Special Issue on “Single-cell Omics Analysis”

We are very pleased to announce a special issue, to be published in the spring of 2020, on "Single-cell Omics Analysis" in the journal Genomics, Proteomics & Bioinformatics(GPB). The cell has been primarily studied as a part of its bulk population for decades until recent

The advances of traditional Chinese medicine in the treatment of liver diseases in 2019

Background:Currently,the treatment of liver diseases remains an unsolved problem due to its complicated etiology and pathogenesis.Traditional Chinese medicine(TCM)has been used for liver disease treatment for thousands of years.Disease treatment using TCM compounds conforms to the concept of“holism”,which coincides with the complicated pathogenic mechanisms of liver diseases.However,the mechanisms have not been clearly explained due to the complex components and multi-targets,which is a big obstacle TCM’s popularity and application.In recent years,studying the mechanisms and identifying the novel ingredients in herbal medicines are becoming a hot spot for many researchers.Therefore,we obtained literature in PubMed and summarized the progress of TCM’s active ingredients and formulas in treating various liver diseases in 2019.Based on the literature,flavonoids,polysaccharides,saponins,and alkaloids,as well as Chinese medicine formulas,such as Ba-Bao pill and Yin-Chen-Hao decoction,have attracted much attention.In addition,we also focused on the application of new omics analysis techniques,such as metabolomics,network pharmacology,and other omics analyses in the study of TCM formulas.

Brain organoids are new tool for drug screening of neurological diseases

At the level of in vitro drug screening,the development of a phenotypic analysis system with highcontent screening at the core provides a strong platform to support high-throughput drug screening.There are few systematic reports on brain organoids,as a new three-dimensional in vitro model,in terms of model stability,key phenotypic fingerprint,and drug screening schemes,and particula rly rega rding the development of screening strategies for massive numbers of traditional Chinese medicine monomers.This paper reviews the development of brain organoids and the advantages of brain organoids over induced neurons or cells in simulated diseases.The paper also highlights the prospects from model stability,induction criteria of brain organoids,and the screening schemes of brain organoids based on the characteristics of brain organoids and the application and development of a high-content screening system.

A new era in healthcare:The integration of artificial intelligence and microbial

The convergence of artificial intelligence(AI)and microbial therapeutics offers promising avenues for novel discoveries and therapeutic interventions.With the exponential growth of omics datasets and rapid advancements in AI technology,the next generation of AI is increasingly prevalent in microbiology research.In microbial research,AI is instrumental in the classification and functional annotation of microorganisms.Machine learning algorithms facilitate efficient and accurate categorization of microbial taxa,enabling the identification of functional traits and metabolic pathways within microbial communities.Additionally,AI-driven protein design strategies hold promise for engineering enzymes with enhanced catalytic activities and stabilities.By predicting protein structures,functions,and interactions,AI algorithms enable the rational design of proteins and enzymes tailored for specific applications.AI systems are already present in clinical microbiology laboratories in the form of expert rules used by some automated susceptibility testing and identification systems.In the future,microbiology technologists will rely more heavily on AI for initial screening,allowing them to focus on diagnostic challenges and complex technical interpretations.AI-driven approaches hold immense promise in advancing our understanding of microbial ecosystems,accelerating drug discovery processes,and fostering the development of groundbreaking therapeutic interventions.This review aims to summarize common algorithms in AI and their applications within microbiology and synthetic biology.We provide a comprehensive evaluation of AI’s utility in microbial research,discussing both its advantages and challenges.Finally,we explore future research directions and the bottlenecks faced by AI in the microbial field.

Genomic and transcriptional changes in response to pinene tolerance and overproduction in evolved Escherichia coli

α-Pinene is an important monoterpene,which is widely used as a flavoring agent and in fragrances,pharmaceuticals and biofuels.Although an evolved strain Escherichia coli YZFP,which had higher tolerance to pinene and titer,has been successfully used to produce high levels of pinene,the pinene titer is much lower than that of hemiterpene(isoprene)and sesquiterpenes(farnesene)to date.Moreover,the overall cellular physiological and metabolic changes caused by higher tolerance to pinene and overproduction of pinene remains unclear.To reveal the mechanism of Escherichia coli YZFP with the higher tolerance to pinene and titer,a comparative genomics and transcriptional level analyses combining with CRISPR activation(CRISPRa)and interference(CRISPRi)were carried out.The results show that the tolerance to pinene and the overproduction of pinene in E.coli may be associated with:1)the mutations of the DXP pathway genes,the rpoA and some membrane protein genes,and their upregulations of transcription levels;and 2)the mutations of some genes and their downregulation of transcriptional levels.These comparative omics analyses provided some genetic modification strategies to further improve pinene production.Overexpression of the mutated cbpA,tabA,pitA,rpoA,sufBCDS,mutS,ispH,oppF,dusB,dnaK,dxs,dxr and flgFGH genes further improved pinene production.This study also demonstrated that combining comparative omics analysis with CRISPRa and CRISPRi is an efficient technology to quickly find a new metabolic engineering strategy.