Systems and Synthetic Biology最新文献_第10页

On an infrastructure to support sharing and aggregating pre- and post-publication systems biology research data. 在一个基础设施上，以支持共享和聚合出版前和出版后的系统生物学研究数据。

Systems and Synthetic Biology Pub Date : 2012-06-01 Epub Date: 2012-08-03 DOI: 10.1007/s11693-012-9095-x

Mark Slaymaker, James Osborne, Andrew Simpson, David Gavaghan

{"title":"On an infrastructure to support sharing and aggregating pre- and post-publication systems biology research data.","authors":"Mark Slaymaker, James Osborne, Andrew Simpson, David Gavaghan","doi":"10.1007/s11693-012-9095-x","DOIUrl":"https://doi.org/10.1007/s11693-012-9095-x","url":null,"abstract":"The move towards in silico experimentation has resulted in the use of computational models, in addition to traditional experimental models, to generate the raw data that is analysed and published as research findings. This change requires new methods to be introduced to facilitate independent validation of the underlying models and the reported results. The promotion of co-operative research has the potential to help to both validate results and explore wider problem areas. In this paper we leverage and extend two existing software frameworks to develop an infrastructure that has the potential to both promote the sharing of data between researchers pre-publication and enable access to the data for interested parties post-publication. The pre-publication sharing of data would enable larger problem spaces to be explored by distributed research groups; enabling access to the data post-publication would allow reviewers and the wider community to independently verify the published results which would, in the longer term, help to increase confidence in published results. The framework is used to perform reproducible and numerically validated individual-based computational experiments into the onset of colorectal cancer. Existing results are verified and new insights into the top-down versus bottom-up hypothesis of colorectal crypt invasion are given.","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-012-9095-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31476983","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: 1

Microbial synthetic biology for human therapeutics. 用于人类治疗的微生物合成生物学。

Systems and Synthetic Biology Pub Date : 2012-06-01 Epub Date: 2012-06-02 DOI: 10.1007/s11693-012-9092-0

Aastha Jain, Pooja Bhatia, Archana Chugh

{"title":"Microbial synthetic biology for human therapeutics.","authors":"Aastha Jain, Pooja Bhatia, Archana Chugh","doi":"10.1007/s11693-012-9092-0","DOIUrl":"10.1007/s11693-012-9092-0","url":null,"abstract":"The emerging field of synthetic biology holds tremendous potential for developing novel drugs to treat various human conditions. The current study discusses the scope of synthetic biology for human therapeutics via microbial approach. In this context, synthetic biology aims at designing, engineering and building new microbial synthetic cells that do not pre-exist in nature as well as re-engineer existing microbes for synthesis of therapeutic products. It is expected that the construction of novel microbial genetic circuitry for human therapeutics will greatly benefit from the data generated by 'omics' approaches and multidisciplinary nature of synthetic biology. Development of novel antimicrobial drugs and vaccines by engineering microbial systems are a promising area of research in the field of synthetic biology for human theragnostics. Expression of plant based medicinal compounds in the microbial system using synthetic biology tools is another avenue dealt in the present study. Additionally, the study suggest that the traditional medicinal knowledge can do value addition for developing novel drugs in the microbial systems using synthetic biology tools. The presented work envisions the success of synthetic biology for human therapeutics via microbial approach in a holistic manner. Keeping this in view, various legal and socio-ethical concerns emerging from the use of synthetic biology via microbial approach such as patenting, biosafety and biosecurity issues have been touched upon in the later sections.","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424199/pdf/11693_2012_Article_9092.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31476980","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

Quantum-like model for the adaptive dynamics of the genetic regulation of E. coli's metabolism of glucose/lactose. 大肠杆菌葡萄糖/乳糖代谢遗传调控自适应动力学的类量子模型。

Systems and Synthetic Biology Pub Date : 2012-06-01 Epub Date: 2012-04-11 DOI: 10.1007/s11693-012-9091-1

Masanari Asano, Irina Basieva, Andrei Khrennikov, Masanori Ohya, Yoshiharu Tanaka, Ichiro Yamato

引用次数: 35

Gene network analysis of Aeromonas hydrophila for novel drug target discovery. 嗜水气单胞菌基因网络分析用于新药靶点发现。

Systems and Synthetic Biology Pub Date : 2012-06-01 Epub Date: 2012-05-22 DOI: 10.1007/s11693-012-9093-z

Vijai Singh, Dharmendra Kumar Chaudhary, Indra Mani

{"title":"Gene network analysis of Aeromonas hydrophila for novel drug target discovery.","authors":"Vijai Singh, Dharmendra Kumar Chaudhary, Indra Mani","doi":"10.1007/s11693-012-9093-z","DOIUrl":"https://doi.org/10.1007/s11693-012-9093-z","url":null,"abstract":"Increasing the multi-drug resistance Aeromonas hydrophila creates a health problem regularly thus, an urgent needs to develop and screen potent antibiotics for controlling of the infections. There are many studies have focused on interactions between specific drugs, little is known about the system properties of a full drug interaction in gene network. Thus, an attractive approach for developing novel antibiotics against DNA gyrase, an enzyme essential for DNA replication, transcription, repair and recombination mechanisms which is important for bacterial growth and cell division. Homology modeling method was used to generate the 3-D structure of B subunit of DNA gyrase (gyrB) using known crystal structure. The active amino acids in 3-D structure of gyrB were targeted for structure based virtual screening of potent drugs by molecular docking. Number of drugs and analogs were selected and used for docking against gryB. The drugs Cinodine I, Cyclothialidine and Novobiocin were found to be more binding affinity with gyrB-drug interaction. The homology of gyrB protein sequence of A. hydrophila resembles with other species of Aeromonas closely showed relationship in phylogenetic tree. We have also demonstrated the gene network interactions of gyrB with other cellular proteins which are playing the key role in gene regulation. These findings provide new insight to understand the 3-D structure of gyrB which can be used in structure-based drug discovery; and development of novel, potent and specific drug against B subunit of DNA gyrase.","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-012-9093-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31476981","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

Systems biology beyond degree, hubs and scale-free networks: the case for multiple metrics in complex networks. 超越程度、集线器和无标度网络的系统生物学:复杂网络中多重指标的案例。

Systems and Synthetic Biology Pub Date : 2012-06-01 Epub Date: 2012-05-29 DOI: 10.1007/s11693-012-9094-y

Soumen Roy

引用次数: 31

Mathematical modeling of fission yeast Schizosaccharomyces pombe cell cycle: exploring the role of multiple phosphatases. 分裂酵母分裂糖酵母pombe细胞周期的数学建模:探索多种磷酸酶的作用。

Systems and Synthetic Biology Pub Date : 2011-12-01 Epub Date: 2011-12-08 DOI: 10.1007/s11693-011-9090-7

P Anbumathi, Sharad Bhartiya, K V Venkatesh

{"title":"Mathematical modeling of fission yeast Schizosaccharomyces pombe cell cycle: exploring the role of multiple phosphatases.","authors":"P Anbumathi, Sharad Bhartiya, K V Venkatesh","doi":"10.1007/s11693-011-9090-7","DOIUrl":"https://doi.org/10.1007/s11693-011-9090-7","url":null,"abstract":"Unlabelled: Cell cycle is the central process that regulates growth and division in all eukaryotes. Based on the environmental condition sensed, the cell lies in a resting phase G0 or proceeds through the cyclic cell division process (G1→S→G2→M). These series of events and phase transitions are governed mainly by the highly conserved Cyclin dependent kinases (Cdks) and its positive and negative regulators. The cell cycle regulation of fission yeast Schizosaccharomyces pombe is modeled in this study. The study exploits a detailed molecular interaction map compiled based on the published model and experimental data. There are accumulating evidences about the prominent regulatory role of specific phosphatases in cell cycle regulations. The current study emphasizes the possible role of multiple phosphatases that governs the cell cycle regulation in fission yeast S. pombe. The ability of the model to reproduce the reported regulatory profile for the wild-type and various mutants was verified though simulations.Electronic supplementary material: The online version of this article (doi:10.1007/s11693-011-9090-7) contains supplementary material, which is available to authorized users.","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-011-9090-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31093305","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: 5

In silico description of cobalt and nickel assimilation systems in the genomes of methanogens. 甲烷菌基因组中钴和镍同化系统的计算机描述。

Systems and Synthetic Biology Pub Date : 2011-12-01 Epub Date: 2011-10-15 DOI: 10.1007/s11693-011-9087-2

P Chellapandi

{"title":"In silico description of cobalt and nickel assimilation systems in the genomes of methanogens.","authors":"P Chellapandi","doi":"10.1007/s11693-011-9087-2","DOIUrl":"https://doi.org/10.1007/s11693-011-9087-2","url":null,"abstract":"Methanogens are a diverse group of organisms that can live in a wide range of environments. Herein, cobalt and tungsten assimilation pathways have proposed to be established in the genomes of Methanococcus maripaludies C5 and Methanosarcina mazei Go1, respectively. All of the proteins involved in the proposed pathways were identified from public domain databases and then complied manually to reconstruct the pathways. The function of proteins with unknown function was assigned by a combined prediction approach. Totally, 17 proteins were identified to cobalt transport and assimilation processes whereas 7 proteins reported to tungsten assimilation system. Phylogenetic analysis of this study revealed that heavy metal transporter of methanogens could be evolved from closely related members in the different genera of methanogens. Nevertheless, genes encoding for metal resistance proteins could be originated from thermophilic and sulfur reducing bacteria. Many metalloenzymes in methanogens were very unique to the species of methanogens. It implied that these metal ions were utilized to produce the precursors for energy driven processes of methanogens. This study suggested that in combination of systems models and evolutionary inference can only correlate metabolic fluxes and physiological changes in methanogens. In silico models of this study will provide insights to design experiments for heavy metal assimilation processes of methanogens growing under heavy metal-rich environments and or in a laboratory condition.","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-011-9087-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31093304","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

Modulating ectopic gene expression levels by using retroviral vectors equipped with synthetic promoters. 利用携带合成启动子的逆转录病毒载体调节异位基因表达水平。

Systems and Synthetic Biology Pub Date : 2011-12-01 Epub Date: 2011-11-20 DOI: 10.1007/s11693-011-9089-0

Joshua P Ferreira, Ryan W S Peacock, Ingrid E B Lawhorn, Clifford L Wang

{"title":"Modulating ectopic gene expression levels by using retroviral vectors equipped with synthetic promoters.","authors":"Joshua P Ferreira, Ryan W S Peacock, Ingrid E B Lawhorn, Clifford L Wang","doi":"10.1007/s11693-011-9089-0","DOIUrl":"https://doi.org/10.1007/s11693-011-9089-0","url":null,"abstract":"Unlabelled: The human cytomegalovirus and elongation factor 1α promoters are constitutive promoters commonly employed by mammalian expression vectors. These promoters generally produce high levels of expression in many types of cells and tissues. To generate a library of synthetic promoters capable of generating a range of low, intermediate, and high expression levels, the TATA and CAAT box elements of these promoters were mutated. Other promoter variants were also generated by random mutagenesis. Evaluation using plasmid vectors integrated at a single site in the genome revealed that these various synthetic promoters were capable of expression levels spanning a 40-fold range. Retroviral vectors were equipped with the synthetic promoters and evaluated for their ability to reproduce the graded expression demonstrated by plasmid integration. A vector with a self-inactivating long terminal repeat could neither reproduce the full range of expression levels nor produce stable expression. Using a second vector design, the different synthetic promoters enabled stable expression over a broad range of expression levels in different cell lines.Electronic supplementary material: The online version of this article (doi:10.1007/s11693-011-9089-0) contains supplementary material, which is available to authorized users.","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-011-9089-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31093306","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: 31

Characterizing the memory of the GAL regulatory network in Saccharomyces cerevisiae. 表征酿酒酵母中GAL调控网络的记忆。

Systems and Synthetic Biology Pub Date : 2011-12-01 Epub Date: 2011-09-20 DOI: 10.1007/s11693-011-9086-3

Vishwesh V Kulkarni, Venkatesh Kareenhalli, Ganesh A Viswananthan, Marc Riedel

引用次数: 1

A systems view of the protein expression process. 蛋白质表达过程的系统观点。

Systems and Synthetic Biology Pub Date : 2011-12-01 Epub Date: 2011-10-19 DOI: 10.1007/s11693-011-9088-1

Sucheta Gokhale, Dimpal Nyayanit, Chetan Gadgil

{"title":"A systems view of the protein expression process.","authors":"Sucheta Gokhale, Dimpal Nyayanit, Chetan Gadgil","doi":"10.1007/s11693-011-9088-1","DOIUrl":"https://doi.org/10.1007/s11693-011-9088-1","url":null,"abstract":"Unlabelled: Many biological processes are regulated by changing the concentration and activity of proteins. The presence of a protein at a given subcellular location at a given time with a certain conformation is the result of an apparently sequential process. The rate of protein formation is influenced by chromatin state, and the rates of transcription, translation, and degradation. There is an exquisite control system where each stage of the process is controlled both by seemingly unregulated proteins as well as through feedbacks mediated by RNA and protein products. Here we review the biological facts and mathematical models for each stage of the protein production process. We conclude that advances in experimental techniques leading to a detailed description of the process have not been matched by mathematical models that represent the details of the process and facilitate analysis. Such an exercise is the first step towards development of a framework for a systems biology analysis of the protein production process.Electronic supplementary material: The online version of this article (doi:10.1007/s11693-011-9088-1) contains supplementary material, which is available to authorized users.","PeriodicalId":22161,"journal":{"name":"Systems and Synthetic Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s11693-011-9088-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31093308","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