Biophysics Reports

2021 Vol. 7, No. 2

Cover Story

The transport of cargo proteins to specific subcellular destinations is crucial for the different secretory and endocytic traffic pathways. One of the most important steps in maintaining the accuracy of this process is the recruitment of adaptor protein (AP) complexes to the membrane for recognizing and packaging cargo proteins into nascent vesicles. Adaptor protein complex 3 (AP-3) is a heterotetrametric complex implicated in the trafficking of cargo proteins from the trans-Golgi network (TGN) and/or endosomes to lysosomes or lysosome-related organelles (LROs). This complex is also involved in the biogenesis of synaptic vesicles (SVs) in neurons and of dense core vesicles (DCVs) in endocrine cells as well as in the recycling of receptors in immune cells and the regulation of planar cell polarity (PCP) proteins. Functional defects in AP-3 cause multiple abnormalities in cellular vesicle trafficking and related organelle function, leading to various disorders, such as Hermansky-Pudlak syndrome (HPS). However, the molecular mechanism underlying AP-3 has not been fully elucidated, and further investigations are needed to understand AP-3-mediated trafficking, its associated molecules and its related roles in inherited diseases. Here, we review the current understanding of AP-3 in cellular vesicle trafficking, especially focusing on mammalian systems.

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MINI-REVIEW

Potential of adipose derived stem cell preparations in neurological repair and regeneration

Laura Combes, Xenia Sawkulycz, Wen-Hui Fang, Baoqiang Guo, Mark Slevin

2021, 7(2): 81-90. doi: 10.52601/bpr.2021.200025

Abstract(1403)

PDF(80)

Abstract:
Stem cell therapy is a promising treatment for neurogenerative disease as well as inflammatory and immune mediated diseases. Decades of preclinical research has demonstrated stem cell ability to differentiate into multiple cell lineages and be utilised in regeneration and repair with their immunomodulatory and immunosuppressive properties. This work has provided the fundamental scientific knowledge needed to launch various clinical trials studying stem cell therapy in autoimmune disorders, stroke, and other tissue injury. Despite the early success many of these promising therapies are yet to breakthrough into clinical use. In this review, we highlight the recent developments in the use of stem cells as therapeutic agents for neurological conditions as well as their failures and how the clinical translation can be improved.

REVIEW

AP-3 adaptor complex-mediated vesicle trafficking

Zhuo Ma, Md. Nur Islam, Tao Xu, Eli Song

2021, 7(2): 91-100. doi: 10.52601/bpr.2021.200051

Abstract(2672)

PDF(191)

Abstract:
The transport of cargo proteins to specific subcellular destinations is crucial for the different secretory and endocytic traffic pathways. One of the most important steps in maintaining the accuracy of this process is the recruitment of adaptor protein (AP) complexes to the membrane for recognizing and packaging cargo proteins into nascent vesicles. Adaptor protein complex 3 (AP-3) is a heterotetrametric complex implicated in the trafficking of cargo proteins from the trans-Golgi network (TGN) and/or endosomes to lysosomes or lysosome-related organelles (LROs). This complex is also involved in the biogenesis of synaptic vesicles (SVs) in neurons and of dense core vesicles (DCVs) in endocrine cells as well as in the recycling of receptors in immune cells and the regulation of planar cell polarity (PCP) proteins. Functional defects in AP-3 cause multiple abnormalities in cellular vesicle trafficking and related organelle function, leading to various disorders, such as Hermansky-Pudlak syndrome (HPS). However, the molecular mechanism underlying AP-3 has not been fully elucidated, and further investigations are needed to understand AP-3-mediated trafficking, its associated molecules and its related roles in inherited diseases. Here, we review the current understanding of AP-3 in cellular vesicle trafficking, especially focusing on mammalian systems.

Live-cell fluorescence imaging of ciliary dynamics

Quanlong Lü, Chuanmao Zhang, Christopher J. Westlake

2021, 7(2): 101-110. doi: 10.52601/bpr.2021.210005

Abstract(2335)

PDF(128)

Abstract:
The cilium was one of the first organelles observed through a microscope. Motile cilia appear as oscillating cell appendages and have long been recognized to function in cell motility. In contrast, the far more widespread non-motile cilia, termed primary cilia, were thought to be vestigial and largely ignored following their initial description over a century ago. Only in the last two decades has the critical function of primary cilia been elucidated. Primary cilia play essential roles in signal transduction, chemical sensation, mechanosensation and light detection. Various microscopy approaches have been important for characterizing the structure, dynamics and function of the cilia. In this review, we discuss the application of live-cell imaging technologies and their contribution to our current understanding of ciliary processes.

Genetic variation and function: revealing potential factors associated with microbial phenotypes

Xiaolin Liu, Yue Ma, Jun Wang

2021, 7(2): 111-126. doi: 10.52601/bpr.2021.200040

Abstract(988)

PDF(47)

Abstract:
Innovations in sequencing technology have generated voluminous microbial and host genomic data, making it possible to detect these genetic variations and analyze the function influenced by them. Recently, many studies have linked such genetic variations to phenotypes through association or comparative analysis, which have further advanced our understanding of multiple microbial functions. In this review, we summarized the application of association analysis in microbes like Mycobacterium tuberculosis, focusing on screening of microbial genetic variants potentially associated with phenotypes such as drug resistance, pathogenesis and novel drug targets etc.; reviewed the application of additional comparative genomic or transcriptomic methods to identify genetic factors associated with functions in microbes; expanded the scope of our study to focus on host genetic factors associated with certain microbes or microbiome and summarized the recent host genetic variations associated with microbial phenotypes, including susceptibility and load after infection of HIV, presence/absence of different taxa, and quantitative traits of microbiome, and lastly, discussed the challenges that may be encountered and the apparent or potential viable solutions. Gene-function analysis of microbe and microbiome is still in its infancy, and in order to unleash its full potential, it is necessary to understand its history, current status, and the challenges hindering its development.

Mammalian mitochondrial iron–sulfur cluster biogenesis and transfer and related human diseases

Wenxin Zhang, Li Xu, Hongting Zhao, Kuanyu Li

2021, 7(2): 127-141. doi: 10.52601/bpr.2021.200038

Abstract(2746)

PDF(85)

Abstract:
As a cofactor, iron–sulfur (Fe–S) cluster binds to proteins or enzymes that play important roles in various important biological processes, including DNA synthesis and repair, mitochondrial function, gene transcription and translation. In mammals, the core components involved in Fe–S cluster biosynthesis are considered to include the scaffold protein ISCU, cysteine desulfurase NFS1 and its accessory proteins ISD11 and ACP, and frataxin (FXN). Proteins involved in Fe–S cluster transfer have been found to include HSC20/HSPA9, as chaperone system, and Fe–S cluster carriers. The biosynthesis and transfer of Fe–S clusters to Fe–S recipients require fine-tune regulation. Recently, significant progress has been made in the structure and mechanism of mitochondrial Fe–S biosynthesis and transfer. Based on, especially, the development of DNA sequencing technology, bioinformatics, and gene editing technology, diseases caused by mutations of Fe–S cluster-related genes have been revealed in recent years, promoting the rapid development in the field of Fe–S and human health. This review focuses on the function of genes involved in Fe–S cluster biosynthesis and transfer and on the diseases caused by the mutations of the related genes. Finally, some questions we are facing are raised, new hypotheses presented, and the perspectives discussed.

RESEARCH ARTICLE

Anti-oxidative effect of zinc in human umbilical cord mesenchymal stem cells

Xiaodan Lu, Yifan Lin, Xiuying Lin, Qiang Zhang, Zihang Wang, Xuguang Mi, Ruobing Wang, Xiaofang Zhang, Xu Luan, Yan Liu, Bing Li, Yan Tan, Yanqiu Fang

2021, 7(2): 142-151. doi: 10.52601/bpr.2021.200046

Abstract(1215)

PDF(55)

Abstract:
Human umbilical cord mesenchymal stem cells (HUC-MSCs) are pluripotent and functional in many biological processes, by which releasing secretary factors to promote the self-repairing of damaged tissue or developing into functional cell at local organ. However, there is a high risk that oxidative stress would reduce the pluripotency and factor-secretion during the preparation and transplantation. Therefore, reducing oxidative stress is expected to improve the efficacy of HUC-MSCs therapy. Zinc (Zn) is an essential trace element which involves in the resistance of oxidative stress. To investigate Zn-regulated signaling pathways, we have profiled the gene expression at transcriptome level in primary HUC-MSCs treated with zinc sulfate, followed with GO and KEGG gene enrichment analysis. Zn treatment improved signal pathways for mineral absorption, cell growth, and cell death. Zn deficiency was mimicked by TPEN administration, which suppressed cell proliferation and reduced the expression of HUC-MSCs surface stem cell markers CD73, CD90 and CD105 by flow cytometry. Nuclear factor erythrocyte 2 related factor 2 (Nrf2) plays an important role in antioxidant biological processes. In vitro treatment of Zn significantly increased Nrf2 and Sirt3 expression at gene level and protein level respectively. Zn supplementation inhibited TPEN-induced failure of cell survival and reversed the reduction of Nrf2 and Sirt3 expression, which further reduced the production of ROS. Zn successfully presented its anti-oxidation effect by activating Nrf2/Sirt3 signaling pathway in HUC-MSCs. Zn supplementation may improve the efficacy of HUC-MSCs therapy with reduced oxidative stress.

Optimizing weighting functions for cryo-electron microscopy

Jing Cheng, Xinzheng Zhang

2021, 7(2): 152-158. doi: 10.52601/bpr.2021.210001

Abstract(1802)

PDF(105)

Abstract:
The frequency-dependent signal to noise ratio of cryo-electron microscopy data varies dramatically with the frequency and with the type of the data. During different steps of data processing, data with distinct SNR are used for calculations. Thus, specific weighting function based on the particular SNR should be designed to optimize the corresponding calculation. Here, we deduced these weighting functions by maximizing the signal to noise ratio of cross correlated coefficients. Some of our weighting functions for refinement resemble that used in the existing software packages. However, weighting functions we deduced for motion correction, particle picking and the refinement with overlapping densities differ from those employed by existing programs. Our new weighting functions may improve the calculation in these steps.