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  1. Article ; Online: Mass Spectrometry-Based Proteomics for Biomarker Discovery.

    Cao, Zhijun / Yu, Li-Rong

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2486, Page(s) 3–17

    Abstract: Proteomics plays a pivotal role in systems medicine, in which pharmacoproteomics and toxicoproteomics have been developed to address questions related to efficacy and toxicity of drugs. Mass spectrometry is the core technology for quantitative proteomics, ...

    Abstract Proteomics plays a pivotal role in systems medicine, in which pharmacoproteomics and toxicoproteomics have been developed to address questions related to efficacy and toxicity of drugs. Mass spectrometry is the core technology for quantitative proteomics, providing the capabilities of identification and quantitation of thousands of proteins. The technology has been applied to biomarker discovery and understanding the mechanisms of drug action. Both stable isotope labeling of proteins or peptides and label-free approaches have been incorporated with multidimensional LC separation and tandem mass spectrometry (LC-MS/MS) to increase the coverage and depth of proteome analysis. A protocol of such an approach exemplified by dimethyl labeling in combination with 2D-LC-MS/MS is described. With further development of novel proteomic tools and increase in sample throughput, the full spectrum of mass spectrometry-based proteomic research will greatly advance systems medicine.
    MeSH term(s) Biomarkers ; Chromatography, Liquid/methods ; Proteome/analysis ; Proteomics/methods ; Tandem Mass Spectrometry/methods
    Chemical Substances Biomarkers ; Proteome
    Language English
    Publishing date 2022-04-18
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, P.H.S.
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2265-0_1
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  2. Article ; Online: Noonan syndrome: rhGH treatment and PTPN11 mutation.

    Wu, Xian / Wu, Jiali / Yuan, Yi / Yang, Li / Yu, Lirong

    Molecular genetics & genomic medicine

    2023  Volume 11, Issue 11, Page(s) e2266

    Abstract: Objective: To analyze the clinical data and genetic characteristics of Noonan syndrome, both the effect and side effects of recombinant human growth hormone (rhGH) treatment.: Methods: We collected clinical data from 8 children with Noonan syndrome ... ...

    Abstract Objective: To analyze the clinical data and genetic characteristics of Noonan syndrome, both the effect and side effects of recombinant human growth hormone (rhGH) treatment.
    Methods: We collected clinical data from 8 children with Noonan syndrome diagnosed from November 2017 to June 2021. The diagnosis was clarified by exome second-generation sequencing and parental PCR-NGS validation and interpretation of the preceding evidence, and growth hormone therapy was administered. Of the cases, four males and four females were seen for slow height growth and the median age at diagnosis was 8 years 7 months (1 year 7 months to 12 years 6 months).
    Results: Here, 7 children were treated with rhGH. Compared to the pre-treatment period, the growth rate increased after rhGH treatment [3.7 ± 0.5 cm/year before treatment and 8.0 ± 1.0 cm/year after treatment, p < 0.01], with the maximum growth rate between 3 and 6 months of treatment and decreasing with the duration of treatment thereafter. The growth hormone treatment was discontinued and the orthopedic consultation was ordered with regular follow-up, which was considered to be related to the PTPN11 mutation.
    Conclusion: Noonan syndrome is characterized by slow growth, short stature, mental retardation, peculiar facial features, structural heart abnormalities and abnormal bone metabolism. and osteochondroma was found after case 2 rhGH treatment. Genetic examination is mostly caused by PTPN11 mutation. It is recommended to pay attention to bone metabolism abnormalities before growth hormone treatment, especially in children with PTPN11 mutations.
    MeSH term(s) Child ; Male ; Female ; Humans ; Noonan Syndrome/drug therapy ; Noonan Syndrome/genetics ; Noonan Syndrome/diagnosis ; Human Growth Hormone/therapeutic use ; Genetic Testing ; Recombinant Proteins/genetics ; Mutation ; Protein Tyrosine Phosphatase, Non-Receptor Type 11/genetics
    Chemical Substances Human Growth Hormone (12629-01-5) ; Recombinant Proteins ; PTPN11 protein, human (EC 3.1.3.48) ; Protein Tyrosine Phosphatase, Non-Receptor Type 11 (EC 3.1.3.48)
    Language English
    Publishing date 2023-08-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2734884-2
    ISSN 2324-9269 ; 2324-9269
    ISSN (online) 2324-9269
    ISSN 2324-9269
    DOI 10.1002/mgg3.2266
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  3. Article ; Online: Analysis of quality of life in children and adolescents with type 1 diabetes mellitus.

    Yu, Lirong / Du, Xiangping / Wu, Xian / Yuan, Yi

    Minerva surgery

    2022  Volume 77, Issue 6, Page(s) 636–638

    MeSH term(s) Humans ; Adolescent ; Child ; Diabetes Mellitus, Type 1 ; Quality of Life ; Surveys and Questionnaires ; Glycated Hemoglobin
    Chemical Substances Glycated Hemoglobin A
    Language English
    Publishing date 2022-01-28
    Publishing country Italy
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 3067899-7
    ISSN 2724-5438
    ISSN (online) 2724-5438
    DOI 10.23736/S2724-5691.21.09327-8
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  4. Article ; Online: Modeling Clinical Phenotype Variability: Consideration of Genomic Variations, Computational Methods, and Quantitative Proteomics.

    Bai, Jane P F / Yu, Li-Rong

    Journal of pharmaceutical sciences

    2022  Volume 112, Issue 4, Page(s) 904–908

    Abstract: Advances in biomedical and computer technologies have presented the modeling community the opportunity for mechanistically modeling and simulating the variability in a disease phenotype or in a drug response. The capability to quantify response ... ...

    Abstract Advances in biomedical and computer technologies have presented the modeling community the opportunity for mechanistically modeling and simulating the variability in a disease phenotype or in a drug response. The capability to quantify response variability can inform a drug development program. Quantitative systems pharmacology scientists have published various computational approaches for creating virtual patient populations (VPops) to model and simulate drug response variability. Genomic variations can impact disease characteristics and drug exposure and response. Quantitative proteomics technologies are increasingly used to facilitate drug discovery and development and inform patient care. Incorporating variations in genomics and quantitative proteomics may potentially inform creation of VPops to model and simulate virtual patient trials, and may help account for, in a predictive manner, phenotypic variations observed clinically.
    MeSH term(s) Proteomics ; Genomics ; Drug Development ; Phenotype ; Biological Variation, Population
    Language English
    Publishing date 2022-10-21
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 3151-3
    ISSN 1520-6017 ; 0022-3549
    ISSN (online) 1520-6017
    ISSN 0022-3549
    DOI 10.1016/j.xphs.2022.10.016
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  5. Article ; Online: Characterization of Phosphorylated Proteins Using Mass Spectrometry.

    Yu, Li-Rong / Veenstra, Timothy D

    Current protein & peptide science

    2020  Volume 22, Issue 2, Page(s) 148–157

    Abstract: Phosphorylation is arguably the most important post-translational modification that occurs within proteins. Phosphorylation is used as a signal to control numerous physiological activities ranging from gene expression to metabolism. Identifying ... ...

    Abstract Phosphorylation is arguably the most important post-translational modification that occurs within proteins. Phosphorylation is used as a signal to control numerous physiological activities ranging from gene expression to metabolism. Identifying phosphorylation sites within proteins was historically a challenge as it required either radioisotope labeling or the use of phospho-specific antibodies. The advent of mass spectrometry (MS) has had a major impact on the ability to qualitatively and quantitatively characterize phosphorylated proteins. In this article, we describe MS methods for characterizing phosphorylation sites within individual proteins as well as entire proteome samples. The utility of these methods is illustrated in examples that show the information that can be gained using these MS techniques.
    MeSH term(s) Amino Acid Sequence ; Chromatography, Affinity/instrumentation ; Chromatography, Affinity/methods ; Chromatography, Liquid ; Humans ; Peptide Mapping/methods ; Phosphopeptides/classification ; Phosphopeptides/isolation & purification ; Phosphoproteins/classification ; Phosphoproteins/isolation & purification ; Phosphorylation ; Protein Processing, Post-Translational ; Proteome/classification ; Proteome/isolation & purification ; Proteomics/instrumentation ; Proteomics/methods ; Tandem Mass Spectrometry
    Chemical Substances Phosphopeptides ; Phosphoproteins ; Proteome
    Language English
    Publishing date 2020-11-23
    Publishing country United Arab Emirates
    Document type Journal Article ; Review
    ZDB-ID 2045662-1
    ISSN 1875-5550 ; 1389-2037
    ISSN (online) 1875-5550
    ISSN 1389-2037
    DOI 10.2174/1389203721999201123200439
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  6. Article ; Online: COL1A1 regulates the apoptosis of embryonic stem cells by mediating the PITX1/TBX4 signaling.

    Du, Xiangping / Wu, Xinle / Yu, Lirong / Min, Wu / Chen, Gan / Liu, Fadi / Li, Jian

    Birth defects research

    2023  Volume 116, Issue 1, Page(s) e2277

    Abstract: Purpose: The purpose of this study is to explore the regulatory function of COL1A1 against the apoptosis of embryonic stem cells (ESCs) and the potential function in congenital talipes equinovarus (CTEV).: Methods: Muscle tissues were collected from ... ...

    Abstract Purpose: The purpose of this study is to explore the regulatory function of COL1A1 against the apoptosis of embryonic stem cells (ESCs) and the potential function in congenital talipes equinovarus (CTEV).
    Methods: Muscle tissues were collected from 20 children with CTEV and 20 children without CTEV, followed by detecting the expression of COL1A1 using the RT-PCR method. COL1A1 was knocked down in H1 and H9 human ESCs using the RNA interference technology, followed by determining the level of COL1A1, PITX1, TBX4, HOXD10, Fas, FasL, and Bax using the Western blotting assay.
    Results: COL1A1 was found markedly upregulated in muscle tissues of CTEV children. In H1 and H9 human ESCs, compared to the empty vector, COL1A1, PITX1, TBX4, HOXD10, Fas, FasL, and Bax were found notably downregulated after transfected with the siRNA targeting COL1A1.
    Conclusion: COL1A1 induced the apoptosis of ESCs by mediating the PITX1/TBX4 signaling and might be a potential target for treating CTEV.
    MeSH term(s) Child ; Humans ; Apoptosis/genetics ; bcl-2-Associated X Protein/genetics ; Clubfoot/genetics ; Embryonic Stem Cells ; T-Box Domain Proteins/genetics
    Chemical Substances bcl-2-Associated X Protein ; T-Box Domain Proteins ; TBX4 protein, human ; COL1A1 protein, human
    Language English
    Publishing date 2023-12-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2104792-3
    ISSN 2472-1727
    ISSN (online) 2472-1727
    DOI 10.1002/bdr2.2277
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  7. Article ; Online: Typology in Vernacular Architecture—Qianmo Tower Post Station in Mingyue Village

    Li Yunzhang / Zhu Yuhong / Yu Lirong / Bi Zhongsong / Huang Guanjun

    E3S Web of Conferences, Vol 237, p

    2021  Volume 03019

    Abstract: The acceleration of the modernization process has promoted the improvement of rural residential construction technology and efficiency, but the rural buildings have not inherited and developed the regional traditional characteristics on this basis, ... ...

    Abstract The acceleration of the modernization process has promoted the improvement of rural residential construction technology and efficiency, but the rural buildings have not inherited and developed the regional traditional characteristics on this basis, instead, there has been a blind trend of urban architectural styles in different regions, resulting in a phenomenon of the homogenization of development. The design of qianmota post station uses the typological analysis method to excavate and inherit the characteristics of the local traditional buildings in Mingyue village, then combines the characteristics with new technologies and materials to restore the local architecture in the hearts of the villagers in Mingyue village. It is restored in two aspects: the architectural appearance of the traditional houses in Western Sichuan and the spiritual symbol of the church.
    Keywords Environmental sciences ; GE1-350
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher EDP Sciences
    Document type Article ; Online
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  8. Article ; Online: ArfA and SarA small GTPases involved in growth, patulin biosynthesis and virulence of Penicillium expansum

    Zhang, Feng / Zhang, Xuemei / Gong, Di / Yu, Lirong / Prusky, Dov / Sionov, Edward / Bi, Yang / Zong, Yuanyuan

    Postharvest Biology and Technology. 2023 Nov., v. 205 p.112506-

    2023  

    Abstract: Although the Sar/Arf GTPase belonging to a small family of GTPases contributes to growth of fungi, its function in postharvest fungi has not been characterized. Here, ArfA and SarA gene deletion mutants were generated in Penicillium expansum. We found ... ...

    Abstract Although the Sar/Arf GTPase belonging to a small family of GTPases contributes to growth of fungi, its function in postharvest fungi has not been characterized. Here, ArfA and SarA gene deletion mutants were generated in Penicillium expansum. We found that ΔArfA and ΔSarA exhibited attenuated colony growth and rough colony morphology, as well as insufficient spore development. ΔArfA also increased hyphal branches. Stress experiments showed that knocking out the ArfA or SarA genes affected cell wall integrity of the P. expansum strain. In addition, ΔArfA and ΔSarA significantly downregulated the expression of genes controlling spore development (wetA, abaA and brlA) and MAPK pathway regulators (Fus3, Kss1, Hog1 and Mpk1). Absence of ArfA and SarA reduced patulin production, and the related gene expression was significantly limited. ΔArfA showed attenuated virulence in infected fruit and downregulated PG and PL gene expression. However, ΔSarA had no significant effect on fungal virulence. Taken together, both ArfA and SarA contribute to the growth, development and patulin biosynthesis in P. expansum. ArfA is also involved in the virulence of P. expansum in fruit.
    Keywords Biological Sciences ; Penicillium expansum ; biosynthesis ; cell walls ; fruits ; fungi ; gene deletion ; gene expression ; guanosinetriphosphatase ; hyphae ; patulin ; spores ; technology ; virulence ; Sar/Arf GTPase ; Growth ; Development
    Language English
    Dates of publication 2023-11
    Publishing place Elsevier B.V.
    Document type Article ; Online
    ZDB-ID 1082798-5
    ISSN 1873-2356 ; 0925-5214
    ISSN (online) 1873-2356
    ISSN 0925-5214
    DOI 10.1016/j.postharvbio.2023.112506
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  9. Article ; Online: Ultrasonography-Guided Combination with Elbow Arthrography-Assisted Minimally Invasive Treatment of Radial Neck Fractures in Young Children.

    Du, Xiangping / Yu, Lirong / Wu, Xinle / Chen, Gan / Xiong, Zhigang / Jiang, Qiqing

    publication RETRACTED

    Computational and mathematical methods in medicine

    2022  Volume 2022, Page(s) 6840716

    Abstract: Background: A radius neck fracture in children is a common fracture that not only affects the growth and development of children but also has a certain impact on the function of children's elbow joints.: Objective: To probe into the application value ...

    Abstract Background: A radius neck fracture in children is a common fracture that not only affects the growth and development of children but also has a certain impact on the function of children's elbow joints.
    Objective: To probe into the application value of ultrasonography- (US-) guided combination with elbow arthrography in the minimally invasive treatment of radial neck fractures in young children, summarize its clinical effect and provide a minimally invasive, safe, effective, and reliable method for treating radial neck fractures in young children.
    Methods: Seventy-three patients with type III or IV radial neck fractures were treated from June 2013 to December 2020 and were divided into the Métaizeau group (
    Results: In comparison with the
    Conclusion: In the minimally invasive treatment of radial neck fractures, US-guided combination with elbow arthrography in young children has better efficacy and high safety. It can be widely promoted and applied clinically.
    MeSH term(s) Arthrography ; Child ; Child, Preschool ; Elbow/diagnostic imaging ; Fracture Fixation, Internal/methods ; Humans ; Radius/diagnostic imaging ; Radius/surgery ; Radius Fractures/diagnostic imaging ; Radius Fractures/surgery ; Retrospective Studies ; Treatment Outcome ; Ultrasonography
    Language English
    Publishing date 2022-07-04
    Publishing country United States
    Document type Journal Article ; Retracted Publication
    ZDB-ID 2252430-7
    ISSN 1748-6718 ; 1748-670X ; 1027-3662
    ISSN (online) 1748-6718
    ISSN 1748-670X ; 1027-3662
    DOI 10.1155/2022/6840716
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  10. Article: Prevalence, Virulence, and Antibiotics Gene Profiles in

    Xie, Xinmei / Pan, Zihao / Yu, Yong / Yu, Lirong / Wu, Fan / Dong, Jing / Wang, Tiancheng / Li, Lin

    Microorganisms

    2023  Volume 11, Issue 2

    Abstract: Lactococcus ... ...

    Abstract Lactococcus garvieae
    Language English
    Publishing date 2023-02-02
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms11020379
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