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12 results for “droplet digital PCR”
Droplet digital PCR (ddPCR) as a tool for investigating dynamics of cryptic symbionts
<p>Interactions among symbiotic organisms and their hosts are major drivers of ecological and evolutionary processes. Monitoring the infection patterns among natural populations and identifying factors affecting these interactions is critical for understanding symbiont-host relationships. However, many of these interactions remain understudied since the knowledge about the symbiont species is lacking and hinders the development of appropriate tools. In this study, we developed a digital droplet PCR (ddPCR) assay based on apicomplexan COX1 gene to detect an undescribed agamococcidian symbiont. We show that the method gives precise and reproducible results and enables detecting cryptic symbionts in low target concentration. We further exemplify the assay's use to survey seasonally sampled natural host (Pygospio elegans) populations for symbiont infection dynamics. We found that symbiont prevalence differs spatially but does not show seasonal changes. Infection load differed between populations and was low in spring and significantly increased towards fall in all populations. We also found that the symbiont prevalence is affected by host length and population density. Larger hosts were more likely to be infected and high host densities were found to have lower probability of infection. The observed variations could be due to characteristics of both symbiont and host biology, especially the seasonal variation in encounter rates. Our findings show that the developed ddPCR assay is a robust tool for detecting undescribed symbionts that are otherwise difficult to quantify, enabling further insight into the impact cryptic symbionts have on their hosts.</p>
Data from: Drop it all: Extraction-free detection of non-indigenous marine species through optimized direct-droplet digital PCR
<p>Molecular biosecurity surveillance programs increasingly use environmental DNA (eDNA) for detecting marine non-indigenous species (NIS). However, the current molecular detection workflow is cumbersome, prone to errors and delays, and is limited in providing knowledge about eDNA beyond the spatial and temporal extent of the sampling. These limitations can hinder management efforts and restrict the "opportunity window" for a rapid response to new marine NIS incursions. Emerging innovative field-deployable digital droplet PCR (ddPCR) systems offer improved workflow efficiency by autonomously analyzing targeted free-floating extra-cellular eDNA (free-eDNA) signals. Despite their potential, these systems have not been tested in marine environments. Thus, an aquarium study was conducted with three distinct marine NIS: <span>the Mediterranean fanworm <em>Sabella spallanzanii</em>, the ascidian clubbed tunicate <em>Styela clava</em>, and the brown bryozoan <em>Bugula neritina</em></span> to evaluate the detectability of free-eDNA in seawater. The detectability of targeted free-eDNA was assessed by directly analyzing aquarium water samples using an optimized species-specific ddPCR assay, without filtration or DNA extraction, so-called, "direct-ddPCR". The results demonstrated the consistent detection of <em>Sabella spallanzanii</em> and <em>Bugula neritina</em> free-eDNA when these organisms were present in high abundance. Once organisms were removed, the free-eDNA signal exponentially declined, noting that free-eDNA persisted between 24-72 hours. Results indicate that organism biomass, specimen characteristics (e.g., stress and viability), and species-specific biological differences may influence free-eDNA detectability. These results are critical for implementing <em>in-situ</em> nucleic acid automated continuous sensing systems for marine biosurveillance, enabling point-of-need detection and <span>rapid management response to biosecurity threats. </span></p>
Drop it all: Extraction-free detection of non-indigenous marine species through optimized direct-droplet digital PCR
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Droplet digital PCR (ddPCR) as a tool for investigating dynamics of cryptic symbionts
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MRD Monitoring by Digital Droplet PCR in the Early Period After Allo-HSCT to Predict Patients at High Risk of Relapse
ClinicalTrials.gov study NCT06000306. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Droplet Digital PCR and PCR-free BIOSensors for the Detection of Resistance-associated SNPs in Pneumocystis Jirovecii
ClinicalTrials.gov study NCT06431958. IPD Sharing: YES. Countries: 1. Publications: 7.
Evaluation of Droplet Digital PCR Rapid Detection Method and Precise Diagnosis and Treatment for Suspected Sepsis
ClinicalTrials.gov study NCT05190861. IPD Sharing: NO. Countries: 1. Publications: 2.
Epigenetic age-predictions in mice using pyrosequencing, droplet digital PCR or barcoded bisulfite amplicon sequencing
GEO Series GSE156193. Mus musculus. 111 samples. Type: Methylation profiling by high throughput sequencing.
Rapid high-resolution measurement of DNA replication timing by droplet digital PCR
GEO Series GSE114480. Homo sapiens. 2 samples. Type: Other.
Droplet-digital PCR for the Detection of Circulating Cell-free DNA in Patients With Cystic Echinococcosis: an Exploratory Study
ClinicalTrials.gov study NCT05769790. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Digital Droplet PCR analysis of organoids generated from mouse mammary tumors demonstrates proof-of-concept capture of tumor heterogeneity
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Droplet Digital PCR Combines With Transcriptome Analysis in Early Warning of Sepsis in the Emergency Department
ClinicalTrials.gov study NCT06028178. IPD Sharing: YES. Countries: 0. Publications: 0.
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OpenNeuro
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