Engineering biology最新文献_第6页

Long-range order and short-range disorder in Saccharomyces cerevisiae biofilm 酿酒酵母生物膜中的长程有序和短程无序

Engineering biology Pub Date : 2019-03-14 DOI: 10.1049/enb.2018.5008

Vincent Piras, Adam Chiow, Kumar Selvarajoo

{"title":"Long-range order and short-range disorder in Saccharomyces cerevisiae biofilm","authors":"Vincent Piras, Adam Chiow, Kumar Selvarajoo","doi":"10.1049/enb.2018.5008","DOIUrl":"10.1049/enb.2018.5008","url":null,"abstract":"<div>\u0000 <p>Biofilm, a colony forming cooperative response of microorganisms under environmental stress, is a major concern for food safety, water safety and drug resistance. Most current works focus on controlling biofilm growth by targeting single genes. Here, the authors investigated transcriptome-wide expressions of the yeast Saccharomyces cerevisiae biofilm in wildtype, and six previously identified biofilm regulating overexpression strains. Using statistical distributions for low expression filter (TPM > 5), Pearson auto- and cross-correlations reveal a strong transcriptome-wide invariance among all genotypes. The 50 highly expressed genes, however, differ significantly between the genotypes. Principal components analysis shows the global similarity between most overexpression strains. Thus, though single overexpression strains may show significant favourable local and acute expression changes (short-range disorder), the almost unperturbed global and collective structure between the genotypes indicate gradual adaptive response converging to original stable biofilm states (long-range order). Hierarchical clustering and gene ontology show 11 groups of local (e.g. mitochondria processes, amine and nucleotide metabolic processes) and 6 groups of global (e.g. transcription, translation and cell cycle) processes for all genotypes. The overall data indicate that there is a strong global regulatory structure that keeps the overall biofilm stable in all investigated strains.</p>\u0000 </div>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"3 1","pages":"12-19"},"PeriodicalIF":0.0,"publicationDate":"2019-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/enb.2018.5008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46325841","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

Thermofluidic chip containing virtual thermal wells 包含虚拟热阱的热流体芯片

Engineering biology Pub Date : 2019-03-11 DOI: 10.1049/enb.2018.5010

Andrew J. Ferguson, Matthew J. Hayes, Blair C. Kirkpatrick, Yen-chun Lin, Vijay Narayan, Albert Prak

引用次数: 2

Education and training for industrial biotechnology and engineering biology 工业生物技术和工程生物学的教育和培训

Engineering biology Pub Date : 2018-06-11 DOI: 10.1049/enb.2018.0001

Camille J. Delebecque, Jim Philp

引用次数: 7

Editorial: BioPart Datasheets 编辑:BioPart数据表

Engineering biology Pub Date : 2018-03-27 DOI: 10.1049/enb.2018.0003

Prof Richard I Kitney, Dr Chueh Loo Poh

引用次数: 0

Engineering biology and the grand challenges: Do we need a new R&D&I model? 工程生物学和重大挑战:我们是否需要一个新的研发与创新模式?

Engineering biology Pub Date : 2018-02-28 DOI: 10.1049/enb.2017.0024

Denis Gauvreau, David Winickoff, Jim Philp

{"title":"Engineering biology and the grand challenges: Do we need a new R&D&I model?","authors":"Denis Gauvreau, David Winickoff, Jim Philp","doi":"10.1049/enb.2017.0024","DOIUrl":"https://doi.org/10.1049/enb.2017.0024","url":null,"abstract":"<div>\u0000 <p>Facing up to the grand challenges posed to society today requires a policy that counts the cost of environmental damage, such as carbon emissions and air pollution. Technologies have arrived to address climate mitigation, but relatively few of these are biotechnologies. Biotechnologies in environmental applications suffer a variety of inhibitors – political, social and technical, and yet the potential cannot be denied. The greatest technical promise for future biotechnology mobilisation may be the standardisation of engineering biology that allows more rapid and less expensive reduction to practice. However, decades of metabolic engineering for bio-based chemicals and materials have brought many research successes but few commercial-scale products. To address this gap between laboratory and market, new models of R&D&I may be needed to speed up the process. In past, haste has not mattered. For the proposed generation and those that follow, there is a need for policy makers to abandon this complacency as recent evidence is showing that time is running out to keep global warming within internationally agreed limits.</p>\u0000 </div>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"2 1","pages":"2-6"},"PeriodicalIF":0.0,"publicationDate":"2018-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/enb.2017.0024","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"109174946","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

Data model for biopart datasheets 生物制品数据表的数据模型

Engineering biology Pub Date : 2018-02-28 DOI: 10.1049/enb.2017.0020

Iñaki Sainz de Murieta, Matthieu Bultelle, Richard I. Kitney

{"title":"Data model for biopart datasheets","authors":"Iñaki Sainz de Murieta, Matthieu Bultelle, Richard I. Kitney","doi":"10.1049/enb.2017.0020","DOIUrl":"10.1049/enb.2017.0020","url":null,"abstract":"<div>\u0000 <p>This study introduces a new data model, based on the DICOM-SB (see glossary of terms for definition of acronyms) standard for synthetic biology, that is capable of describing/incorporating the data, metadata and ancillary information from detailed characterisation experiments – to present DNA components (bioparts) in datasheets. The data model offers a standardised mechanism to associate bioparts with data and information about component performance – in a particular biological context (or a range of contexts, e.g. chassis). The data model includes the raw, experimental data for each characterisation run, and the protocol details needed to reliably reproduce the experiment. In addition, it provides metrics (e.g. relative promoter units, synthesis/growth rates etc.) that constitute the main content of a biopart datasheet. The data model has been developed to directly link to DICOM-SB, but also to be compatible with existing data standards, e.g. SBOL and SBML. It has been implemented within the latest version of the API that enables access to the SynBIS information system. The work should contribute significantly to the current standardisation effort in synthetic biology. The standard data model for datasheets is seen as a necessary step towards effective interoperability between part repositories, and between repositories and BioCAD applications.</p>\u0000 </div>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"2 1","pages":"7-18"},"PeriodicalIF":0.0,"publicationDate":"2018-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/enb.2017.0020","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"98341559","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: 3

Synthetic biology UK: progress, paradigms and prospects 英国合成生物学:进展、范例和前景

Engineering biology Pub Date : 2017-12-20 DOI: 10.1049/enb.2017.0022

Lionel J. Clarke

{"title":"Synthetic biology UK: progress, paradigms and prospects","authors":"Lionel J. Clarke","doi":"10.1049/enb.2017.0022","DOIUrl":"10.1049/enb.2017.0022","url":null,"abstract":"<div>\u0000 <p>Drawing comparisons with the study of scientific revolutions by Thomas Kuhn over 50 years ago it is possible to frame synthetic biology as a new paradigm, approaching biology and its potential for redesign from an engineering and information management standpoint. This may help relate it to current thinking about potentially revolutionary future developments stemming from the recent and very rapidly progressing convergence of relevant technologies. However, striking differences from Kuhn's historic examples may also be noted – not only a greater awareness today of potential impacts that highlights the importance of explicitly incorporating broader issues of responsibility and governance but also the rapid growth in numbers of new researchers and entrepreneurs to the field globally which could accelerate the paradigm-shift process. The UK Synthetic Biology Roadmap 2012 and subsequent 2016 Strategy set out to develop a mechanism to respond nationally to this wider perspective, and examples, both UK and global, are drawn upon to help assess current progress towards the realisation of an ‘engineering biology’ paradigm.</p>\u0000 </div>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"1 2","pages":"66-70"},"PeriodicalIF":0.0,"publicationDate":"2017-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/enb.2017.0022","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"103579831","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

High rates of fuel consumption are not required by insulating motifs to suppress retroactivity in biochemical circuits 在生化回路中，绝缘基序抑制反作用并不需要高的燃料消耗率

Engineering biology Pub Date : 2017-12-14 DOI: 10.1049/enb.2017.0017

Abhishek Deshpande, Thomas E. Ouldridge

引用次数: 6

Comprehensive web-based broker for bio-technology design and manufacturing 综合性的基于网络的生物技术设计和制造中介

Engineering biology Pub Date : 2017-12-13 DOI: 10.1049/enb.2017.0019

Stefan Claesen, Anna Stone, Mark van Rossum, Richard I. Kitney

引用次数: 1

Analytical approach for the calculation of promoter activities based on fluorescent protein expression data 基于荧光蛋白表达数据计算启动子活性的分析方法

Engineering biology Pub Date : 2017-10-25 DOI: 10.1049/enb.2017.0002

Konstantinos Markakis, Aitor De Las Heras, Alistair Elfick

{"title":"Analytical approach for the calculation of promoter activities based on fluorescent protein expression data","authors":"Konstantinos Markakis, Aitor De Las Heras, Alistair Elfick","doi":"10.1049/enb.2017.0002","DOIUrl":"10.1049/enb.2017.0002","url":null,"abstract":"<div>\u0000 <p>Characterisation of promoters, repressors, enhancers and so on, is not only essential for unravelling the inner workings of gene regulation, but also to enable the rational engineering of novel synthetic elements. Each putative regulatory region requires experimental assessment across a range of chassis and growth conditions, in order to be categorised as a fully defined functional element. In most studies, promoter activity is represented as the magnitude of a reporter signal, usually fluorescence, normalised to the biomass, as given by the optical density (OD). Such experimental values are often obtained from a coupled time-series experiment. Applying simple mathematical reasoning, a tool that describes promoter activity at each time point has been implemented. Protein expression and maturation, are modelled as first-order differential equations, taking into account the degradation and maturation rates which need to be known in advance. The promoter activity is then expressed based on the measured values of fluorescence and OD with a formula derived by mathematical manipulations of the defined quantities and the differential equations that comprise the model. Continuous expressions for fluorescence and OD are obtained from Gaussian process regression. Validation of the tool with experimental data from several constructs showed the expected behaviour of promoter activities.</p>\u0000 </div>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"1 2","pages":"77-85"},"PeriodicalIF":0.0,"publicationDate":"2017-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/enb.2017.0002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"103621382","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