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Jiang H.-Y.,CAS South China Sea Institute of Oceanology | Jiang H.-Y.,Guangdong Entomological Institute South China Institute of Endangered Animals | Hu C.-Q.,CAS South China Sea Institute of Oceanology | Yang H.-P.,Guangzhou DE AOU Biotechnology Technology Co. | And 5 more authors.
Phytotaxa | Year: 2015

Halamphora yongxingensis sp. nov., a marine benthic diatom isolated from an intertidal reef around the Yongxing Island, South China Sea (16° 58’ 43.3” N, 112° 14’ 41.7” E), is described in this study on the basis of light and electron microscopy. This diatom is also compared with related taxa such as Halamphora subturgida (Hustedt) Levkov and Amphora subtropica Wachnicka & Gaiser. In addition, phylogenetic analyses based on 18S rDNA and rbcL gene were also conducted. The results revealed that H. yongxingensis was clustered into the Halamphora clade, closely related to Halamphora montana (Krasske) Levkov. We discuss morphological differences between H. yongxingensis and H. montana. © 2015 Magnolia Press.

Li Y.,South China University of Technology | Shi L.,South China University of Technology | Pan A.,South China University of Technology | Cao W.,Guangzhou DE AOU Biotechnology Technology Co. | And 5 more authors.
Journal of Microbiological Methods | Year: 2014

Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB) leads to serious health problems as a chronic respiratory infectious disease. Here we established a real-time fluorescence loop-mediated isothermal amplification assay (RealAmp) using a portable ESE Quant tube scanner as a convenient rapid detection method for MTB. The method efficacy from sputum samples was further investigated, and the reaction time was only 20min with the detection limit low to 102CFU/ml concentration of MTB. We assessed a total of 1067 samples by the RealAmp assay, comparing the results with smear microscopy and conventional culture methods. To examine whether the failure to detect TB by culturing is due to low sensitivity or true absence, we examined the culture negative samples by commercial real time PCR MTB detection kit, and the results were compared with RealAmp. The data showed that RealAmp assay had a higher positive rate than that of sputum smear and culture methods. RealAmp had a sensitivity of 96.70% and a specificity of 91.55% when compared with culture. In addition, its sensitivity and specificity were 95.29% and 86.88% respectively compared with examination of smear samples using light microscopy. The sensitivity of RealAmp in comparison to real time PCR was 98.25% and specificity was 99.11% in validation of culture negative samples.The present study revealed the newly established RealAmp assay as a convenient, efficient, sensitive and specific method that could be an alternative for rapid detection of MTB and a tool to validate culture and smear negative samples. Furthermore, the portability of the ESE Quant tube scanner also contributed to the promising application for grassroots and field detection of MTB. © 2014.

Di H.,South China University of Technology | Di H.,Guangzhou DE AOU Biotechnology Technology Co. | Ye L.,South China University of Technology | Yan H.,South China University of Technology | And 5 more authors.
Biochemical and Biophysical Research Communications | Year: 2014

Listeria monocytogenes, an important food-borne pathogen, causes high mortality rate of listeriosis. Pan-genomic comparisons revealed the species genome of L. monocytogenes is highly stable but not completely clonal. The population structure of this species displays at least four evolutionary lineages (I-IV). Isolates of different lineages displayed distinct genetic, phenotypic and ecologic characteristics, which appear to affect their ability to be transmitted through foods and to cause human disease, as well as their ability to thrive in markedly phage-rich environments. CRISPR (clustered regularly interspaced short palindrome repeats), a recently described adaptive immunity system, not only confers defense against invading elements derived from bacteriophages or plasmids in many bacteria and archaeal, but also displays strains-level variations in almost any given endowed species. This work was aimed to investigate CRISPR diversity in L. monocytogenes strains of different lineages and estimated the potential practicability of the CRISPR-based approach to resolve this species' biodiversity. Only a third of strains contained all three CRISPR loci (here defined as LMa, LMb and LMc) at same time. Combined the strain-level variations in presence/absence of each CRISPR locus and its relative size and spacer arrangements, a total of 29 CRISPR genotypes and 11 groups were defined within a collection of 128 strains covering all serotypes. The CRISPR-based approach showed powerful ability to subtype the more commonly food-borne isolates of serotype 1/2a (lineage II) and serotypes 1/2b (lineage I), but limited by the absence of typical CRISPR structure in many lineage I isolates. Strikingly, we found a long associated cas1 gene as well as two self-targeting LMb spacers accidently homologous with endogenous genes in a fraction of serotype 1/2a isolations, demonstrated that CRISPR I B system might involve in bacterial physiology besides antiviral immunity. © 2014 Elsevier Inc. All rights reserved.

Yi M.,Guangdong Inspection and Quarantine Technology Center | Ling L.,Guangdong Inspection and Quarantine Technology Center | Neogi S.B.,Osaka Prefecture University | Neogi S.B.,International Center for Diarrhoeal Diseases Research | And 7 more authors.
Food Control | Year: 2014

We evaluated the usefulness of the loop-mediated isothermal amplification (LAMP) using a portable ESE Quant tube scanner as a rapid and simple method for the detection of Vibrio parahaemolyticus, an important pathogen causing seafood-borne gastroenteritis. The real time LAMP (RT-LAMP) assay using a hemolysin gene (tlh/ldh)-specific primers was verified using V.parahaemolyticus strains (n=91) from different countries and other non-target strains to check the utility of this method. Both the sensitivity and specificity of the RT-LAMP using 3 pairs of tlh/ldh-specific primers developed in this study were excellent (100%). The detection limit of the RT-LAMP was as low as 7 Colony forming unit per reaction and detection time was only 20min. Comparative evaluation of the target bacterial strains with the RT-LAMP using ESE Quant tube scanner, API 20E system and conventional RT-PCR method revealed that the RT-LAMP assay developed in this study is simpler and more rapid than the latter two methods. Therefore, the RT-LAMP method using the easily portable ESE Quant tube scanner can be considered as an effective tool for the rapid screening of V.parahaemolyticus strains in environmental and clinical samples, especially, in remote areas of developing countries during epidemic periods. © 2014 Elsevier Ltd.

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