Article
Multidisciplinary Sciences
Mark Blaxter, John M. Archibald, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Federica Di Palma, Richard Durbin, Scott V. Edwards, Jennifer A. M. Graves, Kevin J. Hackett, Neil Hall, Erich D. Jarvis, Rebecca N. Johnson, Elinor K. Karlsson, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, Kerstin Lindblad-Toh, Jose V. Lopez, Nancy A. Moran, Gene E. Robinson, Oliver A. Ryder, Beth Shapiro, Pamela S. Soltis, Tandy Warnow, Guojie Zhang, Harris A. Lewin
Summary: Life on Earth has evolved from simplicity to complexity, with bacteria and archaea excelling in metabolic diversification and eukaryotes displaying morphological innovation. The Earth BioGenome Project proposes sequencing the genomes of all known eukaryotic species to create a digital library of life, which will help address evolutionary and ecological questions and provide insights into speciation, adaptation, and organismal dependencies within ecosystems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Philip C. J. Donoghue, Chris Kay, Anja Spang, Gergely Szollosi, Anna Nenarokova, Edmund R. R. Moody, Davide Pisani, Tom A. Williams
Summary: The origin of eukaryotes is a highly debated topic in evolutionary biology, with multiple theories trying to explain the acquisition of eukaryotic characteristics. The main controversy stems from differing views on the defining characteristics of eukaryotes. By defining eukaryotes phylogenetically, we can clarify areas of agreement and test disagreements among hypotheses. Some hypotheses make predictions about the phylogenetic origins of eukaryotic genes, while others differ in the order of key evolutionary steps that cannot currently be distinguished phylogenetically.
Article
Multidisciplinary Sciences
Landen Gozashti, Scott W. Roy, Bryan Thornlow, Alexander Kramer, Manuel Ares, Russell Corbett-Detig
Summary: There is significant variation in intron numbers across eukaryotic genomes, and the major drivers of intron content during evolution remain unclear. This study identified 27,563 introns derived from specialized transposons called Introners in 175 eukaryotic genomes, indicating that Introners may explain the episodic nature of intron gain across the eukaryotic tree of life. Species with Introners span diverse phylogenetic backgrounds, and aquatic organisms are more likely to contain Introners. The mechanistic diversity of Introners suggests convergent evolution from nonautonomous transposable elements.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Microbiology
Anja Spang
Summary: The origin of complex cellular life is a puzzling topic in evolutionary research, with wide variations in perspectives depending on world views and contexts. This article shares a biological perspective on the origin of eukaryotic cells, specifically focusing on the question of whether an archaeon was the ancestor of eukaryotes.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Food Science & Technology
En Yu, Wenguang Wang, Naoki Yamaji, Shuichi Fukuoka, Jing Che, Daisei Ueno, Tsuyu Ando, Fenglin Deng, Kiyosumi Hori, Masahiro Yano, Ren Fang Shen, Jian Feng Ma
Summary: The low cadmium accumulation in rice is shown to be due to the duplication of the manganese/cadmium transporter gene. Introducing this allele into an elite rice cultivar can reduce cadmium accumulation in the grain grown in Cd-contaminated soil without affecting grain yield and quality. This study not only reveals the molecular mechanism behind low cadmium accumulation but also provides a useful target for breeding rice cultivars with low cadmium accumulation.
Article
Multidisciplinary Sciences
Laura Eme, Daniel Tamarit, Eva F. Caceres, Courtney W. Stairs, Valerie De Anda, Max E. Schoen, Kiley W. Seitz, Nina Dombrowski, William H. Lewis, Felix Homa, Jimmy H. Saw, Jonathan Lombard, Takuro Nunoura, Wen-Jun Li, Zheng-Shuang Hua, Lin-Xing Chen, Jillian F. Banfield, Emily St John, Anna-Louise Reysenbach, Matthew B. Stott, Andreas Schramm, Kasper U. Kjeldsen, Andreas P. Teske, Brett J. Baker, Thijs J. G. Ettema
Summary: Through analysis of an expanded genomic sampling of Asgard archaea, this study reveals that eukaryotes are placed within Asgard archaea as a well-nested clade and a sister lineage to Hodarchaeales. The study also shows that genome evolution in Asgard archaea involved more gene duplication and fewer gene loss events compared to other archaea.
Article
Biochemistry & Molecular Biology
Jose Cerca
Summary: Studying the concepts and definitions of parallel and convergent evolution is crucial for understanding evolutionary patterns. A consolidated framework is proposed to address the inconsistencies and confusion in existing concepts and definitions. This framework aims to harmonize the concepts of parallel and convergent evolution with natural selection and the idea of similarity.
Review
Biochemistry & Molecular Biology
Jose Gabriel Nino Barreat, Aris Katzourakis
Summary: Paleovirology studies ancient viruses and their coevolution with hosts, providing insights into the diversity, origins, and evolution of eukaryotic DNA viruses. By examining viral families integrated in eukaryotic genomes, paleovirology has expanded our knowledge of viral diversity, host ranges, and evolution timeline, leading to the discovery of new families of viral integrating dsDNA viruses and transposons. Future research in paleovirology will continue to enhance our understanding of antiviral immunity, viral diversity, and potential applications in uncovering more secrets of the viral world.
TRENDS IN MICROBIOLOGY
(2022)
Review
Plant Sciences
An Yong Hu, Shu Nan Xu, Dong Ni Qin, Wen Li, Xue Qiang Zhao
Summary: The article reviews the important role of silicon in mediating phosphorus imbalance in plants, including silicon uptake and accumulation, the role of phosphate transporters, and the effects of silicon under phosphorus deficiency and excess phosphorus stress. The results show that silicon plays a significant role in regulating phosphorus imbalance in plants.
Article
Engineering, Marine
Barrie Dale
Summary: Molecular trees and geochemical markers suggest the divergence of dinoflagellates as early eukaryotes around 650 million years ago. However, the traditional fossil record of dinoflagellate cysts begins during the Triassic about 230 million years ago. A re-evaluation of the pre-Triassic record reveals that many microfossils called acritarchs are actually dinoflagellate cysts, representing missing fossil evidence. Traditional diagnostic criteria for dinoflagellate cysts were biased towards thecate species, but a new approach based on comparing with living cysts includes athecate species. The earliest acritarchs had a cell wall made of sporopollenin-like material, which provided survival advantages in a microbial-dominated world.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2023)
Article
Biology
Yirong Wang, Xiaolu Tang, Jian Lu
Summary: The evolution of microRNAs in bilaterian animals has been extensively studied, with a focus on both convergent and divergent evolution. Recent evidence suggests that the miRNA pathway might have already existed in the last common ancestor of eukaryotes, and differences in animal and plant lineages arise from lineage-specific innovations and losses. The miRNA repertoire has expanded through de novo creation and duplication processes, with many newly emerged miRNAs being lineage-specific. MiRNA clustering and seed mimicry contribute to the convergent molecular evolution of miRNAs, and miRNAs from different sources can converge to degrade maternal mRNAs during animal development. MiRNAs can evolve across species due to changes in sequence, seed shifting, arm switching, and spatiotemporal expression patterns, resulting in variations in target sites among orthologous miRNAs.
BIOLOGICAL REVIEWS
(2023)
Article
Multidisciplinary Sciences
Francois Osiurak, Nicolas Claidiere, Alexandre Bluet, Joel Brogniart, Salome Lasserre, Timothe Bonhoure, Laura Di Rollo, Neo Gorry, Yohann Polette, Alix Saude, Giovanni Federico, Natalie Uomini, Emanuelle Reynaud
Summary: Understanding the evolution of human technology is crucial for solving the mystery of our origins. Current theories suggest that technology evolves through the accumulation of advantageous modifications and the selective retention of these variations. Another explanation is that technical reasoning supports high-fidelity transmission in the context of cumulative technological culture, allowing individuals to converge to optimal solutions. In a microsociety experiment, we tested these competing hypotheses and found that the system improved over generations, accompanied by an increased understanding and progressive convergence of solutions. These findings highlight the role of technical reasoning in the cultural evolution of technology.
Article
Biochemical Research Methods
Peiyan Han, Yuan Ma, Zongheng Fu, Zhou Guo, Jiangnan Xie, Yi Wu, Ying-jin Yuan
Summary: Researchers have successfully achieved genetic inversion and deletion in yeast through directed evolution of Rci recombinase. This DNA inversion system, with specificity and reversibility, can serve as an on/off transcriptional switch and function on linear chromosomes.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Shuai Luo, Peng Zhang, Wei Miao, Jie Xiong
Summary: This study provides the first comprehensive genome-wide identification of GPCRs in ciliates, identifying 492 GPCRs in 24 ciliates. GPCRs in ciliates can be assigned to four families, with most belonging to family A. Gene duplication events play a role in the expansion of the GPCR superfamily in ciliates. This study improves our understanding of the evolution and function of GPCRs in ciliates.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Jory Thiel, Muzaffar A. Khan, Roel M. Wouters, Richard J. Harris, Nicholas R. Casewell, Bryan G. Fry, R. Manjunatha Kini, Stephen P. Mackessy, Freek J. Vonk, Wolfgang Wuster, Michael K. Richardson
Summary: Convergence is the phenomenon where similar phenotypes evolve independently in different lineages. Resistance to toxins in animals is an example of convergence, where molecular adaptations have evolved to counteract the harmful effects of toxins. However, resistance adaptations may carry fitness costs if they disrupt the normal physiology of the resistant animal.
BIOLOGICAL REVIEWS
(2022)
Article
Physics, Multidisciplinary
Maziyar Jalaal, Nico Schramma, Antoine Dode, Helene de Maleprade, Christophe Raufaste, Raymond E. Goldstein
PHYSICAL REVIEW LETTERS
(2020)
Article
Physics, Multidisciplinary
David B. Stein, Gabriele De Canio, Eric Lauga, Michael J. Shelley, Raymond E. Goldstein
Summary: Studies have shown a transition from spatially disordered cytoskeleton to an ordered state with cell-spanning vortical flow during streaming in the oocyte development of fruit flies.
PHYSICAL REVIEW LETTERS
(2021)
Article
Mechanics
George T. Fortune, Alan Worley, Ana B. Sendova-Franks, Nigel R. Franks, Kyriacos C. Leptos, Eric Lauga, Raymond E. Goldstein
Summary: Circular milling behavior is observed in a plant-animal worm, and is investigated experimentally and theoretically from a fluid dynamical viewpoint. Singularities such as source dipoles and Stokes quadrupoles are expected to dominate the flow fields generated by a mill, unlike other systems modeled as force dipoles. A model treating a circular mill as a rigid rotating disc that generates a Stokes flow captures basic experimental results and provides insights into the emergence and stability of multiple mill systems.
JOURNAL OF FLUID MECHANICS
(2021)
Editorial Material
Physics, Multidisciplinary
Pierre A. Haas, Raymond E. Goldstein, Diana Cholakova, Nikolai Denkov, Stoyan K. Smoukov
PHYSICAL REVIEW LETTERS
(2021)
Article
Physics, Multidisciplinary
Pierre A. Haas, Raymond E. Goldstein
Summary: The diffusive threshold for true Turing instabilities in reaction-diffusion systems may be lower for N > 2, as shown by analysis of random matrices describing the dynamics. As N increases, the diffusive threshold becomes more likely to be smaller and physical, with many-species instabilities unable to be described by reduced models with fewer diffusing species in most cases.
PHYSICAL REVIEW LETTERS
(2021)
Article
Physics, Fluids & Plasmas
Nicolas Bruot, Pietro Cicuta, Hermes Bloomfield-Gadelha, Raymond E. Goldstein, Jurij Kotar, Eric Lauga, Francois Nadal
Summary: The oscillation frequencies of eukaryotic flagella are high, requiring an understanding of global unsteady flows. A direct Lagrangian measurement of this unsteady flow was conducted for the first time, indicating that tracer particles display elliptical Lissajous figures in the microscale regime.
PHYSICAL REVIEW FLUIDS
(2021)
Article
Physics, Multidisciplinary
Francesco Boselli, Jerome Jullien, Eric Lauga, Raymond E. Goldstein
Summary: The cilia bundles in MCCs behave as active vortices, limiting their rate of work and shearing the tissue at a finite but low area coverage, which mirrors findings for other sparse distributions such as cell receptors and leaf stomata.
PHYSICAL REVIEW LETTERS
(2021)
Article
Biology
Thomas C. Day, Stephanie S. Hohn, Seyed A. Zamani-Dahaj, David Yanni, Anthony Burnetti, Jennifer Pentz, Aurelia R. Honerkamp-Smith, Hugo Wioland, Hannah R. Sleath, William C. Ratcliff, Raymond E. Goldstein, Peter J. Yunker
Summary: The prevalence of multicellular organisms is due to their ability to form complex structures. This study quantifies the statistics of cellular neighborhoods in two different multicellular eukaryotes and finds that the cell neighborhood sizes closely fit a gamma distribution. This suggests that gamma-distributed cell neighborhood sizes are a general feature of multicellularity, providing predictability in cell packing.
Article
Physics, Multidisciplinary
George T. Fortune, Nuno M. Oliveira, Raymond E. Goldstein
Summary: This study investigates the growth of biofilms in confined spaces. By utilizing a poroelastic framework, the radial growth mechanism of biofilms is revealed, and it is found that the growth of biofilms is limited by the Poisson's ratio of the matrix.
PHYSICAL REVIEW LETTERS
(2022)
Article
Biology
Daniel J. Richter, Romain Watteaux, Thomas Vannier, Jade Leconte, Paul Fremont, Gabriel Reygondeau, Nicolas Maillet, Nicolas Henry, Gaetan Benoit, Ophelie Da Silva, Tom O. Delmont, Antonio Fernandez-Guerra, Samir Suweis, Romain Narci, Cedric Berney, Damien Eveillard, Frederick Gavory, Lionel Guidi, Karine Labadie, Eric Mahieu, Julie Poulain, Sarah Romac, Simon Roux, Celine Dimier, Stefanie Kandels, Marc Picheral, Sarah Searson, Tara Oceans Coordinators, Stephane Pesant, Jean-Marc Aury, Jennifer R. Brum, Claire Lemaitre, Eric Pelletier, Peer Bork, Shinichi Sunagawa, Fabien Lombard, Lee Karp-Boss, Chris Bowler, Matthew B. Sullivan, Eric Karsenti, Mahendra Mariadassou, Ian Probert, Pierre Peterlongo, Patrick Wincker, Colomban de Vargas, Maurizio Ribera D'Alcala, Daniele Iudicone, Olivier Jaillon
Summary: This study assesses the global structure of plankton geography by analyzing metagenomes of plankton communities sampled from oceans worldwide. The findings demonstrate the influence of ocean currents on plankton biogeography and reveal characteristic timescales of community dynamics.
Article
Physics, Multidisciplinary
Pierre A. Haas, Maria A. Gutierrez, Nuno M. Oliveira, Raymond E. Goldstein
Summary: Recent theoretical work has shown that clonal microbes can stabilize microbial communities by switching between different phenotypes. This switching can be stochastic or in response to environmental factors. The study explores the ecological effects of responsive switching and shows that it can stabilize coexistence, even when stochastic switching does not affect community stability.
PHYSICAL REVIEW RESEARCH
(2022)
Article
Chemistry, Physical
Christophe Raufaste, Simon Cox, Raymond E. Goldstein, Adriana Pesci
Summary: This study investigates the collapse of a catenoidal soap film when the supporting rings are moved beyond a critical separation. By dividing the catenoid with a glass plate, two identical hemicatenoids with a surface Plateau border (SPB) on the plate are formed. The collapse of the hemicatenoids is governed by frictional forces arising from viscous dissipation in the SPBs. Numerical studies confirm the relationship between the frictional force and the capillary number on wet surfaces. This study is significant for understanding the fragmentation of bubbles in highly confined geometries.
Article
Physics, Fluids & Plasmas
Raymond E. Goldstein, Adriana Pesci, Christophe Raufaste, James D. Shemilt
Summary: The study investigates a robust geometric feature in the collapse of catenoidal soap films of various viscosities, which is found to be universal and independent of film viscosity prior to the pinchoff event. The approach to the conical structures is viewed as passage close to an unstable fixed point of conical similarity solutions. The overall analysis provides the basis for the systematic study of more complex problems of surface instabilities triggered by deformations of the supporting boundaries.
Article
Biochemical Research Methods
Jess Berry, Francois J. Peaudecerf, Nicole A. Masters, Keith B. Neeves, Raymond E. Goldstein, Matthew T. Harper
Summary: Cardiovascular disease is a leading cause of death worldwide, with myocardial infarction being triggered by blood clots. Developing new anti-platelet drugs is an active area of research, with in vitro models using human blood showing potential in improving relevance. The study developed a microfluidic device for generating occlusive thrombi and demonstrated its ability to monitor the effect of anti-thrombotic drugs in an unbiased and objective manner.
Article
Physics, Fluids & Plasmas
Pierre A. Haas, Raymond E. Goldstein
Summary: The study derives a shell theory for large intrinsic bending deformations by asymptotically expanding three-dimensional incompressible morphoelasticity in the limit of a thin shell, highlighting geometric material anisotropy and the elastic role of cell constriction. Using the invagination of the green alga Volvox as a model developmental event, the results of this theory are shown to differ from those of classical shell theory and reveal how geometric effects stabilize invagination.