[Predicting response to non-small cell lung cancer immunotherapy using pre-treatment contrast-enhanced CT texture-based classification]

Objective: To explore the value of pre-treatment contrast-enhanced computed tomography (CT)-based texture analysis in predicting response to non-small cell lung cancer (NSCLC) immunotherapy. Methods: From January to July 2018, a total of 51 lesions from 42 patients with advanced non-small cell lung cancer receiving immunotherapy at Shanghai Chest Hospital were selected in this retrospective study. Pre-treatment contrast-enhanced CT-based texture features were extracted by MaZda software. Ten optimal texture features were chosen based on three different methods: Fisher coefficient, mutual information measure (MI) and minimization of classification error probability combined average correlation coefficients(POE+ ACC), respectively. According to the efficacy of the first immunotherapy, 51 lesions were divided into non-progressive disease (non-PD, n=26) and progressive disease (PD, n=25). The differences were tested in each texture feature set between the two groups. The immunotherapy effects of target lesions were analyzed by principal component analysis(PCA), linear discriminant analysis (LDA) and nonlinear discriminant analysis (NDA). The sensitivity, specificity, accuracy, positive-predictive value (PPV) and negative-predictive value (NPV) were calculated. The area under the curve (AUC) was used to quantify the predictive accuracy of the three analysis models for each texture feature set and compare them with the actual classification results. Results: In all of three texture feature sets, the texture parameter differences of Perc.50%, Perc.90%, "S(5, 5)SumEntrp" and "S(4, 4)SumEntrp" were higher in PD group than those in non-PD group (all P<0.05). The classification result of texture feature set chosen by POE+ ACC and analyzed by NDA was identified as the best model (AUC=0.802, 95%CI: 0.674-0.930), and its sensitivity, specificity, accuracy, PPV and NPV were 72%, 88.5%, 80.4%, 85.7%, 76.7%, respectively. Conclusion: Pre-treatment contrast-enhanced CT-based texture characteristics of NSCLC may function as non-invasive biomarkers for the evaluation of response to immunotherapy.

Effect of dietary taurine supplementation on metabolome variation in plasma of Nile tilapia

Taurine has been considered as an essential nutrient for many aquaculture species. While dietary taurine supplementation is highly recommended, novelty studies on taurine metabolism in fish are needed. The present study aimed to provide insight into the molecular mechanisms involved in multiple metabolome changes in Nile tilapia (Oreochromis niloticus) by studying plasma metabolic profile changes in response to graded levels of dietary taurine supplementation. The analysis used proton nuclear magnetic resonance-based metabolomics. Four groups of tilapias were fed with four diets supplemented with 0.0, 0.4, 0.8 and 1.2% taurine for 84 days. Fish plasma was sampled at multiple time points to provide an accurate snapshot of specific metabolic profiles during growth. Under the effect of taurine supplementation, 21 and 12 metabolites in tilapia plasma shown significant changes in terms of time-dependence and diet-dependence, respectively. These metabolic changes in tilapia plasma were mainly associated with energy and amino acid metabolism, lipids, nucleotides and protein metabolism. The results indicate that 0.8% taurine supplementation could significantly improve the carbohydrate synthesis, protein digestion and absorption, and fat deposition of tilapia and thereby promoted growth and development of tilapia.

DNA-rescuable allosteric inhibition of aptamer II ligand affinity by aptamer I element in the shortened Vibrio cholerae glycine riboswitch

Glycine riboswitches contain two aptamers and turn on the expression of downstream genes in bacteria. Although full-length glycine riboswitches were shown to exhibit no glycine-binding cooperativity, the truncated glycine riboswitches were confirmed to bind two glycine molecules cooperatively. Thorough understanding of the ligand-binding cooperativity may shed light on the molecular basis of the cooperativity and help design novel intricate biosensing genetic circuits for application in synthetic biology. A previously proposed sequential model does not readily provide explanation for published data showing a deleterious mutation in the first aptamer inhibiting the glycine binding of the second one. Using the glycine riboswitch from Vibrio cholerae as a model system, we have identified a region in the first aptamer that modulates the second aptamer function especially in the shortened glycine riboswitch. Importantly, this modulation can be rescued by the addition of a complementary oligodeoxynucleotide, demonstrating the feasibility of developing this system into novel genetic circuits that sense both glycine and a DNA signal.

Characterizing the dynamics of the leader-linker interaction in the glycine riboswitch with site-directed spin labeling

Site-directed spin labeling with continuous wave electron paramagnetic resonance (EPR) spectroscopy was utilized to characterize dynamic features of the kink–turn motif formed through a leader–linker interaction in the Vibrio cholerae glycine riboswitch. Efficient incorporation of spin-labels into select sites within the phosphate backbone of the leader–linker region proceeded via splinted ligation of chemically synthesized spin-labeled oligonucleotides to in vitro transcribed larger RNA fragments. The resultant nitroxide EPR line shapes have spectral characteristics consistent with a kink–turn motif and reveal differential backbone dynamics that are modulated by the presence of magnesium, potassium, and glycine.

Specific RNA-binding antibodies with a four-amino-acid code

Numerous large non-coding RNAs are rapidly being discovered, and many of them have been shown to play vital roles in gene expression, gene regulation, and human diseases. Given their often structured nature, specific recognition with an antibody fragment becomes feasible and may help define the structure and function of these non-coding RNAs. As demonstrated for protein antigens, specific antibodies may aid in RNA crystal structure elucidation or the development of diagnostic tools and therapeutic drugs targeting disease-causing RNAs. Recent success and limitation of RNA antibody development has made it imperative to generate an effective antibody library specifically targeting RNA molecules. Adopting the reduced chemical diversity design and further restricting the interface diversity to tyrosines, serines, glycines, and arginines only, we have constructed a RNA-targeting Fab library. Phage display selection and downstream characterization showed that this library yielded high-affinity Fabs for all three RNA targets tested. Using a quantitative specificity assay, we found that these Fabs are highly specific, possibly due to the alternate codon design we used to avoid consecutive arginines in the Fab interface. In addition, the effectiveness of the minimal Fab library may challenge our view of the protein-RNA binding interface and provide a unique solution for future design of RNA-binding proteins.

Site-directed spin-labeling strategies and electron paramagnetic resonance spectroscopy for large riboswitches

Genetic regulation effected by RNA riboswitches is governed by ligand-induced structural reorganization with modulation of RNA conformation and dynamics. Characterization of the conformational states of riboswitches in the presence or absence of salts and ligands is important for understanding how interconversion of riboswitch RNA folding states influences function. The methodology of site-directed spin labeling (SDSL) coupled with electron paramagnetic resonance (EPR) spectroscopy is suitable for such studies, wherein site-specific incorporation of a nitroxide radical spin probe allows for local dynamics and conformational changes to be investigated. This chapter reviews a strategy for SDSL-EPR studies of large riboswitches and uses the full length 232 nucleotide (nt) kink-turn motif-containing Vibrio cholerae (VC) glycine riboswitch as an example. Spin-labeling strategies and the challenges of incorporating spin labels into large riboswitches are reviewed and the approach to overcome these challenges is described. Results are subsequently presented illustrating changes in dynamics within the labeled region of the VC glycine riboswitch as observed using SDSL-EPR.

An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches

Comprised of two aptamers connected by a short nucleotide linker, the glycine riboswitch was the first example of naturally occurring RNA elements reported to bind small organic molecules cooperatively. Earlier works have shown binding of glycine to the second aptamer allows tertiary interactions to be made between the two aptamers, which facilitates binding of a separate glycine molecule to the first aptamer, leading to glycine-binding cooperativity. Prompted by a distinctive protection pattern in the linker region of a minimal glycine riboswitch construct, we have identified a highly conserved (>90%) leader-linker duplex involving leader nucleotides upstream of the previously reported consensus glycine riboswitch sequences. In >50% of the glycine riboswitches, the leader-linker interaction forms a kink-turn motif. Characterization of three glycine ribsowitches showed that the leader-linker interaction improved the glycine-binding affinities by 4.5- to 86-fold. In-line probing and native gel assays with two aptamers in trans suggested synergistic action between glycine-binding and interaptamer interaction during global folding of the glycine riboswitch. Mutational analysis showed that there appeared to be no ligand-binding cooperativity in the glycine riboswitch when the leader-linker interaction is present, and the previously measured cooperativity is simply an artifact of a truncated construct missing the leader sequence.

Improvement of the crystallizability and expression of an RNA crystallization chaperone

Crystallizing RNA has been an imperative and challenging task in the world of RNA research. Assistive methods such as chaperone-assisted RNA crystallography (CARC), employing monoclonal antibody fragments (Fabs) as crystallization chaperones have enabled us to obtain RNA crystal structures by forming crystal contacts and providing initial phasing information. Despite the early successes, the crystallization of large RNA-Fab complex remains a challenge in practice. The possible reason for this difficulty is that the Fab scaffold has not been optimized for crystallization in complex with RNA. Here, we have used the surface entropy reduction (SER) technique for the optimization of ΔC209 P4-P6/Fab2 model system. Protruding lysine and glutamate residues were mutated to a set of alanines or serines to construct Fab2SMA or Fab2SMS. Expression with the shake flask approach was optimized to allow large scale production for crystallization. Crystal screening shows that significantly higher crystal-forming ratio was observed for the mutant complexes. As the chosen SER residues are far away from the CDR regions of the Fab, the same set of mutations can now be directly applied to other Fabs binding to a variety of ribozymes and riboswitches to improve the crystallizability of Fab-RNA complex.

Reactions of phosphate and phosphorothiolate diesters with nucleophiles: comparison of transition state structures

A series of methyl aryl phosphorothiolate esters (SP) were synthesized and their reactions with pyridine derivatives were compared to those for methyl aryl phosphate esters (OP). Results show that SP esters react with pyridine nucleophiles via a concerted S(N)2(P) mechanism. Brønsted analysis suggests that reactions of both SP and OP esters proceed via transition states with dissociative character. The overall similarity of the transition state structures supports the use of phosphorothiolates as substrate analogues to probe mechanisms of enzyme-catalyzed phosphoryl transfer reactions.

Enhanced field emission from injector-like ZnO nanostructures with minimized screening effect

Injector-like zinc oxide (ZnO) nanostructures have been synthesized on Si substrate by the vapour phase transport method. Samples with different areal densities were obtained by controlling the temperature. The field emission properties of the injector-like ZnO nanostructures showed a clear dependence on the areal density of the nanostructures, which is due to the screening effect. The samples with a needle length of 850 nm and an areal density of 1 × 10(8) cm(-2) showed the lowest field emission turn-on field of 1.85 V µm(-1) at a current density of 10 µA cm(-2), and the current density reaches 1 mA cm(-2) at an applied field of 4.7 V µm(-1).

Nano-structural bioactive gradient coating fabricated by computer controlled plasma-spraying technology

The poor mechanical property of hydroxyapatite was the major problem for load bearing and implant coating in clinical applications. To overcome this weakness, a bioactive gradient coating with a special design composition of hydroxyapatite (HA), ZrO2, Ti, bioglass was developed. This 120 microm coating with an upper layer of 30-50 microm porous HA produced by computer controlled plasma spraying which maintained energy level of the plasma which ensure proper melting of powder. The crystal size of the coating was 18.6-26.2 nm. Transformation of t-ZrO2 to m-ZrO2 reduced the thermal stress that weakened the coating and lowered down interfacial strength of the coating and metal substrate. Thermal stress of sprayed coating was 16.4 MPa which was much smaller than the sample without thermal treatment of 67.1 MPa. Interfacial strength between the coating and metal substrate was 53 MPa which is much higher than conventional Hydroxyapatite coating. Based on XRD analysis crystallinity of HA approached 98%. Therefore, high temperature treatment improved long term stability of the coating through improved crystallinity of hydroxyapatite and reduced other impure calcium phosphate phase.

Synthesis of 2'-C-difluoromethylribonucleosides and their enzymatic incorporation into oligonucleotides

[Chemical reaction: See text] Nucleosides bearing a branched ribose have significant promise as therapeutic agents and biotechnological and biochemical tools. Here we describe synthetic entry into a new subclass of these analogues, 2'-C-beta-difluoromethylribonucleosides. We constructed the glycosylating agent 4 in three steps from 1,3,5-tri-O-benzoyl-alpha-D-ribofuranose 1. The key steps included nucleophilic addition of difluoromethyl phenyl sulfone to 2-ketoribose 2 followed by mild and efficient reductive desulfonation. Ribofuranose 4 glycosylated bis(trimethylsilyl)uracil directly, giving difluoromethyluridine 7 efficiently after deprotection. Conversion of 4 to the corresponding ribofuranosyl bromide allowed efficient access to C, A, and G analogues. A related approach starting from methyl D-ribofuranose offered synthetic entry into the diastereomeric manifold, 2'-C-alpha-difluoromethyl-arabino-alpha-pyrimidine. To incorporate 2'-C-beta-difluoromethyluridine into an oligodeoxynucleotide we converted 7 to the bisphosphate and carried out successive ligation reactions using T4 RNA ligase and T4 DNA ligase. Analogous to natural RNA linkages, the resulting oligonucleotide undergoes hydroxide-catalyzed backbone scission at the difluoromethyluridine residue via internal transphosphorylation.

New strategies for exploring RNA's 2'-OH expose the importance of solvent during group II intron catalysis

The 2'-hydroxyl group contributes inextricably to the functional behavior of many RNA molecules, fulfilling numerous essential chemical roles. To assess how hydroxyl groups impart functional behavior to RNA, we developed a series of experimental strategies using an array of nucleoside analogs. These strategies provide the means to investigate whether a hydroxyl group influences function directly (via hydrogen bonding or metal ion coordination), indirectly (via space-filling capacity, inductive effects, and sugar conformation), or through interactions with solvent. The nucleoside analogs span a broad range of chemical diversity, such that quantitative structure activity relationships (QSAR) now become possible in the exploration of RNA biology. We employed these strategies to investigate the spliced exons reopening (SER) reaction of the group II intron. Our results suggest that the cleavage site 2'-hydroxyl may mediate an interaction with a water molecule.