scholarly journals Homogenization of Endosymbiont Communities Hosted by Equatorial Corals during the 2016 Mass Bleaching Event

2020 ◽  
Vol 8 (9) ◽  
pp. 1370
Author(s):  
Sudhanshi S. Jain ◽  
Lutfi Afiq-Rosli ◽  
Bar Feldman ◽  
Oren Levy ◽  
Jun Wei Phua ◽  
...  
Keyword(s):  
Thermal Tolerance ◽  
High Throughput Sequencing ◽  
Quantitative Polymerase Chain Reaction ◽  
Global Scale ◽  
Bleaching Event ◽  
Reef Corals ◽  
Qpcr Method ◽  
Polymerase Chain ◽  
Limited Change

Thermal stress drives the bleaching of reef corals, during which the endosymbiotic relationship between Symbiodiniaceae microalgae and the host breaks down. The endosymbiont communities are known to shift in response to environmental disturbances, but how they respond within and between colonies during and following bleaching events remains unclear. In 2016, a major global-scale bleaching event hit countless tropical reefs. Here, we investigate the relative abundances of Cladocopium LaJeunesse & H.J.Jeong, 2018 and Durusdinium LaJeunesse, 2018 within and among Pachyseris speciosa colonies in equatorial Singapore that are known to host both these Symbiodiniaceae clades. Bleached and unbleached tissues from bleaching colonies, as well as healthy colonies, during and following the bleaching event were sampled and analyzed for comparison. The nuclear ribosomal internal transcribed spacer (ITS) regions were separately amplified and quantified using a SYBR Green-based quantitative polymerase chain reaction (qPCR) method and Illumina high-throughput sequencing. We found Cladocopium to be highly abundant relative to Durusdinium. The relative abundance of Durusdinium, known to be thermally tolerant, was highest in post-bleaching healthy colonies, while bleached and unbleached tissues from bleaching colonies as well as tissue from healthy colonies during the event had depressed proportions of Durusdinium. Given the importance of Durusdinium for thermal tolerance and stress response, it is surprising that bleached tissue showed limited change over healthy tissue during the bleaching event. Moreover, colonies were invariably dominated by Cladocopium during bleaching, but a minority of colonies were Durusdinium-dominant during non-bleaching times. The detailed characterization of Symbiodiniaceae in specific colonies during stress and recovery will provide insights into this crucial symbiosis, with implications for their responses during major bleaching events.

scholarly journals Identification and Functional Characterization of a Cold-Related Protein, BcHHP5, in Pak-Choi (Brassica rapa ssp. chinensis)

2018 ◽  
Vol 20 (1) ◽  
pp. 93
Author(s):  
Jin Wang ◽  
Feiyi Huang ◽  
Xiong You ◽  
Xilin Hou
Keyword(s):  
Brassica Rapa ◽  
Abiotic Stresses ◽  
Quantitative Polymerase Chain Reaction ◽  
Functional Characterization ◽  
Regulation Mechanism ◽  
Pak Choi ◽  
Negative Effect ◽  
Polymerase Chain ◽  
Related Proteins

In plants, heptahelical proteins (HHPs) have been shown to respond to a variety of abiotic stresses, including cold stress. Up to the present, the regulation mechanism of HHP5 under low temperature stress remains unclear. In this study, BcHHP5 was isolated from Pak-choi (Brassica rapa ssp. chinensis cv. Suzhouqing). Sequence analysis and phylogenetic analysis indicated that BcHHP5 in Pak-choi is similar to AtHHP5 in Arabidopsis thaliana. Structure analysis showed that the structure of the BcHHP5 protein is relatively stable and highly conservative. Subcellular localization indicated that BcHHP5 was localized on the cell membrane and nuclear membrane. Furthermore, real-time quantitative polymerase chain reaction (RT-qPCR) analysis showed that BcHHP5 was induced to express by cold and other abiotic stresses. In Pak-choi, BcHHP5-silenced assay, inhibiting the action of endogenous BcHHP5, indicated that BcHHP5-silenced might have a negative effect on cold tolerance, which was further confirmed. All of these results indicate that BcHHP5 might play a role in abiotic response. This work can serve as a reference for the functional analysis of other cold-related proteins from Pak-choi in the future.

scholarly journals Characterization of Fecal Microbiota across Seven Chinese Ethnic Groups by Quantitative Polymerase Chain Reaction

PLoS ONE ◽  
2014 ◽  
Vol 9 (4) ◽  
pp. e93631 ◽  
Author(s):  
Lai-yu Kwok ◽  
Jiachao Zhang ◽  
Zhuang Guo ◽  
Qimu Gesudu ◽  
Yi Zheng ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Ethnic Groups ◽  
Quantitative Polymerase Chain Reaction ◽  
Fecal Microbiota ◽  
Chain Reaction ◽  
Polymerase Chain

scholarly journals The Distribution and Detection of Grapevine red blotch virus in its Host Depend on Time of Sampling and Tissue Type

Plant Disease ◽  
2018 ◽  
Vol 102 (11) ◽  
pp. 2187-2193 ◽  
Author(s):  
Felicia J. Setiono ◽  
Debotri Chatterjee ◽  
Marc Fuchs ◽  
Keith L. Perry ◽  
Jeremy R. Thompson
Keyword(s):  
Polymerase Chain Reaction ◽  
Seasonal Variations ◽  
Quantitative Polymerase Chain Reaction ◽  
Virus Titer ◽  
Tissue Type ◽  
Chain Reaction ◽  
Variable Distribution ◽  
Qpcr Method ◽  
Polymerase Chain ◽  
Virus Distribution

Grapevine red blotch virus (GRBV) is the causal agent of grapevine red blotch, an emerging disease that affects cultivated grapevine such as Vitis vinifera. The ability to detect viruses in grapevine is often hindered by low virus titers compounded by a variable distribution in the plant and seasonal variations. In order to examine these two variables in relation to GRBV, we developed a quantitative polymerase chain reaction (qPCR) method that incorporates both internal and external references to enhance assay robustness. In greenhouse-grown vines infected with GRBV, qPCR identified highest virus titers in the petioles of fully expanded leaves and significantly reduced levels of virus in the shoot extremities. In vineyard-grown vines infected with GRBV, the virus titer in July and October 2016 followed a pattern similar to that found for the greenhouse-grown plants but, most strikingly, close to half (44%) of the samples analyzed in June 2015 tested negative for infection. The technique presented and results obtained highlight the variability of virus distribution in its host and provide a useful guide for selecting the best tissues for optimal GRBV diagnosis.

Comparison of culture and qPCR methods in detection of mycobacteria from drinking waters

2013 ◽  
Vol 59 (4) ◽  
pp. 280-286 ◽  
Author(s):  
Noora H.J. Räsänen ◽  
Helena Rintala ◽  
Ilkka T. Miettinen ◽  
Eila Torvinen
Keyword(s):  
Surface Water ◽  
Quantitative Polymerase Chain Reaction ◽  
Water Source ◽  
Assimilable Organic Carbon ◽  
Environmental Mycobacteria ◽  
Drinking Waters ◽  
Qpcr Method ◽  
Sensitive Tool ◽  
Different Types ◽  
Polymerase Chain

Environmental mycobacteria are common bacteria in man-made water systems and may cause infections and hypersensitivity pneumonitis via exposure to water. We compared a generally used cultivation method and a quantitative polymerase chain reaction (qPCR) method to detect mycobacteria in 3 types of drinking waters: surface water, ozone-treated surface water, and groundwater. There was a correlation between the numbers of mycobacteria obtained by cultivation and qPCR methods, but the ratio of the counts obtained by the 2 methods varied among the types of water. The qPCR counts in the drinking waters produced from surface or groundwater were 5 to 34 times higher than culturable counts. In ozone-treated surface waters, both methods gave similar counts. The ozone-treated drinking waters had the highest concentration of assimilable organic carbon, which may explain the good culturability. In warm tap waters, qPCR gave 43 times higher counts than cultivation, but both qPCR counts and culturable counts were lower than those in the drinking waters collected from the same sites. The TaqMan qPCR method is a rapid and sensitive tool for total quantitation of mycobacteria in different types of clean waters. The raw water source and treatments affect both culturability and total numbers of mycobacteria in drinking waters.

scholarly journals Characterization of the interactions between procoagulant albumin and human endothelial cells

Blood ◽  
1993 ◽  
Vol 82 (9) ◽  
pp. 2684-2692
Author(s):  
KJ Faucette ◽  
LA Fitzgerald ◽  
L Liu ◽  
CJ Parker ◽  
GM Rodgers
Keyword(s):  
Endothelial Cells ◽  
Umbilical Vein ◽  
Quantitative Polymerase Chain Reaction ◽  
Scavenger Receptor ◽  
Kinase C ◽  
Normal Human ◽  
Membrane Bound ◽  
Polymerase Chain ◽  
Umbilical Vein Endothelial Cells

Normal human plasma contains procoagulant albumin (PC-Al), an anionic form of albumin that induces tissue factor (TF) activity in human umbilical vein endothelial cells (HUVEC) and monocytes. In this study, we investigated both the interactions between HUVEC and PC-Al and the mechanism by which PC-Al induces TF activity. Binding of PC-Al to HUVEC was specific and reversible. Further studies indicated that membrane- bound PC-Al was not internalized by HUVEC. A potential receptor on HUVEC was suggested by studies in which the capacity of a variety of reagents to inhibit the activity of PC-Al was quantitated. Induction of TF activity by PC-Al was antagonized by dextran sulfate, heparin, fucoidan, and concanavalin A but not by ovalbumin, polyglutamic acid, or polyvinyl sulfate. This competition profile bears similarities to those reported for scavenger receptors that have been identified on both HUVEC and monocytes. Involvement of protein kinase C (PKC) in the PC-Al-induced enhancement of TF activity was suggested by experiments in which staurosporine, an inhibitor of PKC, suppressed the activity of PC-Al. The induction of TF activity by PC-Al was further characterized by using a quantitative polymerase chain reaction assay. Increased TF mRNA was first seen after 1 hour of incubation with PC-Al. Maximal observed expression occurred at 2 hours, but at 5 hours, expression had significantly decreased. Monocytes could also be induced to express TF mRNA after a 2-hour incubation with PC-Al. These results suggest that the functionally relevant binding of PC-Al to HUVEC may be mediated through interactions with a membrane constituent that has some of the properties of a scavenger receptor and that this interaction augments TF activity by enhancing transcription of TF mRNA, at least in part, by a mechanism that is dependent on activation of PKC.

Molecular and biokinetic characterization of methylotrophic denitrification using nitrate and nitrite as terminal electron acceptors

2008 ◽  
Vol 58 (2) ◽  
pp. 359-365 ◽  
Author(s):  
Vladimir Baytshtok ◽  
Sungpyo Kim ◽  
Ran Yu ◽  
Hongkeun Park ◽  
Kartik Chandran
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Stable Isotope Probing ◽  
Electron Acceptors ◽  
Methylotrophic Bacteria ◽  
Chain Reaction ◽  
Relative Population ◽  
Polymerase Chain ◽  
Abundance And Diversity ◽  
Nitrate And Nitrite

Although methanol is a widely employed carbon source for denitrification, relatively little is known on the abundance and diversity of methylotrophic bacteria in activated sludge. The primary aim of this study was to specifically identify bacteria that metabolized methanol in a sequencing batch denitrifying reactor (SBDR), using a novel technique, stable isotope probing (SIP) of 13C labeled DNA. A secondary aim was to quantitatively track dominant methylotrophic bacteria in the SBDR exposed to different terminal electron acceptors. SIP enabled 13C 16S rDNA clone libraries revealed that SBDR methylotrophic populations were related to Methyloversatilis spp. and Hyphomicrobium spp. Based on newly developed quantitative polymerase chain reaction (qPCR) assays, Hyphomicrobium spp. were more abundant than Methyloversatilis spp. throughout the period of SBDR operation. The relative population abundance was stable despite a shift in electron acceptor from nitrate to nitrite (keeping the same methanol dose). However, the shift to nitrite resulted in a significant decrease in denitrification biokinetics on both nitrate and nitrite.

scholarly journals Enumeration of viable and non-viable larvated Ascaris eggs with quantitative PCR

2012 ◽  
Vol 10 (4) ◽  
pp. 594-604 ◽  
Author(s):  
Maria Raynal ◽  
Eric N. Villegas ◽  
Kara L. Nelson
Keyword(s):  
Polymerase Chain Reaction ◽  
Detection Limit ◽  
Quantitative Polymerase Chain Reaction ◽  
High Heat ◽  
Chain Reaction ◽  
Direct Microscopy ◽  
Development Stages ◽  
Target Dna ◽  
Qpcr Method ◽  
Polymerase Chain

The goal of this study was to further develop an incubation-quantitative polymerase chain reaction (qPCR) method for quantifying viable Ascaris eggs by characterizing the detection limit and number of template copies per egg, determining the specificity of the method, and testing the method with viable and inactivated larvated eggs. The number of template copies per cell was determined by amplifying DNA from known numbers of eggs at different development stages; the value was estimated to be 32 copies. The specificity of the method was tested against a panel of bacteria, fungi, protozoa and helminths, and no amplification was found with non-target DNA. Finally, fully larvated eggs were inactivated by four different treatments: 254 nm ultraviolet light, 2,000 ppm NH3-N at pH 9, moderate heat (48 °C) and high heat (70 °C). Concentrations of treated eggs were measured by direct microscopy and incubation-qPCR. The qPCR signal decreased following all four treatments, and was in general agreement with the decrease in viable eggs determined by microscopy. The incubation-qPCR method for enumerating viable Ascaris eggs is a promising approach that can produce results faster than direct microscopy, and may have benefits for applications such as assessing biosolids.

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