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The SARS-CoV-2 proteome shares regions of conservation with endemic human coronaviruses (CoVs), but it remains unknown to what extent these may be cross-recognized by the antibody response. Here, we study cross-reactivity using a highly multiplexed peptide assay (PepSeq) to generate an epitope-resolved view of IgG reactivity across all human CoVs in both COVID-19 convalescent and negative donors. PepSeq resolves epitopes across the SARS-CoV-2 Spike and Nucleocapsid proteins that are commonly targeted in convalescent donors, including several sites also recognized in some uninfected controls. By comparing patterns of homologous reactivity between CoVs and using targeted antibody-depletion experiments, we demonstrate that SARS-CoV-2 elicits antibodies that cross-recognize pandemic and endemic CoV antigens at two Spike S2 subunit epitopes. We further show that these cross-reactive antibodies preferentially bind endemic homologs. Our findings highlight sites at which the SARS-CoV-2 response appears to be shaped by previous CoV exposures and which have the potential to raise broadly neutralizing responses., Competing Interests: The authors declare no competing interests., (© 2020 The Author(s).)

A high-resolution understanding of the antibody response to SARS-CoV-2 is important for the design of effective diagnostics, vaccines and therapeutics. However, SARS-CoV-2 antibody epitopes remain largely uncharacterized, and it is unknown whether and how the response may cross-react with related viruses. Here, we use a multiplexed peptide assay ('PepSeq') to generate an epitope-resolved view of reactivity across all human coronaviruses. PepSeq accurately detects SARS-CoV-2 exposure and resolves epitopes across the Spike and Nucleocapsid proteins. Two of these represent recurrent reactivities to conserved, functionally-important sites in the Spike S2 subunit, regions that we show are also targeted for the endemic coronaviruses in pre-pandemic controls. At one of these sites, we demonstrate that the SARS-CoV-2 response strongly and recurrently cross-reacts with the endemic virus hCoV-OC43. Our analyses reveal new diagnostic and therapeutic targets, including a site at which SARS-CoV-2 may recruit common pre-existing antibodies and with the potential for broadly-neutralizing responses.

Background: This study tested whether exposure to e-cigarette advertising affects the subliminal-spontaneous or automatic-attitudes towards e-cigarettes as a more pleasant or safer alternative to cigarettes among non-smoking young adults., Methods: 187 young adult (mean age=21.9; SD=4.1) current non-smokers who had never used an e-cigarette were randomly assigned to one of the 3 conditions that involved viewing magazine advertisements. Two of the 3 conditions were experimental conditions where thematically different [harm-reduction ("Health") vs. social enhancement ("Social") focused] e-cigarette ads were interspersed among ads of everyday objects. The third condition was the control condition in which participants viewed ads of everyday objects only. Participants provided data on explicit (e.g., harm perceptions) and implicit [e.g., Implicit Association Test (IAT), Affect Misattribution Procedure (AMP)] measures after viewing the ads., Results: Relative to the Control condition, participants in the Social condition showed 2.8 times higher odds of being open to using an e-cigarette in the future. Participants in the Health condition showed significantly higher implicit attitudes towards e-cigarettes as a safer alternative to cigarettes than participants in the Control condition. E-cigarette stimuli elicited more positive spontaneous affective reactions among participants in the Social condition than participants in the Health condition., Conclusions: E-cigarette ads may implicitly promote e-cigarettes as a reduced-harm cigarette alternative. Marketing of e-cigarette use as a way to enhance social life or self-image may encourage non-smoking young adults to try e-cigarettes. Findings may inform regulations on e-cigarette marketing., Competing Interests: No conflict declared., (Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.)

Background: Not much is currently understood regarding the contexts of cigarette and e-cigarette use among dual users. Proper application of e-cigarettes to smoking cessation or tobacco harm reduction would require an understanding of when and why dual users use cigarettes versus e-cigarettes. This study sought to elucidate the contexts of cigarette versus e-cigarette use among dual users., Methods: Twelve focus group discussions were conducted with 62 young adult current daily e-cigarette users [63% men; mean age = 25.1 (Standard Deviation = 5.5)]. Almost all participants either concurrently smoked cigarettes or had been recent dual users. Data were analyzed following principles of inductive deduction., Results: Results indicated that dual users' use of cigarettes is influenced by particular activities (e.g., before/after eating), strong craving or need for stimulation (e.g., in response to stress), places/situations (e.g., when cigarette smokers are nearby; outdoors), use of other substances (alcohol, coffee), and unavailability of an e-cigarette when needed. In addition to particular activities and places/situations that are conducive to e-cigarette use, use of e-cigarette when cigarette is not available or where cigarette smoking is not permitted emerged as contexts specific to e-cigarette use., Conclusions: For habitual cigarette smokers wanting to quit tobacco smoking, switching over completely to e-cigarettes may require skills of cognitive-behavioral management. Future research needs to ascertain the characteristics of dual users who use e-cigarettes as cessation aids versus as cigarette alternative when cigarette is unavailable or smoking is not permitted.

Matrix metalloproteinases (MMPs) play incompletely understood roles in health and disease. Knowing the MMP cleavage preferences is essential for a better understanding of the MMP functions and design of selective inhibitors. To elucidate the cleavage preferences of MMPs, we employed a high-throughput multiplexed peptide-centric profiling technology involving the cleavage of 18,583 peptides by 18 proteinases from the main sub-groups of the MMP family. Our results enabled comparison of the MMP substrates on a global scale, leading to the most efficient and selective substrates. The data validated the accuracy of our cleavage prediction software. This software allows us and others to locate, with nearly 100% accuracy, the MMP cleavage sites in the peptide sequences. In addition to increasing our understanding of both the selectivity and the redundancy of the MMP family, our study generated a roadmap for the subsequent MMP structural-functional studies and efficient substrate and inhibitor design., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Objective: To gain an in-depth understanding of what young adult electronic- or e-cigarette users like or dislike about e-cigarettes. We aimed to determine the reasons that may encourage young adults to use e-cigarettes or discourage them from using e-cigarettes., Design: Twelve focus group discussions were conducted with 62 current daily e-cigarette users (63% men) of mean age = 25.1 years (standard deviation = 5.5). Data were analysed following principles of inductive content analysis., Results: Results indicated 12 categories of reasons for liking e-cigarettes (e.g., recreation, smoking cessation) and 6 categories of reasons for not liking e-cigarettes (e.g. poor product quality, poor smoking experience)., Conclusions: Young adults' motives for using or not using e-cigarettes appear to be varied and their relative importance in terms of predicting e-cigarette use initiation, dependence, and cigarette/e-cigarette dual use needs to be carefully studied in population-based, empirical studies. The current findings suggest that e-cigarettes may serve social, recreational, and sensory expectancies that are unique relative to cigarettes and not dependent on nicotine. Further, successful use of e-cigarettes in smoking cessation will likely need higher standards of product quality control, better nicotine delivery efficiency and a counselling component that would teach smokers how to manage e-cigarette devices while trying to quit smoking cigarettes.

Background: E-cigarette use outcome expectancies and their relationships with demographic and e-cigarette use variables are not well understood. Based on past cigarette as well as e-cigarette use research, we generated self-report items to assess e-cigarette outcome expectancies among college students. The objective was to determine different dimensions of e-cigarette use expectancies and their associations with e-cigarette use and use susceptibility., Methods: Self-report data were collected from 307 multiethnic 4- and 2-year college students [M age=23.5 (SD=5.5); 65% Female; 35% current cigarette smokers] in Hawaii. Data analyses were conducted by using factor and regression analyses., Results: Exploratory factor analysis among e-cigarette ever-users indicated 7 factors: 3 positive expectancy factors (social enhancement, affect regulation, positive sensory experience) and 4 negative expectancy factors (negative health consequences, addiction concern, negative appearance, negative sensory experience). Confirmatory factor analysis among e-cigarette never-users indicated that the 7-factor model fitted reasonably well to the data. Being a current cigarette smoker was positively associated with positive expectancies and inversely with negative expectancies. Higher positive expectancies were significantly associated with greater likelihood of past-30-day e-cigarette use. Except addiction concern, higher negative expectancies were significantly associated with lower likelihood of past-30-day e-cigarette use. Among e-cigarette never-users, positive expectancy variables were significantly associated with higher intentions to use e-cigarettes in the future, adjusting for current smoker status and demographic variables., Conclusions: E-cigarette use expectancies determined in this study appear to predict e-cigarette use and use susceptibility among young adults and thus have important implications for future research., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Enterotoxigenic anaerobic Bacteroides fragilis is a significant source of inflammatory diarrheal disease and a risk factor for colorectal cancer. Two distinct metalloproteinase types (the homologous 1, 2, and 3 isoforms of fragilysin (FRA1, FRA2, and FRA3, respectively) and metalloproteinase II (MPII)) are encoded by the B. fragilis pathogenicity island. FRA was demonstrated to be important to pathogenesis, whereas MPII, also a potential virulence protein, remained completely uncharacterized. Here, we, for the first time, extensively characterized MPII in comparison with FRA3, a representative of the FRA isoforms. We employed a series of multiplexed peptide cleavage assays to determine substrate specificity and proteolytic characteristics of MPII and FRA. These results enabled implementation of an efficient assay of MPII activity using a fluorescence-quenched peptide and contributed to structural evidence for the distinct substrate cleavage preferences of MPII and FRA. Our data imply that MPII specificity mimics the dibasic Arg↓Arg cleavage motif of furin-like proprotein convertases, whereas the cleavage motif of FRA (Pro-X-X-Leu-(Arg/Ala/Leu)↓) resembles that of human matrix metalloproteinases. To the best of our knowledge, MPII is the first zinc metalloproteinase with the dibasic cleavage preferences, suggesting a high level of versatility of metalloproteinase proteolysis. Based on these data, we now suggest that the combined (rather than individual) activity of MPII and FRA is required for the overall B. fragilis virulence in vivo.

The aim of this study was to elucidate the presence of vitamin E homologues in medicinal plants. To identify various homologues in the matrix of medicinal plant samples, a method for simultaneous determination was developed using ESI(+)-LC-MS3. A complete separation of each homologue was achieved within 20 min using a PFP column and an isocratic elution system of water/methanol (10:90, v/v) at a flow rate of 0.5 mL/min. The ESI-MS condition for each homologue was optimized, and the m/z value and the fragmentation pathway of each homologue were summarized. This LC-MS3 method made it possible to detect the homologues without the effect of matrix; therefore, high sensitive analysis was established, and then, the MS3 makes it possible to extract from plants with methanol only. The LC-MS3 method was applied to identify the eight vitamin E homologues in 11 medicinal plants.

We investigated the gene regulatory mechanism of a previously engineered riboswitch +thiMN(15)#19 that turns on gene expression in response to thiamine pyrophosphate (TPP). In vitro enzymatic probing was performed to identify the secondary structures of the OFF conformations predicted by Mfold. Interestingly, enzymatic probing data of the riboswitch and its variants indicated that the riboswitch in its OFF state adopts two distinct structures. Moreover, further in vivo experiments suggested that both OFF structures contribute to the riboswitch function. A deeper understanding of how riboswitches function at the molecular level should enhance our ability to design synthetic riboswitches with new or improved characteristics.

The preparation of posttranslationally modified proteins is required to investigate the function and structure of modified proteins. However, homogeneously modified proteins are not easily isolated from natural sources or prepared using modification enzymes. Non-natural amino acid mutagenesis has enabled us to incorporate modified amino acids into specific positions of proteins in both cell-free and in-cell translation systems using tRNAs that are aminoacylated with modified amino acids. Here, we developed a method of double incorporation of modified amino acids and fluorescent non-natural amino acids in a quantitative, position-specific manner to obtain modified and fluorescently labeled proteins. To introduce methyllysine, dimethyllysine, trimethyllysine, and acetyllysine, frameshift and amber suppressor tRNAs aminoacylated with modified lysines were synthesized by chemical aminoacylation and supplied to an Escherichia coli cell-free translation system. The immunodetection of the translation products indicated that the modified lysines were incorporated into streptavidin and histone H3 in a quantitative, position-specific manner. Calmodulin derivatives containing a fluorescent non-natural amino acid at the N-terminal region and modified lysines at the Lys115 position were also synthesized, and their binding activity to a calmodulin-binding peptide was analyzed by fluorescence correlation spectroscopy. The results obtained here demonstrate that this method is useful in preparing and analyzing naturally occurring and non-natural modified proteins., (Copyright © 2010 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.)

We designed a synthetic riboswitch containing an OFF and an ON riboswitch units fused in tandem. The resulting complex riboswitch functions as a chemical band-pass filter circuit.

After the recent discovery of bacterial riboswitches, synthetic riboswitches have been engineered by using natural and artificial RNA aptamers. In contrast to natural riboswitches, the majority of synthetic riboswitches in bacteria reported to date are ON switches that activate gene expression in response to the aptamer ligand. In this study, we adopted a mechanism-guided approach to design libraries predisposed to contain OFF riboswitches that respond to thiamine pyrophosphate (TPP). The first library design exploited a pseudo-Shine-Dalgarno (SD) sequence located near the 3'-end of the TPP aptamer, which would be less accessible to the ribosome when the aptamer is bound to TPP. In the second library, an SD sequence was strategically placed in the aptamer's P1 stem, which is stabilized upon ligand binding. OFF riboswitches were obtained by dual genetic selection of these libraries. The results underscore the importance of effective library design to achieve desired riboswitch functions.

Engineered gene switches and circuits that can sense various biochemical and physical signals, perform computation, and produce predictable outputs are expected to greatly advance our ability to program complex cellular behaviors. However, rational design of gene switches and circuits that function in living cells is challenging due to the complex intracellular milieu. Consequently, most successful designs of gene switches and circuits have relied, to some extent, on high-throughput screening and/or selection from combinatorial libraries of gene switch and circuit variants. In this study, we describe a generic and efficient platform for selection and screening of gene switches and circuits in Escherichia coli from large libraries. The single-gene dual selection marker tetA was translationally fused to green fluorescent protein (gfpuv) via a flexible peptide linker and used as a dual selection and screening marker for laboratory evolution of gene switches. Single-cycle (sequential positive and negative selections) enrichment efficiencies of >7000 were observed in mock selections of model libraries containing functional riboswitches in liquid culture. The technique was applied to optimize various parameters affecting the selection outcome, and to isolate novel thiamine pyrophosphate riboswitches from a complex library. Artificial riboswitches with excellent characteristics were isolated that exhibit up to 58-fold activation as measured by fluorescent reporter gene assay.

We have developed a novel method to attach a fluorescent label at the N terminus of proteins through a four-base codon-mediated incorporation of a fluorescent hydroxy acid and subsequent cleavage of the ester bond in a cell-free translation system. We found that a fluorescent-labeled p-amino-L-phenyllactic acid was successfully incorporated downstream of N-terminal tag peptides in response to a CGGG codon, and the tag peptides could be removed through ester cleavage to leave the fluorescent hydroxy acid at the N terminus of the proteins. Immunoprecipitation analysis revealed that ester cleavage occurred spontaneously during the translation reaction. The efficiency of the ester cleavage and the yield of the labeled proteins were dependent on the peptide tag sequence. We demonstrate that the insertion of an asparagine residue between the N-terminal T7 tag and the fluorescent hydroxy acid achieved both quantitative ester cleavage and efficient expression of the labeled proteins. The present method is a potential tool for N-terminal specific labeling of proteins with various compounds.

Saturation mutagenesis is a useful technique for the structural and functional analyses of proteins and for protein engineering. However, the extensive mutagenesis of genes and expression of mutated proteins are tedious and time-consuming. We have developed a simple and rapid method for the expression of mutated proteins with comprehensive single amino acid substitutions from single mutated genes having a four-base codon in a cell-free translation system. Twenty types of tRNA that were aminoacylated with one of the 20 proteinogenic amino acids and that contained a four-base anticodon were prepared by chemical aminoacylation. In the presence of one of the aminoacyl-tRNAs, a streptavidin mRNA with a four-base codon at the Tyr83 position was expressed in an Escherichia coli cell-free translation system. The N-terminus of the expressed proteins was fluorescently labeled using a fluorescent-labeled initiator Met-tRNA. Fluorescence imaging of an SDS-PAGE gel showed that all the amino acids are incorporated in response to the four-base codon; however, the incorporation efficiency was dependent on the structure of the side chains. Streptavidin mutants with comprehensive amino acid substitutions at the Tyr83, Arg84, and Tyr54 positions were used for analyzing their biotin-binding activity by dot blot analysis. These results demonstrate that this method is effective for the expression and analysis of mutated proteins with comprehensive amino acid substitutions at desired positions.

Biotinylation is useful for the detection, purification and immobilization of proteins. It is performed by chemical modification, although position-specific and quantitative biotinylation is rarely achieved. We developed a position-specific biotinylation method using biotinylated non-natural amino acids. We showed that biotinylated p-aminophenylalanine derivatives were incorporated into a protein more efficiently than biotinylated lysine derivatives in a cell-free translation system. In addition, the biotinylated p-aminophenylalanines overcame the serious position-dependency observed for biotinylated lysines. The present method will be useful for detection and purification of proteins along with comprehensive exploration of surface-exposed residues and oriented immobilization of proteins.

The locations of the pole and rotation axis of asteroid 25143 Itokawa were derived from Asteroid Multiband Imaging Camera data on the Hayabusa spacecraft. The retrograde pole orientation had a right ascension of 90.53 degrees and a declination of -66.30 degrees (52000 equinox) or equivalently 128.5 degrees and -89.66 degrees in ecliptic coordinates with a 3.9 degrees margin of error. The surface area is 0.393 square kilometers, the volume is 0.018378 cubic kilometers with a 5% margin of error, and the three axis lengths are 535 meters by 294 meters by 209 meters. The global Itokawa revealed a boomerang-shaped appearance composed of two distinct parts with partly faceted regions and a constricted ring structure.

Novel non-natural amino acids carrying a dansyl fluorescent group were designed, synthesized, and incorporated into various positions of streptavidin by using a CGGG four-base codon in an Escherichia coli in vitro translation system. 2,6-Dansyl-aminophenylalanine (2,6-dnsAF) was found to be incorporated into the protein more efficiently than 1,5-dansyl-lysine, 2,6-dansyl-lysine, and 1,5-dansyl-aminophenylalanine. Fluorescence measurements indicate that the position-specific incorporation of the 2,6-dnsAF is a useful technique to probe protein structures. These results also indicate that well-designed non-natural amino acids carrying relatively large side chains can be accepted as substrates of the translation system.

Horseradish peroxidase mutants containing L-p-phenylazophenylalanine (azoAla) at various positions were synthesized by using an Escherichia coli in vitro translation system. Among the 15 mutants examined, four mutants containing a single azoAla unit at the 6th, 68th, 142nd, and 179th positions, respectively, retained the peroxidase activity. The activity of the Phe68azoAla mutant was higher when the azobenzene group was in the cis form than in the trans form. On the contrary, the activity of the Phe179azoAla mutant disappeared when the azobenzene group was photoisomerized to the cis form, but recovered in the trans form. In the latter mutant, therefore, an on/off photoswitching of the peroxidase activity was attained.