Development of ListeriaBase and comparative analysis of Listeria monocytogenes

Background: Listeria consists of both pathogenic and non-pathogenic species. Reports of similarities between the genomic content between some pathogenic and non-pathogenic species necessitates the investigation of these species at the genomic level to understand the evolution of virulence-associated genes. With Listeria genome data growing exponentially, comparative genomic analysis may give better insights into evolution, genetics and phylogeny of Listeria spp., leading to better management of the diseases caused by them. Description: With this motivation, we have developed ListeriaBase, a web Listeria genomic resource and analysis platform to facilitate comparative analysis of Listeria spp. ListeriaBase currently houses 850,402 protein-coding genes, 18,113 RNAs and 15,576 tRNAs from 285 genome sequences of different Listeria strains. An AJAX-based real time search system implemented in ListeriaBase facilitates searching of this huge genomic data. Our in-house designed comparative analysis tools such as Pairwise Genome Comparison (PGC) tool allowing comparison between two genomes, Pathogenomics Profiling Tool (PathoProT) for comparing the virulence genes, and ListeriaTree for phylogenic classification, were customized and incorporated in ListeriaBase facilitating comparative genomic analysis of Listeria spp. Interestingly, we identified a unique genomic feature in the L. monocytogenes genomes in our analysis. The Auto protein sequences of the serotype 4 and the non-serotype 4 strains of L. monocytogenes possessed unique sequence signatures that can differentiate the two groups. We propose that the aut gene may be a potential gene marker for differentiating the serotype 4 strains from other serotypes of L. monocytogenes. Conclusions: ListeriaBase is a useful resource and analysis platform that can facilitate comparative analysis of Listeria for the scientific communities. We have successfully demonstrated some key utilities of ListeriaBase. The knowledge that we obtained in the analyses of L. monocytogenes may be important for functional works of this human pathogen in future. ListeriaBase is currently available at http://listeria.um.edu.my

Development of ListeriaBase and comparative analysis of \u3ci\u3eListeria monocytogenes\u3c/i\u3e

Background: Listeria consists of both pathogenic and non-pathogenic species. Reports of similarities between the genomic content between some pathogenic and non-pathogenic species necessitates the investigation of these species at the genomic level to understand the evolution of virulence-associated genes. With Listeria genome data growing exponentially, comparative genomic analysis may give better insights into evolution, genetics and phylogeny of Listeria spp., leading to better management of the diseases caused by them. Description: With this motivation, we have developed ListeriaBase, a web Listeria genomic resource and analysis platform to facilitate comparative analysis of Listeria spp. ListeriaBase currently houses 850,402 protein-coding genes, 18,113 RNAs and 15,576 tRNAs from 285 genome sequences of different Listeria strains. An AJAX-based real time search system implemented in ListeriaBase facilitates searching of this huge genomic data. Our in-house designed comparative analysis tools such as Pairwise Genome Comparison (PGC) tool allowing comparison between two genomes, Pathogenomics Profiling Tool (PathoProT) for comparing the virulence genes, and ListeriaTree for phylogenic classification, were customized and incorporated in ListeriaBase facilitating comparative genomic analysis of Listeria spp. Interestingly, we identified a unique genomic feature in the L. monocytogenes genomes in our analysis. The Auto protein sequences of the serotype 4 and the non-serotype 4 strains of L. monocytogenes possessed unique sequence signatures that can differentiate the two groups. We propose that the aut gene may be a potential gene marker for differentiating the serotype 4 strains from other serotypes of L. monocytogenes. Conclusions: ListeriaBase is a useful resource and analysis platform that can facilitate comparative analysis of Listeria for the scientific communities. We have successfully demonstrated some key utilities of ListeriaBase. The knowledge that we obtained in the analyses of L. monocytogenes may be important for functional works of this human pathogen in future. ListeriaBase is currently available at http://listeria.um.edu.my

Urban Conservation As A Development Strategy to Revitalize Real Estate Market: An Analysis Of Property Transactions In Georgetown Penang

Penang is well known for its heritage character especially in the city of Georgetown with more than 200 years of urban history. To retain its heritage character, the state and local governments have implemented various conservation policies and identified a heritage zone in the inner city of Georgetown. In many parts of the world, designation as a heritage property would have increased a property’s value and this is one of the reasons put forward for urban effects of conservation related policies on the heritage property market. In this paper, we focus the analysis on data from property transactions and price to intervention strategies, socio-economic and political changes. Our analysis of the transaction date and price trends shows that urban conservation has a potential to be a viable real estate development strategy for Georgetown. Even with conservation policies to place, the demand for old buildings in the conservation zones has not diminished but has shown relatively high transaction counts and high price of heritage properties

CoryneBase: <i>Corynebacterium</i> Genomic Resources and Analysis Tools at Your Fingertips

<div><p>Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for <i>Corynebacterium</i> with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of <i>Corynebacterium</i> where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive <i>Corynebacterium</i> data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of <i>Corynebacterium</i> genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at <a href="http://corynebacterium.um.edu.my/" target="_blank">http://corynebacterium.um.edu.my/</a>.</p></div

Bacterial subcellular localization analysis.

<p>PSORTb 3.0 predicted the percentage of the proteins that are localized in each compartment of bacterial cell.</p

Pathogenomics profiling.

<p>Clustered heat map generated by PathoProT comparing all the genomes of <i>Corynebacterium</i> with 50% sequence identity and completeness thresholds. The data are sorted by hierarchical clustering on both strains and virulence genes to bring similarities together. Cluster relationships are indicated by dendrograms along the left and top of the heat map, and the state of virulence genes being present or absent may indicate functional relationships among strains.</p

Feature diagram showing the overall functionalities of CoryneBase.

<p>Screenshots of CoryneBase web pages with five distinct features accessible from the navigation bar on top: browse, search, tools, genome browser, and download. Four bioinformatic tools are incorporated in CoryneBase: standard BLAST, VFDB BLAST, PGC, and PathoProT.</p

Erratum to: Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) (Autophagy, 12, 1, 1-222, 10.1080/15548627.2015.1100356

No abstract available