The reactions of the hydroxymethyl radical with 1,3-dimethyluracil and 1,3-dimethylthymine

Hydroxymethyl radicals .CH2OH, generated by the radiolysis of methanol (0.5 mol dm-3) in N2O-saturated aqueous solutions, were reacted with 1,3-dimethyluracil or 1,3-dimethylthymine (10(-3) mol dm-3). The products were identified and their G values determined. It has been concluded that in 1,3-dimethyluracil .CH2OH attack occurs only at C(6) while in 1,3-dimethylthymine there is partitioning between addition (two-thirds) and H-abstraction from the C(5)-methyl group (one-third). A rate constant for CH2OH addition to 1,3-dimethyluracil of about 10(4) dm3 mol-1 s-1 is estimated. Complexities that may arise in the radiolysis of pyrimidines such as 1,3-dimethylthymine, apparently as a consequence of the formation of 5-alkylidenepyrimidines, are discussed. A value of 0.15 has been estimated for the disproportionation/combination ratio for the hydroxymethyl radical self-termination reaction.     

A multinomial model for estimating the size of a whale population from incomplete census data

This paper adapts the removal method of population size estimation to the problem of estimating the size of the western Arctic stock of bowhead whales. The whales are counted during their spring migration as they pass two census camps located near Point Barrow, Alaska. Whales seen at the first camp are "removed" from the population of concern to the second camp, where only whales missed by the first camp are counted. If both camps were in operation throughout the migration and if the probability of missing a whale were constant, the removal method would provide a population size estimate based on a trinomial model in which the size of the population would be the number of trials, whales counted by each camp would provide the observed cell totals, and whales missed by both camps would represent an unobserved cell total. Since the probability of missing a whale depends on visibility, we model the population size as the sum of the number of trials of several independent trinomial distributions, each of which represents a particular visibility condition occurring during the census. To account for the fact that watch cannot be maintained at both camps throughout the migration, we derive a confidence interval estimate of the number of trials under a more general model allowing for incomplete observation of totals within particular cells as well as for completely unobserved cells.     

Phylogenetic analysis of ten black yeast species using nuclear small subunit rRNA gene sequences

The nuclear small subunit rRNA genes of authentic strains of the black yeastsExophiala dermatitidis, Wangiella dermatitidis, Sarcinomyces phaeomuriformis, Capronia mansonii, Nadsoniella nigra var.hesuelica, Phaeoannellomyces elegans, Phaeococcomyces exophialae, Exophiala jeanselmei var.jeanselmei andE. castellanii were amplified by PCR and directly sequenced. A putative secondary structure of the nuclear small subunit rRNA ofExophiala dermatitidis was predicted from the sequence data. Alignment with corresponding sequences fromNeurospora crassa andAureobasidium pullulans was performed and a phylogenetic tree was constructed using the neighbor-joining method. The obtained topology of the tree was confirmed by bootstrap analysis. Based upon this analysis all fungi studied formed a well-supported monophyletic group clustering as a sister group to one group of the Plectomycetes (Trichocomaceae and Onygenales). The analysis confirmed the close relationship postulated betweenExophiala dermatitidis, Wangiella dermatitidis andSarcinomyces phaeomuriformis. This monophyletic clade also contains the teleomorph speciesCapronia mansonii thus confirming the concept of a teleomorph connection of the genusExophiala to a member of the Herpotrichiellaceae. However,Exophiala castellanii did not belong to this clade. Therefore, this species is not the anamorph ofCapronia mansonii as it was postulated.     

The reactions of OH radicals with D-ribose in deoxygenated and oxygenated aqueous solution

Aqueous solution ofD-ribose (10^?2M) saturated with N₂O and N₂O/O₂ (4/1) were γ-irradiated (dose rate: 3.85 x 10¹⁸ eV.g^?1.h^?1) at room temperature. The following products were identified:D-ribonic acid (1). D-erythro-pentos-2-ulose (2). D-erythro-pentos-4-ulose (3),D-erythro-pentos-3-ulose (4), D-ribo-pentodialdose (5), 2-deoxy-D-erythro-pentonic acid (6), 2-deoxypentos-3-ulose (7)(7), 4-deoxylpentos-3-ulose (8), 3-deoxypentos-4-ulose (9), 3-deoxypentos-2-ulose (10), 5-deoxypentos-4-ulose (11), erythrose (12), erythro-tetrodialdose (13), erythronic acid (14), threose/erythrulose (15). threonic acid (16), 2-deoxytetrose (17), and glyceraldehyde (18). In deoxygenated solutions, 13, 14, and 16 were absent. In the presence of oxygen, the formation of 6–11 and 17 was suppressed. From quantitative measurements, G-values were calculated for both deoxygenated and oxygenated conditions. Five different, primary, ribosyl radicals are formed which, in deoxygenated solution, undergo disproportionation reactions (to give 1-5), and transformations such as elimination of water and carbon monoxide followed by disproportionation reactions (to give6-12.17). Material-balance considerations indicate the formation of dimers (not measured). In oxygenated solutions, oxygen rapidly adds to the primary ribosyl radicals, thus preventing the transformation reactions, and the main products are 1–5 and 13. Possible mechanistic routes are discussed. The attack of HO radicals on D-ribose involves C-1, ～20%; C-2 and C-4, ～35%: C-3, ～ 20%; and C-5, ～25%     

Mutational change of membrane architecture. Mutants of Escherichia coli K12 missing major proteins of the outer cell envelope membrane

Mutant of Escherichia coli have been analyzed which miss two of the major proteins of the outer cell envelope membrane. The two proteins I and II1, normally are present at high concentrations (about 10⁵ copies per cell).In such mutants, as compared with wild type, the phospholipid-to-protein ratio in the outer membrane has increased by a factor of 2.3 causing a considerable difference in density between wild type and mutant membranes. The concentrations of two other major components of the outer membrane, lipopolysaccharide and Braun's lipoprotein, did not change.The protein-deficient mutants do not exhibit gross functional defects in vitro. An increased sensitivity to EDTA and a slight such increase to dodecyl sulfate (but not to deoxycholate or Triton X-100) was observed, loss of so-called periplasmic enzymes was not found, and other differences to wild type are marginal. The mutants can grow with normal morphology. It is not possible, however, to prepare “ghosts” (particles of size and shape of the cell without murein, surrounded by a derivative of the outer membrane, and posssessing the major proteins of this membrane) from them. This fact confirms our earlier suggestion that the proteins in question are required for the shape maintenance phenomenon in ghosts, and the mutants reject the speculation that these proteins are involved in the expression of the genetic information specifying cellular shape.Freeze-fracturing showed that in mutant cells, and in sharp contrast to wild type, the far predominant fracture plane is within the outer membrane. The concentration of the well known densely packed particles at the outer, concave leaflet of this fracture plane is greatly reduced. It was not possible, however, to clearly establish that one or the other protein is part of these particles because these ultrastructural differences were not apparent in mutants missing either one of the proteins only. The biochemical and ultrastructural data allow the conclusion that the loss of two major proteins and the concomitant increase of phospholipid concentration has changed the architecture of the outer membrane from a highly oriented structure. with a large fraction of protein-protein interaction, to one predominantly exhibiting planar lipid bilayer characteristics. E. coli thus can assemble rather different outer membranes, afact excluding that outer membrane formatin constitutes a highly ordered or strictly sequential assembly-line process.     

Intratumor heterogeneity of biomarker expression in breast carcinomas

Small biopsy samples are used increasingly to assess the biomarker expression for prognostic information and for monitoring therapeutic responses prior to and during neoadjuvant therapy. The issue of intratumor heterogeneity of expression of biomarkers, however, has raised questions about the validity of the assessment of biomarker expression based on limited tissue samples. We examined immunohistochemically the expression of HER-2neu (p185^erbB-2), epidermal growth factor receptor (EGFR), Bcl-2, p53, and proliferating cell nuclear antigen (PCNA) in 30 breast carcinomas using archived, paraffin embedded tissue and determined the extent of intratumor heterogeneity. Each section was divided into four randomly oriented discrete regions, each containing a portion of the infiltrating carcinoma. For each tumor, the entire lesion and four regions were analyzed for the expression of these markers. Scores of both membrane and cytoplasmic staining of HER-2neu and EGFR, scores of cytoplasmic staining of Bcl-2, and scores of nuclear staining of both p53 and PCNA were recorded. The intensity of staining and the proportion of immunostained cells were determined. A semiquantitative immunoscore was calculated by determining the sum of the products of the intensity and corresponding proportion of stained tumor cells. We analyzed both invasive (IDC) and in situ (DCIS) carcinomas. The Wilcoxon signed-rank test was used for paired comparisons between overall and regional immunoscores and between overall and regional percentages of stained cells. Spearman's correlation coefficients were used to assess the level of agreement of overall biomarker expression with each of the regions. Generalized linear models were used to assess overall and pair-wise differences in the absolute values of percent changes between overall and regional expression of biomarkers. For IDCs, there were no statistically significant differences in the expression of the biomarkers in terms of either the percentage of cells staining or the immunoscores when comparing the entire tumor with each region except for the lower EGFR expression of arbitrarily selected region 1 and lower p53 expression of region 1 compared to that of the entire tumor section. For DCIS, there were no statistically significant differences in the expression of the biomarkers between the entire tumor and each region except in PCNA of region 2 compared to that of entire tumor section. Positive correlation of immunoscores was observed between the entire tumor and each region as well as across all four regions for IDC. Similar observations were noted with DCIS except for HER-2neu and PCNA. No statistically significant differences were observed in the absolute values of percent changes of biomarker expression between overall and the four regions for both DCIS and IDC. Therefore, no significant intratumor heterogeneity in the expression of HER-2neu, Bcl-2, and PCNA was observed in IDC. Minor regional variations were observed for EGFR and p53 in IDC. Similarly, no significant regional variation in the expression of markers was observed in DCIS except for PCNA.     

猪源肠球菌的分离及生物特性的初报

本研究从猪粪便中分离了肠球菌两珠,经菌种鉴定两珠菌均为屡肠球菌。其生物特性的研究表明：可耐受15的胆盐和6％NaCI高盐,在pH3．0条件下可存活,对绝大多数抗生素耐药。     

The energetics of rearrangement and water elimination reactions in the radiolysis of the DNA bases in aqueous solution (eaq- and *OH attack): DFT calculations

DFT calculations on the relative stability of various nucleobase radicals induced by e(aq)(-) and (*)OH have been carried out for assessing the energetics of rearrangements and water elimination reactions, taking the solvent effect of water into account. Uracil and thymine radical anions are protonated fast at O2 and O4, whereby the O2-protonated anions are higher in energy (50 kJ mol(-1), equivalent to a 9-unit lower pK(a)). The experimentally observed pK(a)=7 is thus that of the O4-protonated species. Thermodynamically favored protonation occurs slowly at C6 (driving force, thymine: 49 kJ mol(-1), uracil: 29 kJ mol(-1)). The cytosine radical anion is rapidly protonated by water at N3. Final protonation at C6 is disfavored here. The kinetically favored pyrimidine C5 (*)OH adducts rearrange into the thermodynamically favored C6 (*)OH adducts (driving force, thymine: 42 kJ mol(-1)). Very similar in energy is a water elimination that leads to the Ura-5-methyl radical. Purine (*)OH adducts at C4 and C5 (plus C2 in guanine) eliminate water in exothermic reactions, while water elimination from the C8 (*)OH adducts is endothermic. The latter open the ring en route to the FAPY products, an H transfer from the C8(*)OH to N9 being the most likely process.