Download the Free Unbound MEDLINE PubMed App to your smartphone or tablet.
Available for iPhone, iPad, iPod touch, and Android.
naked DNA [keywords]
The seven human sirtuins are a family of ubiquitously expressed and evolutionarily conserved NAD(+)-dependent deacylases/mono-ADP ribosyltransferases that regulate numerous cellular and organismal functions, including metabolism, cell cycle, and longevity. Here, we report the discovery that all seven sirtuins have broad-range antiviral properties. We demonstrate that small interfering RNA (siRNA)-mediated knockdown of individual sirtuins and drug-mediated inhibition of sirtuin enzymatic activity increase the production of virus progeny in infected human cells. This impact on virus growth is observed for both DNA and RNA viruses. Importantly, sirtuin-activating drugs inhibit the replication of diverse viruses, as we demonstrate for human cytomegalovirus, a slowly replicating DNA virus, and influenza A (H1N1) virus, an RNA virus that multiplies rapidly. Furthermore, sirtuin defense functions are evolutionarily conserved, since CobB, the sirtuin homologue in Escherichia coli, protects against bacteriophages. Altogether, our findings establish sirtuins as broad-spectrum and evolutionarily conserved components of the immune defense system, providing a framework for elucidating a new set of host cell defense mechanisms and developing sirtuin modulators with antiviral activity.We live in a sea of viruses, some of which are human pathogens. These pathogenic viruses exhibit numerous differences: DNA or RNA genomes, enveloped or naked virions, nuclear or cytoplasmic replication, diverse disease symptoms, etc. Most antiviral drugs target specific viral proteins. Consequently, they often work for only one virus, and their efficacy can be compromised by the rapid evolution of resistant variants. There is a need for the identification of host proteins with broad-spectrum antiviral functions, which provide effective targets for therapeutic treatments that limit the evolution of viral resistance. Here, we report that sirtuins present such an opportunity for the development of broad-spectrum antiviral treatments, since our findings highlight these enzymes as ancient defense factors that protect against a variety of viral pathogens.
- Comparative cytogenetic mapping of rRNA genes among naked catfishes: implications for genomic evolution in the Bagridae family. [Journal Article]
- Genet Mol Res 2014; 13(4):9533-42.
In the present study, the karyotype and chromosomal characteristics of 9 species of the Bagridae fish family were investigated using conventional Giemsa staining as well as dual-color fluorescence in situ hybridization to detect the 18S and 5S rDNA sites. In addition to describing the karyotype of several Bagridae catfishes, we established molecular cytogenetic techniques to study this group. The 9 species contained a diploid chromosomal number, varying from 50 (Pseudomystus siamensis) to 62 (Hemibagrus wyckii), while none contained heteromorphic sex chromosomes. 18S rDNA sites were detected in only 1 chromosomal pair among all species evaluated. However, 3 different patterns were observed for the distribution of the 5S rDNA: 2 sites were found in the genus Mystus and in P. siamensis, multiple sites were observed in the genus Hemibagrus, and a syntenic condition for the 18S and 5S rDNA sites was identified in H. wyckii. The extensive variation in the number and chromosomal position of rDNA clusters observed among these Bagridae species may be related to the intense evolutionary dynamics of rDNA-repeated units, which generates divergent chromosomal distribution patterns even among closely related species. In summary, the distribution of repetitive DNA sequences provided novel, useful information regarding the evolutionary relationships between Bagridae fishes.
- Highly sensitive DNA detection using cascade amplification strategy based on hybridization chain reaction and enzyme-induced metallization. [JOURNAL ARTICLE]
- Biosens Bioelectron 2014 Nov 26.:520-526.
A novel highly sensitive colorimetric assay for DNA detection using cascade amplification strategy based on hybridization chain reaction and enzyme-induced metallization was established. The DNA modified superparamagnetic beads were demonstrated to capture and enrich the target DNA in the hybridization buffer or human plasma. The hybridization chain reaction and enzyme-induced silver metallization on the gold nanoparticles were used as cascade signal amplification for the detection of target DNA. The metalization of silver on the gold nanoparticles induced a significant color change from red to yellow until black depending on the concentration of the target DNA, which could be recognized by naked eyes. This method showed a good specificity for the target DNA detection, with the capabilty to discriminate single-base-pair mismatched DNA mutation (single nucleotide polymorphism). Meanwhile, this approach exhibited an excellent anti-interference capability with the convenience of the magentic seperation and washing, which enabled its usage in complex biological systems such as human blood plasma. As an added benefit, the utilization of hybridization chain reaction and enzyme-induced metallization improved detection sensitivity down to 10pM, which is about 100-fold lower than that of traditional unamplified homogeneous assays.
- Electroporation-enhanced delivery of nucleic acid vaccines. [JOURNAL ARTICLE]
- Expert Rev Vaccines 2014 Dec 9.:1-10.
The naked delivery of nucleic acid vaccines is notoriously inefficient, and an enabling delivery technology is required to direct efficiently these constructs intracellularly. A delivery technology capable of enhancing nucleic acid uptake in both cells in tissues and in culture is electroporation (EP). EP is a physical delivery mechanism that increases the permeability of mammalian cell membranes and allows the trafficking of large macromolecules into the cell. EP has now been used extensively in the clinic and been shown to be an effective method to increase both the uptake of the construct and the breadth and magnitude of the resulting immune responses. Excitingly, 2014 saw the announcement of the first EP-enhanced DNA vaccine Phase II trial demonstrating clinical efficacy. This review seeks to introduce the reader to EP as a technology to enhance the delivery of DNA and RNA vaccines and highlight several published clinical trials using this delivery modality.
- Rapid and Sensitive PCR-Dipstick DNA Chromatography for Multiplex Analysis of the Oral Microbiota. [Journal Article]
- Biomed Res Int 2014.:180323.
A complex of species has been associated with dental caries under the ecological hypothesis. This study aimed to develop a rapid, sensitive PCR-dipstick DNA chromatography assay that could be read by eye for multiplex and semiquantitative analysis of plaque bacteria. Parallel oligonucleotides were immobilized on a dipstick strip for multiplex analysis of target DNA sequences of the caries-associated bacteria, Streptococcus mutans, Streptococcus sobrinus, Scardovia wiggsiae, Actinomyces species, and Veillonella parvula. Streptavidin-coated blue-colored latex microspheres were to generate signal. Target DNA amplicons with an oligonucleotide-tagged terminus and a biotinylated terminus were coupled with latex beads through a streptavidin-biotin interaction and then hybridized with complementary oligonucleotides on the strip. The accumulation of captured latex beads on the test and control lines produced blue bands, enabling visual detection with the naked eye. The PCR-dipstick DNA chromatography detected quantities as low as 100 pg of DNA amplicons and demonstrated 10- to 1000-fold higher sensitivity than PCR-agarose gel electrophoresis, depending on the target bacterial species. Semiquantification of bacteria was performed by obtaining a series of chromatograms using serial 10-fold dilution of PCR-amplified DNA extracted from dental plaque samples. The assay time was less than 3 h. The semiquantification procedure revealed the relative amounts of each test species in dental plaque samples, indicating that this disposable device has great potential in analysis of microbial composition in the oral cavity and intestinal tract, as well as in point-of-care diagnosis of microbiota-associated diseases.
- A framework for modelling gene regulation which accommodates non-equilibrium mechanisms. [JOURNAL ARTICLE]
- BMC Biol 2014 Dec 5; 12(1):102.
BackgroundGene regulation has, for the most part, been quantitatively analysed by assuming that regulatory mechanisms operate at thermodynamic equilibrium. This formalism was originally developed to analyse the binding and unbinding of transcription factors from naked DNA in eubacteria. Although widely used, it has made it difficult to understand the role of energy-dissipating, ¿epigenetic¿ mechanisms, such as DNA methylation, nucleosome remodelling and post-translational modification of histones and co-regulators, which act together with transcription factors to regulate gene expression in eukaryotes.ResultsHere, we introduce a graph-based framework which can accommodate non-equilibrium mechanisms. A gene-regulatory system is described as a graph, which specifies the DNA microstates (vertices), the transitions between microstates (edges) and the transition rates (edge labels). The graph yields a stochastic master equation for how microstate probabilities change over time. We show that this framework has broad scope by providing new insights into three very different ad hoc models, of steroid-hormone responsive genes, of inherently-bounded chromatin domains and of the yeast PHO5 gene. We find, moreover, surprising complexity in the regulation of PHO5, which has not yet been experimentally explored, and we show that this complexity is an inherent feature of being away from equilibrium. At equilibrium, microstate probabilities do not depend on how a microstate is reached but, away from equilibrium, each path to a microstate can contribute to its steady-state probability. Systems that are far from equilibrium thereby become history-dependent and the resulting complexity is a fundamental challenge. To begin addressing this, we introduce a graph-based concept of independence, which can be applied to sub-systems that are far from equilibrium, and prove that history-dependent complexity can be circumvented when sub-systems operate independently.ConclusionAs epigenomic data becomes increasingly available, we anticipate that gene function will come to be represented by graphs, as gene structure has been represented by sequences, and that the methods introduced here will provide a broader foundation for understanding how genes work.
- Protective immunity of grass carp immunized with DNA vaccine encoding the vp7 gene of grass carp reovirus using carbon nanotubes as a carrier molecule. [JOURNAL ARTICLE]
- Fish Shellfish Immunol 2014 Nov 25; 42(2):325-334.
The uses of single walled carbon nanotubes (SWCNTs) as carriers for DNA delivery have received considerable attention in cell studies. DNA vaccination of fish has been shown to elicit durable transgene expression, but no reports exist on intramuscular administration of SWCNTs-DNA vaccine electrostatic complexes which prepared through non-covalent conjugation. In this study, we injected grass carp intramuscularly with a plasmid vector containing a major capsid protein gene (vp7) of grass carp reovirus as a) naked pcDNA-vp7, b) SWCNTs-pcDNA-vp7, c) empty plasmid vector, or phosphate buffered saline. After intramuscular administration, the ability of the different immune treatments to induce transgene expression was analyzed. The results indicated that higher levels of transcription and expression of the vp7 gene could be detected in muscle tissues of grass carp 28 days intramuscular injection in SWCNTs-pcDNA-vp7 treatment groups compare with naked pcDNA-vp7 treatment groups. Moreover, the serum respiratory burst activity, complement activity, lysozyme activity, superoxide dismutase activity, immune-related genes, antibody levels and relative percentage survival were significantly enhanced in fish immunized with SWCNTs-pcDNA-vp7 vaccine. The data in this study suggested that SWCNTs were promising carriers for plasmid DNA vaccine and might be used to vaccinate fish by intramuscular approach.
- Applications of metal ions and liquid crystals for multiplex detection of DNA. [JOURNAL ARTICLE]
- J Colloid Interface Sci 2015 Feb 1.:149-153.
Many cations such as sodium ions have strong influence on anchoring behaviors of liquid crystals (LC). Since DNA is negatively charged and forms complex with metal ions, it is possible to form DNA/metal ions complex on surfaces to disrupt orientations of LC. This phenomenon is used to establish a principle for detecting surface immobilized DNA by using LC. In contrast, peptide nucleic acid (PNA) is electroneutral. It does not complex with metal ions or affect the orientations of LC. Therefore, PNA can be used as a probe to hybridize with specific DNA with a unique sequence, and the principle mentioned above can be used to detect the DNA target by using metal ions and LC. Based on this method, a 600bp DNA target in buffer can be detected with a limit of detection at 10fM. Unlike other fluorescence-based DNA assays, this LC-based detection method does not require labeling of DNA, and the test result can be viewed with the naked eye under a polarized microscope.
- Binding-induced collapse of DNA nano-assembly for naked-eye detection of ATP with plasmonic gold nanoparticles. [JOURNAL ARTICLE]
- Biosens Bioelectron 2014 Oct 18.:171-175.
The detection of small molecules depends heavily on complicated GC-MS (Gas chromatography-mass spectrometry), HPLC (High-performance liquid chromatography) and some other complicated instruments that are not suitable for point of care detection. Here, we have demonstrated a fast (in 10min), simple (instrument-free) and effective detection platform for small molecule-ATP. In our design, we engineered the hybridization region of aptamer and assembled it into a superstructure to avoid the exposed flexible ends. The binding of ATP triggered the collapse of the superstructures to produce single stranded DNA that can obviously tune the plasmonic coupling of unmodified gold nanoparticles (AuNPs). Compared to detection platforms based on fully hybridized aptamer double helix, the detection time was significantly decreased to 10min. The resulting color change can be recognized by naked eyes. Our detection is highly specific and selective. Furthermore, a logic gate with multiplexed detection capability for ATP and DNA were demonstrated.
- A facile label-free colorimetric aptasensor for acetamiprid based on the peroxidase-like activity of hemin-functionalized reduced graphene oxide. [JOURNAL ARTICLE]
- Biosens Bioelectron 2014 Oct 6.:39-46.
A facile aptasensor has been developed for the colorimetric detection of acetamiprid by using the hemin-functionalized reduced graphene oxide (hemin-rGO) composites. The as-prepared hemin-rGO composites possessed both the ability of rGO to physically adsorb the aptamers and the peroxidase-like activity of hemin that could catalyse 3,3,5,5-tetramethylbenzidine (TMB) in the presence of H2O2, to produce a solution with blue color. The well-dispersed hemin-rGO composites coagulated completely at the proper salt concentration; however, the coagulation of hemin-rGO was vanished when abundant aptamers were adsorbed on its surface because the attached negatively charged DNA backbone increased individual hemin-rGO electrostatic repulsion. In the detection scheme, acetamiprid with different concentrations was firstly incubated with the same amount of aptamer. The more acetamiprid in the tested solution, the less free aptamers were absorbed on the hemin-rGO surface, making the composites coagulate to a higher degree in the presence of the optimum NaCl concentration. As a consequence, the content of hemin-rGO in the supernatant was decreased after centrifugation, which catalysed oxidation of TMB in the presence of H2O2 to produce light blue color with a low absorbance. The color variation relavant to the acetamiprid concentration can be judged by the naked eyes and easily monitored by the inexpensive UV-vis spectrometer. Such designed aptasensor displayed a linear response for acetamiprid in the range from 100nM to 10μM with a detection limit of 40nM (S/N=3). This colorimetric aptasensing platform offers great advantages including the simple operation process, low-cost portable instrument, and user-friendly applications.