Article
Biotechnology & Applied Microbiology
Sophie Vaud, Nicole Pearcy, Marko Hanzevacki, Alexander M. W. Van Hagen, Salah Abdelrazig, Laudina Safo, Muhammad Ehsaan, Magdalene Jonczyk, Thomas Millat, Sean Craig, Edward Spence, James Fothergill, Rajesh Reddy Bommareddy, Pierre-Yves Colin, Jamie Twycross, Paul A. Dalby, Nigel P. Minton, Christof M. Jaeger, Dong-Hyun Kim, Jianping Yu, Pin-Ching Maness, Sean Lynch, Carrie A. Eckert, Alex Conradie, Samantha J. Bryan
Summary: Ethylene is a widely used small hydrocarbon gas in the chemical industry, but its production contributes to significant CO2 emissions, highlighting the need for a sustainable alternative. Research has shown that a combination of genome-scale metabolic modeling, continuous fermentation, and protein evolution can accelerate the development of a high-efficiency ethylene-producing E. coli strain, resulting in a 49-fold increase in production.
METABOLIC ENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Prisciluis Caheri Salas-Navarrete, Arturo Ivan Montes de Oca Miranda, Alfredo Martinez, Luis Caspeta
Summary: This study used adaptive laboratory evolution (ALE) and whole-genome analysis to generate strains of Saccharomyces cerevisiae tolerant to high temperatures, acetic acid, and acidic pH. Through a year of evolution, two strains were selected, TAT12 and AT22, which were capable of growing and producing ethanol in conditions previously inhibitory to their ancestors. Whole-genome sequencing and transcriptomic analysis showed mutations in key genes related to stress response and replication, confirming the importance of these mutations in enhancing the tolerance of S. cerevisiae to harsh environments.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Plant Sciences
Jesus Martinez-Gomez, Tara A. M. Atluri, Irving Jason Rose, Aaliyah J. Holliday, Christopher F. Strock, Jonathan P. Lynch, William B. Miller, Dennis Wm. Stevenson, Chelsea D. Specht
Summary: This study characterizes the developmental morphology and anatomy of various umbellate inflorescences in monocots and analyzes their evolutionary context. It identifies three convergent developmental programs for generating umbellate inflorescences and discusses the morphological modifications necessary for such complex structures. The study also introduces a new variant of metatopy called horizontal concaulesence.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Erol S. Kavvas, Christopher P. Long, Anand Sastry, Saugat Poudel, Maciek R. Antoniewicz, Yang Ding, Elsayed T. Mohamed, Richard Szubin, Jonathan M. Monk, Adam M. Feist, Bernhard O. Palsson
Summary: This study characterizes the genotype-fitness maps of E.coli strains during adaptive laboratory evolution, providing insights into the mechanisms of microbial adaptation. The results show convergence in overall phenotypic measures across different strains, with the exception of divergence in NADPH production mechanisms. Transcriptomic adaptations involve increased expression of growth promoting genes and decreased expression of stress response and structural components. The study also identifies trade-offs in the regulatory network and correlates between causal mutations and systems-level adaptations.
Article
Biotechnology & Applied Microbiology
Nicolas T. Wirth, Nicolas Gurdo, Nicolas Krink, Angela Vidal-Verdu, Stefano Donati, Tune Wulff, Lorena Fernandez-Cabezon, Pablo I. Nikel
Summary: Acetyl-coenzyme A is a metabolic hub that can be rewired in Pseudomonas putida to create novel network connectivities and improve microbial production. This can be achieved through growth-coupling strategies and large-scale structural chromosome rearrangements.
METABOLIC ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Ana Garona, Nils F. Huelter, Devani Romero Picazo, Tal Dagan
Summary: Plasmids, extrachromosomal genetic elements in prokaryotes, play a crucial role in microbial ecology and evolution. Cell division-induced genetic drift (segregational drift) leads to rapid extinction of novel plasmid alleles, and the mode of plasmid inheritance is an important determinant of plasmid allele dynamics. Phylogenetic reconstruction shows that plasmid-encoded genes evolve at a slower rate compared to chromosomal genes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Biochemistry & Molecular Biology
Vanessa Polet Carrillo-Carrasco, Jorge Hernandez-Garcia, Sumanth K. Mutte, Dolf Weijers
Summary: The signaling molecule auxin is found in various life kingdoms. It has primarily been studied as a phytohormone regulating growth and development in land plants. Recent advancements in genomic and transcriptomic data, along with phylogenetic inference, have allowed us to trace the evolutionary history of auxin biology in bryophytes and streptophyte algae. This review examines auxin biosynthesis, transport, physiological and molecular responses, as well as its role as a chemical messenger in ecological communication. Validating predicted orthologs will further our understanding of the conserved properties of auxin biology among streptophytes.
Article
Biochemistry & Molecular Biology
Fabricio Almeida-Silva, Yves Van de Peer
Summary: Angiosperms have a complex history of whole-genome duplications, with varying numbers and ages of duplication events across different clades. These duplications have impacted plant genomes by selectively retaining genes involved in specific functions. Protein-protein interaction networks and gene regulatory networks enriched in these duplicated genes show strong selection pressure on gene sequences and interactions. Duplicated genes are predominantly involved in dosage-sensitive processes such as transcription regulation, cell cycle, translation, photosynthesis, and carbon metabolism.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Gao Wang, Trung Phan, Shengkai Li, Jing Wang, Yan Peng, Guo Chen, Junle Qu, Daniel Goldman, Simon A. Levin, Kenneth Pienta, Sarah Amend, Robert H. Austin, Liyu Liu
Summary: Experimental robobiological physics explores the impact of genetic diversity and different landscapes on the survival of autonomous robots, shedding light on biological evolution.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Psychology, Multidisciplinary
Severi Luoto, Marco Antonio Correa Varella
Summary: The COVID-19 pandemic has led to global turmoil, with differences in policies implemented by political leaders varying based on sex. Female leaders emphasize minimizing human suffering, while male leaders focus on short-term economic consequences and risk-taking. These sex differences are rooted in evolutionary processes and the sexual differentiation of the mammalian brain.
FRONTIERS IN PSYCHOLOGY
(2021)
Review
Cell Biology
Harold M. McNamara, Beatrice Ramm, Jared E. Toettcher
Summary: Technological advances have contributed to recent developments in developmental biology, such as light sheet imaging for studying single-cell dynamics and single-cell genomic methods for cataloguing cell types and gene expression states. Synthetic approaches are also emerging to understand development processes from the bottom up, including synthetic circuits for signaling delivery and recording, and synthetic reconstitution of pattern formation on multicellular scales.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Article
Immunology
Yoram Vodovotz, Derek Barclay, Jinling Yin, Robert H. Squires, Ruben Zamora
Summary: The study investigated immune/inflammatory responses in children with Pediatric Acute Liver Failure (PALF) across different age groups, revealing significant differences in inflammatory mediators levels. By analyzing these differences, the study hypothesized on possible pathological inflammation and utilized multiple machine learning approaches to gain insights into the complex inflammatory disease.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Computer Science, Information Systems
Kaizheng Liu, Ming Yang, Zhen Ling, Huaiyu Yan, Yue Zhang, Xinwen Fu, Wei Zhao
Summary: This article presents a novel manual reverse engineering framework for discovering communication protocols of embedded Linux-based IoT systems. By analyzing the communication protocol of the WeMo smart plug as an example, the framework exposes severe design flaws in the protocol.
IEEE INTERNET OF THINGS JOURNAL
(2021)
Article
Biology
Vishhvaan Gopalakrishnan, Dena Crozier, Kyle J. Card, Lacy D. Chick, Nikhil P. Krishnan, Erin McClure, Julia Pelesko, Drew F. K. Williamson, Daniel Nichol, Soumyajit Mandal, Robert A. Bonomo, Jacob G. Scott
Summary: A morbidostat is a bioreactor that uses antibiotics to control bacterial growth, making it suitable for studying antibiotic resistance evolution. We present a low-cost morbidostat called the EVolutionary biorEactor (EVE) that can be constructed by students with minimal engineering and programming experience. We validate EVE in a real classroom setting by evolving replicate Escherichia coli populations under chloramphenicol challenge, providing students the opportunity to learn about bacterial growth and antibiotic resistance.
Review
Evolutionary Biology
Pierre De Wit, Ellika Faust, Leon Green, Marlene Jahnke, Ricardo T. Pereyra, Marina Rafajlovic
Summary: The article summarizes the progress in Marine Evolutionary Biology over the past decade as presented in the Evolutionary Applications Special Issue. This issue, consisting of original papers and reviews, is a small contribution to the broader field of evolutionary biology, highlighting the importance of collaboration and knowledge exchange among researchers. The establishment of the Linnaeus Centre for Marine Evolutionary Biology (CeMEB) has played a crucial role in studying evolutionary processes in the marine environment under global change, with contributions from researchers worldwide. This Special Issue provides a snapshot of the current state of the field and serves as an important foundation for future research.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Berta Verd, Erik Clark, Karl R. Wotton, Hilde Janssens, Eva Jimenez-Guri, Anton Crombach, Johannes Jaeger
Article
Biology
Juan Jose Fraire-Zamora, Johannes Jaeger, Jerome Solon
Article
Multidisciplinary Sciences
Eva Jimenez-Guri, Karl R. Wotton, Johannes Jaeger
ROYAL SOCIETY OPEN SCIENCE
(2018)
Article
Evolutionary Biology
Elise Parey, Anton Crombach
GENOME BIOLOGY AND EVOLUTION
(2019)
Article
Biology
Berta Verd, Nicholas A. M. Monk, Johannes Jaeger
Article
History & Philosophy Of Science
James DiFrisco, Johannes Jaeger
BIOLOGY & PHILOSOPHY
(2019)
Article
Biochemistry & Molecular Biology
James DiFrisco, Johannes Jaeger
Article
Ecology
Julie Marin, Guillaume Achaz, Anton Crombach, Amaury Lambert
JOURNAL OF EVOLUTIONARY BIOLOGY
(2020)
Article
Biology
Sara Zeppilli, Tobias Ackels, Robin Attey, Nell Klimpert, Kimberly D. Ritola, Stefan Boeing, Anton Crombach, Andreas T. Schaefer, Alexander Fleischmann
Summary: This study identified distinct populations of mitral and tufted cells in the mammalian olfactory bulb, unveiling their molecular mechanisms and gene expression profiles. Additionally, a new computational approach for integrating data was proposed, offering new insights into the functional roles of mitral and tufted cell subtypes.
Letter
Biochemistry & Molecular Biology
Johannes Jaeger, Nick Monk
Article
Biology
Johannes Jaeger, Nick Monk
Summary: Modularity is crucial in adaptive complex systems, with phenotypic traits as modules that can vary independently. The genotype-phenotype map is proposed to be functionally modular, and dynamical modularity may be more widely applicable than structural decomposition. This approach provides a shared conceptual foundation for developmental and evolutionary biology, and offers a new account of process homology.
Article
Biology
James DiFrisco, Johannes Jaeger
Summary: The paper investigates the concept of homology in ontogenetic processes, focusing on insect segmentation and vertebrate somitogenesis as examples. The authors propose six criteria of process homology, combining recognized indicators and novel criteria derived from dynamical systems modelling. The study shows how these criteria apply to animal segmentation and other ontogenetic processes and situates the proposed dynamical framework in relation to similar research programmes.
Article
Art
Gemma Anderson, Berta Verd, Johannes Jaeger
Article
Mathematics, Interdisciplinary Applications
Amir Masoud Abdol, Damjan Cicin-Sain, Jaap A. Kaandorp, Anton Crombach