Qin Qi

Union Hospital

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Michael R. Gillings

Macquarie University

Sasha G. Tetu

Macquarie University

Vaheesan Rajabal

Macquarie University

Timothy M. Ghaly

Macquarie University

Yang Song

Research Center for Eco-Environmental Sciences

Erqun Song

Southwest University

Bingwei Yang

Chinese Academy of Medical Sciences & Peking Union Medical College

Anahit Penesyan

Macquarie University

Zhanqi Dong

Southwest University

Min‐Hui Pan

Southwest University

Cooperative Institutions

University of Oslo

Chinese Academy of Sciences

Southwest University

Nanchang University

Shanghai University of Traditional Chinese Medicine

Fudan University

Chinese Academy of Medical Sciences & Peking Union Medical College

Huazhong University of Science and Technology

Norwegian Institute of Public Health

Yueyang Hospital

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[Analysis on molecular characteristic of VP7 and NSP4].

Yongkun Huang Qin Qi Zongliu Hou Hailin Li Ge-Sheng Wen

To explore the molecular characteristics and molecular variation of human rotavirus (HRV) strains and to understand the relationship between clinical characteristics and epidemiology of different HRV-VP7 and NSP4.Double-strand RNA of rotavirus extracted from stool samples was used as the template for reverse transcription of gene VP7, which was followed by nested PCR for VP7 typing. NSP4 genes from 22 epidemic strains of human rotavirus isolated in Kunming in 2002 and 2003 were amplified with RT-PCR. Then cDNAs were sequenced and compared with 4 human rotavirus NSP4 (Wa, KUN, AU-1, Hochi)) and 3 animal rotavirus NSP4 (EW, OSU, SA11) available in the GenBank while the epidemic strains of human rotavirus isolated in different areas of China were compared, using the Clustal-mp, DNAssist, MEGA2 software. The G serotype of VP7 was analysed by PCR.Serotype G1 was prevalent in 2002 while serotype G3 was the prevalent in Kumming in 2003. The NSP4 genes from 22 epidemic strains of human rotavirus isolated in Kunming in 2002 and 2003 belonged to Wa with highly conservative amino acid. Samples isolated in the same years but not in the same area shared higher homology. Symptoms associated with heavy diarrhea did not seem to be associated with NSP4 molecular variation (P > 0.05).Obvious variations of VP7 typing were seen in the same season, as well as in different areas and years. Due to the stable nature of NSP4, it seem to be a better candidate for vaccine production, than VP7.

Molecular Epidemiology

Homology

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A Multiplex CRISPR/Cas9 System for Use as an Anti-BmNPV Therapeutic

Zhanqi Dong Qin Qi Zhigang Hu Peng Chen Liang Huang

Clustered regularly interspaced short palindromic repeats/associated protein 9 nuclease (CRISPR/Cas9) technology guided by a single-guide RNA (sgRNA) has recently opened a new avenue for antiviral therapy. A unique capability of the CRISPR/Cas9 system is multiple genome engineering. However, there are few applications in insect viruses by a single Cas9 enzyme targeting two or more sgRNA at different genomic sites for simultaneous production of multiple DNA breaks. To address the need for multi-gene editing and sustained delivery of multiplex CRISPR/Cas9-based genome engineering tools, we developed a one-vector (pSL1180-Cas9-U6-sgRNA) system to express multiple sgRNA and Cas9 protein to excise Bombyx mori nucleopolyhedrovirus (BmNPV) in insect cells. Here, ie-1, gp64, lef-11, and dnapol genes were screened and identified as multiple sgRNA editing sites according to the BmNPV system infection and DNA replication mechanism. Furthermore, we constructed a multiplex editing vector sgMultiple to efficiently regulate multiplex gene editing steps and inhibit BmNPV replication after viral infection. This is the first report that describes the application of multiplex CRISPR/Cas9 system inhibiting insect virus replication. This multiplex system can significant enable the potential of CRISPR/Cas9-based multiplex genome engineering in transgenic silkworms.

Subgenomic mRNA

Multiplex

Genome Engineering

10.20944/preprints201811.0159.v1

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Moxibustion improves experimental colitis in rats with Crohn’s disease by regulating bile acid enterohepatic circulation and intestinal farnesoid X receptor

Journal of Integrative Medicine (2023)

Jiacheng Shen Qin Qi Dong Kwan Han Yuan Lü Rong Huang

Moxibustion

Farnesoid X receptor

10.1016/j.joim.2023.01.001

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Gut Microflora and Critical Patients

Testowy IndexCopernicus (2010)

Qin Qi

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The genomic basis of adaptation to the fitness cost of rifampicin resistance inPseudomonas aeruginosa

Proceedings of the Royal Society B Biological Sciences (2016)

Qin Qi Macarena Toll‐Riera Karl Heilbron Gail M. Preston R. Craig MacLean

Antibiotic resistance carries a fitness cost that must be overcome in order for resistance to persist over the long term. Compensatory mutations that recover the functional defects associated with resistance mutations have been argued to play a key role in overcoming the cost of resistance, but compensatory mutations are expected to be rare relative to generally beneficial mutations that increase fitness, irrespective of antibiotic resistance. Given this asymmetry, population genetics theory predicts that populations should adapt by compensatory mutations when the cost of resistance is large, whereas generally beneficial mutations should drive adaptation when the cost of resistance is small. We tested this prediction by determining the genomic mechanisms underpinning adaptation to antibiotic-free conditions in populations of the pathogenic bacterium Pseudomonas aeruginosa that carry costly antibiotic resistance mutations. Whole-genome sequencing revealed that populations founded by high-cost rifampicin-resistant mutants adapted via compensatory mutations in three genes of the RNA polymerase core enzyme, whereas populations founded by low-cost mutants adapted by generally beneficial mutations, predominantly in the quorum-sensing transcriptional regulator gene lasR . Even though the importance of compensatory evolution in maintaining resistance has been widely recognized, our study shows that the roles of general adaptation in maintaining resistance should not be underestimated and highlights the need to understand how selection at other sites in the genome influences the dynamics of resistance alleles in clinical settings.

Experimental Evolution

Pleiotropy

10.1098/rspb.2015.2452

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Citations (29)

Uncovering bacterial hosts of class 1 integrons in an urban coastal aquatic environment with a single-cell fusion-polymerase chain reaction technology

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Qin Qi Timothy M. Ghaly Anahit Penesyan Vaheesan Rajabal Jeremy AC Stacey

Abstract Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbour class 1 integrons. We developed a modified version of epicPCR ( e mulsion, p aired i solation and c oncatenation p olymerase c hain r eaction) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multi-gene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts towards hotspots of class 1 integron-mediated dissemination of AMR. Synopsis We present a novel single-cell genomic surveillance technology for identifying environmental bacterial hosts of a class of mobile genetic elements that are linked to anthropogenic pollution and contribute to the dissemination of antimicrobial resistance.

Horizontal Gene Transfer

10.1101/2023.02.09.527782

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Wetting behaviors of the Ti2AlC ceramics by nickel and aluminum fillers

Materials Letters (2018)

Chengjie Lu Liangbo Sun Qin Qi Jie Zhang Gilles Hug

Characterization

Wetting transition

10.1016/j.matlet.2018.02.077

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Establishment of a baculovirus-inducible CRISPR/Cas9 system for antiviral research in transgenic silkworms

Applied Microbiology and Biotechnology (2018)

Zhanqi Dong Liang Huang Feifan Dong Zhigang Hu Qin Qi

10.1007/s00253-018-9295-8

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Citations (23)

Effects of multiple reflected P waves on crack-tip stress and crack propagation in directional fracturing blasting

Mechanics of Advanced Materials and Structures (2024)

Peng Qiu Qin Qi Qinyuan Li Hong Su

Directional fracturing blasting is effective for rock engineering, but it is inevitably disturbed by multiple reflected waves from different directions in natural rock mass due to discontinuous boundaries. Reflected waves affect both crack-tip stress and crack propagation, hence affect the results of directional fracturing blasting. In this paper, with the aid of high-speed photography, an optical caustics method is used to study effects of multiple reflected P waves on a directional blast-induced crack in a polymethyl methacrylate (PMMA) plate, specifically on crack path, crack fracturing mode, crack-tip stress and crack velocity. Crack-tip stress field is indicated by the shape of caustics pattern. Before the loading of reflected P waves, the mode I directional crack driven by blast-induced gases propagates in a straight path; crack-tip stress field is K-dominated, and crack-tip caustics pattern is consistent with classical caustics theory. On the contrary, under the loading of reflected P waves, the directional crack changes to be mixed-mode I + II and propagates in a curved path; Crack-tip stress field is non-K-dominated due to transient stress superposition of reflected P waves, and crack-tip caustics pattern is consistent with modified caustics theory. Transient stress superposition is not obvious for reflected P waves with a longer reflection distance. The tension loading of reflected P waves plays a more important role than the compression loading, which increases crack-tip stress intensity factors and crack velocity. This study provides a comprehensive understanding of effects of multiple reflected P waves from different directions on directional fracturing blasting.

Stress wave

10.1080/15376494.2024.2416475

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NSUN5 is Upregulated and Positively Correlated with Translation in Human Cancers: A Bioinformatics-based Study

Research Square (Research Square) (2020)

Xiaowen Zhang Yan Huang Lu-yi Wu Qin Qi Rui Zhong

Abstract The role of RNA m 5 C (5-methylcytosine) and RNA m 5 C methyltransferases (RCMTs, including NSUN1, NSUN2, NSUN3, NSUN4, NSUN5, NSUN6, NSUN7 and TRDMT1) in human cancers remains largely unknown. In this study, GEPIA2 was used to compare the expression of RCMTs in human cancers and that in associated normal tissues, and to analyze the prognosis value of NSUN5 expression. UALCAN was used to compare the methylation level of NSUN5 promoter in human cancers and that in associated normal tissues. LinkedOmics was used perform BPs (biological processes), CCs (cellular components), MFs (molecular functions) and KEGG pathways analyses of NSUN5-correlated genes in each cancer one by one. We found that six RCMTs (NSUN1-NSUN5 and TRDMT1), especially NSUN5, were generally upregulated in human cancers, that the hypomethylation of NSUN5 promoter may be responsible for its upregulation, and that overexpressed NSUN5 predicted poorer prognosis and was positively correlated with translation in human cancers. The function of NSUN5 in human cancers and its mechanism need to be validated by biological experiments.

KEGG

10.21203/rs.3.rs-92585/v1

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Citations (2)