Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae

As the use of synthetic biology both in industry and in academia grows, there is an increasing need to ensure biocontainment. There is growing interest in engineering bacterial- and yeast-based safeguard (SG) strains. First-generation SGs were based on metabolic auxotrophy; however, the risk of cross-feeding and the cost of growth-controlling nutrients led researchers to look for other avenues. Recent strategies include bacteria engineered to be dependent on nonnatural amino acids and yeast SG strains that have both transcriptional- and recombinational-based biocontainment. We describe improving yeast Saccharomyces cerevisiae-based transcriptional SG strains, which have near-WT fitness, the lowest possible escape rate, and nanomolar ligands controlling growth. We screened a library of essential genes, as well as the best-performing promoter and terminators, yielding the best SG strains in yeast. The best constructs were fine-tuned, resulting in two tightly controlled inducible systems. In addition, for potential use in the prevention of industrial espionage, we screened an array of possible "decoy molecules" that can be used to mask any proprietary supplement to the SG strain, with minimal effect on strain fitness

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  </p

Manipulating the 3D organization of the largest synthetic yeast chromosome

Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field. Here, we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp yeast chromosome resulting from extensive genome streamlining and modification. We developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction. Besides the drastic sequence changes, we further manipulated the 3D structure of synIV to explore spatial gene regulation. Surprisingly, we found few gene expression changes, suggesting that positioning inside the yeast nucleoplasm plays a minor role in gene regulation. Lastly, we tethered synIV to the inner nuclear membrane via its hundreds of loxPsym sites and observed transcriptional repression of the entire chromosome, demonstrating chromosome-wide transcription manipulation without changing the DNA sequences. Our manipulation of the spatial structure of synIV sheds light on higher-order architectural design of the synthetic genomes. </p

Identification of Orbital Angular Momentum by Support Vector Machine in Ocean Turbulence

With the advancement of underwater communication technology, the traditional modulation dimension has been introduced, developed and utilized. In addition, orbital angular momentum (OAM) is utilized as the modulation dimension for optical underwater communication to obtain larger spectrum resources. The OAM features are extracted using a histogram of oriented gradient and trained using the support vector machine method with a gradient direction histogram feature. The topological charge value of the OAM was used to identify the classification labels, and the ocean turbulence caused by different temperatures and salinity were analyzed. Experimentation results showed that the recognition accuracy for the OAM under the Laguerre–Gaussian beam rates of 1~5, 1~6, 1~7, 1~8, 1~9, and 1~10 was 98.93%, 98.89%, 97.33%, 96.66%, 95.40%, and 95.33%, respectively. The proposed method achieved a high recognition accuracy and performed efficiently under strong turbulence. Our research explored a new technique that provides a new idea for the demodulation of OAM in optical underwater communication

Channel Polarization Scheme for Ocean Turbulence Channels in Underwater Visible Light Communication

Underwater wireless communication technology plays an important role in marine environment monitoring and ecological protection. Underwater optical wireless communications (UWOCs) can currently achieve a transmission distance of hundreds of meters, and the rate can reach hundreds of Mbps or even Gbps, with low power consumption and high-speed features. In addition, UWOC also has the advantages of a small transceiver size and strong anti-electromagnetic interference ability, which is especially suitable for scenarios where underwater volume and power consumption are relatively limited. However, UWOC systems face problems such as unstable transceiver ends, ocean turbulence, and so on, resulting in reduced communication reliability and limited transmission distance. Establishing a stable and reliable communication link is critical to extending the communication distance of the UWOC system. In this paper, a model of ocean turbulence channels is established based on the power spectrum inversion method. The transmission characteristics of orbital angular momentum (OAM) light in an ocean turbulence channel are studied, then the mode selection of OAM light is determined. At the same time, the polarization coding technique is applied to the underwater OAM communication system for the first time. The simulation results show that this scheme can effectively extend the communication distance and reduce the system bit error rate

Research on Orbital Angular Momentum Recognition Technology Based on a Convolutional Neural Network

In underwater wireless optical communication (UWOC), a vortex beam carrying orbital angular momentum has a spatial spiral phase distribution, which provides spatial freedom for UWOC and, as a new information modulation dimension resource, it can greatly improve channel capacity and spectral efficiency. In a case of the disturbance of a vortex beam by ocean turbulence, where a Laguerre–Gaussian (LG) beam carrying orbital angular momentum (OAM) is damaged by turbulence and distortion, which affects OAM pattern recognition, and the phase feature of the phase map not only has spiral wavefront but also phase singularity feature, the convolutional neural network (CNN) model can effectively extract the information of the distorted OAM phase map to realize the recognition of dual-mode OAM and single-mode OAM. The phase map of the Laguerre–Gaussian beam passing through ocean turbulence was used as a dataset to simulate and analyze the OAM recognition effect during turbulence caused by different temperature ratios and salinity. The results showed that, during strong turbulence Cn2=1.0×10−13K2m−2/3, when different ω = −1.75, the recognition rate of dual-mode OAM (ℓ = ±1~±5, ±1~±6, ±1~±7, ±1~±8, ±1~±9, ±1~±10) had higher recognition rates of 100%, 100%, 100%, 100%, 98.89%, and 98.67% and single-mode OAM (ℓ = 1~5, 1~6, 1~7, 1~8, 1~9, 1~10) had higher recognition rates of 93.33%, 92.77%, 92.33%, 90%, 87.78%, and 84%, respectively. With the increase in ω, the recognition accuracy of the CNN model will gradually decrease, and in a fixed case, the dual-mode OAM has stronger anti-interference ability than single-mode OAM. These results may provide a reference for optical communication technologies that implement high-capacity OAM

Highly Effective Anti-Organic Fouling Performance of a Modified PVDF Membrane Using a Triple-Component Copolymer of P(Stx-co-MAAy)-g-fPEGz as the Additive

In this study, a triple-component copolymer of P(Stx-co-MAAy)-g-fPEGz containing hydrophobic (styrene, St), hydrophilic (methacrylic acid, MAA), and oleophobic (perfluoroalkyl polyethylene glycol, fPEG) segments was synthesized and used as an additive polymer to prepare modified PVDF membrane for enhanced anti-fouling performance. Two compositions of St:MAA at 4:1 and 1:1 for the additive and two blending ratios of the additive:PVDF at 1:9 and 3:7 for the modified membranes were specifically examined. The results showed that the presence of the copolymer additive greatly affected the morphology and performance of the modified PVDF membranes. Especially, in a lower ratio of St to MAA (e.g., St:MAA at 1:1 versus 4:1), the additive polymer and therefore the modified PVDF membrane exhibited both better hydrophilic as well as oleophobic surface property. The prepared membrane can achieve a water contact angle at as low as 48.80&deg; and display an underwater oil contact angle at as high as 160&deg;. Adsorption experiments showed that BSA adsorption (in the concentration range of 0.8 to 2 g/L) on the modified PVDF membrane can be reduced by as much as 93%. From the filtration of BSA solution, HA solution, and oil/water emulsion, it was confirmed that the obtained membrane showed excellent resistance to these organic foulants that are often considered challenging in membrane water treatment. The performance displayed slow flux decay during filtration and high flux recovery after simple water cleaning. The developed membrane can therefore have a good potential to be used in such applications as water and wastewater treatment where protein and other organic pollutants (including oils) may cause severe fouling problems to conventional polymeric membranes