Article
Multidisciplinary Sciences
Ronghui Zhu, Jesus M. del Rio-Salgado, Jordi Garcia-Ojalvo, Michael B. Elowitz
Summary: This study explores synthetic circuits that generate multiple stable states, providing insights into natural cell fate control circuit structures and enabling engineering of multicellular programs requiring interactions among distinct cell types.
Review
Biology
Abdurrahman Pharmacy Yusuf, Murtala Bello Abubakar, Ibrahim Malami, Kasimu Ghandi Ibrahim, Bilyaminu Abubakar, Muhammad Bashir Bello, Naeem Qusty, Sara T. Elazab, Mustapha Umar Imam, Athanasios Alexiou, Gaber El-Saber Batiha
Summary: Zinc was established more than half a century ago as an essential micronutrient for normal human physiology, with around 10% of the human proteome potentially binding zinc. Proteins with zinc-binding domains play key roles in epigenetic modifications, such as DNA methylation and histone modifications, regulating transcription under physiological and pathological conditions. Zinc metalloproteins in epigenetics, mainly zinc metalloenzymes and zinc finger proteins, interact as writers, erasers, readers, editors, and feeders to maintain the epigenome's functioning.
Article
Biology
Lisa Baumgartner, Dominik Handler, Sebastian Wolfgang Platzer, Changwei Yu, Peter Duchek, Julius Brennecke
Summary: The chromatin occupancy of Rhino at piRNA source loci in Drosophila germline cells is determined by histone marks and maternally inherited piRNAs. We identified a zinc finger protein called Kipferl as a critical cofactor for Rhino in ovaries, which recruits Rhino to specific loci and stabilizes it on chromatin. In kipferl mutant flies, Rhino is lost from target chromatin loci and accumulates on pericentromeric Satellite arrays, leading to decreased levels of transposon targeting piRNAs and impaired fertility.
Article
Biochemistry & Molecular Biology
Serhan Ozyildirim, Saltuk Bugra Baltaci
Summary: Zinc is essential for the structure and function of numerous enzymes and transcription factors in the human body. It plays a crucial role in heart development and is associated with various congenital heart defects. Zinc is involved in cell signaling, enzymatic responses, and the pathogenesis of cardiovascular diseases. However, the relationship between zinc and the cardiovascular system is complex and not fully understood.
BIOLOGICAL TRACE ELEMENT RESEARCH
(2023)
Article
Computer Science, Artificial Intelligence
Chakkarai Sathyaseelan, L. Ponoop Prasad Patro, Thenmalarchelvi Rathinavelan
Summary: Zinc finger (ZnF) is an important class of nucleic acid and protein recognition domain with diverse structures and biological functions. In order to accurately predict ZnF motifs, researchers collected 74 ZnF sequence patterns and used Pfam HMM profiles for prediction. They developed a web server called ZnF-Prot that can predict 31 ZnF domains in protein sequences of any organism.
PATTERN RECOGNITION
(2023)
Article
Plant Sciences
James Mutemachani Mapodzeke, Muhammad Faheem Adil, Shafaque Sehar, Muhammad Fazal Karim, Muhammad Abu Bakar Saddique, Younan Ouyang, Imran Haider Shamsi
Summary: This review discusses the roles of zinc in plant development and stresses, including its uptake and utilization processes. It also highlights strategies aimed at optimizing plant zinc nutrition levels.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Plant Sciences
A. Carolina Puentes-Romero, Sebastian A. Gonzalez, Enrique Gonzalez-Villanueva, Carlos R. Figueroa, Simon Ruiz-Lara
Summary: The research indicates that Arabidopsis ZINC FINGER 4 (AtZAT4) plays a crucial role in pollen development and maturation, with its subcellular localization in the nucleus, contributing to the regulation of genes associated with reproductive development. The study of Atzat4 (+/) heterozygous mutant revealed significant reductions in gene expression, leading to impaired pollen tube development and reduced seed viability. These findings suggest a role for AtZAT4 in fertilization and seed viability through the regulation of gene expression during reproductive development.
Article
Cell Biology
Hongsheng Liu, Yingzhi Qin, Na Zhou, Dongjie Ma, Yingyi Wang
Summary: ZNF280A plays a tumor-promoting role in LUAD, with a positive correlation with tumor grade, pathological stage, and lymphatic metastasis, and a negative relationship with patient survival. Its effects on cell proliferation, apoptosis, cell cycle, and cell migration may contribute to the development of LUAD.
CELL DEATH & DISEASE
(2021)
Article
Cell Biology
Bin Yang, Haiyu Tang, Nan Wang, Jian Gu, Qin Wang
Summary: Abnormal hypermethylation of the ZNF334 gene, which downregulates its expression, was detected in CRC tissues. TET1 was identified to be involved in regulating the methylation level of ZNF334. A constructed targeted demethylation system successfully upregulated ZNF334 expression and inhibited CRC growth.
CELL DEATH & DISEASE
(2023)
Review
Chemistry, Inorganic & Nuclear
Kiwon Ok, Milos R. Filipovic, Sarah L. J. Michel
Summary: ZF proteins, including the emerging CCCH class, are widespread eukaryotic proteins that play crucial roles in gene regulation, with a particular focus on tristetraprolin (TTP). Various methods have been explored to modulate TTP activity, including targeting with exogenous metals and endogenous signaling molecules. Research has been conducted on using metals such as Fe, Cu, Cd, Au, and H2S to target TTP, with attention to new methods for monitoring metal exchange and RNA binding.
EUROPEAN JOURNAL OF INORGANIC CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Ranjeet Maurya, Aparna Swaminathan, Uzma Shamim, Smriti Arora, Pallavi Mishra, Aakarshan Raina, Varsha Ravi, Bansidhar Tarai, Sandeep Budhiraja, Rajesh Pandey
Summary: The emergence of multiple SAR-CoV-2 variants during the COVID-19 pandemic has led to an increased understanding of the host-immune kinetics associated with these variants. A longitudinal investigation revealed a robust antiviral response in Omicron infection, which was largely absent in the Pre-VOC and Delta waves. The study also highlighted differential protein-protein interactions and gene expression patterns, particularly in relation to zinc finger proteins, that contribute to the immune response.
Review
Chemistry, Multidisciplinary
Gezhi Kong, Mengyi Xiong, Lu Liu, Ling Hu, Hong-Min Meng, Guoliang Ke, Xiao-Bing Zhang, Weihong Tan
Summary: DNA origami, as a sophisticated nanostructure, offers predictable and programmable scaffolds for precise protein assembly. The emerging application of DNA origami-based protein networks in various fields, such as enzymatic reaction regulation and bionics, provides great potential for future research and development. Challenges and opportunities in this research field are also discussed to inspire more innovative studies and applications.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Chemistry, Multidisciplinary
Guoping Li, Aidan C. Manning, Alex Bagi, Xinyu Yang, Priyanka Gokulnath, Michail Spanos, Jonathan Howard, Patricia P. Chan, Thadryan Sweeney, Robert Kitchen, Haobo Li, Brice D. Laurent, Sary F. Aranki, Maria Kontaridis, Louise C. Laurent, Kendall Van Keuren-Jensen, Jochen Muehlschlegel, Todd M. Lowe, Saumya Das
Summary: The study highlights the crucial role of transfer RNA-derived small RNAs in different stress responses and introduces a new sequencing technique for generating a comprehensive abundance landscape of cellular and extracellular tDRs. It also reveals that extracellular tDRs have distinct fragmentation signatures which are better indicators of different stress responses than miRNAs.
Article
Engineering, Electrical & Electronic
Chen Zhu, Wenxing Zhong
Summary: Modularization is an effective method for high-power wireless power transfer (WPT) by modifying the number of modules. However, the cross couplings among modules complicate power transfer paths, making it difficult to achieve stable output regulation. This article proposes a decoupling control method to compensate for the adverse effects of cross couplings, allowing individual output control for each module. A 7-kW two-module WPT prototype is built for experimental verification.
IEEE TRANSACTIONS ON POWER ELECTRONICS
(2023)
Article
Chemistry, Multidisciplinary
Alessandro Alcinesio, Idil Cazimoglu, Gabriella Raye Kimmerly, Vanessa Restrepo Schild, Ravinash Krishna Kumar, Hagan Bayley
Summary: The authors applied modular design to construct modular synthetic tissues, assembling different functional 3D-printed building blocks for storing and releasing reagents, performing logic operations, responding to magnetic fields, and encapsulating living cells. They successfully built synthetic tissues capable of transmitting electrical signals and assembled hybrid tissues composed of both synthetic modules and modules containing living cells. By incorporating mutant protein nanopores within the building blocks, they created modular synthetic tissues with electrical outputs modulated by chemical inputs.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Multidisciplinary Sciences
Nemi Vora, Peter R. Christensen, Jeremy Demarteau, Nawa Raj Baral, Jay D. Keasling, Brett A. Helms, Corinne D. Scown
Summary: Mechanical recycling of polymers downgrades their usability, while chemical recycling offers a more sustainable way to recover chemical feedstocks. The cost and carbon footprint of chemically recycled PDKs are significantly lower than producing virgin resin, providing a strong incentive for recovering and recycling future polymer waste.
Editorial Material
Biotechnology & Applied Microbiology
Corinne D. Scown, Jay D. Keasling
Summary: Producing commodity chemicals in bacteria that thrive on industrial air pollution can capture more greenhouse gases than it emits.
NATURE BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Jeremy Demarteau, Nemi Vora, Jay D. Keasling, Brett A. Helms, Corinne D. Scown
Summary: The efficiency of monomer recovery in the chemical recycling of plastic waste has been a major consideration for sustainability. However, this study also highlights the costs, energy consumption, and carbon emissions associated with resin production. By applying systems analysis, a less intensive process for the production of polydiketoenamine (PDK) resins is proposed, resulting in cost reduction and lower greenhouse gas emissions. The study emphasizes the importance of targeted collection and sorting for achieving practical savings.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2022)
Article
Automation & Control Systems
Murat Arcak
Summary: A major challenge for safety-critical engineering systems is their limited scalability in certifying stability and performance properties. This article proposes a compositional approach to derive system-level guarantees from dissipativity properties and interconnection structure of subsystems. This method is particularly suitable for subsystems amenable to standard analytical and computational methods.
IEEE CONTROL SYSTEMS MAGAZINE
(2022)
Article
Automation & Control Systems
He Yin, Peter Seiler, Murat Arcak
Summary: This paper presents a method for analyzing the stability of feedback systems with neural network controllers and provides two stability theorems. These theorems combine Lyapunov theory with local quadratic constraints to handle both linear and nonlinear systems and can incorporate various types of perturbations.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2022)
Review
Plant Sciences
Xu Lu, Lijin Huang, Henrik Scheller, Jay D. Keasling
Summary: Terpenoid glycosides derived from medicinal plants have shown significant curative effects in the treatment of various diseases. UDP-dependent glycosyltransferases in plants play a crucial role in the biosynthesis of bioactive glycosides. In this review, the characteristics, evolution, and recent advances in terpenoid UDP-glycosyltransferases (UGTs) in medicinal plants over the past 20 years are summarized, providing a reference for the study of glycosylation and biosynthetic pathways of medicinal terpenoids in plants.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Chemistry, Organic
Bo Pang, Edmund I. Graziani, Jay D. Keasling
Summary: Researchers have created a new analog of rapamycin called 23-desmethyl rapamycin, which has reduced inhibitory effects on the growth of Saccharomyces cerevisiae. The ternary complex formed between FKBP12, 23-desmethyl rapamycin, and the FKBP12-rapamycin-binding domain of mTOR has a shorter lifespan compared to the complex derived from rapamycin.
TETRAHEDRON LETTERS
(2022)
Article
Biochemical Research Methods
Kevin Yin, Pablo Cruz-Morales, Christopher M. Whitford, Jay D. Keasling
Summary: Polycyclopropanated (POP) compounds have the potential to be a more energy-dense alternative to current jet and rocket fuels, but further development is needed. This protocol outlines the production of polycyclopropanated fatty acids in Streptomyces, though the production of POP in other hosts has yet to be demonstrated. This method serves as a baseline for the future development of POP and other polyketide products. For more information, please refer to Cruz-Morales et al. (2022).
Article
Multidisciplinary Sciences
Xiaoyue Chen, Graham A. Hudson, Charlotte Mineo, Bashar Amer, Edward E. K. Baidoo, Samantha A. Crowe, Yuzhong Liu, Jay D. Keasling, Henrik V. Scheller
Summary: Methyl jasmonate (MeJA) is a known elicitor of plant specialized metabolism, including triterpenoid saponins. In this study, we leveraged MeJA-induced saponin biosynthesis in S. vaccaria and identified multiple enzymes that catalyze the oxidation and glycosylation of triterpenoids. We also discovered the biosynthetic pathway for the rare nucleotide sugar UDP-d-fucose. Our findings enable the production and optimization of high-value saponins in microorganisms and plants through synthetic biology approaches.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Lucas Waldburger, Mitchell G. Thompson, Alexandra J. Weisberg, Namil Lee, Jeff H. H. Chang, Jay D. Keasling, Patrick M. M. Shih
Summary: Transcription start sites (TSSs) play a fundamental role in understanding gene expression and regulation. Agrobacteria are prokaryotes widely used in plant biotechnology due to their ability to transfer DNA into host plant genomes. However, the genome-wide transcriptional regulation of agrobacteria, especially in less-studied lineages, remains poorly understood. A study using differential RNA-seq and an optimized algorithm has successfully identified thousands of TSSs with nucleotide resolution for representatives of each lineage, providing a framework for understanding the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. The importance of parameter optimization in genome-wide TSS identification and genomics is also highlighted by the optimized algorithm.
Article
Food Science & Technology
Vayu Maini Rekdal, Nabila Rodriguez-Valeron, Mikel Olaizola Garcia, Diego Prado Vasquez, Pia M. Sorensen, Rasmus Munk, Jay D. Keasling
Summary: This study explores novel culinary applications of Neurospora intermedia, an edible fungus traditionally used in Java, Indonesia. The fungus can be used to produce oncom-like meat alternatives and enzymes for starch-to-sugar conversion. It also adds orange color and distinct volatile aroma to dishes. The novel foods produced in this study received favorable ratings in consumer trials.
INTERNATIONAL JOURNAL OF GASTRONOMY AND FOOD SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Aidan E. Cowan, Sarah H. Klass, Peter H. Winegar, Jay D. Keasling
Summary: Anthropogenic carbon emissions are causing rapid climate change and posing risks to ecosystems and human society. Innovations in microbial fermentation enable the production of fuels, chemicals, and materials without the use of fossil resources, thus reducing carbon emissions. Recent advances in microbial fermentation aim to increase product yield and efficiency, while also lowering production costs to compete economically with fossil-derived chemicals.
CURRENT OPINION IN SYSTEMS BIOLOGY
(2023)
Review
Automation & Control Systems
Katherine S. Schweidel, He Yin, Stanley W. Smith, Murat Arcak
Summary: We propose a safe-by-design trajectory planning and tracking framework for nonlinear dynamical systems, which uses a hierarchy of system models. The framework combines a low-fidelity model for planning and a high-fidelity model for tracking, ensuring safety and limiting the error states between the two models. The framework allows online planning and offline controller design, providing flexibility and safety in the choice of models.
ANNUAL REVIEWS IN CONTROL
(2022)
Article
Automation & Control Systems
He Yin, Peter Seiler, Ming Jin, Murat Arcak
Summary: A method is proposed to learn neural network controllers with stability and safety guarantees through imitation learning. Convex stability and safety conditions are derived for linear time-invariant systems with neural network controllers by merging Lyapunov theory with local quadratic constraints. These conditions are incorporated in the imitation learning process to minimize the loss and maximize the volume of the region of attraction.
IEEE CONTROL SYSTEMS LETTERS
(2022)
Article
Automation & Control Systems
Katherine S. Schweidel, Murat Arcak
Summary: This letter extends the concept of delta dissipativity from game theory to general interconnections of dynamical systems. The main contribution is a compositionality result that presents conditions for a large-scale interconnection of delta dissipative systems to remain delta dissipative. The letter also analyzes the stability and asymptotic stability of equilibrium points for the interconnected systems and introduces a sum-of-squares program for verifying delta dissipativity of a polynomial system. The results are illustrated with examples.
IEEE CONTROL SYSTEMS LETTERS
(2022)
