Multimaterial bioprinting—minus the printer: Synthetic bacterial patterning with UV-responsive genetic circuits

2020 ◽  
pp. 147807712096337
Author(s):  
Gizem Gumuskaya
Keyword(s):  
Industrial Revolution ◽  
Vibrio Fischeri ◽  
Raw Material ◽  
Genetic Circuit ◽  
Elastic Tissue ◽  
Genetic Circuits ◽  
Bacterial Colony ◽  
Synthetic Dna ◽  
Macro Scale ◽  
Bacterial Lawn

In this paper, we argue that synthetic biology can help us employ living systems’ unique capacity for self-construction and biomaterial production toward developing novel architectural fabrication paradigms, in which both the raw material production and its refinement into a target structure can be merged into a single computational process embedded in the living structure itself. To demonstrate, here we introduce bioPheme, a novel biofabrication method for engineering bacteria to build biomaterial(s) of designer’s choice into arbitrary 2D geometries specified via transient UV tracing. To this end, we present the design, construction, and testing of the enabling synthetic DNA circuit, which, once inserted into a bacterial colony, allows the bacteria to execute spatial computation by interacting with one another based on the if-then rules encoded in this circuit. At the heart of this genetic circuit is a pair of UV sensor – actuator, and a pair of cell-to-cell signal transmitter – receptor modules, created with genes extracted from the virus λ Phage and marine bacterium Vibrio fischeri, respectively. These modules are wired together to help designers engineer bacteria to build macro-scale structures with seamlessly integrated biomaterials, thereby bridge the molecular and architectural scales. In this way, a bacterial lawn can be programmed to produce different objects with complementary biomaterial compositions, such as a biomineralized superstructure and an elastic tissue filling in-between. In summary, this paper focuses on how scientists’ increasing ability to harness the innate computational capacity of living cells can help designers create self-constructing structures for architectural biofabrication. Through the discussions in this paper, we aim to initiate a shift in today’s biodesign practices toward a greater appreciation and adoption of bottom-up governance of living structures. We are confident that such a paradigm shift will allow for more efficient and sustainable biofabrication systems in the 4th industrial revolution and beyond.

scholarly journals Synthetic and systems biology principles in the design of programmable oncolytic virus immunotherapies for glioblastoma

2021 ◽  
Vol 50 (2) ◽  
pp. E10
Author(s):  
Dileep D. Monie ◽  
Archis R. Bhandarkar ◽  
Ian F. Parney ◽  
Cristina Correia ◽  
Jann N. Sarkaria ◽  
...  
Keyword(s):  
Systems Biology ◽  
Synthetic Biology ◽  
Laboratory Data ◽  
Immunological Response ◽  
Analytical Framework ◽  
Oncolytic Viruses ◽  
Genetic Circuit ◽  
Genetic Circuits ◽  
Synthetic Dna ◽  
Network Analyses

Oncolytic viruses (OVs) are a class of immunotherapeutic agents with promising preclinical results for the treatment of glioblastoma (GBM) but have shown limited success in recent clinical trials. Advanced bioengineering principles from disciplines such as synthetic and systems biology are needed to overcome the current challenges faced in developing effective OV-based immunotherapies for GBMs, including off-target effects and poor clinical responses. Synthetic biology is an emerging field that focuses on the development of synthetic DNA constructs that encode networks of genes and proteins (synthetic genetic circuits) to perform novel functions, whereas systems biology is an analytical framework that enables the study of complex interactions between host pathways and these synthetic genetic circuits. In this review, the authors summarize synthetic and systems biology concepts for developing programmable, logic-based OVs to treat GBMs. Programmable OVs can increase selectivity for tumor cells and enhance the local immunological response using synthetic genetic circuits. The authors discuss key principles for developing programmable OV-based immunotherapies, including how to 1) select an appropriate chassis, a vector that carries a synthetic genetic circuit, and 2) design a synthetic genetic circuit that can be programmed to sense key signals in the GBM microenvironment and trigger release of a therapeutic payload. To illustrate these principles, some original laboratory data are included, highlighting the need for systems biology studies, as well as some preliminary network analyses in preparation for synthetic biology applications. Examples from the literature of state-of-the-art synthetic genetic circuits that can be packaged into leading candidate OV chassis are also surveyed and discussed.

scholarly journals CRIMoClo plasmids for modular assembly and orthogonal chromosomal integration of synthetic circuits in Escherichia coli

2019 ◽  
Vol 13 (1) ◽  
Author(s):  
Stefano Vecchione ◽  
Georg Fritz
Keyword(s):  
Escherichia Coli ◽  
Synthetic Biology ◽  
Integrated Circuits ◽  
High Efficiency ◽  
Genetic Circuit ◽  
Dna Assembly ◽  
Chromosomal Integration ◽  
Golden Gate ◽  
Genetic Circuits ◽  
E Coli

Abstract Background Synthetic biology heavily depends on rapid and simple techniques for DNA engineering, such as Ligase Cycling Reaction (LCR), Gibson assembly and Golden Gate assembly, all of which allow for fast, multi-fragment DNA assembly. A major enhancement of Golden Gate assembly is represented by the Modular Cloning (MoClo) system that allows for simple library propagation and combinatorial construction of genetic circuits from reusable parts. Yet, one limitation of the MoClo system is that all circuits are assembled in low- and medium copy plasmids, while a rapid route to chromosomal integration is lacking. To overcome this bottleneck, here we took advantage of the conditional-replication, integration, and modular (CRIM) plasmids, which can be integrated in single copies into the chromosome of Escherichia coli and related bacteria by site-specific recombination at different phage attachment (att) sites. Results By combining the modularity of the MoClo system with the CRIM plasmids features we created a set of 32 novel CRIMoClo plasmids and benchmarked their suitability for synthetic biology applications. Using CRIMoClo plasmids we assembled and integrated a given genetic circuit into four selected phage attachment sites. Analyzing the behavior of these circuits we found essentially identical expression levels, indicating orthogonality of the loci. Using CRIMoClo plasmids and four different reporter systems, we illustrated a framework that allows for a fast and reliable sequential integration at the four selected att sites. Taking advantage of four resistance cassettes the procedure did not require recombination events between each round of integration. Finally, we assembled and genomically integrated synthetic ECF σ factor/anti-σ switches with high efficiency, showing that the growth defects observed for circuits encoded on medium-copy plasmids were alleviated. Conclusions The CRIMoClo system enables the generation of genetic circuits from reusable, MoClo-compatible parts and their integration into 4 orthogonal att sites into the genome of E. coli. Utilizing four different resistance modules the CRIMoClo system allows for easy, fast, and reliable multiple integrations. Moreover, utilizing CRIMoClo plasmids and MoClo reusable parts, we efficiently integrated and alleviated the toxicity of plasmid-borne circuits. Finally, since CRIMoClo framework allows for high flexibility, it is possible to utilize plasmid-borne and chromosomally integrated circuits simultaneously. This increases our ability to permute multiple genetic modules and allows for an easier design of complex synthetic metabolic pathways in E. coli.

Omission of Data in Wrigley’s “Reconsidering the Industrial Revolution”

2020 ◽  
Vol 51 (2) ◽  
pp. 297-299
Author(s):  
Manish Kumar
Keyword(s):  
Urban Growth ◽  
Industrial Revolution ◽  
Value Added ◽  
Raw Material ◽  
Agricultural Change ◽  
England And Wales

In “Reconsidering the Industrial Revolution: England and Wales,” Wrigley omits vital information from the section “Urban Growth and Agricultural Change.” Arguing that by 1800, English agriculture was able to provide not only food for the rising population but also raw material for the industries, he cites wool and leather as the two largest industries in terms of value added in 1801 and leaves out building and cotton entirely. Therein lies the problem.

Intellectual Property Rights on Traditional Knowledge and their Significance in Sustainable Societal Development

2017 ◽  
pp. 157-185
Author(s):  
P. Pushpangadan ◽  
T. P. Ijinu
Keyword(s):  
Industrial Revolution ◽  
Life Support ◽  
Value Added ◽  
Primary Source ◽  
Developed Countries ◽  
Raw Material ◽  
Benefit Sharing ◽  
Access And Benefit Sharing ◽  
Special Value ◽  
The Developed Countries

Rich biodiversity and equally rich cultural heritages are the two invaluable assets of most of the Third World Counties (TWC). Biogenetic resources are the primary source of valuable genes, chemicals, drugs, pharmaceuticals, natural dyes, gums, resins, enzymes or proteins of great health, nutritional and economic importance. Biodiversity regulates and maintains overall health of the life support systems on earth and is the source from which human race derives food, fodder, fuel, fibre, shelter, medicine and raw material for meeting his other multifarious needs and industrial goods required for the ever changing and ever increasing needs and aspirations. TWC members are still at the receiving end as far as the development of special value added products and herbal technologies are concerned. The developed countries, on the other hand, are emerging as super powers with their biotechnological strength. IPRs emerged strongly during the industrial revolution and it has been an important driving force behind rapid industrial growth and prosperity of the Western countries during the last 3 centuries. Nowadays Access and Benefit Sharing issues have become a central theme for subsequent detailed discussions and decision making under CBD, TRIPS and the WIPO. It is therefore increasingly urgent for the CBD to make ABS work as was intended. The entry into force of the Nagoya Protocol represents a step in this direction. In India, we can be proud of having the distinction of the first country in experimenting a benefit-sharing model that implemented in Letter and Spirit Article 8(j) of CBD.

scholarly journals Security Challenges in Industry 4.0 PLC Systems

2021 ◽  
Vol 11 (21) ◽  
pp. 9785
Author(s):  
Janusz Hajda ◽  
Ryszard Jakuszewski ◽  
Szymon Ogonowski
Keyword(s):  
Industrial Development ◽  
Information Technologies ◽  
Industrial Revolution ◽  
Raw Material ◽  
The Internet ◽  
Security Measures ◽  
Industrial Control Systems ◽  
Digital Revolution ◽  
Digitally Controlled ◽  
Risk Sources

The concept of the fourth industrial revolution assumes the integration of people and digitally controlled machines with the Internet and information technologies. At the end of 2015, more than 20 billion machines and devices were connected to the Internet, with an expected growth to half a trillion by 2030. The most important raw material for this digital revolution is data, which when properly stored, analyzed and secured, constitute the basis for the development of any business. In times of rapid industrial development, automation of production processes and systems integration via networks, the effective protection of the cyber-physical systems of a plant is particularly important. To minimize the risks associated with Internet access, one must define all the possible threats and determine their sources in the plant and block or minimize the possibility of sabotage or data loss. This article analyzes the security measures used in industrial systems. In particular, risk management and the study of the risk sources in terms of human, hardware and software aspects in networked PLC and SCADA systems are discussed. Methods of improving the architecture of industrial networks and their management are proposed in order to increase the level of security. Additionally, the safety of the communication protocols with PLCs in industrial control systems is discussed.

scholarly journals Genetic Circuits Combined with Machine Learning Provides Fast Responding Living Sensors

2020 ◽  
Author(s):  
Behide Saltepe ◽  
Eray Ulaş Bozkurt ◽  
Murat Alp Güngen ◽  
A. Ercüment Çiçek ◽  
Urartu Özgür Şafak Şeker
Keyword(s):  
Response Time ◽  
Short Term Memory ◽  
Cost Effective ◽  
Genetic Circuit ◽  
Analyte Concentration ◽  
Genetic Circuits ◽  
Wide Range ◽  
Biomedical Diagnostics ◽  
Long Short Term Memory ◽  
Increasing Demand

AbstractWhole cell biosensors (WCBs) have become prominent in many fields from environmental analysis to biomedical diagnostics thanks to advanced genetic circuit design principles. Despite increasing demand on cost effective and easy-to-use assessment methods, a considerable amount of WCBs retains certain drawbacks such as long response time, low precision and accuracy. Furthermore, the output signal level does not correspond to a specific analyte concentration value but shows comparative quantification. Here, we utilized a neural network-based architecture to improve the aforementioned features of WCBs and engineered a gold sensing WCB which has a long response time (18 h). Two Long-Short Term-Memory (LSTM)-based networks were integrated to assess both ON/OFF and concentration dependent states of the sensor output, respectively. We demonstrated that binary (ON/OFF) network was able to distinguish between ON/OFF states as early as 30 min with 78% accuracy and over 98% in 3 h. Furthermore, when analyzed in analog manner, we demonstrated that network can classify the raw fluorescence data into pre-defined analyte concentration groups with high precision (82%) in 3 h. This approach can be applied to a wide range of WCBs and improve rapidness, simplicity and accuracy which are the main challenges in synthetic biology enabled biosensing.

scholarly journals Un paradigma diferente del management: teletrabajo. / A different paradigm of management : teleworking.

2020 ◽  
pp. 7-17
Author(s):  
Gabriel Maresca
Keyword(s):  
Information Technology ◽  
Industrial Revolution ◽  
Work Organization ◽  
Raw Material ◽  
Potential Development ◽  
Historical Times ◽  
Technology And Communication ◽  
New Forms Of Work ◽  
Material Input

En la actualidad estamos transitando los primeros vestigios de una nueva revolución sociocultural y económica tanto a nivel local como global, a raíz de la implantación de las tecnologías de la información y de la comunicación (TICs) en muchas de las actividades que realizan los seres humanos y las organizaciones, y el gran desarrollo potencial de aplicación que ofrece a todos los campos disciplinares. Tal como ocurrió en su momento histórico con la revolución industrial, hoy se manifiesta a través de la necesidad de obtener información como principal insumo y materia prima para el éxito de las organizaciones. Es decir, la posibilidad de acceder a una mayor cantidad y calidad de información en todo momento y lugar, representa actualmente el alimento escencial para subsistir y obtener los mejores beneficios en cualquier sistema productivo. Podríamos decir, que toda actividad donde participan los individuos, ya sea de ocio, educativa o productiva, intervienen en mayor o menor grado las tecnologías de la información y de la comunicación, y nos “exige” de alguna manera, a no detenernos en adquirir constantemente conocimiento del manejo sobre éstas, adaptándonos al avance vertiginoso que nos impone, y acompañando de la mejor manera su evolución. Este contexto fue el que permitió, principalmente, el acceso a nuevas formas de organización del trabajo, dando inicio a la modalidad del teletrabajo o trabajo a distancia, cada vez más utilizada por las organizaciones, y ofreciendo amplios beneficios tanto a los empresarios como a los trabajadores. ABSTRACT: Today we are moving the first traces of a new socio-cultural and economic revolution both locally and globally, following the implementation of information technology and communication (ICT) in many of the activities performed by humans and organizations, and the potential development of application that provides all disciplinary fields. As happened in historical times with the industrial revolution, it is now manifested by the need for information as the main raw material input and for the success of organizations. That is, the ability to access a greater quantity and quality of information anytime, anywhere, now accounts essential to survive and get the best benefits in any food production system. We could say that every activity where individuals involved, whether recreational, educational or productive, involved in varying degrees of information technology and communication, and we “require” somehow not stop in acquiring knowledge management constantly on them, adapting to the rapid advance imposed on us, and the best way to accompany its evolution. This context was allowed mainly access to new forms of work organization, starting mode of teleworking or telecommuting increasingly used by organizations, and providing extensive benefits to both employers and the workers.

scholarly journals Trade-offs in Robustness to Perturbations of Bacterial Population Controllers

2020 ◽  
Author(s):  
Cameron McBride ◽  
Domitilla Del Vecchio
Keyword(s):  
Population Size ◽  
Cell Population ◽  
Resource Sharing ◽  
Genetic Circuit ◽  
Genetic Circuits ◽  
Genetic Population ◽  
Considerable Difficulty ◽  
Trade Offs ◽  
Multiple Cell ◽  
Circuit Components

AbstractSynthetic biology applications have the potential to have lasting impact; however, there is considerable difficulty in scaling up engineered genetic circuits. One of the current hurdles is resource sharing, where different circuit components become implicitly coupled through the host cell’s pool of resources, which may destroy circuit function. One potential solution around this problem is to distribute genetic circuit components across multiple cell strains and control the cell population size using a population controller. In these situations, perturbations in the availability of cellular resources, such as due to resource sharing, will affect the performance of the population controller. In this work, we model a genetic population controller implemented by a genetic circuit while considering perturbations in the availability of cellular resources. We analyze how these intracellular perturbations and extracellular disturbances to cell growth affect cell population size. We find that it is not possible to tune the population controller’s gain such that the population density is robust to both extracellular disturbances and perturbations to the pool of available resources.

scholarly journals Identification of a Transcriptomic Network Underlying the Wrinkly and Smooth Phenotypes of Vibrio fischeri

2020 ◽  
Vol 203 (3) ◽  
Author(s):  
Alba Chavez-Dozal ◽  
William Soto ◽  
Michele K. Nishiguchi
Keyword(s):  
Biofilm Formation ◽  
Marine Bacterium ◽  
Vibrio Fischeri ◽  
Life History Strategy ◽  
Complex Form ◽  
Bacterial Colony ◽  
Content Type ◽  
Naturally Occurring ◽  
Light Organs ◽  
Genetic Mechanisms

ABSTRACT Vibrio fischeri is a cosmopolitan marine bacterium that oftentimes displays different colony morphologies, switching from a smooth to a wrinkly phenotype in order to adapt to changes in the environment. This wrinkly phenotype has also been associated with increased biofilm formation, an essential characteristic for V. fischeri to adhere to substrates, to suspended debris, and within the light organs of sepiolid squids. Elevated levels of biofilm formation are correlated with increased microbial survival of exposure to environmental stressors and the ability to expand niche breadth. Since V. fischeri has a biphasic life history strategy between its free-living and symbiotic states, we were interested in whether the wrinkly morphotype demonstrated differences in its expression profile in comparison to the naturally occurring and more common smooth variant. We show that genes involved in major biochemical cascades, including those involved in protein sorting, oxidative stress, and membrane transport, play a role in the wrinkly phenotype. Interestingly, only a few unique genes are specifically involved in macromolecule biosynthesis in the wrinkly phenotype, which underlies the importance of other pathways utilized for adaptation under the conditions in which Vibrio bacteria are producing this change in phenotype. These results provide the first comprehensive analysis of the complex form of genetic activation that underlies the diversity in morphologies of V. fischeri when switching between two different colony morphotypes, each representing a unique biofilm ecotype. IMPORTANCE The wrinkly bacterial colony phenotype has been associated with increased squid host colonization in V. fischeri. The significance of our research is in identifying the genetic mechanisms that are responsible for heightened biofilm formation in V. fischeri. This report also advances our understanding of gene regulation in V. fischeri and brings to the forefront a number of previously overlooked genetic networks. Several loci that were identified in this study were not previously known to be associated with biofilm formation in V. fischeri.

scholarly journals In Silico Design and Analysis of Genetic Circuit-Based Whole-Cell Biosensors for Detecting Groundwater Contaminants

2020 ◽  
Author(s):  
Samuel Fajemilua ◽  
Solomon Bada ◽  
M. Ahsanul Islam
Keyword(s):  
Salicylic Acid ◽  
Continuous Monitoring ◽  
Analytical Techniques ◽  
Genetic Circuit ◽  
Genetic Circuits ◽  
Natural Habitats ◽  
Whole Cell ◽  
Mathematical Simulations ◽  
Harmful Effects ◽  
Biology Research

AbstractContaminants of emerging concern (CEC) such as tetracycline, erythromycin, and salicylic acid in groundwater can seriously endanger the environment and human health due to their widespread and everlasting harmful effects. Thus, continuous monitoring of various CEC concentrations in groundwater is essential to ensure the safety, security, and biodiversity of natural habitats. CECs can be detected using whole-cell biosensors for environmental surveillance and monitoring purposes, as they provide a cheaper and more robust alternative to traditional and expensive analytical techniques. In this study, various genetic circuit designs are considered to model three biosensors using the genetic design automation (GDA) software, iBioSim. The genetic circuits were designed to detect multiple CECs, including atrazine, salicylic acid, and tetracycline simultaneously to produce quantitative fluorescent outputs. The biosensor responses and the viability of the genetic circuit designs were further analysed using ODE-based mathematical simulations in iBioSim. The designed circuits and subsequent biosensor modelling presented here, thus, not only show the usefulness and importance of GDA tools, but also highlight their limitations and shortcomings that need to overcome in the future; thereby, providing a practical guidance for further improvement of such tools, so that they can be more effectively and routinely used in synthetic biology research.

Sign in / Sign up

Export Citation Format

Share Document