Objective To detect the diatom population diversity in Dianchi by constructing a 18S rDNA clone library. Methods DNA from diatoms in 6 water samples of Dianchi was amplified with diatom 18S rDNA specific primer.The 18S rDNA clone library was constructed, and clones were randomly selected for sequence. Sequence alignment was performed by BLAST. The diatom population distribution in Dianchi was analyzed and the phylogenetic tree of diatom 18S rDNA in Dianchi waters was established with the MEGA v7.0.14 software. Results Two hundred and forty clones were sequenced, with 167 diatom sequences obtained, including 11 diatom species such as Stephanodiscus, Diatoma, and Melosira. There were certain differences in diatom population distribution among the 6 samples. Conclusion The population distribution of diatom species in Dianchi shows unique features and the sequence analysis of diatom 18S rDNA has a certain reference value to the inference of forensic drowning sites.
China ; DNA, Ribosomal/genetics* ; Diatoms/classification* ; Drowning ; Forensic Sciences ; Humans ; Phylogeny ; RNA, Ribosomal, 18S/genetics*

The taxonomy of Acanthamoeba spp., an amphizoic amoeba which causes granulomatous amoebic encephalitis and chronic amoebic keratitis, has been revised many times. The taxonomic validity of some species has yet to be assessed. In this paper, we analyzed the morphological characteristics, nuclear 18s rDNA and mitochondrial 16s rDNA sequences and the Mt DNA RFLP of the type strains of four Acanthamoeba species, which had been previously designated as A. divionensis, A. parasidionensis, A. mauritaniensis, and A. rhysodes. The four isolates revealed characteristic group II morphology. They exhibited 18S rDNA sequence differences of 0.2-1.1% with each other, but more than 2% difference from the other compared reference strains. Four isolates formed a different clade from that of A. castellanii Castellani and the other strains in morphological group II on the phylogenetic tree. In light of these results, A. paradivionensis, A. divionensis, and A. mauritaniensis should be regarded as synonyms for A. rhysodes.
Acanthamoeba/*classification/*genetics ; Animals ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 18S/genetics

Siraitia grosvenorii is a traditional Chinese medicine also as edible food. This study selected six candidate reference genes by real-time quantitative PCR, the expression stability of the candidate reference genes in the different samples was analyzed by using the software and methods of geNorm, NormFinder, BestKeeper, Delta CT method and RefFinder, reference genes for S. grosvenorii were selected for the first time. The results showed that 18SrRNA expressed most stable in all samples, was the best reference gene in the genetic analysis. The study has a guiding role for the analysis of gene expression using qRT-PCR methods, providing a suitable reference genes to ensure the results in the study on differential expressed gene in synthesis and biological pathways, also other genes of S. grosvenorii.
Cucurbitaceae ; genetics ; RNA, Ribosomal, 18S ; genetics ; Real-Time Polymerase Chain Reaction ; methods ; Reference Standards

The paper is aimed to identify SNP in Sarcandra glabra and Chloranthus spicatus, and authenticate S. glabra from Ch. spicatus and the mixture by using PCR amplification of specific alleles. SNPs in the ITS sequences of S. glabra and Ch. spicatus were found by ClustulX 2. 1 program and Bioedit software. Primers for authentic S. glabra and Ch. spicatus was designed according to the SNP site, and ITS sequence universal primers plus to the authentic primer to construct a multi-PCR reaction system, and then optimized the PCR reaction system. Five hundred and eighty band special for S. glabra and 470 bp band special for Ch. spicatus were found by using multi-PCR reaction. The multi-PCR reaction system could be applied to identify S. glabra and Ch. spicatus's leaves.
DNA, Plant ; analysis ; genetics ; DNA, Ribosomal ; genetics ; DNA, Ribosomal Spacer ; analysis ; genetics ; Magnoliopsida ; classification ; genetics ; Plant Leaves ; genetics ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; RNA, Ribosomal ; genetics ; RNA, Ribosomal, 18S ; genetics ; RNA, Ribosomal, 5.8S ; genetics ; Species Specificity

In this study, we used traditional morphological and molecular identification methods to preliminarily identify two strains of dermatophytes. The two strains were observed under the microscope. And then the dermatophytes were cultured on Sabouraud's dextrose agar (SDA). The 18S rRNA regions of the two dermatophyte strains were amplified by polymerase chain reaction (PCR), and the PCR products were sequenced and compared with GenBank data. BLAST tools and DNAMAN software were used to analyze the sequences. To further determine highly homologous sequences, a phylogenetic tree was constructed using the Neighbor-Joining method. The two strains of dermatophytes were identified by traditional morphological identification as Epidermophyton floccosum and Microsporum ferrugineum. The 18S rRNA sequence analyses showed high similarities to Cladosporium cladosporioides isolate C115LM-UFPR and Ascomycete sp. LB68A1A2. Epidermophyton and Cladosporium belong to dermatophyte, while Microsporum ferrugineum and Ascomycete belong to microsporum. The two novel strains of dermatophytes were therefore identified as Cladosporium cladosporioides isolate C115LM-UFPR (JN650537, Cladosporium) and Ascomycete sp. LB68A1A2 (AY770409, Ascomycete sp).
Arthrodermataceae ; cytology ; genetics ; isolation & purification ; Humans ; Hyphae ; cytology ; RNA, Fungal ; genetics ; RNA, Ribosomal, 18S ; genetics ; Skin ; microbiology

Subgenus classification of Acanthamoeba remains uncertain. Twenty-three reference strains of Acanthamoeba including 18 (neo)type-strains were subjected for classification at the subgenus level by riboprinting. PCR/RFLP analysis of 18S rRNA gene (rDNA). On the dendrogram reconstructed on the basis of riboprint analyses, two type-strains (A. astronyxis and A. tubiashi) of morphological group 1 diverged early from the other strains and were quite distinct from each other. Four type-strains of morphological group 3, A. culbertsoni, A. palestinensis, A. healyi were considered taxonomically valid, but A. pustulosa was regarded as an invalid synonym of A. palestinensis. Strains of morphological group 2 were classified into 6 subgroups. Among them, A. griffini which has an intron in its 18S rDNA was the most divergent from the remaining strains. Acanthamoeba castellanii Castellani, A. quina Vil3, A. lugdunensis L3a, A. polyphaga Jones, A. triangularis SH621, and A. castellanii Ma strains belonged to a subgroup, A. castellanii complex. However, A. quina and A. lugdunensis were regarded as synonyms of A. castellanii. The Chang strain could be regarded as A. hatchetti. Acanthamoeba mauritaniensis, A. divionensis, A. paradivionensis could be considered as synonyms of A. rhysodes. Neff strain was regarded as A. polyphaga rather than as A. castellanii. It is likely that riboprinting can be applied for rapid identification of Acanthamoeba isolated from the clinical specimens and environments.
Acanthamoeba/genetics ; Acanthamoeba/classification* ; Animal ; DNA, Protozoan/analysis ; Polymerase Chain Reaction/methods* ; Polymorphism, Restriction Fragment Length* ; RNA, Protozoan/genetics ; RNA, Protozoan/analysis* ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 18S/analysis*

The present study was performed to trace the decisive evidence for mixed infection of 2 Myxobolus species, M. episquamalis and Myxobolus sp., in the gray mullet, Mugil cephalus, from Korean waters. Mullets with whitish cyst-like plasmodia on their scales were collected near a sewage plant in Yeosu, southern part of Korea, in 2009. The cysts were mainly located on scales and also found in the intestine. The spores from scales were oval in a frontal view, tapering anteriorly to a blunt apex, and measured 7.2 microm (5.8-8.0) in length and 5.3 microm (4.7-6.1) in width. Two polar capsules were pyriform and extended over the anterior half of the spore, measuring 3.5 microm (2.3-4.8) in length and 2.0 microm (1.5-2.2) in width. In contrast, the spores from the intestine were ellipsoidal, 10.4 microm (9.0-11.9) in length and 8.4 microm (7.3-10.1) in width. The polar capsules were pyriform but did not extend over the anterior half of the spore, 3.7 microm (2.5-4.5) in length and 2.2 microm (1.8-2.9) in width. The nucleotide sequences of the 18S rDNA gene of the 2 myxosporean spores from scales and intestine showed 88.1% identity to each other and 100% identity with M. episquamalis and 94.5% identity with M. spinacurvatura from mullet, respectively. By the above findings, it is first confirmed that mullets from the Korean water are infected with 2 myxosporean species, M. episquamalis and Myxobolus sp.
Animals ; Fish Diseases/epidemiology/*parasitology ; Myxobolus/classification/*genetics ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Republic of Korea/epidemiology ; *Smegmamorpha ; Species Specificity

Amoebic keratitis (AK) caused by Acanthamoeba is one of the most serious corneal infections. AK is frequently misdiagnosed initially as viral, bacterial, or fungal keratitis, thus ensuring treatment delays. Accordingly, the early detection of Acanthamoeba would contribute significantly to disease management and selection of an appropriate anti-amoebic therapy. Recently, the loop-mediated isothermal amplification (LAMP) method has been applied to the clinical diagnosis of a range of infectious diseases. Here, we describe a rapid and efficient LAMP-based method targeting Acanthamoeba 18S rDNA gene for the detection of Acanthamoeba using clinical ocular specimens in the diagnosis of AK. Acanthamoeba LAMP assays detected 11 different strains including all AK-associated species. The copy number detection limit for a positive signal was 10 DNA copies of 18S rDNA per reaction. No cross-reactivity with the DNA of fungi or other protozoa was observed. The sensitivity of LAMP assay was higher than those of Nelson primer PCR and JDP primer PCR. In the present study, LAMP assay based on directly heat-treated samples was found to be as efficient at detecting Acanthamoeba as DNA extracted using a commercial kit, whereas PCR was only effective when commercial kit-extracted DNA was used. This study showed that the devised Acanthamoeba LAMP assay could be used to diagnose AK in a simple, sensitive, and specific manner.
Acanthamoeba/*genetics ; Animals ; Base Sequence ; Humans ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques/*methods ; RNA, Ribosomal, 18S/*genetics ; Sensitivity and Specificity

In order to transform main active ingredient of volatile oil, endophytic fungi were screened from the root of Atractylodes lancea. Transformation method was used in vitro. The changes of volatile oil were traced by gas chromatography. One endophytic fungus (strain ALG-13) which could uitilize volatile oil selectively was screened. Single factor experiment were conducted for exploring the effects of various factors that including kinds of carbon source, speed, liquid volume, pH and concentration of plant tissue on degradation by this strain. Subsequently, the main affecting factors carbon source, speed, pH and liquid volume were optimized using orthogonal array design. Results showed that endophytic fungus ALG-13 selectively used the volatile oil, change the relative percentage of the main components of volatile oil, Atractylon and Atractydin were increased, While, beta-eudesmol and Atractylol decreased. After selectively degradation by fungus, volatile oil components percentage were closer to the geo-herbs. Strain ALG-13 was identified as Bionectria ochroleuca according to its morphological characteristics and systematic analysis of ITS sequence. The optimal conditions were as follows: sucrose used as carbon source, rotating speed was 200 r x min(-1), initial pH for medium was 4.5, 50 mL liquid was added in 250 mL flask. The endophytic fungus ALG-13 could degrade the volatile oil selectively, which was benefit for forming geoherbs A. lancea volatile oil composition.
Atractylodes ; chemistry ; microbiology ; Fungi ; classification ; genetics ; isolation & purification ; metabolism ; Oils, Volatile ; chemistry ; metabolism ; Phylogeny ; RNA, Ribosomal, 18S ; genetics

We performed a molecular genetic study on the sequences of 18S ribosomal RNA (ITS1 region) gene in 4-day-old adult worms of Macroorchis spinulosus recovered in mice experimentally infected with metacercariae from crayfish in Jeollanam-do Province, Korea. The metacercariae were round, 180 µm in average diameter, encysted with 2 layers of thick walls, but the stylet on the oral sucker was not clearly seen. The adult flukes were oval shape, and 760-820 µm long and 320-450 µm wide, with anterolateral location of 2 large testes. The phylogenetic tree based on ITS1 sequences of 6 M. spinulosus samples showed their distinguished position from other trematode species in GenBank. The most closely resembled group was Paragonimus spp. which also take crayfish or crabs as the second intermediate host. The present study is the first molecular characterization of M. spinulosus and provided a basis for further phylogenetic studies to compare with other trematode fauna in Korea.
Animals ; DNA, Ribosomal Spacer/*genetics ; Metacercariae/classification/cytology/genetics/isolation & purification ; Mice ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Trematoda/*classification/cytology/*genetics/isolation & purification