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1. chinaXiv:201607.00041 [pdf]

Computations of superstring amplitudes in pure spinor formalism via Cadabra

Sun, Kesheng; Ding, Xiangmao; Sun, Fei; Zhang, Haibin
Subjects: Physics >> The Physics of Elementary Particles and Fields

In this paper, we will illustrate how computer algebra system Cadabra is used in computing the supersymmetric amplitude in pure spinor formalism and provide the source code that computes the tree-level massless 5-gluon amplitude.

submitted time 2016-07-13 Hits3501Downloads922 Comment 1

2. chinaXiv:201605.01727 [pdf]

Cilostazol inhibits plasmacytoid dendritic cell activation and antigen presentation

Sun, Fei; Yin, Zhao; Shi, Quan-Xing; Zhao, Bei; Wang, Shou-Li; Yu, Hai-Sheng; Zhang, Li-Guo
Subjects: Biology >> Biophysics

Background Cilostazol, an anti-platelet drug for treating coronary heart disease, has been reported to modulate immune cell functions. Plasmacytoid dendritic cells (pDCs) have been found to participate in the progression of atherosclerosis mainly through interferon a (IFN-alpha) production. Whether cilostazol influences pDCs activation is still not clear. In this study, we aimed to investigate the effects of cilostazol on cell activation and antigen presentation of pDCs in vitro in this study. Methods Peripheral blood mononuclear cells isolated by Ficoll centrifugation and pDCs sorted by flow cytometry were used in this study. After pretreated with cilostazol for 2 h, cells were stimulated with CpG-A, R848 or virus for 6 h or 20 h, or stimulated with CpG-B for 48 h and then co-cultured with naive T cell for five days. Cytokines in supernatant and intracellular cytokines were analyzed by ELISA or flow cytometry respectively. Results Our data indicated that cilostazol could inhibit IFN-alpha and tumor necrosis factor a (TNF-alpha) production from pDCs in a dose-dependent manner. In addition, the ability of priming naive T cells of pDCs was also impaired by cilostazol. The inhibitory effect was not due to cell killing since the viability of pDCs did not change upon cilostazol treatment. Conclusion Cilostazol inhibits pDCs cell activation and antigen presentation in vitro, which may explain how cilostazol protects against atherosclerosis.

submitted time 2016-05-15 Hits1768Downloads844 Comment 0

3. chinaXiv:201605.01525 [pdf]

Three-dimensional super-resolution protein localization correlated with vitrified cellular context

Liu, Bei; Xue, Yanhong; Zhao, Wei; Chen, Yan; Fan, Chunyan; Gu, Lusheng; Zhang, Yongdeng; Zhang, Xiang; Sun, Lei; Huang, Xiaojun; Ding, Wei; Sun, Fei; Ji, Wei; Xu, Tao; Liu, Bei; Gu, Lusheng; Zhang, Yongdeng; Xu, Tao; Zhao, Wei; Chen, Yan
Subjects: Biology >> Biophysics

We demonstrate the use of cryogenic super-resolution correlative light and electron microscopy (csCLEM) to precisely determine the spatial relationship between proteins and their native cellular structures. Several fluorescent proteins (FPs) were found to be photoswitchable and emitted far more photons under our cryogenic imaging condition, resulting in higher localization precision which is comparable to ambient super-resolution imaging. Vitrified specimens were prepared by high pressure freezing and cryo-sectioning to maintain a near-native state with better fluorescence preservation. A 2-3-fold improvement of resolution over the recent reports was achieved due to the photon budget performance of screening out Dronpa and optimized imaging conditions, even with thin sections which is at a disadvantage when calculate the structure resolution from label density. We extended csCLEM to mammalian cells by introducing cryo-sectioning and observed good correlation of a mitochondrial protein with the mitochondrial outer membrane at nanometer resolution in three dimensions.

submitted time 2016-05-12 Hits1520Downloads904 Comment 0

4. chinaXiv:201605.01471 [pdf]

A novel mitochondrial carrier protein Mme1 acts as a yeast mitochondrial magnesium exporter

Cui, Yixian; Zhao, Shanke; Wang, Juan; Wang, Xudong; Fan, Qiangwang; Zhou, Bing; Gao, Bingquan; Sun, Fei
Subjects: Biology >> Biophysics >> Biochemistry & Molecular Biology

The homeostasis of magnesium (Mg2+), an abundant divalent cation indispensable for many biological processes including mitochondrial functions, is underexplored. Previously, two mitochondrial Mg2+ importers, Mrs2 and Lpe10, were characterized for mitochondrial Mg2+ uptake. We now show that mitochondrial Mg2+ homeostasis is accurately controlled through the combined effects of previously known importers and a novel exporter, Mme1 (mitochondrial magnesium exporter 1). Mme1 belongs to the mitochondrial carrier family and was isolated for its mutation that is able to suppress the mrs2 Delta respiration defect. Deletion of MME1 significantly increased steady-state mitochondrial Mg2+ concentration, while overexpression decreased it. Measurements of Mg2+ exit from proteoliposomes reconstituted with purified Mme1 provided definite evidence for Mme1 as an Mg2+ exporter. Our studies identified, for the first time, a mitochondrial Mg2+ exporter that works together with mitochondrial importers to ensure the precise control of mitochondrial Mg2+ homeostasis. (C) 2015 Elsevier B.V. All rights reserved.

submitted time 2016-05-12 Hits971Downloads492 Comment 0

5. chinaXiv:201605.01409 [pdf]

Expression, purification, crystallization and crystallographic study of the Aspergillus terreus aromatic prenyltransferase AtaPT

Gao, Bingquan; Sun, Fei; Gao, Bingquan; Chen, Ridao; Liu, Xiao; Dai, Jungui; Chen, Ridao; Liu, Xiao; Dai, Jungui; Liu, Xiao
Subjects: Biology >> Biophysics

Prenylated aromatics are produced by aromatic prenyltransferases during the secondary metabolism of bacteria, fungi and plants. The prenylation of nonprenylated precursors can lead to great chemical diversity and extensive biological properties. Aspergillus terreus aromatic prenyltransferase (AtaPT), which has recently been discovered and characterized, is such an enzyme and is responsible for the prenylation of various aromatic compounds. Here, recombinant AtaPT was overexpressed in Escherichia coli, purified and crystallized. Diffraction data were collected to a resolution of 1.71 angstrom and the crystal belonged to space group P2(1)2(1)2, with unit-cell parameters a = 96.2, b = 135.8, c = 69.5 angstrom, alpha = beta = gamma = 90 degrees. Analysis of the calculated Matthews coefficient and the self-rotation function suggested that there are two AtaPT molecules in the asymmetric unit.

submitted time 2016-05-12 Hits912Downloads489 Comment 0

6. chinaXiv:201605.01402 [pdf]

PGE2 Elevates IL-23 Production in Human Dendritic Cells via a cAMP Dependent Pathway

Shi, Quanxing; Yin, Zhao; Zhao, Bei; Sun, Fei; Wang, Shouli; Yu, Haisheng; Yin, Xiangyun; Zhang, Liguo
Subjects: Biology >> Biophysics >> Cell Biology

PGE2 elevates IL-23 production in mouse dendritic cells while inhibits IL-23 production in isolated human monocytes. Whether this differential effect of PGE2 on IL-23 production is cell-type-or species-specific has not been investigated in detail. The present study was designed to investigate the effect of PGE2 on IL-23 production in human DCs and the possible underlying mechanisms. Human monocytes derived dendritic cells (Mo-DCs) were pretreated with or without PGE2. Then the cells were incubated with zymosan. Our results demonstrated that PGE2 promoted zymosan-induced IL-23 production in a concentration dependent manner. In addition, it was found that PGE2 is also able to elevate MyD88-mediated IL-23 p19 promoter activity. More importantly, ELISA data demonstrated that db-cAMP, a cAMP analog, and forskolin, an adenylate cyclase activator, can mimic the effect of PGE2 on zymosan-induced IL-23 production, and rp-cAMP, a protein kinase A (PKA) inhibitor, can block the effect of PGE2. Moreover, PGE2 can increase zymosan-induced expression of the mRNA levels of both p19 and p40 subunits, which was mimicked by db-cAMP and forskolin. Our data suggest that PGE2 elevates the production of IL-23 in humanMo-DCs via a cAMP dependent pathway.

submitted time 2016-05-12 Hits1227Downloads657 Comment 0

7. chinaXiv:201605.01243 [pdf]

Acyl-CoA Dehydrogenase Drives Heat Adaptation by Sequestering Fatty Acids

Ma, Dengke K.; Lu, Alice Y.; Horvitz, H. Robert; Li, Zhijie; Sun, Fang; Sun, Fei; Chen, Sidi; Horvitz, H. Robert; Rothe, Michael; Menzel, Ralph
Subjects: Biology >> Biophysics >> Biochemistry & Molecular Biology

Cells adapt to temperature shifts by adjusting levels of lipid desaturation and membrane fluidity. This fundamental process occurs in nearly all forms of life, but its mechanism in eukaryotes is unknown. We discovered that the evolutionarily conserved Caenorhabditis elegans gene acdh-11 (acyl-CoA dehydrogenase [ACDH]) facilitates heat adaptation by regulating the lipid desaturase FAT-7. Human ACDH deficiency causes the most common inherited disorders of fatty acid oxidation, with syndromes that are exacerbated by hyperthermia. Heat upregulates acdh-11 expression to decrease fat-7 expression. We solved the high-resolution crystal structure of ACDH-11 and established the molecular basis of its selective and high-affinity binding to C11/C12-chain fatty acids. ACDH-11 sequesters C11/C12-chain fatty acids and prevents these fatty acids from activating nuclear hormone receptors and driving fat-7 expression. Thus, the ACDH-11 pathway drives heat adaptation by linking temperature shifts to regulation of lipid desaturase levels and membrane fluidity via an unprecedented mode of fatty acid signaling.

submitted time 2016-05-11 Hits820Downloads418 Comment 0

8. chinaXiv:201605.01198 [pdf]

A novel fully automatic scheme for fiducial marker-based alignment in electron tomography

Han, Renmin; Zhang, Fa; Han, Renmin; Sun, Fei; Liu, Zhiyong; Sun, Fei; Sun, Fei
Subjects: Biology >> Biophysics >> Biochemistry & Molecular Biology

Although the topic of fiducial marker-based alignment in electron tomography (ET) has been widely discussed for decades, alignment without human intervention remains a difficult problem. Specifically, the emergence of subtomogram averaging has increased the demand for batch processing during tomographic reconstruction; fully automatic fiducial marker-based alignment is the main technique in this process. However, the lack of an accurate method for detecting and tracking fiducial markers precludes fully automatic alignment. In this paper, we present a novel, fully automatic alignment scheme for ET. Our scheme has two main contributions: First, we present a series of algorithms to ensure a high recognition rate and precise localization during the detection of fiducial markers. Our proposed solution reduces fiducial marker detection to a sampling and classification problem and further introduces an algorithm to solve the parameter dependence of marker diameter and marker number. Second, we propose a novel algorithm to solve the tracking of fiducial markers by reducing the tracking problem to an incomplete point set registration problem. Because a global optimization of a point set registration occurs, the result of our tracking is independent of the initial image position in the tilt series, allowing for the robust tracking of fiducial markers without pre-alignment. The experimental results indicate that our method can achieve an accurate tracking, almost identical to the current best one in IMOD with half automatic scheme. Furthermore, our scheme is fully automatic, depends on fewer parameters (only requires a gross value of the marker diameter) and does not require any manual interaction, providing the possibility of automatic batch processing of electron tomographic reconstruction. (C) 2015 Elsevier Inc. All rights reserved.

submitted time 2016-05-11 Hits1189Downloads742 Comment 0

9. chinaXiv:201605.00758 [pdf]

A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules

Shan, Hong; Yin, Chang-Cheng; Sun, Fei; Wang, Zihao; Zhang, Fa; Wang, Zihao; Zhang, Fa; Wang, Zihao; Sun, Fei; Xiong, Yong; Sun, Fei;
Subjects: Biology >> Biophysics >> Cell Biology

Single particle analysis, which can be regarded as an average of signals from thousands or even millions of particle projections, is an efficient method to study the three-dimensional structures of biological macromolecules. An intrinsic assumption in single particle analysis is that all the analyzed particles must have identical composition and conformation. Thus specimen heterogeneity in either composition or conformation has raised great challenges for high-resolution analysis. For particles with multiple conformations, inaccurate alignments and orientation parameters will yield an averaged map with diminished resolution and smeared density. Besides extensive classification approaches, here based on the assumption that the macromolecular complex is made up of multiple rigid modules whose relative orientations and positions are in slight fluctuation around equilibriums, we propose a new method called as local optimization refinement to address this conformational heterogeneity for an improved resolution. The key idea is to optimize the orientation and shift parameters of each rigid module and then reconstruct their three-dimensional structures individually. Using simulated data of 80S/70S ribosomes with relative fluctuations between the large (60S/50S) and the small (40S/30S) subunits, we tested this algorithm and found that the resolutions of both subunits are significantly improved. Our method provides a proof-of-principle solution for high-resolution single particle analysis of macromolecular complexes with dynamic conformations.

submitted time 2016-05-05 Hits1127Downloads657 Comment 0

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