GFCNet: Utilizing graph feature collection networks for coronavirus knowledge graph embeddings.

In response to fighting COVID-19 pandemic, researchers in machine learning and artificial intelligence have constructed some medical knowledge graphs (KG) based on existing COVID-19 datasets, however, these KGs contain a considerable amount of semantic relations which are incomplete or missing. In this paper, we focus on the task of knowledge graph embedding (KGE), which serves an important solution to infer the missing relations. In the past, there have been a collection of knowledge graph embedding models with different scoring functions to learn entity and relation embeddings published. However, these models share the same problems of rarely taking important features of KG like attribute features, other than relation triples, into account, while dealing with the heterogeneous, complex and incomplete COVID-19 medical data. To address the above issue, we propose a graph feature collection network (GFCNet) for COVID-19 KGE task, which considers both neighbor and attribute features in KGs. The extensive experiments conducted on the COVID-19 drug KG dataset show promising results and prove the effectiveness and efficiency of our proposed model. In addition, we also explain the future directions of deepening the study on COVID-19 KGE task.

LbDSF, the Lysobacter brunescens Quorum-Sensing System Diffusible Signaling Factor, Regulates Anti- Xanthomonas XSAC Biosynthesis, Colony Morphology, and Surface Motility.

Lysobacter species are emerging as novel sources of antibiotics, but the regulation of these antibiotics has not been thoroughly elucidated to date. In this work, we identified a small diffusible signaling factor (DSF) molecule (LbDSF) that regulates the biosynthesis of a novel Xanthomonas-specific antibiotic compound (XSAC) in Lysobacter brunescens OH23. LbDSF was isolated from the culture broth of L. brunescens OH23, and the chemical structure of the molecule was determined by NMR and MS. The LbDSF compound induced GUS expression in a reporter strain of Xanthomonas campestris pv. campestris FE58, which contained the gus gene under the control of a DSF-inducible engXCA promoter. LbDSF production was found to be linked to the enoyl-CoA hydratase RpfF and dependent on the two-component regulatory system RpfC (hybrid sensor histidine kinase)/RpfG (response regulator), and LbDSF production was increased 6.72 times in the ΔrpfC compared to wild-type OH23. LbDSF-regulated XSAC production was dramatically decreased in ΔrpfF, ΔrpfC, and ΔrpfG. Additionally, a significant reduction in surface motility and a number of changes in colony morphology was observed in the ΔrpfF, ΔrpfC, and ΔrpfG compared to the wild-type OH23. The exogenous LbDSF significantly increased XSAC production in wild-type OH23 and recovered the XSAC biosynthetic ability in ΔrpfF. Taken together, these results showed that LbDSF is a fatty-acid-derived DSF that positively regulates XSAC biosynthesis, cell morphology, and surface motility. Moreover, the RpfC/RpfG quorum-sensing signal transduction pathway mediates XSAC biosynthesis. These findings may facilitate antibiotic production through genetic engineering in Lysobacter spp.

Development of a simple, low-cost and eurytopic medium based on Pleurotus eryngii for lactic acid bacteria.

Lactic acid bacteria (LAB) are a group of important beneficial microorganisms for human, but their growth is restricted to the habitats with rich nutrients. In order to develop a simple, low-cost and efficient medium based on the mushroom Pleurotus eryngii, this study evaluated the effects of different treatment methods for the mushroom, concentration of the mushroom, buffers, tween 80, MgSO4·7H2O, MnSO4·4H2O, CuSO4·5H2O, riboflavin and ascorbic acid on the growth of Lactococcus lactis subsp. lactis SLPE1-3. An optimized medium was developed, which was composed of the mushroom at 200 g/L, the buffer sodium acetate at 5 g/L, and riboflavin at 0.5 mg/L. The mushroom was ground, boiled and filtered for the filtrate in advance. In this optimized medium which was named as PSR medium, the population density of SLPE1-3 sharply reached 2.13 × 10(9) CFU/mL within 18 h of incubation, and still maintained 1.17 × 10(8) CFU/mL at 120 h. In addition, this study found that 6 kinds of LAB could grow almost well, and maintained high survival in PSR medium compared to M17 or MRS medium, including Lactococcus lactis subsp. lactis, Lactobacillus plantarum, Lactococcus lactis subsp. cremoris, Lactobacillus paracasei, Pediococcus pentosaceus and Lactobacillus rhamnosus. These results showed that PSR medium was a simple, low cost and eurytopic medium for the cultivation of LAB, and could replace MRS or M17 medium in the food industry, biomedicine and laboratory.