Biology Meets Computation

2017 ◽  
Author(s):  
Arlindo Oliveira
Keyword(s):  
Synthetic Biology ◽  
Computational Biology ◽  
Systematic Approach ◽  
Biological Systems ◽  
Deep Understanding ◽  
Decisive Role ◽  
Computer Models ◽  
Living Cells ◽  
Open The Doors ◽  
The Way

This chapter describes how computers played a decisive role in the sequencing and understanding of the genomes of humans and other organisms. The discovery of the structure of DNA, by Watson and Crick, opened the way to a systematic approach to biology, based on the study of the way DNA encodes the proteins in all living cells. The area that became known as computational biology, or bioinformatics, aims at modelling, simulating, and understanding the behaviour of biological systems, using computer models and algorithms. Such a deep understanding will enable us to create computer models of cells and of entire organisms and even, in the future, open the doors to the creation of entirely new lifeforms, a field known as synthetic biology.

Integrating the whole from the sum of the parts: vignettes in computational biology

2017 ◽  
Vol 1 (3) ◽  
pp. 241-243
Author(s):  
Jeffrey Skolnick
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
Synthetic Biology ◽  
Personalized Medicine ◽  
Computational Biology ◽  
Biological Systems ◽  
Deep Understanding ◽  
Biological Processes ◽  
Practical Applications ◽  
Biological Variables

As is typical of contemporary cutting-edge interdisciplinary fields, computational biology touches and impacts many disciplines ranging from fundamental studies in the areas of genomics, proteomics transcriptomics, lipidomics to practical applications such as personalized medicine, drug discovery, and synthetic biology. This editorial examines the multifaceted role computational biology plays. Using the tools of deep learning, it can make powerful predictions of many biological variables, which may not provide a deep understanding of what factors contribute to the phenomena. Alternatively, it can provide the how and the why of biological processes. Most importantly, it can help guide and interpret what experiments and biological systems to study.

scholarly journals A Synthetic Microbial Operational Amplifier

2017 ◽  
Author(s):  
Ji Zeng ◽  
Jaewook Kim ◽  
Areen Banerjee ◽  
Rahul Sarpeshkar
Keyword(s):  
Transcription Factor ◽  
Synthetic Biology ◽  
Operational Amplifier ◽  
Biological Systems ◽  
Logic Gates ◽  
Living Cells ◽  
Output Stage ◽  
Cellular Circuits ◽  
Differential Transcription ◽  
Insight Into

AbstractSynthetic biology has created oscillators, latches, logic gates, logarithmically linear circuits, and load drivers that have electronic analogs in living cells. The ubiquitous operational amplifier, which allows circuits to operate robustly and precisely has not been built with bio-molecular parts. As in electronics, a biological operational-amplifier could greatly improve the predictability of circuits despite noise and variability, a problem that all cellular circuits face. Here, we show how to create a synthetic 3-stage inducer-input operational amplifier with a differential transcription-factor stage, a CRISPR-based push-pull stage, and an enzymatic output stage with just 5 proteins including dCas9. Our ‘Bio-OpAmp’ expands the toolkit of fundamental circuits available to bioengineers or biologists, and may shed insight into biological systems that require robust and precise molecular homeostasis and regulation.One Sentence SummaryA synthetic bio-molecular operational amplifier that can enable robust, precise, and programmable homeostasis and regulation in living cells with just 5 protein parts is described.

scholarly journals Self-adaptive Biosystems Through Tunable Genetic Parts and Circuits

2020 ◽  
Author(s):  
Vittorio Bartoli ◽  
Mario di Bernardo ◽  
Thomas E. Gorochowski
Keyword(s):  
Synthetic Biology ◽  
Biological Systems ◽  
Living Cells ◽  
Complex Environments ◽  
Control Engineering ◽  
Physiological Conditions ◽  
Recent Advances ◽  
The Face ◽  
The Creation ◽  
Self Adaptive

Biological systems often need to operate in complex environments where conditions can rapidly change. This is possible due to their inherent ability to sense changes and adapt by adjusting their behavior in response. Here, we detail recent advances in the creation of synthetic genetic parts and circuits whose behaviors can be dynamically tuned through a variety of intra- and extra-cellular signals. We show how this capability lays the foundation for implementing control engineering schemes in living cells and allows for the creation of biological systems that are able to self-adapt, ensuring their functionality is maintained in the face of varying environmental and physiological conditions. We end by discussing some of the broader implications of this technology for the safe deployment of synthetic biology.

scholarly journals Self-adaptive Biosystems Through Tunable Genetic Parts and Circuits

2020 ◽  
Author(s):  
Vittorio Bartoli ◽  
Mario di Bernardo ◽  
Thomas E. Gorochowski
Keyword(s):  
Synthetic Biology ◽  
Biological Systems ◽  
Living Cells ◽  
Complex Environments ◽  
Control Engineering ◽  
Physiological Conditions ◽  
Recent Advances ◽  
The Face ◽  
The Creation ◽  
Self Adaptive

Biological systems often need to operate in complex environments where conditions can rapidly change. This is possible due to their inherent ability to sense changes and adapt their behavior in response. Here, we detail recent advances in the creation of synthetic genetic parts and circuits whose behaviors can be dynamically tuned through a variety of intra- and extra-cellular signals. We show how this capability lays the foundation for implementing control engineering schemes in living cells and allows for the creation of biological systems that are able to self-adapt, ensuring their functionality is maintained in the face of varying environmental and physiological conditions. We end by discussing some of the broader implications of this technology for the safe deployment of synthetic biology.

Life as a Raw Material: Illusions of Control

Somatechnics ◽  
2012 ◽  
Vol 2 (2) ◽  
pp. 250-262 ◽  
Author(s):  
Oron Catts ◽  
Ionat Zurr
Keyword(s):  
Synthetic Biology ◽  
Cognitive Engineering ◽  
Raw Material ◽  
Future Scenarios ◽  
Short History ◽  
Know How ◽  
Political Forces ◽  
History Of ◽  
The Way

The paper discusses and critiques the concept of the single engineering paradigm. This concepts allude to a future in which the control of matter and life, and life as matter, will be achieved by applying engineering principles; through nanotechnology, synthetic biology and, as some suggest, geo-engineering, cognitive engineering and neuro-engineering. We outline some issues in the short history of the field labelled as Synthetic Biology. Furthermore; we examine the way engineers, scientists, designers and artists are positioned and articulating the use of the tools of Synthetic Biology to expose some of the philosophical, ethical and political forces and considerations of today as well as some future scenarios. We suggest that one way to enable the possibilities of alternative frames of thought is to open up the know-how and the access to these technologies to other disciplines, including artistic.

Foto-Etnografi dalam Proses Penciptaan Karya Seni Fotografi

Panggung ◽  
2013 ◽  
Vol 23 (2) ◽  
Author(s):  
Arief Datoem
Keyword(s):  
Social Life ◽  
Systematic Approach ◽  
Deep Understanding ◽  
Digital Photography ◽  
Cultural Representation ◽  
Visual Anthropology ◽  
Artistic Creation ◽  
Ethnographic Approach ◽  
The Subject ◽  
Emotional Approach

ABSTRACT This article aims at deepening the possibility of utilizing the art of photography that is rich of sig- nificance of the socio-cultural representation. The visual ethnographic field or photo-ethnography, which is relatively new, can provide assistance and answer for this. Therefore, the author has tried a form of collaboration between the photo-ethnographic approach and the sense approach in doing his research on the subject in order to obtain the deep understanding and the truth significance attached to them. The method of digital photography art creation which is intuitively the basis of the art cre- ation in digital domain, then was tried to be formulated, based on heuristics research in the process of the art of digital photography. This concept was developed from the experience in the field of digital photography and visual anthropology, guided by the basic theories of creativity, quantum theory in art, and theory of artistic creation that has existed before. Through emotional approach as a method, along with the structured systematic approach of photo-ethnography and with the deep awareness of the environment and social life of the subject leads to the creation of the image that tends to be better and more meaningful, more productive in a social sense, and offers a credible empiric documentation. Keywords: photo-ethnography, photography art works  ABSTRAK Artikel ini dibuat dalam upaya melakukan pendalaman mengenai kemungkinan peman- faatan seni fotografi yang kaya makna representasi sosio-kultural. Bidang etnografi visual atau foto-etnografi yang relatif masih baru, dapat memberikan bantuan dan jawaban un- tuk hal ini. Oleh karena itu penulis mencoba suatu bentuk kolaborasi antara pendekatan foto-etnografi dengan pendekatan rasa ketika melakukan penelitian terhadap subjek agar diperoleh pemahaman mendalam serta makna kebenaran yang menyertainya. Metode penciptaan seni fotografi digital yang merupakan dasar dari penciptaan seni secara intu- itif dalam domain digital, kemudian dicoba dirumuskan, berdasarkan penelaahan heu- ristik dalam proses seni fotografi digital. Konsep ini dikembangkan dari pengalaman di bidang fotografi digital dan antropologi visual, dipandu oleh teori-teori dasar kreativitas, teori kuantum dalam seni, dan teori penciptaan seni yang telah ada sebelumnya. Melalui pendekatan emosional sebagai metode, disertai dengan pendekatan sistematis yang ter- struktur dari foto-etnografi dan dengan kesadaran yang mendalam mengenai lingkungan dan kehidupan sosial subjek mengarah pada penciptaan gambaran yang cenderung lebih baik dan lebih bermakna, lebih produktif dalam arti sosial, dan menawarkan dokumentasi empiris yang kredibel. Kata kunci: foto-etnografi, karya seni fotografi

scholarly journals Quantitative linear dichroism imaging of molecular processes in living cells made simple by open software tools

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Alexey Bondar ◽  
Olga Rybakova ◽  
Josef Melcr ◽  
Jan Dohnálek ◽  
Petro Khoroshyy ◽  
...  
Keyword(s):  
Biological Systems ◽  
Linear Dichroism ◽  
Quantitative Information ◽  
Living Cells ◽  
Software Tools ◽  
Model Systems ◽  
Membrane Properties ◽  
Polarization Microscopy ◽  
Molecular Processes ◽  
Wide Range

AbstractFluorescence-detected linear dichroism microscopy allows observing various molecular processes in living cells, as well as obtaining quantitative information on orientation of fluorescent molecules associated with cellular features. Such information can provide insights into protein structure, aid in development of genetically encoded probes, and allow determinations of lipid membrane properties. However, quantitating and interpreting linear dichroism in biological systems has been laborious and unreliable. Here we present a set of open source ImageJ-based software tools that allow fast and easy linear dichroism visualization and quantitation, as well as extraction of quantitative information on molecular orientations, even in living systems. The tools were tested on model synthetic lipid vesicles and applied to a variety of biological systems, including observations of conformational changes during G-protein signaling in living cells, using fluorescent proteins. Our results show that our tools and model systems are applicable to a wide range of molecules and polarization-resolved microscopy techniques, and represent a significant step towards making polarization microscopy a mainstream tool of biological imaging.

scholarly journals Independent control of amplitude and period in a synthetic oscillator circuit with modified repressilator

2022 ◽  
Vol 5 (1) ◽  
Author(s):  
Fengyu Zhang ◽  
Yanhong Sun ◽  
Yihao Zhang ◽  
Wenting Shen ◽  
Shujing Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Synthetic Biology ◽  
Biological Systems ◽  
Reporter Genes ◽  
Quantitative Model ◽  
Theoretical Level ◽  
Independent Control ◽  
Oscillator Circuit ◽  
Biological Circuits

AbstractSynthetic Biology aims to create predictable biological circuits and fully operational biological systems. Although there are methods to create more stable oscillators, such as repressilators, independently controlling the oscillation of reporter genes in terms of their amplitude and period is only on theoretical level. Here, we introduce a new oscillator circuit that can be independently controlled by two inducers in Escherichia coli. Some control components, including σECF11 and NahR, were added to the circuit. By systematically tuning the concentration of the inducers, salicylate and IPTG, the amplitude and period can be modulated independently. Furthermore, we constructed a quantitative model to forecast the regulation results. Under the guidance of the model, the expected oscillation can be regulated by choosing the proper concentration combinations of inducers. In summary, our work achieved independent control of the oscillator circuit, which allows the oscillator to be modularized and used in more complex circuit designs.

From Never Born Proteins to Minimal Living Cells: Two Projects in Synthetic Biology

2006 ◽  
Vol 36 (5-6) ◽  
pp. 605-616 ◽  
Author(s):  
Pier Luigi Luisi ◽  
Cristiano Chiarabelli ◽  
Pasquale Stano
Keyword(s):  
Synthetic Biology ◽  
Living Cells
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