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A knowledge integration strategy for the selection of a robust multi-stress biomarkers panel for Bacillus subtilis

Synthetic and Systems Biotechnology 2023年第1期8卷 97-106页

作者： Yiming Huang Nishant Sinha Anil Wipat Jaume Bacardit Interdisciplinary Computing and Complex BioSystems(ICOS)Group School of ComputingNewcastle UniversityUK Department of Neurology Perelman School of MedicineUniversity of PennsylvaniaUSA

One challenge in the engineering of biological systems is to be able to recognise the cellular stress states of bacterial hosts,as these stress states can lead to suboptimal growth and lower yields of target *** enable the design of genetic circuits for reporting or mitigating the stress states,it is important to identify a relatively reduced set of gene biomarkers that can reliably indicate relevant cellular growth states in *** advances in high-throughput omics technologies have enhanced the identification of molecular biomarkers specific states in bacteria,motivating computational methods that can identify robust biomarkers for experimental characterisation and *** on identifying gene expression biomarkers to sense various stress states in Bacillus subtilis,this study aimed to design a knowledge integration strategy for the selection of a robust biomarker panel that generalises on external datasets and *** developed a recommendation system that ranks the candidate biomarker panels based on complementary information from machine learning model,gene regulatory network and co-expression *** identified a recommended biomarker panel showing high stress sensing power for a variety of conditions both in the dataset used for biomarker identification(mean f1-score achieved at 0.99),as well as in a range of independent datasets(mean f1-score achieved at 0.98).We discovered a significant correlation between stress sensing power and evaluation metrics such as the number of associated regulators in a *** gene regulatory network(GRN)and the number of associated modules in a *** co-expression network(CEN).GRNs and CENs provide information relevant to the diversity of biological processes encoded by biomarker *** demonstrate that quantitatively relating meaningful evaluation metrics with stress sensing power has the potential for recognising biomarkers that show better sensitivity and robustness to an exte

关键词： transcriptomics analysis System biology Biomarker discovery Machine learning

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Transcriptome analysis of molecular mechanisms underlying facial nerve injury repair in rats

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Neural Regeneration Research 2021年第11期16卷 2316-2323页

作者： Qian-Qian Cao Shuo Li Yan Lu Di Wu Wei Feng Yong Shi Lu-Ping Zhang Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education Co-innovation Center of NeuroregenerationNantong UniversityNantongJiangsu ProvinceChina Department of Otolaryngology Affiliated Hospital of Nantong UniversityNantongJiangsu ProvinceChina Department of Otolaryngology Head and Neck SurgeryEyeEarNose and Throat HospitalFudan UniversityShanghaiChina

Although the transcriptional alterations inside the facial nucleus after facial nerve injury have been well studied,the gene expression changes in the facial nerve trunk after injury are still *** this study,we established an adult rat model of facial nerve crush injury by compressing the right lateral extracranial nerve *** sequencing,differential gene expression analysis,and cluster analysis of the injured facial nerve trunk were performed,and 39 intersecting genes with significant variance in expression were *** Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway analyses of the 39 intersecting genes revealed that these genes are mostly involved in leukocyte cell-cell adhesion and phagocytosis and have essential roles in regulating nerve *** real-time polymerase chain reaction assays were used to validate the expression of pivotal ***,nine pivotal genes that contribute to facial nerve recovery were identified,including Arhgap30,Akr1b8,C5ar1,Csf2ra,Dock2,Hcls1,Inpp5d,Sla,and *** Schwann cells were isolated from the sciatic nerve of neonatal *** knocking down Akr1b8 in Schwann cells with an Akr1b8-specific small interfering RNA plasmid,expression levels of monocyte chemoattractant protein-1 and interleukin-6 were decreased,while cell proliferation and migration were not obviously *** findings suggest that Akr1b8 likely regulates the interaction between Schwann cells and macrophages through regulation of cytokine expression to promote facial nerve *** study is the first to reveal a transcriptome change in the facial nerve trunk after facial nerve injury,thereby revealing the potential mechanism underlying repair of facial nerve *** study was approved by the Animal Ethics Committee of Nantong University,China in 2018(approval No.S20180923-007).

关键词： Akr1b8 cell proliferation facial nerve injury Gene-Act Networks inflammatory response RNA-Seq Schwann cells transcriptomics analysis

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Underlying mechanisms of the antagonistic effects of Bifidobacterium adolescentis CCFM1108 on Penicillium expansum:Based on comparative transcriptome analysis

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Food Bioscience 2022年第3期47卷 954-963页

作者： Leilei Yu Nanzhen Qiao Chaozhi Wei Qianjue Hu Qixiao Zhai Bowen Yan Jianxin Zhao Hao Zhang Wei Chen Fengwei Tian State Key Laboratory of Food Science and Technology Jiangnan UniversityWuxi214122China School of Food Science and Technology Jiangnan UniversityWuxi214122China National Engineering Research Center for Functional Food Jiangnan UniversityWuxi214122China Department of Agricultural Food and Nutritional ScienceUniversity of AlbertaEdmontonAB T6G 2R3Canada

Penicillium expansum is the primary postharvest pathogen that attacks fruits and vegetables and threatens human *** adolescentis CCFM1108 has been previously demonstrated to inhibit the growth of Penicillium expansum and patulin production;however,its modes of action remain ***-seq analysis was used to investigate the underlying antifungal mechanism of metabolites produced by B .adolescents *** expression of genes in the control group and three treatment groups (1/2 MIC CFS,1/4 MIC CFS,and acid treatment groups) was determined and further compared using GO and KEGG *** inhibitory metabolites were found to participate in the dysfunction of the mitochondrial membrane,affecting energy metabolism,reactive oxidative species production,and patulin *** with the mixture of multiple metabolites of Bifidobacterium ,the acid mixture affected gene expression in a more significant manner by inhibiting all critical genes included in the patulin biosynthetic *** changes in the patulin biosynthetic were verified by qRT-PCR in the presence of ***,the present study provides a clear perspective on the antifungal mechanism of metabolites produced by a *** strain through transcriptome analysis and suggests that acid mixtures could be potential candidates for the postharvest control of P .expansum .

关键词： B.adolescentis P.expansum transcriptomics analysis Antifungal compounds Patulin biosynthesis

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