Genome Writing:Current Progress and Related Applications

The ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic writing technologies are required to build such an artificial genome. Recently, the partially-completed synthetic yeast genome project represents a milestone in this field. In this mini review, we briefly introduce the techniques for de novo genome synthesis and genome editing. Furthermore, we summarize recent research progresses and highlight several applications in the synthetic genome field. Finally, we discuss current challenges and future prospects. Keywords: Synthetic biology, Genome writing, Genome editing, Bioethics, Biosafet

The anti-cholestatic effects of Coptis chinensis Franch. alone and combined with Tetradium ruticarpum (A. Jussieu) T. G. Hartley: dual effects on fecal metabolism and microbial diversity

Introduction: Drug dosages and combinations are the main factors that affect the efficacy of pleiotropic traditional Chinese medicine (TCM). Coptis chinensis Franch. (CF) is a representative TCM with multiple effects and is often combined with Tetradium ruticarpum (A. Jussieu) T. G. Hartley (TR) to treat cholestasis. The present study assessed the influence of CF dose and its combination with TR on the efficacy of CF in cholestasis treatment, including their effects on fecal metabolism and fecal microorganisms.Methods: Rats with α-naphthylisothiocyanate (ANIT, 50 mg/kg)-induced cholestasis were administered low (0.3 g/kg) and high (0.6 g/kg) doses of CF, as well as CF combined with TR at doses of 0.6 g/kg and 0.9 g/kg, respectively. The anti-cholestatic effects of these treatments were assessed by determining their anti-inflammatory, hypolipidemic, and anti-oxidative stress properties. Additionally, fecal metabolomics and fecal microorganisms were analyzed.Results: Low dose CF had a more potent hypolipidemic effect than high dose CF, whereas high dose CF had more potent anti-inflammatory and anti-oxidative stress effects. Combination with TR enhanced the hypolipidemic effect, but antagonized the anti-inflammatory effect, of CF. Analyses of fecal metabolomics and fecal microorganisms showed differences in the regulation of lipid- and amino acid metabolism-related pathways, including pathways of linoleic acid, tyrosine, and arachidonic acid metabolism, and amino acid biosynthesis between different doses of CF as well as between different doses of CF in combination with TR. These differences may contribute to differences in the anti-cholestatic effects of these preparations.Conclusion: CF dose influences its anti-cholestatic efficacy. The combination with TR had synergistic or antagonistic effects on the properties of CF, perhaps by altering fecal metabolism and fecal microbial homeostasis

Histone demethylase JMJD6 regulates cellular migration and proliferation in adipose-derived mesenchymal stem cells

Abstract Background Adipose-derived mesenchymal stem cells (ADSCs) have been extensively explored as a promising therapeutic agent due to their differentiation, proliferation and migration abilities. The epigenetic mechanisms that regulate the fate of mesenchymal stem cells (MSCs) have been described in detail. However, the epigenetic modulation of ADSCs proliferation and migration is poorly understood. Methods The present study examined histone demethylases roles and expression by RT-PCR, as well as through siRNA screening and ChIP-qPCR assay. Cellular proliferation and migration assays were employed in shRNA-mediated JMJD6 knockdown and control ADSCs. PDE1C inhibition studies were conducted to confirm its role in JMJD6-mediated epigenetic regulation of ADSCs. Results The data demonstrate that the histone demethylase JMJD6 plays a critical role in regulating the proliferation and migration of ADSCs by removing H4R3me2a at the promoter regions of PDEC1 and suppressing PDEC1 expression. Importantly, the depletion of JMJD6 in ADSCs significantly increased cellular proliferation and motility, which was associated with increases in PDE1C expression and decreases in the levels of both cAMP and cGMP. The increase in proliferation and migration was reversed by treatment with a PDE1C inhibitor, suggesting that JMJD6 attenuates the proliferation and migration of ADSCs as an epigenetic regulator and PDE1C partially contributes to the JMJD6-mediated regulation. Conclusions Taken together, our results indicate for the first time that JMJD6 plays an important role in the regulation of ADSCs proliferation and migration through the modulation of PDE1C expression

SuperCall: A Secure Interface For Isolated Execution Environment to Dynamically Use External Services

Recent years have seen many virtualization-based Isolated Execution Environments (IEE) proposed in the literature to protect a Piece of Application Logic (PAL) against attacks from an untrusted guest kernel. A prerequisite of these IEE system is that the PAL is small and self-contained. Therefore, a PAL is deprived of channels to interact with the external execution environment including the kernel and application libraries. As a result, the PAL can only perform limited tasks such as memory-resident computation with inflexible utilization of system resources. To protect more sophisticated tasks, the application developer has to segment it into numerous PALs satisfying the IEE prerequisite, which inevitably lead to development inefficiency and more erroneous code. In this paper, we propose SuperCall, a new function call interface for a PAL to safely and efficiently call external untrusted code in both the kernel and user spaces. It not only allows flexible interactions between a PAL and untrusted environments, but also improved the utilization of resources, without compromising the security of the PAL. We have implemented SuperCall on top of a tiny hypervisor. To demonstrate and evaluate SuperCall, we use it to build a PAL as part of a password checking program. The experiment results show that SuperCall improves the development efficiency and incurs insignificant performance overhead. ? Institute for Computer Sciences, Social Informatics and Telecommunications Engineering 2015.EI193-21116

Application of combined model of stepwise regression analysis and artificial neural network in data calibration of miniature air quality detector

Abstract In this paper, six types of air pollutant concentrations are taken as the research object, and the data monitored by the micro air quality detector are calibrated by the national control point measurement data. We use correlation analysis to find out the main factors affecting air quality, and then build a stepwise regression model for six types of pollutants based on 8 months of data. Taking the stepwise regression fitting value and the data monitored by the miniature air quality detector as input variables, combined with the multilayer perceptron neural network, the SRA-MLP model was obtained to correct the pollutant data. We compared the stepwise regression model, the standard multilayer perceptron neural network and the SRA-MLP model by three indicators. Whether it is root mean square error, average absolute error or average relative error, SRA-MLP model is the best model. Using the SRA-MLP model to correct the data can increase the accuracy of the self-built point data by 42.5% to 86.5%. The SRA-MLP model has excellent prediction effects on both the training set and the test set, indicating that it has good generalization ability. This model plays a positive role in scientific arrangement and promotion of miniature air quality detectors. It can be applied not only to air quality monitoring, but also to the monitoring of other environmental indicators

SuperCall: A Secure Interface For Isolated Execution Environment to Dynamically Use External Services

Recent years have seen many virtualization-based Isolated Execution Environments (IEE) proposed in the literature to protect a Piece of Application Logic (PAL) against attacks from an untrusted guest kernel. A prerequisite of these IEE system is that the PAL is small and self-contained. Therefore, a PAL is deprived of channels to interact with the external execution environment including the kernel and application libraries. As a result, the PAL can only perform limited tasks such as memory-resident computation with inflexible utilization of system resources. To protect more sophisticated tasks, the application developer has to segment it into numerous PALs satisfying the IEE prerequisite, which inevitably lead to development inefficiency and more erroneous code. In this paper, we propose SuperCall, a new function call interface for a PAL to safely and efficiently call external untrusted code in both the kernel and user spaces. It not only allows flexible interactions between a PAL and untrusted environments, but also improved the utilization of resources, without compromising the security of the PAL. We have implemented SuperCall on top of a tiny hypervisor. To demonstrate and evaluate SuperCall, we use it to build a PAL as part of a password checking program. The experiment results show that SuperCall improves the development efficiency and incurs insignificant performance overhead. ? Institute for Computer Sciences, Social Informatics and Telecommunications Engineering 2015.EI193-21116

River blockage and impulse wave evolution of the Baige landslide in October 2018: insights from coupled DEM-CFD analyses

On 11 October 2018, the Baige landslide in Southwest China blocked the Jinsha River and induced waves amplifying the landslide-affected area significantly. Devastating flood damage was caused by the consequent dam breach. Such a complex sequence can lead to catastrophic consequences but has rarely been fully reproduced. This paper investigates the landslide-river interaction of the first Baige landslide based on coupled discrete element method (DEM) and computational fluid dynamics (CFD) analyses. To this end, the volume of fluid (VOF) and virtual sphere model are adopted to realise impacted river tracing and accurate terrain modelling. The damming process and impulse wave evolution of the first event are well represented. In addition, the simulated cumulative landslide spreading path, deposit geometry, maximum wave elevation and cumulative wave erosion area satisfactorily match the survey results. Our findings further indicate that the movement path and deposit morphology of the Baige landslide are mainly affected by local terrain, while the propagation of impulse waves is driven by the sliding mass and modulated by the riverbank and hydrodynamic conditions. In particular, we discussed the evolution patterns of impulse waves caused by river damming landslides, encompassing run-up on the opposite bank and quasi-3D propagation along the river direction. This research provides a valuable guide for the practical simulation of river blockage and impulse wave evolution and supports the mitigation of landslide disasters in mountainous areas.This research was supported by the National Natural Science Foundation of China (52079020, 51579032), the LiaoNing Revitalization Talents Program (XLYC2002036) and the China Scholarship Council (CSC) (File No. 202006060115)

Comprehensive Detection of Particle Radiation Effects on the Orbital Platform of the Upper Stage of the Chinese CZ-4C Carrier Rocket

Based on the characteristics of space particle radiation in the Sun-synchronous orbit (SSO), a space particle radiation effect comprehensive measuring instrument (SPRECMI) was installed on the orbital platform of the upper stage of the Chinese CZ-4C carrier rocket, which can acquire the high-energy proton energy spectra, linear energy transfer (LET) spectra of particles, and radiation dose rate. The particle radiation detection data were obtained at 1000 km altitude for the first time, which can be used mainly for scientific research of the space environment, in-orbit fault analysis, and the operational control management of spacecraft, and can also serve as reference data for component validation tests. After SPRECMI’s development, accelerator calibration and simulations were conducted, and the results demonstrated that all the measured indicators, including the high-energy proton spectra (energy range: 21.8–275.0 MeV, precision: 6 rad, sensitivity: 6.2 µrad/h), and the LET spectra (range: 0.001–37.20 MeV/(mg/cm2), >37.2 MeV/(mg/cm2)), met the relevant requirements. Furthermore, the in-orbit flight test revealed that the detection results of the load components were consistent with the physical characteristics of the particle radiation environment of the spacecraft’s orbit

Intake of Vitamin B12 and Folate and Biomarkers of Nutrient Status of Women within Two Years Postpartum

Background: Little is known about variation in vitamin B12 and folate status among Chinese women 2 years postpartum. This study assessed intake of vitamin B12 and folate and biomarkers of nutrient status among Chinese women postpartum. Methods: Demographic information, multi-/single-nutrient supplementation, dietary data, serum vitamin B12 and serum folate were assessed in 982 women within 2 years postpartum, using ten investigation sites in Zhejiang Province from the National Nutritional Study 2016–2017, which is a nationally representative cross-sectional study, to form a representative provincial sample of Zhejiang Province. The dietary diversity score (DDS) was used for assessing the dietary pattern. Results: Vitamin B12 increased slightly at the early stage of postpartum and then dropped over time. Serum folate level elevated with postpartum time. The median serum vitamin B12 concentration was 494.59 (373.21–650.20) pg/mL, and folate was 7.58 (5.02–10.34) ng/mL. Correspondingly, vitamin B12 levels suggesting marginal deficiency (200–300 pg/mL) and deficiency (<200 pg/mL) resulted as 9.27% and 3.26%, respectively, and folate level suggesting deficiency (<3 ng/mL) was 9.16%. Multi-/single-nutrient supplementation during pregnancy was associated with log-transformed serum vitamin B12 and folate level after adjusting for potential confounders (vitamin B12: ß (SE) = 0.124 (0.028), p < 0.001; folate: 0.128 (0.035), <0.001). Additionally, postpartum nutrient supplementation was associated with log-transformed serum folate level, especially for lactating women (ß (SE) = 0.204 (0.062), p = 0.001). Increased DDS was significantly associated with elevated serum vitamin B12 and folate levels (vitamin B12: ß (SE) = 0.028 (0.011), p = 0.011; folate: 0.030 (0.014), 0.031). In addition, age and educational level were influencing factors for serum vitamin B12 and folate concentrations among postpartum women. Conclusion: Serum vitamin B12 level decreased and folate level increased with postpartum age among Chinese women. Nutrient supplementation during pregnancy was related to elevated serum vitamin B12 and folate concentrations. Postpartum nutrient supplementation was associated with the increased serum folate level of lactating women. Dietary diversity was related to increased serum vitamin B12 and folate levels, especially among postpartum women with younger age and lower educational level