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Decoding early myelopoiesis from dynamics of core endogenous network

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Science China(Life Sciences) 2017年第6期60卷 627-646页

作者： Hang Su Gaowei Wang ruoshi yuan Junqiang Wang Ying Tang Ping Ao Xiaomei Zhu Key Laboratory of Systems Biomedicine(Ministry of Education) Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghai 200240China School of Biomedical Engineering Shanghai Jiao Tong UniversityShanghai 200240China Department of Physics and Astronomy Shanghai Jiao Tong UniversityShanghai 200240China State Key Laboratory for Oncogenes and Related Genes Shanghai Cancer InstituteShanghai Jiao Tong University School of MedicineShanghai 200240China Shanghai Center for Quantitative Life Sciences and Physics Department Shanghai UniversityShanghai 200444China

A decade ago mainstream molecular biologists regarded it impossible or biologically ill-motivated to understand the dynamics of complex biological phenomena, such as cancer genesis and progression, from a network perspective. Indeed, there are numerical difficulties even for those who were determined to explore along this direction. Undeterred, seven years ago a group of Chinese scientists started a program aiming to obtain quantitative connections between tumors and network dynamics. Many interesting results have been obtained. In this paper we wish to test such idea from a different angle: the connection between a normal biological process and the network dynamics. We have taken early myelopoiesis as our biological model. A standard roadmap for the cell-fate diversification during hematopoiesis has already been well established experimentally, yet little was known for its underpinning dynamical mechanisms. Compounding this difficulty there were additional experimental challenges, such as the seemingly conflicting hematopoietic roadmaps and the cell-fate inter-conversion events. With early myeloid cell-fate determination in mind, we constructed a core molecular endogenous network from well-documented gene regulation and signal transduction knowledge. Turning the network into a set of dynamical equations, we found computationally several structurally robust states. Those states nicely correspond to known cell phenotypes. We also found the states connecting those stable *** reveal the developmental routes—how one stable state would most likely turn into another stable state. Such interconnected network among stable states enabled a natural organization of cell-fates into a multi-stable state landscape. Accordingly, both the myeloid cell phenotypes and the standard roadmap were explained mechanistically in a straightforward manner. Furthermore,recent challenging observations were also explained naturally. Moreover, the landscape visually enables a prediction o

关键词： developmental scheme early myeloid cell-fate determination endogenous network stable state transition state landscape

Statistical analysis can fail to reveal underlying true biological mechanism:a demonstration of expression profile generation

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Statistical analysis can fail to reveal underlying true biol...

Potential Function in Dynamical Systems and the Relation with Lyapunov Function

第37届中国控制会议

作者： Runtan Cheng Xiaomei Zhu ruoshi yuan Ping Ao Key Laboratory of Systems Biomedicine (Ministry of Education) Shanghai Center for Systems Biomedicine Shanghai Jiao Tong University Shanghai Center for Quantitative Life Sciences and Physics Department Shanghai University

In the life science, data show an exponential increase trend with the development of biotechnology. Statistical analysis is a powerful tool to find useful information in tremendous amount of data. However, biological systems always contain serious errors where data-driven biostatistics may meet barriers. Different and complementary approaches are needed. Endogenous network theory is a mechanism-driven method which can quantitatively analyze regulation networks. Steady states expression profiles and potential landscape of a dynamic network could be found by this theory. Simulations of stochastic effects indicate that in systems with large noise, data-driven biostatistics can fail to reveal the true biological mechanism.

关键词： dynamics landscape stochasticity expression profile network

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Potential Function in Dynamical Systems and the Relation wit...

Insights into skeletal stem cells

第三十届中国控制会议

作者： yuan ruoshi,MA Yian,yuan Bo,AO Ping Shanghai Jiao Tong University,800 Dongchuan Road,Minhang District,Shanghai 200240,P.R.China

＜正＞One of the present authors has proposed a novel treatment of stochastic processes leading to the construction of potential functions for dynamics described by stochastic differential equations（SDEs）.The approach transforms the deterministic part of the original system into three components:a potential function,a frictional force and a Lorentz *** potential function drives the dynamics and determines the final steady state distribution that has both local and global *** note that such a potential is closely related to the classical Lyapunov *** this paper,we first provide a brief review on the decomposition framework and then give a constructive proof on the equivalence of two fundamental concepts:the global Lyapunov function in engineering and the potential function in physics,establishing a bridge between the two distinct fields. This result reveals the physical meaning of Lyapunov functions,thus suggests new approaches on the largely unsolved problem: constructing Lyapunov functions for general nonlinear systems,through the analogy with existing methods on potential functions. In addition,we show another connection that the Lyapunov equation is a reduced form of the generalized Einstein relation for linear *** inheriting from a physical treatment of stochastic processes,this work demonstrates a stochastic view of deterministic systems together with the deterministic rules that govern stochastic behaviors.

关键词： Lyapunov Function Potential Function Lyapunov Equation Limit Cycle Non-equilibrium Process

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Bone Research 2022年第4期10卷 679-695页

作者： Qiwen Li ruoshi Xu Kexin Lei Quan yuan State Key Laboratory of Oral Diseases National Clinical Research Center for Oral DiseasesWest China Hospital of StomatologySichuan UniversityChengdu 610041China

The tissue-resident skeletal stem cells(SSCs),which are self-renewal and multipotent,continuously provide cells(including chondrocytes,bone cells,marrow adipocytes,and stromal cells)for the development and homeostasis of the skeletal *** recent decade,utilizing fluorescence-activated cell sorting,lineage tracing,and single-cell sequencing,studies have identified various types of SSCs,plotted the lineage commitment trajectory,and partially revealed their properties under physiological and pathological *** this review,we retrospect to SSCs identification and functional *** discuss the principles and approaches to identify bona fide SSCs,highlighting pioneering findings that plot the lineage atlas of *** roles of SSCs and progenitors in long bone,craniofacial tissues,and periosteum are systematically *** further focus on disputes and challenges in SSC research.

关键词： skeletal utilizing sorting

Saliva: potential diagnostic value and transmission of 2019-nCoV

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International Journal of Oral Science 2020年第2期12卷 83-88页

作者： ruoshi Xu Bomiao Cui Xiaobo Duan Ping Zhang Xuedong Zhou Quan yuan State Key Laboratory of Oral Diseases&National Clinical Research Center for Oral Diseases&West China Hospital of Stomatology Sichuan UniversityChengduChina State Key Laboratory of Oral Diseases&Human Saliva Laboratory&National Clinical Research Center for Oral Diseases&West China Hospital of Stomatology Sichuan UniversityChengduChina

2019-n Co V epidemic was firstly reported at late December of 2019 and has caused a global outbreak of COVID-19 ***,a biofluid largely generated from salivary glands in oral cavity,has been reported 2019-n Co V nucleic acid *** lungs,salivary glands and tongue are possibly another hosts of 2019-n Co V due to expression of *** contact or short-range transmission of infectious saliva droplets is a primary mode for 2019-n Co V to disseminate as claimed by WHO,while long-distance saliva aerosol transmission is highly environment dependent within indoor space with aerosol-generating procedures such as dental *** far,no direct evidence has been found that 2019-n Co V is vital in air flow for long ***,to prevent formation of infectious saliva droplets,to thoroughly disinfect indoor air and to block acquisition of saliva droplets could slow down2019-n Co V *** review summarizes diagnostic value of saliva for 2019-n Co V,possibly direct invasion into oral tissues,and close contact transmission of 2019-n Co V by saliva droplets,expecting to contribute to 2019-n Co V epidemic control.

关键词： invasion aerosol value

Obstacle avoidance transplanting method on Kinect visual processing

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International Journal of Agricultural and Biological Engineering 2021年第5期14卷 72-78页

作者： Xin Jin ruoshi Li Jiangtao Ji Yanwei yuan Mingyong Li College of Agricultural Equipment Engineering Henan University of Science and TechnologyLuoyang 471003HenanChina Collaborative Innovation Center of Machinery Equipment Advanced Manufacturing of Henan Province Luoyan 471003HenanChina Chinese Academy of Agricultural Mechanization Sciences Beijing 100020China

In modern facility agriculture,to improve the quality and efficiency of transplanting,the application of transplanting robots based on visual processing is becoming more and more *** order to reduce the damage to plants during the transplanting process and reduce the damage rate of plant stems,leaves and substrates,a transplanting method based on Kinect visual processing combined with an inclined transplanting manipulator was *** the research,the Kinect visual processing was used to obtain and process the seedling height information and leaf edge information,and the working coordinate system of the transplanting manipulator was established and applied to plan the obstacle avoidance *** with the oblique manipulator,the obstacle avoidance transplanting method was *** the structural design and force analysis of the seedling transplanting device,the key parameters that affect the transplanting quality were obtained,and the optimal transplanting performance parameters were obtained through *** the experiment,with the aid of the Kinect vision processing system,the designed obstacle avoidance transplanting manipulator had a leaf damage degree of 4.70%,a stem bending rate of 16.67%,substrate integrity of 83.45%and a transplanting quality parameter of 87.36%.The time for a single seedling transplanting was(8.32±0.40)*** experiment result proves that the obstacle avoidance transplanting method based on Kinect visual processing can effectively reduce the damage to seedlings when ensuring the transplanting efficiency.

关键词： Kinect vision processing oblique-type transplanting robot path planning obstacle avoidance

AFF4 regulates osteogenic differentiation of human dental follicle cells

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International Journal of Oral Science 2020年第4期12卷 287-297页

作者： Qingyue Xiao Yuning Zhang Xingying Qi Yaqian Chen Rui Sheng ruoshi Xu Quan yuan Chenchen Zhou State Key Laboratory of Oral Diseases&National Clinical Research Center for Oral Diseases&West China Hospital of Stomatology Sichuan UniversityChengduChina State Key Laboratory of Oral Diseases&National Clinical Research Center for Oral Diseases&Department of Cariology and Endodontology West China Hospital of StomatologySichuan UniversityChengduChina State Key Laboratory of Oral Diseases&National Clinical Research Center for Oral Diseases&Department of Oral Implantology West China Hospital of StomatologySichuan UniversityChengduChina State Key Laboratory of Oral Diseases&National Clinical Research Center for Oral Diseases&Department of Pediatric Dentistry West China Hospital of StomatologySichuan UniversityChengduChina

As a member of the AFF(AF4/FMR2)family,AFF4 is a transcription elongation factor that is a component of the super elongation ***4 serves as a scaffolding protein that connects transcription factors and promotes gene transcription through elongation and chromatin ***,we investigated the effect of AFF4 on human dental follicle cells(DFCs)in osteogenic *** this study,we found that small interfering RNA-mediated depletion of AFF4 resulted in decreased alkaline phosphatase(ALP)activity and impaired *** addition,the expression of osteogenic-related genes(DLX5,SP7,RUNX2 and BGLAP)was significantly *** contrast,lentivirus-mediated overexpression of AFF4 significantly enhanced the osteogenic potential of human ***,we found that both the mRNA and protein levels of ALKBH1,a critical regulator of epigenetics,changed in accordance with AFF4 expression *** of ALKBH1 in AFF4-depleted DFCs partially rescued the impairment of osteogenic *** data indicated that AFF4 promoted the osteogenic differentiation of DFCs by upregulating the transcription of ALKBH1.

关键词： impaired impairment alkaline

Application of nano-patterned InGaN fabricated by selfassembled Ni nano-masks in green InGaN/GaN multiple quantum wells

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Journal of Semiconductors 2023年第4期44卷 86-91页

作者： ruoshi Peng Shengrui Xu Xiaomeng Fan Hongchang Tao Huake Su yuan Gao Jincheng Zhang Yue Hao Wide Bandgap Semiconductor Technology Disciplines State Key Laboratory School of MicroelectronicsXi'dian UniversityXi'an 710071China

The nano-patterned InGaN film was used in green InGaN/GaN multiple quantum wells(MQWs)structure,to relieve the unpleasantly existing mismatch between high indium content InGaN and GaN,as well as to enhance the light *** different self-assembled nano-masks were formed on InGaN by annealing thin Ni layers of different ***,the InGaN films were etched into nano-patterned *** with the green MQWs structure grown on untreated InGaN film,which on nano-patterned InGaN had better luminous *** them the MQWs performed best when 3 nm thick Ni film was used as mask,because that optimally balanced the effects of nano-patterned InGaN on the crystal quality and the light output.

关键词： GaN InGaN nano-mask nano-patterned MQWs

METTL3-mediated m^(6)A RNA methylation regulates dorsal lingual epithelium homeostasis

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International Journal of Oral Science 2022年第3期14卷 287-296页

作者： Qiuchan Xiong Caojie Liu Xin Zheng Xinyi Zhou Kexin Lei Xiaohan Zhang Qian Wang Weimin Lin Ruizhan Tong ruoshi Xu Quan yuan State Key Laboratory of Oral Diseases&National Clinical Research Center for Oral Diseases&West China Hospital of Stomatology Sichuan UniversityChengduChina Department of Thoracic Oncology Cancer Centerand Laboratory of Clinical Cell TherapyWest China HospitalSichuan UniversityChengduChina

The dorsal lingual epithelium,which is composed of taste buds and keratinocytes differentiated from K14^(+)basal cells,discriminates taste compounds and maintains the epithelial barrier.N6-methyladenosine(m^(6)A)is the most abundant mRNA modification in eukaryotic *** METTL3-mediated m^(6)A modification regulates K14^(+)basal cell fate during dorsal lingual epithelium formation and regeneration remains *** we show knockout of Mettl3 in K14^(+)cells reduced the taste buds and enhanced *** of Mettl3 led to increased basal cell proliferation and decreased cell division in taste *** Mettl3 knock-in mice showed little impact on taste buds or keratinization,but displayed increased proliferation of cells around taste buds in a protective manner during post-irradiation ***,we revealed that the most frequent m^(6)A modifications were enriched in Hippo and Wnt signaling,and specific peaks were observed near the stop codons of Lats1 and *** study elucidates that METTL3 is essential for taste bud formation and could promote the quantity recovery of taste bud after radiation.

关键词： METTL3-mediated m^(6)A RNA methylation regulates dorsal lingual epithelium homeostasis RNA