scholarly journals Eukaryotic systems broaden the scope of synthetic biology

2009 ◽  
Vol 187 (5) ◽  
pp. 589-596 ◽  
Author(s):  
Karmella A. Haynes ◽  
Pamela A. Silver
Keyword(s):  
Synthetic Biology ◽  
Nucleic Acids ◽  
Cell Biology ◽  
Cell Behavior ◽  
Cellular Functions ◽  
Complex Cells ◽  
Cellular Processes ◽  
Challenges And Opportunities ◽  
Foundational Work ◽  
Biology Research

Synthetic biology aims to engineer novel cellular functions by assembling well-characterized molecular parts (i.e., nucleic acids and proteins) into biological “devices” that exhibit predictable behavior. Recently, efforts in eukaryotic synthetic biology have sprung from foundational work in bacteria. Designing synthetic circuits to operate reliably in the context of differentiating and morphologically complex cells presents unique challenges and opportunities for progress in the field. This review surveys recent advances in eukaryotic synthetic biology and describes how synthetic systems can be linked to natural cellular processes in order to manipulate cell behavior and to foster new discoveries in cell biology research.

scholarly journals Bioelectrical understanding and engineering of cell biology

2020 ◽  
Vol 17 (166) ◽  
pp. 20200013 ◽  
Author(s):  
Zoe Schofield ◽  
Gabriel N. Meloni ◽  
Peter Tran ◽  
Christian Zerfass ◽  
Giovanni Sena ◽  
...  
Keyword(s):  
Systems Biology ◽  
Cell Biology ◽  
Genetic Basis ◽  
Control Cell ◽  
Status Quo ◽  
Cell Behaviour ◽  
Cellular Processes ◽  
Mechanical Responses ◽  
Predictive Understanding ◽  
Biology Research

The last five decades of molecular and systems biology research have provided unprecedented insights into the molecular and genetic basis of many cellular processes. Despite these insights, however, it is arguable that there is still only limited predictive understanding of cell behaviours. In particular, the basis of heterogeneity in single-cell behaviour and the initiation of many different metabolic, transcriptional or mechanical responses to environmental stimuli remain largely unexplained. To go beyond the status quo , the understanding of cell behaviours emerging from molecular genetics must be complemented with physical and physiological ones, focusing on the intracellular and extracellular conditions within and around cells. Here, we argue that such a combination of genetics, physics and physiology can be grounded on a bioelectrical conceptualization of cells. We motivate the reasoning behind such a proposal and describe examples where a bioelectrical view has been shown to, or can, provide predictive biological understanding. In addition, we discuss how this view opens up novel ways to control cell behaviours by electrical and electrochemical means, setting the stage for the emergence of bioelectrical engineering.

Hydrodynamically-Confined Microflows for Cell Adhesion Strength Measurement

2010 ◽  
Author(s):  
Kevin V. Christ ◽  
Kevin T. Turner
Keyword(s):  
Cell Adhesion ◽  
Adhesion Strength ◽  
Cell Biology ◽  
Microfluidic Devices ◽  
Cell Behavior ◽  
Shear Stresses ◽  
Strength Measurement ◽  
Coated Surfaces ◽  
Biology Research ◽  
Standard Techniques

Cell adhesion plays a fundamental role in numerous physiological and pathological processes, and measurements of the adhesion strength are important in fields ranging from basic cell biology research to the development of implantable biomaterials. Our group and others have recently demonstrated that microfluidic devices offer advantages for characterizing the adhesion of cells to protein-coated surfaces [1,2]. Microfluidic devices offer many advantages over conventional assays, including the ability to apply high shear stresses in the laminar regime and the opportunity to directly observe cell behavior during testing. However, a key disadvantage is that such assays require cells to be cultured inside closed microchannels. Assays based on closed channels restrict the types of surfaces that can be examined and are not compatible with many standard techniques in cell biology research. Furthermore, while techniques for cell culture in microchannels have become common, maintaining the viability of certain types of cells in channels remains a challenge.

scholarly journals Novel roles for mammalian septins: from vesicle trafficking to oncogenesis

2001 ◽  
Vol 114 (5) ◽  
pp. 839-844 ◽  
Author(s):  
B. Kartmann ◽  
D. Roth
Keyword(s):  
Plasma Membrane ◽  
Recent Work ◽  
Cell Biology ◽  
Vesicle Trafficking ◽  
Family Members ◽  
Protein Family ◽  
Cellular Functions ◽  
Cellular Processes ◽  
Sequence Homologies ◽  
Genome Analyses

In recent years a convergence of various aspects of cell biology has become apparent, and yet investigators are only beginning to grasp the underlying unifying mechanisms. Among the proteins that participate in diverse aspects of cell biology are the septins. These are a group of novel GTPase proteins that are broadly distributed in many eukaryotes except plants. Although septins were originally identified as a protein family involved in cytokinesis in yeast, recent advances in the field have now ascribed additional functions to these proteins. In particular, the number of known mammalian septin family members has increased dramatically as more data has become available through genome analyses. We suggest a classification for the mammalian septins based on the sequence homologies in their highly divergent N- and C-termini. Recent work suggests novel functions for septins in vesicle trafficking, oncogenesis and compartmentalization of the plasma membrane. Given the ability of the septins to bind GTP and phosphatidylinositol 4,5-bisphosphate in a mutually exclusive manner, these proteins might be crucial elements for the spatial and/or temporal control of diverse cellular functions. As the functions of the septins become unraveled, our understanding of seemingly different cellular processes may move a step further.

scholarly journals The Multiple Faces of MNT and Its Role as a MYC Modulator

Cancers ◽  
2021 ◽  
Vol 13 (18) ◽  
pp. 4682
Author(s):  
Judit Liaño-Pons ◽  
Marie Arsenian-Henriksson ◽  
Javier León
Keyword(s):  
Cell Proliferation ◽  
Transcriptional Repression ◽  
Cell Biology ◽  
Essential Role ◽  
Present Knowledge ◽  
Special Focus ◽  
Cellular Functions ◽  
Cellular Processes ◽  
Tumor Cell Survival

MNT is a crucial modulator of MYC, controls several cellular functions, and is activated in most human cancers. It is the largest, most divergent, and most ubiquitously expressed protein of the MXD family. MNT was first described as a MYC antagonist and tumor suppressor. Indeed, 10% of human tumors present deletions of one MNT allele. However, some reports show that MNT functions in cooperation with MYC by maintaining cell proliferation, promoting tumor cell survival, and supporting MYC-driven tumorigenesis in cellular and animal models. Although MAX was originally considered MNT’s obligate partner, our recent findings demonstrate that MNT also works independently. MNT forms homodimers and interacts with proteins both outside and inside of the proximal MYC network. These complexes are involved in a wide array of cellular processes, from transcriptional repression via SIN3 to the modulation of metabolism through MLX as well as immunity and apoptosis via REL. In this review, we discuss the present knowledge of MNT with a special focus on its interactome, which sheds light on the complex and essential role of MNT in cell biology.

scholarly journals Mammalian synthetic biology for studying the cell

2016 ◽  
Vol 216 (1) ◽  
pp. 73-82 ◽  
Author(s):  
Melina Mathur ◽  
Joy S. Xiang ◽  
Christina D. Smolke
Keyword(s):  
Synthetic Biology ◽  
Cell Biology ◽  
Mammalian Cells ◽  
Regulatory Networks ◽  
Dynamic Control ◽  
Model Systems ◽  
Cellular Mechanisms ◽  
Cellular Processes ◽  
Regulatory Processes ◽  
Multicellular Interactions

Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology.

scholarly journals Eukaryo: An AR and VR Application for Cell Biology

2016 ◽  
Vol 16 (1) ◽  
pp. 7-14
Author(s):  
Douglas Yuen ◽  
Markus Santoso ◽  
Stephen Cartwright ◽  
Christian Jacob
Keyword(s):  
Cell Biology ◽  
High Performance ◽  
Large Scale ◽  
Eukaryotic Cell ◽  
Cellular Functions ◽  
3 Dimensional ◽  
Cellular Processes ◽  
Head Mounted Displays ◽  
Biological Environment ◽  
Immersive Visualization

Eukaryo is a simulated bio-molecular world that allows users to explore the complex environment within a biological cell. Eukaryo was developed using Unity, leveraging the capabilities and high performance of a commercial game engine. Through the use of MiddleVR, our tool can support a wide variety of interaction platforms including 3D virtual reality (VR) environments, such as head-mounted displays, augmented reality (AR) headsets, and large scale immersive visualization facilities. Our interactive, 3-dimensional model demonstrates key functional elements of a generic eukaryotic cell. Users are able to use multiple modes to explore the cell, its structural elements, its organelles, and some key metabolic processes. In contrast to textbook diagrams and even videos, Eukaryo immerses users directly in the biological environment, giving a more effective demonstration of how cellular processes work, how compartmentalization affects cellular functions, and how the machineries of life operate.

scholarly journals Physical bioenergetics: Energy fluxes, budgets, and constraints in cells

2021 ◽  
Vol 118 (26) ◽  
pp. e2026786118
Author(s):  
Xingbo Yang ◽  
Matthias Heinemann ◽  
Jonathon Howard ◽  
Greg Huber ◽  
Srividya Iyer-Biswas ◽  
...  
Keyword(s):  
Cell Biology ◽  
Biochemical Networks ◽  
Energy Budgets ◽  
Living Matter ◽  
Cellular Functions ◽  
Cellular Processes ◽  
Energy Flows ◽  
Open Questions ◽  
Nonequilibrium Physics ◽  
Energetic Constraints

Cells are the basic units of all living matter which harness the flow of energy to drive the processes of life. While the biochemical networks involved in energy transduction are well-characterized, the energetic costs and constraints for specific cellular processes remain largely unknown. In particular, what are the energy budgets of cells? What are the constraints and limits energy flows impose on cellular processes? Do cells operate near these limits, and if so how do energetic constraints impact cellular functions? Physics has provided many tools to study nonequilibrium systems and to define physical limits, but applying these tools to cell biology remains a challenge. Physical bioenergetics, which resides at the interface of nonequilibrium physics, energy metabolism, and cell biology, seeks to understand how much energy cells are using, how they partition this energy between different cellular processes, and the associated energetic constraints. Here we review recent advances and discuss open questions and challenges in physical bioenergetics.

scholarly journals Bend, Push, Stretch: Remarkable Structure and Mechanics of Single Intermediate Filaments and Meshworks

Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1960
Author(s):  
K. Tanuj Sapra ◽  
Ohad Medalia
Keyword(s):  
Intermediate Filaments ◽  
Eukaryotic Cell ◽  
Coiled Coils ◽  
Cellular Functions ◽  
Mechanical Pressure ◽  
Mechanical Feature ◽  
Cellular Processes ◽  
Nuclear Lamins ◽  
Filament Networks ◽  
And Function

The cytoskeleton of the eukaryotic cell provides a structural and functional scaffold enabling biochemical and cellular functions. While actin and microtubules form the main framework of the cell, intermediate filament networks provide unique mechanical properties that increase the resilience of both the cytoplasm and the nucleus, thereby maintaining cellular function while under mechanical pressure. Intermediate filaments (IFs) are imperative to a plethora of regulatory and signaling functions in mechanotransduction. Mutations in all types of IF proteins are known to affect the architectural integrity and function of cellular processes, leading to debilitating diseases. The basic building block of all IFs are elongated α-helical coiled-coils that assemble hierarchically into complex meshworks. A remarkable mechanical feature of IFs is the capability of coiled-coils to metamorphize into β-sheets under stress, making them one of the strongest and most resilient mechanical entities in nature. Here, we discuss structural and mechanical aspects of IFs with a focus on nuclear lamins and vimentin.

scholarly journals The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)

2020 ◽  
Vol 17 (2-3) ◽  
Author(s):  
Dagmar Waltemath ◽  
Martin Golebiewski ◽  
Michael L Blinov ◽  
Padraig Gleeson ◽  
Henning Hermjakob ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Data Model ◽  
Computational Models ◽  
Life Sciences ◽  
The Past ◽  
Challenges And Opportunities ◽  
Stakeholder Workshop ◽  
Software Engineers ◽  
Future Work ◽  
Modeling In Biology

AbstractThis paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.

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