Revision of the Massarineae (Pleosporales, Dothideomycetes).

We here taxonomically revise the suborder Massarineae (Pleosporales, Dothideomycetes, Ascomycota). Sequences of SSU and LSU nrDNA and the translation elongation factor 1-alpha gene (tef1) are newly obtained from 106 Massarineae taxa that are phylogenetically analysed along with published sequences of 131 taxa in this suborder retrieved from GenBank. We recognise 12 families and five unknown lineages in the Massarineae. Among the nine families previously known, the monophyletic status of the Dictyosporiaceae, Didymosphaeriaceae, Latoruaceae, Macrodiplodiopsidaceae, Massarinaceae, Morosphaeriaceae, and Trematosphaeriaceae was strongly supported with bootstrap support values above 96 %, while the clades of the Bambusicolaceae and the Lentitheciaceae are moderately supported. Two new families, Parabambusicolaceae and Sulcatisporaceae, are proposed. The Parabambusicolaceae is erected to accommodate Aquastroma and Parabambusicola genera nova, as well as two unnamed Monodictys species. The Parabambusicolaceae is characterised by depressed globose to hemispherical ascomata with or without surrounding stromatic tissue, and multi-septate, clavate to fusiform, hyaline ascospores. The Sulcatisporaceae is established for Magnicamarosporium and Sulcatispora genera nova and Neobambusicola. The Sulcatisporaceae is characterised by subglobose ascomata with a short ostiolar neck, trabeculate pseudoparaphyses, clavate asci, broadly fusiform ascospores, and ellipsoid to subglobose conidia with or without striate ornamentation. The genus Periconia and its relatives are segregated from the Massarinaceae and placed in a resurrected family, the Periconiaceae. We have summarised the morphological and ecological features, and clarified the accepted members of each family. Ten new genera, 22 new species, and seven new combinations are described and illustrated. The complete ITS sequences of nrDNA are also provided for all new taxa for use as barcode markers.

Associations of PD-L1, PD-L2, and HLA class I expression with responses to immunotherapy in patients with advanced sarcoma: post hoc analysis of a phase 1/2 trial.

BACKGROUND: Although immunotherapy is thought to be a promising cancer treatment, most patients do not respond to immunotherapy. In this post hoc analysis of a phase 1/2 study, associations of programmed death ligand 1 (PD-L1), PD-L2, and HLA class I expressions with responses to dendritic cells (DCs)-based immunotherapy were investigated in patients with advanced sarcoma. METHODS: This study enrolled 35 patients with metastatic and/or recurrent sarcomas who underwent DC-based immunotherapy. The associations of PD-L1, PD-L2, and HLA class I expressions in tumor specimens, which were resected before immunotherapy, with immune responses (increases of IFN-γ and IL-12) and oncological outcomes were evaluated. RESULTS: Patients who were PD-L2 (+) showed lower increases of IFN-γ and IL-12 after DC-based immunotherapy than patients who were PD-L2 (-). The disease control (partial response or stable disease) rates of patients who were PD-L1 (+) and PD-L1 (-) were 0% and 22%, respectively. Disease control rates of patients who were PD-L2 (+) and PD-L2 (-) were 13% and 22%, respectively. Patients who were PD-L1 (+) tumors had significantly poorer overall survival compared with patients who were PD-L1 (-). No associations of HLA class I expression with the immune response or oncological outcomes were observed. CONCLUSIONS: This study suggests that PD-L1 and PD-L2 are promising biomarkers of DC-based immunotherapy, and that addition of immune checkpoint inhibitors to DC-based immunotherapy may improve the outcomes of DC-based immunotherapy.

Adaptive optical phase estimation using time-symmetric quantum smoothing.

Quantum parameter estimation has many applications, from gravitational wave detection to quantum key distribution. The most commonly used technique for this type of estimation is quantum filtering, using only past observations. We present the first experimental demonstration of quantum smoothing, a time-symmetric technique that uses past and future observations, for quantum parameter estimation. We consider both adaptive and nonadaptive quantum smoothing, and show that both are better than their filtered counterparts. For the problem of estimating a stochastically varying phase shift on a coherent beam, our theory predicts that adaptive quantum smoothing (the best scheme) gives an estimate with a mean-square error up to 2sqrt[2] times smaller than nonadaptive filtering (the standard quantum limit). The experimentally measured improvement is 2.24+/-0.14.

Inhibiting effects of Streptococcus salivarius on competence-stimulating peptide-dependent biofilm formation by Streptococcus mutans.

INTRODUCTION: The effects of Streptococcus salivarius on the competence-stimulating peptide (CSP)-dependent biofilm formation by Streptococcus mutans were investigated. METHODS: Biofilms were grown on 96-well microtiter plates coated with salivary components in tryptic soy broth without dextrose supplemented with 0.25% sucrose. Biofilm formations were stained using safranin and quantification of stained biofilms was performed by measuring absorbance at 492 nm. RESULTS: S. mutans formed substantial biofilms, whereas biofilms of S. salivarius were formed poorly in the medium conditions used. Furthermore, in combination cultures, S. salivarius strongly inhibited biofilm formation when cultured with S. mutans. This inhibition occurred in the early phase of biofilm formation and was dependent on inactivation of the CSP of S. mutans, which is associated with competence, biofilm formation, and antimicrobial activity of the bacterium, and is induced by expression of the comC gene. Comparisons between the S. mutans clinical strains FSC-3 and FSC-3DeltaglrA in separate dual-species cultures with S. salivarius indicated that the presence of the bacitracin transport ATP-binding protein gene glrA caused susceptibility to inhibition of S. mutans biofilm formation by S. salivarius, and was also associated with the regulation of CSP production by com gene-dependent quorum sensing systems. CONCLUSION: It is considered that regulation of CSP by glrA in S. mutans and CSP inactivation by S. salivarius are important functions for cell-to-cell communication between biofilm bacteria and oral streptococci such as S. salivarius. Our results provide useful information for understanding the ecosystem of oral streptococcal biofilms, as well as the competition between and coexistence of multiple species in the oral cavity.

Melain G, a cysteine protease from green fruits of the bead tree, Melia azedarach: a protease affected by specific amino acids at P3 position.

A protease (melain G) was isolated from the greenish fruits of the bead tree, Melia azedarach var. japonica Makino. Melain G shares 110 identical amino acid residues (50%) with papain, 112 (51%) with actinidain, and 91 (41%) with stem bromelain. From the sites cleaved in the oxidized insulin B-chain and synthetic oligopeptide substrates by melain G, the enzyme preferred small amino acid residues such as Gly or Ser at the P2 position and negatively charged residues such as glutamic or cysteic acid at the P3 position. This is clearly different from the specificity of papain, which prefers the large hydrophobic amino acid residues such as Phe, Val, and Leu at the P2 position. Accordingly, it is presumed that the bottom of the S2 pocket of melain G is shallow due to the presence of a Phe residue, and a bulky P2 substrate (for example Phe residue) is not preferred by the enzyme. Negatively charged residues at the P3 position of substrates well suited the S3 site of melain G for making a salt bridge. It is likely that Arg61 is the S3 position of melain G by analogy with papain.

Amino acid sequence and some properties of phytolacain G, a cysteine protease from growing fruit of pokeweed, Phytolacca americana.

A protease, phytolacain G, has been found to appear on CM-Sepharose ion-exchange chromatography of greenish small-size fruits of pokeweed, Phytolacca americana L, from ca. 2 weeks after flowering, and increases during fruit enlargement. Reddish ripe fruit of the pokeweed contained both phytolacain G and R. The molecular mass of phytolacain G was estimated to be 25.5 kDa by SDS-PAGE. Its amino acid sequence was reconstructed by automated sequence analysis of the peptides obtained after cleavage with Achromobacter protease I, chymotrypsin, and cyanogen bromide. The enzyme is composed of 216 amino acid residues, of which it shares 152 identical amino acid residues (70%) with phytolacain R, 126 (58%) with melain G, 108 (50%) with papain, 106 (49%) with actinidain, and 96 (44%) with stem bromelain. The amino acid residues forming the substrate binding S(2) pocket of papain, Tyr67, Pro68, Trp69, Val133, and Phe207, were predicted to be replaced by Trp, Met, His, Ala, and Ser in phytolacain G, respectively. As a consequence of these substitutions, the S(2) pocket is expected to be less hydrophobic in phytolacain G than in papain.

Role of thymidine phosphorylase and dihydropyrimidine dehydrogenase in tumour progression and sensitivity to doxifluridine in gastric cancer patients.

This study was designed to investigate the role of thymidine phosphorylase (TP) and dihydropyrimidine dehydrogenase (DPD) on tumour progression and sensitivity to 5'-deoxy-5-fluorouridine (5'-DFUR). Tumour tissue was obtained from surgically resected samples from 93 patients with primary gastric cancer. Tumour TP and DPD expression levels were determined by the enzyme-linked immunosorbent assay (ELISA) system and compared with several clinicopathological factors and in vitro sensitivity to 5'-DFUR. DPD showed no correlation with any clinicopathological factors. However, the TP level was significantly correlated with the depth of tumour, lymphatic invasion and venous invasion. In comparison with 5'-DFUR sensitivity, there was a weak inverse correlation between the DPD level and the sensitivity to 5'-DFUR (r(s)=-0.361). Furthermore, the TP/DPD ratio showed a significant correlation with 5'-DFUR sensitivity (r(s)=0.634). In a subgroup of patients with postoperative 5'-DFUR administration, the survival rate was significantly better in patients with a high TP/DPD ratio (n=8) than in those with low TP/DPD ratio (n=14) (P=0.0140). These results suggest that sensitivity to 5'-DFUR is predictable by measurement of both TP and DPD levels.

Superior antitumour activity of S-1 in tumours with a high dihydropyrimidine dehydrogenase activity.

To elucidate the mechanism of the enhanced antitumour activity of S-1 (1 M tegafur, 0.4 M 5-chloro-2, 4-dihydroxypyridine, and 1 M potassium oxonate) in terms of the phosphorylation and degradation pathways of 5-fluorouracil (5-FU) metabolism, we investigated tumoral thymidylate synthase (TS) content, dihydropyrimidine dehydrogenase (DPD) activity, the TS inhibition rate (TS-IR), and 5-FU incorporated into RNA (F-RNA) in four human gastric cancer xenografts (MKN-28, MKN-74, GCIY and GT3TKB) and compared the results obtained with S-1 with those obtained with 5-FU and UFT (1 M tegafur, 4 M uracil). 5-FU was administered intraperitoneally (i.p.) to mice at a dose of 50 mg/kg, three times, on days 0, 4 and 8. S-1 and UFT were administered orally at doses of 10 and 24 mg/kg, respectively, once a day, for 9 consecutive days. Antitumour activity was evaluated as the maximum inhibition of tumour growth in each animal. S-1 showed a better antitumour activity than 5-FU and UFT in tumours with a high DPD activity (GCIY and GT3TKB). There were inverse correlations between the antitumour activity and both TS content and DPD activity in the 5-FU and UFT groups. However, no such correlations were observed in the S-1 group. In GCIY and GT3TKB xenografts, TS-IR was significantly higher in the S-1 group than in the 5-FU or UFT groups. In GT3TKB xenografts, the F-RNA level was significantly higher in the S-1 group than in the 5-FU or UFT groups. The superior cytotoxicity of S-1 appears to be attributable to both an increased inhibition of DNA synthesis and an enhanced blockade of RNA function against tumours with a high DPD activity.

Retinal vessel changes in galactose-fed dogs.

BACKGROUND: Retinal lesions similar to those in human early-stage diabetic retinopathy have been reported to occur in dogs fed galactose for long periods. Investigations of retinal changes, however, have been limited to studies of the intact retinal vasculature isolated by trypsin digestion. OBJECTIVE: To document the onset and progression of retinal lesions in galactose-fed dogs by the common clinical techniques of fundus color photography and fluorescein angiography. METHODS: Fourteen 6-month-old male beagles made aphakic in 1 eye were divided into a control group (4 dogs), receiving a diet containing 30% cellulose, and a galactosemic group (10 dogs), receiving a diet containing 30% galactose. The progression of retinal changes in these dogs was periodically monitored by color fundus photography and fluorescein angiography. RESULTS: Dogs fed a 30% galactose diet for 28 to 41 months were observed by fluorescein angiography and color fundus photography to develop, in order of frequency, microaneurysms, retinal hemorrhages, intraretinal microvascular abnormalities, retinal nonperfused areas, and varicose and serpiginous veins. These findings are similar to the early clinical retinal changes observed in humans with diabetes. CONCLUSION: These results confirm that galactosemic dogs are an appropriate and suitable animal model for investigating human diabetic retinopathy.

Cleavage specificity of cucumisin, a plant serine protease.

Cucumisin was isolated from prince melon sarcocarp by means of a simple purification procedure. Serine protease inhibitors such as soybean trypsin inhibitor, ovomucoid, and aprotinin had no effect on the enzyme activity. alpha 2-Macroglobulin showed 38% inhibition of the original caseinolytic activity of cucumisin. The favorable synthetic substrates for cucumisin were Glt-Ala-Ala-Pro-Leu-pNA and Suc-Ala-Ala-Pro-Phe-pNA. The constant (kcat/Km) for Suc-Ala-Pro-Ala-pNA was found to be 30 times greater than that for Suc-Ala-Ala-Ala-pNA. The substrate specificity of cucumisin for oligopeptides and proteins was shown to be broad.

Identification of the reactive histidine of cucumisin, a plant serine protease: modification with peptidyl chloromethyl ketone derivative of peptide substrate.

A radioactive peptidyl chloromethyl ketone derived from substrates of cucumisin, 3H-labeled Z-Ala-Ala-Pro-Phe-chloromethyl ketone (3H-ZAAPFCK), was synthesized. When cucumisin was incubated with a 100-fold molar excess of 3H-ZAAPFCK for 16 h, 98% of the cucumisin activity was inhibited and about 0.93 mol of 3H-ZAAPFCK was incorporated in 1 mol of cucumisin. The 3H-ZAAPFCK-modified cucumisin was reduced and pyridylethylated, and then digested by trypsin. The radioactive peptide fragment was isolated and its amino acid sequence was determined. The radioactive fragment contained 32 amino acid residues and the sequence around the labeled residue was found to be -Asp-Thr-Asn-Gly-(His)-Gly-Thr-His-Thr-Ala-. This sequence is analogous to that around the reactive site histidine residue of the subtilisin family.

Determination of pepstatin-sensitive carboxyl proteases by using pepstatinyldansyldiaminopropane (dansyl-pepstatin) as an active site titrant.

N-Pepstatinyl-N'-dansyldiaminopropane (dansyl-pepstatin) was prepared by the coupling of pepstatin A and N-dansyl-diaminopropane. The dansyl-pepstatin obtained strongly inhibited pepsin activity by forming a 1:1 complex. The fluorescence of the dansyl group (excitation at 320 nm, and emission near 520 nm) increased with the formation of the complex. The increase in fluorescence of dansyl-pepstatin solution was proportional to the amount of added pepsin, chymosin and cathepsin D until dansyl-pepstatin was saturated by these enzymes and at higher protease concentrations the fluorescence did not increase further. Therefore, the net amounts of active pepstatin-sensitive carboxyl proteases could be determined by detecting the inflection point of increased fluorescence upon addition of the protease to a dansyl-pepstatin solution of known concentration. Moreover, the protease concentrations of many samples were obtained easily by measurements of increased fluorescence compared with that caused by authentic protease solution. The minimum detectable amount of pepsin was about 20 pmol. On the other hand, the fluorescence did not increase upon mixing with inactivated pepsin, chymotrypsin, or trypsin. The K(i) value of dansyl-pepstatin for pepsin was similar to that of pepstatin A. It was possible to determine the amount of chymosin contained in rennet by this method. The inactivation curve of pepsin in pH 6.5 buffer was also determined quickly and easily by the use of this method. This assay method for pepstatin-sensitive carboxyl proteases is very simple and easy, and it is possible to determine the net amounts of active pepstatin-sensitive carboxyl proteases even in crude mixtures.

Mode of antibacterial action by gramicidin S.

To elucidate the mode of antibacterial action by gramicidin S (GS), a detailed experiment on GS distribution on bacteria cells was carried out. 14C-Labeled gramicidin S ([14C]GS) was incubated with cells of Gram-positive Bacillus subtilis and Gram-negative Escherichia coli, and the amount of [14C]GS adsorbed on the cells was measured. Adsorption on B. subtilis cells was observed from 1 microgram/ml of [14C]GS. As the concentration of [14C]GS increased, the amount adsorbed on B. subtilis increased discontinuously, producing a curve which had three plateaus. On the other hand, [14C]GS was not easily adsorbed on E. coli cells at lower concentrations, but the amount adsorbed increased above 6 micrograms/ml, and the cells were temporarily saturated with GS at 10 micrograms/ml, which is the minimum inhibitory concentration for E. coli. The amount of [14C]GS adsorbed on the protoplast membrane of B. subtilis was the same as that of natural cells. However, the amount of [14C]GS adsorbed on the cell wall dropped to about 20% of that of natural bacteria. These facts indicate that GS is adsorbed on the cell membrane of bacteria particularly. The uptake of amino acid or glucose in B. subtilis was inhibited by GS. Therefore, it is concluded that GS damages the phospholipid bilayer of the cell membrane by adsorption, and prevents the functioning of the cell membrane. The amount of [14C]GS adsorbed on the spheroplast membrane of E. coli increased remarkably as compared with natural cells, even at a lower concentration of GS. The poor GS adsorption on E. coli cells may be due to the permeability barrier of the E. coli cell wall.

Amino acid sequence around the reactive serine of cucumisin from melon fruit.

Cucumisin is a diisopropyl fluorophosphate-sensitive enzyme. The inactivation by DFP is accompanied by the formation of 1 mol of labeled serine residue per mol of enzyme. From the soluble portion of the chymotryptic digest of the diisopropyl phosphoryl derivative of cucumisin, two peptides containing phosphorus were isolated; their amino acid sequences were determined to be Gly-Thr-Ser(P)-Met and Asn-Ile-Ile-Ser-Gly-Thr-Ser(P)-Met, respectively. The four residues Gly-Thr-Ser-Met in the above amino acid sequence are identical with those of subtilisin.

Amino acid sequence and some properties of phytolacain R, a cysteine protease from full-growth fruits of pokeweed, Phytolacca americana.

A cysteine protease, phytolacain R from full-growth greenish fruits of pokeweed, Phytolacca americana L, was purified to electrophoretic homogeneity by a simple purification procedure employing CM-Sepharose ion-exchange chromatography. The enzyme was present in low content in the young fruits about 50 d after flowering but gradually accumulated in growing fruits. Its molecular mass was estimated to be ca. 23 kDa by SDS-PAGE, and its sugar content was zero. Its amino acid sequence was established by automated sequence analysis of the peptides obtained by cleavage with Achromobacter protease I, chymotrypsin, trypsin, and cyanogen bromide. The enzyme is composed of 218 amino acid residues, of which it shares 110 residues (50%) with papain, 104 (47%) with actinidain, and 87 (40%) with stem bromelain. The amino acid residues forming the substrate-binding the S2 pocket of papain, Tyr61, Tyr67, Pro68, Trp69, Val133, and Phe207, were predicted to be replaced by Gly, Trp, Met, His, Ala, and Met in phytolacain R, respectively. As a consequence of these substitutions, the S2 pocket is expected to be less hydrophobic in phytolacain R than in papain.

Adsorption of 14C-labeled gramicidin S on cell of bacteria.

Gramicidin S (GS) containing 14C-labeled proline was synthesized by a solid-phase method, and the labeled GS dihydrochloride was obtained as crystals. The labeled GS exhibited same antibacterial activity as natural GS. Strains sensitive to GS (B. subtilis and S. aureus) and an insensitive strain (E. coli) were treated with the labeled GS, and the amount of the labeled GS adsorbed on the cells was measured. GS was adsorbed rapidly on the cells of the sensitive strains; the amount adsorbed increased linearly with GS concentration up to 1-1.5 microgram/ml, and at a lower rate at above 1.5 microgram/ml. GS molecules covered most of the cell surface at the minimum inhibitory concentration of 1.5 microgram/ml; the number of molecules adsorbed per cell was 1.3-1.4 x 10(6). No GS was adsorbed by the insensitive strain.

Isolation and characterization of pepsinogen from Trimeresurus flavoviridis (Habu snake).

Pepsinogen was isolated from the gastric mucosa of Trimeresurus flavoviridis (Habu snake) by DEAE-cellulose and DEAE-Sepharose ion-exchange chromatographies, and Sephacryl S-200 gel-chromatography. The yield calculated from the crude extract was 29% with 6.2-fold purification. The purified pepsinogen gave a single band on both native- and SDS-PAGE. As no other active enzyme was detected on the chromatographies, it was concluded that the Habu snake has one major pepsinogen. The molecular mass of the pepsinogen was estimated to be 38 kDa by SDS-PAGE. The sequence of the N-terminal 26 amino acid residues was determined and compared with those of other pepsinogens. The N-terminal structure of Habu snake pepsinogen was more homologous with those of mammalian pepsinogens C than those of mammalian pepsinogens A. The pepsinogen was rapidly converted to pepsin by way of an intermediate form induced by acidification. The optimum pH of Habu snake pepsin for bovine hemoglobin was 1.5-2.0, and it retained full activity at pH 6.2 and 30 degrees C on incubation for 30 min. The optimum temperature for the snake pepsin was 50 degrees C and it was stable at 40 degrees C on incubation for 10 min. The proteolytic activity of the pepsin toward bovine hemoglobin was about two times higher than that of porcine pepsin A, however, the activity toward oxidized bovine insulin B-chain was lower than that of porcine pepsin A, and it did not hydrolyze oligopeptides. The specificity for oxidized bovine insulin B-chain of the pepsin was different from that of porcine pepsin A. Habu snake pepsin was inhibited by pepstatin A but not by serine, cysteine, or metallo protease inhibitors.

Prosopagnosia without topographagnosia and object agnosia associated with a lesion confined to the right occipitotemporal region.

A patient is presented who developed prosopagnosia with a recent occipitotemporal infarct in the distribution of the right posterior cerebral artery. He did not have topographical agnosia or object agnosia. He regained the ability to recognize faces of familiar persons, whereas he remained unable to identify faces of persons whom he met after the disease onset. This case demonstrates that prosopagnosia may occur as a deficit of matching a perceived face to a memory store of the face, and that the failure to recognize unfamiliar faces may be due to the inability to form memory stores of new faces. These deficits can occur in association with a lesion confined to the right occipitotemporal region.

Reserpine-induced reduction of in vivo binding of SCH 23390 and N-methylspiperone and its reversal by d-amphetamine.

In order to clarify the role of endogenous dopamine in the binding of [3H]SCH23390 and [3H]N-methylspiperone to the mouse striatum in vivo, the effects of reserpine and the reversal of these effects by d-amphetamine were investigated. Radioactivity was measured in the striatum and cerebellum following i.v. injection of each ligand into control and drug-treated mice. The ratio of radioactivity in the striatum to that in the cerebellum, plotted as a function of time, showed a linear correlation. Pretreatment with reserpine 24 h prior to injection of tracer significantly decreased the in vivo binding of both [3H]SCH23390 and [3H]N-methyl-spiperone in a dose-dependent manner. Saturation experiments indicated that these changes in in vivo binding were due mainly to changes in apparent affinity rather than to the number of binding sites available. Administration of d-amphetamine to reserpine-treated mice reversed the effect of reserpine in a dose-dependent manner. Blockade of dopamine D1 receptors with SCH23390 did not prevent the reversal by d-amphetamine of [3H]N-methylspiperone binding in vivo; however, treatment with haloperidol did prevent the effect of d-amphetamine on [3H]SCH23390 binding. These results suggest that dopamine D2 receptor-mediated neurotransmission might itself regulate the binding of dopamine to receptors in vivo.

Reduced size of right hippocampus in 39- to 80-year-old normal subjects carrying the apolipoprotein E epsilon4 allele.

Hippocampal size on magnetic resonance imaging was compared between normal subjects with the apolipoprotein E (apo E) epsilon4 allele (epsilon4/4, epsilon4/3, and epsilon4/2) and those without the epsilon4 allele (epsilon3/3, epsilon3/2, and epsilon2/2) in the age range of 39-80 years. The Mini-Mental State Examination (MMSE) scores did not differ between the two groups. The right hippocampal area and its ratio to hemisphere area and intracranial cavity area were significantly smaller in epsilon4 carriers than non-carriers, whereas hemisphere area did not differ between the two groups. These results suggest that as early as their forties, apo E epsilon4 allele carriers have a markedly smaller right hippocampus with no apparent cognitive impairment, which may have some significance in the high prevalence of the epsilon4 allele in Alzheimer's disease as well as other conditions that cause dementia.