Systems and Synthetic Biology最新文献_第9页

Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches. 利用计算生物学和系统生物学方法重建和可视化毕赤酵母CBS7435的碳水化合物、n -糖基化途径。

Systems and Synthetic Biology Pub Date : 2013-06-01 Epub Date: 2012-12-30 DOI: 10.1007/s11693-012-9102-2

Akriti Srivastava, Pallavi Somvanshi, Bhartendu Nath Mishra

{"title":"Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches.","authors":"Akriti Srivastava, Pallavi Somvanshi, Bhartendu Nath Mishra","doi":"10.1007/s11693-012-9102-2","DOIUrl":"https://doi.org/10.1007/s11693-012-9102-2","url":null,"abstract":"Pichia pastoris is an efficient expression system for production of recombinant proteins. To understand its physiology for building novel applications it is important to understand and reconstruct its metabolic network. The metabolic reconstruction approach connects genotype with phenotype. Here, we have attempted to reconstruct carbohydrate metabolism pathways responsible for high biomass density and N-glycosylation pathways involved in the post translational modification of proteins of P. pastoris CBS7435. Both these metabolic pathways play a crucial role in heterologous protein production. We report novel, missing and unannotated enzymes involved in the target metabolic pathways. A strong possibility of cellulose and xylose metabolic processes in P. pastoris CBS7435 suggests its use in the area of biofuels. The reconstructed metabolic networks can be used for increased yields and improved product quality, for designing appropriate growth medium, for production of recombinant therapeutics and for making biofuels. ","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-012-9102-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32035572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

Designing de novo: interdisciplinary debates in synthetic biology. 重新设计:合成生物学的跨学科辩论。

Systems and Synthetic Biology Pub Date : 2013-06-01 Epub Date: 2013-04-09 DOI: 10.1007/s11693-013-9106-6

Ana Delgado, Manuel Porcar

{"title":"Designing de novo: interdisciplinary debates in synthetic biology.","authors":"Ana Delgado, Manuel Porcar","doi":"10.1007/s11693-013-9106-6","DOIUrl":"https://doi.org/10.1007/s11693-013-9106-6","url":null,"abstract":"Synthetic biology is often presented as a promissory field that ambitions to produce novelty by design. The ultimate promise is the production of living systems that will perform new and desired functions in predictable ways. Nevertheless, realizing promises of novelty has not proven to be a straightforward endeavour. This paper provides an overview of, and explores the existing debates on, the possibility of designing living systems de novo as they appear in interdisciplinary talks between engineering and biological views within the field of synthetic biology. To broaden such interdisciplinary debates, we include the views from the social sciences and the humanities and we point to some fundamental sources of disagreement within the field. Different views co-exist, sometimes as controversial tensions, but sometimes also pointing to integration in the form of intermediate positions. As the field is emerging, multiple choices are possible. They will inform alternative trajectories in synthetic biology and will certainly shape its future. What direction is best is to be decided in reflexive and socially robust ways. ","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-013-9106-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32037157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 21

A primer to 'bio-objects': new challenges at the interface of science, technology and society. “生物物体”入门:科学、技术和社会界面的新挑战。

Systems and Synthetic Biology Pub Date : 2013-06-01 Epub Date: 2013-02-26 DOI: 10.1007/s11693-013-9104-8

Peter Dabrock, Matthias Braun, Jens Ried, Uwe Sonnewald

引用次数: 10

ATP4A gene regulatory network for fine-tuning of proton pump and ion channels. 质子泵和离子通道微调的ATP4A基因调控网络。

Systems and Synthetic Biology Pub Date : 2013-06-01 Epub Date: 2013-01-09 DOI: 10.1007/s11693-012-9103-1

Vijai Singh, Indra Mani, Dharmendra Kumar Chaudhary

{"title":"ATP4A gene regulatory network for fine-tuning of proton pump and ion channels.","authors":"Vijai Singh, Indra Mani, Dharmendra Kumar Chaudhary","doi":"10.1007/s11693-012-9103-1","DOIUrl":"https://doi.org/10.1007/s11693-012-9103-1","url":null,"abstract":"The ATP4A encodes α subunit of H(+), K(+)-ATPase that contains catalytic sites of the enzyme forming pores through cell membrane which allows the ion transport. H(+), K(+)-ATPase is a membrane bound P-type ATPase enzyme which is found on the surface of parietal cells and uses the energy derived from each cycle of ATP hydrolysis that can help in exchanging ions (H(+), K(+) and Cl(-)) across the cell membrane secreting acid into the gastric lumen. The 3-D model of α-subunit of H(+), K(+)-ATPase was generated by homology modeling. It was evaluated and validated on the basis of free energies and amino acid residues. The inhibitor binding amino acid active pockets were identified in the 3-D model by molecular docking. The two drugs Omeprazole and Rabeprazole were found more potent interactions with generated model of α-subunit of H(+), K(+)-ATPase on the basis of their affinity between drug-protein interactions. We have generated ATP4A gene regulatory networks for interactions with other proteins which involved in regulation that can help in fine-tuning of proton pump and ion channels. These findings provide a new dimension for discovery and development of proton pump inhibitors and gene regulation of the ATPase. It can be helpful in better understanding of human physiology and also using synthetic biology strategy for reprogramming of parietal cells for control of gastric ulcers. ","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-012-9103-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32037155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

A quantitative study of gene regulatory pathways in Bacillus subtilis for virulence and competence phenotype by quorum sensing. 枯草芽孢杆菌毒力和能力表型基因调控途径的群体感应定量研究。

Systems and Synthetic Biology Pub Date : 2013-06-01 Epub Date: 2013-03-05 DOI: 10.1007/s11693-013-9105-7

Ashwani Kumar, Tiratha Raj Singh

{"title":"A quantitative study of gene regulatory pathways in Bacillus subtilis for virulence and competence phenotype by quorum sensing.","authors":"Ashwani Kumar, Tiratha Raj Singh","doi":"10.1007/s11693-013-9105-7","DOIUrl":"https://doi.org/10.1007/s11693-013-9105-7","url":null,"abstract":"Quorum sensing (QS) is a process which allows a population of bacteria to coordinately regulate gene expression of their entire community. Bacillus subtilis is a soil organism which uses QS to alternate between competence for DNA uptake and sporulation. We propose a model to describe the components involved in QS and to analyze reaction species involved in the regulation of QS machinery. We targeted only those QS phenotypes for which the genetic organization and molecular characterization of the components are fully elucidated. We have analyzed simulations for concentration of different species involved in competence as well as sporulation pathways at diverse time period using quantitative methods. It was observed that there is possibility of achieving different measurement from reactions taken place between species by applying irreversible Michaelis-Menten kinetic law. We obtain variation in measurement on changing parameters such as concentrations ranging from 0.3 to 50 μM in stepwise manner by setting end time in the range of 0.1-100 ms. Additionally we observe covariance between different reaction species involved in QS by fluctuating their quantities in real-time simulations. Our model mimics correctly the phenotype for competence and virulence. We concluded that time factor play major role to determine rate kinetics of diverse reaction species as compared to their concentrations and support the hypothesis of getting genetic stability while colonies are in synchronization. ","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-013-9105-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32037156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Lysine overproducing Corynebacterium glutamicum is characterized by a robust linear combination of two optimal phenotypic states. 赖氨酸过量产生谷氨酸棒状杆菌的特点是两种最佳表型状态的强大线性组合。

Systems and Synthetic Biology Pub Date : 2013-06-01 Epub Date: 2013-04-17 DOI: 10.1007/s11693-013-9107-5

Meghna Rajvanshi, Kalyan Gayen, K V Venkatesh

{"title":"Lysine overproducing Corynebacterium glutamicum is characterized by a robust linear combination of two optimal phenotypic states.","authors":"Meghna Rajvanshi, Kalyan Gayen, K V Venkatesh","doi":"10.1007/s11693-013-9107-5","DOIUrl":"https://doi.org/10.1007/s11693-013-9107-5","url":null,"abstract":"A homoserine auxotroph strain of Corynebacterium glutamicum accumulates storage compound trehalose with lysine when limited by growth. Industrially lysine is produced from C. glutamicum through aspartate biosynthetic pathway, where enzymatic activity of aspartate kinase is allosterically controlled by the concerted feedback inhibition of threonine plus lysine. Ample threonine in the medium supports growth and inhibits lysine production (phenotype-I) and its complete absence leads to inhibition of growth in addition to accumulating lysine and trehalose (phenotype-II). In this work, we demonstrate that as threonine concentration becomes limiting, metabolic state of the cell shifts from maximizing growth (phenotype-I) to maximizing trehalose phenotype (phenotype-II) in a highly sensitive manner (with a Hill coefficient of 4). Trehalose formation was linked to lysine production through stoichiometry of the network. The study demonstrated that the net flux of the population was a linear combination of the two optimal phenotypic states, requiring only two experimental measurements to evaluate the flux distribution. The property of linear combination of two extreme phenotypes was robust for various medium conditions including varying batch time, initial glucose concentrations and medium osmolality. ","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-013-9107-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32037158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Analysis of the multicopper oxidase gene regulatory network of Aeromonas hydrophila. 嗜水气单胞菌多铜氧化酶基因调控网络分析。

Systems and Synthetic Biology Pub Date : 2012-12-01 Epub Date: 2012-08-23 DOI: 10.1007/s11693-012-9096-9

Vijai Singh, Indra Mani, Dharmendra Kumar Chaudhary

引用次数: 6

Gene regulatory network modeling using literature curated and high throughput data. 利用文献和高通量数据建立基因调控网络模型。

Systems and Synthetic Biology Pub Date : 2012-12-01 Epub Date: 2012-12-07 DOI: 10.1007/s11693-012-9100-4

Vishwesh V Kulkarni, Reza Arastoo, Anupama Bhat, Kalyansundaram Subramanian, Mayuresh V Kothare, Marc C Riedel

{"title":"Gene regulatory network modeling using literature curated and high throughput data.","authors":"Vishwesh V Kulkarni, Reza Arastoo, Anupama Bhat, Kalyansundaram Subramanian, Mayuresh V Kothare, Marc C Riedel","doi":"10.1007/s11693-012-9100-4","DOIUrl":"10.1007/s11693-012-9100-4","url":null,"abstract":"Building on the linear matrix inequality (LMI) formulation developed recently by Zavlanos et al. (Automatica: Special Issue Syst Biol 47(6):1113-1122, 2011), we present a theoretical framework and algorithms to derive a class of ordinary differential equation (ODE) models of gene regulatory networks using literature curated data and microarray data. The solution proposed by Zavlanos et al. (Automatica: Special Issue Syst Biol 47(6):1113-1122, 2011) requires that the microarray data be obtained as the outcome of a series of controlled experiments in which the network is perturbed by over-expressing one gene at a time. We note that this constraint may be relaxed for some applications and, in addition, demonstrate how the conservatism in these algorithms may be reduced by using the Perron-Frobenius diagonal dominance conditions as the stability constraints. Due to the LMI formulation, it follows that the bounded real lemma may easily be used to make use of additional information. We present case studies that illustrate how these algorithms can be used on datasets to derive ODE models of the underlying regulatory networks. ","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528886/pdf/11693_2012_Article_9100.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31917207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Are we doing synthetic biology? 我们在做合成生物学吗?

Systems and Synthetic Biology Pub Date : 2012-12-01 Epub Date: 2012-12-05 DOI: 10.1007/s11693-012-9101-3

Manuel Porcar, Juli Peretó

引用次数: 17

Optimizing bioethanol production by regulating yeast growth energy. 通过调节酵母生长能量优化生物乙醇生产。

Systems and Synthetic Biology Pub Date : 2012-12-01 Epub Date: 2012-11-10 DOI: 10.1007/s11693-012-9099-6

Emad Y Moawad

{"title":"Optimizing bioethanol production by regulating yeast growth energy.","authors":"Emad Y Moawad","doi":"10.1007/s11693-012-9099-6","DOIUrl":"https://doi.org/10.1007/s11693-012-9099-6","url":null,"abstract":"The goal of this work is to optimize production of bio-ethanol by fermentation through regulating yeast growth energy (YGE), and provide the mechanism of ethanol production from food-waste leachate (FWL) using yeast (S. cerevisiae) as inoculums to be predictable and controllable. The wide range of reduced sugar concentration (RSC) which is commonly administered from low (35 g per liter) to very high (100 g per liter) is responsible for costs increasing besides risks of FWL contamination and death of yeast cells. A mathematical model is presented to describe yeast growth energy (YGE) due to RSC doses along with predicting the amounts of ethanol yield by each dose to identify the optimum one. Simulations of the presented model showed that YGE, energy intake (EI), and their produced ethanol energy (PEE) are always balanced during fermentation process according to the law of conservation of energy. For a better fermentation rate in a continuous process and a large-scale production; YGE should be less than half of EI and more than its quarter (i.e. [Formula: see text]) which keeps the residual energy less than YGE to avoid risks of osmotic stresses or aging of cells allowing the survival of all yeast cells as long as possible to maximize ethanol production and decrease productivity costs. ","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-012-9099-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31917206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 19