Dataset Information

Diagnostic PCR can be used to illuminate meiofaunal diets and trophic relationships.

ABSTRACT: Analysis of the meiofaunal food web is hampered because few prey have features that persist long enough in a predator's digestive tract to allow identification to species. Hence, at least for platyhelminth predators, direct observations of prey preference are almost nonexistent, and where they occur, prey identification is often limited to phylum. Studies using an in vitro approach are rare because they are extremely time-consuming and are subject to the criticism that predators removed from their natural environment may exhibit altered behaviors. Although PCR-based approaches have achieved wide application in food-web analysis, their application to meiofaunal flatworms suffers from a number of limitations. Most importantly, the microscopic size of both the predator and prey does not allow for removal of prey material from the digestive tract of the predator, and thus the challenge is to amplify prey sequences in the presence of large quantities of predator sequence. Here, we report on the successful use of prey-taxon-specific primers in diagnostic PCR to identify, to species level, specific prey items of 13 species of meiofaunal flatworms. Extension of this method will allow, for the first time, the development of a species-level understanding of trophic interactions among the meiofauna.

SUBMITTER: Maghsoud H

PROVIDER: S-EPMC4110740 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Diagnostic PCR can be used to illuminate meiofaunal diets and trophic relationships.

Maghsoud Hanna H Weiss Austin A Smith Julian P S JP Litvaitis Marian K MK Fegley Stephen R SR

Invertebrate biology : a quarterly journal of the American Microscopical Society and the Division of Invertebrate Zoology/ASZ 20140601 2

Analysis of the meiofaunal food web is hampered because few prey have features that persist long enough in a predator's digestive tract to allow identification to species. Hence, at least for platyhelminth predators, direct observations of prey preference are almost nonexistent, and where they occur, prey identification is often limited to phylum. Studies using an <i>in vitro</i> approach are rare because they are extremely time-consuming and are subject to the criticism that predators removed f ...[more]

PMID: 25071364

Similar Datasets

Project description:Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8-2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life.IMPORTANCESingle-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers' efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.

Project description:To meet the unprecedented requirement of diagnostic testing for SARS-CoV-2, a large number of diagnostic kits were authorized by concerned authorities for diagnostic use within a short period of time during the initial phases of the ongoing pandemic. We undertook this study to evaluate the inter-test agreement and other key operational features of 5 such commercial kits that have been extensively used in India for routine diagnostic testing for COVID-19. The five commercial kits were evaluated, using a panel of positive and negative respiratory samples, considering the kit provided by National Institute of Virology, Indian Council of Medical Research (2019-nCoV Kit) as the reference. The positive panel comprised of individuals who fulfilled the 3 criteria of being clinically symptomatic, having history of contact with diagnosed cases and testing positive in the reference kit. The negative panel included both healthy and disease controls, the latter being drawn from individuals diagnosed with other respiratory viral infections. The same protocol of sample collection, same RNA extraction kit and same RT-PCR instrument were used for all the kits. Clinical samples were collected from a panel of 92 cases and 60 control patients, who fulfilled our inclusion criteria. The control group included equal number of healthy individuals and patients infected with other respiratory viruses (n = 30, in each group). We observed varying sensitivity and specificity among the evaluated kits, with LabGun COVID-19 RT-PCR kit showing the highest sensitivity and specificity (94% and 100% respectively), followed by TaqPath COVID-19 Combo and Allplex 2019-nCoV assays. The extent of inter-test agreement was not associated with viral loads of the samples. Poor correlation was observed between Ct values of the same genes amplified using different kits. Our findings reveal the presence of wide heterogeneity and sub-optimal inter-test agreement in the diagnostic performance of the evaluated kits and hint at the need of adopting stringent standards for fulfilling the quality assurance requirements of the COVID-19 diagnostic process.

Dataset Information

Diagnostic PCR can be used to illuminate meiofaunal diets and trophic relationships.

Publications

Diagnostic PCR can be used to illuminate meiofaunal diets and trophic relationships.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets