Defining Bacterial RNA-RNA Interactomes Using CLASH.

Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen accounting for high mortality rates among infected patients. Transcriptomic regulation by small RNAs (sRNAs) has been shown to regulate networks promoting antibiotic resistance and virulence in S. aureus. Yet, the biological role of most sRNAs during MRSA host infection remains unknown. To fill this gap, in collaboration with the lab of Jai Tree, we performed comprehensive RNA-RNA interactome analyses in MRSA using CLASH under conditions that mimic the host environment. Here we present a detailed version of this optimized CLASH (cross-linking, ligation, and sequencing of hybrids) protocol we recently developed, which has been tailored to explore the RNA interactome in S. aureus as well as other Gram-positive bacteria. Alongside, we introduce a compilation of helpful Python functions for analyzing folding energies of putative RNA-RNA interactions and streamlining sRNA and mRNA seed discovery in CLASH data. In the accompanying computational demonstration, we aim to establish a standardized strategy to evaluate the likelihood that observed chimeras arise from true RNA-RNA interactions.

Renewable and Functional Latexes Synthesized by Polymerization-Induced Self-Assembly for UV-Curable Films.

After the development of polymer coatings and films based on renewable resources, there remains a challenge of combining the advantages of water-borne acrylic latexes with the excellent physical properties of cross-linked solvent-borne coatings. After polymerization, the renewable 4-oxocyclopentenyl acrylate (4CPA) is capable of undergoing photocyclodimerization under UV light, yielding a cross-linked polyacrylate. In this work, we investigate the polymerization-induced self-assembly (PISA) of 4CPA with several renewable acrylic monomers in the presence of a macro-RAFT agent. The produced latexes have a small particle size, good colloidal stability, and are free of volatile organic compounds. After film formation and UV curing, flexible to rigid films can be obtained depending on the monomer composition and UV irradiation time. The cross-linked films show promise as oil and water barriers in paper coating applications. This work outlines the development and application of renewable and functional cross-linkable latexes synthesized by PISA.

In vitro enzymatic degradation of the PTMC/cross-linked PEGDA blends.

Introduction: Poly(1,3-trimethylene carbonate) (PTMC) is a flexible amorphous polymer with good degradability and biocompatibility. The degradation of PTMC is critical for its application as a degradable polymer, more convenient and easy-to-control cross-linking strategies for preparing PTMC are required. Methods: The blends of poly(trimethylene carbonate) (PTMC) and cross-linked poly(ethylene glycol) diacrylate (PEGDA) were prepared by mixing photoactive PEGDA and PTMC and subsequently photopolymerizing the mixture with uv light. The physical properties and in vitro enzymatic degradation of the resultant PTMC/cross-linked PEGDA blends were investigated. Results: The results showed that the gel fraction of PTMC/cross-linked PEGDA blends increased while the swelling degree decreased with the content of PEGDA dosage. The results of in vitro enzymatic degradation confirmed that the degradation of PTMC/cross-linked PEGDA blends in the lipase solution occurred under the surface erosion mechanism, and the introduction of the uv cross-linked PEGDA significantly improved the resistance to lipase erosion of PTMC; the higher the cross-linking degree, the lower the mass loss. Discussion: The results indicated that the blends/cross-linking via PEGDA is a simple and effective strategy to tailor the degradation rate of PTMC.

Advantages and limitations of UV cross-linking analysis of protein-RNA interactomes in microbes.

RNA-binding proteins (RBPs) govern the lifespan of nearly all transcripts and play key roles in adaptive responses in microbes. A robust approach to examine protein-RNA interactions involves irradiating cells with UV light to form covalent adducts between RBPs and their cognate RNAs. Combined with RNA or protein purification, these procedures can provide global RBP censuses or transcriptomic maps for all target sequences of a single protein in living cells. The recent development of novel methods has quickly populated the RBP landscape in microorganisms. Here, we provide an overview of prominent UV cross-linking techniques which have been applied to investigate RNA interactomes in microbes. By assessing their advantages and caveats, this technical evaluation intends to guide the selection of appropriate methods and experimental design as well as to encourage the use of complementary UV-dependent techniques to inspect RNA-binding activity.

Analysis of RNA-Protein Interaction Networks Using RNP-MaP.

RNA-protein interactions regulate a myriad of biological functions through formation of ribonucleoprotein complexes. These complexes may consist of one or more RNA-protein interaction network(s) providing additional layers of regulatory potential to the RNA. Moreover, since the protein-binding also regulates local and global structure of the RNA by structurally remodeling the latter, it is important to correlate RNA nucleotide flexibility with the site of protein-binding. We have discussed methods for chemical probing of structure of the RNA in the protein-free and protein-bound states in the preceding chapters. In this chapter, we describe a ribonucleoprotein mutational profiling (RNP-MaP) method for probing RNA-protein interaction networks.

Streamlined Purification of RNA-Protein Complexes Using UV Cross-Linking and RNA Antisense Purification.

RNA-protein interactions are important in development and disease, but identification of novel RNA-protein interactions remains challenging. Here, we describe an updated capture method to identify direct and specific RNA-protein interactions. First, RNA and protein are covalently cross-linked in living cells by treatment with UV light at 254 nanometers wavelength. The antisense purification approach is dependent upon nucleic acid hybridization between biotinylated DNA probes and a target RNA. Target protein:RNA:DNA complexes are enriched by capture on streptavidin magnetic beads and purified through several denaturing washes that remove nonspecific protein and nucleic acid interactors. Mass spectrometry is used to identify proteins that are specifically enriched in the target RNA capture. This method has been applied to discover the protein interactions of noncoding RNAs but can be used to capture any RNA where the target sequence is known.

The Non-Canonical Iron-Responsive Element of IRE-tvcp12 Hairpin Structure at the 3'-UTR of Trichomonas vaginalis TvCP12 mRNA That Binds TvHSP70 and TvACTN-3 Can Regulate mRNA Stability and Amount of Protein.

Trichomonas vaginalis is one of the most common sexually transmitted parasites in humans. This protozoan has high iron requirements for growth, metabolism, and virulence. However, iron concentrations also differentially modulate T. vaginalis gene expression as in the genes encoding cysteine proteinases TvCP4 and TvCP12. Our goal was to identify the regulatory mechanism mediating the upregulation of tvcp12 under iron-restricted (IR) conditions. Here, we showed by RT-PCR, Western blot, and immunocytochemistry assays that IR conditions increase mRNA stability and amount of TvCP12. RNA electrophoretic mobility shift assay (REMSA), UV cross-linking, and competition assays demonstrated that a non-canonical iron-responsive element (IRE)-like structure at the 3'-untranslated region of the tvcp12 transcript (IRE-tvcp12) specifically binds to human iron regulatory proteins (IRPs) and to atypical RNA-binding cytoplasmic proteins from IR trichomonads, such as HSP70 and α-Actinin 3. These data were confirmed by REMSA supershift and Northwestern blot assays. Thus, our findings show that a positive gene expression regulation under IR conditions occurs at the posttranscriptional level possibly through RNA-protein interactions between atypical RNA-binding proteins and non-canonical IRE-like structures at the 3'-UTR of the transcript by a parallel mechanism to the mammalian IRE/IRP system that can be applied to other iron-regulated genes of T. vaginalis.

Electrospun UV-cross-linked polyvinylpyrrolidone fibers modified with polycaprolactone/polyethersulfone microspheres for drug delivery.

Electrospun fibers, often used as drug delivery systems, have two drawbacks - in the first stage of their action a sudden active substance burst release occurs and they have a relatively small capacity for a drug. In this work the fibers are modified by the addition of drug-loaded microspheres acting as micro-containers for the drug and increasing the total drug capacity of the system. Its release from such a structure is slowed down by placing the microspheres inside the fibers so they are covered with an outer layer of fiber-forming polymer. The work presents a new method (microsphere suspension electrospinning) of obtaining polyvinylpyrrolidone fibers cross-linked with UV light modified with polycaprolactone/polyethersulphone microspheres loaded with active substance - rhodamine 640 as a marker or ampicillin as a drug example. The influence of UV-cross-linking time and the microspheres addition on the degradation, mechanical strength and transport properties of fibrous mats was investigated. The mats were insoluble in water, in some cases mechanically stronger, their drug capacity was increased and the burst effect was eliminated. The antibacterial properties of ampicillin-loaded mats were confirmed. The product of proposed suspension electrospinning process has application potential as a drug delivery system.

RNA binding protein BOULE forms aggregates in mammalian testis.

Amyloids have traditionally been considered pathologic protein aggregates which contribute to neurodegeneration. New evidence however increasingly suggests that non-pathological amyloids are formed in animals during normal development. Amyloid-like aggregate formation was originally thought to be a conserved feature of animal gametogenesis. This hypothesis was based on findings which suggest that regulated amyloid formations govern yeast meiosis by way of meiosis-specific RNA binding proteins. Additional support came from studies which demonstrate that DAZL, a mammalian gametogenesis-specific RNA binding protein, also forms SDS-resistant aggregates in vivo. Here, we report evidence of aggregated BOULE formations, another DAZ family protein, during sperm development. Data suggest that in mouse testis, BOULE forms SDS-resistant amyloid-like aggregates. BOULE aggregate formation correlates with dynamic developmental expression during spermatogenesis but disappeared in Boule knockout testis. We also mapped essential small region in vitro BOULE aggregations, immediately downstream DAZ repeats, and found that aggregations positively correlated with temperature. We also performed enhanced UV cross-linking immunoprecipitation on BOULE aggregates from mouse testes and found that aggregates bind with a large number of spermatogenesis-related mRNAs. These findings provide insight into the amyloidogenic properties of gametogenesis-specific RNA binding proteins as a conserved feature in mammalian reproduction. Further investigation is warranted to understand the functional significance of BOULE amyloid-like formation during mouse spermatogenesis.

Adhesive Films Based on Benzoxazine Resins and the Photoreactive Epoxyacrylate Copolymer.

UV-cross-linkable and thermally curable self-adhesive structural tapes (SATs) were compounded using solid commercial benzoxazine resins (Araldite MT 35700 and Araldite MT 35910) and a photoreactive epoxyacrylate copolymer (EAC). As initiators of benzoxazine resin polymerization and epoxy component cationic polymerization, two kinds of latent curing agents (LCAs) were tested, i.e., amine type and ionic liquid type. The influence of the benzoxazine resin and the LCA type on the UV-cross-linking process, the self-adhesive features and thermal curing behavior of UV-cross-linked tapes, as well as the shear strength of cured aluminum/SAT/aluminum joints and thermal stability of adhesives were investigated. It was found that the amine additive and the benzoxazine resin take part in the UV-cross-linking process of the EAC as hydrogen donors, which is confirmed by an increase in cohesion (+86%) and a decrease in adhesion (-25%) of SATs. The highest results of adhesion to steel (47 N/25 mm) and overlap shear strength (11.1 MPa) values were registered for SATs based on Araldite MT 35910 and contained 7.5 wt. parts of the amine-type hardener. The formation of a polyacrylate-benzoxazine network has a significant impact on the course of the thermal curing process and the thermomechanical properties of adhesive joints, which was also confirmed by the Cure Index calculation.

Post-transcriptional control of fungal cell wall synthesis.

Pathogenic fungi hide from their hosts by camouflage, obscuring immunogenic cell wall components such as beta-glucan with innocuous coverings such as mannoproteins and alpha-glucan that are less readily recognised by the host. Attempts to understand how such processes are regulated have met with varying success. Typically studies focus on understanding the transcriptional response of fungi to either their reservoir environment or the host. However, such approaches do not fully address this research question, due to the layers of post-transcriptional and post-translational regulation that occur within a cell. Although in animals the impact of post-transcriptional and post-translational regulation has been well characterised, our knowledge of these processes in the fungal kingdom is more limited. Mutations in RNA-binding proteins, like Ssd1 and Candida albicans Slr1, affect cell wall composition and fungal virulence indicating that post-transcriptional regulation plays a key role in these processes. Here, we review the current state of knowledge of fungal post-transcriptional regulation, and link this to potential mechanisms of immune evasion by drawing on studies from model yeast and plant pathogenic fungi. We highlight several RNA-binding proteins that regulate cell wall synthesis and could be involved in local translation of cell wall components. Expanding our knowledge on post-transcriptional regulation in human fungal pathogens is essential to fully comprehend fungal virulence strategies and for the design of novel antifungal therapies.

Photo-Cross-Linked Single-Ion Conducting Polymer Electrolyte for Lithium-Metal Batteries.

Polymer electrolytes are considered potential key enablers for lithium-metal batteries due to their compatibility with the lithium-metal negative electrode. Herein, cross-linked self-standing single-ion conducting polymer electrolytes are obtained via a facile UV-initiated radical polymerization using pentaerythritol tetraacrylate as the cross-linker and lithium (3-methacryloyloxypropylsulfonyl)-(trifluoromethylsulfonyl)imide as the ionic functional group. Incorporating propylene carbonate as charge-transport supporting additive allowed for achieving single-ion conductivities of 0.21 mS cm-1 at 20 °C and 0.40 mS cm-1 at 40 °C, while maintaining a suitable electrochemical stability window for 4 V-class positive electrodes (cathodes). As a result, this single-ion polymer electrolyte featured good cycling stability and rate capability in Li||LiFePO4 and Li||LiNi0.6 Mn0.2 Co0.2 O2 cells. These results render this polymer electrolyte as potential alternative to liquid electrolytes for high-energy lithium-metal batteries.

Nanoporous Block Copolymer Membranes with Enhanced Solvent Resistance Via UV-Mediated Cross-Linking Strategies.

In this work, a block copolymer (BCP) consisting of poly((butyl methacrylate-co-benzophenone methacrylate-co-methyl methacrylate)-block-(2-hydroxyethyl methacrylate)) (P(BMA-co-BPMA-co-MMA)-b-P(HEMA)) is prepared by a two-step atom-transfer radical polymerization (ATRP) procedure. BCP membranes are fabricated applying the self-assembly and nonsolvent induced phase separation (SNIPS) process from a ternary solvent mixture of tetrahydrofuran (THF), 1,4-dioxane, and dimethylformamide (DMF). The presence of a porous top layer of the integral asymmetric membrane featuring pores of about 30 nm is confirmed via scanning electron microscopy (SEM). UV-mediated cross-linking protocols for the nanoporous membrane are adjusted to maintain the open and isoporous top layer. The swelling capability of the noncross-linked and cross-linked BCP membranes is investigated in water, water/ethanol mixture (1:1), and pure ethanol using atomic force microscopy, proving a stabilizing effect of the UV cross-linking on the porous structures. Finally, the influence of the herein described cross-linking protocols on water-flux measurements for the obtained membranes is explored. As a result, an increased swelling resistance for all tested solvents is found, leading to an increased water flux compared to the pristine membrane. The herein established UV-mediated cross-linking protocol is expected to pave the way to a new generation of porous and stabilized membranes within the fields of separation technologies.

Re-evaluating expanding intravenous catheters in medical practice.

BACKGROUND: Intravenous catheters are common and essential devices within medical practice. Their placement can be difficult, leading to application of several technologies to improve success. Functionally expanding catheters were once an exciting technology, derailed clinically by hypersensitivity reactions. The exact cause of reactions, attributed to Aquavene catheter materials, remains unknown. AIMS: To reinvestigate functionally expanding intravenous catheters. MATERIALS AND METHODS: The history of the functionally expanding intravenous catheter is presented here along with its utility in current medical practice, potential for further investigation, and possible redesign of these once promising devices. RESULTS: This review demonstrates clinical utility and a lack of definitive cause for failure of the previous functionally expanding intravenous catheter design. As Aquavene materials themselves are commonly considered the cause of hypersensitivity reactions which removed expanding intravenous catheters from the market, this review found several possible substitutes for this material for use in any redesign. DISCUSSION AND CONCLUSION: The functionally expanding intravenous catheter failed due to hypersensitivity reactions in patients. Alternative materials exist for a possible redesign on this once promising clinical product.

Identification of lncRNA-Protein Interactions by CLIP and RNA Pull-Down Assays.

The emerging data indicates that long noncoding RNAs (lncRNAs) are involved in fundamental biological processes, and their deregulation may lead to oncogenesis and other diseases. LncRNA fulfil its biological functions at least in part by interacting with distinctive proteins. Here, we described two methods to identify the direct or indirect interactions between lncRNA and proteins: cross-linking and immunoprecipitation (CLIP) and RNA pull-down assay. CLIP methods enable yield a list of lncRNAs that directly interact target protein in living cells, whereas immunoprecipitation of biotin-labeled RNA (RNA pull-down) assay represents a method for identification of proteins that directly and indirectly bind with a particular target lncRNA of interest.

Multi-physics modeling and finite element formulation of corneal UV cross-linking.

The UV cross-linking technique applied to the cornea is a popular and effective therapy for eye diseases such as keratoconus and ectatic disorders. The treatment strengthens the cornea by forming new cross-links via photochemical reactions and, in turn, prevents the disease from further developing. To better understand and capture the underlying mechanisms, we develop a multi-physics model that considers the migration of the riboflavin (i.e., the photo-initializer), UV light absorption, the photochemical reaction that forms the cross-links, and biomechanical changes caused by changes to the microstructure. Our model is calibrated to a set of nanoindentation tests on UV cross-linked corneas from the literature. Additionally, we implement our multi-physics model numerically into a commercial finite element software. We also compare our simulation against a set of inflation tests from the literature. The simulation capability allows us to make quantitative predictions of a therapy's outcomes in full 3-D, based on the actual corneal geometry; it also helps medical practitioners with surgical planning.

Single-Nucleotide-Resolution Sequencing of N6-Methyldeoxyadenosine.

Use of methylation-specific antibodies with methylated-DNA-immunoprecipitation sequencing allows for the mapping of methylated DNA, such as N6-methyldeoxyadenosine (6mA). However, such mapping methods only detect methylated DNA at low resolution. Here, we describe 6mA Cross-linking Exonuclease sequencing (6mACE-seq), which utilizes 6mA-specific antibodies cross-linked to 6mA sites to protect 6mA-DNA fragments from subsequent exonuclease treatment. This allowed 6mACE-seq to map human-genome-wide 6mA at single-nucleotide resolution.

Protocol for High-Yield Production of Photo-Leucine-Labeled Proteins in Escherichia coli.

UV-cross-linking mass spectrometry is an emerging technique to obtain structural information of biomacromolecules and their complexes in vivo and in vitro. In particular, certain photo-reactive amino acids (pA) such as photo-leucine (pLeu) and photo-methionine can provide unique short-distance information on the structural core regions of proteins. Here, we present a protocol for high-yield incorporation of pLeu in proteins recombinantly expressed in Escherichia coli. The protein of interest is expressed at high cell densities, which reduces the required amount of the pA by a factor of 10, as compared to the standard protocols, while maintaining high incorporation rates. For the two chaperones, trigger factor and SecB, up to 3 mg of pLeu-labeled protein were thus obtained from 100 mL of cell culture, with label incorporation rates of up to 34%. For trigger factor, UV-induced cross-linking leads to the identification of 12 cross-links that are in agreement with the published three-dimensional structures. The accessibility of milligram amounts of pLeu-labeled proteins at low costs will be highly useful to address structural biology questions.

Fabrication of Aligned Biomimetic Gellan Gum-Chitosan Microstructures through 3D Printed Microfluidic Channels and Multiple In Situ Cross-Linking Mechanisms.

In this study we use a combination of ionic- and photo-cross-linking to develop a fabrication method for producing biocompatible microstructures using a methacrylated gellan gum (a polyanion) and chitosan (a polycation) in addition to lithium phenyl-2,4,6-trimethylbenzoylphosphinate (LAP) as the photoinitiator. This work involves the development of a low-cost, portable 3D bioprinter and a customized extrusion mechanism for controlled introduction of the materials through a 3D printed microfluidic nozzle, before being cross-linked in situ to form robust microstructure bundles. The formed microstructures yielded a diameter of less than 1 µm and a tensile strength range of ∼1 MPa. This study is the first to explore and achieve GGMA:CHT microstructure fabrication by means of controlled in-line compaction and photo-cross-linking through 3D printed microfluidic channels.

Mapping Exosome-Substrate Interactions In Vivo by UV Cross-Linking.

The RNA exosome complex functions in both the accurate processing and rapid degradation of many classes of RNA in eukaryotes and Archaea. Functional and structural analyses indicate that RNA can either be threaded through the central channel of the exosome or more directly access the active sites of the ribonucleases Rrp44 and Rrp6, but in most cases, it remains unclear how many substrates follow each pathway in vivo. Here we describe the method for using an UV cross-linking technique termed CRAC to generate stringent, transcriptome-wide mapping of exosome-substrate interaction sites in vivo and at base-pair resolution.