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Inference of gene regulatory networks (GRNs) is one of the major challenges in molecular biology, understanding of which can reveal the regulatory relationship between transcription factors (TFs) and target genes. Although in the past decades many methods were developed to reconstruct GRNs, the accuracy of traditional methods can be further improved. In this work, we proposed a new method, GRN-LightGBM (Light Gradient Boosting Machine), to reconstruct GRNs. GRN-LightGBM is a non-linear. Ordinary differential equations (ODEs) model established by LightGBM, which is considering regulatory and target genes for a specific gene. Furthermore, GRN-LightGBM utilizes time-series data, steady-state data, and temporal time-delay data together to evaluate the features of regulatory genes important for target genes. GRN-LightGBM is evaluated both in the DREAM4 simulated datasets and Escherichia coli real datasets. The results show that the proposed method outperforms other popular inference algorithms in terms of area under the receiver operating characteristic curve (AUROC) and area under the precision-recall curve (AUPR).

Synthetic biology is a new interdisciplinary research area that uses engineering principles as guidelines for biological investigation. With research goals to modify existing biological systems or to create new ones, the recent applications of synthetic biology have expanded approaches and tools for conventional biological research. In this article, we first briefly review the development and progress of synthetic biology over the past decade. Although the contributions of synthetic biology to basic life science research, human health, environmental protection, and even economic growth have been widely observed, potential biosafety, biosecurity, and ethical risks related to synthetic biology have also emerged in recent years as technology becomes less expensive, more mature, and more accessible. We provide a brief assessment of the risks associated with the possible misuse or abuse of this technology in various areas and discuss concerns from three points of view: biosafety, biosecurity risks, and ethics. Finally, to address challenges arising from the rapid progress of synthetic biology, technical, ethical, and regulatory measures were developed or discussed in recent years, including laboratory level precautionary measures for biosafety and biosecurity related to synthetic biology (such as genetic safeguards and firewalls), ethical codes of conduct for biological scientists, and regulations or oversight rules from personal, national, and international perspectives. A brief summary of these efforts is provided. Keywords: Synthetic biology, Biosafety, Biosecurity, Ethics, Genetic firewall, Genetic safeguard, Code of conduct, Governance regulation

Dietary omega-3 long-chain polyunsaturated fatty acids docosahexaenoic acid (DHA, C22:6) can be synthesized in microalgae Crypthecodinium cohnii; however, its productivity is still low. Here, we established a new protocol termed as “chemical modulator based adaptive laboratory evolution” (CM-ALE) to enhance lipid and DHA productivity in C. cohnii. First, ACCase inhibitor sethoxydim based CM-ALE was applied to redirect carbon equivalents from starch to lipid. Second, CM-ALE using growth modulator sesamol as selection pressure was conducted to relive negative effects of sesamol on lipid biosynthesis in C. cohnii, which allows enhancement of biomass productivity by 30% without decreasing lipid content when sesamol was added. After two-step CM-ALE, the lipid and DHA productivity in C. cohnii was respectively doubled to a level of 0.046 g/L/h and 0.025 g/L/h in culture with addition of 1 mM sesamol, demonstrating that this two-step CM-ALE could be a valuable approach to maximize the properties of microalgae.

The heterotrophic microalga Crypthecodinium cohnii accumulates lipids with a high fraction of docosahexaenoic acid (DHA). However, lack of genomic information limits the understanding of its physiological metabolism for better DHA production. In this study, de novo assembly of the C. cohnii transcriptome from three growth stages (i.e., fast growth, fatty acid accumulation and DHA conversion stages) was conducted, leading to identification of a total of 82,106 unigenes with an N50 of 1822 bp, among which 64.7% were annotated based on sequence similarity to known genes in the database. In addition, pathway enrichment analysis showed that transcripts related to fatty acid biosynthesis, starch and sucrose metabolism as well as biosynthesis of unsaturated fatty acids were significantly up-regulated during late-stage fermentation. Interestingly, several polyketide synthases (PKSs) and multiple fatty acid desaturases potentially involved in DHA biosynthesis were identified in the C. cohnii transcriptome, most of which were significantly up-regulated during lipid and DHA accumulation, implying that C. cohnii might utilize a combination of PKS systems and desaturase steps for DHA biosynthesis. The results were further confirmed by qRT-PCR and GC–MS-based metabolomic analyses. Overall, integrative analysis of de novo transcriptomic and metabolomic data provided important functional genomic information necessary for not only a better understanding of C. cohnii growth and DHA biosynthesis but also future genetic engineering of industry-important C. cohnii.

Docosahexaenoic acid (DHA, C22: 6), which can be synthesized by the heterotrophic microalga Crypthecodinium cohnii, has received significant interest recently, due to its important roles in human health. However, the high production cost caused by low productivity and yield is still a major hurdle for industrial production of DHA using C. cohnii. The reduction of starch content has been found to be a promising mean to drive more carbon source to lipid biosynthesis in C. cohnii; however, it usually affects cell growth negatively, which limits its practical application. In this study, atmospheric and room temperature plasma mutagenesis associated with high-throughput screening based on iodine vapour was developed to identify a starch-deficient C. cohnii mutant 16D. The mutant 16D accumulated more biomass, lipid and DHA, with less starch and extracellular polysaccharide. The productivity and the yield of DHA were elevated 1.7 and 1.3 fold, reaching levels of 57.7 mg/L-h and 52.0 mg/g, respectively, in fed-batch fermentation, which are the highest reported so far for DHA production using C. cohnii. LC- and GC–MS based metabolomic analyses revealed multiple possible mechanisms relevant to increased growth and lipid content in mutant 16D, including strengthened Embden-Meyerhof, Krebs cycle and pentose phosphate pathways to provide more CoA, ATP and NADPH for supporting growth and lipid accumulation; and a significant increase in the intracellular abundance of tagatose, which was demonstrated to be involved in lipid content enhancement possibly by activating the triacylglycerol biosynthesis pathway in mutant 16D. The study presents a new strain improvement strategy for DHA-producing C. cohnii and new insights for switching metabolism from starch to growth and lipid in C. cohnii. In addition, the study also demonstrates the inductive effects of tagatose on lipogenesis in heterotrophic microalgae.

Metallic Pd and PdO electrodes were prepared by using Pd and PdCl2 slurries, respectively, and their electrochemical performance as a cathode for oxygen reduction reaction in intermediate temperature solid oxide fuel cells was evaluated by electrochemical impedance spectroscopy (EIS) and direct current polarization (DC polarization). The electrochemical activity of metallic Pd was much higher than that of PdO for the reaction of oxygen reduction; below the decomposition temperature, a thin layer of PdO formed on the surface of metallic Pd electrode, which increased its polarization resistance. The decomposition temperature of PdO decreased from 810 to 750 °C as oxygen partial pressure decreased from 20 to 5 kPa, and was further lowered under the influence of the applied current during DC polarization test. The charge transfer resistance of PdO increased by decreasing oxygen partial pressure, while that of metallic Pd was less sensitive to it.

The stability of La 0.6 Sr 0.4 Co 0.2 Fe 0.8 O 3− δ impregnated Y 2 O 3 stabilized ZrO 2 (LSCF–YSZ) cathodes was investigated under the condition of open circuit or current polarization at 750 °C in air. The electrochemical measurement and the microstructure characteristic show that the flattening of LSCF particles has great contribution to the increase of resistance of LSCF–YSZ cathodes after 500 h heat treatment at 750 °C. Microstructure coarsening and the damage of well-connected porous structure are main reasons of the performance degradation for LSCF–YSZ cathodes testing at 200 mA cm −2 and 750 °C in air. Higher current density of 500 mA cm −2 applying on cathodes accelerates degradation processes. X-ray photoelectron spectroscopy (XPS) shows that Sr concentration on the cathode surface decreases after current polarization, which plays a main role in performance activation processes observed at the beginning stage. The enhancement of cobalt activity in LSCF lattice by current polarization increases the conductivity and decreases the stability of LSCF–YSZ cathodes.

La 0.8 Sr 0.2 MnO 3 (LSM)-coated Ba 0.5 Sr 0.5 Co 0.8 Fe 0.2 O 3 (BSCF) composite powder (LSM-BSCF) was synthesized by a novel solid-solution method and investigated electrochemically as a cathode material for intermediate temperature solid oxide fuel cells. The cathode combined the merits of LSM and BSCF cathodes through an extended triple phase boundary and stabilized microstructure and demonstrated a polarization resistance between 0.61 and 0.09 Ω cm 2 at 600 to 750 °C. Compared with high performance cathodes prepared by solution impregnation, this LSM-BSCF cathode greatly improved performance stability.

The performance degradation of composite cathodes of La 0.6 Sr 0.4 Co 0.2 Fe 0.8 O 3− δ and Gd-doped ceria (LSCF–GDC), prepared by impregnating the porous GDC scaffold with a nitrate solution containing La, Sr, Co and Fe in desired composition, is investigated at 750 °C and open circuit in air for 500 h. The performance of the impregnated LSCF–GDC composite cathodes deteriorates after testing at 750 °C for 500 h; the electrode polarization resistance ( R p ) increases from 0.38 to 0.83 Ω cm 2 , and the electrode ohmic resistance ( R o ) increases from 1.79 to 2.14 Ω cm 2 . The grain growth and coarsening of impregnated LSCF nanoparticles are responsible for the performance degradation of the cathodes. XPS analysis shows the enrichment of cobalt on the surface of the infiltrated LSCF–GDC cathodes and such surface segregation could also contribute to the degradation of the electrocatalytic activity of the cathodes. Introducing MgO and LaNi 0.6 Fe 0.4 O 3 phases can effectively suppress the coarsening of LSCF nanoparticles and enhance the stability of the cathodes. However, the enhancing effect is related to the conductivity and electrocatalytic activity of the introduced phases.

LaCo0.6Ni0.4O3−δ (LCN64) was prepared through the polymeric steric entrapment precursor route with Polyvinyl alcohol (PVA) as the entrapment agent and was evaluated as a contact material between the metallic interconnect and the cathode in planar intermediate temperature solid oxide fuel cell stacks (IT-SOFC). The ratio of PVA to metal nitrates and the calcination temperature of the precursor were optimized for the process. The electrical conductivity and thermal expansion coefficient (TEC) of the synthesized LCN64 and its chemical compatibility with SUS 430 were also characterized. The results indicate that 1:4 is a proper ratio of PVA to metal nitrates for process control and safety management; and calcination of the precursor at temperatures above 650 °C leads to formation of single perovskite phase LCN64. The conductivity of fully sintered LCN64 is above 1150 S cm−1 in the temperature range between 100 °C and 800 °C, which is higher than those of conventional contact materials La1−xSrxMnO3 (LSM) and LaNiyFe1−yO3 (LNF). The average TEC is 17.22 × 10−6 K−1 at temperatures below 900 °C, which is higher than those of the metallic interconnect and cell components. Mn and Cr elements contained in SUS 430 migrated into the porous LCN64 layer at 800 °C without chemically forming resistive phases.

The contact resistance and chemical compatibility of LaCo 0.6 Ni 0.4 O 3−δ (LCN) coated Ni–Mo–Cr alloy are investigated at 750 °C in air for more than 530 h to simulate the contact situation of cathode/contact layer/interconnect in SOFC stacks. With La 0.72 Sr 0.18 MnO 3 (LSM) as the cathode, the area specific resistance (ASR) of LSM/LCN/Ni–Mo–Cr alloy assembly increases to a maximum of 240 mΩ cm 2 during the early stage of the test, and decreases after 55 h to a steady level of ∼220 mΩ cm 2 till the end of the test. The contribution of formed oxide scale on the alloy to the measured ASR is negligible, compared to that of big AgLaMo 2 O 8 particles sporadically distributed in LCN matrix. AgLaMo 2 O 8 is formed of evaporated Mo from the alloy, Ag from the testing lead and La from the LCN before the oxide scale on the alloy is well developed. This reaction is expected to cease once the oxide scale is fully established.

Solution impregnated La 0.8 Sr 0.2 Co 0.8 Ni 0.2 O 3 + Gd-doped CeO 2 (LSCN + GDC) cathodes for intermediate temperature solid oxide fuel cells (IT-SOFC) are prepared and their electrochemical properties are evaluated and compared with the conventional LSCN cathodes. The results indicate that the cathode performance can be enhanced by the presence of the nanosized microstructure produced with the solution impregnation method. It is determined that the amount of LSCN loading in the LSCN + GDC composite cathode needs to be higher than 35 wt% in order to achieve a performance superior to that of the conventional LSCN cathode. The optimum amount of LSCN loading is in the range of 45–55 wt% with an activation energy near 1.32 eV for oxygen reduction. At temperatures between 600 and 750 °C, the polarization resistance of the 55 wt% LSCN loaded LSCN + GDC cathode is in the range of 1.07 and 0.08 Ω cm 2 , which is only about one half of that for the conventional cathode.