Editorial Material
Chemistry, Multidisciplinary
Russell Johnson, Frances S. Ligler
Summary: Professor Frances S. Ligler was inducted into the National Inventors Hall of Fame in 2017 for her inventions in portable optical biosensors. In an interview with Nature Chemistry, Professor Ligler discusses the challenges of developing new sensor designs into reliable products and shares some pitfalls to avoid in the development process.
Review
Plant Sciences
Gen-ichiro Arimura
Summary: Plants under threat from herbivores can devise survival strategies by sensing and responding to elicitors secreted by herbivores. These elicitors activate diverse plant defense mechanisms, increasing resistance to herbivores. Insights into the cellular pathways involved in plant-herbivore interactions are leading to potential agricultural applications.
TRENDS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Piercarlo Valdesolo
Summary: Epistemic emotions such as awe and wonder can have both beneficial and potentially destructive consequences for individuals and societies. It is important to specify the conditions under which these states promote individual well-being and societal flourishing.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2021)
Editorial Material
Biochemistry & Molecular Biology
Chris C. Rodgers, Badr F. Albanna, Michele N. Insanally
Summary: Decisions can be made internally and implicitly, engaging non-sensory neurons in the sensory cortex, as revealed by a new study.
Review
Plant Sciences
Geertje M. F. van der Heijden, Ashley D. C. Proctor, Kim Calders, Chris J. Chandler, Richard Field, Giles M. Foody, Sruthi M. Krishna Moorthy, Stefan A. Schnitzer, Catherine E. Waite, Doreen S. Boyd
Summary: This article reviews the application of remote sensing technology in studying the ecology of lianas. Lianas are important components of tropical ecosystems, but little is known about their distribution in forest canopies. Remote sensing technology can help overcome the limitations of traditional field methods and provide important insights into liana ecology.
JOURNAL OF ECOLOGY
(2022)
Editorial Material
Hematology
Elisabetta Castoldi
Summary: In this issue of Blood, Mohammed et al. present a detailed atomic-resolution structure of factor V (FV) short, a splice variant associated with bleeding. This structure, encompassing the entire B domain of FV short, sheds light on its distinct functional properties.
Article
Computer Science, Artificial Intelligence
Richard Evans, Jose Hernandez-Orallo, Johannes Welbl, Pushmeet Kohli, Marek Sergot
Summary: This paper examines the meaning of making sense of a sensory sequence in unsupervised learning, proposing a symbolic causal theory construction method and introducing the APPERCEPTION ENGINE computer implementation. The system can generate interpretable causal theories from small amounts of data and performs well in various domains, even achieving human-level performance in sequence induction intelligence tests.
ARTIFICIAL INTELLIGENCE
(2021)
Article
Computer Science, Artificial Intelligence
Richard Evans, Matko Bosnjak, Lars Buesing, Kevin Ellis, David Pfau, Pushmeet Kohli, Marek Sergot
Summary: The paper presents a neuro-symbolic framework for distilling interpretable theories from raw sensory experiences, by mapping sensory input to disjunctive input through a neural network. The weights of the network and the rules of the theory are jointly solved as a single SAT problem.
ARTIFICIAL INTELLIGENCE
(2021)
Article
Green & Sustainable Science & Technology
Jose Carlos Canizares, Samantha Marie Copeland, Neelke Doorn
Summary: Resilience is a major concept in development, climate adaptation, and related domains. While originally a descriptive concept for ecosystems, subsequent applications distorted its meaning by framing it as a transformative and normative quality. The article proposes an alternative philosophical account based on C.S. Holling's original work, highlighting resilience as a transformative social-ecological property with intrinsic ecological value, organizational virtue, and a virtuous understanding of human-nature relations. This interpretation clarifies the relations between resilience and related terms, providing a firm foundation for further normative work.
Editorial Material
Biochemistry & Molecular Biology
Michal Komorowski
Summary: This article discusses the complexity of cellular signaling systems and examines the mechanisms and consequences of different responses to combinations of BMP ligands in the BMP pathway.
Review
Genetics & Heredity
Kirsten Seale, Steve Horvath, Andrew Teschendorff, Nir Eynon, Sarah Voisin
Summary: This article reviews the changes in DNA methylation during aging and the statistical tools used to quantify them. It also explores the evidence linking DNA methylation to aging phenotypes and strategies for extending healthspan and lifespan. Finally, it discusses theories on the mechanistic causes of epigenetic aging.
NATURE REVIEWS GENETICS
(2022)
Editorial Material
Immunology
Kouji Kobiyama, Ken J. Ishii
Summary: mRNA vaccines owe their success in part to methylation, which masks the immunostimulatory properties of the mRNA. However, the immunological mechanisms of adjuvanticity are still unclear. Two new studies have revealed distinct mechanisms for the innate sensing of this hidden adjuvant.
Article
History & Philosophy Of Science
Ashley Coates
Summary: According to the powerful qualities view, properties are seen as both powerful and qualitative, offering an attractive alternative to the views that properties are pure powers or pure qualities. The claimed identity between powerfulness and qualitativity can be made coherent with a particular conception of both the qualitativity and powerfulness of properties.
Review
Clinical Neurology
Hunter R. Schone, Chris Baker, Joel Katz, Lone Nikolajsen, Katleho Limakatso, Herta Flor, Tamar R. Makin
Summary: Phantom limb pain (PLP) is a common experience for individuals who have undergone limb amputation, but its characteristics vary greatly. The lack of reliable data has made it challenging to understand the mechanisms of PLP and find effective treatments. However, recent research provides an opportunity to re-examine our assumptions about PLP and its treatments. This review aims to generate consensus on the best ways to study and treat PLP, addressing conceptual and methodological challenges and offering potential solutions. The hope is that a critical evaluation of foundational knowledge will lead to more informed decisions in testing interventions and guide the development of new PLP treatments.
JOURNAL OF NEUROLOGY NEUROSURGERY AND PSYCHIATRY
(2022)
Article
Ecology
Hannes Palang, Anita Zarina, Anu Printsmann
Summary: This paper investigates the potential use of cultural explosion theory and path dependence approach in exploring landscape change. Through a case study on post-Soviet military areas, it is found that both approaches are useful in understanding landscape change.
Review
Biotechnology & Applied Microbiology
Mihris Ibnu Saleem Naduthodi, Nico J. Claassens, Sarah 'Adamo, John van der Oost, Maria J. Barbosa
Summary: The high cost of phototrophic cultivation is the main obstacle in commercializing biofuels and other products produced by microalgae, and improving microalgal productivity is seen as a potential solution. While synthetic biology methods have been used to engineer downstream production pathways in some microalgal strains, exploration of enhancing upstream photosynthetic and carbon fixation metabolism for growth and yield improvement in microalgae is limited. Strategies to increase reducing power generation from light and enhance CO2 assimilation through the Calvin cycle or synthetic alternatives are described as key areas for improvement. Optimism is expressed for breakthroughs in microalgal research with recent technological advancements.
TRENDS IN BIOTECHNOLOGY
(2021)
Editorial Material
Biotechnology & Applied Microbiology
Nico J. Claassens
Summary: The study by Hong et al. demonstrates that expressing the metabolic core of rGlyP heterologously can act as a sink for anaerobic conversion of glycerol, which is an efficient one-carbon assimilating pathway. Engineering this pathway in diverse hosts could facilitate the transition towards renewable, one-carbon-based bioproduction.
TRENDS IN BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Dorian Leger, Silvio Matassa, Elad Noor, Alon Shepon, Ron Milo, Arren Bar-Even
Summary: The translation discusses the increasing pressure on the environment due to population growth and changes in dietary patterns, emphasizing the need for a revolution in the way natural resources are harnessed. It also highlights the potential of cultivating microbial biomass to produce single-cell protein (SCP) for protein-rich feed and food supplements, and the lack of quantitative comparison between traditional agriculture and photovoltaic-driven SCP systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Henning Kirst, Bryan H. Ferlez, Steffen N. Lindner, Charles A. R. Cotton, Arren Bar-Even, Cheryl A. Kerfeld
Summary: This article introduces a prototype technology using bacterial microcompartments to synthesize formate. The technology utilizes oxygen-sensitive glycyl radical enzyme and a phosphate acyltransferase to convert formate into pyruvate, and provides a well-defined environment for efficient formate growth.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemical Research Methods
M. Stoekl, N. J. Claassens, S. N. Lindner, E. Klemm, D. Holtmann
Summary: This article introduces the research on the conversion of carbon dioxide into chemical raw materials through electrochemical and microbial processes. Existing gaps for the realization of hybrid microbial electrosynthesis processes are evaluated.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Biology
Helena Schulz-Mirbach, Alexandra Mueller, Tong Wu, Pascal Pfister, Selcuk Aslan, Lennart Schada von Borzyskowski, Tobias J. Erb, Arren Bar-Even, Steffen N. Lindner, Ahmad S. Khalil
Summary: This study reveals the high flexibility of the cellular amination network, both in terms of transaminase promiscuity and adaptability to new connections and ammonium entry points. By constructing an Escherichia coli glutamate auxotrophic strain, the researchers systematically studied the ability of different amino acids to serve as amine sources, and found that several amino acids are able to complement the auxotrophy by producing glutamate or converting to glutamate via transamination reactions.
Review
Biotechnology & Applied Microbiology
Enrico Orsi, Nico J. Claassens, Pablo I. Nikel, Steffen N. Lindner
Summary: Recent studies have challenged the traditional view of metabolism and discovered the plasticity of metabolic networks, which can be harnessed for bioproduction by establishing unnatural connections between metabolic nodes.
BIOTECHNOLOGY ADVANCES
(2022)
Review
Chemistry, Physical
Suzan Yilmaz, Akos Nyerges, John van der Oost, George M. Church, Nico J. Claassens
Summary: Metabolic engineering has the potential to transform the chemical industry and support the transition into a circular bioeconomy by modifying cellular biocatalysts to convert sustainable substrates into desired products. However, despite decades of research, its industrial application has been limited. To fully unleash its potential, it is crucial to optimize the synthetic and native metabolic networks of cell factories at the system and genome-wide level, incorporating machine learning and efficient screening or selection approaches.
Article
Biochemistry & Molecular Biology
Thijs Nieuwkoop, Barbara R. Terlouw, Katherine G. Stevens, Richard A. Scheltema, Dick de Ridder, John van der Oost, Nico J. Claassens
Summary: It has been found that codon usage affects translation efficiency and protein production levels. This study utilized a synonymous codon-randomized library of the red fluorescent protein coding sequence to investigate the correlations between codon usage and protein production. The results showed that the first eight codons near the translation initiation site play a crucial role in protein production, with mRNA secondary structure being a key determinant rather than Codon Adaptation Index (CAI). These findings suggest that optimizing protein production should focus on reducing mRNA secondary structure formation with the first few codons, rather than relying solely on CAI-based codon optimization strategies.
NUCLEIC ACIDS RESEARCH
(2023)
Editorial Material
Chemistry, Multidisciplinary
Olufemi E. Bankefa, Nico J. Claassens
Summary: In this issue of Chem, Zhang et al. present a new system that utilizes CO2 and electricity to produce biomass and bioplastic. Their hybrid chemical and biological system employs an electrochemical process to generate soluble two-carbon (C2) mediators, which are then used to support the growth of Pseudomonas putida bacterium.
Article
Biotechnology & Applied Microbiology
Lyon Bruinsma, Sebastian Wenk, Nico J. Claassens, Vitor A. P. Martins dos Santos
Summary: In this study, the carbon metabolism of the industrially important bacterium Pseudomonas putida was engineered to utilize one-carbon compounds such as methanol, formate, and CO2 as sustainable microbial feedstocks for the production of chemicals and fuels. The functionality of the C1-assimilation module was demonstrated and successfully extended to include methanol and CO2. This research lays the foundation for further engineering P. putida as a sustainable and versatile cell factory that can utilize formate, methanol, and CO2 as sole feedstocks.
METABOLIC ENGINEERING
(2023)
Review
Biochemical Research Methods
Michele Partipilo, Nico J. Claassens, Dirk Jan Slotboom
Summary: The construction of synthetic cells from scratch is an ambitious goal in the field of science and technology. To achieve life-like systems, minimal enzymatic modules are needed to support the processes underlying life. The availability of reduced nicotinamide cofactors is crucial for a synthetic cell, and this study proposes guidelines for reducing these cofactors enclosed in phospholipid vesicles. Specific enzymes, called transhydrogenases, may be necessary to overcome potential limitations in the electron carrier system.
ACS SYNTHETIC BIOLOGY
(2023)
Review
Biochemical Research Methods
Jan L. Kruesemann, Vittorio Rainaldi, Charles A. R. Cotton, Nico J. Claassens, Steffen N. Lindner
Summary: Methanol is a promising feedstock for industrial bioproduction due to its renewable production, high solubility, and limited microbial toxicity. The first enzymatic oxidation step to formaldehyde is a key challenge for its bio-industrial application. Different types of methanol dehydrogenases (MDH) can catalyze this reaction using NAD+, O2, or PQQ as an electron acceptor. NAD-dependent MDH have high energetic efficiency but mediocre kinetics, while O2-dependent methanol oxidases require high oxygen concentrations and do not conserve energy. PQQ-dependent MDH provide a good compromise between energy efficiency and kinetics, making them a promising solution for industry.
CURRENT OPINION IN BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Florent Collas, Beau B. Dronsella, Armin Kubis, Karin Schann, Sebastian Binder, Nils Arto, Nico J. Claassens, Frank Kensy, Enrico Orsi
Summary: In order to promote the sustainability of the biobased economy, novel bioprocesses based on renewable resources are needed. Formate, a C1 molecule generated from CO2 and renewable energy, is increasingly proposed as a carbon and energy source for microbial fermentations. However, its conversion into value-added compounds has been limited. In this study, the bacterium C. necator was engineered as a cell factory for the biological conversion of formate into crotonate, a relevant platform chemical. A small-scale cultivation setup and a heterologous crotonate pathway were developed, resulting in significantly improved productivity and yield compared to the control strain. This work demonstrates the integration of bioprocess and metabolic engineering approaches for the upgrading of formate into a value-added chemical.
METABOLIC ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Sebastian Wenk, Nico J. Claassens, Steffen N. Lindner
Summary: Synthetic biology modifies biological systems to create new parts, devices, and organisms, while systems biology deciphers the design principles of biological systems. Both disciplines are interconnected, as synthetic biology studies require understanding of the biological system, and systems biology benefits from new biological systems generated through synthetic biology approaches.
CURRENT OPINION IN SYSTEMS BIOLOGY
(2022)