Synthetic promoter design for cyanobacteria with deep-learning models

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Design of synthetic promoters for cyanobacteria with generative deep-learning model

Deep generative models, which can approximate complex data distribution from large datasets, are widely used in biological dataset analysis. In particular, they can identify and unravel hidden traits encoded within a complicated nucleotide sequence, allowing us to design genetic parts with accuracy. Here, we provide a deep-learning based generic framework to design and evaluate synthetic promoters for cyanobacteria using generative models, which was in turn validated with cell-free transcription assay. We developed a deep generative model and a predictive model using a variational autoencoder and convolutional neural network, respectively. Using native promoter sequences of the model unicellular cyanobacterium Synechocystis sp. PCC 6803 as a training dataset, we generated 10 000 synthetic promoter sequences and predicted their strengths. By position weight matrix and k-mer analyses, we confirmed that our model captured a valid feature of cyanobacteria promoters from the dataset. Furthermore, critical subregion identification analysis consistently revealed the importance of the -10 box sequence motif in cyanobacteria promoters. Moreover, we validated that the generated promoter sequence can efficiently drive transcription via cell-free transcription assay. This approach, combining in silico and in vitro studies, will provide a foundation for the rapid design and validation of synthetic promoters, especially for non-model organisms

Polypyrrole–MnO₂‑Coated Textile-Based Flexible-Stretchable Supercapacitor with High Electrochemical and Mechanical Reliability

Carbon-nanotube (CNT)-based textile supercapacitors with MnO₂ nanoparticles have excellent power and energy densities, but MnO₂ nanoparticles can be delaminated during charge–discharge cycles, which results in significant degradation in capacitance. In this study, polypyrrole conductive polymer was coated on top of MnO₂ nanoparticles that are deposited on CNT textile supercapacitor to prevent delamination of MnO₂ nanoparticles. An increase of 38% in electrochemical energy capacity to 461 F/g was observed, while cyclic reliability also improved, as 93.8% of energy capacity was retained over 10 000 cycles. Energy density and power density were measured to be 31.1 Wh/kg and 22.1 kW/kg, respectively. An in situ electrochemical–mechanical study revealed that polypyrrole–MnO₂-coated CNT textile supercapacitor can retain 98.5% of its initial energy capacity upon application of 21% tensile strain and showed no observable energy storage capacity change upon application of 13% bending strain. After imposing cyclic bending of 750 000 cycles, the capacitance was retained to 96.3%. Therefore, the results from this study confirmed for the first time that the polypyrrole–MnO₂-coated CNT textile can reliably operate with high energy and power densities with in situ application of both tensile and bending strains

Polyphenols Coordinated with Cu (II) in an Aqueous System Build Ion-Channel Coatings on Hair Surfaces

Recently, developments in the field of cosmetics have led to a renewed interest in hair dyeing. However, damage to the hair during the dyeing process has increased hesitation in attempting hair dyeing. As a result, hair dyes with minimal side effects have been in constant demand, and are being developed. In this study, natural-extract polyphenols, pyrogallol, and gallic acid are coordinated by CuCl2 in a NaCl aqueous solution to form an oligomer, which creates an ion-channel coating on the hair surface to protect it. This work attempts to develop fast, simple, and damage-free hair-dye ingredients based on pyrogallol and gallic acid. The morphology and elements of polyphenols coated on hair are characterized. The results reveal that the hair is dyed with the polyphenol-based dye reagent successfully. Moreover, the thickness of the dyed hair continuously rises ten times after dyeing. The tensile strength of the dyed hair is also measured, showing an upward and downward trend. These results reflect the fact that pyrogallol and gallic acid are considered to be the essential and functional polyphenols, and can build ion blocks on hair, which can create new multifunctional coating materials

Polyphenols Coordinated with Cu (II) in an Aqueous System Build ion-Channel Coatings on Hair Surfaces

Recently, developments in the field of cosmetics have led to a renewed interest in hair dyeing. However, damage to the hair during the dyeing process has increased hesitation in attempting hair dyeing. As a result, hair dyes with minimal side effects have been in constant demand, and are being developed. In this study, natural-extract polyphenols, pyrogallol, and gallic acid are coordinated by CuCl2 in a NaCl aqueous solution to form an oligomer, which creates an ion-channel coating on the hair surface to protect it. This work attempts to develop fast, simple, and damage-free hair-dye ingredients based on pyrogallol and gallic acid. The morphology and elements of polyphenols coated on hair are characterized. The results reveal that the hair is dyed with the polyphenol-based dye reagent successfully. Moreover, the thickness of the dyed hair continuously rises ten times after dyeing. The tensile strength of the dyed hair is also measured, showing an upward and downward trend. These results reflect the fact that pyrogallol and gallic acid are considered to be the essential and functional polyphenols, and can build ion blocks on hair, which can create new multifunctional coating materials

Coagulation parameters and plasma total homocysteine levels in Behcet's disease

Behcet's disease (BD) is a multisystemic inflammatory disorder of unknown etiology that is sometimes associated with thrombosis in addition to systemic manifestations. However, the mechanism of hypercoagulability is not known. We evaluated the coagulation and fibrinolytic activities and the plasma total homocysteine levels of Korean BD patients in two cross-sectional studies. In the first study regarding coagulation and fibrinolytic activities, the levels of fibrinogen and von Willebrand factor (vWF) antigen were significantly higher in the BD patients than in the healthy controls (387.7+/-24.3 versus 240.6+/-8.8 mg/dl, p<0.001, and 131.9+/-8.8 versus 105.2+/-0.3%, p<0.01, respectively). The level of antithrombin III (AT III) was significantly lower in the BD patients (92.8+/-3.2 versus 106.3+/-2.6%, p<0.005). No differences were observed in the levels of plasminogen, protein C, or protein S activities. Activated protein C (APC) resistance was not observed in any BD patients. In the second study, the plasma total homocysteine levels of patients with a history of thrombosis (11.9+/-3.0 micromol/l) or disease activity (12.5+/-3.8 micromol/l) were found to be significantly higher than those of the controls (9.2+/-2.6 micromol/l, p<0.05, both). The plasma homocysteine concentrations in the thrombosis patients were positively correlated with plasma vWF levels; a relationship which suggests injury of the vascular endothelium (Spearman coefficient=0.857, p<0.01). Therefore, coagulation abnormality did not contribute to thrombotic complications, and higher levels of homocysteine may play a role in the hypercoagulablity of BD patients.This project has been supported by Grant No. 03-1997- 0101 from the Seoul National University Hospital Research Fund and in part by the Cancer Research Foundation of America (SWC) and by the U.S. Department of Agriculture, under Agreement No. 581950-9-001 (SWC)

Study on structure and electrochemical properties of carbon-coated monoclinic Li3V2(PO4)(3) using synchrotron based in situ X-ray diffraction and absorption

Monoclinic Li3V2(PO4)(3), is a highly promising cathode material for lithium-ion rechargeable batteries. It has good ion mobility and high lithium capacity due to its ability to reversibly extract all three lithium ions. Here, we present, a systematic investigation of phase transitions and volume variations that occur during lithium extraction from the carbon-coated monoclinic phase of Li3V2(PO4)(3) by synchrotron based in situ X-ray diffraction and X-ray absorption spectroscopy. This monoclinic Li3V2(PO4)(3) illustrates complex behavior of four successive two-phase transitions upon extraction of all three lithium ions between 3.0 and 4.8 V vs. Li/Li+. Each XRD pattern of the intermediate compositions can be fully indexed in the monoclinic space group P2(1)/n, with net volume reduction of 6.47%. In situ V K-edge XANES in combination with study of structural parameters is applied to find the vanadium valence state at plateau regions, which highlights the variations in electrochemical potential constraining to extraction of lithium ion from different crystal sites. (C) 2013 Elsevier B. V. All rights reserved.

Genomic Characterization of a Newly Isolated Rhizobacteria Sphingomonas panacis Reveals Plant Growth Promoting Effect to Rice

This article reports the full genome sequence of Sphingomonas panacis DCY99(T) (=KCTC 42347(T) =JCM30806(T)), which is a Gram-negative rod-shaped, non-spore forming, motile bacterium isolated from rusty ginseng root in South Korea. A draft genome of S. panacis DCY99T and a single circular plasmid were generated using the PacBio platform. Antagonistic activity experiment showed S. panacis DCY99T has the plant growth promoting effect. Thus, the genome sequence of S. panacis DCY99T may contribute to biotechnological application of the genus Sphingomonas in agriculture