Synthetic chromosome fusion: Effects on mitotic and meiotic genome structure and function.

We designed and synthesized synI, which is ∼21.6% shorter than native chrI, the smallest chromosome in Saccharomyces cerevisiae. SynI was designed for attachment to another synthetic chromosome due to concerns surrounding potential instability and karyotype imbalance and is now attached to synIII, yielding the first synthetic yeast fusion chromosome. Additional fusion chromosomes were constructed to study nuclear function. ChrIII-I and chrIX-III-I fusion chromosomes have twisted structures, which depend on silencing protein Sir3. As a smaller chromosome, chrI also faces special challenges in assuring meiotic crossovers required for efficient homolog disjunction. Centromere deletions into fusion chromosomes revealed opposing effects of core centromeres and pericentromeres in modulating deposition of the crossover-promoting protein Red1. These effects extend over 100 kb and promote disproportionate Red1 enrichment, and thus crossover potential, on small chromosomes like chrI. These findings reveal the power of synthetic genomics to uncover new biology and deconvolute complex biological systems.

Octree Representation Improves Data Fidelity of Cardiac CT Images and Convolutional Neural Network Semantic Segmentation of Left Atrial and Ventricular Chambers.

PURPOSE: To assess whether octree representation and octree-based convolutional neural networks (CNNs) improve segmentation accuracy of three-dimensional images. MATERIALS AND METHODS: Cardiac CT angiographic examinations from 100 patients (mean age, 67 years ± 17 [standard deviation]; 60 men) performed between June 2012 and June 2018 with semantic segmentations of the left ventricular (LV) and left atrial (LA) blood pools at the end-diastolic and end-systolic cardiac phases were retrospectively evaluated. Image quality (root mean square error [RMSE]) and segmentation fidelity (global Dice and border Dice coefficients) metrics of the octree representation were compared with spatial downsampling for a range of memory footprints. Fivefold cross-validation was used to train an octree-based CNN and CNNs with spatial downsampling at four levels of image compression or spatial downsampling. The semantic segmentation performance of octree-based CNN (OctNet) was compared with the performance of U-Nets with spatial downsampling. RESULTS: Octrees provided high image and segmentation fidelity (median RMSE, 1.34 HU; LV Dice coefficient, 0.970; LV border Dice coefficient, 0.843) with a reduced memory footprint (87.5% reduction). Spatial downsampling to the same memory footprint had lower data fidelity (median RMSE, 12.96 HU; LV Dice coefficient, 0.852; LV border Dice coefficient, 0.310). OctNet segmentation improved the border segmentation Dice coefficient (LV, 0.612; LA, 0.636) compared with the highest performance among U-Nets with spatial downsampling (Dice coefficients: LV, 0.579; LA, 0.592). CONCLUSION: Octree-based representations can reduce the memory footprint and improve segmentation border accuracy.Keywords CT, Cardiac, Segmentation, Supervised Learning, Convolutional Neural Network (CNN), Deep Learning Algorithms, Machine Learning Algorithms© RSNA, 2021.

Optogenetic Control of Heterologous Metabolism in E. coli.

Multiobjective optimization of microbial chassis for the production of xenobiotic compounds requires the implementation of metabolic control strategies that permit dynamic distribution of cellular resources between biomass and product formation. We addressed this need in a previous study by engineering the T7 RNA polymerase to be thermally responsive. The modified polymerase is activated only after the temperature of the host cell falls below 18 °C, and Escherichia coli cells that employ the protein to transcribe the heterologous lycopene biosynthetic pathway exhibit impressive improvements in productivity. We have expanded our toolbox of metabolic switches in the current study by engineering a version of the T7 RNA polymerase that drives the transition between biomass and product formation upon stimulation with red light. The engineered polymerase is expressed as two distinct polypeptide chains. Each chain comprises one of two photoactive components from Arabidopsis thaliana, phytochrome B (PhyB) and phytochrome-integrating factor 3 (PIF3), as well as the N- or C-terminus domains of both, the vacuolar ATPase subunit (VMA) intein of Saccharomyces cerevisiae and the polymerase. Red light drives photodimerization of PhyB and PIF3, which then brings together the N- and C-terminus domains of the VMA intein. Trans-splicing of the intein follows suit and produces an active form of the polymerase that subsequently transcribes any sequence that is under the control of a T7 promoter. The photodimerization also involves a third element, the cyanobacterial chromophore phycocyanobilin (PCB), which too is expressed heterologously by E. coli. We deployed this version of the T7 RNA polymerase to control the production of lycopene in E. coli and observed tight control of pathway expression. We tested a variety of expression configurations to identify one that imposes the lowest metabolic burden on the strain, and we subsequently optimized key parameters such as the source, moment, and duration of photostimulation. We also identified targets for future refinement of the circuit. In summary, our work is a significant advance for the field and greatly expands on previous work by other groups that have used optogenetic circuits to control heterologous metabolism in prokaryotic hosts.

Multi-particulate Systems: Cutting-edge Technology for Controlled Drug Delivery.

BACKGROUND: In the last two decades, multi-particulate dosage forms have caught the attention of formulation scientists due to their tremendous potential as a drug delivery system with a broad range of applications. METHODS: Recent patented technologies are focused on designing multi-particulate systems that can enhance therapeutic efficacy and oral bioavailability with minimum systemic toxicity. The technologies offer opportunities to the manufacturers for increasing their market share, especially for competitive generics, and also establishing intellectual property positions. RESULTS: The present paper provides an overview of advanced technologies and patents, based on different principles, for designing multi-particulate dosage forms. The review covers basic characteristics of the current technologies, the mechanisms by which they overcome the limitations of conventional oral dosage forms, and their applications. CONCLUSION: Comprehensive knowledge of these technologies will expedite further development and platform technologies for multi-particulate controlled drug delivery systems.