Delivery of DNA into Human Cells by Functionalized Lignin Nanoparticles

Lignin is an aromatic plant cell wall polymer that is generated in large quantities as a low-value by-product by the pulp and paper industry and by biorefineries that produce renewable fuels and chemicals from plant biomass. Lignin structure varies among plant species and as a function of the method used for its extraction from plant biomass. We first explored the impact of this variation on the physico-chemical properties of lignin nanoparticles (LNPs) produced via a solvent exchange procedure and then examined whether LNPs produced from industrial sources of lignin could be used as delivery vehicles for DNA. Spherical LNPs were formed from birch and wheat BioLignin™ and from poplar thioglycolic acid lignin after dissolving the lignin in tetrahydrofuran (THF) and dialyzing it against water. Dynamic light scattering indicated that the diameter of these LNPs was dependent on the initial concentration of the lignin, while electrophoretic light scattering indicated that the LNPs had a negative zeta potential, which became less negative as the diameter increased. The dynamics of LNP formation as a function of the initial lignin concentration varied as a function of the source of the lignin, as did the absolute value of the zeta potential. After coating the LNPs with cationic poly-l-lysine, an electrophoretic mobility shift assay indicated that DNA could adsorb to LNPs. Upon transfection of human A549 lung carcinoma basal epithelial cells with functionalized LNPs carrying plasmid DNA encoding the enhanced green fluorescent protein (eGFP), green foci were observed under the microscope, and the presence of eGFP in the transfected cells was confirmed by ELISA. The low cytotoxicity of these LNPs and the ability to tailor diameter and zeta potential make these LNPs of interest for future gene therapy applications.

GCM2 Variants in Familial and Multiglandular Primary Hyperparathyroidism

Context Multiglandular and familial parathyroid disease constitute important fractions of primary hyperparathyroidism (PHPT). Germline missense variants of GCM2, a regulator of parathyroid development, were observed in familial isolated hyperparathyroidism (FIHP) and sporadic PHPT. However, as these previously-reported GCM2 variants occur at relatively high frequencies in the population, understanding their potential clinical utility will require both additional penetrance data and functional evidence relevant to tumorigenicity. Objective Determine the frequency of GCM2 variants-of-interest among patients with sporadic multigland or familial parathyroid disease, and assess their penetrance. Design and Patients DNA encoding PHPT-associated GCM2 germline-variants were PCR-amplified and sequenced from 107 patients with either sporadic multigland or suspected/confirmed familial parathyroid tumors. Results GCM2 variants were observed in 9 of 107 cases (8.4%): Y282D in 4 patients (6.3%) with sporadic multigland disease; Y394S in 2 patients (11.1%) with familial PHPT and three (4.8%) with sporadic multigland disease. Compared with the general population, Y282D was enriched 5.9-fold in multigland disease but its penetrance was very low (0.02%). Y394S was enriched 79-fold in sporadic multigland disease and 93-fold in familial PHPT, but its penetrance was low (1.33%, 1.04% respectively). Conclusions Observed in vitro activating GCM2 variant alleles are significantly overrepresented in PHPT patients with multiglandular or familial disease compared with the general population, yet penetrance values are very low i.e. most individuals with these variants in the population have a very low risk of developing PHPT. The potential clinical utility of detecting these GCM2 variants requires further investigation, including assessing their possible role as pathogenic/low-penetrance alleles.

Sus sp. DNA ENCODING cyt b GENE DETECTION TEST ON SOFT GEL CANDY SAMPLES USING PCR METHOD

Softgel candy is soft-textured confectionery processed by the addition of several components such as gum, pectin, starch and gelatin, to obtain a supple product and packed after aging treatment first. Gelatin is one of the main components in the manufacture of soft candy derived from the hydrolysis of collagen connective tissue and animal bone that serves as the nature of gelling agents, stabilizers or emulsifiers. However, the gelatin used in products not yet labeled halal Indonesian Council of Ulama (MUI) is particularly vulnerable to pork gelatin, since pork gelatin is cheaper than cattle. The purpose of this study was to test the contaminants of pig DNA on 17 samples of soft candles not labeled halal MUI. This research used Polymerase Chain Reaction (PCR) method. Seventeen samples were isolated by DNA, then spectrophotometry was performed, followed by PCR. The PCR product is run electrophoresis. Visualize the DNA with a UV gel documentation. Primer used is primer gene encoding cyt b DNA pork. Results showed that 17 samples were negative contaminants, while the positive control of pork showed a DNA band of 149 bp. This shows that Softgel Candy 17 samples do not contain pork gelatin.

A New Conservative Hyperchaotic System-Based Image Symmetric Encryption Scheme with DNA Coding

In the current paper, a new conservative hyperchaotic system is proposed. We make a quantitative analysis of the complexity of the conservative hyperchaotic system from several different aspects, such as phase diagrams, bifurcation diagrams, Lyapunov exponents, and Kaplan–Yorke dimension. The complexity of chaotic time series is tested with various measurement tools, such as the scale index, the multiscale sample entropy and approximate entropy, TESTU01, and NIST test. In addition, a novel hyperchao-based image encryption scheme with dynamic DNA coding is proposed. The encryption algorithm consists of line-by-line scrambling and diffusion of DNA encoding characters. The dynamic DNA coding mechanism is introduced by using the chaotic sequence. The generation of the intermediate secret keys is related to the sum of the image DNA code, and the ciphertext feedback mechanism of the DNA encoding image is introduced in the diffusion procedure. Simulation experiments and various security analyses show that this algorithm has a good effect on encryption, high time efficiency, and can effectively resist brute force attacks, statistical attacks, chosen-plaintext attacks, and differential attacks.

Evidence for the Involvement of Pleckstrin Homology Domain-Containing Proteins in the Transport of Enterocin DD14 (EntDD14); a Leaderless Two-Peptide Bacteriocin

Bacteriocins synthesis is initiated from an inactive precursor, which is composed of an N-terminal leader peptide attached to a C-terminal pro-peptide. However, leaderless bacteriocins (LLB) do not possess this N-terminal leader peptide nor undergo post-translational modifications. These atypical bacteriocins are observed to be immediately active after their translation in the cytoplasm. However, although considered to be simple, the biosynthetic pathway of LLB remains to be fully understood. Enterocin DD14 (EntDD14) is a two-peptide LLB produced by Enterococcus faecalis 14, which is a strain isolated from meconium. In silico analysis of DNA encoding EntDD14 located a cluster of 10 genes ddABCDEFGHIJ, where ddE and ddF encode the peculiar DdE and DdF proteins, carrying pleckstrin homology (PH) domains. These modules are quite common in Eucarya proteins and are known to be involved in intracellular signaling or cytoskeleton organization. To elucidate their role within the EntDD14 genetic determinants, we constructed deletion mutants of the ddE and ddF genes. As a result, the mutants were unable to export EntDD14 outside of the cytoplasm even though there was a clear expression of structural genes ddAB encoding EntDD14, and genes ddHIJ encoding an ABC transporter. Importantly, in these mutant strains (ΔddE and ΔddF), EntDD14 was detected by mass spectrometry in the intracellular soluble fraction exerting, upon its accumulation, a toxic effect on the producing strain as revealed by cell-counting and confocal microscopy analysis. Taken together, these results clearly indicate that PH domain-containing proteins, such as DdE and DdF, are involved in the transport of the leaderless two-peptide EntDD14.

From sequence to yield: deep learning for protein production systems

Recent progress in laboratory automation has enabled rapid and large-scale characterization of strains engineered to express heterologous proteins, paving the way for the use of machine learning to optimize production phenotypes. The ability to predict protein expression from DNA sequence promises to deliver large efficiency gains and reduced costs for strain design. Yet it remains unclear which models are best suited for this task or what is the size of training data required for accurate prediction. Here we trained and compared thousands of predictive models of protein expression from sequence, using a large screen of Escherichia coli strains with varying levels of GFP expression. We consider models of increasing complexity, from linear regressors to convolutional neural networks, trained on datasets of variable size and sequence diversity. Our results highlight trade-offs between prediction accuracy, data diversity, and DNA encoding methods. We provide robust evidence that deep neural networks can outperform classic models with the same amount of training data, achieving prediction accuracy over 80% when trained on approximately 2,000 sequences. Using techniques from Explainable AI, we show that deep learning models capture sequence elements that are known to correlate with expression, such as the stability of mRNA secondary structure. Our results lay the groundwork for the more widespread adoption of deep learning for strain engineering across the biotechnology sector.

Bacterial LomR Induces the Vibriophage VP882 VqmA-Directed Quorum-Sensing Lysogeny-Lysis Transition

The bacterial cell-cell communication process called quorum sensing enables groups of bacteria to synchronously alter behavior in response to changes in cell population density. Quorum sensing relies on the production, release, accumulation, and detection of extracellular signal molecules called autoinducers. Here, we investigate a mechanism employed by a vibriophage to surveil host quorum sensing and tune its lysogeny-lysis decision to host cell density. The phage possesses a gene called vqmAPhage encoding a quorum-sensing receptor homologous to vibrio VqmA. Both VqmA receptors can detect the host bacteria-produced autoinducer called DPO. DPO-bound VqmAPhage launches the phage lysis process. We discover that the bacterial host produces an inducer of the VqmAPhage-directed quorum-sensing lysogeny-lysis transition. Production of the inducer appears to be widespread among bacteria. A screen of the Escherichia coli Keio collection for mutants impaired for inducer production revealed lomR, located in a prophage, and encoding a poorly understood protein. In the E. coli screening strain, lomR is interrupted by DNA encoding an insertion element. The 3’ domain of this LomR protein is sufficient to induce VqmAPhage-directed lysis. Alanine-scanning mutagenesis showed that substitution at either of two key residues abrogates inducer activity. Full-length LomR is similar to the outer membrane porin OmpX in E. coli and Vibrio parahaemolyticus O3:K6, and OmpT in Vibrio cholerae C6706, and indeed, OmpX and OmpT can induce VqmAPhage-directed activity. Possibly, development of the LomR, OmpX, or OmpT proteins as tools to direct phage lysis of host cells could be used to control bacteria in medical or industrial settings.

Delivery of dCas9 CRISPR System Into the Hard Transfection Cells by Magnetofection Approach

Background: The CRISPR-Cas9 system, a powerful tool, has revolutionized genome engineering in eukaryotic cells and living organisms. However, this approach poses unique concerns and limitations when used by conventional transfection methods, including limited packaging size and low delivery efficiency. Here, we aim at assessing the transfection efficiency of DNA encoding for the CRISPR-Cas9 system by PEI coated Magnetic NanoParticle (MNPs) to improve the delivery of CRISPR/Cas9 constructs into eukaryotic cells. Results: Superparamagnetic iron oxide nanoparticles (SPIONs) coated with polyethylenimine (PEI) and then complexed with pCXLE-dCas9VPH-T2A-GFP-shP53 plasmid DNA. We used HEK-293 (human embryonic kidney) and Human foreskin fibroblasts (HFF) cells to express GFP after transfection to evaluate delivery efficiency with MNPs and Lipofection methods. PEI-coated nanoparticles with magnetic iron oxide core were synthesized by co-precipitation technique resulting in an average size of ~ 20 nm in diameter. Characterization of Magnetic Nano Particle (MNPs) revealed that particles have narrow size distribution sufficient colloidal stability. The result showed that the magnetofection method with an efficiency around 85.7% for HEK-293 and 28.2% for HFF. Also, transfection efficiency by lipofection method was 83.2% and 7.89% for HEK-293 and HFF respectively. Conclusion: The magnetofection was revealed to be more efficient than classic Lipofectamine transfection as measured by GFP expression. We show that PEI-MNPs enable effective delivery and improved safety of plasmids encoding CRISPR/Cas9 into eukaryote cells.