Article
Multidisciplinary Sciences
A. J. Shore, R. A. Wood, I. B. Butler, A. Yu Zhuravlev, S. McMahon, A. Curtis, F. T. Bowyer
Summary: Through exceptional preservation, a phylogenetic connection between Ediacaran and Cambrian metazoans is established. The discovery of three-dimensional, pyritized soft tissue in Namacalathus provides evidence of a lophotrochozoan affinity and suggests deep roots of modern lophotrochozoan phyla in the Ediacaran period. This supports molecular phylogenies and demonstrates the early development of biomineralization abilities in these ancient organisms.
Article
Biochemistry & Molecular Biology
Zhidan Li, Yiming Zhang, Stephen J. Bush, Chao Tang, Li Chen, Dan Zhang, Araxi O. Urrutia, Jing-wen Lin, Lu Chen
Summary: Alternative splicing is a widespread phenomenon in eukaryotic genomes that increases transcriptomic diversity. MeDAS is a database resource that allows users to study alternative splicing in a developmental context and provides detailed time course data for various species.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell Biology
Logan R. Myler, Charles G. Kinzig, Nanda K. Sasi, George Zakusilo, Sarah W. Cai, Titia de Lange
Summary: This study investigated the evolutionary origins of the shelterin complex, which is comprised of TRF1, TRF2, Rap1, TIN2, TPP1, and POT1. The study revealed that TRF1 emerged in vertebrates through duplication of a TRF2-like ancestor, and provided insights into the biology of shelterin and its evolution from ancestral telomeric DNA-binding proteins.
GENES & DEVELOPMENT
(2021)
Review
Cell Biology
Benjamin Tajer, Aaron M. Savage, Jessica L. Whited
Summary: Regenerative ability varies greatly among different animal species, making it challenging to compare molecular processes. However, through analyzing the salamander limb blastema, which has been extensively studied for over 200 years and is supported by a wide range of molecular tools, researchers can gain valuable insights for comparing regenerative abilities and studying human limb regeneration.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Xuye Yuan, Yu Zhu, David Ruiz-Carrillo, Tatsuhiko Kadowaki
Summary: Most members of the TMEM16 family act as Ca2+-activated chloride channels or phospholipid scramblases, playing different physiological roles. The family is highly conserved in eukaryotes, but the origin and evolution of its subfamilies in Metazoa are still unclear. Through evolutionary genomics analysis, this study reveals the evolutionary history of the TMEM16 family, identifying vertebrate-specific subfamilies and ancient subfamilies present in many metazoan species. The findings suggest that the TMEM16 family has evolved through gene gain and loss, with purifying selection maintaining protein structures and functions.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Likui Feng, Matthew T. Gordon, Ying Liu, Kari B. Basso, Rebecca A. Butcher
Summary: The authors identify the biosynthetic roles of individual megasynthetase domains and additional enzymes required for nemamide biosynthesis in the canal-associated neurons of C. elegans. They also discover a trafficking mechanism involving at least five additional enzymes for transferring intermediates between a PKS and an NRPS system. This mechanism expands the biosynthetic potential of the PKS-NRPS system and is likely important for the regulation of nemamide biosynthesis.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Deepesh D. Gaikwad, Nilima S. Bangar, Mayura M. Apte, Armaan Gvalani, Rashmi S. Tupe
Summary: This study discovers that the interaction between aldosterone and glycated albumin in diabetic nephropathy can cause oxidative stress, reduce levels of antioxidants and glycation detoxifying enzymes, and result in renal cell damage.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Multidisciplinary Sciences
Richard G. Stockey, Alexandre Pohl, Andy Ridgwell, Seth Finnegan, Erik A. Sperling
Summary: The decline in background extinction rates of marine animals through geologic time is linked to the synergistic impacts of oxygen and temperature on aerobic respiration, making marine animals more vulnerable to ocean warming events during periods of limited surface oxygenation. Physiological theory predicts that atmospheric oxygen is the dominant predictor of extinction vulnerability for marine animals.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Hajime Julie Yuasa
Summary: This study characterized the Tryptophan indole-lyase (TIL) enzymes from two metazoans, Nematostella vectensis and Bradysia coprophila, and found that they have low but significant activity with higher affinity for L-Trp compared to bacterial TILs. Analysis of chimeric enzymes revealed that the high affinity of Bradysia coprophila TIL is not accidental but due to the cooperative effect of multiple residues.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Nicolas S. M. Robert, Fatih Sarigol, Bob Zimmermann, Axel Meyer, Christian R. Voolstra, Oleg Simakov
Summary: This study analyzed 49 animal genomes and discovered the largest gains of synteny in the last common ancestor of bilaterians and cnidarians. Depending on their node of emergence, the novel syntenic blocks exhibit distinct functional compositions and gene density properties. These findings provide insights into the regulatory properties of microsyntenic blocks in animal genomes.
Review
Neurosciences
David Ramos-Vicente, Seth G. N. Grant, Alex Bayes
Summary: Glutamate is the major excitatory neurotransmitter in both vertebrate and invertebrate nervous systems. The evolution of glutamate receptors is more complex than anticipated, with recent research proposing a new classification system for ionotropic glutamate receptors. Additionally, the evolution of animal metabotropic glutamate receptors has resulted in the formation of four classes instead of three previously recognized.
Article
Endocrinology & Metabolism
Min Zhao, Emmanuelle Gelize, Rinath Levy, Alexandre Moulin, Frederic Azan, Marianne Berdugo, Marie-Christine Naud, Justine Guegan, Kimberley Delaunay, Eric Pussard, Patricia Lassiaz, Irene Bravo-Osuna, Rocio Herrero-Vanrell, Francine Behar-Cohen
Summary: The study found that MR is overexpressed in the retina of diabetic individuals, and local application of spironolactone can reduce the pathological features of retinopathy, suggesting it may be a novel therapeutic option for diabetic retinopathy.
Article
Ecology
Eisuke Hayakawa, Christine Guzman, Osamu Horiguchi, Chihiro Kawano, Akira Shiraishi, Kurato Mohri, Mei-Fang Lin, Ryotaro Nakamura, Ryo Nakamura, Erina Kawai, Shinya Komoto, Kei Jokura, Kogiku Shiba, Shuji Shigenobu, Honoo Satake, Kazuo Inaba, Hiroshi Watanabe
Summary: Biochemical identification and expression analysis suggest the presence of peptidergic neurons in early stages of nervous system evolution in Cnidaria and Ctenophora. A comprehensive survey of short peptides in early-branching lineages revealed the expression of neuropeptides associated with sensory, muscular, and digestive systems in ctenophores. Comparisons of genetic characteristics showed similarities between neuropeptide-expressing cells in Cnidaria, Ctenophora, and Bilateria, suggesting a common evolutionary origin of metazoan peptidergic nervous systems.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Peripheral Vascular Disease
Lara Matilla, Eva Jover, Mattie Garaikoetxea, Ernesto Martin-Nunez, Vanessa Arrieta, Amaia Garcia-Pena, Adela Navarro, Amaya Fernandez-Celis, Alicia Gainza, Virginia Alvarez, Diego Alvarez de la Rosa, Rafael Sadaba, Frederic Jaisser, Natalia Lopez-Andres
Summary: There are sex differences in the pathophysiology of aortic valve (AV) calcification in patients with aortic stenosis. Aldosterone (Aldo) promotes proteoglycan synthesis in valve interstitial cells (VICs) via the mineralocorticoid receptor (MR). The MR/Aldo pathway plays a role in fibrosis in women and in early AV calcification in men.
Article
Geology
Brian M. Kelley, Meiyi Yu, Daniel J. Lehrmann, Demir Altiner, Jonathan L. Payne
Summary: This study investigates the tempo of biotic recovery following the end-Permian mass extinction. The findings suggest that reef recovery from severe environmental perturbation can require several million years, even after favorable conditions return, highlighting the importance of modern reef conservation.
Correction
Biotechnology & Applied Microbiology
Oliver M. Selmoni, Diane Maitre, Julien Roux, Laetitia G. E. Wilkins, Lucas Marques da Cunha, Etienne L. M. Vermeirssen, Susanne Knoerr, Marc Robinson-Rechavi, Claus Wedekind
Review
Biotechnology & Applied Microbiology
Sara S. Fonseca Costa, Marc Robinson-Rechavi, Jurgen A. Ripperger
BRIEFINGS IN FUNCTIONAL GENOMICS
(2020)
Article
Genetics & Heredity
Qingyu Chen, Ramona Britto, Ivan Erill, Constance J. Jeffery, Arthur Liberzon, Michele Magrane, Jun-ichi Onami, Marc Robinson-Rechavi, Jana Sponarova, Justin Zobel, Karin Verspoor
GENOMICS PROTEOMICS & BIOINFORMATICS
(2020)
Article
Biology
Jialin Liu, Michael Frochaux, Vincent Gardeux, Bart Deplancke, Marc Robinson-Rechavi
Article
Evolutionary Biology
Kamil S. Jaron, Jens Bast, Reuben W. Nowell, T. Rhyker Ranallo-Benavidez, Marc Robinson-Rechavi, Tanja Schwander
Summary: Systematic characterization of genomic features in 26 parthenogenetic animals revealed no consistent patterns across transitions to asexuality, indicating lineage-specific rather than general consequences of parthenogenesis. Only parthenogens of hybrid origin showed high heterozygosity levels, while non-hybrid parthenogens appeared largely homozygous, regardless of the cellular mechanism underlying parthenogenesis.
JOURNAL OF HEREDITY
(2021)
Article
Biochemistry & Molecular Biology
Frederic B. Bastian, Julien Roux, Anne Niknejad, Aurelie Comte, Sara S. Fonseca Costa, Tarcisio Mendes de Farias, Sebastien Moretti, Gilles Parmentier, Valentine Rech de Laval, Marta Rosikiewicz, Julien Wollbrett, Amina Echchiki, Angelique Escoriza, Walid H. Gharib, Mar Gonzales-Porta, Yohan Jarosz, Balazs Laurenczy, Philippe Moret, Emilie Person, Patrick Roelli, Komal Sanjeev, Mathieu Seppey, Marc Robinson-Rechavi
Summary: Bgee is a database that allows retrieval and comparison of gene expression patterns in multiple animal species using curated healthy wild-type data, enabling the detection of expression conditions for any single gene across different species. It integrates various data types and ensures consistent data annotation and processing for cross-species comparisons.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Patrick Tran Van, Yoann Anselmetti, Jens Bast, Zoe Dumas, Nicolas Galtier, Kamil S. Jaron, Koen Martens, Darren J. Parker, Marc Robinson-Rechavi, Tanja Schwander, Paul Simion, Isa Schon
Summary: Ostracods, as one of the oldest crustacean groups, have been lacking genome resources, hindering genomic research. However, researchers successfully assembled and annotated reference genomes for three species of nonmarine ostracods using Illumina-based sequencing technology. These genomes provide a basis for further developing ostracods as models for evolutionary and ecological research.
G3-GENES GENOMES GENETICS
(2021)
Article
Biochemical Research Methods
Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz
Summary: Assigning new sequences to known protein families and subfamilies is crucial for many functional, comparative and evolutionary genomics analyses. However, relying solely on the closest sequence in a reference database for assignment can lead to misassignments, as a query sequence may not necessarily belong to the same subfamily as its closest sequence. To overcome this issue, a novel alignment-free protein subfamily assignment method called OMAmer has been introduced, which provides better and quicker subfamily-level assignments compared to methods relying on the closest sequence.
Article
Biochemistry & Molecular Biology
Jialin Liu, Rebecca R. Viales, Pierre Khoueiry, James P. Reddington, Charles Girardot, Eileen E. M. Furlong, Marc Robinson-Rechavi
Summary: Inter-species comparisons reveal an hourglass expression pattern during embryogenesis, with a higher proportion of conserved enhancers at the phylotypic period. Positive selection is detected on developmental enhancers at early and late stages, with a depletion at the phylotypic period, suggesting positive selection as an evolutionary mechanism underlying the hourglass pattern of animal evolution.
Article
Ecology
Tina Begum, Martha Liliana Serrano-Serrano, Marc Robinson-Rechavi
Summary: The study investigates comparative methods for gene function evolution, finding that both phylogenetic independent contrasts and pairwise comparisons lose power to detect functional evolution trends when the functional trait accelerates for a long time following duplication, with better power of phylogenetic contrasts under intermediate scenarios. Improved pairwise comparisons are robust to bias, and both approaches perform equally well under rapid shifts in traits.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Giulia Zancolli, Maarten Reijnders, Robert M. Waterhouse, Marc Robinson-Rechavi
Summary: Animals have evolved specialized organs and anatomical structures to produce and release potent bioactive molecules, known as venoms, for the purpose of subduing prey or predators. A comparative analysis of venom gland transcriptomes from 20 venomous species reveals a strong convergence in gene expression profiles, indicating that different animals have independently adopted similar molecular mechanisms to perform the same function. The study also highlights the presence of stress response mechanisms in venom glands to cope with toxin production, as well as regulatory networks for epithelial development and maintenance.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Ecology
Jelisaveta Djordjevic, Zoe Dumas, Marc Robinson-Rechavi, Tanja Schwander, Darren James Parker
Summary: Sexually dimorphic phenotypes are primarily caused by sex-biased gene expression during development. This study examined sex-biased gene expression during development in a hemimetabolous stick insect and compared it to a holometabolous fly. The results showed significant differences in the dynamics of sex-biased gene expression between the two insect species.
Article
Ecology
Darren J. Parker, Kamil S. Jaron, Zoe Dumas, Marc Robinson-Rechavi, Tanja Schwander
Summary: Sex chromosomes have evolved repeatedly across different species, with similar consequences such as accelerated evolution and increased accumulation of sexually antagonistic alleles. In Timema stick insects, the X chromosome has remained consistent in size and gene content over 30 million years of evolution, showing limited association with sexually biased genes.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2022)
Article
Biochemical Research Methods
David Laloum, Marc Robinson-Rechavi
Summary: The study investigates the evolutionary origins of gene expression rhythmicity and suggests that rhythmicity of protein expression could be favored by selection to minimize costs. Furthermore, the study found that rhythmic gene expression may help reduce expression noise and genes under stronger purifying selection tend to be rhythmically expressed at the mRNA level. The adaptive role of rhythmic expression is supported by the observation that rhythmic genes are highly expressed yet tissue-specific.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tina Begum, Marc Robinson-Rechavi
Summary: Investigating how gene function evolves is crucial in evolutionary biology, and this can be done by comparing functional genomics results between species and genes. While pairwise comparisons are commonly used, they may lead to biased results due to the phylogenetic relatedness of genes. Phylogenetic comparative methods, although more accurate, rely on strong assumptions. Reanalysis of gene trees revealed biases and challenges in implementing phylogenetic methods in empirical gene studies.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)