Fluorescence in situ hybridization in paraffin tissue sections: pretreatment protocol

Fluorescence in situ hybridization has found wide application in the enumeration of gene and chromosome copy number both in isolated cells and in tissue sections. However, the technique has been less widely used than would be expected in formalin-fixed paraffin processed (archival) tissue. This article describes a method for assessing archival tissue sections, following pretreatment, before applying DNA probes, that gives consistent, reliable results.     

‘寒富’苹果二倍体及其同源四倍体叶片超微结构和叶绿素荧光参数特征

采用扫描电镜和石蜡切片法,以‘寒富’苹果二倍体及经秋水仙素加倍获得的同源四倍体植株为材料,比较两种倍性植株叶片超微结构、叶绿素含量及叶绿素荧光参数的日变化规律。结果显示:(1)与二倍体植株相比较,其同源四倍体叶片厚度、栅海比、气孔长、气孔宽、分别增加了15.1%、16.1%、70.5%、27.2%,而气孔密度显著减少了58.7%;其同源四倍体叶保卫细胞中叶绿体数和叶绿素含量分别比二倍体植株高出125.3%、37.7%。(2)‘寒富’苹果同源四倍体与其二倍体的叶绿素荧光参数PSⅡ的原初光能转化效率(Fv/Fm)、PSⅡ的潜在光化学效率(Fv/F0)和以吸收光能为基础的光合性能指数(PI)值的日变化趋势相似,但PI平均值比二倍体显著高出38.6%。研究表明,同源四倍体较二倍体叶片在形态上更大、更厚,气孔更大、密度更小,栅海比更大,表现出抗病的叶片结构;同时同源四倍体较二倍体含有更高的叶绿素含量,表现更优良的光合特性。     

A proteomic profile of synoviocyte lesions microdissected from formalin-fixed paraffin-embedded synovial tissues of rheumatoid arthritis

Background

Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic inflammation of the synovial joints. Early intervention followed by early diagnosis can result in disease remission; however, both early stage diagnosis and provision of effective treatment have been impeded by the heterogeneity of RA, which details of pathological mechanism are unclear. Regardless of numerous investigations of RA by means of genomic and proteomic approaches, proteins interplaying in RA synovial tissues that contain various types of synoviocytes, are not yet sufficiently understood. Hence we have conducted an HPLC/mass spectrometry-based exploratory proteomic analysis focusing on synoviocyte lesions laser-microdissected (LMD) from formalin-fixed paraffin-embedded (FFPE) synovial tissues (RA, n = 15; OA, n = 5), where those of Osteoarthritis (OA) were used as the control.

Results

A total of 508 proteins were identified from the RA and OA groups. With the semi-quantitative comparisons, the spectral index (SpI), log2 protein ratio (R_SC) based on spectral counting, and statistical G-test, 98 proteins were found to be significant (pair-wise p < 0.05) to the RA synovial tissues. These include stromelysin-1 (MMP3), proteins S100-A8 and S100-A9, plastin-2, galectin-3, calreticulin, cathepsin Z, HLA-A, HLA-DRB1, ferritin, neutrophil defensin 1, CD14, MMP9 etc.

Conclusions

Our results confirmed the involvement of known RA biomarkers such as stromelysin-1 (MMP3) and proteins S100-A8 and S100-A9, and also that of leukocyte antigens such as HLA-DRB1. Network analyses of protein–protein interaction for those proteins significant to RA revealed a dominant participation of ribosome pathway (p = 5.91 × 10⁻⁴⁵), and, interestingly, the associations of the p53 signaling (p = 2.34 × 10⁻⁵). An involvement of proteins including CD14, S100-A8/S100-A9 seems to suggest an activation of the NF-kB/MAPK signaling pathway. Our strategy of laser-microdissected FFPE-tissue proteomic analysis in Rheumatoid Arthritis thus demonstrated its technical feasibility in profiling proteins expressed in synovial tissues, which may play important roles in the RA pathogenesis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12014-015-9091-8) contains supplementary material, which is available to authorized users.     

Observation on Flower Bud Differentiation of Crape Myrtle in Red Soil Environment

Flower bud differentiation is a key component of plant blooming biology and understanding how it works is vital for flowering regulation and plant genetic breeding, increasing the number and quality of flowering. Red soil is the most widely covered soil type in the world, and it is also the most suitable soil type for crape myrtle planting. The flower buds of crape myrtle (Lagerstroemia indica) planted in red soil were employed as experimental materials in this study, and the distinct periods of differentiation were identified using stereomicroscopy and paraffin sectioning. We optimized the steps of dehydration, transparency, embedding, sectioning and staining when employing paraffin sections. When seen under a microscope, this optimization can make the cell structure of paraffin sections obvious, the tissue structure complete, and the staining clear and natural. The flower bud differentiation process is divided into 7 periods based on anatomical observations of the external morphology and internal structure during flower bud differentiation: undifferentiated period, start of differentiation period, inflorescence differentiation period, calyx differentiation period, petal differentiation period, stamen differentiation period, and pistil differentiation period. The differentiation time is concentrated from the end of May to mid-June. Crape myrtle flower bud differentiation is a complicated process, and the specific regulatory mechanism and affecting elements need to be investigated further.     

Application of 2-D DIGE to formalin-fixed, paraffin-embedded tissues

The ability to investigate the proteome of formalin-fixed, paraffin-embedded (FFPE) tissues can be considered a major recent achievement in the field of clinical proteomics. However, gel-based approaches to the investigation of FFPE tissue proteomes have lagged behind, mainly because of insufficient quality of full-length protein extracts. Here, the 2-D DIGE technology was investigated for applicability to FFPE proteins, for internal reproducibility among replicate FFPE extracts, and for comparability between FFPE and fresh-frozen tissue profiles. The 2-D DIGE patterns obtained upon labeling and electrophoresis of replicate FFPE tissue extracts were highly reproducible, with satisfactory resolution and complexity. Moreover, the implementation of DIGE enabled to highlight and characterize the consistent differences found in the FFPE profiles compared with fresh-frozen profiles, represented by an acidic shift, directly correlated to the protein pI value, and by a reduction in spot signal intensity, directly correlated to molecular weight and percentage of lysine residues. Being constantly and reproducibly present in all FFPE tissue extract replicates at similar extents, these modifications do not appear to hinder the comparative analysis of FFPE tissue extracts by 2-D DIGE, opening the way to its application for the differential proteomic investigation of archival tissue repositories.     

The use of whole genome amplification in the study of human disease

The availability of large amounts of genomic DNA is of critical importance for many of the molecular biology assays used in the analysis of human disease. However, since the amount of patient tissue available is often limited and as particular foci of interest may consist of only a few hundred cells, the yield of DNA is often insufficient for extensive analysis. To address this problem, several whole genome amplification (WGA) methodologies have been developed. Initial WGA approaches were based on the polymerase chain reaction (PCR). However, recent reports have described the use of non-PCR-based linear amplification protocols for WGA. Using these methods, it is possible to generate microgram quantities of DNA starting with as little as 1mg of genomic DNA. This review will provide an overview of WGA approaches and summarize some of the uses for amplified DNA in various high-throughput genetic applications.     

3种桉树组培苗不定根发生发育过程的解剖学观察

以巨尾桉‘GL9’、尾巨桉‘DH32-29’和尾边桉‘XF35’3种桉树无性系组培生根苗为材料,采用常规石蜡切片技术,对石蜡切片制作过程中的固定环节进行了优化,观察了桉树不定根的发育过程。结果表明:(1)采用FAA固定液固定材料,可获得染色清晰,组织完整的桉树根系切片。(2)‘GL9’和‘DH32-29’在生根诱导8d后生出不定根,生根类型为皮部生根;‘XF35’在生根诱导12d后生出不定根,生根类型为愈伤组织生根;‘GL9’不定根的根尖和根基处均有细胞旺盛分裂,‘DH32-29’不定根只在根尖有细胞旺盛分裂,‘XF35’不定根则只在其根基处有大量旺盛分裂的细胞。     

Comparison of Water,Oils and Emulsifiable Adjuvant Oils as Formulating Agents for <Emphasis Type="Italic">Metarhizium Anisopliae</Emphasis> for Use in Control of <Emphasis Type="Italic">Boophilus Microplus</Emphasis>

Studies were conducted to identify oil-based formulating agents (paraffinic oil, palm oil and emulsifiable adjuvant oils (EAOs)) for Metarhizium anisopliae that were superior to water with simple surfactants using a germination test and a bioassay against Boophilus microplus. Germination of conidia in all formulations, except 10% coconut EAO, produced more than 68% germination at 24 h and nearly 100% at 48 h. Coconut oil (average survival time (AST)=4.6±0.28 days) and 10% liquid paraffin EAO (AST=4.4±0.15 days) enhanced the pathogenicity of M. anisopliae to B. microplus relative to water (AST=8.4±0.42 days). M. anisopliae in 10% liquid paraffin EAO was the most effective formulation having a moderately high germination after 24 h and a low AST as well as a high AST in the control. In the second experiment, germination of conidia in 2% liquid paraffin EAO and 2% Cropspray was higher than in 2% Codacide oil at 24 h, however, all treatments reached 100% germination after 48 h. The ASTs of the EAO based M. anisopliae formulations (Average AST=6.4±0.54 days) were similar but lower that the ASTs of the controls (Average AST=9.6±0.28 days).