Biophysics Reports

2018 Vol. 4, No. 4

Cover Story

Through the efforts of Dr. Shizhang Bei, the State Council of China approved the transformation of the Beijing Institute of Experimental Biology into the Institute of Biophysics (IBP), Chinese Academy of Sciences (CAS) on 26th September, 1958. In the sixty years since its establishment, the direction of the Institute of Biophysics has been in line with principles proposed by Dr. Bei:integrate theory with practice, align work with national needs, and strive to reach and surpass global standards. The Institute has attracted a group of outstanding scientists and made many great accomplishments in scientific research, leading and promoting research and development in China on radiobiology, cosmology, cell biology, enzymology, structural biology, membrane biology, neurobiology, biocybernetics, and biophysical engineering. In doing so, it has made an important contribution to the development of the life sciences in China. This special issue of the 60th anniversary of the founding of the Institute of Biophysics aims to further enhance cooperation and communication between the Institute and academic colleagues in the field.

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The road to a first-class research institute: creating an exceptional environment, recruiting outstanding scientists, producing high-impact work,and nurturing a culture of innovation-preface to the 60th anniversary special issue

Ruiming Xu

2018, 4(4): 167-169. doi: 10.1007/s41048-018-0069-8

Abstract(88)

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Abstract:

Roles of H3K36-specific histone methyltransferases in transcription: antagonizing silencing and safeguarding transcription fidelity

Chang Huang, Bing Zhu

2018, 4(4): 170-177. doi: 10.1007/s41048-018-0063-1

Abstract(342)

PDF(122)

Abstract:
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.

Cancer stem cells and tumorigenesis

Pingping Zhu, Zusen Fan

2018, 4(4): 178-188. doi: 10.1007/s41048-018-0062-2

Abstract(1241)

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Abstract:
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.

Structural roles of lipid molecules in the assembly of plant PSII-2LHCII supercomplex

Xin Sheng, Xiuying Liu, Peng Cao, Mei Li, Zhenfeng Liu

2018, 4(4): 189-203. doi: 10.1007/s41048-018-0068-9

Abstract(797)

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Abstract:
In plants, photosystem Ⅱ (PSⅡ) associates with light-harvesting complexes Ⅱ (LHCⅡ) to form PSⅡ-LHCⅡ supercomplexes. They are multi-subunit supramolecular systems embedded in the thylakoid membrane of chloroplast, functioning as energy-converting and water-splitting machinery powered by light energy. The high-resolution structure of a PSⅡ-LHCⅡ supercomplex, previously solved through cryo-electron microscopy, revealed 34 well-defined lipid molecules per monomer of the homodimeric system. Here we characterize the distribution of lipid-binding sites in plant PSⅡ-LHCⅡ supercomplex and summarize their arrangement pattern within and across the membrane. These lipid molecules have crucial roles in stabilizing the oligomerization interfaces of plant PSⅡ dimer and LHCⅡ trimer. Moreover, they also mediate the interactions among PSⅡ core subunits and contribute to the assembly between peripheral antenna complexes and PSⅡ core. The detailed information of lipid-binding sites within PSⅡ-LHCⅡ supercomplex may serve as a framework for future researches on the functional roles of lipids in plant photosynthesis.

PTB/nPTB: master regulators of neuronal fate in mammals

Jing Hu, Hao Qian, Yuanchao Xue, Xiang-Dong Fu

2018, 4(4): 204-214. doi: 10.1007/s41048-018-0066-y

Abstract(1243)

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Abstract:
PTB was initially discovered as a polypyrimidine tract-binding protein (hence the name), which corresponds to a specific RNA-binding protein associated with heterogeneous ribonucleoprotein particle (hnRNP I). The PTB family consists of three members in mammalian genomes, with PTBP1 (PTB) expressed in most cell types, PTBP2 (also known as nPTB or brPTB) exclusively found in the nervous system, and PTBP3 (also known as ROD1) predominately detected in immune cells. During neural development, PTB is down-regulated, which induces nPTB, and the expression of both PTB and nPTB becomes diminished when neurons mature. This programed switch, which largely takes place at the splicing level, is critical for the development of the nervous system, with PTB playing a central role in neuronal induction and nPTB guarding neuronal maturation. Remarkably, sequential knockdown of PTB and nPTB has been found to be necessary and sufficient to convert non-neuronal cells to the neuronal lineage. These findings, coupled with exquisite understanding of the molecular circuits regulated by these RNA-binding proteins, establish a critical foundation for their future applications in regenerative medicine.

Hessian single-molecule localization microscopy using sCMOS camera

Fudong Xue, Wenting He, Fan Xu, Mingshu Zhang, Liangyi Chen, Pingyong Xu

2018, 4(4): 215-221. doi: 10.1007/s41048-018-0065-z

Abstract(149)

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Abstract:
Single-molecule localization microscopy (SMLM) has the highest spatial resolution among the existing super-resolution imaging techniques, but its temporal resolution needs further improvement. An sCMOS camera can effectively increase the imaging rate due to its large field of view and fast imaging speed. Using an sCMOS camera for SMLM imaging can significantly improve the imaging time resolution, but the unique single-pixel-dependent readout noise of sCMOS cameras severely limits their application in SMLM imaging. This paper develops a Hessian-based SMLM (Hessian-SMLM) method that can correct the variance, gain, and offset of a single pixel of a camera and effectively eliminate the pixeldependent readout noise of sCMOS cameras, especially when the signal-to-noise ratio is low. Using Hessian-SMLM to image mEos3.2-labeled actin was able to significantly reduce the artifacts due to camera noise.

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

2018, 4(4): 222-232. doi: 10.1007/s41048-018-0064-0

Abstract(113)

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Abstract:
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.