Dataset Information

Evaluating and mitigating clinical samples matrix effects on TX-TL cell-free performance.

ABSTRACT: Cell-free biosensors are promising tools for medical diagnostics, yet their performance can be affected by matrix effects arising from the sample itself or from external components. Here we systematically evaluate the performance and robustness of cell-free systems in serum, plasma, urine, and saliva using two reporter systems, sfGFP and luciferase. In all cases, clinical samples have a strong inhibitory effect. Of the different inhibitors, only RNase inhibitor mitigated matrix effects. However, we found that the recovery potential of RNase inhibitor was partially muted by interference from glycerol contained in the commercial buffer. We solved this issue by designing a strain producing an RNase inhibitor protein requiring no additional step in extract preparation. Furthermore, our new extract yielded higher reporter levels than previous conditions and tempered interpatient variability associated with matrix effects. This systematic evaluation and improvements of cell-free system robustness unified across many types of clinical samples is a significant step towards developing cell-free diagnostics for a wide range of conditions.

SUBMITTER: Voyvodic PL

PROVIDER: S-EPMC9374283 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Evaluating and mitigating clinical samples matrix effects on TX-TL cell-free performance.

Voyvodic Peter L PL Conejero Ismael I Mesmoudi Khouloud K Renard Eric E Courtet Philippe P Cattoni Diego I DI Bonnet Jerome J

Scientific reports 20220812 1

Cell-free biosensors are promising tools for medical diagnostics, yet their performance can be affected by matrix effects arising from the sample itself or from external components. Here we systematically evaluate the performance and robustness of cell-free systems in serum, plasma, urine, and saliva using two reporter systems, sfGFP and luciferase. In all cases, clinical samples have a strong inhibitory effect. Of the different inhibitors, only RNase inhibitor mitigated matrix effects. However, ...[more]

PMID: 35962056

Similar Datasets

Project description:The spread of invasive species is considered a major threat to biodiversity, second only to habitat loss. Red Imported Fire Ants (Solenopsis invicta) are a globally invasive species with negative impacts reported on native invertebrate and vertebrate species. Federally endangered Houston Toads (Bufo [=Anaxyrus] houstonensis), endemic to Texas, are among the vertebrates reportedly negatively impacted by Red Imported Fire Ants (RIFA). Threats posed by RIFA to Houston Toads needed to be explicitly characterized. Large-scale chemical treatments to suppress RIFA and facilitate brood survival in Attwater's prairie-chickens (Tympanuchus cupido attwateri) at the Attwater Prairie Chicken National Wildlife Refuge (APCNWR) afforded us an opportunity to experimentally examine the influence of RIFA abundance on juvenile Houston Toad growth and survival. We also sought to examine whether juvenile Houston Toads could grow and survive in a vegetation type similar to a historic species locality. We conducted a terrestrial mesocosm experiment to test whether the application of bait-driven suppressant decreased counts of RIFA relative to untreated sites. We examined whether counts of native ant and non-ant native invertebrates were higher in response to potential decreases in RIFA. We compared growth and survival rates in juvenile Houston Toads among treated and untreated sites, expecting juvenile growth and survival to be higher in response to potentially decreased RIFA counts and increased native invertebrate counts. We saw lower counts of RIFA in treated prairies, but we also observed a decrease in native ant counts possibly due to chemical treatment. Therefore, the application of bait-driven suppressant may not affect RIFA alone. We saw no difference in counts of non-ant invertebrates among treated and untreated sites. Juvenile Houston Toads did not differ in growth and survival among treated and untreated sites. We recognize that the lack of a relationship between juvenile growth and survival with a treatment effect, and therefore RIFA abundance, may be limited to APCNWR. We encourage additional experimental studies to elucidate RIFA impacts at other sites. We extrapolated apparent survival estimates from our study to one year. These appear comparable to juvenile survivorship required in simulations for Houston Toad population persistence and on this basis, we recommend that APCNWR be re-evaluated as a reintroduction site for Houston Toads. We also recommend further studies to potentially broaden the regulatory definition of Houston Toad habitat beyond the current restrictive view of canopied forest alone. Such studies would need to examine the utility of native grasslands as dispersal corridors/upland habitat for juvenile Houston Toads. Our findings emphasize the utility of experimental studies in directly examining the influence of perceived threats to imperiled species and the role of such clarifications in adapting recovery efforts.

Dataset Information

Evaluating and mitigating clinical samples matrix effects on TX-TL cell-free performance.

Publications

Evaluating and mitigating clinical samples matrix effects on TX-TL cell-free performance.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets