Qingdai Liu

Food storage material silver nanoparticles interfere with DNA replication fidelity and bind with DNA

Nanosilver is increasingly used in the food industry and biomedical applications. A lot of studies have been done to investigate the potential toxicity of nanosilver. But information on whether or how nanosilver particles bring changes in genetic materials remains scant. In this study, the replication fidelity of the rpsL gene was quantified when nanosilver particles were present in polymerase chain reactions (PCRs) or cell cultures of E. coli transformed with the wild-type rpsL gene. Three types of nanosilver (silver nanopowder, SN; silver-copper nanopowder, SCN; and colloidal silver, CS) were tested. The results showed that the replication fidelity of the rpsL gene was differentially compromised by all three kinds of nanosilver particle compared with that without nanosilver. This assay could be expanded and applied to any other materials to preliminarily assess their potential long-term toxicity as a food additive or biomedical reagent. Moreover, we found that nanosilver materials bind with genomic DNA under atomic force microscopy, and this might be an explanation for the compromised DNA replication fidelity.

DNA binding and aggregation by carbon nanoparticles

Significant environmental and health risks due to the increasing applications of engineered nanoparticles in medical and industrial activities have been concerned by many communities. The interactions between nanomaterials and genomes have been poorly studied so far. This study examined interactions of DNA with carbon nanoparticles (CNP) using atomic force microscopy (AFM). We experimentally assessed how CNP affect DNA molecule and bacterial growth of Escherichia coli. We found that CNP were bound to the DNA molecules during the DNA replication in vivo. The results revealed that the interaction of DNA with CNP resulted in DNA molecule binding and aggregation both in vivo and in vitro in a dose-dependent manner, and consequently inhabiting the E. coli growth. While this was a preliminary study, our results showed that this nanoparticle may have a significant impact on genomic activities.

In vitro functional characterization of the Na+/H+ antiporters in Corynebacterium glutamicum

Corynebacterium glutamicum, typically used as industrial workhorse for amino acid production, is a moderately salt-alkali-tolerant microorganism with optimal growth at pH 7-9. However, little is known about the mechanisms of salt-alkali tolerance in C. glutamicum. Here, the catalytic capacity of three putative Na(+)/H(+) antiporters from C. glutamicum (designated as Cg-Mrp1, Cg-Mrp2 and Cg-NhaP) were characterized in an antiporter-deficient Escherichia coli KNabc strain. Only Cg-Mrp1 was able to effectively complement the Na(+)-sensitive of E. coli KNabc. Cg-Mrp1 exhibited obvious Na(+)(Li(+))/H(+) antiport activities with low apparent Km values of 1.08 mM and 1.41 mM for Na(+) and Li(+), respectively. The Na(+)/H(+) antiport activity of Cg-Mrp1 was optimal in the alkaline pH range. All three antiporters showed detectable K(+)/H(+) antiport activitiy. Cg-NhaP also exhibited Na(+)(Li(+),Rb(+))/H(+) antiport activities but at lower levels of activity. Interestingly, overexpression of Cg-Mrp2 exhibited clear Na(+)(K(+))/H(+) antiport activities. These results suggest that C. glutamicum Na(+)(K(+))/H(+) antiporters may have overlapping roles in coping with salt-alkali and perhaps high-osmolarity stress.

Influences of gold and silver nanoparticles in loop-mediated isothermal amplification reactions

Loop-mediated isothermal amplification (LAMP) performed with protein DNA polymerase Bst and DNA chains was influenced by nanoparticles in different ways. The effects of different concentrations of gold nanoparticles (AuNPs) with diameters 10 and 20 nm and silver nanoparticles (AgNPs) 1–10 nm in diameter on the amplification of the pR72H gene of Vibrio parahaemolyticus were investigated. AuNPs with a diameter of 10 nm in 0.6–60 nM concentration accelerated initiation of the LAMP reaction, 3 nM AuNPs reduced the reaction time by about 10 min, whereas 20 nm AuNPs did not, although neither size increased the yield after 60 min. AgNPs inhibited the LAMP reaction both in speed and yield at concentrations of 0.6–60 nM; the yield of amplification was reduced by 50% and 80% for 12 and 60 nM, respectively, after reaction for 1 h. This indicated that strong bactericidal effects of silver are also observed in its nanoparticles. The molecular mechanism of AuNPs and AgNPs in LAMP needs to be explored further, although their size-related electronic, magnetic and optical properties, as well as their ability to affect protein denaturation, or hydrophilic/hydrophobic effects may be involved.

Improvement of rolling circle amplification efficiency with gold nanoparticles

Abstract Rolling circle amplification of plasmid has become increasingly popular as a technique to clone and amplify DNA sequences. We have found that 15 μg mL−1 gold nanoparticles could increase the rolling circle amplification yield and shorten the reaction time from 12 to 8 hours. Although the mutation frequencies were calculated as 2.43‰, the rolling circle amplification fidelity was sufficient for DNA manipulation. Furthermore, gold nanoparticles were found to bind specifically to rolling circle amplification products.

Carbon nanotubes altering specificity of repeated PCR and DNA integrity properties.

We have investigated the impact of aqueous suspension of single-walled carbon nanotubes (SWCNTs) and multi-walled carbon nanotubes (MWCNTs) on performance of repeated PCR, and discussed their thermal impact on DNA characteristics. Both SWCNTs and MWCNTs are found significantly enhancing the specificity of the repeated PCR and capable of inhibition of long DNA thermal degradation. SWCNTs performed a better specificity in repeated PCR than MWCNTs did. MWCNT-DNA binding was more favorable for protecting long DNA from thermal degradation than SWCNT-DNA binding. The results suggested that CNTs are very useful in repeated PCR working on limited amount of DNA resources.

Carbon Nanopowder Binds with DNA and May Induce DNA Aggregation

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.

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

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.

Analysis of the Chlorophyll a Fluorescence Transient of Spirodela polyrhiza by JIP-Test

Chlorophyll a fluorescence has been used as non-invasive probe for stress physiology and environmental investigation. The changes of photosynthetic apparatus in Spirodela polyrrhiza was studied by using chlorophyll a fluorescence technique and JIP-test. During L-serine-induced senescence, photosynthetic performance index (PI), reaction center (RC) decreased gradually and reached zero on the 8th day of cultivation. However, the oxygen evolving complex (OEC) remained nearly 60% and the capacity of Hill reaction remained about 43%. JIP-test also offers a platform to analyze the energy flux in fronds.

Measuring the Effect of Chromate Pollution on Duckweed Half-Fronds by Chlorophyll Fluorescence

Accumulated chromate from the medium was responsible for the inhibition of the photosystem II. In this study, we focused on the alteration of the photosynthetic apparatus through analysis of the Chlorophyll a fluorescence of duckweed half-fronds. Chromate induced the K step on the fluorescence transient in 6-BA treated half-fronds. Chromate affected several targets of photosynthetic II apparatus. The oxygen evolving complex (OEC) was the more highly sensitive to chromate than the reaction center (RC) in 6-BA treated half-fronds. We showed that 6-BA treated half-fronds would be taken as a potential useful system to estimate the effect of water pollution.