arXiv: Subcellular Processes最新文献

Modeling protein target search in human chromosomes 人类染色体中蛋白质靶标搜索模型

arXiv: Subcellular Processes Pub Date : 2019-09-19 DOI: 10.1103/PHYSREVRESEARCH.3.013055

Markus Nyberg, T. Ambjörnsson, P. Stenberg, L. Lizana

{"title":"Modeling protein target search in human chromosomes","authors":"Markus Nyberg, T. Ambjörnsson, P. Stenberg, L. Lizana","doi":"10.1103/PHYSREVRESEARCH.3.013055","DOIUrl":"https://doi.org/10.1103/PHYSREVRESEARCH.3.013055","url":null,"abstract":"Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple diffusion: diffusion-limited association rates may underestimate $in~vitro$ measurements up to several orders of magnitude. Moreover, the rates increase if the DNA is coiled rather than straight. Here we model how this works $in~vivo$ in mammalian cells. We use chromatin-chromatin contact data from state-of-the-art Hi-C experiments to map the protein target-search onto a network problem. The nodes represent a DNA segment and the weight of the links is proportional to measured contact probabilities. We then put forward a master equation for the density of searching protein that allows us to calculate the association rates across the genome analytically. For segments where the rates are high, we find that they are enriched with active genes and have high RNA expression levels. This paper suggests that the DNA's 3D conformation is important for protein search times $in~vivo$ and offers a method to interpret protein-binding profiles in eukaryotes that cannot be explained by the DNA sequence itself.","PeriodicalId":384479,"journal":{"name":"arXiv: Subcellular Processes","volume":"83 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115736048","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: 5

Murburn concept: A facile explanation for oxygen-centered cellular respiration 默本概念:对以氧为中心的细胞呼吸的简单解释

arXiv: Subcellular Processes Pub Date : 2017-03-16 DOI: 10.14748/bmr.v28.4450

K. Manoj

引用次数: 17

CAN GRAPHENE BILAYERS BE THE MEMBRANE MIMETIC MATERIALS? ION CHANNELS IN GRAPHENE-BASED NANOSTRUCTURES 石墨烯双层能否成为膜类材料?石墨烯基纳米结构中的离子通道

arXiv: Subcellular Processes Pub Date : 2016-12-01 DOI: 10.17725/rensit.2016.08.154

O. Gradov, M. Gradova

引用次数: 1

"MS-Patch-Clamp" or the Possibility of Mass Spectrometry Hybridization with Patch-Clamp Setups for Single Cell Metabolomics and Channelomics “ms -膜片钳”或质谱杂交与膜片钳设置单细胞代谢组学和通道组学的可能性

arXiv: Subcellular Processes Pub Date : 2015-10-30 DOI: 10.11648/j.ab.20150306.11

O. Gradov, M. Gradova

{"title":"\"MS-Patch-Clamp\" or the Possibility of Mass Spectrometry Hybridization with Patch-Clamp Setups for Single Cell Metabolomics and Channelomics","authors":"O. Gradov, M. Gradova","doi":"10.11648/j.ab.20150306.11","DOIUrl":"https://doi.org/10.11648/j.ab.20150306.11","url":null,"abstract":"In this projecting work we propose a mass spectrometric patch-clamp equipment with the capillary performing both a local potential registration at the cell membrane and the analyte suction simultaneously. This paper provides a current literature analysis comparing the possibilities of the novel approach proposed with the known methods, such as scanning patch-clamp, scanning ion conductance microscopy, patch clamp based on scanning probe microscopy technology, quantitative subcellular secondary ion mass spectrometry or \"ion microscopy\", live single-cell mass spectrometry, in situ cell-by-cell imaging, single-cell video-mass spectrometry, etc. We also consider the ways to improve the informativeness of these methods and particularly emphasize the trend at the increasing of the analysis complexity. We propose here the way to improve the efficiency of the cell trapping to the capillary during MS-path-clamp, as well as to provide laser surface ionization using laser trapping and tweezing of cells with the laser beam transmitted through the capillary as a waveguide. It is also possible to combine the above system with the microcolumn separation system or capillary electrophoresis as an optional direction of further development of the complex of analytical techniques emerging from the MS variation of patch-clamp.","PeriodicalId":384479,"journal":{"name":"arXiv: Subcellular Processes","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124361364","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: 7

Certain amplified genomic-DNA fragments (AGFs) may be involved in cell cycle progression and chloroquine is found to induce the production of cell-cycle-associated AGFs (CAGFs) in Plasmodium falciparum 某些扩增的基因组dna片段(AGFs)可能参与细胞周期进程，氯喹可诱导恶性疟原虫细胞周期相关AGFs (CAGFs)的产生

arXiv: Subcellular Processes Pub Date : 2015-10-12 DOI: 10.4236/OALIB.1102447

Gao-De Li

引用次数: 5

Cell bystander effect induced by radiofrequency electromagnetic fields and magnetic nanoparticles 射频电磁场与磁性纳米颗粒诱导的细胞旁观者效应

arXiv: Subcellular Processes Pub Date : 2015-06-03 DOI: 10.2174/1573413712666151124195846

G. Goya, L. Asín, M. P. Calatayud, A. Trés, M. Ibarra

引用次数: 16

Thermodynamics of Error Correction 误差修正热力学

arXiv: Subcellular Processes Pub Date : 2015-04-24 DOI: 10.1103/PhysRevX.5.041039

P. Sartori, S. Pigolotti

{"title":"Thermodynamics of Error Correction","authors":"P. Sartori, S. Pigolotti","doi":"10.1103/PhysRevX.5.041039","DOIUrl":"https://doi.org/10.1103/PhysRevX.5.041039","url":null,"abstract":"Information processing at the molecular scale is limited by thermal fluctuations. This can cause undesired consequences in copying information since thermal noise can lead to errors that can compromise the functionality of the copy. For example, a high error rate during DNA duplication can lead to cell death. Given the importance of accurate copying at the molecular scale, it is fundamental to understand its thermodynamic features. In this paper, we derive a universal expression for the copy error as a function of entropy production and {cred work dissipated by the system during wrong incorporations}. Its derivation is based on the second law of thermodynamics, hence its validity is independent of the details of the molecular machinery, be it any polymerase or artificial copying device. Using this expression, we find that information can be copied in three different regimes. In two of them, work is dissipated to either increase or decrease the error. In the third regime, the protocol extracts work while correcting errors, reminiscent of a Maxwell demon. As a case study, we apply our framework to study a copy protocol assisted by kinetic proofreading, and show that it can operate in any of these three regimes. We finally show that, for any effective proofreading scheme, error reduction is limited by the chemical driving of the proofreading reaction.","PeriodicalId":384479,"journal":{"name":"arXiv: Subcellular Processes","volume":"59 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114495896","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: 56

Theory of cargo and membrane trafficking 货物和膜运输理论

arXiv: Subcellular Processes Pub Date : 2014-12-03 DOI: 10.1016/B978-0-12-394447-4.40009-X

L. Forêt, L. Brusch, F. Julicher

引用次数: 1

Cryoelectron Microscopy as a Functional Instrument for Systems Biology, Structural Analysis & Experimental Manipulations with Living Cells. A comprehensive review of the current works 低温电子显微镜作为系统生物学、结构分析和活细胞实验操作的功能仪器。对当前工作的全面回顾

arXiv: Subcellular Processes Pub Date : 2014-09-15 DOI: 10.15407/CRYO24.03.193

O. Gradov, M. Gradova

{"title":"Cryoelectron Microscopy as a Functional Instrument for Systems Biology, Structural Analysis & Experimental Manipulations with Living Cells. A comprehensive review of the current works","authors":"O. Gradov, M. Gradova","doi":"10.15407/CRYO24.03.193","DOIUrl":"https://doi.org/10.15407/CRYO24.03.193","url":null,"abstract":"The aim of this paper is to give an introductory review of the cryoelectron microscopy as a complex data source for the most of the system biology branches, including the most perspective non-local approaches known as \"localomics\" and \"dynamomics\". A brief summary of various cryoelectron mi-croscopy methods and corresponding system biological ap-proaches is given in the text. The above classification can be considered as a useful framework for the primary comprehen-sions about cryoelectron microscopy aims and instrumental tools. We do not discuss any of these concepts in details, but merely point out that their methodological complexity follows only from the structure-functional complexity of biological systems which are investigated in this manner. We also postu-late that one can employ some of the cryoelectron microscopic techniques not only for observation, but also for modification and structural refunctionalization of some biological and similar soft matter objects and microscopic samples. In other worlds, we start with the cryoelectron microscopy as a tool for the sys-tem biology and progress to its applying as an instrument for system biology and functional biomimetics; i.e. \"system cryobi-ology\" goes over into \"synthetic cryobiology\" or \"cryogenic biomimetics\". All these conclusions can be deduced from the most recent works of the latest years, including just submitted foreign papers. This article provides an up-to-date description of the conceptual basis for the novel view on the computational cryoelectron microscopy (in silico) approaches and the data mining principles which lie at the very foundation of modern structural analysis and reconstruction.","PeriodicalId":384479,"journal":{"name":"arXiv: Subcellular Processes","volume":"149 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131813641","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: 4

Epigenetics: What it is about? 表观遗传学:它是关于什么的?

arXiv: Subcellular Processes Pub Date : 2014-01-20 DOI: 10.7124/BC.000873

E. Saade, V. Ogryzko

引用次数: 3