AIMS Biophysics最新文献_第7页

The effects of temperature on streptavidin-biotin binding using affinity isothermal titration calorimetry 用亲和等温滴定量热法研究温度对链霉亲和素-生物素结合的影响

IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology

AIMS Biophysics

Pub Date : 2020-06-16 DOI: 10.3934/biophy.2020018

K. Mpye, S. Gildenhuys, Salerwe Mosebi

An entropically-driven binding interaction at a certain temperature may change to an enthalpically-driven process at another temperature, depending on the polarization state of the groups that are involved in binding. The streptavidin-biotin complex has been extensively studied across biological, medical, chemical and material science fields using various techniques, however, not much has been reported on this interaction across a broad temperature range, between 2 °C and 40 °C using biophysical techniques. In this study, we determined how the forces involved in the streptavidin-biotin complex formation are affected by the reaction temperature using the Affinity ITC (TA Instruments). We observed that this complex formation is a spontaneous binding process, indicated by a negative Gibbs energy (ΔG) at all temperatures tested. The observed negative heat capacity (ΔCp) ~ −459.9 cal/mol K highlights the polar solvation of the interaction that corresponds to a decreasing enthalpy (more negative) (ΔH) with increasing reaction temperature. The stoichiometry (n) of 0.98 was estimated at 25 °C. An increase in reaction temperature resulted in an almost two-fold increase or more in n, notably from 1.59 to 3.41 between 30 °C and 40 °C. Whereas, at lower reaction temperatures, 2 °C to 10 °C, higher molar binding ratios were recorded, i.e. 2.74 to 5.76. We report an enthalpically-driven interaction between 30 °C and 40 °C whereas, an entropically-favourable interaction is observed at lower temperatures, suggestive of an interaction dominated by nonpolar interactions at lower temperatures and polar interactions at higher temperatures. Consequently, alterations in the polarisation state of streptavidin result in moderate binding affinity of biotin to streptavidin at higher reaction temperatures, K D 10-4 ≤ 10-5 M.

根据参与结合的基团的极化状态，在某一温度下由熵驱动的结合相互作用可能在另一温度下转变为焓驱动的过程。链霉亲和素-生物素复合物已经在生物、医学、化学和材料科学领域使用各种技术进行了广泛的研究，然而，使用生物物理技术在2°C至40°C的广泛温度范围内对这种相互作用的报道并不多。在这项研究中，我们使用Affinity ITC (TA Instruments)确定了参与链霉亲和素-生物素复合物形成的力如何受到反应温度的影响。我们观察到这种复合物的形成是一个自发的结合过程，在所有测试温度下都有负的吉布斯能(ΔG)。观察到的负热容(ΔCp) ~ - 459.9 cal/mol K突出了相互作用的极性溶剂化，对应于随着反应温度的升高焓减小(更负)(ΔH)。在25°C时，估计其化学计量量n为0.98。反应温度的升高导致n几乎增加两倍或更多，特别是在30°C和40°C之间从1.59增加到3.41。然而，在较低的反应温度下(2 ~ 10℃)，摩尔结合率较高，为2.74 ~ 5.76。我们报告了在30°C和40°C之间焓驱动的相互作用，而在较低温度下观察到熵有利的相互作用，这表明在较低温度下由非极性相互作用和较高温度下的极性相互作用主导的相互作用。因此，链霉亲和素的极化状态的改变导致生物素在较高的反应温度下与链霉亲和素具有中等的结合亲和力，K D 10-4≤10-5 M。

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引用次数: 6

Calorimetry and FTIR reveal the ability of URG7 protein to modify the aggregation state of both cell lysate and amylogenic α-synuclein 量热法和FTIR揭示了URG7蛋白改变细胞裂解物和淀粉样α-突触核蛋白聚集状态的能力

IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology

AIMS Biophysics

Pub Date : 2020-06-15 DOI: 10.3934/biophy.2020015

J. Dandurand, A. Ostuni, M. Armentano, M. Crudele, V. Dolce, Federica Marra, V. Samouillan, F. Bisaccia

Differential scanning calorimetry and FITR analyses allowed to investigate the role of URG7 (up-regulated gene clone 7) protein involved in the development of hepatocellular carcinoma induced by hepatitis B virus infection, on the physical structure both of lysates of human hepatoblastoma cells (HepG2) stressed with tunicamycin and α-synuclein, one of the proteins associated with neurogenerative diseases. The protein-water interfacial region was identified and correlated with protein structure. DSC results confirm through the interfacial water behavior that URG7 is able to act in two ways: it maintains the interfacial water stability and controls the mobile fraction level, thereby the flexibility and the protein folding. The mobile water phase increases strongly for cells exposed to α-synuclein, demonstrating an important influence on water hydration. FTIR results evidenced an increase of about 30% of cross β structures in cells exposed to α-synuclein, associated with aggregated proteins. In stress conditions, URG7 was able to maintain the same fraction of mobile water as untreated cells. URG7 was able to restore the water reorientation ability around the complex lysate system and reduced abnormal protein folding.

差示扫描量热法和FITR分析可以研究URG7（上调基因克隆7）蛋白在乙型肝炎病毒感染诱导的肝细胞癌发生中的作用、对膜霉素和α-突触核蛋白应激的人肝母细胞瘤细胞（HepG2）裂解物的物理结构的影响，与神经源性疾病相关的蛋白质之一。确定了蛋白质-水界面区，并将其与蛋白质结构联系起来。DSC结果通过界面水行为证实，URG7能够通过两种方式发挥作用：它保持界面水的稳定性并控制流动部分的水平，从而提高灵活性和蛋白质折叠。暴露于α-突触核蛋白的细胞的流动水相强烈增加，表明对水的水合作用有重要影响。FTIR结果证明，在暴露于α-突触核蛋白的细胞中，与聚集蛋白相关的交叉β结构增加了约30%。在应激条件下，URG7能够保持与未处理细胞相同的流动水份额。URG7能够恢复复杂裂解物系统周围的水重新定向能力，并减少异常蛋白质折叠。

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引用次数: 3

Towards virtual surgery planning: the modified Blalock-Taussig Shunt 走向虚拟手术计划：改良的Blalock Taussig Shunt

IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology

AIMS Biophysics

Pub Date : 2020-06-03 DOI: 10.3934/biophy.2020014

Stephen J. Haller, R. Gerrah, S. Rugonyi

A modified Blalock-Taussig shunt (MBTS) is an aortopulmonary shunt to establish or augment pulmonary perfusion in congenital cardiac defects with limited pulmonary blood flow. Proper function of this shunt is of utmost importance. In clinical practice, prediction of flow in an MBTS relies on previous experience. In the research field, computational modeling techniques have been developed to simulate flow in an MBTS and predict its performance. These techniques are promising but also time consuming and prone to uncertainties; therefore not yet suitable for clinical practice. Here we present a simplified, patient-based computational model to predict mean circulatory flow characteristics after MBTS insertion. Simulations performed over a range of pulmonary vascular resistances, were compared to data from: i) previous modeling studies; ii) data from the specific patient modeled, and iii) a cohort of patients with MBTS. Model predictions were within one standard deviation from cohort data; and within 1% from results of previous (more complex) computational models. In comparison to previous studies, our model is computationally stable with significantly shorter computational time to perform simulations. We envision that our approach could be used in the future to perform virtual surgeries, quickly testing different surgical scenarios using the patient own geometrical and physiological characteristics, to aid surgeons in decision making.

改良的Blalock-Taussig分流（MBTS）是一种主动脉-肺动脉分流，用于在肺血流量有限的先天性心脏缺陷中建立或增加肺灌注。这种分流器的正确功能至关重要。在临床实践中，MBTS中流量的预测依赖于以前的经验。在研究领域，已经开发了计算建模技术来模拟MBTS中的流动并预测其性能。这些技术很有前景，但也很耗时，而且容易产生不确定性；因此还不适合临床实践。在这里，我们提出了一个简化的、基于患者的计算模型来预测MBTS插入后的平均循环流量特征。将对一系列肺血管阻力进行的模拟与以下数据进行比较：i）先前的建模研究；ii）来自所建模的特定患者的数据，以及iii）患有MBTS的患者队列。模型预测与队列数据的偏差在一个标准差以内；并且与先前（更复杂的）计算模型的结果相差在1%以内。与之前的研究相比，我们的模型在计算上是稳定的，执行模拟的计算时间明显更短。我们设想，我们的方法将来可以用于进行虚拟手术，利用患者自身的几何和生理特征快速测试不同的手术场景，以帮助外科医生做出决策。

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引用次数: 0

Analysis of a normal and aero helmet on an elite cyclist in the dropped position 一名优秀自行车运动员在落点位置上的普通头盔和空气动力头盔的分析

IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology

AIMS Biophysics

Pub Date : 2020-03-22 DOI: 10.3934/biophy.2020005

Pedro Forte, D. Marinho, T. Barbosa, J. Morais

Cyclists use to wear different helmets and adopt different body positions on the bicycle to minimize resistance. The aim of this study was to compare a standard helmet with the new aero road helmets in a bicycle-cyclist system by CFD on the dropped position. An elite level road cyclist volunteered to this research. The cyclist was scanned on his racing bicycle on the dropped position wearing competition gear and a standard helmet and an aero road helmet. A three-dimensional domain around the cyclist with 7 m of length, 2.5 m of width and 2.5 m of height and meshed with more than 43 million of prismatic and tetrahedral elements. The numerical simulations were conducted at 11.11 m/s. The numerical simulations outputs were viscous, pressure and total drag and coefficient of drag. The standard helmet presented a viscous drag of 10.52 N, a pressure drag of 16.51 N and a total drag of 21.98 N. The aero road helmet presented a pressure drag of 7.40 N, a viscous drag of 12.56 N and a total drag of 19.96 N. Moreover, the aero road helmet presented a lower viscous, pressure and total drag coefficient in comparison to the standard helmet. It is possible to conclude that an aero road helmet imposes less drag in comparison to a standard helmet.

骑自行车的人戴不同的头盔，在自行车上采取不同的身体姿势，以尽量减少阻力。本研究的目的是通过CFD对标准头盔与新型空气动力道路头盔在自行车系统中的掉落位置进行比较。一位优秀的公路自行车手自愿参加这项研究。这名自行车手戴着比赛装备、标准头盔和航空头盔，在他的赛车上被扫描。骑行者周围的一个三维区域，长7米，宽2.5米，高2.5米，由超过4300万个棱柱体和四面体单元网格组成。数值模拟以11.11 m/s的速度进行。数值模拟结果包括粘性、压力、总阻力和阻力系数。标准安全帽的粘性阻力为10.52 N，压力阻力为16.51 N，总阻力为21.98 N，气动安全帽的压力阻力为7.40 N，粘性阻力为12.56 N，总阻力为19.96 N，且与标准安全帽相比，气动安全帽的粘性系数、压力系数和总阻力系数均较低。可以得出结论，与标准头盔相比，航空安全帽施加的阻力更小。

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引用次数: 4

Structural changes in thyroid hormone receptor-beta by T3 binding and L330S mutational interactions T3结合和L330S突变相互作用对甲状腺激素受体β结构的影响

IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology

AIMS Biophysics

Pub Date : 2020-03-17 DOI: 10.3934/biophy.2020003

T. R. Lamichhane, H. P. Lamichhane

The point mutations like L330S in the ligand binding domain (LBD) of thyroid hormone receptor-beta (THR-β) make the structural changes as reflected by Ramachandran plots, solvent accessible surface area, radial distribution functions, root mean square deviations and fluctuations, and interaction and internal energies of the LBD residues. By using nanoscale molecular dynamics (NAMD) simulations, the structural features of T3 liganded, unliganded and mutated THR-β LBD are compared to explore the molecular insights in euthyroid, hypothyroid and resistance to thyroid hormones (RTH) states, respectively. The L330S-mutant causes steric hindrance while binding T3 into THR-β LBD causing RTH in the thyroid patients.

甲状腺激素受体-β (THR-β)的配体结合域(LBD)发生L330S等点突变后，其结构发生了变化，反映在Ramachandran图、溶剂可及表面积、径向分布函数、均方根偏差和波动、LBD残基的相互作用和内能等方面。通过纳米尺度分子动力学(NAMD)模拟，比较了T3配体、未配体和突变的THR-β LBD的结构特征，分别探讨了甲状腺功能正常、甲状腺功能低下和甲状腺激素抵抗(RTH)状态的分子意义。l330s突变体在将T3结合到THR-β LBD时引起位阻，导致甲状腺患者发生RTH。

引用次数: 4

The potential of lipid soluble thiamine in the treatment of cancer 脂溶性硫胺素治疗癌症的潜力

IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology

AIMS Biophysics

Pub Date : 2020-02-09 DOI: 10.3934/biophy.2020002

D. Lonsdale, C. Marrs

The resurgence of interest in cancer metabolism has linked alterations in the regulation and exploitation of metabolic pathways with an anabolic phenotype that increases biomass production for the replication of new daughter cells. To support the increase in the metabolic rate of cancer cells, a coordinated increase in the supply of nutrients, such as glucose, as well as micronutrients functioning as enzyme cofactors is required. The majority of co-enzymes are derivatives of water-soluble vitamins such as niacin, folate, pantothenic acid, pyridoxine, biotin, riboflavin and thiamine (Vitamin B1). Continuous dietary intake of these micronutrients is essential for maintaining normal health. How cancer cells adaptively regulate cellular homeostasis of cofactors and how they can regulate expression and function of metabolic enzymes in cancer is under-appreciated. Exploitation of cofactor-dependent metabolic pathways with the advent of anti-folates highlights the potential vulnerabilities and importance of vitamins in cancer biology. Vitamin supplementation products are easily accessible and patients often perceive them as safe and beneficial without full knowledge of their effects. Thus, understanding the significance of enzyme cofactors in cancer cell metabolism will provide for important dietary strategies and new molecular targets to reduce disease progression. Recent studies have demonstrated the significance of thiamine-dependent enzymes in cancer cell metabolism. Therefore, this hypothesis discusses the current knowledge in the alterations in thiamine availability, homeostasis, and exploitation of thiamine-dependent pathways by cancer cells.

对癌症代谢的兴趣的复苏将代谢途径的调节和利用的改变与合成代谢表型联系起来，合成代谢表型增加了用于新子细胞复制的生物量。为了支持癌细胞代谢率的增加，需要协调增加营养物质的供应，如葡萄糖，以及作为酶辅助因子的微量营养素。大多数辅酶是水溶性维生素的衍生物，如烟酸、叶酸、泛酸、吡哆醇、生物素、核黄素和硫胺素(维生素B1)。从饮食中持续摄入这些微量营养素对维持正常健康至关重要。癌细胞如何自适应调节辅助因子的细胞稳态，以及它们如何调节肿瘤代谢酶的表达和功能尚不清楚。随着抗叶酸的出现，对辅助因子依赖性代谢途径的开发突出了维生素在癌症生物学中的潜在脆弱性和重要性。维生素补充产品很容易获得，患者往往认为它们是安全有益的，而不完全了解它们的效果。因此，了解酶辅助因子在癌细胞代谢中的重要性将为重要的饮食策略和减少疾病进展的新分子靶点提供依据。近年来的研究证实了硫胺素依赖性酶在癌细胞代谢中的重要作用。因此，这一假设讨论了目前对硫胺素可用性、体内平衡和癌细胞利用硫胺素依赖途径的改变的了解。

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引用次数: 2

Peptide AEDL alters chromatin conformation via histone binding 肽AEDL通过组蛋白结合改变染色质构象

IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology

AIMS Biophysics

Pub Date : 2020-01-31 DOI: 10.3934/biophy.2020001

Larisa I. Fedoreyeva, Boris F. Vanyushin, Ekaterina N. Baranova

Eukaryotic DNA is tightly packed into chromatin, a DNA–protein structure that exists as transcriptionally permissive euchromatin or repressive heterochromatin. Post-translational modification of histones plays a key role in regulating chromatin dynamics. Short peptides derived from various sources are known to function as epigenetic modulators; however, their mechanisms of action are poorly understood. We addressed this issued by investigating the effect of peptide AEDL on chromatin structure in tobacco (Nicotiana tabacum L.), a commercially important plant species. The chromatin of tobacco interphase cells is characterized by the presence of zones of transcriptionally active domains and particular domains of condensed chromatin of cells that partially coincide with heterochromatin zones. Chromatin decondensation and the formation of euchromatin, accompanied by the activation of genes expression activity, are a determining factor in responses to stressful effects. Our results show that plants grown in the presence of 10 −7 M peptide AEDL transformed condensed chromatin domains from 45% in control cells to 25%. Histone modifications, which constitute the so-called histone code, play a decisive role in the control of chromatin structure. Fluorescence quenching experiments using fluorescein isothiocyanate-labeled histones revealed that the linker histone H1 and complexes of core H3 and H1 histones with DNA bound to peptide AEDL in a 1: 1 molar ratio. The peptide was found to bind to the N-terminal lysine residue of H1 and the lysine residue at position 36 of the H3 C terminus. These interactions of histones H1 and H3 with AEDL peptide loosened the tightly packed chromatin structure, getting transcriptionally active euchromatin. Our findings provide novel insight into the mechanism of gene regulation by short peptides and have implications for breeding more resistant or productive varieties of tobacco and other crops.

真核DNA紧密地包裹在染色质中，染色质是一种DNA-蛋白质结构，以转录允许的常染色质或抑制性异染色质的形式存在。组蛋白的翻译后修饰在调节染色质动力学中起着关键作用。已知衍生自各种来源的短肽具有表观遗传学调节剂的功能；然而，人们对它们的作用机制知之甚少。我们通过研究肽AEDL对烟草（Nicotiana tabacum L.）染色质结构的影响来解决这一问题，烟草是一种重要的商业植物。烟草间期细胞的染色质的特征是存在转录活性结构域区域和与异染色质区域部分重合的细胞浓缩染色质的特定结构域。染色质去凝聚和常染色质的形成，伴随着基因表达活性的激活，是对应激反应的决定因素。我们的结果表明，在10−7M肽AEDL存在下生长的植物将浓缩染色质结构域从对照细胞中的45%转化为25%。组蛋白修饰构成了所谓的组蛋白密码，在控制染色质结构中起着决定性作用。使用异硫氰酸荧光素标记的组蛋白的荧光猝灭实验显示，连接组蛋白H1以及核心H3和H1组蛋白与DNA的复合物以1∶1摩尔比结合到肽AEDL。发现该肽与H1的N-末端赖氨酸残基和H3C末端36位的赖氨酸残余基结合。组蛋白H1和H3与AEDL肽的这些相互作用松动了紧密堆积的染色质结构，获得了转录活性的常染色质。我们的发现为短肽的基因调控机制提供了新的见解，并对培育更具抗性或生产力的烟草和其他作物品种具有启示。

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引用次数: 2

A generalization of the Shell Theorem.Electric potential of charged spheres and charged vesicles surrounded by electrolyte 壳层定理的推广电解质包围的带电球体和带电囊泡的电势

IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology

AIMS Biophysics

Pub Date : 2020-01-25 DOI: 10.3934/biophy.2020007

Istv'an P. Sug'ar

引用次数: 6

Imaging flow cytometry methods for quantitative analysis of label-free crystalline silica particle interactions with immune cells. 成像流式细胞术方法定量分析无标记结晶二氧化硅颗粒与免疫细胞的相互作用。

IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology

AIMS Biophysics

Pub Date : 2020-01-01 Epub Date: 2020-05-26 DOI: 10.3934/biophy.2020012

Bradley Vis, Jonathan J Powell, Rachel E Hewitt

Exposure to respirable fractions of crystalline silica quartz dust particles is associated with silicosis, cancer and the development of autoimmune conditions. Early cellular interactions are not well understood, partly due to a lack of suitable technological methods. Improved techniques are needed to better quantify and study high-level respirable crystalline silica exposure in human populations. Techniques that can be applied to complex biological matrices are pivotal to understanding particle-cell interactions and the impact of particles within real, biologically complex environments. In this study, we investigated whether imaging flow cytometry could be used to assess the interactions between cells and crystalline silica when present within complex biological matrices. Using the respirable-size fine quartz crystalline silica dust Min-u-sil® 5, we first validated previous reports that, whilst associating with cells, crystalline silica particles can be detected solely through their differential light scattering profile using conventional flow cytometry. This same property reliably identified crystalline silica in association with primary monocytic cells in vitro using an imaging flow cytometry assay, where darkfield intensity measurements were able to detect crystalline silica concentrations as low as 2.5 μg/mL. Finally, we ultilised fresh whole blood as an exemplary complex biological matrix to test the technique. Even after the increased sample processing required to analyse cells within whole blood, imaging flow cytometry was capable of detecting and assessing silica-association to cells. As expected, in fresh whole blood exposed to crystalline silica, neutrophils and cells of the monocyte/macrophage lineage phagocytosed the particles. In addition to the use of this technique in in vitro exposure models, this method has the potential to be applied directly to ex vivo diagnostic studies and research models, where the identification of crystalline silica association with cells in complex biological matrices such as bronchial lavage fluids, alongside additional functional and phenotypic cellular readouts, is required.

暴露于可吸入的结晶二氧化硅石英粉尘颗粒与矽肺病、癌症和自身免疫性疾病的发展有关。早期的细胞相互作用还没有被很好地理解，部分原因是缺乏合适的技术方法。需要改进技术来更好地量化和研究人群中高水平可吸入结晶二氧化硅暴露。可以应用于复杂生物基质的技术对于理解粒子-细胞相互作用以及粒子在真实的、复杂的生物环境中的影响至关重要。在这项研究中，我们研究了成像流式细胞术是否可以用于评估复杂生物基质中细胞与结晶二氧化硅之间的相互作用。使用可呼吸大小的细石英晶体二氧化硅粉尘Min-u-sil®5，我们首先验证了先前的报道，虽然与细胞相关，但晶体二氧化硅颗粒可以通过传统流式细胞术的差异光散射谱进行检测。利用成像流式细胞术测定，在体外可靠地鉴定出与原代单核细胞相关的结晶二氧化硅，其中暗场强度测量能够检测到低至2.5 μg/mL的结晶二氧化硅浓度。最后，我们利用新鲜全血作为典型的复杂生物基质来测试该技术。即使在分析全血细胞所需的更多样品处理之后，成像流式细胞术也能够检测和评估二氧化硅与细胞的关联。正如预期的那样，在暴露于结晶二氧化硅的新鲜全血中，中性粒细胞和单核/巨噬细胞谱系的细胞吞噬了颗粒。除了在体外暴露模型中使用该技术外，该方法还具有直接应用于体外诊断研究和研究模型的潜力，其中需要识别与复杂生物基质(如支气管洗洗液)中细胞相关的结晶二氧化硅，以及额外的功能和表型细胞读数。

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引用次数: 3

Data formats for modelling the spatial structure of chromatin based on experimental positions of nucleosomes 基于核小体实验位置的染色质空间结构建模数据格式

IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology

AIMS Biophysics

Pub Date : 2019-07-16 DOI: 10.3934/BIOPHY.2019.3.83

M. Mörl, Tilo Zülske, R. Schöpflin, G. Wedemann

In the nucleus of eukaryotic cells, DNA is wrapped around histone proteins, forming units termed nucleosomes. Nucleosome chains fold into chromatin. Despite extensive experimental advancement, many fundamental features of chromatin remain uncertain. Since all cell types and states cannot be profiled experimentally, especially in solution and in vivo, computer simulations are valuable tools for research. Most computer simulation models of chromatin are coarse-grained and describe the main characteristics of 3D chromatin packing. Newer models include experimentally derived positions of nucleosomes. While it is common practice in other disciplines, such as systems biology, to make experimental data publicly available, data from computer simulations of chromatin models are not usually published. Thus, data standard exchange formats are lacking, and we address this issue in the present work. We analysed the workflow, from experimental determination of the positions of nucleosomes through to analysis of outputs from simulated computer models. We defined standardized formats based on Extensible Markup Language (XML) for artefacts generated by steps in this workflow. We found that XML is useful since it is easy to transform XML-based-files by applying Extensible Stylesheet Language Transformations (XSLT) to other formats. We demonstrate the viability of this approach and the associated file formats using a complete example of computer simulation of chromatin domains based on experimentally determined nucleosome positions. The XML schemas and examples are published in an open source repository.

在真核细胞的细胞核中，DNA包裹在组蛋白周围，形成称为核小体的单元。核小体链折叠成染色质。尽管实验取得了广泛进展，但染色质的许多基本特征仍不确定。由于所有细胞类型和状态都无法通过实验来描述，尤其是在溶液和体内，因此计算机模拟是有价值的研究工具。大多数染色质的计算机模拟模型都是粗粒度的，并描述了3D染色质堆积的主要特征。较新的模型包括实验推导的核小体位置。虽然在系统生物学等其他学科中，公开实验数据是一种常见的做法，但染色质模型的计算机模拟数据通常不会公布。因此，缺乏数据标准交换格式，我们在目前的工作中解决了这个问题。我们分析了工作流程，从核小体位置的实验确定到模拟计算机模型输出的分析。我们为该工作流中的步骤生成的工件定义了基于可扩展标记语言（XML）的标准化格式。我们发现XML很有用，因为通过将可扩展样式表语言转换（XSLT）应用于其他格式，可以很容易地转换基于XML的文件。我们使用基于实验确定的核小体位置的染色质结构域的计算机模拟的完整示例来证明这种方法和相关文件格式的可行性。XML模式和示例发布在一个开源存储库中。

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引用次数: 2