Extension of the crRNA enhances Cpf1 gene editing in vitro and in vivo.

Engineering of the Cpf1 crRNA has the potential to enhance its gene editing efficiency and non-viral delivery to cells. Here, we demonstrate that extending the length of its crRNA at the 5 end can enhance the gene editing efficiency of Cpf1 both in cells and in vivo. Extending the 5 end of the crRNA enhances the gene editing efficiency of the Cpf1 RNP to induce non-homologous end-joining and homology-directed repair using electroporation in cells. Additionally, chemical modifications on the extended 5 end of the crRNA result in enhanced serum stability. Also, extending the 5 end of the crRNA by 59 nucleotides increases the delivery efficiency of Cpf1 RNP in cells and in vivo cationic delivery vehicles including polymer nanoparticle. Thus, 5 extension and chemical modification of the Cpf1 crRNA is an effective method for enhancing the gene editing efficiency of Cpf1 and its delivery in vivo

The Computational Techniques Developed to Analyze DNA Gel Images

The analysis of gel electrophoresis images is very crucial for molecular biologists to comprehend and interpret their experimental results. Thus, enhancing current mathematical methods and developing new accurate ones is very important and challenging task for bioinformaticians. For example, enhancing the commonly used mathematical method in gel analysis known as "Fitting method estimation" and proposing a new efficient method entitled "Ruler estimation" for preprocessing a given image and detecting lanes and bands automatically. Both mathematical methods implemented in our newly developed software. Three mathematical models namely, linear, quadratic and cubic fitting are tested for the accuracy of detecting the bands and lanes in the gel image to determine the best fitting model. A friendly user interface is developed for this new program using MATLB GUI to extract useful bimolecular information accurately and automatically. The new software has the ability to manually add or delete any band(s) and estimate the size of any unknown band(s) on the gel. Moreover, the similarity and (dis)similarity between lanes "samples" are estimated based on comparing the numbers and sizes of bands to generate a phylogram tree

Characterization of the aerosol produced by infrared femtosecond laser ablation of polyacrylamide gels for the sensitive inductively coupled plasma mass spectrometry detection of selenoproteins

A 2D high repetition rate femtosecondlaserablation strategy (2-mm wide lane) previously developed for the detection of selenoproteins in gel electrophoresis by inductively coupled plasma mass spectrometry was found to increase signal sensitivity by a factor of 40 compared to conventional nanosecond ablation (0.12-mm wide lane) [G. Ballihaut, F. Claverie, C. Pécheyran, S. Mounicou, R. Grimaud and R. Lobinski, Sensitive Detection of Selenoproteins in Gel Electrophoresis by High Repetition Rate FemtosecondLaserAblation-Inductively Coupled Plasma Mass Spectrometry, Anal. Chem. 79 (2007) 6874–6880]. Such improvement couldn't be explained solely by the difference of amount of material ablated, and then, was attributed to the aerosol properties. In order to validate this hypothesis, the characterization of the aerosolproduced by nanosecond and high repetition rate femtosecondlaserablation of polyacrylamidegels was investigated. Our 2D high repetition rate femtosecondlaserablation strategy of 2-mm wide lane was found to produce aerosols of similar particle size distribution compared to nanosecond laserablation of 0.12-mm wide lane, with 38% mass of particles < 1 µm. However, at high repetition rate, when the ablated surface was reduced, the particle size distribution was shifted toward thinner particle diameter (up to 77% for a 0.12-mm wide lane at 285 µm depth). Meanwhile, scanning electron microscopy was employed to visualize the morphology of the aerosol. In the case of larger ablation, the fine particles ejected from the sample were found to form agglomerates due to higher ablation rate and then higher collision probability. Additionally, investigations of the plasma temperature changes during the ablation demonstrated that the introduction of such amount of polyacrylamidegel particles had very limited impact on the ICP source (ΔT~ 25 ± 5 K). This suggests that the cohesion forces between the thin particles composing these large aggregates were weak enough to have negligible impact on the ICPMS detection

Chloroquine-enhanced gene delivery mediated by carbon nanotubes

Polyethyleneimine-coated double-walled carbon nanotubes (DWCNTs) were used for dual gene and drug delivery, after loading the DWCNTs with the drug chloroquine, a lysosomotropic compound that is able to promote escape from the lysosomal compartment. Different forms of functionalization of the DWCNTs were examined in order to optimize this system. They included the testing of different treatments on DWCNTs to optimize the loading and delivery of chloroquine and the selection of a cationic polymer for coating the DWCNTs for optimum DNA binding and delivery. An acid oxidation treatment of DWCNTs was selected for optimum chloroquine loading together with polyethyleneimine as optimum cationic coating agent for plasmid DNA binding. Optimization of the conditions for choroquine-enhanced gene delivery were developed using luciferase expression as a model system. We have demonstrated that chloroquine-loading increases the ability of polyethyleneimine-coated DWCNTs to deliver functional nucleic acid to human cells. Cell viability tests have shown no cytotoxicity of the functionalized DWCNTs at the concentrations needed for optimum gene delivery. These results support the potential applications of this methodology in gene therapy

The influence of natural pulmonary surfactant on the efficacy of siRNA-loaded dextran nanogels

Aim: Topical administration of siRNA nanocarriers is a promising approach in the treatment of pulmonary disorders. Pulmonary surfactant, covering the entire alveolar surface of mammalian lungs, will be one of the first interfaces that siRNA nanocarriers encounter upon inhalation therapy. Therefore, it is of outstanding importance to evaluate the impact of pulmonary surfactant on the performance of siRNA nanocarriers. Materials & methods: The effect of natural lung-derived surfactants on the siRNA delivery capacity of dextran nanogels (DEX-NGs) was evaluated in vitro using flow cytometry and confocal microscopy. Results: Although the interaction with pulmonary surfactant decreases the cellular internalization of siRNA-loaded DEX-NGs significantly, the gene silencing potential of siRNA-loaded DEX-NGs was maintained. On the other hand, cationic lipid-based siRNA nanocarriers (Lipofectamine (TM) RNAiMAX) were incompatible with pulmonary surfactants. Conclusion: Our data suggest that pulmonary surfactant can enhance the intracellular siRNA delivery by DEX-NGs, thereby possibly providing new therapeutic opportunities

Microchip electrophoresis bioanalytical applications

Microchip electrophoresis (MCE) is a novel analytical technique resulting from miniaturization of capillary electrophoresis (CE) to a planar microfabricated separation device. The consequences of the transfer of CE to MCE in terms of benefits and drawbacks have been identified and commented. The strategies developed to overcome the unfavourable features of the chip with respect to the capillary are briefly described. A method for simultaneous separation of catecholamines and their cationic metabolites has been developed on the microchip. The addition of three modifiers was required to resolve all analytes. The sensitivity of on-chip amperometric detection has been improved by employing an enzyme-catalyzed reaction on the amperometric electrode, as well as by using a carbon nanotube-modified electrode. The developed analytical methodology has been successfully applied for a direct on-chip determination of catecholamines and their metabolites in a mouse brain homogenate. The feasibility of performing affinity measurements as well as isoelectric focusing on the microchip has been demonstrated and available applications of these two electrophoretic modes on a chip have been reviewed. A commercial Shimadzu microchip station has for the first time been applied for high-throughput microchip isoelectric focusing of therapeutic proteins and obtained results have been compared to conventional capillary isoelectric focusing

An Automated Dna Strands Detection System Featuring 32-Bit Arm7tdmi Microcontroller And Vga-Cmos Digital Image Sensor.

Genetic DNA recognition is a routine experiment for detecting the origin of the species. Electrophoresis is one of the processes for such detection which has been used extensively. Pengecaman genetik DNA ialah eksperimen rutin untuk mengesan asal usul sesuatu spesis. Proses electrophoresis ialah salah satu proses pengecaman yang digunakan secara meluas

Computer simulation of pulsed field gel runs allows the quantitation of radiation-induced double-strand breaks in yeast

A procedure for the quantification of double-strand breaks in yeast is presented that utilizes pulsed field gel electrophoresis (PFGE) and a comparison of the observed DNA mass distribution in the gel lanes with calculated distributions. Calculation of profiles is performed as follows. If double-strand breaks are produced by sparsely ionizing radiation, one can assume that they are distributed randomly in the genome, and the resulting DNA mass distribution in molecular length can be predicted by means of a random breakage model. The input data for the computation of molecular length profiles are the breakage frequency per unit length, , as adjustable parameter, and the molecular lengths of the intact chromosomes. The obtained DNA mass distributions in molecular length must then be transformed into distributions of DNA mass in migration distance. This requires a calibration of molecular length vs. migration distance that is specific for the gel lane in question. The computed profiles are then folded with a Lorentz distribution with adjusted spread parameter to account for and broadening. The DNA profiles are calculated for different breakage frequencies and for different values of , and the parameters resulting in the best fit of the calculated to the observed profile are determined

Diffusiophoretic manipulation of particles in a drop deposited on a hydrogel

We report an experimental study on the manipulation of colloidal particles in a drop sitting on a hydrogel. The manipulation is achieved by diffusiophoresis, which describes a directed motion of particles induced by solute gradients. By letting the solute concentrations for the drop and the hydrogel be different, we control the motion of particles in a stable suspension, which is otherwise difficult to achieve. We show that diffusiophoresis can cause the particles to move either toward or away from the liquid-air interface depending on the direction of the solute gradient and the surface charge of the particles. We measure the particle adsorption experimentally and rationalize the results with a one-dimensional numerical model. We show that diffusiophoretic motion is significant at the lengthscale of a drop deposited on a hydrogel, which suggests a simple method for the deposition of particles on hydrogels