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
Multidisciplinary Sciences
Luna Rizik, Loai Danial, Mouna Habib, Ron Weiss, Ramez Daniel
Summary: Researchers have utilized the perceptgene technology to create synthetic gene circuits based on the computational properties of neuronal networks. These circuits can perform non-binary logic computation and signal processing, and can be modified for different tasks by adjusting parameters.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Tianchi Chen, M. Ali Al-Radhawi, Christopher A. Voigt, Eduardo D. Sontag
Summary: A design for genetically encoded counters using repressor-based circuits is proposed, allowing for scalable computation and bypassing limitations on maximal circuit genes per cell. The design utilizes distributed computation with specialized cell types and connector modules for interconnecting single-bit counters to achieve an N-bit counter. An optimization framework is used to determine gate parameters and guide the construction of novel gates, moving towards circuits capable of finite automaton computation akin to central processing units.
Review
Chemistry, Multidisciplinary
Qiwen Wang, Zhehui Hu, Zhixuan Li, Tiangang Liu, Guangkai Bian
Summary: Engineered living materials (ELMs) represent a significant paradigm shift in material design, possessing unique living attributes and unprecedented potential in various fields. This review provides an overview of the latest research progress and design strategies for ELMs derived from bacteria, fungi, and plants, and offers valuable references for future ELM design and application. The investigation into synergistic application possibilities among different species of ELMs provides beneficial information for researchers and practitioners in this field.
ADVANCED MATERIALS
(2023)
Review
Biotechnology & Applied Microbiology
Roberto Di Blasi, Annalise Zouein, Tom Ellis, Francesca Ceroni
Summary: Construction of DNA-encoded programs is crucial in synthetic biology, with Golden Gate toolkits now dominating due to their modular design. Future advances include accessory packs for cloning toolkits to facilitate editing, orthogonality, advanced regulation, and integration into synthetic chromosome construction.
TRENDS IN BIOTECHNOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Angel Leon-Buitimea, Francisco de Jesus Balderas-Cisneros, Cesar Rodolfo Garza-Cardenas, Javier Alberto Garza-Cervantes, Jose Ruben Morones-Ramirez
Summary: With the rise of antibiotic-resistant bacterial infections, there is a global health crisis. Overuse, inappropriate prescribing, and lack of innovation have led to an increase in microorganisms that can overcome traditional antimicrobial treatments. Synthetic biology offers a promising strategy to develop new antimicrobial therapies through the engineering of control systems in microbial cells.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
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)
Review
Chemistry, Multidisciplinary
Marcelo D. T. Torres, Jicong Cao, Octavio L. Franco, Timothy K. Lu, Cesar de la Fuente-Nunez
Summary: Antibiotic resistance poses a significant global health challenge, with the need for innovative strategies becoming more urgent. Antimicrobial peptides (AMPs) offer a natural template for the discovery, design, and production of antibiotics, potentially leading the way for future advancements in peptide drug discovery through computational and synthetic biology approaches.
Review
Biochemical Research Methods
Yan Huang, Xiaojun Lin, Siyang Yu, Ruiyue Chen, Weizhao Chen
Summary: This review summarizes the progress and issues in the use of synthetic biology to construct gut-engineered probiotics for live therapeutics.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Biochemical Research Methods
Yan Huang, Xiaojun Lin, Siyang Yu, Ruiyue Chen, Weizhao Chen
Summary: Intestinal engineered probiotics show promise in treating specific diseases, but there are design and safety issues that restrict their widespread application.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Engineering, Electrical & Electronic
Jamie A. Davies
Summary: Synthetic morphogenesis is a new engineering discipline that genetically engineers cells to create designed shapes and structures. Devices in this field utilize natural shape-generating processes from embryonic development, but artificially manipulate them according to a technologist's preferences. Synthetic morphogenesis enables the construction of two-way interfaces between living organisms and electronic devices, facilitating unprecedented information flow and control.
PROCEEDINGS OF THE IEEE
(2022)
Review
Biology
Stefano Rosa, Chiara Bertaso, Paolo Pesaresi, Simona Masiero, Andrea Tagliani
Summary: Protein-protein interactions play a key role in regulating cell physiology and metabolism. By utilizing protein domains in genetic circuits, synthetic biology has enabled the design of circuits that can impact transcriptional outputs and cellular metabolism, with potential applications in biosensing and diagnostics. Additionally, engineered PPIs can be utilized in the development of new drugs targeting specific cellular and extracellular proteins.
Editorial Material
Oncology
Krishneel Prasad, Ryan S. Cross, Misty R. Jenkins
Summary: Synthetic biology has allowed for rewiring natural cellular responses to treat disease, as exemplified by CAR T cells as immunotherapy for cancer. Current research focuses on using noncanonical signaling pathways and synthetic gene circuitry to enhance the antitumor properties of engineered T cells. Two recent studies explore how these new technologies can achieve this goal, one using machine learning to predict CAR T cell phenotype and the other engineering controllable transcriptional regulators using synthetic zinc fingers. These studies expand the possibilities for future gene circuits and demonstrate how cellular therapy can respond to various environmental cues.
MOLECULAR ONCOLOGY
(2023)
Review
Cell Biology
Maysam Mansouri, Martin Fussenegger
Summary: Cell therapy approaches utilizing engineered mammalian cells for on-demand production of therapeutic agents in the patient's body have advanced beyond proof-of-concept in translational medicine. Customized therapeutic cells can sense user-defined signals, process them, and respond programmably. Various methods of controlling cell behavior, including open-loop and closed-loop systems, are discussed, along with therapeutic applications of engineered cells in early disease diagnosis and treatment. Emerging technologies like digital devices also show potential for future incorporation into cell-based therapies.
Article
Engineering, Biomedical
Diana R. Fonseca, Ana Moura, Victoria Leiro, Ricardo Silva-Carvalho, Berta N. Estevinho, Catarina L. Seabra, Patricia C. Henriques, Monica Lucena, Catia Teixeira, Paula Gomes, Paula Parreira, M. Cristina L. Martins
Summary: The bioengineered approach of grafting MSI-78A onto chitosan microspheres enhances its bactericidal performance against Helicobacter pylori. The conjugation does not compromise the antimicrobial activity of MSI-78A and even boosts its effectiveness against H. pylori, making it a potential alternative for antibiotic therapy.
ACTA BIOMATERIALIA
(2022)
Review
Chemistry, Multidisciplinary
Marcelo D. T. Torres, Jicong Cao, Octavio L. Franco, Timothy K. Lu, Cesar de la Fuente-Nunez
Summary: Antibiotic resistance poses a significant global health challenge, with the need for innovative strategies becoming more urgent. Antimicrobial peptides (AMPs) offer a natural template for the discovery, design, and production of antibiotics, potentially leading the way for future advancements in peptide drug discovery through computational and synthetic biology approaches.
Review
Immunology
Nicholas Palmer, Jacqueline R. M. A. Maasch, Marcelo D. T. Torres, Cesar de la Fuente-Nunez
Summary: Antimicrobial resistance is a growing concern, with only two new classes of antibiotics approved for human use since the 1960s. Molecular dynamics simulation is a valuable tool for understanding antibiotic mechanisms and can lay the groundwork for new antibiotic discovery. Antimicrobial peptides show promise in combating resistance due to their lower tendency to induce resistance compared to small-molecule antibiotics.
INFECTION AND IMMUNITY
(2021)
Article
Biochemistry & Molecular Biology
Tzu-Chieh Tang, Eleonore Tham, Xinyue Liu, Kevin Yehl, Alexis J. Rovner, Hyunwoo Yuk, Cesar de la Fuente-Nunez, Farren J. Isaacs, Xuanhe Zhao, Timothy K. Lu
Summary: A hydrogel-based encapsulation system, known as DEPCOS, has been developed to provide deployable physical containment for genetically modified microorganisms, preventing their escape and protecting them against environmental insults. It also allows for controlled lifespan and easy retrieval of bacteria, showcasing versatility in executing useful functions such as cell-cell communication and heavy metal sensing.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Angela Cesaro, Marcelo D. T. Torres, Rosa Gaglione, Eliana Dell'Olmo, Rocco Di Girolamo, Andrea Bosso, Elio Pizzo, Henk P. Haagsman, Edwin J. A. Veldhuizen, Cesar de la Fuente-Nunez, Angela Arciello
Summary: Encrypted peptides in the human proteome have been found to have potent antimicrobial activity against drug-resistant bacteria, without causing bacterial resistance. Blood may serve as an important source of antimicrobials.
Article
Engineering, Biomedical
Marcelo D. T. Torres, Marcelo C. R. Melo, Orlando Crescenzi, Eugenio Notomista, Cesar de la Fuente-Nunez
Summary: By mining the human proteome, researchers identified 2,603 encrypted peptide antibiotics with antibacterial activity and low bacterial resistance, which target pathogenic bacteria by modulating their membranes and demonstrate anti-infective properties in mouse infection models. Additionally, peptides from the same geographical region show synergistic antimicrobial effects.
NATURE BIOMEDICAL ENGINEERING
(2022)
Article
Chemistry, Multidisciplinary
Xavier Arque, Marcelo D. T. Torres, Tania Patino, Andreia Boaro, Samuel Sanchez, Cesar de la Fuente-Nunez
Summary: The increasing resistance of bacteria to antibiotics is a major global public health threat. Current antibiotic treatments are hindered by poor delivery to the infection site, leading to off-target effects and drug resistance. This study presents micro- and nanomotors that autonomously deliver antibiotics to specific areas, showing effective bactericidal activity against Gram-positive and Gram-negative bacteria in vitro by rapidly depolarizing their membrane. This technology provides a much-needed tool to direct therapeutics to infection sites and combat drug-resistant infections.
Editorial Material
Respiratory System
Lucia Ageitos, Cesar de la Fuente-Nunez
ARCHIVOS DE BRONCONEUMOLOGIA
(2022)
Editorial Material
Biotechnology & Applied Microbiology
Cesar de la Fuente-Nunez
Summary: This study utilizes artificial intelligence to find candidate peptide antibiotics in the human gut microbiome.
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Marcelo D. T. Torres, Lucas F. de Lima, Andre L. Ferreira, William R. de Araujo, Paul Callahan, Antonio Davila, Benjamin S. Abella, Cesar de la Fuente-Nunez
Summary: This study presents a rapid, accurate, inexpensive, and scalable test for diagnosing COVID-19 at the point-of-care. The method showed high sensitivity, specificity, and accuracy in the testing.
Article
Public, Environmental & Occupational Health
David Garcia-Garcia, Enrique Morales, Cesar De La Fuente-Nunez, Isabel Vigo, Eva S. Fonfria, Cesar Bordehore
Summary: Accurate detection of early COVID-19 cases is crucial to reduce infections and deaths. This study used seroprevalence data and a new methodology to analyze the initial spread of SARS-CoV-2 infections in the US. Results showed that the virus likely entered the country on December 28, 2019, and on average a month earlier than previously recorded.
SPATIAL AND SPATIO-TEMPORAL EPIDEMIOLOGY
(2022)
Correction
Engineering, Biomedical
Marcelo D. T. Torres, Marcelo C. R. Melo, Laurice Flowers, Orlando Crescenzi, Eugenio Notomista, Cesar de la Fuente-Nunez
NATURE BIOMEDICAL ENGINEERING
(2022)
Editorial Material
Engineering, Biomedical
Fangping Wan, Cesar de la Fuente-Nunez
Summary: A machine-learning pipeline is used to identify effective antimicrobial peptides by progressively narrowing down the search space of polypeptide chain sequences.
NATURE BIOMEDICAL ENGINEERING
(2023)
News Item
Biochemistry & Molecular Biology
Angela Cesaro, Cesar de la Fuente-Nunez
NATURE CHEMICAL BIOLOGY
(2023)
Review
Multidisciplinary Sciences
Felix Wong, Cesar de la Fuente-nunez, James J. Collins
Summary: Despite advancements in various fields, infectious diseases still pose a significant threat to public health. Combating pathogen outbreaks, pandemics, and antimicrobial resistance requires interdisciplinary efforts. With the integration of systems and synthetic biology, artificial intelligence (AI) has emerged as a valuable tool in anti-infective drug discovery, understanding infection biology, and accelerating diagnostics. This review explores the current progress supported by AI and discusses potential future applications in controlling infectious disease outbreaks and pandemics.
