Optimization of on-bead emulsion polymerase chain reaction based on single particle analysis

Siu, Ryan Ho Ping; Liu, Yang; Chan, Kaitlin Hao Yi; Ridzewski, Clara; Slaughter, Liane Siu; Wu, Sean M.

doi:10.1016/j.talanta.2020.121593

Cited by 5 publications

(2 citation statements)

References 40 publications

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“…Specifically, the emulsion MDA can be prepared with any reaction mix, either primase MDA [ 29 ] or standard MDA, and vortexing is a low-cost alternative to microfluidic devices or microdroplet generators. Optimization parameters like the ratio of surfactant to reaction mix, vortexing speed and duration, vortexing technique (pulsing or continuous), shape of the tube, and co-adjuvants like hydrogel particles or beads influence the emulsion quality, ensuring more uniform and smaller droplet size [ 58 , 60 , 62 , 63 ]. These parameters must be revisited to demonstrate the advantage of the reduced MDA reactions using a vortex in future studies.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples

Ospino,

Engel,

Ruiz-Navas

et al. 2024

ISME Communications

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Combining multiple displacement amplification (MDA) with metagenomics enables analysis of environmental or host-associated samples with extremely low DNA concentrations that would otherwise not be appropriate for high-throughput sequencing. Although amplification bias and non-specific amplification have been reported from MDA-amplified samples, the impact of MDA on metagenomic datasets is not well understood. In this study, we compared three MDA methods (i.e., bulk MDA, emulsion MDA, and primase MDA) for metagenomic analysis of two different picogram-range DNA template concentrations (approx. 1 and 100 pg) derived from a microbial community standard “mock community” and two low biomass environmental samples (i.e., borehole fluid and groundwater). We assessed the impact of MDA on metagenome-based community composition, assembly quality, functional profiles, and binning. We found amplification bias against high GC content genomes but relatively low non-specific amplification such as chimeras, artifacts, or contamination for all MDA methods. We observed MDA-associated representational bias for microbial community profiles, especially for low-input DNA and with the primase MDA method. Nevertheless, similar taxa were represented in MDA-amplified libraries to those of unamplified samples. The MDA libraries were highly fragmented, but similar functional profiles to the unamplified libraries were obtained for bulk MDA and emulsion MDA at higher DNA input and across these MDA libraries for the groundwater sample. Medium to low-quality bins were possible for the high input bulk MDA metagenomes for the most simple microbial communities, borehole fluid, and mock community. Overall, our results suggest that MDA-based amplification should be avoided, but that it is nonetheless possible to access meaningful taxonomic and functional information from samples with extremely low DNA concentration where direct metagenomics analysis would otherwise not be feasible.

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Section: Discussionmentioning

confidence: 99%

Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples

Ospino,

Engel,

Ruiz-Navas

et al. 2024

ISME Communications

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“…Surface nanodroplets refer to droplets at a solid–liquid interface that have at least one dimension less than 1 μm . Nanodroplets have been studied because of their various and novel applications, such as biosensors, chemical analysis, and even gene therapy. − For example, phase-changeable nanodroplets were used to combat complex bacterial biofilms by physical cavitation and concurrent deep antibiotic release . Nanodroplets have unusual physical properties, such as contact line tension and evaporation aspects, which are generally neglected in macroscopic droplet studies .…”

Section: Introductionmentioning

confidence: 99%

Influence of the Dissolved Gas on the Interfacial Properties of Decane Surface Nanodroplets

et al. 2022

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Surface nanodroplets have received extensive attention recently due to their potential in the fabrication of functional materials with nanostructures and chemical reactions at micro-and nanoscales. Although the effect of dissolved gas in water has been realized in some important processes such as spontaneous emulsification of oil droplets in water, its roles in the wetting behavior of surface nanodroplets at the hydrophobic interface have been largely neglected. Here, we focused on the influence of dissolved gas on the interfacial properties of surface nanodroplets and characterized their morphological evolution when exposed to different air-saturated water samples. Results indicated that the morphology of surface nanodroplets barely changed in airoversaturated cold water. However, their contact angle first decreases gradually in deionized water, increases immediately after replacement with degassed water, and eventually decreases gradually with time. Furthermore, the surface tension of nanodroplets would change similarly after the injection of degassed water. We considered these changes to be caused by the removal or reduction of the enriched gas at the substrate interface, in which the surface hydrophobicity was changed. Our findings could shed some light on the wetting behavior of nanodroplets at the hydrophobic surface in different air-saturated water samples and inspire the microscale manipulation and reaction of surface nanodroplets.

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Improved PCR-DGGE analysis by emulsion-PCR for the determination of food geographical origin: A case study on Greek PDO “avgotaracho Mesolonghiou”

Dimitrakopoulou

Panteleli

Vantarakis

2021

Current Research in Food Science

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Optimization of on-bead emulsion polymerase chain reaction based on single particle analysis

Cited by 5 publications

References 40 publications

Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples

Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples

Influence of the Dissolved Gas on the Interfacial Properties of Decane Surface Nanodroplets

Improved PCR-DGGE analysis by emulsion-PCR for the determination of food geographical origin: A case study on Greek PDO “avgotaracho Mesolonghiou”

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