Use of methacrylate De-embedding protocols for in situ hybridization on semithin plastic sections with multiple detection strategies

Posttranscriptional control over rapid development and ciliogenesis in Marsilea

Marsilea vestita is a semiaquatic fern that produces its spores (meiotic products) as it undergoes a process of natural desiccation. During the period of desiccation, the spores mature, and produce large quantities of pre-mRNA, which is partially processed and stored in nuclear speckles and can remain stable during a period of extended quiescence in the dry spore. Rehydration of the spores initiates a highly coordinated developmental program, featuring nine successive mitotic division cycles that occur at precise times and in precise planes within the spore wall to produce 39 cells, 32 of which are spermatids. The spermatids then undergo de novo basal body formation, the assembly of a massive cytoskeleton, nuclear and cell elongation, and finally ciliogenesis, before being released from the spore wall. The entire developmental program requires only 11 h to reach completion, and is synchronous in a population of spores rehydrated at the same time. Rapid development in this endosporic gametophyte is controlled posttranscriptionally, where stored pre-mRNAs, many of which are intron-retaining transcripts, are unmasked, processed, and translated under tight spatial and temporal control. Here, we describe posttranscriptional mechanisms that exert temporal and spatial control over this developmental program, which culminates in the production of ∼140 ciliary axonemes in each spermatozoid.

A novel immunofluorescent computed tomography (ICT) method to localise and quantify multiple antigens in large tissue volumes at high resolution

Current immunofluorescence protocols are limited as they do not provide reliable antibody staining within large tissue volumes (mm³) and cannot localise and quantify multiple antigens or cell populations in the same tissue at high resolution. To address this limitation, we have developed an approach to three-dimensionally visualise large tissue volumes (mm³) at high resolution (<1 µm) and with multiple antigen labelling, for volumetric and quantitative analysis. This is made possible through computer reconstruction of serial sectioned and sequentially immunostained butyl-methyl methacrylate (BMMA) embedded tissue. Using this novel immunofluorescent computed tomography (ICT) approach, we have three-dimensionally reconstructed part of the murine lower eyelid that contains the meibomian gland and localised cell nuclei (DAPI), Ki67 and cytokeratin 1 (CK1), as well as performing non-linear optical (NLO) microscopy imaging of collagen, to assess cell density, cell proliferation, gland keratinisation and gland volume respectively. Antigenicity was maintained after four iterative stains on the same tissue, suggesting that there is no defined limit to the number of antigens that can be immunostained for reconstruction, as long as the sections remain intact and the previous antibody has been successfully eluted. BMMA resin embedding also preserved fluorescence of transgenic proteins. We propose that ICT may provide valuable high resolution, three-dimensional biological maps of multiple biomolecules within a single tissue or organ to better characterise and quantify tissue structure and function.

An immunocytochemical procedure for protein localization in various nematode life stages combined with plant tissues using methylacrylate-embedded specimens

Plant-parasitic nematodes possess a large number of proteins that are secreted in planta, allowing them to be successful parasites of plants. The majority of these proteins are synthesized mainly in the nematode subventral and dorsal glands as well as in other organs. To improve the immunovisualization of these proteins, we adapted a methacrylate embedding method for the localization of proteins inside nematode tissues, and extracellularly when secreted in planta or within plant cells. An important advantage is that the method is applicable for all nematode stages: preparasitic as well as parasitic stages, including large mature females. Herein, the method has been successfully applied for the localization of four nematode secreted proteins, such as Mi-MAP-1, Mi-CBM2-bearing proteins, Mi-PEL3, and Mi-6D4. In addition, we could also localize 14-3-3 proteins, as well as two cytoskeletal proteins, by double-immunolabeling on preparasitic juveniles. Superior preservation of nematode and plant morphology, allowed more accurate protein localization as compared with other methods. Besides excellent epitope preservation, dissolution of methacrylate from tissue sections unmasks target proteins and thereby drastically increases antibody access.

Improvements in histological quality and signal retention following in situ hybridization in early chick embryos using plastic resin and recolorization

We describe a novel method that allows reliable detection of in situ hybridization signals in thin sections of plastic embedded embryos. Sections from plastic embedded embryos are thinner and have superior histological quality compared to paraffin, gelatin, agarose embedded sections or cryosections; however, plastic resin traditionally has not been used as an embedding medium following in situ hybridization because of loss of signal. When signal is detected with alkaline phosphatase and NBT/BCIP, the resulting colored precipitate is subject to fading when samples are exposed to organic compounds. The colored precipitate can be redeposited by repeating the NBT/BCIP reaction following plastic sectioning. This recolorization shows no loss of specificity, because signal is detected only where the anti-digoxigenin/alkaline phosphatase conjugated antibody is bound to the riboprobe. Strong signals can be detected without recolorization; however, weaker signals require the recolorization step. This novel method of re-depositing colored precipitate after processing and sectioning allows accurate determination of the location of gene expression and study of this expression in high quality histological sections of early chick embryos.

Localization of mRNAs and proteins in methyl methacrylate-embedded tissues

Precise localization of proteins and mRNA in histological sections is necessary for evaluating spatial gene expression patterns. Here we report sensitive detection of the gene products in fish tissues by immunohistochemistry (IHC) and in situ hybridization (ISH) assays on sections of whole specimens and vertebra embedded in methyl methacrylate (MMA) resin. This plastic resin favors easy preparation of various specimen types and enables preparation of large sections with well-preserved cell morphology. IHC analysis of the muscle regulatory factor MyoD in transverse sections of juvenile cod revealed MyoD-positive cells in the dorsolateral parts of the adaxial muscle. ISH revealed less spatially restricted signals of the bone morphogenic protein bmp4 in muscle and brain. To assess the applicability of ISH on sections of bony tissue, col1a1 and col2a1 expression was investigated in non-decalcified vertebra sections of Atlantic salmon. The former was identified in both chondrocytes and osteoblasts, whereas the latter was mostly evident in chondrocytes. We conclude that MMA resin offers easy preparation of large and problematic tissues and the possibility of carrying out both IHC and ISH analyses using standard protocols.

Analysis of barley (Hordeum vulgare) grain development using three-dimensional digital models

Analysis of gene expression in the developing barley caryopsis requires effective instruments for visualization of the grain and the 3D expression patterns. Digital models of developing barley (Hordeum vulgare) grains were reconstructed from serial sections to visualize the complex three-dimensional (3D) grain anatomy, to generate and analyse 3D expression patterns, and to quantify tissues during growth. The models provide detailed spatial descriptions of developing grains at anthesis, at the syncytial stage of endosperm development and at the onset of starch accumulation, visualizing and quantifying 18 tissues or tissue complexes. Total caryopsis volumes and volume changes of specific tissues between the stages were determined, and proportions of ovule- and non-ovule-tissues and ratios of filial to maternal tissues were calculated from the model data. To generate and analyse 3D expression patterns, data from mRNA localization by in situ hybridizations were integrated into the models. At the onset of starch accumulation, cell-wall invertase (HvCWINV1) mRNA is mainly localized in the transfer cells and to a lesser degree in zones of the starchy endosperm. Using the model, an expression gradient across the grain was visualized. The expression pattern in the upper region of the caryopsis resembles that found in the median region at an earlier stage, indicating the presence of a developmental gradient. At anthesis, mRNA of the protease nucellin was visualized in a distinct zone of the nucellus near the antipodal cells.

Contribution of resident endoneurial macrophages to the local cellular response in experimental autoimmune neuritis

Macrophages are intimately involved in the pathogenesis of inflammatory neuropathies. The contribution of resident endoneurial macrophages is unknown since their differentiation from infiltrating macrophages is difficult due to missing cellular markers. Previous studies demonstrated the participation of resident macrophages in Wallerian degeneration and the pathogenesis of hereditary neuropathies. The question arises whether resident macrophages are involved in experimental autoimmune neuritis (EAN) where they could contribute to immunosurveillance and antigen presentation. To address this question we used bone marrow chimeric rats, allowing the differentiation between resident and hematogenous cells. Immunohistochemistry and in situ hybridization were applied on to identify and characterize resident macrophages in terms of morphological features, expression of activation markers, proliferation, phagocytosis, and MHC-II expression. Endoneurial macrophages of resident origin were detectable at all stages of disease with a contribution of at least 27% of the total macrophages. They appeared activated by morphological and immunohistochemical criteria and proliferated early. MHC-II-positive resident macrophages were observed that had phagocytosed myelin. These results demonstrate that the macrophage response in EAN is partly of intrinsic origin. The rapid activation and proliferation of resident endoneurial macrophages points toward an active role of these cells in inflammatory peripheral nerve disease, especially early in disease.

Cement Proteins of the Tube-building Polychaete Phragmatopoma californica

The mineralized tube of the sandcastle worm Phragmatopoma californica is made from exogenous mineral particles (sand, shell, etc.) glued together with a cement secreted from the "building organ" on the thorax of the worm. The glue is a cross-linked mixture of three highly polar proteins. The complete sequences of Pc-1 (18 kDa) and Pc-2 (21 kDa) were deduced from cDNAs derived from previously reported peptide sequences (Waite, J. H., Jensen, R., and Morse, D. E. (1992) Biochemistry 31, 5733-5738). Both proteins are basic (pI approximately 10) and exhibit Gly-rich peptide repeats. The consensus repeats in Pc-1 and -2 are VGGYGYGGKK (15 times), and HPAVXHKALGGYG (eight times), respectively, in which X denotes an intervening nonrepeated sequence and Y is modified to 3,4-dihydroxyphenyl-l-alanine (Dopa). The third protein, Pc-3, was deduced from the cement to be about 80 mol % phosphoserine/serine, and the cDNA was obtained by exploiting the presence of poly-serine repeats. Pc-3 consists of a family of at least seven variants with 60-90 mol % serine most of which is phosphorylated in the cement. Pc-1, -2, and -3 contain cysteine some of which reacts to form 5-S-cysteinyl-Dopa cross-links during the setting process.

Differential segregation and modification of mRNA during spermiogenesis in Marsilea vestita

We are interested in the mechanisms that underlie cell fate determination in the endosporic male gametophytes of the fern, Marsilea vestita. Synchronous development is initiated by placing dry spores into water and involves the translation of stored mRNAs, with little transcription. Nine division cycles produce 32 spermatids surrounded by 7 sterile cells, and then each spermatid differentiates into a multiciliate gamete. Here, we focus on changes in the distribution of particular proteins, mRNAs, and patterns of polyadenylation as essential prerequisites for cell fate determination and gametogenesis. Earlier, we showed that alpha- and beta-tubulin proteins become concentrated in spermatogenous initials, and that centrin mRNA is translated only in spermatogenous initials. In situ hybridizations reveal that centrin, cyclin B, and beta-tubulin mRNAs are present in both sterile and spermatogenous cells, but that transcripts encoding RNA helicase and PRP-19 (a spliceosome component) become localized in spermatogenous cells. The targeted destruction of these two transcripts by RNAi treatments does not affect the numbers of division cycles, but the gametophytes exhibit anomalous patterns of cytokinesis, and a subsequent failure of spermatid differentiation. Thus, cell fate determination in the gametophyte involves localized translation, and the localization of mRNAs for proteins involved in transcript processing. We found differences in polyadenylation levels in sterile and spermatogenous cells that match the distribution of cytoplasmic poly(A) polymerase (PAP), which, in immunolocalizations, is abundant in spermatogenous cells, but undetectable in sterile cells. The activation of translation in spermatogenous initials, but not in sterile cells, may be under the control of mRNA processing enzymes, which become localized either as proteins or mRNAs in the spermatogenous subdomains before any divisions occur.

Cell cycle arrest allows centrin translation but not basal body formation during spermiogenesis inMarsilea

Spermiogenesis in the water fern Marsilea vestita is a rapid process that requires the de novo formation of basal bodies in a cytoplasmic particle known as a blepharoplast. Spermiogenesis is activated by placing dry spores into water and is dependent upon the translation of new proteins from stored mRNAs with little, if any, new transcription. We looked at the necessity of cell division cycles in the gametophyte as a prerequisite for the activation of centrin translation and for the consequent formation of blepharoplasts. Cell cycle arrest was induced by treatments of gametophytes with hydroxyurea, with olomoucine, or after RNAi, employing dsRNA derived from Marsilea cyclin A or cyclin B. In all cases, centrin is translated from stored mRNA at the normal time, approximately 4 hours after imbibition, and it accumulates to maximal levels ∼6 hours after imbibition. In spite of the fact that centrin is translated at essentially normal times and accumulates to nearly normal levels, no blepharoplasts form in the gametophytes where division cycles have been disrupted. These results provide a clear demonstration that the new translation of centrin, by itself, is insufficient for blepharoplast formation, the de novo formation of basal bodies, and the assembly of a motile apparatus.

Co-localization of multiple antigens and specific DNA. A novel method using methyl methacrylate-embedded semithin serial sections and catalyzed reporter deposition

Co-localization of proteins and nucleic acid sequences by in situ hybridization and immunohistochemistry is frequently difficult as the process necessary to detect the target structure of one technique may negatively affect the target of the other. Morphological impairment may also limit the application of the two techniques on sensitive tissue. To overcome these problems we developed a method to perform in situ hybridization and immunohistochemistry on semithin sections of methyl methacrylate-embedded tissue. Microwave-stimulated antigen retrieval, signal amplification by catalyzed reporter deposition, and fluorescent dyes were used for both techniques, yielding high sensitivity and excellent morphological preservation compared to conventional paraffin sections. Co-localization of in situ hybridization and immunohistochemistry signals with high morphological resolution was achieved on single sections as well as on adjacent multiple serial sections, using computerized image processing. The latter allowed for the co-localization of multiple antigens and a specific DNA sequence at the same tissue level. The method was successfully applied to radiation bone marrow chimeric rats created by transplanting wild-type Lewis rat bone marrow into TK-tsa transgenic Lewis rats, in an attempt to trace and characterize TK-tsa transgenic cells. It also proved useful in the co-localization of multiple antigens in peripheral nerve biopsies.

Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms

As a technique allowing simultaneous visualization, identification, enumeration and localization of individual microbial cells, fluorescence in situ hybridization (FISH) is useful for many applications in all fields of microbiology. FISH not only allows the detection of culturable microorganisms, but also of yet-to-be cultured (so-called unculturable) organisms, and can therefore help in understanding complex microbial communities. In this review, methodological aspects, as well as problems and pitfalls of FISH are discussed in an examination of past, present and future applications.

In search of molecular dovetails in mussel byssus: from the threads to the stem

We recently described the cDNA sequence for a unique collagenous protein, preCol-P, in the byssal threads of the marine mussel Mytilus edulis. The translated amino acid sequence encodes an unprecedented block-copolymer-like sequence with a central collagenous domain flanked by elastin-like sequences. Here, we report on the presence of two additional variants of preCol-P. The distribution of these variants in M. edulis foot tissue was examined by reverse transcription followed by polymerase chain reaction (RT-PCR) and in situ hybridization techniques. One of the variants, P33, exhibits a graded distribution with decreasing concentrations along the longitudinal axis of the foot. The second variant, P22, is expressed only at the base of the mussel's foot. In situ hybridization confirms the exclusive expression of preCol-P variant P22 in the stem gland. We propose that this variant may represent a molecular ‘dovetail’ between the proximal thread and the byssal stem, imparting extensibility and elastic recoil to the ring portion of the stem.

Bacterial symbiont transmission in the wood-boring shipworm Bankia setacea (Bivalvia: Teredinidae)

The Teredinidae (shipworms) are a morphologically diverse group of marine wood-boring bivalves that are responsible each year for millions of dollars of damage to wooden structures in estuarine and marine habitats worldwide. They exist in a symbiosis with cellulolytic nitrogen-fixing bacteria that provide the host with the necessary enzymes for survival on a diet of wood cellulose. These symbiotic bacteria reside in distinct structures lining the interlamellar junctions of the gill. This study investigated the mode by which these nutritionally essential bacterial symbionts are acquired in the teredinid Bankia setacea. Through 16S ribosomal DNA (rDNA) sequencing, the symbiont residing within the B. setacea gill was phylogenetically characterized and shown to be distinct from previously described shipworm symbionts. In situ hybridization using symbiont-specific 16S rRNA-directed probes bound to bacterial ribosome targets located within the host gill coincident with the known location of the gill symbionts. These specific probes were then used as primers in a PCR-based assay which consistently detected bacterial rDNA in host gill (symbiont containing), gonad tissue, and recently spawned eggs, demonstrating the presence of symbiont cells in host ovary and offspring. These results suggest that B. setacea ensures successful inoculation of offspring through a vertical mode of symbiont transmission and thereby enables a broad distribution of larval settlement.

Effect of bone decalcification procedures on DNA in situ hybridization and comparative genomic hybridization. EDTA is highly preferable to a routinely used acid decalcifier

Decalcification is routinely performed for histological studies of bone-containing tissue. Although DNA in situ hybridization (ISH) and comparative genomic hybridization (CGH) have been successfully employed on archival material, little has been reported on the use of these techniques on archival decalcified bony material. In this study we compared the effects of two commonly used decalcifiers, i.e. , one proprietary, acid-based agent (RDO) and one chelating agent (EDTA), in relation to subsequent DNA ISH and CGH to bony tissues (two normal vertebrae, six prostate tumor bone metastases with one sample decalcified by both EDTA and RDO). We found that RDO-decalcified tissue was not suited for DNA ISH in tissue sections with centromere-specific probes, whereas we were able to adequately determine the chromosomal status of EDTA-decalcified material of both control and tumor material. Gel electrophoresis revealed that no DNA could be successfully retrieved from RDO-treated material. Moreover, in contrast to RDO-decalcified tumor material, we detected several chromosomal imbalances in the EDTA-decalcified tumor tissue by CGH analysis. Furthermore, it was possible to determine the DNA ploidy status of EDTA- but not of RDO-decalcified material by DNA flow cytometry. Decalcification of bony samples by EDTA is highly recommended for application in DNA ISH and CGH techniques.