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TU tagging

Binbin Ding, Linliang Zhang, Zhifei Li, Yi Zhong, Qiaopeng Tang, Yali Qin, Mingzhou Chen
Mitophagy is a form of autophagy that selectively removes damaged mitochondria. Impaired mitochondria can be tagged by the kinase PINK1, which triggers recruitment of the E3-ubiquitin ligase Parkin and subsequent mitochondrial sequestration within autophagosomes. We previously found that human parainfluenza virus type 3 (HPIV3) infection induces autophagy, but the type and mechanisms of autophagy induction remain unknown. Here, we show that matrix protein (M) of HPIV3 translocates to mitochondria and interacts with Tu translation elongation factor mitochondrial (TUFM)...
April 12, 2017: Cell Host & Microbe
Ling Li, Hongli Jin, Hualei Wang, Zengguo Cao, Na Feng, Jianzhong Wang, Yongkun Zhao, Xuexing Zheng, Pengfei Hou, Nan Li, Hang Chi, Pei Huang, Cuicui Jiao, Qian Li, Lina Wang, Tiecheng Wang, Weiyang Sun, Yuwei Gao, Changchun Tu, Guixue Hu, Songtao Yang, Xianzhu Xia
Rabies virus (RABV) is a neurotropic virus that causes serious disease in humans and animals worldwide. It has been reported that different RABV strains can result in divergent prognoses in animal model. To identify host factors that affect different infection processes, a kinetic analysis of host proteome alterations in mouse brains infected with different virulent RABV strains was performed using isobaric tags for a relative and absolute quantification (iTRAQ)-liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach, and this analysis identified 147 differentially expressed proteins (DEPs) between the pathogenic challenge virus standard (CVS)-11 strain and the attenuated SRV9 strain...
March 28, 2017: Oncotarget
Zhuchi Tu, Weili Yang, Sen Yan, An Yin, Jinquan Gao, Xudong Liu, Yinghui Zheng, Jiezhao Zheng, Zhujun Li, Su Yang, Shihua Li, Xiangyu Guo, Xiao-Jiang Li
CRISPR-Cas9 is a powerful new tool for genome editing, but this technique creates mosaic mutations that affect the efficiency and precision of its ability to edit the genome. Reducing mosaic mutations is particularly important for gene therapy and precision genome editing. Although the mechanisms underlying the CRSIPR/Cas9-mediated mosaic mutations remain elusive, the prolonged expression and activity of Cas9 in embryos could contribute to mosaicism in DNA mutations. Here we report that tagging Cas9 with ubiquitin-proteasomal degradation signals can facilitate the degradation of Cas9 in non-human primate embryos...
February 3, 2017: Scientific Reports
Shu-Chi Wang, Kuan-Ru Lai, Chia-Yang Li, Chi-Shiun Chiang, Guann-Yi Yu, Naoya Sakamoto, Wen-Yu Tu, Meng-Hsuan Hsieh, Jee-Fu Huang, Wan-Long Chuang, Chia-Yen Dai, Ming-Lung Yu
Hepatitis C virus (HCV)-induced hepatic stress is associated with increased oxidative DNA damage and has been implicated in hepatic inflammation. However, HCV infection and replication are uneven and vary among individual hepatocytes. To investigate the effect of the viral load on host DNA damage, we used an Enhanced Yellow Fluorescent Protein gene (EYFP)-tagged HCV virus to distinguish between HCV intracellular high viral load (HVL) cells and low viral load (LVL) cells. The cell sorting efficiency was confirmed by the high expression of the HCV polyprotein...
2017: PloS One
K Hwang, J Meier, J Yung, R Stafford
PURPOSE: Echo planar imaging (EPI) is known to exhibit gross geometric distortion caused by multiple factors, including B0 inhomgeneity and transient eddy currents. However, diffusion weighted (DW) EPI has become indispensable for diagnosis and therapy assessment. We propose a methodology for quantifying distortion in EPI sequences that does not require the use of dedicated spatial accuracy phantoms, enabling flexibility in phantom design for QA of distortion effects in EPI protocols...
June 2016: Medical Physics
Chao-Hui Li, Lan-Zhen Yan, Wen-Zan Ban, Qiu Tu, Yong Wu, Lin Wang, Rui Bi, Shuang Ji, Yu-Hua Ma, Wen-Hui Nie, Long-Bao Lv, Yong-Gang Yao, Xu-Dong Zhao, Ping Zheng
Tree shrews have a close relationship to primates and have many advantages over rodents in biomedical research. However, the lack of gene manipulation methods has hindered the wider use of this animal. Spermatogonial stem cells (SSCs) have been successfully expanded in culture to permit sophisticated gene editing in the mouse and rat. Here, we describe a culture system for the long-term expansion of tree shrew SSCs without the loss of stem cell properties. In our study, thymus cell antigen 1 was used to enrich tree shrew SSCs...
February 2017: Cell Research
Anqi Tu, Qiang Ma, Hua Bai, Zhenxia Du
Triacylglycerols (TAGs) as the major component of milk fat are significant factors to ensure the healthy growth of infants. An efficient method for identifying TAGs in human milk (HM) and infant formula (IF) was established using supercritical fluid chromatograph (SFC) coupled with quadruple time-of-flight mass spectrometry (Q-TOF-MS). The results indicated the feasibility of this method with satisfactory recoveries (>80%) and correlation coefficients (r(2)⩾0.993). More than 60 TAGs in HM and 50 TAGs in IF were identified...
April 15, 2017: Food Chemistry
Xiaokun Li, Youlin Zhang, Bin Xue, Xianggui Kong, Xiaomin Liu, Langping Tu, Yulei Chang, Hong Zhang
Assay technologies capable of detecting biomarker concentrations in unprocessed whole blood samples are fundamental for applications in medical diagnostics. SERS nano-tags integrated fiber-optic biosensor (FOB) was realized for the first time for in situ immunoassay in whole blood. The reliability and sensitivity of this method rely, in a large extent, on the quality and properties of the SERS nano-tags. The constructed silica-coated Ag SERS nano-tags as labels were used in a rapid and specific in situ FOB immune sensor to detect alpha fetoprotein (AFP) in unprocessed blood samples...
June 15, 2017: Biosensors & Bioelectronics
Joanne Trinh, Emil K Gustavsson, Carles Vilariño-Güell, Stephanie Bortnick, Jeanne Latourelle, Marna B McKenzie, Chelsea Szu Tu, Ekaterina Nosova, Jaskaran Khinda, Austen Milnerwood, Suzanne Lesage, Alexis Brice, Meriem Tazir, Jan O Aasly, Laura Parkkinen, Hazal Haytural, Tatiana Foroud, Richard H Myers, Samia Ben Sassi, Emna Hentati, Fatma Nabli, Emna Farhat, Rim Amouri, Fayçal Hentati, Matthew J Farrer
BACKGROUND: Leucine-rich repeat kinase 2 (LRRK2) mutation 6055G→A (Gly2019Ser) accounts for roughly 1% of patients with Parkinson's disease in white populations, 13-30% in Ashkenazi Jewish populations, and 30-40% in North African Arab-Berber populations, although age of onset is variable. Some carriers have early-onset parkinsonism, whereas others remain asymptomatic despite advanced age. We aimed to use a genome-wide approach to identify genetic variability that directly affects LRRK2 Gly2019Ser penetrance...
November 2016: Lancet Neurology
Sheng-Wen Wu, Jia-Hung Liou, Kun-Tu Yeh, Tung-Wei Hung, Horng-Rong Chang
PURPOSE: Human polyomaviruses (PV) has been associated with oncogenicity; however, the association between human bladder cancer and PV remains inconclusive. Moreover, whether PV has the interaction with p53 in tumorigenesis and their prognostic significance on human bladder cancer has yet to be determined. MATERIALS AND METHODS: Bladder tumor specimens and clinical parameters from 74 patients with urothelial carcinoma were collected. Immunohistochemical analysis using monoclonal antibodies specific to PV large tumor antigen (TAg) and p53 protein was performed to investigate the involvement of PV in human bladder tumorigenesis and the prognostic significance of TAg and p53 expressions using Cox proportional hazards model...
August 25, 2016: Urology Journal
T Erickson, T Nicolson
Transcriptomic studies are important tools for understanding the development and function of the different cell types that make up complex tissues. Zebrafish (Danio rerio) is a valuable organism for modeling key aspects of vertebrate development, cell biology, and human disease. However, the small size of individual larvae and relative scarcity of certain cell types in zebrafish can hamper efforts to collect enough pure material for cell type-specific transcriptomic studies. Thus, there is a need in the zebrafish field for spatially and temporally resolved gene expression assays...
2016: Methods in Cell Biology
Sukhdeep Singh, Marco Y Hein, A Francis Stewart
We introduce msVolcano, a web application for the visualization of label-free mass spectrometric data. It is optimized for the output of the MaxQuant data analysis pipeline of interactomics experiments and generates volcano plots with lists of interacting proteins. The user can optimize the cutoff values to find meaningful significant interactors for the tagged protein of interest. Optionally, stoichiometries of interacting proteins can be calculated. Several customization options are provided to the user for flexibility, and publication-quality outputs can also be downloaded (tabular and graphical)...
September 2016: Proteomics
Salem Alkanaimsh, Kalimuthu Karuppanan, Andrés Guerrero, Aye M Tu, Bryce Hashimoto, Min Sook Hwang, My L Phu, Lucas Arzola, Carlito B Lebrilla, Abhaya M Dandekar, Bryce W Falk, Somen Nandi, Raymond L Rodriguez, Karen A McDonald
To optimize the expression, extraction and purification of plant-derived tetrameric recombinant human butyrylcholinesterase (prBChE), we describe the development and use of plant viral amplicon-based gene expression system; Tobacco Mosaic Virus (TMV) RNA-based overexpression vector (TRBO) to express enzymatically active FLAG-tagged plant made recombinant butyrylcholinesterase (rBChE) in Nicotiana benthamiana leaves using transient agroinfiltration. Two gene expression cassettes were designed to express the recombinant protein in either the ER or to the apoplastic compartment...
2016: Frontiers in Plant Science
Xiangfeng Wang, Fudi Zhong, Cheuk Hang Woo, Yansong Miao, Michael A Grusak, Xiaobo Zhang, Jumin Tu, Yum Shing Wong, Liwen Jiang
Iron (Fe) is an essential micronutrient for humans. Fe deficiency disease is widespread and has led to extensive studies on the mechanisms of Fe uptake and storage, especially in staple food crops such as rice. However, studies of functionally related genes in rice and other crops are often time and space demanding. Here, we demonstrate that transgenic Arabidopsis suspension culture cells and Arabidopsis plants can be used as an efficient expression system for gain-of-function study of selected transporters, using Fe transporters as a proof-of-principle...
March 2017: Protoplasma
Ilaria Guella, Daniel M Evans, Chelsea Szu-Tu, Ekaterina Nosova, Stephanie F Bortnick, Jennifer G Goldman, John C Dalrymple-Alford, Gert J Geurtsen, Irene Litvan, Owen A Ross, Lefkos T Middleton, Laura Parkkinen, Matthew J Farrer
OBJECTIVE: The relationship between Parkinson disease (PD), PD with dementia (PDD), and dementia with Lewy bodies (DLB) has long been debated. Although PD is primarily considered a motor disorder, cognitive impairment is often present at diagnosis, and only ∼20% of patients remain cognitively intact in the long term. Alpha-synuclein (SNCA) was first implicated in the pathogenesis of the disease when point mutations and locus multiplications were identified in familial parkinsonism with dementia...
June 2016: Annals of Neurology
Brittany A Simone, Tu Dan, Ajay Palagani, Lianjin Jin, Sunny Y Han, Christopher Wright, Jason E Savage, Robert Gitman, Meng Kieng Lim, Juan Palazzo, Minesh P Mehta, Nicole L Simone
PURPOSE: Metastatic breast cancer is devastating and triple negative breast cancers (TNBC) have a higher propensity for metastasis. Improved local control upfront in this aggressive cancer could potentially decrease its propensity toward metastasis. We sought to determine if using caloric restriction (CR) as a systemic therapy, combined with radiation therapy (IR) to the primary tumor, may impact metastatic disease. METHODS: An orthotopic mouse model using a highly metastatic, luciferase-tagged TNBC cell line (4T1), was used to generate palpable tumors...
September 2016: Cell Cycle
Christina Chatzi, Yingyu Zhang, Rongkun Shen, Gary L Westbrook, Richard H Goodman
Despite representing only a small fraction of hippocampal granule cells, adult-generated newborn granule cells have been implicated in learning and memory (Aimone et al., 2011). Newborn granule cells undergo functional maturation and circuit integration over a period of weeks. However, it is difficult to assess the accompanying gene expression profiles in vivo with high spatial and temporal resolution using traditional methods. Here we used a novel method ["thiouracil (TU) tagging"] to map the profiles of nascent mRNAs in mouse immature newborn granule cells compared with mature granule cells...
January 2016: ENeuro
Liang Ma, Chunlai Tu, Phuong Le, Shweta Chitoor, Sung Jun Lim, Mohammad U Zahid, Kai Wen Teng, Pinghua Ge, Paul R Selvin, Andrew M Smith
Quantum dots are fluorescent nanoparticles used to detect and image proteins and nucleic acids. Compared with organic dyes and fluorescent proteins, these nanocrystals have enhanced brightness, photostability, and wavelength tunability, but their larger size limits their use. Recently, multidentate polymer coatings have yielded stable quantum dots with small hydrodynamic dimensions (≤10 nm) due to high-affinity, compact wrapping around the nanocrystal. However, this coating technology has not been widely adopted because the resulting particles are frequently heterogeneous and clustered, and conjugation to biological molecules is difficult to control...
March 16, 2016: Journal of the American Chemical Society
Xiangdong Tu, Jian Zeng, Xuewen Cong, Xiao Zhang, Aizhen Yan
OBJECTIVE: To explore the source of small supernumerary marker chromosome in a case. METHODS: G-banded karyotyping, fluorescence in situ hybridization, multiple sequence tagged sites (STS) of the Y chromosome, and Illumima Human Cyto SNP-12 Beadchip analysis were carried out. RESULTS: The karyotype was mos 46,X,+mar1[21]/46,X,+mar2[78]. Y chromosome STS analysis has displayed the presence of sy84, sY86, USP9Y and DDX3Y genes from the AZFa region, and sY1227 of the AZFb region, while sY1228, sY1015, sY127, sY134 from the AZFb region, and sY254 and sY255 from the AZFc region were missing...
February 2016: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
Timothy Erickson, Teresa Nicolson
BACKGROUND: Sensory hair cells are exquisitely sensitive to mechanical stimuli and as such, are prone to damage and apoptosis during dissections or in vitro manipulations. Thiouracil (TU)-tagging is a noninvasive method to label cell type-specific transcripts in an intact organism, thereby meeting the challenge of how to analyze gene expression in hair cells without the need to sort cells. We adapted TU-tagging to zebrafish to identify novel transcripts expressed in the sensory hair cells of the developing acoustico-lateralis organs...
2015: BMC Genomics
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