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Effects of sampling strategies and DNA extraction methods on eDNA metabarcoding: A case study of estuarine fish diversity monitoring

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Zoological research 2022年第2期43卷 192-204页

作者： Hui-Ting Ruan Rui-Li Wang Hong-Ting Li Li Liu Tian-Xu Kuang Min Li Ke-Shu Zou University Joint Laboratory of Guangdong Province Hong Kong and Macao Region on Marine Bioresource Conservation and ExploitationCollege of Marine ScienceSouth China Agricultural UniversityGuangzhouGuangdong 510642China Key Laboratory for Sustainable Utilization of Open-sea Fishery Ministry of Agriculture and Rural AffairsSouth China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouGuangdong 510300China southern Marine Science and Engineering Guangdong Laboratory(Guangzhou) GuangzhouGuangdong 511458China Guangzhou CAOMUFAN Ecological research limited company GuangzhouGuangdong 510520China College of Marine Sciences Shanghai Ocean UniversityShanghai 201306China

Environmental DNA(eDNA)integrated with metabarcoding is a promising and powerful tool for species composition and biodiversity assessment in aquatic ecosystems and is increasingly applied to evaluate fish *** date,however,no standardized eDNA-based protocol has been established to monitor fish *** this study,we investigated and compared two filtration methods and three DNA extraction methods using three filtration water volumes to determine a suitable approach for eDNA-based fish diversity monitoring in the Pearl River Estuary(PRE),a highly anthropogenically disturbed estuarine *** to filtration-based precipitation,direct filtration was a more suitable method for eDNA metabarcoding in the *** combined use of DNeasy Blood and Tissue Kit(BT)and traditional phenol/chloroform(PC)extraction produced higher DNA yields,amplicon sequence variants(ASVs),and Shannon diversity indices,and generated more homogeneous and consistent community composition among *** to the other combined protocols,the PC and BT methods obtained better species detection,higher fish diversity,and greater consistency for the filtration water volumes of 1000 and 2000 mL,*** eDNA metabarcoding protocols were more sensitive than bottom trawling in the PRE fish surveys and combining two techniques yielded greater taxonomic ***,combining traditional methods with eDNA analysis enhanced *** results indicate that methodological decisions related to eDNA metabarcoding should be made with caution for fish community monitoring in estuarine ecosystems.

关键词： eDNA metabarcoding Fish diversity Sampling strategies DNA extraction Estuarine ecosystem

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Inhibition of REDD1 sensitizes bladder urothelial carcinoma to paclitaxel by inhibiting autophagy

Inhibition of REDD1 sensitizes bladder urothelial carcinoma ...

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2017年中国肿瘤标志物学术大会暨第十一届肿瘤标志物青年科学家论坛

作者： Qinghai Zeng Jianye Liu Peiguo Cao Jingjing Li Xiaoming Liu Xiaojun Fan Ling Liu Yan Cheng Wei Xiong Jigang Li Hao Bo Yuxing Zhu Fei Yang Jun Hu Ming Zhou Yanhong Zhou Qiong Zou Jianda Zhou Ke Cao Department of Dermatology Third Xiangya HospitalCentral South University Department of Urology Third Xiangya HospitalCentral South University Department of Oncology Third Xiangya HospitalCentral South University Department of Plastic Surgery Third Xiangya HospitalCentral South University Department of Gastroenterology Third Xiangya HospitalCentral South University research Service office Third Xiangya HospitalCentral South University Outpatient service office Third Xiangya HospitalCentral South University Department of Pharmacology School of Pharmaceutical SciencesCentral South University Cancer research institute and Key Laboratory of Carcinogenesis of Ministry of Health Central South University Department of Pathology Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of MedicineCentral South University institute of Reproductive and Stem Cell Engineering Central South University School of Public Health Central South University Department of Tissue-bank Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of MedicineCentral South University Department of Pathology Third Xiangya HospitalCentral South University

Purpose: Regulated in development and DNA damage response-1(REDD1) is a stress related protein and is involved in the progression of cancer. The role and regulatory mechanism of REDD1 in bladder urothelial carcinoma(BUC), however, is yet unidentified. Experimental Design: The expression of REDD1 in BUC was detected by western blot and immunohistochemistry. The correlation between REDD1 expression and clinical features in BUC patients were assessed. The effects of REDD1 on cellular proliferation, apoptosis, autophagy, and paclitaxel sensitivity were determined both in vitro and in vivo. Then the targeted-regulating mechanism of REDD1 by microRNAs was explored. Results: Here the significant increase of REDD1 expression is detected in BUC tissue, and REDD1 is firstly reported as an independent prognostic factor in BUC patients. Silencing REDD1 expression in T24 and EJ cells decreased cell proliferation, increased apoptosis, and decreased autophagy, whereas the ectopic expression of REDD1 in RT4 and BIU87 cells had the opposite effect. Additionally, the REDD1-mediated proliferation, apoptosis, and autophagy are found to be negatively regulated by miR-22 in vitro, which intensify the paclitaxel sensitivity via inhibition of the well-acknowledged REDD1-EEF2 K-autophagy axis. AKT/mTOR signaling initially activated or inhibited in response to silencing or enhancing REDD1 expression and then recovered rapidly. Lastly, the inhibited REDD1 expression by either RNAi or miR-22 sensitizes BUC tumor cells to paclitaxel in a subcutaneous transplant sarcoma model in vivo. Conclusion: REDD1 is confirmed as an oncogene in BUC, and antagonizing REDD1 could be a potential therapeutic strategy to sensitize BUC cells to paclitaxel.

关键词： REDD1 autophagy miR-22 paclitaxel sensitivity bladder urothelial carcinom

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Engineering the next generation of theranostic biomaterials with synthetic biology

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Bioactive Materials 2024年第2期32卷 514-529页

作者： Xiang Wang Qianyi Liang Yixuan Luo Jianwen Ye Yin Yu Fei Chen Center for Materials Synthetic Biology CAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen518055China School of Biology and Biological Engineering South China University of TechnologyGuangzhou510006China

Biomaterials have evolved from inert materials to responsive entities,playing a crucial role in disease diagnosis,treatment,and ***,their advancement is hindered by limitations in chemical and mechanical *** biology enabling the genetically reprograming of biological systems offers a new *** has achieved remarkable progresses in cell reprogramming,engineering designer cells for diverse *** biology also encompasses cell-free systems and rational design of biological *** review focuses on the application of synthetic biology in theranostics,which boost rapid development of advanced *** introduce key fundamental concepts of synthetic biology and highlight frontier applications thereof,aiming to explore the intersection of synthetic biology and *** integration holds tremendous promise for advancing biomaterial engineering with programable complex functions.

关键词： Theranostic biomaterials Synthetic biology Genetic circuit Programmable Living

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Contactin-associated protein-like 2(CNTNAP2)mutations impair the essentialα-secretase cleavages,leading to autism-like phenotypes

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Signal Transduction and Targeted Therapy 2024年第4期9卷 1625-1636页

作者： Qing Zhang Mengen Xing Zhengkai Bao Lu Xu Yang Bai Wanqi Chen Wenhao Pan Fang Cai Qunxian Wang Shipeng Guo Jing Zhang Zhe Wang Yili Wu Yun Zhang Jia-Da Li Weihong Song Oujiang Laboratory(Zhejiang Lab for Regenerative Medicine Vision and Brain Health)Zhejiang Key Laboratory of Alzheimer's DiseaseZhejiang Provincial Clinical Research Center for Mental DisordersSchool of Mental Health and Wenzhou Kangning HospitalThe Second Affiliated Hospital and Yuying Children's HospitalInstitute of AgingWenzhou Medical UniversityWenzhouZhejiang 325035China Townsend Family Laboratories Department of PsychiatryBrain Research CenterThe University of British Columbia2255 Wesbrook MallVancouverBC V6T 1Z3Canada Chongqing Key Laboratory of Translational Medical research in Cognitive development and Learning and Memory Disorders Ministry of Education Key Laboratory of Child Development and DisordersChildren's Hospital of Chongqing Medical UniversityChongqing 400014China Center for Medical Genetics Hunan Key Laboratory of Animal Models for Human DiseasesHunan Key Laboratory of Medical GeneticsHunan International Scientific and Technological Cooperation Base of Animal Models for Human DiseasesSchool of Life SciencesCentral South UniversityChangsha 410078 HunanChina The National Clinical research Center for Geriatric Disease Xuanwu HospitalCapital Medical UniversityBeijing 100053Chin

Mutations in the Contactin-associated protein-like 2(CNTNAP2)gene are associated with autism spectrum disorder(ASD),and ectodomain shedding of the CNTNAP2 protein plays a role in its ***,key enzymes involved in the C-terminal cleavage of CNTNAP2 remain largely unknown,and the effect of ASD-associated mutations on this process and its role in ASD pathogenesis remain *** this report we showed that CNTNAP2 undergoes sequential cleavages by furin,ADAM10/17-dependent a-secretase and presenilindependent *** identified that the cleavage sites of ADAM10 and ADAM17 in CNTNAP2 locate at its C-terminal residue I79 and L96,and the main a-cleavage product C79 by ADAM10 is required for the subsequent y-secretase cleavage to generate CNTNAP2 intracellular domain(CICD).ASD-associated CNTNAP2 mutations impair the a-cleavage to generate C79,and the inhibition leads to ASDIlike repetitive and social behavior abnormalties in the Cntnap2l1254T knock-in ***,exogenous expression of 79 improves autism-ike phenotypes in the Cntnap2^(11254T) knock-in and Cntnap2^(-/-)knockout *** data demonstrates that the a-secretase is essential for CNTNAP2 processing and its *** study indicates that inhibition of the cleavage by pathogenic mutations underlies ASD pathogenesis,and upregulation of its C-terminal fragments could have therapeutical potentials for ASD treatment.

关键词： NAP2 cleavage subsequent

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Structure,variation and assembly processes of bacterial communities in different root-associated niches of tomato under periodic drought and nitrogen addition

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Pedosphere 2024年第5期34卷 892-904页

作者： Dan HE Ruifeng GAO Honghong DONG Xiaodi LIU Lijuan REN Qinglong WU Qing YAO Honghui ZHU southern Marine Science and Engineering Guangdong Laboratory(Guangzhou) Guangzhou 511458China Key Laboratory of Agricultural Microbiomics and Precision Application(MARA) State Key Laboratory of Applied Microbiology Southern ChinaInstitute of MicrobiologyGuangdong Academy of SciencesGuangzhou 510070China College of Plant Protection South China Agricultural UniversityGuangzhou 510642China Department of Ecology Institute of HydrobiologyJinan UniversityGuangzhou 510632China College of Horticulture South China Agricultural UniversityGuangzhou 510642China

Root-associated bacteria play a vital role in the growth and adaptation of host plants to drought *** bacteria can be classified as rhizoplane and rhizosphere bacteria based on their distance from the root *** plants are often exposed to periodic drought and nitrogen(N)addition throughout their life cycle,but the impacts of these factors on the plant and root-associated bacteria are not well *** gain insight into this relationship,we conducted an experiment to monitor the effects of periodic drought and N addition on rhizoplane and rhizosphere bacteria of tomato *** and N addition had interactive effects on plant and soil properties,which varied with the timing of *** were clear divergences in community traits such as alpha diversity,beta diversity,and network topological features between the two types of *** rhizoplane bacteria showed lower alpha diversity but higher beta diversity and were more sensitive to drought and N addition than the rhizosphere *** addition could downsize the effects of drought on rhizoplane bacterial community *** higher proximity to the root might induce a community to develop more cooperation between different members to cope with plant metabolites,as revealed by the more connected and modularized community network of the rhizoplane *** at the seedling stage had great legacy effects on plant and soil *** may enhance selection,cause the dominance of deterministic processes in the assembly of rhizoplane bacteria,and reduce bacterial community network *** conclusion,N addition could interact with drought in affecting tomato plants and their root-associated bacteria,depending on the timing of drought and the fineness of root *** higher sensitivity of rhizoplane bacteria to drought and N addition calls for more research due to their higher proximity and importance to plants in future environmental changes.

关键词： alpha diversity beta diversity community composition co-occurrence network drought stress node-level network feature rhizoplane bacteria rhizospherebacteria

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Fabrication of GaN-based LEDs with 22° undercut sidewalls by inductively coupled plasma reactive ion etching

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Chinese Physics B 2013年第10期22卷 445-448页

作者：王波宿世臣何苗陈弘吴汶波张伟伟王巧陈虞龙高优张力朱克宝雷严 Laboratory of Nanophotonic Functional Materials and Devices Institute of Optoelectronic Materials and TechnologySouth China Normal University Key Laboratory for Renewable Energy Chinese Academy of SciencesBeijing Key Laboratory for New Energy Materials and DevicesBeijing National Laboratory for Condense Matter PhysicsInstitute of PhysicsChinese Academy of Sciences

We use a simple and controllable method to fabricate GaN-based light-emitting diodes （LEDs） with 22° undercut sidewalls by the successful implementation of the inductively coupled plasma reactive ion etching （ICP-RIE）. Our exper- iment results show that the output powers of the LEDs with 22° undercut sidewalls are 34.8 rnW under a 20-mA current injection, 6.75% higher than 32.6 mW, the output powers of the conventional LEDs under the same current injection.

关键词： GaN light-emitting diode (LED) undercut

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Deadlock-free dynamic resource assignment in multi-robot systems with multiple missions:application in wireless sensor networks

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控制理论与应用（英文版） 2010年第1期8卷 12-19页

作者： P.M.BALLAL A.C.TRIVEDI V.GIORDANO J.MIRELES Jr. F.L.LEWIS Automation & Robotics research institute University of Texas at Arlington

In unstructured environments, dynamic resource assignment is required for effective cooperation of robot teams. In some scenarios, robots are in charge of executing multiple missions simultaneously. This creates risks of deadlock due to the presence of shared resources among various missions. The main contribution of this paper is the development of a novel approach that combines the one-step look-ahead deadlock avoidance policy with dynamic resource assignment. The dynamicresource assignment is achieved using greedy resource assignment for multi-mission robot teams in the framework of a matrix-based discrete event controller. Simulation results are presented in MATLAB to discuss in detail the proposed control strategy. The paper also discusses the toolkit developed in LabVIEW which is used to implement this control framework using a suitable example.

关键词： Discrete event systems Wireless sensor networks Deadlock avoidance Petri nets

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A Seismic Facies Analysis to Determine the Relative Age and History of the Al Idrissi Mud Volcano from Offshore Larache Located in the NW Moroccan Atlantic Margin

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Open Journal of Geology 2023年第3期13卷 203-220页

作者： Asher Hategekamungu Nadia Mhammdi Mohamed Amine Manar Asmae Bernachid Geophysics and Natural Hazards Laboratory GEOPAC Research Centre Scientific Institute Mohammed V University in Rabat Rabat Morocco Department of Petroleum Exploration Direction and south Offshore Office National des Hydrocarbures et des Mines (ONHYM) Rabat Morocco

Formed on top of the Gulf of Cadiz, the Al Idrissi mud volcano is the shallowest and largest mud volcano in the El Arraiche mud volcano field of the northwestern Moroccan margin. The development and morphology of mud volcanoes from the El Arraiche mud volcanoes group have been studied at a large scale. However, the time interval related to their formation period still needs to be better understood. In this regard, we interpreted and analyzed the seismic facies from the 2D reflection data of the GEOMARGEN-1 campaign, which took place in 2011. The aim was to identify the seismic sequences and draw the Al Idrissi mud volcano system to determine the formation period of the Al Idriss mud volcano. And as a result, the Al Idrissi mud volcano system is made of both buried and superficial bicone and was identified along with the Upper Tortonian to Messinian-Upper Pliocene facies. As the initial mud volcano extrusive edifice, the buried bicone was formed in the Late-Messinian to Early-Pliocene period. However, the superficial bicone, as the final extrusive edifice, was included in the Late Pliocene. In this case, the timing interval between the buried and superficial bicone is equivalent to the Late-Messinian to Upper-Pliocene period. Therefore, the latter corresponds to the Al Idrissi mud volcano formation period.

关键词： Northwestern Moroccan Margin Al Idrissi Mud Volcano 2D Reflection Data from the GEOMARGEN-1 Campaign Seismic Signatures Analysis Formation Period

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Effect of In_x Ga_(1-x )N “continuously graded” buffer layer on InGaN epilayer grown by metalorganic chemical vapor deposition

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Chinese Physics B 2013年第10期22卷 401-405页

作者：钱卫宁宿世臣陈弘马紫光朱克宝何苗卢平元王耿卢太平杜春花王巧吴汶波张伟伟 Laboratory of Nanophotonic Functional Materials and Devices Institute of Opto-electronic Materials & TechnologySouth China Normal University Key Laboratory for Renewable Energy Chinese Academy of SciencesBeijing Key Laboratory for New Energy Materials and DevicesBeijing National Laboratory for Condense Matter PhysicsInstitute of PhysicsChinese Academy of Sciences

In this paper we report on the effect of an lnxGal xN continuously graded buffer layer on an InGaN epilayer grown on a GaN template. In our experiment, three types of buffer layers including constant composition, continuously graded composition, and the combination of constant and continuously graded composition are used. Surface morphologies, crystalline quality, indium incorporations, and relaxation degrees of InGaN epilayers with different buffer layers are investigated. It is found that the InxGa1-xN continuously graded buffer layer is effective to improve the surface morphology, crystalline quality, and the indium incorporation of the InGaN epilayer. These superior characteristics of the continuously graded buffer layer can be attributed to the sufficient strain release and the reduction of dislocations.

关键词： InGaN reciprocal space map indium incorporation surface morphology

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Influence of social capital on the livelihood strategies of farmers under China's rural revitalization strategy in poor mountain areas: A case study of the Liangshan Yi autonomous prefecture

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Journal of Mountain Science 2022年第4期19卷 958-973页

作者： HE Ren-wei GUO Shi-li DENG Xian ZHOU Kui institute of City Situation Survey research Beijing Academy of Social SciencesBeijing 100101China School of Resources and Environment Xichang CollegeXichang 615013China China Western Economic research Center Southwestern University of Finance and EconomicsChengdu 611130China office Service Center of Standing Committee of Neijiang Municipal People’s Congress Neijing 641000China

Social capital in the form of social resources or social networks is one of the most important livelihood capital of farmers, which can increase the labor productivity of poor households and increase income. It is important to explore the reasons underlying the livelihood strategy choices of farmers from the perspective of social capital under China’s rural revitalization strategy. In this study, the Liangshan Yi Autonomous Prefecture, a povertystricken mountainous area in southwestern China, was selected as the case study area, and multivariable linear regression models were constructed to analyze the influence of social capital on livelihood *** results are as follows:(1) Individual social capital had a positive effect on non-agricultural livelihood strategies. On average, with a one-unit increase in individual social capital, the ratio of farmers’ nonagricultural income to total productive income(Income_Rto) increased by 0.002% and 0.062%,respectively. Collective social capital, with the Peasant Economic cooperation Organization(PECO) as the carrier, had a negative effect on the non-agricultural livelihood strategies of farmers;on average, with a oneunit increase in PECO, Income_Rto decreased by approximately 0.053%. However, this effect was only significant in the river valley area.(2) The income differences among the different livelihood strategy types were explained by the livelihood strategy choices of farmers. As non-agricultural work can bring more benefits, the labor force exhibited one-way migration from villages to cities, resulting in a lack of the subject of rural revitalization. It is necessary to implement effective measures to highlight the role of PECO in increasing agricultural income for farmers. Finally,based on the above conclusions,policy recommendations with respect to livelihood transformation of farmers and rural sustainable development are discussed.

关键词： Social capital Livelihood strategies Village types Rural revitalization Poor mountain areas Liangshan Yi Autonomous Prefecture

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