Evaluation of the Ability of Aqueous Lignin-Carbohydrate Complex Extracted from Botanical Waste to Scavenge Reactive Oxygen Species by Using an Electron Spin Resonance Method

Lignin-carbohydrate complexes (LCCs) were extracted from botanical waste, Quercus acutissima, rice bran, peanut husks, tofu refuse, and used green tea leaves. The contents of the lignin and phenolic hydroxyl groups in the LCCs taken from these samples were positively correlated. The capacity of scavenging reactive oxygen species was evaluated by employing an electron spin resonance method for its superoxide dismutase (SOD)-like activity. The lignin content and the SOD-like activity of LCC from Quercus acutissima were much greater than those of other LCCs. These findings suggest that the SOD-like activity of LCCs depends on the lignin content

GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures

BACKGROUND: We introduce GASH, a new, publicly accessible program for structural alignment and superposition. Alignments are scored by the Number of Equivalent Residues (NER), a quantitative measure of structural similarity that can be applied to any structural alignment method. Multiple alignments are optimized by conjugate gradient maximization of the NER score within the genetic algorithm framework. Initial alignments are generated by the program Local ASH, and can be supplemented by alignments from any other program. RESULTS: We compare GASH to DaliLite, CE, and to our earlier program Global ASH on a difficult test set consisting of 3,102 structure pairs, as well as a smaller set derived from the Fischer-Eisenberg set. The extent of alignment crossover, as well as the completeness of the initial set of alignments are examined. The quality of the superpositions is evaluated both by NER and by the number of aligned residues under three different RMSD cutoffs (2,4, and 6Å). In addition to the numerical assessment, the alignments for several biologically related structural pairs are discussed in detail. CONCLUSION: Regardless of which criteria is used to judge the superposition accuracy, GASH achieves the best overall performance, followed by DaliLite, Global ASH, and CE. In terms of CPU usage, DaliLite CE and GASH perform similarly for query proteins under 500 residues, but for larger proteins DaliLite is faster than GASH or CE. Both an http interface and a simple object application protocol (SOAP) interface to the GASH program are available at

Distorted antibody repertoire developed in the absence of pre-B cell receptor formation

The pre-B cell receptor (pre-BCR), consisting of the μ heavy chain (μHC) and the surrogate light chain (SLC, Vpre-B and λ5), plays important roles during B cell development. The formation of the pre-BCR, which enables the nascent immunoglobulin HC to associate with the SLC, is considered a prerequisite for B cell development. However, a significant number of peripheral mature (leaky) B cells exist in SLC-deficient mice. These leaky B cells develop in the absence of pre-BCR and do not undergo the pre-BCR checkpoint. The antibody repertoires of leaky B cells thus reflect the absence of pre-BCR function. To investigate how the absence of the pre-BCR is circumvented by these leaky-B cells and examine the effect of the pre-BCR checkpoint on the antibody system, we analyzed the antibody repertoires of λ5-deficient (λ5−/−) mice using next-generation sequencing. In λ5−/− mice, spleen B cells displayed different patterns of VDJ-usage, relative to those in wild-type (WT) mice. Moreover, leaky B cells were neither derived from unusual B2 cells, characterized by particular LC gene rearrangements in the absence of pre-BCR signaling, nor from B1 cells, originating from different B cell progenitors. Analysis of the CDR-H3 amino acid sequences of μ-chain repertoires revealed that certain bone marrow B cells with particular CDR-H3 profiles undergo clonal expansion in λ5−/− mice. Part of these CDR-H3s contain arginine(s) in the middle of the CDR-H3 loop in λ5−/− mice, whereas few arginine(s) exist in this middle loop in WT CDR-H3s in the absence of clonal expansion. This CDR-H3 feature in λ5−/− mice presumably reflects the role of the pre-BCR in autoantibody regulation, since arginine(s) are often found in the antigen-binding site of autoantibodies. Here, we present a unique viewpoint on the role of pre-BCR, by assessing the whole antibody repertoire formed in SLC-deficient mice

Roles of MIWI, MILI and PLD6 in small RNA regulation in mouse growing oocytes

he mouse PIWI-interacting RNA (piRNA) pathway produces a class of 26–30-nucleotide (nt) small RNAs and is essential for spermatogenesis and retrotransposon repression. In oocytes, however, its regulation and function are poorly understood. In the present study, we investigated the consequences of loss of piRNA-pathway components in growing oocytes. When MILI (or PIWIL2), a PIWI family member, was depleted by gene knockout, almost all piRNAs disappeared. This severe loss of piRNA was accompanied by an increase in transcripts derived from specific retrotransposons, especially IAPs. MIWI (or PIWIL1) depletion had a smaller effect. In oocytes lacking PLD6 (or ZUCCHINI or MITOPLD), a mitochondrial nuclease/phospholipase involved in piRNA biogenesis in male germ cells, the piRNA level was decreased to 50% compared to wild-type, a phenotype much milder than that in males. Since PLD6 is essential for the creation of the 5΄ ends of primary piRNAs in males, the presence of mature piRNA in PLD6-depleted oocytes suggests the presence of compensating enzymes. Furthermore, we identified novel 21–23-nt small RNAs, termed spiRNAs, possessing a 10-nt complementarity with piRNAs, which were produced dependent on MILI and independent of DICER. Our study revealed the differences in the biogenesis and function of the piRNA pathway between sexes

EDITORIAL

Ligand-mediated drug delivery systems have enormous potential for improving the efficacy of cancer treatment. In particular, Arg-Gly-Asp peptides are promising ligand molecules for targeting α_vβ₃/α_vβ₅ integrins, which are overexpressed in angiogenic sites and tumors, such as intractable human glioblastoma (U87MG). We here achieved highly efficient drug delivery to U87MG tumors by using a platinum anticancer drug-incorporating polymeric micelle (PM) with cyclic Arg-Gly-Asp (cRGD) ligand molecules. Intravital confocal laser scanning microscopy revealed that the cRGD-linked polymeric micelles (cRGD/m) accumulated rapidly and had high permeability from vessels into the tumor parenchyma compared with the PM having nontargeted ligand, “cyclic-Arg-Ala-Asp” (cRAD). As both cRGD/m- and cRAD-linked polymeric micelles have similar characteristics, including their size, surface charge, and the amount of incorporated drugs, it is likely that the selective and accelerated accumulation of cRGD/m into tumors occurred <i>via</i> an active internalization pathway, possibly transcytosis, thereby producing significant antitumor effects in an orthotopic mouse model of U87MG human glioblastoma

Annual report by The Japanese Association for Thoracic Surgery

All data regarding cardiovascular surgery and thoracic surgery were obtained from NCD, whereas data regarding esophageal surgery were collected from survey questionnaire by The Japanese Association for Thoracic Surgery forms because NCD of esophageal surgery does not include non-surgical cases (i.e., patients with adjuvant chemotherapy or radiation alone). Based on the change in data aggregation, there are several differences between this 2015 annual report and previous annual reports: the number of institutions decreased in each category from 578 (2014) to 568 (2015) in cardiovascular, from 762 to 714 in general thoracic and from 626 to 571 in esophageal surgery. Because more than two departments in the same institute registered their data to NCD individually, we cannot calculate correct number of institutes in this survey. Then, the response rate is not indicated in the category of cardiovascular surgery (Table 1), and the number of institutions classified by the operation number is also not calculated in the category of cardiovascular surgery (Table 2)