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The index of ideality of correlation improves the predictive potential of models of the antioxidant activity of tripeptides from frog skin (Litoria rubella).

Comput Biol Med 2021 Apr 3;133:104370. Epub 2021 Apr 3.

Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milano, Italy.

It is usually held that good-quality models for the biological activity of peptides must take into account their 3D architecture and descriptors of quantum mechanics. However, the present study shows that it is possible to build up models without these complex calculations. The structure of tripeptides represented by sequences of one-symbol abbreviations of the corresponding amino acids serves to build up quantitative structure-activity relationships for the antioxidant activity of tripeptides from frog skin. Read More

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Synthesis of six-membered carbocyclic ring α,α-disubstituted amino acids and arginine-rich peptides to investigate the effect of ring size on the properties of the peptide.

Bioorg Med Chem 2021 Mar 19;38:116111. Epub 2021 Mar 19.

Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.

Cell-penetrating peptides (CPPs) have been attracting attention as tools for intracellular delivery of membrane-impermeant functional molecules. Among the variety of CPPs that have been developed, many are composed of both natural and unnatural amino acids. We previously synthesized α,α-disubstituted α-amino acids (dAAs) containing a five-membered carbocyclic ring in its side chain and revealed the utility of dAAs for the development of novel CPPs. Read More

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Synthesis and biological evaluation of 2-(4-alkoxy-3-cyano)phenylpyrimidine derivatives with 4-amino or 4-hydroxy as a pharmacophore element binding with xanthine oxidase active site.

Bioorg Med Chem 2021 Apr 2;38:116117. Epub 2021 Apr 2.

Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang 110016, China. Electronic address:

Xanthine oxidase is the rate-limiting enzyme critical for the synthesis of uric acid, and therefore xanthine oxidase inhibitors are considered as one of the promising therapies for hyperuricemia and gout. In our previous study, series of 2-(4-alkoxy-3-cyano)phenyl-6-oxo-1,6-dihydropyrimidine-5-carboxylic acids and 2-(4-alkoxy-3-cyano)phenyl-6-imino-1,6-dihydropyrimidine-5-carboxylic acids were synthesized that presented excellent in vitro xanthine oxidase inhibitory potency. Interestingly, molecular docking studies revealed that the interaction behavior of these compounds with xanthine oxidase was changed after the conversion from a hydroxy group to amine group. Read More

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The endemic Chamaecytisus albidus is nodulated by symbiovar genistearum of Bradyrhizobium in the Moroccan Maamora Forest.

Syst Appl Microbiol 2021 Mar 26;44(3):126197. Epub 2021 Mar 26.

Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Faculté des Sciences, Université Mohammed V de Rabat, 4, Avenue Ibn Battouta, Rabat, Morocco. Electronic address:

Out of 54 isolates from root nodules of the Moroccan-endemic Chamaecytisus albidus plants growing in soils from the Maamora cork oak forest, 44 isolates formed nodules when used to infect their original host plant. A phenotypic analysis showed the metabolic diversity of the strains that used different carbohydrates and amino acids as sole carbon and nitrogen sources. The isolates grew on media with pH values ranging from 6 to 8. Read More

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Comparative study on different organic acids for promoting Solanum nigrum L. hyperaccumulation of Cd and Pb from the contaminated soil.

Chemosphere 2021 Mar 31;278:130446. Epub 2021 Mar 31.

Key Lab of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, PR China. Electronic address:

Organic acids-assisted phytoremediation is a promising strategy to remove metal pollutants from the soil. However, few reports have focused on the mechanisms of organic acids promoting the uptake of heavy metals by hyperaccumulators. In this study, 5 types of organic acids, namely polybasic carboxylic acids, acidic amino acids, acidic plant growth regulators, phosphoric and gluconic acids, were comprehensively investigated the effects on the solubility of Cd and Pb in the soil along with their uptake by Cd hyperaccumulator Solanum nigrum L. Read More

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Design, synthesis, biological evaluation and molecular dynamics of LAR inhibitors.

Comput Biol Chem 2021 Mar 30;92:107481. Epub 2021 Mar 30.

Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China. Electronic address:

In this study, firstly, the pharmacophore model was established based on LAR inhibitors. ZINC database and drug-like database were screened by Hypo-1-LAR model, and the embryonic compound ZINC71414996 was obtained. Based on this compound, we designed 9 compounds. Read More

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Composition and profiles of volatile organic compounds during waste decomposition by the anaerobic bacteria purified from landfill.

Waste Manag 2021 Apr 7;126:466-475. Epub 2021 Apr 7.

College of Environmental Science and Engineering, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing 100871, PR China. Electronic address:

Volatile organic compounds (VOCs) become concerned pollutants in landfill gases, and their composition and concentration varied significantly during waste decomposition. Many environmental factors are known to affect VOC emissions, while the effect of indigenous bacteria in wastes on VOC production remains elusive. In this study, a simplified anaerobic degradation experiment, with the single substrate and the purified bacteria from a landfill, was set up to measure the degradation process and the dynamic changes of VOCs. Read More

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Determination of amino acids that favour the α region using Ramachandran propensity plots. Implications for α-sheet as the possible amyloid intermediate.

J Struct Biol 2021 Apr 7:107738. Epub 2021 Apr 7.

College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK. Electronic address:

In amyloid diseases an insoluble amyloid fibril forms via a soluble oligomeric intermediate. It is this intermediate that mediates toxicity and it has been suggested, somewhat controversially, that it has the α-sheet structure. Nests and α-strands are similar peptide motifs in that alternate residues lie in the α and γ regions of the Ramachandran plot for nests, or α and α regions for α-strands. Read More

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Crystal structure of BRP39, a signaling glycoprotein expressed during mammary gland apoptosis at 2.6 Å resolution.

J Struct Biol 2021 Apr 7:107737. Epub 2021 Apr 7.

Department of Chemistry, University of California Davis, Davis, California, 95616, United States; Department of Molecular and Cellular Biology, University of California Davis, Davis, California, 95616, United States.

Breast regression protein 39 (BRP39) is a 39 kDa protein that is a member of chitolectin class of glycosyl hydrolase family 18 (GH18). High expression levels of BRP39 have been detected in breast carcinoma. It helps in proliferation of cells during the progression of this disease and may act as a signaling factor. Read More

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Gene duplication and subsequent functional diversification of maltase in fig wasp (Chalcidoidea, Hymenoptera).

Int J Biol Macromol 2021 Apr 7. Epub 2021 Apr 7.

Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China. Electronic address:

Maltase can catalyze the hydrolysis of α-1,4-glucosidic linkages and release α-d-glucoses that are used as a source of energy by insects. Maltase has been extensively studied in Lepidoptera and Diptera, while the characterization and evolutionary history of maltase are largely unknown in Hymenoptera. Here, we undertook a bioinformatics study and identified 105 maltase genes in 12 fig wasp species. Read More

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Preparation of the peroxisome proliferator-activated receptor α polyclonal antibody: Its application in fatty liver hemorrhagic syndrome.

Int J Biol Macromol 2021 Apr 7. Epub 2021 Apr 7.

Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China. Electronic address:

Peroxisome proliferator-activated receptor α (PPARα) play a key role in the regulation of metabolic homeostasis, inflammation, cellular growth, and differentiation. To further explore the potential role of PPARα in the energy homeostasis of fatty liver hemorrhagic syndrome (FLHS), we reported the prokaryotic expression and purification of chicken PPARα subunit protein, and successfully prepared a polyclonal antibody against PPARα recombinant protein. The 987 bp PPARα subunit genes were cloned into the pEASY-T3 clone vector. Read More

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The therapeutic potentials of apelin in obesity-associated diseases.

Mol Cell Endocrinol 2021 Apr 7:111278. Epub 2021 Apr 7.

RESTORE UMR1301 INSERM, 5070 CNRS, Université Paul Sabatier.

Apelin, a peptide with several active isoforms ranging from 36 to 12 amino acids and its receptor APJ, a G-protein-coupled receptor, are widely distributed. However, apelin has emerged as an adipokine more than fifteen years ago, integrating the field of inter-organs interactions. The apelin/APJ system plays important roles in several physiological functions both in rodent and humans such as fluid homeostasis, cardiovascular physiology, angiogenesis, energy metabolism. Read More

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Genome-wide association study of serum metabolites in the African American Study of Kidney Disease and Hypertension.

Kidney Int 2021 Apr 7. Epub 2021 Apr 7.

Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore MD, USA; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore MD, USA; Division of Nephrology, Department of Medicine, Johns Hopkins University, Baltimore MD, USA.

The genome-wide association study (GWAS) is a powerful means to study genetic determinants of disease traits and generate insights into disease pathophysiology. To date, few GWAS of circulating metabolite levels have been performed in African Americans with chronic kidney disease. Hypothesizing that novel genetic-metabolite associations may be identified in a unique population of African Americans with a lower glomerular filtration rate (GFR), we conducted a GWAS of 652 serum metabolites in 619 participants (mean measured glomerular filtration rate 45 mL/min/1. Read More

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Characterization of Prototheca CYP51/ERG11 as a possible target for therapeutic drugs.

Med Mycol 2021 Apr 10. Epub 2021 Apr 10.

Department of Microbiology, Dokkyo Medical University School of Medicine, Tochigi 321-0293, Japan.

Prototheca spp. are achlorophyllous algae, ubiquitous in nature. An increasing number of human and animal cases of Prototheca infection (protothecosis) are reported, and antifungal azoles, which inhibit sterol 14α-demethylase (CYP51/ERG11) involved in ergosterol biosynthesis, have empirically been used for the treatment of protothecosis. Read More

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An ultra-high affinity protein-protein interface displaying sequence-robustness.

Protein Sci 2021 Apr 10. Epub 2021 Apr 10.

Biochemistry and Structural Biology, Lund University, Lund, Sweden.

Protein-protein interactions are crucial in biology and play roles in for example, the immune system, signalling pathways, and enzyme regulation. Ultra-high affinity interactions (K , <0.1 nM) occur in these systems, however, structures and energetics behind stability of ultra-high affinity protein-protein complexes are not well understood. Read More

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Coronavirus genomic nsp14-ExoN, structure, role, mechanism, and potential application as a drug target.

Authors:
Mohammed Tahir

J Med Virol 2021 Apr 10. Epub 2021 Apr 10.

Department of Biology, University of Sulaimani, Iraq, Kurdistan region, Sulaimanyah city.

The recent coronavirus disease 2019 (COVID-19), causing a global pandemic with devastating effects on healthcare and social-economic systems, has no special antiviral therapies available for human coronaviruses (CoVs). The severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) possesses a non-structural protein (nsp14), with amino terminal domain coding for a proofreading exoribonuclease (ExoN) that is required for high-fidelity replication. The ability of CoVs during genome replication and transcription to proofread and exclude mismatched nucleotides has long hindered the development of anti-CoV drugs. Read More

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Extraction and detection of guanosine 5'-diphosphate-3'-diphosphate in amino acid starvation cells of Clavibacter michiganensis.

Braz J Microbiol 2021 Apr 10. Epub 2021 Apr 10.

Beijing Key Laboratory of Seed Disease Testing and Control, Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China.

Guanosine 5'-diphosphate-3'-diphosphate (ppGpp) is a small molecule nucleotide alarmone that can accumulate under the amino acid starvation state and trigger the stringent response. This study reported the extraction of ppGpp from the Gram-positive bacteria Clavibacter michiganensis through methods using formic acid, lysozyme, or methanol. Following extraction, ppGpp was detected through ultra-high-performance liquid chromatography (UHPLC) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Read More

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Thiazole-amino acids: influence of thiazole ring on conformational properties of amino acid residues.

Amino Acids 2021 Apr 10. Epub 2021 Apr 10.

Faculty of Chemistry, University of Opole, 45-052, Opole, Poland.

Post-translational modified thiazole-amino acid (Xaa-Tzl) residues have been found in macrocyclic peptides (e.g., thiopeptides and cyanobactins), which mostly inhibit protein synthesis in Gram + bacteria. Read More

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Computational characterizations of GDP-mannose 4,6-dehydratase (NoeL) Rhizobial proteins.

Curr Genet 2021 Apr 10. Epub 2021 Apr 10.

Department of Sciences, Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand.

A growing body of evidence suggests that Nod Factors molecules are the critical structural components in nitrogen fixation. These molecules have been implicated in plant-microbe signaling. Many enzymes involved in Nod factors biosynthesis; however, the enzymes that decorate (modify) nod factor main structure play a vital role. Read More

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Six-state Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses.

Syst Biol 2021 Apr 10. Epub 2021 Apr 10.

Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA.

Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of 6-state recoding approaches by comparing the performance of analyses on recoded and non-recoded datasets that have been simulated under gradients of compositional heterogeneity or saturation. Read More

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Inhibitors of DNA topoisomerases I and II applied to Candida dubliniensis reduce growth, viability, the generation of petite mutants and toxicity, while acting synergistically with fluconazole.

FEMS Yeast Res 2021 Apr 10. Epub 2021 Apr 10.

Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala. Col. Sto. Tomás, 11340 México City, México.

The increasing resistance of Candida species to azoles emphasizes the urgent need for new antifungal agents with novel mechanisms of action. The aim of this study was to examine the effect of three DNA topoisomerase inhibitors of plant origin (camptothecin, etoposide and curcumin) on the growth of Candida dubliniensis. The phylogenetic analysis showed a close relationship between the topoisomerase enzymes of C. Read More

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Iron chelates hitch a ride on PAT1.

Authors:
James F Collins

J Biol Chem 2021 Mar 20;296:100418. Epub 2021 Mar 20.

Food Science & Human Nutrition Department, University of Florida, Gainesville, Florida, USA. Electronic address:

The nicotianamine-iron chelate [NA-Fe], which is found in many plant-based foods, has been recently described as a new form of bioavailable iron in mice and chickens. How NA-Fe is assimilated from the diet, however, remains unclear. The current investigation by Murata et al. Read More

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Trans-editing by aminoacyl-tRNA synthetase-like editing domains.

Enzymes 2020 8;48:69-115. Epub 2020 Sep 8.

Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States. Electronic address:

Aminoacyl-tRNA synthetases (aaRS) are ubiquitous enzymes responsible for aminoacyl-tRNA (aa-tRNA) synthesis. Correctly formed aa-tRNAs are necessary for proper decoding of mRNA and accurate protein synthesis. tRNAs possess specific nucleobases that promote selective recognition by cognate aaRSs. Read More

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September 2020

Putting amino acids onto tRNAs: The aminoacyl-tRNA synthetases as catalysts.

Enzymes 2020 8;48:39-68. Epub 2020 Sep 8.

Department of Chemistry, Wayne State University, Detroit, MI, United States. Electronic address:

In this chapter we consider the catalytic approaches used by aminoacyl-tRNA synthetase (AARS) enzymes to synthesize aminoacyl-tRNA from cognate amino acid and tRNA. This ligase reaction proceeds through an activated aminoacyl-adenylate (aa-AMP). Common themes among AARSs include use of induced fit to drive catalysis and transition state stabilization by class-conserved sequence and structure motifs. Read More

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September 2020

Engineering aminoacyl-tRNA synthetases for use in synthetic biology.

Enzymes 2020 8;48:351-395. Epub 2020 Sep 8.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States. Electronic address:

Within the broad field of synthetic biology, genetic code expansion (GCE) techniques enable creation of proteins with an expanded set of amino acids. This may be invaluable for applications in therapeutics, bioremediation, and biocatalysis. Central to GCE are aminoacyl-tRNA synthetases (aaRSs) as they link a non-canonical amino acid (ncAA) to their cognate tRNA, allowing ncAA incorporation into proteins on the ribosome. Read More

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September 2020

Aminoacyl-tRNA synthetases as drug targets.

Enzymes 2020 14;48:321-350. Epub 2020 Oct 14.

Institute for Advanced Biosciences (IAB), Structural Biology of Novel Drug Targets in Human Diseases, INSERM U1209, CNRS UMR 5309, University Grenoble Alpes, Grenoble, France. Electronic address:

Aminoacyl-tRNA synthetases (AARSs) have been considered very attractive drug-targets for decades. This interest probably emerged with the identification of differences in AARSs between prokaryotic and eukaryotic species, which provided a rationale for the development of antimicrobials targeting bacterial AARSs with minimal effect on the homologous human AARSs. Today we know that AARSs are not only attractive, but also valid drug targets as they are housekeeping proteins that: (i) play a fundamental role in protein translation by charging the corresponding amino acid to its cognate tRNA and preventing mistranslation mistakes [1], a critical process during fast growing conditions of microbes; and (ii) present significant differences between microbes and humans that can be used for drug development [2]. Read More

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October 2020

Aminoacyl-tRNA synthetases in cell signaling.

Authors:
Peng Yao Paul L Fox

Enzymes 2020 12;48:243-275. Epub 2020 Jun 12.

Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States. Electronic address:

Aminoacyl-tRNA synthetases (ARSs) are a family of essential "housekeeping" enzymes ubiquitous in the three major domains of life. ARSs uniquely connect the essential minimal units of both major oligomer classes-the 3-nucleotide codons of oligonucleotides and the amino acids of proteins. They catalyze the esterification of amino acids to the 3'-end of cognate transfer RNAs (tRNAs) bearing the correct anticodon triplet to ensure accurate transfer of information from mRNA to protein according to the genetic code. Read More

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Non-canonical functions of human cytoplasmic tyrosyl-, tryptophanyl- and other aminoacyl-tRNA synthetases.

Enzymes 2020 12;48:207-242. Epub 2020 Jun 12.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Aminoacyl-tRNA synthetases catalyze the aminoacylation of their cognate tRNAs. Here we review the accumulated knowledge of non-canonical functions of human cytoplasmic aminoacyl-tRNA synthetases, especially tyrosyl- (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS). Human TyrRS and TrpRS have an extra domain. Read More

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Noncanonical inputs and outputs of tRNA aminoacylation.

Enzymes 2020 12;48:117-147. Epub 2020 Jun 12.

Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Strasbourg, France. Electronic address:

The aminoacylation reaction is one of most extensively studied cellular processes. The so-called "canonical" reaction is carried out by direct charging of an amino acid (aa) onto its corresponding transfer RNA (tRNA) by the cognate aminoacyl-tRNA synthetase (aaRS), and the canonical usage of the aminoacylated tRNA (aa-tRNA) is to translate a messenger RNA codon in a translating ribosome. However, four out of the 22 genetically-encoded aa are made "noncanonically" through a two-step or indirect route that usually compensate for a missing aaRS. Read More

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The evolution of aminoacyl-tRNA synthetases: From dawn to LUCA.

Enzymes 2020 8;48:11-37. Epub 2020 Sep 8.

Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain; Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia, Spain. Electronic address:

The origin of all extant life on earth is intimately linked to the establishment of the principal components of the Genetic Code. Aminoacyl-tRNA synthetases (aaRS), by virtue of their universality and essential functions in protein synthesis, count among the biomolecules that evolved to a level of complexity comparable to their extant state before the advent of the Last Universal Common Ancestor (LUCA). Despite the enormous technical difficulties in analyzing such an ancient process, proposals have been put forward to describe the emergence and evolution of the two aaRS families. Read More

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September 2020