Biophysical reports最新文献_第10页

Temperature-dependent elastic properties of DNA. DNA的温度依赖性弹性特性。

Biophysical reports Pub Date : 2022-08-05 eCollection Date: 2022-09-14 DOI: 10.1016/j.bpr.2022.100067

Marc Rico-Pasto, Felix Ritort

引用次数: 2

NEU1 and NEU3 enzymes alter CD22 organization on B cells. NEU1和NEU3酶改变B细胞上CD22的组织。

Biophysical reports Pub Date : 2022-07-22 eCollection Date: 2022-09-14 DOI: 10.1016/j.bpr.2022.100064

Hanh-Thuc Ton Tran, Caishun Li, Radhika Chakraberty, Christopher W Cairo

{"title":"NEU1 and NEU3 enzymes alter CD22 organization on B cells.","authors":"Hanh-Thuc Ton Tran, Caishun Li, Radhika Chakraberty, Christopher W Cairo","doi":"10.1016/j.bpr.2022.100064","DOIUrl":"https://doi.org/10.1016/j.bpr.2022.100064","url":null,"abstract":"The B cell membrane expresses sialic-acid-binding immunoglobulin-like lectins, also called Siglecs, that are important for modulating immune response. Siglecs have interactions with sialoglycoproteins found on the same membrane (cis-ligands) that result in homotypic and heterotypic receptor clusters. The regulation and organization of these clusters, and their effect on cell activation, is not clearly understood. We investigated the role of human neuraminidase enzymes NEU1 and NEU3 on the clustering of CD22 on B cells using confocal microscopy. We observed that native NEU1 and NEU3 activity influence the cluster size of CD22. Using single-particle tracking, we observed that NEU3 activity increased the lateral mobility of CD22, which was in contrast to the effect of exogenous bacterial NEU enzymes. Moreover, we show that native NEU1 and NEU3 activity influenced cellular Ca2+ levels, supporting a role for these enzymes in regulating B cell activation. Our results establish a role for native NEU activity in modulating CD22 organization and function on B cells.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100064"},"PeriodicalIF":0.0,"publicationDate":"2022-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/7c/15/main.PMC9680808.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40705904","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

Dominant geometrical factors of collective cell migration in flexible 3D gelatin tube structures. 柔性三维明胶管结构中细胞集体迁移的主要几何因素。

Biophysical reports Pub Date : 2022-07-22 eCollection Date: 2022-09-14 DOI: 10.1016/j.bpr.2022.100063

Mitsuru Sentoku, Kento Iida, Hiromichi Hashimoto, Kenji Yasuda

{"title":"Dominant geometrical factors of collective cell migration in flexible 3D gelatin tube structures.","authors":"Mitsuru Sentoku, Kento Iida, Hiromichi Hashimoto, Kenji Yasuda","doi":"10.1016/j.bpr.2022.100063","DOIUrl":"https://doi.org/10.1016/j.bpr.2022.100063","url":null,"abstract":"Collective cell migration is a dynamic and interactive behavior of cell cohorts essential for diverse physiological developments in living organisms. Recent studies have revealed the importance of three-dimensional (3D) topographical confinements to regulate the migration modes of cell cohorts in tubular confinement. However, conventional in vitro assays fail to observe cells' behavior in response to 3D structural changes, which is necessary for examining the geometric regulation factors of collective migration. Here, we introduce a newly developed assay for fabricating flexible 3D structures of capillary microtunnels to examine the behavior of vascular endothelial cells (ECs) as they progress through the successive transition across wide or narrow tube structures. The microtunnels with altered diameters were formed inside gelatin-gel blocks by photo-thermal etching with micrometer-sized spot heating of the focused infrared laser absorption. The ECs migrated and spread two-dimensionally on the inner surface of gelatin capillary microtunnels as a monolayer instead of filling the entire capillary. In the straight cylindrical topographical constraint, leading ECs exhibited no apparent diameter dependence for the maximum peak migration velocity. However, widening the diameter in the narrow-wide structures caused a decrease in migration velocity following in direct proportion to the diameter increase ratio, whereas narrowing the diameter in wide-narrow microtunnels increased the speed without obvious correlation between velocity change and diameter change. The results demonstrated the ability of the newly developed flexible 3D gelatin tube structures for collective cell migration, and the findings provide insights into the dominant geometric factor of the emerging migratory modes for endothelial migration as asymmetric fluid flow-like behavior in the borderless cylindrical cell sheets.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100063"},"PeriodicalIF":0.0,"publicationDate":"2022-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/af/0e/main.PMC9680702.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40705900","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

Cell cycle-dependent endocytosis of DNA-wrapped single-walled carbon nanotubes by neural progenitor cells. 神经祖细胞对dna包裹单壁碳纳米管细胞周期依赖的内吞作用。

Biophysical reports Pub Date : 2022-06-15 eCollection Date: 2022-09-14 DOI: 10.1016/j.bpr.2022.100061

Swetha Chandrasekar, Sophia Kuipa, Ana I Vargas, Tetyana Ignatova, Slava V Rotkin, Sabrina S Jedlicka

{"title":"Cell cycle-dependent endocytosis of DNA-wrapped single-walled carbon nanotubes by neural progenitor cells.","authors":"Swetha Chandrasekar, Sophia Kuipa, Ana I Vargas, Tetyana Ignatova, Slava V Rotkin, Sabrina S Jedlicka","doi":"10.1016/j.bpr.2022.100061","DOIUrl":"https://doi.org/10.1016/j.bpr.2022.100061","url":null,"abstract":"While exposure of C17.2 neural progenitor cells (NPCs) to nanomolar concentrations of carbon nanotubes (NTs) yields evidence of cellular substructure reorganization and alteration of cell division and differentiation, the mechanisms of NT entry are not understood. This study examines the entry modes of (GT)20 DNA-wrapped single-walled carbon nanotubes (SWCNTs) into NPCs. Several endocytic mechanisms were examined for responsibility in nanomaterial uptake and connections to alterations in cell development via cell-cycle regulation. Chemical cell-cycle arrest agents were used to synchronize NPCs in early G1, late G1/S, and G2/M phases at rates (>80%) aligned with previously documented levels of synchrony for stem cells. Synchronization led to the highest reduction in SWCNT internalization during the G1/S transition of the cell cycle. Concurrently, known inhibitors of endocytosis were used to gain control over established endocytic machineries (receptor-mediated endocytosis (RME), macropinocytosis (MP), and clathrin-independent endocytosis (CIE)), which resulted in a decrease in uptake of SWCNTs across the board in comparison with the control. The outcome implicated RME as the primary mechanism of uptake while suggesting that other endocytic mechanisms, though still fractionally responsible, are not central to SWCNT uptake and can be supplemented by RME when compromised. Thereby, endocytosis of nanomaterials was shown to have a dependency on cell-cycle progression in NPCs.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100061"},"PeriodicalIF":0.0,"publicationDate":"2022-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/be/13/main.PMC9680777.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40705903","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

Diffusion and interaction dynamics of the cytosolic peroxisomal import receptor PEX5. 细胞膜过氧物酶体导入受体 PEX5 的扩散和相互作用动力学。

IF 2.4

Biophysical reports Pub Date : 2022-06-08 DOI: 10.1016/j.bpr.2022.100055

S Galiani, K Reglinski, P Carravilla, A Barbotin, I Urbančič, J Ott, J Sehr, E Sezgin, F Schneider, D Waithe, P Hublitz, W Schliebs, R Erdmann, C Eggeling

{"title":"Diffusion and interaction dynamics of the cytosolic peroxisomal import receptor PEX5.","authors":"S Galiani, K Reglinski, P Carravilla, A Barbotin, I Urbančič, J Ott, J Sehr, E Sezgin, F Schneider, D Waithe, P Hublitz, W Schliebs, R Erdmann, C Eggeling","doi":"10.1016/j.bpr.2022.100055","DOIUrl":"10.1016/j.bpr.2022.100055","url":null,"abstract":"Cellular functions rely on proper actions of organelles such as peroxisomes. These organelles rely on the import of proteins from the cytosol. The peroxisomal import receptor PEX5 takes up target proteins in the cytosol and transports them to the peroxisomal matrix. However, its cytosolic molecular interactions have so far not directly been disclosed. Here, we combined advanced optical microscopy and spectroscopy techniques such as fluorescence correlation spectroscopy and stimulated emission depletion microscopy with biochemical tools to present a detailed characterization of the cytosolic diffusion and interaction dynamics of PEX5. Among other features, we highlight a slow diffusion of PEX5, independent of aggregation or target binding, but associated with cytosolic interaction partners via its N-terminal domain. This sheds new light on the functionality of the receptor in the cytosol as well as highlighting the potential of using complementary microscopy tools to decipher molecular interactions in the cytosol by studying their diffusion dynamics.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":"2 2","pages":"None"},"PeriodicalIF":2.4,"publicationDate":"2022-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/8f/8d/main.PMC9586885.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10853977","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

Erratum: Diagnosing and mitigating method-based avidity artifacts that confound polyubiquitin-binding assays. 勘误:诊断和减轻方法为基础的狂热伪影，混淆多泛素结合测定。

Biophysical reports Pub Date : 2022-05-18 eCollection Date: 2022-06-08 DOI: 10.1016/j.bpr.2022.100058

Allyn J Schoeffler, Elizabeth Helgason, Nataliya Popovych, Erin C Dueber

引用次数: 0

Identifying vaccine escape sites via statistical comparisons of short-term molecular dynamics 通过短期分子动力学的统计比较确定疫苗逃逸位点

Biophysical reports Pub Date : 2022-04-01 DOI: 10.1016/j.bpr.2022.100056

Madhusudan Rajendran, M. C. Ferran, G. Babbitt

引用次数: 5

Unbiased retrieval of frequency-dependent mechanical properties from noisy time-dependent signals. 从噪声时变信号中无偏检索频率相关力学特性。

Biophysical reports Pub Date : 2022-03-30 eCollection Date: 2022-09-14 DOI: 10.1016/j.bpr.2022.100054

Shada Abuhattum, Hui-Shun Kuan, Paul Müller, Jochen Guck, Vasily Zaburdaev

{"title":"Unbiased retrieval of frequency-dependent mechanical properties from noisy time-dependent signals.","authors":"Shada Abuhattum, Hui-Shun Kuan, Paul Müller, Jochen Guck, Vasily Zaburdaev","doi":"10.1016/j.bpr.2022.100054","DOIUrl":"https://doi.org/10.1016/j.bpr.2022.100054","url":null,"abstract":"The mechanical response of materials to dynamic loading is often quantified by the frequency-dependent complex modulus. Probing materials directly in the frequency domain faces technical challenges such as a limited range of frequencies, long measurement times, or small sample sizes. Furthermore, many biological samples, such as cells or tissues, can change their properties upon repetitive probing at different frequencies. Therefore, it is common practice to extract the material properties by fitting predefined mechanical models to measurements performed in the time domain. This practice, however, precludes the probing of unique and yet unexplored material properties. In this report, we demonstrate that the frequency-dependent complex modulus can be robustly retrieved in a model-independent manner directly from time-dependent stress-strain measurements. While applying a rolling average eliminates random noise and leads to a reliable complex modulus in the lower frequency range, a Fourier transform with a complex frequency helps to recover the material properties at high frequencies. Finally, by properly designing the probing procedure, the recovery of reliable mechanical properties can be extended to an even wider frequency range. Our approach can be used with many state-of-the-art experimental methods to interrogate the mechanical properties of biological and other complex materials.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100054"},"PeriodicalIF":0.0,"publicationDate":"2022-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9680806/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40705899","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

PySOFI: an open source Python package for SOFI. PySOFI:用于SOFI的开源Python包。

Biophysical reports Pub Date : 2022-03-30 eCollection Date: 2022-06-08 DOI: 10.1016/j.bpr.2022.100052

Yuting Miao, Shimon Weiss, Xiyu Yi

引用次数: 0

Chromatin as self-returning walks: From population to single cell and back. 自我回归的染色质:从群体到单细胞再回来。

Biophysical reports Pub Date : 2022-03-09 DOI: 10.1016/j.bpr.2021.100042

Anne R Shim, Kai Huang, Vadim Backman, Igal Szleifer

引用次数: 1