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A new method has been developed to reassign the rare codon AGA in Escherichia coli by engineering an orthogonal tRNA/aminoacyl-tRNA synthetase pair derived from Methanocaldococcus jannaschii. The tRNA mutant was introduced with a UCU anticodon, and the synthetase was evolved to correctly recognize the modified tRNA anticodon loop and to selectively charge a target noncanonical amino acid (NAA) onto the tRNA. In order to maximize the efficiency of AGA codon reassignment, while avoiding the lethal effects caused by global codon reassignment in cellular proteins, an inducible promoter (araBAD) was utilized to provide temporal controls for overexpression of the aminoacyl-tRNA synthetase and switch on codon reassignment. Using this system, we were able to efficiently incorporate p-acetylphenylalanine, O-methyl-tyrosine, and p-iodophenylalanine into proteins in response to AGA codons. Also, we found that E. coli strain GM10 was optimal in achieving the highest AGA reassignment rates. The successful reassignment of AGA codons reported here provides a new avenue to further expand the genetic code., (© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Previously, a non-human DNA fragment named NV-F was isolated from a patient with non-A-E fulminant hepatitis. This sequence encoded an incomplete open reading frame (the NV-F antigen). In this study, we developed a western blot assay to detect serum anti-NV-F antibodies. Serum samples from 347 patients with severe hepatitis (ALT > fivefold ULN) were analyzed to understand the prevalence and distribution of the NV-F associated virus (HnFV) infection. Of these patients, acute HnFV infection was diagnosed (by positive serum NV-F DNA) in 34 patients (9.8%). However, none of these 34 serum samples were positive for serum anti-NV-F antibodies. In the remaining patients negative for serum NV-F DNA, 62 (17.9%) were positive for serum anti-NV-F antibodies. Liver biopsy samples from 35 severe hepatitis patients were submitted for immunohistochemistry and electron microscopy examination. Of them, seven were positive for hepatic NV-F antigen expression. Electron microscopy identified a novel virus-like particle in all of the seven NV-F antigen-positive liver tissues but not in the remaining 28 NV-F antigen-negative liver tissues. Longitudinal serum sample analysis revealed transient positivity of serum NV-F DNA in three of the seven patients during the clinical courses. Seroconversion of anti-NV-F antibody from negative to positive was found in four of the seven patients and all positive anti-NV-F antibodies were detected in the convalescent phases. In conclusion, in patients with severe hepatitis, a novel hepatotropic virus, temporarily named HnFV, was found in liver tissues expressing the NV-F antigen. Serum anti-NV-F antibodies were detected in the convalescent serum samples., (© 2015 Wiley Periodicals, Inc.)

Helicobacter pylori infection occurs in more than half of the world's population and is the main cause for gastric cancer. A series of lifestyle and nutritional factors, such as tobacco smoking and obesity, have been found to elevate the risk for cancer development. In this study, we sought to determine the immunological aspects during H. pylori infection and gastric cancer development. We found that B cells from H. pylori-infected patients presented altered composition and function compared to uninfected patients. IL-10-expressing CD24+CD38+ B cells were upregulated in H. pylori-infected patients, contained potent regulatory activity in inhibiting T cell pro-inflammatory cytokine secretion, and responded directly to H. pylori antigen stimulation. Interestingly, in H. pylori-infected smoking subjects and obese subjects, the number of IL-10+ B cells and CD24+CD38+ B cells were reduced compared to H. pylori-infected asymptomatic subjects. Regulatory functions mediated by CD24+CD38+ B cells were also impaired. In addition, gastric cancer positive patients had reduced IL-10-producing B cell frequencies after H. pylori-stimulation. Altogether, these data suggest that in H. pylori-infection, CD24+CD38+ B cell is upregulated and plays a role in suppressing pro-inflammatory responses, possibly through IL-10 production, a feature that was not observed in smoking and obese patients.

The preclinical development of anticancer drugs including immunotherapeutics and targeted agents relies on the ability to detect minimal residual tumor burden as a measure of therapeutic efficacy. Real-time quantitative (qPCR) represents an exquisitely sensitive method to perform such an assessment. However, qPCR-based applications are limited by the availability of a genetic defect associated with each tumor model under investigation. Here, we describe an off-the-shelf qPCR-based approach to detect a broad array of commonly used preclinical murine tumor models. In particular, we report that the mRNA coding for the envelope glycoprotein 70 (gp70) encoded by the endogenous murine leukemia virus (MuLV) is universally expressed in 22 murine cancer cell lines of disparate histological origin but is silent in 20 out of 22 normal mouse tissues. Further, we detected the presence of as few as 100 tumor cells in whole lung extracts using qPCR specific for gp70, supporting the notion that this detection approach has a higher sensitivity as compared with traditional tissue histology methods. Although gp70 is expressed in a wide variety of tumor cell lines, it was absent in inflamed tissues, non-transformed cell lines, or pre-cancerous lesions. Having a high-sensitivity biomarker for the detection of a wide range of murine tumor cells that does not require additional genetic manipulations or the knowledge of specific genetic alterations present in a given neoplasm represents a unique experimental tool for investigating metastasis, assessing antitumor therapeutic interventions, and further determining tumor recurrence or minimal residual disease.

The 2-naphthol analogue of tyrosine, 2-amino-3-(6-hydroxy-2-naphthyl)propanoic acid (NpOH), has been genetically introduced into proteins in Escherichia coli . This is achieved through the directed evolution of orthogonal aminoacyl-tRNA synthetase/tRNA pairs that selectively charge the target amino acid in response to the amber stop codon, UAG. Moreover, chemoselective azo coupling reactions have been revealed between the 2-naphthol group and diazotized aniline derivatives that are substituted with an electron donating moiety. The coupling reactions required a very mild condition (pH 7) with great reaction rate (less than 2 h at 0 °C), high efficiency, and excellent selectivity.

For more than 2 centuries active immunotherapy has been at the forefront of efforts to prevent infectious disease [Waldmann TA (2003) Nat Med 9:269-277]. However, the decreased ability of the immune system to mount a robust immune response to self-antigens has made it more difficult to generate therapeutic vaccines against cancer or chronic degenerative diseases. Recently, we showed that the site-specific incorporation of an immunogenic unnatural amino acid into an autologous protein offers a simple and effective approach to overcome self-tolerance. Here, we characterize the nature and durability of the polyclonal IgG antibody response and begin to establish the generality of p-nitrophenylalanine (pNO(2)Phe)-induced loss of self-tolerance. Mutation of several surface residues of murine tumor necrosis factor-alpha (mTNF-alpha) independently to pNO(2)Phe leads to a T cell-dependent polyclonal and sustainable anti-mTNF-alpha IgG autoantibody response that lasts for at least 40 weeks. The antibodies bind multiple epitopes on mTNF-alpha and protect mice from severe endotoxemia induced by lipopolysaccharide (LPS) challenge. Immunization of mice with a pNO(2)Phe(43) mutant of murine retinol-binding protein (RBP4) also elicited a high titer IgG antibody response, which was cross-reactive with wild-type mRBP4. These findings suggest that this may be a relatively general approach to generate effective immunotherapeutics against cancer-associated or other weakly immunogenic antigens.

NV-F is a novel hepatotropic viruslike agent. To investigate the impact of the NV-F agent during chronic hepatitis C virus (HCV) infection, 101 consecutive patients with chronic HCV infection were evaluated. NV-F DNA in serum samples and NV-F antigen expression in liver tissues were assessed. All patients subsequently received a 6-month course of interferon-based antiviral therapy. Of the 101 patients, 30 (29.7%) were positive for serum NV-F DNA. Immunohistochemical analysis revealed positive NV-F antigen expression in the liver in 14 of these 30 patients. Patients positive for serum NV-F DNA had significantly higher serum aminotransferase levels (P < .001) and higher Knodell histology activity index values (P < .001). The sustained virological response rate for HCV clearance was not significantly different between patients with and those without detectable serum NV-F DNA. In conclusion, coinfection of the NV-F agent in chronic HCV infection is associated with more severe hepatitis activity.

We have devised a phage display system in which an expanded genetic code is available for directed evolution. This system allows selection to yield proteins containing unnatural amino acids should such sequences functionally outperform ones containing only the 20 canonical amino acids. We have optimized this system for use with several unnatural amino acids and provide a demonstration of its utility through the selection of anti-gp120 antibodies. One such phage-displayed antibody, selected from a naïve germline scFv antibody library in which six residues in V(H) CDR3 were randomized, contains sulfotyrosine and binds gp120 more effectively than a similarly displayed known sulfated antibody isolated from human serum. These experiments suggest that an expanded "synthetic" genetic code can confer a selective advantage in the directed evolution of proteins with specific properties.

The ability to selectively induce a strong immune response against self-proteins, or increase the immunogenicity of specific epitopes in foreign antigens, would have a significant impact on the production of vaccines for cancer, protein-misfolding diseases, and infectious diseases. Here, we show that site-specific incorporation of an immunogenic unnatural amino acid into a protein of interest produces high-titer antibodies that cross-react with WT protein. Specifically, mutation of a single tyrosine residue (Tyr(86)) of murine tumor necrosis factor-alpha (mTNF-alpha) to p-nitrophenylalanine (pNO(2)Phe) induced a high-titer antibody response in mice, whereas no significant antibody response was observed for a Tyr(86) --> Phe mutant. The antibodies generated against the pNO(2)Phe are highly cross-reactive with native mTNF-alpha and protect mice against lipopolysaccharide (LPS)-induced death. This approach may provide a general method for inducing an antibody response to specific epitopes of self- and foreign antigens that lead to a neutralizing immune response.

By use of the yeast two-hybrid system, hepatitis C virus (HCV) F protein was found to interact with a cellular protein named prefoldin 2. The interaction was confirmed by confocal immunofluorescence microscopy as well as coimmunoprecipitation experiments. Prefoldin 2 is a subunit of a hexameric molecular chaperone complex, named prefoldin, which delivers nascent actin and tubulin proteins to the eukaryotic cytosolic chaperonin for facilitated folding. Functional prefoldin spontaneously assembles from its six subunits (prefoldin 1-6). In the yeast three-hybrid system, it was found that expression of HCV F protein impeded the interaction between prefoldin 1 and 2. By performing immunofluorescence experiment and non-denaturing gel electrophoresis, it was shown that expression of HCV F protein resulted in aberrant organization of tubulin cytoskeleton. Since HCV replication requires intact microtubule and actin polymerization, HCV F protein may serve as a modulator to prevent high level of HCV replication and thus contributes to viral persistence in chronic HCV infection.

By performing nonspecific polymerase chain reaction followed by elimination of chromosome-derived sequences, foreign DNA fragments were obtained from the serum of a patient with non-A-E hepatitis. One of the sequences, named NV-F, contained a partial open reading frame and was detected in 17 (24.6%) of 69 patients with non-A-E hepatitis, including 1 with fulminant hepatitis (vs. in 5 [2.8%] of 180 healthy individuals). A peptide was synthesized accordingly, to detect serum anti-NV-F antibody, which was found in 49 (75.4%) of 65 patients positive for NV-F. This DNA fragment was sensitive to S1 nuclease digestion. Cesium chloride gradient analysis revealed that the NV-F-associated particles had buoyant densities of 1.33-1.39 and 1.22-1.25 g/mL. Immunofluorescence analysis revealed that the novel antigen was present in the hepatocytes of patients infected with NV-F. In conclusion, we have identified a novel single-stranded DNA fragment derived from a virus-like agent associated with human hepatitis.

The unnatural amino acid p-nitrophenylalanine (pNO2-Phe) was genetically introduced into proteins in Escherichia coli in response to the amber nonsense codon with high fidelity and efficiency by means of an evolved tRNA/aminoacyl-tRNA synthetase pair from Methanocuccus jannaschii. It was shown that pNO2-Phe efficiently quenches the intrinsic fluorescence of Trp in a distance-dependent manner in a model GCN4 basic region leucine zipper (bZIP) protein. Thus, the pNO2-Phe/Trp pair should be a useful biophysical probe of protein structure and function.

[reaction: see text] Photolysis of 3 in argon-saturated 2-propanol led to formation of 5 via intermolecular H-atom abstraction followed by lactonization. Irradiation of 4 in 2-propanol gave compounds 6 and 7 that also come from intermolecular H-atom abstraction. In contrast, photolysis of an oxygen-saturated solution of 3 in 2-propanol yields products 8, 9, and 10, which were all formed from intramolecular H-atom abstraction and trapping of the corresponding biradical with oxygen. Laser flash photolysis of 3 in methanol showed formation of biradical 3BR (lambda(max) 330 nm, and tau = 50 ns) via intramolecular H-atom abstraction as the main photoreactivity of 3. Biradical 3BR decayed into photoenols 3Z and 3E (lambda(max) 390 nm, tau = 6.5 micros and tau = 162 micros, respectively). In comparison, laser flash photolysis of 4 yielded photoenols 4Z and 4E (lambda(max) 390 nm, tau = 15 micros and tau = 3.6 ms, respectively). Thus photoenol 3E is unusually short-lived, and therefore it does not undergo the intramolecular lactonization as we have observed for the analogous photoenol 1E. Photoenol 3Z decays back to 3 via an intramolecular 1,5-H shift, whereas photoenol 3E reforms 3 efficiently via the solvent with the aid of the ortho ester group. The intramolecular lactonization of photoenols 1E and 3E must be a slow process, presumably because the photoenols are rigid and the hydroxyl group is inhibited, by intramolecular hydrogen bonding, from acquiring the correct geometry for lactonization. Thus only photoenols that are resistant to reformation of their ketone via the solvent are long-lived enough to undergo lactonization and release the alcohol moiety.

A cDNA encoding hepatitis C virus NS5A protein was isolated from the serum of a patient with hepatocellular carcinoma. The NS5A(HCC) was localized in both the cytoplasmic and nuclear fractions of Huh-7 cells. Immunoprecipitation and electrophoresis experiments showed four major phosphorylated species of NS5A(HCC), p58, p56, p53, and p50. Two mutants (NS5A(HCC-NLSmt) and NS5A(HCC-TSmt)) carrying mutations on the putative nuclear localization signal were engineered. NS5A(HCC-NLSmt) was localized exclusively in the cytoplasm, whereas some forms of NS5A(HCC-TSmt) can be transported into the nucleus. These NS5A(HCC) mutant proteins were capable of transactivating c-fos and SV40 promoters. However, the transactivation efficiency was not dependent on its capability of nuclear localization. Subsequently, interaction between NS5A(HCC) mutants and Grb2 was studied. While capable of transactivating oncogenic promoters, NS5A(HCC-TSmt) could not interact with Grb2. Our results suggested that other cytosolic pathways independent of Grb2-mediated mechanisms were involved in the transactivation activity of HCV NS5A.

The dynamics of singlet 3,5-dichloro-2-biphenylnitrene and the products of its rearrangement were monitored by pico- and nanosecond laser flash photolysis and the results were consistent with the predictions of DFT and ab initio molecular orbital calculations.

We report a general method to display peptide-containing unnatural amino acids on filamentous M13 phage. Five distinct unnatural amino acids were site-specifically incorporated at the N-terminal of the M13 phage minor coat protein pIII. Phages that contain p-azidophenylalanine can undergo a highly specific azide-alkyne [3 + 2] cycloaddition reaction with an alkyne-derivatized fluorophore. The generalization of phage display to include unnatural amino acids should significantly increase the scope of phage display technology.

Ar matrix photolysis of 1- and 2-naphthyl azides 3 and 4 at 313 nm initially affords the singlet naphthyl nitrenes, (1)()1 and (1)()2. Relaxation to the corresponding lower energy, persistent triplet nitrenes (3)()1 and (3)()2 competes with cyclization to the azirines 15 and 18, which can also be formed photochemically from the triplet nitrenes. On prolonged irradiation, the azirines can be converted to the seven-membered cyclic ketenimines 10 and 13, respectively, as described earlier by Dunkin and Thomson. However, instead of the o-quinoid ketenimines 16 and 19, which are the expected primary ring-opening products of azirines 15 and 18, respectively, we observed their novel bond-shift isomers 17 and 20, which may be formally regarded as cyclic nitrile ylides. The existence of such ylidic heterocumulenes has been predicted previously, but this work provides the first experimental observation of such species. The factors which are responsible for the special stability of the ylidic species 17 and 20 are discussed.

Phenyl azide, 2,6-diethylphenyl azide, 2,6-diisopropylphenyl azide, and 2,4,6-tri-tert-butylphenyl azide were studied by laser flash photolysis (LFP) methods. LFP (266 nm) of the azides in glassy 3-methylpentane at 77 K produces the transient UV-vis absorption spectra of the corresponding singlet nitrenes. At 77 K, the singlet nitrenes relax to the corresponding triplet nitrenes. The triplet nitrenes are persistent at 77 K and their spectra were recorded. The rate constants of singlet to triplet intersystem crossing were determined at this temperature. LFP of 2,4,6-tri-tert-butyl phenyl azide in pentane at ambient temperature again produces a singlet nitrene, which is too short-lived to detect by nanosecond spectroscopy under these conditions. Unlike the other azides, the first detectable intermediate produced upon LFP of 2,4,6-tri-tert-butyl phenyl azide at ambient temperature is the benzazirine (285 nm) which has a lifetime of 62 ns controlled by ring opening to a didehydroazepine. The results are interpreted with the aid of Density Functional Theoretical and Molecular Orbital Calculations.

To identify genes that are frequently downregulated in hepatocellular carcinoma (HCC), a panel of putative underexpressed genes was first established by an in-house cDNA macroarray method. Two different assays, semiquantitative RT-PCR combined with Northern analysis and customized cDNA microarray analysis, were used to screen through these genes and the results were compared. Several genes, some with unknown function, were confirmed to be downregulated by both the methods. The effect of a downregulated gene, BMAL2, on cell proliferation was examined. Overexpression of antisense BMAL2 RNA in 293EBNA cells resulted in reduced cell cycle time, increased plating efficiency in soft agar, diminished TNF-alpha-induced increment of CPP32/caspase-3 activity, and a reduced proportion of cells in the G2 phase with a concomitantly increased proportion of cells in the S phase. In conclusion, by combining three different methods, we have obtained a panel of frequently down regulated genes in HCC, including BMAL2. Antisense overexpression of BMAL2 enhances cell proliferation.

The photochemistry of ortho-biphenyl azide (1a) has been studied by laser flash photolysis (LFP), with UV-vis and IR detection of the transient intermediates formed. LFP (266 nm) of 1a in glassy 3-methylpentane at 77 K releases singlet ortho-biphenylnitrene (1b) (lambda(max) = 410 nm, tau = 59 +/- 6 ns), which under these conditions decays cleanly to the lower energy triplet state. In fluid solution at 298 K, 1b rapidly (tau < 10 ns) partitions between formation of isocarbazole (4) (lambda(max) = 430 nm, tau = 70 ns) and benzazirine (1e) (lambda(max) = 305 nm, tau = 12 ns). Isocarbazole 4 undergoes a 1,5-hydrogen shift, with k(H)/k(D) = 3.4 at 298 K to form carbazole 9 and smaller amounts of two other isocarbazoles (7 and 8). Benzazirine 1e ring-opens reversibly to azacycloheptatetraene (1f), which serves as a reservoir for singlet nitrene 1b. Azacycloheptatetraene 1f ultimately forms carbazole 9 on the millisecond time scale by the pathway 1f --> 1e --> 1b --> 4 --> 9. The energies of the transient intermediates and of the transition structures connecting them were successfully predicted by CASPT2/6-31G calculations. The electronic and vibrational spectra of the intermediates, computed by density functional theory, support the assignment of the transient spectra, observed in the formation of 9 from 1a.

The structures of halogen atom-benzene complexes were investigated by modern DFT and ab initio computational methods. The spectroscopic properties of the complexes are also predicted and are in good agreement with experiment where such data have been reported. The fluorine atom-benzene complex is predicted to be a sigma complex due to the strength of a C-F bond. The chlorine atom-benzene complex is predicted to have an eta(1) pi complex structure, which is only slightly more favorable (1.1 kcal/mol with the BH&HLYP/6-311++G method including the ZPE correction) than a sigma complex but is significantly more stable (4.4 kcal/mol with the BH&HLYP/6-311++G method including the ZPE correction) than the eta(6) pi complex. The bromine and iodine benzene complexes are also predicted to prefer an eta(1) pi complex structure.

As a model for riboflavin, lumiflavin was investigated using density functional theory methods (B3LYP/6-31G* and B3LYP/6-31+G**) with regard to the proposed cascade of intermediates formed after excitation to the triplet state, followed by electron-transfer, proton-transfer, and radical[bond]radical coupling reactions. The excited triplet state of the flavin is predicted to be 42 kcal/mol higher in energy than the singlet ground state, and the pi radical anion lies 45.1 kcal/mol lower in energy than the ground-state flavin and a free electron in the gas phase. The former value compares to a solution-phase triplet energy of 49.8 kcal/mol of riboflavin. For the radical anion, the thermodynamically favored position to accept a proton on the flavin ring system is at N(5). A natural population analysis also provided spin density information for the radicals and insight into the origin of the relative stabilities of the six different calculated hydroflavin radicals. The resulting 5H-LF* radical can then undergo radical[bond]radical coupling reactions, with the most thermodynamically stable adduct being formed at C(4'). Vibrational spectra were also calculated for the transient species. Experimental time-resolved infrared spectroscopic data obtained using riboflavin tetraacetate are in excellent agreement with the calculated spectra for the triplet flavin, the radical anion, and the most stable hydroflavin radical.