Designing fluorescent biosensors using circular permutations of riboswitches.

RNA-based fluorescent (RBF) biosensors have been applied to detect a variety of metabolites in vitro and in live cells. They are designed by combining the ligand sensing domain of natural riboswitches with in vitro selected fluorogenic aptamers. Different biosensor topologies have been developed to accommodate the diversity of riboswitch structures. Here we show that circular permutation of the riboswitch ligand sensing domain also gives functional biosensors, using the SAM-I riboswitch as our model. We reveal that this design can enhance fluorescence turn-on and ligand binding affinity compared to the non-permuted topology.

GEMM-I riboswitches from Geobacter sense the bacterial second messenger cyclic AMP-GMP.

Cyclic dinucleotides are an expanding class of signaling molecules that control many aspects of bacterial physiology. A synthase for cyclic AMP-GMP (cAG, also referenced as 3'-5', 3'-5' cGAMP) called DncV is associated with hyperinfectivity of Vibrio cholerae but has not been found in many bacteria, raising questions about the prevalence and function of cAG signaling. We have discovered that the environmental bacterium Geobacter sulfurreducens produces cAG and uses a subset of GEMM-I class riboswitches (GEMM-Ib, Genes for the Environment, Membranes, and Motility) as specific receptors for cAG. GEMM-Ib riboswitches regulate genes associated with extracellular electron transfer; thus cAG signaling may control aspects of bacterial electrophysiology. These findings expand the role of cAG beyond organisms that harbor DncV and beyond pathogenesis to microbial geochemistry, which is important to environmental remediation and microbial fuel cell development. Finally, we have developed an RNA-based fluorescent biosensor for live-cell imaging of cAG. This selective, genetically encodable biosensor will be useful to probe the biochemistry and cell biology of cAG signaling in diverse bacteria.

Angiotensin II type 1 receptor antagonist attenuates lung fibrosis in hyperoxia-exposed newborn rats.

Bronchopulmonary dysplasia (BPD) remains a major cause of morbidity and mortality during the first year of life, and many infants have significant respiratory problems throughout childhood. Currently no effective therapy is clinically available to prevent the long-term pulmonary sequelae of BPD. Previous research has demonstrated that the renin-angiotensin system is up-regulated in human lung fibroblasts. Angiotensin II type 1 receptor (AT1R) antagonists and AT1R short interfering RNA diminished hyperoxia-increased collagen expression, whereas AT2R antagonists did not have any effects on these hyperoxia-induced changes. The in vivo therapeutic effects of AT1R antagonists on hyperoxia-induced lung fibrosis remain unknown. The present study assessed the effects of an AT1R antagonist (losartan) on preventing hyperoxia-induced lung fibrosis in newborn rats. Rat pups were exposed to 7 days of > 95% O2 and an additional 2 weeks of 60% O2. AT1R antagonist-treated pups were injected intraperitoneally with losartan at a dose of 10 mg/kg/day from postnatal days 1 to 7 and a dose of 5 mg/kg/day from postnatal days 8 to 21. Control group pups were injected with an equal volume of normal saline. AT1R antagonist treatment attenuated the hyperoxia-induced lung fibrosis on postnatal days 7 and 21 and also decreased the hyperoxia-induced expression of extracellular signal-regulated protein kinase and α-smooth muscle actin. AT1R antagonist treatment did not affect body weight or lung weight of the rats. These data suggest that AT1R antagonist may offer a novel therapeutic strategy for preventing hyperoxia-induced lung fibrosis.

Engineering the Composition of Microfibers to Enhance the Remodeling of a Cell-Free Vascular Graft.

The remodeling of vascular grafts is critical for blood vessel regeneration. However, most scaffold materials have limited cell infiltration. In this study, we designed and fabricated a scaffold that incorporates a fast-degrading polymer polydioxanone (PDO) into the microfibrous structure by means of electrospinning technology. Blending PDO with base polymer decreases the density of electrospun microfibers yet did not compromise the mechanical and structural properties of the scaffold, and effectively enhanced cell infiltration. We then used this technique to fabricate a tubular scaffold with heparin conjugated to the surface to suppress thrombosis, and the construct was implanted into the carotid artery as a vascular graft in animal studies. This graft significantly promoted cell infiltration, and the biochemical cues such as immobilized stromal cell-derived factor-1α further enhanced cell recruitment and the long-term patency of the grafts. This work provides an approach to optimize the microfeatures of vascular grafts, and will have broad applications in scaffold design and fabrication for regenerative engineering.

Coronary CT angiography-based estimation of myocardial perfusion territories for coronary artery FFR and wall shear stress simulation.

This study aims to apply a CCTA-derived territory-based patient-specific estimation of boundary conditions for coronary artery fractional flow reserve (FFR) and wall shear stress (WSS) simulation. The non-invasive simulation can help diagnose the significance of coronary stenosis and the likelihood of myocardial ischemia. FFR is often regarded as the gold standard to evaluate the functional significance of stenosis in coronary arteries. In another aspect, proximal wall shear stress ([Formula: see text]) can also be an indicator of plaque vulnerability. During the simulation process, the mass flow rate of the blood in coronary arteries is one of the most important boundary conditions. This study utilized the myocardium territory to estimate and allocate the mass flow rate. 20 patients are included in this study. From the knowledge of anatomical information of coronary arteries and the myocardium, the territory-based FFR and the [Formula: see text] can both be derived from fluid dynamics simulations. Applying the threshold of distinguishing between significant and non-significant stenosis, the territory-based method can reach the accuracy, sensitivity, and specificity of 0.88, 0.90, and 0.80, respectively. For significantly stenotic cases ([Formula: see text] [Formula: see text] 0.80), the vessels usually have higher wall shear stress in the proximal region of the lesion.

NaDDBS as a dispersion agent for multiwalled carbon nanotubes in capillary EKC separation of nucleotides.

A novel pseudostationary phase (PSP) of multiwalled carbon nanotubes (MWCNTs) dispersed with sodium dodecylbenzenesulfonate (NaDDBS) was used for the EKC separation of nucleotides. NaDDBS has a long hydrophobic chain and a benzylsulfonate group. It suspends more MWCNTs (about 100-fold) than SDS, and the π-π interaction between the benzene ring of NaDDBS and MWCNTs prolongs the slurry suspension time. Using NaDDBS as a surfactant can reduce the required amount of MWCNTs and decrease the baseline noise. To produce a stable suspension, the optimum ratio (w/w) of MWCNTs to NaDDBS was investigated with turbidimetry. In this context, several parameters affecting EKC separation were studied, including buffer pH, composition, concentration, and the organic modifier. Use of NaDDBS (8 mg/L)/MWCNTs (0.8 mg/L) as the PSP in a phosphate buffer (30 mM, pH 8) yielded complete resolution of seven geometric isomers of a nucleoside monophosphate. In stacking mode, with 10% MeOH in the sample plug, the mixture of nucleoside mono-, di-, and tri-phosphates was satisfactorily separated in phosphate buffer (50 mM, pH 9). The results indicate that nucleotides with bases containing more electron-withdrawing groups interact more strongly with MWCNTs. The system has been used to separate oligonucleotides, and to analyze nucleotides in a complex matrix sample.

Functionalized carbon nanotubes as the pseudostationary phase for capillary EKC separation of non-steroidal anti-inflammatory drugs.

Functionalized multiwalled carbon nanotubes (f-MWCNTs) can serve as the pseudostationary phase (PSP) for the capillary EKC separation of non-steroidal anti-inflammatory drugs (NSAIDs). To increase their hydrophilicity, we treated MWCNTs, with a sonochemical process in a concentrated nitric/sulfuric acid mixture. The oxidized MWCNTs were then characterized by FT-IR, transmission electron microscopy, and X-ray photoelectron spectroscopy. We evaluated the potential of the PSP and the effects of buffer composition, pH, addition of organic modifier, and injection temperature on the NSAID separation. The PSP created a network structure of pi-pi interactions, hydrophobic forces, hydrogen bonding, and electrostatic interactions to separate NSAIDs, providing a different separation mode from SDS micelles. We achieved complete separation of six NSAIDs using a mixture of a borate buffer (75 mM, pH 10) with methanol (5%, v/v) containing 0.02 mg/mL f-MWCNTs, an applied voltage of +12 kV and detection at 214 nm. Better precision was obtained with a low injection temperature. The method was also satisfactorily applied to the analysis of NSAIDs spiked into a urine sample.

Comparison of plasma and chemical modifications of poly-L-lactide-co-caprolactone scaffolds for heparin conjugation.

Biodegradable polymers have potential as a scaffold material for making small diameter artery bypass grafts. To resist thrombosis, maintain biocompatibility and enhance the remodeling of the grafts, it is crucial to modify polymer scaffolds so that the grafts have antithrombogenic capacity and allow cell infiltration. In this study, two methods of aminolysis on electrospun poly-L-lactide-co-caprolactone (PLCL) microfiber vascular grafts are compared: plasma treatment method and Fmoc-PEG-diamine insertion method. Both methods successfully inserted amino groups on the polymer graft for heparin conjugation. However, plasma treatment resulted in significantly higher initial heparin density and higher heparin stability on PLCL microfibers than Fmoc-PEG-diamine treatment. In addition, mechanical testing demonstrated that the plasma treatment method maintained PLCL microfiber tensile strength after heparin conjugation. Fmoc-PEG-diamine insertion method compromised the mechanical property due to partial fiber melting and structure disruption. Subcutaneous implantation of the grafts in a rat model showed that heparin coating with both methods promoted cell infiltration. This study provides a rationale to optimize the biomolecule conjugation on electrospun PLCL scaffolds, and will have applications in tissue engineering vascular grafts and other tissues.

Staurosporine-induced G2/M arrest in primary effusion lymphoma BCBL-1 cells.

Staurosporine, an inhibitor of protein kinase C, is a potential antitumor drug and its derivatives are used as anticancer drugs in clinical trials. Human herpesvirus 8 (HHV-8) is implicated in all forms of Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), and multicentric Castleman's disease (MCD), indicating it to be a DNA tumor virus. It is difficult to culture cell lines derived from KS patients; we therefore used a cell line derived from PEL (BCBL-1) to investigate whether staurosporine affects the HHV-8-related tumors. Our results show that staurosporine treatment reduces the cell viability of BCBL-1 cells and causes cell cycle arrest in the G2/M phase. The G2/M arrest was associated with the decrease in the expression of Cdc2 and cyclin B. Furthermore, the induction of the HHV-8 lytic cycle was not observed under the staurosporine treatment.