High-resolution in situ hybridization to whole-mount zebrafish embryos

The in situ hybridization (ISH) technique allows the sites of expression of particular genes to be detected. This protocol describes ISH of digoxigenin-labeled antisense RNA probes to whole-mount zebrafish embryos. In our method, PCR-amplified sequence of a gene of interest is used as a template for the synthesis of an antisense RNA probe, which is labeled with digoxigenin-linked nucleotides. Embryos are fixed and permeabilized before being soaked in the digoxigenin-labeled probe. We use conditions that favor specific hybridization to complementary mRNA sequences in the tissue(s) expressing the corresponding gene. After washing away excess probe, hybrids are detected by immunohistochemistry using an alkaline phosphatase-conjugated antibody against digoxigenin and a chromogenic substrate. The whole procedure takes only 3 days and, because ISH conditions are the same for each probe tested, allows high throughput analysis of zebrafish gene expression during embryogenesis.     

在拔尖人才教学中开设斑马鱼原位杂交实验探索

为更好地响应教育部"拔尖人才"计划,四川大学生物科学国家级实验教学示范中心在"拔尖人才"教学中,特引进世界第二大模式生物——斑马鱼,设置了"斑马鱼发育相关基因crip2原位杂交实验",新颖的实验内容激发了学生的积极性,培养了学生的创新能力。     

Whole amount in situ hybridization and transgene via microinjection in zebrafish]

Zebrafish is new model organism to study development of the vertebrate. In this report, we chose a fragment of gene GATA-1 which specifically expressed in zebrafish hematopoiesis system as probe to carry on whole amount in situ hybridization. Then we transported reporter gene driven by GATA-1 promoter into the embryos via microinjection approach and observed the spatial and temporal expression pattern of GFP. Our results demonstrated that efficient and reliable technology of whole amount in situ hybridization and microinjection in zebrafish was established.     

斑马鱼高分辨率整胚原位杂交实验方法与流程

整胚原位杂交技术是利用反义RNA探针检测体内mRNA表达的一项技术, 在利用模式动物研究基因时空表达方面有着重要的应用。如何使用该技术得到特异、高敏感度的表达结果, 对每一个使用该技术的实验室来说都很重要。本实验室参照常规的实验方法, 对该技术加以改进, 使之更加灵敏, 结果更加特异。文章主要以斑马鱼为例, 介绍了整胚原位杂交技术的发展历史, 并重点介绍了本实验室所用的整胚原位杂交实验流程, 同时还分析了实验结果不理想的原因及其解决方法。     

Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques

The ribosomal-RNA (rRNA) approach to microbial evolution and ecology has become an integral part of environmental microbiology. Based on the patchy conservation of rRNA, oligonucleotide probes can be designed with specificities that range from the species level to the level of phyla or even domains. When these probes are labelled with fluorescent dyes or the enzyme horseradish peroxidase, they can be used to identify single microbial cells directly by fluorescence in situ hybridization. In this Review, we provide an update on the recent methodological improvements that have allowed more reliable quantification of microbial populations in situ in complex environmental samples, with a particular focus on the usefulness of group-specific probes in this era of ever-growing rRNA databases.     

Measurement of telomere length in haematopoietic cells using in situ hybridization techniques

The DNA of human chromosomes terminates in several kilobases of telomere repeats that are gradually lost with; age and with replication in vitro. Defective telomere maintenance has been shown to be causally linked to cell cycle exit and apoptosis. In order to overcome the limitations imposed by Southern blotting, we have established a quantitative fluorescence in situ hybridization (Q-FISH) technique. This technique allows estimation of telomere length in specific chromosome arms from metaphase cell preparations. Furthermore, we have extended quantitative in situ hybridization to flow cytometry (flow FISH) in order to obtain information on the mean telomere repeat content in suspended cells. Telomere length in granulocytes, monocytes, CD8 and CD4 T lymphocytes and natural killer cells was found to differ slightly in the peripheral blood of adults. However, strikingly longer telomeres were observed in B lymphocytes (approximately 1.3 kb longer), suggesting a functional role for telomere maintenance in this cell subset. In summary, Q-FISH and flow FISH represent new methods for measuring telomere length in single cells and allow studies of telomere dynamics in haematopoietic subpopulations at various stages of normal and abnormal antigen responses.     

斑马鱼整体原位杂交法研究MMP15a的发育相关表达的初步观察

克隆斑马鱼基质金属蛋白酶15a（MMP15a）基因,并研究其在斑马鱼胚胎早期发育中的时空表达状况。收集不同发育时期的斑马鱼胚胎,制备DIG标记的MMP15a RNA探针,采用全胚胎原位杂交方法研究MMP15a基因在胚胎斑马鱼的表达。结果MMP15a基因在胚胎受精后一个细胞时期就开始表达,从受精后24h起,在眼睛处表达明显,从受精后48h MMP15a在胸鳍和耳囊有特异性表达至到受精后96h。MMP15a在斑马鱼胚胎发育不同时期表达明显,且在胸鳍和耳囊处有持续表达。     

整体原位杂交法初步研究MMP11b在斑马鱼胚胎发育过程中的表达

克隆斑马鱼基质金属蛋白酶11b（MMP11b）基因,并研究其在斑马鱼胚胎早期发育中的时空表达状况。收集不同发育时期的斑马鱼胚胎,制备DIG标记的MMP11b RNA探针,采用全胚胎原位杂交方法研究MMP11b基因在斑马鱼胚胎的表达。MMP11b基因在胚胎受精后一个细胞时期就开始表达,并且一直持续到96h,从受精后24h起,在耳囊处表达明显,在受精后48h时期在胸鳍和肛门处也有特异性表达。MMP11b在斑马鱼胚胎发育不同时期表达明显,且在耳囊处有持续表达。     

Non-radioactive in situ hybridization

Summary A number of immunocytochemical detection systems for determining the chromosomal localization of specific nucleic acid sequences by non-radioactive in situ hybridization have been compared. The procedures were: 1. the peroxidase/diaminobenzidine (PO/DAB) combination, either or not gold/silver intensificated; 2. alkaline phosphatase marking using the nitro-blue tetrazolium plus bromochloro-indolyl phosphate substrate combination (AP/NBT+CIP); and 3. immunogold with or without silver enhancement. The procedures were first tested and optimized in dot blot experiments and then applied to in situ hybridization. As hybridization probes, both a middle-repetitive and a unique sequence (modified with 2-acetyl-aminofluorene (AAF)) were used. The advantages and dis-advantages of the various methods for reflection contrast (RC) or transmission electron microscopic (TEM) visualization of hybrids are discussed.     

Comparative aneugenicity of doxorubicin and its derivative idarubicin using fluorescence in situ hybridization techniques

The present study was designed to evaluate and compare the aneugenicity of idarubicin and doxorubicin, topoisomerase-targeting anticancer anthracyclines, using fluorescence in situ hybridization techniques. It was found that idarubicin and doxorubicin treatment (12 mg/kg) induced sperm meiotic delay of 24h. To determine the frequencies of disomic and diploid sperm, groups of 5 male Swiss albino mice were treated with 3, 6 and 12 mg/kg idarubicin or doxorubicin. Significant increases in the frequencies of disomic and diploid sperm were caused by treatment with all doses of idarubicin and the two highest doses of doxorubicin compared with the controls. Moreover, both compounds significantly increased the frequency of diploid sperm, indicating that complete meiotic arrest occurred. The observation that XX- and YY-sperm significantly prevailed XY-sperm indicates missegregation during the second meiotic division. The results suggest also that earlier prophase stages contribute relatively less to idarubicin and doxorubicin-induced aneuploidy. Effects of the same doses were investigated by the bone-marrow micronucleus test. Significant increases in the frequencies of micronuclei were found after treatment with all doses of both compounds. The responses were also directly correlated with bone marrow suppression. Idarubicin was more toxic than doxorubicin. Exposure to 12 mg/kg of idarubicin and doxorubicin yielded 3.82 and 2.64% micronuclei, respectively, and of these an average of 58.3 and 62.8%, respectively, showed centromeric signals, indicating their formation by whole chromosomes and reflecting the aneugenic activity of both compounds. Correspondingly, about 41.7 and 37.2% of the induced micronuclei, respectively, were centromere-negative, demonstrating that both compounds not only induce chromosome loss but also DNA strand breaks. Based on our data, aneuploidy assays such as sperm-fluorescence in situ hybridization assay and micronucleus test complemented by fluorescence in situ hybridization with centromeric DNA probes have been to some extent validated to be recommended for the assessment of aneuploidogenic effects of chemicals.     

Multiple fluorescence in situ hybridization

A method for multiple fluorescence in situ hybridization is described allowing the simultaneous detection of more than three target sequences with only three fluorescent dyes (FITC, TRITC, AMCA), respectively emitting in the green, red, and blue. This procedure is based on the labeling of (DNA) probes with more than one hapten and visualisation in multiple colors. The possibility to detect multiple targets simultaneously is important for prenatal diagnosis and the detection of numerical and/or structural chromosome aberrations in tumor diagnosis. It may form the basis for an in situ hybridization based chromosome banding technique.     

Ontogeny of the GnRH systems in zebrafish brain: in situ hybridization and promoter-reporter expression analyses in intact animals

The ontogeny of two gonadotropin-releasing-hormone (GnRH) systems, salmon GnRH (sGnRH) and chicken GnRH-II (cGnRH-II), was investigated in zebrafish (Danio rerio). In situ hybridization (ISH) first detected sGnRH mRNA-expressing cells at 1 day post-fertilization (pf) anterior to the developing olfactory organs. Subsequently, cells were seen along the ventral olfactory organs and the olfactory bulbs, reaching the terminal nerve (TN) ganglion at 5–6 days pf. Some cells were detected passing posteriorly through the ventral telencephalon (10–25 days pf), and by 25–30 days pf, sGnRH cells were found in the hypothalamic/preoptic area. Continuous documentation in live zebrafish was achieved by a promoter-reporter expression system. The expression of enhanced green fluorescent protein (EGFP) driven by the sGnRH promoter allowed the earlier detection of cells and projections and the migration of sGnRH neurons. This expression system revealed that long leading processes, presumably axons, preceded the migration of the sGnRH neuron somata. cGnRH-II mRNA expressing cells were initially detected (1 day pf) by ISH analysis at lateral aspects of the midbrain and later on (starting at 5 days pf) at the midline of the midbrain tegmentum. Detection of red fluorescent protein (DsRed) driven by the cGnRH-II promoter confirmed the midbrain expression domain and identified specific hindbrain and forebrain cGnRH-II-cells that were not identified by ISH. The forebrain DsRed-expressing cells seemed to emerge from the same site as the sGnRH-EGFP-expressing cells, as revealed by co-injection of both constructs. These studies indicate that zebrafish TN and hypothalamic sGnRH cell populations share a common embryonic origin and migratory path, and that midbrain cGnRH-II cells originate within the midbrain. This study was supported by the US-Israel Bi-national Agricultural Research and Development (BARD) Foundation (grant 3428-03).     

Characterization of SV40-transformed human cells by immunofluorescence and fluorescent in situ hybridization techniques

We have performed immunofluorescent and fluorescent in situ hybridization studies in order to better clarify the integration of SV40 DNA in human fibroblast cell lines. Most of the cells were T-antigen positive by immunocytochemical studies, while in all the cells we detected the integrated viral DNA by in situ hybridization. Both techniques are easy and useful to perform but the molecular genetic method gives a more specific signal with the possibility of localizing molecular hybrids in the nucleus and in the cytoplasm of the transformed cells.     

Application of in situ hybridization, cytochemical and immunocytochemical techniques for the investigation of peroxisomes

 In situ hybridization, cytochemical and immunocytochemical techniques have contributed significantly to the understanding of the biology of peroxisomes, since they permit in situ demonstration of the sites of synthesis and distribution of peroxisomal proteins without the necessity of homogenization and subcellular fractionation of tissues or cultured cells. This article reviews the results of research on mammalian peroxisomal metabolism, biogenesis and proliferation in which morphological techniques have played a significant role in the elucidation of the biological problem. Some new data on peroxisomal heterogeneity and morphogenesis are included. The morphological methods applied have made it possible to characterize the differences in distribution of mRNAs encoding peroxisomal proteins in different tissues, as well as to monitor the marked heterogeneity in the protein composition and in the activity of specific enzymes in the peroxisomal population of single cells, or in tissues with complex organization (e.g. liver and kidney). In addition, the dynamic alterations and high plasticity of the peroxisomal compartment – partly dependent on contact of the peroxisomes to the microtubular network – are presented.     

Advances in fluorescence in situ hybridization

The techniques of in situ hybridization (ISH) are widely applied for analyzing the genetic make-up and RNA expression patterns of individual cells. This review focusses on a number of advances made over the last 5 years in the fluorescence ISH (FISH) field, i.e., Fiber-FISH, Multi-colour chromosome painting, Comparative Genomic Hybridization, Tyramide Signal Amplification and FISH with Polypeptide Nucleic Acid and Padlock probes.