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
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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 Abstract:
Ethnopharmacological relevanceTraditionally, the leaves of Catha edulis Forsskal (Khat) are consumed by the people of Yemen primarily for its recreational effect, and secondarily, for achieving certain tasks. Additionally, Yemeni diabetics chew such leaves in the belief that this can control their elevated blood glucose level. AimsThis review focuses on outlining the findings of studies that have been conducted to display the glycemic effect of Catha edulis, while trying to balance it with findings of the association of its chewing with the development of type 2 diabetes mellitus (DM). Materials and methodsThe search strategy adopted was based on a comprehensive research in Medline, PubMed, Web of Science, JSTOR, Scopus and Cochrane for articles, proceeding abstracts and theses to identify complete reports written in the English language about the glycemic effect of Catha edulis in humans and animals from 1976 to 2016. In addition, bibliographies were also reviewed to find additional reports not otherwise published. Thirty seven records were identified of which, 25 eligible studies were included in the meta-analysis using blood glucose as an outcome measurement. Studies were divided into four subgroups according to the experimental model, namely; non-diabetic animals, diabetic animals, non-diabetic humans and diabetic humans. The pooled mean difference (MD) of blood glucose between experimental and control were calculated using random effects model of the weighted mean difference of blood glucose with 95% confidence interval (CI). Heterogeneity between studies was tested using I2 statistic and a value of P<0.05 was considered to indicate statistical significance. ResultsThe scientific reports in the literature prevailed that the glycemic effect of Catha eduliswere greatly conflicting with the majority of studies indicating that Catha edulis has a mild hypoglycemic effect. However, the meta-analysis indicted that the overall result showed an insignificant reduction in blood glucose (MD=−9.70, 95% CI: −22.17 to 2.76, P=0.13, with high heterogeneity between subgroups, I2=88.2%, P<0.0001). In addition, pooled mean difference of blood glucose of non-diabetic animals, diabetic animals and non-diabetic humans showed an insignificant reduction in blood glucose (MD=−18.55, 95% CI: −39.55 to 2.50, P<0.08, MD=−52.13%, 95% CI: −108.24 to 3.99, P=0.07 and MD=−2.71%, 95% CI: −19.19 to −13.77, P=0.75) respectively. Conversely, a significant elevation in the pooled mean difference of blood glucose in diabetic humans was indicated (MD=67.18, 95% CI: 36.93–97.43, P<0.0001). The conflict shown in the glycemic effect of Catha edulis is thought to be cultivar-related, while demographic and epidemiological reports suggested that chewing Catha edulis might be a predisposing factor contributing to the development of type 2 DM. ConclusionIt was difficult to draw a meaningful conclusion from both the systematic and the meta-analysis with respect to the glycemic effect of Catha edulis since the meta-analysis results were insignificant with high heterogeneity among subgroups and are greatly conflicting. The variation is most likely due to unadjusted experimental factors or is related to Catha edulis itself, such as the differences in the phytochemical composition. Therefore, it is highly recommended that further studies of the glycemic effect of the cultivar of Catha edulis being studied should come with the identification and quantification of phytochemical content so that a meaningful assessment can be made with regard to its hypoglycemic properties. In addition, well-controlled clinical studies should be conducted to confirm whether or not chewing Catha edulis is associated with the development of type 2 DM, since this would be a source of concern seeing that the plant is widely consumed in certain populations. Source: Journal of Ethnopharmacology Author: Alsalahi A, Mohamed R, Alyousefi NA, Alshagga MA, Shwter AN, Al-Maqtari A, Ahmed RH, Mohamed Z. Status: A paid open access option is available for this journal at ScienceDirect Abstract:
Background: The regulation of specific target genes by transcription factors is central to our understanding of gene network control in developmental and physiological processes yet how target specificity is achieved is still poorly understood. This is well illustrated by the Hox family of transcription factors as their limited in vitro DNA-binding specificity contrasts with their clear in vivo functional specificity. Results: We generated genome-wide binding profiles for three Hox proteins, Ubx, Abd-A and Abd-B, following transient expression in Drosophila Kc167 cells, revealing clear target specificity and a striking influence of chromatin accessibility. In the absence of the TALE class homeodomain cofactors Exd and Hth, Ubx and Abd-A bind at a very similar set of target sites in accessible chromatin, whereas Abd-B binds at an additional specific set of targets. Provision of Hox cofactors Exd and Hth considerably modifies the Ubx genome-wide binding profile enabling Ubx to bind at an additional novel set of targets. Both the Abd-B specific targets and the cofactor-dependent Ubx targets are in chromatin that is relatively DNase1 inaccessible prior to the expression of Hox proteins/Hox cofactors. Conclusions: Our experiments demonstrate a strong role for chromatin accessibility in Hox protein binding and suggest that Hox protein competition with nucleosomes has a major role in Hox protein target specificity in vivo. Source: EPIGENETICS & CHROMATIN (1756-8935) Author: Beh CY, El-Sharnouby S, Chatzipli A, Russell S, Choo SW, White R. Status: Free Full Text available at BioMed Central 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: Full text available at liebertpub |