Article
Biology
Marc W. Van Goethem, Andrew R. Osborn, Benjamin P. Bowen, Peter F. Andeer, Tami L. Swenson, Alicia Clum, Robert Riley, Guifen He, Maxim Koriabine, Laura Sandor, Mi Yan, Chris G. Daum, Yuko Yoshinaga, Thulani P. Makhalanyane, Ferran Garcia-Pichel, Axel Visel, Len A. Pennacchio, Ronan C. O'Malley, Trent R. Northen
Summary: The study utilized long-read sequencing and metatranscriptomic analysis to investigate nearly 3,000 biosynthetic gene clusters (BGCs) encoding microbial secondary metabolites in biocrust samples, highlighting the crucial role of BGCs in maintaining phylogenetic niches within biocrusts. The research revealed significant changes in BGC expression under different light conditions during wetting processes, indicating complex dynamics of BGCs in response to environmental stimuli.
COMMUNICATIONS BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Agerdanio Andrade de Souza, Brenda Lorena Sanchez Ortiz, Rosemary de Carvalho Rocha Koga, Priscila Faimann Sales, Divino Bruno da Cunha, Ana Luiza Mantovaneli Guerra, Gisele Custodio de Souza, Jose Carlos Tavares Carvalho
Summary: Plant-derived products may offer promising strategies in the treatment of Neglected Tropical Diseases (NTDs). This study focused on the species Trattinnickia rhoifolia Willd, commonly known as Breu sucuruba, in the Amazon region, identifying its potential therapeutic activities including antimicrobial, antioxidant, anti-inflammatory, antiviral, antifungal, anesthetic, and antiparasitic properties. Further exploration of its pharmacological potential, especially in addressing NTDs in the Brazilian Amazon, is warranted.
Article
Microbiology
Yanlei Sun, Bo Chen, Xinlin Li, Ying Yin, Chengshu Wang
Summary: Fungal chemical ecology is largely mediated by metabolites produced by biosynthetic gene clusters (BGCs) with antibiotic activities. In the insect pathogen Metarhizium robertsii, a supercluster consisting of three BGCs is controlled by an embedded master regulator. This supercluster collectively produces four classes of chemicals and contributes to the fungus's ability to combat diverse bacteria. The findings reveal a novel strategy employed by fungi to manage effective adaptations to different environments.
Article
Biochemistry & Molecular Biology
Kolade O. Faloye, Manish K. Tripathi, Stephen A. Adesida, Samuel A. Oguntimehin, Yemisi M. Oyetunde, Adetola H. Adewole, Ifeoluwa I. Ogunlowo, Esther A. Idowu, Uduak I. Olayemi, Olamide D. Dosumu
Summary: This study evaluated the antimalarial effect of ginger rhizome and identified gingerenone A as the hit molecule. Molecular docking and simulation techniques were used to assess the antimalarial potential. The study also identified eight phytochemicals in ginger rhizome, and demonstrated its significant antimalarial activity.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Mehmet Direnc Mungan, Theresa Anisja Harbig, Naybel Hernandez Perez, Simone Edenhart, Evi Stegmann, Kay Nieselt, Nadine Ziemert
Summary: This article introduces a web server called SeMa-Trap, which helps researchers prioritize genes for genetic engineering in the drug discovery process. SeMa-Trap uses transcriptome analysis to identify co-expression patterns between specific genes and the target gene clusters, and provides interactive result pages for comparing and exploring expression patterns.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Kunpeng Zhang, Nuohan Wang, Xinqiang Gao, Qiang Ma
Summary: This study investigates the tissue-specific regulatory network of terpenoid biosynthesis in Artemisia argyi through integrated metabolomic and transcriptomic analysis. Key genes and transcription factors related to terpenoid metabolism were identified, providing a foundation for future metabolic engineering.
Article
Marine & Freshwater Biology
Sabrina Heiser, Andrew J. Shilling, Charles D. Amsler, James B. McClintock, Bill J. Baker
Summary: Understanding the spatial distribution of intraspecific variation is crucial for identifying drivers of ecosystem structure. Secondary metabolites, such as chemical defenses, vary among organisms. In a study on Antarctic red macroalga Plocamium sp., 15 chemogroups were found. These chemogroups affect the feeding rates and reproduction of the amphipod Paradexamine fissicauda, which feeds on Plocamium sp.
Article
Microbiology
J. L. Weissman, Marie Peras, Tyler P. Barnum, Jed A. Fuhrman
Summary: Trait inference from mixed-species microbial communities is a central problem in microbial ecology. The authors developed a tool, gRodon, for predicting the maximum growth rate of an organism based on its genomic data. This predictor can be applied to mixed-species communities to estimate the average community-wide maximum growth rate. The authors also provided an improved predictor for metagenomic data that corrects a persistent bias and showed the importance of data preprocessing for accurate predictions.
Review
Chemistry, Multidisciplinary
Ronglu Yu, Jia Liu, Yi Wang, Hong Wang, Huawei Zhang
Summary: Aspergillus niger, a common and important fungal species, produces various biomolecules with wide applications as secondary metabolites. This review comprehensively summarizes the biological and chemical aspects of A. niger strains, including their sources, BGCs, secondary metabolites, biological properties, and biosynthetic pathways. Future perspectives on the discovery of more functional biomolecules derived from A. niger are also provided.
FRONTIERS IN CHEMISTRY
(2021)
Article
Ecology
Paul V. A. Fine, Diego Salazar, Roberta E. Martin, Margaret R. Metz, Tracy M. Misiewicz, Gregory P. Asner
Summary: This study explores an integrative approach that combines spectral data with plant metabolomics data to study secondary metabolites in Protium tree species. The research found strong correlations between many secondary metabolites and VSWIR spectra of Protium, as well as significant correlations in phenolics content between juvenile and canopy trees of the same species.
Review
Plant Sciences
Panchsheela Nogia, Pratap Kumar Pati
Summary: The study focuses on the important roles of secondary metabolites (SMs) in plant growth, defense, development, and survival, as well as explores the transport mechanisms of SMs and the potential of engineering transporters to enhance metabolite production.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Aya Yoshimura, Rio Saeki, Ryusuke Nakada, Shota Tomimoto, Takahiro Jomori, Keisuke Suganuma, Toshiyuki Wakimoto
Summary: Most bacterial biosynthetic gene clusters (BGCs) are silent under normal culture conditions but can be conditionally expressed in response to external stimuli. Bacterial membrane vesicles (MVs) have been found to mimic exogenous stimulants and can activate silent BGCs. In this study, Burkholderia multivorans MVs were used to induce silent metabolites in various bacteria, and the mechanism was found to involve quorum sensing inhibition and interspecies communication through MV exchange.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Shinji Kishimoto, Ayumi Minami, Yoshimitsu Aoki, Yuya Matsubara, Shogo Watanabe, Kenji Watanabe
Summary: Pathogenic fungi of Aspergillus section Fumigati are capable of producing various secondary metabolites. This study reports the isolation of fumimycin and a new compound named lentofuranine from A. lentulus. These compounds were found to be assembled through a nonenzymatic condensation involving a polyketide intermediate from the terrein biosynthetic pathway and a highly reactive azlactone intermediate. The formation of an unusual carbon skeleton is attributed to the reactivity of azlactone.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Microbiology
Stephanie D. Jurburg, Francois Buscot, Antonis Chatzinotas, Narendrakumar M. Chaudhari, Adam T. Clark, Magda Garbowski, Matthias Grenie, Erik F. Y. Hom, Canan Karakoc, Susanne Marr, Steffen Neumann, Mika Tarkka, Nicole M. van Dam, Alexander Weinhold, Anna Heintz-Buschart
Summary: This article examines the impact of technical biases and noise introduced during sample preparation and data collection on the estimation of molecular diversity. It also explores how novel methods from community ecology can improve the interpretation and integration of multivariate molecular data.
Article
Pharmacology & Pharmacy
Benedito Matheus Dos Santos, Glaucio Monteiro Ferreira, Mauricio Temotheo Tavares, Julio Cesar De Bona, Mario Hiroyuki Hirata, Vanderlucia Fonseca De Paula, Klaus Casaro Saturnino, Andreimar Martins Soares, Mirian Machado Mendes
Summary: The study showed that lupeol, a triterpenoid from Zanthoxylum monogynum, has the potential to inhibit coagulant, phospholipasic, and myotoxic activities of bothropic venom. It interacts with snake venom toxins such as thrombin-like toxin Jararacussin-I and acidic PLA(2) toxin BthA-I, demonstrating its pharmacological potential for the treatment of bothropic accidents.
Article
Ecology
Ana M. Aldana, Marcos B. Carlucci, Paul V. A. Fine, Pablo R. Stevenson
Article
Evolutionary Biology
Carlos Daniel Cadena, Felipe Zapata, Ivan Jimenez
SYSTEMATIC BIOLOGY
(2018)
Review
Ecology
Timothy R. Baker, R. Toby Pennington, Kyle G. Dexter, Paul V. A. Fine, Helen Fortune-Hopkins, Euridice N. Honorio, Isau Huamantupa-Chuquimaco, Bente B. Klitgard, Gwilym P. Lewis, Haroldo C. de Lima, Peter Ashton, Christopher Baraloto, Stuart Davies, Michael J. Donoghue, Maria Kaye, W. John Kress, Caroline E. R. Lehmann, Abel Monteagudo, Oliver L. Phillips, Rodolfo Vasquez
TRENDS IN ECOLOGY & EVOLUTION
(2017)
Article
Biochemistry & Molecular Biology
Catriona Munro, Stefan Siebert, Felipe Zapata, Mark Howison, Alejandro Damian-Serrano, Samuel Church, Freya Goetz, Philip Pugh, Steven Haddock, Casey Dunn
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2018)
Article
Multidisciplinary Sciences
Casey W. Dunn, Felipe Zapata, Catriona Munro, Stefan Siebert, Andreas Hejnol
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Multidisciplinary Sciences
Felipe Zapata, Daniel Villarroel
Article
Plant Sciences
Natalie Henkhaus, Madelaine Bartlett, David Gang, Rebecca Grumet, Ingrid Jordon-Thaden, Argelia Lorence, Eric Lyons, Samantha Miller, Seth Murray, Andrew Nelson, Chelsea Specht, Brett Tyler, Thomas Wentworth, David Ackerly, David Baltensperger, Philip Benfey, James Birchler, Sreekala Chellamma, Roslyn Crowder, Michael Donoghue, Jose Pablo Dundore-Arias, Jacqueline Fletcher, Valerie Fraser, Kelly Gillespie, Lonnie Guralnick, Elizabeth Haswell, Mitchell Hunter, Shawn Kaeppler, Stefan Kepinski, Fay-Wei Li, Sally Mackenzie, Lucinda McDade, Ya Min, Jennifer Nemhauser, Brian Pearson, Peter Petracek, Katie Rogers, Ann Sakai, Delanie Sickler, Crispin Taylor, Laura Wayne, Ole Wendroth, Felipe Zapata, David Stern
Article
Plant Sciences
Sonal Singhal, Adam B. Roddy, Christopher DiVittorio, Ary Sanchez-Amaya, Claudia L. Henriquez, Craig R. Brodersen, Shannon Fehlberg, Felipe Zapata
Summary: This study investigates the rapid diversification and disparification of the woody plant lineage Encelia in the deserts of the Americas, showing that it originated in the hot deserts of North America and diversified rapidly with fast rates of phenotypic evolution and extreme disparity. Multiple instances of gene flow between species were uncovered, highlighting how interspecific gene flow and high trait lability can enable exceptionally fast diversification across steep environmental gradients.
Article
Multidisciplinary Sciences
August Guang, Mark Howison, Felipe Zapata, Charles Lawrence, Casey W. Dunn
Summary: treeinform is a method that utilizes phylogenetic information across species to improve transcriptome assemblies within species. It helps identify and correct the error of mistaking different transcripts of the same gene as transcripts from multiple closely related genes.
Article
Multidisciplinary Sciences
Christopher T. DiVittorio, Sonal Singhal, Adam B. Roddy, Felipe Zapata, David D. Ackerly, Bruce G. Baldwin, Craig R. Brodersen, Alberto Burquez, Paul V. A. Fine, Mayra Padilla Flores, Elizabeth Solis, Jaime Morales-Villavicencio, David Morales-Arce, Donald W. Kyhos
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Octavio Aburto-Oropeza, Carlos Manuel Burelo-Ramos, Exequiel Ezcurra, Paula Ezcurra, Claudia L. Henriquez, Sula E. Vanderplank, Felipe Zapata
Summary: Climatic oscillations during the Pleistocene, particularly the Last Interglacial period, led to significant changes in global sea level and the spatial distribution of marine and terrestrial ecosystems. The study provides evidence of an extant, inland mangrove ecosystem as a relict of the Last Interglacial period, demonstrating the long-lasting impact of sea level changes on tropical landscapes and species ranges.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Sarah J. Jacobs, Michael C. Grundler, Claudia L. Henriquez, Felipe Zapata
Summary: The definition and biological reality of plant species have been debated in evolutionary biology, with some biologists suggesting that taxonomists create species subjectively. By analyzing phenomic and genomic data in Escallonia, it was found that taxonomic species did not match patterns of variation in nature, suggesting the existence of objective plant species independent of taxonomy. The study also showed that evolutionary forces beyond gene flow play a role in maintaining species cohesion.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Michael J. Landis, Ignacio Quintero, Martha M. Munoz, Felipe Zapata, Michael J. Donoghue
Summary: Geographical features have an impact on species dispersal, extinction, and speciation. This study uses a Bayesian hierarchical modeling framework to transform regional features into evolutionary rates. The results show that distance between regions affects dispersal rates and speciation rates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Evolutionary Biology
Michael C. Grundler, Daniel L. Rabosky, Felipe Zapata
Summary: Understanding phenotypic disparity across the tree of life requires accurate inference of evolutionary rate heterogeneity. In this study, a method for inferring among-lineage evolutionary rate heterogeneity in both continuous and discrete traits is described. The method uses dynamic programming and maximum likelihood estimators to accurately reconstruct rates of trait evolution and reduces computational costs. This method expands the tools available for detecting macroevolutionary rate heterogeneity and demonstrates the utility of fast, approximate methods for studying biodiversity dynamics on a large scale.
SYSTEMATIC BIOLOGY
(2022)
Article
Evolutionary Biology
Ioana Anghel, Sarah J. Jacobs, Merly Escalona, Mohan P. A. Marimuthu, Colin W. Fairbairn, Eric Beraut, Oanh Nguyen, Erin Toffelmier, H. Bradley Shaffer, Felipe Zapata
Summary: Sandblossoms, Linanthus parryae, is a widespread annual plant species that has played a central role in evolutionary biology. By assembling its genome, it will allow us to revisit the role of evolutionary forces in geographic landscapes and uncover its adaptations to arid environments.
JOURNAL OF HEREDITY
(2022)
Article
Biochemistry & Molecular Biology
Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby
Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun
Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko
Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun
Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan
Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling
Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu
Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson
Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris
Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)