Correlative light and electron microscopy using immunolabeled sections.

In correlative microscopy, light microscopy provides the overview and orientation of the complex cells and tissue, while electron microscopy offers the detailed localization and correlation of subcellular structures. In this chapter we offer detailed high-quality electron microscopical preparation methods for optimum preservation of the cellular ultrastructure. From such preparations serial thin sections are collected and used for comparative histochemical, immunofluorescence, and immunogold staining.In light microscopy histological stains identify the orientation of the sample and immunofluorescence labeling facilitates to find the region of interest, namely, the labeled cells expressing the macromolecule under investigation. Sections, labeled with immunogold are analyzed by electron microscopy in order to identify the label within the cellular architecture at high resolution.

Biostratigraphy, mineralogy and geochemistry of the Trabakua Pass and Ermua sections in Spain: Paleocene-Eocene transition

Isotopic, geochemical and bulk mineralogical analyses in the Trabakua and Ermua sections, Basque Basin, reveal major changes across the Paleocene-Eocene transition. Expanded sedimentary records exhibit a gradual decrease of 1.0 parts per thousand in delta(13)C values in the lower part of Zone P5 followed by a more rapid 3 parts per thousand negative excursion. The 3 parts per thousand delta(13)C excursion is associated with an abrupt decrease in carbonate sedimentation, increased detrital flux and decreased grain size which suggest changes in marine/atmospheric currents and/or size and structure of the ocean carbon reservoir. The clays recognized at Trabakua record a deep burial diagenesis as indicated by two generations of chlorite, the presence of mixed-layers chlorite-smectite and illite-smectite, the absence of smectite and the near absence of kaolinite. The very low delta(18)O values (<-3.5 parts per thousand) throughout the Trabakua and Ermua sections reflect diagenetic alteration rather than paleotemperatures. Because of deep burial diagenesis and very poorly preserved microfossils, the Trabakua Pass and Ermua sections are not optimal potential stratotypes for the Paleocene-Eocene boundary.

Immunofluorescence test on Schistosoma mansoni worm paraffin sections (IgM-IFT) for the study of schistosomiasis transmission in Campinas, São Paulo, Brazil

The detection of IgM antibodies for Schistosoma mansoni using gut-associated antigens (IgM-IFT) was compared to the parasitological Kato-Katz method for study of the transmission of schistosomiasis in an urban area in Campinas. About 400 schoolchildren whose ages ranged from 6 to 18 years, were observed for a period of two years. Blood samples on filter paper and fecal samples were collected, at intervals of six months. Serological (IgM-IFT) prevalence rates of 1.2%, 4.3%, 3.6%, 2.9% and 3.4% were obtained in five surveys carried out. S. mansoni eggs were detected in only one child out of the 225 children (0.4%) who were submitted to the Kato-Katz method (three slides for each fecal sample) in the 1st survey. Sixty eight children who submitted five blood samples, one for each survey, were found IFT negative throughout the study. No child was found to be IFT positive in all five surveys, and only four children showed IFT positive results in at least four surveys. Seroconversion from IFT negative to positive was observed from the 1st to the 2nd survey in six chidren, from the 2nd to the 3rd survey in three children, from the 3rd to the 4th survey in four children, and from the 4th to the 5th survey in two cases. However, confirmation of S. mansoni infection using the fecal examination was not possible in any of the cases. Also, in most of them the IFT result oscillated from negative to positive and vice versa. Our data implied that recent transmission of schistosomiasis in the study area was not possible.

Orthogonal organic and aqueous-based washes of tissue sections to enhance protein sensitivity by MALDI imaging mass spectrometry.

Imaging mass spectrometry (IMS) is an emergent and innovative approach for measuring the composition, abundance and regioselectivity of molecules within an investigated area of fixed dimension. Although providing unprecedented molecular information compared with conventional MS techniques, enhancement of protein signature by IMS is still necessary and challenging. This paper demonstrates the combination of conventional organic washes with an optimized aqueous-based buffer for tissue section preparation before matrix-assisted laser desorption/ionization (MALDI) IMS of proteins. Based on a 500 mM ammonium formate in water-acetonitrile (9:1; v/v, 0.1% trifluororacetic acid, 0.1% Triton) solution, this buffer wash has shown to significantly enhance protein signature by profiling and IMS (~fourfold) when used after organic washes (70% EtOH followed by 90% EtOH), improving the quality and number of ion images obtained from mouse kidney and a 14-day mouse fetus whole-body tissue sections, while maintaining a similar reproducibility with conventional tissue rinsing. Even if some protein losses were observed, the data mining has demonstrated that it was primarily low abundant signals and that the number of new peaks found is greater with the described procedure. The proposed buffer has thus demonstrated to be of high efficiency for tissue section preparation providing novel and complementary information for direct on-tissue MALDI analysis compared with solely conventional organic rinsing.

Detection of Trypanosoma cruzi DNA within murine cardiac tissue sections by in situ polymerase chain reaction

The use of in situ techniques to detect DNA and RNA sequences has proven to be an invaluable technique with paraffin-embedded tissue. Advances in non-radioactive detection systems have further made these procedures shorter and safer. We report the detection of Trypanosoma cruzi, the causative agent of Chagas disease, via indirect and direct in situ polymerace chain reaction within paraffin-embedded murine cardiac tissue sections. The presence of three T. cruzi specific DNA sequences were evaluated: a 122 base pair (bp) sequence localized within the minicircle network, a 188 bp satellite nuclear repetitive sequence and a 177 bp sequence that codes for a flagellar protein. In situ hybridization alone was sensitive enough to detect all three T. cruzi specific DNA sequences.

Carbon isotope excursions and microfacies changes in marine Permian-Triassic boundary sections in Hungary

Several Permian-Triassic boundary sections occur in various structural units within Hungary. These sections represent different facies zones of the western Palaeotethys margin. The Gardony core in the NE part of the Transdanubian Range typically represents the inner ramp, while the Balvany section in the Bukk Mountains of northern Hungary represents an outer ramp setting. The two sections have different patterns for their delta(13)C values. The Balvany section shows a continuous change towards more negative delta(13)C values starting at the first biotic decline, followed by a sharp, quasi-symmetric negative peak at the second decline. The appearance of the delta(13)C peak has no relationship to the lithology and occurs within a shale with low overall carbonate content, indicating that the peak is not related to diagenesis or other secondary influences. Instead, the shift and the peak reflect primary processes related to changes in environmental conditions. The continuous shift in delta(13)C values is most probably related to a decrease in bioproductivity, whereas the sharp peak can be attributed to an addition of C strongly depleted in (13)C to the ocean-atmosphere system. The most plausible model is a massive release of methane-hydrate. The quasi-symmetric pattern suggests a rapid warming-cooling cycle or physical unroofing of sediments through slope-failure and releasing methane-hydrate. The Gidony-1 core shows a continuous negative delta(13)C shift starting below the P-T boundary. However, the detailed analyses revealed a sharp delta(13)C peak in the boundary interval, just below the major biotic decline, although its magnitude doesn't reach that observed in the Balvany section. Based on careful textural examination and high-resolution stable isotope microanalyses we suggest that the suppression of the delta(13)C peak that is common in the oolitic boundary sections is due to combined effects of condensed sedimentation, sediment reworking and erosion, as well as perhaps diagenesis. (c) 2005 Elsevier B.V All rights reserved.

Cutting artefacts and cutting process in vitreous sections for cryo-electron microscopy.

Cryo-electron microscopy of vitreous sections (CEMOVIS) has recently been shown to provide images of biological specimens with unprecedented quality and resolution. Cutting the sections remains however the major difficulty. Here, we examine the parameters influencing the quality of the sections and analyse the resulting artefacts. They are in particular: knife marks, compression, crevasses, and chatter. We propose a model taking into account the interplay between viscous flow and fracture. We confirm that crevasses are formed on only one side of the section, and define conditions by which they can be avoided. Chatter is an effect of irregular compression due to friction of the section of the knife edge and conditions to prevent this are also explored. In absence of crevasses and chatter, the bulk of the section is compressed approximately homogeneously. Within this approximation, it is possible to correct for compression by a simple linear transformation for the bulk of the section. A research program is proposed to test and refine our understanding of the sectioning process.

Organisation structurale du noyau et de microtubules de cellules de mammifères observés par cryo-microscopie électronique de sections hydratées

RESUME L'architecture nucléaire ainsi que l'ultrastructure des microtubules ont été abondamment étudiées par des méthodes cytochimiques utilisant des échantillons fixés chimiquement, enrobés dans des résines ou fixés à basse température. Les échantillons fixés à basse température pouvant aussi avoir été substitués, déshydratés et enrobés dans des résines pour la plupart hydrophiles. Ici, nous avons étendu ces études en utilisant la microscopie électronique effectuée sur des sections hydratées (CEMOVIS) permettant d'observer les échantillons dans un état le plus proche de leur état natif. De plus, nous avons effectué de la tomographie électronique sur des sections hydratées (TOVIS) afin d'obtenir une vision tridimensionnelle de : 1) la périphérie du noyau et de la région périchromatinienne et 2) de la lumière des microtubules. Concernant l'architecture nucléaire Nos observations montrent que le nucléole et la chromatine condensée sont facilement visualisés grâce à la texture spécifique qu'ils arborent. Au contraire, la visualisation de domaines nucléaires importants et spécialement ceux qui contiennent des ribonucléoprotéines, est rendue difficile, à cause du faible contraste qui caractérise l'espace interchromatinien. Ceci est essentiellement dû à la quantité d'information présente dans le volume de la section qui semble être superposée, lorsque observée sur des micrographies en deux dimensions. La tomographie nous a permis de mieux visualiser les différentes régions du noyau. Les mottes de chromatine condensée sont décorées à leur périphérie (région périchromatinienne), par nombre de fibrilles et granules. Des tunnels d'espace interchromatinien sont occasionnellement observés en train de traverser des régions de chromatine condensée favorisant l'accès aux pores nucléaires. Enfin, nous avons pu, au niveau d'un pore unique, observer la plupart des structures caractéristiques du complexe de pore nucléaire. Concernant l'ultrastructure des microtubules: Nous avons démontré que la polarité d'un microtubule observé in situ en section transversale, par CEMOVIS, est directement déduite de l'observation de la chiralité de ses protofilaments. Cette chiralité, a été établie précédemment comme étant liée à la morphologie des sous unités de tubuline. La tomographie électronique effectuée sur des sections hydratées, nous a permis d'observer les microtubules dans leur contexte cellulaire avec une résolution suffisante pour visualiser des détails moléculaires, comme les monomères de tubuline. Ainsi, des molécules n'ayant pas encore été caractérisées, ont été observées dans la lumière des microtubules. Ces observations ont été effectuées autant sur des cellules observées en coupe par CEMOVIS que sur des cellules congelées dans leur totalité par immersion dans un bain d'éthane liquide. Enfin, nous avons montré que les microtubules étaient aussi de formidables objets, permettant une meilleure compréhension des artéfacts de coupe occasionnés lors de la préparation des échantillons par CEMOVIS. Les buts des études qui seront menées â la suite de ce travail seront de 1) essayer de localiser des domaines nucléaires spécifiques par des approches cytochimiques avant la congélation des cellules. 2) Appliquer des méthodes de moyennage afin d'obtenir un modèle tridimensionnel de la structure du complexe de pore nucléaire dans son contexte cellulaire. 3) Utiliser des approches biochimiques afin de déterminer la nature exacte des particules qui se trouvent dans la lumière des microtubules. ABSTRACT Nuclear architecture as well as microtubule ultrastructure have been extensively investigated by means of different methods of ultrastructural cytochemistry using chemically fixed and resin embedded samples or following cryofixation, cryosubstitution and embedding into various, especially partially hydrophilic resins. Here, we extend these studies using cryoelectron microscopy of vitreous sections (CEMOVIS) which allows one to observe the specimen as close as possible to its native state. Furthermore, we applied cryoelectron tomography of vitreous sections (TOVIS) in order to obtain athree-dimensional view of: 1) the nuclear periphery, and of the perichromatin region, and 2) the microtubule lumen. Concerning the nuclear architecture: Our observations show that nucleoli and condensed chromatin are well recognisable due to their specific texture. Conversely, the visualisation of other important nuclear domains, especially those containing ribonucleoproteins, is seriously hampered by a generally low contrast of the interchromatin region. This is mainly due to the plethora of information superposed in the volume of the section observed on two-dimensional micrographs. Cryoelectron tomography allowed us to better visualise nuclear regions. Condensed chromatin clumps are decorated on their periphery, the perichromatin region, by numerous fibrils and granules. Tunnels of interchromatin space can occasionally be found as crossing condensed chromatin regions, thus, allowing the access to nuclear pores. Finally, we were able to use TOVIS to directly distinguish most of the nuclear pore complex structures, at the level of a single pore. Concerning the microtubule ultrastructure: We have demonstrated that the polarity of across-sectioned microtubule observed in situ by CEMOVIS wás directly deducible from the visualisation of the tubulin protofiíaments' chirality. This chirality has been established before as related to the shape. of the tubulin subunits. Cryoelectron tomography allowed us to observe microtubules in their cellular context at a resolution sufficient to resolve molecular details such as their tubulin monomers. In this way, uncharacterized molecules were visualised in the microtubule lumen. These observations were made either on samples prepared by CEMOVIS or plunge freezing of whole cells. Finally, we have shown that microtubules are also relevant objects for the understanding of cutting artefacts, when performing CEMOVIS. The goals of our further studies will be to: 1) try to speciifically target different nuclear domains by cytochemical approaches in situ, prior to cryofixation. 2) Apply averaging methods in order to obtain a three-dimensional model of the nuclear pore complex at work, in its cellular context. 3) Use biochemical analysis combined in a second time to immunocytochemical approaches, to determine the exact nature of the microtubule's luminal particles.

Granular layer in the periplasmic space of gram-positive bacteria and fine structures of Enterococcus gallinarum and Streptococcus gordonii septa revealed by cryo-electron microscopy of vitreous sections.

High-resolution structural information on optimally preserved bacterial cells can be obtained with cryo-electron microscopy of vitreous sections. With the help of this technique, the existence of a periplasmic space between the plasma membrane and the thick peptidoglycan layer of the gram-positive bacteria Bacillus subtilis and Staphylococcus aureus was recently shown. This raises questions about the mode of polymerization of peptidoglycan. In the present study, we report the structure of the cell envelope of three gram-positive bacteria (B. subtilis, Streptococcus gordonii, and Enterococcus gallinarum). In the three cases, a previously undescribed granular layer adjacent to the plasma membrane is found in the periplasmic space. In order to better understand how nascent peptidoglycan is incorporated into the mature peptidoglycan, we investigated cellular regions known to represent the sites of cell wall production. Each of these sites possesses a specific structure. We propose a hypothetic model of peptidoglycan polymerization that accommodates these differences: peptidoglycan precursors could be exported from the cytoplasm to the periplasmic space, where they could diffuse until they would interact with the interface between the granular layer and the thick peptidoglycan layer. They could then polymerize with mature peptidoglycan. We report cytoplasmic structures at the E. gallinarum septum that could be interpreted as cytoskeletal elements driving cell division (FtsZ ring). Although immunoelectron microscopy and fluorescence microscopy studies have demonstrated the septal and cytoplasmic localization of FtsZ, direct visualization of in situ FtsZ filaments has not been obtained in any electron microscopy study of fixed and dehydrated bacteria.

JULIDE: a software tool for 3D reconstruction and statistical analysis of autoradiographic mouse brain sections.

In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

Using immunoglobulin Y as an alternative antibody for the detection of hepatitis A virus in frozen liver sections

An increasing amount of research has been conducted on immunoglobulin Y (IgY) because the use of IgY offers several advantages with respect to diagnostic testing, including its easy accessibility, low cost and translatability to large-scale production, in addition to the fact that it can be ethically produced. In a previous work, immunoglobulin was produced and purified from egg yolks (IgY) reactive to hepatitis A virus (HAV) antigens. In the present work, this anti-HAV-specific IgY was used in an indirect immunofluorescence assay to detect viral antigens in liver biopsies that were obtained from experimentally infected cynomolgus monkeys. Fields that were positive for HAV antigen were detected in liver sections using confocal microscopy. In conclusion, egg yolks from immunised hens may be a reliable source for antibody production, which can be employed for immunological studies.