Molecular chemistry of plant protein structure at a cellular level by synchrotron-based FTIR spectroscopy: Comparison of yellow (Brassica rapa) and Brown (Brassica napus) canola seed tissues

The objective of this study was to use synchrotron light sourced FTIR microspectroscopy as a novel approach to characterize protein molecular structure of plant tissue: compared yellow and brown Brassica canola seed within cellular dimensions. Differences in the molecular chemistry and the structural-chemical characteristics were identified between two type of plant tissues. The yellow canola seeds contained a relatively lower (P < 0.05) percentage of model-fitted -helices (33 vs. 37), a higher (P < 0.05) relative percentage of model-fitted β-sheets (27 vs. 21) and a lower (P < 0.05) ratio of -helices to β-sheets (1.3 vs. 1.9) than the brown seeds. These results may indicate that the protein value of the yellow canola seeds as food or feed was different from that of the brown canola seeds. The cluster analysis and principal component analysis did not show clear differences between the yellow and brown canola seed tissues in terms of protein amide I structures, indicating they are related to each other. Both yellow and brown canola seeds contain the same proteins but in different ratios.     

Identification and location of albumin-like antigens in third-stage larva of W. bancrofti, in adult forms of Litomosoides chagasfilhoi and in the free-living nematode Caenorhabditis elegans

Antigens resembling those of host proteins have been identified on the surface of several filarial parasites, such as immunoglobulins and serum albumins. The origin of albumin-like antigens on filarial parasites remains unclear. Several authors suggested that they have been adsorbed, or that they were metabolic waste products from nutritional utilization of human albumin, or perhaps a contamination with human products. This study searched for human albumin-like antigens by Western blot and ultrastructural analyses on filarial parasites, third stage of W. bancrofti and adult females of Litomosoides chagasfilhoi, and on the free-living Caenorhabditis elegans nematode. Our results showed approximately 67kDa proteins recognized by anti-human albumin antibodies on extracts and excretory-secretory (ES) products of the third-stage W. bancrofti. Similar albumin-like proteins were also detected on the filarial parasite L. chagasfilhoi and on C. elegans extracts. The immunocytochemistry analysis showed human albumin-like antigens on similar tissues of these nematodes. These results provide evidence that these proteins have antigenic similarity and similar distribution in nematodes tissues. Our observations suggest that albumin-like antigens presented on filarial parasites are not acquired from the host, but rather are shared antigenic determinants found even in the third-stage larvae recovered from the invertebrate host.     

An elegant nano-injection machinery for sabotaging the host: Role of Type III secretion system in virulence of different human and animal pathogenic bacteria

Various Gram-negative bacteria possess a specialized membrane-bound protein secretion system known as the Type III secretion system (T3SS), which transports the bacterial effector proteins into the host cytosol thereby helping in bacterial pathogenesis. The T3SS has a special needle-like translocon that can sense the contact with the host cell membrane and translocate effectors. The export apparatus of T3SS recognizes these effector proteins bound to chaperones and translocates them into the host cell. Once in the host cell cytoplasm, these effector proteins result in modulation of the host system and promote bacterial localization and infection. Using molecular biology, bioinformatics, genetic techniques, electron microscopic studies, and mathematical modeling, the structure and function of the T3SS and the corresponding effector proteins in various bacteria have been studied. The strategies used by different human pathogenic bacteria to modulate the host system and thereby enhance their virulence mechanism using T3SS have also been well studied. Here we review the history, evolution, and general structure of the T3SS, highlighting the details of its comparison with the flagellar export machinery. Also, this article provides mechanistic details about the common role of T3SS in subversion and manipulation of host cellular processes. Additionally, this review describes specific T3SS apparatus and the role of their specific effectors in bacterial pathogenesis by considering several human and animal pathogenic bacteria.     

基于FTIR比较分析鸡骨草与毛鸡骨草的化学组分

采用傅里叶变换红外光谱法分析鸡骨草与毛鸡骨草的红外光谱特征及其化学成分的差异。采集鸡骨草和毛鸡骨草两种药材整株和不同部位的FTIR图,运用二阶导数谱和半定量分析研究不同谱图间的差异。结果显示鸡骨草与毛鸡骨草均含挥发油、三萜类、黄酮、皂苷、多糖类等化学成分。黄酮类、皂苷类、多糖类成分含量均以毛鸡骨草高。"指纹"区的特征光谱显示,鸡骨草根部的黄酮类成分含量少于茎部、而皂苷类和多糖类成分含量高于茎部;毛鸡骨草黄酮类和皂苷类成分含量以叶部最高,根部最低;多糖类成分叶部最高,根部和茎部较低但二者含量相近。FTIR技术可以快速鉴别出鸡骨草与毛鸡骨草主要化学成分的差异,避免了用单一成分来衡量药材质量的优劣。     

A method of correlative light and electron microscopy for yeast cells

Correlative light and electron microscopy (CLEM) is a method of imaging in which the same specimen is observed by both light microscopy and electron microscopy. Specifically, CLEM compares images obtained by light and electron microscopy and makes a correlation between them. After the advent of fluorescent proteins, CLEM was extended by combining electron microscopy with fluorescence microscopy to enable molecular-specific imaging of subcellular structures with a resolution at the nanometer level. This method is a powerful tool that is used to determine the localization of specific molecules of interest in the context of subcellular structures. Knowledge of the localization of target proteins coupled with the functions of the structures to which they are localized yields valuable information about the molecular functions of these proteins. However, this method has been mostly applied to adherent cells due to technical difficulties in immobilizing non-adherent target cells, such as yeasts, during sample preparation. We have developed a method of CLEM applicable to yeast cells. In this report, we detail this method and present its extension to Live CLEM. The Live CLEM method enabled us to link the dynamic properties of molecules of interest to cellular ultrastructures in the yeast cell. Since yeasts are premier organisms in molecular genetics, combining CLEM with yeast genetics promises to provide important new findings for understanding the molecular basis of the function of cellular structures.     

基于模糊聚类分析和曲线拟合的FTIR不同产地鸡骨草、毛鸡骨草鉴别分析

利用傅里叶变换红外光谱技术结合模糊聚类分析法和曲线拟合对鸡骨草、毛鸡骨草进行产地鉴别。选用曼哈顿距离单位计算的相异度聚类分析结果最优,5个产地鸡骨草都可完全区分开来,毛鸡骨草则只能鉴别出3个产地,南宁和钦州2个产地发生重叠;为了进一步鉴别不同产地鸡骨草和毛鸡骨草,对鸡骨草和毛鸡骨草平均红外谱图中1 034 cm-1吸收峰进行曲线拟合,野生鸡骨草拟合出11个子峰,其他各产地鸡骨草均只能拟合出9个子峰,上林产毛鸡骨草拟合出9个子峰,其他各产地毛鸡骨草均只能拟合出8个子峰,而且不同产地鸡骨草和毛鸡骨草拟合出的子峰位置和归一化强度都不完全相同;模糊聚类分析法和曲线拟合法有机结合能够使产地鉴别结果更加准确。     

微波消解-火焰原子吸收光谱法测定毛鸡骨草中的6种微量元素

用浓硝酸微波消解的方法处理样品,采用火焰原子吸收光谱法测定中药毛鸡骨草中Fe、Cu,Mg、Ca、Mn、Zn 6种微量元素的含量.结果表明毛鸡骨草含有丰富的人体必需微量元素,各元素的回收率在98.00%-102.20%之间.该方法操作简单,结果准确,是毛鸡骨草中微量元素测定的理想方法.     

Histological assessment of SJL/J mice treated with the antioxidants coenzyme Q10 and resveratrol

The muscular dystrophies (MDs) are genetic disorders of muscle degeneration due to mutations in genes that encode a wide variety of proteins. Dysferlinopathy are characterized by the absence of dysferlin in skeletal muscle and an autosomal recessive mode of inheritance. Both histological and ultrastructural pathology have been well established in dysferlinopathy patients and dysferlin-deficient animal models. To our knowledge the effect of antioxidant supplementation on this level has not been described previously. This article therefore focuses on the histopathology to reveal the effect of antioxidant supplementation. The study aimed to determine, at cellular level, the histopathological changes in the SJL/J mouse model following a 90 day trial with antioxidant supplementation. Markedly reduced inflammatory insult in the more affected quadriceps muscles of animals treated with high doses of CoQ10 and a combination of resveratrol/CoQ10 were observed. The outcome provides evidence that high doses of antioxidant supplementation resulted in decreased dystrophic markers and enhanced tissue integrity at cellular level.     

Glycosylation patterns of human alpha2-macroglobulin: Analysis of lectin binding by electron microscopy

Human alpha2-macroglobulin (α2M) is a 720 kDa glycoprotein that presents two ultrastructural conformations: slow (S-α2M) and fast (F-α2M). α2M acts mainly as a proteinase scavenger, but an immunomodulatory role was also proposed. This work studies the effect of desialylation and deglycosylation on the structure patterns of α2M by ultrastructural analysis of lectin-induced aggregates, which represents a new approach that had never been previously used. Transmission electron microscopy (TEM) analysis showed the loss of S-α2M conformation after deglycosylation, indicating that glycosidic side-chains contribute to the molecular stability of S-α2M. TEM proved to be an important tool to analyze the effect of biochemical changes on α2M, yielding an objective qualitative control of its morphological state. Certain carbohydrate residues did not vary between the α2M conformations, since both bound similarly ConA and WGA lectins. However, the binding of PNA and BSI-B₄ was slightly lower in F-α2M than in S-α2M. Among the neuraminidases used to desialylate both conformations of α2M that from Arthrobacter ureafaciens was the most effective. Incubation with the lectins ConA or SNA, respectively specific for mannosyl and sialyl residues, led to dose-dependent patterns of aggregation of α2M molecules, mediated by lectin binding and clearly visualized by TEM.     

Immunolocalization of the short neuropeptide F receptor in queen brains and ovaries of the red imported fire ant (Solenopsis invicta Buren)

Background

Insect neuropeptides are involved in diverse physiological functions and can be released as neurotransmitters or neuromodulators acting within the central nervous system, and as circulating neurohormones in insect hemolymph. The insect short neuropeptide F (sNPF) peptides, related to the vertebrate neuropeptide Y (NPY) peptides, have been implicated in the regulation of food intake and body size, and play a gonadotropic role in the ovaries of some insect species. Recently the sNPF peptides were localized in the brain of larval and adult Drosophila. However, the location of the sNPF receptor, a G protein-coupled receptor (GPCR), has not yet been investigated in brains of any adult insect. To elucidate the sites of action of the sNPF peptide(s), the sNPF receptor tissue expression and cellular localization were analyzed in queens of the red imported fire ant, Solenopsis invicta Buren (Hymenoptera), an invasive social insect.

Results

In the queen brains and subesophageal ganglion about 164 cells distributed in distinctive cell clusters (C1-C9 and C12) or as individual cells (C10, C11) were immuno-positive for the sNPF receptor. Most of these neurons are located in or near important sensory neuropils including the mushroom bodies, the antennal lobes, the central complex, and in different parts of the protocerebrum, as well as in the subesophageal ganglion. The localization of the sNPF receptor broadly links the receptor signaling pathway with circuits regulating learning and feeding behaviors. In ovaries from mated queens, the detection of sNPF receptor signal at the posterior end of oocytes in mid-oogenesis stage suggests that the sNPF signaling pathway may regulate processes at the oocyte pole.

Conclusions

The analysis of sNPF receptor immunolocalization shows that the sNPF signaling cascade may be involved in diverse functions, and the sNPF peptide(s) may act in the brain as neurotransmitter(s) or neuromodulator(s), and in the ovaries as neurohormone(s). To our knowledge, this is the first report of the cellular localization of a sNPF receptor on the brain and ovaries of adult insects.     

核仁的细胞辐射应激功能研究进展

核仁是细胞核内核糖体合成、 加工的场所。 最近研究发现核仁参与多种细胞过程, 其中最为重要的就是细胞应激反应。 核仁作为细胞应激感受器, 调控ARF等多种蛋白的定位及P53等关键蛋白的活性等, 从而介导细胞的应激反应。 对核仁的细胞辐射应激功能研究进展进行了综述。 Nucleoli is the sites for ribosome synthesis and processing, however, recent approaches have revealed that it is also involved in variety of cellular processes, especially the cellular stress response. As sensors, nucleoli regulate the localization of nucleolar proteins, such as (Alternate Reading Frame, ARF), and the activation of key factors, such as P53, and consequently mediate the cellular stress response. In this paper, recent progress in the studies on nucleolar functions in cellular stress response to radiation is reviewed.     

Libraries of random-sequence polypeptides produced with high yield as carboxy-terminal fusions with ubiquitin

Summary Libraries of random-sequence polypeptides have been shown to be valuable sources of novel molecules possessing a variety of useful biologic-like activities, some of which may hold promise as potential vaccines and therapeutics. Previous random peptide expression systems were limited to low levels of peptide production and often to short sequences. Here we describe a series of libraries designed for increased polypeptide length. Cloned as carboxy-terminal extensions of ubiquitin, the fusions were produced inE. coli at high levels, and were purified to homogeneity. The majority of the extension proteins examined could be cleaved from ubiquitin by treatment with a ubiquitin-fusion hydrolase. The libraries described here are appropriate sources of novel polypeptides with desired binding or catalytic function, as well as tools with which to examine inherent properties of proteins as a whole. Toward the latter goal, we have examined structural properties of random-sequence proteins purified from these libraries. Quite surprisingly, fluorescence emission spectra of intrinsic tryptophan residues in several purified fusion proteins, under native-like and denaturing conditions, often resemble those expected for folded and unfolded states, respectively. The results presented here detail an important expansion in the range of potential uses for random-sequence polypeptide libraries.     

胡椒生物碱提取、几何结构以及红外光谱的研究

以海南胡椒果为原料,95%乙醇溶液为溶剂,采用回流法提取胡椒生物碱。通过调节pH值除去胡椒酸,乙醚除去脂溶物,用丙酮为溶剂重结晶纯化胡椒生物碱,并用高效液相色谱仪检测其纯度,以及对胡椒生物碱进行了红外光谱表征。同时运用密度泛函B3LYP/6-31G(d, p)方法,对胡椒生物碱的结构进行优化、频率和能量的计算,得到四种构型(构型Ⅰ胡椒碱、构型Ⅱ异胡椒碱、构型Ⅲ异胡椒脂碱和构型Ⅳ胡椒脂碱)的64种构象的稳定结构,并利用吉布斯自由能计算常温(298.15 K)下四种构型分子体系稳定构象的热力学平衡分布。并对实验红外光谱与理论红外光谱的特征峰进行了对比。结果表明,所提取的胡椒生物碱主要以构型Ⅰ中的构象1结构存在,即胡椒碱结构;经纯化后得到胡椒碱含量为7%,纯度达99%。经分析建立的胡椒生物碱提取、分离和纯化方法效果良好,建立的胡椒生物碱模型能与实验结果相吻合。该研究对指导胡椒生物碱的提取、结构模型的建立、表征和应用有重大意义。     

C2C12 myoblast sensitivity to different apoptotic chemical triggers

Apoptosis is a form of cell death crucial for normal development and tissue homeostasis. Its typical features include chromatin changes, nuclear breakdown, plasma membrane blebbing and splitting of cellular content into apoptotic bodies, that progressively undergo phagocytosis.Apoptosis is considered essential for skeletal muscle development, where defective cells are deleted during differentiation. In addition, it plays a relevant role in several muscle myopathies, as well as in denervation and disuse.The aim of this study was to evaluate muscle cell sensitivity to different apoptotic triggers, acting through different mechanisms of action. Chemical agents, active against distinct intracellular targets, such as mitochondrial respiratory chain and DNA, have been chosen to better highlight cell death mechanisms. To induce apoptosis, C2C12 myoblasts have been exposed to H₂O₂, staurosporine, cisplatin and etoposide, at different doses and incubation times, and they have been analysed by flow cytometry, scanning and transmission electron microscopy.Flow cytometry analysis revealed a certain subdiploid peak after all treatments. The best apoptotic effect was observable, as confirmed at reverted microscope, at minimum doses and after the major exposure time.At ultrastructural level programmed cell death has been observed. Characteristic chromatin condensation and margination, as well as apoptotic bodies, frequently appeared, even if in the presence of secondary necrosis; surface blebs were also observed during scanning microscopic observation.In particular, exposure to H₂O₂ or staurosporine showed the largest number of myoblasts in late apoptotic stages and in secondary necrosis. Cisplatin treatments revealed few early apoptotic cells. The analysis of etoposide-induced apoptosis was in agreement with data obtained from flow cytometry, indicating a significant increase of apoptotic cell number.These results suggest that all conditions are able to induce apoptosis in C2C12 myoblasts, which occurs, considering trigger mechanisms of action, mostly following the mitochondrial pathway, if not excluding that due to DNA damage. Therefore, mitochondria permeability alteration is an important step in skeletal muscle programmed cell death. This last conclusion seems to have a significant relevance in understanding the mechanisms involved in muscle disorders, denervation and chronic muscle disuse, conditions frequently characterized by a decline in mitochondrial content and by an increase of mitochondrial apoptosis susceptibility.     

基于近红外光谱油分检测的玉米单倍体鉴别方法研究

目前,在单倍体育种技术中,可先使用低场核磁共振方法定量测得玉米单倍体与二倍体的油分,再依据二者油分差异鉴别单倍体,该方法在实际育种工作中已取得初步应用,但核磁共振鉴别单倍体方法存在速度慢、价格贵、维护难等缺点,难以获得大范围应用。近红外光谱技术有诸多优点并在各领域取得广泛应用,相关研究也表明该技术可用于玉米单倍体的定性鉴别,但是目前该方法用于鉴别单倍体实验研究时涉及的玉米品种相对较少,对于某些品种识别效果较差,且内部机理类似于黑盒,难以指明单倍体、二倍体两类种子是依据何种物质的差别进行区分,有时难以获得农业领域专家认可。根据花粉直感效应的原理,玉米单倍体与二倍体存在明显的油分区别,通过油分鉴别单倍体原理直观明白,易于被业内专家接受。因此,提出了一种先定量得到油分,再依据定量分析所得油分进行分类的方法,即首先使用玉米单籽粒的近红外光谱定量回归分析得到各籽粒的油分含量,再利用定量分析所得的油分值,并使用最小平方误差方法对单倍体、二倍体混合籽粒进行定性分类。实验结果表明近红外定量分析方法的识别精度与核磁共振方法相当,与几种定性分析方法比较,在训练集规模相同时,近红外定量分析方法所得识别率优于几种定性分析方法,进一步表明近红外定量分析方法鉴别单倍体具有一定优势,可满足育种行业精度要求,能够为尽快实现单倍体工程化育种提供保障。     

Ultrastructural architecture of colonies of different morphologies produced by phenotypic switching of a clinical strain of Candida tropicalis and biofilm formation by variant phenotypes

Candida tropicalis has been identified as one of the most prevalent pathogenic yeast species of the Candida-non-albicans (CNA) group. Study of switching in C. tropicalis has not been the subject of extensive research. Therefore, we investigated switching event and characterized the ultrastructural architecture of different phenotypes and biofilm produced in a C. tropicalis clinical strain. Cells switched heritably, reversibly, and at a high frequency between four phenotypes readily distinguishable by the shape of colonies formed on agar at 25°C. SEM analysis was used to verify the architecture of whole Candida colonies at ultrastructural level. The smooth phenotype (parental phenotype) colony showed a hemispherical shape character, while the semi-smooth was characterized by the presence of shallow marginal depressions. The ring and rough phenotypes exhibited more complex architecture and were characterized by the presence of deep central and peripheral depressions areas. The biofilm-forming ability varied among the switch phenotypes. After 12h incubation, the smooth phenotype formed less biofilm compared to the other phenotypes (P<0.05). The electron microscopy analysis revealed that filamentation (pseudohyphae) was associated with ring and rough colonies. The ultrastructural analysis allowed the observation of the arrangement of individual cells within the colonies. At the deep central and peripheral depressions areas of the ring and rough colonies extracellular material was seen in different arrangements. The data presented here open new avenues to study a possible role for extracellular material in the formation and maintenance of the architecture of switch phenotypes in C. tropicalis. It is therefore essential that more strains be investigated to determine the biological significance of extracellular material in C. tropicalis phenotypic switching phenomenon.     

On graphene melting

Dynamics of disordering of graphene upon heating has been studied by computer simulation. The mechanism governing the formation of seeds for a three-dimensional grid of entangled carbon chains into which graphene is transformed upon melting has been analyzed in detail. It has been shown that the emergence of these seeds is preceded by the disruption of several interatomic bonds, accompanied with the formation of large rings or groups of adjacent rings and the formation of penta- and heptagons of their C–C bonds. The results of this work on the whole agree with the Lindemann–Lozovik criterion. The melting temperature is estimated as T_m ~ 5100 K.     

Comparative genomics and functional annotation of bacterial transporters

Transport proteins are difficult to study experimentally, and because of that their functional characterization trails that of enzymes. The comparative genomic analysis is a powerful approach to functional annotation of proteins, which makes it possible to utilize the genomic sequence data from thousands of organisms. The use of computational techniques allows one to identify candidate transporters, predict their structure and localization in the membrane, and perform detailed functional annotation, which includes substrate specificity and cellular role.

We overview the main techniques of analysis of transporters' structure and function. We consider the most popular algorithms to identify transmembrane segments in protein sequences and to predict topology of multispanning proteins. We describe the main approaches of the comparative genomics, and how they may be applied to the analysis of transporters, and provide examples showing how combinations of these techniques is used for functional annotation of new transporter specificities in known families, characterization of new families, and prediction of novel transport mechanisms.     

Highly charged clusters of fullerenes: charge mobility and appearance sizes

Clusters of fullerenes (C60,C70)(n) are produced in a gas aggregation source and are multiply ionized in collisions with highly charged Xe(20+,30+) ions. Their stabilities and decay processes are analyzed with high-resolution time-of-flight mass spectrometry. Fullerene clusters in charge states up to q=5 have been observed and appearance sizes are found to be as small as n(app)=5, 10, 21, and 33 for q=2, 3, 4, and 5, respectively. The analysis of the multicoincident fragmentation spectra indicates a high charge mobility. This is in contrast to charge localization effects which have been reported for Ar(q+)(n) rare gas clusters. Clusters of fullerenes are found to be conducting when multiply charged.