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Pencirian bakteria asid laktik dan sebatian aroma ikan pekasam

Tan WC, Lim SJ, Wan Aida Wan Mustapha

Sains Malaysiana, 2017;46:439-448.

Dalam kajian ini, bakteria asid laktik (LAB) serta sebatian aroma ikan pekasam daripada spesies yang berbeza
ditentukan. Persampelan ikan pekasam iaitu tilapia, loma, lampam, sepat dan gelama diperoleh daripada pembekal
Perusahaan Ikan Pekasam Kiah di Kuala Kangsar, Perak. Penentuan spesies LAB dijalankan melalui kaedah pencairan
bersiri, pengkulturan LAB, ujian katalase, ujian pewarnaan spora serta ujian pengesanan Gram bakteria dan morfologi.
Pengesahan spesies LAB dijalankan melalui pengekstrakan asid deoksiribonukleik (DNA), amplifikasi dengan tindak
balas rantaian polimerasi (PCR), analisis elektroforesis gel dan penjujukan DNA. Hasil jujukan DNA yang diperoleh
dibandingkan dengan jujukan dalam pangkalan data GenBank di NCBI menggunakan BLAST. Didapati Lactobacillus
brevis KB290 DNA dan Lactobacillus casei W56 wujud dalam pekasam tilapia, Lactobacillus plantarum 16 dalam
pekasam lampam, Lactobacillus casei BD-II kromosom dan Lactobacillus plantarum WCFS1 dalam pekasam sepat,
Corynebacterium vitaeruminis DSM 20294 dan Streptococcus anginosus C1051 dalam pekasam gelama. Manakala
Staphylococcus carnosus subsp. carnosus TM300 kromosom adalah LAB dominan dalam pekasam loma. Sementara
itu, sebatian aroma ditentukan melalui kaedah pengekstrakan cecair menggunakan pelarut metanol dan heksana.
Pemprofilan sebatian aroma dijalankan dengan kromatografi gas-spektometer jisim (GC-MS). Sebatian aroma dalam
ekstrak metanol dan heksana daripada lima jenis ikan pekasam dibandingkan. Bilangan sebatian aroma yang diekstrak
menggunakan metanol adalah lebih banyak berbanding dengan yang menggunakan heksana. Sebatian aroma yang
paling banyak dikesan adalah daripada pekasam loma. Asid karboksilik merupakan sebatian yang paling dominan
dalam ikan pekasam dan memberi bau hamis serta tengik.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry
Fulltext PRELIMINARY ASSESSMENT OF THE DISTRIBUTION OF PM2.5-BOUND POLYCYCLIC AROMATIC HYDROCARBONS IN PRIMARY SCHOOL ENVIRONMENTS IN KUALA LUMPUR

MOHAMAD FIRDAUS ISMAIL, MUHAMMAD FAIS FADZIL, NORHAYATI MOHD TAHIR, NORHAYATI MOHD TAHIR, MOHD TALIB LATIF, NOORLIN MOHAMAD

UMT Journal of Undergraduate Research, 2019;1(2):51-58.
MyJurnal

Fine particulate matter (aerodynamic diameter ≤2.5 μm) (PM2.5) has become a major concern because it can adsorb chemicals e.g. polycyclic aromatic hydrocarbons (PAHs) onto its surface. Although PAHs are priority pollutants that can cause adverse health effect, there is still limited information concerning indoor exposures to PAHs in Malaysia. This study aimed to characterise the distribution of PAHs bounded to PM2.5in primary school environments. Indoor and outdoor PM2.5 were collected between May and July 2017 using low volume samplers (LVS) at three public primary schools in the Federal Territory of Kuala Lumpur. PAHs were extracted by ultrasonic extraction with Dichloromethane: n-Hexane (1:1, v/v) as the extraction solvent and analysed using gas chromatography coupled with mass spectrometer (GC-MS). Based on the results, the average total concentration of PAHs (∑PAHs) ranged from 3.8 to 10.1 ng m-3and 1.6 to 8.0 ng m-3for outdoors and indoors, respectively. PAHs in PM2.5samples indicated the potential contribution of combustion at high temperature and indoor sources and the infiltration of outdoor PAHs were the important sources for outdoor and indoor, respectively. In addition, the diagnostic ratio analysis showed that vehicular emissions were the most predominant sources of PAHs in school environments.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry
Other factors to consider in the formation of chloropropandiol fatty esters in oil processes

Ramli MR, Siew WL, Ibrahim NA, Kuntom A, Abd Razak RA

Food Addit Contam Part A Chem Anal Control Expo Risk Assess, 2015;32(6):817-24.
PMID: 25798697 DOI: 10.1080/19440049.2015.1032368

This paper examines the processing steps of extracting palm oil from fresh fruit bunches in a way that may impact on the formation of chloropropandiol fatty esters (3-MCPD esters), particularly during refining. Diacylglycerols (DAGs) do not appear to be a critical factor when crude palm oils are extracted from various qualities of fruit bunches. Highly hydrolysed oils, in spite of the high free fatty acid (FFA) contents, did not show exceptionally high DAGs, and the oils did not display a higher formation of 3-MCPD esters upon heat treatment. However, acidity measured in terms of pH appears to have a strong impact on 3-MCPD ester formation in the crude oil when heated at high temperatures. The differences in the extraction process of crude palm oil from current commercial processes and that from a modified experimental process showed clearly the effect of acidity of the oil on the formation of 3-MCPD esters. This paper concludes that the washing or dilution step in palm oil mills removes the acidity of the vegetative materials and that a well-optimised dilution/washing step in the extraction process will play an important role in reducing formation of 3-MCPD esters in crude palm oil upon further heat processing.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry
Optimization of palm oil physical refining process for reduction of 3-monochloropropane-1,2-diol (3-MCPD) ester formation

Zulkurnain M, Lai OM, Tan SC, Abdul Latip R, Tan CP

J Agric Food Chem, 2013 Apr 3;61(13):3341-9.
PMID: 23464796 DOI: 10.1021/jf4009185

The reduction of 3-monochloropropane-1,2-diol (3-MCPD) ester formation in refined palm oil was achieved by incorporation of additional processing steps in the physical refining process to remove chloroester precursors prior to the deodorization step. The modified refining process was optimized for the least 3-MCPD ester formation and acceptable refined palm oil quality using response surface methodology (RSM) with five processing parameters: water dosage, phosphoric acid dosage, degumming temperature, activated clay dosage, and deodorization temperature. The removal of chloroester precursors was largely accomplished by increasing the water dosage, while the reduction of 3-MCPD esters was a compromise in oxidative stability and color of the refined palm oil because some factors such as acid dosage, degumming temperature, and deodorization temperature showed contradictory effects. The optimization resulted in 87.2% reduction of 3-MCPD esters from 2.9 mg/kg in the conventional refining process to 0.4 mg/kg, with color and oil stability index values of 2.4 R and 14.3 h, respectively.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry
Fulltext Optimization of headspace solid phase microextraction (HS-SPME) for the extraction of volatile organic compounds (VOCs) in MD2 pineapple

Syaidatul Faraha Zainuddin, Siti Raihan Zakaria, Norashikin Saim, Rossuriati Dol Hamid, Rozita Osman

Science Letters, 2020;14(2):58-70.
MyJurnal

Headspace solid phase microextraction (HS-SPME) was employed for the extraction of volatile organic compounds (VOCs) in MD2 pineapple (Ananas comosus L. var. comosus cv. MD2). Optimisation of HS-SPME operating parameters was conducted using three-factor, three-level Box–Behnken response surface experimental design to evaluate the interactive effects of temperature (30 – 50 ºC), extraction time (10 – 30 min) and salting effect (1 – 3 g of salt addition) on the amount of selected VOCs. Determination of VOCs was done using gas chromatography with spectrometry detector (GC-MSD). Extraction temperature was found to be significant (p < 0.05) in increasing the amount of selected VOCs (ethyl acetate, methyl isobutyrate and butanoic acid methyl ester). Based on the maximum amount of these VOCs, the optimum operating extraction conditions for HS-SPME were set up at temperature of 30 °C, time of 29 min and salt addition of 1 g. The optimized HS-SPME conditions were employed for the extraction of VOCs from pineapple of different varieties.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry
Fulltext Optimization of Cat's Whiskers Tea (Orthosiphon stamineus) Using Supercritical Carbon Dioxide and Selective Chemotherapeutic Potential against Prostate Cancer Cells

Al-Suede FS, Khadeer Ahamed MB, Abdul Majid AS, Baharetha HM, Hassan LE, Kadir MO, et al.

Evid Based Complement Alternat Med, 2014;2014:396016.
PMID: 25276215 DOI: 10.1155/2014/396016

Cat's whiskers (Orthosiphon stamineus) leaves extracts were prepared using supercritical CO2 (SC-CO2) with full factorial design to determine the optimum extraction parameters. Nine extracts were obtained by varying pressure, temperature, and time. The extracts were analysed using FTIR, UV-Vis, and GC-MS. Cytotoxicity of the extracts was evaluated on human (colorectal, breast, and prostate) cancer and normal fibroblast cells. Moderate pressure (31.1 MPa) and temperature (60°C) were recorded as optimum extraction conditions with high yield (1.74%) of the extract (B2) at 60 min extraction time. The optimized extract (B2) displayed selective cytotoxicity against prostate cancer (PC3) cells (IC50 28 µg/mL) and significant antioxidant activity (IC50 42.8 µg/mL). Elevated levels of caspases 3/7 and 9 in B2-treated PC3 cells suggest the induction of apoptosis through nuclear and mitochondrial pathways. Hoechst and rhodamine assays confirmed the nuclear condensation and disruption of mitochondrial membrane potential in the cells. B2 also demonstrated inhibitory effects on motility and colonies of PC3 cells at its subcytotoxic concentrations. It is noteworthy that B2 displayed negligible toxicity against the normal cells. Chemometric analysis revealed high content of essential oils, hydrocarbon, fatty acids, esters, and aromatic sesquiterpenes in B2. This study highlights the therapeutic potentials of SC-CO2 extract of cat's whiskers in targeting prostate carcinoma.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry
One pot synthesis, molecular structure and spectroscopic studies (X-ray, IR, NMR, UV-Vis) of novel 2-(4,6-dimethoxy-1,3,5-triazin-2-yl) amino acid ester derivatives

El-Faham A, Soliman SM, Osman SM, Ghabbour HA, Siddiqui MR, Fun HK, et al.

Spectrochim Acta A Mol Biomol Spectrosc, 2016 Apr 15;159:184-98.
PMID: 26845586 DOI: 10.1016/j.saa.2016.01.051

Novel series of 2-(4,6-dimethoxy,1,3,5-triazin-2-yl) amino acid ester derivatives were synthesized using simple one pot method in methanol. The products were obtained in high yields and purities as observed from their spectral data, elemental analyses, GC-MS and X-ray crystallographic analysis. The B3LYP/6-311G(d,p) calculated molecular structures are well correlated with the geometrical parameters obtained from the X-ray analyses. The spectroscopic properties such as IR vibrational modes, NMR chemical shifts and UV-Vis electronic transitions were discussed both experimentally and theoretically. The IR vibrational frequencies showed good correlations with the experimental data (R(2)=0.9961-0.9995). The electronic spectra were assigned based on the TD-DFT results. Intense electronic transition band is calculated at 198.1nm (f=0.1389), 204.2nm (f=0.2053), 205.0 (f=0.1704) and 205.7 (0.2971) for compounds 6a-i, respectively. The molecular orbital energy levels contributed in the longest wavelength transition band were explained. For all compounds, the experimental wavelengths showed red shifts compared to the calculations due to the solvent effect. The NMR chemical shifts were calculated using GIAO method. The NBO analyses were performed to predict the stabilization energies due to the electron delocalization processes occur in the studied systems.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry
Occurrence, distribution, and dechlorination of polychlorinated biphenyls and health risk assessment in Selangor River basin

Sakai N, Dayana E, Abu Bakar A, Yoneda M, Nik Sulaiman NM, Ali Mohd M

Environ Monit Assess, 2016 Oct;188(10):592.
PMID: 27679511

Polychlorinated biphenyls (PCBs) were monitored in surface water collected in the Selangor River basin, Malaysia, to identify the occurrence, distribution, and dechlorination process as well as to assess the potential adverse effects to the Malaysian population. Ten PCB homologs (i.e., mono-CBs to deca-CBs) were quantitated by using gas chromatography-mass spectrometry (GC/MS). The total concentration of PCBs in the 10 sampling sites ranged from limit of detection to 7.67 ng L(-1). The higher chlorinated biphenyls (tetra-CBs to deca-CBs) were almost not detected in most of the sampling sites, whereas lower chlorinated biphenyls (mono-CBs, di-CBs, and tri-CBs) dominated more than 90 % of the 10 homologs in all the sampling sites. Therefore, the PCB load was estimated to be negligible during the sampling period because PCBs have an extremely long half-life. The PCBs, particularly higher chlorinated biphenyls, could be thoroughly dechlorinated to mono-CBs to tri-CBs by microbial decomposition in sediment or could still be accumulated in the sediment. The lower chlorinated biphenyls, however, could be resuspended or desorbed from the sediment because they have faster desorption rates and higher solubility, compared to the higher chlorinated biphenyls. The health risk for the Malaysia population by PCB intake that was estimated from the local fish consumption (7.2 ng kg(-1) bw day(-1)) and tap water consumption (1.5 × 10(-3)-3.1 × 10(-3) ng kg(-1) bw day(-1)) based on the detected PCB levels in the surface water was considered to be minimal. The hazard quotient based on the tolerable daily intake (20 ng kg(-1) bw day(-1)) was estimated at 0.36.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry/methods
Nutrient improvement using statistical optimization for growth of Schizophyllum commune, and its antifungal activity against wood degrading fungi of rubberwood

Teoh YP, Don MM, Ujang S

Biotechnol Prog, 2012 Jan-Feb;28(1):232-41.
PMID: 21990033 DOI: 10.1002/btpr.714

Two statistical tools, Plackett-Burman design (PBD) and Box-Behnken design (BBD) were used to optimize the mycelia growth of Schizophyllum commune with different nutrient components. Results showed that 32.92 g/L of biomass were produced using a medium consisting of 18.74 g/L yeast extract, 38.65 g/L glucose, and 0.59 g/L MgSO(4).7H(2)O. The experimental data fitted well with the model predicted values within 0.09 to 0.77% error. The biomass was also tested for antifungal activity against wood degrading fungi of rubberwood. Results showed that the minimum inhibitory concentration (MIC) values for antifungal activity range from 0.16 to 5.00 μg/μL. The GC-MS analysis indicated that this fungus produced several compounds, such as glycerin, 2(3H)-furanone, 5-heptyldihydro-, 4H-pyran-4-one, 2,3-dihydro-3,5-dihydroxy-6-methyl-, and triacetin.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry/methods
Fulltext Nutrient and Sensory Metabolites Profiling of Averrhoa Carambola L. (Starfruit) in the Context of Its Origin and Ripening Stage by GC/MS and Chemometric Analysis

Ramadan NS, Wessjohann LA, Mocan A, Vodnar DC, El-Sayed NH, El-Toumy SA, et al.

Molecules, 2020 May 22;25(10).
PMID: 32455938 DOI: 10.3390/molecules25102423

Averrhoa carambola L. is a tropical tree with edible fruit that grows at different climatic conditions. Despite its nutritive value and reported health benefits, it is a controversial fruit owing to its rich oxalate content. The present study aimed at investigating aroma and nutrient primary metabolites distribution in A. carambola fruits grown in Indonesia, Malaysia (its endemic origin) versus Egypt, and at different ripening stages. Two techniques were employed to assess volatile and non-volatile metabolites including headspace solid-phase micro-extraction (HS-SPME) joined with gas chromatography coupled with mass-spectrometry (GC-MS) and GC-MS post silylation, respectively. Twenty-four volatiles were detected, with esters amounting for the major class of volatiles in Egyptian fruit at ca. 66%, with methyl caproate as the major component, distinguishing it from other origins. In contrast, aldehydes predominated tropically grown fruits with the ether myristicin found exclusively in these. Primary metabolites profiling led to the identification of 117 metabolites viz. sugars, polyols and organic acids. Fructose (38-48%) and glucose (21-25%) predominated sugar compositions in ripe fruits, whereas sorbitol was the major sugar alcohol (2.4-10.5%) in ripe fruits as well. Oxalic acid, an anti-nutrient with potential health risks, was the major organic acid detected in all the studied fruits (1.7-2.7%), except the Malaysian one (0.07%). It increases upon fruit ripening, including considerable amounts of volatile oxalate esters detected via SPME, and which must not be omitted in total oxalate determinations for safety assessments.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry
Novel solid-phase membrane tip extraction and gas chromatography with mass spectrometry methods for the rapid analysis of triazine herbicides in real waters

Sanagi MM, Muhammad SS, Hussain I, Ibrahim WA, Ali I

J Sep Sci, 2015 Feb;38(3):433-8.
PMID: 25421899 DOI: 10.1002/jssc.201400912

Novel, fast, selective, eco-friendly and reproducible solid-phase membrane tip extraction and gas chromatography with mass spectrometry methods were developed and validated for the analysis of triazine herbicides (atrazine and secbumeton) in stream and lake waters. The retention times of atrazine and secbumeton were 7.48 and 8.51 min. The solid-phase membrane tip extraction was carried out in semiautomated dynamic mode on multiwall carbon nanotubes enclosed in a cone-shaped polypropylene membrane cartridge. Acetone and methanol were found as the best preconditioning and desorption solvents, respectively. The extraction and desorption times for these herbicides were 15.0 and 10.0 min, respectively. The percentage recoveries of atrazine and secbumeton were 88.0 and 99.0%. The linearity range was 0.50-80.0 μg/L (r(2) > 0.994), with detection limits (<0.47 μg/L, S/N = 3) and good reproducibility (<8.0%). The ease of operation, eco-friendly nature, and low cost of solid-phase membrane tip extraction made these methods novel. The Solid-phase membrane tip extraction method was optimized by considering the effect of extraction time, desorbing solvents and time.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry
Novel sol-gel hybrid methyltrimethoxysilane-tetraethoxysilane as solid phase extraction sorbent for organophosphorus pesticides

Wan Ibrahim WA, Veloo KV, Sanagi MM

J Chromatogr A, 2012 Mar 16;1229:55-62.
PMID: 22326188 DOI: 10.1016/j.chroma.2012.01.022

A novel sol-gel hybrid methyltrimethoxysilane-tetraethoxysilane (MTMOS-TEOS) was produced and applied as sorbent for solid phase extraction (SPE). Five selected organophosphorus pesticides (OPPs) were employed as model compounds to evaluate the extraction performance of the synthesized sol-gel organic-inorganic hybrid MTMOS-TEOS. Analysis was performed using gas chromatography-mass spectrometry. Several important SPE parameters were optimized. Under the optimum extraction conditions, the method using the sol-gel organic-inorganic hybrid MTMOS-TEOS as SPE sorbent showed good linearity in the range of 0.001-1 μg L(-1), good repeatability (RSD 2.1-3.1%, n=5), low limits of detection at S/N=3 (0.5-0.9 pg mL(-1)) and limit of quantification (1-3 pg mL(-1), S/N=10). The performance of the MTMOS-TEOS SPE was compared to commercial C18 Supelclean SPE since C18 SPE is widely used for OPPs. The MTMOS-TEOS SPE method LOD was 500-600 × lower than the LOD of commercial C18 SPE. The LOD achieved with the sol-gel organic-inorganic hybrid MTMOS-TEOS SPE sorbent allowed the detection of these OPPs in drinking water well below the level set by European Union (EU) at 0.1 μg L(-1) of each pesticides. The developed MTMOS-TEOS SPE method was successfully applied to real sample analysis of the selected OPPs from several water samples and its application extended to the analysis of several fruits samples. Excellent recoveries and RSDs of the OPPs were obtained from the various water samples (recoveries: 97-111%, RSDs 0.4-2.8%, n=3) and fruit samples (recoveries: 96-111%), RSDs 1-4%, n=5) using the sol-gel organic-inorganic hybrid MTMOS-TEOS SPE sorbent. Recoveries and RSDs of OPPs from river water samples and fruit samples using C18 Supelclean SPE sorbent were 91-97%, RSD 0.9-2.6, n=3 and 86-96%, RSD 3-8%, n=5, respectively). The novel sol-gel hybrid MTMOS-TEOS SPE sorbent demonstrate the potential as an alternative inexpensive extraction sorbent for OPPs with higher sensitivity for the OPPs.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry/methods*
Mutagenic and antimutagenic assessment of methanol leaf extract of Myristica fragrans (Houtt.) using in vitro and in vivo genetic assays

Akinboro A, Mohamed KB, Asmawi MZ, Othman AS, Ying TH, Maidin SM

Drug Chem Toxicol, 2012 Oct;35(4):412-22.
PMID: 22149219 DOI: 10.3109/01480545.2011.638300

The role of diets in causing cancers necessitates the ongoing search for natural antimutagens of promising anticancer therapeutics. This study determined the potential anticancer efficacy of the leaf extract of Myristica fragrans (Houtt.). Methanol leaf extract of M. fragrans (Houtt.) alone was screened for mutagenicity in the bacterial reverse mutation (Ames) test, using the Salmonella typhimurium TA100 strain, the Allium cepa, and the mouse in vivo bone marrow micronucleus tests. The antimutagenicity of this extract against benzo[a]pyrene- and cyclophosphamide-induced mutations was evaluated. An antioxidant test on the extract was performed with 2,2-diphenyl-1-picrylhydrazyl, using butylated hydroxyanisole (BHA) and butylated hydroxytoluene (BHT) as the standards, whereas its phytochemicals were elucidated by following the gas chromatography/mass spectrometry protocol. In S. typhimurium (TA100), the mutagenicity ratio at 200,500 and 1,000 µg/well was >2. Cell division in the A. cepa root tips and mouse bone marrow was significantly (P ≤ 0.05) inhibited at 2,000 and 4,000 mg/kg, whereas the observed chromosomal aberrations and micronucleated polychromatic erythrocytes were non-dose-related and were insignificantly (P ≥ 0.05) different from the negative control. Inhibition of benzo[a]pyrene- and cyclophosphamide-induced mutagenicity by this extract was above 40%. Half-maximal inhibitory concentration of the extract in the antioxidant test was lower than that of BHA and BHT. Phytochemical compounds, possessing antioxidant activity, may be responsible for the observed effects, suggesting a strong antimutagenic activity of the MeOH leaf extract of M. fragrans, a necessary characteristic of a promising anticancer agent.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry
Multivariate study of parameters in the determination of pesticide residues in apple by headspace solid phase microextraction coupled to gas chromatography-mass spectrometry using experimental factorial design

Abdulra'uf LB, Tan GH

Food Chem, 2013 Dec 15;141(4):4344-8.
PMID: 23993624 DOI: 10.1016/j.foodchem.2013.07.022

Solid-phase microextraction (SPME) is a solvent-less sample preparation method which combines sample preparation, isolation, concentration and enrichment into one step. In this study, multivariate strategy was used to determine the significance of the factors affecting the solid phase microextraction of pesticide residues (fenobucarb, diazinon, chlorothalonil and chlorpyrifos) using a randomised factorial design. The interactions and effects of temperature, time and salt addition on the efficiency of the extraction of the pesticide residues were evaluated using 2(3) factorial designs. The analytes were extracted with 100 μm PDMS fibres according to the factorial design matrix and desorbed into a gas chromatography-mass spectrometry detector. The developed method was applied for the analysis of apple samples and the limits of detection were between 0.01 and 0.2 μg kg(-)(1), which were lower than the MRLs for apples. The relative standard deviations (RSD) were between 0.1% and 13.37% with average recovery of 80-105%. The linearity ranges from 0.5-50 μg kg(-)(1) with correlation coefficient greater than 0.99.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry/methods*
Molecular docking of compounds from Clinacanthus nutans extract detected by GC-MS analysis with the SARS-CoV-2 main protease and ACE2 protein

Ismail NZ, Adebayo IA, Mohamad Zain NN, Arsad H

Nat Prod Res, 2021 May 05.
PMID: 33949277 DOI: 10.1080/14786419.2021.1919104

Clinacanthus nutans has been reported to have many medicinal properties and it is traditionally used in treating viral lesions. This study aims to determine the molecular docking of C. nutans compounds detected by Gas Chromatography-Mass Spectrometry (GC-MS) with the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 main protease) protein and its host receptor angiotensin-converting enzyme 2 (ACE2) protein using the AutoDock 4.2 tool. The drug-likeness and molecular docking analyses showed that fourteen compounds of C. nutans satisfied the Lipinski's rule of five and they exhibited good inhibitory effects against the SARS-Cov-2 main protease and ACE2 proteins. In addition, the glyceryl 2-linolenate compound was found to have the most potent binding affinities with both proteins. The results provide useful insights into the molecular inhibitory interactions of C. nutans compounds detected by GC-MS analysis with the targeted SARS-CoV-2 main protease and ACE2 protein.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry
Molecular docking and molecular dynamic simulations of apoptosis proteins with potential anticancer compounds present in Clinacanthus nutans extract using gas chromatography-mass spectrometry

Ismail NZ, Mohamed WAS, Ab Rahim N, Hashim NM, Adebayo IA, Mohamad Zain NN, et al.

J Biomol Struct Dyn, 2023;41(13):6104-6120.
PMID: 35899385 DOI: 10.1080/07391102.2022.2101530

Clinacanthus nutans is a medicinal plant recognised for its anticancer properties. We previously discovered that the C. nutans extract had the most potent inhibitory effect on MCF7 breast cancer cell and significantly induced apoptosis. However, there is a scarcity of studies demonstrating the molecular interactions of C. nutans-derived chemical compounds associated with apoptosis-related proteins. Therefore, the objective of this study was to determine the potential chemical compounds found in the C. nutans extract and examine their interactions with the targeted apoptotic proteins using molecular docking and molecular dynamic simulations. To address this objective, the compounds found in the SF2 extract of C. nutans were analysed using Gas Chromatography-Mass Spectrometry (GC-MS). The molecular interaction of the compounds with the targeted apoptotic proteins were determined using molecular docking and molecular dynamic simulations. GC-MS analysis revealed a total of 32 compounds in the SF2 extract. Molecular docking analysis showed that compound β-amyrenol had the highest binding affinity for MDM2-P53 (-7.26 kcal/mol), BCL2 (-11.14 kcal/mol), MCL1-BAX (-6.42 kcal/mol), MCL1-BID (-6.91 kcal/mol), and caspase-9 (-12.54 kcal/mol), whereas campesterol had the highest binding affinity for caspase-8 (-10.11 kcal/mol) and caspase-3 (-10.14 kcal/mol). These selected compounds were subjected to molecular dynamic simulation at 310 K for 100 ns. The results showed that the selected protein-ligand conformation complexes were stable, compact, and did not alter much when compared to the protein references. The findings indicate that β-amyrenol and campesterol are potentially significant compounds that might provide insight into the molecular interactions of the compounds with the apoptosis-related proteins.Communicated by Ramaswamy H. Sarma.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry
Modeling of crude oil biodegradation using two phase partitioning bioreactor

Fakhru'l-Razi A, Peyda M, Ab Karim Ghani WA, Abidin ZZ, Zakaria MP, Moeini H

Biotechnol Prog, 2014 Jul-Aug;30(4):797-805.
PMID: 24692323 DOI: 10.1002/btpr.1911

In this work, crude oil biodegradation has been optimized in a solid-liquid two phase partitioning bioreactor (TPPB) by applying a response surface methodology based d-optimal design. Three key factors including phase ratio, substrate concentration in solid organic phase, and sodium chloride concentration in aqueous phase were taken as independent variables, while the efficiency of the biodegradation of absorbed crude oil on polymer beads was considered to be the dependent variable. Commercial thermoplastic polyurethane (Desmopan®) was used as the solid phase in the TPPB. The designed experiments were carried out batch wise using a mixed acclimatized bacterial consortium. Optimum combinations of key factors with a statistically significant cubic model were used to maximize biodegradation in the TPPB. The validity of the model was successfully verified by the good agreement between the model-predicted and experimental results. When applying the optimum parameters, gas chromatography-mass spectrometry showed a significant reduction in n-alkanes and low molecular weight polycyclic aromatic hydrocarbons. This consequently highlights the practical applicability of TPPB in crude oil biodegradation.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry
Microenvironmental Interplay Predominated by Beneficial Aspergillus Abates Fungal Pathogen Incidence in Paddy Environment

Fan X, Matsumoto H, Wang Y, Hu Y, Liu Y, Fang H, et al.

Environ Sci Technol, 2019 Nov 19;53(22):13042-13052.
PMID: 31631659 DOI: 10.1021/acs.est.9b04616

Rice fungal pathogens, responsible for severe rice yield loss and biotoxin contamination, cause increasing concerns on environmental safety and public health. In the paddy environment, we observed that the asymptomatic rice phyllosphere microenvironment was dominated by an indigenous fungus, Aspergillus cvjetkovicii, which positively correlated with alleviated incidence of Magnaporthe oryzae, one of the most aggressive plant pathogens. Through the comparative metabolic profiling for the rice phyllosphere microenvironment, two metabolites were assigned as exclusively enriched metabolic markers in the asymptomatic phyllosphere and increased remarkably in a population-dependent manner with A. cvjetkovicii. These two metabolites evidenced to be produced by A. cvjetkovicii in either a phyllosphere microenvironment or artificial media were purified and identified as 2(3H)-benzofuranone and azulene, respectively, by gas chromatography coupled to triple quadrupole mass spectrometry and nuclear magnetic resonance analyses. Combining with bioassay analysis in vivo and in vitro, we found that 2(3H)-benzofuranone and azulene exerted dissimilar actions at the stage of infection-related development of M. oryzae. A. cvjetkovicii produced 2(3H)-benzofuranone at the early stage to suppress MoPer1 gene expression, leading to inhibited mycelial growth, while azulene produced lately was involved in blocking of appressorium formation by downregulation of MgRac1. More profoundly, the microenvironmental interplay dominated by A. cvjetkovicii significantly blocked M. oryzae epidemics in the paddy environment from 54.7 to 68.5% (p < 0.05). Our study first demonstrated implication of the microenvironmental interplay dominated by indigenous and beneficial fungus to ecological balance and safety of the paddy environment.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry
Fulltext Microbial Biodegradation of Paraffin Wax in Malaysian Crude Oil Mediated by Degradative Enzymes

Adlan NA, Sabri S, Masomian M, Ali MSM, Rahman RNZRA

Front Microbiol, 2020;11:565608.
PMID: 33013795 DOI: 10.3389/fmicb.2020.565608

The deposition of paraffin wax in crude oil is a problem faced by the oil and gas industry during extraction, transportation, and refining of crude oil. Most of the commercialized chemical additives to prevent wax are expensive and toxic. As an environmentally friendly alternative, this study aims to find a novel thermophilic bacterial strain capable of degrading paraffin wax in crude oil to control wax deposition. To achieve this, the biodegradation of crude oil paraffin wax by 11 bacteria isolated from seawater and oil-contaminated soil samples was investigated at 70°C. The bacteria were identified as Geobacillus kaustophilus N3A7, NFA23, DFY1, Geobacillus jurassicus MK7, Geobacillus thermocatenulatus T7, Parageobacillus caldoxylosilyticus DFY3 and AZ72, Anoxybacillus geothermalis D9, Geobacillus stearothermophilus SA36, AD11, and AD24. The GCMS analysis showed that strains N3A7, MK7, DFY1, AD11, and AD24 achieved more than 70% biodegradation efficiency of crude oil in a short period (3 days). Notably, most of the strains could completely degrade C37-C40 and increase the ratio of C14-C18, especially during the initial 2 days incubation. In addition, the degradation of crude oil also resulted in changes in the pH of the medium. The degradation of crude oil is associated with the production of degradative enzymes such as alkane monooxygenase, alcohol dehydrogenase, lipase, and esterase. Among the 11 strains, the highest activities of alkane monooxygenase were recorded in strain AD24. A comparatively higher overall alcohol dehydrogenase, lipase, and esterase activities were observed in strains N3A7, MK7, DFY1, AD11, and AD24. Thus, there is a potential to use these strains in oil reservoirs, crude oil processing, and recovery to control wax deposition. Their ability to withstand high temperature and produce degradative enzymes for long-chain hydrocarbon degradation led to an increase in the short-chain hydrocarbon ratio, and subsequently, improving the quality of the oil.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry
Fulltext Methodological issues in a prospective study on plasma concentrations of persistent organic pollutants and pancreatic cancer risk within the EPIC cohort

Gasull M, Pumarega J, Kiviranta H, Rantakokko P, Raaschou-Nielsen O, Bergdahl IA, et al.

Environ Res, 2019 Feb;169:417-433.
PMID: 30529143 DOI: 10.1016/j.envres.2018.11.027

BACKGROUND: The use of biomarkers of environmental exposure to explore new risk factors for pancreatic cancer presents clinical, logistic, and methodological challenges that are also relevant in research on other complex diseases.
OBJECTIVES: First, to summarize the main design features of a prospective case-control study -nested within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort- on plasma concentrations of persistent organic pollutants (POPs) and pancreatic cancer risk. And second, to assess the main methodological challenges posed by associations among characteristics and habits of study participants, fasting status, time from blood draw to cancer diagnosis, disease progression bias, basis of cancer diagnosis, and plasma concentrations of lipids and POPs. Results from etiologic analyses on POPs and pancreatic cancer risk, and other analyses, will be reported in future articles.
METHODS: Study subjects were 1533 participants (513 cases and 1020 controls matched by study centre, sex, age at blood collection, date and time of blood collection, and fasting status) enrolled between 1992 and 2000. Plasma concentrations of 22 POPs were measured by gas chromatography - triple quadrupole mass spectrometry (GC-MS/MS). To estimate the magnitude of the associations we calculated multivariate-adjusted odds ratios by unconditional logistic regression, and adjusted geometric means by General Linear Regression Models.
RESULTS: There were differences among countries in subjects' characteristics (as age, gender, smoking, lipid and POP concentrations), and in study characteristics (as time from blood collection to index date, year of last follow-up, length of follow-up, basis of cancer diagnosis, and fasting status). Adjusting for centre and time of blood collection, no factors were significantly associated with fasting status. Plasma concentrations of lipids were related to age, body mass index, fasting, country, and smoking. We detected and quantified 16 of the 22 POPs in more than 90% of individuals. All 22 POPs were detected in some participants, and the smallest number of POPs detected in one person was 15 (median, 19) with few differences by country. The highest concentrations were found for p,p'-DDE, PCBs 153 and 180 (median concentration: 3371, 1023, and 810 pg/mL, respectively). We assessed the possible occurrence of disease progression bias (DPB) in eight situations defined by lipid and POP measurements, on one hand, and by four factors: interval from blood draw to index date, tumour subsite, tumour stage, and grade of differentiation, on the other. In seven of the eight situations results supported the absence of DPB.
CONCLUSIONS: The coexistence of differences across study centres in some design features and participant characteristics is of relevance to other multicentre studies. Relationships among subjects' characteristics and among such characteristics and design features may play important roles in the forthcoming analyses on the association between plasma concentrations of POPs and pancreatic cancer risk.

Matched MeSH terms: Gas Chromatography-Mass Spectrometry

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