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Abstract Urea (Ua) is produced in DNA as the result of oxidative damage to thymine and guanine. It was previously reported that Klenow fragment (Kf) exo− incorporated dATP opposite Ua, and that DNA polymerase β was blocked by Ua. We report here the following nucleotide incorporations opposite Ua by various DNA polymerases: DNA polymerase α, dATP and dGTP (dATP > dGTP); DNA polymerase δ, dATP; DNA polymerase ζ, dATP; Kf exo−, dATP; Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4), dGTP and dATP (dGTP > dATP); and DNA polymerase η, dCTP, dGTP, dATP, and dTTP (dCTP > dGTP > dATP > dTTP). DNA polymerases β and ε were blocked by Ua. Elongation by DNA polymerases δ and ζ stopped after inserting dATP opposite Ua. Importantly, the elongation efficiency to full-length beyond Ua using DNA polymerase η and Dpo4 were almost the same as that of natural DNA. Graphical abstract

We demonstrate a second harmonic generation (SHG) of 116 mW at 461 nm in a periodically poled lithium niobate waveguide when the power of the 922 nm fundamental light is coupled into the waveguide was 350 mW. The waveguide is 12.5 μm wide, 12.0 μm thick, 22 mm long, and has a 1 mm long slab window at the output facet of the waveguide. The temperature acceptance bandwidth of the phase-matching curve of the SHG is approximately 0.5 °C. The SHG system demonstrates good beam quality and is reliable for cold atom experiments, including research on optical lattice clocks.

The functional role of fatty acid 2-hydroxylase (FA2H) is controversial in the field of cancer biology due to the dual role of FA2H, particularly related to its interaction with triple-negative breast cancer (TNBC). A previous biochemical- and clinical-focused study suggested that FA2H could dampen TNBC aggressiveness. However, another epidemiological study demonstrated that FA2H expression is associated with shorter disease-free survival in TNBC cases. We reported that FA2H is a peroxisome proliferator-activated receptor α (PPARα)-regulated gene in human breast cancer MDA-MB-231 cells, in vitro experimental models for TNBC analysis. PPARα activation by its ligand reportedly results in an aggressive MDA-MB-231 cell phenotype, as well as estrogen receptor α (ERα)-positive MCF-7 cells. The results of this study show that i) MDA-MB-231 cells express very low levels of FA2H compared to the MCF-7 cells, reflecting a low basal-level PPARα-driven transcriptional activity compared to the MCF-7 cells, and ii) the increased FA2H expression stimulates the MDA-MB-231 and MCF-7 breast cancer cell migration without affecting proliferation. Taken together, our findings indicate that FA2H might be a breast cancer cell migration stimulator, independently of the ERα expression status.

The spread of the novel coronavirus disease (COVID-19) has caused a global pandemic. Exiting agents that act on proteins including 3-chymotrypsin-like protease (3CLpro), papain-like protease (PLpro), helicase, RNA-dependent RNA polymerase (RdRp), spike glycoprotein (S protein), and others in similar viruses [1,2] are likely used as antiviral drugs against the novel coronavirus (SARS-CoV-2). Data on Chemical Abstract Service show that the potential drug candidates against 3CLpro and RdRp are more than those against other targets [2].

Assisting the elderly to or from a toilet for excretion is a heavy burden, and staff at nursing homes and families at home have problems such as backache and tiredness. There are several previous studies on standing up from a chair, bed, or toilet seat but almost no studies on the series of actions required for excretion (i.e., from a bed to a transfer apparatus and from the transfer apparatus to the toilet seat). The difference in the physical burden (muscular strength) for helpers when using the Norisukesan II, a transfer-type wheelchair developed in collaboration with the authors, and an ordinary wheelchair when transferring a patient to or from a toilet for excretion was studied by biometrics with surface electromyogram (EMG) patterns. We chose a total of 11 healthy adult examinees, 10 males and one female, with an average age of 47.7±9.7. Muscle activity was measured at eight positions: right and left biceps brachii muscles, right and left quadriceps femoris muscles, upper right and left trapezius muscles, and right and left waist muscles. The results showed that if the transfer-type wheelchair was used, the muscle activity of the helpers’ biceps brachii muscles decreased by 70%, that of the quadriceps femoris muscles decreased by 60%, that of the trapezius muscles decreased by 70%, and that of the waist muscles decreased by 40%, when compared to using the ordinary wheelchair. It was therefore quantitatively clarified that assisting patients with the transfer-type wheelchair could reduce the assisting burden significantly, as the helpers did not have to tightly hold or turn the patients.

Self-annealing behaviors of the electrodeposited silver films which preferentially orient in (001) and (111) directions were investigated by in situ EBSP analysis. In the (001)-oriented film, self-annealing starts in storage for a few hours at R. T. and is almost complete after storage for 6 h at R. T. (001)- and (212)-oriented recrystallized grains mainly nucleate, and (001)-oriented grains mainly grow up. In the (111)-oriented film, self-annealing starts in storage for 15 min at R. T. and is almost complete after storage for 1 h at R. T. (111)-, (001)- and (212)-oriented recrystallized grains mainly nucleate, and (111)-oriented grains mainly grow up. The size of recrystallized grains induced in the (111)-oriented film by self-annealing is approximately half that in the (001)-oriented film although the rate of recrystallization in the (111)-oriented film is faster than that in the (001)-oriented one. The area fraction of the preferential orientation after completion of recrystallization saturates in approximately 70% and 50% in the (001)- and (111)-oriented films, respectively.

There is adequate evidence for the carcinogenicity of cadmium (Cd). However, a significant unaddressed question remains as to how this metal actually causes malignant transformation (tumor initiation). Since it has been shown that Cd only has the weak direct interaction potential with DNA, the metal is recognized as an indirect genotoxicant and mutagen. Currently, Cd-mediated "epigenetic" modifications, such as changes in DNA methylation resulting in alteration in target gene expression, coupled with cancer progression, are the focus of mechanistic research. We have reported that the apolipoprotein E (ApoE) gene, a suppressor of cell invasion, is an early Cd target, and is involved in the malignant transformation of TRL 1215 rodent liver cells. Cd exposure suppresses ApoE expression which can be re-activated with 5-aza-2'-deoxycytidine, a DNA demethylating agent. In the present study, we sought direct evidence of Cd-induced DNA hypermethylation of the ApoE promoter region by performing bisulfite sequencing and real-time quantitative methylation-specific PCR. Our data clearly suggest that Cd can down-regulate the expression of ApoE via introduction of excess DNA methylation in the promoter region of ApoE during malignant transformation of TRL 1215 cells.

Chitin, which is a major component of house dust mites (HDM), fungi, crustaceans, etc., can activate immune cells, suggesting that it contributes to development of allergic disorders such as asthma. Although the pathophysiological sensitization route of asthmatic patients to allergens is considered via the respiratory tract, the roles of intranasally-administered chitin in development of asthma remain unclear. After ovalbumin (OVA) challenge, development of airway inflammation was profoundly exacerbated in mice sensitized with OVA in the presence of chitin. The exacerbation was dependent on IL-33, but not IL-25, thymic stromal lymphopoietin or IL-17A. Chitin enhanced IL-33-dependent IL-1β production by dendritic cells (DCs). Furthermore, chitin- and IL-33-stimulated DC-derived IL-1β promoted OVA-specific Th2 cell activation, resulting in aggravation of OVA-induced airway inflammation. These findings indicate the adjuvant activity of chitin via a new mechanism and provide important clues for development of therapeutics for allergic disorders caused by HDM, fungi and crustaceans.

TAL2 is a transcription factor required in the normal development of mouse brain. In a previous study, we demonstrated that the expression of Tal2 gene is induced by the complex of all-trans retinoic acid (atRA) and retinoic acid receptor α (RARα) in mouse embryonal carcinoma P19 cells. atRA is also known to be important in inducing P19 cells to differentiate into the neural lineage. Therefore, we believe that the function of TAL2 in neural differentiation may be clarified by utilizing P19 cells. As the atRA-RARα complex induced the expression of Tal2, we focused on the regulatory region that is involved in its transcription. The atRA-RARα complex occupies a characteristic retinoic acid response element (RARE) located in the promoter of target genes. Therefore, we searched for RARE on the mouse Tal2 and found that a RARE-like element was located in the intron. We also found that a TATA-box-like element was located in the 5'-region of Tal2. Involvement between transcriptional activity and the TATA-box-like element was confirmed in the luciferase assay, and TATA-box binding protein was bound to this element upstream of Tal2 in P19 cells. atRA signaling activated the transcription through the RARE-like element, and RARα was bound to this element on Tal2 in P19 cells. In addition, the interaction between these elements on Tal2 was shown in the chromatin immunoprecipitation assay. These results suggest that the transcription of Tal2 is coordinately mediated by two distal regulatory elements.

Guanine is the most readily oxidized of the four DNA bases, and guanine oxidation products cause G:C-T:A and G:C-C:G transversions through DNA replication. 8-Oxo-7,8-dihydroguanine (8-oxoG) causes G:C-T:A transversions but not G:C-C:G transversions, and is more readily oxidized than guanine. This review covers four major findings. (i) 2,2,4-Triamino-5(2H)-oxazolone (Oz) is produced from guanine and 8-oxoG under various oxidative conditions. Guanine is incorporated opposite Oz by DNA polymerases, except REV1. (ii) Several enzymes exhibit incision activity towards Oz. (iii) Since the redox potential of GG is lower than that of G, contiguous GG sequences are more readily oxidized by a one-electron oxidant than a single guanine, and OzOz is produced from GG in double-stranded DNA. Unlike most DNA polymerases, DNA polymerase ζ efficiently extends the primer up to full-length across OzOz. (iv) In quadruplex DNA, 3′-guanine is mainly damaged by one-electron oxidation in quadruplex DNA, and this damage depends on the highest occupied molecular orbital (HOMO). The oxidation products in quadruplex DNA are different from those in single-stranded or double-stranded DNA.

Cadmium is a transition metal that is classified as human carcinogen by the International Agency for Research on Cancer (IARC) with multiple target sites. Many studies using various model systems provide evidence of cadmium-induced malignancy formation in vivo or malignant cell transformation in vitro. Nonetheless, further studies are needed to completely understand the mechanisms of cadmium carcinogenicity. Our prior studies have utilized a rat liver epithelial cell line (TRL 1215) as a model for cadmium-induced malignant transformation. In the present study, we focused on the molecular mechanisms of this malignant transformation, especially with regard to hyper-invasiveness stimulated by cadmium transformation. By performing a series of biochemical analyses on cadmium transformed cells, it was determined that cadmium had significantly down-regulated the expression of apolipoprotein E (ApoE). ApoE was recently established as a suppressor of cell invasion. A key factor in the suppression of ApoE by cadmium appeared to be that the metal evoked a 5-aza-2'-deoxycytidine-sensitive hypermethylation of the regulatory region of ApoE, coupled with interference of the action of liver X receptor α (LXRα), a transcriptional regulator for ApoE. Furthermore, the expression of LXRα itself was suppressed by cadmium-mediated epigenetic modification. Re-expression of ApoE clearly abrogated the cell invasion stimulated by cadmium-induced malignant transformation. Together, the current results suggest that the cadmium-mediated enhanced cell invasion is linked to down-regulation of ApoE during malignant transformation these liver cells.

In a previous study, we showed that formylmethylflavin (FMF) can bind to cysteine. In this study, FMF was reacted with native peptides (CG and CKLVFF) containing an N-terminal cysteine. The formation of flavin-CG and flavin-CKLVFF was confirmed using HPLC and ESI-MS. Storage of flavin-CKLVFF in DMSO at −30 °C for 7 days resulted in no detectable deposition. In contrast, flavin-CKLVFF formed deposits when stored in water at −30 °C for 1 day, but no deposit was observed in the aqueous solution of flavin-CKLVFF after 7 days storage in the presence of 0.1% Triton X-100.

Electrodeposited silver layers obtained from high-cyanide silver plating solution are widely applied for connectors and switches of automobiles. However, few groups have discussed the relationship between the crystal structure of silver layers and their properties. In this study, the effect of the concentration of Se, added as a brightener to high-cyanide silver plating solution, was investigated by XRD and EBSD analysis for electrodeposited silver layers with {200} orientation. By optimizing the concentration of Se in the silver plating solution, the {200} orientation ratio of the silver layer was increased to as high as 94%. Since the diffusion of Cu from the Cu substrate used in this study into the silver layer was inhibited, the silver layer with the high {200} orientation ratio exhibited good electrical contact resistance of the surface of 1.3mΩ after a heating test performed at 200°C for 74h. In addition, the silver layer had good bend formability. The results of XRD analysis confirmed that the recrystallization of the electrodeposited silver layer occurred at room temperature within several hours, thus increasing the {200} orientation ratio of the silver layer.

Guanine is the most easily oxidized among the four DNA bases, and some guanine-rich sequences can form quadruplex structures. In a previous study using 6-mer DNA d(TGGGGT), which is the shortest oligomer capable of forming quadruplex structures, we demonstrated that guanine oxidation products of quadruplex DNA differ from those of single-stranded DNA. Therefore, the hotooxidation products of double-stranded DNA (dsDNA) may also differ from that of quadruplex or single-stranded DNA, with the difference likely explaining the influence of DNA structures on guanine oxidation pathways. In this study, the guanine oxidation products of the dsDNA d(TGGGGT)/d(ACCCCA) were analyzed using HPLC and electrospray ionization-mass spectrometry (ESI-MS). As a result, the oxidation products in this dsDNA were identified as 2,5-diamino-4H-imidazol-4-one (Iz), 8-oxo-7,8-dihydroguanine (8oxoG), dehydroguanidinohydantoin (Ghox), and guanidinohydantoin (Gh). The major oxidation products in dsDNA were consistent with a combination of each major oxidation product observed in single-stranded and quadruplex DNA. We previously reported that the kinds of the oxidation products in single-stranded or quadruplex DNA depend on the ease of deprotonation of the guanine radical cation (G•+) at the N1 proton. Similarly, this mechanism was also involved in dsDNA. Deprotonation in dsDNA is easier than in quadruplex DNA and more difficult in single-stranded DNA, which can explain the formation of the four oxidation products in dsDNA.

Nuclear transcription factor nuclear factor-kappa B (NF-κB) has diverse pathophysiological functions, and NF-κB inhibitors are considered to be candidates for multiple therapeutic applications. We previously reported a novel triazine-based NF-κB inhibitor, 2-anilino-4,6-dichloro-1,3,5-triazine (NI241), that directly inhibits DNA binding of NF-κB. Here, we report synthesis of a series of triazine derivatives and evaluation of their structure-activity relationships for NF-κB inhibition. We found that 2-amino-4,6-dichloro-1,3,5-triazine substructure is essential for the inhibitory activity of the lead compound NI241, and modification of NI241 by introduction of an m-methoxy substituent on the phenyl ring afforded the more potent derivative 28. The structure-activity relationships identified in this study suggested a possible mechanism of irreversible NF-κB inhibition by NI241, and should be helpful in the design of other NF-κB inhibitors.

The nucleobase derivative, 2,2,4-triamino-5(2H)-oxazolone (Oz), is an oxidation product of guanine or of 8-oxo-7,8-dihydroguanine that causes G-to-C transversions in DNA. Human NEIL1 (hNEIL1) and NTH1 (hNTH1) are homologues of two prokaryotic base excision repair enzymes, FPG/NEI and NTH, respectively. Here, we demonstrated that hNEIL1 and hNTH1 cleave Oz sites as efficiently as 5-hydroxyuracil sites. Thus, hNEIL1 and hNTH1 can repair Oz lesions. Furthermore, the nicking activities of these enzymes are largely independent of nucleobases opposite Oz; this finding indicates that removing Oz from Oz:G and Oz:A base pairs might cause an increase in the rate of point mutations in human cells.

DNA is constantly exposed to endogenous and exogenous oxidative stresses. Damaged DNA can cause mutations, which may increase the risk of developing cancer and other diseases. G:C-C:G transversions are caused by various oxidative stresses. 2,2,4-Triamino-5(2H)-oxazolone (Oz), guanidinohydantoin (Gh)/iminoallantoin (Ia) and spiro-imino-dihydantoin (Sp) are known products of oxidative guanine damage. These damaged bases can base pair with guanine and cause G:C-C:G transversions. In this study, the stabilization energies of these bases paired with guanine were calculated in vacuo and in water. The calculated stabilization energies of the Ia:G base pairs were similar to that of the native C:G base pair, and both bases pairs have three hydrogen bonds. By contrast, the calculated stabilization energies of Gh:G, which form two hydrogen bonds, were lower than the Ia:G base pairs, suggesting that the stabilization energy depends on the number of hydrogen bonds. In addition, the Sp:G base pairs were less stable than the Ia:G base pairs. Furthermore, calculations showed that the Oz:G base pairs were less stable than the Ia:G, Gh:G and Sp:G base pairs, even though experimental results showed that incorporation of guanine opposite Oz is more efficient than that opposite Gh/Ia and Sp.

Self-annealing behavior of an electrodeposited Ag film which has been preferentially oriented in (001) direction was investigated by electron backscatter diffraction pattern (EBSP) analysis. There are few clear grains of micrometer order in the initial state just after electrodepositing. The result shows that the electrodeposited film would be in amorphous state or could be consisted of very fine grains which size cannot be analyzed by EBSP. Self-annealing starts in storage at R.T. for a few hours and recrystallization almost completes in the storage time of 6 h. Recrystallized grains with relatively random orientation and a few micrometer order size have nucleate in storage time of a few hours. Afterward, (001) oriented grains preferentially grow in the self-annealing process. During self-annealing, the area fraction of (001) oriented grains increases rapidly and saturates in the range from 70 % to 80 % at the storage time over 6 h. The area fraction of (111) oriented grains slightly increases with increasing storage time, but it becomes at most 10 % even when self-annealing process has completed. On the contrary, the area fraction of (101) oriented grains decreases with increasing storage time and it becomes almost 0 % at the storage time over 6 h. Two patterns were found for formation of (001) oriented grains. One is that (001) orientation occurs at the same time as recrystallization and (001) oriented grains grow. In the other pattern, recrystallized grains oriented to near (001) in self-annealing process, subsequently the grains tilted from (001) are rotated to (001) by further storage.

Severe combined immune deficiency (SCID) mice were more sensitive to systemic delivery of bleomycin (BLM) than the wild-type strain, and died from esophagitis. Lung injury in the SCID mice by its intratracheal injection, however, was of comparable degree but with less lymphocyte infiltration than that in the wild-type mice. Macrophages and lymphocytes increased transiently in bronchoalveolar lavage fluid of SCID mice, whereas their increase in wild-type was continuous. Unsustainable inflammation in the lung might reduce BLM-induced lung injury in BLM-sensitive SCID mice.

We fabricated direct-bonded quasi-phase-matched (QPM) LiNbO3 (LN) ridge waveguides for difference frequency generation (DFG) in the 2.7-µm wavelength range, and obtained a conversion efficiency of 87%/W. We showed that dips in the DFG tuning curve originated from the absorption of H2O in air and the O–H absorption in the LN crystal exhibited no influence on DFG when we used the type-0 phase-matching condition. We confirmed that the direct-bonded QPM-LN ridge waveguide is suitable for achieving high-efficiency DFG in the 2.7-µm range.

The feasibility of making ferrite at ambient temperature from aqueous solutions of simulated acid mine drainage was investigated following our previous report. In this paper, qualitative and quantitative effects of coexisting ions such as Mn(II), Zn(II), Al(III) and Si(IV), on ferrite formation were investigated.As the first step, influences of several coexisting ions on the settling volume of the precipitates were investigated. In the case of Mn(II) or Zn(II) coexisting system, which are well known to have the capacity to substitute to the part of the lattice of ferrite, the settling volume increased a little, but in the case of Al(III) or Si(IV) coexisting system, which are known to impede ferrite formation, the settling volume considerably increased. However, the interference of Al(III) or Si(IV) to ferrite formation was weakened in the sludge recycling system.Secondly, their influences on the yield of magnetite or ferrite, which are calculated by the total oxygen consumption in the aerial oxidation reaction test, were investigated. The yield of magnetite decreases with an increase of Al(III) or Si(IV), but their interferences on ferrite formation were weakened in the presence of restored magnetite seed.Thirdly, their influences on the reaction rate in the aging process were also examined by solid-solid reaction test in which Fe(OH)2, FeOOH and coexisting ions reacted directly in reduction atmosphere and at a fixed pH. The reaction coefficient considerably decreased not only by Al(III) or Si(IV), but also by Mn(II) or Zn(II), which are estimated not to impede ferrite formation.

Photosensitized oxidation of guanine provides various oxidation products, including 8-oxoguanine (8-oxoG) and imidazolone. Riboflavin (vitamin B2) is known as an effective photosensitizer for oxidation of guanine. Here, we show the user-friendly synthesis and photoreaction of a flavin-linked oligonucleotide; the practical synthesis of a hydroxyethyl-flavin (2) from commercially available riboflavin; and the preparation of a flavin-linked oligonucleotide using the phosphoramidite of 2. To demonstrate the usefulness of this method, the flavin-linked oligomer flavin-5′-d(T6CCT6)-3′ was synthesized. Flavin-5′-d(T6CCT6)-3′ and its complementary 5′-d(A6G8-oxoGA6)-3′ were irradiated under UV light (366 nm) at neutral pH. Enzymatic digestion of the irradiated mixture with P1 nuclease and alkaline phosphatase indicated that the 8-oxoG residue was oxidized to imidazolone. These results demonstrate that 8-oxoG is effectively oxidized to imidazolone by photosensitization of the terminal flavin via a hole-transfer mechanism, and imidazolone is formed by one-electron oxidation of 8-oxoG at neutral pH.

Mutations induced by oxidative DNA damage can cause diseases such as cancer. In particular, G:C-T:A and G:C-C:G transversions are caused by oxidized guanine and have been observed in the p53 and K-ras genes. We focused on an oxidized form of guanine, 2,2,4-triamino-5(2H)-oxazolone (Oz), as a cause of G:C-C:G transversions based on our earlier elucidation that DNA polymerases (Pols) α, β, γ, ε, η, I, and IV incorporate dGTP opposite Oz. The nucleotide insertion and extension of Pols δ, ζ, ι, κ, and REV1, belonging to the B- and Y-families of DNA polymerases, were analyzed for the first time. Pol δ incorporated dGTP, in common with other replicative DNA polymerases. Pol ζ incorporated dGTP and dATP, and the efficiency of elongation up to full-length beyond Oz was almost the same as that beyond G. Although nucleotide incorporation by Pols ι or κ was also error-prone, they did not extend the primer. On the other hand, the polymerase REV1 predominantly incorporated dCTP opposite Oz more efficiently than opposite 8-oxo-7,8-dihydroguanine, guanidinohydantoin, or tetrahydrofuran. Here, we demonstrate that Pol ζ can efficiently replicate DNA containing Oz and that REV1 can prevent G:C-C:G transversions caused by Oz.