Identification of Traditional Chinese Medicine Seahorses Using Graphene Oxide-based Fluorescent Sensing Technology / 中国实验方剂学杂志

ObjectiveTo establish a method for seahorse identification based on graphene oxide fluorescence sensing technology， and to provide a new research idea for identification of traditional Chinese medicine. MethodThe fluorophore FAM was labeled at the 5' end of the specificity upstream primer Ja-F of Hippocampus japonicus as the nucleic acid probe FAM-ssDNA （single strand DNA）. The recognition site of RNA polymerase Ⅱ was added to its specific downstream primer Ja-R as Ja-R1. The seahorse samples were amplified with Ja-F/Ja-R1 primers， and the ssDNA of H. japonicus was obtained by reverse transcription of the amplification products using vitro transcription method. The 20 μL nucleic acid probe FAM-ssDNA （500 nmol·L-1） was incubated at 90 ℃ for 5 min， and was gradually cooled to room temperature. Different volume of graphene oxide solution （100 mg·L-1） and Tris hydroxymethyl amino methane HCl （Tris-HCl） buffer （50 mmol·L-1） were added into each probe solution to make a final reaction volume of 1 mL. The fluorescence intensity of each sample was measured after mixing and placing different times at room temperature away from the light. So that the most appropriate graphene oxide concentration and reaction time were screened for constructing the best nucleic acid probe-graphene oxide biosensor. Adding probe complementary sequence FAM-ssDNA-match solution into the nucleic acid probe-graphene oxide solution， the fluorescence intensity of the reaction mixture was measured after being placed different times at room temperature. Therefore， the optimal reaction time of fluorescence recovery was screened and the feasibility of the sensor was tested. The sensitivity was detected via adding ddH2O as the blank control and different concentration H. japonicus ssDNA into each nucleic acid probe-graphene oxide solution， respectively. Finally， the commercial hippocampal were identified using the optimal experimental condition， and the feasibility of this method for the identification of Chinese medicinal materials was verified. ResultThe fluorescence of 1 mL reaction mixture including 10 nmol·L-1 nucleic acid probe FAM-ssDNA and 12 mg·L-1 go solution for 20 min at room temperature away from the light could be completely quenched. Feasibility test of the biosensor showed that when probe complementary sequence FAM-ssDNA-match solution （final concentration 90 nmol·L-1） was added to the biosensor solution and reacted 1 h reaction at room temperature， the fluorescence signal was significantly enhanced. Sensitivity test showed that the minimum concentration of ssDNA detected by this method was about 10 mg·L-1. This method was used to detect commercial seahorses， and only H. japonicus samples had obvious fluorescence signal. ConclusionThe graphene oxide-based fluorescent sensing technology could be used for zoological origin survey of commercial hippocampus.

Investigation of Single-stranded Deoxyribonucleic Acid Translocation Through α-Hemolysin Nanopore with Ionic Liquid Supporting Electrolytes / 分析化学

Due to the difference in spatial configuration and charge of the bases in a DNA molecule, characteristic translocation current pulses through a single nanopore could be obtained. This could become the basis of DNA sequencing method. However, due to the fast translocation speed (sub-micro seconds) and the small current change (about pA), it is still a challenge to obtain the accurate molecular substructure with present electronic techniques. In this work, in order to control the translocation behavior of ssDNA, two kinds of ionic liquids with high viscosity and conductivity were introduced to establish a viscosity gradient with the α-hemolysin single nanopore interface and the acidity of the solution was optimized. The trans chamber contained pure BmimPF6 and the cis chamber contained 1 mol/ L BmimCl and 10 mmol/ L Tris-HCl ( pH 5. 5 ). Preliminary experiment results under this electrolyte configuration showed that poly ( dC) 15 , poly ( dC) 15 , poly(dC) 30 and poly(dC) 50 exhibited obvious long duration pulses with high current suppression ratio. The blocking depth reached more than 95％ of long blocking events. The duration time of long blocking events prolonged to tens or hundreds of milliseconds. Meanwhile, the peak-peak of baseline noise was reduced by about 30％ .

Study on Interaction of Protamine and Single-stranded DNA by Current Pulses Through Single Nanopore / 分析化学

Single nanopore current pulse method is a new, rapid and simple detection method, which is promising for single-molecule DNA sequencing and bio-sensing. Due to the short duration and the low current amplitude of the pulses caused by molecular translocation under normal conditions, pulse detection system with fast response and high sensitivity is required. In this work, based on a lab-established pulse detection system, the effect of protamine in the regulation of single-stranded (ssDNA) current pulses with α-hemolysin (α-HL) single nanopore interface was investigated. Experimental results showed that the pulses positive charged protamine and negative ssDNA probes were both well observed with the established system, and both the pulse amplitude and duration of ssDNA were increased as a result of interaction with protamine. This study provides a way to improve the resolving power of current pulses based on molecular interactions.

Possible Role of Single Stranded DNA Binding Protein 3 on Skin Hydration by Regulating Epidermal Differentiation

BACKGROUND: Skin hydration is a common problem both in elderly and young people as dry skin may cause irritation, dermatological disorders, and wrinkles. While both genetic and environmental factors seem to influence skin hydration, thorough genetic studies on skin hydration have not yet been conducted. OBJECTIVE: We used a genome-wide association study (GWAS) to explore the genetic elements underlying skin hydration by regulating epidermal differentiation and skin barrier function. METHODS: A GWAS was conducted to investigate the genetic factors influencing skin hydration in 100 Korean females along with molecular studies of genes in human epidermal keratinocytes for functional study in vitro. RESULTS: Among several single nucleotide polymorphisms identified in GWAS, we focused on Single Stranded DNA Binding Protein 3 (SSBP3) which is associated with DNA replication and DNA damage repair. To better understand the role of SSBP3 in skin cells, we introduced a calcium-induced differentiation keratinocyte culture system model and found that SSBP3 was upregulated in keratinocytes in a differentiation dependent manner. When SSBP3 was overexpressed using a recombinant adenovirus, the expression of differentiation-related genes such as loricrin and involucrin was markedly increased. CONCLUSION: Taken together, our results suggest that genetic variants in the intronic region of SSBP3 could be determinants in skin hydration of Korean females. SSBP3 represents a new candidate gene to evaluate the molecular basis of the hydration ability in individuals.

Identification of circo-like virus-Brazil genomic sequences in raw sewage from the metropolitan area of São Paulo: evidence of circulation two and three years after the first detection

BACKGROUND Two novel viruses named circo-like virus-Brazil (CLV-BR) hs1 and hs2 were previously discovered in a Brazilian human fecal sample through metagenomics. CLV-BR hs1 and hs2 possess a small circular DNA genome encoding a replication initiator protein (Rep), and the two genomes exhibit 92% nucleotide identity with each other. Phylogenetic analysis based on the Rep protein showed that CLV-BRs do not cluster with circoviruses, nanoviruses, geminiviruses or cycloviruses. OBJECTIVE The aim of this study was to search for CLV-BR genomes in sewage and reclaimed water samples from the metropolitan area of São Paulo, Brazil, to verify whether the first detection of these viruses was an isolated finding. METHODS Sewage and reclaimed water samples collected concomitantly during the years 2005-2006 were purified and concentrated using methodologies designed for the study of viruses. A total of 177 treated reclaimed water samples were grouped into five pools, as were 177 treated raw sewage samples. Nucleic acid extraction, polymerase chain reaction (PCR) amplification and Sanger sequencing were then performed.e FINDINGS CLV-BR genomes were detected in two pools of sewage samples, p6 and p9. Approximately 28% and 51% of the CLV-BR genome was amplified from p6 and p9, respectively, including 76% of the Rep gene. The detected genomes are most likely related to CLV-BR hs1. Comparative analysis showed several synonymous substitutions within Rep-encoding sequences, suggesting purifying selection for this gene, as has been observed for other eukaryotic circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses. MAIN CONCLUSION The results therefore indicated that CLV-BR has continued to circulate in Brazil two and three years after first being detected.

Effects of silencing single-stranded DNA-binding protein 1 gene on proliferation and DNA repair of submandibular gland cells after irradiation / 中华放射医学与防护杂志

Objective To investigate the effects of silencing the gene of single-stranded DNA-binding protein 1 (SSB1) on proliferation and DNA repair of rat submandibular gland (SMG) cells after irradiation, and explore the relationship between SSB1 and DNA damage repair. Methods Primary rat SMG cells were obtained by mechanical-enzyme digestion and identified by immunohistochemistry. The cells were divided into three groups, including blank control, negative control and shRNA transfection group. The shRNA was transfected into cells by recombinant adenovirus vector. Real-time quantitative PCR ( qRT-PCR) was used to detect the expression of SSB1 after silencing. The cell viability was detected by CCK-8 assay. Immunofluorescence analysis was performed to observe the dynamic formation of γ-H2AX foci. Results The SMG cells were positively stained for both Pan CK and α-Amylase. The efficiency of shRNA transfection was about 90%at 72 h post-transfection. Compared with the blank control group, the expression of SSB1 was significantly decreased in the cells transfected with shRNA (t=16. 24, P<0. 05). The cell viability of shRNA transfection group without irradiation was decreased indistinctively and became lower than the blank control group significantly until 120 h(t=3. 29, P<0. 05). After radiation with 5 Gy of γ-rays, the cell viability of shRNA transfection group was lower than that of the control groups significantly (F=10. 19-30. 13, P<0. 05). Silencing the expression of SSB1 could increase the number ofγ-H2AX foci in SMG cells at different time of radiation. Conclusions After silencing of the expression of SSB1, the SMG cells could be more radiosensitive, which indicats that SSB1 may play an important role in DNA damage repair after radiation.

Effects of silencing single-stranded DNA-binding protein 1 gene on proliferation and DNA repair of submandibular gland cells after irradiation / 中华放射医学与防护杂志

Objective To investigate the effects of silencing the gene of single-stranded DNA-binding protein 1 (SSB1) on proliferation and DNA repair of rat submandibular gland (SMG) cells after irradiation, and explore the relationship between SSB1 and DNA damage repair. Methods Primary rat SMG cells were obtained by mechanical-enzyme digestion and identified by immunohistochemistry. The cells were divided into three groups, including blank control, negative control and shRNA transfection group. The shRNA was transfected into cells by recombinant adenovirus vector. Real-time quantitative PCR ( qRT-PCR) was used to detect the expression of SSB1 after silencing. The cell viability was detected by CCK-8 assay. Immunofluorescence analysis was performed to observe the dynamic formation of γ-H2AX foci. Results The SMG cells were positively stained for both Pan CK and α-Amylase. The efficiency of shRNA transfection was about 90%at 72 h post-transfection. Compared with the blank control group, the expression of SSB1 was significantly decreased in the cells transfected with shRNA (t=16. 24, P<0. 05). The cell viability of shRNA transfection group without irradiation was decreased indistinctively and became lower than the blank control group significantly until 120 h(t=3. 29, P<0. 05). After radiation with 5 Gy of γ-rays, the cell viability of shRNA transfection group was lower than that of the control groups significantly (F=10. 19-30. 13, P<0. 05). Silencing the expression of SSB1 could increase the number ofγ-H2AX foci in SMG cells at different time of radiation. Conclusions After silencing of the expression of SSB1, the SMG cells could be more radiosensitive, which indicats that SSB1 may play an important role in DNA damage repair after radiation.

DNA damage to human genetic disorders with neurodevelopmental defects

Although some mutations are beneficial and are the driving force behind evolution, it is important to maintain DNA integrity and stability because it contains genetic information. However, in the oxygen-rich environment we live in, the DNA molecule is under constant threat from endogenous or exogenous insults. DNA damage could trigger the DNA damage response (DDR), which involves DNA repair, the regulation of cell cycle checkpoints, and the induction of programmed cell death or senescence. Dysregulation of these physiological responses to DNA damage causes developmental defects, neurological defects, premature aging, infertility, immune system defects, and tumors in humans. Some human syndromes are characterized by unique neurological phenotypes including microcephaly, mental retardation, ataxia, neurodegeneration, and neuropathy, suggesting a direct link between genomic instability resulting from defective DDR and neuropathology. In this review, rare human genetic disorders related to abnormal DDR and damage repair with neural defects will be discussed.

Assessing extent of single stranded DNA damage in oral mucosal cells of patients with oral squamous cell carcinoma and its correlation with TNM staging.

Context: This study was carried out on the assumption that oral mucosal cells might show DNA damage in oral squamous cell carcinoma (OSCC). Aims: To evaluate the extent of DNA damage in oral smears of patients with OSCC and determine correlation if any of the extent of DNA damage to TNM staging of oral cancer. Settings and design: A randomized controlled study at a regional cancer centre was designed for this project. Smears were taken from lesion proper of 30 patients with OSCC and from the buccal mucosa of 30 normal healthy volunteers. Materials and methods: Collected cells were centrifuged and single-cell gel electrophoresis (SCGE) assay was performed. DNA damage was visualized under a fluorescent microscope. Statistical analysis used : Mean DNA damage levels of both the groups were measured and statistically analyzed with students' test. The extent of DNA damage was correlated with the TNM stages by employing the one way ANOVA 'F' technique. Results: High statistical significance (P < 0.0001) was found in DNA damage levels between control and study groups. A stepwise increase in DNA damage levels with high statistical significance (P < 0.005) was also found between all the TNM stages. Conclusions: Statistically significant increased DNA damage levels in OSCC patients and their correlation to clinical staging suggest that comet assay may be used effectively to assess the prognosis of OSCC.

Detection of alphaB-crystallin mRNA using Single-stranded DNA Probe in Oligodendrocytes of the Developing Chick Retina / 체질인류학회지

In situ hybridization (ISH) using single-stranded DNA probe (ssDNA probe) is a useful method for observing the specific transcripts in cells, since it is convenient to prepare probe which is specific and sensitive. In this study, ssDNA probe for detection of alphaB-crystallin (aBC) mRNA, transcript of a heat shock protein, was prepared and aBC mRNA-expressed cells were spatiotemporally observed in the retina of the developing chick embryos. Single-stranded antisense probe produced by reverse transcription and polymerase chain reaction was identified as a specific probe for aBC mRNA in comparison to negative control using sense probe and immunohistochemistry for aBC protein. In the ISH experiment, aBC mRNA was expressed only in the peripapillary glial cells which are a specific cell type located in the avian retina adjacent to the optic nerve at E12 and E14 retinas. At E16, a small number of aBC mRNA-expressed cells were identified in the nerve fiber layer (NFL) of the retina. At E18, aBC mRNA-expressed cells were observed in the ganglion cell layer (GCL) as well as the NFL. At E20, the number of aBC mRNA-expressed cells was increased in the GCL and the NFL. Based on the same localization of nkx2.2 immunoreactive cells and aBC mRNA-expressed cells, aBC mRNA-expressed cells were identified as oligodendrocytes. These results indicate that ssDNA probe for aBC mRNA detection is very useful tool for oligodendrocyte research such as distribution, migration and differentiation of the cells.

Asymmetric PCR method in generation of HBV ssDNA for pyrosequencing / 西安交通大学学报·英文版

Objective: To explore the optimal primer ratio and concentration of asymmetric polymerase chain reaction (A-PCR) in producing hepatitis B virus (HBV) single-stranded DNA (ssDNA) for pyrosequencing. Methods: A-PCR was carried out to generate HBV ssDNA with forward to reverse primers of different ratios (50:1, 100:1) and concentrations (13.0 pmol/25μL and 0.14 pmol/25μL, 19.5 pmol/25μL and 0.21 pmol/25μL), and the product yield and quality were compared respectively. Results: The forward to reverse primer ratio of 50:1 provided better yield and concentration of 19.5 pmol/25μL and 0.21 pmol//25μL generated a clearer band. Conclusion: A simple and feasible method to produce HBV ssDNA for pyrosequencing in batch is established.