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Biophysics Reports

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https://www.readbyqxmd.com/read/28317014/metadp-a-comprehensive-web-server-for-disease-prediction-of-16s-rrna-metagenomic-datasets
#1
Xilin Xu, Aiping Wu, Xinlei Zhang, Mingming Su, Taijiao Jiang, Zhe-Ming Yuan
High-throughput sequencing-based metagenomics has garnered considerable interest in recent years. Numerous methods and tools have been developed for the analysis of metagenomic data. However, it is still a daunting task to install a large number of tools and complete a complicated analysis, especially for researchers with minimal bioinformatics backgrounds. To address this problem, we constructed an automated software named MetaDP for 16S rRNA sequencing data analysis, including data quality control, operational taxonomic unit clustering, diversity analysis, and disease risk prediction modeling...
2016: Biophysics Reports
https://www.readbyqxmd.com/read/28317013/simulated-microgravity-potentiates-generation-of-reactive-oxygen-species-in-cells
#2
Fanlei Ran, Lili An, Yingjun Fan, Haiying Hang, Shihua Wang
Microgravity (MG) and space radiation are two major environmental factors of space environment. Ionizing radiation generates reactive oxygen species (ROS) which plays a key role in radiation-induced DNA damage. Interestingly, simulated microgravity (SMG) also increases ROS production in various cell types. Thus, it is important to detect whether SMG could potentiate ROS production induced by genotoxins including radiation, especially at a minimal level not sufficient to induce detectable ROS. In this study, we treated mouse embryonic stem (MES) cells with H2O2 and SMG for 24 h...
2016: Biophysics Reports
https://www.readbyqxmd.com/read/28317012/using-3drpc-for-rna-protein-complex-structure-prediction
#3
Yangyu Huang, Haotian Li, Yi Xiao
3dRPC is a computational method designed for three-dimensional RNA-protein complex structure prediction. Starting from a protein structure and a RNA structure, 3dRPC first generates presumptive complex structures by RPDOCK and then evaluates the structures by RPRANK. RPDOCK is an FFT-based docking algorithm that takes features of RNA-protein interactions into consideration, and RPRANK is a knowledge-based potential using root mean square deviation as a measure. Here we give a detailed description of the usage of 3dRPC...
2016: Biophysics Reports
https://www.readbyqxmd.com/read/28317011/thermodynamic-aspects-of-atp-hydrolysis-of-actomyosin-complex
#4
Xuejun C Zhang, Wei Feng
No abstract text is available yet for this article.
2016: Biophysics Reports
https://www.readbyqxmd.com/read/28018966/crystal-structures-of-mdfa-complexed-with-acetylcholine-and-inhibitor-reserpine
#5
Ming Liu, Jie Heng, Yuan Gao, Xianping Wang
The DHA12 family of transporters contains a number of prokaryotic and eukaryote membrane proteins. Some of these proteins share conserved sites intrinsic to substrate recognition, structural stabilization and conformational changes. For this study, we chose the MdfA transporter as a model DHA12 protein to study some general characteristics of the vesicular neurotransmitter transporters (VNTs), which all belong to the DHA12 family. Two crystal structures were produced for E. coli MdfA, one in complex with acetylcholine and the other with potential reserpine, which are substrate and inhibitor of VNTs, respectively...
2016: Biophysics Reports
https://www.readbyqxmd.com/read/28018965/regulation-of-metabolism-by-the-mediator-complex
#6
Dou Yeon Youn, Alus M Xiaoli, Jeffrey E Pessin, Fajun Yang
The Mediator complex was originally discovered in yeast, but it is conserved in all eukaryotes. Its best-known function is to regulate RNA polymerase II-dependent gene transcription. Although the mechanisms by which the Mediator complex regulates transcription are often complicated by the context-dependent regulation, this transcription cofactor complex plays a pivotal role in numerous biological pathways. Biochemical, molecular, and physiological studies using cancer cell lines or model organisms have established the current paradigm of the Mediator functions...
2016: Biophysics Reports
https://www.readbyqxmd.com/read/28018964/structure-determination-of-a-human-virus-by-the-combination-of-cryo-em-and-x-ray-crystallography
#7
Zheng Liu, Tom S Y Guu, Jianhao Cao, Yinyin Li, Lingpeng Cheng, Yizhi Jane Tao, Jingqiang Zhang
Virus 3D atomic structures provide insight into our understanding of viral life cycles and the development of antiviral drugs. X-ray crystallography and cryo-EM have been used to determine the atomic structure of viruses. However, limited availability of biological samples, biosafety issues due to virus infection, and sometimes inherent characteristics of viruses, pose difficulties on combining both methods in determining viral structures. These have made solving the high resolution structure of some medically important viruses very challenging...
2016: Biophysics Reports
https://www.readbyqxmd.com/read/28018963/uniporter-substrate-binding-and-transport-reformulating-mechanistic-questions
#8
Xuejun C Zhang, Lei Han
Transporters are involved in material transport, signaling, and energy input in all living cells. One of the fundamental questions about transporters is concerned with the precise role of their substrate in driving the transport process. This is particularly important for uniporters, which must utilize the chemical potential of substrate as the only energy source driving the transport. Thus, uniporters present an excellent model for the understanding of how the difference in substrate concentration across the membrane is used as a driving force...
2016: Biophysics Reports
https://www.readbyqxmd.com/read/27819029/combining-biophysical-methods-to-analyze-the-disulfide-bond-in-sh2-domain-of-c-terminal-src-kinase
#9
Dongsheng Liu, David Cowburn
The Src Homology 2 (SH2) domain is a structurally conserved protein domain that typically binds to a phosphorylated tyrosine in a peptide motif from the target protein. The SH2 domain of C-terminal Src kinase (Csk) contains a single disulfide bond, which is unusual for most SH2 domains. Although the global motion of SH2 domain regulates Csk function, little is known about the relationship between the disulfide bond and binding of the ligand. In this study, we combined X-ray crystallography, solution NMR, and other biophysical methods to reveal the interaction network in Csk...
2016: Biophysics Reports
https://www.readbyqxmd.com/read/27819028/symmetry-mismatch-reconstruction-of-genomes-and-associated-proteins-within-icosahedral-viruses-using-cryo-em
#10
Xiaowu Li, Hongrong Liu, Lingpeng Cheng
Although near-atomic resolutions have been routinely achieved for structural determination of many icosahedral viral capsids, structures of genomes and associated proteins within the capsids are still less characterized because the genome information is overlapped by the highly symmetric capsid information in the virus particle images. We recently developed a software package for symmetry-mismatch structural reconstruction and determined the structures of the genome and RNA polymerases within an icosahedral virus for the first time...
2016: Biophysics Reports
https://www.readbyqxmd.com/read/27819027/exploring-the-inside-details-of-virions-by-electron-microscopy
#11
EDITORIAL
Zheng Liu, Jingqiang Zhang
No abstract text is available yet for this article.
2016: Biophysics Reports
https://www.readbyqxmd.com/read/27819026/radiolabeled-cyclic-rgd-peptides-as-radiotracers-for-tumor-imaging
#12
REVIEW
Jiyun Shi, Fan Wang, Shuang Liu
The integrin family comprises 24 transmembrane receptors, each a heterodimeric combination of one of 18α and one of 8β subunits. Their main function is to integrate the cell adhesion and interaction with the extracellular microenvironment with the intracellular signaling and cytoskeletal rearrangement through transmitting signals across the cell membrane upon ligand binding. Integrin αvβ3 is a receptor for the extracellular matrix proteins containing arginine-glycine-aspartic (RGD) tripeptide sequence. The αvβ3 is generally expressed in low levels on the epithelial cells and mature endothelial cells, but it is highly expressed in many solid tumors...
2016: Biophysics Reports
https://www.readbyqxmd.com/read/27471749/radioligand-saturation-binding-for-quantitative-analysis-of-ligand-receptor-interactions
#13
Chengyan Dong, Zhaofei Liu, Fan Wang
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, K d, and the maximum density of receptors, B max. The entire (125)I-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...
2015: Biophysics Reports
https://www.readbyqxmd.com/read/27340693/pseudomonas-sp-lz-q-continuously-degrades-phenanthrene-under-hypersaline-and-hyperalkaline-condition-in-a-membrane-bioreactor-system
#14
Yiming Jiang, Haiying Huang, Mengru Wu, Xuan Yu, Yong Chen, Pu Liu, Xiangkai Li
GRAPHICAL ABSTRACT: HASH(0x32615e0) ABSTRACT: 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...
2015: Biophysics Reports
https://www.readbyqxmd.com/read/27340692/e2-2-a-novel-immunohistochemical-marker-for-both-human-and-monkey-plasmacytoid-dendritic-cells
#15
Jianping Ma, Haisheng Yu, Xiangyun Yin, Menglan Cheng, Quanxing Shi, Zhao Yin, Xiaohua Nie, Wang Shouli, Liguo Zhang
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...
2015: Biophysics Reports
https://www.readbyqxmd.com/read/27340691/visualizing-the-ensemble-structures-of-protein-complexes-using-chemical-cross-linking-coupled-with-mass-spectrometry
#16
Zhou Gong, Yue-He Ding, Xu Dong, Na Liu, E Erquan Zhang, Meng-Qiu Dong, Chun Tang
GRAPHICAL ABSTRACT: HASH(0x3b29bc8) ABSTRACT: 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...
2015: Biophysics Reports
https://www.readbyqxmd.com/read/27340690/implications-for-directionality-of-nanoscale-forces-in-bacterial-attachment
#17
Jan J T M Swartjes, Deepak H Veeregowda
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...
2015: Biophysics Reports
https://www.readbyqxmd.com/read/27340689/thermodynamics-of-gpcr-activation
#18
Xuejun C Zhang, Ye Zhou, Can Cao
No abstract text is available yet for this article.
2015: Biophysics Reports
https://www.readbyqxmd.com/read/26942225/transcriptomic-analysis-of-human-breast-cancer-cells-reveals-differentially-expressed-genes-and-related-cellular-functions-and-pathways-in-response-to-gold-nanorods
#19
Teng Zhou, Yipeng Du, Taotao Wei
Breast cancer is the leading cause of cancer deaths in women. 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...
2015: Biophysics Reports
https://www.readbyqxmd.com/read/26942224/the-application-of-traditional-transmission-electron-microscopy-for-autophagy-research-in-caenorhabditis-elegans
#20
Attila L Kovács
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...
2015: Biophysics Reports
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