A new frontier in synthetic biology: automated design of small RNA devices in bacteria

The quest to construct artificial cells from the bottom-up using simple building blocks has received much attention over recent decades and is one of the grand challenges in synthetic biology. Cell mimics that are encapsulated by lipid membranes are a particularly powerful class of artificial cells due to their biocompatibility and the ability to reconstitute biological machinery within them. One of the key obstacles in the field centres on the following: how can membrane-based artificial cells be generated in a controlled way and in high-throughput? In particular, how can they be constructed to have precisely defined parameters including size, biomolecular composition and spatial organization? Microfluidic generation strategies have proved instrumental in addressing these questions. This article will outline some of the major principles underpinning membrane-based artificial cells and their construction using microfluidics, and will detail some recent landmarks that have been achieved.

Download Full-text

Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality

ACS Synthetic Biology ◽

10.1021/acssynbio.6b00306 ◽

2017 ◽

Vol 6 (7) ◽

pp. 1180-1193 ◽

Cited By ~ 19

Author(s):

Irene Otero-Muras ◽

Julio R. Banga

Keyword(s):

Synthetic Biology ◽

Pareto Optimality ◽

Automated Design ◽

Design Framework

Download Full-text

Small RNA regulators in bacteria: powerful tools for metabolic engineering and synthetic biology

Applied Microbiology and Biotechnology ◽

10.1007/s00253-014-5569-y ◽

2014 ◽

Vol 98 (8) ◽

pp. 3413-3424 ◽

Cited By ~ 42

Author(s):

Zhen Kang ◽

Chuanzhi Zhang ◽

Junli Zhang ◽

Peng Jin ◽

Juan Zhang ◽

...

Keyword(s):

Metabolic Engineering ◽

Synthetic Biology ◽

Small Rna

Download Full-text

Changing Infrastructural Practices: Routine and Reproducibility in Automated Interdisciplinary Bioscience

Science Technology & Human Values ◽

10.1177/0162243919893757 ◽

2019 ◽

Vol 45 (6) ◽

pp. 1220-1241

Author(s):

Robert Meckin

Keyword(s):

Synthetic Biology ◽

Research Productivity ◽

Interdisciplinary Collaboration ◽

Biological Materials ◽

Automated Design ◽

Manual Labor ◽

Research Infrastructures ◽

Epistemic Culture ◽

New Research

Proponents of engineering and design approaches to biology aim to make interdisciplinary bioscience research faster and more reproducible. This paper outlines and deploys a practice-based approach to analyses of infrastructure that focuses on the routine epistemic activities and charts how two such routines are unsettled and resettled in the background of epistemic culture. This paper describes attempts to bring about new research infrastructures in synthetic biology using robotics and software-enabled design. A focus on the skills of pipetting shows how established manual labor has to be reconfigured to fit with novel robotic automations. An analysis of curating frozen materials shows that automated design presents new problems for the established activities of storing and retrieving biological materials. These movements, while transient, have implications for organizing interdisciplinary collaboration, research productivity, and enabling greater reproducibility. This paper explores the idea of infrastructure as practice and shows how this has important implications for studies of research infrastructures. This article discusses the main contributions of this approach for analysts of infrastructure in terms of movements, temporalities, and ethics and offers suggestions for what the research implies for synthetic biology.

Download Full-text

Small RNA drugs for prion disease: a new frontier

Expert Opinion on Drug Discovery ◽

10.1517/17460441.2013.818976 ◽

2013 ◽

Vol 8 (10) ◽

pp. 1265-1284 ◽

Cited By ~ 7

Author(s):

Amrit S Boese ◽

Anna Majer ◽

Reuben Saba ◽

Stephanie A Booth

Keyword(s):

Prion Disease ◽

Small Rna ◽

New Frontier

Download Full-text

NSUN6, an RNA methyltransferase of 5-mC controls glioblastoma response to Temozolomide (TMZ) via NELFB and RPS6KB2 interaction.

10.1101/2021.08.11.455957 ◽

2021 ◽

Author(s):

Chidiebere U Awah ◽

Jan Winter ◽

Claudiane M Mazdoom ◽

Olorunseun Ogunwobi

Keyword(s):

Small Rna ◽

Survival Benefit ◽

Alkylating Agents ◽

Present Evidence ◽

General Transcription Factor ◽

New Frontier ◽

Transcription Factor Complexes ◽

Methyl Cytosine ◽

Control Translation ◽

Mgmt Promoter Status

Nop2/Sun RNA methyltransferase (NSUN6) is an RNA 5 - methyl cytosine (5mC) transferase with little information known of its function in cancer and response to cancer therapy. Here, we show that NSUN6 methylates both large and small RNA in glioblastoma and controls glioblastoma response to temozolomide with or without influence of the MGMT promoter status, with high NSUN6 expression conferring survival benefit to glioblastoma patients and in other cancers. Mechanistically, our results show that NSUN6 controls response to TMZ therapy via 5mC mediated regulation of NELFB and RPS6BK2. Taken together, we present evidence that show that NSUN6 mediated 5mC deposition regulates transcriptional pause (by accumulation of NELFB and the general transcription factor complexes (POLR2A, TBP, TFIIA, TFIIE) on the preinitiation complex at TATA binding site to control translation machinery in glioblastoma response to alkylating agents. Our findings open a new frontier into controlling of transcriptional regulation by RNA methyltransferase and 5mC.

Download Full-text