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Trinucleotide repeat sequences (TRSs), consisting of 10 unique classes of repeats in DNA, are members of microsatellites and abundantly and non-randomly distributed in many eukaryotic genomes. The lengths of TRSs are mutable, and the expansions of several TRSs are implicated in hereditary neurological diseases. However, the underlying causes of the biased distribution and the dynamic properties of TRSs in the genome remain elusive. Here, we examined the effects of TRSs on nucleosome formation in vivo by histone H4–S47C site-directed chemical cleavages, using well-defined yeast minichromosomes in which each of the ten TRS classes resided in the central region of a positioned nucleosome. We showed that (AAT)12 and (ACT)12 act as strong nucleosome-promoting sequences, while (AGG)12 and (CCG)12 act as nucleosome-excluding sequences in vivo. The local histone binding affinity scores support the idea that nucleosome formation in TRSs, except for (AGG)12, is mainly determined by the affinity for the histone octamers. Overall, our study presents a framework for understanding the nucleosome-forming abilities of TRSs.

Introduction Measurement of blood Favipiravir (FPV) levels and accumulation of data in COVID-19 patients are critical for assessing FPV efficacy and safety. We performed a retrospective study based on measurements of blood levels of FPV and related factors in COVID-19 patients admitted to our hospital. Furthermore, we also investigated the association between blood FPV levels and uric acid level alterations before and after FPV administration. Methods We enrolled 27 COVID-19 patients who had received FPV treatment at Hokushin General Hospital from April 1 to December 31, 2020. Age, gender, COVID-19 severity, presence of comorbidities, and laboratory data for each subject were investigated to identify factors that correlate with blood FPV levels. Uric acid levels were measured before and after FPV administration and a difference between the levels (i.e., a change of uric acid level) was evaluated. Results When a significant univariate variable was input by the stepwise method and a combination of variables that maintained statistical superiority was searched, serum ferritin was the only factor that independently affected blood FPV level. Furthermore, in the high-FPV group (20 μg/mL or more), a significant increase in uric acid levels was observed after FPV administration. The increment value was significantly larger than that in the low-FPV group (less than 20 μg/mL). Conclusions Ferritin level was an important independent factor inversely affecting blood FPV level. Furthermore, a high blood FPV level induced the elevation of uric acid levels in COVID-19 treatment.

In eukaryotic genomes, the nucleosome is the structural and functional unit, and its position and dynamics are important for gene expression control and epigenetic regulation. Epigenetics is an important mechanism in development and homeostasis, and aberrant epigenetics is a common feature in cancer. Although understanding the mechanistic basis that determines nucleosome positioning in vivo is important for elucidating chromatin function and epigenetic regulation, a suitable experimental system to examine such mechanisms is still being developed. Herein, we examined nucleosome organization in yeast minichromosomes, using a parallel mapping method we previously developed that involve site-directed chemical cleavage and micrococcal nuclease digestion. This parallel mapping is capable of revealing the differences in the occupancy and the stability of individual nucleosomes in the minichromosome. Based on the previously characterized minichromosome, we engineered a set of new minichromosomes, aimed at strengthening the positioning of the nucleosomes. The site-directed chemical mapping method demonstrated that the nucleosome positioning in the newly designed yeast minichromosome system was significantly more stable. This system will be useful for elucidating the determinants of nucleosome organization, such as DNA sequences and/or nucleosome binding proteins, and for determining the relationships between nucleosome dynamics and epigenetic regulation, which are targets for therapeutic agents.

Micrococcal nuclease (MNase) has been widely used for analyses of nucleosome locations in many organisms. However, due to its sequence preference, the interpretations of the positions and occupancies of nucleosomes using MNase have remained controversial. Next-generation sequencing (NGS) has also been utilized for analyses of MNase-digests, but some technical biases are commonly present in the NGS experiments. Here, we established a gel-based method to map nucleosome positions in Saccharomyces cerevisiae, using isolated nuclei as the substrate for the histone H4 S47C-site-directed chemical cleavage in parallel with MNase digestion. The parallel mapping allowed us to compare the chemically and enzymatically cleaved sites by indirect end-labeling and primer extension mapping, and thus we could determine the nucleosome positions and the sizes of the nucleosome-free regions (or nucleosome-depleted regions) more accurately, as compared to nucleosome mapping by MNase alone. The analysis also revealed that the structural features of the nucleosomes flanked by the nucleosome-free region were different from those within regularly arrayed nucleosomes, showing that the structures and dynamics of individual nucleosomes strongly depend on their locations. Moreover, we demonstrated that the parallel mapping results were generally consistent with the previous genome-wide chemical mapping and MNase-Seq results. Thus, the gel-based parallel mapping will be useful for the analysis of a specific locus under various conditions.

In this study, we investigated the interaction between apple polyphenols (AP; mainly consisting of procyanidin (PC) from an apple) and staphylococcal enterotoxin A (SEA), and the inhibitory effects of AP on SEA activity. According to the degree of polymerization, in particularly highly polymerized PC (more than pentamer) strongly interacted with SEA. The binding affinity of AP with SEA molecules was determined using Biacore analysis. AP reacted with SEA immobilized on a Biacore sensor chip. After treatment with pepsin and pancreatin, to examine the changes of binding affinity of AP in intragastric conditions, AP maintained interaction with SEA. We examined whether AP inhibits the proliferation and interferon-γ (IFN-γ) production induced by SEA in mouse spleen cells. AP strongly inactivated the proliferation and IFN-γ production induced by SEA. These results suggest that AP, which has a higher degree of polymerization, inactivates stronger biological activity of SEA through interaction with SEA. Our studies are the first to demonstrate the relationship between the degree of polymerization of AP and the inhibitory effects on SEA activities.

A chromanone glycoside, 5-β- d -glucopyranosyloxy-7-hydroxy-2-isopropylchromanone, and two acylphloroglucinol glycosides, 2-(3-methylbutyryl)phloroglucinol-4,6-di-C-β- d -glucopyranoside and 2-isobutyrylphloroglucinol-1,5-di-O-β- d -glucopyranoside, along with 15 known compounds were isolated from the bracts of hops (Humulus lupulus L.). Their structures were elucidated based on spectroscopic data, including TOFMS and 1D/2D NMR.

Aqueous–aqueous two-phase (AATP) systems composed of polyethylene glycol (PEG) (molecular mass, Mr:1000–8000) and dextran (Mr:40,000) were evaluated for purification of maltose binding protein tagged-histone deacetylase (MBP-HDAC) by counter-current chromatography (CCC). CCC purification of an MBP-HDAC from Escherichia coli cell-lysate was successfully demonstrated with a 7.0% PEG 3350–10% dextran T40 system containing 10 mM potassium phosphate buffer at pH 9.0. After CCC purification, both polymers in the CCC fractions were easily removed by ultrafiltration in a short period of time. The collected fractions containing target protein were analyzed by an HPLC-based in vitro assay as well as sodium dodecyl sulfate polyacrylamide gel electrophoresis. MBP tag was digested from fusion HDAC during the CCC separation and native HDAC was purified by one-step operation with well preserved deacetyl enzyme activity.

High-speed counter-current chromatography (HSCCC) using the type-J coil planet centrifuge was applied to compositional analysis of tea catechins and separation of other food-related polyphenols. The HSCCC separation of nine different standard compounds and those from extracts of commercial tea leaves was performed with a two-phase solvent system composed of tert-butyl methyl ether-acetonitrile-0.1% aqueous trifluoroacetic acid (TFA) (2:2:3, v/v/v) by eluting the upper organic phase at a flow rate of 2 ml/min. The main compounds in the extract of non-fermented green tea were found to be monomeric catechins, their galloylated esters and caffeine. In addition to these compounds, oxidized pigments, such as hydrophobic theaflavins (TFs) and polar thearubigins (TRs) were also separated and detected from the extracts of semi-fermented oolong tea and fermented black tea. Furthermore, several food-related polyphenols, such as condensed catechin oligomers (procyanidins), phenolic acids and flavonol glycosides were clearly separated under the same HSCCC condition. These separation profiles of HSCCC provide useful information about the hydrophobic diversity of these bioactive polyphenols present in various types of teas and food products.

Glucosyltransferase (GTF), a cariogenic factor of Streptococcus sobrinus (SS), was extracted from a large quantity of cell culture medium by batch extraction with aqueous polymer two‐phase systems (APTPs). The small quantity of the extract was further purified by countercurrent chromatography (CCC) using polyethylene glycol (PEG) 8000‐dextran T500 system at pH 9.2, by eluting the impurities with the upper mobile phase at 1.0 mL/min. After the elution, the GTF still remaining in the dextran‐rich lower stationary phase was collected. The GTF fractions were subjected to hydroxyapatite chromatography to eliminate polymers, such as PEG 8000 and dextran T500. Purified fractions were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS‐PAGE) and GTF enzyme activity, which rose over 270 fold from that in the original culture medium.

A novel sequential chromatographic technique was applied to the comprehensive separation of polyphenols and related compounds from a hop bract extract. Over 100 types of constituents were effectively isolated from only 25 g of extract in high yields by high-speed countercurrent chromatography followed by hydrophilic interaction chromatography and reversed-phase high performance liquid chromatography. Among the materials isolated, the structures of 39 compounds were elucidated on the basis of their spectroscopic data including electrospray ionization time-of-flight mass spectrometry and one-dimensional/two-dimensional nuclear magnetic resonance. Three new compounds, 1 known compound identified for the first time in plants, and 20 known compounds that have not been reported in hops, were found. The hop bract extract also contained an abundance of highly oligomeric proanthocyanidins, which consisted of B-type procyanidin structures.

We studied here the antiallergic effect of apple condensed tannins (ACT) administered orally to a type I allergy model mouse transplanted with an IgEL a2 hybridoma secreting anti-2,4,6-trinitrophenyl (TNP) immunoglobulin E (IgE). The oral administration of ACT significantly inhibited the ear swelling responses at 1 h after antigen-stimulation with picryl chloride. The response was dose dependent within 0.1 to 10 mg/mouse. The inhibition of the ear swelling response reached the maximal level (90% inhibition) when ACT was administered 2 h before the antigen challenge. These findings suggest that ACT has an antiallergic effect on type I allergic symptoms.

A crude apple polyphenol (CAP) fraction partially purified from unripe apples was found to inhibit adipose differentiation in mouse fibroblast 3T3-L1 cells. CAP inhibited the increase in intracellular levels of glycerophosphate-3-dehydrogenase (GPDH), one of the most important enzymes in the pathway for triacylglycerol biosynthesis, that occurs upon differentiation of 3T3-L1 cells into adipocytes and decreased the triglyceride content of the cells. In particular, apple condensed tannins (ACT), purified from CAP, inhibited the increase in GPDH activity when these cells differentiated. In contrast, phloridzin, (+)-catechin, and (−)-epicatechin, which were also present in the CAP fraction, decreased the triglyceride content of the cells but did not inhibit the increase in GPDH activity These results suggest that ACT such as procyanidins inhibit the differentiation of preadipocytes into adipocytes.

Counter-current chromatography (CCC) using a cross-axis coil planet centrifuge (X-axis CPC) was applied to the purification of glucosyltransferase (GTF) from a cell-lysate of cariogenic bacteria. The purification was performed using an aqueous polymer two-phase system composed of 4.4% (w/w) polyethylene glycol (PEG) 8000–6% (w/w) dextran T500 containing 10 mM phosphate buffer at pH 9.2 by eluting the upper phase (UP) at 1.0 ml/min. The bacterial GTF in the cell-lysate of Streptococcus mutans was selectively retained in the dextran-rich lower stationary phase. The column contents were diluted and subjected to hydroxyapatite (HA) chromatography to remove the polymers from the GTF. Fractions eluted with 500 mM potassium phosphate buffer were analyzed by GTF enzymatic activity as well as sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS–PAGE). The GTF purity in the final product was increased about 87 times as that in the cell-lysate with a good recovery rate of about 79% through this purification process.

The inhibitory effects of apple polyphenols (APP) on the synthesis of water-insoluble glucans by glucosyltransferases (GTF) of streptococci of the mutans group and on the sucrose-dependent adherence of the bacterial cells were examined in vitro. APP markedly inhibited the activity of GTF purified from the cariogenic bacterial cells. However, APP showed no significant effect on the growth of the cariogenic bacteria. The strongest GTF inhibitors in APP were apple condensed tannins (ACT), a mixture of procyanidins. The 50% inhibitory doses of ACT against the GTF of S. sobrinus and that of S. mutans were 1.5 microgram/mL and 5 microgram/mL, respectively. The ACT efficacy largely depended upon the degree of polymerization. Interestingly, while the other polyphenols known to inhibit GTF such as tannic acid markedly inhibited salivary alpha-amylase activity, APP and ACT only scarcely inhibited that enzyme activity. This means that APP and ACT might selectively inhibit the bacterial GTF activity under oral conditions.

The anti-allergic activities of polyphenol fractions extracted from immature fruits of apple (Rosaceae, Malus sp.) were evaluated by in vitro assays. A crude apple polyphenol (CAP) fraction, which had been obtained from the juice of immature apples by reverse-phase column chromatography, was further purified by LH-20 column chromatography to obtain an apple condensed tannin (ACT) fraction consisting of linear oligomeric epicatechins from the dimer to pentadecamer. ACT strongly inhibited the release of histamine from rat basophilic leukemia (RBL-2H3) cells stimulated by the antigen-stimulation and from rat peritoneal mast cells stimulated by compound 48/80. The IC50 values for histamine release were 30 micrograms/ml and 25 micrograms/ml, respectively. ACT also inhibited hyaluronidase activity and the increase in intracellular free calcium concentration in RBL-2H3 cells stimulated with the antigen. These results suggest that ACT affected early signal transduction including the calcium influx.

It was confirmed that the flexible arm region of HU alpha forms an antiparallel beta-sheet and that all of the residues of phenylalanines, together with some of leucines and/or valines, form a hydrophobic core within the dimer of HU alpha. HU alpha protein alone is thermally labile and melts at 38 degrees C, but it becomes remarkably stabilized and melts at 59 degrees C in the presence of DNA. Several resonances from both HU alpha and DNA perturbed by their complex formation, notably those of His C-2 and C-4 protons, downfield shifted C alpha protons in the antiparallel beta-sheet, as well as Arg C delta and Lys C epsilon protons. The results indicated that a beta-sheet region of HU alpha binds to DNA, and also showed that rapid equilibrium occurs on the NMR time scale between bound and unbound states of HU alpha. A few intermolecular nuclear Overhauser effects (NOEs) were also observed between the protein and H1' protons of DNA in the complex, suggesting that HU alpha binds primarily to the minor groove of DNA.