Technique and Application of Single-molecule Fluorescence in situ Hybridization / 生物化学与生物物理进展

Single molecule fluorescence in situ hybridization (smFISH) is a method for imaging single mRNA molecule in fixed cell or tissue using oligonucleotide probes coupled with fluorophores. It can realize real-time study of interested transcripts by RNA localization and quantification. smFISH is widely suitable for many types of biological samples such as cell and tissue sections. It was invented in 1982 which opened up the application of visualizing single molecules. However, due to its shortcomings such as poor binding specificity, Raj et al. optimized this technique in 2008, using 48 independent probes that were separately coupled with fluorophores to locate transcripts. In contrast, methods using multiple labeled probes can distinguish false positive or false negative results due to a single probe misbinding or unbinding event. However, with the continuous application of the technique, it was found that the scheme still has many technical defects, such as low probe specificity, weak fluorescence intensity, low hybridization efficiency, and high background fluorescence. Since then, a series of derivative technologies have been developed. For example, HCR-FISH is a multi-fluorescence in situ hybridization method based on orthogonal amplification and hybridization chain reaction, which significantly improves the problem of weak signal. SeqFISH amplifies the signal and reduces nonspecific binding by continuously hybridizing the mRNA in the cell, imaging it, and stripping the probe in order to barcode RNA. MERFISH utilizes combination labeling, continuous imaging and other technologies to increase detection throughput, and uses binary barcodes to offset single-molecule labeling and detection errors, with more advanced built-in error correction functions to effectively improve the accuracy of results. ClampFISH uses biological orthogonal click chemistry to effectively lock the probe around the target and prevent the probe from disengaging in amplification microscopy. RNAscope amplifies its own signal while simultaneously suppressing the background by using novel probe design strategy and hybridization-based signal amplification system. Split-FISH uses splitting probes for signal enhancement to accurately detect single RNA molecule in complex tissue environments. AmpFISH achieves imaging of short RNA molecules by preparing long single-strand DNA concatemers through controlled rolling circle amplification. CircFISH uses two unique sets of probes (PC probes and PL probes) to distinguish between linear and circular RNAs. π-FISH rainbow enables simultaneous detection of DNA, RNA, and proteins at the single-molecule level with π-FISH target probes. HT-smFISH is more suitable for large or high throughput form of systematic experiments. With the development of technology, the subsequent data analysis process is particularly important. Different analysis software, such as dotdotdot and FISH-quant v2, also improve the process of smFISH. The excellent ability of smFISH to visualize single molecule of RNA makes that it is widely used in basic biological disciplines such as tumor biology, developmental biology, neurobiology, botany, virology. In this paper, we reviewed the basic principle of smFISH technology, its development process and improvement, limitations of smFISH technology and how to avoid them, its derivative technologies include HCR-FISH, SeqFISH, MERFISH, ClampFISH, RNAscope, Split-FISH, AmpFISH, CircFISH, π-FISH rainbow and HT-smFISH. The application progress of smFISH in different biological disciplines, such as developmental biology, tumor biology, neurobiology. Finally, the development prospect of smFISH technology is prospected.

Concordance of identifying the presence or absence of KIR genes by Flow-rSSO and PCR-SBT methods: a comparative study / 中国输血杂志

【Objective】 To study the concordance of identifying the presence or absence of KIR genes using flow reverse sequence-specific oligonucleotide probe (Flow-rSSO) hybridization and sequencing based typing-PCR (PCR-SBT) methods. 【Methods】 A total number of 131 cases of DNA samples from Han population were subjected to identify the presence or absence of all 16 KIR genes by Flow-rSSO method, and then sequenced at coding sequence for all 14 functional KIR genes using our in-house KIR PCR-SBT assay. The concordance of identifying the presence or absence of all functional KIR genes by Flow-rSSO and PCR-SBT was analyzed. Samples with inconsistent initial results were re-tested using the Flow-rSSO commercial kits with different Lot number, and further tested using the PCR-SSP commercial kit. 【Results】 The presence or absence of 14 functional KIR genes for 129 of 131 samples were completely in accordance via the PCR-SBT and Flow-rSSO methods. Two samples, one with 3DL1 negative, the other with both 2DS3 and 2DS5 negative initially-identified by Flow-rSSO, were actually all positive tested by PCR-SBT. Further retest by Flow-rSSO commercial kits with different Lot number and PCR-SSP commercial kit indicated that the two samples were all positive, which agreed well with PCR-SBT results. 【Conclusion】 In this paper, the initial test results of the presence or absence of KIR genes identified by Flow-rSSO for 2 samples were wrong, which indicated the importance of carrying out the quality control for reagents in KIR gene testing.

Colorimetric microwell plate reverse-hybridization assay for Mycobacterium tuberculosis detection

Direct smear examination using Ziehl-Neelsen staining for pulmonary tuberculosis (PTB) diagnosis is inexpensive and easy to use, but has the major limitation of low sensitivity. Rapid molecular methods are becoming more widely available in centralized laboratories, but they depend on timely reporting of results and strict quality assurance obtainable only from costly commercial kits available in high burden nations. This study describes a pre-commercial colorimetric method, Detect-TB, for detecting Mycobacterium tuberculosis DNA in which an oligonucleotide probe is fixed onto wells of microwell plates and hybridized with biotinylated polymerase chain reaction amplification products derived from clinical samples. The probe is capable of hybridising with the IS6110 insertion element and was used to specifically recognise the M. tuberculosis complex. When combined with an improved silica-based DNA extraction method, the sensitivity of the test was 50 colony-forming units of the M. tuberculosis reference strain H37Rv. The results that were in agreement with reference detection methods were observed in 95.2 percent (453/476) of samples included in the analysis. Sensitivity and specificity for 301 induced sputum samples and 175 spontaneous sputum samples were 85 percent and 98 percent, and 94 percent and 100 percent, respectively. This colorimetric method showed similar specificity to that described for commercially available kits and may provide an important contribution for PTB diagnosis.

Application of rapid identification for Streptpcoccus mutans, Streptpcoccus sobrinus and Streptpcoccus sanguis in the native dental plaque biofilm by fluorescence in situ hybridization / 中华微生物学和免疫学杂志

Objective To examine Streptpcoccus mutans,Streptpcoccus sobrinus and Streptpcoccus sanguis in the early formation of native dental plaque biofilm. Methods An experimental dental plaque biofilm model in the oral cavity was established using enamel slabs. The spatial distribution of S. mutans, S.sobrinus and S. sanguis in the early colonization of dental plaque biofilms on the enamel surface was observed bv in situ, real-time and dynamic observations and optical sections utilizing confocal laser scanning microscopy(CLSM) and fluorescence in situ hybridization(FISH). The experiment data were analyzed with One-Way AVOVA, α=0.05 using SPSS11.5. Results Dental biofilm had a certain degree of thickness and various forms in three-dimensioned structure. The bacteria in the structure were sparse at the inner layers and the outer layers. In the middle layers the bacteria were closely compacted. There were many voids traversing from the outside of the biofilm to the enamel surface. At the initial stage of dental biofilm formation, the scanned average thickness of S. mutans,S. sobrinus and S. sanguis increased with time elapsing,the mean thicknesses of 1 h biofilms were 20.43 μm,11.50 μm and 14.76 μm,respectively,and those of 24 h were the thickest in terms of average level,the mean values were 70.25 μm,75.40 μm and 79.98 μm,respectively. Conclusion The fluorescence in situ hybridization combined with CLSM are thought to be convenient and sensitive to detect S. mutans, S. sobrinus and S. sanguis in the dental plaque biofilms.

Comparison of Three Radiolabeled Probes for PCR-Hybridization to Detect Mycobacterium tuberculosis / 대한진단검사의학회지

BACKGROUND: Three homemade radiolabeled probes to detect DNA of Mycobacterium tuberculosis by PCR-hybridization (PCRH) assay were compared in order to select the most sensitive and economic probe with the longest lifespan. METHODS: One full length probe, probe 1, prepared by the random priming method and two oligonucleotide probes, probes 2 and 3, prepared by the 5' end-labeling method were designed and assessed for sensitivity, specificity, and life span. The detection limit of each probe was determined on sample membranes containing serially diluted M. tuberculosis DNA from 5 ng to 5 fg on weekly intervals. To assess the specificity of each probe, DNA samples from 4 species of nontuberculous mycobacteria (NTM) and 9 species of bacteria other than mycobacteria were also tested. RESULTS: Each probe with PCRH showed the same detection limits of 50 fg of M. tuberculosis DNA after a 48-hr film exposure time. There were no nonspecific reactions to bacteria when tested for specificity. When we defined the life span of each probe as the longest period for detecting the lowest detection limits of M. tuberculosis DNA, the life spans of probes 1, 2, and 3 after a 3-hour film exposure were 7, 0, and 0 weeks, respectively. For probes 2 and 3, no band was visible even on the day of preparation. The life spans after a 48-hour film exposure were 9, 3, and 2 weeks for probes 1, 2 and 3, respectively. CONCLUSIONS: Probe 1, a full length probe prepared by the random priming method, was more sensitive and was a cheaper probe with a longer life span compared to probes 2 and 3, oligoprobes prepared by the 5' end-labeling method.

Detection of Mycobactrium tuberculosis by in situ hybridization / 결핵

BACKGROUND: A presumptive histopathologic diagnosis of tuberculosis is commonly based on the finding of acid- fast bacilli upon microscopic examination of a diagnostic specimens. Although this traditional histochemical staining methodis satisfactory, it is time-consuming and not species-specific. For more specific assessment, in situ hybridization assay with oligonucleotide probes is introduced. METHODS: The human surgical specimens were obtained from tuberculosis patients(,)and experimental specimens were made by injecting fresh rat liver with cultured M. tuberculosis organisms into fresh rat liver. Oligonucleotide probes complementary to ribosomal RNA portion were synthesized and labeled with multiple biotin molecules. For a rapid detection, all procedures were carried out using manual capillary action technology on the Microprobe staining system. RESULTS: The in situ hybridization assay produced a positive reaction in experimental specimens (80-90% sensitivity) after pepsin- HCl pre-treatment for a good permeabilization of probes, but reliable result was not obtained from human surgical specimens. CONCLUSION: It is, therefore, suggested that biotin- labeled oligonucleotide probes have considerable potential for identification and in situ detection of M. tuberculosis but, there are some barriers to overcome for the diagnostic use of this method.

Quick identification of haemophilus influenza with reverse dot blot / 实用儿科临床杂志

Objective To study the way of quick identification of haemophilus influenzae with reverse dot blot.Methods Oligonucleotide probe which is specially targeted to 16SrDNA of haemophilus influenzae was designed, then fixed the probe to nylon membranes, and hybridized with the production of gain with the universal primers.Results The universal primers could hybridize the target sequence from common pathogenic bacteria by PCR, and oligonucleotide probe could hybridize with haemophilus influenza specially and could not hybridize with other bacterias. It proved that the probe was of highly speciality.Conclusion Reverse dot blot is a good method of quickly identification of haemophilus influenzae.

Use of 16S-rRNA Hybridization Probes to Detect the Cellulolytic Bacteria in Rumen / 微生物学通报

In this study, the general bacterial probe and specific cellulolytic bacterial probes were used to quantify the bacteria in rumen. The total RNA were extracted and then hybridized with general bacterial probe after a dilution of concentration. The result showed that there was a high correlation between the hybridization signal and the dilution of total bacterial RNA. Based on the result above, the quantities of three cellulolytic bacteria in rumen sample were detected. The comparative RNA percentage of three cellulolytic bacteria to total bacterial RNA were similar to the previous reports. It can be concluded that the quantification of bacteria in rumen could be conducted by this approach, and which could be used in future research.

Rapid Species Identification of Mycobacterium tuberculosis by rpoB Gene Micro Array / 微生物学通报

Rapid species identification of Mycobacterium tuberculosis by rpoB gene micro array.Based on the gene micro array of rpoB,the standard strains of 21 mycobacteria and 8 non-mycobacteria,126 clinical isolated of mycobacteria were detected by PCR-reverse dot blot hybridization assay.360bp DNA fragment was amplified from all mycobacteria tested and was not found in all nonmycobacteria except Hemolytic streptococcus and Corynebacterium pseudodiphtheriticum.The result of specimens were detected by the probe which is composed of 21 oligonucleotide was that probe-Mycobacterium fortuitum cross hybridizated with Mycobacterium platypoecilus while the other probes were specific.The 89 strains of the all 126 strains isolated from clinical specimens were identified to be mycobacterium tuberculosis,the percentage was 70.6%(89/126),while the other 9 strains were identified to be unmycobacterium tuberculosis and the the percentage was 9.2%(9/98).Identification of Mycobacteria by rpoB gene micro array is a rapid and effective method which is of considerable value in clinical territory.