Development of a cob-18S rRNA Gene Real-Time PCR Assay for Quantifying Pfiesteria shumwayae in the Natural Environment

Despite the fact that the heterotrophic dinoflagellate Pfiesteria shumwayae is an organism of high interest due to alleged toxicity, its abundance in natural environments is poorly understood. To address this inadequacy, a real-time quantitative PCR assay based on mitochondrial cytochrome b (cob) and18S rRNA gene was developed and P. shumwayae abundance was investigated in several geographic locations. First, cob and its 5′-end region were isolated from a P. shumwayae culture, revealing three different copies, each consisting of an identical cob coding region and an unidentified region (X) of variable length and sequence. The unique sequences in cob and the X region were then used to develop a P. shumwayae-specific primer set. This primer set was used with reported P. shumwayae-specific 18S primers in parallel real-time PCRs to investigate P.shumwayae abundance from Maine to North Carolina along the U.S. east coast and along coasts in Chile, Hawaii, and China. Both genes generally gave similar results, indicating that this species was present, but at low abundance (mostly <10 cells · ml⁻¹), in all the American coast locations investigated (with the exception of Long Island Sound, where which both genes gave negative results). Genetic variation was detected by use of both genes in most of the locations, and while cob consistently detected P. shumwayae or close genetic variants, some of the 18S PCR products were unrelated to P. shumwayae. We conclude that (i) the real-time PCR assay developed is useful for specific quantification of P. shumwayae, and (ii) P. shumwayae is distributed widely at the American coasts, but normally only as a minor component of plankton even in high-risk estuaries (Neuse River and the Chesapeake Bay).     

Development of a real-time PCR probe for quantification of the heterotrophic dinoflagellate Cryptoperidiniopsis brodyi (Dinophyceae) in environmental samples

A TaqMan format real-time PCR probe was developed against the internal transcribed spacer 2 ribosomal DNA region for the specific detection and quantification of Cryptoperidiniopsis brodyi in environmental samples. The assay specificity was confirmed by testing against related dinoflagellates and verified by sequencing PCR amplicons from natural water samples. Phylogenetic analysis of the sequenced environmental samples also showed that this assay is specific to C. brodyi. The C. brodyi-specific assay was used in conjunction with Pfiesteria piscicida- and Pfiesteria shumwayae-specific real-time PCR assays to investigate the temporal variations of C. brodyi, P. piscicida, and P. shumwayae abundance in the Derwent estuary, Tasmania. The 18-month field survey from November 2004 to April 2006 revealed that C. brodyi occurred in all seasons at very low densities, mostly below 25 cells liter(-1), with higher abundance (maximum, 112 cells liter(-1)) in April and May. P. piscicida was detected only once, in May 2005 at 60 cells liter(-1). P. shumwayae was not detected during the survey.     

Low abundance distribution of Pfiesteria piscicida in Pacific and Western Atlantic as detected by mtDNA-18S rDNA real-time polymerase chain reaction

Information on the abundance of Pfiesteria piscicida in thenatural environment is needed for understanding the ecologicalroles of this dinoflagellate. In this study, a real-time polymerasechain reaction (PCR) assay was developed using mitochondrialcytochrome b upstream region and 18S rDNA (PpmtDNA and Pp18S),and the geographic and temporal distribution of P. piscicidawas investigated in several locations. Both PpmtDNA and Pp18Sgenerally gave similar results, indicating that P. piscicidawas present at all studied regions along the American coast(from Maine to North Carolina along the US Atlantic coast andLos Lagos along the Chilean Pacific coast). Despite its widespreaddistribution, P. piscicida was only detected in 36% of the 431water samples analyzed, and its abundance was generally low(<1.0–1.5 cells mL^–1). Populations detected atthe five stations in the Neuse River (North Carolina) and twostations in Chesapeake Bay (Maryland) were genetically homogeneous,whereas those from other locations appeared to be geneticallydiverse. It can be concluded that (i) the PpmtDNA–Pp18Sreal-time PCR assay is sensitive and specific for detectingand quantifying P. piscicida in the natural environment and(ii) P. piscicida is widespread along the American coasts, butnormally only as a minor component of plankton even in the high-riskestuaries (Neuse River, Chesapeake Bay).     

Detection of Sclerotinia sclerotiorum in Planta by a Real-time PCR Assay

Stem rot caused by Sclerotinia sclerotiorum is a very serious disease on oilseed rape worldwide. In this study, a pair of polymerase chain reaction (PCR) primers was designed based on the nucleotide sequence of a DNA region amplified by a microsatellite primer M13. The primer pair amplified a 252-bp fragment from all S. sclerotiorum isolates collected from oilseed rapes at different locations in different years, but not from any other fungus tested. Using this pair of primers, a real-time PCR assay was developed to rapidly detect early infection of S. sclerotiorum on petals of oilseed rape. The real-time PCR assay developed in this study could help growers make a timely decision on fungicide application.     

Detection of the Dinozoans Pfiesteria piscicida and P. shumwayae: a review of detection methods and geographic distribution

Molecular methods, including conventional PCR, real-time PCR, denaturing gradient gel electrophoresis, fluorescent fragment detection PCR, and fluorescent in situ hybridization, have all been developed for use in identifying and studying the distribution of the toxic dinoflagellates Pfiesteria piscicida and P. shumwayae. Application of the methods has demonstrated a worldwide distribution of both species and provided insight into their environmental tolerance range and temporal changes in distribution. Genetic variability among geographic locations generally appears low in rDNA genes, and detection of the organisms in ballast water is consistent with rapid dispersal or high gene flow among populations, but additional sequence data are needed to verify this hypothesis. The rapid development and application of these tools serves as a model for study of other microbial taxa and provides a basis for future development of tools that can simultaneously detect multiple targets.     

Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR

Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR). The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen® method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affected by length polymorphism and may provide sufficiently small targets, a crucial criterion for enhancing accuracy and reproducibility of the detection technique. An in silico analysis of 33 primer sets targeting the 18S rRNA gene was performed to select the primer set with the best potential for real-time Q-PCR: short amplicon length; good fungal specificity and coverage. The best consensus between specificity, coverage and amplicon length among the 33 sets tested was the primer set FR1 / FF390. This in silico analysis of the specificity of FR1 / FF390 also provided additional information to the previously published analysis on this primer set. The specificity of the primer set FR1 / FF390 for Fungi was validated in vitro by cloning - sequencing the amplicons obtained from a real time Q-PCR assay performed on five independent soil samples. This assay was also used to evaluate the sensitivity and reproducibility of the method. Finally, fungal abundance in samples from 24 soils with contrasting physico-chemical and environmental characteristics was examined and ranked to determine the importance of soil texture, organic carbon content, C∶N ratio and land use in determining fungal abundance in soils.     

细菌感染后家蚕幼虫中肠差异表达基因的鉴定（英文）

作为遭遇各种微生物的前线, 昆虫的消化道在免疫反应中起到重要的作用。为了研究家蚕Bombyx mori肠道免疫反应, 我们利用基于ACP (annealing control primer)的反转录PCR技术, 从中肠组织中鉴定得到18个在经口器感染绿脓杆菌Pseudomonas aeruginosa 和金黄色葡萄球菌Staphylococcus aureus后的差异表达基因,并利用荧光定量PCR分析了其中4个基因在感染后24 h内的动态变化。结果表明： 肽聚糖识别蛋白-L1（PGRP-L1)和一个丝氨酸蛋白酶前体基因特异性地受绿脓杆菌感染后上调; 30kP蛋白酶A基因受绿脓杆菌和金黄色葡萄球菌2种细菌感染后上调。我们的研究鉴定了经口器感染后家蚕中肠中参与入侵细菌识别和免疫信号途径的基因, 可为对这些基因进一步的功能研究提供线索。     

Electrophoretic mobility anomalies associated with PCR amplification of the intergenic spacer region between 16S and 23S ribosomal RNA genes of Fusobacterium necrophorum.

PCR amplification of the intergenic spacer region (ISR) between 16S and 23S rRNA genes among subspecies of the anaerobic bacterium Fusobacterium necrophorum gave identical patterns, with two forms of ISR identified. However, extra bands resulting from anomalous electrophoretic mobility of amplified DNA fragments with certain primer combinations were encountered. Therefore, PCR assays relying solely on banding patterns may be unreliable, and supporting sequence analysis is essential for correct culture identification.     

三线闭壳龟18SrRNA基因序列的测定

用分子遗传标记进行物种鉴别准确可靠,本文应用18SrRNA序列测定研究中药材三线闭壳龟的进化与种类鉴定.应用PCR直接测序技术测定三线闭壳龟肌肉18srRNA基因部分核苷酸序列.结果表明,所测序列为678bp,其中GC占多数(54.1%).讨论了DNA测序技术在龟鳖类等中药材鉴定方面的应用.     

低温对鲤鱼的5个基因在不同组织中表达量的影响

本研究应用实时荧光定量 PCR技术对抑制性消减杂交所得到的鲤鱼不同温度下差异表达的5个基因做进一步的研究.结果表明: 水温由16℃降至4℃(骤降点)的过程中,在鲤鱼的肝、肠组织中,LKE-25基因的表达量呈下降趋势,而LKE-62基因则呈上升趋势;在肾脏组织中,LKE-48-1、 LKE-48-2和LKE-59基因的表达量呈上升趋势,且随着4℃维持时间的延长,其表达量逐渐下降.LKE-25和LKE-59基因在4℃同一尾鱼的心脏、脑、肝、脾、肾、肠组织中的表达量上有很大差异,其中LKE-25基因在心、LKE-59基因在肾组织中的表达量最高 .本实验所研究的5个基因在不同温度、不同组织表达量的显著差异,证明了这些基因与水温相关且有组织特异性 [动物学报 54(3):460-466,2008].     

Genetic diversity of the black mangrove (Avicennia germinans L.) in Colombia

This study analyzed the genetic diversity and patterns of genetic structure in Colombian populations of Avicennia germinans L. using microsatellite loci. A lower genetic diversity was found on both the Caribbean (Ho = 0.439) and the Pacific coasts (Ho = 0.277) than reported for the same species in other locations of Central American Pacific, suggesting the deterioration of genetic diversity. All the populations showed high inbreeding coefficients (0.131–0.462) indicating heterozygotes deficience. The genetic structure between the Colombian coasts separated by Central American Isthmus was high (F_RT = 0.39) and the analyses of the genetic patterns of A. germinans revealed a clear differentiation of populations and no-recent gene flow evidence between coasts. Genetic structure was found within each coast (F_ST = 0.10 for the Caribbean coast and F_ST = 0.22 for the Pacific coast). The genetic patterns along the two coasts appear to reflect a forcing by local geomorphology and marine currents. Both coasts constitute a different Evolutionary Significant Unit, so we suggest for future transplantations plans that propagules or saplings of the populations of the Caribbean coast should not be mixed with those of the Pacific Colombian coast. Besides, we suggest that reforestation efforts should carefully distinguish propagules sources within each coast.     

Genetic characterization of Cylindrospermopsis raciborskii (cyanobacteria) isolates from diverse geographic origins based on nifH and cpcBA-IGS nucleotide sequence analysis

Isolates of the toxic, N(2)-fixing species Cylindrospermopsis raciborskii from various geographic locations were analyzed with respect to their genetic diversity based on the nifH and cpcBA-IGS genes. Gene sequences clustered according to their geographic origin, with the nifH sequences separating into European, Australian, and American groups and the cpcBA-IGS sequences separating into American and European or Australian groups. PCR primers for both genes were designed to exclusively amplify DNA from Cylindrospermopsis species, and an additional primer set for cpcBA-IGS was designed to specifically amplify the American C. raciborskii strains.     

Anguilla rostrata glass eel ingress into two, U.S. east coast estuaries: patterns, processes and implications for adult abundance

A time series of American eel Anguilla rostrata glass eel abundance, timing and size from Little Egg Inlet, New Jersey (16 years) and Beaufort Inlet, North Carolina (18 years) was used to provide a better understanding of ingress patterns at two, U.S. east coast estuaries. There was no evidence of synchronous declines in abundance between the two locations; however, at the Little Egg Inlet site, glass eels arrived later in the season and at significantly smaller sizes over the duration of the series. One significant linkage between sites was revealed: abundance was positively correlated with winter precipitation. Precipitation differed between sites annually and was correlated with El Niño at Beaufort Inlet and, to a lesser extent, the North Atlantic Oscillation at Little Egg Inlet. It is hypothesized that glass eels may use freshwater signals to enhance recruitment to local estuaries, thus influencing year-class strength, yet the relationship between year-class strength and adult abundance remains unresolved.     

Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities,and estimation of sequencing bias against 18S

Universal primers for SSU rRNA genes allow profiling of natural communities by simultaneously amplifying templates from Bacteria, Archaea, and Eukaryota in a single PCR reaction. Despite the potential to show relative abundance for all rRNA genes, universal primers are rarely used, due to various concerns including amplicon length variation and its effect on bioinformatic pipelines. We thus developed 16S and 18S rRNA mock communities and a bioinformatic pipeline to validate this approach. Using these mocks, we show that universal primers (515Y/926R) outperformed eukaryote-specific V4 primers in observed versus expected abundance correlations (slope = 0.88 vs. 0.67–0.79), and mock community members with single mismatches to the primer were strongly underestimated (threefold to eightfold). Using field samples, both primers yielded similar 18S beta-diversity patterns (Mantel test, p < 0.001) but differences in relative proportions of many rarer taxa. To test for length biases, we mixed mock communities (16S + 18S) before PCR and found a twofold underestimation of 18S sequences due to sequencing bias. Correcting for the twofold underestimation, we estimate that, in Southern California field samples (1.2–80 μm), there were averages of 35% 18S, 28% chloroplast 16S, and 37% prokaryote 16S rRNA genes. These data demonstrate the potential for universal primers to generate comprehensive microbiome profiles.     

Plasmodium vivax: parasitemia determination by real-time quantitative PCR in Aotus monkeys

Plasmodium vivax and Plasmodium falciparum are the two prevalent human malaria species. A Colombian P. vivax wild strain has been adapted in Aotus nancymaae monkeys for use in further biological and immunological studies. We present data validating a real-time PCR assay quantifying P. vivax parasitemia, using the small subunit ribosomal RNA genes as an amplification target. P. vivax species-specific primers were designed on the 18S ribosomal gene V8 region, for amplifying both asexual and sporozoite ssrRNA genes. The assay detects amplification products bound to fluorescent SYBR-Green I dye using Perkin-Elmer GeneAmp-5700-SDS. Linear range standard curves from 6 DNA concentration logs (+0.99 correlation coefficients) were obtained. Standard curves were constructed using a plasmid containing target gene for real-time PCR amplification. This P. vivax specific assay is very sensitive, having a three parasite detection limit, and is reproducible and accurate. It involves a "closed-tube" PCR, avoids time-consuming post-PCR manipulation, and decreases potential PCR contamination.     

Identification of Lactobacillus crispatus by polymerase chain reaction targeting S-layer protein gene

AIMS: This study aimed to develop a polymerase chain reaction (PCR) method to identify Lactobacillus crispatus. METHODS AND RESULTS: A primer set (CbsA2F-CbsA2R) for amplifying conserved regions of S-layer genes was designed to identify Lact. crispatus and the specificity of this set was compared with that of another primer set (Cri 16SI-Cri 16SII) which has been reported as a species-specific primer set targeting the 16S rRNA gene. Among species in the Lact. acidophilus A1-A4 groups, when KOD polymerase was used for amplification, the primer set CbsA2F-CbsA2R gave PCR products with Lact. crispatus strains only. However, when Taq polymerase was used, this primer set gave products with one Lact. amylovorus strain as well as with Lact. crispatus strains. The primer set Cri 16SI-Cri 16SII gave PCR products with Lact. crispatus strains and two Lact. acidophilus strains, regardless of whether the polymerase used was KOD or Taq. CONCLUSIONS: A PCR targeting the S-layer gene and amplified with KOD polymerase can identify Lact. crispatus accurately and rapidly. SIGNIFICANCE AND IMPACT OF THE STUDY: To the authors' knowledge, this is the first paper to provide a PCR method for the specific identification of Lact. crispatus.     

Detection of methicillin- and aminoglycoside-resistant genes and simultaneous identification of S. aureus using triplex real-time PCR Taqman assay

In this study we describe a triplex real-time PCR assay that enables the identification of S. aureus and detection of two important antibiotic resistant genes simultaneously using real-time PCR technology in a single assay. In this triplex real-time PCR assay, the mecA (methicillin resistant), femA (species specific S. aureus) and aacA-aphD (aminoglycoside resistant) genes were detected in a single test using dual-labeled Taqman probes. The assay gives simultaneous information for the identification of S. aureus and detection of methicillin and aminoglycoside resistance in staphylococcal isolates. 152 clinical isolates were subjected to this triplex real-time PCR assay. The results of the triplex real-time PCR assay correlated with the results of the phenotypic antibiotic susceptibility testing. The results obtained from triplex real-time PCR assay shows that the primer and probe sets were specific for the identification of S. aureus and were able to detect methicillin- and aminoglycoside-resistant genes. The entire assay can be performed within 3 h which is a very rapid method that can give simultaneous information for the identification of S. aureus and antibiotic resistance pattern of a staphylococcal isolate. The application of this rapid method in microbiology laboratories would be a valuable tool for the rapid identification of the S. aureus isolates and determination of their antibiotic resistance pattern with regards to methicillin and aminoglycosides.