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Identifying the substrate proteins of U-box E3s E4B and CHIP by orthogonal ubiquitin transfer.
Bhuripanyo K, Wang Y, Liu X, Zhou L, Liu R, Duong D, Zhao B, Bi Y, Zhou H, Chen G, Seyfried NT, Chazin WJ, Kiyokawa H, Yin J
(2018) Sci Adv 4: e1701393
MeSH Terms: Amino Acid Sequence, Bacteriophages, Biocatalysis, Cyclin-Dependent Kinase 4, Endoplasmic Reticulum Stress, HEK293 Cells, Humans, Mutant Proteins, Mutation, Peptides, Proteolysis, Reproducibility of Results, Signal Transduction, Substrate Specificity, Tumor Suppressor Protein p53, Tumor Suppressor Proteins, Ubiquitin, Ubiquitin-Protein Ligase Complexes, Ubiquitin-Protein Ligases, Ubiquitination
Show Abstract · Added March 24, 2018
E3 ubiquitin (UB) ligases E4B and carboxyl terminus of Hsc70-interacting protein (CHIP) use a common U-box motif to transfer UB from E1 and E2 enzymes to their substrate proteins and regulate diverse cellular processes. To profile their ubiquitination targets in the cell, we used phage display to engineer E2-E4B and E2-CHIP pairs that were free of cross-reactivity with the native UB transfer cascades. We then used the engineered E2-E3 pairs to construct "orthogonal UB transfer (OUT)" cascades so that a mutant UB (xUB) could be exclusively used by the engineered E4B or CHIP to label their substrate proteins. Purification of xUB-conjugated proteins followed by proteomics analysis enabled the identification of hundreds of potential substrates of E4B and CHIP in human embryonic kidney 293 cells. Kinase MAPK3 (mitogen-activated protein kinase 3), methyltransferase PRMT1 (protein arginine -methyltransferase 1), and phosphatase PPP3CA (protein phosphatase 3 catalytic subunit alpha) were identified as the shared substrates of the two E3s. Phosphatase PGAM5 (phosphoglycerate mutase 5) and deubiquitinase OTUB1 (ovarian tumor domain containing ubiquitin aldehyde binding protein 1) were confirmed as E4B substrates, and β-catenin and CDK4 (cyclin-dependent kinase 4) were confirmed as CHIP substrates. On the basis of the CHIP-CDK4 circuit identified by OUT, we revealed that CHIP signals CDK4 degradation in response to endoplasmic reticulum stress.
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20 MeSH Terms
Exact Topological Inference for Paired Brain Networks Persistent Homology.
Chung MK, Vilalta-Gil V, Lee H, Rathouz PJ, Lahey BB, Zald DH
(2017) Inf Process Med Imaging 2017: 299-310
MeSH Terms: Algorithms, Brain, Brain Mapping, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity
Show Abstract · Added March 21, 2018
We present a novel framework for characterizing paired brain networks using techniques in hyper-networks, sparse learning and persistent homology. The framework is general enough for dealing with any type of paired images such as twins, multimodal and longitudinal images. The exact nonparametric statistical inference procedure is derived on testing monotonic graph theory features that do not rely on time consuming permutation tests. The proposed method computes the exact probability in quadratic time while the permutation tests require exponential time. As illustrations, we apply the method to simulated networks and a twin fMRI study. In case of the latter, we determine the statistical significance of the heritability index of the large-scale reward network where every voxel is a network node.
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9 MeSH Terms
Genetic Interactions with Age, Sex, Body Mass Index, and Hypertension in Relation to Atrial Fibrillation: The AFGen Consortium.
Weng LC, Lunetta KL, Müller-Nurasyid M, Smith AV, Thériault S, Weeke PE, Barnard J, Bis JC, Lyytikäinen LP, Kleber ME, Martinsson A, Lin HJ, Rienstra M, Trompet S, Krijthe BP, Dörr M, Klarin D, Chasman DI, Sinner MF, Waldenberger M, Launer LJ, Harris TB, Soliman EZ, Alonso A, Paré G, Teixeira PL, Denny JC, Shoemaker MB, Van Wagoner DR, Smith JD, Psaty BM, Sotoodehnia N, Taylor KD, Kähönen M, Nikus K, Delgado GE, Melander O, Engström G, Yao J, Guo X, Christophersen IE, Ellinor PT, Geelhoed B, Verweij N, Macfarlane P, Ford I, Heeringa J, Franco OH, Uitterlinden AG, Völker U, Teumer A, Rose LM, Kääb S, Gudnason V, Arking DE, Conen D, Roden DM, Chung MK, Heckbert SR, Benjamin EJ, Lehtimäki T, März W, Smith JG, Rotter JI, van der Harst P, Jukema JW, Stricker BH, Felix SB, Albert CM, Lubitz SA
(2017) Sci Rep 7: 11303
MeSH Terms: Age Factors, Aged, Atrial Fibrillation, Body Mass Index, Chromosomes, Human, Pair 4, Epistasis, Genetic, Female, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Hypertension, Male, Middle Aged, Odds Ratio, Polymorphism, Single Nucleotide, Reproducibility of Results, Risk Factors, Sex Characteristics
Show Abstract · Added March 14, 2018
It is unclear whether genetic markers interact with risk factors to influence atrial fibrillation (AF) risk. We performed genome-wide interaction analyses between genetic variants and age, sex, hypertension, and body mass index in the AFGen Consortium. Study-specific results were combined using meta-analysis (88,383 individuals of European descent, including 7,292 with AF). Variants with nominal interaction associations in the discovery analysis were tested for association in four independent studies (131,441 individuals, including 5,722 with AF). In the discovery analysis, the AF risk associated with the minor rs6817105 allele (at the PITX2 locus) was greater among subjects ≤ 65 years of age than among those > 65 years (interaction p-value = 4.0 × 10). The interaction p-value exceeded genome-wide significance in combined discovery and replication analyses (interaction p-value = 1.7 × 10). We observed one genome-wide significant interaction with body mass index and several suggestive interactions with age, sex, and body mass index in the discovery analysis. However, none was replicated in the independent sample. Our findings suggest that the pathogenesis of AF may differ according to age in individuals of European descent, but we did not observe evidence of statistically significant genetic interactions with sex, body mass index, or hypertension on AF risk.
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19 MeSH Terms
An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass Spectrometry Collision Cross Section Measurements.
Stow SM, Causon TJ, Zheng X, Kurulugama RT, Mairinger T, May JC, Rennie EE, Baker ES, Smith RD, McLean JA, Hann S, Fjeldsted JC
(2017) Anal Chem 89: 9048-9055
MeSH Terms: Calibration, Ion Mobility Spectrometry, Laboratories, Lipids, Mass Spectrometry, Molecular Structure, Nitrogen, Proteins, Reproducibility of Results
Show Abstract · Added December 17, 2018
Collision cross section (CCS) measurements resulting from ion mobility-mass spectrometry (IM-MS) experiments provide a promising orthogonal dimension of structural information in MS-based analytical separations. As with any molecular identifier, interlaboratory standardization must precede broad range integration into analytical workflows. In this study, we present a reference drift tube ion mobility mass spectrometer (DTIM-MS) where improvements on the measurement accuracy of experimental parameters influencing IM separations provide standardized drift tube, nitrogen CCS values (CCS) for over 120 unique ion species with the lowest measurement uncertainty to date. The reproducibility of these CCS values are evaluated across three additional laboratories on a commercially available DTIM-MS instrument. The traditional stepped field CCS method performs with a relative standard deviation (RSD) of 0.29% for all ion species across the three additional laboratories. The calibrated single field CCS method, which is compatible with a wide range of chromatographic inlet systems, performs with an average, absolute bias of 0.54% to the standardized stepped field CCS values on the reference system. The low RSD and biases observed in this interlaboratory study illustrate the potential of DTIM-MS for providing a molecular identifier for a broad range of discovery based analyses.
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9 MeSH Terms
Assessment of unilateral ureter obstruction with multi-parametric MRI.
Wang F, Takahashi K, Li H, Zu Z, Li K, Xu J, Harris RC, Takahashi T, Gore JC
(2018) Magn Reson Med 79: 2216-2227
MeSH Terms: Algorithms, Animals, Contrast Media, Diffusion, Disease Models, Animal, Fibrosis, Image Interpretation, Computer-Assisted, Kidney, Kidney Cortex, Magnetic Resonance Imaging, Mice, Mice, Inbred C57BL, Reproducibility of Results, Signal-To-Noise Ratio, Ureter, Ureteral Obstruction
Show Abstract · Added August 17, 2017
PURPOSE - Quantitative multi-parametric MRI (mpMRI) methods may allow the assessment of renal injury and function in a sensitive and objective manner. This study aimed to evaluate an array of MRI methods that exploit endogenous contrasts including relaxation rates, pool size ratio (PSR) derived from quantitative magnetization transfer (qMT), chemical exchange saturation transfer (CEST), nuclear Overhauser enhancement (NOE), and apparent diffusion coefficient (ADC) for their sensitivity and specificity in detecting abnormal features associated with kidney disease in a murine model of unilateral ureter obstruction (UUO).
METHODS - MRI scans were performed in anesthetized C57BL/6N mice 1, 3, or 6 days after UUO at 7T. Paraffin tissue sections were stained with Masson trichrome following MRI.
RESULTS - Compared to contralateral kidneys, the cortices of UUO kidneys showed decreases of relaxation rates R and R , PSR, NOE, and ADC. No significant changes in CEST effects were observed for the cortical region of UUO kidneys. The MRI parametric changes in renal cortex are related to tubular cell death, tubular atrophy, tubular dilation, urine retention, and interstitial fibrosis in the cortex of UUO kidneys.
CONCLUSION - Measurements of multiple MRI parameters provide comprehensive information about the molecular and cellular changes produced by UUO. Magn Reson Med 79:2216-2227, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
© 2017 International Society for Magnetic Resonance in Medicine.
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16 MeSH Terms
Comparative analysis of chimeric ZFP-, TALE- and Cas9-piggyBac transposases for integration into a single locus in human cells.
Luo W, Galvan DL, Woodard LE, Dorset D, Levy S, Wilson MH
(2017) Nucleic Acids Res 45: 8411-8422
MeSH Terms: Bacterial Proteins, CRISPR-Associated Protein 9, CRISPR-Cas Systems, Cell Line, Tumor, DNA Transposable Elements, Endonucleases, Gene Knockout Techniques, Gene Targeting, Gene Transfer Techniques, Humans, Hypoxanthine Phosphoribosyltransferase, Mutagenesis, Insertional, Recombinant Fusion Proteins, Reproducibility of Results, Transcription Activator-Like Effector Nucleases, Transcription Activator-Like Effectors, Transposases, Zinc Fingers
Show Abstract · Added September 11, 2017
Integrating DNA delivery systems hold promise for many applications including treatment of diseases; however, targeted integration is needed for improved safety. The piggyBac (PB) transposon system is a highly active non-viral gene delivery system capable of integrating defined DNA segments into host chromosomes without requiring homologous recombination. We systematically compared four different engineered zinc finger proteins (ZFP), four transcription activator-like effector proteins (TALE), CRISPR associated protein 9 (SpCas9) and the catalytically inactive dSpCas9 protein fused to the amino-terminus of the transposase enzyme designed to target the hypoxanthine phosphoribosyltransferase (HPRT) gene located on human chromosome X. Chimeric transposases were evaluated for expression, transposition activity, chromatin immunoprecipitation at the target loci, and targeted knockout of the HPRT gene in human cells. One ZFP-PB and one TALE-PB chimera demonstrated notable HPRT gene targeting. In contrast, Cas9/dCas9-PB chimeras did not result in gene targeting. Instead, the HPRT locus appeared to be protected from transposon integration. Supplied separately, PB permitted highly efficient isolation of Cas9-mediated knockout of HPRT, with zero transposon integrations in HPRT by deep sequencing. In summary, these tools may allow isolation of 'targeted-only' cells, be utilized to protect a genomic locus from transposon integration, and enrich for Cas9-mutated cells.
Published by Oxford University Press on behalf of Nucleic Acids Research 2017.
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18 MeSH Terms
Application and evaluation of NODDI in the cervical spinal cord of multiple sclerosis patients.
By S, Xu J, Box BA, Bagnato FR, Smith SA
(2017) Neuroimage Clin 15: 333-342
MeSH Terms: Adult, Cervical Cord, Diffusion Magnetic Resonance Imaging, Feasibility Studies, Female, Humans, Image Interpretation, Computer-Assisted, Middle Aged, Multiple Sclerosis, Relapsing-Remitting, Neurites, Reproducibility of Results
Show Abstract · Added March 14, 2018
INTRODUCTION - There is a need to develop imaging methods sensitive to axonal injury in multiple sclerosis (MS), given the prominent impact of axonal pathology on disability and outcome. Advanced multi-compartmental diffusion models offer novel indices sensitive to white matter microstructure. One such model, neurite orientation dispersion and density imaging (NODDI), is sensitive to neurite morphology, providing indices of apparent volume fractions of axons (v), isotropic water (v) and the dispersion of fibers about a central axis (orientation dispersion index, ODI). NODDI has yet to be studied for its sensitivity to spinal cord pathology. Here, we investigate the feasibility and utility of NODDI in the cervical spinal cord of MS patients.
METHODS - NODDI was applied in the cervical spinal cord in a cohort of 8 controls and 6 MS patients. Statistical analyses were performed to test the sensitivity of NODDI-derived indices to pathology in MS (both lesion and normal appearing white matter NAWM). Diffusion kurtosis imaging (DKI) and diffusion tensor imaging (DTI) analysis were also performed to compare with NODDI.
RESULTS - A decrease in NODDI-derived v was observed at the site of the lesion ( < 0.01), whereas a global increase in ODI was seen throughout white matter ( < 0.001). DKI-derived mean kurtosis (MK) and radial kurtosis (RK) and DTI-derived fractional anisotropy (FA) and radial diffusivity (RD) were all significantly different in MS patients ( < 0.02), however NODDI provided higher contrast between NAWM and lesion in all MS patients.
CONCLUSION - NODDI provides unique contrast that is not available with DKI or DTI, enabling improved characterization of the spinal cord in MS.
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11 MeSH Terms
Genome-wide association and pathway analysis of left ventricular function after anthracycline exposure in adults.
Wells QS, Veatch OJ, Fessel JP, Joon AY, Levinson RT, Mosley JD, Held EP, Lindsay CS, Shaffer CM, Weeke PE, Glazer AM, Bersell KR, Van Driest SL, Karnes JH, Blair MA, Lagrone LW, Su YR, Bowton EA, Feng Z, Ky B, Lenihan DJ, Fisch MJ, Denny JC, Roden DM
(2017) Pharmacogenet Genomics 27: 247-254
MeSH Terms: Adult, Anthracyclines, Cohort Studies, Demography, Female, Genome-Wide Association Study, Humans, Male, Middle Aged, Reproducibility of Results, Signal Transduction, Stroke Volume, Ventricular Function, Left
Show Abstract · Added March 14, 2018
BACKGROUND - Anthracyclines are important chemotherapeutic agents, but their use is limited by cardiotoxicity. Candidate gene and genome-wide studies have identified putative risk loci for overt cardiotoxicity and heart failure, but there has been no comprehensive assessment of genomic variation influencing the intermediate phenotype of anthracycline-related changes in left ventricular (LV) function. The purpose of this study was to identify genetic factors influencing changes in LV function after anthracycline chemotherapy.
METHODS - We conducted a genome-wide association study (GWAS) of change in LV function after anthracycline exposure in 385 patients identified from BioVU, a resource linking DNA samples to de-identified electronic medical record data. Variants with P values less than 1×10 were independently tested for replication in a cohort of 181 anthracycline-exposed patients from a prospective clinical trial. Pathway analysis was performed to assess combined effects of multiple genetic variants.
RESULTS - Both cohorts were middle-aged adults of predominantly European descent. Among 11 candidate loci identified in discovery GWAS, one single nucleotide polymorphism near PR domain containing 2, with ZNF domain (PRDM2), rs7542939, had a combined P value of 6.5×10 in meta-analysis. Eighteen Kyoto Encyclopedia of Gene and Genomes pathways showed strong enrichment for variants associated with the primary outcome. Identified pathways related to DNA repair, cellular metabolism, and cardiac remodeling.
CONCLUSION - Using genome-wide association we identified a novel candidate susceptibility locus near PRDM2. Variation in genes belonging to pathways related to DNA repair, metabolism, and cardiac remodeling may influence changes in LV function after anthracycline exposure.
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13 MeSH Terms
Breast tissue stiffness estimation for surgical guidance using gravity-induced excitation.
Griesenauer RH, Weis JA, Arlinghaus LR, Meszoely IM, Miga MI
(2017) Phys Med Biol 62: 4756-4776
MeSH Terms: Breast, Breast Neoplasms, Female, Gravitation, Humans, Magnetic Resonance Imaging, Reproducibility of Results, Surgery, Computer-Assisted
Show Abstract · Added July 23, 2018
Tissue stiffness interrogation is fundamental in breast cancer diagnosis and treatment. Furthermore, biomechanical models for predicting breast deformations have been created for several breast cancer applications. Within these applications, constitutive mechanical properties must be defined and the accuracy of this estimation directly impacts the overall performance of the model. In this study, we present an image-derived computational framework to obtain quantitative, patient specific stiffness properties for application in image-guided breast cancer surgery and interventions. The method uses two MR acquisitions of the breast in different supine gravity-loaded configurations to fit mechanical properties to a biomechanical breast model. A reproducibility assessment of the method was performed in a test-retest study using healthy volunteers and was further characterized in simulation. In five human data sets, the within subject coefficient of variation ranged from 10.7% to 27% and the intraclass correlation coefficient ranged from 0.91-0.944 for assessment of fibroglandular and adipose tissue stiffness. In simulation, fibroglandular content and deformation magnitude were shown to have significant effects on the shape and convexity of the objective function defined by image similarity. These observations provide an important step forward in characterizing the use of nonrigid image registration methodologies in conjunction with biomechanical models to estimate tissue stiffness. In addition, the results suggest that stiffness estimation methods using gravity-induced excitation can reliably and feasibly be implemented in breast cancer surgery/intervention workflows.
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High spatial correspondence at a columnar level between activation and resting state fMRI signals and local field potentials.
Shi Z, Wu R, Yang PF, Wang F, Wu TL, Mishra A, Chen LM, Gore JC
(2017) Proc Natl Acad Sci U S A 114: 5253-5258
MeSH Terms: Animals, Brain, Brain Mapping, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Neurons, Neurovascular Coupling, Reproducibility of Results, Rest, Saimiri, Somatosensory Cortex
Show Abstract · Added May 4, 2017
Although blood oxygenation level-dependent (BOLD) fMRI has been widely used to map brain responses to external stimuli and to delineate functional circuits at rest, the extent to which BOLD signals correlate spatially with underlying neuronal activity, the spatial relationships between stimulus-evoked BOLD activations and local correlations of BOLD signals in a resting state, and whether these spatial relationships vary across functionally distinct cortical areas are not known. To address these critical questions, we directly compared the spatial extents of stimulated activations and the local profiles of intervoxel resting state correlations for both high-resolution BOLD at 9.4 T and local field potentials (LFPs), using 98-channel microelectrode arrays, in functionally distinct primary somatosensory areas 3b and 1 in nonhuman primates. Anatomic images of LFP and BOLD were coregistered within 0.10 mm accuracy. We found that the point spread functions (PSFs) of BOLD and LFP responses were comparable in the stimulus condition, and both estimates of activations were slightly more spatially constrained than local correlations at rest. The magnitudes of stimulus responses in area 3b were stronger than those in area 1 and extended in a medial to lateral direction. In addition, the reproducibility and stability of stimulus-evoked activation locations within and across both modalities were robust. Our work suggests that the intrinsic resolution of BOLD is not a limiting feature in practice and approaches the intrinsic precision achievable by multielectrode electrophysiology.
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11 MeSH Terms