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Opto-fluidically multiplexed assembly and micro-robotics

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Light(Science & Applications) 2024年第3期13卷 544-554页

作者： Elena Erben Weida Liao Antonio Minopoli Nicola Maghelli Eric Lauga Moritz Kreysing Max Planck Institute of Molecular Cell biology and Genetics Dresden 01307Germany center for systems biology Dresden 01307Germany Institute of Biological and Chemical systems–Biological Information Processing.Karlsruhe Institute of Technology(KIT) Eggenstein-Leopoldshafen 76344Germany Department of Applied Mathematics and Theoretical Physics University of CambridgeCambridge CB30WAUK

Techniques for high-definition micromanipulations,such as optical tweezers,hold substantial interest across a wide range of ***,their applicability remains constrained by material properties and laser *** while microfluidic manipulations have been suggested as an alternative,their inherent capabilities are limited and further hindered by practical challenges of implementation and *** we show that the iterative application of laser-induced,localized flow fields can be used for the relative positioning of multiple micro-particles,irrespectively of their material *** to the standing theoretical proposal,our method keeps particles mobile,and we show that their precision manipulation is non-linearly accelerated via the multiplexing of temperature stimuli below the heat diffusion *** resulting flow fields are topologically rich and mathematically *** represent unprecedented microfluidic control capabilities that are illustrated by the actuation of humanoid micro-robots with up to 30 degrees of freedom,whose motions are sufficiently well-defined to reliably communicate personal characteristics such as gender,happiness and *** results constitute high-definition micro-fluidic manipulations with transformative potential for assembly,micro-manufacturing,the life sciences,robotics and optohydraulically actuated micro-factories.

关键词： manipulation fluid assembly

Bacillus cereus AR156 primes induced systemic resistance by suppressing miR825/825 and activating defense-related genes in Arabidopsis

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Journal of Integrative Plant biology 2016年第4期58卷 426-439页

作者： Dongdong Niu Jing Xia Chunhao Jiang Beibei Qi Xiaoyu Ling Siyuan Lin Weixiong Zhang Jianhua Guo Hailing Jin Hongwei Zhao Department of Plant Pathology College of Plant Protection Nanjing Agriculture University Department of Plant Pathology and Microbiology Center for Plant Cell Biology and Institute for Integrative Genome Biology University of California Department of Computer Science and Engineering Washington University in St Louis The Institute for systems biology Jianghan University

Small RNAs play an important role in plant immune responses. However, their regulatory function in induced systemic resistance（ISR） is nascent. Bacillus cereus AR156 is a plant growth-promoting rhizobacterium that induces ISR in Arabidopsis against bacterial infection. Here,by comparing small RNA profiles of Pseudomonas syringae pv. tomato（Pst） DC3000-infected Arabidopsis with and without AR156 pretreatment, we identified a group of Arabidopsis micro RNAs（mi RNAs） that are differentially regulated by AR156 pretreatment. mi R825 and mi R825 are two mi RNA generated from a single mi RNA *** blot analysis indicated that they were significantly downregulated in Pst DC3000-infected plants pretreated with AR156, in contrast to the plants without AR156 pretreatment. mi R825 targets two ubiquitin-protein ligases,while mi R825 targets toll-interleukin-like receptor（TIR）-nucleotide binding site（NBS） and leucine-rich repeat（LRR）type resistance（R） genes. The expression of these target genes negatively correlated with the expression of mi R825 and mi R825. Moreover, transgenic plants showing reduced expression of mi R825 and mi R825 displayed enhanced resistance to Pst DC3000 infection, whereas transgenic plants overexpressing mi R825 and mi R825 were more susceptible. Taken together, our data indicates that Bacillus cereus AR156 pretreatment primes ISR to Pst infection by suppressing mi R825 and mi R825 and activating the defense related genes they targeted.

关键词： Induced systemic resistance ISR micro RNA plant innate immunity small RNA

Mutual interaction of microbiota and host immunity during health and diseases

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Biophysics Reports 2021年第4期7卷 326-340页

作者： Di Wu Yinlian Zhang Suwei Dong Chao Zhong Institute of systems Biomedicine Department of ImmunologyBeijing Key Laboratory of Tumor Systems BiologyPeking University Health Science Center State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical BiologySchool of Pharmaceutical SciencesPeking University

Microbiota–host interaction has attracted more and more attentions in recent years. The association between microbiota and host health is largely attributed to its influence on host immune ***-derived antigens and metabolites play a critical role in shaping the host immune system,including regulating its development, activation, and function. However, during various diseases the microbiota–host communication is frequently found to be disordered. In particular, gut microbiota dysbiosis associated with or led to the occurrence and progression of infectious diseases, autoimmune diseases, metabolic diseases, and neurological diseases. Pathogenic microbes and their metabolites disturb the protective function of immune system, and lead to disordered immune responses that usually correlate with disease exacerbation. In the other hand, the immune system also regulates microbiota composition to keep host homeostasis. Here, we will discuss the current advances of our knowledge about the interactions between microbiota and host immune system during health and diseases.

关键词： Microbiota Microbial-derived antigens and metabolites Immune system Composition of microbiota Host health and diseases

Experimental identification of a comb-shaped chaotic region in multiple parameter spaces simulated by the Hindmarsh–Rose neuron model

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Chinese Physics B 2014年第3期23卷 179-185页

作者：贾冰 center for Computational System biology School of Mathematical Science Fudan University

A comb-shaped chaotic region has been simulated in multiple two-dimensional parameter spaces using the Hindmarsh-Rose （HR） neuron model in many recent studies, which can interpret almost all of the previously simulated bifurcation processes with chaos in neural firing patterns. In the present paper, a comb-shaped chaotic region in a two- dimensional parameter space was reproduced, which presented different processes of period-adding bifurcations with chaos with changing one parameter and fixed the other parameter at different levels. In the biological experiments, different period-adding bifurcation scenarios with chaos by decreasing the extra-cellular calcium concentration were observed from some neural pacemakers at different levels of extra-cellular 4-aminopyridine concentration and from other pacemakers at different levels of extra-cellular caesium concentration. By using the nonlinear time series analysis method, the determin- istic dynamics of the experimental chaotic firings were investigated. The period-adding bifurcations with chaos observed in the experiments resembled those simulated in the comb-shaped chaotic region using the HR model. The experimental results show that period-adding bifurcations with chaos are preserved in different two-dimensional parameter spaces, which provides evidence of the existence of the comb-shaped chaotic region and a demonstration of the simulation results in dif- ferent two-dimensional parameter spaces in the HR neuron model. The results also present relationships between different firing patterns in two-dimensional parameter spaces.

关键词： chaos neural firing bifurcation Hindmarsh-Rose model

Synchronization transition of a coupled system composed of neurons with coexisting behaviors near a Hopf bifurcation

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Chinese Physics B 2014年第5期23卷 180-190页

作者：贾冰 center for Computational System biology School of Mathematical ScienceFudan University

The coexistence of a resting condition and period-1 firing near a subcritical Hopf bifurcation point, lying between the monostable resting condition and period-1 firing, is often observed in neurons of the central nervous systems. Near such a bifurcation point in the Morris-Lecar （ML） model, the attraction domain of the resting condition decreases while that of the coexisting period-1 firing increases as the bifurcation parameter value increases. With the increase of the coupling strength, and parameter and initial value dependent synchronization transition processes from non-synchronization to compete synchronization are simulated in two coupled ML neurons with coexisting behaviors： one neuron chosen as the resting condition and the other the coexisting period-1 firing. The complete synchronization is either a resting condition or period-1 firing dependent on the initial values of period-1 firing when the bifurcation parameter value is small or middle and is period- 1 firing when the parameter value is large. As the bifurcation parameter value increases, the probability of the initial values of a period- 1 firing neuron that lead to complete synchronization of period- 1 firing increases, while that leading to complete synchronization of the resting condition decreases. It shows that the attraction domain of a coexisting behavior is larger, the probability of initial values leading to complete synchronization of this behavior is higher. The bifurcations of the coupled system are investigated and discussed. The results reveal the complex dynamics of synchronization behaviors of the coupled system composed of neurons with the coexisting resting condition and period-1 firing, and are helpful to further identify the dynamics of the spatiotemporal behaviors of the central nervous system.

关键词： synchronization neuronal network Hopf bifurcation coexistence

Neural plasticity and adult neurogenesis: the deep biology perspective

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Neural Regeneration Research 2019年第2期14卷 201-205页

作者： Anna Maria Colangelo Giovanni Cirillo Lilia Alberghina Michele Papa Hans V.Westerhoff Laboratory of Neuroscience "R.Levi-Montalcini" Dept.of Biotechnology and Biosciences University of Milano-Bicocca SYSBIO Centre of systems biology University of Milano-Bicocca NeuroMI Milan center for Neuroscience University of Milano-Bicocca Laboratory of Morphology of Neuronal Network Department of Public Medicine University of Campania "Luigi Vanvitelli" Synthetic systems biology and Nuclear Organization University of Amsterdam Molecular Cell Physiology VU University Amsterdam and Infrastructure Systems Biology at NL (ISBE.NL) Amsterdam NL and Systems Biology School for Chemical Engineering and Analytical Science University of Manchester

The recognition that neurogenesis does not stop with adolescence has spun off research towards the reduction of brain disorders by enhancing brain regeneration. Adult neurogenesis is one of the tougher problems of developmental biology as it requires the generation of complex intracellular and pericellular anatomies, amidst the danger of neuroinflammation. We here review how a multitude of regulatory pathways optimized for early neurogenesis has to be revamped into a new choreography of time dependencies. Distinct pathways need to be regulated, ranging from neural growth factor induced differentiation to mitochondrial bioenergetics, reactive oxygen metabolism, and apoptosis. Requiring much Gibbs energy consumption, brain depends on aerobic energy metabolism, hence on mitochondrial activity. Mitochondrial fission and fusion, movement and perhaps even mitoptosis, thereby come into play. All these network processes are interlinked and involve a plethora of molecules. We recommend a deep thinking approach to adult neurobiology.

关键词： neurogenesis adult brain neuroregeneration neuron differentiation nerve growth factor energy homeostasis mitochondria deep biology systems biology

Bio-Review 2021: Inspiring the future of Biochemical Engineering

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Chinese Journal of Chemical Engineering 2021年第2期34卷 1-3页

作者： Yan Sun Department of Biochemical Engineering School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology(Ministry of Education)Tianjin UniversityTianjin 300350China

Biochemical Engineering(BCE)discipline had largely developed from fermentation technology studies from 1950s through 1960s when fermentation emerged as the core technology able to address multiple industrial needs ranging from health care products such as antibiotics;food products such as single cell proteins,amino acids,organic acids,and vitamins;liquid fuels and chemicals such as ethanol and acetic acid;and industrial enzymes.

关键词： acetic ethanol vitamin

Data-based prediction and causality inference of nonlinear dynamics

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Science China Mathematics 2018年第3期61卷 403-420页

作者： Huanfei Ma Siyang Leng Luonan Chen School of Mathematical Sciences Soochow University Institute of Industrial Science The University of Tokyo Key Laboratory of systems biology Innovation Center for Cell Signaling NetworkInstitute of Biochemistry and Cell Biology Shanghai Institutes for Biological SciencesChinese Academy of Sciences

Natural systems are typically nonlinear and complex, and it is of great interest to be able to reconstruct a system in order to understand its mechanism, which cannot only recover nonlinear behaviors but also predict future dynamics. Due to the advances of modern technology, big data becomes increasingly accessible and consequently the problem of reconstructing systems from measured data or time series plays a central role in many scientific disciplines. In recent decades, nonlinear methods rooted in state space reconstruction have been developed, and they do not assume any model equations but can recover the dynamics purely from the measured time series data. In this review, the development of state space reconstruction techniques will be introduced and the recent advances in systems prediction and causality inference using state space reconstruction will be presented. Particularly, the cutting-edge method to deal with short-term time series data will be focused ***, the advantages as well as the remaining problems in this field are discussed.

关键词： nonlinear system prediction causality inference time series data

Aptamer-Based DNA Materials for the Separation and Analysis of Biological Particles

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Transactions of Tianjin University 2021年第6期27卷 450-459页

作者： Chenxu Zhu Chi Yao Dayong Yang Frontiers Science center for Synthetic biology Key Laboratory of Systems Bioengineering(MOE)School of Chemical Engineering and TechnologyTianjin UniversityTianjin 300350China

DNA is a biological macromolecule that carries genetic information in *** provides a series of predominant bio-logical advantages,such as sequence programmability,high biocompatibility,and low *** such,it is a unique polymer material that shows great potential for application in biological and medical *** aptamers are short DNA sequences with a specific ability of molecular *** its discovery,the application prospect of DNA materials has broadened,especially for the separation and analysis of biological *** this review,the functions and characteristics of DNA aptamers are introduced,and the applications of DNA materials in cell/exosome separation and cancer detection are *** application prospect and possible challenges of DNA materials are predicted.

关键词： DNA materials DNA aptamer Biological particle separation Disease analysis