Implementation and Validation of the Teleshake Unit for DNA IQ™ Robotic Extraction and Development of a Large Volume DNA IQ™ Method

Standardized high-throughput biomonitoring using DNA metabarcoding: Strategies for the adoption of automated liquid handlers

Reliable and comprehensive monitoring data are required to trace and counteract biodiversity loss. High-throughput metabarcoding using DNA extracted from community samples (bulk) or from water or sediment (environmental DNA) has revolutionized biomonitoring, given the capability to assess biodiversity across the tree of life rapidly with feasible effort and at a modest price. DNA metabarcoding can be upscaled to process hundreds of samples in parallel. However, while automated high-throughput analysis workflows are well-established in the medical sector, manual sample processing still predominates in biomonitoring laboratory workflows limiting the upscaling and standardization for routine monitoring applications. Here we present an automated, scalable, and reproducible metabarcoding workflow to extract DNA from bulk samples, perform PCR and library preparation on a liquid handler. Key features are the independent sample replication throughout the workflow and the use of many negative controls for quality assurance and quality control. We generated two datasets: i) a validation dataset consisting of 42 individual arthropod specimens of different species, and ii) a routine monitoring dataset consisting of 60 stream macroinvertebrate bulk samples. As a marker, we used the mitochondrial COI gene. Our results show that the developed single-deck workflow is free of laboratory-derived contamination and produces highly consistent results. Minor deviations between replicates are mostly due to stochastic differences for low abundant OTUs. Thus, we successfully demonstrated that robotic liquid handling can be used reliably from DNA extraction to final library preparation on a single deck, thereby substantially increasing throughput, reducing costs, and increasing data robustness for biodiversity assessments and monitoring.

Critical review of forensic trace evidence analysis and the need for a new approach

The historical development, contributions and limitations of the two traditional approaches to trace evidence analysis are reviewed. The first approach was as generalist practitioner, looking broadly at an assemblage of many different particle types. The second was that of specialist practitioner, with attention focused on one specific particle type. Four factors have significantly impacted the effectiveness of these approaches: (1) increasing technological capabilities, (2) increasing complexity in the character of manufactured materials, (3) changes in forensic laboratory management, and (4) changing scientific and legal expectations. The effectiveness of each approach is assessed within the context of these changes. More recently, new technologies have been applied to some trace evidence problems, intended to address one or more limitations. This has led to a third approach founded on discrete, highly technical methods addressing specific analytical problems. After evaluating the contributions and limitations of this third approach, we consider the different ways that technologies could be developed to address unmet needs in forensic trace evidence analysis. The route toward effective use of new technologies is contrasted with how forensic science laboratories are currently choosing and employing them. The conclusion is that although new technologies are contributing, we are not on a path that will result in their most effective and appropriate use. A new approach is required. Based on an analysis of the contributions of each of the three exisiting approaches, seven characteristics of an effective trace evidence analysis capability were determined: (1) particle traces should be a major problem-solving tool, (2) there should be readily available, straightforward methods to enable their use, (3) all available and potentially useful particle types should be considered, (4) decisions to use them should be made in the context of each case, guided by what they can contribute to the case and how efficiently they can do so, (5) analyses should be conducted using appropriate technologies, (6) findings should be timely and directly integrated with case-specific problems, and (7) new technologies should be used to improve the overall effectiveness of the capability. Clearly new technologies have the potential to revolutionize forensic trace evidence, but just as clearly some of the traditional capabilities have been rendered ineffective, or lost entirely, by the way we have come to approach the problem. Having critically defined the current limitations of and the desired outcomes, the next focus should be consideration of alternative approaches that might achieve such a result.

Competition for DNA binding sites using Promega DNA IQ™ paramagnetic beads

The Promega DNA IQ™ system is easily amenable to automation and has been an integral part of standard operating procedures for many forensic laboratories including those of the Royal Canadian Mounted Police (RCMP) since 2004. Due to some failure to extract DNA from samples that should have produced DNA using our validated automated DNA IQ™-based protocol, the competition for binding sites on the DNA IQ™ magnetic beads was more closely examined. Heme from heavily blooded samples interfered slightly with DNA binding. Increasing the concentration of Proteinase K during lysis of these samples did not enhance DNA recovery. However, diluting the sample lysate following lysis prior to DNA extraction overcame the reduction in DNA yield and preserved portions of the lysates for subsequent manual or automated extraction. Dye/chemicals from black denim lysates competed for binding sites on the DNA IQ™ beads and significantly reduced DNA recovery. Increasing the size or number of black denim cuttings during lysis had a direct adverse effect on DNA yield from various blood volumes. The dilution approach was successful on these samples and permitted the extraction of high DNA yields. Alternatively, shortening the incubation time for cell lysis to 30 min instead of the usual overnight at 56 °C prevented competition from black denim dye/chemicals and increased DNA yields.