scholarly journals Standards. The building blocks of complexity

2021 ◽  
Author(s):  
Juli Peretó ◽  
Manuel Porcar
Keyword(s):  
Synthetic Biology ◽  
Mechanical Design ◽  
Building Blocks ◽  
Open Science ◽  
Research And Innovation ◽  
Living Things ◽  
Key Factor ◽  
Cellular Context ◽  
Cultural Standards ◽  
Biological World

Without standards, the world as we know it would not be possible. International and supra-cultural standards and norms have been a key factor in engineering, as well as in the development of industrial societies. Despite the obvious successes in electronic and mechanical design, other technological areas present difficulties for the application of standards. In the field of biotechnology and synthetic biology – which aims at studying living things from an engineering perspective – standards are desirable, but whether they can be widely adopted remains to be proved. This monograph reviews the sociological and scientific aspects of standardisation and delves into the more problematic facets of universal standardisation, especially in the biological field. Are standards possible in synthetic biology at all? What are the limitations to the universal use of modular and interchangeable parts in a cellular context? Could it be that the biological world resists standardisation, similarly to the field of software engineering, where these attempts have not progressed? And should some kind of standard be applicable in synthetic biology, what qualities might be required in an environment of open science and responsible research and innovation?

Probing the Substrate Promiscuity of Isopentenyl Phosphate Kinase as a Platform for Hemiterpene Analogue Production

2019 ◽  
Author(s):  
Sean Lund ◽  
Taylor Courtney ◽  
Gavin Williams
Keyword(s):  
Synthetic Biology ◽  
Building Blocks ◽  
Isoprenoid Biosynthesis ◽  
Thermoplasma Acidophilum ◽  
Substrate Promiscuity ◽  
Enzymatic Pathways ◽  
First Time ◽  
Rate Limiting ◽  
Alcohol Dependent ◽  
Isopentenyl Phosphate

Isoprenoids are a large class of natural products with wide-ranging applications. Synthetic biology approaches to the manufacture of isoprenoids and their new-to-nature derivatives are limited due to the provision in Nature of just two hemiterpene building blocks for isoprenoid biosynthesis. To address this limitation, artificial chemo-enzymatic pathways such as the alcohol-dependent hemiterpene pathway (ADH) serve to leverage consecutive kinases to convert exogenous alcohols to pyrophosphates that could be coupled to downstream isoprenoid biosynthesis. To be successful, each kinase in this pathway should be permissive of a broad range of substrates. For the first time, we have probed the promiscuity of the second enzyme in the ADH pathway, isopentenyl phosphate kinase from Thermoplasma acidophilum, towards a broad range of acceptor monophosphates. Subsequently, we evaluate the suitability of this enzyme to provide non-natural pyrophosphates and provide a critical first step in characterizing the rate limiting steps in the artificial ADH pathway.<br>

The fuzzy structure of populations

2002 ◽  
Vol 80 (12) ◽  
pp. 2235-2241 ◽  
Author(s):  
James A Schaefer ◽  
Chris C Wilson
Keyword(s):  
Rangifer Tarandus ◽  
Human Perception ◽  
Fuzzy Classification ◽  
Resolving Power ◽  
Biological Organization ◽  
Philosophical Foundations ◽  
Living Things ◽  
Biological World ◽  
Multiple Clusters ◽  
Management And Conservation

The human perception of biological organization has profound implications for the study, management, and conservation of living things. Traditional methods of classification, which imply all-or-nothing group membership, are inconsistent with the modern synthesis, which stresses variability and unique individuals. We propose that fuzzy classification, which allows fractional membership in multiple clusters, can more realistically denote many forms of biological organization, such as populations. We used fuzzy clustering to depict the ambiguous structure of a migratory caribou (Rangifer tarandus) herd, based on affinities in space use, and walleye (Stizostedion vitreum) stocks, based on genetic dissimilarities among multilocus genotypes. In both cases, fuzzy memberships conveyed the degree of uncertainty of belonging while resolving cluster memberships for unambiguous and problematic individuals. Vagueness implies that borderline group identity cannot be remedied with more resolving power. Fuzzy classification is more in tune with the empirical and philosophical foundations of our discipline and can reconcile our need to classify with an inherently vague biological world.

Biochemistry: A Very Short Introduction

2021 ◽  
Author(s):  
Mark Lorch
Keyword(s):  
Synthetic Biology ◽  
Chemical Reactions ◽  
Biochemical Reactions ◽  
Short Introduction ◽  
Chemical Structures ◽  
Living Things ◽  
Historical Figures ◽  
Key Concepts ◽  
Current Science

Biochemistry: A Very Short Introduction discusses the key concepts of biochemistry, as well as the historical figures in the field and the molecules they studied. From bacteria to humans, all living things are composed of cells of one type or another, all of which have fundamentally the same chemistry. Biochemistry is the study of the chemical reactions within these cells; the molecules that are created, manipulated, and destroyed as a result of them; and the chemical structures such as DNA on which these biochemical reactions take place. This VSI considers the current science and innovations in the field. It also looks at the interaction between biochemistry, biotechnology, and synthetic biology.

scholarly journals Societal impact of synthetic biology: responsible research and innovation (RRI)

2016 ◽  
Vol 60 (4) ◽  
pp. 371-379 ◽  
Author(s):  
Daniel Gregorowius ◽  
Anna Deplazes-Zemp
Keyword(s):  
Synthetic Biology ◽  
Technology Assessment ◽  
Ethical Issues ◽  
Responsible Research And Innovation ◽  
Societal Impact ◽  
Biotechnological Applications ◽  
Research And Innovation ◽  
Challenges And Opportunities ◽  
Living Organisms ◽  
Responsible Research

Synthetic biology is an emerging field at the interface between biology and engineering, which has generated many expectations for beneficial biomedical and biotechnological applications. At the same time, however, it has also raised concerns about risks or the aim of producing new forms of living organisms. Researchers from different disciplines as well as policymakers and the general public have expressed the need for a form of technology assessment that not only deals with technical aspects, but also includes societal and ethical issues. A recent and very influential model of technology assessment that tries to implement these aims is known as RRI (Responsible Research and Innovation). In this paper, we introduce this model and its historical precursor strategies. Based on the societal and ethical issues which are presented in the current literature, we discuss challenges and opportunities of applying the RRI model for the assessment of synthetic biology.

scholarly journals An open toolkit for tracking open science partnership implementation and impact

2019 ◽  
Vol 3 ◽  
pp. 1442 ◽  
Author(s):  
E. Richard Gold ◽  
Sarah E. Ali-Khan ◽  
Liz Allen ◽  
Lluis Ballell ◽  
Manoel Barral-Netto ◽  
...  
Keyword(s):  
Annual Report ◽  
Open Data ◽  
Structured Interview ◽  
Open Science ◽  
Social Scientists ◽  
Policy Makers ◽  
Ethical Concerns ◽  
Research And Innovation ◽  
Survey Form ◽  
The Impact

Serious concerns about the way research is organized collectively are increasingly being raised. They include the escalating costs of research and lower research productivity, low public trust in researchers to report the truth, lack of diversity, poor community engagement, ethical concerns over research practices, and irreproducibility. Open science (OS) collaborations comprise of a set of practices including open access publication, open data sharing and the absence of restrictive intellectual property rights with which institutions, firms, governments and communities are experimenting in order to overcome these concerns. We gathered two groups of international representatives from a large variety of stakeholders to construct a toolkit to guide and facilitate data collection about OS and non-OS collaborations. Ultimately, the toolkit will be used to assess and study the impact of OS collaborations on research and innovation. The toolkit contains the following four elements: 1) an annual report form of quantitative data to be completed by OS partnership administrators; 2) a series of semi-structured interview guides of stakeholders; 3) a survey form of participants in OS collaborations; and 4) a set of other quantitative measures best collected by other organizations, such as research foundations and governmental or intergovernmental agencies. We opened our toolkit to community comment and input. We present the resulting toolkit for use by government and philanthropic grantors, institutions, researchers and community organizations with the aim of measuring the implementation and impact of OS partnership across these organizations. We invite these and other stakeholders to not only measure, but to share the resulting data so that social scientists and policy makers can analyse the data across projects.

scholarly journals Interventions to Promote a Healthy Sexuality among School Adolescents: A Scoping Review

2021 ◽  
Vol 11 (11) ◽  
pp. 1155
Author(s):  
Fernanda Loureiro ◽  
Margarida Ferreira ◽  
Paula Sarreira-de-Oliveira ◽  
Vanessa Antunes
Keyword(s):  
Open Science ◽  
Multidisciplinary Teams ◽  
Adolescent Sexual Behavior ◽  
Scoping Reviews ◽  
Key Factor ◽  
Nurses Role ◽  
Healthy Sexuality ◽  
Science Framework ◽  
Meta Analyses

Schools are particularly suitable contexts for the implementation of interventions focused on adolescent sexual behavior. Sexual education and promotion have a multidisciplinary nature. Nurses’ role and the spectrum of the carried-out interventions is not clear. We aimed to identify interventions that promote a healthy sexuality among school adolescents. Our review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews and was registered in the Open Science Framework. Published articles on sexuality in adolescents in school contexts were considered. The research limitations included primary studies; access in full text in English, Spanish, or Portuguese; and no data publication limitation. Research was carried out on the EBSCOhost, PubMed, SciELO, and Web of Science platforms; gray literature and the bibliographies of selected articles were also searched. A total of 56 studies were included in the sample. The studies used a broad range of research methods, and 10 types of interventions were identified. Multi-interventional programs and socio-emotional interventions showed a greater impact on long-term behavioral changes, and continuity seemed to be a key factor. Long-term studies are needed to reach a consensus on the effectiveness of interventions. Nurses’ particular role on the multidisciplinary teams was found to be a gap in the research, and must be further explored.

scholarly journals Engineering a Minimal Cloning Vector from a pUC18 Plasmid Backbone with an Extended Multiple Cloning Site

2018 ◽  
Author(s):  
Jens Staal ◽  
Wouter De Schamphelaire ◽  
Rudi Beyaert
Keyword(s):  
Synthetic Biology ◽  
Molecular Biology ◽  
Restriction Enzyme ◽  
Essential Role ◽  
Building Blocks ◽  
Cloning Vector ◽  
Multiple Cloning Site ◽  
Unique Restriction ◽  
Plasmid Backbone

Minimal plasmids play an essential role in many intermediate steps in molecular biology. They can for example be used to assemble building blocks in synthetic biology or be used as intermediate cloning plasmids that are ideal for PCR-based mutagenesis methods. A small backbone also opens up for additional unique restriction enzyme cloning sites. Here we describe the generation of pICOz, a 1185 bp fully functional high-copy cloning plasmid with an extended multiple cloning site (MCS). To our knowledge, this is the smallest high-copy cloning vector ever described.

scholarly journals The Sustainability Argument for Open Science

2021 ◽  
Author(s):  
Gisela Govaart ◽  
Simon M. Hofmann ◽  
Evelyn Medawar
Keyword(s):  
Climate Change ◽  
Greenhouse Gas ◽  
Scientific Progress ◽  
Building Blocks ◽  
Open Science ◽  
Academic Environments ◽  
Science Practices ◽  
Research Activities ◽  
Systemic Level ◽  
Climate Crisis

Ever-increasing anthropogenic greenhouse gas emissions narrow the timeframe for humanity to mitigate the climate crisis. Scientific research activities are resource demanding and, consequently, contribute to climate change; at the same time, scientists have a central role in advancing knowledge, also on climate-related topics. In this opinion piece, we discuss (1) how open science – adopted on an individual as well as on a systemic level – can contribute to making research more environmentally friendly, and (2) how open science practices can make research activities more efficient and thereby foster scientific progress and solutions to the climate crises. While many building blocks are already at hand, systemic changes are necessary in order to create academic environments that support open science practices and encourage scientists from all fields to become more carbon-conscious, ultimately contributing to a sustainable future.

Mechanical Design of Antichiral-Reentrant Hybrid Intravascular Stent

2018 ◽  
Vol 10 (10) ◽  
pp. 1850105 ◽  
Author(s):  
Xiao Li Ruan ◽  
Jie Jie Li ◽  
Xiao Ke Song ◽  
Hong Jian Zhou ◽  
Wei Xing Yuan ◽  
...  
Keyword(s):  
Large Scale ◽  
Mechanical Design ◽  
Experimental Tests ◽  
Building Blocks ◽  
Industrial Applications ◽  
Mechanical Effect ◽  
Parametric Models ◽  
Element Analysis ◽  
Specific Strength ◽  
Intravascular Stents

Chiral and reentrant metastructures with auxetic deformation abilities can serve as the building blocks in many industrial applications because of their light weight, high specific strength, energy absorption properties. In this paper, we report an innovative tubular-like structure by a combined mechanical effect of antichiral and reentrant. 2D antichiral-reentrant hybrid structures consisting of circular nodes and tangentially-connected ligaments are predesigned and fabricated using laser cutting technology with high-resolution. The elastic properties and auxeticity of the plane structure are analyzed and compared based on finite element analysis (FEA) and experimental results. For the first time, the antichiral-reentrant hybrid intravascular stents with the auxetic feature are proposed and parametric models are devised with good geometrical structure demonstrated. A series of large-scale stents are manufactured with stereolithography apparatus (SLA) additive manufacturing technique, and their mechanical behaviors are investigated in both experimental tests and FEA. As the selected antichiral-reentrant hybrid stents with tailored expansion ability are subjected to radial loading by the dilation of the balloon, stents undergo identifiable deformation mechanism due to the beam-like ligaments and circular node elements in the varied geometrical design, resulting in the distinct stress outcomes in plaque. It is also demonstrated that the antichiral-reentrant hybrid stents with tunable auxeticity possess robust mechanical properties through implantation inside the obstructed lesion.

Metaphors and other slippery creatures

2019 ◽  
Vol 52 (2) ◽  
pp. 345-352
Author(s):  
James E. Strick
Keyword(s):  
Cell Biology ◽  
New Technologies ◽  
Building Blocks ◽  
State University ◽  
Arizona State University ◽  
Living Things ◽  
History Of ◽  
Dialectical Relationship ◽  
Rich Material ◽  
And Function

What are cells? How are they related to each other and to the organism as a whole? These questions have exercised biology since Schleiden and Schwann (1838–1839) first proposed cells as the key units of structure and function of all living things. But how do we try to understand them? Through new technologies like the achromatic microscope and the electron microscope. But just as importantly, through the metaphors our culture has made available to biologists in different periods and places. These two new volumes provide interesting history and philosophy of the development of cell biology. Reynolds surveys the field's changing conceptual structure by examining the varied panoply of changing metaphors used to conceptualize and explain cells – from cells as empty boxes, as building blocks, to individual organisms, to chemical factories, and through many succeeding metaphors up to one with great currency today: cells as social creatures in communication with others in their community. There is some of this approach in the Visions edited collection as well. But this collection also includes rich material on the technologies used to visualize cells and their dialectical relationship with the epistemology of the emerging distinct discipline of cell biology. This volume centres on, but is not limited to, ‘reflections inspired by [E.V.] Cowdry's [1924 volume] General Cytology’; it benefits from a conference on the Cowdry volume as well as a 2011 Marine Biological Lab/Arizona State University workshop on the history of cell biology.

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