• Journal of Microbiology and Biotechnology
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• v.16 no.5
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• pp.740-747
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• 2006

Amplification by universal consensus sequences in pathogenic bacterial DNA would allow rapid identification of pathogenic bacteria, and amplification of genus-specific and species-specific sequences of pathogenic bacterial DNA might be used for genotyping at the genus and species levels. For design of probes for molecular diagnostics, several tools are available as stand-alone programs or as Web application. However, since most programs can design only a few probe sets at one time, they are not suitable for large-scale and automatic probes design. Therefore, for high-throughput design of specific probes in diagnostic array development, an automated design tool is necessary. Thus, we developed a Web-based automatic system for design of genus-specific and species-specific probes for pathogen detection. The system is available at http://www.miprobe.com.

• Parasites, Hosts and Diseases
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• v.38 no.3
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• pp.191-194
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• 2000

Genus specific antigenicity of the 10 kDa protein in cyst fluid (CF) of Taenia solium metacestodes was demonstrated by comparative immunoblot analysis. When CFs from taeniid metacestodes of T. saginata, T. solium, T. taeniaeformis and T. crassiceps were probed with specific monoclonal antibody (mAb) raised against 150 kDa protein of T. solium metacestodes, specific antibody reactions were observed in 7 and 10 kDa proteins of T. solium and in 7/8 kDa of T. saginata, T. taeniaeformis and T. crasiceps. The mAb did not react with any protein in hydatid fluid of Echinococcus granulosus and E. multilocularis. This result revealed that the 10 kDa peptide of T. solium metacestodes and its equivalent proteins of different Taenia metacestodes are genus specific antigens that are shared among different Taenia species.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.399-401
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• 2005

MIPROBE is a web-based tool for design of universal, genus-specific, and species-specific primers and probes. The main functions of MIPROBE are collection of target gene sequences, construction of consensus sequences, collection of candidate primers and probes, and evaluation of candidates by BLAST. Biologists with little computer skills can easily use MIPROBE to design large-scale universal, genus-, and species-specific primers and probes. This software is available at http://www.miprobe.com. Also detailed descriptions of how to use the program are found at this site.

• Korean Journal of Veterinary Service
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• v.35 no.4
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• pp.289-294
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• 2012

Mycoplasmas are highly fastidious bacteria, difficult to culture and slow growing. Infections with Mycoplasma species can cause a variety of problems in living organisms and in vitro cell cultures. In this study, we investigated the usefulness of a genus-specific consensus PCR analysis method to detect Mycoplasma species. The developed consensus primer pairs MycoF and MycoR were designed specifically to amplify the 16S ribosomal RNA gene (rRNA) of Mycoplasma species by the optimized PCR system. The developed consensus PCR system effectively amplified 215 bp of Mycoplasma genus-specific region of 16S rRNA. In conclusion, we recommend this consensus PCR for monitoring Mycoplasma species in animals, human and cell culture system.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.12
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• pp.1887-1894
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• 2007

In this paper, a rapid and reliable gene-targeted species-specific polymerase chain reaction (PCR) technique based on a two-step process was established to identify bifidobacteria in dairy products. The first step was the PCR assay for genus Bifidobacterium with genus specific primers followed by the second step, which identified the species level with species-specific primer mixtures. Ten specific primer pairs, designed from nucleotide sequences of the 16-23S rRNA region, were developed for the Bifidobacterium species including B. angulatum, B. animalis, B. bifidum, B. breve, B. catenulatum, B. infantis, B. longum, B. minimum, B. subtile, and B. thermophilum. This technique was applied to the identification of Bifidobacterium species isolated from 6 probiotic products, and four different Bifidobacterium spp. (B. bifidum, B. longum, B. infantis, and B. breve) were identified. The findings indicated that the 16S-23S rDNA gene-targeted species-specific PCR technique is a simple and reliable method for identification of bifidobacteria in probiotic products. PCR combined with Denaturing Gradient Gel Electrophoresis (DGGE) for identification of the bifidobacteria was also evaluated and compared with the gene-targeted species-specific technique. Results indicated that for fermented milk products consistency was found for both species-specific PCR and PCR-DGGE in detecting species. However, in some lyophilized products, the bands corresponding to these species were not visualized in the DGGE profile but the specific PCR gave a positive result.

• Genomics & Informatics
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• v.16 no.4
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• pp.23.1-23.5
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• 2018

Virus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the development of genome sequence analysis technology, there is an increasing demand for virus taxonomy to be extended from in vivo and in vitro to in silico. In this study, we verified the consistency of the current International Committee on Taxonomy of Viruses taxonomy using an in silico approach, aiming to identify the specific sequence for each virus. We applied this approach to norovirus in Caliciviridae, which causes 90% of gastroenteritis cases worldwide. First, based on the dogma "protein structure determines its function," we hypothesized that the specific sequence can be identified by the specific structure. Firstly, we extracted the coding region (CDS). Secondly, the CDS protein sequences of each genus were annotated by the conserved domain database (CDD) search. Finally, the conserved domains of each genus in Caliciviridae are classified by RPS-BLAST with CDD. The analysis result is that Caliciviridae has sequences including RNA helicase in common. In case of Norovirus, Calicivirus coat protein C terminal and viral polyprotein N-terminal appears as a specific domain in Caliciviridae. It does not include in the other genera in Caliciviridae. If this method is utilized to detect specific conserved domains, it can be used as classification keywords based on protein functional structure. After determining the specific protein domains, the specific protein domain sequences would be converted to gene sequences. This sequences would be re-used one of viral bio-marks.

• ALGAE
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• v.33 no.1
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• pp.37-48
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• 2018

Alaria is the second largest genus of the Laminariales, which is distributed far into the northern Pacific and Atlantic oceans. Due to its high morphological plasticity, over 100 specific and sub-specific names have been used in Alaria, this has been tailored down to the present 17 species through morphological revision and molecular phylogenetic analysis. Endemic species of Alaria from Russian Far East have not been thoroughly revised since their original description, and few of them were confirmed using molecular data until recently. We carried out morphological and molecular studies on A. paradisea which is an endemic species distributed on the Kurile Islands, first described by Miyabe and Nagai in 1932 as Pleuropterum paradiseum. The range of morphological variability and its distribution was re-evaluated using the type specimen as well as other specimens. Analyses of partial mitochondrial cytochrome c oxidase subunit 1 and nuclear-encoded internal transcribed spacer sequences showed that A. paradisea nested within the genus Alaria, but differs morphologically from any other Alaria species in having additional sporophylls with a central midrib (${\beta}-sporophylls$). Our results showed that A. paradisea clearly belongs to the genus Alaria based on DNA data, although the key morphological character that was used to include this species to the genus Pleuropterum, ${\beta}-sporophylls$, is stable and distinguishes it from other Alaria species.

• Journal of the East Asian Society of Dietary Life
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• v.18 no.5
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• pp.753-759
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• 2008

The principal objective of this study was to develop the optimum oligonucleotide primers for the simple detection of Campylobacter in food samples. In order to achieve this goal, a variety of oligonucleotide primers were designed via the modification of 16S rDNA, ceuE and mapA sequences of Campylobacter. Through the subsequent analysis of the specificity and sensitivity of primers, two types of oligonucleotide primers, CB4 and CJ1, were selected for Campylobacter genus-specific and C. jejuni species-specific primers, respectively. The detection limit was found to be $10^0{\sim}10^1$ cells per reaction with the prepared cell suspension, however, the sensitivity in the meat samples was less, at $10^1{\sim}10^2$. We suggested that PCR inhibitors such as hemoglobin or immunoglobulin in pork or beef influenced.

• Animal Systematics, Evolution and Diversity
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• v.36 no.2
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• pp.107-112
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• 2020

A new genus Parkiana Cho, gen. nov., belonging to Torodorinae of Lecithoceridae, is described from Madagascar, with two new species: P. matutinalis Cho & Agassiz, sp. nov. and P. andasibensis Cho & Agassiz, sp. nov. Although superficially similar to Thubdora Park, 2018, some of their morphological characters, such as wing venation, are unique and the species of the genus are grouped apart from Thubdora in a preliminary phylogenetic analysis based on COI barcode sequences. In addition to the specific descriptions, adults and genitalia for the two new species are illustrated.

• Journal of Korean Society of Forest Science
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• v.51 no.1
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• pp.36-40
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• 1981

The patterns of isoperoxidase in needle-leaves of 23 species of the genus Pinus were analyzed by means of starch gel electrophoresis. Each species had a unique band pattern. In all, 56 isoperoxidase bands were identified, of which 9 to 35 isoperoxidase bands were possessed by single species. No single band was common to all Pinus species but when band patterns were grouped into 7 types, type II was considered to be the specific to genus Pinus. The results of this experiment indicated that various Pinus species had their more or less specific band patterns of peroxidase.