Browsing by Author "Li, Yi"

Now showing 1 - 8 of 8
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    A Randomized Control Trial of Ravulizumab for Treatment of Patients With COVID-19 Infection and Kidney Injury
    (Elsevier, 2022) Memon, Aliza A.; Ahmed, Hasban; Li, Yi; Wongboonsin, Janewit; Hundert, Joshua; Benoit, Stefanie; Chaudhari, Advika; Sher, Jawad; Ghimire, Pratima; Hopkins, Rebecca; Patel, Jay; Stegman, Melinda; Lim, Kenneth; Azzi, Jamil; Siedlecki, Andrew M.; Medicine, School of Medicine
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    Genetic variants in the genes encoding rho GTPases and related regulators predict cutaneous melanoma-specific survival
    (Wiley, 2017-08-15) Liu, Shun; Wang, Yanru; Xue, William; Liu, Hongliang; Xu, Yinghui; Shi, Qiong; Wu, Wenting; Zhu, Dakai; Amos, Christopher I.; Fang, Shenying; Lee, Jeffrey E.; Hyslop, Terry; Li, Yi; Han, Jiali; Wei, Qingyi; Epidemiology, School of Public Health
    Rho GTPases control cell division, motility, adhesion, vesicular trafficking and phagocytosis, which may affect progression and/or prognosis of cancers. Here, we investigated associations between genetic variants of Rho GTPases-related genes and cutaneous melanoma-specific survival (CMSS) by re-analyzing a published melanoma genome-wide association study (GWAS) and validating the results in another melanoma GWAS. In the single-locus analysis of 36,018 SNPs in 129 Rho-related genes, 427 SNPs were significantly associated with CMSS (p < 0.050 and false-positive report probability <0.2) in the discovery dataset, and five SNPs were replicated in the validation dataset. Among these, four SNPs (i.e., RHOU rs10916352 G > C, ARHGAP22 rs3851552 T > C, ARHGAP44 rs72635537 C > T and ARHGEF10 rs7826362 A > T) were independently predictive of CMSS (a meta-analysis derived p = 9.04 × 10-4 , 9.58 × 10-4 , 1.21 × 10-4 and 8.47 × 10-4 , respectively). Additionally, patients with an increasing number of unfavorable genotypes (NUGs) of these loci had markedly reduced CMSS in both discovery dataset and validation dataset (ptrend =1.47 × 10-7 and 3.12 × 10-5 ). The model including the NUGs and clinical variables demonstrated a significant improvement in predicting the five-year CMSS. Moreover, rs10916352C and rs3851552C alleles were significantly associated with an increased mRNA expression levels of RHOU (p = 1.8 × 10-6 ) and ARHGAP22 (p = 5.0 × 10-6 ), respectively. These results may provide promising prognostic biomarkers for CM personalized management and treatment.
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    Genetic variants of PDGF signaling pathway genes predict cutaneous melanoma survival
    (Impact Journals, 2017-08-14) Li, Hong; Wang, Yanru; Liu, Hongliang; Shi, Qiong; Li, Hongyu; Wu, Wenting; Zhu, Dakai; Amos, Christopher I.; Fang, Shenying; Lee, Jeffrey E.; Li, Yi; Han, Jiali; Wei, Qingyi; Epidemiology, School of Public Health
    To investigate whether genetic variants of platelet-derived growth factor (PDGF) signaling pathway genes are associated with survival of cutaneous melanoma (CM) patients, we assessed associations of single-nucleotide polymorphisms in PDGF pathway with melanoma-specific survival in 858 CM patients of M.D. Anderson Cancer Center (MDACC). Additional data of 409 cases from Harvard University were also included for further analysis. We identified 13 SNPs in four genes (COL6A3, NCK2, COL5A1 and PRKCD) with a nominal P < 0.05 and false discovery rate (FDR) < 0.2 in MDACC dataset. Based on linkage disequilibrium, functional prediction and minor allele frequency, a representative SNP in each gene was selected. In the meta-analysis using MDACC and Harvard datasets, there were two SNPs associated with poor survival of CM patients: rs6707820 C>T in NCK2 (HR = 1.87, 95% CI = 1.35-2.59, Pmeta = 1.53E-5); and rs2306574 T>C in PRKCD (HR = 1.73, 95% CI = 1.33-2.24, Pmeta = 4.56E-6). Moreover, CM patients in MDACC with combined risk genotypes of these two loci had markedly poorer survival (HR = 2.47, 95% CI = 1.58-3.84, P < 0.001). Genetic variants of rs6707820 C>T in NCK2 and rs2306574 T>C in PRKCD of the PDGF signaling pathway may be biomarkers for melanoma survival.
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    Genome-wide association studies identify multiple genetic loci influencing eyebrow color variation in Europeans
    (Elsevier, 2019) Peng, Fuduan; Zhu, Gu; Hysi, Pirro G.; Eller, Ryan J.; Chen, Yan; Li, Yi; Hamer, Merel A.; Zeng, Changqing; Hopkins, Racquel L.; Jacobus, Case L.; Wallace, Paige L.; Uitterlinden, André G.; Ikram, M. Arfan; Duffy, David L.; Nijsten, Tamar; Medland, Sarah E.; Spector, Timothy D.; Walsh, Susan; Martin, Nicholas G.; Liu, Fan; Kayser, Manfred; Biology, School of Science
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    Genome-wide meta-analysis identifies multiple novel associations and ethnic heterogeneity of psoriasis susceptibility
    (Nature Publishing Group, 2015-04-23) Yin, Xianyong; Low, Hui Qi; Wang, Ling; Li, Yonghong; Ellinghaus, Eva; Han, Jiali; Estivill, Xavier; Sun, Liangdan; Zuo, Xianbo; Shen, Changbing; Zhu, Caihong; Zhang, Anping; Sanchez, Fabio; Padyukov, Leonid; Catanese, Joseph J.; Krueger, Gerald G.; Duffin, Kristina Callis; Mucha, Sören; Weichenthal, Michael; Weidinger, Stephan; Lieb, Wolfgang; Foo, Jia Nee; Li, Yi; Sim, Karseng; Liany, Herty; Irwan, Ishak; Teo, Yikying; Theng, Colin T. S.; Gupta, Rashmi; Bowcock, Anne; De Jager, Philip L.; Qureshi, Abrar A.; de Bakker, Paul I. W.; Seielstad, Mark; Liao, Wilson; Ståhle, Mona; Franke, Andre; Zhang, Xuejun; Liu, Jianjun; Department of Dermatology, IU School of Medicine
    Psoriasis is a common inflammatory skin disease with complex genetics and different degrees of prevalence across ethnic populations. Here we present the largest trans-ethnic genome-wide meta-analysis (GWMA) of psoriasis in 15,369 cases and 19,517 controls of Caucasian and Chinese ancestries. We identify four novel associations at LOC144817, COG6, RUNX1 and TP63, as well as three novel secondary associations within IFIH1 and IL12B. Fine-mapping analysis of MHC region demonstrates an important role for all three HLA class I genes and a complex and heterogeneous pattern of HLA associations between Caucasian and Chinese populations. Further, trans-ethnic comparison suggests population-specific effect or allelic heterogeneity for 11 loci. These population-specific effects contribute significantly to the ethnic diversity of psoriasis prevalence. This study not only provides novel biological insights into the involvement of immune and keratinocyte development mechanism, but also demonstrates a complex and heterogeneous genetic architecture of psoriasis susceptibility across ethnic populations.
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    Integrin α 5 Is Regulated by miR-218-5p in Endothelial Progenitor Cells
    (Wolters Kluwer, 2022) Liu, Jialing; Li, Yi; Lyu, Lingna; Xiao, Liang; Memon, Aliza A.; Yu, Xin; Halim, Arvin; Patel, Shivani; Osman, Abdikheyre; Yin, Wenqing; Jiang, Jie; Naini, Said; Lim, Kenneth; Zhang, Aifeng; Williams, Jonathan D.; Koester, Ruth; Qi, Kevin Z.; Fucci, Quynh-Anh; Ding, Lai; Chang, Steven; Patel, Ankit; Mori, Yutaro; Chaudhari, Advika; Bao, Aaron; Liu, Jia; Lu, Tzong-Shi; Siedlecki, Andrew; Medicine, School of Medicine
    Kidney endothelial cells are sensitive to hypoxic injury. This cell type expresses integrin α5 (ITGA5), which is essential to the Tie2 signaling cascade. The microRNA miR-218 is known to increase after hypoxia, but the microRNA’s role in regulating ITGA5 protein synthesis is unclear. In this study, the authors found that miR-218-5p specifically binds to ITGA5 mRNA in human kidney-derived endothelial progenitor cells (EPCs). In an animal model of ischemia/reperfusion injury, cells pretreated with an miR-218-5p mimic were delivered efficiently, whereas an animal model containing an miR-218-2 deletion specific to angioblasts resulted in kidney dysgenesis and impaired migration of mouse kidney-derived EPCs. Understanding the regulation of prominent signaling pathways in EPCs may inform optimization of therapeutic techniques for addressing kidney endothelial cell injury.
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    Isolation and Analysis of a Mycobacteriophage Specific to Mycobacterium Smegmatis
    (2015-12-15) Collins, Angela J.; Ghazali, Danish M.; Li, Yi; Ha, Soo; Clase, Kari L.; Hatfull, Graham
    BACKGROUND: Bacteriophages are viruses that kill bacteria. It is estimated that there are roughly 1031 types of bacteriophages in the world, and that every bacterium has an average of 10 bacteriophages that can infect it. A mycobacteriophage is a type of bacteriophage which has a mycobacterial species as its host. There are 30 known clusters, or types, or mycobacteriophages which all contain very distinct genetic structures, but there are still countless mycobacteriophage populations that need to be isolated. Now that microorganisms are becoming resistant to many antibiotics, the study of bacteriophages is increasingly important because they have an incredibly untapped potential to treat resistant bacteria, eradicate bacterial contaminants in food products, promote ulcer healing, control bacterial growth during fermentation, and much more. The goal of this project was to discover new bacteriophages that might contribute to novel medical solutions. MATERIALS AND METHODS: We plated 29 agar plates for 8 different samples. One sample resulted in plaque growth, from which we performed 9 streak tests, underwent a dilution series and filtration to eliminate the contamination, and harvested a High Titer Lysate. After isolating and purifying the phage genomic DNA, we analyzed the sample and quantified the DNA using a Nanodrop spectrophotometer, and we used agarose gel electrophoresis to separate and analyze the DNA fragments. Finally, we used electron mycrocopy to visualize the physical structure and confirm the successful isolation of a single mycobacteriophage population. DISCUSSION: The cloudiness of the plaque produced by the bacteriophage suggests it is a temperate phage, meaning it switchs between two behavior types regarding replication and survival. Analysis of the physical structure of the mycobacteriophage reveals more information about its genomic DNA; its large capsid diameter suggests lengthy indwelling genomic DNAand its relatively long tail suggests a large tape-measure gene. We were unble to analyze the agarose gel electrophoresis results due to time constraints. However, the results of the genomic DNA sequence will hopefully prove that our bacteriophage is a distinct population. CONCLUSION: We successfully captured, isolated, and purified a single bacteriophage species from the local environment of West Lafayette, Indiana. Upon isolating a single bacteriophage species, we then isolated, purified, restricted, and analyzed the genomic DNA of the phage. Finally, we documented our findings on the Bacteriophage Database as FelixElFago (http://phagesdb.org/phages/FelixElFago/) and sent our DNA to the Sequencing Center.
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    Phase-resolved electrical detection of coherently coupled magnonic devices
    (AIP, 2021-05) Li, Yi; Zhao, Chenbo; Amin, Vivek P.; Zhang, Zhizhi; Vogel, Michael; Xiong, Yuzan; Sklenar, Joseph; Divan, Ralu; Pearson, John; Stiles, Mark D.; Zhang, Wei; Hoffmann, Axel; Novosad, Valentyn; Physics, School of Science
    We demonstrate the electrical detection of magnon–magnon hybrid dynamics in yttrium iron garnet/Permalloy (YIG/Py) thin film bilayer devices. Direct microwave current injection through the conductive Py layer excites the hybrid dynamics consisting of the uniform mode of Py and the first standing spin wave (n = 1) mode of YIG, which are coupled via interfacial exchange. Both the two hybrid modes, with Py- or YIG-dominated excitations, can be detected via the spin rectification signals from the conductive Py layer, providing phase resolution of the coupled dynamics. The phase characterization is also applied to a nonlocally excited Py device, revealing the additional phase shift due to the perpendicular Oersted field. Our results provide a device platform for exploring hybrid magnonic dynamics and probing their phases, which are crucial for implementing coherent information processing with magnon excitations.