Biology subjects

Pascual-Garrigos, A.

Publications and source records attributed to Pascual-Garrigos, A..

3 recordsLinked to original sources

bioRxiv2025

Detection of five viruses commonly implicated with Bovine Respiratory Disease using loop-mediated isothermal amplification

Herein, we present novel quantitative loop-mediated isothermal amplification (qLAMP) and reverse-transcription qLAMP (RT-qLAMP) assays for the detection of five viruses commonly implicated with the onset and progression of bovine respiratory disease (BRD): Bovine Alphaherpesvirus Type 1 (BHV-1), Bovine Adenovirus Type 3 (BAV-3), Bovine Respiratory Syncytial Virus (BRSV), Bovine Viral Diarrhea Virus Type 1 (BVDV-1), and Bovine Parainfluenza Virus Type 3 (BPIV-3). Using contrived samples spiked with whole viruses, we found that our extraction-free assays have limits of detection between 30 and 1,057 copies per reaction (1.8% final sample concentration) with minimal sample processing. Using dual-tipped swabs and 1.4 mL resuspension volumes, these limits of detection are on the order of 2 x 105 copies per swab for BAV-3 and BHV-1 and between 6.31 x 106 to 8.22 x 106 copies per swab in the case of BPIV-3, BRSV, and BVDV-1. Analytical sensitivities ranged from 73 - 100% and analytical specificities ranged from 90 - 100%. Additionally, we introduced a streamlined pipeline to minimize the experimental workload to design, screen, select, and characterize LAMP performance for developing assays. The assays targeting these BRD viruses can be utilized to develop colorimetric LAMP assays that enable the sensitive and specific detection of these viruses chute side to aid in diagnosing and treating BRD. The associated development pipeline enables more rapid development of LAMP-based diagnostic tools targeting emerging pathogens.

bioengineering↗

bioRxiv2024

qByte: Open-source isothermal fluorimeter for democratizing analysis of nucleic acids, proteins and cells

Access to affordable and reliable scientific instrumentation remains a significant barrier to the democratization of healthcare and scientific research. In the field of biotechnology, in particular, the complexity, cost, and infrastructure requirements of many instruments continue to limit their accessibility, especially in resource-limited environments. Despite the recent increase in the development of open-source tools, driven by advances in digital fabrication and electronic prototyping, few of these projects have reached large-scale implementation or validation in real-world settings. Here, we present qByte, an open-source, 8-tube isothermal fluorimeter designed to overcome these barriers by offering a cost-effective ($60) yet production-ready solution. qByte leverages standard digital manufacturing and Printed Circuit Board (PCB) assembly techniques and is designed to be portable, making it ideal for both laboratory and field use. The device has been benchmarked against commercial real-time thermocyclers and spectrophotometers, showing comparable results across four key applications: nucleic acid amplification and detection, analysis of protein activity and stability, genetic construct characterization, and bacterial viability tests. Further testing including the on-site diagnosis of human parasites in Kumasi, Ghana, and field work in Patagonia, Chile, validated qBytes reliability in real-world conditions. Taken together, our results proved qByte as flexible and reliable equipment for a variety of biological tests and applications, while its affordability and open-source design simplify further development and allow adaptation to the needs of future users.

bioengineering↗

bioRxiv2024

Colorimetric CRISPR Biosensor: A Case Study with Salmonella Typhi

There is a critical need to implement a sensitive and specific point-of-care (POC) biosensor that addresses the instrument limitations and manufacturing challenges faced in resource-constrained contexts. In this paper we focus on enteric fever which is a highly contagious and prevalent infection in low- and middle-income countries. Although easily treatable, its ambiguous symptoms paired with a lack of fast, accurate and affordable diagnostics lead to incorrect treatments which exacerbate the disease burden, including increasing antibiotic resistance. In this study, we develop a readout module for CRISPR-Cas12a that produces a colorimetric output that is visible to the naked eye and can act as a cascade signal amplifier in any CRISPR assay based on trans-cleavage. We achieve this by immobilizing an oligo covalently linked to a {beta}-galactosidase (LacZ) enzyme, which is cleaved in the presence of DNA target-activated CRISPR-Cas12a. Upon cleavage, the colorimetric enzyme is released, and the supernatant transferred to an environment containing X-Gal producing an intense blue color. This method is capable of detecting amplified bacterial genomic DNA and has a lower limit of detection (LoD) to standard fluorescent assays while removing the requirement for costly equipment. Furthermore, it remained active after lyophilization, allowing for the possibility of shipment without cold chain, significantly reducing deployment costs. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/606709v1_figSc1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@d66787org.highwire.dtl.DTLVardef@2708eaorg.highwire.dtl.DTLVardef@ba5a86org.highwire.dtl.DTLVardef@8d4f48_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOScheme 1.C_FLOATNO Mechanism of CRISPR-Cas12a, and the signal output produced by enzyme trans-cleavage and the release of LacZ. 1) Initial set-up of inactivated system. 2) DNA isolation and amplification. 3) DNA addition to the biosensor. 4) CRISPR recognition of the DNA target and indiscriminate cleavage of all DNA. 5) LacZ release to the supernatant. 6) Transfer to an X-Gal environment. 7) X-Gal cleavage by LacZ and chromophore oxidation to the intensive blue indigo [illustration created with BioRender.com]. C_FIG

synthetic biology↗