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From Mutation Signature to Molecular Mechanismin the RNA World: A Case of SARS-CoV-2

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Genomics, Proteomics & Bioinformatics 2020年第6期18卷 627-639页

作者： Jun Yu China National Center for Bioinformation Beijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100190China

As a positive-sense single-strand RNA virus,coronavirus(CoV)possesses some of the largest genomes among RNA viruses,∼30 Kb in size and encodes more than two-dozen proteins that ensure a long-lasting parasitic cellular life leveraging on both informational inheritability and operational integrity by constantly changing the underlying molecular constituents toward harmony with those of the hosts whose genomes harbor over 20,000 genes and 2–3 Gb in sizes.We,taking the advantage of the unprecedented accumulation of genomic sequences,interrogate mutation spectra of SARS-CoV-2 as a whole or of the major clades in details using comprehensive genomic tools and structure chemistry principles.

关键词： details harmony sizes

Probiotics intervention in colorectal cancer:From traditional approaches to novel strategies

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Chinese Medical Journal 2024年第1期137卷 8-20页

作者： Suki Ha Xiang Zhang Jun Yu Institute of Digestive Disease and Department of Medicine and Therapeutics State Key Laboratory of Digestive DiseaseLi Ka Shing Institute of Health SciencesThe Chinese University of Hong KongHong Kong SARChina

The intestine harbors a large population of microorganisms that interact with epithelial cells to maintain host healthy physiological status.These intestinal microbiota engage in the fermentation of non-digestible nutrients and produce beneficial metabolites to regulate host homeostasis,metabolism,and immune response.The disruption of microbiota,known as dysbiosis,has been implicated in many intestinal diseases,including colorectal cancer(CRC).As the third most common cancer and the second leading cause of cancer-related death worldwide,CRC poses a significant health burden.There is an urgent need for novel interventions to reduce CRC incidence and improve clinical outcomes.Modulating the intestinal microbiota has emerged as a promising approach for CRC prevention and treatment.Current research efforts in CRC probiotics primarily focus on reducing the incidence of CRC,alleviating treatment-related side effects,and potentiating the efficacy of anticancer therapy,which is the key to successful translation to clinical practice.This paper aims to review the traditional probiotics and new interventions,such as next-generation probiotics and postbiotics,in the context of CRC.The underlying mechanisms of probiotic anti-cancer effects are also discussed,including the restoration of microbial composition,reinforcement of gut barrier integrity,induction of cancer cell apoptosis,inactivation of carcinogens,and modulation of host immune response.This paper further evaluates the novel strategy of probiotics as an adjuvant therapy in boosting the efficacy of chemotherapy and immunotherapy.Despite all the promising findings presented in studies,the evaluation of potential risks,optimization of delivery methods,and consideration of intra-patient variability of gut microbial baseline must be thoroughly interpreted before bench-to-bedside translation.

关键词： colorectal cancer probiotics gut microbiota dysbiosis adjuvant therapy immune modulation gut barrrier

MHC class I-LILRB3 delivers a punch to eliminate precancerous cells

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Cellular & Molecular Immunology 2022年第6期19卷 655-656页

作者： Chi Chun Wong Jun Yu Institute of Digestive Disease Department of Medicine and TherapeuticsState Key Laboratory of Digestive DiseaseLi Ka Shing Institute of Health SciencesThe Chinese University of Hong KongHong Kong SARChina

In the study by Ayukawa et al.[1],the authors presented an innate defense mechanism whereby normal epithelial cells actively remove precancerous cells from the epithelium via mechanical extrusion(Fig.1).

关键词： precancerous epithelium

Uncovering novel human gut virome using ultra-deep metagenomic sequencing

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Chinese Medical Journal 2022年第20期135卷 2395-2397页

作者： Harry Cheuk Hay Lau Jun Yu Institute of Digestive Disease and Department of Medicine and Therapeutics State Key Laboratory of Digestive DiseaseLi Ka Shing Institute of Health Sciencesthe Chinese University of Hong KongHong Kong SARChina

Human gastrointestinal tract harbors trillions of commensal microbes including bacteria,viruses,and fungi to form an ecological community,commonly known as the gut microbiome.Being the second most dominant taxonomic kingdom in the gut(5.8%of total microbiome DNA),enteric viruses are increasingly acknowledged for their roles in shaping the overall composition of the gut microbiome and maintaining human health.[1,2]Recent advancements in metagenomic sequencing have brought breakthrough in deciphering the features and functions of the gut virome.

关键词： breakthrough harbor gut

A Scientist Guerilla Fighter in the Frontiers of Bioinformatics--In Memory of Bailin Hao

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Genomics, Proteomics & Bioinformatics 2018年第5期16卷 307-309页

作者： Jun Yu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

The well-known physicist and bioinformaticist, Professor,Academician of Chinese Academy of Sciences (the Academy),and the former director of Institute of Theoretical Physics (the Institute; 1990–1994), Mr. Bailin Hao, passed away early this year (March 7, 2018). In the cover of this issue of Genomics,Proteomics&Bioinformatics (GPB), the Editorial Board has decided to publish his art-processed portrait in memory of

关键词： A Scientist Guerilla Fighter in the Frontiers of Bioinformatics

Evolution of copper species during heat treatment and its effect on CO oxidation reaction on CuCeZrO_(y) catalyst synthesized by a facile solvent-free route

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Journal of Rare Earths 2024年第4期42卷 660-667页

作者： Guangying Fu Dongsen Mao Jun Yu Qiangsheng Guo School of Chemical and Environmental Engineering Shanghai Institute of TechnologyShanghai21418 China The ZeoMat Group Qingdao Institute of Bioenergy and Bioprocess TechnologyCASQingdao26611China

Several ternary oxides CuCeZrO_(y)(CCZ)were synthesized by a facile grinding method followed by calcination at high temperatures,and used as catalysts for CO oxidation at low temperatures.The influences of calcination temperature(400-600℃)on the physicochemical properties of the assynthesized ternary oxides were investigated by thermogravimetric analysis/differential scanning calorimetry(TGA/DSC),X-ray diffraction(XRD),transmission electron microscopy(TEM),Raman,inductively coupled plasma-optical emission spectrometry(ICP-OES),N_(2) adsorption,H_(2)-temperature programmed reduction(H_(2)-TPR),and X-ray photoelectron spectroscopy(XPS)characterizations.The results show that the increase in calcination temperature from 400 to 500℃is conducive to the high dispersion of CuOx on catalyst surface and the incorporation of Cu species into the support to form the Cu-Ce-Zr-O solid solution.Further raising of calcination temperature from 500 to 600℃,however,leads to the segregation of Cu species from the solid solution to aggregate on support surface and growth of highly dispersed CuOx nanoparticles.The highest catalytic activity is acquired over the CCZ calcined at 500℃,which can be ascribed to the largest contents of Cu+species and oxygen vacancies owing to the formation of the maximum amount of Cu-Ce-Zr-O solid solution.

关键词： CuCeZrO_(y)catalyst co oxidation Calcination temperature Grinding method Oxalate precursor Rare earths

A Time for Celebration: 40th Anniversary of GSC and 15th Anniversary of BIG,CAS

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Genomics, Proteomics & Bioinformatics 2018年第6期16卷 387-388页

This special collection of Genomics, Proteomics&Bioinformatics (GPB) is dedicated to anniversary celebrations of two organizations, of which GPB is an official journal under their auspices. One is the Genetics Society of China (GSC), which was established 40 years ago, and the other is the Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS),

关键词： GSC

On the ultimate finishing line of the Human Genome Project

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The Innovation 2021年第3期2卷 13-14页

作者： Jun Yu Songnian Hu University of Chinese Academy of Sciences Beijing 100190China The Institute of Microbiology Chinese Academy of SciencesBeijing 100101China

The Human Genome Project(HGP)has paved the way for the Digital Personal Genomes(DPG),whereby a person’s complete genome sequence serves as the primary entry for the Digital Healthcare Systems(DHS).If the goal is to deliver PDG on demand,affordability,mainly the cost,becomes one of the primary issues.However,as a once-in-a-lifetime event,a total cost of US$100 is close to$1 per year contribution.Therefore,what remains is still largely an engineering challenge,since a multi-fold reduction of the current per-genome sequencing cost may be achievable by increasing the scale of operation and the degree of automation over 5–10 years.The second issue is to differentiate scientific achievements from what is applicable to the healthcare systems and human well-being in general.The original thought of HGP is to understand the genetics of cancers—an idea or a proposal was made and debated in the early 1980s,and it is still clear that we need both high-quality genome sequences and time to fully understand their encoded biological information;the success of HGP lies on the separation of these two goals.

关键词： Human finishing lifetime

Precision Medicine: What Do We Expect in the Scope of Basic Biomedical Sciences?

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Genomics, Proteomics & Bioinformatics 2016年第1期14卷 1-3页

作者： Jun Yu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences

The era of Precision Medicine （PM） has entered its execution phase where acquisition of human genome variation data is already leading the charge [1,2]. PM has come a long way to this phase from the Human Genome Project started some 25 years ago [3,4]; it marks the beginning of disease-centric research in the field of biomedical sciences. Other than deliver- ing high-coverage human genomes by millions--of course tai- lored to patients and common diseases--in the next decade or so, what else do we expect to have and what should we be doing to make the best out of PM projects beyond the current expectation of genetics？

关键词： Precision Medicine What Do We Expect in the Scope of Basic Biomedical Sciences We PM than gene