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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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CONTENTS
Biophysics Reports    2016, 2 (5-6): 0-0.   DOI:
Abstract   PDF (4843KB)
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CONTENTS
Biophysics Reports    2018, 4 (2): 0-0.   DOI:
Abstract   PDF (1221KB)
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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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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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CONTENTS
Biophysics Reports    2018, 4 (3): 0-0.   DOI:
Abstract   PDF (1167KB)
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Biophysics Reports    DOI:
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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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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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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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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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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Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL
Zhou Gong, Zhu Liu, Xu Dong, Yue-He Ding, Meng-Qiu Dong, Chun Tang
Biophysics Reports    2017, 3 (4-6): 100-108.   DOI: 10.1007/s41048-017-0044-9
Abstract   PDF (788KB)
Chemical cross-linking coupled with mass spectroscopy (CXMS) is a powerful technique for investigating protein structures. CXMS has been mostly used to characterize the predominant structure for a protein, whereas cross-links incompatible with a unique structure of a protein or a protein complex are often discarded. We have recently shown that the so-called over-length cross-links actually contain protein dynamics information. We have thus established a method called DynaXL, which allow us to extract the information from the over-length cross-links and to visualize protein ensemble structures. In this protocol, we present the detailed procedure for using DynaXL, which comprises five steps. They are identification of highly confident cross-links, delineation of protein domains/subunits, ensemble rigidbody refinement, and final validation/assessment. The DynaXL method is generally applicable for analyzing the ensemble structures of multi-domain proteins and protein-protein complexes, and is freely available at www.tanglab.org/resources.
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CONTENTS
Biophysics Reports    2017, 3 (1-3): 0-0.   DOI:
Abstract   PDF (5527KB)
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Docking-based inverse virtual screening: methods, applications, and challenges
Xianjin Xu, Marshal Huang, Xiaoqin Zou
Biophysics Reports    2018, 4 (1): 1-16.   DOI: 10.1007/s41048-017-0045-8
Abstract   PDF (610KB)
Identifying potential protein targets for a small-compound ligand query is crucial to the process of drug development. However, there are tens of thousands of proteins in human alone, and it is almost impossible to scan all the existing proteins for a query ligand using current experimental methods. Recently, a computational technology called docking-based inverse virtual screening (IVS) has attracted much attention. In docking-based IVS, a panel of proteins is screened by a molecular docking program to identify potential targets for a query ligand. Ever since the first paper describing a docking-based IVS program was published about a decade ago, the approach has been gradually improved and utilized for a variety of purposes in the field of drug discovery. In this article, the methods employed in dockingbased IVS are reviewed in detail, including target databases, docking engines, and scoring function methodologies. Several web servers developed for non-expert users are also reviewed. Then, a number of applications are presented according to different research purposes, such as target identification, side effects/toxicity, drug repositioning, drug-target network development, and receptor design. The review concludes by discussing the challenges that docking-based IVS needs to overcome to become a robust tool for pharmaceutical engineering.
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AIM interneurons mediate feeding suppression through the TYRA-2 receptor in C. elegans
Jiajun Fu, Haining Zhang, Wenming Huang, Xinyu Zhu, Yi Sheng, Eli Song, Tao Xu
Biophysics Reports    2018, 4 (1): 17-24.   DOI: 10.1007/s41048-018-0046-2
Abstract   PDF (1528KB)
Feeding behavior is the most fundamental behavior in C. elegans. Our previous results have dissected the central integration circuit for the regulation of feeding, which integrates opposing sensory inputs and regulates feeding behavior in a nonlinear manner. However, the peripheral integration that acts downstream of the central integration circuit to modulate feeding remains largely unknown. Here, we find that a Gai/o-coupled tyramine receptor, TYRA-2, is involved in peripheral feeding suppression. TYRA-2 suppresses feeding behavior via the AIM interneurons, which receive tyramine/octopamine signals from RIM/RIC neurons in the central integration circuit. Our results reveal previously unidentified roles for the receptor TYRA-2 and the AIM interneurons in feeding regulation, providing a further understanding of how biogenic amines tyramine and octopamine regulate feeding behavior.
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The application of CorrSightTM in correlative light and electron microscopy of vitrified biological specimens
Xiaomin Li, Jianlin Lei, Hong-Wei Wang
Biophysics Reports    2018, 4 (3): 143-152.   DOI: 10.1007/s41048-018-0059-x
Abstract   PDF (3677KB)
Correlative light and electron microscopy is a powerful technique for identification and determination of the structures of interested macromolecules in situ. Combined with sample vitrification, it would be much easier to preserve the native state of macromolecule complexes and distinguish them from the crowded structure environment. In this article, we present a detailed process for the application of the CorrSight system, a light microscope equipped with a cryo module, in combination with a cryo-electron microscope. A relatively long course of up to 7-8 h for cryo module preparation and multichannel light microscopy imaging of vitrified specimen can be sustained. Correlation of light and electron microscopy images at both grid levels to locate squares and square level to locate target particles, and verification of target particles can be performed with the help of AutoEMation software. Cryo-electron tomography is used for obtaining the three-dimensional structure information.
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Electron microscopy combined with spatial analysis: quantitative mapping of the nano-assemblies of plasma membrane-associating proteins and lipids
Yong Zhou, John F. Hancock
Biophysics Reports    DOI: 10.1007/s41048-018-0060-4
Abstract   PDF (697KB)
The plasma membrane (PM) is a complex environment consisting of[700 species of lipids and many different types of membrane-associating proteins.These lipids and membrane proteins are distributed heterogeneously into nanometer-sized domains,called nanoclusters.The lateral spatial segregation in the PM gives rise to different curvature and lipid composition,which determines the efficiency of effector binding and signal transmission.Here,we describe an electron microscopy (EM)-spatial mapping technique to quantify the extent of nanoclusters formation in the PM.The nano-assemblies in the PM are quantified via expressing the GFP-tagged proteins or lipid-binding domains in the cells, which are then immunolabeled with the gold nanoparticles pre-coupled to the anti-GFP antibody.The gold nanoparticles are visualized via the transmission EM at high magnification.The statistical analysis of the Ripley's K-function calculates the spatial distribution of the gold nanoparticles.Important spatial parameters,such as the extent of nanoclustering,the clustered fraction,the number of proteins per cluster,the optimal size of a nanocluster,and the number of proteins localized to the PM,can be calculated.Further detailed aggregation pattern,such as the populations of monomers,dimers,trimers, and higher ordered oligomers,can also be extracted from the spatial analysis.The EM-bivariate analysis quantifies the extent of co-localization between two different components in the PM and provides key information on the protein-protein and the protein-lipid interactions over a long-distance scale from 8 to 240 nm.
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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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Roles of H3K36-specific histone methyltransferases in transcription: antagonizing silencing and safeguarding transcription fidelity
Chang Huang, Bing Zhu
Biophysics Reports    DOI: 10.1007/s41048-018-0063-1
Abstract   PDF (778KB)
Histone H3K36 methylation is well-known for its role in active transcription. In Saccharomyces cerevisiae, H3K36 methylation is mediated solely by SET2 during transcription elongation. In metazoans, multiple H3K36-specific methyltransferases exist and contribute to distinct biochemical activities and subsequent functions. In this review, we focus on the H3K36-specific histone methyltransferases in metazoans, and discuss their enzymatic activity regulation and their roles in antagonizing Polycomb silencing and safeguarding transcription fidelity.
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Proteomic analysis of insulin secretory granules in INS-1 cells by protein correlation profiling
Min Li, Wen Du, Maoge Zhou, Li Zheng, Eli Song, Junjie Hou
Biophysics Reports    DOI: 10.1007/s41048-018-0061-3
Abstract   PDF (1545KB)
Insulin secretory granules (ISGs), a group of distinguishing organelles in pancreatic β cells, are responsible for the storage and secretion of insulin to maintain blood glucose homeostasis. The molecular mechanisms of ISG biogenesis, maturation, transportation, and exocytosis are still largely unknown because the proteins involved in these distinct steps have not been fully identified. Subcellular fractionation by density gradient centrifugation has been successfully employed to analyze the proteomes of numerous organelles. However, use of this method to elucidate the ISG proteome is limited by co-fractionated contaminants because ISGs are very dynamic and have abundant exchanges or contacts with other organelles, such as the Golgi apparatus, lysosomes, and endosomes. In this study, we developed a new strategy for identifying ISG proteins by protein correlation profiling (PCP)-based proteomics, which included ISG purification by OptiPrep density gradient centrifugation, label-free quantitative proteome, and identification of ISG proteins by correlating fractionation profiles between candidates and known ISG markers. Using this approach, we were able to identify 81 ISG proteins. Among them, TM9SF3, a nine-transmembrane protein, was considered a high confidence ISG candidate protein highlighted in the PCP network. Further biochemical and immunofluorescence assays indicated that TM9SF3 localized in ISGs, suggesting that it is a potential new ISG marker.
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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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Dissection of structural dynamics of chromatin fibers by single-molecule magnetic tweezers
Xue Xiao, Liping Dong, Yi-Zhou Wang, Peng-Ye Wang, Ming Li, Guohong Li, Ping Chen, Wei Li
Biophysics Reports    DOI: 10.1007/s41048-018-0064-0
Abstract   PDF (1694KB)
The accessibility of genomic DNA, as a key determinant of gene-related processes, is dependent on the packing density and structural dynamics of chromatin fiber. However, due to the highly dynamic and heterogeneous properties of chromatin fiber, it is technically challenging to study these properties of chromatin. Here, we report a strategy for dissecting the dynamics of chromatin fibers based on singlemolecule magnetic tweezers. Using magnetic tweezers, we can manipulate the chromatin fiber and trace its extension during the folding and unfolding process under tension to investigate the dynamic structural transitions at single-molecule level. The highly accurate and reliable in vitro single-molecule strategy provides a new research platform to dissect the structural dynamics of chromatin fiber and its regulation by different epigenetic factors during gene expression.
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Phenylboronic acid-functionalized magnetic nanoparticles for one-step saccharides enrichment and mass spectrometry analysis
Xiangdong Xue, Yuanyuan Zhao, Xu Zhang, Chunqiu Zhang, Anil Kumar, Xiaoning Zhang, Guozhang Zou, Paul C. Wang, Jinchao Zhang, Xing-Jie Liang
Biophysics Reports    DOI: 10.1007/s41048-015-0002-3
Abstract   PDF (1530KB)
In this work, 2-(2-aminoethoxy) ethanolblocked phenylboronic acid-functionalized magnetic nanoparticles (blocked PMNPs) were fabricated for selective enrichment of different types of saccharides. The phenylboronic acid was designed for capturing the cis-diols moieties on saccharides molecules, and the 2-(2-aminoethoxy) ethanol can deplete the nonspecific absorption of peptides and proteins which always coexisted with saccharides. For mass spectrometry analysis, the PMNPs bound saccharides can be directly applied onto the MALDI plate with matrix without removing the PMNPs. By PMNPs, the simple saccharide (glucose) could be detected in pmol level. The complex saccharides can also be reliably purified and analyzed; 16 different Nglycans were successfully identified fromovalbumin, and the high-abundance N-glycans can be detected even when the ovalbumin was in very low concentration (2 μg). In human milk, ten different oligosaccharides were identified, and the lactose can still be detected when the human milk concentration was low to 0.01 μL.
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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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Fabrication and modification of implantable optrode arrays for in vivo optogenetic applications
Lulu Wang, Kang Huang, Cheng Zhong, Liping Wang, Yi Lu
Biophysics Reports    2018, 4 (2): 82-93.   DOI: 10.1007/s41048-018-0052-4
Abstract   PDF (11462KB)
Recent advances in optogenetics have established a precisely timed and cell-specific methodology for understanding the functions of brain circuits and the mechanisms underlying neuropsychiatric disorders. However, the fabrication of optrodes, a key functional element in optogenetics, remains a great challenge. Here, we report reliable and efficient fabrication strategies for chronically implantable optrode arrays. To improve the performance of the fabricated optrode arrays, surfaces of the recording sites were modified using optimized electrochemical processes. We have also demonstrated the feasibility of using the fabricated optrode arrays to detect seizures in multiple brain regions and inhibit ictal propagation in vivo. Furthermore, the results of the histology study imply that the electrodeposition of composite conducting polymers notably alleviated the inflammatory response and improved neuronal survival at the implant/neural-tissue interface. In summary, we provide reliable and efficient strategies for the fabrication and modification of customized optrode arrays that can fulfill the requirements of in vivo optogenetic applications.
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Cancer stem cells and tumorigenesis
Pingping Zhu, Zusen Fan
Biophysics Reports    DOI: 10.1007/s41048-018-0062-2
Abstract   PDF (766KB)
Cancer is one of the most serious diseases all over the world, and the cancer stem cell (CSC) model accounts for tumor initiation, metastasis, drug resistance, and relapse. The CSCs within tumor bulk have the capacity to self-renew, differentiate, and give rise to a new tumor. The self-renewal of CSCs is precisely regulated by various modulators, including Wnt/β-catenin signaling, Notch signaling, Hedgehog signaling, transcription factors, chromatin remodeling complexes, and non-coding RNAs. CSCs reside in their niches that are also involved in the self-renewal maintenance of CSCs and protection of CSCs from chemotherapy, radiotherapy, and even endogenous damages. Moreover, CSCs can also remodel their niches to initiate tumorigenesis. The mutual interactions between CSCs and their niches play a critical role in the regulation of CSC self-renewal and tumorigenesis as well. Many surface markers of CSCs have been identified, and these markers become first choices for CSC targeting. Due to heterogeneity and plasticity, targeting CSCs is still a big challenge for tumor elimination. In this review, we summarize recent progresses on the biological features of CSCs and targeting strategies against CSCs.
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Evaluation of RNA secondary structure prediction for both base-pairing and topology
Yunjie Zhao, Jun Wang, Chen Zeng, Yi Xiao
Biophysics Reports    2018, 4 (3): 123-132.   DOI: 10.1007/s41048-018-0058-y
Abstract   PDF (1535KB)
Secondary structures of RNAs are crucial to the understanding of their tertiary structures and functions. At present, many theoretical methods are widely used to predict RNA secondary structures. The performance of these methods has been evaluated but only for their ability of base-pairing prediction. However, the topology of a RNA secondary structure is more important for understanding its tertiary structure and function, especially for long RNAs. In this paper, we constructed a new non-redundant RNA database containing 73 RNA with lengths of 50-300 nucleotides and benchmarked four popular algorithms for both base pairing and topology. The results show that the prediction accuracy of secondary structure topology is only 38%, in contrast to 70% for that of base pairing. Furthermore, the topological consistency is not strongly correlated to the base-pairing consistency. Our results will be helpful to understand the limitations of RNA secondary structure prediction methods from a different point of view and also to their improvements in future.
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