179,545 results match your criteria acid residues


Effect of rare coding variants of charged amino acid residues on the function of human organic anion transporting polypeptide 1B3 (SLCO1B3).

Biochem Biophys Res Commun 2021 Apr 11;557:1-7. Epub 2021 Apr 11.

College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou Industrial Park, Suzhou, Jiangsu, 215123, China. Electronic address:

Human organic anion transporting polypeptide 1B3 (OATP1B3, gene symbol SLCO1B3) is a liver-specific uptake transporter. Its function was reported to be largely affected by some positively charged amino acid residues. However, so far the effect of naturally occurring genetic variants of charged residues on OATP1B3's function has not been explored yet. Read More

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Two strains of a novel begomovirus encoding Rep proteins with identical β1 strands but different β5 strands are not compatible in replication.

Arch Virol 2021 Apr 14. Epub 2021 Apr 14.

División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C. Camino a la Presa de San José 2055, Lomas 4a Sección, C.P. 78216, San Luis Potosí, S.L.P., Mexico.

Geminiviruses have genomes composed of single-stranded DNA molecules and encode a rolling-circle replication (RCR) initiation protein ("Rep"), which has multiple functions. Rep binds to specific repeated DNA motifs ("iterons"), which are major determinants of virus-specific replication. The particular amino acid (aa) residues that determine the preference of a geminivirus Rep for specific iterons (i. Read More

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An arginine residue in the outer segment of hASIC1a TM1 affects both proton affinity and channel desensitization.

J Gen Physiol 2021 May;153(5)

Department of Basic Sciences, Tsinghua University School of Medicine, Beijing, China.

Acid-sensing ion channels (ASICs) respond to changes in pH in the central and peripheral nervous systems and participate in synaptic plasticity and pain perception. Understanding the proton-mediated gating mechanism remains elusive despite the of their structures in various conformational states. We report here that R64, an arginine located in the outer segment of the first transmembrane domain of all three isoforms of mammalian ASICs, markedly impacts the apparent proton affinity of activation and the degree of desensitization from the open and preopen states. Read More

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Colloidal gold-based lateral flow immunoassay with inline cleanup for rapid on-site screening of carbendazim in functional foods.

Anal Bioanal Chem 2021 Apr 13. Epub 2021 Apr 13.

Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.

In this study, for the first time, we propose a sensitive colloidal gold-based lateral flow immunoassay (LFIA) that can be used to detect carbendazim residues in functional foods. The adoption of inline cleanup LFIA strips effectively improved background interference to reduce misjudgment of results. First, the hapten 2-(methylamino)-1H-benzo[d]imidazole-5-carboxylic acid was used to establish the carbendazim immunoassay method. Read More

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Characterization of amino acid residues of T-cell receptors interacting with HLA-A*02-restricted antigen peptides.

Ann Transl Med 2021 Mar;9(6):495

Department of Proctology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China.

Background: The present study aimed to explore residues' properties interacting with HLA-A*02-restricted peptides on T-cell receptors (TCRs) and their effects on bond types of interaction and binding free energy.

Methods: We searched the crystal structures of HLA-A*02-restricted peptide-TCR complexes from the Protein Data Bank (PDB) database and subsequently collected relevant parameters. We then employed Schrodinger to analyze the bond types of interaction and Gromacs 2019 to evaluate the TCR-antigen peptide complex's molecular dynamics simulation. Read More

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Diversity of 3' variable region of cagA gene in Helicobacter pylori strains isolated from Chinese population.

Gut Pathog 2021 Apr 13;13(1):23. Epub 2021 Apr 13.

State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China.

Background: The cytotoxin-associated gene A (cagA) is one of the most important virulence factors of Helicobacter pylori (H. pylori). There is a highly polymorphic Glu-Pro-Ile-Tyr-Ala (EPIYA) repeat region in the C-terminal of CagA protein. Read More

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Monomeric a-synuclein (aS) inhibits amyloidogenesis of human prion protein (hPrP) by forming a stable aS-hPrP hetero-dimer.

Prion 2021 Dec;15(1):37-43

United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Tokai National Higher Education and Research System, Gifu, Japan.

Intermolecular interaction between hPrP and αS was investigated using high-speed atomic force microscopy, dynamic light scattering, and nuclear magnetic resonance. We found that hPrP spontaneously gathered and naturally formed oligomers. Upon addition of monomer αS with a disordered conformation, poly-dispersive property of hPrP was lost, and hetero-dimer formation started quite coherently, and further oligomerization was not observed. Read More

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December 2021

Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures.

Authors:
Jingyi Cao Yi Xue

Nucleic Acids Res 2021 Apr 13. Epub 2021 Apr 13.

School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China.

RNA structures play a fundamental role in nearly every aspect of cellular physiology and pathology. Gaining insights into the functions of RNA molecules requires accurate predictions of RNA secondary structures. However, the existing thermodynamic folding models remain less accurate than desired, even when chemical probing data, such as selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) reactivities, are used as restraints. Read More

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An anti-HER2 nanobody binds to its antigen HER2 via two independent paratopes.

Int J Biol Macromol 2021 Apr 10. Epub 2021 Apr 10.

Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, 5000 Rožna Dolina, Nova Gorica, Slovenia. Electronic address:

High-resolution structural data of complexes between antibodies and membrane receptors still represent a demanding task. In this study, we used complementary sets of experimental data to obtain a structural model of the complex formed by the human epidermal growth factor receptor 2 (HER2) and its specific nanobody A10. First we identified by NMR the residues that bind or rearrange as a consequence of the complex formation. Read More

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Origin and evolution of nonulosonic acid synthases and their relationship with bacterial pathogenicity revealed by a large-scale phylogenetic analysis.

Microb Genom 2021 Apr;7(4)

Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz-PR, Algacyr Munhoz Mader street, 3775, Curitiba, Paraná, Brazil.

Nonulosonic acids (NulOs) are a group of nine-carbon monosaccharides with different functions in nature. -acetylneuraminic acid (Neu5Ac) is the most common NulO. It covers the membrane surface of all human cells and is a central molecule in the process of self-recognition via SIGLECS receptors. Read More

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Acyl Donor Stringency and Dehydroaminoacyl Intermediates in β-Lactam Formation by a Non-ribosomal Peptide Synthetase.

ACS Chem Biol 2021 Apr 13. Epub 2021 Apr 13.

Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States.

Condensation (C) domains in non-ribosomal peptide synthetases catalyze peptide elongation steps whereby activated amino acid or peptidyl acyl donors are coupled with specific amino acid acceptors. In the biosynthesis of the β-lactam antibiotic nocardicin A, an unusual C domain converts a seryl tetrapeptide into its pentapeptide product containing an integrated β-lactam ring. While indirect evidence for the intermediacy of a dehydroalanyl species has been reported, here we describe observation of the elusive enzyme-bound dehydroamino acyl intermediate generated from the corresponding -threonyl tetrapeptide and partitioned into pentapeptide products containing either a dehydrobutyrine residue or an embedded β-lactam. Read More

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Novel Wx alleles generated by base editing for improvement of rice grain quality.

J Integr Plant Biol 2021 Apr 13. Epub 2021 Apr 13.

School of Life Sciences, Shandong Normal University, Ji'nan, 250014, China.

Amylose content (AC), which is regulated by the Waxy (Wx) gene, is a major indicator of eating and cooking quality in rice (Oryza sativa). Thus far, only a limited number of mutations in the N-terminal domain of Wx were found to have a major impact on the AC of rice grains and no mutations with such effects were reported for other regions of the Wx protein. Here, nucleotide substitutions in the middle region of Wx were generated by adenine and cytosine base editors. Read More

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Characterization of an L-α,β-diaminopropionic acid polymer with comb-like structure isolated from a poly(ε-L-lysine)-producing Streptomyces sp.

Appl Microbiol Biotechnol 2021 Apr 12. Epub 2021 Apr 12.

Department of Life Science and Biotechnology, Graduate School of Science and Engineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka, 564-8680, Japan.

Polymers of basic amino acids function as polycationic compounds under physiological conditions and exhibit intriguing biological properties, such as antimicrobial and antiviral activities, immunopotentiating ability, and DNA-binding activity. Poly(ε-L-lysine) (ε-PL) produced by some strains of Streptomyces spp. is a cationic homopolymer of L-lysine linking between ε-amino and α-carboxylic acid functional groups and has been used as a food preservative based on its biocompatibility and biodegradability. Read More

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Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.

Sci Rep 2021 Apr 12;11(1):7929. Epub 2021 Apr 12.

Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan.

The emergence of drug-resistant bacteria has become a major problem worldwide. Bacterial dipeptidyl peptidases 7 and 11 (DPP7s and DPP11s), belonging to the family-S46 peptidases, are important enzymes for bacterial growth and are not present in mammals. Therefore, specific inhibitors for these peptidases are promising as potential antibiotics. Read More

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GyrA Tower Domain Interacts with QnrB1 Loop B and Plays an Important Role in QnrB1 Protection from Quinolone Inhibition.

Antimicrob Agents Chemother 2021 Apr 12. Epub 2021 Apr 12.

Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA;

The Qnr pentapeptide repeat proteins interact with DNA gyrase and protect it from quinolone inhibition. The two external loops, particularly the larger loop B, of Qnr proteins are essential for quinolone protection of DNA gyrase. The specific QnrB1 interaction sites on DNA gyrase are not known. Read More

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A combined approach based on matrix solid-phase dispersion extraction assisted by titanium dioxide nanoparticles and liquid chromatography to determine polyphenols from grape residues.

J Chromatogr A 2021 Mar 31;1644:462128. Epub 2021 Mar 31.

Analytical Chemistry Department. Faculty of Chemistry. Universidad Complutense de Madrid. 28040-Madrid, Spain.

A simple and efficient low-cost matrix solid phase dispersion (MSPD) extraction assisted by TiO nanoparticles and diatomaceous earth has been developed for the extraction of phenolic compounds from grape and grape pomace wastes. Experimental conditions for MSPD extraction were optimized by a factorial design and a surface response methodology. The simultaneous identification and quantification of eight main natural polyphenols (caffeic, p-coumaric, dihydroxybenzoic and gallic acid, rutin, resveratrol, quercetin and catechin) was possible by combining MSPD and capillary liquid chromatography coupled to a diode array detection and a mass simple quadrupole analyzer (cLC-DAD-MS). Read More

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Design, synthesis, modelling studies and biological evaluation of 1,3,4-oxadiazole derivatives as potent anticancer agents targeting thymidine phosphorylase enzyme.

Bioorg Chem 2021 Mar 29;111:104873. Epub 2021 Mar 29.

Shobhaben Pratapbhai Patel School of Pharmacy Technology Management, SVKM's NMIMS, Mumbai, India. Electronic address:

A series of novel 1,3,4-oxadiazole derivatives with substituted phenyl ring were designed and synthesized with an objective of discovering newer anti-cancer agents targeting thymidine phosphorylase enzyme (TP). The 1,3,4-oxadiazole derivatives were synthesized by simple and convenient methods in the lab. Chemical structure of the all the synthesized compounds were characterized by IR, H NMR and mass spectral methods and evaluated for cytotoxicity by MTT method against two breast cancer cell lines (MCF-7 and MDA-MB-231). Read More

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Directed evolution of feruloyl esterase from Lactobacillus acidophilus and its application for ferulic acid production.

Bioresour Technol 2021 Mar 17;332:124967. Epub 2021 Mar 17.

Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China.

Producing ferulic acid (FA) from the natural substrate with feruloyl esterase is promising in industries, screening and engineering new enzymes with high efficiency to increase the FA yield is of great concern. Here, the feruloyl esterase of Lactobacillus acidophilus (FAELac) was heterologous expressed and the FAELac with different oligomerization states was separated. Interestingly, the activity of dimer was 37-fold higher than high-polymer. Read More

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Advances in Molecular Understanding of α-Helical Membrane-Active Peptides.

Acc Chem Res 2021 Apr 12. Epub 2021 Apr 12.

CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic.

ConspectusBiological membranes separate the interior of cells or cellular compartments from their outer environments. This barrier function of membranes can be disrupted by membrane-active peptides, some of which can spontaneously penetrate through the membranes or open leaky transmembrane pores. However, the origin of their activity/toxicity is not sufficiently understood for the development of more potent peptides. Read More

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Attenuation of Human Lysozyme Amyloid Fibrillation by ACE Inhibitor Captopril: A Combined Spectroscopy, Microscopy, Cytotoxicity, and Docking Study.

Biomacromolecules 2021 Apr 12. Epub 2021 Apr 12.

RI-B-NT Research Institute of Bioinformatics and Nanotechnology, Franziusallee 177, 24148 Kiel, Germany.

Misfolding proteins could form oligomers or amyloid fibers, which can cause a variety of amyloid-associated diseases. Thus, the inhibition of protein misfolding and fibrillation is a promising way to prevent and treat these diseases. Captopril (CAP) is an angiotensin-converting enzyme inhibitor (ACEI) that is widely used to treat diseases such as hypertension and heart failure. Read More

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Comparative analysis of C chemical shifts of β-sheet amyloid proteins and outer membrane proteins.

J Biomol NMR 2021 Apr 12. Epub 2021 Apr 12.

Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA.

Cross-β amyloid fibrils and membrane-bound β-barrels are two important classes of β-sheet proteins. To investigate whether there are systematic differences in the backbone and sidechain conformations of these two families of proteins, here we analyze the C chemical shifts of 17 amyloid proteins and 7 β-barrel membrane proteins whose high-resolution structures have been determined by NMR. These 24 proteins contain 373 β-sheet residues in amyloid fibrils and 521 β-sheet residues in β-barrel membrane proteins. Read More

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Optimal pH shift of the NADH oxidase from Lactobacillus rhamnosus with a single mutation.

Biotechnol Lett 2021 Apr 12. Epub 2021 Apr 12.

School of Pharmacy, Jiangsu University, Zhenjiang, 212013, People's Republic of China.

Objective: To improve the activity of a water-forming NADH oxidase from Lactobacillus rhamnosus under neutral or alkaline pH for coupling NAD-dependent dehydrogenases with an alkaline optimal pH.

Results: The water-forming NADH oxidase from Lactobacillus rhamnosus was engineered by replacing the aspartic acid or glutamic acid with arginine on the surface. The mutant D251R improved the activity with a 112%, 111%, and 244% relative activity to the wild-type at pH 6. Read More

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Substitution of histone H3 arginine 72 to alanine leads to deregulation of isoleucine biosynthesis in budding yeast Saccharomyces cerevisiae.

Biochem Cell Biol 2021 Apr 11. Epub 2021 Apr 11.

IISER Bhopal, 189785, Bhopal, India, 462066;

Histone residues play an essential role in the regulation of various biological processes. In the present study, we have utilized the H3/H4 histone mutant library to probe functional aspects of histone residues in amino acid biosynthesis. We found that histone residue H3R72 plays a crucial role in the regulation of isoleucine biosynthesis. Read More

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Isolated Pea Resistant Starch Substrates with Different Structural Features Modulate the Production of Short-Chain Fatty Acids and Metabolism of Microbiota in Anaerobic Fermentation In Vitro.

J Agric Food Chem 2021 Apr 12. Epub 2021 Apr 12.

College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi 710062, China.

Resistant starches (RSs) with different structural features were isolated from both native and pullulanase-debranched and acid-hydrolyzed pea starches. Their microscopic changes, short-chain fatty acids (SCFA) composition, microbiota communities, and structural characteristics of the corresponding fermenta residues by the end of 24 h of the in vitro fermentation period were investigated. The microbial fermentation clearly caused numerous cracks and erosion on the RS granule surface. Read More

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Biocatalysts Based on Peptide and Peptide Conjugate Nanostructures.

Authors:
Ian W Hamley

Biomacromolecules 2021 Apr 12. Epub 2021 Apr 12.

Department of Chemistry, University of Reading, RG6 6AD Reading, United Kingdom.

Peptides and their conjugates (to lipids, bulky N-terminals, or other groups) can self-assemble into nanostructures such as fibrils, nanotubes, coiled coil bundles, and micelles, and these can be used as platforms to present functional residues in order to catalyze a diversity of reactions. Peptide structures can be used to template catalytic sites inspired by those present in natural enzymes as well as simpler constructs using individual catalytic amino acids, especially proline and histidine. The literature on the use of peptide (and peptide conjugate) α-helical and β-sheet structures as well as turn or disordered peptides in the biocatalysis of a range of organic reactions including hydrolysis and a variety of coupling reactions (e. Read More

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Improving Cβ-stereoselectivity of L-threonine Aldolase for Synthesis of L-threo-4-methylsulfonylphenylserine by Modulating Substrate-binding Pocket for Orientation Control of Substrate Entrance.

Chemistry 2021 Apr 11. Epub 2021 Apr 11.

Fuzhou University, college of biological science and engineering, CHINA.

L-threonine aldolase form Actinocorallia herbida (AhLTA) is an ideal catalyst for producing L-threo-4-methylsulfonylphenylserine [(2S, 3R)-1b], a key chiral precursor for florfenicol and thiamphenicol. The moderate Cβ-stereoselectivity is the main obstacle for the industrial application of AhLTA. To address this issue, combinatorial active-site saturation test (CAST) joined with sequence conservatism analysis were applied to engineer the AhLTA toward improved Cβ-stereoselectivity. Read More

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New Cationic -[Re(CO)(deeb)B2] Complex, Where B2 Is a Benzimidazole Derivative, as a Potential New Luminescent Dye for Proteins Separated by SDS-PAGE.

Front Chem 2021 25;9:647816. Epub 2021 Mar 25.

Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.

Sodium-dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) can be used to separate proteins based mainly on their size such as in denaturing gels. Different staining methods have been reported to observe proteins in the gel matrix, where the most used dyes are generally anionic. Anionic dyes allow for interactions with protonated amino acids, retaining the dye in the proteins. Read More

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Identification of Critical Residues in the Carboxy Terminus of the Dopamine Transporter Involved in the G Protein βγ-Induced Dopamine Efflux.

Front Pharmacol 2021 24;12:642881. Epub 2021 Mar 24.

Department of Molecular, Cellular and Biomedical Sciences, CUNY School of Medicine at City College of New York, New York, NY, United States.

The dopamine transporter (DAT) plays a crucial role in the regulation of brain dopamine (DA) homeostasis through the re-uptake of DA back into the presynaptic terminal. In addition to re-uptake, DAT is also able to release DA through a process referred to as DAT-mediated DA efflux. This is the mechanism by which potent and highly addictive psychostimulants, such as amphetamine (AMPH) and its analogues, increase extracellular DA levels in motivational and reward areas of the brain. Read More

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Structural elucidation and antidiabetic activity of fucosylated chondroitin sulfate from sea cucumber Stichopus japonicas.

Carbohydr Polym 2021 Jun 20;262:117969. Epub 2021 Mar 20.

Weihai Marine Organism & Medical Technology Research Institute, Harbin Institute of Technology, Weihai, 264209, PR China; Weihai Huiankang Biotechnology Co., Ltd, Weihai 264200, PR China. Electronic address:

A fucosylated chondroitin sulfate was isolated from the body wall of sea cucumber Stichopus japonicus (FCSsj), whose structure was characterized by NMR spectroscopy and HILIC-FTMS. At the ratio of 1.00:0. Read More

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Simultaneous determination of short-chain fatty alcohols in aged oil and biodiesels by stable isotope labeling assisted liquid chromatography-mass spectrometry.

Talanta 2021 Jul 9;229:122223. Epub 2021 Mar 9.

Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, 430074, People's Republic of China. Electronic address:

Short-chain fatty alcohols (SCFAs) are one of the reactants for the production of biodiesels. The SCFA residues at the trace level have a significant impact on biodiesel quality. However, the analysis of SCFAs in aged biodiesels has not been reported so far, which is probably due to the unavailability of an appropriate analytical method for the simultaneous determination of SCFAs. Read More

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