Stabilization of RNA through absorption by functionalized mesoporous silicate nanospheres

Characterization of the Molecular Events Underlying the Establishment of Axillary Meristem Region in Pepper

Plant architecture is a major motif of plant diversity, and shoot branching patterns primarily determine the aerial architecture of plants. In this study, we identified an inbred pepper line with fewer lateral branches, 20C1734, which was free of lateral branches at the middle and upper nodes of the main stem with smooth and flat leaf axils. Successive leaf axil sections confirmed that in normal pepper plants, for either node n, Pn (Primordium n) < 1 cm and Pn+1 < 1 cm were the critical periods between the identification of axillary meristems and the establishment of the region, whereas Pn+3 < 1 cm was fully developed and formed a completely new organ. In 20C1734, the normal axillary meristematic tissue region establishment and meristematic cell identity confirmation could not be performed on the axils without axillary buds. Comparative transcriptome analysis revealed that "auxin-activated signaling pathway", "response to auxin", "response to abscisic acid", "auxin biosynthetic process", and the biosynthesis of the terms/pathways, such as "secondary metabolites", were differentially enriched in different types of leaf axils at critical periods of axillary meristem development. The accuracy of RNA-seq was verified using RT-PCR for some genes in the pathway. Several differentially expressed genes (DEGs) related to endogenous phytohormones were targeted, including several genes of the PINs family. The endogenous hormone assay showed extremely high levels of IAA and ABA in leaf axils without axillary buds. ABA content in particular was unusually high. At the same time, there is no regular change in IAA level in this type of leaf axils (normal leaf axils will be accompanied by AM formation and IAA content will be low). Based on this, we speculated that the contents of endogenous hormones IAA and ABA in 20C1734 plant increased sharply, which led to the abnormal expression of genes in related pathways, which affected the formation of Ams in leaf axils in the middle and late vegetative growth period, and finally, nodes without axillary buds and side branches appeared.

Biocompatible FePO4 Nanoparticles: Drug Delivery, RNA Stabilization, and Functional Activity

FePO4 NPs are of special interest in food fortification and biomedical imaging because of their biocompatibility, high bioavailability, magnetic property, and superior sensory performance that do not cause adverse organoleptic effects. These characteristics are desirable in drug delivery as well. Here, we explored the FePO4 nanoparticles as a delivery vehicle for the anticancer drug, doxorubicin, with an optimum drug loading of 26.81% ± 1.0%. This loading further enforces the formation of Fe3+ doxorubicin complex resulting in the formation of FePO4-DOX nanoparticles. FePO4-DOX nanoparticles showed a good size homogeneity and concentration-dependent biocompatibility, with over 70% biocompatibility up to 80 µg/mL concentration. Importantly, cytotoxicity analysis showed that Fe3+ complexation with DOX in FePO4-DOX NPs enhanced the cytotoxicity by around 10 times than free DOX and improved the selectivity toward cancer cells. Furthermore, FePO4 NPs temperature-stabilize RNA and support mRNA translation activity showing promises for RNA stabilizing agents. The results show the biocompatibility of iron-based inorganic nanoparticles, their drug and RNA loading, stabilization, and delivery activity with potential ramifications for food fortification and drug/RNA delivery.

SNAPflex: a paper-and-plastic device for instrument-free RNA and DNA extraction from whole blood

Nucleic acid amplification tests (NAATs), which amplify and detect pathogen nucleic acids, are vital methods to diagnose diseases, particularly in cases where patients exhibit low levels of infection. For many blood-borne pathogens such as HIV or Plasmodium falciparum, it is necessary to first extract pathogen RNA or DNA from patient blood prior to NAAT analysis. Traditional nucleic acid extraction methods are expensive, resource-intensive and are often difficult to deploy to resource-limited areas where many blood-borne infections are widespread. Here, we describe a portable, paper-and-plastic device, called SNAPflex, for instrument-free nucleic acid extraction from whole blood, which builds upon our previous work for RNA extraction using a pressure-driven extraction system. SNAPflex shows improved HIV RNA extraction from simulated patient samples compared to traditional extraction methods as well as long-term stability of extracted RNA without the need for cold storage. We further demonstrated successful extraction and recovery of P. falciparum DNA from cultured parasites in whole blood. SNAPflex was designed to be easily manufacturable and deployable to resource-limited settings.

Quantities of Intra- and Extracellular DNA Reveal Information About Activity and Physiological State of Methanogenic Archaea

Although being a common aim of many microbial ecology studies, measuring individual physiological conditions of a microbial group or species within a complex consortium is still a challenge. Here, we propose a novel approach that is based on the quantification of sequentially extracted extracellular (exDNA) and intracellular DNA (iDNA) and reveals information about cell lysis and activity of methanogenic archaea within a biogas-producing microbial community. We monitored the methane production rates of differently treated batch anaerobic cultures and compared the concentrations of the alpha subunit of the methyl coenzyme M reductase gene of methanogenic archaea in extracellular and intracellular DNA fractions and in the classically extracted total DNA pool. Our results showed that this fine-tuned DNA approach coupled with the interpretation of the ratio between free exDNA and iDNA considerably improved microbial activity tracking compared to the classical extraction/quantification of total DNA. Additionally, it allowed to identify and quantify methanogenic populations that are inactive and those that are strongly influenced by cell lysis. We argue that despite the need of further studies, this method represents a novel approach to gain specific physiological information from a complex environmental sample and holds the potential to be applied to other microbes of interest.

Adsorption of annealed branched polymers on curved surfaces

The behavior of annealed branched polymers near adsorbing surfaces plays a fundamental role in many biological and industrial processes. Most importantly single stranded RNA in solution tends to fold up and self-bind to form a highly branched structure. Using a mean field theory, we both perturbatively and numerically examine the adsorption of branched polymers on surfaces of several different geometries in a good solvent. Independent of the geometry of the wall, we observe that as branching density increases, surface tension decreases. However, we find a coupling between the branching density and curvature in that a further lowering of surface tension occurs when the wall curves towards the polymer, but the amount of lowering of surface tension decreases when the wall curves away from the polymer. We find that for branched polymers confined into spherical cavities, most of branch-points are located in the vicinity of the interior wall and the surface tension is minimized for a critical cavity radius. For branch polymers next to sinusoidal surfaces, we find that branch-points accumulate at the valleys while end-points on the peaks.

Mesoporous silica nanoparticles with redox-responsive surface linkers for charge-reversible loading and release of short oligonucleotides

Aimed at high loading and controlled release of oligonucleotides with short sequences of base-pairs, a novel series of mesoporous silica nanoparticles with three different pore sizes (3.5-5.0 nm) but the same cleavable surface linkers (MSN-Linker-Cys) were synthesized. The small particle size (∼70 nm) with radially aligned pore structure and the well-defined surface linkers terminated with amino groups led to unprecedentedly high adsorption capacities of a model oligo DNA (21 bp in length) into MSN-Linker-Cys particles, where MSN with a medium pore size of 4.5 nm exhibited the highest adsorption capacity (190 mg g(-1)). The electrostatic attraction forces between amino groups on the surfaces and phosphate groups of DNA led to N/P ratios less than 1 in the particles, and retained the loaded DNA molecules inside the particles albeit with some degree of premature release observed. Triggered by the presence of reducing agents mimicking those found inside cells, the disulfide bond was shown to be cleaved in the organic linkers, generating a thiol group terminated surface. As a consequence, the most efficient release of DNA was found for MSN-Linker-Cys at neutral pH. A sustained responsive release with lower premature release ratio was obtained after a PEG polymer was conjugated to the free amines on the particle surface post adsorption of DNA. This nanocarrier design was based on the understanding and tuning of the molecular interactions between oligonucleotides and the cationic linkers. Thus, it is expected to lay the possibility for the development of innovative and strategic approaches for advancing related gene delivery technology.