Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens

Totoiu, Christian A.; Phillips, Jessica M.; Reese, Aspen T.; Majumdar, Sudipta; Girguis, Peter R.; Raston, Colin L.; Weiss, Gregory A.

doi:10.1371/journal.pone.0225807

Cited by 17 publications

(16 citation statements)

References 37 publications

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“…Considering this outcome, we did not expect successful amplification of the 202 bp sequence and did not attempt to extract DNA from the formalin fixed tissue any further. Recently published, more advanced protocols might overcome these limitations, but do require special equipment [ 40 ]. A definitive morphological identification was possible and comparable to other publications [ 41 ].…”

Section: Discussionmentioning

confidence: 99%

First Autochthonous Infection of a Cat with Dirofilaria immitis in Austria

et al. 2021

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This case report is about a seven-year-old male neutered European Shorthair cat infected by Dirofilaria immitis as the first reported autochthonous Dirofilaria immitis infection in Austria. There was no history of periods abroad. Echocardiography showed suspected D. immitis in the right cardiac chamber with increased pulmonary pressure and ascites. Surgical removal of the heartworms was performed. Twenty adult heartworms were removed by transvenous jugular approach under general anesthesia and stored in 4% formalin. Five out of 20 specimens were examined via light and stereomicroscopy and feline heartworm infection was confirmed. Amplification of a 203 bp or 724 bp fragment of the cytochrome c oxidase subunit I gene was unsuccessful. After surgery the cat developed acute renal failure but recovered quickly. One year later, the cat underwent a control examination including echocardiography and blood work. There were no more D. immitis detectable at echocardiography. Lung pressure was mildly increased. Complete blood count and creatinine were unremarkable. The Knott’s test and Dirofilaria-Antigen-test produced negative results. The cat did not show any clinical signs during the follow-up period. The aim of this case report is to highlight the growing risk of acquiring infection with D. immitis not only for Austrian dogs, but also for cats. This case report represents the first report of autochthonous D. immitis infection in Austria. Moreover, even if the prognosis in cats with caval syndrome due to feline heartworm disease is guarded to poor, surgical removal of the filariae can be a successful treatment option.

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Section: Discussionmentioning

confidence: 99%

First Autochthonous Infection of a Cat with Dirofilaria immitis in Austria

et al. 2021

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“…Nonetheless, recent advances in DNA extraction and library preparation have made DNA from museum samples more accessible (Paireder et al, 2013;Sørensen et al, 2016;Totoiu et al, 2020). In particular, target capture techniques have enabled the sequencing of fragmented and low-yield DNA from vertebrate dried museum skin and bone preparations, as well as dried invertebrate, plant and fungal specimens (Ávila-Arcos et al, 2012;Bakker et al, 2020;Blaimer et al, 2016;Leavitt et al, 2019;Rowe et al, 2011;Sánchez Barreiro et al, 2017;Schmid et al, 2018;Staats et al, 2013;St Laurent et al, 2018;Tsai et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Genomic library preparation and hybridization capture of formalin‐fixed tissues and allozyme supernatant for population genomics and considerations for combining capture‐ and RADseq‐based single nucleotide polymorphism data sets

O’Connell

Mulder

Wynn

et al. 2021

Molecular Ecology Resources

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Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high-throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic DNA from dried and fluid-preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples, but the amenability of these samples to HTS has not yet been assessed. Here, we compared the performance of a target-capture approach using alternative sources of genomic DNA from 10 specimens of spring salamanders (Plethodontidae: Gyrinophilus porphyriticus) collected between 1985 and 1990: allozyme supernatants, allozyme homogenate pellets and formalin-fixed tissues. We designed capture probes based on double-digest restriction-site associated sequencing (RADseq) derived loci from frozen blood samples available for seven of the specimens and assessed the success and consistency of capture and RADseq approaches.This study design enabled direct comparisons of data quality and potential biases among the different data sets for phylogenomic and population genomic analyses.We found that in phylogenetic analyses, all enrichment types for a given specimen clustered together. In principal component space all capture-based samples clustered together, but RADseq samples did not cluster with corresponding capture-based samples. Single nucleotide polymorphism calls were on average 18.3% different between enrichment types for a given individual, but these discrepancies were primarily due to differences in heterozygous/homozygous single nucleotide polymorphism calls. We demonstrate that both allozyme supernatant and formalin-fixed samples can be successfully used for population genomic analyses and we discuss ways to identify and reduce biases associated with combining capture and RADseq data.

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“…[27][28][29] This approach has been successful for generating such material high in green chemistry credentials, without the need for surfactants and harsh chemicals, thereby minimising the waste stream, with the processing simple and low costing, using low molecular weight solvents and under continuous flow conditions. The angled VFD with an optimal tilt angle of 45 o (maximum cross vector between centrifugal and gravity) spun at high rotational speeds has remarkably diverse range of applications beyond the exfoliation of 2D materials, including scrolling of graphene directly from graphite flakes, laser assisted controlled slicing of carbon nanotubes, controlling chemical reactivity and selectivity, biocatalysis and probing the structure of self-organised systems, [30][31][32][33][34][35][36] also incorporating green chemistry principles within the processing.…”

Section: Introductionmentioning

confidence: 99%