Article
Biochemical Research Methods
Chaitanya Aluru, Mona Singh
Summary: The study introduces a reconciliation-based framework that considers the relative positions of protein domains within extant sequences to uncover tandem domain duplications accurately. By developing an integer linear programming approach and a heuristic algorithm, the researchers are able to identify single and tandem domain duplication events with high accuracy. Through extensive simulation studies and testing on an orthogroup with complex domain duplication patterns, the effectiveness of the approach is demonstrated.
Article
Plant Sciences
Yun-Hai Lu, Intikhab Alam, Yan-Qing Yang, Ya-Cen Yu, Wen-Chao Chi, Song-Biao Chen, Boulos Chalhoub, Li-Xi Jiang
Summary: The YABBY gene family, present in all seed plants, plays crucial roles in plant growth and development, including polarity establishment, leaf and flower formation, and response to hormonal signals and environmental stress. Through identification of 364 YABBY genes in 37 Brassicaceae genomes, it was found that these genes are largely conserved across species but exhibit considerable functional divergence.
Article
Multidisciplinary Sciences
Dia A. Ghose, Kaitlyn E. Przydzial, Emily M. Mahoney, Amy E. Keating, Michael T. Laub
Summary: The evolution of novel functions in biology relies on gene duplication and divergence, creating large paralogous protein families. However, the specificity of these paralogs to their interaction partners can be sensitive to mutation. Through deep mutational scanning, it was demonstrated that a family of bacterial signaling proteins exhibits marginal specificity, with individual substitutions leading to substantial cross-talk between pathways. These findings suggest that the evolution of bacterial signaling proteins is constrained by sequence space crowding, and that evolution selects for good enough rather than optimized phenotypes in paralogs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Fisheries
Shang Geng, Tianjun Xu, Yuena Sun
Summary: In this study, we identified 27 ChemR genes in miiuy croaker and analyzed their characteristics, including gene structure, evolutionary mechanism, and expression levels upon bacterial infection. The results showed that these genes underwent tandem and segmental duplication events during evolution, and teleost fishes' ChemRs may have a higher evolutionary dynamic compared to vertebrates. Additionally, 21 positively selected codons were detected in vertebrate ChemRs under Model 8, and certain genes were significantly up-regulated upon Vibrio harveyi infection, providing valuable information for further functional analysis.
FISH & SHELLFISH IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Colin J. Shew, Paulina Carmona-Mora, Daniela C. Soto, Mira Mastoras, Elizabeth Roberts, Joseph Rosas, Dhriti Jagannathan, Gulhan Kaya, Henriette O'Geen, Megan Y. Dennis
Summary: Evidence shows that in humans, paralogous segmental duplication genes exhibit different expression patterns, possibly due to relaxed selection or neofunctionalization. While ancestral paralogs show greater expression conservation with chimpanzee orthologs, certain derived paralogs may retain or supplant ancestral functions.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Lars H. Kruse, Austin T. Weigle, Mohammad Irfan, Jesus Martinez-Gomez, Jason D. Chobirko, Jason E. Schaffer, Alexandra A. Bennett, Chelsea D. Specht, Joseph M. Jez, Diwakar Shukla, Gaurav D. Moghe
Summary: Large enzyme families catalyze metabolic diversification by using diverse chemical scaffolds, but it is not clear how these families achieve functional diversity. In this study, using BAHD acyltransferases as a model, the researchers compiled published activities and used orthologous groups to predict the utilization and origins of BAHD enzymes in plants. The results not only describe how BAHD enzymes contributed to the evolution of multiple chemical phenotypes in the plant world, but also propose an approach for improved functional annotation of plant enzyme families using biocuration.
Review
Plant Sciences
Yuanpeng Fang, Junmei Jiang, Xiaolong Hou, Jiyuan Guo, Xiangyang Li, Degang Zhao, Xin Xie
Summary: The evolution of gene families is crucial for understanding the evolutionary history and biodiversity of plants, as well as explaining their tolerance to environmental stresses. Studying the molecular evolution of plant gene families helps to gain insights into these important processes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Alberto M. Rivera, Damien B. Wilburn, Willie J. Swanson
Summary: The rapid evolution of fertilization proteins has led to diversity in molecular structure and function. The study focuses on the ZP-N domains in vertebrate egg coat glycoproteins, which have diversified in structure and function. The modular ZP-N domains are associated with another domain type and have a stabilizing network absent in free domains.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
History & Philosophy Of Science
Phil Corkum
Summary: Metaphysical explanations are typically considered to be independent of our epistemic situation, but recent studies have shown that certain distributed properties play a key role in metaphysical explanations. These explanations have shown a failure in salience, and further research is needed to determine how to represent the semantics of salience effectively.
Review
Cell Biology
Narendra Pratap Singh, Robb Krumlauf
Summary: Gene duplication and divergence play a significant role in the generation of morphological diversity and emergence of novel features in vertebrates. Although genome sequencing has improved our understanding of gene and regulatory element evolution, progress in studying protein function conservation and divergence has been slow. Some studies have explored the functional evolution of related proteins, but understanding of protein function variation within gene families remains limited.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biology
Yi Lei, Liandong Yang, Haifeng Jiang, Juan Chen, Ning Sun, Wenqi Lv, Shunping He
Summary: The study revealed that genome duplications in representative Cyprinidae fish facilitated phenotypic diversity in the Hb gene family, resulting in repeated evolutionary transitions and species-specific changes in gene content.
SCIENCE CHINA-LIFE SCIENCES
(2021)
Article
Genetics & Heredity
Alejandro Alvarez-Lugo, Arturo Becerra
Summary: Gene duplication is a crucial process in the emergence of new genes and functions, with a high ratio of paralogs found in certain enzymatic classes among prokaryotes. Around 20-40% of prokaryotic enzymes are estimated to have paralogs, with free-living enzymes showing higher ratios compared to intracellular organisms. Similar genomic and biochemical traits are shared among phylogenetically close phyla and even some unrelated phyla with similar lifestyles, suggesting gene duplication is associated with environmental adaptation.
FRONTIERS IN GENETICS
(2021)
Article
Immunology
Lee K. Campbell, Rhiannon M. Peery, Katharine E. Magor
Summary: TRIM genes play important roles in development, innate immunity and viral restriction. This study investigated the TRIM gene repertoire in the domestic mallard duck and found 57 TRIM genes, which belong to all 12 subfamilies. Comparison of C-IV TRIM proteins among reptiles, birds and mammals revealed independent origins in these lineages. The expression analysis showed that C-IV TRIMs have high expression in immune relevant sites and low expression in immune privileged sites. The evolution of TRIM genes in birds suggests potential immune genes and viral targets.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Zoology
Yahui Zhao, Zushi Huang, Jinqing Huang, Chunguang Zhang, Fanwei Meng
Summary: The study found that eye-degenerated species in Sinocyclocheilus are polyphyletic, showing varying degrees of photoreceptor defects. While S. anophthalmus is classified as an eye-normal species, it exhibits high levels of eye degeneration and significant differences in eye-related gene expression compared to other eye-normal species.
INTEGRATIVE ZOOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Sophie Fouchecourt, Valerie Fillon, Christelle Marrauld, Caroline Callot, Sarah Ronsin, Floriane Picolo, Cecile Douet, Benoit Piegu, Philippe Monget
Summary: Gene duplications increase genetic and phenotypic diversity. PHF7 gene is a highly duplicated gene family in the chicken genome, which is also likely to occur in other bird species. By screening the chicken BAC library and using FISH technology, we identified and located 10 PHF7-like loci on five Gallus gallus chromosomes. The sequenced BAC sequences revealed additional duplicated genes in these genomic regions.
Article
History & Philosophy Of Science
Beckett Sterner
BIOLOGY & PHILOSOPHY
(2015)
Article
Biology
Beckett Sterner, Scott Lidgard
JOURNAL OF THE HISTORY OF BIOLOGY
(2018)
Article
Mathematical & Computational Biology
Nico M. Franz, Beckett W. Sterner
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2018)
Article
History & Philosophy Of Science
Beckett Sterner
PHILOSOPHY OF SCIENCE
(2019)
Article
Mathematical & Computational Biology
Samuel Cusimano, Beckett Sterner
ACTA BIOTHEORETICA
(2020)
Article
History & Philosophy Of Science
Beckett Sterner, Joeri Witteveen, Nico Franz
HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES
(2020)
Article
Statistics & Probability
Michael Cullan, Scott Lidgard, Beckett Sterner
JOURNAL OF APPLIED STATISTICS
(2020)
Article
History & Philosophy Of Science
Beckett Sterner, Steve Elliott, Nate Upham, Nico Franz
Summary: Modeling zoonotic disease risks requires consideration of the robustness of background assumptions and phylogenetic inference, as different taxonomic assumptions may affect the objectivity of risk assessments and the consistency of policy decisions.
HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES
(2021)
Article
History & Philosophy Of Science
Beckett Sterner, Christopher DiTeresi
Summary: Making sense of scientific success or failure is crucial to inform scientists' next steps, with the realism debate focusing on truth or reliability explanations. This paper aims to expand on Arthur Fine's practice-oriented project by introducing design specifications and track records to enhance understanding of scientific modeling practices, while maintaining a deflationary stance on the realism debate.
EUROPEAN JOURNAL FOR PHILOSOPHY OF SCIENCE
(2021)
Article
Environmental Sciences
Nathan S. Upham, Jorrit H. Poelen, Deborah Paul, Quentin J. Groom, Nancy B. Simmons, Maarten P. M. Vanhove, Sandro Bertolino, DeeAnn M. Reeder, Cristiane Bastos-Silveira, Atriya Sen, Beckett Sterner, Nico M. Franz, Marcus Guidoti, Lyubomir Penev, Donat Agosti
Summary: Lockdowns during the pandemic have highlighted the issue of biological dark data, where published data is disconnected from digital knowledge resources, limiting analysis. Building digitally connected knowledge graphs can help identify host-pathogen interactions quickly and strengthen human and planetary health systems.
LANCET PLANETARY HEALTH
(2021)
Article
Cultural Studies
Beckett Sterner, Steve Elliott
Summary: Biodiversity science is at a critical juncture as different actors negotiate norms for governing biodiversity data portals. The management of these portals can either correct or perpetuate historical and current inequities. Researchers and Indigenous Peoples are implementing strategies to influence the recognition of key participants in data management and use. The FAIR and CARE Data Principles are notable efforts in this regard, with FAIR prioritizing machine understanding of data meanings and CARE emphasizing Indigenous Peoples and their data sovereignty. Together, FAIR and CARE represent a strategy for institutionalizing international norms for digital repositories.
SCIENCE AS CULTURE
(2023)
Article
Mathematical & Computational Biology
Beckett Sterner, Steve Elliott, Edward E. Gilbert, Nico M. Franz
Summary: How to share and reuse billions of species observations worldwide? The traditional ideal of standardizing all datasets and aggregating them into a centralized repository has limitations, which warrants exploring alternatives. To facilitate community deliberation and evaluation, a conceptual framework is developed to show how different organizational models, regulative ideals, and heuristic strategies can be combined to form shared infrastructures supporting data reuse. The evidence suggests that a pluralistic ideal is better suited for biodiversity data, considering the relationships between stakeholders.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
History & Philosophy Of Science
Beckett Sterner
Summary: The concept of ambiguity in data science is still controversial. While many believe that polysemy undermines reasoning and communication, some historians, philosophers, and social scientists argue that polysemy can be generative and strategically valuable. Recent quantitative results from linguistics also suggest that polysemy can improve human communication efficiency. This article presents a new conceptual typology that synthesizes prior research and explores the value of polysemy in scientific research practices. The author proposes that studying historical patterns of partial synonyms can provide insights into these issues.
Article
History & Philosophy Of Science
Beckett Sterner
BIOLOGY & PHILOSOPHY
(2017)