Biophysics and Physicobiology最新文献_第7页

How evolution builds up complexity?: In vitro evolution approaches to witness complexification in artificial molecular replication systems 进化是如何构建复杂性的?:人工分子复制系统中复杂化的体外进化方法

Biophysics and Physicobiology Pub Date : 2022-02-15 DOI: 10.2142/biophysico.bppb-v19.0005

Taro Furubayashi, N. Ichihashi

{"title":"How evolution builds up complexity?: In vitro evolution approaches to witness complexification in artificial molecular replication systems","authors":"Taro Furubayashi, N. Ichihashi","doi":"10.2142/biophysico.bppb-v19.0005","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0005","url":null,"abstract":"How can evolution assemble lifeless molecules into a complex living organism? The emergent process of biological complexity in the origin of life is a big mystery in biology. In vitro evolution of artificial molecular replication systems offers unique experimental opportunities to probe possible pathways of a simple molecular system approaching a complex life-like system. This review focuses on experimental efforts to examine evolvability of molecules in vitro from the pioneering Spiegelman’s experiment to our latest research on an artificial RNA self-replication system. Genetic translation and compartmentalization are shown to enable sustainable replication and evolution. Latest studies are revealing that coevolution of self-replicating “host replicators” and freeloading “parasitic replicators” is crucial to extend evolvability of a molecular replication system for continuous evolution and emergence of diversity. Intense competition between hosts and parasites would have existed even before the origin of life and contributed to generating complex molecular ecosystems. This review article is an extended version of the Japanese article “An in vitro evolutionary journey of an artificial RNA replication system towards biological complexity” published in SEIBUTSU-BUTSURI Vol.61, p.240–244 (2021).”","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90863068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A variety of photoreceptors and the frontiers of optogenetics 各种光感受器和光遗传学的前沿

Biophysics and Physicobiology Pub Date : 2022-02-09 DOI: 10.2142/biophysico.bppb-v19.0004

S. Tokutomi, S. Tsunoda

引用次数: 0

Ionic strength-sensitive and pH-insensitive interactions between C-reactive protein (CRP) and an anti-CRP antibody. c -反应蛋白(CRP)和抗CRP抗体之间离子强度敏感和ph不敏感的相互作用。

Biophysics and Physicobiology Pub Date : 2022-02-09 eCollection Date: 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0003

Yuka Oka, Shota Ushiba, Naruto Miyakawa, Madoka Nishio, Takao Ono, Yasushi Kanai, Yohei Watanabe, Shinsuke Tani, Masahiko Kimura, Kazuhiko Matsumoto

{"title":"Ionic strength-sensitive and pH-insensitive interactions between C-reactive protein (CRP) and an anti-CRP antibody.","authors":"Yuka Oka, Shota Ushiba, Naruto Miyakawa, Madoka Nishio, Takao Ono, Yasushi Kanai, Yohei Watanabe, Shinsuke Tani, Masahiko Kimura, Kazuhiko Matsumoto","doi":"10.2142/biophysico.bppb-v19.0003","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0003","url":null,"abstract":"C-reactive protein (CRP) is an important biomarker of infection and inflammation, as CRP is one of the most prominent acute-phase proteins. CRP is usually detected using anti-CRP antibodies (Abs), where the intermolecular interactions between CRP and the anti-CRP Ab are largely affected by the pH and ionic strength of environmental solutions. Therefore, it is important to understand the environmental effects of CRP-anti-CRP Ab interactions when designing highly sensitive biosensors. Here, we investigated the efficiency of fluorescently labeled CRP-anti-CRP monoclonal antibody (mAb) interactions at different pHs and ionic strengths. Our results indicate that the affinity was insensitive to pH changes in the range of 5.9 to 8.1, while it was significantly sensitive to ionic strength changes. The binding affinity decreased by 55% at an ionic strength of 1.6 mM, when compared to that under a physiological condition (~150 mM). Based on the isoelectric focusing results, both the labeled CRP and anti-CRP mAb were negatively charged in the studied pH range, which rendered the system insensitive to pH changes, but sensitive to ionic strength changes. The decreased ionic strength led to a significant enhancement of the repulsive force between CRP and the anti-CRP mAb. Although the versality of the findings is not fully studied yet, the results provide insights into designing highly sensitive CRP sensors, especially field-effect transistor-based sensors.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190003"},"PeriodicalIF":0.0,"publicationDate":"2022-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/cc/ec/19_e190003.PMC8926308.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40691091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural diversity of cysteine desulfurases involved in iron-sulfur cluster biosynthesis 参与铁硫簇生物合成的半胱氨酸脱硫酶的结构多样性

Biophysics and Physicobiology Pub Date : 2022-02-08 DOI: 10.2142/biophysico.bppb-v19.0001

T. Fujishiro, R. Nakamura, K. Kunichika, Yasuhiro Takahashi

引用次数: 4

Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast 出芽酵母DNA双链断裂修复过程中染色体动力学的数学模型

Biophysics and Physicobiology Pub Date : 2022-02-01 DOI: 10.1101/2022.02.01.478611

Shinjiro Nakahata, Tetsushi Komoto, Masashi Fujii, A. Awazu

{"title":"Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast","authors":"Shinjiro Nakahata, Tetsushi Komoto, Masashi Fujii, A. Awazu","doi":"10.1101/2022.02.01.478611","DOIUrl":"https://doi.org/10.1101/2022.02.01.478611","url":null,"abstract":"During the repair of double-strand breaks (DSBs) in DNA, active mobilizations for conformational changes in chromosomes have been widely observed in eukaryotes, from yeast to animal and plant cells. DSB-damaged loci in the yeast genome showed increased mobility and relocation to the nuclear periphery. However, the driving forces behind DSB-induced chromatin dynamics remain unclear. In this study, mathematical models of normal and DSB-damaged yeast chromosomes were developed to simulate their structural dynamics. The effects of histone degradation in the whole nucleus and the change in the physical properties of damaged loci due to the binding of SUMOylated repair proteins were considered in the model of DSB-induced chromosomes based on recent experimental results. The simulation results reproduced DSB-induced changes to structural and dynamical features by which the combination of whole nuclear histone degradation and the rigid structure formation of repair protein accumulations on damaged loci were suggested to be primary contributors to the process by which damaged loci are relocated to the nuclear periphery.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90363096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Live-cell imaging of bio-metal species. 生物金属物种的活细胞成像。

Biophysics and Physicobiology Pub Date : 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0047

Tasuku Hirayama, Koichiro Ishimori

{"title":"Live-cell imaging of bio-metal species.","authors":"Tasuku Hirayama, Koichiro Ishimori","doi":"10.2142/biophysico.bppb-v19.0047","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0047","url":null,"abstract":"Bioinorganic species play essential roles in living organisms. Figure 1 shows the elements found in living things so far, and most of them are known as essential elements for human beings [1]. In particular, the concentrations of the inorganic species must be controlled within each appropriate range because the dysfunctions of the homeostasis of inorganic species often cause diseases. Revealing the relationship between the dysfunction of inorganic species' homeostasis and diseases must lead to the development of new drugs for the treatment of the diseases such as cancer and neurodegenerative diseases. Live-cell imaging is a powerful method to investigate the alteration of inorganic species in living cells and has contributed to elucidating the roles and functions of inorganic species in living systems. We organized the symposium, “Live-cell Imaging of Bio-metal Species,” at the 60th Annual Meeting of the Biophysical Society of Japan to introduce recent advances in imaging technologies for metal ions and inorganic species. This symposium is co-supported by Scientific Research on Innovative Areas, “Integrated Bio-metal Science” [2]. One of the ultimate goals of this area is to decipher the behaviors of bioinorganic species from whole organisms to molecular levels. In this context, cutting-edge methods to visualize bioinorganic species are required. In this symposium, we invited six upcoming researchers working on imaging of inorganic species to present their recent achievements.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"19 ","pages":"e190047"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/70/17/19_e190047.PMC9895318.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9303282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Activation mechanism of the bacterial flagellar dual-fuel protein export engine. 细菌鞭毛双燃料蛋白输出引擎的激活机制。

Biophysics and Physicobiology Pub Date : 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0046

Tohru Minamino, Miki Kinoshita, Yusuke V Morimoto, Keiichi Namba

{"title":"Activation mechanism of the bacterial flagellar dual-fuel protein export engine.","authors":"Tohru Minamino, Miki Kinoshita, Yusuke V Morimoto, Keiichi Namba","doi":"10.2142/biophysico.bppb-v19.0046","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0046","url":null,"abstract":"Bacteria employ the flagellar type III secretion system (fT3SS) to construct flagellum, which acts as a supramolecular motility machine. The fT3SS of Salmonella enterica serovar Typhimurium is composed of a transmembrane export gate complex and a cytoplasmic ATPase ring complex. The transmembrane export gate complex is fueled by proton motive force across the cytoplasmic membrane and is divided into four distinct functional parts: a dual-fuel export engine; a polypeptide channel; a membrane voltage sensor; and a docking platform. ATP hydrolysis by the cytoplasmic ATPase complex converts the export gate complex into a highly efficient proton (H+)/protein antiporter that couples inward-directed H+ flow with outward-directed protein export. When the ATPase ring complex does not work well in a given environment, the export gate complex will remain inactive. However, when the electric potential difference, which is defined as membrane voltage, rises above a certain threshold value, the export gate complex becomes an active H+/protein antiporter to a considerable degree, suggesting that the export gate complex has a voltage-gated activation mechanism. Furthermore, the export gate complex also has a sodium ion (Na+) channel to couple Na+ influx with flagellar protein export. In this article, we review our current understanding of the activation mechanism of the dual-fuel protein export engine of the fT3SS. This review article is an extended version of a Japanese article, Membrane voltage-dependent activation of the transmembrane export gate complex in the bacterial flagellar type III secretion system, published in SEIBUTSU BUTSURI Vol. 62, p165-169 (2022).","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"19 ","pages":"e190046"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/22/61/19_e190046.PMC9751260.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10428174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Development of the force field for cyclosporine A. 环孢素A的力场研究进展。

Biophysics and Physicobiology Pub Date : 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0045

Tsutomu Yamane, Toru Ekimoto, Mitsunori Ikeguchi

引用次数: 0

Creation of supramolecular biomembrane by the bottom-up self-assembly: Where material science meets biophysics. 自底向上自组装的超分子生物膜:材料科学与生物物理学的交集。

Biophysics and Physicobiology Pub Date : 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0043

Kazuma Yasuhara, Kenichi Morigaki

引用次数: 1

Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation of mouse embryonic stem cells. 在小鼠胚胎干细胞早期分化过程中，X染色体的表观遗传结构变化促进了Xic配对。

Biophysics and Physicobiology Pub Date : 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0018

Tetsushi Komoto, Masashi Fujii, Akinori Awazu

{"title":"Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation of mouse embryonic stem cells.","authors":"Tetsushi Komoto, Masashi Fujii, Akinori Awazu","doi":"10.2142/biophysico.bppb-v19.0018","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0018","url":null,"abstract":"X chromosome inactivation center (Xic) pairing occurs during the differentiation of embryonic stem (ES) cells from female mouse embryos, and is related to X chromosome inactivation, the circadian clock, intra-nucleus architecture, and metabolism. However, the mechanisms underlying the identification and approach of X chromosome pairs in the crowded nucleus are unclear. To elucidate the driving force of Xic pairing, we developed a coarse-grained molecular dynamics model of intranuclear chromosomes in ES cells and in cells 2 days after the onset of differentiation (2-day cells) by considering intrachromosomal epigenetic-structural feature-dependent mechanics. The analysis of the experimental data showed that X-chromosomes exhibit the rearrangement of their distributions of open/closed chromatin regions on their surfaces during cell differentiation. By simulating models where the excluded volume effects of closed chromatin regions are stronger than those of open chromatin regions, such rearrangement of open/closed chromatin regions on X-chromosome surfaces promoted the mutual approach of the Xic pair. These findings suggested that local intrachromosomal epigenetic features may contribute to the regulation of cell species-dependent differences in intranuclear architecture.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"19 ","pages":"1-14"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/85/e1/19_e190018.PMC9174021.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10309217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0