Fluorescence-based Multiplex PCR-Single Strand Conformation Polymorphism (SSCP) Analysis of 16S Ribosomal DNA Using Capillary Electrophoresis

The rRNA genetic locus is found in all prokaryotic organisms, and is highly conservative, although its relatively stable variations are found frequently in different bacteria. The utility of this locus as a taxonomic and phylogenetic tool has been reported widely. This study, aimed at 16S rRNA gene (16S rDNA) and with the help of biomolecular methods, attempted to achieve the goal of rapid identification of common pathogens. In this study, 333 clinical isolated pathogenic bacteria were collected. Two pairs of primers were chosen and labeled with different fluorescent dyes and then used to amplify the genomic DNA extracted from bacteria. The PCR products were then detected by capillary electrophoresis-single strand conformation polymorphism (CE-SSCP). In order to pursue higher resolution and peak-separation effect, a high efficient separating medium, liner polyacrylamidedel (LPA), was put to use in this study. Finally, every bacteria colony generated distinct patterns from each other, which were easily to be used for identification. These results indicated that PCR-CE-SSCP was a rapid identification method for bacterial identification, with the aspects of high efficiency and high precision. Compared with traditional method, this technology is of great utility for clinical use especially for its high sensitivity.

An automated fluorescent single strand conformation polymorphism technique for high throughput mutation screening

Objective To develop a high throughput mutational detection method by mutiple fluorescence-labeled polymerase chain reaction(PCR)products.Methods A total of 27 known mutations including 22 substitutions,3 insertions(1,2 and 7 bp)and 2 deletions(1 and 2 bp)in the hepatocyte nuclear factor(HNF)-4α,glucokinase and HNF-1α genes were tested.During nested PCR,amplified fragments were labeled with three fluorescent dyes.PCR products were visualized with an ABI-377 fluorescence sequencer using 5% glycerol or 10% sucrose in nondenaturing gel conditions.Results Twenty-five of 27 variants(93%)could be detected by combining 5% glycerol and 10% sucrosegel matrix conditions.Twenty-two of 27(82%)and 18 of 27(67%)variants were identified using 5%glycerol and 10% sucrose conditions,respectively.Conclusion This fluorescence-based PCR single strand conformation polymorphism technique represents a simple,non-hazardous,time-saving and sensitive method for high throughput mutation detection.

Single nucleotide polymorphisms in the CDH17 gene of colorectal carcinoma

AIM:To investigate the relationship between c.343A>G and c.2216A>C polymorphism sites in the CDH17 gene and colorectal carcinoma.METHODS:Ninety-three non-consanguineous colorectal carcinoma patients admitted to the Department of Oncology at the First Affiliated Hospital of Zhengzhou University were included in this study.Ninety-three peripheral venous blood samples,of approximately one milliliter from each patient,were collected betweenDecember 2009 and August 2010.The genomic DNA of these peripheral venous blood samples were extracted and purified using a Fermentas Genomic DNA Purification Kit(Fermentas,CA) according to the manufacturer' s protocol.The single nucleotide polymorphisms(SNPs) of the liver-intestine cadherin(CDH17) gene c.343A>G and c.2216A>C were determined by the polymerase chain reaction-single strand conformation polymorphism method(PCR-SSCP) in 93 peripheral venous blood samples from patients suffering with colorectal carcinoma.Typical samples that showed different migration bands in SSCP were confirmed by sequencing.Directed DNA sequencing was used to check the correctness of the genotype results from the PCR-SSCP method.RESULTS:There was a significant association between the c.2216 A>C SNPs of the CDH17 gene and the tumor-node-metastasis(TNM) grade,as well as with lymph node status,in 93 peripheral venous blood samples from colorectal carcinoma patients.The genotype frequencies of A/C,A/A,and C/C were 12.90%,33.33% and 53.76%,respectively.There was a significant correlation between lymph node metastasis,TNM grade,and the genotype distribution(P < 0.05).The C/C genotype raised the risk of lymph node metastasis and the TNM grade.There was a significant difference in the TNM grade and lymph node metastasis between the A/A and C/C genotypes(P = 0.003 and P = 0.013,respectively).Patients with colorectal carcinoma carrying the C allele tended to have a higher risk of lymph node metastasis and have a higher TNM grade.The difference between the TNM grades,as well as the lymph node metastasis of the two alleles,was statistically significant(P < 0.01).CONCLUSION:The SNPs of the CDH17 gene c.2216 A>C might be clinically important in the prognosis of colorectal carcinoma.

Role of detection of microsatellite instability in Chinese with hereditary nonpolyposis colorectal cancer or ordinary hereditary colorectal cancer

AIM： To detect microsatellite instability （MSI） in patients with hereditary nonpolyposis colorectal cancer or ordinary hereditary colorectal cancer and to provide criteria for screening the kindreds with hereditary nonpolyposis colorectal cancer at molecular level.METHODS： MSI was detected in the specimens from 20 cases with HNPCC, 20 cases with ordinary hereditary colorectal cancer and 20 cases with sporadic colorectal cancer by means of polymerase chain reaction-single strand conformation polymorphism. RESULTS： The positive rate of MSI was 85% （17/20） in HNPCC group, 40% （8/20） in ordinary hereditary colorectal cancer group and 10% （2/20） in the sporadic colorectal cancer group respectively. The differences were significant. The mean ages of the three groups were 43.6, 52.2, and 61.8 years respectively, which increased gradually. The incidence of right hemicolon cancer was 64.7%, 37.5%, and 0% respectively, which decreased gradually and had significant difference. The expression ratio of BAT26 and BAT25 was 94.1% respectively, which was highest in the 5 gene sites studied. The incidence of poorly differentiated adenocarcinoma was 70.6% in HNPCC group among high frequency microsatellite instability （MSI-H）, which was higher than the other two groups, which had 50% and 50% respectively. CONCLUSION： The incidence of MSI-H is higher in HNPCC group. The detection of MSI is simple and economical and has high correlation with the clinicopathologic feature of HNPCC and can be used as a screening method to detect the germ line mutation of the mismatch repair gene.

Noise exposure induced cochlear hair cell death pathways in guinea pig

Objective To understand the mechanism of noise exposure induced outer hair cells(OHCs) death pathways. Methods Thirty two guinea pigs were used in this study. The animals were either exposed for 4 h/day to broadband noise at 122 dB SPL (A-weighted) for 2 consecutive days or perfused with MNNG. After auditory test, the cochleae of animals were dissected. Propidium iodide (PI), a DNA intercalating fluorescent probe, was used to trace morphological changes in OHC nuclei. F-actin staining was used to determine missing OHCs. Caspase-3 was detected in living organ of Corti whole mounts using the fluorescent probe. The single strand DNA (ssDNA) in apoptotic OHCs in guinea pigs and apoptosis inducing factor (AIF) in hair cells in guinea pigs were examined by immunohistology method. Whole mounts of organ of Corti were prepared. Morphological and fluorescent changes were examined under a confocal microscope. Results (1) Both apoptotic and necrotic hair cells appeared following noise exposure. (2) Noise exposure induced single strand DNA in apoptotic OHCs but not in the normal OHCs. (3) Either after noise exposure or after MNNG perfusion, apoptotic OHCs were featured by nuclear condensation or fragmentation with caspase-3 activation, whereas necrotic OHCs were characterized by nuclear swelling without caspase-3 activation. (4) In normal organ of Corti, AIF was located in the mitochondria areas. After noise exposure, AIF was translocated from mitochondria in apoptotic and necrotic OHCs. Conclusion These findings indicate that noise exposure damages DNA in the OHC, which triggers action of Caspase-3. Subsequently, AIF is translocated to the nucleus, leading to DNA damage and OHCs death.

Boosting genome editing in plants with single transcript unit surrogate reporter systems

CRISPR-Cas-based genome editing holds immense promise for advancing plant genomics and crop enhancement.However,the challenge of low editing activity complicates the identification of editing events.In this study,we introduce multiple single transcript unit surrogate reporter(STU-SR)systems to enhance the selection of genome-edited plants.These systems use the same single guide RNAs designed for endogenous genes to edit reporter genes,establishing a direct link between reporter gene editing activity and that of endogenous genes.Various strategies are used to restore functional reporter genes after genome editing,including efficient single-strand annealing(SSA)for homologous recombination in STUSR-SSA systems.STU-SR-base editor systems leverage base editing to reinstate the start codon,enriching C-to-T and A-to-G base editing events.Our results showcase the effectiveness of these STU-SR systems in enhancing genome editing events in the monocot rice,encompassing Cas9 nuclease-based targeted mutagenesis,cytosine base editing,and adenine base editing.The systems exhibit compatibility with Cas9 variants,such as the PAM-less SpRY,and are shown to boost genome editing in Brassica oleracea,a dicot vegetable crop.In summary,we have developed highly efficient and versatile STU-SR systems for enrichment of genome-edited plants.

Study of ss-DNA Adsorption and Nano-mechanical Properties on Mica Substrate with Surface Forces Apparatus

Many DNA?based devices need to build stable and controllable DNA films on surfaces. However, the most com?monly used method of film characterization, namely, the probe?like microscopes which may destroy the sample and substrate. Surface Forces Apparatus(SFA) technique, specializing in surface interaction studies, is introduced to investigate the e ects of DNA concentration on the formation of single?stranded DNA(ss?DNA) film. The result demonstrates that 50 ng/μL is the lowest concentration that ss?DNA construct a dense layer on mica. Besides, it is also indicated that at di erent DNA concentrations, ss?DNA exhibit diverse morphology: lying flat on surface at 50 ng/μL while forming bilayer or cross?link at 100 ng/μL, and these ss?DNA structures are stable enough due to the repeatabil?ity even under the load of 15 mN/m. At the same time, an obvious adhesion force is measured:/m at 100 ng/μL, respectively, which is attributed to the ion?correlation e ect. M-6.5 mN/m at 50 ng/μL and-5.3 mNoreover, the atomic force microscopy(AFM) images reveal the entire surface is covered with wormlike ss?DNA and the measured surface roughness(1.8±0.2 nm) also matches well with the film thickness by SFA. The desorption behaviors of ss?DNA layer from mica surface occur by adding sodium salt into gap bu er, which is mainly ascribed to the decreased ion?ion cor?relation force. This paper employing SFA and AFM techniques to characterize the DNA film with flexibility and stable mechanical ability achieved by ion bridging method, is helpful to fabricate the DNA?based devices in nanoscale.

应用聚合酶链反应-单链构象多态性技术分析结节性硬化症基因突变

目的 检测结节性硬化症基因外显子突变。方法 应用聚合酶链反应 单链构象多态性 (PCR SSCP)技术分析 2 8例结节性硬化症患者TSC1和TSC2基因外显子突变情况。结果 2 8例中有 4例发生TSC1基因突变 ,其中包括 1个无义突变、2个错义突变和 1个移码突变 ;有 13例患者发生TSC2基因突变 ,其中包括 2个无义突变、2个移码突变、1个缺失和 8个错义突变。有 2例患者在TSC1及TSC2基因上均发生突变 ,另有 2例患者在TSC2核苷位 1960上出现同样突变。TSC1突变患者和TSC2突变患者之间临床表现无明显差异。结论 突变广泛分布于TSC1及TSC2基因各个外显子上 ,没有集聚于某个外显子 。

Drosophila RecQ5 is required for efficient SSA repair and suppression of LOH in vivo

RecQ5 in mammalian cells has been suggested to suppress inappropriate homologous recombination.However,the specific pathway(s)in which it is involved and the underlining mechanism(s)remain poorly understood.We took advantage of genetic tools in Drosophila to investigate how Drosophila RecQ5(dRecQ5)functions in vivo in homologous recombination-mediated double strand break(DSB)repair.We generated null alleles of dRecQ5 using the targeted recombination technique.The mutant animals are homozygous viable,but with growth retardation during development.The mutants are sensitive to both exogenous DSB-inducing treatment,such as gamma-irradiation,and endogenously induced double strand breaks(DSBs)by I-Sce I endonuclease.In the absence of dRecQ5,single strand annealing(SSA)-mediated DSB repair is compromised with compensatory increases in either inter-homologous gene conversion,or non-homologous end joining(NHEJ)when inter-chromosomal homologous sequence is unavailable.Loss of function of dRecQ5 also leads to genome instability in loss of heterozygosity(LOH)assays.Together,our data demonstrate that dRecQ5 functions in SSA-mediated DSB repair to achieve its full efficiency and in suppression of LOH in Drosophila.

p53 mutation, EGFR gene amplification and loss of heterozygosity on chromosome 10, 17?p in human gliomas

To further illustrate the roles of p53 gene, epidermal growth factor receptor (EGFR) gene and loss of heterozygosity (LOH) on chromosome 10 and 17?p in human glioma progression Methods p53 mutations were scanned in 50 gliomas with various malignant grades using the polymerase chain reaction single strand conformation polymorphism (PCR SSCP) assay, and were confirmed by direct sequencing LOH for chromosome 10, 17?p and amplification of the EGFR gene were also assessed using Southern blot analysis Results p53 mutations were found in 9 of 17 high grade astrocytomas (53%), 1 of 15 low grade astrocytomas (7%), and the only subject of eppendymoblastoma but in none of the 10 medulloblastomas and 7 eppendymomas The majority of gliomas (38/50) analyzed here retained both 17?p alleles The frequency of p53 mutations was 13% in this group of tumors and increased to 50% (6/12) in tumors with one 17?p allele ( P <0 025) LOH on chromosome 10 was found in 35% (6/17) of high grade astrocytomas, in 10% (1/10) of medulloblastomas, but in 0% of low grade gliomas EGFR gene amplification was found in 9 high grade gliomas, 60% (6/9) of which also presented LOH for chromosome 10 Conclusions These results indicate that p53 inactivation is a common genetic event in astrocytoma progression that may be more strongly associated with the progression of astrocytomas than with their origin Absence of p53 mutations in 50% of the tumors with one 17?p allele suggests that a tumor suppressor gene other than p53 may be located on chromosome 17?p and involved in progression to malignancy of some gliomas The loss of alleles on chromosome 10 and the amplification of the EGFR gene appear to be restricted to high grade tumors, suggesting that these events may be related to tumor progression rather than initiation