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Detecting peroxiredoxin hyperoxidation by one-dimensional isoelectric focusing
Zhenbo Cao, Neil J. Bulleid
Biophysics Reports    2015, 1 (1): 14-17.   DOI: 10.1007/s41048-015-0007-y
Abstract   PDF (408KB)
The activity of typical 2-cys peroxiredoxin (Prxs) can be regulated by hyperoxidation with a consequent loss of redox activity. Here we developed a simple assay to monitor the level of hyperoxidation of different typical 2-cys prxs simultaneously. This assay only requires standard equipment and can compare different samples on the same gel. It requires much less time than conventional 2D gels and gives more information than Western blotting with an antibody specific for hyperoxidized peroxiredoxin. This method could also be used to monitor protein modification with a charge difference such as phosphorylation.
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Implications for directionality of nanoscale forces in bacterial attachment
Jan J. T. M. Swartjes, Deepak H. Veeregowda
Biophysics Reports    2015, 1 (3): 120-126.   DOI: 10.1007/s41048-016-0019-2
Abstract   PDF (1432KB)
Adhesion and friction are closely related and play a predominant role in many natural processes. From the wall-clinging feet of the gecko to bacteria forming a biofilm, in many cases adhesion is a necessity to survive. The direction in which forces are applied has shown to influence the bond strength of certain systems tremendously and can mean the difference between adhesion and detachment. The spatula present on the extension of the feet of the gecko can either attach or detach, based on the angle at which they are loaded. Certain proteins are known to unfold at different loads, depending on the direction at which the load is applied and some bacteria have specific receptors which increase their bond strength in the presence of shear. Bacteria adhere to any man-made surface despite the presence of shear forces due to running fluids, air flow, and other causes. In bacterial adhesion research, however, adhesion forces are predominantly measured perpendicularly to surfaces, whereas other directions are often neglected. The angle of shear forces acting on bacteria or biofilms will not be at a 90 angle, as shear induced by flow is often along the surface. Measuring at different angles or even lateral to the surface will give a more complete overview of the adhesion forces and mechanism, perhaps even resulting in alternative means to discourage bacterial adhesion or promote removal.
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Physics-based RNA structure prediction
Xiaojun Xu, Shi-Jie Chen
Biophysics Reports    2015, 1 (1): 2-13.   DOI: 10.1007/s41048-015-0001-4
Abstract   PDF (1685KB)
Despite the success of RNA secondary structure prediction for simple, short RNAs, the problem of predicting RNAs with long-range tertiary folds remains. Furthermore, RNA 3D structure prediction is hampered by the lack of the knowledge about the tertiary contacts and their thermodynamic parameters. Low-resolution structural modeling enables us to estimate the conformational entropies for a number of tertiary folds through rigorous statistical mechanical calculations. The models lead to 3D tertiary folds at coarse-grained level. The coarse-grained structures serve as the initial structures for all-atom molecular dynamics refinement to build the final all-atom 3D structures. In this paper, we present an overview of RNA computational models for secondary and tertiary structures' predictions and then focus on a recently developed RNA statistical mechanical model—the Vfold model. The main emphasis is placed on the physics behind the models, including the treatment of the non-canonical interactions in secondary and tertiary structure modelings, and the correlations to RNA functions.
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Biophysics Reports: focus on theoretical and technical advances
Tao Xu
Biophysics Reports    2015, 1 (1): 1-1.   DOI: 10.1007/s41048-015-0010-3
Abstract   PDF (301KB)
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An efficient two-step subcellular fractionation method for the enrichment of insulin granules from INS-1 cells
Yan Chen, Zhiping Xia, Lifen Wang, Yong Yu, Pingsheng Liu, Eli Song, Tao Xu
Biophysics Reports    2015, 1 (1): 34-40.   DOI: 10.1007/s41048-015-0008-x
Abstract   PDF (1234KB)
Insulin is one of the key regulators for blood glucose homeostasis. More than 99% of insulin is secreted from the pancreatic β-cells. Within each β-cell, insulin is packaged and processed in insulin secretary granules (ISGs) before its exocytosis. Insulin secretion is a complicated but well-organized dynamic process that includes the budding of immature ISGs (iISGs) from the trans-Golgi network, iISG maturation, and mature ISG (mISG) fusion with plasma membrane. However, the molecular mechanisms involved in this process are largely unknown. It is therefore crucial to separate and enrich iISGs and mISGs before determining their distinct characteristics and protein contents. Here, we developed an efficient two-step subcellular fractionation method for the enrichment of iISGs and mISGs from INS-1 cells: OptiPrep gradient purification followed by Percoll solution purification. We demonstrated that by using this method, iISGs and mISGs can be successfully distinguished and enriched. This method can be easily adapted to investigate SGs in other cells or tissues, thereby providing a useful tool for elucidating the mechanisms of granule maturation and secretion.
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Phosphorylation and function of DGAT1 in skeletal muscle cells
Jinhai Yu, Yiran Li, Fei Zou, Shimeng Xu, Pingsheng Liu
Biophysics Reports    2015, 1 (1): 41-50.   DOI: 10.1007/s41048-015-0004-1
Abstract   PDF (5854KB)
Aberrant intramuscular triacylglycerol (TAG) storage in human skeletal muscle is closely related to insulin insensitivity. Excessive lipid storage can induce insulin resistance of skeletal muscle, and under severe conditions, lead to type 2 diabetes. The balance of interconversion between diacylglycerol and TAG greatly influences lipid storage and utilization. Diacylglycerol O-acyltransferase 1 (DGAT1) plays a key role in this process, but its activation and phosphorylation requires further dissection. In this study, 12 putative conserved phosphorylation sites of DGAT1 were identified by examining amino acid conservation of DGAT1 in different species. Another 12 putative phosphorylation sites were also found based on bioinformatics predictions and previous reports. Meanwhile, several phosphorylation sites of DGAT1 were verified by phosphorylation mass spectrometry analysis of purified DGAT1 from mouse myoblast C2C12 cells. Using single point mutations, a regulatory role of 3 putative phosphorylation sites was dissected. Finally, using truncation mutations, a potential domain of DGAT1 that was involved in the regulation of enzymatic activity was revealed. This study provides useful information for further understanding DGAT1 activity regulation.
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Visualizing the Ensemble Structures of Protein Complexes Using Chemical Cross-Linking Coupled with Mass Spectrometry
Zhou Gong, Yue-He Ding, Xu Dong, Na Liu, E. Erquan Zhang, Meng-Qiu Dong, Chun Tang
Biophysics Reports    2015, 1 (3): 127-138.   DOI: 10.1007/s41048-015-0015-y
Abstract   PDF (1992KB)
Chemical cross-linking coupled with mass spectrometry (CXMS) identifies protein residues that are close in space, and has been increasingly used for modeling the structures of protein complexes. Here we show that a single structure is usually sufficient to account for the intermolecular cross-links identified for a stable complex with sub-μmol/L binding affinity. In contrast,we show that the distance between two cross-linked residues in the different subunits of a transient or fleeting complex may exceed the maximum length of the cross-linker used, and the cross-links cannot be fully accounted for with a unique complex structure. We further show that the seemingly incompatible cross-links identified with high confidence arise from alternative modes of protein-protein interactions. By converting the intermolecular crosslinks to ambiguous distance restraints, we established a rigid-body simulated annealing refinement protocol to seek the minimum set of conformers collectively satisfying the CXMS data. Hence we demonstrate that CXMS allows the depiction of the ensemble structures of protein complexes and elucidates the interaction dynamics for transient and fleeting complexes.
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Transcriptomic analysis of human breast cancer cells reveals differentially expressed genes and related cellular functions and pathways in response to gold nanorods
Teng Zhou, Yipeng Du, Taotao Wei
Biophysics Reports    2015, 1 (2): 106-114.   DOI: 10.1007/s41048-015-0005-0
Abstract   PDF (1703KB)
Breast cancer is the leading cause of cancer deaths inwomen.Recent advances in nanomedicine have shown that gold nanorods (AuNRs), as multifunctional drug delivery and photothermal therapeutic agents, have potential for use in cancer therapy. However, the effect of AuNRs on the transcriptome of breast cancer cells is unknown. In the present study, cells of the triple-negative human breast cancer cell line MDA-MB-231, which has high metastatic activity, were treated with AuNRs for transcriptomic analysis using RNA-seq technology. In total, 3126 genes were found to be up-regulated and 3558 genes were found to be downregulated inAuNR-treatedMDA-MB-231 cells. These differentially expressed genes presumably take part in multiple biological pathways, including glycolysis and regulation of the actin cytoskeleton, and impact a variety of cellular functions, including chemoattractant activity. The distinct gene expression profile of MDA-MB-231 cells treated with AuNRs provides a foundation for further screening and validation of important genes involved in the interaction between AuNRs and MDA-MB-231 cells.
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Solubilization and purification of recombinant modified C-reactive protein from inclusion bodies using reversible anhydride modification
Lawrence A. Potempa, Zhen-Yu Yao, Shang-Rong Ji, János G. Filep, Yi Wu
Biophysics Reports    2015, 1 (1): 18-33.   DOI: 10.1007/s41048-015-0003-2
Abstract   PDF (2149KB)
The precise function of C-reactive protein (CRP) as a regulator of inflammation in health and disease continues to evolve. The true understanding of its role in host defense responses has been hampered by numerous reports of comparable systems with contradictory interpretations of CRP as a stimulator, suppressor, or benign contributor to such processes. These discrepancies may be explained in part by the existence of a naturally occurring CRP isoform, termed modified CRP (i.e., mCRP), that is expressed when CRP subunits are dissociated into monomeric structures. The free mCRP subunit undergoes a non-proteolytic conformational change that has unique solubility, antigenicity, and bioactivity compared to the subunits that remain associated in the native, pentameric CRP molecule (i.e., pCRP). As specific reagents have been developed to identify and quantify mCRP, it has become apparent that this isoform can be formed spontaneously in calcium-free solutions. Furthermore, mCRP can be expressed on perturbed cell membranes with as little as 24-48 h incubation in tissue culture. Because mCRP has the same size as pCRP subunits as evaluated by SDS-PAGE, its presence in a pCRP reagent would not be apparent using this technique to evaluate purity. Finally, because many antibody reagents purported to be specific for "CRP" contains some, or substantial specificity tomCRP, antigen-detection techniques using such reagents may fail to distinguish the specific CRP isoform detected. All these caveats concerning CRP structures and measurements suggest that the aforementioned contradictory studies may reflect to some extent on distinctive bioactivities of mCRP rather than on pCRP. To provide a reliable, abundant supply of mCRP for separate and comparable studies, a recombinant proteinwas engineered and expressed in E. coli (i.e., recombinant mCRP or rmCRP). Synthesized protein was produced as inclusion bodies which proved difficult to solubilize for purification and characterization. Herein, we describe a method using anhydride reagents to effectively solubilize rmCRP and allow for chromatographic purification in high yield and free of contaminating endotoxin. Furthermore, the purified rmCRP reagent represents an excellent comparable protein to the biologically produced mCRP and as a distinctive reagent from pCRP. Deciphering the true function of CRP in both health and disease requires a knowledge, understanding, and reliable supply of each of its structures so to define the distinctive effects of each on the body's response to tissue damaging events.
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Pseudomonas sp. LZ-Q continuously degrades phenanthrene under hypersaline and hyperalkaline condition in a membrane bioreactor system
Yiming Jiang, Haiying Huang, Mengru Wu, Xuan Yu, Yong Chen, Pu Liu, Xiangkai Li
Biophysics Reports    2015, 1 (3): 156-167.   DOI: 10.1007/s41048-016-0018-3
Abstract   PDF (1399KB)
Phenanthrene is one of the most recalcitrant components of crude oil-contaminated wastewater. An efficient phenanthrene-degrading bacterium Pseudomonas sp. strain named LZ-Q was isolated from oil-contaminated soil near the sewage outlet of a petrochemical company. Pseudomonas sp. LZ-Q is able to degrade 1000 mg/L phenanthrene in Bushnell-Hass mineral salt medium. It also degrades other polycyclic aromatic hydrocarbons such as naphthalene, anthracene, pyrene, petrol, and diesel at broad ranges of salinities of 5 g/L to 75 g/L, pHs of 5.0-10.0, and temperatures of 10-42 ℃. Therefore, Pseudomonas sp. LZ-Q could be a good candidate for remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated wastewater. A membrane bioreactor (MBR) was applied to investigate the remediation ability of the strain LZ-Q. Wastewater containing phenanthrene with pH of 8, salinity of 35 g/L, and COD of 500 mg/L was continuously added to the system (HRT = 3 h). Results showed that Pseudomonas sp. LZ-Q is capable of degrading 96% of 20 mg/L phenanthrene and 94% of 500 mg/L COD for 60 days in a continuous mode. These results showed that the MBR system with strain LZ-Q might be a good approach for PAHs' remediation in industrial wastewaters.
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Analysis of chromatin bersin Hela cells with electron tomography
Xiaomin Li, Hongli Feng, Jianguo Zhang, Lei Sun, Ping Zhu
Biophysics Reports    2015, 1 (1): 51-60.   DOI: 10.1007/x41048-015-0009-9
Abstract   PDF (2590KB)
The presence and folding pattern of chromatin in eukaryotic cells remain elusive and controversial. In this study, we prepared ultra-thin sections of Hela cells with three different fixation and sectioning methods, i.e., chemical fixation, high pressure freezing with freeze substitution, and cryo-ultramicro- tomy with SEM-FIB (focused ion beam), and analyzed in vivo architecture of chromatin fibers in Hela nuclei with electron tomography technology. The results suggest that the chromatin fibers in eukaryotic Hela cells are likely organized in an architecture with a diameter of about 30 nm.
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A new dimethyl labeling-based SID-MRM-MS method and its application to three proteases involved in insulin maturation
Dongwan Cheng, Li Zheng, Junjie Hou, Jifeng Wang, Peng Xue, Fuquan Yang, Tao Xu
Biophysics Reports    2015, 1 (2): 71-80.   DOI: 10.1007/s41048-015-0012-1
Abstract   PDF (2339KB)
The absolute quantification of target proteins in proteomics involves stable isotope dilution coupled with multiple reactions monitoring mass spectrometry (SID-MRM-MS). The successful preparation of stable isotope-labeled internal standard peptides is an important prerequisite for the SID-MRM absolute quantification methods. Dimethyl labeling has been widely used in relative quantitative proteomics and it is fast, simple, reliable, cost-effective, and applicable to any protein sample, making it an ideal candidate method for the preparation of stable isotope-labeled internal standards. MRM mass spectrometry is of high sensitivity, specificity, and throughput characteristics and can quantify multiple proteins simultaneously, including low-abundance proteins in precious samples such as pancreatic islets. In this study, a new method for the absolute quantification of three proteases involved in insulin maturation, namely PC1/3, PC2 and CPE, was developed by coupling a stable isotope dimethyl labeling strategy for internal standard peptide preparation with SID-MRM-MS quantitative technology. This method offers a new and effective approach for deep understanding of the functional status of pancreatic β cells and pathogenesis in diabetes.
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Mapping disulfide bonds from sub-micrograms of purified proteins or micrograms of complex protein mixtures
Shan Lu, Yong Cao, Sheng-Bo Fan, Zhen-Lin Chen, Run-Qian Fang, Si-Min He, Meng-Qiu Dong
Biophysics Reports    2018, 4 (2): 68-81.   DOI: 10.1007/s41048-018-0050-6
Abstract   PDF (3008KB)
Disulfide bonds are vital for protein functions, but locating the linkage sites has been a challenge in protein chemistry, especially when the quantity of a sample is small or the complexity is high. In 2015, our laboratory developed a sensitive and efficient method for mapping protein disulfide bonds from simple or complex samples (Lu et al. in Nat Methods 12:329, 2015). This method is based on liquid chromatography-mass spectrometry (LC-MS) and a powerful data analysis software tool named pLink. To facilitate application of this method, we present step-by-step disulfide mapping protocols for three types of samples-purified proteins in solution, proteins in SDS-PAGE gels, and complex protein mixtures in solution. The minimum amount of protein required for this method can be as low as several hundred nanograms for purified proteins, or tens of micrograms for a mixture of hundreds of proteins. The entire workflow-from sample preparation to LC-MS and data analysis-is described in great detail. We believe that this protocol can be easily implemented in any laboratory with access to a fastscanning, high-resolution, and accurate-mass LC-MS system.
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Thermodynamics of GPCR activation
Xuejun C. Zhang, Ye Zhou, Can Cao
Biophysics Reports    2015, 1 (3): 115-119.   DOI: 10.1007/s41048-016-0017-4
Abstract   PDF (594KB)
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The application of traditional transmission electron microscopy for autophagy research in Caenorhabditis elegans
Attila L. Kovács
Biophysics Reports    2015, 1 (2): 99-105.   DOI: 10.1007/s41048-015-0014-z
Abstract   PDF (362KB)
Traditional ultrastructural characterization of autophagic processes remains an important approach to be used in parallel with molecular genetics, light microscopy, and other methods. The special nature of Caenorhabditis elegans as an object for transmission electron microscopy makes its introduction into autophagy research a challenging task. The basis of the protocol to prepare C. elegans samples for autophagy studies was worked out around the turn of the millennium and has been used since then in my laboratory with some modifications. The method described here enables the user to prepare samples for systematic morphologic as well as morphometric investigations to characterize autophagy with a high but still realistic investment of effort.
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Radioligand saturation binding for quantitative analysis of ligand-receptor interactions
Chengyan Dong, Zhaofei Liu, Fan Wang
Biophysics Reports    2015, 1 (3): 148-155.   DOI: 10.1007/s41048-016-0016-5
Abstract   PDF (474KB)
The reversible combination of a ligand with specific sites on the surface of a receptor is one of the most important processes in biochemistry. A classic equation with a useful simple graphical method was introduced to obtain the equilibrium constant, Kd, and the maximum density of receptors, Bmax. The entire 125I-labeled ligand binding experiment includes three parts: the radiolabeling, cell saturation binding assays and the data analysis. The assay format described here is quick, simple, inexpensive, and effective, and provides a gold standard for the quantification of ligand-receptor interactions. Although the binding assays and quantitative analysis have not changed dramatically compared to the original methods, we integrate all the parts to calculate the parameters in one concise protocol and adjust many details according to our experience. In every step, several optional methods are provided to accommodate different experimental conditions. All these refinements make the whole protocol more understandable and user-friendly. In general, the experiment takes one person less than 8 h to complete, and the data analysis could be accomplished within 2 h.
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The advent of structural biology in situ by single particle cryoelectron tomography
Jesús G. Galaz-Montoya, Steven J. Ludtke
Biophysics Reports    DOI: 10.1007/s41048-017-0040-0
Abstract   PDF (4263KB)
Single particle tomography (SPT), also known as subtomogram averaging, is a powerful technique uniquely poised to address questions in structural biology that are not amenable to more traditional approaches like X-ray crystallography, nuclear magnetic resonance, and conventional cryoEM single particle analysis. Owing to its potential for in situ structural biology at subnanometer resolution, SPT has been gaining enormous momentum in the last five years and is becoming a prominent, widely used technique. This method can be applied to unambiguously determine the structures of macromolecular complexes that exhibit compositional and conformational heterogeneity, both in vitro and in situ. Here we review the development of SPT, highlighting its applications and identifying areas of ongoing development.
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Determining the target protein localization in 3D using the combination of FIB-SEM and APEX2
Yang Shi, Li Wang, Jianguo Zhang, Yujia Zhai, Fei Sun
Biophysics Reports    2017, 3 (4-6): 92-99.   DOI: 10.1007/s41048-017-0043-x
Abstract   PDF (1163KB)
Determining the cellular localization of proteins of interest at nanometer resolution is necessary for elucidating their functions. Besides super-resolution fluorescence microscopy, conventional electron microscopy (EM) combined with immunolabeling or clonable EM tags provides a unique approach to correlate protein localization information and cellular ultrastructural information. However, there are still rare cases of such correlation in three-dimensional (3D) spaces. Here, we developed an approach by combining the focus ion beam scanning electron microscopy (FIB-SEM) and a promising clonable EM tag APEX2 (an enhanced ascorbate peroxidase 2) to determine the target protein localization within 3D cellular ultrastructural context. We further utilized this approach to study the 3D localization of mitochondrial dynamics-related proteins (MiD49/51, Mff, Fis1, and Mfn2) in the cells where the target proteins were overexpressed. We found that all the target proteins were located at the surface of the mitochondrial outer membrane accompanying with mitochondrial clusters. Mid49/51, Mff, and hFis1 spread widely around the mitochondrial surface while Mfn2 only exists at the contact sites.
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Co-encapsulation of curcumin and doxorubicin in albumin nanoparticles blocks the adaptive treatment tolerance of cancer cells
Seyed Mohammad Motevalli, Ahmed Shaker Eltahan, Lu Liu, Andrea Magrini, Nicola Rosato, Weisheng Guo, Massimo Bottini, Xing-Jie Liang
Biophysics Reports    2019, 5 (1): 19-30.   DOI: 10.1007/s41048-018-0079-6
Abstract   PDF (4016KB)
The adaptive treatment tolerance (ATT) of cancer cells is the main encumbrance to cancer chemotherapy. A potential solution to this problem is to treat cancer cells with multiple drugs using nanoparticles (NPs). In this study, we tested the co-administration of curcumin (Cur) and doxorubicin (Dox) to MCF-7 resistant breast cancer cells to block the ATTand elicit efficient cell killing. Drugs were co-administered to cells both sequentially and simultaneously. Sequential drug co-administration was carried out by pre-treating the cells with albumin nanoparticles (ANPs) loaded with Cur (Cur@ANPs) followed by treatment with Dox-loaded ANPs (Dox@ANPs). Simultaneous drug co-administration was carried out by treating the cells with ANPs loaded with both the drugs (Cur/Dox@ANPs). We found that the simultaneous drug co-administration led to a greater intra-cellular accumulation of Dox and cell killing with respect to the sequential drug co-administration. However, the simultaneous drug co-administration led to a lower intracellular accumulation of Cur with respect to the sequential drug co-administration. We showed that this result was due to the aggregation and entrapment of Cur in the lysosomes as soon as it was released from Cur@ANPs, a phenomenon called lysosomotropism. In contrast, the simultaneous release of Dox and Cur from Cur/Dox@ANPs into the lysosomes led to lysosomal pH elevation, which, in turn, avoided Cur aggregation, led to lysosome swelling and drug release in the cytosol, and finally provoked efficient cell killing. Our study shed the light on the molecular processes driving the therapeutic effects of anti-cancer drugs co-administered to cancer cells in different manners.
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Accelerating electron tomography reconstruction algorithm ICON with GPU
Yu Chen, Zihao Wang, Jingrong Zhang, Lun Li, Xiaohua Wan, Fei Sun, Fa Zhang
Biophysics Reports    DOI: 10.1007/s41048-017-0041-z
Abstract   PDF (1253KB)
Electron tomography (ET) plays an important role in studying in situ cell ultrastructure in threedimensional space. Due to limited tilt angles, ET reconstruction always suffers from the "missing wedge" problem. With a validation procedure, iterative compressed-sensing optimized NUFFT reconstruction (ICON) demonstrates its power in the restoration of validated missing information for low SNR biological ET dataset. However, the huge computational demand has become a major problem for the application of ICON. In this work, we analyzed the framework of ICON and classified the operations of major steps of ICON reconstruction into three types. Accordingly, we designed parallel strategies and implemented them on graphics processing units (GPU) to generate a parallel program ICON-GPU. With high accuracy, ICON-GPU has a great acceleration compared to its CPU version, up to 83.7×, greatly relieving ICON's dependence on computing resource.
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Energy coupling mechanisms of AcrB-like RND transporters
Xuejun C. Zhang, Min Liu, Lei Han
Biophysics Reports    2017, 3 (4-6): 73-84.   DOI: 10.1007/s41048-017-0042-y
Abstract   PDF (1543KB)
Prokaryotic AcrB-like proteins belong to a family of transporters of the RND superfamily, and as main contributing factor to multidrug resistance pose a tremendous threat to future human health. A unique feature of AcrB transporters is the presence of two separate domains responsible for carrying substrate and generating energy. Significant progress has been made in elucidating the three-dimensional structures of the homo-trimer complexes of AcrB-like transporters, and a three-step functional rotation was identified for this class of transporters. However, the detailed mechanisms for the transduction of the substrate binding signal, as well as the energy coupling processes between the functionally distinct domains remain to be established. Here, we propose a model for the interdomain communication in AcrB that explains how the substrate binding signal from the substrate-carrier domain triggers protonation in the transmembrane domain. Our model further provides a plausible mechanism that explains how protonation induces conformational changes in the substrate-carrier domain. We summarize the thermodynamic principles that govern the functional cycle of the AcrB trimer complex.
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Dye-based mito-thermometry and its application in thermogenesis of brown adipocytes
Tao-Rong Xie, Chun-Feng Liu, Jian-Sheng Kang
Biophysics Reports    2017, 3 (4-6): 85-91.   DOI: 10.1007/s41048-017-0039-6
Abstract   PDF (5803KB)
Mitochondrion is the main intracellular site for thermogenesis and attractive energy expenditure targeting for obesity therapy. Here, we develop a method of mitochondrial thermometry based on Rhodamine B methyl ester, which equilibrates as a thermosensitive mixture of nonfluorescent and fluorescent resonance forms. Using this approach, we are able to demonstrate that the efficacy of norepinephrine-induced thermogenesis is low, and measure the maximum transient rate of temperature increase in brown adipocytes.
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A comprehensive procedure for antiviral inhibitor discovery using EV71 as an example
Lin Cao, Shouhai Zhu, Yaxin Wang, Zhiyong Lou, Yuna Sun
Biophysics Reports    2015, 1 (2): 81-89.   DOI: 10.1007/s41048-015-0006-z
Abstract   PDF (2725KB)
The prevalence of chronic viral infectious diseases, the emergence and re-emergence of new viral infections, and in particular, resistance to currently used antiviral drugs have led to increased demand for new antiviral strategies and reagents. Increased understanding of the molecular mechanisms of viral infection has provided great potential for the discovery of new antiviral agents that target viral proteins or host factors. In this work, we introduce a comprehensive system using enteroviruses 71 (EV71) as an example for leading compound discovery to develop new antiviral.
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Skeletal intramyocellular lipid metabolism and insulin resistance
Yiran Li, Shimeng Xu, Xuelin Zhang, Zongchun Yi, Simon Cichello
Biophysics Reports    2015, 1 (2): 90-98.   DOI: 10.1007/s41048-015-0013-0
Abstract   PDF (428KB)
Lipids stored in skeletal muscle cells are known as intramyocellular lipid (IMCL). Disorders involving IMCL and its causative factor, circulatory free fatty acids (FFAs), induce a toxic state and ultimately result in insulin resistance (IR) in muscle tissue. On the other hand, intramuscular triglyceride (IMTG), the most abundant component of IMCL and an essential energy source for active skeletal muscle, is different from other IMCLs, as it is stored in lipid droplets and plays a pivotal role in skeletal muscle energy homeostasis. This review discusses the association of FFA-induced ectopic lipid accumulation and IR, with specific emphasis on the relationship between IMCL/IMTG metabolism and IR.
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Using integrated correlative cryo-light and electron microscopy to directly observe syntaphilin-immobilized neuronal mitochondria in situ
Shengliu Wang, Shuoguo Li, Gang Ji, Xiaojun Huang, Fei Sun
Biophysics Reports    2017, 3 (1-3): 8-16.   DOI: 10.1007/s41048-017-0035-x
Abstract   PDF (3069KB)
Correlative cryo-fluorescence and cryo-electron microscopy (cryo-CLEM) system has been fast becoming a powerful technique with the advantage to allow the fluorescent labeling and direct visualization of the close-to-physiologic ultrastructure in cells at the same time, offering unique insights into the ultrastructure with specific cellular function. There have been various engineered ways to achieve cryo-CLEM including the commercial FEI iCorr system that integrates fluorescence microscope into the column of transmission electron microscope. In this study, we applied the approach of the cryo-CLEMbased iCorr to image the syntaphilin-immobilized neuronal mitochondria in situ to test the performance of the FEI iCorr system and determine its correlation accuracy. Our study revealed the various morphologies of syntaphilin-immobilized neuronal mitochondria that interact with microtubules and suggested that the cryo-CLEM procedure by the FEI iCorr system is suitable with a half micron-meter correlation accuracy to study the cellular organelles that have a discrete distribution and large size, e.g. mitochondrion, Golgi complex, lysosome, etc.
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E2-2, a novel immunohistochemical marker for both human and monkey plasmacytoid dendritic cells
Jianping Ma, Haisheng Yu, Xiangyun Yin, Menglan Cheng, Quanxing Shi, Zhao Yin, Xiaohua Nie, Wang Shouli, Liguo Zhang
Biophysics Reports    2015, 1 (3): 139-147.   DOI: 10.1007/s41048-016-0023-6
Abstract   PDF (3481KB)
Plasmacytoid dendritic cells (pDCs) play important roles in initiating and regulating immune responses. pDC infiltration has been documented in multiple pathological lesions including infections, tumors, and autoimmune diseases, and the severity of pDC infiltration correlates with disease progression. However, a specific antibody for identifying pDCs by immunohistochemical staining on paraffin-embedded tissue sections is still lacking. Here, we developed a novel antibody targeted E2-2, a transcription factor preferentially expressed in pDCs. The antibody stains the nuclei of pDCs specifically in immunohistochemical analysis of various tissues from both human and rhesus monkey. This novel antibody will serve as a beneficial tool for pDC-related basic research and clinical investigation.
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Choosing proper fluorescent dyes, proteins, and imaging techniques to study mitochondrial dynamics in mammalian cells
Xingguo Liu, Liang Yang, Qi Long, David Weaver, György Hajnóczky
Biophysics Reports    2017, 3 (4-6): 64-72.   DOI: 10.1007/s41048-017-0037-8
Abstract   PDF (459KB)
Mitochondrial dynamics refers to the processes maintaining mitochondrial homeostasis, including mitochondrial fission, fusion, transport, biogenesis, and mitophagy. Mitochondrial dynamics is essential for maintaining the metabolic function of mitochondria as well as their regulatory roles in cell signaling. In this review, we summarize the recently developed imaging techniques for studying mitochondrial dynamics including:mitochondrial-targeted fluorescent proteins and dyes, live-cell imaging using photoactivation, photoswitching and cell fusion, mitochondrial transcription and replication imaging by in situ hybridization, and imaging mitochondrial dynamics by super-resolution microscopy. Moreover, we discuss examples of how to choose and combine proper fluorescent dyes and/or proteins.
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Proton transfer during class-A GPCR activation: do the CWxP motif and the membrane potential act in concert?
Xuejun C. Zhang, Ye Zhou, Can Cao
Biophysics Reports    2018, 4 (3): 115-122.   DOI: 10.1007/s41048-018-0056-0
Abstract   PDF (506KB)
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Exploring the inside details of virions by electron microscopy
Zheng Liu, Jingqiang Zhang
Biophysics Reports    2016, 2 (1): 21-24.   DOI: 10.1007/s41048-016-0022-7
Abstract   PDF (622KB)
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Natural and engineered bacterial outer membrane vesicles
Guangchao Qing, Ningqiang Gong, Xiaohui Chen, Jing Chen, Hong Zhang, Yongchao Wang, Ruifang Wang, Shouwen Zhang, Zhen Zhang, Xianxian Zhao, Yang Luo, Xing-Jie Liang
Biophysics Reports    2019, 5 (4): 184-198.   DOI: 10.1007/s41048-019-00095-6
Abstract   PDF (3119KB)
Bacterial outer membrane vesicle (OMV) is a kind of spherical lipid bilayer nanostructure naturally secreted by bacteria, which has diverse functions such as intracellular and extracellular communication, horizontal gene transfer, transfer of contents to host cells, and eliciting an immune response in host cells. In this review, several methods including ultracentrifugation and precipitation for isolating OMVs were summarized. The latest progresses of OMVs in biomedical fields, especially in vaccine development, cancer treatment, infection control, and bioimaging and detection were also summarized in this review. We highlighted the importance of genetic engineering for the safe and effective application and in facilitating the rapid development of OMVs. Finally, we discussed the bottleneck problems about OMVs in preparation and application at present and put forward our own suggestions about them. Some perspectives of OMVs in biomedical field were also provided.
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CN 10-1302/Q
ISSN 2364-3439
eISSN 2364-3420
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