Displaying publications 1 - 20 of 323 in total

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  1. Extraction, anti-tyrosinase, and antioxidant activities of the collagen hydrolysate derived from Rhopilema hispidum
    Ab Aziz NA, Salim N, Zarei M, Saari N, Yusoff FM
    Prep Biochem Biotechnol, 2021;51(1):44-53.
    PMID: 32701046 DOI: 10.1080/10826068.2020.1789991
    The study was conducted to determine anti-tyrosinase and antioxidant activities of the extracted collagen hydrolysate (CH) derived from Malaysian jellyfish, Rhopilema hispidum. Collagen was extracted using 1:1 (w:v) 0.1 M NaOH solution at temperature 25 °C for 48 hr followed by treatment of 1:2 (w:v) distilled water for another 24 hr and freeze-dried. The extracted collagen was hydrolyzed using papain at optimum temperature, pH and enzyme/substrate ratio [E/S] of 60 °C, 7.0 and 1:50, respectively. CH was found to exhibit tyrosinase inhibitory activity, DPPH radical scavenging and metal ion-chelating assays up to 64, 28, and 83%, respectively, after 8 hr of hydrolysis process. The molecular weight of CH was found <10 kDa consisting of mainly Gly (19.219%), Glu (10.428%), and Arg (8.848%). The UV-visible spectrum analysis showed a major and minor peak at 218 and 276 nm, accordingly. The FTIR spectroscopy confirmed the amide groups in CH. The SEM images demonstrated spongy and porous structure of CH. In the cytotoxicity study, CH has no cytotoxicity against mouse embryonic 3T3 fibroblast cell line with IC50 value >500 µg/ml. Results revealed that the CH generated from this study has a potential to be developed as active ingredient in cosmeceutical application.
    Matched MeSH terms: Amino Acids
  2. Fulltext Side chain similarity comparisons for integrated drug repositioning and potential toxicity assessments in epidemic response scenarios: The case for COVID-19
    Ab Ghani NS, Emrizal R, Makmur H, Firdaus-Raih M
    Comput Struct Biotechnol J, 2020;18:2931-2944.
    PMID: 33101604 DOI: 10.1016/j.csbj.2020.10.013
    Structures of protein-drug-complexes provide an atomic level profile of drug-target interactions. In this work, the three-dimensional arrangements of amino acid side chains in known drug binding sites (substructures) were used to search for similarly arranged sites in SARS-CoV-2 protein structures in the Protein Data Bank for the potential repositioning of approved compounds. We were able to identify 22 target sites for the repositioning of 16 approved drug compounds as potential therapeutics for COVID-19. Using the same approach, we were also able to investigate the potentially promiscuous binding of the 16 compounds to off-target sites that could be implicated in toxicity and side effects that had not been provided by any previous studies. The investigations of binding properties in disease-related proteins derived from the comparison of amino acid substructure arrangements allows for effective mechanism driven decision making to rank and select only the compounds with the highest potential for success and safety to be prioritized for clinical trials or treatments. The intention of this work is not to explicitly identify candidate compounds but to present how an integrated drug repositioning and potential toxicity pipeline using side chain similarity searching algorithms are of great utility in epidemic scenarios involving novel pathogens. In the case of the COVID-19 pandemic caused by the SARS-CoV-2 virus, we demonstrate that the pipeline can identify candidate compounds quickly and sustainably in combination with associated risk factors derived from the analysis of potential off-target site binding by the compounds to be repurposed.
    Matched MeSH terms: Amino Acids
  3. The effect of alkaline extraction and drying techniques on the physicochemical, structural properties and functionality of rice bran protein concentrates
    Abd Rahim FN, Wan Ibadullah WZ, Saari N, Brishti FH, Mustapha NA, Ahmad N, et al.
    Int J Biol Macromol, 2023 Jul 01;242(Pt 3):124908.
    PMID: 37217045 DOI: 10.1016/j.ijbiomac.2023.124908
    Rice bran protein concentrates (RBPC) were extracted using mild alkaline solvents (pH: 8, 9, 10). The physicochemical, thermal, functional, and structural aspects of freeze-drying (FD) and spray-drying (SD) were compared. FD and SD of RBPC had porous and grooved surfaces, with FD having non-collapsed plates and SD being spherical. Alkaline extraction increases FD's protein concentration and browning, whereas SD inhibits browning. According to amino acid profiling, RBPC-FD9's extraction optimizes and preserves amino acids. A tremendous particle size difference was prominent in FD, thermally stable at a minimal maximum of 92 °C. Increased pH extraction gives FD greater exposal surface hydrophobicity and positively relates to denaturation enthalpy. Mild pH extraction and drying significantly impacted solubility, improved emulsion properties, and foaming properties of RBPC as observed in acidic, neutral, and alkaline environments. RBPC-FD9 and RBPC-SD10 extracts exhibit outstanding foaming and emulsion activity in all pH conditions, respectively. Appropriate drying selection, RBPC-FD or SD potentially employed as foaming/emulsifier agent or meat analog.
    Matched MeSH terms: Amino Acids
  4. Fulltext Synthesis and physico-chemical properties of new tetraethylammonium-based amino acid chiral ionic liquids
    Abdul Rahman MB, Jumbri K, Basri M, Abdulmalek E, Sirat K, Salleh AB
    Molecules, 2010 Apr 05;15(4):2388-97.
    PMID: 20428050 DOI: 10.3390/molecules15042388
    This paper reports the synthesis of a series of new tetraethylammonium-based amino acid chiral ionic liquids (CILs). Their physico-chemical properties, including melting point, thermal stability, viscosity and ionic conductivity, have been comprehensively studied. The obtained results indicated that the decomposition for these salts proceeds in one step and the temperature of decomposition (T(onset)) is in the range of 168-210 degrees C. Several new CILs prepared in this work showed high ionic conductivity compared to the amino acid ionic liquids (AAILs) found in the literature.
    Matched MeSH terms: Amino Acids/chemistry*
  5. Synthesis of dipeptide benzoylalanylglycine methyl ester and corrosion inhibitor evaluation by tafel equation
    Abdurrahman J, Wahyuningrum D, Achmad S, Bundjali B
    Sains Malaysiana, 2011;40.
    Corrosion is one of the major problems in petroleum mining and processing industry. The pipelines used to transport crude oil from reservoir to the processing installation were made from carbon steel that is susceptible towards corrosion. One of the best methods to prevent corrosion that occurred at the inner parts of carbon steel pipelines is to use organic corrosion inhibitor. One of the potent organic corrosion inhibitors is amino acids derivatives. In this study, dipeptide compound namely benzoylalanylglycine methyl ester and benzoylalanylglycine have been synthesized. The structure elucidation of the products was performed by IR, MS and NMR spectroscopy. The determination of corrosion inhibition activity utilized the Tafel method. The corrosion inhibition efficiency of glycine methyl ester, benzoylalanine, dipeptide benzoylalanylglycine methyl ester and dipeptide benzoylalanylglycine were 63.34%, 35.86%, 68.40% and 27.72%, respectively. These results showed that the formation of dipeptide benzoylalanylglycine methyl ester, derived from carboxylic protected glycine and amine protected alanine, increased the corrosion inhibition activity due to the loss of acidity center in the structure of glicine and L-alanine that would induce the corrosive environment towards carbon steel.
    Matched MeSH terms: Amino Acids
  6. Biochemical and radical-scavenging properties of sea cucumber (Stichopus vastus) collagen hydrolysates
    Abedin MZ, Karim AA, Latiff AA, Gan CY, Ghazali FC, Barzideh Z, et al.
    Nat Prod Res, 2014;28(16):1302-5.
    PMID: 24670209 DOI: 10.1080/14786419.2014.900617
    The molecular mass distribution, amino acid composition and radical-scavenging activity of collagen hydrolysates prepared from collagen isolated from the sea cucumber Stichopus vastus were investigated. β and α1 chains of the collagen were successfully hydrolysed by trypsin. The molecular mass distribution of the hydrolysates ranged from 5 to 25 kDa, and they were rich in glycine, alanine, glutamate, proline and hydroxyproline residues. The hydrolysates exhibited excellent radical-scavenging activity. These results indicate that collagen hydrolysates from S. vastus can be used as a functional ingredient in food and nutraceutical products.
    Matched MeSH terms: Amino Acids/analysis*
  7. Extraction and characterization of gelatin from the feet of Pekin duck (Anas platyrhynchos domestica) as affected by acid, alkaline, and enzyme pretreatment
    Abedinia A, Ariffin F, Huda N, Nafchi AM
    Int J Biol Macromol, 2017 May;98:586-594.
    PMID: 28174080 DOI: 10.1016/j.ijbiomac.2017.01.139
    The effects of different pretreatments on yield and composition of extraction, physicochemical, and rheological properties of duck feet gelatin (DFG) were investigated. Gelatins were extracted from the whole feet of Pekin duck with an average yield of 4.09%, 3.65%, and 5.75% for acidic (Ac-DFG), alkaline (Al-DFG), and enzymatic (En-DFG) pretreatment on a wet weight basis, respectively. Proteins at 81.38%, 79.41%, 82.55%, and 87.38% were the major composition for Ac-DFG, Al-DFG, En-DFG, and bovine, respectively. Amino acid analysis showed glycine as the predominant amino acid in Ac-DFG, followed by hydroxyproline, proline, and alanine for Ac-DFG, Al-DFG, and En-DFG, respectively. Rheological analysis indicated that the maximum elastic modulus (9972.25Pa) and loss modulus (4956.28Pa) for Ac-DFG gelatin were significantly higher than those of other gelatins. Extracted gelatins contained α1 and α2 chains as the predominant components, and enzymatic gelatin had low molecular weight peptides. Fourier transform infrared spectroscopy showed that the peak of the gelatins was mainly positioned in the amide band region (amides I, II, and III). A considerable loss of molecular-order triple helical structure was also observed after pepsin treatment. In summary, duck feet gelatin has potential to replace as mammalian gelatin in food and pharmaceutical industry.
    Matched MeSH terms: Amino Acids
  8. Metabolomics - the complementary field in systems biology: a review on obesity and type 2 diabetes
    Abu Bakar MH, Sarmidi MR, Cheng KK, Ali Khan A, Suan CL, Zaman Huri H, et al.
    Mol Biosyst, 2015 Jul;11(7):1742-74.
    PMID: 25919044 DOI: 10.1039/c5mb00158g
    Metabolomic studies on obesity and type 2 diabetes mellitus have led to a number of mechanistic insights into biomarker discovery and comprehension of disease progression at metabolic levels. This article reviews a series of metabolomic studies carried out in previous and recent years on obesity and type 2 diabetes, which have shown potential metabolic biomarkers for further evaluation of the diseases. Literature including journals and books from Web of Science, Pubmed and related databases reporting on the metabolomics in these particular disorders are reviewed. We herein discuss the potential of reported metabolic biomarkers for a novel understanding of disease processes. These biomarkers include fatty acids, TCA cycle intermediates, carbohydrates, amino acids, choline and bile acids. The biological activities and aetiological pathways of metabolites of interest in driving these intricate processes are explained. The data from various publications supported metabolomics as an effective strategy in the identification of novel biomarkers for obesity and type 2 diabetes. Accelerating interest in the perspective of metabolomics to complement other fields in systems biology towards the in-depth understanding of the molecular mechanisms underlying the diseases is also well appreciated. In conclusion, metabolomics can be used as one of the alternative approaches in biomarker discovery and the novel understanding of pathophysiological mechanisms in obesity and type 2 diabetes. It can be foreseen that there will be an increasing research interest to combine metabolomics with other omics platforms towards the establishment of detailed mechanistic evidence associated with the disease processes.
    Matched MeSH terms: Amino Acids/metabolism
  9. Effect of Ipomoea aquatica ethanolic extract in streptozotocin (STZ) induced diabetic rats via1H NMR-based metabolomics approach
    Abu Bakar Sajak A, Mediani A, Maulidiani, Mohd Dom NS, Machap C, Hamid M, et al.
    Phytomedicine, 2017 Dec 01;36:201-209.
    PMID: 29157816 DOI: 10.1016/j.phymed.2017.10.011
    BACKGROUND: Ipomoea aquatica (locally known as "kangkung") has previously been reported to have hypoglycemic activities on glucose level in diabetes patients. However, the effect of I. aquatica ethanolic extract on the metabolites in the body has remained unknown.

    PURPOSE: This study provides new insights on the changes of endogenous metabolites caused by I. aquatica ethanolic extract and improves the understanding on the therapeutic efficacy and mechanism of I. aquatica ethanolic extract.

    METHODS: By using a combination of 1H nuclear magnetic resonance (NMR) with multivariate analysis (MVDA), the changes of metabolites due to I. aquatica ethanolic extract administration in obese diabetic-induced Sprague Dawley rats (OB+STZ+IA) were identified.

    RESULTS: The results suggested 19 potential biomarkers with variable importance projections (VIP) above 0.5, which include creatine/creatinine, glucose, creatinine, citrate, carnitine, 2-oxoglutarate, succinate, hippurate, leucine, 1-methylnicotinamice (MNA), taurine, 3-hydroxybutyrate (3-HB), tryptophan, lysine, trigonelline, allantoin, formiate, acetoacetate (AcAc) and dimethylamine. From the changes in the metabolites, the affected pathways and aspects of metabolism were identified.

    CONCLUSION: I. aquatica ethanolic extract increases metabolite levels such as creatinine/creatine, carnitine, MNA, trigonelline, leucine, lysine, 3-HB and decreases metabolite levels, including glucose and tricarboxylic acid (TCA) intermediates. This implies capabilities of I. aquatica ethanolic extract promoting glycolysis, gut microbiota and nicotinate/nicotinamide metabolism, improving the glomerular filtration rate (GFR) and reducing the β-oxidation rate. However, the administration of I. aquatica ethanolic extract has several drawbacks, such as unimproved changes in amino acid metabolism, especially in reducing branched chain amino acid (BCAA) synthesis pathways and lipid metabolism.

    Matched MeSH terms: Amino Acids/metabolism
  10. Fulltext Biochemical changes of fresh and preserved freshwater prawns (Macrobrachium rosenbergii) during storage
    Abu Bakar, F., Salleh, A.B., Razak, C.N.A., Basri, M., Ching, M.K., Son, R.
    International Food Research Journal, 2008;15(2):181-191.
    MyJurnal
    Biochemical analysis was carried out for pH profiles, freshness in terms of K-values, amino acids profiles, total volatile bases (TVB), total volatile acids (TVA) and biogenic amines for fresh and preserved Macrobrachium rosenbergii. Results showed that pH profiles of Macrobrachium rosenbergii explain the inability of this parameter to be used to evaluate the quality of Macrobrachium rosenbergii. Thus changes in pH profiles of Macrobrachium rosenbergii should be combined with indicators such as total volatile acids and total volatile bases. Total volatile acids of the shrimps increased steadily in small amounts throughout the storage period. A rapid increase in TVB at 100C was detected due to the increase in total aerobic bacteria at elevated temperatures. The microbial activities caused the decrease in the amino acids arginine, lysine and histidine which correlated well with the increase in the corresponding biogenic amines such as putrescine, cadaverine and histamine respectively. Preservatives used in this study controlled the production of these biogenic amines without significantly altering the pH of preserved shrimp.
    Matched MeSH terms: Amino Acids
  11. Deciphering the catalytic amino acid residues of l-2-haloacid dehalogenase (DehL) from Rhizobium sp. RC1: An in silico analysis
    Adamu A, Wahab RA, Shamsir MS, Aliyu F, Huyop F
    Comput Biol Chem, 2017 Oct;70:125-132.
    PMID: 28873365 DOI: 10.1016/j.compbiolchem.2017.08.007
    The l-2-haloacid dehalogenases (EC 3.8.1.2) specifically cleave carbon-halogen bonds in the L-isomers of halogenated organic acids. These enzymes have potential applications for the bioremediation and synthesis of various industrial products. One such enzyme is DehL, the l-2-haloacid dehalogenase from Rhizobium sp. RC1, which converts the L-isomers of 2-halocarboxylic acids into the corresponding D-hydroxycarboxylic acids. However, its catalytic mechanism has not been delineated, and to enhance its efficiency and utility for environmental and industrial applications, knowledge of its catalytic mechanism, which includes identification of its catalytic residues, is required. Using ab initio fragment molecular orbital calculations, molecular mechanics Poisson-Boltzmann surface area calculations, and classical molecular dynamic simulation of a three-dimensional model of DehL-l-2-chloropropionic acid complex, we predicted the catalytic residues of DehL and propose its catalytic mechanism. We found that when Asp13, Thr17, Met48, Arg51, and His184 were individually replaced with an alanine in silico, a significant decrease in the free energy of binding for the DehL-l-2-chloropropionic acid model complex was seen, indicating the involvement of these residues in catalysis and/or structural integrity of the active site. Furthermore, strong inter-fragment interaction energies calculated for Asp13 and L-2-chloropropionic acid, and for a water molecule and His184, and maintenance of the distances between atoms in the aforementioned pairs during the molecular dynamics run suggest that Asp13 acts as the nucleophile and His184 activates the water involved in DehL catalysis. The results of this study should be important for the rational design of a DehL mutant with improved catalytic efficiency.
    Matched MeSH terms: Amino Acids/metabolism*; Amino Acids/chemistry
  12. Fulltext Review article : phytase: application in food industry
    Afinah, S., Yazid, A.M, Anis Shobirin, M.H, Shuhaimi, M.
    International Food Research Journal, 2010;17(1):13-21.
    MyJurnal
    Phytates have been considered as a threat in human diet due to its antinutrients behaviour which
    known as strong chelators of divalent minerals such as Ca2+, Mg2+, Zn2+ and Fe2+. Phytic acid has a potential for binding positively charged proteins, amino acids, and/or multivalent cations or minerals in foods. The resulting complexes are insoluble, difficult for humans to hydrolyze during digestion, and thus, typically are nutritionally less available for absorption. The reduction of this phytates can be achieved through both enzymatic and nonenzymatic removal. Enzymatic degradation includes addition of either isolated form of wild-type or recombinant exogenous phytate-degrading enzymes microorganisms in the food matrix. Non-enzymatic hydrolysis of phytate occurred in the final food during food processing or physical separation of phytate-rich parts of the plants seed. The application of phytase with respect to breadmaking process, probiotics, animal feed supplement and transgenic crops are emphasised in this paper.
    Matched MeSH terms: Amino Acids
  13. Tocotrienol offers better protection than tocopherol from free radical-induced damage of rat bone
    Ahmad NS, Khalid BA, Luke DA, Ima Nirwana S
    Clin Exp Pharmacol Physiol, 2005 Sep;32(9):761-70.
    PMID: 16173934
    1. Free radicals generated by ferric nitrilotriacetate (FeNTA) can activate osteoclastic activity and this is associated with elevation of the bone resorbing cytokines interleukin (IL)-1 and IL-6. In the present study, we investigated the effects of 2 mg/kg FeNTA (2 mg iron/kg) on the levels of serum IL-1 and IL-6 with or without supplementation with a palm oil tocotrienol mixture or alpha-tocopherol acetate in Wistar rats. 2. The FeNTA was found to elevate levels of IL-1 and IL-6. Only the palm oil tocotrienol mixture at doses of 60 and 100 mg/kg was able to prevent FeNTA-induced increases in IL-1 (P < 0.01). Both the palm oil tocotrienol mixture and alpha-tocopherol acetate, at doses of 30, 60 and 100 mg/kg, were able to reduce FeNTA-induced increases in IL-6 (P < 0.05). Therefore, the palm oil tocotrienol mixture was better than pure alpha-tocopherol acetate in protecting bone against FeNTA (free radical)-induced elevation of bone-resorbing cytokines. 3. Supplementation with the palm oil tocotrienol mixture or alpha-tocopherol acetate at 100 mg/kg restored the reduction in serum osteocalcin levels due to ageing, as seen in the saline (control) group (P < 0.05). All doses of the palm oil tocotrienol mixture decreased urine deoxypyridinoline cross-link (DPD) significantly compared with the control group, whereas a trend for decreased urine DPD was only seen for doses of 60 mg/kg onwards of alpha-tocopherol acetate (P < 0.05). 4. Bone histomorphometric analyses have shown that FeNTA injections significantly lowered mean osteoblast number (P < 0.001) and the bone formation rate (P < 0.001), but raised osteoclast number (P < 0.05) and the ratio of eroded surface/bone surface (P < 0.001) compared with the saline (control) group. Supplementation with 100 mg/kg palm oil tocotrienol mixture was able to prevent all these FeNTA-induced changes, but a similar dose of alpha-tocopherol acetate was found to be effective only for mean osteoclast number. Injections of FeNTA were also shown to reduce trabecular bone volume (P < 0.001) and trabecular thickness (P < 0.05), whereas only supplementation with 100 mg/kg palm oil tocotrienol mixture was able to prevent these FeNTA-induced changes.
    Matched MeSH terms: Amino Acids/urine
  14. Synthesis, characterization, monoamine oxidase inhibition, molecular docking and dynamic simulations of novel 2,1-benzothiazine-2,2-dioxide derivatives
    Ahmad S, Zaib S, Jalil S, Shafiq M, Ahmad M, Sultan S, et al.
    Bioorg Chem, 2018 10;80:498-510.
    PMID: 29996111 DOI: 10.1016/j.bioorg.2018.04.012
    In this research work, we report the synthesis and biological evaluation of two new series of 1-benzyl-4-(benzylidenehydrazono)-3,4-dihydro-1H-benzo[c] [1,2]thiazine 2,2-dioxides and 1-benzyl-4-((1-phenylethylidene)hydrazono)-3,4-dihydro-1H-benzo[c][1,2]thiazine 2,2-dioxides. The synthetic plan involves the mesylation of methyl anthranilate with subsequent N-benzylation of the product. The methyl 2-(N-benzylmethylsulfonamido)benzoate was subjected to cyclization reaction in the presence of sodium hydride to obtain 1-benzyl-1H-benzo[c][1,2]thiazin-4(3H)-one 2,2-dioxide which was treated with hydrazine hydrate to get corresponding hydrazone precursor. Finally, the titled compounds were obtained by reaction of hydrazone with various substituted aldehydes and ketones. The synthesized derivatives were subjected to carry out their inhibition activities against monoamine oxidases along with modelling investigations to evaluate their binding interactions and dynamic stability during the docking studies. The inhibition profile of potent compounds was found as competitive for both the isozymes. The compounds were more selective inhibitors of MAO-A as compared to MAO-B. Moreover, drug likeness profile of the derivatives was evaluated to have an additional insight into the physicochemical properties. The molecular dynamic simulations predicted the behaviour of amino acids with the active site residues.
    Matched MeSH terms: Amino Acids
  15. Fulltext 1H-NMR-Based Metabolomics: An Integrated Approach for the Detection of the Adulteration in Chicken, Chevon, Beef and Donkey Meat
    Akhtar MT, Samar M, Shami AA, Mumtaz MW, Mukhtar H, Tahir A, et al.
    Molecules, 2021 Jul 30;26(15).
    PMID: 34361796 DOI: 10.3390/molecules26154643
    Meat is a rich source of energy that provides high-value animal protein, fats, vitamins, minerals and trace amounts of carbohydrates. Globally, different types of meats are consumed to fulfill nutritional requirements. However, the increasing burden on the livestock industry has triggered the mixing of high-price meat species with low-quality/-price meat. This work aimed to differentiate different meat samples on the basis of metabolites. The metabolic difference between various meat samples was investigated through Nuclear Magnetic Resonance spectroscopy coupled with multivariate data analysis approaches like principal component analysis (PCA) and orthogonal partial least square-discriminant analysis (OPLS-DA). In total, 37 metabolites were identified in the gluteal muscle tissues of cow, goat, donkey and chicken using 1H-NMR spectroscopy. PCA was found unable to completely differentiate between meat types, whereas OPLS-DA showed an apparent separation and successfully differentiated samples from all four types of meat. Lactate, creatine, choline, acetate, leucine, isoleucine, valine, formate, carnitine, glutamate, 3-hydroxybutyrate and α-mannose were found as the major discriminating metabolites between white (chicken) and red meat (chevon, beef and donkey). However, inosine, lactate, uracil, carnosine, format, pyruvate, carnitine, creatine and acetate were found responsible for differentiating chevon, beef and donkey meat. The relative quantification of differentiating metabolites was performed using one-way ANOVA and Tukey test. Our results showed that NMR-based metabolomics is a powerful tool for the identification of novel signatures (potential biomarkers) to characterize meats from different sources and could potentially be used for quality control purposes in order to differentiate different meat types.
    Matched MeSH terms: Amino Acids/analysis
  16. Fulltext Antibiofilm activity, compound characterization, and acute toxicity of extract from a novel bacterial species of paenibacillus
    Alasil SM, Omar R, Ismail S, Yusof MY
    Int J Microbiol, 2014;2014:649420.
    PMID: 24790603 DOI: 10.1155/2014/649420
    The effectiveness of many antimicrobial agents is currently decreasing; therefore, it is important to search for alternative therapeutics. Our study was carried out to assess the in vitro antibiofilm activity using microtiter plate assay, to characterize the bioactive compounds using Ultra Performance Liquid Chromatography-Diode Array Detection and Liquid Chromatography-Mass Spectrometry and to test the oral acute toxicity on Sprague Dawley rats of extract derived from a novel bacterial species of Paenibacillus strain 139SI. Our results indicate that the crude extract and its three identified compounds exhibit strong antibiofilm activity against a broad range of clinically important pathogens. Three potential compounds were identified including an amino acid antibiotic C8H20N3O4P (MW 253.237), phospholipase A2 inhibitor C21H36O5 (MW 368.512), and an antibacterial agent C14H11N3O2 (MW 253.260). The acute toxicity test indicates that the mortality rate among all rats was low and that the biochemical parameters, hematological profile, and histopathology examination of liver and kidneys showed no significant differences between experimental groups (P > 0.05). Overall, our findings suggest that the extract and its purified compounds derived from novel Paenibacillus sp. are nontoxic exhibiting strong antibiofilm activity against Gram-positive and Gram-negative pathogens that can be useful towards new therapeutic management of biofilm-associated infections.
    Matched MeSH terms: Amino Acids
  17. Fulltext TranCEP: Predicting the substrate class of transmembrane transport proteins using compositional, evolutionary, and positional information
    Alballa M, Aplop F, Butler G
    PLoS One, 2020;15(1):e0227683.
    PMID: 31935244 DOI: 10.1371/journal.pone.0227683
    Transporters mediate the movement of compounds across the membranes that separate the cell from its environment and across the inner membranes surrounding cellular compartments. It is estimated that one third of a proteome consists of membrane proteins, and many of these are transport proteins. Given the increase in the number of genomes being sequenced, there is a need for computational tools that predict the substrates that are transported by the transmembrane transport proteins. In this paper, we present TranCEP, a predictor of the type of substrate transported by a transmembrane transport protein. TranCEP combines the traditional use of the amino acid composition of the protein, with evolutionary information captured in a multiple sequence alignment (MSA), and restriction to important positions of the alignment that play a role in determining the specificity of the protein. Our experimental results show that TranCEP significantly outperforms the state-of-the-art predictors. The results quantify the contribution made by each type of information used.
    Matched MeSH terms: Amino Acids
  18. Fulltext Optimizing the acceleration of Cheddar cheese ripening using response surface methodology by microbial protease without altering its quality features
    Alhelli AM, Mohammed NK, Khalil ES, Hussin ASM
    AMB Express, 2021 Mar 22;11(1):45.
    PMID: 33751265 DOI: 10.1186/s13568-021-01205-9
    Cheddar cheese proteolysis were accelerated employing Penicillium candidum PCA1/TT031 protease into cheese curd. In the present study, several of the significant factors such as protease purification factor (PF), protease concentration and ripening time were optimized via the response surface methodology (RSM). The ideal accelerated Cheddar cheese environment consisted of 3.12 PF, 0.01% (v/v) protease concentration and 0.6/3 months ripening time at 10 °C. The RSM models was verified to be the most proper methodology for the maintain of chosen Cheddar cheese. Under this experimental environment, the pH, acid degree value (ADV), moisture, water activity (aw), soluble nitrogen (SN)%, fat and overall acceptability were found to be 5.4, 6.6, 35%, 0.9348, 18.8%, 34% and 13.6, respectively of ideal Cheddar cheese. Furthermore, the predicted and experimental results were in significant agreement, which confirmed the validity and reliability of the suggested method. In spite of the difference between the ideal and commercial Cheddar cheese in the concentration of some of amino acids and free fatty acids, the sensory evaluation did not show any significant difference in aroma profile between them.
    Matched MeSH terms: Amino Acids
  19. Comparison of free amino acids, antioxidants, soluble phenolic acids, cytotoxicity and immunomodulation of fermented mung bean and soybean
    Ali NM, Yeap SK, Yusof HM, Beh BK, Ho WY, Koh SP, et al.
    J Sci Food Agric, 2016 Mar 30;96(5):1648-58.
    PMID: 26009985 DOI: 10.1002/jsfa.7267
    BACKGROUND: Mung bean and soybean have been individually reported previously to have antioxidant, cytotoxic and immunomodulatory effects, while fermentation is a well-known process to enhance the bioactive compounds that contribute to higher antioxidant, cytotoxic and immunomodulation effects. In this study, the free amino acids profile, soluble phenolic acids content, antioxidants, cytotoxic and immunomodulatory effects of fermented and non-fermented mung bean and soybean were compared.

    RESULTS: Fermented mung bean was recorded to have the highest level of free amino acids, soluble phenolic acids (especially protocatechuic acid) and antioxidant activities among all the tested products. Both fermented mung bean and soybean possessed cytotoxicity activities against breast cancer MCF-7 cells by arresting the G0/G1 phase followed by apoptosis. Moreover, fermented mung bean and soybean also induced splenocyte proliferation and enhanced the levels of serum interleukin-2 and interferon-γ.

    CONCLUSION: Augmented amounts of free amino acids and phenolic acids content after fermentation enhanced the antioxidants, cytotoxicity and immunomodulation effects of mung bean and soybean. More specifically, fermented mung bean showed the best effects among all the tested products. This study revealed the potential of fermented mung bean and soybean as functional foods for maintenance of good health.

    Matched MeSH terms: Amino Acids/metabolism; Amino Acids/chemistry*
  20. Genetic Diversity of Recent Infectious Bursal Disease Viruses Isolated From Vaccinated Poultry Flocks in Malaysia
    Aliyu HB, Hair-Bejo M, Omar AR, Ideris A
    Front Vet Sci, 2021;8:643976.
    PMID: 33959650 DOI: 10.3389/fvets.2021.643976
    Vaccination is an essential component in controlling infectious bursal disease (IBD), however, there is a lack of information on the genetic characteristics of a recent infectious bursal disease virus (IBDV) that was isolated from IBD vaccinated commercial flocks in Malaysia. The present study investigated 11 IBDV isolates that were isolated from commercial poultry farms. The isolates were detected using reverse transcription-polymerase chain reaction (RT-PCR) targeting the hypervariable region (HVR) of VP2. Based on the HVR sequences, five isolates (IBS536/2017, IBS624/2017, UPM766/2018, UPM1056/2018, and UPM1432/2019) were selected for whole-genome sequencing using the MiSeq platform. The nucleotide and amino acid (aa) sequences were compared with the previously characterized IBDV strains. Deduced aa sequences of VP2HVR revealed seven isolates with 94-99% aa identity to very virulent strains (genogroup 3), two isolates with 97-100% aa identity to variant strains (genogroup 2), and two strains with 100% identity to the vaccine strain (genogroup 1) of IBDV. The phylogenetic analysis also showed that the isolates formed clusters with the respective genogroups. The characteristic motifs 222T, 249K, 286I, and 318D are typical of the variant strain and were observed for UPM1219/2019 and UPM1432/2019. In comparison, very virulent residues such as 222A, 249Q, 286T, and 318G were found for the vvIBDV, except for the UPM1056/2018 strain with a A222T substitution. In addition, the isolate has aa substitutions such as D213N, G254D, S315T, S317R, and A321E that are not commonly found in previously reported vvIBDV strains. Unlike the other vvIBDVs characterized in this study, UPM766/2018 lacks the MLSL aa residues in VP5. The aa tripeptides 145/146/147 (TDN) of VP1 were conserved for the vvIBDV, while a different motif, NED, was observed for the Malaysian variant strain. The phylogenetic tree showed that the IBDV variant clustered with the American and Chinese variant viruses and are highly comparable to the novel Chinese variants, with 99.9% identity. Based on the sequences and phylogenetic analyses, this is the first identification of an IBDV variant being reported in Malaysia. Further research is required to determine the pathogenicity of the IBDV variant and the protective efficacy of the current IBD vaccines being used against the virus.
    Matched MeSH terms: Amino Acids
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