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Keywords = Bento Lab

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7 pages, 403 KB  
Technical Note
Technical Note: Rapid Species Barcoding Using Bento Lab Mobile Laboratory
by Karolina Mahlerová, Lenka Vaňková, Marcin Tomsia and Daniel Vaněk
Forensic Sci. 2024, 4(4), 566-572; https://doi.org/10.3390/forensicsci4040038 - 14 Oct 2024
Viewed by 1655
Abstract
In scenarios when the morphological identification of samples is not feasible, the utilization of molecular analyses becomes an imperative. However, that can often be challenging in conditions where standard molecular laboratories cannot be established. In this study, we present a simplified and field-friendly [...] Read more.
In scenarios when the morphological identification of samples is not feasible, the utilization of molecular analyses becomes an imperative. However, that can often be challenging in conditions where standard molecular laboratories cannot be established. In this study, we present a simplified and field-friendly protocol of the previously published Triplex PCR Assay for the identification of mammalian and plant sample origin using a fully portable molecular laboratory from Bento Lab (Bento Bioworks Ltd., London, UK), effectively eliminating the need for a traditional laboratory setup. The protocol in combination with correctly selected kits enables DNA extraction, result evaluation based on electrophoresis, and direct use of the PCR products for downstream analyses such as Sanger sequencing and third-generation sequencing; therefore, enabling the use of molecular analysis directly in situ or for educational purposes in a classroom. Full article
(This article belongs to the Special Issue Innovations and New Aspects in Forensic Practice)
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13 pages, 1234 KB  
Article
Rapid Oxford Nanopore Technologies MinION Sequencing Workflow for Campylobacter jejuni Identification in Broilers on Site—A Proof-of-Concept Study
by Clara Marin, Francisco Marco-Jiménez, Llucia Martínez-Priego, Griselda De Marco-Romero, Vicente Soriano-Chirona, Laura Lorenzo-Rebenaque and Giuseppe D’Auria
Animals 2022, 12(16), 2065; https://doi.org/10.3390/ani12162065 - 13 Aug 2022
Cited by 7 | Viewed by 4732
Abstract
Campylobacter is recognised as one of the most important foodborne bacteria, with a worldwide health and socioeconomic impact. This bacterium is one of the most important zoonotic players in poultry, where efficient and fast detection methods are required. Current official culture methods for [...] Read more.
Campylobacter is recognised as one of the most important foodborne bacteria, with a worldwide health and socioeconomic impact. This bacterium is one of the most important zoonotic players in poultry, where efficient and fast detection methods are required. Current official culture methods for Campylobacter enumeration in poultry usually include >44 h of culture and >72 h for identification, thus requiring at least five working shifts (ISO/TS 10272-2:2017). Here, we have assembled a portable sequencing kit composed of the Bento Lab and the MinION and developed a workflow for on-site farm use that is able to detect and report the presence of Campylobacter from caecal samples in less than five hours from sampling time, as well as the relationship of Campylobacter with other caecal microbes. Beyond that, our workflow may offer a cost-effective and practical method of microbiologically monitoring poultry at the farm. These results would demonstrate the possibility of carrying out rapid on-site screening to monitor the health status of the poultry farm/flock during the production chain. Full article
(This article belongs to the Collection Current Advances in Poultry Research)
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18 pages, 11615 KB  
Article
Takeaways from Mobile DNA Barcoding with BentoLab and MinION
by Jia Jin Marc Chang, Yin Cheong Aden Ip, Chin Soon Lionel Ng and Danwei Huang
Genes 2020, 11(10), 1121; https://doi.org/10.3390/genes11101121 - 24 Sep 2020
Cited by 45 | Viewed by 10930
Abstract
Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for [...] Read more.
Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). Here, we assembled a portable sequencing setup comprising the BentoLab and MinION and developed a workflow capable of processing 32 samples simultaneously. We demonstrated this enhanced capability out at sea, where we collected samples and barcoded them onboard a dive vessel moored off Sisters’ Islands Marine Park, Singapore. In under 9 h, we generated 105 MinION barcodes, of which 19 belonged to fresh metazoans processed immediately after collection. Our setup is thus viable and would greatly fortify existing portable DNA barcoding capabilities. We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. A total of 80% of the R10.3 nanopore barcodes also had zero base ambiguities, compared to 50–60% for R9.4.1, suggesting an improved homopolymer resolution and making the use of R10.3 highly recommended. Full article
(This article belongs to the Special Issue MetaGenomics Sequencing In Situ)
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