Biology subjects

Barksdale, S.

Publications and source records attributed to Barksdale, S..

3 recordsLinked to original sources

bioRxiv2021

Nanotrap Particles Improve Nanopore Sequencing of SARS-CoV-2 and Other Respiratory Viruses

Presented here is a magnetic hydrogel particle enabled workflow for capturing and concentrating SARS-CoV-2 from diagnostic remnant swab samples that significantly improves sequencing results using the Oxford Nanopore Technologies MinION sequencing platform. Our approach utilizes a novel affinity-based magnetic hydrogel particle, circumventing low input sample volumes and allowing for both rapid manual and automated high throughput workflows that are compatible with nanopore sequencing. This approach enhances standard RNA extraction protocols, providing up to 40x improvements in viral mapped reads, and improves sequencing coverage by 20-80% from lower titer diagnostic remnant samples. Furthermore, we demonstrate that this approach works for contrived influenza virus and respiratory syncytial virus samples, suggesting that it can be used to identify and improve sequencing results of multiple viruses in VTM samples. These methods can be performed manually or on a KingFisher Apex system.

microbiology↗

bioRxiv2020

Nanotrap(R) particles improve detection of SARS-CoV-2 for pooled sample methods, extraction-free saliva methods, and extraction-free medium methods

Here we present a rapid and versatile method for capturing and concentrating SARS-CoV-2 from transport medium and saliva using affinity-capture magnetic hydrogel particles. We demonstrate that the method concentrates virus prior to RNA extraction, thus significantly improving detection of the virus using a real-time RT-PCR assay across a range of viral titers, from 100 to 1,000,000 viral copies/mL; in particular, detection of virus in low viral load samples is enhanced when using the method coupled with the IDT 2019-nCoV CDC EUA Kit. This method is compatible with commercially available nucleic acid extraction kits, as well with a simple heat and detergent method. Using transport medium diagnostic remnant samples that previously had been tested for SARS-CoV-2 using either the Abbott RealTime SARS-CoV-2 EUA Test (n=14) or the Cepheid Xpert Xpress SARS-CoV-2 EUA Test (n=35), we demonstrate that our method not only correctly identifies all positive samples (n = 17) but also significantly improves detection of the virus in low viral load samples. The average improvement in cycle threshold (Ct) value as measured with the IDT 2019-nCoV CDC EUA Kit was 3.1; n = 10. Finally, to demonstrate that the method could potentially be used to enable pooled testing, we spiked infectious virus or a confirmed positive diagnostic remnant sample into 5 mL and 10 mL of negative transport medium and observed significant improvement in the detection of the virus from those larger sample volumes.

microbiology↗

bioRxiv2019

Intraperitoneal treatment with antimicrobial peptide rescues mice from a pulmonary Francisella infection

Our long-term goal is to identify new antimicrobial peptides that might be effective against pneumonic Francisella infection in mice. Previously, our group searched the peptidome of the American alligator for novel cationic antimicrobial peptides and identified a naturally-occurring C-terminal fragment of apolipoprotein C-1, which we called Apo6. This peptide was found to have antibacterial activity against the ESKAPE pathogens, including those exhibiting multi-drug resistance. In this work, we tested Apo6 and synthetic derivatives for antibacterial activity against Francisella tularensis including the virulent strain F. tularensis SchuS4. Francisella is inherently highly resistant to the cyclic peptide polymyxin antibiotics and beta-lactam antibiotics. We found that our synthetic peptide derivatives (called GATR peptides), designed with increased hydrophobicity and charge, had generally stronger in vitro antimicrobial activity against Francisella than the parent peptide Apo6. The GATR peptides had a greater effect on the bacterial membrane than the Apo6 peptide and were able to bind Francisella LPS, suggesting their mechanism of action against Francisella. Cytotoxicity experiments showed low cytotoxicity for most of the GATR peptides, and whole organism toxicity studies in the waxworm allowed us to down-select to two our lead peptides, GATR-3 and GATR-6. These peptides were tested in a murine pulmonary tularemia model. We found that the GATR-3 peptide rescued 50-60% of mice from lethal tularemia infection when administered systemically through the intraperitoneal route. This peptide is a candidate for further pre-clinical studies for a potential peptide-based approach to tularemia.

microbiology↗