Integrating Molecular Models Into CryoEM Heterogeneity Analysis Using Scalable High-resolution Deep Gaussian Mixture Models

Resolving the structural variability of proteins is often key to understanding the structure–function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with machine learning algorithms, provides a way to reveal the dynamics within the protein system from noisy micrographs. Here, we introduce an improved computational method that uses Gaussian mixture models for protein structure representation and deep neural networks for conformation space embedding. By integrating information from molecular models into the heterogeneity analysis, we can analyze continuous protein conformational changes using structural information at the frequency of 1/3 Å⁻¹, and present the results in a more interpretable form.     

Regulation of cuticular and postpharyngeal hydrocarbons in the slave-making ant Polyergus rufescens: effect of Formica rufibarbis slaves

The purpose of this study was to compare cuticular hydrocarbon profiles of slave-making Polyergus rufescens ants reared alone or with their Formica rufibarbis slaves. Chemical analyses showed that due to the close contacts occurring when the Formica were tending the Polyergus, the synthesis of the cuticular hydrocarbons carried by the slaves was enhanced in the slave-makers. The postpharyngeal hydrocarbon levels increased during the first 15 days of life, whether or not the Polyergus were exposed to Formica. Our findings suggest that Polyergus is able to secrete all components of their cuticular hydrocarbon blend and that none are acquired through contact with Formica. In addition to presenting our experimental evidence, several hypotheses are proposed to explain the synthesis and regulation of hydrocarbon blends borne when these two species cohabitate within a single colony.     

A theoretical model for F-actin remodeling in vascular smooth muscle cells subjected to cyclic stretch

A constrained mixture theory model was developed and used to estimate remodeling of F-actin in vascular smooth muscle cells that were subjected to 10% equibiaxial stretching for up to 30min. The model was based on a synthesis of data on time-dependent changes in atomic force microscopy measured cell stiffness and immunofluorescence measured focal adhesion associated vinculin as well as data on stress fiber stiffness and pre-stretch. Results suggest that an observed acute (after 2min of stretching) increase in cell stiffness is consistent with an increased stretch of the originally present F-actin plus an assembly of new F-actin having nearly homeostatic values of stretch. Moreover, the subsequent (after 30min of stretching) decrease in cell stiffness back towards the baseline value is consistent with a replacement of the overstretched original filaments with the new (reassembled), less stretched filaments. That is, overall cell response is consistent with a recently proposed concept of "tensional homeostasis" whereby cells seek to maintain constant certain mechanical factors via a remodeling of intracellular and transmembrane proteins. Although there is a need to refine the model based on more comprehensive data sets, using multiple experimental approaches, the present results suggest that a constrained mixture theory can capture salient features of the dynamics of F-actin remodeling and that it offers some advantages over many past methods of modeling, particularly those based on classical linearized viscoelasticity.     

Revisiting sugar-fat mixtures: sweetness and creaminess vary with phenotypic markers of oral sensation

Genetic variation in oral sensation presumably influences ingestive behaviors through sensations arising from foods and beverages. Here, we investigated the influence of taste phenotype [6-n-propylthiouracil (PROP) bitterness, fungiform papillae (FP) density] on sweet and creamy sensations from sugar/fat mixtures. Seventy-nine subjects (43 males) reported the sweetness and creaminess of water or milk (skim, whole, heavy cream) varying in sucrose (0-20% w/v) on the general Labeled Magnitude Scale. Sweetness grew with sucrose concentration and when shifting from water to milk mixtures--the growth was greatest for those tasting PROP as most bitter. At higher sucrose levels, increasing fat blunted the PROP-sweet relationship, whereas at lower levels, the relationship was effectively eliminated. Perceived sweetness of the mixture exceeded that predicted from the sum of components at low sucrose concentrations (especially for those tasting PROP most bitter) but fell below predicted at high concentrations, irrespective of fat level. Creaminess increased greatly with fat level and somewhat with sucrose. Those tasting PROP most bitter perceived greater creaminess in the heavy cream across all sucrose levels. Perceived creaminess was somewhat lower than predicted, irrespective of PROP bitterness. The FP density generally showed similar effects as PROP on sweetness and creaminess, (but to a lesser degree) and revealed potential taste-somatosensory interactions in weakly sweet stimuli. These data support that taste phenotype affects the nature of enhancement or suppression of sweetness and creaminess in liquid fat/sugar mixtures. Taste phenotype effects on sweetness and creaminess likely involve differential taste, retronasal olfactory, and somatosensory contributions to these perceptual experiences.     

葡糖酸醋杆菌内源复制片段的克隆

采用改进的碱裂解法提取Gluconacetobacter hansenii ATCC23769自发不产膜突变体的内源隐蔽质粒。用不同的限制性内切酶对混合质粒直接进行酶切,酶切后的片段混合物与pUC18载体连接构建重组载体。重组载体回转入G.hansenii ATCC23769获得隐蔽质粒上具有复制能力的片段,序列结果分析表明:该片段上没有某些其他质粒所具有的Rep蛋白。利用该片段,构建了能同时在大肠杆菌和葡糖酸醋杆菌中复制的质粒载体,体内的抗生素抗性实验证明该载体具有良好的稳定性。     

A structural analysis of the catalytic mechanism of methionine sulfoxide reductase A from Neisseria meningitidis

The methionine sulfoxide reductases (Msrs) are thioredoxin-dependent oxidoreductases that catalyse the reduction of the sulfoxide function of the oxidized methionine residues. These enzymes have been shown to regulate the life span of a wide range of microbial and animal species and to play the role of physiological virulence determinant of some bacterial pathogens. Two structurally unrelated classes of Msrs exist, MsrA and MsrB, with opposite stereoselectivity towards the R and S isomers of the sulfoxide function, respectively. Both Msrs share a similar three-step chemical mechanism including (1) the formation of a sulfenic acid intermediate on the catalytic Cys with the concomitant release of the product—methionine, (2) the formation of an intramonomeric disulfide bridge between the catalytic and the regenerating Cys and (3) the reduction of the disulfide bridge by thioredoxin or its homologues. In this study, four structures of the MsrA domain of the PilB protein from Neisseria meningitidis, representative of four catalytic intermediates of the MsrA catalytic cycle, were determined by X-ray crystallography: the free reduced form, the Michaelis-like complex, the sulfenic acid intermediate and the disulfide oxidized forms. They reveal a conserved overall structure up to the formation of the sulfenic acid intermediate, while a large conformational switch is observed in the oxidized form. The results are discussed in relation to those proposed from enzymatic, NMR and theoretical chemistry studies. In particular, the substrate specificity and binding, the catalytic scenario of the reductase step and the relevance and role of the large conformational change observed in the oxidized form are discussed.     

Oxidised LDL up-regulate CD36 expression by the Nrf2 pathway in 3T3-L1 preadipocytes

The effect of oxLDL on CD36 expression has been assessed in preadipocytes induced to differentiate. Novel evidence is provided that oxLDL induce a peroxisome proliferator-activated receptor gamma-independent CD36 overexpression, by up-regulating nuclear factor erythroid 2 (NF-E2)-related factor 2 (Nrf2). The nuclear translocation of Nrf2 appeared to depend on PKC pathway activation. In adipocytes, the CD36 up-regulation may indicate a compensation mechanism to meet the demand of excess oxLDL and oxidised lipids in blood, reducing the risk of atherogenesis. Besides strengthening the hypothesis that oxLDL can contribute to the onset of insulin-resistance, data herein presented highlight the significance of oxLDL-induced CD36 overexpression within the cellular defence response.     

复合益生菌对白羽肉鸡肌肉品质的影响及作用机理

【目的】探究饮水中添加复合益生菌制剂(地衣芽孢杆菌、枯草芽孢杆菌和丁酸梭菌)对肉鸡肌肉品质的影响及作用机理。【方法】试验随机选取360只1日龄白羽肉仔鸡,随机分为3个处理组：对照组(CON),正常饮水;低剂量益生菌组(LG),饮水添加0.2%复合益生菌;高剂量益生菌组(HG),饮水添加0.4%复合益生菌,试验为期42d。【结果】与CON组相比,LG组和HG组显著增加肉鸡7、35和42 d平均体重,显著提高HG组肉鸡21-28、28-35、35-42阶段的平均日增重(P<0.05),LG组仅显著提高35-42阶段平均日增重;显著提高胸肌45 min、24 h、48 h红度和24 h黄度,降低24 h和48 h亮度及48 h滴水损失和蒸煮损失。HG组胸肌粗蛋白和粗脂肪含量显著高于CON组,而LG组差异不显著;两组均可降低胸肌灰分含量。添加复合益生菌可显著提高总抗氧化能力(total antioxidant capacity,T-AOC),而总超氧化物歧化酶(total-superoxide dismutase,T-SOD)、过氧化氢酶(catalase,CAT)含量有上升趋势;显著上...     

Multiple inhibitory pathways shape odor-evoked responses in lobster olfactory projection neurons

This study characterizes odor-evoked responses of the glomerular output neurons of the spiny lobster olfactory lobe, and implicates previously identified γ-aminobutyric acid (GABA)- and histamine-mediated inhibitory pathways in shaping these responses. Odor-evoked responses were more complex than electrically evoked responses, with up to three distinct components: a brief, short-latency (fast) depolarization, a longer-duration, longer-latency (slow) depolarization, and a slow hyperpolarization. Seventy-seven percent of all responses contained the hyperpolarization, while only 31% and 23% contained the fast and slow depolarizations, respectively. The broader tuning of the hyperpolarization relative to the other two components suggests that the hyperpolarization mediates lateral inhibitory interactions across olfactory glomeruli. Perfusing the brain with the GABA-receptor antagonist picrotoxin increased the amplitude of the hyperpolarization, while the histamine-receptor antagonist cimetidine decreased the hyperpolarization in some instances but increased it in others. Pharmacological enhancement or suppression of the hyperpolarization could mask or unmask, respectively, the slow depolarization. Both antagonists could also cause the appearance of the fast depolarization when it was not apparent prior to treatment. We conclude that GABA- and histamine-mediated inhibition contributes to the overall pattern of the response of projection neurons to odors by regulating the relative strength of these three distinct types of input. Accepted: 17 September 1997