Two real-time quantitative PCR detection systems that contained DNA Green saturated fluorescent dye for detection of Salmonella Enteritidis and Ly Green saturated fluorescent dye for detection of Salmonella spp. were constructed. Furthermore, the specificity of the amplification system increased with the addition of graphene quantum dots. The R2 values of the standard curves were 0.999 (S. Enteritidis) and 0.998 (Salmonella spp.), respectively. The sensitivities of the two amplification systems were evaluated based on three aspects: genomic DNA (1.36 fg/μL, 1.36 fg/μL); bacterial cell without enrichment (2.49 CFU/mL, 2.49 CFU/mL); plasmid containing Gene ID:1828390769 (11.6 copies/μL) and plasmid containing Gene ID:3335471 (1.08 copies/μL). Detection results of fruits and vegetables artificially contaminated with Salmonella showed that the traditional culture method exhibits a lower detection rate than the molecular detection method, and the culture time of the Selective Luria-Bertani broth (SLB) was short. The detection rate was increased compared with that of the Buffered Peptone Water-Selenite Cystine broth (BPW-SC). The two detection systems exhibit high sensitivity and specificity and are suitable for detecting Salmonella in ready-to-eat fruits and vegetables.

Development of a rapid detection method for real-time fluorescent quantitative PCR of Salmonella spp. and Salmonella Enteritidis in ready-to-eat fruits and vegetables

Hot start (HS) PCR is an excellent alternative for high-throughput real time PCR due to its ability to prevent nonspecific amplification at low temperature. Development of a cost-effective and simple HS PCR technique to guarantee high-throughput PCR specificity and consistency still remains a great challenge. In this study, we systematically investigated the HS characteristics of QDs triggered in real time PCR with EvaGreen and SYBR Green I dyes by the analysis of amplification curves, standard curves and melting curves. Two different kinds of DNA polymerases, Pfu and Taq, were employed. Here we showed that high specificity and efficiency of real time PCR were obtained in a plasmid DNA and an error-prone two-round PCR assay using QD-based HS PCR, even after an hour preincubation at 50 °C before real time PCR. Moreover, the results obtained by QD-based HS PCR were comparable to a commercial Taq antibody DNA polymerase. However, no obvious HS effect of QDs was found in real time PCR using Taq DNA polymerase. The findings of this study demonstrated that a cost-effective high-throughput real time PCR based on QD triggered HS PCR could be established with high consistency, sensitivity and accuracy.

Development of a high-throughput real time PCR based on a hot-start alternative for Pfu mediated by quantum dots.

Quantum dots (QDs) are of great interest due to their unique chemical and physical properties. Recently, a hot start (HS) polymerase chain reaction (PCR) amplification performance based on QDs with a high-fidelity Pfu DNA polymerase has been reported. However, whether QDs can trigger HS effects with other high-fidelity or conventional DNA polymerases is yet to be understood. In the present study, we studied the QD-triggered HS effects with four high-fidelity and three conventional DNA polymerases, and the HS effect comparisons among them were also made. It was found that QDs could trigger a distinct HS PCR amplification performance with all the four tested high-fidelity DNA polymerases, and specific target DNA could be well amplified even if the PCR mixture was pre-incubated for 2 h at 50°C. On the contrary, the HS effects were not prominent with all the three conventional Taq DNA polymerases. Specifically, the fidelity of Pfu is not sacrificed in the presence of QDs, even after a 1 h pre-incubation at 50°C before PCR. Furthermore, the electrophoresis results preliminarily demonstrated that QDs prefer to adsorb high-fidelity polymerases rather than conventional ones, which might result in the QD-triggered HS effects on PCR performance by using high-fidelity DNA polymerases.

/pdf/a-hot-start-alternative-for-high-fidelity-dna-polymerase-7uwkzg3mna.pdf

A hot start alternative for high-fidelity DNA polymerase amplification mediated by quantum dots

We review and summarize the progress of studies of LEAFY genes Sequence com- parative analysis of the orthologs of genes isolated from a wide variety of plant species showed high similarity in coding sequence at the nucleotide and amino acid levels but different copy numbers, especially in diploid angiosperms Orthologous genes, however, have variant ex- pression patterns in different plants Phylogenetic analysis of the predicted protein sequences of the orthologs supported the currently accepted theory of phylogenetic partnerships of plant species the information summarized here is helpful not only for better understanding the mechanisms of plant flowering but also for further promoting studies of the evolution of flowering plants

Studies of {\sl LEAFY} homologue genes in higher plants

Using sol-gel method,the regenerated SF(silk fibroin)/nano-TiO_2 composite films were prepared,the structures and properties of these films were characterized through AFM,FT-IR and two-dimensional correlation FT-IR spectroscopyThe experimental results show that,the nano-TiO_2 particles are well dispersed in the silk fibroin filmsIt is believed that the intermolecular hydrogen bonding between the nano particles and the silk fibroin induces the rearrangement of the silk fibroin molecularThe conformation of the silk fibroin is transited,and the sequence of the transition is in the order of random coil structure to βsheet structure and then α-helix structure

Effect of Nano-TiO_2 on the Conformation Transition of Silk Fibroin Films

Quantitative real-time PCR (qPCR), as an important quantitative technique for nucleic acids, has been widely used in many fields including clinical diagnosis, molecular biology, and cancer research. However, non-specific amplification products are still a frequent problem in qPCR. In this study, we investigated the effects of QDs on real-time amplification based on either SYBR Green I or EvaGreen. It was found that QDs could raise the amplification sensitivity and thus enhance the efficiency using SYBR Green I detection system. In the case of EvaGreen detection systems, addition of QDs also led to a better correlation coefficient than without QDs. EvaGreen-based system gave sharper peaks for melting curves than SYBR Green I. The experiments indicated that the polymerase activity could be partially blocked by QDs at the pre-PCR temperatures, resulting in the improvement of PCR specificity. These results indicated that CdTe QDs could be used as a descent qPCR enhancer. Good amplification fidelity in QDs-facilitated qPCR was also a plus that has not been reported elsewhere.

CdTe quantum dots enhance feasibility of EvaGreen-based real-time PCR with decent amplification fidelity.

The interaction between nanomaterials and genomes is getting more and more attention. Such studies are getting involved into several fields: environment safety, food safety, nanobiotechnology and drug development. Direct interaction between nanoparticles and DNA in vitro has been reported in several studies, but data for in vivo binding between genomic DNA and nanoparticles are rare. In this study, we presented that carbon nanopowder (CNP) is able to bind with DNA both in vitro and in vivo. Interestingly, CNP binds to DNA with a relatively high density and may induce DNA aggregation.

Carbon Nanopowder Binds with DNA and May Induce DNA Aggregation

/pdf/correlation-analysis-between-english-chinese-translation-68es874xan.pdf

Correlation Analysis between English-Chinese Translation-Based Writing Error Types and Language Gene Polymorphisms for Chinese Graduate Students

Local gene network pattern (LGNP) is a useful tool to display complex relationship between multiple genes. A diabetes-specific local gene network (LGN) was constructed with 29 genes (including 9 diabetes susceptibility genes and 20 extra genes to join them) that participate in 30 biological pathways. Further analysis indicated diabetes-specific LGN has close relations with carbohydrate metabolism, lipid metabolism, amino acid metabolism, cofactor and vitamin metabolism. Especially, molecular links demonstrated diabetes was associated with alanine and nicotinamide metabolism, consistent with previous reports. Preliminary six microarray data revealed that some key nutrient metabolism related genes were de-regulated in insulin treated muscles, providing clues how to transform diabetes-specific-LGNP with personalized nutrient formula in future.

Molecular Association between Diabetes-Specific Local Gene Network and Nutrient Metabolism Modules

LEAFY(LFY) gene plays a critical role on the formation of floral meristem. A fragment of LFY homologous gene about 900 bp was amplified by polymerase chain reaction (PCR) using a pair of degenerate primers and the genomic DNA of Albizzia julibrssin Durazz. The fragment of LFY homologous gene is named Albizzia julibrssin Durazz LFY. The sequence analysis indicates that there is an intron of 496 bp, and two exons, one being 123 bp and the other 284 bp, in the fragment, and the exons encode 120 amino acids. It is also found that the amino acids homology reaches 90%~97% of the other LFY homologous genes, and especially for Acacia mangium, Acacia auriculiformis, the homology reaches the highest level (97%). The result suggests that Albizzia julibrssin Durazz LFY gene is the highly conserved as other LFY homologous genes.

Notice of Retraction Cloning and Analysis of LEAFY Homologous Gene from Albizzia julibrssin Durazz

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