Tailoring structural and optical properties of ZnO system through elemental Mn Doping through First-principles calculations

In this study, band structure and optical properties of Manganese (Mn) doped ZnO are investigated adopting first-principles study calculations. It is observed that, by addition of Mn in ZnO crystal, the electrical properties like conductivity and dielectric function of material have been improved. The elastic constants for the elements are also calculated which shows that the element is stable after addition of dopant. The computational study is done on CASTEP and Material Studio. The ZnO system is simulated and atoms of Mn has been added replacing Zn atoms. The properties that studied are band structure and optics including conductivity, reflectivity, dielectric function, absorption and refractive index. Furthermore, this study also includes calculation of Elastic constants, XRD Spectra, Phonon dispersion and Temperature profile of doped ZnO systems. The computational study produced promising results and experimental approach can be adopted to reinforce the outcomes of this study.</p

Novel endosomolytic compounds enable highly potent delivery of antisense oligonucleotides

The therapeutic and research potentials of oligonucleotides (ONs) have been hampered in part by their inability to effectively escape endosomal compartments to reach their cytosolic and nuclear targets. Splice-switching ONs (SSOs) can be used with endosomolytic small molecule compounds to increase functional delivery. So far, development of these compounds has been hindered by a lack of high-resolution methods that can correlate SSO trafficking with SSO activity. Here we present in-depth characterization of two novel endosomolytic compounds by using a combination of microscopic and functional assays with high spatiotemporal resolution. This system allows the visualization of SSO trafficking, evaluation of endosomal membrane rupture, and quantitates SSO functional activity on a protein level in the presence of endosomolytic compounds. We confirm that the leakage of SSO into the cytosol occurs in parallel with the physical engorgement of LAMP1-positive late endosomes and lysosomes. We conclude that the new compounds interfere with SSO trafficking to the LAMP1-positive endosomal compartments while inducing endosomal membrane rupture and concurrent ON escape into the cytosol. The efficacy of these compounds advocates their use as novel, potent, and quick-acting transfection reagents for antisense ONs

The viral protein corona directs viral pathogenesis and amyloid aggregation

Artificial nanoparticles accumulate a protein corona layer in biological fluids, which significantly influences their bioactivity. As nanosized obligate intracellular parasites, viruses share many biophysical properties with artificial nanoparticles in extracellular environments and here we show that respiratory syncytial virus (RSV) and herpes simplex virus type 1 (HSV-1) accumulate a rich and distinctive protein corona in different biological fluids. Moreover, we show that corona pre-coating differentially affects viral infectivity and immune cell activation. In addition, we demonstrate that viruses bind amyloidogenic peptides in their corona and catalyze amyloid formation via surface-assisted heterogeneous nucleation. Importantly, we show that HSV-1 catalyzes the aggregation of the amyloid beta-peptide (A beta(42)), a major constituent of amyloid plaques in Alzheimer's disease, in vitro and in animal models. Our results highlight the viral protein corona as an acquired structural layer that is critical for viral-host interactions and illustrate a mechanistic convergence between viral and amyloid pathologies.Peer reviewe

Pharmaceutical insights into improving oligonucleotide delivery and efficacy

The power of gene therapy lies in their capacity to target a disease on a genetic level. Nucleic acid containing therapeutics can be utilized to treat, diagnose or prevent a possible disease or condition. However, the successful delivery of such molecules constitutes a major limitation. The field of gene therapy is revolving around finding the ideal balance between efficacious and safe delivery of gene therapeutics and oligonucleotides (ONs). Different chemistries and delivery vectors were investigated for such purpose. In paper I, the synergism between low generation peptide dendrimers and lipids demonstrated high transfection efficiency of splice-switching ONs compared to peptide dendrimers alone. 20 peptide dendrimers/lipid mixtures were tested to deliver a splice-switching ON in a HeLa Luc/705 reporter cell line (a cervical cancer cell line). Under serum-free conditions optimal complexes displayed 30-fold higher correction levels compared to untreated cells. However, their activity was abolished under serum condition. Surprisingly, sucrose addition to the formulation completely restored complexes efficacy in the presence of serum. Optimal sucrose-containing formulation altered the biodistribution profile more towards the liver and less towards the kidneys following systemic delivery in mice. The in vitro and in vivo results obtained with sucrose addition demonstrated the potential positive effect of excipient addition on the formulation efficacy and biodistribution behavior. Paper II was based on our findings in paper I aiming to optimize the transfection efficacy under serum conditions. We screened different sugar and polymer excipients with the optimal peptide dendrimer and buffer from our previous study. Using this approach, splicing correction levels increased to 95-fold higher in a HeLa Luc/705 reporter cell line compared to untreated cells. We also noticed the enhancement effects of excipients in other reporter cell lines derived from osteosarcoma, hepatocyte-carcinoma and neuroblastoma cells. Cytotoxicity assays highlighted the safety of the formulations which encouraged us to check their biodistribution in mice. We noticed that biodistribution profiles of the ON were influenced by the type of formulations suggesting that excipients can preferentially direct ON therapeutics to certain organs. Despite the success of the approaches used in papers I and II, the presence of many components in the formulation can make them difficult to reproduce. We therefore synthesized another class of peptide dendrimers with lipophilic components (fatty acids or hydrophobic amino acids) conjugated to their core. In paper III, we screened different lipophilic dendrimers and evaluated the efficacy of the transfection of splice-switching ONs in reporter cell models. Factors as composition, stereochemistry, and formulation buffer were investigated. We noticed that 3rd generation peptide dendrimers were more efficient than 2nd generation peptide dendrimers. The effect of stereochemistry was more evident in 3rd generation peptide dendrimers favoring D-amino acid composed dendrimers. Variable results were obtained in different cell lines and levels of correction with the optimal formulation reached 93-fold over untreated in HeLa Luc/705 cells. Toxicity levels were minimal, yet Polyvinyl alcohol 18 (PVA18) addition increased the toxicity of the best candidates. The potential efficacy of the lipophilic peptide dendrimers is inspiring for future optimization and evaluation of different conjugates and /or cargos. Paper IV addressed the possibility to apply a new strategy in which ONs are targeting the DNA structure (anti-gene ONs). Such strategy was tested in a Huntington disease (HD) cell model. HD is a neurodegenerative disorder caused by CAG•CTG repeat expansion at exon 1 of Huntingtin gene (HTT) leading to formation of mutant HTT (mHTT) transcript and protein. The utilized anti-gene ONs were composed of Locked nucleic acids (LNA)/DNA mixmer and are complementary to the template strand of HTT. We were able to down-regulate HTT mRNA using various anti-gene ONs lengths, LNA content, and fatty acid modifications. We observed that high LNA content was necessary for activity. However, ON length and phosphorothioate (PS) content had minimal impact. Additionally, ON containing palmitoyl-modified LNA were superior to conventional LNA/DNA mixmers in serum starvation conditions. Finally, it was apparent that the number and positioning of palmitoyl-modified LNA nucleotides greatly affected activity. Overall, our screening highlighted optimal designs of anti-gene ONs targeting HTT DNA. Further investigation may include other chemistries and other classes of trinucleotide repeat (TNR) disorders

Oligonucleotide–Palladacycle Conjugates as Splice-Correcting Agents

2&#8217;-O-Methylribo phosphorothioate oligonucleotides incorporating cyclopalladated benzylamine conjugate groups at their 5&#8217;-termini have been prepared and their ability to hybridize with a designated target sequence was assessed by conventional UV melting experiments. The oligonucleotides were further examined in splice-switching experiments in human cervical cancer (HeLa Luc/705), human liver (HuH7_705), and human osteosarcoma (U-2 OS_705) reporter cell lines. Melting temperatures of duplexes formed by the modified oligonucleotides were approximately 5 &#176;C lower than melting temperatures of the respective unmodified duplexes. The cyclopalladated oligonucleotides functioned as splice-correcting agents in the HeLa Luc/705 cell line somewhat more efficiently than their unmodified counterparts. Furthermore, the introduction of this chemical modification did not induce toxicity in cells. These results demonstrate the feasibility of using covalently metalated oligonucleotides as therapeutic agents

Optimization of culture conditions for biodiesel production from Egyptian isolate Penicillium commune NRC2016

Abstract Background Biodiesel is a type of renewable energy, an ideal substitute for petroleum diesel fuel. The present study concerns about optimization of culture conditions for biodiesel production by Penicillium commune NRC2016. Results The maximum lipid production from P. commune NRC2016 was investigated using basal liquid medium with initial pH 7.0, incubation temperature 20 °C, and after 5 days of incubation time at static condition. Six types of agro-industrial by-products (broken rice, rice straw, wheat bran, corn stalk, sweet sorghum, and bagasse) were separately used as components of semi-solid fermentation media. The highest lipid accumulation was recorded with sweet sorghum 99.1 mg/g as compared with the other by-products. Biodiesel obtained from P. commune NRC2016 was blended “B5” and the physical properties were determined and found to be as follows: density 0.8 g/ml, viscosity 2.1 mm2/s, flash point 77.0 °C, cloud point − 1.5 °C, iodine value 42.3 g I2/100 g, acid value 2.1 mg/g, pour point − 1.7 °C, and cetane number 47.8 min. Conclusions This work revealed the optimization of culture conditions for biodiesel production from Egyptian fungal strain P. commune NRC2016

Design, construction and field testing of a manually feeding semiautomatic sugarcane dud chipper

Abstract Sugarcane is the main sugar crop, and sugar is an important agricultural product in Egypt. There are many problems with the technology used in the current planting method of sugarcane, which has a great impact on the planting quality of sugarcane, which have a series of problems, such as low cutting efficiency and poor quality. Therefore, the aim of the current study was to design, construct, and field testing of a semiautomatic sugarcane bud chipper assisted with pivot knives for cutting sugarcane buds and germinating them in plastic trays inside a greenhouse until they reached an average length of 35 cm, and then planting them in the field. In the field tests five cutting speeds (35, 40, 45, 50, and 56 rpm. (Revolution Per minute), three cutting knives (1.5, 2.0, and 2.5 mm) were used for cutting sugarcane stalks with four different diameters (1.32, 1.82, 2.43, and 2.68 cm). The obtained results showed that the values of the damage index and invisible losses were within acceptable limits (ranging between − 1.0 and 0.0) for all the variables under the test. Still, the lowest damage index and invisible losses were recorded with the buds that were cut with a knife of 1.5 mm thickness and cutting speeds less than 50 rpm. The skipping rate increases with the increase in cutting speed and stalk diameter, ranging between 0.0 to 13%. The maximum machine productivity was 110 Buds per minute at a cutting speed of 35 rpm and stalk diameter of 1.32 cm. The paper's findings have important application values for promoting the designing and development of sugarcane bud chipper and sugarcane planting technology in the future

Sugar and Polymer Excipients Enhance Uptake and Splice-Switching Activity of Peptide-Dendrimer/Lipid/Oligonucleotide Formulations

Non-viral transfection vectors are commonly used for oligonucleotide (ON) delivery but face many challenges before reaching the desired compartments inside cells. With the support of additional compounds, it might be more feasible for a vector to endure the barriers and achieve efficient delivery. In this report, we screened 18 different excipients and evaluated their effect on the performance of peptide dendrimer/lipid vector to deliver single-stranded, splice-switching ONs under serum conditions. Transfection efficiency was monitored in four different reporter cell lines by measuring splice-switching activity on RNA and protein levels. All reporter cell lines used had a mutated human &beta;-globin intron 2 sequence interrupting the luciferase gene, which led to an aberrant splicing of luciferase pre-mRNA and subsidence of luciferase protein translation. In the HeLa Luc/705 reporter cell line (a cervical cancer cell line), the lead excipients (Polyvinyl derivatives) potentiated the splice-switching activity up to 95-fold, compared to untreated cells with no detected cytotoxicity. Physical characterization revealed that lead excipients decreased the particle size and the zeta potential of the formulations. In vivo biodistribution studies emphasized the influence of formulations as well as the type of excipients on biodistribution profiles of the ON. Subsequently, we suggest that the highlighted impact of tested excipients would potentially assist in formulation development to deliver ON therapeutics in pre-clinical and clinical settings

Lipophilic Peptide Dendrimers for Delivery of Splice-Switching Oligonucleotides

Non-viral transfection reagents are continuously being developed in attempt to replace viral vectors. Among those non-viral vectors, dendrimers have gained increasing interest due to their unique molecular structure and multivalency. However, more improvements are still needed to achieve higher efficacy and lower toxicity. In this study, we have examined 18 peptide dendrimers conjugated to lipophilic moieties, such as fatty acids or hydrophobic amino acids, that were previously explored for siRNA. Reporter cells were employed to investigate the transfection of single strand splice-switching oligonucleotides (ONs) using these peptide dendrimers. Luciferase level changes reflecting efficiency varied with amino acid composition, stereochemistry, and complexation media used. 3rd generation peptide dendrimers with D-amino acid configuration were superior to L-form. Lead formulations with 3rd generation, D-amino acid peptide dendrimers increased the correction level of the delivered ON up to 93-fold over untreated HeLa Luc/705 cells with minimal toxicity. To stabilize the formed complexes, Polyvinyl alcohol 18 (PVA18) polymer was added. Although PVA18 addition increased activity, toxicity when using our best candidates G 2,3KL-(Leu)4 (D) and G 2,3KL-diPalmitamide (D) was observed. Our findings demonstrate the potential of lipid-conjugated, D-amino acid-containing peptide dendrimers to be utilized as an effective and safe delivery vector for splice-switching ONs