Spatial imaging of glycoRNA in single cells with ARPLA.

Little is known about the biological roles of glycosylated RNAs (glycoRNAs), a recently discovered class of glycosylated molecules, because of a lack of visualization methods. We report sialic acid aptamer and RNA in situ hybridization-mediated proximity ligation assay (ARPLA) to visualize glycoRNAs in single cells with high sensitivity and selectivity. The signal output of ARPLA occurs only when dual recognition of a glycan and an RNA triggers in situ ligation, followed by rolling circle amplification of a complementary DNA, which generates a fluorescent signal by binding fluorophore-labeled oligonucleotides. Using ARPLA, we detect spatial distributions of glycoRNAs on the cell surface and their colocalization with lipid rafts as well as the intracellular trafficking of glycoRNAs through SNARE protein-mediated secretory exocytosis. Studies in breast cell lines suggest that surface glycoRNA is inversely associated with tumor malignancy and metastasis. Investigation of the relationship between glycoRNAs and monocyte-endothelial cell interactions suggests that glycoRNAs may mediate cell-cell interactions during the immune response.

Synthesis of hierarchical mesoporous cerium titanate brannerite and uranyl adsorption properties at pH 3.8.

Cerium titanates possessing brannerite structure are produced by employing soft and hard templates via sol-gel processing. Powders synthesized with various hard template sizes and template to brannerite weight ratios are composed of nanoscale 'building blocks' with size ∼20-30 nm and characterized on macro-, nano- and atomic scales. These polycrystalline oxide powders exhibit specific surface area up to ∼100 m2 g-1, pore volume ∼0.4 cm3 g-1, and uranyl adsorption capacity ∼0.221 mmol (53 mg) U per gram powder. Remarkably, the materials possess significant proportion of mesopores with 5-50 nm pores representing 84-98% of total pore volume, which facilitate fast accessibility of the adsorbate to the internal surfaces of the adsorbent with adsorbed uranyl reaching over 70% of the full capacity within 15 min of contact. These mesoporous cerium titanate brannerites synthesized by the soft chemistry route are highly homogenous, stable at least in 2 mol L-1 acidic or basic solution, and may attract attention for other applications like catalysis at high temperature.

PNA-Assisted DNAzymes to Cleave Double-Stranded DNA for Genetic Engineering with High Sequence Fidelity.

DNAzymes have been widely used in many sensing and imaging applications but have rarely been used for genetic engineering since their discovery in 1994, because their substrate scope is mostly limited to single-stranded DNA or RNA, whereas genetic information is stored mostly in double-stranded DNA (dsDNA). To overcome this major limitation, we herein report peptide nucleic acid (PNA)-assisted double-stranded DNA nicking by DNAzymes (PANDA) as the first example to expand DNAzyme activity toward dsDNA. We show that PANDA is programmable in efficiently nicking or causing double strand breaks on target dsDNA, which mimics protein nucleases and can act as restriction enzymes in molecular cloning. In addition to being much smaller than protein enzymes, PANDA has a higher sequence fidelity compared with CRISPR/Cas under the condition we tested, demonstrating its potential as a novel alternative tool for genetic engineering and other biochemical applications.

Distinct Roles of Shewanella oneidensis Thioredoxin in Regulation of Cellular Responses to Hydrogen and Organic Peroxides.

The thioredoxin (Trx) and glutaredoxin (Grx) antioxidant systems are deeply involved in bacterial response to oxidative stress, but to date, we know surprisingly little about the roles of these systems in response to reactive oxygen species (ROS) other than hydrogen peroxide (H2O2). In this study, we used Shewanella oneidensis, an environmental bacterium, as a research model to investigate the roles of Trx and Grx in oxidative stress response because it has functionally intertwined ROS responsive regulators OxyR and OhrR. We found that Trx1 is the major thiol/disulfide redox system and that in its absence a Grx system becomes essential under normal conditions. Although overshadowed by Trx1 in the wild type, Trx2 can fully replace Trx1 in physiology when overproduced. Trx1 is required for OxyR to function as a repressor but, more importantly, plays a critical role in the cellular response to organic peroxide (OP) by mediating the redox status of OhrR but not OP scavenger OhrA. While none of the trx and grx genes are OxyR dependent, trxA and trxC are affected by OhrR indirectly. Additional data suggest that depletion of glutathione is likely the cue to trigger induced expression of trxA and trxC These findings underscore the particular importance of Trx in the bacterial OP stress response.IMPORTANCE The Trx and Grx systems are deeply involved in bacterial responses to H2O2-induced oxidative stress. However, little is known about their roles in response to other ROS, such as organic peroxides (OPs). In this study, we used S. oneidensis as a research model to investigate the interplay between Trx/Grx and OxyR/OhrR. We show that Trxs mediate the redox status of transcriptional OP-responding regulator OhrR. Although none of the trx or grx genes are directly controlled by OxyR or OhrR, expression of trxA and trxC is induced by tert-butyl hydroperoxide (t-BHP). We further show that the trxA and trxC genes respond to effects of glutathione (GSH) depletion rather than oxidation. These findings underscore the particular importance of Trx in the bacterial OP stress response.

Defining the binding determinants of Shewanella oneidensis OxyR: Implications for the link between the contracted OxyR regulon and adaptation.

It is well-established that OxyR functions as a transcriptional activator of the peroxide stress response in bacteria, primarily based on studies on Escherichia coli Recent investigations have revealed that OxyRs of some other bacteria can regulate gene expression through both repression and activation or repression only; however, the underlying mechanisms remain largely unknown. Here, we demonstrated in γ-proteobacteriumShewanella oneidensis regulation of OxyR on expression of major catalase gene katB in a dual-control manner through interaction with a single site in the promoter region. Under non-stress conditions, katB expression was repressed by reduced OxyR (OxyRred), whereas when oxidized, OxyR (OxyRoxi) outcompeted OxyRred for the site because of substantially enhanced affinity, resulting in a graded response to oxidative stress, from repression to derepression to activation. The OxyR-binding motif is characterized as a combination of the E. coli motif (tetranucleotides spaced by heptanucleotide) and palindromic structure. We provided evidence to suggest that the S. oneidensis OxyR regulon is significantly contracted compared with those reported, probably containing only five members that are exclusively involved in oxygen reactive species scavenging and iron sequestering. These characteristics probably reflect the adapting strategy of the bacteria that S. oneidensis represents to thrive in redox-stratified microaerobic and anaerobic environments.

Novel chemical synthesis and characterization of CeTi(2)O(6) brannerite.

Cerium titanate CeTi2O6 was prepared by a new soft chemistry route in aqueous solution. A suite of characterization techniques, including X-ray diffraction, thermal analysis, vibrational spectroscopy, and scanning and transmission electron spectroscopy, were employed to investigate the brannerite structure formation and its bulk properties. The synthesized powder formed the brannerite crystal structure upon calcination at temperatures as low as 800 °C. Samples sintered at 1350 °C possess a high level of crystallinity. X-ray absorption near-edge structure results indicate the presence of six-coordinated Ce(4+) in the brannerite samples.

Synthesis of hexa aza cages, SarAr-NCS and AmBaSar and a study of their metal complexation, conjugation to nanomaterials and proteins for application in radioimaging and therapy.

A novel hexa aza cage, N(1)-(4-isothiocyanatobenzyl)-3,6,10,13,16,19-hexaazabicyclo[6.6.6]icosane-1,8-diamine (SarAr-NCS) was synthesized in good yield and characterized by (1)H NMR and electrospray mass spectrometry. A new method for the synthesis of the related N(1)-(4-carboxybenzyl)-3,6,10,13,16,19-hexaazabicyclo[6.6.6]icosane-1,8-diamine (AmBaSar) using the p-carboxybenzaldehyde is reported. The complexation of Cu(2+), Co(2+) and Zn(2+) by the two ligands over a range of pHs was found to be similar to the parent derivative SarAr. SarAr-NCS was conjugated to both silica particles (≈90 nm diam.) and the model B72.3 murine antibody. The SarAr-NCSN-silica particles were radiolabeled with Cu(2+) doped (64)Cu and the number of ligands conjugated was calculated to be an average of 7020 ligands per particle. Conjugation of SarAr-NCS to the B72.3 antibody was optimized over a range of conditions. The SarAr-NCSN-B72.3 conjugate was stored in buffer and as a lyophilized powder at 4 °C over 38 days. Its radiolabeling efficiency, stability and immunoreactivity were maintained. The development of a high yielding synthesis of SarAr-NCS should provide an entry point for a wide range of Cu and Zn radiometal PET imaging agents and potentially radiotherapeutic agents with (67)Cu.

Optimizing radiolabeling amine-functionalized silica nanoparticles using SarAr-NCS for applications in imaging and radiotherapy.

Silica nanoparticles functionalized with amine groups and in the size range of approximately 60-94 nm were produced by combining sol-gel processing and emulsion technology. Hexa-aza cage ligand SarAr-NCS was conjugated to the silica nanoparticles and subsequently radiolabeled with a solution of (57)Co(2+)-doped carrier Co(2+). The number of Co(2+) ions bound to the silica particles at pH 7 was used to determine the average number of available SarAr-NCS ligands conjugated to a silica particle. For organically modified silica particles of 94.0 and 59.5 nm diameter, the maximum number of metal binding sites was determined to be 11700 and 3270 sites per particle, respectively. For silica particles (63.5 nm peak diameter) produced using an water-in-oil emulsion, the calculated average was 4480 on the particle surface. The number of SarAr-NCS conjugated on the particles was easily controlled, potentially providing for a range of products for applications in the risk assessment of particles and theranostic imaging or radiotherapy when radiolabeled with a suitable radioisotope such as (64)Cu or (67)Cu.

Formation of silica nanoparticles in microemulsions.

Silica nanoparticles for controlled release applications have been produced by the reaction of tetramethylorthosilicate (TMOS) inside the water droplets of a water-in-oil microemulsion, under both acidic (pH 1.05) and basic (pH 10.85) conditions. In-situ FTIR measurements show that the addition of TMOS to the microemulsion results in the formation of silica as TMOS, preferentially located in the oil phase, diffuses into the water droplets. Once in the hydrophilic domain, hydrolysis occurs rapidly as a result of the high local concentration of water. Varying the pH of the water droplets from 1.05 to 10.85, however, considerably slows the hydrolysis reaction of TMOS. The formation of a dense silica network occurs rapidly under basic conditions, with IR indicating the slower formation of more disordered silica in acid. SAXS analysis of the evolving particles shows that approximately 11 nm spheres are formed under basic conditions; these are stabilized by a water/surfactant layer on the particle surface during formation. Under acidic conditions, highly uniform approximately 5 nm spheres are formed, which appear to be retained within the water droplets (approximately 6 nm diameter) and form an ordered micelle nanoparticle structure that exhibits sufficient longer-range order to generate a peak in the scattering at q approximately equal to 0.05 A-1. Nitrogen adsorption analysis reveals that high surface area (510 m2/g) particles with an average pore size of 1 nm are formed at pH 1.05. In contrast, base synthesis results in low surface area particles with negligible internal porosity.

Quantum dot and silica nanoparticle doped polymer optical fibers.

A novel and highly versatile doping method has been developed to allow active dopants, including materials incompatible with the polymer matrix, to be incorporated into microstructured polymer optical fibers through the use of nanoparticles. The incorporation of quantum dots and silica nanoparticles containing Rhodamine isothiocyanate is demonstrated.

Electroacoustic Study of Concentrated Oil-in-Water Emulsions.

Electroacoustics was used to study SDS-stabilized sunflower oil-in-water emulsions, with oil volume fractions between 2% and 50%. The dynamic mobility of the oil droplets was measured; the size and electric charge on the drops were calculated using formulas derived for dilute and concentrated systems and the results were compared. The relation derived for concentrated systems appears to be valid up to at least 50% provided the particles remain within the size range of the instrument, which shifts upward with rising concentration. Conductivity and pH had little effect on particle properties in the range studied; higher oil volume fraction (φ) had a substantial influence on the particle size produced in a homogenizer, but not on the zeta potential. Both median size and spread decreased with increases in φ. In contrast, both size and charge were hardly affected at volume fractions less than 10%. Dilution of the emulsion with a surfactant solution of the same composition as the water phase changed neither the particle size nor the zeta potential. The temperature of the emulsification process had a significant influence on the particle size but the zeta potential was hardly affected. Surfactant concentration had some effect on size at low volume fractions but not for φ>10%. The electroacoustic method hence could be applied to analyze both the dilute and the concentrated emulsions directly. Copyright 2001 Academic Press.