Iron-based ferritin nanocore as a contrast agent

Self-assembling protein cages have been exploited as templates for nanoparticle synthesis. The ferritin molecule, a protein cage present in most living systems, stores excess soluble ferrous iron in the form of an insoluble ferric complex within its cavity. Magnetic nanocores formed by loading excess iron within an engineered ferritin from Archaeoglobus fulgidus (AfFtn-AA) were studied as a potential magnetic resonance (MR) imaging contrast agent. The self-assembly characteristics of the AfFtn-AA were investigated using dynamic light scattering technique and size exclusion chromatography. Homogeneous size distribution of the assembled nanoparticles was observed using transmission electron microscopy. The magnetic properties of iron-loaded AfFtn-AA were studied using vibrating sample magnetometry. Images obtained from a 3.0 T whole-body MRI scanner showed significant brightening of T1 images and signal loss of T2 images with increased concentrations of iron-loaded AfFtn-AA. The analysis of the MR image intensities showed extremely high R2 values (5300 mM^(−1) s^(−1)) for the iron-loaded AfFtn-AA confirming its potential as a T2 contrast agent

Thermodynamically Stable DNA Code Design using a Similarity Significance Model

DNA code design aims to generate a set of DNA sequences (codewords) with minimum likelihood of undesired hybridizations among sequences and their reverse-complement (RC) pairs (cross-hybridization). Inspired by the distinct hybridization affinities (or stabilities) of perfect double helix constructed by individual single-stranded DNA (ssDNA) and its RC pair, we propose a novel similarity significance (SS) model to measure the similarity between DNA sequences. Particularly, instead of directly measuring the similarity of two sequences by any metric/approach, the proposed SS works in a way to evaluate how more likely will the undesirable hybridizations occur over the desirable hybridizations in the presence of the two measured sequences and their RC pairs. With this SS model, we construct thermodynamically stable DNA codes subject to several combinatorial constraints using a sorting-based algorithm. The proposed scheme results in DNA codes with larger code sizes and wider free energy gaps (hence better cross-hybridization performance) compared to the existing methods.Comment: To appear in ISIT 202

Spatial organisation of enzymes in the biosynthetic limonene production pathway in Escherichia coli

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Construction of bio-constrained code for DNA data storage

With extremely high density and durable preservation, DNA data storage has become one of the most cutting-edge techniques for long-term data storage. Similar to traditional storage which impose restrictions on the form of encoded data, data stored in DNA storage systems are also subject to two biochemical constraints, i.e., maximum homopolymer run limit and balanced GC content limit. Previous studies used successive process to satisfy these two constraints. As a result, the process suffers low efficiency and high complexity. In this paper, we propose a novel content-balanced run-length limited (C-RLL) code with an efficient code construction method, which generates short DNA sequences that satisfy both constraints at one time. Besides, we develop an encoding method to map binary data into long DNA sequences for DNA data storage, which ensures both local and global stability in terms of satisfying the biochemical constraints. The proposed encoding method has high effective code rate of 1.917 bits per nucleotide and low coding complexity

Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen

A synthetic genetic system is designed and characterized that allows Escherichia coli to sense and eradicate Pseudomonas aeruginosa, providing a novel antimicrobial strategy that could potentially be applied to fighting infectious pathogens

Optimized code design for constrained DNA data storage with asymmetric errors

With ultra-high density and preservation longevity, deoxyribonucleic acid (DNA)-based data storage is becoming an emerging storage technology. Limited by the current biochemical techniques, data might be corrupted during the processes of DNA data storage. A hybrid coding architecture consisting of modified variable-length run-length limited (VL-RLL) codes and optimized protograph low-density parity-check (LDPC) codes is proposed in order to suppress error occurrence and correct asymmetric substitution errors. Based on the analyses of the different asymmetric DNA sequencer channel models, a series of the protograph LDPC codes are optimized using a modified extrinsic information transfer algorithm (EXIT). The simulation results show the better error performance of the proposed protograph LDPC codes over the conventional good codes and the codes used in the existing DNA data storage system. In addition, the theoretical analysis shows that the proposed hybrid coding scheme stores ~1.98 bits per nucleotide (bits/nt) with only 1% gap from the upper boundary (2 bits/nt)

Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL)

8 Pág.Synthetic biology aims to develop novel biological systems and increase their reproducibility using engineering principles such as standardization and modularization. It is important that these systems can be represented and shared in a standard way to ensure they can be easily understood, reproduced, and utilized by other researchers. The Synthetic Biology Open Language (SBOL) is a data standard for sharing biological designs and information about their implementation and characterization. Previously, this standard has only been used to represent designs in systems where the same design is implemented in every cell; however, there is also much interest in multicellular systems, in which designs involve a mixture of different types of cells with differing genotype and phenotype. Here, we show how the SBOL standard can be used to represent multicellular systems, and, hence, how researchers can better share designs with the community and reliably document intended system functionality.This work was supported in part by NSF Expeditions in Computing Program Award No. 1522074 as part of the Living Computing Project and by the Defense Advanced Research Projects Agency under Contract No. W911NF-17-2-0098. The views, opinions, and/or findings expressed are of the author(s) and should not be interpreted as representing official views or policies of the Department of Defense or the U.S. Government. A.G.-M. was supported by the SynBio3D project of the UK Engineering and Physical Sciences Research Council (No.EP/R019002/1) and the European CSA on biological standardization BIOROBOOST (EU Grant No. 820699)Peer reviewe

Building a global alliance of biofoundries (vol 10, 2040, 2019)

The original version of this Comment contained errors in the legend of Figure 2, in which the locations of the fifteenth and sixteenth GBA members were incorrectly given as '(15) Australian Genome Foundry, Macquarie University; (16) Australian Foundry for Advanced Biomanufacturing, University of Queensland.'. The correct version replaces this with '(15) Australian Foundry for Advanced Biomanufacturing (AusFAB), University of Queensland and (16) Australian Genome Foundry, Macquarie University'. This has been corrected in both the PDF and HTML versions of the Comment

Web based visualization interface for the assessment of osteoarthritis using MRI

The main objective of the research project is to design and develop a web-based visualization interface for the assessment of osteoarthritis. This involves the development of semi-automatic segmentation method, cartilage measurement technique, and 2D/3D visualization techniques/interfaces for the knee joint (e.g. bones and cartilage). The project focused on analyzing the articular cartilage thickness of the knee joint using MR images. The following were carried out in the project. 1. A web-based 3D visualization interface has been developed. Using this interface, it is possible to visualize the knee joint in 3D and perform quantitative measurement of anatomical structures. The interface also enables the visibility of 3D structures to be interactively changed. This enables clinician to view structures that would otherwise be obstructed. This interface was subsequently developed using Java to make it web-based. A new 3D trackback function was developed to facilitate the studying of 3D model and 2D images by allowing clinician to click on the 3D model to retrieve corresponding image and highlight the point of interest on the image. 2. A program to visualise both anatomical and quantitative MR images was developed to facilitate the examining of quantitative MR images during diagnosis. 3. A MR noise removal technique which utilized differential evolution for parameters selection has been developed. 4. A semi-automatic segmentation method for the cartilage has been developed to delineate articular cartilage using MR images. 5. A cartilage thickness measurement and visualization program has been developed which measures the articular cartilage thickness using segmented images derived from the semi-automatic segmentation program. An interface that aids segmentation process has been developed. This interface allows clinician to use prior region of interest to initiate the segmentation of bone and cartilage.SUG 9/0

A manganese–ferritin nanocomposite as an ultrasensitive T2 contrast agent

T 2 contrast is gaining importance in high field strength MRI. We report a strategy for developing a T2 contrast agent from paramagnetic metal ions synthesized within an engineered protein cage. The manganese–ferritin nanocomposite showed high T2 relaxivity indicating its potential as an ultrasensitive T2 contrast agent