Biophysics (Nagoya-shi, Japan)最新文献_第3页

Morphological and physiological characteristics of dermal photoreceptors in Lymnaea stagnalis. 海蚕皮肤光感受器的形态和生理特征。

Biophysics (Nagoya-shi, Japan) Pub Date : 2014-11-11 eCollection Date: 2014-01-01 DOI: 10.2142/biophysics.10.77

Satoshi Takigami, Hiroshi Sunada, Tetsuro Horikoshi, Manabu Sakakibara

{"title":"Morphological and physiological characteristics of dermal photoreceptors in Lymnaea stagnalis.","authors":"Satoshi Takigami, Hiroshi Sunada, Tetsuro Horikoshi, Manabu Sakakibara","doi":"10.2142/biophysics.10.77","DOIUrl":"https://doi.org/10.2142/biophysics.10.77","url":null,"abstract":"Dermal photoreceptors located in the mantle of Lymnaea stagnalis were histologically and physiologically characterized. Our previous study demonstrated that the shadow response from dermal photoreceptors induces the whole-body withdrawal response. Through the interneuron, RPeD11, we detected that the light-off response indirectly originated from a dermal photoreceptor. Previous observations, based on behavioral pharmacology, revealed that cyclic guanosine monophosphate acts as a second messenger in the dermal photoreceptor. Furthermore, gastropods possess dermal photoreceptors containing rhodopsin, as a photopigment, and another photo-sensitive protein, arrestin, responsible for terminating the light response. Thus, we chose three antibodies, anti-cGMP, anti-rhodopsin, and anti-β-arrestin, to identify the dermal photoreceptor molecules in Lymnaea mantle. Extracellular recording, using a suction electrode on the mantle, revealed a light off-response from the right parietal nerve. Overlapping structures, positive against each of the antibodies, were also observed. Numerous round, granular particles of 3-47 μm in diameter with one nucleus were distributed around pneumostome and/or inside the mantle. The cells surrounding the pneumostome area, located 10 μm beneath the surface, tended to have smaller cell soma ranging from 3 to 25 μm in diameter, while cells located in other areas were distributed uniformly inside the mantle, with a larger diameter ranging from 12 to 47 μm. The histological examination using back-filing Lucifer Yellow staining of the right parietal nerve with the three dermal photoreceptor antibodies confirmed that these overlapping-stained structures were dermal photoreceptors in Lymnaea. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"10 ","pages":"77-88"},"PeriodicalIF":0.0,"publicationDate":"2014-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2142/biophysics.10.77","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34734066","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: 4

Myosin V is a biological Brownian machine. 肌凝蛋白V是一种生物布朗机器。

Biophysics (Nagoya-shi, Japan) Pub Date : 2014-11-01 eCollection Date: 2014-01-01 DOI: 10.2142/biophysics.10.69

Keisuke Fujita, Mitsuhiro Iwaki

引用次数: 0

Structural and mutation studies of two DNA demethylation related glycosylases: MBD4 and TDG. 两种DNA去甲基化相关糖基酶:MBD4和TDG的结构和突变研究。

Biophysics (Nagoya-shi, Japan) Pub Date : 2014-10-18 eCollection Date: 2014-01-01 DOI: 10.2142/biophysics.10.63

Hideharu Hashimoto

{"title":"Structural and mutation studies of two DNA demethylation related glycosylases: MBD4 and TDG.","authors":"Hideharu Hashimoto","doi":"10.2142/biophysics.10.63","DOIUrl":"https://doi.org/10.2142/biophysics.10.63","url":null,"abstract":"Two mammalian DNA glycosylases, methyl-CpG binding domain protein 4 (MBD4) and thymine DNA glycosylase (TDG), are involved in active DNA demethylation via the base excision repair pathway. Both MBD4 and TDG excise the mismatch base from G:X, where X is uracil, thymine, and 5-hydroxymethyluracil (5hmU). In addition, TDG excises 5mC oxidized bases i.e. when X is 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) not 5-hydroxymethylcytosine (5hmC). A MBD4 inactive mutant and substrate crystal structure clearly explains how MBD4 glycosylase discriminates substrates: 5mC are not able to be directly excised, but a deamination process from 5mC to thymine is required. On the other hand, TDG is much more complicated; in this instance, crystal structures show that TDG recognizes G:X mismatch DNA containing DNA and G:5caC containing DNA from the minor groove of DNA, which suggested that TDG might recognize 5mC oxidized product 5caC like mismatch DNA. In mutation studies, a N157D mutation results in a more 5caC specific glycosylase, and a N191A mutation inhibits 5caC activity while that when X=5fC or T remains. Here I revisit the recent MBD4 glycos ylase domain co-crystal structures with DNA, as well as TDG glycosylase domain co-crystal structures with DNA in conjunction with its mutation studies. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"10 ","pages":"63-8"},"PeriodicalIF":0.0,"publicationDate":"2014-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2142/biophysics.10.63","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34734064","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: 5

Familial clustering of mice consistent to known pedigrees enabled by the genome profiling (GP) method. 通过基因组分析(GP)方法使小鼠的家族聚类与已知系谱一致。

Biophysics (Nagoya-shi, Japan) Pub Date : 2014-09-06 eCollection Date: 2014-01-01 DOI: 10.2142/biophysics.10.55

Harshita Sharma, Fumihito Ohtani, Parmila Kumari, Deepti Diwan, Naoko Ohara, Tetsuya Kobayashi, Miho Suzuki, Naoto Nemoto, Yoshibumi Matsushima, Koichi Nishigaki

{"title":"Familial clustering of mice consistent to known pedigrees enabled by the genome profiling (GP) method.","authors":"Harshita Sharma, Fumihito Ohtani, Parmila Kumari, Deepti Diwan, Naoko Ohara, Tetsuya Kobayashi, Miho Suzuki, Naoto Nemoto, Yoshibumi Matsushima, Koichi Nishigaki","doi":"10.2142/biophysics.10.55","DOIUrl":"https://doi.org/10.2142/biophysics.10.55","url":null,"abstract":"Familial clustering without any prerequisite knowledge becomes often necessary in Behavioral Science, and forensic studies in case of great disasters like Tsunami and earthquake requiring body-identification without any usable information. However, there has been no well-established method for this purpose although conventional ones such as short tandem repeats (STR) and single nucleotide polymorphism (SNP), which might be applied with toil and moil to some extent. In this situation, we could find that the universal genome distance-measuring method genome profiling (GP), which is made up of three elemental techniques; random PCR, micro-temperature gradient gel electrophoresis (μTGGE), and computer processing for normalization, can do this purpose with ease when applied to mouse families. We also confirmed that the sequencing approach based on the ccgf (commonly conserved genetic fragment appearing in the genome profile) was not completely discriminative in this case. This is the first demonstration that the familial clustering can be attained without a priori sequence information to the level of discriminating strains and sibling relationships. This method can complement the conventional approaches in preliminary familial clustering. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"10 ","pages":"55-62"},"PeriodicalIF":0.0,"publicationDate":"2014-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4629661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34732709","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: 3

Ultrasensitive enzyme-linked immunosorbent assay (ELISA) of proteins by combination with the thio-NAD cycling method. 结合硫代nad循环法的超灵敏酶联免疫吸附测定(ELISA)。

Biophysics (Nagoya-shi, Japan) Pub Date : 2014-09-05 eCollection Date: 2014-01-01 DOI: 10.2142/biophysics.10.49

Satoshi Watabe, Hiromi Kodama, Mugiho Kaneda, Mika Morikawa, Kazunari Nakaishi, Teruki Yoshimura, Atsushi Iwai, Toshiaki Miura, Etsuro Ito

{"title":"Ultrasensitive enzyme-linked immunosorbent assay (ELISA) of proteins by combination with the thio-NAD cycling method.","authors":"Satoshi Watabe, Hiromi Kodama, Mugiho Kaneda, Mika Morikawa, Kazunari Nakaishi, Teruki Yoshimura, Atsushi Iwai, Toshiaki Miura, Etsuro Ito","doi":"10.2142/biophysics.10.49","DOIUrl":"https://doi.org/10.2142/biophysics.10.49","url":null,"abstract":"An ultrasensitive method for the determination of proteins is described that combines an enzyme-linked immunosorbent assay (ELISA) and a thionicotinamide-adenine dinucleotide (thio-NAD) cycling method. A sandwich method using a primary and a secondary antibody for antigens is employed in an ELISA. An androsterone derivative, 3α-hydroxysteroid, is produced by the hydrolysis of 3α-hydroxysteroid 3-phosphate with alkaline phosphatase linked to the secondary antibody. This 3α-hydroxysteroid is oxidized to a 3-ketosteroid by 3α- hydroxysteroid dehydrogenase (3α-HSD) with a cofactor thio-NAD. By the opposite reaction, the 3-ketosteroid is reduced to a 3α-hydroxysteroid by 3α-HSD with a cofactor NADH. During this cycling reaction, thio-NADH accumulates in a quadratic function-like fashion. Accumulated thio-NADH can be measured directly at an absorbance of 400 nm without any interference from other cofactors. These features enable us to detect a target protein with ultrasensitivity (10(-19) mol/assay) by measuring the cumulative quantity of thio-NADH. Our ultrasensitive determination of proteins thus allows for the detection of small amounts of proteins only by the application of thio-NAD cycling reagents to the usual ELISA system. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"10 ","pages":"49-54"},"PeriodicalIF":0.0,"publicationDate":"2014-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2142/biophysics.10.49","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34732708","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: 32

Reconstitution of intracellular environments in vitro and in artificial cells. 体外和人工细胞内细胞内环境的重建。

Biophysics (Nagoya-shi, Japan) Pub Date : 2014-08-07 eCollection Date: 2014-01-01 DOI: 10.2142/biophysics.10.43

Kei Fujiwara, Miho Yanagisawa, Shin-Ichiro M Nomura

引用次数: 11

Effect of the MotB(D33N) mutation on stator assembly and rotation of the proton-driven bacterial flagellar motor. MotB(D33N)突变对质子驱动细菌鞭毛马达定子组装和旋转的影响。

Biophysics (Nagoya-shi, Japan) Pub Date : 2014-06-14 eCollection Date: 2014-01-01 DOI: 10.2142/biophysics.10.35

Shuichi Nakamura, Tohru Minamino, Nobunori Kami-Ike, Seishi Kudo, Keiichi Namba

{"title":"Effect of the MotB(D33N) mutation on stator assembly and rotation of the proton-driven bacterial flagellar motor.","authors":"Shuichi Nakamura, Tohru Minamino, Nobunori Kami-Ike, Seishi Kudo, Keiichi Namba","doi":"10.2142/biophysics.10.35","DOIUrl":"https://doi.org/10.2142/biophysics.10.35","url":null,"abstract":"The bacterial flagellar motor generates torque by converting the energy of proton translocation through the transmembrane proton channel of the stator complex formed by MotA and MotB. The MotA/B complex is thought to be anchored to the peptidoglycan (PG) layer through the PG-binding domain of MotB to act as the stator. The stator units dynamically associate with and dissociate from the motor during flagellar motor rotation, and an electrostatic interaction between MotA and a rotor protein FliG is required for efficient stator assembly. However, the association and dissociation mechanism of the stator units still remains unclear. In this study, we analyzed the speed fluctuation of the flagellar motor of Salmonella enterica wild-type cells carrying a plasmid encoding a nonfunctional stator complex, MotA/B(D33N), which lost the proton conductivity. The wild-type motor rotated stably but the motor speed fluctuated considerably when the expression level of MotA/B(D33N) was relatively high compared to MotA/B. Rapid accelerations and decelerations were frequently observed. A quantitative analysis of the speed fluctuation and a model simulation suggested that the MotA/B(D33N) stator retains the ability to associate with the motor at a low affinity but dissociates more rapidly than the MotA/B stator. We propose that the stator dissociation process depends on proton translocation through the proton channel. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"10 ","pages":"35-41"},"PeriodicalIF":0.0,"publicationDate":"2014-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4629662/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34732706","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: 5

Uncovering the mechanism for selective control of the visible and near-IR absorption bands in bacteriochlorophylls a, b and g. 揭示了细菌叶绿素a、b和g的可见光和近红外吸收波段的选择性控制机制。

Biophysics (Nagoya-shi, Japan) Pub Date : 2014-06-07 eCollection Date: 2014-01-01 DOI: 10.2142/biophysics.10.25

Jun-Ichi Fujisawa, Morio Nagata

{"title":"Uncovering the mechanism for selective control of the visible and near-IR absorption bands in bacteriochlorophylls a, b and g.","authors":"Jun-Ichi Fujisawa, Morio Nagata","doi":"10.2142/biophysics.10.25","DOIUrl":"https://doi.org/10.2142/biophysics.10.25","url":null,"abstract":"Bacteriochlorophylls (BChls) play an important role as light harvesters in photosynthetic bacteria. Interestingly, bacteriochlorophylls (BChls) a, b, and g selectively tune their visible (Qx) and near IR (Qy) absorption bands by the substituent changes. In this paper, we theoretically study the mechanism for the selective control of the absorption bands. Density functional theory (DFT) and time-dependent DFT (TD-DFT) and four-orbital model analyses reveal that the selective red-shift of the Qy band with the substituent change from BChl a to b occurs with the lower-energy shift of the (HOMO, LUMO) excited state directly induced by the molecular-orbital energy changes. In contrast, the Qx band hardly shifts by the cancellation between the higher- and lower-energy shifts of the (HOMO-1, LUMO) excited state directly induced by the molecular-orbital energy changes and configuration interaction, respectively. On the other hand, with the substituent changes from BChl a to g, the Qx band selectively blue-shifts by the larger higher-energy shift of the (HOMO-1, LUMO) excited state directly induced by the molecular-orbital energy shifts than the lower-energy shift due to the configuration interaction. In contrast, the Qy band hardly shifts by the cancellation between the higher- and lower-energy shifts of the (HOMO, LUMO) excited state directly induced by the molecular-orbital energy changes and configuration interaction, respectively. Our work provides the important knowledge for understanding how nature controls the light-absorption properties of the BChl dyes, which might be also useful for design of porphyrinoid chromophores. ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"10 ","pages":"25-34"},"PeriodicalIF":0.0,"publicationDate":"2014-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4629652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34732705","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: 2

Optimal terminal sequences for continuous or serial isothermal amplification of dsRNA with norovirus RNA replicase. 诺如病毒RNA复制酶连续或连续等温扩增dsRNA的最佳末端序列。

Biophysics (Nagoya-shi, Japan) Pub Date : 2014-03-01 eCollection Date: 2014-01-01 DOI: 10.2142/biophysics.10.15

Hidenao Arai, Koichi Nishigaki, Naoto Nemoto, Miho Suzuki, Yuzuru Husimi

{"title":"Optimal terminal sequences for continuous or serial isothermal amplification of dsRNA with norovirus RNA replicase.","authors":"Hidenao Arai, Koichi Nishigaki, Naoto Nemoto, Miho Suzuki, Yuzuru Husimi","doi":"10.2142/biophysics.10.15","DOIUrl":"https://doi.org/10.2142/biophysics.10.15","url":null,"abstract":"The norovirus RNA replicase (NV3D(pol), 56 kDa, single chain monomeric protein) can amplify double-stranded (ds) RNA isothermally. It will play an alternative role in the in vitro evolution against traditional Qβ RNA replicase, which cannot amplify dsRNA and consists of four subunits, three of which are borrowed from host E.coli. In order to identify the optimal 3'-terminal sequence of the RNA template for NV3D(pol), an in vitro selection using the serial transfer was performed for a random library having the 3'-terminal sequence of ---UUUUUUNNNN-3'. The population landscape on the 4-dimensional sequence space of the 17(th) round of transfer gave a main peak around ---CAAC-3'. In the preceding studies on the batch amplification reaction starting from a single-stranded RNA, a template with 3'-terminal C-stretch was amplified effectively. It was confirmed that in the batch amplification the ---CCC-3' was much more effective than the ---CAAC-3', but in the serial transfer condition in which the ----CAAC-3' was sustained stably, the ---CCC-3' was washed out. Based on these results we proposed the existence of the \"shuttle mode\" replication of dsRNA. We also proposed the optimal terminal sequences of RNA for in vitro evolution with NV3D(pol). ","PeriodicalId":91456,"journal":{"name":"Biophysics (Nagoya-shi, Japan)","volume":"10 ","pages":"15-23"},"PeriodicalIF":0.0,"publicationDate":"2014-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2142/biophysics.10.15","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34732704","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

α-helix formation rate of oligopeptides at subzero temperatures. 低温下寡肽α-螺旋的形成速率。

Biophysics (Nagoya-shi, Japan) Pub Date : 2014-02-18 eCollection Date: 2014-01-01 DOI: 10.2142/biophysics.10.9

Zhi-Jie Qin, Akio Shimizu, Jinsong Li, Masamichi Ikeguchi, Masaji Shinjo, Hiroshi Kihara

引用次数: 1