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  1. Fulltext Autofluorescence study and selected cyanidin quantification in the Jewel orchids Anoectochilus sp. and Ludisia discolor
    Poobathy R, Zakaria R, Murugaiyah V, Subramaniam S
    PLoS One, 2018;13(4):e0195642.
    PMID: 29649288 DOI: 10.1371/journal.pone.0195642
    Anoectochilus sp. and Ludisia discolor are known as Jewel orchids. Both species are terrestrial wild orchids that grow in shaded areas of forests. The Jewel orchids are renowned for the beauty of their leaves, which are dark-green laced with silvery or golden veins. The orchids are used as a cure in various parts of Asia. Overharvesting and anthropogenic disturbances threaten the existence of the Jewel orchids in the wild, necessitating human intervention in their survival. An understanding of the structure and adaptations of a plant may assist in its survival when propagated outside of its habitat. In this study, ex vitro leaves of Anoectochilus sp. and L. discolor were subjected to freehand sectioning, and then inspected through brightfield and fluorescence microscopy. The study indicated that all parts of both plants presented typical monocotyledonous characteristics except the leaves. The leaves displayed dorsiventrality with distinct palisade and spongy mesophyll layers. The spongy mesophyll layer contained cells which fluoresced a bright red when exposed to ultraviolet, blue, and green light wavelengths, hinting at the presence of anthocyanins for photoprotection. Cyanidin was detected in the leaves of L. discolor, as enumerated through high performance liquid chromatography (HPLC). The observations indicated that Anoectochilus sp. and L. discolor are well-adapted to live under shaded conditions with minimal exposure to light.
    Matched MeSH terms: Plant Leaves/metabolism; Orchidaceae/metabolism
  2. Restoring the IL-1β/NF-κB-induced impaired chondrogenesis by diallyl disulfide in human adipose-derived mesenchymal stem cells via attenuation of reactive oxygen species and elevation of antioxidant enzymes
    Bahrampour Juybari K, Kamarul T, Najafi M, Jafari D, Sharifi AM
    Cell Tissue Res, 2018 08;373(2):407-419.
    PMID: 29582166 DOI: 10.1007/s00441-018-2825-y
    Strategies based on mesenchymal stem cell (MSC) therapy for restoring injured articular cartilage are not effective enough in osteoarthritis (OA). Due to the enhanced inflammation and oxidative stress in OA microenvironment, differentiation of MSCs into chondrocytes would be impaired. This study aims to explore the effects of diallyl disulfide (DADS) on IL-1β-mediated inflammation and oxidative stress in human adipose derived mesenchymal stem cells (hADSCs) during chondrogenesis. MTT assay was employed to examine the effects of various concentrations of DADS on the viability of hADSCs at different time scales to obtain non-cytotoxic concentration range of DADS. The effects of DADS on IL-1β-induced intracellular ROS generation and lipid peroxidation were evaluated in hADSCs. Western blotting was used to analyze the protein expression levels of IκBα (np), IκBα (p), NF-κB (np) and NF-κB (p). Furthermore, the gene expression levels of antioxidant enzymes in hADSCs and chondrogenic markers at days 7, 14 and 21 of differentiation were measured using qRT-PCR. The results showed that addition of DADS significantly enhanced the mRNA expression levels of antioxidant enzymes as well as reduced ROS elevation, lipid peroxidation, IκBα activation and NF-κB nuclear translocation in hADSCs treated with IL-1β. In addition, DADS could significantly increase the expression levels of IL-1β-induced impaired chondrogenic marker genes in differentiated hADSCs. Treatment with DADS may provide an effective approach to prevent the pro-inflammatory cytokines and oxidative stress as catabolic causes of chondrocyte cell death and enhance the protective anabolic effects by promoting chondrogenesis associated gene expressions in hADSCs exposed to OA condition.
    Matched MeSH terms: Antioxidants/metabolism*; Cell Nucleus/metabolism; Glycosaminoglycans/metabolism; Malondialdehyde/metabolism; RNA, Messenger/metabolism; NF-kappa B/metabolism*; Reactive Oxygen Species/metabolism*; Intracellular Space/metabolism; Interleukin-1beta/metabolism*; Mesenchymal Stromal Cells/metabolism*; NF-KappaB Inhibitor alpha/metabolism
  3. Fulltext Structure of polyhydroxyalkanoate (PHA) synthase PhaC from Chromobacterium sp. USM2, producing biodegradable plastics
    Chek MF, Kim SY, Mori T, Arsad H, Samian MR, Sudesh K, et al.
    Sci Rep, 2017 07 13;7(1):5312.
    PMID: 28706283 DOI: 10.1038/s41598-017-05509-4
    Polyhydroxyalkanoate (PHA) is a promising candidate for use as an alternative bioplastic to replace petroleum-based plastics. Our understanding of PHA synthase PhaC is poor due to the paucity of available three-dimensional structural information. Here we present a high-resolution crystal structure of the catalytic domain of PhaC from Chromobacterium sp. USM2, PhaC Cs -CAT. The structure shows that PhaC Cs -CAT forms an α/β hydrolase fold comprising α/β core and CAP subdomains. The active site containing Cys291, Asp447 and His477 is located at the bottom of the cavity, which is filled with water molecules and is covered by the partly disordered CAP subdomain. We designated our structure as the closed form, which is distinct from the recently reported catalytic domain from Cupriavidus necator (PhaC Cn -CAT). Structural comparison showed PhaC Cn -CAT adopting a partially open form maintaining a narrow substrate access channel to the active site, but no product egress. PhaC Cs -CAT forms a face-to-face dimer mediated by the CAP subdomains. This arrangement of the dimer is also distinct from that of the PhaC Cn -CAT dimer. These findings suggest that the CAP subdomain should undergo a conformational change during catalytic activity that involves rearrangement of the dimer to facilitate substrate entry and product formation and egress from the active site.
    Matched MeSH terms: Acyltransferases/metabolism; Biodegradable Plastics/metabolism
  4. Efficacy of surgical laser therapy in the management of oral pigmented lesions: A systematic review
    Abduljabbar T, Vohra F, Akram Z, Ghani SMA, Al-Hamoudi N, Javed F
    J. Photochem. Photobiol. B, Biol., 2017 Aug;173:353-359.
    PMID: 28641206 DOI: 10.1016/j.jphotobiol.2017.06.016
    BACKGROUND: Oral pigmentation, especially in the gingiva poses esthetic problems. Laser therapy has been widely used for cosmetic therapy in dentistry. The aim of the present study was to systematically review the efficacy of surgical laser therapy (SLT) in the management of oral pigmented lesions (OPL).

    MATERIALS AND METHODS: The addressed focused question was "Is SLT effective in the management of OPL?" Databases (MEDLINE via PubMed; EMBASE; Cochrane Central Register of Controlled Trials and Cochrane Oral Health Group Trials Register databases) were searched from 1970 up to and including February 2017.

    RESULTS: Ten studies were included. The reported number of OPL ranged between 8 and 140. Oral pigmented sites included, gingiva, buccal and labial mucosa, alveolar mucosa and lips. Lasers used in the studies included Q-switched alexandrite, Neodymium-doped yttrium aluminium garnet, diode, Erbium: yttrium aluminium garnet and carbon dioxide laser. Laser wavelength, power output and number of irradiations were 635-10,600nm, 1-10W and 1 to 9 times, respectively. The follow up period ranged from 6 to 24months. All studies reported SLT to be effective in the treatment of OPL. In five studies, recurrence of OPL occurred which ranged from 21.4% to 45%.

    CONCLUSIONS: Lasers are effective in the management of OPL including physiologic gingival pigmentation, smokers' melanosis and pigmentation in Laugier-Hunziker syndrome. Different laser types (CO2, Er:YAG and Diode) showed comparable outcomes in the treatment of OPL.

    Matched MeSH terms: Gingiva/metabolism; Mouth Mucosa/metabolism
  5. Fulltext De novo transcriptome analysis shows differential expression of genes in salivary glands of edible bird's nest producing swiftlets
    Looi QH, Amin H, Aini I, Zuki M, Omar AR
    BMC Genomics, 2017 07 03;18(1):504.
    PMID: 28673247 DOI: 10.1186/s12864-017-3861-9
    BACKGROUND: Edible bird's nest (EBN), produced from solidified saliva secretions of specific swiftlet species during the breeding season, is one of the most valuable animal by-products in the world. The composition and medicinal benefits of EBN have been extensively studied, however, genomic and transcriptomic studies of the salivary glands of these birds have not been conducted.

    RESULTS: The study described the transcriptomes of salivary glands from three swiftlet species (28 samples) generated by RNASeq. A total of 14,835 annotated genes and 428 unmapped genes were cataloged. The current study investigated the genes and pathways that are associated with the development of salivary gland and EBN composition. Differential expression and pathway enrichment analysis indicated that the expression of CREB3L2 and several signaling pathways involved in salivary gland development, namely, the EGFR, BMP, and MAPK signaling pathways, were up-regulated in swiftlets producing white EBN (Aerodramus fuciphagus) and black EBN (Aerodramus maximus) compared with non-EBN-producing swiftlets (Apus affinis). Furthermore, MGAT, an essential gene for the biosynthesis of N-acetylneuraminic acid (sialic acid), was highly expressed in both white- and black-nest swiftlets compared to non-EBN-producing swiftlets. Interspecies comparison between Aerodramus fuciphagus and Aerodramus maximus indicated that the genes involved in N-acetylneuraminic and fatty acid synthesis were up-regulated in Aerodramus fuciphagus, while alanine and aspartate synthesis pathways were up-regulated in Aerodramus maximus. Furthermore, gender-based analysis revealed that N-glycan trimming pathway was significantly up-regulated in male Aerodramus fuciphagus from its natural habitat (cave) compared to their female counterpart.

    CONCLUSIONS: Transcriptomic analysis of salivary glands of different swiftlet species reveal differential expressions of candidate genes that are involved in salivary gland development and in the biosynthesis of various bioactive compounds found in EBN.

    Matched MeSH terms: Birds/metabolism*; Salivary Glands/metabolism*
  6. Effects of single and co-immobilization on the product specificity of type I pullulanase from Anoxybacillus sp. SK3-4
    Kahar UM, Chan KG, Sani MH, Mohd Noh NI, Goh KM
    Int J Biol Macromol, 2017 Nov;104(Pt A):322-332.
    PMID: 28610926 DOI: 10.1016/j.ijbiomac.2017.06.054
    Type I pullulanase from Anoxybacillus sp. SK3-4 (PulASK) is an unusual debranching enzyme that specifically hydrolyzes starch α-1,6 linkages at long branches producing oligosaccharides (≥G8), but is nonreactive against short branches; thus, incapable of producing reducing sugars (G1-G7). We report on the effects of both single and co-immobilization of PulASK on product specificity. PulASK was purified and immobilized through covalent attachment to three epoxides (ReliZyme EP403/M, Immobead IB-150P, and Immobead IB-150A) and an amino-epoxide (ReliZyme HFA403/M) activated supports. Following immobilization, all PulASK derivatives were active on both short and long branches in starch producing reducing sugars (predominantly maltotriose) and oligosaccharides (≥G8), respectively, a feature that is absent in the free enzyme. This study also demonstrated that co-immobilization of PulASK and α-amylase from Anoxybacillus sp. SK3-4 (TASKA) on ReliZyme HFA403/M significantly changed the product specificity compared to the free enzymes alone or individually immobilized enzymes. In conclusion, individual or co-immobilization caused changes in the product specificity, presumably due to changes in the enzyme binding pocket caused by the influence of carrier surface properties (hydrophobic or hydrophilic) and the lengths of the spacer arms.
    Matched MeSH terms: Enzymes, Immobilized/metabolism*; Glycoside Hydrolases/metabolism*
  7. Identification of three homologous latex-clearing protein (lcp) genes from the genome of Streptomyces sp. strain CFMR 7
    Nanthini J, Ong SY, Sudesh K
    Gene, 2017 Sep 10;628:146-155.
    PMID: 28711667 DOI: 10.1016/j.gene.2017.07.039
    Rubber materials have greatly contributed to human civilization. However, being a polymeric material does not decompose easily, it has caused huge environmental problems. On the other hand, only few bacteria are known to degrade rubber, with studies pertaining them being intensively focusing on the mechanism involved in microbial rubber degradation. The Streptomyces sp. strain CFMR 7, which was previously confirmed to possess rubber-degrading ability, was subjected to whole genome sequencing using the single molecule sequencing technology of the PacBio® RS II system. The genome was further analyzed and compared with previously reported rubber-degrading bacteria in order to identify the potential genes involved in rubber degradation. This led to the interesting discovery of three homologues of latex-clearing protein (Lcp) on the chromosome of this strain, which are probably responsible for rubber degrading activities. Genes encoding oxidoreductase α-subunit (oxiA) and oxidoreductase β-subunit (oxiB) were also found downstream of two lcp genes which are located adjacent to each other. In silico analysis reveals genes that have been identified to be involved in the microbial degradation of rubber in the Streptomyces sp. strain CFMR 7. This is the first whole genome sequence of a clear-zone-forming natural rubber- degrading Streptomyces sp., which harbours three Lcp homologous genes with the presence of oxiA and oxiB genes compared to the previously reported Gordonia polyisoprenivorans strain VH2 (with two Lcp homologous genes) and Nocardia nova SH22a (with only one Lcp gene).
    Matched MeSH terms: Rubber/metabolism; Streptomyces/metabolism
  8. A novel role for estrogen-induced signaling in the colorectal cancer gender bias
    Haziman AA, Ravinderan S, Thangavelu T, Thomas W
    Ir J Med Sci, 2019 May;188(2):389-395.
    PMID: 30014247 DOI: 10.1007/s11845-018-1867-1
    Colorectal cancer (CRC) is a malignancy whose incidence is increasing globally, and there is a gender difference in the increasing risk. Evidence from hormone replacement therapy studies points to a role for circulating estrogens in suppressing the development of CRC. Estrogen receptor-β has been identified as a tumor suppressor, but other actions of estrogen may also contribute to the difference in CRC incidence between men and women. The KCNQ1/KCNE3 potassium channel is regulated by estrogen in order to modulate chloride secretion during the menstrual cycle; the effect of estrogen on the colon is to promote fluid conservation during the implantation window. KCNQ1 is also a tumor suppressor in CRC, and its sustained expression has been linked to suppression of the Wnt/β-catenin signaling pathway that contributes to CRC tumor progression. KCNQ1 regulation may represent a link between the normal physiological actions of estrogen in the colon and the hormone's apparent tumor-suppressive effects in CRC development.
    Matched MeSH terms: Estrogens/metabolism*; Colorectal Neoplasms/metabolism*
  9. Diatom Nitzschia navis-varingica (Bacillariophyceae) and its domoic acid production from the mangrove environments of Malaysia
    Tan SN, Teng ST, Lim HC, Kotaki Y, Bates SS, Leaw CP, et al.
    Harmful Algae, 2016 12;60:139-149.
    PMID: 28073557 DOI: 10.1016/j.hal.2016.11.003
    The distribution of the toxic pennate diatom Nitzschia was investigated at four mangrove areas along the coastal brackish waters of Peninsular Malaysia. Eighty-two strains of N. navis-varingica were isolated and established, and their identity confirmed morphologically and molecularly. Frustule morphological characteristics of the strains examined are identical to previously identified N. navis-varingica, but with a sightly higher density of the number of areolae per 1μm (4-7 areolae). Both LSU and ITS rDNAs phylogenetic trees clustered all strains in the N. navis-varingica clade, with high sequence homogeneity in the LSU rDNA (0-0.3%), while the intraspecific divergences in the ITS2 data set reached up to 7.4%. Domoic acid (DA) and its geometrical isomers, isodomoic A (IA) and isodomoic B (IB), were detected in cultures of N. navis-varingica by FMOC-LC-FLD, and subsequently confirmed by LC-MS/MS, with selected ion monitoring (SIM) and multiple reaction monitoring (MRM) runs. DA contents ranged between 0.37 and 11.06pgcell-1. This study demonstrated that the toxigenic euryhaline diatom N. navis-varingica is widely distributed in Malaysian mangrove swamps, suggesting the risk of amnesic shellfish poisoning and the possibility of DA contamination in the mangrove-related fisheries products.
    Matched MeSH terms: Kainic Acid/metabolism; Diatoms/metabolism*
  10. Modelling of polyhydroxyalkanoate synthase from Aquitalea sp. USM4 suggests a novel mechanism for polymer elongation
    Teh AH, Chiam NC, Furusawa G, Sudesh K
    Int J Biol Macromol, 2018 Nov;119:438-445.
    PMID: 30048726 DOI: 10.1016/j.ijbiomac.2018.07.147
    Polyhydroxyalkanoate (PHA) synthase, PhaC, is a key enzyme in the biosynthesis of PHA, a type of bioplastics with huge potential to replace petroleum-based plastics. While two structures have been determined, the exact mechanism remains unclear partly due to the absence of a tunnel for product passage. A model of the class I PhaC from Aquitalea sp. USM4, characterised with Km of 394 μM and kcat of 476 s-1 on 3-(R)-hydroxybutyryl-CoA, revealed a three-branched channel at the dimeric interface. Two of them are opened to the solvent and are expected to serve as the putative routes for substrate entrance and product exit, while the third is elongated in the class II PhaC1 model from Pseudomonas aeruginosa, indicating a role in accommodating the hydroxyalkanoate (HA) moiety of a HA-CoA substrate. Docking of the two tetrahedral intermediates, formed during the transfer of the growing PHA chain from the catalytic Cys to a new molecule of substrate and back to Cys, suggests a common elongation mechanism requiring the HA moiety of the ligand to rotate ~180°. Substrate specificity is determined in part by a bulky Phe/Tyr/Trp residue in the third branch in class I, which is conserved as Ala in class II to create room for longer substrates.
    Matched MeSH terms: Acyltransferases/metabolism*; Polyhydroxyalkanoates/metabolism*
  11. Antioxidant and functional properties of protein hydrolysates obtained from squid pen chitosan extraction effluent
    Shavandi A, Hu Z, Teh S, Zhao J, Carne A, Bekhit A, et al.
    Food Chem, 2017 Jul 15;227:194-201.
    PMID: 28274422 DOI: 10.1016/j.foodchem.2017.01.099
    Squid pens were subjected to alkali hydrolysis to extract chitin and chitosan. Proteins present in the alkaline extraction wastewater were recovered at pH 3, 4, 5 and 6, and were subjected to hydrolysis by trypsin, pepsin and a bacterial protease called HT for 1, 2, 4 and 24h. Hydrolysis of the extracted proteins with either trypsin or HT generated more antioxidant activity than hydrolysis with pepsin. Higher ACE-inhibitory activity was generated in the trypsin and pepsin hydrolysates than in the HT hydrolysate. Squid pen protein recovered from chitosan processing waste alkaline solution can be a potential source of bioactive peptides for addition to foods. The antioxidant and ACE-inhibitory activities of the extracted proteins were initially low and increased upon incubation with the proteases. Pepsin generated significantly lower (P<0.05) antioxidant activities compared to trypsin and HT, while trypsin and pepsin hydrolysates exhibited higher ACE-inhibitory activity than HT (P<0.05).
    Matched MeSH terms: Peptide Hydrolases/metabolism; Chitosan/metabolism
  12. Probing the interaction of 2,4-dichlorophenoxyacetic acid with human serum albumin as studied by experimental and computational approaches
    Tayyab S, Francis JA, Kabir MZ, Ghani H, Mohamad SB
    Spectrochim Acta A Mol Biomol Spectrosc, 2019 Jan 15;207:284-293.
    PMID: 30267976 DOI: 10.1016/j.saa.2018.09.033
    To characterize the binding of a widely used herbicide, 2,4-dichlorophenoxyacetic acid (2,4-D) to the major transporter in human circulation, human serum albumin (HSA), multi-spectroscopic approaches such as fluorescence, absorption and circular dichroism along with computational methods were employed. Analysis of the fluorescence and absorption spectroscopic data confirmed the 2,4-D-HSA complex formation. A static quenching mechanism was evident from the inverse temperature dependence of the KSV values. The complex was stabilized by a weak binding affinity (Ka = 5.08 × 103 M-1 at 298 K). Quantitative analysis of thermodynamic data revealed participation of hydrophobic and van der Waals interactions as well as hydrogen bonds in the binding process. Circular dichroism and three-dimensional fluorescence spectral results showed structural (secondary and tertiary) changes in HSA as well as microenvironmental perturbation around protein fluorophores (Trp and Tyr residues) upon 2,4-D binding. Addition of 2,4-D to HSA was found to improve protein's thermal stability. Competitive displacement results as well as computational analyses suggested preferred location of the 2,4-D binding site as Sudlow's site I (subdomain IIA) in HSA.
    Matched MeSH terms: Herbicides/metabolism*; 2,4-Dichlorophenoxyacetic Acid/metabolism*
  13. A Protein Decomplexation Strategy in Snake Venom Proteomics
    Tan CH, Tan KY, Tan NH
    Methods Mol Biol, 2019;1871:83-92.
    PMID: 30276733 DOI: 10.1007/978-1-4939-8814-3_5
    Snake venoms are complex mixtures of proteins and peptides that play vital roles in the survival of venomous snakes. As with their diverse pharmacological activities, snake venoms can be highly variable, hence the importance of understanding the compositional details of different snake venoms. However, profiling venom protein mixtures is challenging, in particular when dealing with the diversity of protein subtypes and their abundances. Here we described an optimized strategy combining a protein decomplexation method with in-solution trypsin digestion and mass spectrometry of snake venom proteins. The approach involves the integrated use of C18 reverse-phase high-performance liquid chromatography (RP-HPLC), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and nano-electrospray ionization tandem mass spectrometry (nano-ESI-LC-MS/MS).
    Matched MeSH terms: Peptides/metabolism; Snake Venoms/metabolism*
  14. Quantum mechanical tunnelling through the catalytic effects of A2451 ribosomal residue during a stepwise peptide bond formation
    Monajemi H, Md Zain S, Ishida T, Wan Abdullah WAT
    Biochem. Cell Biol., 2019 08;97(4):497-503.
    PMID: 30444637 DOI: 10.1139/bcb-2018-0220
    The search for the mechanism of ribosomal peptide bond formation is still ongoing. Even though the actual mechanism of peptide bod formation is still unknown, the dominance of proton transfer in this reaction is known for certain. Therefore, it is vital to take the quantum mechanical effects on proton transfer reaction into consideration; the effects of which were neglected in all previous studies. In this study, we have taken such effects into consideration using a semi-classical approach to the overall reaction mechanism. The M06-2X density functional with the 6-31++G(d,p) basis set was used to calculate the energies of the critical points on the potential energy surface of the reaction mechanism, which are then used in transition state theory to calculate the classical reaction rate. The tunnelling contribution is then added to the classical part by calculating the transmission permeability and tunnelling constant of the reaction barrier, using the numerical integration over the Boltzmann distribution for the symmetrical Eckart potential. The results of this study, which accounts for quantum effects, indicates that the A2451 ribosomal residue induces proton tunnelling in a stepwise peptide bond formation.
    Matched MeSH terms: Peptides/metabolism; Ribosomes/metabolism*
  15. Integrated Eutopic Endometrium and Non-Depleted Serum Quantitative Proteomic Analysis Identifies Candidate Serological Markers of Endometriosis
    Manousopoulou A, Hamdan M, Fotopoulos M, Garay-Baquero DJ, Teng J, Garbis SD, et al.
    Proteomics Clin Appl, 2019 05;13(3):e1800153.
    PMID: 30488576 DOI: 10.1002/prca.201800153
    BACKGROUND: Endometriosis affects about 4% of women in the reproductive age and is associated with subfertility. The aim of the present study is to examine the integrated quantitative proteomic profile of eutopic endometrium and serum from women with endometriosis compared to controls in order to identify candidate disease-specific serological markers.

    METHODS: Eutopic endometrium and serum from patients with endometriosis (n = 8 for tissue and n = 4 for serum) are, respectively, compared to endometrium and serum from females without endometriosis (n = 8 for tissue and n = 4 for serum) using a shotgun quantitative proteomics method. All study participants are at the proliferative phase of their menstrual cycle.

    RESULTS: At the tissue and serum level, 1214 and 404 proteins are differentially expressed (DEPs) in eutopic endometrium and serum, respectively, of women with endometriosis versus controls. Gene ontology analysis shows that terms related to immune response/inflammation, cell adhesion/migration, and blood coagulation are significantly enriched in the DEPs of eutopic endometrium, as well as serum. Twenty-one DEPs have the same trend of differential expression in both matrices and can be further examined as potential disease- and tissue-specific serological markers of endometriosis.

    CONCLUSIONS: The present integrated proteomic profiling of eutopic endometrium and serum from women with endometriosis identify promising serological markers that can be further validated in larger cohorts for the minimally invasive diagnosis of endometriosis.

    Matched MeSH terms: Endometriosis/metabolism*; Endometrium/metabolism*
  16. Fulltext Maintenance of active chromatin states by HMGN2 is required for stem cell identity in a pluripotent stem cell model
    Garza-Manero S, Sindi AAA, Mohan G, Rehbini O, Jeantet VHM, Bailo M, et al.
    Epigenetics Chromatin, 2019 12 12;12(1):73.
    PMID: 31831052 DOI: 10.1186/s13072-019-0320-7
    BACKGROUND: Members of the HMGN protein family modulate chromatin structure and influence epigenetic modifications. HMGN1 and HMGN2 are highly expressed during early development and in the neural stem/progenitor cells of the developing and adult brain. Here, we investigate whether HMGN proteins contribute to the chromatin plasticity and epigenetic regulation that is essential for maintaining pluripotency in stem cells.

    RESULTS: We show that loss of Hmgn1 or Hmgn2 in pluripotent embryonal carcinoma cells leads to increased levels of spontaneous neuronal differentiation. This is accompanied by the loss of pluripotency markers Nanog and Ssea1, and increased expression of the pro-neural transcription factors Neurog1 and Ascl1. Neural stem cells derived from these Hmgn-knockout lines also show increased spontaneous neuronal differentiation and Neurog1 expression. The loss of HMGN2 leads to a global reduction in H3K9 acetylation, and disrupts the profile of H3K4me3, H3K9ac, H3K27ac and H3K122ac at the Nanog and Oct4 loci. At endodermal/mesodermal genes, Hmgn2-knockout cells show a switch from a bivalent to a repressive chromatin configuration. However, at neuronal lineage genes whose expression is increased, no epigenetic changes are observed and their bivalent states are retained following the loss of HMGN2.

    CONCLUSIONS: We conclude that HMGN1 and HMGN2 maintain the identity of pluripotent embryonal carcinoma cells by optimising the pluripotency transcription factor network and protecting the cells from precocious differentiation. Our evidence suggests that HMGN2 regulates active and bivalent genes by promoting an epigenetic landscape of active histone modifications at promoters and enhancers.

    Matched MeSH terms: Chromatin/metabolism*; Histones/metabolism; Nerve Tissue Proteins/metabolism; Neurons/metabolism; HMGN1 Protein/metabolism; HMGN2 Protein/metabolism*; Pluripotent Stem Cells/metabolism; Octamer Transcription Factor-3/metabolism; Basic Helix-Loop-Helix Transcription Factors/metabolism; Neural Stem Cells/metabolism; Nanog Homeobox Protein/metabolism
  17. Fulltext Microbial Decolorization of Triazo Dye, Direct Blue 71: An Optimization Approach Using Response Surface Methodology (RSM) and Artificial Neural Network (ANN)
    Zin KM, Effendi Halmi MI, Abd Gani SS, Zaidan UH, Samsuri AW, Abd Shukor MY
    Biomed Res Int, 2020;2020:2734135.
    PMID: 32149095 DOI: 10.1155/2020/2734135
    The release of wastewater from textile dyeing industrial sectors is a huge concern with regard to pollution as the treatment of these waters is truly a challenging process. Hence, this study investigates the triazo bond Direct Blue 71 (DB71) dye decolorization and degradation dye by a mixed bacterial culture in the deficiency source of carbon and nitrogen. The metagenomics analysis found that the microbial community consists of a major bacterial group of Acinetobacter (30%), Comamonas (11%), Aeromonadaceae (10%), Pseudomonas (10%), Flavobacterium (8%), Porphyromonadaceae (6%), and Enterobacteriaceae (4%). The richest phylum includes Proteobacteria (78.61%), followed by Bacteroidetes (14.48%) and Firmicutes (3.08%). The decolorization process optimization was effectively done by using response surface methodology (RSM) and artificial neural network (ANN). The experimental variables of dye concentration, yeast extract, and pH show a significant effect on DB71 dye decolorization percentage. Over a comparative scale, the ANN model has higher prediction and accuracy in the fitness compared to the RSM model proven by approximated R2 and AAD values. The results acquired signify an efficient decolorization of DB71 dye by a mixed bacterial culture.
    Matched MeSH terms: Carbon/metabolism; Nitrogen/metabolism
  18. Starch granules as Pickering emulsifiers: Role of octenylsuccinylation and particle size
    Li S, Li C, Yang Y, He X, Zhang B, Fu X, et al.
    Food Chem, 2019 Jun 15;283:437-444.
    PMID: 30722895 DOI: 10.1016/j.foodchem.2019.01.020
    The present study aimed at investigating the effects of octenylsuccinylation and particle size on the emulsifying properties of starch granules as Pickering emulsifiers. Starch spherulites (1-5 μm), native rice starch (5-10 μm), waxy maize starch (10-20 μm) and waxy potato starch (20-30 μm) were modified with octenylsuccinic anhydride. Results showed that octenylsuccinylation caused a significant increase in the contact angle, and there was a weak positive linear correlation with the emulsifying capacity of the starch granules. After octenylsuccinylation, smaller particles of octenylsuccinate-starch granules exhibited better emulsifying properties with smaller droplet size and lower creaming index. Overall, both octenylsuccinylation and particle size have important effects on the emulsifying properties of starch granules as Pickering stabilizers. This study could be useful in the design and development of starch-based Pickering emulsifiers, and provide potential applications in the food and pharmaceutical industries.
    Matched MeSH terms: Zea mays/metabolism; Solanum tuberosum/metabolism
  19. Fulltext The Value of H3K27me3 Immunohistochemistry in Differentiating Malignant Peripheral Nerve Sheath Tumour with Its Histologic Mimickers
    Mustapar N, Zawawi MSF, Tuan Sharif SE
    Asian Pac J Cancer Prev, 2020 Mar 01;21(3):699-705.
    PMID: 32212796 DOI: 10.31557/APJCP.2020.21.3.699
    BACKGROUND: Diagnosis of malignant peripheral nerve sheath tumor (MPNST) is rather challenging due to its divergent morphologic heterogeneity and lack of specific ancillary test. The emergence of H3K27 trimethylation (H3K27me3) as a new immunohistochemistry (IHC) marker for MPNST have recently available to assist pathologists in differentiating MPNST from other histologic mimics. We aim to study the expression pattern of H3K27me3 in MPNST and its histologic mimickers and their association with the clinicopathological data.

    METHODOLOGY: A total of 59 benign and malignant spindle cell tumours (18 MPNST and 41 of its histologic mimickers which included 10 schwannoma, 13 neurofibroma, 4 synovial sarcoma, 3 fibrosarcoma, 2 gastrointestinal stromal tumour (GIST), 4 leiomyosarcoma, 1 spindle cell liposarcoma, 1 solitary fibrous tumour, 2 low grade fibromyxoid sarcoma and 1 unclassified spindle cell sarcoma), diagnosed from January 1998 to April 2018 in Hospital Universiti Sains Malaysia (HUSM) were tested for H3K27me3 by IHC. The MPNST histological grade was assessed based on the French Fe'de' ration Nationale des Centres de LutteContre le Cancer (FNCLCC) for 3 tiers system (low grade, intermediate grade and high grade). The clinicopathological data were retrieved from the patients' record.

    RESULTS: A total of 61.1% (11/18 MPNST) showed loss of H3K27me3 expression which is statistically significant as compared to its histologic mimics (p<0.001). Similar findings (p=0.026) were also observed in high grade MPNST (81.8%), intermediate grade MPNST (100%) and 0% in low grade MPNST.

    CONCLUSION: H3K27me3, combined with other panel of markers, is useful in MPNST diagnosis to differentiate it from the histological mimickers.

    Matched MeSH terms: Histones/metabolism*; Nerve Sheath Neoplasms/metabolism
  20. Fulltext Phylogenetic relationships of Pseudo-nitzschia subpacifica (Bacillariophyceae) from the Mexican Pacific, and its production of domoic acid in culture
    Quijano-Scheggia SI, Olivos-Ortiz A, Garcia-Mendoza E, Sánchez-Bravo Y, Sosa-Avalos R, Salas Marias N, et al.
    PLoS One, 2020;15(4):e0231902.
    PMID: 32330168 DOI: 10.1371/journal.pone.0231902
    Pseudo-nitzschia is a cosmopolitan genus, some species of which can produce domoic acid (DA), a neurotoxin responsible for the Amnesic Shellfish Poisoning (ASP). In this study, we identified P. subpacifica for the first time in Todos Santos Bay and Manzanillo Bay, in the Mexican Pacific using SEM and molecular methods. Isolates from Todos Santos Bay were cultivated under conditions of phosphate sufficiency and deficiency at 16°C and 22°C to evaluate the production of DA. This toxin was detected in the particulate (DAp) and dissolved (DAd) fractions of the cultures during the exponential and stationary phases of growth of the cultures. The highest DA concentration was detected during the exponential phase grown in cells maintained in P-deficient medium at 16°C (1.14 ± 0.08 ng mL-1 DAd and 4.71 ± 1.11 × 10-5 ng cell-1 of DAp). In P-sufficient cultures DA was higher in cells maintained at 16°C (0.25 ± 0.05 ng mL-1 DAd and 9.41 ± 1.23 × 10-7 ng cell-1 of DAp) than in cells cultured at 22°C. Therefore, we confirm that P. subpacifica can produce DA, especially under P-limited conditions that could be associated with extraordinary oceanographic events such as the 2013-2016 "Blob" in the northeastern Pacific Ocean. This event altered local oceanographic conditions and possibly generated the presence of potential harmful species in areas with economic importance on the Mexican Pacific coast.
    Matched MeSH terms: Kainic Acid/metabolism; Diatoms/metabolism*
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