Article
Engineering, Environmental
Wankui Jiang, Yali Liu, Zhijian Ke, Lu Zhang, Mingliang Zhang, Yidong Zhou, Hui Wang, Chenglong Wu, Jiguo Qiu, Qing Hong
Summary: The study found that CehA genes from different hosts are highly conserved but exhibit significant substrate preferences. Point mutations can affect the substrate specificity of CehA genes. Considering the presence of transposable elements in the flanking regions of cehA, it is speculated that hosts may have acquired the ability to hydrolyze carbamate pesticides and their substrate preferences through horizontal gene transfer and genetic copying errors.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Biotechnology & Applied Microbiology
Veera Hamalainen, Juan De Dios Barajas-Lopez, Yana Berlina, Rafael Alvarez-Rafael, Klara Birikh
Summary: The study successfully addressed the issue of endoglucanase being diverted by other substrates through enzyme engineering and evolution, leading to improved substrate specificity and enhanced activity towards high molecular weight substrates. These findings hold potential applications in the bioeconomy sector, such as second-generation biofuels and biomaterials from lignocellulosic biomass.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Lisa Michelle Barber, Zakir Hussain, Merlin Thomas, Andrew Hung
Summary: Phosphorylation of GLO1 alters its structure and affects its activity and interaction with substrates, potentially leading to cellular damage.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Computer Science, Theory & Methods
Fabian Castiblanco, Camilo Franco, J. Tinguaro Rodriguez, Javier Montero
Summary: This paper investigates the reciprocal fuzzy preference relations within fuzzy relations, proposing a general framework for their transformation based on the concept of reciprocal functions. It demonstrates that reciprocal relations have their own preference structure and examines their compatibility with standard preference structures.
FUZZY SETS AND SYSTEMS
(2021)
Article
Nutrition & Dietetics
Shan-Shan Zhang, Yu-Fei Hou, Shao-Jing Liu, Sen Guo, Chi-Tang Ho, Nai-Sheng Bai
Summary: This study found that flavonoids-rich A. tenuissimum flower can effectively inhibit α-glucosidase activity, improving glycolipid metabolic disorders and inflammation in type 2 diabetes patients.
Article
Chemistry, Multidisciplinary
Sudarshan Behera, Sundaram Balasubramanian
Summary: Research has found that proteins coated with a polymer surfactant coating can form a liquid phase without the need for a solvent. However, these solvent-free protein liquids (SFPL) exhibit reduced catalytic rates compared to aqueous solutions. This study identifies the location and dynamics of substrates in SFPL as contributing factors to the reduced enzyme activity.
Article
Agriculture, Multidisciplinary
Shang Wang, Yan Xu, Xiao-Wei Yu
Summary: In this study, the mechanism of a propeptide in fungal lipases was explored using Rhizopus chinensis lipase as a research model. Molecular dynamics simulations showed that the propeptide inhibited the lid movement of the lipase and identified a key region on the propeptide. Subsequent mutation experiments confirmed the important role of this region in catalytic efficiency and substrate specificity of the lipase.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Nuwan Gunarathna, Anjalie Amarasinghe, Sunil Wijesundara, Devika Iddawela, Susiji Wickramasinghe
Summary: This study determined the presence and prevalence of Naegleria species in the water bodies of North-Western Province of Sri Lanka through molecular characterization and phylogenetic analysis. The prevalence of Naegleria species and N. fowleri in the study area were 23.07% and 1.92%. Bayesian analysis revealed different clade formations among the isolates, indicating the need for further investigations to confirm these findings.
Article
Biophysics
Joel Jose Montalvo-Acosta, Edmund R. S. Kunji, Jonathan J. Ruprecht, Francois Dehez, Christophe Chipot
Summary: Research has shown that cardiolipins play a minor stabilizing role in the structure of the mitochondrial ADP/ATP carrier (AAC), particularly in the formation of interdomain salt bridges and hydrogen bonds. Additionally, cardiolipins contribute to preserving the pseudosymmetric structure of AAC, making it more compactly organized.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Ajit Kumar, Prabhaker Yadav, Aftab Usmani, Syed Ainul Hussian, Sandeep Kumar Gupta
Summary: The Ganges river dolphin is an endangered cetacean that has experienced a significant reduction in distribution range due to increasing anthropogenic activities. The study of its complete mitochondrial genome provides insights important for identifying evolutionary relationships and monitoring the endangered species. Phylogenetic analysis showed that the river dolphins studied were polyphyletic, with Platanista having a more basal placement than other river dolphins like Lipotes, Inia, and Pontoporia.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Food Science & Technology
Meiping Li, Xiying Zhao, Manjun Xu
Summary: This study investigates the chemical composition, antimicrobial, and antioxidant activities of essential oil from Allium tenuissimum L. flowers. The essential oil contains 72 volatile components, with terpenoid compounds and sulfurous compounds, especially dimethyl trisulfide, being the most abundant. The oil demonstrates significant antimicrobial efficiency against various pathogens and exhibits high stability to UV. Additionally, the essential oil shows strong radical-scavenging effects, making it a potential natural antibacterial and antioxidant agent in the food industry.
Article
Biochemistry & Molecular Biology
Jing Zhang, Ling-Xiao Gao, Wei Chen, Jian-Jiang Zhong, Chao Qian, Wen-Wen Zhou
Summary: Doxorubicin, a widely used antitumor drug, is currently produced through a chemical conversion method, which is costly and environmentally polluting. In this study, we expressed and optimized the key enzyme, cytochrome daunorubicin C-14 hydroxylase, for doxorubicin production. Through rational design, we obtained a mutant enzyme, DoxA(P88Y), which showed a 56% increase in bioconversion efficiency compared to the wild-type enzyme. Molecular dynamics simulation revealed the enhanced binding stability between the mutant enzyme and the substrate, daunorubicin, contributing to the improved catalytic activity. This work provides a foundation for further development of doxorubicin and facilitates its industrial production.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Marzieh Dehghan Shasaltaneh, Elmira Naghdi, Zahra Moosavi-Nejad
Summary: This study investigates the interactions between RNase A and cCMP through molecular docking and molecular dynamics simulation. The results indicate that cCMP-RNase A complexes are stabilized through hydrophobic interaction, hydrogen bonding, and π-π stacking interaction. The enzyme-ligand docking study shows three phases of binding modes, and experimental methods confirm the activation and inhibition of substrate at different concentrations of cCMP.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Jamille A. Bitencourt, Paulo R. A. M. Affonso, Robson T. C. Ramos, Horacio Schneider, Iracilda Sampaio
Summary: In this study, the researchers conducted a comprehensive molecular phylogenetic analysis of the Achiridae family using both nuclear and mitochondrial genes. The results confirmed the monophyletism of Achiridae and identified non-monophyletic genera within the family. The study also provided evidence for the origin of Achiridae in estuaries and the independent evolution of some lineages in marine or freshwater habitats. Additionally, the researchers proposed a scenario for the diversification of New World soles involving marine incursions and geographic barriers. The dependence of Achiridae on estuaries was found to have driven the recent divergence of many species.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Giacinto De Vivo, Fabio Crocetta, Miriam Ferretti, Roberto Feuda, Salvatore D'Aniello
Summary: By investigating 74 lophotrochozoan genomes, we discovered that the common ancestor of Lophotrochozoa possessed at least seven paralog groups of opsins, with divergent evolutionary histories in different phyla. Moreover, we identified opsin-related pseudopsins in Bilateria for the first time, potentially crucial in unraveling opsin evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Tomas Curtis, James C. Lendemer
Summary: Catillaria fungoides is newly reported in North America based on collections from the temperate eastern United States. A detailed description, distribution map, and images are provided. The species is likely widespread but often overlooked due to its inconspicuous appearance.
Article
Biodiversity Conservation
Erin A. Manzitto-Tripp, James C. Lendemer, Christy M. McCain
Summary: This study examines the drivers of species rarity in North American lichens. The results show that most lichens are rare and their distribution is influenced by geographical regions, mode of reproduction, substrate type, and other factors. The uneven representation of lichens across trait categories is also highlighted.
DIVERSITY AND DISTRIBUTIONS
(2022)
Review
Plant Sciences
Elisabeth B. Ward, Marlyse C. Duguid, Sara E. Kuebbing, James C. Lendemer, Mark A. Bradford
Summary: Ericoid mycorrhizal (ErM) shrubs commonly found in forest understories can have significant effects on soil carbon and nitrogen dynamics. ErM fungi and plants have unique traits that can contribute to organic matter accumulation and nutrient limitation. Further study of ErM effects is important for understanding the interaction of different mycorrhizal types in changing environmental conditions.
Bibliography
Plant Sciences
James C. Lendemer
Article
Mycology
Susan Egbert, Jordan R. Hoffman, R. Troy McMullin, James C. Lendemer, John L. Sorensen
Summary: Lichenized fungi are known for producing a variety of secondary metabolites, with usnic acid being the most well-studied. This study identified functional gene clusters responsible for usnic acid production in Cladonia rangiferina, a species previously thought to lack this ability. However, other species, such as C. stygia and C. oricola, truly lacked the gene clusters and could not produce usnic acid. These findings highlight the importance of using sensitive LC-MS methods for comprehensive characterization of lichen secondary metabolite profiles.
Article
Biodiversity Conservation
Gregory M. Mueller, Kelmer Martins Cunha, Tom W. May, Jessica L. Allen, James R. S. Westrip, Catia Canteiro, Diogo Henrique Costa-Rezende, Elisandro Ricardo Drechsler-Santos, Aida M. Vasco-Palacios, Antony Martyn Ainsworth, Genivaldo Alves-Silva, Frank Bungartz, Amanda Chandler, Susana C. Goncalves, Irmgard Krisai-Greilhuber, Reda Irsenaite, John Bjarne Jordal, Thiago Kosmann, James Lendemer, Richard Troy McMullin, Armin Mesic, Viviana Motato-Vasquez, Yoshihito Ohmura, Rikke Reese Naesborg, Claudia FerMi, Irja Saar, Diego Simijaca, Rebecca Yahr, Anders Dahlberg
Summary: Fungal species are also vulnerable to the threats faced by animals and plants, and recent efforts have led to an increase in the number of published fungal assessments. The 597 assessed fungal species in the 2022-1 IUCN Red List update provide the first global review of the extinction risk and threats faced by fungi. Nearly 50% of the assessed species are threatened, with habitat loss/degradation, climate change, invasive species, and pollution identified as the primary threats.
Bibliography
Plant Sciences
James C. Lendemer
Article
Mycology
Jordan R. Hoffman, Kenneth G. Karol, Yoshihito Ohmura, Cloe S. Pogoda, Kyle G. Keepers, Robert T. McMullin, James C. Lendemer
Summary: This study investigates the mitochondrial genome diversity and variation in lichen obligate symbioses, specifically focusing on the Cladonia genus. The results show that mitochondrial genome size and structure differ among species, suggesting a correlation with reproductive morphology and evolutionary history.
Bibliography
Plant Sciences
James C. Lendemer
Article
Plant Sciences
James C. Lendemer, Jason P. Hollinger
Summary: Schadonia saulskellyana is a newly discovered species in the southern Appalachian Mountains in the eastern United States. It is primarily found on conifer bark and is especially abundant in the endangered high-elevation spruce-fir forests of the region.
Bibliography
Plant Sciences
James C. Lendemer
Article
Ecology
Natalia M. Koch, James C. Lendemer, Erin A. Manzitto-Tripp, Christy McCain, Daniel E. Stanton
Summary: Carbon-concentrating mechanisms (CCMs) are widespread in photosynthetic organisms and are associated with significant shifts in vascular plants. However, little is known about the impact of CCMs on the distribution of other terrestrial photosynthetic organisms. This study examines the importance of CCMs in lichen communities and demonstrates that CCM status is a key functional trait that affects lichen ecology and distribution. The responses of lichens with CCMs to temperature and precipitation differ from those without CCMs, contrary to our understanding of lichen physiology.
Article
Plant Sciences
Olivia A. Asher, John Howieson, James C. Lendemer
Summary: Platismatia lichens are common and widespread, but there have been limited molecular phylogenetic studies on them. This study presents an expanded phylogeny of Platismatia based on newly generated ITS sequences. The results confirm the distinction between P. wheeleri and the widespread P. glauca. The study also suggests that Platismatia could be a useful model for future research on reproductive mode, biogeography, and speciation in lichens.
Article
Plant Sciences
Tomas Curtis, Dennis P. Waters, James C. Lendemer
Summary: This article reports on the newly discovered species Bilimbia fuscoviridis in North America. It is widespread in the temperate eastern United States and adjacent Canada, frequently found on shaded calcareous and siliceous rocks near waterways. Despite its inconspicuous appearance and absence of diagnostic secondary metabolites, the species is likely common but often overlooked.
JOURNAL OF THE TORREY BOTANICAL SOCIETY
(2023)
Article
Plant Sciences
James C. Lendemer
Summary: Herpothallon rubrogranulosum is a unique lichen species with limited distribution but local abundance. Previously confused with H. rubroechinatum, the two species differ markedly in the size of their pseudoisidia.
JOURNAL OF THE TORREY BOTANICAL SOCIETY
(2022)