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Multi-objective Optimization Conceptual Design of Product Structure Based on Variable Length gene expression

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Chinese Journal of Mechanical Engineering 2011年第1期24卷 42-49页

作者： WEI Xiaopeng ZHAO Tingting JU Zhenhe ZHANG Shi LI Xiaoxiao School of Management Dalian University of Technology Dalian 116023 China Key Laboratory of Advanced Design and Intelligent Computing of Ministry of Education Dalian University Dalian 116622 China New Energy Center Shenyang Institute of Engineering Shenyang 110136 China Liaoning Solar Energy R＆D Co. Ltd. Shenyang 110136 China Institute of Systems Engineering Northeastern University Shenyang 110004 China

It is a complicated problem for the bottom-to-top adaptive conceptual design of complicated products between structure and function. Reliable theories demand to be found in order to determine whether the structure accords with the requirement of design. For the requirement generally is dynamic variety as time passes, new requirements will come, and some initial requirements can no longer be used. The number of product requirements, the gene length expressing requirements, the structure of the product, and the correlation matrix are varied with individuation of customer requirements of the product. By researching on the calculation mechanisms of dynamic variety, the approaches of gene expression and variable length gene expression are proposed. According to the diversity of structure selection in conceptual design and mutual relations between structure and function as well as structure and structure, the correlation matrixes between structure and function as well as structure and structure are defined. By the approach of making the sum of the elements of correlation matrix maximum, the mathematical models of multi-object optimization for structure design are provided based on variable requirements. An improved genetic algorithm called segment genetic algorithm is proposed based on optimization preservation simple genetic algorithm. The models of multi-object optimization are calculated by the segment genetic algorithm and hybrid genetic algorithm. An example for the conceptual design of a washing machine is given to show that the proposed method is able to realize the optimization structure design fitting for variable requirements. In addition, the proposed approach can provide good Pareto optimization solutions, and the individuation customer requirements for structures of products are able to be resolved effectively.

关键词： gene expression multi-object optimization conceptual design genetic algorithm

Substrate concentration effect on gene expression in genetic circuits with additional positive feedback

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Science China(Technological Sciences) 2018年第8期61卷 1175-1183页

作者： WU LuLu WANG Pei Lü JinHu Academy of Mathematics and Systems Science Chinese Academy of Sciences School of Mathematical Sciences University of Chinese Academy of Sciences School of Mathematics and Statistics Henan University School of Automation Science and Electrical Engineering State Key Laboratory of Software Development Environment and Beijing Advanced Innovation Center for Big Data and Brain Machine Intelligence Beihang University

In gene regulatory networks, gene regulation loops often occur with multiple positive feedback, multiple negative feedback and coupled positive and negative feedback forms. In above gene regulation loops, auto-activation loops are ubiquitous regulatory motifs. This paper aims to investigate a two-component dual-positive feedback genetic circuit, which consists of a double negative feedback circuit and an additional positive feedback loop(APFL). We study effect of substrate concentration on gene expression in the single and the networked systems with APFLs, respectively. We find that substrate concentration can tune stochastic switch behavior in the signal system and then we explore relationship of substrate concentration with positive feedback strength in aspect of stochastic switch behavior. Furthermore, we also discuss gene expression and stochastic switch behavior in the networked systems with APFLs. Based on analysis in the networked systems, we discover that genes express in some specific cells and do not express in the other cells when the expression achieves its steady state. These results can be used to well explain the character of regionalization in the expression of genes and the phenomenon of gene differentiation.

关键词： substrate concentration additional positive feedback loop stochastic switch behavior gene expression gene differ-entiation

gene expression analysis of cytokines and MMPs in melatonin and rhBMP-2 enhanced bone remodeling

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World Journal of Orthopedics 2024年第11期15卷 1075-1087页

作者： Marina Ribeiro Paulini Letícia Ferreira Montarele Dimitrius Leonardo Pitol Gisele Giannocco Bruno Fiorelini Pereira Daniela Vieira Buchaim Carlos Henrique Bertoni Reis Rogério Leone Buchaim Joao Paulo Mardegan Issa Department of Basic and Oral Biology University of São PauloRibeirao Preto 14040-904Brazil Instituto de Ciências Ambientais Químicas e FarmacêuticasFederal University of São PauloDiadema 09972-270Brazil Medical School University Center of AdamantinaAdamantina 17800-000Brazil Postgraduate Program in Structural and Functional Interactions in Rehabilitation University of MariliaMarilia 17525-902Brazil Department of Biological Sciences Bauru School of DentistryUniversity of São PauloBauru 17012-901Brazil Department of Basic and Oral Biology Ribeirão Preto School of DentistryUniversity of São PauloRibeirao Preto 14040-904Brazil

BACKGROUND In the medical and dental fields,there is a need for studies of new therapeutic approaches for the treatment of bone defects that cause extensive bone *** may be an important endogenous biological factor for bone remodeling,and growth factors may enhance the repair *** To evaluate the gene expression of cytokines(IL-1β,IL-6,IL-10 and TNF-α),markers of osteoclastogenesis(RANK,RANKL and OPG)and MMPs(MMP-1,MMP-2,MMP-8 and MMP-13)from the treatment of melatonin associated with an osteogenic membrane and rhBMP-2 on the recovery of a bone *** Sixty-four rats were used and divided into 9 experimental groups and were formed according to the treatment carried out in the region of the bone lesion,which varied between the combination of 1,10 and 100μmol/L of *** expression analysis was performed using real time-PCR by reading the concentration of total RNA and reverse *** There were differences between groups when compared with clot or scaffold control,and improvement with a higher concentration of melatonin or *** combination melatonin(1μg)with 5μg of rhBMP-2,using the guided bone regeneration technique,demonstrated some effects,albeit mild,on bone repair of critical bone *** This indicates that the approach for administering these substances needs to be reassessed,with the goal of ensuring their direct application to the affected ***,future research must be carried out,seeking to produce materials with these ideal characteristics.

关键词： Bone repair Melatonin gene expression Rhbmp-2 Scaffold Tissue engineering Guided bone regeneration

gene expression in cisplatin ototoxicity and protection with p53 inhibitor

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Journal of Otology 2009年第2期4卷 61-70页

作者： Donald Coling Richard Salvi Center for Hearing & Deafness 137 Cary HallUniversity at Buffalo

Cisplatin damages cochlear hair cells and spiral ganglion neurons through cell death signaling pathways that are not fully understood. We used focused apoptosis gene microarrays to study early changes in gene expres- sion in cochlear cultures from P3 neonatal rats treated with cisplatin (0.2 mM). After 12 hours of cisplatin treat- ment, more than 50% of the 96 genes on the array showed a significant decrease in expression, consistent with widespread cell death. However, after 3 hours of cisplatin treatment, 10 genes showed significant increase in ex- pression in total cochlear tissue. In experiments with subsets of cochlear tissues, at 3h, cisplatin induced increased expression of 12 genes in the cochlear sensory epithelium (basilar membrane) and 11 genes in the spiral ganglion (tissue of Rosenthal’s canal, containing the spiral ganglion). These included pro- and anti-apoptotic genes in- volved in the p53 signaling pathway, TNF receptor family, NF-kappaB pathway, death domain family, death effec- tor domain family, Bcl-2 family, CARD family, TRAF family, and GTP signal transduction. Although the changes in gene expression showed an overlap between basilar membrane and spiral ganglion, other changes, which may reflect the unique response of each tissue, were also observed. Pifithrin-α blocked cisplatin-induced up-regulation of genes in the p53 signaling pathway when assayed by both superarray and real time PCR. The data add to our understanding of the involvement of p53 in cisplatin-induced ototoxicity and otoprotection, conferred by the p53 inhibitor Pifithrin-α.

关键词： cisplatin p53 Pifithrin-α gene expression ototoxicity cochlea hair cells spiral ganglion neurons

gene expression profiling and mechanism study of neural stem cells response to surface chemistry

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Regenerative Biomaterials 2014年第1期1卷 37-47页

作者： Ying Wang Shenglian Yao Qingyuan Meng Xiaolong Yu Xiumei Wang Fuzhai Cui Institute for regenerative medicine and biomimetic materials School of materials science and engineeringTsinghua UniversityBeijing 100084China Department of anatomy histology and embryologySchool of basic medical sciencesCapital Medical UniversityBeijing 100069China Department of material science and chemical engineering Hainan UniversityHaikou 570228China

To declare the mechanisms of neural stem cells(NSCs)in response to material surface chemistry,NSCs were exposed to the self-assemble monolayers of alkanethiolates on gold surfaces terminated with amine(NH2),hydroxyl(OH)and methyl(CH3)for *** morphological responses of NSCs were recorded;the gene expression profilings were detected by genechips;the gene expressions data of NSCs responded to different chemical groups were declared through the gene ontology term and pathway *** showed that cells behaved dissimilar on the three chemical groups,the adhesion,proliferation and migration were easier on the NH2 and OH groups;the gene expressions of NSCs were induced differently,either,involved in several functional processes and signaling ***3 group induced genes enriched much in chemistry reactions and death processes,whereas many genes of cellular nucleotide metabolism were ***2 group induced NSCs to express many genes of receptors on membrane,and participated in cellular signal transduction of cell adhesion and interactions,or associated with axon *** group was similar to NH2 group to induce the membrane response,but it also down regulated metabolism of ***,it declared the chemical groups affected NSCs through inner way and the NH2,OH and CH3 groups triggered the cellular gene expression in different signaling pathways.

关键词： neural stem cell chemical group biomaterial gene expression receptor signaling pathway

gene expression profile of degenerated cervical intervertebral disc tissues in rats

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Chinese Journal of Traumatology 2004年第6期7卷 330-340页

作者：王拥军吕维加施杞周重建张强周泉卞琴刘梅梁智仁 Research Institute of Spine Shanghai University of Traditional Chinese Medicine Shanghai 200032 China Department of Orthopaedics Medical College of Hongkong University Hongkong China Department of Orthopaedics Changzheng Hospital Second Military Medical University Shanghai 200032 China

Objective: To analyze the gene expression profile of degenerated cervical intervertebral disc of Sprague Dawley rats on a large ***: Degenerated models of Sprague Dawley rats of 9 months old (degeneration group, n=9) and normal Sprague Dawley rats of 3 months old (control group, n=9) were prepared, respectively. mRNA was obtained from the cervical intervertebral disc of rats in both groups, respectively, and then labelled by Cy5 and Cy3 fluorescence respectively after reverse transcription to obtain intervertebral disc cDNA probes. cDNA probes were hybridized with BiostarR-40s gene expression profile chips and scanned by laser scanner. The results were treated with portrait analysis, standardization management, and ratio analysis with ***: Compared with the rats in the control group, (9.6)% (381 pieces in total) gene expression changed obviously in the rats in the degeneration group, among which, the gene expression quantities of 171 pieces increased significantly (r=the ratio of the degeneration group to the control group >(2.0)), 52 pieces of which had certain function. While the gene expression quantities of 211 pieces decreased significantly (rgene chip technology can be used to analyze the gene expression profile of degenerated intervertebral disc of rats in parallel, in quantity and on a large scale, which helps to testify the representative genes and protein expression, and plays an important role in clarifying the pathogenesis of degenerated intervertebral disc.

关键词： Intervertebral disc gene expression Rats

Effect of Long-Term Intake of Y^(3+) in Drinking Water on gene expression in Brains of Rats

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Journal of Rare Earths 2006年第3期24卷 369-373页

作者：杨维东张萍刘洁生薛艳芳 Department of Biotechnology Jinan University Guangzhou 510632 China

The rats were fed with water dissolved Y^3＋ at different levels （0, 53.4, 5340 mg·L^-1） for 7 months. The gene expression in brain tissue was detected with oligonucleotide microarray. The results show that, compared to the control, 789 genes express differentially, 507 over-expressed genes and 282 under-expressed genes in the high-dose group （5340 mg· L^-1）, of which, most were related to cell receptor, cell signal and transmission, and ionic passage. 44 genes were found to express differentially including 32 over-expressed genes and 12 under-expressed genes in the low-dose group （53. 40 mg· L^-1）, of which, most were related to cell skeleton and movement, immunity, and DNA binding protein. These resuits suggest that Y^3. can change the expression of some genes, which may be responsible for the toxicity of rare earths on learning and memory.

关键词： gene expression rats cRNA rare earths

Synergistic Effect of Auto-Activation and Small RNA Regulation on gene expression

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Chinese Physics Letters 2010年第9期27卷 237-240页

作者：熊礼平马余强汤雷翰 National Laboratory of Solid State Microstructures Nanjing University Nanjing 210093 Laboratory of Soft Condensed Matter Physics and Interdisciplinary Research Soot-hOw University Suzhou 215006 Department of Physics Hong Kong Baptist University Kowloon Tong Hong Kong

Auto-activation and small ribonucleic acid （RNA）-mediated regulation are two important mechanisms in controlling gene expression. We study the synergistic effect of these two regulations on gene expression. It is found that under this combinatorial regulation, gene expression exhibits bistable behaviors at the transition regime, while each of these two regulations, if working solely, only leads to monostability. Within the stochastic framework, the base pairing strength between sRNA and mRNA plays an important role in controlling the transition time between on and off states. The noise strength of protein number in the off state approaches 1 and is smaller than that in the on state. The noise strength also depends on which parameters, the feedback strength or the synthesis rate of small RNA, are tuned in switching the new insight into gene-regulation mechanism and can be gene expression on and off. Our findings may provide applied in synthetic biology.

关键词： NON-coding RNA geneTIC regulation gene expression COMBINATORIAL analysis STOCHASTIC processes SYNTHETIC biology

SDG714 Regulates Specific gene expression and Consequently Affects Plant Growth via H3K9 Dimethylation

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Journal of Integrative Plant Biology 2010年第4期52卷 420-430页

作者： Bo Ding Yan Zhu Zhong-Yuan Bu Wen-Hui Shen Yu Yu Ai-Wu Dong State KeyLaboratory of genetic Engineering Institute of Plant Biology School of Life Sciences Fudan University Shanghai 200433 China Institut de Biologie Moleculaire des Plantes du CNRS Universite Louis Pasteur de Strasbourg 67084 Strasbourg Cedex France B. Ding and Y. Zhu contributed equally to this paper

Histone lysine methylation is known to be involved in the epigenetic regulation of gene expression in all eukaryotes including plants. Here we show that the rice SDG714 is primarily responsible for dimethylation but not trimethylaUon on histone H3K9 in vivo. Overexpression of YFP-SDG714 in Arabidopsis significantly inhibits plant growth and this inhibition is associated with an enhanced level of H3K9 dimethylation. Our microarray results show that many genes essential for the plant growth and development were downregulated in transgenic Arabidopsis plants overexpressing YFP-SDG714. By chromatin immunoprecipitation analysis, we show that YFP-SDG714 is targeted to specific chromatin regions and dimethylate the H3Kg, which is linked with heterochromatinization and the downregulation of genes. Most interestingly, when YFP-SDG714 production is stopped, the inhibited plants can partially restore their growth, suggesting that the perturbation of gene expression caused by YFP-SDG714 is revertible. Taken together, our results point to an important role of SDG714 in H3K9 dimethylation, suppression of gene expression and plant growth, and provide a potential method to regulate gene expression and plant development by an on-off switch of SDG714 expression.

关键词： HISTONES gene expression ARABIDOPSIS PLANT growth METHYLATION