Biological Chemistry最新文献_第10页

Highlight: on the past and the future of cellular microcompartments. 重点:关于细胞微室的过去和未来。

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2023-04-25 DOI: 10.1515/hsz-2023-0153

Milos Galic, Christian Ungermann, Katia Cosentino

引用次数: 0

Computational resolution in single molecule localization - impact of noise level and emitter density. 单分子定位的计算分辨率——噪声水平和发射器密度的影响。

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2023-04-25 DOI: 10.1515/hsz-2022-0301

Mathias Hockmann, Stefan Kunis, Rainer Kurre

{"title":"Computational resolution in single molecule localization - impact of noise level and emitter density.","authors":"Mathias Hockmann, Stefan Kunis, Rainer Kurre","doi":"10.1515/hsz-2022-0301","DOIUrl":"https://doi.org/10.1515/hsz-2022-0301","url":null,"abstract":"Classical fluorescence microscopy is a powerful technique to image biological specimen under close-to-native conditions, but light diffraction limits its optical resolution to 200-300 nm-two orders of magnitude worse than the size of biomolecules. Assuming single fluorescent emitters, the final image of the optical system can be described by a convolution with the point spread function (PSF) smearing out details below the size of the PSF. In mathematical terms, fluorescence microscopy produces bandlimited space-continuous images that can be recovered from their spatial samples under the conditions of the classical Shannon-Nyquist theorem. During the past two decades, several single molecule localization techniques have been established and these allow for the determination of molecular positions with sub-pixel accuracy. Without noise, single emitter positions can be recovered precisely - no matter how close they are. We review recent work on the computational resolution limit with a sharp phase transition between two scenarios: 1) where emitters are well-separated with respect to the bandlimit and can be recovered up to the noise level and 2) closely distributed emitters which results in a strong noise amplification in the worst case. We close by discussing additional pitfalls using single molecule localization techniques based on structured illumination.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2023-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9367349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

The readily retrievable pool of synaptic vesicles. 突触囊泡易于恢复的池。

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2023-04-25 DOI: 10.1515/hsz-2022-0298

Sai Krishnan, Jürgen Klingauf

引用次数: 1

Nuclear redox processes in land plant development and stress adaptation. 陆地植物发育和逆境适应中的核氧化还原过程。

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2023-04-25 DOI: 10.1515/hsz-2022-0288

Sabine Zachgo

引用次数: 3

The role of lysosomes in lipid homeostasis. 溶酶体在脂质稳态中的作用。

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2023-04-25 DOI: 10.1515/hsz-2022-0287

Florian Fröhlich, Ayelén González Montoro

引用次数: 2

Modulation of self-organizing circuits at deforming membranes by intracellular and extracellular factors. 胞内和胞外因子对变形膜自组织回路的调节。

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2023-04-25 DOI: 10.1515/hsz-2022-0290

Anastasiia Sokolova, Milos Galic

引用次数: 1

Setting up a data management infrastructure for bioimaging. 建立生物成像的数据管理基础设施。

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2023-04-25 DOI: 10.1515/hsz-2022-0304

Susanne Kunis, Karen Bernhardt, Michael Hensel

{"title":"Setting up a data management infrastructure for bioimaging.","authors":"Susanne Kunis, Karen Bernhardt, Michael Hensel","doi":"10.1515/hsz-2022-0304","DOIUrl":"https://doi.org/10.1515/hsz-2022-0304","url":null,"abstract":"While the FAIR (Findable, Accessible, Interoperable, and Re-usable) principles are well accepted in the scientific community, there are still many challenges in implementing them in the day-to-day scientific process. Data management of microscopy images poses special challenges due to the volume, variety, and many proprietary formats. In particular, appropriate metadata collection, a basic requirement for FAIR data, is a real challenge for scientists due to the technical and content-related aspects. Researchers benefit here from interdisciplinary research network with centralized data management. The typically multimodal structure requires generalized data management and the corresponding acquisition of metadata. Here we report on the establishment of an appropriate infrastructure for the research network by a Core Facility and the development and integration of a software tool MDEmic that allows easy and convenient processing of metadata of microscopy images while providing high flexibility in terms of customization of metadata sets. Since it is also in the interest of the core facility to apply standards regarding the scope and serialization formats to realize successful and sustainable data management for bioimaging, we report on our efforts within the community to define standards in metadata, interfaces, and to reduce the barriers of daily data management.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2023-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9312789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Loss of respiratory complex I subunit NDUFB10 affects complex I assembly and supercomplex formation. 呼吸复合体I亚基NDUFB10的缺失影响复合体I的组装和超复合体的形成。

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2023-04-25 DOI: 10.1515/hsz-2022-0309

Tasnim Arroum, Marie-Theres Borowski, Nico Marx, Frank Schmelter, Martin Scholz, Olympia Ekaterini Psathaki, Michael Hippler, José Antonio Enriquez, Karin B Busch

{"title":"Loss of respiratory complex I subunit NDUFB10 affects complex I assembly and supercomplex formation.","authors":"Tasnim Arroum, Marie-Theres Borowski, Nico Marx, Frank Schmelter, Martin Scholz, Olympia Ekaterini Psathaki, Michael Hippler, José Antonio Enriquez, Karin B Busch","doi":"10.1515/hsz-2022-0309","DOIUrl":"https://doi.org/10.1515/hsz-2022-0309","url":null,"abstract":"The orchestrated activity of the mitochondrial respiratory or electron transport chain (ETC) and ATP synthase convert reduction power (NADH, FADH2) into ATP, the cell's energy currency in a process named oxidative phosphorylation (OXPHOS). Three out of the four ETC complexes are found in supramolecular assemblies: complex I, III, and IV form the respiratory supercomplexes (SC). The plasticity model suggests that SC formation is a form of adaptation to changing conditions such as energy supply, redox state, and stress. Complex I, the NADH-dehydrogenase, is part of the largest supercomplex (CI + CIII2 + CIVn). Here, we demonstrate the role of NDUFB10, a subunit of the membrane arm of complex I, in complex I and supercomplex assembly on the one hand and bioenergetics function on the other. NDUFB10 knockout was correlated with a decrease of SCAF1, a supercomplex assembly factor, and a reduction of respiration and mitochondrial membrane potential. This likely is due to loss of proton pumping since the CI P P -module is downregulated and the P D -module is completely abolished in NDUFB10 knock outs.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2023-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9313652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Neuronal stress granules as dynamic microcompartments: current concepts and open questions. 作为动态微室的神经元应激颗粒:当前概念和悬而未决的问题。

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2023-04-25 DOI: 10.1515/hsz-2022-0302

Anna-Carina Söhnel, Roland Brandt

{"title":"Neuronal stress granules as dynamic microcompartments: current concepts and open questions.","authors":"Anna-Carina Söhnel, Roland Brandt","doi":"10.1515/hsz-2022-0302","DOIUrl":"https://doi.org/10.1515/hsz-2022-0302","url":null,"abstract":"Stress granules are cytosolic, membraneless RNA-protein complexes that form in the cytosol in response to various stressors. Stress granules form through a process termed liquid-liquid phase separation, which increases the local concentration of RNA and protein within the granules, creates dynamic sorting stations for mRNAs and associated proteins, and modulates the availability of mRNA for protein translation. We introduce the concept that neuronal stress granules act as dynamic cytosolic microcompartments in which their components differentially cycle in and out, monitoring the cellular environment. We discuss that neuronal stress granules have distinctive features and contain substructures in which individual components interact transiently. We describe that neuronal stress granules modulate protein expression at multiple levels and affect the proteoform profile of the cytoskeletal protein tau. We argue that a better knowledge of the regulation of stress granule dynamics in neurons and the modulation of their material state is necessary to understand their function during physiological and pathological stress responses. Finally, we delineate approaches to determine the behavior and regulation of critical stress granule organizers and the physical state of stress granules in living neurons.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2023-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9367357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Molecular determinants of protein half-life in chloroplasts with focus on the Clp protease system. 叶绿体中蛋白质半衰期的分子决定因素，重点是Clp蛋白酶系统。

IF 3.7 4区生物学

Biological Chemistry Pub Date : 2023-04-25 DOI: 10.1515/hsz-2022-0320

Lioba Inken Winckler, Nico Dissmeyer

{"title":"Molecular determinants of protein half-life in chloroplasts with focus on the Clp protease system.","authors":"Lioba Inken Winckler, Nico Dissmeyer","doi":"10.1515/hsz-2022-0320","DOIUrl":"https://doi.org/10.1515/hsz-2022-0320","url":null,"abstract":"Proteolysis is an essential process to maintain cellular homeostasis. One pathway that mediates selective protein degradation and which is in principle conserved throughout the kingdoms of life is the N-degron pathway, formerly called the 'N-end rule'. In the cytosol of eukaryotes and prokaryotes, N-terminal residues can be major determinants of protein stability. While the eukaryotic N-degron pathway depends on the ubiquitin proteasome system, the prokaryotic counterpart is driven by the Clp protease system. Plant chloroplasts also contain such a protease network, which suggests that they might harbor an organelle specific N-degron pathway similar to the prokaryotic one. Recent discoveries indicate that the N-terminal region of proteins affects their stability in chloroplasts and provides support for a Clp-mediated entry point in an N-degron pathway in plastids. This review discusses structure, function and specificity of the chloroplast Clp system, outlines experimental approaches to test for an N-degron pathway in chloroplasts, relates these aspects into general plastid proteostasis and highlights the importance of an understanding of plastid protein turnover.","PeriodicalId":8885,"journal":{"name":"Biological Chemistry","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2023-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9314676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0