The design and engineering of synthetic genomes.

Synthetic genomics seeks to design and construct entire genomes to mechanistically dissect fundamental questions of genome function and to engineer organisms for diverse applications, including bioproduction of high-value chemicals and biologics, advanced cell therapies, and stress-tolerant crops. Recent progress has been fuelled by advancements in DNA synthesis, assembly, delivery and editing. Computational innovations, such as the use of artificial intelligence to provide prediction of function, also provide increasing capabilities to guide synthetic genome design and construction.

Automation and Expansion of EMMA Assembly for Fast-Tracking Mammalian System Engineering.

With applications from functional genomics to the production of therapeutic biologics, libraries of mammalian expression vectors have become a cornerstone of modern biological investigation and engineering. Multiple modular vector platforms facilitate the rapid design and assembly of vectors. However, such systems approach a technical bottleneck when a library of bespoke vectors is required.

EMMA-CAD: Design Automation for Synthetic Mammalian Constructs.

Computational design tools are the cornerstone of synthetic biology and have underpinned its rapid development over the past two decades. As the field has matured, the scale of biological investigation has expanded dramatically, and researchers often must rely on computational tools to operate in the high-throughput investigational space. This is especially apparent in the modular design of DNA expression circuits, where complexity is accumulated rapidly.

Formulating and Deploying Strength Amplification Controllers for Lower-Body Walking Exoskeletons.

Augmenting the physical strength of a human operator during unpredictable human-directed (volitional) movements is a relevant capability for several proposed exoskeleton applications, including mobility augmentation, manual material handling, and tool operation. Unlike controllers and augmentation systems designed for repetitive tasks (e.g.

Postsynthetic Modification of ZIF-8 Membranes via Membrane Surface Ligand Exchange for Light Hydrocarbon Gas Separation Enhancement.

The ability to tailor the pore structure of metal-organic framework (MOF) membranes enables synthesis of new or modified MOF membranes with enhanced separation characteristics. This work employs a modified version of solvent-assisted ligand exchange, termed membrane surface ligand exchange (MSLE), to modify the pore structure of zeolitic imidazolate framework-8 (ZIF-8) membranes. This paper is the first to perform a time-based, ex situ characterization and gas permeation study of ZIF-8 MSLE with 5,6-DBIM (DBIM, dimethylbenzimidazole) to effectively narrow the ZIF-8 pores, enhance light hydrocarbon gas-phase separations, and give insight into the exchange mechanism with respect to time and temperature.

Technical Note: Validation and implementation of a wireless transponder tracking system for gated stereotactic ablative radiotherapy of the liver.

Purpose: Tracking soft-tissue targets has recently been cleared as a new application of Calypso, an electromagnetic wireless transponder tracking system, allowing for gated treatment of the liver based on the motion of the target volume itself. The purpose of this study is to describe the details of validating the Calypso system for wireless transponder tracking of the liver and to present the clinical workflow for using it to deliver gated stereotactic ablative radiotherapy (SABR).

Methods: A commercial 3D diode array motion system was used to evaluate the dynamic tracking accuracy of Calypso when tracking continuous large amplitude motion.

Commissioning of a motion system to investigate dosimetric consequences due to variability of respiratory waveforms.

A commercially available six-dimensional (6D) motion system was assessed for accuracy and clinical use in our department. Positional accuracy and respiratory waveform reproducibility were evaluated for the motion system. The system was then used to investigate the dosimetric consequences of respiratory waveform variation when an internal target volume (ITV) approach is used for motion management.

Implementation of an in-house visual feedback system for motion management during radiation therapy.

In this Technical Note, we describe an in-house video goggles feedback system assembled using several commercially available products. This goggle video feed-back system is currently being used at University of Louisville and Mayo Clinic for both CT simulation and linac treatment delivery. The setup details, including specific recommendations, are provided, along with an alternative option for using the video goggles system.

Site-specific tolerance tables and indexing device to improve patient setup reproducibility.

While the implementation of tools such as image-guidance and immobilization devices have helped to prevent geometric misses in radiation therapy, many treatments remain prone to error if these items are not available, not utilized for every fraction, or are misused. The purpose of this project is to design a set of site-specific treatment tolerance tables to be applied to the treatment couch for use in a record and verify (R&V) system that will insure accurate patient setup with minimal workflow interruption. This project also called for the construction of a simple indexing device to help insure reproducible patient setup for patients that could not be indexed with existing equipment.

Percent depth-dose distribution discrepancies from very small volume ion chambers.

As very small ion chambers become commercially available, medical physicists may be inclined to use them during the linear accelerator commissioning process to better characterize the beam in steep dose gradient areas. For this work, a total of eight different ion chambers (volumes from 0.007 cc to 0.

Quantification of planning target volume margin when using a robotic radiosurgery system to treat lung tumors with spine tracking.

Purpose: The use of fiducial markers or direct tumor visualization allows for tumor tracking and ultimately smaller planning target volume (PTV) margins in the treatment of lung tumors, yet many patients are either not amenable to fiducial marker placement or their tumors are unable to be visualized on orthogonal-axis x-ray images. Spine tracking is an alternative method for tumor localization but is limited by the assumption that the location of the lung tumor relative to the spine is constant. The purpose of this study was to quantify the additional PTV margin needed when spine tracking is used to ensure the internal target volume (ITV) receives the prescription dose during treatment.

The efficacy of mitomycin-C in the treatment of laryngotracheal stenosis.

Objective: The purpose of this study is to evaluate whether the addition of topical mitomycin-C (MMC) application to the wound site after endoscopic treatment of laryngotracheal stenosis (LTS) resulted in measurable improvement in clinical outcomes.

Study Design And Setting: A retrospective chart review of patients with LTS treated by the senior author over a 6-year period was performed. The treatment groups were stratified into two main categories: 1) endoscopic treatment alone and 2) endoscopic treatment + topical MMC.

A novel method to correct for pitch and yaw patient setup errors in helical tomotherapy.

An accurate means of determining and correcting for daily patient setup errors is important to the cancer outcome in radiotherapy. While many tools have been developed to detect setup errors, difficulty may arise in accurately adjusting the patient to account for the rotational error components. A novel, automated method to correct for rotational patient setup errors in helical tomotherapy is proposed for a treatment couch that is restricted to motion along translational axes.

Quantitative assessment of gene targeting in vitro and in vivo by the pancreatic transcription factor, Pdx1. Importance of chromatin structure in directing promoter binding.

The transcription factor Pdx1 is expressed in the pancreatic beta-cell, where it is believed to regulate several beta-cell-specific genes. Whereas binding by Pdx1 to elements of beta-cell genes has been demonstrated in vitro, almost none of these genes has been demonstrated to be a direct binding target for Pdx1 within cells (where complex chromatin structure exists). To determine which beta-cell promoters are bound by Pdx1 in vivo, we performed chromatin immunoprecipitation assays using Pdx1 antiserum and chromatin from beta-TC3 cells and Pdx1-transfected NIH3T3 cells and subsequently quantitated co-immunoprecipitated promoters using real-time PCR.