Bashir, R. | Search bioRxiv

bioRxiv2020

Computationally assisted design and selection of maneuverable biological walking machines

The intriguing opportunities enabled by the use of living components in biological machines have spurred the development of a variety of muscle-powered bio-hybrid robots in recent years. Among them, several generations of bio-hybrid walkers have been established as reliable platforms to study untethered locomotion. However, despite these advances, such technology is not mature yet, and major challenges remain. This study takes steps to address two of them: the lack of systematic design approaches, common to bio-hybrid robotics in general, and in the case of bio-hybrid walkers specifically, the lack of maneuverability. We then present here a dual-ring biobot, computationally designed and selected to exhibit robust forward motion and rotational steering. This dual-ring biobot consists of two independent muscle actuators and a 4-legged scaffold asymmetric in the fore/aft direction. The integration of multiple muscles within its body architecture, combined with differential electrical stimulation, allows the robot to maneuver. The dual-ring robot design is then fabricated and experimentally tested, confirming computational predictions and turning abilities. Overall, our design approach based on modeling, simulation, and fabrication exemplified in this robot represents a route to efficiently engineer biological machines with adaptive functionalities.

bioengineering↗

bioRxiv2020

Rapid Isothermal Amplification and Portable Detection System for SARS-CoV-2

The COVID-19 pandemic provides an urgent example where a gap exists between availability of state-of-the-art diagnostics and current needs. As assay details and primer sequences become widely known, many laboratories could perform diagnostic tests using methods such as RT-PCR or isothermal RT-LAMP amplification. A key advantage of RT-LAMP based approaches compared to RT-PCR is that RT-LAMP is known to be robust in detecting targets from unprocessed samples. In addition, RT-LAMP assays are performed at a constant temperature enabling speed, simplicity, and point-of-use testing. Here, we provide the details of an RT-LAMP isothermal assay for the detection of SARS-CoV-2 virus with performance comparable to currently approved tests using RT-PCR. We characterize the assay by introducing swabs in virus spiked synthetic nasal fluids, moving the swab to viral transport medium (VTM), and using a volume of that VTM for performing the amplification without an RNA extraction kit. The assay has a Limit-of-Detection (LOD) of 50 RNA copies/L in the VTM solution within 20 minutes, and LOD of 5000 RNA copies/L in the nasal solution. Additionally, we show the utility of this assay for real-time point-of-use testing by demonstrating detection of SARS-CoV-2 virus in less than 40 minutes using an additively manufactured cartridge and a smartphone-based reader. Finally, we explore the speed and cost advantages by comparing the required resources and workflows with RT-PCR. This work could accelerate the development and availability of SARS-CoV-2 diagnostics by proving alternatives to conventional laboratory benchtop tests. Significance StatementAn important limitation of the current assays for the detection of SARS-CoV-2 stem from their reliance on time- and labor-intensive and laboratory-based protocols for viral isolation, lysis, and removal of inhibiting materials. While RT-PCR remains the gold standard for performing clinical diagnostics to amplify the RNA sequences, there is an urgent need for alternative portable platforms that can provide rapid and accurate diagnosis, potentially at the point-of-use. Here, we present the details of an isothermal amplification-based detection of SARS-CoV-2, including the demonstration of a smartphone-based point-of-care device that can be used at the point of sample collection.

bioengineering↗