Article
Biology
Elena Righetti, Cansu Uluseker, Ozan Kahramanogullari
Summary: Synthetic biology offers new perspectives in various industries but developing applications in this field is often time-consuming and costly. Computational models can be used to design biological circuits in a computer setting, providing a virtual lab environment for better understanding of molecular pathways. The relationship between signal fidelity and noise in gene expression is crucial for the successful functioning of engineered organisms.
Article
Materials Science, Multidisciplinary
Rakesha Chandra Dash
Summary: In this research, a stochastic model is developed to analyze the impact of random wind speed fluctuations on the power output of galloping-based piezoelectric energy harvesters (GPEHs). Monte Carlo simulations are employed to evaluate the system performance under different degrees of randomness in wind speed and aerodynamic coefficients. The findings indicate that random variations in the galloping force coefficients have a more significant influence on the electrical power output compared to wind speed, and the non-linear galloping force coefficient has a more pronounced effect on power output than the linear coefficient.
MECHANICS OF ADVANCED MATERIALS AND STRUCTURES
(2023)
Article
Biology
Lucy Ham, Marcel Jackson, Michael P. H. Stumpf
Summary: Single-cell expression profiling reveals extensive cell-to-cell variability at the transcriptomic and proteomic level, posing challenges in inferring dynamics and causes of variability. New mathematical models and experimental set-ups are proposed to distinguish intrinsic and extrinsic noise, providing insights into understanding the origins and effects of cell-to-cell variability.
News Item
Multidisciplinary Sciences
Philip Ball
Summary: A pair of studies highlight ethical and legal concerns surrounding the status of lab-grown human embryo models.
Article
Physics, Fluids & Plasmas
Euan Joly-Smith, Zitong Jerry Wang, Andreas Hilfinger
Summary: Inferring functional relationships within complex networks from static snapshots of a subset of variables is a common problem in science. Researchers demonstrated a method using static population snapshots to infer properties of gene expression dynamics, and validated the theory through experiments with gene expression reporters. The study also derived correlation conditions for detecting closed-loop feedback regulation in gene regulatory networks.
Review
Biochemistry & Molecular Biology
Yaron Ilan
Summary: The constrained disorder principle (CDP) defines systems based on their degree of disorder bounded by dynamic boundaries. The principle explains stochasticity in living and non-living systems. Denis Noble described the importance of stochasticity in biology, emphasizing stochastic processes at molecular, cellular, and higher levels in organisms as having a role beyond simple noise. The CDP and Noble's theories (NT) claim that biological systems use stochasticity. This paper presents the CDP and NT, discussing common notions and differences between the two theories. The paper presents the CDP-based concept of taking the disorder beyond its role in nature to correct malfunctions of systems and improve the efficiency of biological systems. The use of CDP-based algorithms embedded in second-generation artificial intelligence platforms is described. In summary, noise is inherent to complex systems and has a functional role. The CDP provides the option of using noise to improve functionality.
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY
(2023)
Article
Mathematical & Computational Biology
Meiling Chen, Tianshou Zhou, Jiajun Zhang
Summary: The transcription of genes in single cells is discussed as a probabilistic process, with emphasis on the relationship between variance and mean expression. It is revealed that the sign of a key parameter beta in this relationship is entirely controlled by external regulation, rather than promoter structure, and is determined by the independence or correlation of regulators as stochastic variables. The findings suggest that external regulation governs the mean-noise relationship more so than promoter sequence.
MATHEMATICAL BIOSCIENCES AND ENGINEERING
(2021)
Article
Ecology
Zachariah Gompert, Samuel M. Flaxman, Jeffrey L. Feder, Luis-Miguel Chevin, Patrik Nosil
Summary: Our ability to predict natural phenomena is limited by incomplete information, as demonstrated by Laplace's demon. Research using analytical models and computer simulations illustrates how data limits in a Bayesian framework influence our ability to predict evolution, highlighting the importance of more accurate knowledge for improved prediction.
Review
Biotechnology & Applied Microbiology
Kangsan Kim, Minjeong Kang, Byung-Kwan Cho
Summary: In recent years, there has been increasing interest in gut commensal engineering for therapeutic applications. Recent advancements in synthetic biology and systems biology have enabled effective utilization of gut commensals for therapy and diagnosis, including the rational design of synthetic microbial consortia and the construction of synthetic cells that can detect specific signals in the intestine and deliver therapeutic drugs in real-time.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Editorial Material
Biochemical Research Methods
Michael B. Sheets, Joshua T. Atkinson, Mark P. Styczynski, Emily R. Aurand
Summary: As engineering biology continues to have increasing impacts, it is crucial to introduce the field early on in an accessible manner. However, teaching engineering biology faces challenges such as limited representation in widely used scientific textbooks or curricula, as well as its interdisciplinary nature. To address this, we have developed an adaptable curriculum module that provides a versatile slide deck designed by engineering biology experts to cover the fundamental principles and applications of the field. Free and accessible through a public website, this module can be used independently or integrated into existing curricula, aiming to enhance the ease of teaching current engineering biology topics and promote public engagement with the field.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemical Research Methods
Salva Duran-Nebreda, Jordi Pla, Blai Vidiella, Jordi Pinero, Nuria Conde-Pueyo, Ricard Sole
Summary: This article discusses the characteristics of multicellular entities and their spatial patterns related to functions, as well as the repeating distributions in biological structures. It introduces patterning modules and synthetic gene circuits, along with the phenomenon of symmetry-breaking demonstrated through experimental results.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Yuval Elani
Summary: The construction of artificial cells is a major challenge today, with potential applications in clinical and industrial settings. Artificial cells currently cannot match the complexity of biological cells, leading researchers to explore hybrid living/synthetic systems that combine the advantages of both.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Layla Malouf, Diana A. Tanase, Giacomo Fabrini, Ryan A. Brady, Miguel Paez-Perez, Adrian Leathers, Michael J. Booth, Lorenzo Di Michele
Summary: This paper demonstrates how microphase separation can be used to engineer synthetic cells with programmable morphology and compartment-targeted activity. The synthetic cells are self-assembled from amphiphilic DNA nanostructures and can undergo lipid deposition and phase-selective etching to generate core-shell condensates, a porous pseudo-membrane, cytoplasm analog, and membrane-less organelles. The research exemplifies how architectural and functional complexity can emerge from a limited number of distinct building blocks.
Article
Computer Science, Artificial Intelligence
Joel Zirkle, Leonid L. Rubchinsky
Summary: Neural synchrony in the brain is often intermittent, with specific temporal patterns that may be correlated with behavior. Channel noise affects not only synchrony strength but also the temporal patterning of synchrony, potentially contributing to observed short desynchronization dynamics in experimental studies.
Review
Biotechnology & Applied Microbiology
Javad Aminian-Dehkordi, Shadi Rahimi, Mehdi Golzar-Ahmadi, Amritpal Singh, Javiera Lopez, Rodrigo Ledesma-Amaro, Ivan Mijakovic
Summary: Synthetic biology offers new solutions for environmental protection by developing remediation systems using genetically engineered microbes and plants, and utilizing computational methods for design and application to detect and respond to specific pollutants.
BIOTECHNOLOGY ADVANCES
(2023)
