Browsing by Author "Miller, Ryan"

Now showing 1 - 2 of 2
  • Thumbnail Image
    AssemblyTron: Flexible automation of DNA assembly with Opentrons OT-2 lab robots
    Bryant, John A., Jr.; Kellinger, Mason; Longmire, Cameron; Miller, Ryan; Wright, R. Clay (Oxford University Press, 2022-12-22)
    As one of the newest fields of engineering, synthetic biology relies upon a trial-and-error Design-Build-Test-Learn approach to simultaneously learn how function is encoded in biology and attempt to engineer it. Many software and hardware platforms have been developed to automate, optimize, and algorithmically perform each step of the Design-Build-Test-Learn cycle. However, there are many fewer options for automating the Build step. Build typically involves DNA assembly, which remains manual, low throughput, and unreliable in most cases and limits our ability to advance the science and engineering of biology. Here, we present AssemblyTron: an open-source python package to integrate j5 DNA assembly design software outputs with build implementation in Opentrons liquid handling robotics with minimal human intervention. We demonstrate the versatility of AssemblyTron through several scarless, multipart DNA assemblies beginning from fragment amplification. We show that AssemblyTron can perform PCRs across a range of fragment lengths and annealing temperatures by using an optimal annealing temperature gradient calculation algorithm. We then demonstrate that AssemblyTron can perform Golden Gate and homology-dependent in vivo assemblies with comparable fidelity to manual assemblies by simultaneously building four four-fragment assemblies of chromoprotein reporter expression plasmids. Finally, we used AssemblyTron to perform site-directed mutagenesis reactions via homology-dependent in vivo assembly also achieving comparable fidelity to manual assemblies as assessed by sequencing. AssemblyTron can reduce the time, training, costs, and wastes associated with synthetic biology, which along with open-source and affordable automation, will further foster the accessibility of synthetic biology and accelerate biological research and engineering.
  • Thumbnail Image
    First-in-man histotripsy of hepatic tumors: the THERESA trial, a feasibility study
    Vidal-Jove, Joan; Serres, Xavier; Vlaisavljevich, Eli; Cannata, Jon; Duryea, Alex; Miller, Ryan; Merino, Xavier; Velat, Manuela; Kam, Yossi; Bolduan, Ryan; Amaral, Joseph; Hall, Timothy; Xu, Zhen; Lee, Fred T., Jr.; Ziemlewicz, Timothy J. (Taylor & Francis, 2022-12-31)
    Rationale Current hepatic locoregional therapies are limited in terms of effectiveness and toxicities. Given promising pre-clinical results, a first in-human trial was designed to assess the technical effectiveness and safety profile of histotripsy, a noninvasive, non-thermal, non-ionizing focused ultrasound therapy that creates precise, predictable tissue destruction, in patients with primary and secondary liver tumors. Methods A multicenter phase I trial (Theresa Study) was performed in a single country with 8 weeks of planned follow-up. Eight of fourteen recruited patients were deemed eligible and enrolled in the study. Hepatic histotripsy, was performed with a prototype system (HistoSonics, Inc., Ann Arbor, MI). Eleven tumors were targeted in the 8 patients who all had unresectable end-stage multifocal liver tumors: colorectal liver metastases (CRLM) in 5 patients (7 tumors), breast cancer metastases in 1 (1 tumor), cholangiocarcinoma metastases in 1 (2 tumors), and hepatocellular carcinoma (HCC) in 1 (1 tumor). The primary endpoint was acute technical success, defined as creating a zone of tissue destruction per planned volume assessed by MRI 1-day post-procedure. Safety (device-related adverse events) through 2 months was a secondary endpoint. Results The 8 patients had a median age of 60.4 years with an average targeted tumor diameter of 1.4cm. The primary endpoint was achieved in all procedures. The secondary safety profile endpoint identified no device-related adverse events. Two patients experienced a continuous decline in tumor markers during the eight weeks following the procedure. Conclusions This first-in-human trial demonstrates that hepatic histotripsy effectively destroys liver tissue in a predictable manner, correlating very well with the planned histotripsy volume, and has a high safety profile without any device-related adverse events. Based on these results, the need for more definitive clinical trials is warranted.