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Fulltext Evolutionary and genomic analysis of four SARS-CoV-2 isolates circulating in March 2020 in Sri Lanka; Additional evidence on multiple introduction and further transmission

Satharasinghe DA, Parakatawella PMSDK, Premarathne JMKJK, Jayasooriya LJPAP, Prathapasinghe GA, Yeap SK

Epidemiol Infect, 2021 03 16;149:e78.
PMID: 33722321 DOI: 10.1017/S0950268821000583

The molecular epidemiology of the virus and mapping helps understand the epidemics' evolution and apply quick control measures. This study provides genomic evidence of multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) introductions into Sri Lanka and virus evolution during circulation. Whole-genome sequences of four SARS-CoV-2 strains obtained from coronavirus disease 2019 (COVID-19) positive patients reported in Sri Lanka during March 2020 were compared with sequences from Europe, Asia, Africa, Australia and North America. The phylogenetic analysis revealed that the sequence of the sample of the first local patient collected on 10 March, who contacted tourists from Italy, was clustered with SARS-CoV-2 strains collected from Italy, Germany, France and Mexico. Subsequently, the sequence of the isolate obtained on 19 March also clustered in the same group with the samples collected in March and April from Belgium, France, India and South Africa. The other two strains of SARS-CoV-2 were segregated from the main cluster, and the sample collected from 16 March clustered with England and the sample collected on 30 March showed the highest genetic divergence to the isolate of Wuhan, China. Here we report the first molecular epidemiological study conducted on circulating SARS-CoV-2 in Sri Lanka. The finding provides the robustness of molecular epidemiological tools and their application in tracing possible exposure in disease transmission during the pandemic.

Matched MeSH terms: Amino Acids/analysis
Fulltext A Comparative Characterization of Physicochemical and Antioxidants Properties of Processed Heterotrigona itama Honey from Different Origins and Classification by Chemometrics Analysis

Shamsudin S, Selamat J, Sanny M, A R SB, Jambari NN, Khatib A

Molecules, 2019 Oct 29;24(21).
PMID: 31671885 DOI: 10.3390/molecules24213898

Stingless bee honey produced by Heterotrigona itama from different botanical origins was characterised and discriminated. Three types of stingless bee honey collected from acacia, gelam, and starfruit nectars were analyzed and compared with Apis mellifera honey. The results showed that stingless bee honey samples from the three different botanical origins were significantly different in terms of their moisture content, pH, free acidity, total soluble solids, colour characteristics, sugar content, amino acid content and antioxidant properties. Stingless bee honey was significantly different from Apis mellifera honey in terms of physicochemical and antioxidant properties. The amino acid content was further used in the chemometrics analysis to evaluate the role of amino acid in discriminating honey according to botanical origin. Partial least squares-discriminant analysis (PLS-DA) revealed that the stingless bee honey was completely distinguishable from Apis mellifera honey. Notably, a clear distinction between the stingless bee honey types was also observed. The specific amino acids involved in the distinction of honey were cysteine for acacia and gelam, phenylalanine and 3-hydroxyproline for starfruit, and proline for Apis mellifera honey. The results showed that all honey samples were successfully classified based on amino acid content.

Matched MeSH terms: Amino Acids/analysis
Identification of the amino acids in the Major Histocompatibility Complex class II region of Scottish Blackface sheep that are associated with resistance to nematode infection

Stear A, Ali AOA, Brujeni GN, Buitkamp J, Donskow-Łysoniewska K, Fairlie-Clarke K, et al.

Int J Parasitol, 2019 09;49(10):797-804.
PMID: 31306661 DOI: 10.1016/j.ijpara.2019.05.003

Lambs with the Major Histocompatibility Complex DRB1*1101 allele have been shown to produce fewer nematode eggs following natural and deliberate infection. These sheep also possess fewer adult Teladorsagia circumcincta than sheep with alternative alleles at the DRB1 locus. However, it is unclear if this allele is responsible for the reduced egg counts or merely acts as a marker for a linked gene. This study defined the MHC haplotypes in a population of naturally infected Scottish Blackface sheep by PCR amplification and sequencing, and examined the associations between MHC haplotypes and faecal egg counts by generalised linear mixed modelling. The DRB1*1101 allele occurred predominately on one haplotype and a comparison of haplotypes indicated that the causal mutation or mutations occurred in or around this locus. Additional comparisons with another resistant haplotype indicated that mutations in or around the DQB2*GU191460 allele were also responsible for resistance to nematode infections. Further analyses identified six amino acid substitutions in the antigen binding site of DRB1*1101 that were significantly associated with reductions in the numbers of adult T. circumcincta.

Matched MeSH terms: Amino Acids/analysis*
A comparative study of physicochemical characteristics and functionalities of pinto bean protein isolate (PBPI) against the soybean protein isolate (SPI) after the extraction optimisation

Tan ES, Ying-Yuan N, Gan CY

Food Chem, 2014;152:447-55.
PMID: 24444960 DOI: 10.1016/j.foodchem.2013.12.008

Optimisation of protein extraction yield from pinto bean was investigated using response surface methodology. The maximum protein yield of 54.8 mg/g was obtained with the optimal conditions of: temperature=25 °C, time=1 h and buffer-to-sample ratio=20 ml/g. PBPI was found to obtain high amount of essential amino acids such as leucine, lysine, and phenylalanine compared to SPI. The predominant proteins of PBPI were vicilin and phytohemagglutinins whereas the predominant proteins of SPI were glycinin and conglycinins. Significantly higher emulsifying capacity was found in PBPI (84.8%) compared to SPI (61.9%). Different isoelectric points were found in both PBPI (4.0-5.5) and SPI (4.0-5.0). Also, it was found that PBPI obtained a much higher denaturation temperature of 110.2 °C compared to SPI (92.5 °C). Other properties such as structural information, gelling capacity, water- and oil-holding capacities, emulsion stability as well as digestibility were also reported.

Matched MeSH terms: Amino Acids/analysis
Isolation and characterization of an acidic lethal phospholipase Az from Malayan cobra (Naja naja sputatrix) venom

Tan NH, Arunmozhiarasi A

Biochem. Int., 1989 Apr;18(4):785-92.
PMID: 2764979

An acidic, lethal phospholipase Az was purified to electrophoretic homogeneity from the venom of the Malayan cobra (Naja naja sputatrix). The enzyme has an isoelectric point of 5.58, a molecular weight of 12000, and a medium lethal dose (LD50) of 0.86 micrograms/g in mice by intravenous injection. The enzyme also exhibited weak anticoagulant and edema-forming activities. The amino acid composition of the enzyme is similar to those of other cobra venom phospholipases Az.

Matched MeSH terms: Amino Acids/analysis
Cardiotoxins from the venom of Malayan cobra (Naja naja sputatrix)

Tan NH

Arch Biochem Biophys, 1982 Oct 01;218(1):51-8.
PMID: 7149742
Matched MeSH terms: Amino Acids/analysis
Application of the artificial neural network in quantitative structure-gradient elution retention relationship of phenylthiocarbamyl amino acids derivatives

Tham SY, Agatonovic-Kustrin S

J Pharm Biomed Anal, 2002 May 15;28(3-4):581-90.
PMID: 12008137

Quantitative structure-retention relationship(QSRR) method was used to model reversed-phase high-performance liquid chromatography (RP-HPLC) separation of 18 selected amino acids. Retention data for phenylthiocarbamyl (PTC) amino acids derivatives were obtained using gradient elution on ODS column with mobile phase of varying acetonitrile, acetate buffer and containing 0.5 ml/l of triethylamine (TEA). Molecular structure of each amino acid was encoded with 36 calculated molecular descriptors. The correlation between the molecular descriptors and the retention time of the compounds in the calibration set was established using the genetic neural network method. A genetic algorithm (GA) was used to select important molecular descriptors and supervised artificial neural network (ANN) was used to correlate mobile phase composition and selected descriptors with the experimentally derived retention times. Retention time values were used as the network's output and calculated molecular descriptors and mobile phase composition as the inputs. The best model with five input descriptors was chosen, and the significance of the selected descriptors for amino acid separation was examined. Results confirmed the dominant role of the organic modifier in such chromatographic systems in addition to lipophilicity (log P) and molecular size and shape (topological indices) of investigated solutes.

Matched MeSH terms: Amino Acids/analysis*
Microbial dynamics, metabolomic profiles, and the correlation between them during fermentation of serofluid dish

Wei J, Ren W, Wang L, Liu M, Tian X, Ding G, et al.

J Sci Food Agric, 2020 Dec;100(15):5627-5636.
PMID: 32712996 DOI: 10.1002/jsfa.10690

BACKGROUND: Serofluid dish, a traditional Chinese fermented food, possesses unique flavors and health beneficial effects. These properties are likely due to the sophisticated metabolic networks during fermentation, which are mainly driven by microbiota. However, the exact roles of metabolic pathways and the microbial community during this process remain equivocal.
RESULTS: Here, we investigated the microbial dynamics by next-generation sequencing, and outlined a differential non-targeted metabolite profiling in the process of serofluid dish fermentation using the method of hydrophilic interaction liquid chromatography column with ultra-high-performance liquid chromatography-quadruple time-of-flight mass spectrometry. Lactobacillus was the leading genus of bacteria, while Pichia and Issatchenkia were the dominant fungi. They all accumulated during fermentation. In total, 218 differential metabolites were identified, of which organic acids, amino acids, sugar and sugar alcohols, fatty acids, and esters comprised the majority. The constructed metabolic network showed that tricarboxylic acid cycle, urea cycle, sugar metabolism, amino acids metabolism, choline metabolism, and flavonoid metabolism were regulated by the fermentation. Furthermore, correlation analysis revealed that the leading fungi, Pichia and Issatchenkia, were linked to organic acids, amino acid and sugar metabolism, flavonoids, and several other flavor and functional components. Antibacterial tests indicated the antibacterial effect of serofluid soup against Salmonella and Staphylococcus.
CONCLUSION: This work provides new insights into the complex microbial and metabolic networks during serofluid dish fermentation, and a theoretical basis for the optimization of its industrial production. © 2020 Society of Chemical Industry.

Matched MeSH terms: Amino Acids/analysis
Antinociceptive, antiinflammatory and antipyretic properties of Channa striatus fillet aqueous and lipid-based extracts in rats

Zakaria ZA, Kumar GH, Mat Jais AM, Sulaiman MR, Somchit MN

Methods Find Exp Clin Pharmacol, 2008 Jun;30(5):355-62.
PMID: 18806894 DOI: 10.1358/mf.2008.30.5.1186084

The present study was carried out to elucidate the antinociceptive, antiinflammatory and antipyretic properties of the aqueous and lipid-based extracts of Channa striatus fillet in rats. The antinociceptive activity was assessed using the formalin test, and the antiinflammatory and antipyretic activities were assessed using the carrageenan-induced paw edema and brewer's yeast-induced pyrexia tests, respectively. Both types of extracts were prepared in concentrations of 10%, 50% and 100% by serial dilution in distilled water or dimethyl sulfoxide, respectively, and were administered subcutaneously 30 min prior to each test. Except for the 10% aqueous extract which exhibits activity only in the early phase, the extracts were found to exhibit significant (P < 0.05) activity in the early and late phases of the formalin test. Furthermore, the aqueous and lipid-based extracts were also found to show significant (P < 0.05) antiinflammatory activity, with the former showing a greater effect at the lowest concentration used. The lipidbased, but not the aqueous, extract was found to have significant (P < 0.05) activity in the pyrexia test. In conclusion, the present study demonstrated that C. striatus extracts possess antinociceptive, antiinflammatory and antipyretic activities.

Matched MeSH terms: Amino Acids/analysis
Amino acid and fatty acid composition of an aqueous extract of Channa striatus (Haruan) that exhibits antinociceptive activity

Zakaria ZA, Mat Jais AM, Goh YM, Sulaiman MR, Somchit MN

Clin Exp Pharmacol Physiol, 2007 Mar;34(3):198-204.
PMID: 17250639

1. The present study was performed in order to determine the amino acid and fatty acid composition of an aqueous extract of the freshwater fish Channa striatus, obtained by soaking (1:2, w/v) fresh fillets overnight in a chloroform:methanol (2:1, v/v) solvent, to elucidate the mechanism responsible for its antinociceptive activity and to clarify the relationship between the presence of the amino and fatty acids and the expected activity. 2. The aqueous extract was found to contain all amino acids with the major amino acids glycine, alanine, lysine, aspartic acid and proline making up 35.77 +/- 0.58, 10.19 +/- 1.27, 9.44 +/- 0.56, 8.53 +/- 1.15 and 6.86 +/- 0.78% of the total protein, respectively. 3. In addition, the aqueous extract was found to have a high palmitic acid (C16:0) content, which contributed approximately 35.93 +/- 0.63% to total fatty acids. The other major fatty acids in the aqueous extract were oleic acid (C18:1), stearic acid (C18:0), linoleic acid (C18:2) and arachidonic acid (C20:4), contributing 22.96 +/- 0.40, 15.31 +/- 0.33, 11.45 +/- 0.31 and 7.44 +/- 0.83% of total fatty acids, respectively. 4. Furthermore, the aqueous extract was demonstrated to possess concentration-dependent antinociceptive activity, as expected, when assessed using the abdominal constriction test in mice. 5. It is concluded that the aqueous extract of C. striatus contains all the important amino acids, but only some of the important fatty acids, which are suggested to play a key role in the observed antinociceptive activity of the extract, as well as in the traditionally claimed wound healing properties of the extract.

Matched MeSH terms: Amino Acids/analysis*