Article
Biochemistry & Molecular Biology
Kosuke Seki, Joey L. Galindo, Ashty S. Karim, Michael C. Jewett
Summary: Non-canonical amino acids (ncAAs) can be incorporated into peptides and proteins to create new properties and functions. In this study, a cell-free gene expression system based on Escherichia coli crude extract was developed to rapidly express and characterize functional suppressor tRNAs. The system co-expresses orthogonal tRNAs using endogenous machinery alongside a reporter protein, allowing for easy evaluation of suppression activity. This cell-free workflow can also be used to discover new suppressor tRNAs in metagenomic data. Overall, this system has the potential to accelerate the development of orthogonal translation systems for synthetic biology.
ACS CHEMICAL BIOLOGY
(2023)
Article
Biology
Gabrielle E. Scolaro, Edward L. Braun
Summary: The rates of amino acid substitution during evolutionary time are influenced by the chemical properties of amino acids. Different substitution rates reflect different evolutionary models, which can be shaped by both evolutionary history and environmental factors. This study provides evidence that both history and environment contribute to model differences in protein evolution.
Article
Chemistry, Organic
Han Yang, Zhen Chen, Wenjing Guo, Zhenhua Gu
Summary: A palladium-catalyzed cross-coupling reaction between 3-iodoazetidines and nonheteroaryl boronic acids was reported in this study. The reaction was facilitated by the [1,1'-biphenyl]-2-yldicyclohexylphosphane ligand, leading to the formation of 2-aryl azetidines. Control experiments indicated that the reaction can proceed through either a palladiumhydride/dihydroazete complex or free dihydroazete intermediate followed by hydropalladation.
Article
Multidisciplinary Sciences
Benjamin Klemm, Reece W. Lewis, Irene Piergentili, Rienk Eelkema
Summary: The authors developed a new chemical reaction network (CRN) that allows for control over the deactivation kinetics of artificial materials, enabling them to autonomously respond to their environment. By reversible formation of positive charges and using nucleophilic signals, the deactivation process is controlled. This concept not only offers new opportunities in molecular cargo delivery, but also paves the way for next-generation interactive materials.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Christoffer Norn, Ingemar Andre, Douglas L. Theobald
Summary: Evolutionary pressures and thermodynamic stability constraints play key roles in shaping the global amino acid substitution patterns observed in proteins, as evidenced by a new hybrid biophysical and evolutionary model. This model accurately recapitulates the complex yet universal patterns seen in common amino acid substitution matrices, suggesting that selection for thermodynamically stable proteins and nucleotide mutation bias filtered by genetic code structure are primary drivers behind these patterns.
Article
Ecology
Ulrike Hanz, Philip Riekenberg, Anna de Kluijver, Marcel van der Meer, Jack J. Middelburg, Jasper M. de Goeij, Martijn C. Bart, Erik Wurz, Ana Colaco, Gerard C. A. Duineveld, Gert-Jan Reichart, Hans-Tore Rapp, Furu Mienis
Summary: This study reveals how deep-sea sponge grounds survive in a food-limited environment through stable isotope analysis. Sponge with high microbial abundance utilize dissolved resources and efficient recycling pathways to sustain themselves and other organisms. Additionally, sponges provide organic material to support the otherwise food-limited associated fauna, contributing to the thriving deep-sea ecosystems.
FUNCTIONAL ECOLOGY
(2022)
Article
Geriatrics & Gerontology
George F. F. Pavis, Doaa R. R. Abdelrahman, Andrew J. J. Murton, Benjamin T. T. Wall, Francis B. B. Stephens, Marlou L. L. Dirks
Summary: The decline in muscle protein synthesis rates during short-term disuse does not fully account for muscle atrophy, and 2 days of unilateral knee immobilization does not affect muscle protein breakdown rates. Instead, the muscle negative protein balance associated with brief periods of disuse is primarily driven by reduced basal muscle protein synthesis rates and anabolic resistance to amino acid administration.
JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE
(2023)
Article
Environmental Sciences
Abraham Guerrero, Alexei F. Licea, M. L. Lizarraga-Partida
Summary: The community structure of bacterial populations in selected water masses and sediment samples from the Southern Gulf of Mexico was studied using 16S rRNA sequencing. The results revealed significant differences in bacterial community composition between water masses and sediment samples.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Mikhail Makarov, Jingwei Meng, Vyacheslav Tretyachenko, Pavel Srb, Anna Brezinova, Valerio Guido Giacobelli, Lucie Bednarova, Jiri Vondrasek, A. Keith Dunker, Klara Hlouchova
Summary: The study demonstrates that substitute aromatic residues do not significantly alter the secondary structure of proteins. Although the ATPase activity of the variants decreases by 150-300 times, they still retain phosphotransferase activity, with only His-containing variant being able to perform the reaction effectively.
Article
Microbiology
Keith Dufault-Thompson, Chang Nie, Huahua Jian, Fengping Wang, Ying Zhang
Summary: Microbial acclimation to temperature conditions can lead to changes in cell composition and metabolic efficiency. This study used genome-scale models to simulate the metabolic responses of a deep-sea psychrophilic bacterium under different temperatures. The models predicted differences in metabolic efficiency and rearrangement of metabolic pathways, which were validated through comparisons to transcriptomes. This study highlights the utility of modeling approaches in studying the temperature-driven metabolic responses of extremophilic organisms.
Article
Sport Sciences
Sidney Abou Sawan, Nathan Hodson, Julia M. Malowany, Daniel W. D. West, Cassidy Tinline-Goodfellow, Matthew S. Brook, Kenneth Smith, Philip J. Atherton, Dinesh Kumbhare, Daniel R. Moore
Summary: Resistance training increases muscle strength, thickness, and fiber cross-sectional area. MyoPS increases to a greater extent in males and is associated with muscle hypertrophy, potentially due to altered mTOR localization.
MEDICINE & SCIENCE IN SPORTS & EXERCISE
(2022)
Article
Biochemistry & Molecular Biology
Elias Primetis, Spyridon Chavlis, Pavlos Pavlidis
Summary: In this study, amino acid interactions and substitutions were investigated, revealing that substitutions are associated with the spatial neighborhoods of amino acid residuals, providing insights into the amino acid substitution process.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Sebastian Dengler, Pradeep K. Mandal, Lars Allmendinger, Celine Douat, Ivan Huc
Summary: Incorporating an aromatic foldamer segment into a macrocyclic peptide can influence its conformation and properties. The study reveals that the foldamer helical folding tends to prevail and stretch peptides in a solvent-dependent manner, while peptides also reciprocally affect foldamer helix handedness bias and stabilization. The hybrid macrocycles exhibit resistance towards proteolytic degradation.
Article
Biochemical Research Methods
Yaniv Shlosberg, Yair Farber, Salah Hasson, Valery Bulatov, Israel Schechter
Summary: Rapid identification of pathogenic bacteria is crucial for patient diagnosis in hospitals and environmental monitoring. A new method using synchronous fluorescence has been developed to quantify the concentrations of three amino acids and differentiate six pathogenic bacterial species, showing potential for broad applicability in rapid cell identification.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Andrea Baucon, Annalisa Ferretti, Chiara Fioroni, Luca Pandolfi, Enrico Serpagli, Armando Piccinini, Carlos Neto de Carvalho, Mario Cachao, Thomas Linley, Fernando Muniz, Zain Belaustegui, Alan Jamieson, Girolamo Lo Russo, Filippo Guerrini, Sara Ferrando, Imants Priede
Summary: This study reveals that fish have been inhabiting the deep seafloor since the Early Cretaceous, using various techniques to feed on prey. These findings shed light on the evolutionary history of deep-seafloor fishes and the availability of new food sources in the deep sea.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Agricultural Engineering
Rebecca Serna-Garcia, Panagiotis Tsapekos, Laura Treu, Alberto Bouzas, Aurora Seco, Stefano Campanaro, Irini Angelidaki
Summary: Three inhibitors, including sodium ionophore III (ETH2120), carbon monoxide (CO), and sodium 2bromoethanesulfonate (BES), were assessed for their impact on CO2 biomethanation in microorganisms from Archaea and Bacteria domains. The study demonstrates that ETH2120 and CO can promote methane production while BES does not, indicating the inactivation of archaea. Methylotrophic methanogenesis from methylamines was the main pathway for methane production, and a slight decrease in acetate production with an increase in CH4 production was observed with the addition of 20 kPa of CO. It should be noted that all compounds had effects on the microbial community composition, although the specific effects on CO2 biomethanation were challenging to observe due to the complexity of the environmental samples used as inoculum.
BIORESOURCE TECHNOLOGY
(2023)
Article
Agricultural Engineering
Silvia Greses, Nicola De Bernardini, Laura Treu, Stefano Campanaro, Cristina Gonzalez-Fernandez
Summary: This study investigated the effect of slight pH variations on the microbial dynamics and corresponding functions in anaerobic fermentation of food waste. It was found that a pH of 6.5 promoted the production of acetate, butyrate, and ethanol, while a slight decrease to 6.1 resulted in caproate and H2 production.
BIORESOURCE TECHNOLOGY
(2023)
Article
Agricultural Engineering
Rosemary A. Cripwell, Rebecca My, Laura Treu, Stefano Campanaro, Lorenzo Favaro, Willem H. van Zyl, Marinda Viljoen-Bloom
Summary: This paper addresses the challenges of consolidated bioprocessing for starch to ethanol conversion by expressing additional genes in a robust yeast strain and using low-cost substrates, which leads to improved ethanol productivity and fermentation efficiency.
BIORESOURCE TECHNOLOGY
(2023)
Article
Engineering, Environmental
Mengyuan Ji, Ginevra Giangeri, Muhammad Usman, Chao Liu, Matteo Bosaro, Filippo Sessa, Paolo Canu, Laura Treu, Stefano Campanaro
Summary: This study explored a hybrid strategy using native microorganisms and magnetic biochar (MBC) to degrade plasticizers. The MBC treatment led to the degradation of diethyl phthalate (DP) and the production of various organic products. The study provides evidence of the potential cooperation between native biodegraders and MBC in removing phthalate plasticizers from soil and surface water.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Engineering, Environmental
Mengyuan Ji, Lurui Xiao, Muhammad Usman, Chao Liu, Wenjing Sang, Laura Treu, Stefano Campanaro, Gang Luo, Yalei Zhang
Summary: Microplastics are prevalent in farmland and pose a threat to soil ecology. This study investigated how different microplastics affect methane emission in paddy soil. Results showed that polyvinyl chloride microplastics at 1% concentration had the highest increase in methane production compared to polyethylene and polypropylene microplastics. Microplastics contributed to the accumulation of humus in the soil solution and enriched specific microbial taxa. The findings emphasize the threat of microplastics to greenhouse gas emissions in agricultural fields and suggest potential strategies to reduce methane emissions.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Engineering, Environmental
Ginevra Giangeri, Panagiotis Tsapekos, Maria Gaspari, Parisa Ghofrani-Isfahani, Marie Karen Tracy Hong Lin, Laura Treu, Panagiotis Kougias, Stefano Campanaro, Irini Angelidaki
Summary: The presence of sulfate in anaerobic digestion systems reduces methane yield, as sulfate-reducing bacteria compete with methanogens for substrates. This study demonstrates that the addition of magnetite can enhance methane production and reduce hydrogen sulfide levels. Furthermore, genomic analysis reveals both competitive and cooperative interactions between methanogens and sulfate-reducing bacteria, depending on the specific methanogenic group.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Green & Sustainable Science & Technology
Maria Gaspari, Laura Treu, Victor Borin Centurion, Thomas A. . Kotsopoulos, Stefano Campanaro, Panagiotis G. Kougias
Summary: The present study used genome-centric metagenomics to discover a microorganism called Nigerium sp. and revealed its functionalities within the biogas reactor. Additionally, Candidatus Hydrogenedentes sp. demonstrated the ability for β-oxidation. Transcriptional analysis showed that up-regulated genes were dominantly involved in lipid metabolism, as well as activation of genes encoding cell motility proteins.
JOURNAL OF CLEANER PRODUCTION
(2023)
Article
Engineering, Environmental
Mengyuan Ji, Ginevra Giangeri, Fengbo Yu, Filippo Sessa, Chao Liu, Wenjing Sang, Paolo Canu, Fangbai Li, Laura Treu, Stefano Campanaro
Summary: The study found that magnetic biochar can enhance the degradation of microplastics through advanced oxidation processes, but the synergistic effects of microbes in this process are still uncertain. A long-term incubation experiment was conducted on paddy soil contaminated with polyethylene and polyvinyl chloride microplastics, followed by bioremediation with biochar or magnetic biochar. The results showed that the use of magnetic biochar significantly increased the total organic matter content in samples containing polyvinyl chloride or polyethylene, and resulted in the accumulation of UVA humic and protein/phenol-like substances. Genomic investigation revealed changes in the relative abundance of key genes involved in fatty acids degradation and dehalogenation in different treatments, with a Nocardioides species identified as cooperating with magnetic biochar in microplastic degradation.
JOURNAL OF HAZARDOUS MATERIALS
(2023)