Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences

Bacterial phosphorothioate (PT) DNA modifications are incorporated by Dnd proteins A-E and often function with DndF-H as a restriction-modification (R-M) system, as in Escherichia coli B7A. However, bacteria such as Vibrio cyclitrophicus FF75 lack dndF-H, which points to other PT functions. Here we report two novel, orthogonal technologies to map PTs across the genomes of B7A and FF75 with >90% agreement: single molecule, real-time sequencing and deep sequencing of iodine-induced cleavage at PT (ICDS). In B7A, we detect PT on both strands of G[subscript ps]AAC/G[subscript ps]TTC motifs, but with only 12% of 40,701 possible sites modified. In contrast, PT in FF75 occurs as a single-strand modification at C[subscript ps]CA, again with only 14% of 160,541 sites modified. Single-molecule analysis indicates that modification could be partial at any particular genomic site even with active restriction by DndF-H, with direct interaction of modification proteins with GAAC/GTTC sites demonstrated with oligonucleotides. These results point to highly unusual target selection by PT-modification proteins and rule out known R-M mechanisms.National Natural Science Foundation (China)Ministry of Science and Technology of the People's Republic of China (973 and 863 Programs)Shanghai Municipal Council of Science and Technology. Shanghai Pujiang ProgramNational Science Foundation (U.S.) (CHE-1019990)National Institute of Environmental Health Sciences (ES002109)Singapore. National Research Foundation (Singapore-MIT Alliance for Research and Technology

The Complexity Entropy Analysis of a Supply Chain System Considering Recovery Rate and Channel Service

In this paper, we study a dual-channel closed-loop supply chain in which a manufacturer considers the market waste products recovery and remanufacture, and a retailer considers provide services to customers. We build a Stackelberg game model and a centralized game model in a static and dynamic state, respectively, and analyze the two dynamic models by mathematical analysis and explore the stability and entropy of the two models using bifurcation, the basin of attraction, chaotic attractors, and so on. The influences of service level and profit distribution rate on the system’s profit are discussed. The theoretical results show that higher price adjustment speed will lead to the system lose stability with a larger entropy value. In the Stackelberg game model, the stability of the system increases as the service value and the recovery rate increases; in the centralized model, the stability of the system decreases with the increase of the service value and increases with the recovery rate increases. When the Stackelberg game model is in a stable state, the manufacturer’s profit increases first and then decreases, and the retailer’s profit first decreases and then increases as the service value of the retailer increases. The research will serve as good guidance for both the manufacturer and retailer in dual-channel closed-loop supply chains to improve decision making

Purification, characterization and antigenic species-specific reactivity of vitellogenin of rosy barb (Puntius conchonius Hamilton)

216-220Vitellogenin (Vg) was isolated using gel filtration and ion-exchange chromatography from plasma of rosy barb (Puntius conchonius) treated with estrogen (estradiol-17β). The purified Vg was stained positive for carbohydrate, lipid and phosphorus and was rich in Ala (10.58%), Asp (8.46%), Glu (10.30%), Leu (11.23%), Lys (7.22%) and Val (7.49%). It appeared as a single band of approximately 450 kDa in native PAGE and was reduced to a single band of approximately 167 kDa under SDS-PAGE, suggesting that it is probably composed of three identical polypeptide subunits. Double-immunodiffusion assay showed that the plasma from female rosy barb reacted with the mouse antisera against rosy barb Vg, forming a single immunoprecipitin line, while the plasma from male rosy barb or female zebrafish showed no such reactivity, confirming the existence of the sex- and species-specific reactivity for rosy barb Vg antisera

Elucidating the surface compositions of Pd@PtnL core–shell nanocrystals through catalytic reactions and spectroscopy probes

The catalytic behaviors or properties of bimetallic catalysts are highly dependent on the surface composition, but it has been a grand challenge to acquire such information. In this work, we employ Pd@Pt core-shell nanocrystals with an octahedral shape and tunable Pt shell thickness as a model system to elucidate their surface compositions using catalytic reactions based upon the selective hydrogenation of butadiene and acetylene. Our results indicate that the surface of the core-shell nanocrystals changed from Pt-rich to Pd-rich when they were subjected to calcination under oxygen, a critical step involved in the preparation of many industrial catalysts. The inside-out migration can be attributed to both atomic interdiffusion and the oxidation of Pd atoms during the calcination process. The changes in surface composition were further confirmed using infrared and X-ray photoelectron spectroscopy. This work offers insightful guidance for the development and optimization of bimetallic catalysts toward various reactions

Wnt10b Participates in Regulating Fatty Acid Synthesis in the Muscle of Zebrafish

There are 19 Wnt genes in mammals that belong to 12 subfamilies. Wnt signaling pathways participate in regulating numerous homeostatic and developmental processes in animals. However, the function of Wnt10b in fatty acid synthesis remains unclear in fish species. In the present study, we uncovered the role of the Wnt10b signaling pathway in the regulation of fatty acid synthesis in the muscle of zebrafish. The gene of Wnt10b was overexpressed in the muscle of zebrafish using pEGFP-N1-Wnt10b vector injection, which significantly decreased the expression of glycogen synthase kinase 3β (GSK-3β), but increased the expression of β-catenin, peroxisome proliferators-activated receptor γ (PPARγ), and CCAAT/enhancer binding protein α (C/EBPα). Moreover, the activity and mRNA expression of key lipogenic enzymes ATP-citrate lyase (ACL), acetyl-CoA carboxylase (ACC) and fatty acid synthetase (FAS), and the content of non-esterified fatty acids (NEFA), total cholesterol (TC), and triglyceride (TG) were also significantly decreased. Furthermore, interference of the Wnt10b gene significantly inhibited the expression of β-catenin, PPARγ, and C/EBPα, but significantly induced the expression of GSK-3β, FAS, ACC, and ACL. The content of NEFA, TC, and TG as well as the activity of FAS, ACC, and ACL significantly increased. Thus, our results showed that Wnt10b participates in regulating fatty acid synthesis via β-catenin, C/EBPα and PPARγ in the muscle of zebrafish

Improvement of the Combustion Completeness of Hydrogen Jet Flames within a Mesoscale Tube under Zero Gravity

Microjet hydrogen flames can be directly used as micro heat sources or can be applied in micro propulsion systems. In our previous study, under zero gravity and without an active air supply, the combustion completeness of hydrogen jet flames within a mesoscale tube with an inner diameter of 5 mm was very low. In this study, we were dedicated to improving the combustion efficiency by using a convergent nozzle (tilt angle was around 68°) instead of the previous straight one, and the exit diameter was 0.8 or 0.4 mm. The numerical results demonstrate that the maximum combustion efficiency in the case of d= 0.8 mm was only around 15%; however, the peak value for the case of d = 0.4 mm was around 36%. This happened because with d = 0.4 mm, the fuel jet velocity was around four times that of the d = 0.8 mm case. Hence, the negative pressure in the combustor of d = 0.4 mm decreased to a much lower level compared to that of d = 0.8 mm, which led to an enhancement of the air entrainment ratio. However, the highest combustion efficiency of d = 0.4 mm was still below 36%; therefore, a slightly larger tube or an even smaller nozzle exit diameter will be necessary for further improvements to the combustion efficiency

Numerical Study on Thermal-Hydraulic Performance of Printed Circuit Heat Exchangers during Natural Gas Trans-Critical Liquefaction

Printed Circuit Heat Exchangers (PCHEs) are considered an excellent alternative for the main cryogenic heat exchanger of Floating Liquefied Natural Gas (FLNG) facilities due to their compact structure and strong heat transfer performance. However, it is unclear how to configure the geometry of the PCHE channels to achieve its optimal performance in the trans-critical liquefaction process of natural gas (NG), which is critical for the main heat exchanger. In this paper, we numerically studied the thermal-hydraulic characteristics of PCHEs with different channel types under the specified condition. The results elucidate that all channels have an enhancement of heat transfer near the pseudo-critical point of NG. All the wavy channels could improve the heat transfer performance of PCHEs, where the trapezoidal channel achieves the largest promotion. Compared with the straight channel, the local heat transfer coefficient could be increased by up to 53% in the trapezoidal channel. Additionally, vortex appeared at the bends of the wavy channels, which greatly increase the local friction loss. Among several channels, the total pressure drop of zigzag, fillet and the sinusoidal channel was almost the same, while that of the trapezoidal channel was the largest. Furthermore, we compared the comprehensive performance of different types of channels and found that the benefit of heat transfer enhancement could not offset the penalty of flow deterioration. Our work provides important guidance for the design of PCHEs employed in FLNG