Characterising biomolecular interactions and dynamics with mass photometry

We review recent advances in our ability to characterise biomolecular structure, interactions and associated dynamics by mass photometry (MP), the label-free detection and mass measurement of individual biomolecules in solution. Molecular counting and identification provides direct access to relative abundance, and thereby affinities, while associated dynamics yield on- and off-rates. The molecular resolution afforded by MP enables these measurements as a function of stoichiometry and assembly at equilibrium, as opposed to the majority of existing solution-based methods. Together with future improvements in terms of assays and technological performance, MP is likely to provide mechanistic details of complex biomolecular processes.     

全胸腔镜下肺叶切除联合系统淋巴清扫对肺癌患者血清疼痛相关因子和免疫功能的影响及预后的影响因素分析

摘要 目的：探讨全胸腔镜下肺叶切除（VATS）联合系统淋巴清扫对肺癌患者血清疼痛相关因子和免疫功能的影响,并分析预后的影响因素。方法：选择我院于2014年3月~2016年3月期间收治的肺癌患者116例,采用随机数字表法分为对照组和研究组,各58例。对照组患者给予传统开胸肺叶切除联合系统淋巴清扫治疗,研究组给予VATS联合系统淋巴清扫治疗,对比两组手术相关指标、血清疼痛相关因子和免疫功能,随访记录研究组患者5年生存率,分析预后的影响因素。结果：与对照组相比,研究组手术时间更长,术中出血量更少,术后住院时间、切口长度、引流时间更短（P<0.05）。两组术后1 d去甲肾上腺素（NE）、前列腺素E2（PGE2）、P物质（SP）、皮质醇（Cor）水平均较术前升高,但研究组低于对照组（P<0.05）。两组术后1 d CD3⁺、CD4⁺、CD4⁺/CD8⁺均较术前降低,但研究组高于对照组,CD8+较术前升高,但研究组低于对照组（P<0.05）。单因素分析结果可知：研究组患者的预后与组织分化、吸烟史、病灶直径、临床分期、清扫淋巴结个数有关（P<0.05）。多因素Logistic回归分析结果可知：临床分期、清扫淋巴结个数是研究组患者预后的影响因素（P<0.05）。结论：ATS联合系统淋巴清扫可减轻肺癌患者术后疼痛及免疫抑制,虽然手术时间更长,但可以改善其他围术期指标。此外,临床分期、清扫淋巴结个数是患者预后的影响因素,应引起临床重视。     

Automatic determination of the handedness of single-particle maps of macromolecules solved by CryoEM

Single-Particle Analysis by Cryo-Electron Microscopy is a well-established technique to elucidate the three-dimensional (3D) structure of biological macromolecules. The orientation of the acquired projection images must be initially estimated without any reference to the final structure. In this step, algorithms may find a mirrored version of all the orientations resulting in a mirrored 3D map. It is as compatible with the acquired images as its unmirrored version from the image processing point of view, only that it is not biologically plausible.In this article, we introduce HaPi (Handedness Pipeline), the first method to automatically determine the hand of electron density maps of macromolecules solved by CryoEM. HaPi is built by training two 3D convolutional neural networks. The first determines α-helices in a map, and the second determines whether the α-helix is left-handed or right-handed. A consensus strategy defines the overall map hand. The pipeline is trained on simulated and experimental data. The handedness can be detected only for maps whose resolution is better than 5 Å. HaPi can identify the hand in 89% of new simulated maps correctly. Moreover, we evaluated all the maps deposited at the Electron Microscopy Data Bank and 11 structures uploaded with the incorrect hand were identified.     

An innovative approach in the detection of Toxocara canis excretory/secretory antigens using specific nanobodies

Human toxocariasis is a zoonosis resulting from the migration of larval stages of the dog parasite Toxocara canis into the human paratenic host. Despite its well-known limitations, serology remains the most important tool to diagnose the disease. Our objective was to employ camelid single domain antibody fragments also known as nanobodies (Nbs) for a specific and sensitive detection of Toxocara canis excretory/secretory (TES) antigens. From an alpaca immune Nb library, we retrieved different Nbs with specificity for TES antigens. Based on ELISA experiments, these Nbs did not show any cross-reactivity with Ascaris lumbricoides, Ascaris suum, Pseudoterranova decipiens, Anisakis simplex and Angiostrongylus cantonensis larval antigens. Western blot and immunocapturing revealed that Nbs 1TCE39, 1TCE52 and 2TCE49 recognise shared epitopes on different components of TES antigen. The presence of disulphide bonds in the target antigen seems to be essential for recognition of the epitopes by these three Nbs. Three separate sandwich ELISA formats, using monovalent and bivalent Nbs, were assessed to maximise the detection of TES antigens in solution. The combination of biotinylated, bivalent Nb 2TCE49 on a streptavidin pre-coated plate to capture TES antigens, and Nb 1TCE39 chemically coupled to horseradish peroxidase for detection of the captured TES antigens, yielded the most sensitive ELISA with a limit of detection of 0.650 ng/ml of TES antigen, spiked in serum. Moreover, the assay was able to detect TES antigens in sera from mice, taken 3 days after the animals were experimentally infected with T. canis. The specific characteristics of Nbs make this ELISA not only a promising tool for the detection of TES antigens in clinical samples, but also for a detailed structural and functional study of TES antigens.     

利用系统作图(Systems mapping)研究大肠埃希菌和金黄色葡萄球菌的互作遗传机制

【背景】物种间相互作用是物种进化的重要推动力,然而如何将基因型和表型关联以及确定在物种相互作用过程中起重要作用的基因均面临挑战。【目的】通过系统作图(Systems mapping)得到两种微生物在相互作用过程中起重要作用的SNPs (Single nucleotide polymorphism),以及随着时间的变化,这些SNPs是如何相互联系进而影响大肠埃希菌和金黄色葡萄球菌的相互作用。【方法】分别对45株大肠埃希菌、45株金黄色葡萄球菌进行单独培养和混合共培养,通过实时荧光定量PCR(Real-time quantitative PCR,qPCR)进行绝对定量,得到一定时间内各个菌株的生长量,比较相同菌株在不同培养条件下生长情况,以各个菌株重测序结果为基础,结合系统作图得到在相互作用过程中起重要作用的显著SNPs及其相互联系。【结果】通过系统作图分析,获得具有54对显著SNPs组合的三维曼哈顿图,这些组合中41个显著SNPs来自大肠埃希菌,12个显著SNPs来自金黄色葡萄球菌。在上述SNPs中已有6个SNPs所在的候选基因都可以直接或者间接影响微生物的生长量变化,从而影响两种微生物相互作用方式。它们分别是nhaR(E19056)参与生物膜的形成,rhlE(E832164)与核糖体的组装有关,csiD (E2789300)的表达可以使细胞面对恶劣环境,alk B (E2309274)可以参与DNA的损伤修复,sucA(E759230)和yjjW(E4614704)都参与细胞的代谢过程。【结论】系统作图可以检测到物种在相互作用过程中显著SNPs;物种相互作用过程中不同SNPs遗传效应随着时间变化;细菌的相互作用过程是直接遗传效应、间接遗传效应和上位性效应共同产生的结果。     

Cryo-EM structures of cardiac thin filaments reveal the 3D architecture of troponin

Troponin is an essential component of striated muscle and it regulates the sliding of actomyosin system in a calcium-dependent manner. Despite its importance, the structure of troponin has been elusive due to its high structural heterogeneity. In this study, we analyzed the 3D structures of murine cardiac thin filaments using a cryo-electron microscope equipped with a Volta phase plate (VPP). Contrast enhancement by a VPP enabled us to reconstruct the entire repeat of the thin filament. We determined the orientation of troponin relative to F-actin and tropomyosin, and characterized the interactions between troponin and tropomyosin. This study provides a structural basis for understanding the molecular mechanism of actomyosin system.     

Genomic control for association studies

A dense set of single nucleotide polymorphisms (SNP) covering the genome and an efficient method to assess SNP genotypes are expected to be available in the near future. An outstanding question is how to use these technologies efficiently to identify genes affecting liability to complex disorders. To achieve this goal, we propose a statistical method that has several optimal properties: It can be used with case control data and yet, like family-based designs, controls for population heterogeneity; it is insensitive to the usual violations of model assumptions, such as cases failing to be strictly independent; and, by using Bayesian outlier methods, it circumvents the need for Bonferroni correction for multiple tests, leading to better performance in many settings while still constraining risk for false positives. The performance of our genomic control method is quite good for plausible effects of liability genes, which bodes well for future genetic analyses of complex disorders.     

Targeting of HIV gp120 by oligonucleotide-photosensitizer conjugates. Light-induced damages

The effects of the lysosphingolipid, sphingosylphosphorylcholine (SPC), on the cardiac ryanodine receptor (RyR) were examined. The open probability of cardiac RyR incorporated in lipid bilayers was decreased by cytoplasmic, but not lumenal side application of micromolar concentrations of SPC. Modification of channel function was characterized by the appearance of a long-lived closed state in addition to the brief channel closings observed in the presence and absence of SPC. Open channel kinetics and ion conduction properties, however, were not altered by this compound. These results suggest that SPC, a putative second messenger derived from sphingomyelin, may regulate Ca(2+) release from the sarcoplasmic reticulum by modifying the gating kinetics of the RyR.     

Structure–function relationships of four compression wood types: micromechanical properties at the tissue and fibre level

The mechanisms behind compressive stress generation in gymnosperms are not yet fully understood. Investigating the structure–function relationships at the tissue and cell level, however, can provide new insights. Severe compression wood of all species lacks a S3 layer, has a high microfibril angle in the S2 layer and a high lignin content. Additionally, special features like helical cavities or spiral thickenings appear, which are not well understood in terms of their mechanical relevance, but need to be examined with regard to evolutionary trends in compression wood development. Thin compression wood foils and isolated tracheids of four gymnosperm species [Ginkgo biloba L., Taxus baccata L., Juniperus virginiana L., Picea abies (L.) Karst.] were investigated. The tracheids were isolated mechanically by peeling them out of the solid wood using fine tweezers. In contrast to chemical macerations, the cell wall components remained in their original condition. Tensile properties of tissue foils and tracheids were measured in a microtensile apparatus under wet conditions. Our results clearly show an evolutionary trend to a much more flexible compression wood. An interpretation with respect to compressive stress generation is discussed.     

Applied tissue engineering in the closure of severe burns and chronic wounds using cultured human autologous keratinocytes in a natural fibrin matrix

Whereas in severe burns cultured human epithelial cells may well serve as a life saving method, the true value of tissue-engineered skin products in chronic wound care has yet to be clearly defined. Among other well-known clinical problems, the engraftment rate of commercially available multilayered "sheet grafts" has been shown to vary extremely. Adherence of transplanted cells to the wound bed--especially in the presence of potential wound contamination-- is one of the crucial aspects of this technique. Keratinocyte suspensions in a natural fibrin sealant matrix can potentially treat a variety of skin defects. In acute burn wounds, as well as in chronic wounds the clinical application of this type of tissue-engineered skin substitute demonstrates the capacity of cultured human autologous keratinocytes in a fibrin sealant matrix to adhere to wound beds, attach and spread over the wound resulting in reepithelialization of both acute and chronic wounds. In full thickness burns the combination of this new tool with allogenic dermis is a promising option to achieve complete dermal-epidermal reconstitution by means of tissue engineering and guided tissue repair. When transferring this technique into the treatment of chronic wounds we found an optimal preparation of such recipient wound beds to be crucial to the success. The additional application of continuous negative pressure (vacuum therapy) and preliminary chip skin grafting to optimally prepare the recipient site may be helpful tools to achieve such well-prepared and graftable surfaces. Prospective controlled comparative studies should be designed to further assess the clinical efficacy of this technique.