Quorum sensing activity of Citrobacter amalonaticus L8A, a bacterium isolated from dentalplaque5/18/2016 Abstract:
Cell-cell communication is also known as quorum sensing (QS) that happens in the bacterial cells with the aim to regulate their genes expression in response to increased cell density. In this study, a bacterium (L8A) isolated from dental plaque biofilm was identified as Citrobacter amalonaticus by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Its N-acylhomoserine-lactone (AHL) production was screened by using two types of AHL biosensors namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Citrobacter amalonaticus strain L8A was identified and confirmed producing numerous types of AHL namely N-butyryl-L-homoserine lactone (C4-HSL), N-hexanoyl-L-homoserine lactone (C6-HSL), N-octanoyl-L-homoserine lactone (C8-HSL) and N-hexadecanoyl-L-homoserine lactone (C16-HSL). We performed the whole genome sequence analysis of this oral isolate where its genome sequence reveals the presence of QS signal synthase gene and our work will pave the ways to study the function of the related QS genes in this bacterium. Source; Scientific Reports Author: Goh SY, Khan SA, Tee KK, Abu Kasim NH, Yin WF, Chan KG Status: Full text available at Scientific Reports
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Approximately 20% of global cancer incidence is causally linked to an infectious agent. Epstein-Barr virus (EBV) accounts for around 1% of all virus-associated cancers and is associated with nasopharyngeal carcinoma (NPC). Latent membrane protein 1 (LMP1), the major oncoprotein encoded by EBV, behaves as a constitutively active tumour necrosis factor (TNF) receptor activating a variety of signalling pathways, including the three classic MAPKs (ERK-MAPK, p38 MAPK and JNK/SAPK). The present study identifies novel signalling properties for this integral membrane protein via the induction and secretion of activin A and TGF beta 1, which are both required for LMP1's ability to induce the expression of the extracellular matrix protein, fibronectin. However, it is evident that LMP1 is unable to activate the classic Smad-dependent TGF beta signalling pathway, but rather elicits its effects through the non-Smad arm of TGF beta signalling. In addition, there is a requirement for JNK/SAPK signalling in LMP1-mediated fibronectin induction. LMP1 also induces the expression and activation of the major fibronectin receptor, alpha 5 beta 1 integrin, an effect that is accompanied by increased focal adhesion formation and turnover. Taken together, these findings support the putative role for LMP1 in the pathogenesis of NPC by contributing to the metastatic potential of epithelial cells. Source: SCIENTIFIC REPORTS Author: Morris MA, Dawson CW, Laverick L, Davis AM, Dudman JPR, Ravennthiraraj S, Ahmad Z, Yap LF, Young LS. Status: Full text available at Nature Abstract:
Mycobacteria have been reported to cause a wide range of human diseases. We present the first whole-genome study of a Non-Tuberculous Mycobacterium, Mycobacterium sp. UM_CSW (referred to hereafter as UM_CSW), isolated from a patient diagnosed with bronchiectasis. Our data suggest that this clinical isolate is likely a novel mycobacterial species, supported by clear evidence from molecular phylogenetic, comparative genomic, ANI and AAI analyses. UM_CSW is closely related to the Mycobacterium avium complex. While it has characteristic features of an environmental bacterium, it also shows a high pathogenic potential with the presence of a wide variety of putative genes related to bacterial virulence and shares very similar pathogenomic profiles with the known pathogenic mycobacterial species. Thus, we conclude that this possible novel Mycobacterium species should be tightly monitored for its possible causative role in human infections. Source; PLoS One Author: Choo SW, Dutta A, Wong GJ, Wee WY, Ang MY, Siow CC. Status: Full text available PLoS One Abstract:
Background Nasopharyngeal carcinoma (NPC) is a neoplasm of the epithelial lining of the nasopharynx. Despite various reports linking genomic variants to NPC predisposition, very few reports were done on copy number variations (CNV). CNV is an inherent structural variation that has been found to be involved in cancer predisposition. Methods A discovery cohort of Malaysian Chinese descent (NPC patients, n = 140; Healthy controls, n = 256) were genotyped using Illumina (R) HumanOmniExpress BeadChip. PennCNV and cnvPartition calling algorithms were applied for CNV calling. Taqman CNV assays and digital PCR were used to validate CNV calls and replicate candidate copy number variant region (CNVR) associations in a follow-up Malaysian Chinese (NPC cases, n = 465; and Healthy controls, n = 677) and Malay cohort (NPC cases, n = 114; Healthy controls, n = 124). Results Six putative CNVRs overlapping GRM5, MICA/HCP5/HCG26, LILRB3/LILRA6, DPY19L2, RNase3/RNase2 and GOLPH3 genes were jointly identified by PennCNV and cnvPartition. CNVs overlapping GRM5 and MICA/HCP5/HCG26 were subjected to further validation by Taqman CNV assays and digital PCR. Combined analysis in Malaysian Chinese cohort revealed a strong association at CNVR on chromosome 11q14.3 (P-combined = 1.54x10(-5); odds ratio (OR) = 7.27; 95% CI = 2.96-17.88) overlapping GRM5 and a suggestive association at CNVR on chromosome 6p21.3 (P-combined = 1.29x10(-3); OR = 4.21; 95% CI = 1.75-10.11) overlapping MICA/HCP5/HCG26 genes. Source: PLoS One Author: Low JSY, Chin YM, Mushiroda T, Kubo M, Govindasamy GK, Pua KC, Yap YY, Yap LF, Subramaniam SK, Ong CA, et al. Status: Full text available at Plos One Abstract:
The radioprotective effect of Polyalthia longifolia was studied in mice. P. longifolia treatment showed improvement in mice survival compared to 100% mortality in the irradiated mice. Significant increases in hemoglobin concentration, and red blood cell, white blood cell and platelet counts were observed in the animals pretreated with leaf extract. Pre-irradiation administration of P. longifolia leaf extract also increased the CFU counts of the spleen colony and increased the relative spleen size. A dose-dependent decrease in lipid peroxidation levels was observed in the animals pretreated with P. longifolia. However, although the animals pretreated with P. longifolia exhibited a significant increase in superoxide dismutase and catalase activity, the values remained below normal in both liver and the intestine. Pre-irradiation administration of P. longifolia also resulted in the regeneration of the mucosal crypts and villi of the intestine. Moreover, pretreatment with P. longifolia leaf extract also showed restoration of the normal liver cell structure and a significant reduction in the elevated levels of ALT, AST and bilirubin. These results suggested the radioprotective ability of P. longifolia leaf extract, which is significant for future investigation for human applications in developing efficient, economically viable, non-toxic natural and clinically acceptable novel radioprotectors. (C) 2015 Associazione Italiana di Fisica Medica. Source: PHYSICA MEDICA-EUROPEAN JOURNAL OF MEDICAL PHYSICS Author: Jothy SL, Saito T, Kanwar JR, Chen Y, Aziz A, Yin-Hui L, Sasidharan S. Status: Full text available at UMEprints Abstract:
Objective: The aim of this study was to assess the bactericidal efficacy of antimicrobial photodynamic dynamic therapy (aPDT) as an adjunct to scaling and root planing (SRP) against periodontal pathogens. Background data: SRP followed by laser therapy has better clinical outcomes than conventional SRP alone. Materials and methods: The question addressed was "Does aPDT as an adjunct to SRP exhibit better bactericidal effect against periodontal pathogens than the use of SRP alone in periodontal disease?" MEDLINE (R)/PubMed, Embase, Scopus, Web of Science, and Google Scholar databases were searched from 1977 to December 2015, using different combinations of key words. Review articles, in vitro and experimental studies, and articles in languages other than English were excluded. Results: Seventeen clinical studies were included. Laser wavelengths and duration of irradiation ranged between 470 and 810 nm and 60 and 300 sec, respectively. All studies showed that aPDT application was effective in reducing the counts of periodontal microbes at follow-up. Four studies showed significantly reduced bacterial counts for aPDT as an adjunct to SRP compared with SRP alone. Thirteen studies showed comparable reduction in the counts of periodontal bacteria when aPDT alone or as an adjunct to SRP was compared with SRP alone. Conclusions: The bactericidal efficacy of aPDT as an adjunct to SRP against periodontal pathogens in periodontal disease remains debatable. Source: PHOTOMEDICINE AND LASER SURGERY Author: Akram Z, Al-Shareed SAA, Daood U, Asiri FY, Shah AH, Alqahtani MA, Asiri FY, Vohra F, Javed F. Status: A paid open access option is available for this journal. at Liebertpub Abstract:
Mycobacterium brisbanense is a member of Mycobacterium fortuitum third biovariant complex, which includes rapidly growing Mycobacterium spp. that normally inhabit soil, dust and water, and can sometimes cause respiratory tract infections in humans. We present the first whole-genome analysis of M. brisbanense UM_WWY which was isolated from a 70-year-old Malaysian patient. Molecular phylogenetic analyses confirmed the identification of this strain as M. brisbanense and showed that it has an unusually large genome compared with related mycobacteria. The large genome size of M. brisbanense UM_WWY (similar to 7.7Mbp) is consistent with further findings that this strain has a highly variable genome structure that contains many putative horizontally transferred genomic islands and prophage. Comparative analysis showed that M. brisbanense UM_WWY is the only Mycobacterium species that possesses a complete set of genes encoding enzymes involved in the urea cycle, suggesting that this soil bacterium is able to synthesize urea for use as plant fertilizers. It is likely that M. brisbanense UM_WWY is adapted to live in soil as its primary habitat since the genome contains many genes associated with nitrogen metabolism. Nevertheless, a large number of predicted virulence genes were identified in M. brisbanense UM_WWY that are mostly shared with well-studied mycobacterial pathogens such as Mycobacterium tuberculosis and Mycobacterium abscessus. These findings are consistent with the role of M. brisbanense as an opportunistic pathogen of humans. The whole-genome study of UM_WWY has provided the basis for future work of M. brisbanense. Source: PLOS ONE Author; Wee WY, Tan TK, Jakubovics NS, Choo SW. Full available at PloS One Abstract:
Background The aim was to assess the efficacy of antimicrobial photodynamic therapy (aPDT) in the treatment of aggressive periodontitis (AgP). Methods The addressed focused question was “Is aPDT effective in the treatment of AgP?” MEDLINE/PubMed, EMBASE, Scopus, ISI Web of knowledge and Google-Scholar databases were searched from 1977 till May 2015 using combinations of the following keywords: antimicrobial; photochemotherapy; photodynamic therapy; photosensitizing agents; AgP; scaling and root-planing (SRP). Reviews, case reports, commentaries, and articles published in languages other than English were excluded. Results Seven studies were included. In 5 studies, aPDT was performed as an adjunct to SRP. Laserwavelengths and duration of irradiation ranged between 660–690 nm and 60–120 s, respectively. Laser power output as reported in 2 studies was 75 mW. One study showed significant improvement in periodontal parameters for subjects receiving aPDT as an adjunct to SRP as compared to treatment with SRP alone at follow up. However, comparable periodontal parameters were reported when aPDT as an adjunct to SRP was compared to SRP alone in the treatment of AgP in one study. One study showed comparable outcomes when aPDT was compared to SRP in the treatment of AgP. In two studies, adjunctive antibiotic administration to SRP showed significantly better outcomes when compared to application of adjunctive use of aPDT to SRP. Conclusion aPDT is effective as an adjunct to SRP for the management of AgP, however, further randomized clinical trials with well defined control groups are needed in this regard. Source: PHOTODIAGNOSIS AND PHOTODYNAMIC THERAPY Author: Vohra F, Akram Z, Safii SH, Vaithilingam RD, Ghanem A, Sergis K, Javed F. Status: A paid open access option is available for this journal at ScienceDirect Abstract:
Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through orizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely availableNeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Netsseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server whic were then stored into the MySQL database. The protein-coding genes were ftirther analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CBS, utilizing the model view-controller (MVC) framework. The in-house developed bioinforrnatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Netsserta genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing ofNeisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genonle Comparison tool (PGC) for comparative genornic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my. Source: PEERJ Author: Zheng WN, Mutha NVR, Heydari H, Dutta A, Siow CC, Jakubovis NS, Wee WY, Tan SY, Ang MY, Wong GJ, Choo SW. Status: Full text available at PEERJ Abstract:
A modified silk fibroin scaffold with mimic reconstructed extracellular matrix of decellularized pulp/collagen/fibronectin was proposed for bone tissueengineering in alveolar bone resorption. Silk fibroin scaffolds were fabricated by freeze-drying before modification by coating in a decellularizedpulp/collagen/fibronectin solution. The extracellular matrix reconstruction of the decellularized pulp/collagen/fibronectin and the morphology and biofunctionalities of the modified scaffolds were evaluated. The results showed that decellularized pulp/collagen/fibronectin organized into a dense dendrite structure and adhered in the scaffold in a fibrillar network. The modified scaffold showed predominant biofunctionalities and promise for bone tissueengineering in alveolar bone resorption. Source: Materials Letters Author: Sangkert S, Kamonmattayakul S, Chai WL, Meesane J. Status: A paid open access option is available for this journal at ScienceDirect |