This aim of the study was to isolate and screen potential probiotics from Dioscorea villosa leaves. The potential isolate Y4 was obtained from the Dioscorea villosa leaves, and its ability to grow in a medium containing high NaCl concentrations (2-10%) indicated its negative hemolytic activity. Furthermore, Y4 demonstrated inhibitory activity against human pathogens, such as Klebsiella pneumonia, Staphylococcus aureus, Citrobacter koseri, and Vibrio cholerae, as well as towards a plant pathogen isolate OR-2 (obtained from Citrus sinensis). Some biologically important functional groups of Y4 metabolites, such as sulfoxide; aliphatic ether; 1, 2, 3-trisubstituted, tertiary alcohol: vinyl ether; aromatic amine; carboxylic acid; nitro compound; alkene mono-substituted; and alcohol, were identified through FTIR analysis. The 16S rRNA sequencing and subsequent phylogenetic tree analysis indicated that Y4 and OR-2 are the closest neighbors to Kocuria flava (GenBank accession no. MT773277) and Pantoea dispersa (GenBank accession no. MT766308), respectively. The potential isolate Y4 was found to exhibit adhesion, auto-aggregation, co-aggregation, and weak biofilm activity. It also exhibited a high level of antimicrobial activity and antibiotic susceptibility. The safety of K. flava Y4 isolate, which is proposed to be a probiotic, was evaluated through acute oral toxicity test and biogenic amine production test. Moreover, the preservation potential of isolate Y4 was assessed through application on fruits under different temperatures. Thus, our results confirmed that Kocuria flava Y4 is a prospective probiotic and could also be used for the preservation of fruits.

20 Sep 2022·Briefings in Bioinformatics

ComABAN: refining molecular representation with the graph attention mechanism to accelerate drug discovery

Article

Author: Liu, Yao ; Yan, Huihui ; Sheng, Rong ; Xie, Yuanyuan ; Yuan, Leer

AbstractAn unsolved challenge in developing molecular representation is determining an optimal method to characterize the molecular structure. Comprehension of intramolecular interactions is paramount toward achieving this goal. In this study, ComABAN, a new graph-attention-based approach, is proposed to improve the accuracy of molecular representation by simultaneously considering atom–atom, bond–bond and atom-bond interactions. In addition, we benchmark models extensively on 8 public and 680 proprietary industrial datasets spanning a wide variety of chemical end points. The results show that ComABAN has higher prediction accuracy compared with the classical machine learning method and the deep learning-based methods. Furthermore, the trained neural network was used to predict a library of 1.5 million molecules and picked out compounds with a classification result of grade I. Subsequently, these predicted molecules were scored and ranked using cascade docking, molecular dynamics simulations to generate five potential candidates. All five molecules showed high similarity to nanomolar bioactive inhibitors suppressing the expression of HIF-1α, and we synthesized three compounds (Y-1, Y-3, Y-4) and tested their inhibitory ability in vitro. Our results indicate that ComABAN is an effective tool for accelerating drug discovery.

08 Apr 2022·Huan jing ke xue= Huanjing kexue

[Effects of Burkholderia sp. Y4 on Cadmium Damage and Uptake in Rice Seedlings].

Article

Author: Pang, Jie ; Liu, Ya-Ping ; Liu, Zhong-Qi ; Wang, Chang-Rong ; Zhang, Ya-Hui ; Huang, Yong-Chun ; Liu, Yue-Min ; Zhang, Chang-Bo

In order to investigate the effects of Burkholderia sp. Y4 on rice seedlings under cadmium (Cd) stress, seed germination and vermiculite culture experiments were conducted using low Cd-accumulation xiangzaoxian 24 (X24) and high Cd-accumulation Tyou 705 (T705) varieties. The effects of Burkholderia sp. Y4 on rice growth, oxidative damage caused by Cd, and Cd accumulation were studied. Additionally, the Cd²⁺ flux rates in the elongation zone of rice roots under Burkholderia sp. Y4 application were detected using non-invasive micro-test technology. Burkholderia sp. Y4 alleviated the inhibition effect of Cd on rice seed germination by 13.8%. After inoculation with Burkholderia sp. Y4 for 7 d, the length of rice roots and buds increased by 83.3% and 12.2%, and their dry weight increased by 56.8% and 12.5%, respectively; those in the 10 d Y4 inoculation group increased by 28.6% and 20.0% in length and by 113.2% and 46.0% in dry weight, respectively. Burkholderia sp. Y4 inoculation also alleviated rice oxidative stress damage caused by Cd. The application of strain Y4 significantly reduced the content of the oxidative damage product malondialdehyde (MDA) in the shoots and roots of rice seedlings by 21.5% and 16.9%, respectively. Under Burkholderia sp. Y4 inoculation, the significant changes in antioxidant enzyme SOD and CAT activities caused by Cd stress disappeared in rice roots; those in shoots also decreased from 176.9% and 74.8% to 53.3% and 21.5%, respectively. Conversely, Burkholderia sp. Y4 inhibited Cd uptake by rice seedlings with different genotypes, including the low Cd-accumulation variety X24 and high Cd-accumulation variety T705. The root application of strain Y4 significantly reduced Cd accumulation in the shoots and roots of rice seedlings by 79.2% and 62.7% in T705 and by 57.3% and 24.1% in X24, respectively. The Cd²⁺ flux rate of high Cd-accumulation variety T705 was significantly higher than that of low Cd-accumulation variety X24. Under Burkholderia sp. Y4 inoculation, the yellow membrane was formed on the root surface of rice seedlings, and the Cd²⁺ flux rate in the elongation zone of T705 and X24 roots decreased by 36.0% and 35.0% in 3-day-old seedlings, as well as by 44.6% and 24.9% in 10-day-old seedlings, respectively. In conclusion, Burkholderia sp. Y4 inoculation inhibited the toxic effects of Cd on rice seedling growth through alleviating oxidative stress and damage caused by Cd. Furthermore, the root application of Burkholderia sp. Y4 effectively decreased the Cd²⁺ flux rate in the elongation zone of roots to inhibit the Cd uptake and accumulation in roots and shoots of rice seedlings. This study provides theoretical basis and data support for the application of Burkholderia sp. Y4 as a Cd-reducing and growth-promoting agent for rice in contaminated farmland.

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Indication	Highest Phase	Country/Location	Organization	Date
Peripheral neuralgia	IND Approval	CN	Nanjing Ningdan New Drug Technology Co., Ltd.	18 Jan 2024
Neuralgia	IND Approval	US	Nanjing Ningdan New Drug Technology Co., Ltd.	26 Dec 2023

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