Displaying publications 241 - 260 of 326 in total

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  1. Al-Qaim FF, Mussa ZH, Yuzir A, Latip J, Othman MR
    J Environ Sci (China), 2018 Dec;74:134-146.
    PMID: 30340667 DOI: 10.1016/j.jes.2018.02.019
    Prazosin (PRZ) and levonorgestrel (LNG) are widely used as an anti-disease drugs due to their biological activity in the human body. The frequent detection of these compounds in water samples requires alternative technologies for the removal of both compounds. After electrochemical degradation of PRZ and LNG, the parent compounds could be completely removed after treatment, but the identification and characterization of by-products are necessary as well. In this study, the effects of NaCl concentration and applied voltage were investigated during the electrochemical degradation process. The results revealed that the increase of NaCl concentration and applied voltage could promote the generation of hypochlorite OCl- and then enhance the degradation of PRZ and LNG. After initial study, 6V and 0.2g NaCl were selected for further experiments (96% and 99% removal of PRZ and LNG after 40min, respectively). Energy consumption was also evaluated and calculated for PRZ and LNG at 3, 6 and 8V. Solid phase extraction (SPE) method plays an important role in enhancing the detection limit of by-products. Furthermore, characterization and identification of chlorinated and non-chlorinated by-products were conducted using an accurate liquid chromatography-time of flight/mass spectrometry LC-TOF/MS instrument. The monitoring of products during the electrochemical degradation process was performed at 6V and 0.2g NaCl in a 50mL solution. The results indicated that two chlorinated products were formed during the electrochemical process. The toxicity of by-products toward E. coli bacteria was investigated at 37°C and 20hr incubation time.
    Matched MeSH terms: Chromatography, Liquid
  2. Juvarajah T, Wan-Ibrahim WI, Ashrafzadeh A, Othman S, Hashim OH, Fung SY, et al.
    Breastfeed Med, 2018 11;13(9):631-637.
    PMID: 30362820 DOI: 10.1089/bfm.2018.0057
    BACKGROUND: Bioactive proteins from milk fat globule membrane (MFGM) play extensive roles in cellular processes and defense mechanisms in infants. The aims of this study were to identify differences in protein compositions in human and caprine MFGM using proteomics and evaluate possible nutritional benefits of caprine milk toward an infant's growth, as an alternative when breastfeeding or human milk administration is not possible or inadequate.

    MATERIALS AND METHODS: Human and caprine MFGM proteins were isolated and analyzed, initially by polyacrylamide gel electrophoresis, and subsequently by quadrupole time-of-flight liquid chromatography-mass spectrometry. This was then followed by database search and gene ontology analysis. In general, this method selectively analyzed the abundantly expressed proteins in milk MFGM.

    RESULTS: Human MFGM contains relatively more abundant bioactive proteins compared with caprine. While a total of 128 abundant proteins were detected in the human MFGM, only 42 were found in that of the caprine. Seven of the bioactive proteins were apparently found to coexist in both human and caprine MFGM.

    RESULTS/DISCUSSION: Among the commonly detected MFGM proteins, lactotransferrin, beta-casein, lipoprotein lipase, fatty acid synthase, and butyrophilin subfamily 1 member A1 were highly expressed in human MFGM. On the other hand, alpha-S1-casein and EGF factor 8 protein, which are also nutritionally beneficial, were found in abundance in caprine MFGM. The large number of human MFGM abundant proteins that were generally lacking in caprine appeared to mainly support human metabolic and developmental processes.

    CONCLUSION: Our data demonstrated superiority of human MFGM by having more than one hundred nutritionally beneficial and abundantly expressed proteins, which are clearly lacking in caprine MFGM. The minor similarity in the abundantly expressed bioactive proteins in caprine MFGM, which was detected further, suggests that it is still nutritionally beneficial, and therefore should be included when caprine milk-based formula is used as an alternative.

    Matched MeSH terms: Chromatography, Liquid
  3. Kwan PP, Banerjee S, Shariff M, Yusoff FM
    Vet World, 2019 Sep;12(9):1416-1421.
    PMID: 31749575 DOI: 10.14202/vetworld.2019.1416-1421
    Background and Aim: Malachite green (MG) is an effective antiparasitic and antifungal chemical for treatment of fish. However, MG is reported to be a potential carcinogen. Yet, it is widely used in aquaculture despite its prohibition for use in food-producing animals by the EU and USFDA. The present study quantified MG residues and evaluated the oxidative stress in red tilapia when exposed to subacute and sublethal concentrations of MG.

    Materials and Methods: Red tilapia exposed to subacute (0.105 mg/L for 20 days) and sublethal (0.053 mg/L for 60 days) concentrations were evaluated for total plasma protein, total immunoglobulin, nitroblue tetrazolium activity, malondialdehyde, reduced glutathione (GSH), and catalase (CAT) activity levels. The residues of MG and leuco-MG (LMG) were also quantified in the fish muscles using liquid chromatography-tandem mass spectrometry.

    Results: Fish exposed to subacute concentration showed higher CAT on day 10 in the liver and days 5 and 15 in the spleen, whereas in fish exposed to the sublethal concentration, higher levels of GSH were observed on day 1 in the kidney and day 50 in the spleen. Fish muscle was able to accumulate the sum of MG and LMG of 108.04 µg/kg for subacute (day 20) and 82.68 µg/kg for sublethal (day 60).

    Conclusion: This study showed that red tilapia was able to adapt to the stress caused by exposure to MG at sublethal concentration.

    Matched MeSH terms: Chromatography, Liquid
  4. Alagan A, Jantan I, Kumolosasi E, Azmi N
    Bioinformation, 2019;15(8):535-541.
    PMID: 31719762 DOI: 10.6026/97320630015535
    Phyllanthus amarus Schumach. and Thonn. is a wide spread medicinal herb with various traditional uses. It is well documented for its antioxidant, anti-inflammatory, and hepatoprotective activities. Therefore, it is of interest to evaluate the 80% ethanol extract of Phyllanthus amarus (PA) on spatial memory using the 8-radial arm maze (8-RAM) in mice after induction of neuro inflammation by lipopolysaccharide (LPS) in a 14- and 28-days treatment study. LC-MS/MS was performed to profile the chemical composition in PA extract. Mice were treated orally with 5% v/v tween 20, PA extract (100, 200 and 400 mg/kg), or ibuprofen (IBF 40 mg/kg) for 14 and 28 days. All groups were challenged with LPS (1 mg/kg) via intraperitoneal (i.p.) injection a day prior to the 8-RAM task except for the negative control group which received an i.p. injection of saline. Data obtained were analyzed with one-way ANOVA followed by post hoc Dunnett's test (comparison of all groups against vehicle control). Analysis of LC-MS/MS data revealed the presence of 16 compounds in the PA extract. Administration of PA extract at 200 and 400 mg/kg for 14 and 28 days significantly (*P<0.05) decreased the working and reference memory errors against LPS-induced spatial memory impairment. The observed protective action is possibly due to the putative antineuroinflammatory effects of PA. In conclusion, PA extract possess neuroprotective effects against spatial memory impairment mediated by LPS.
    Matched MeSH terms: Chromatography, Liquid
  5. Chen WL, Ling YS, Lee DJH, Lin XQ, Chen ZY, Liao HT
    Chemosphere, 2020 Mar;242:125268.
    PMID: 31896175 DOI: 10.1016/j.chemosphere.2019.125268
    This study investigated chlorinated transformation products (TPs) and their parent micropollutants, aromatic pharmaceuticals and personal care products (PPCPs) in the urban water bodies of two metropolitan cities. Nine PPCPs and 16 TPs were quantitatively or semi-quantitatively determined using isotope dilution techniques and liquid chromatography-tandem mass spectrometry. TPs and most PPCPs were effectively removed by conventional wastewater treatments in a wastewater treatment plant (WWTP). Chlorinated parabens and all PPCPs (at concentrations below 1000 ng/L) were present in the waters receiving treated wastewater. By contrast, the waters receiving untreated wastewater contained higher levels of PPCPs (up to 9400 ng/L) and more species of chlorinated TPs including chlorinated parabens, triclosan, diclofenac, and bisphenol A. The very different chemical profiles between the water bodies of the two cities of similar geographical and climatic properties may be attributed to their respective uses of chemicals and policies of wastewater management. No apparent increase in the number of species or abundances of TPs was observed in either the chlorinated wastewater or the seawater rich in halogens. This is the first study to elucidate and compare the profiles of multiple TPs and their parent PPCPs in the water bodies of coastal cities from tropical islands. Our findings suggest that chlorinated derivatives of bisphenol A, diclofenac, triclosan, and parabens in the surface water originate from sources other than wastewater disinfection or marine chlorination. Although further studies are needed to identify the origins, conventional wastewater treatments may protect natural water bodies against contamination by those chlorinated substances.
    Matched MeSH terms: Chromatography, Liquid
  6. Hempolchom C, Reamtong O, Sookrung N, Srisuka W, Sakolvaree Y, Chaicumpa W, et al.
    Acta Trop, 2019 Jun;194:82-88.
    PMID: 30922801 DOI: 10.1016/j.actatropica.2019.03.026
    Although several studies have reported pharmacological and immunological activity, as well as the role of black flies in transmitting pathogens to vertebrate hosts through salivary glands (SG) during blood feeding, SG proteomes of the anthropophilic black flies in Thailand have never been reported. Therefore, this study determined the SG proteomes of female S. nigrogilvum and S. nodosum. Sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional (2-DE) gels containing separated SG proteins of individual species were subjected to liquid chromatography-tandem mass spectrometry (LCMS/MS) and an orthologous protein search from eukaryotic organism, nematocera and simuliidae databases for total protein identification. SDS-PAGE and protein staining revealed at least 13 and 9 major protein bands in the SGs of female S. nigrogilvum and S. nodosum, respectively, as well as several minor ones. The 2-DE demonstrated a total of 56 and 41 protein spots for S. nigrogilvum and S. nodosum, respectively. Most of the proteins obtained in both species were enzymes involved in blood feeding, including proteases, apyrases, hyaluronidases, aminopeptidase and elastase. The results obtained in this study provided a new body of knowledge for a better understanding on the role of salivary gland proteins in these black fly species in Thailand.
    Matched MeSH terms: Chromatography, Liquid
  7. Karim ME, Shetty J, Islam RA, Kaiser A, Bakhtiar A, Chowdhury EH
    Pharmaceutics, 2019 Feb 20;11(2).
    PMID: 30791612 DOI: 10.3390/pharmaceutics11020089
    Inorganic nanoparticles hold great potential in the area of precision medicine, particularly for treating cancer owing to their unique physicochemical properties, biocompatibility and improved pharmacokinetics properties compared to their organic counterparts. Here we introduce strontium sulfite nanoparticles as new pH-responsive inorganic nanocarriers for efficient transport of siRNAs into breast cancer cells. We employed the simplest nanoprecipitation method to generate the strontium sulfite nanoparticles (SSNs) and demonstrated the dramatic roles of NaCl and d-glucose in particle growth stabilization in order to produce even smaller nanosize particles (Na-Glc-SSN) with high affinity towards negatively charged siRNA, enabling it to efficiently enter the cancer cells. Moreover, the nanoparticles were found to be degraded with a small drop in pH, suggesting their potential capability to undergo rapid dissolution at endosomal pH so as to release the payload. While these particles were found to be nontoxic to the cells, they showed higher potency in facilitating cancer cell death through intracellular delivery and release of oncogene-specific siRNAs targeting ros1 and egfr1 mRNA transcripts, than the strontium sulfite particles prepared in absence of NaCl and d-glucose, as confirmed by growth inhibition assay. The mouse plasma binding analysis by Q-TOF LC-MS/MS demonstrated less protein binding to smaller particles of Na-Glc-SSNs. The biodistribution studies of the particles after 4 h of treatment showed Na-Glc-SSNs had less off-target distribution than SSNs, and after 24 h, all siRNAs were cleared from all major organs except the tumors. ROS1 siRNA with its potential therapeutic role in treating 4T1-induced breast tumor was selected for subsequent in vivo tumor regression study, revealing that ROS1 siRNA-loaded SSNs exerted more significant anti-tumor effects than Na-Glc-SSNs carrying the same siRNA following intravenous administration, without any systemic toxicity. Thus, strontium sulfite emerged as a powerful siRNA delivery tool with potential applications in cancer gene therapy.
    Matched MeSH terms: Chromatography, Liquid
  8. Wong EYL, Loh GOK, Tan YTF, Peh KK
    Drug Dev Ind Pharm, 2021 Feb;47(2):197-206.
    PMID: 33300818 DOI: 10.1080/03639045.2020.1862177
    OBJECTIVE: The aim of the study was to develop a simple, highthroughput and sensitive LC-MS/MS method and apply to a bioequivalence study of montelukast, a light sensitive drug.

    METHOD: The effects of organic modifiers in mobile phase, protein precipitation agent to plasma sample ratio, and light on montelukast stability in unprocessed and processed human plasma, were evaluated. Validation was conducted in accordance with European Medicines Agency Guideline on bioanalytical method validation.

    RESULTS: No interference peak was observed when acetonitrile was used as an organic modifier. Acetonitrile to plasma ratio of 4:1 produced clean plasma sample. Approximately 3 % of cis isomer was detected in unprocessed plasma samples while 21 % of cis isomer was detected in processed plasma samples after exposing to fluorescent light for 24h. The standard calibration curve was linear over 3.00-1200.00 ng/mL. All method validation parameters were within the acceptance criteria.

    CONCLUSION: The validated method was successfully applied to a bioequivalence study of two montelukast formulations involving 24 healthy Malaysian volunteers. The light stability of a light sensitive drug in unprocessed and processed human plasma samples should be studied prior to pharmacokinetic/bioequivalence studies. Measures could then be taken to protect the analyte in human plasma from light degradation.

    Matched MeSH terms: Chromatography, Liquid
  9. Zèches M, Mesbah K, Loukaci A, Richard B, Schaller H, Sévenet T, et al.
    Planta Med, 1995 Feb;61(1):97.
    PMID: 7701009
    Matched MeSH terms: Chromatography, Liquid
  10. Ahmad SJ, Abdul Rahim MBH, Baharum SN, Baba MS, Zin NM
    J Trop Med, 2017;2017:2189814.
    PMID: 29123551 DOI: 10.1155/2017/2189814
    Natural products continue to play an important role as a source of biologically active substances for the development of new drug. Streptomyces, Gram-positive bacteria which are widely distributed in nature, are one of the most popular sources of natural antibiotics. Recently, by using a bioassay-guided fractionation, an antimalarial compound, Gancidin-W, has been discovered from these bacteria. However, this classical method in identifying potentially novel bioactive compounds from the natural products requires considerable effort and is a time-consuming process. Metabolomics is an emerging "omics" technology in systems biology study which integrated in process of discovering drug from natural products. Metabolomics approach in finding novel therapeutics agent for malaria offers dereplication step in screening phase to shorten the process. The highly sensitive instruments, such as Liquid Chromatography-Mass Spectrophotometry (LC-MS), Gas Chromatography-Mass Spectrophotometry (GC-MS), and Nuclear Magnetic Resonance ((1)H-NMR) spectroscopy, provide a wide range of information in the identification of potentially bioactive compounds. The current paper reviews concepts of metabolomics and its application in drug discovery of malaria treatment as well as assessing the antimalarial activity from natural products. Metabolomics approach in malaria drug discovery is still new and needs to be initiated, especially for drug research in Malaysia.
    Matched MeSH terms: Chromatography, Liquid
  11. Subramaniam S, Raman J, Sabaratnam V, Heng CK, Kuppusamy UR
    Int J Med Mushrooms, 2017;19(10):849-859.
    PMID: 29256840 DOI: 10.1615/IntJMedMushrooms.2017024355
    This study was conducted to evaluate the mycochemical composition and antiglycemic and antioxidant activities of Ganoderma neo-japonicum hot aqueous extracts, prepared at different boiling durations, and polysaccharides isolated from them. Ground basidiocarps of G. neo-japonicum were double-boiled at 100°C for 0.5, 3, or 4 hours, and the antiglycemic activity was assessed by α-amylase and α-glucosidase enzyme inhibition assays. The antioxidant capacity of the crude hot aqueous extracts (AE-1, AE-2, AE-3) was assessed by DPPH and ABTS radical scavenging and ferric-reducing antioxidant power assays. The total phenolics, protein, and sugar in the crude extracts were also determined. The hot aqueous extract (AE-3) containing a significant amount of total sugar and having enhanced antiglycemic and antioxidant activities was selected for polysaccharide isolation. The isolated crude polysaccharide was separated and purified using diethylaminoethyl-cellulose-52 and Sepharose 6B column chromatography. Fourier transform infrared spectroscopy studies of the purified polysaccharide fraction (PF) showed the presence of typical bands corresponding to polysaccharides. The estimated β-glucan concentration in the PF was 39.26%. In general, the PF exhibited significantly lower antioxidant activity than AE-3. Nevertheless, its potency in inhibiting carbohydratehydrolyzing enzymes may have potential in the management of diabetes mellitus.
    Matched MeSH terms: Chromatography, Liquid
  12. Shuib S, Ibrahim I, Mackeen MM, Ratledge C, Hamid AA
    Sci Rep, 2018 Feb 15;8(1):3077.
    PMID: 29449592 DOI: 10.1038/s41598-018-21452-4
    Malic enzyme (ME) plays a vital role in determining the extent of lipid accumulation in oleaginous fungi being the major provider of NADPH for the activity of fatty acid synthase (FAS). We report here the first direct evidence of the existence of a lipogenic multienzyme complex (the lipid metabolon) involving ME, FAS, ATP: citrate lyase (ACL), acetyl-CoA carboxylase (ACC), pyruvate carboxylase (PC) and malate dehydrogenase (MDH) in Cunninghamella bainieri 2A1. Cell-free extracts prepared from cells taken in both growth and lipid accumulation phases were prepared by protoplasting and subjected to Blue Native (BN)-PAGE coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). A high molecular mass complex (approx. 3.2 MDa) consisting of the above enzymes was detected during lipid accumulation phase indicating positive evidence of multienzyme complex formation. The complex was not detected in cells during the balanced phase of growth or when lipid accumulation ceased, suggesting that it was transiently formed only during lipogenesis.
    Matched MeSH terms: Chromatography, Liquid
  13. Wong EHJ, Ng CG, Goh KL, Vadivelu J, Ho B, Loke MF
    Sci Rep, 2018 01 23;8(1):1409.
    PMID: 29362474 DOI: 10.1038/s41598-018-19697-0
    The biofilm-forming-capability of Helicobacter pylori has been suggested to be among factors influencing treatment outcome. However, H. pylori exhibit strain-to-strain differences in biofilm-forming-capability. Metabolomics enables the inference of spatial and temporal changes of metabolic activities during biofilm formation. Our study seeks to examine the differences in metabolome of low and high biofilm-formers using the metabolomic approach. Eight H. pylori clinical strains with different biofilm-forming-capability were chosen for metabolomic analysis. Bacterial metabolites were extracted using Bligh and Dyer method and analyzed by Liquid Chromatography/Quadrupole Time-of-Flight mass spectrometry. The data was processed and analyzed using the MassHunter Qualitative Analysis and the Mass Profiler Professional programs. Based on global metabolomic profiles, low and high biofilm-formers presented as two distinctly different groups. Interestingly, low-biofilm-formers produced more metabolites than high-biofilm-formers. Further analysis was performed to identify metabolites that differed significantly (p-value 
    Matched MeSH terms: Chromatography, Liquid
  14. Benjamin MAZ, Ng SY, Saikim FH, Rusdi NA
    Molecules, 2022 Sep 30;27(19).
    PMID: 36234995 DOI: 10.3390/molecules27196458
    The therapeutic potential of bamboos has acquired global attention. Nonetheless, the biological activities of the plants are rarely considered due to limited available references in Sabah, Malaysia. Furthermore, the drying technique could significantly affect the retention and degradation of nutrients in bamboos. Consequently, the current study investigated five drying methods, namely, sun, shade, microwave, oven, and freeze-drying, of the leaves of six bamboo species, Bambusa multiplex, Bambusa tuldoides, Bambusa vulgaris, Dinochloa sublaevigata, Gigantochloa levis, and Schizostachyum brachycladum. The infused bamboo leaves extracts were analysed for their total phenolic content (TPC) and total flavonoid content (TFC). The antioxidant activities of the samples were determined via the 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and ferric reducing antioxidant power (FRAP) assays, whereas their toxicities were evaluated through the brine shrimp lethality assay (BSLA). The chemical constituents of the samples were determined using liquid chromatography−tandem mass spectrometry (LC-MS/MS). The freeze-drying method exhibited the highest phytochemical contents and antioxidant activity yield, excluding the B. vulgaris sample, in which the microwave-dried sample recorded the most antioxidant and phytochemical levels. The TPC and TFC results were within the 2.69 ± 0.01−12.59 ± 0.09 mg gallic acid equivalent (GAE)/g and 0.77 ± 0.01−2.12 ± 0.01 mg quercetin equivalent (QE)/g ranges, respectively. The DPPH and ABTS IC50 (half-maximal inhibitory concentration) were 2.92 ± 0.01−4.73 ± 0.02 and 1.89−0.01 to 3.47 ± 0.00 µg/mL, respectively, indicating high radical scavenging activities. The FRAP values differed significantly between the drying methods, within the 6.40 ± 0.12−36.65 ± 0.09 mg Trolox equivalent (TE)/g range. The phytochemical contents and antioxidant capacities exhibited a moderate correlation, revealing that the TPC and TFC were slightly responsible for the antioxidant activities. The toxicity assessment of the bamboo extracts in the current study demonstrated no toxicity against the BSLA based on the LC50 (lethal concentration 50) analysis at >1000 µg/mL. LC-MS analysis showed that alkaloid and pharmaceutical compounds influence antioxidant activities, as found in previous studies. The acquired information might aid in the development of bamboo leaves as functional food items, such as bamboo tea. They could also be investigated for their medicinal ingredients that can be used in the discovery of potential drugs.
    Matched MeSH terms: Chromatography, Liquid
  15. Kanakaraju D, Motti CA, Glass BD, Oelgemöller M
    Environ Sci Pollut Res Int, 2016 Sep;23(17):17437-48.
    PMID: 27230148 DOI: 10.1007/s11356-016-6906-8
    Given that drugs and their degradation products are likely to occur as concoctions in wastewater, the degradation of a mixture of two nonsteroidal anti-inflammatory drugs (NSAIDs), diclofenac (DCF) and naproxen (NPX), was investigated by solar photolysis and titanium dioxide (TiO2)-mediated solar photocatalysis using an immersion-well photoreactor. An equimolar ratio (1:1) of both NSAIDs in distilled water, drinking water, and river water was subjected to solar degradation. Solar photolysis of the DCF and NPX mixture was competitive particularly in drinking water and river water, as both drugs have the ability to undergo photolysis. However, the addition of TiO2 in the mixture significantly enhanced the degradation rate of both APIs compared to solar photolysis alone. Mineralization, as measured by chemical oxygen demand (COD), was incomplete under all conditions investigated. TiO2-mediated solar photocatalytic degradation of DCF and NPX mixtures produced 15 identifiable degradants corresponding to degradation of the individual NSAIDs, while two degradation products with much higher molecular weight than the parent NSAIDs were identified by liquid chromatography mass spectrometry (LC-MS) and Fourier transform-ion cyclotron resonance-mass spectrometry (FT-ICR-MS). This study showed that the solar light intensity and the water matrix appear to be the main factors influencing the overall performance of the solar photolysis and TiO2-mediated solar photocatalysis for degradation of DCF and NPX mixtures.
    Matched MeSH terms: Chromatography, Liquid
  16. Wu XY, Zhao ZY, Osman EEA, Wang XJ, Choo YM, Benjamin MM, et al.
    Bioorg Chem, 2024 Feb;143:107103.
    PMID: 38211549 DOI: 10.1016/j.bioorg.2024.107103
    Three undescribed (1-3) and nine known (4-12) platanosides were isolated and characterized from a bioactive extract of the May leaves of Platanus × acerifolia that initially showed inhibition against Staphylococcus aureus. Targeted compound mining was guided by an LC-MS/MS-based molecular ion networking (MoIN) strategy combined with conventional isolation procedures from a unique geographic location. The novel structures were mainly determined by 2D NMR and computational (NMR/ECD calculations) methods. Compound 1 is a rare acylated kaempferol rhamnoside possessing a truxinate unit. 6 (Z,E-platanoside) and 7 (E,E-platanoside) were confirmed to have remarkable inhibitory effects against both methicillin-resistant S. aureus (MIC: ≤ 16 μg/mL) and glycopeptide-resistant Enterococcus faecium (MIC: ≤ 1 μg/mL). These platanosides were subjected to docking analyses against FabI (enoyl-ACP reductase) and PBP1/2 (penicillin binding protein), both of which are pivotal enzymes governing bacterial growth but not found in the human host. The results showed that 6 and 7 displayed superior binding affinities towards FabI and PBP2. Moreover, surface plasmon resonance studies on the interaction of 1/7 and FabI revealed that 7 has a higher affinity (KD = 1.72 μM), which further supports the above in vitro data and is thus expected to be a novel anti-antibacterial drug lead.
    Matched MeSH terms: Chromatography, Liquid
  17. Levitsky LI, Ivanov MV, Goncharov AO, Kliuchnikova AA, Bubis JA, Lobas AA, et al.
    J Proteome Res, 2023 Jun 02;22(6):1695-1711.
    PMID: 37158322 DOI: 10.1021/acs.jproteome.2c00740
    The proteogenomic search pipeline developed in this work has been applied for reanalysis of 40 publicly available shotgun proteomic datasets from various human tissues comprising more than 8000 individual LC-MS/MS runs, of which 5442 .raw data files were processed in total. This reanalysis was focused on searching for ADAR-mediated RNA editing events, their clustering across samples of different origins, and classification. In total, 33 recoded protein sites were identified in 21 datasets. Of those, 18 sites were detected in at least two datasets, representing the core human protein editome. In agreement with prior artworks, neural and cancer tissues were found to be enriched with recoded proteins. Quantitative analysis indicated that recoding the rate of specific sites did not directly depend on the levels of ADAR enzymes or targeted proteins themselves, rather it was governed by differential and yet undescribed regulation of interaction of enzymes with mRNA. Nine recoding sites conservative between humans and rodents were validated by targeted proteomics using stable isotope standards in the murine brain cortex and cerebellum, and an additional one was validated in human cerebrospinal fluid. In addition to previous data of the same type from cancer proteomes, we provide a comprehensive catalog of recoding events caused by ADAR RNA editing in the human proteome.
    Matched MeSH terms: Chromatography, Liquid
  18. Ziganshin RH, Ivanova OM, Lomakin YA, Belogurov AA, Kovalchuk SI, Azarkin IV, et al.
    Mol Cell Proteomics, 2016 Jul;15(7):2366-78.
    PMID: 27143409 DOI: 10.1074/mcp.M115.056036
    Acute inflammatory demyelinating polyneuropathy (AIDP) - the main form of Guillain-Barre syndrome-is a rare and severe disorder of the peripheral nervous system with an unknown etiology. One of the hallmarks of the AIDP pathogenesis is a significantly elevated cerebrospinal fluid (CSF) protein level. In this paper CSF peptidome and proteome in AIDP were analyzed and compared with multiple sclerosis and control patients. A total protein concentration increase was shown to be because of even changes in all proteins rather than some specific response, supporting the hypothesis of protein leakage from blood through the blood-nerve barrier. The elevated CSF protein level in AIDP was complemented by activization of protein degradation and much higher peptidome diversity. Because of the studies of the acute motor axonal form, Guillain-Barre syndrome as a whole is thought to be associated with autoimmune response against neurospecific molecules. Thus, in AIDP, autoantibodies against cell adhesion proteins localized at Ranvier's nodes were suggested as possible targets in AIDP. Indeed, AIDP CSF peptidome analysis revealed cell adhesion proteins degradation, however no reliable dependence on the corresponding autoantibodies levels was found. Proteome analysis revealed overrepresentation of Gene Ontology groups related to responses to bacteria and virus infections, which were earlier suggested as possible AIDP triggers. Immunoglobulin blood serum analysis against most common neuronal viruses did not reveal any specific pathogen; however, AIDP patients were more immunopositive in average and often had polyinfections. Cytokine analysis of both AIDP CSF and blood did not show a systemic adaptive immune response or general inflammation, whereas innate immunity cytokines were up-regulated. To supplement the widely-accepted though still unproven autoimmunity-based AIDP mechanism we propose a hypothesis of the primary peripheral nervous system damaging initiated as an innate immunity-associated local inflammation following neurotropic viruses egress, whereas the autoantibody production might be an optional complementary secondary process.
    Matched MeSH terms: Chromatography, Liquid
  19. da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F, et al.
    Gigascience, 2020 Jan 01;9(1).
    PMID: 31942620 DOI: 10.1093/gigascience/giz152
    BACKGROUND: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked.

    FINDINGS: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.

    CONCLUSIONS: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

    Matched MeSH terms: Chromatography, Liquid
  20. 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: Chromatography, Liquid
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