Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis

Around 80 enzymes are implicated in the generic starch and sucrose pathways. One of these enzymes is sucrose phosphorylase, which reversibly catalyzes the conversion of sucrose and orthophosphate to d-Fructose and alpha-d-glucose 1-phosphate. Here, we present the crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis (BiSP) refined at 1.77 A resolution. It represents the first 3D structure of a sucrose phosphorylase and is the first structure of a phosphate-dependent enzyme from the glycoside hydrolase family 13. The structure of BiSP is composed of the four domains A, B, B', and C. Domain A comprises the (beta/alpha)(8)-barrel common to family 13. The catalytic active-site residues (Asp192 and Glu232) are located at the tips of beta-sheets 4 and 5 in the (beta/alpha)(8)-barrel, as required for family 13 members. The topology of the B' domain disfavors oligosaccharide binding and reduces the size of the substrate access channel compared to other family 13 members, underlining the role of this domain in modulating the function of these enzymes. It is remarkable that the fold of the C domain is not observed in any other known hydrolases of family 13. BiSP was found as a homodimer in the crystal, and a dimer contact surface area of 960 A(2) per monomer was calculated. The majority of the interactions are confined to the two B domains, but interactions between the loop 8 regions of the two barrels are also observed. This results in a large cavity in the dimer, including the entrance to the two active sites.     

Buffalograss germplasm resistance to Blissus occiduus (Hemiptera: Lygaeidae)

Plant germplasm collections may offer genetic variability useful in identifying insect resistance. The goal of this project was to evaluate buffalograss genotypes [Buchlo? dactyloides (Nutt.) Engelm.] for resistance to the chinch bug, Blissus occiduus Barber (Hemiptera: Lygaeidae), and to relate resistance to ploidy level, chinch bug number, and pubescence. Forty-eight buffalograss genotypes from diverse geographic locations were evaluated in replicated studies under greenhouse conditions. Of the genotypes studied, four were highly resistant, 22 were moderately resistant, 19 were moderately susceptible, and three were highly susceptible to chinch bug damage. The mean number of chinch bugs was significantly different among the 48 genotypes. There was no significant correlation between chinch bug resistance and ploidy level or chinch bug resistance and pubescence. These results indicate the genetic source of resistance to chinch bugs exists in buffalograss germplasm. Highly resistant genotypes can be used in breeding programs to further improve buffalograss cultivars.     

Ameliorating role of caffeic acid phenethyl ester (CAPE) against isoniazid-induced oxidative damage in red blood cells

Isoniazid (INH) still remains a first-line drug both for treatment and prophylaxis of tuberculosis, but various organs toxicity frequently develops in patients receiving this drug. We aimed to investigate possible toxic effects of INH on rat red blood cells (RBCs), and to elucidate whether Caffeic acid phenethyl ester (CAPE) prevents a possible toxic effect of INH. Experimental groups were designed as follows: control group, INH group, INH + CAPE group. Compared with the control, the INH caused a significant increase in superoxide dismutase (SOD) activity and malondialdehyde (MDA) levels, and a decrease in glutathione peroxidase (GSH-Px) and catalase (CAT), which are recently used to monitor the development and extent of damage due to oxidative stresses. CAPE administration to INH group ameliorated above changes due to INH.     

Isolation and the characterization of the degradation products of the mediator ABTS-derived radicals formed upon reaction with polyphenols

Two degradation products were obtained from the incubation of the widely used 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), ABTS, radical cations with the polyphenols, (+)-catechin, (-)-epicatechin, and phloroglucinol in acetate buffer (pH 5). The products were purified by reversed-phase chromatography and characterized by UV-visible detection, mass spectrometry, and (1)H NMR spectroscopy. The data allowed us to identify the degradation products as 3-ethyl-6-sulfonate benzothiazolinone imine and the corresponding sulfoxide, 3-ethyl-6-sulfonate benzothiazolone. Elemental composition strongly supported the proposed structures. Our results unequivocally demonstrated that ABTS radicals are not as stable as usually claimed because they could be degraded upon interaction with polyphenols, in addition to being reduced by these antioxidants back to the parent compound. Therefore, it is concluded that caution must be exercised in using ABTS radicals as a basis for the evaluation of antioxidant capacities of pure compounds and/or complex mixtures.     

Effects of chromosome-specific introgression in upland cotton on fiber and agronomic traits

Interspecific chromosome substitution is among the most powerful means of introgression and steps toward quantitative trait locus (QTL) identification. By reducing the genetic "noise" from other chromosomes, it greatly empowers the detection of genetic effects by specific chromosomes on quantitative traits. Here, we report on such results for 14 cotton lines (CS-B) with specific chromosomes or chromosome arms from G. barbadense L. substituted into G. hirsutum and chromosome-specific F2 families. Boll size, lint percentage, micronaire, 2.5% span length, elongation, strength, and yield were measured by replicated field experiments in five diverse environments and analyzed under an additive-dominance (AD) genetic model with genotype and environment interaction. Additive effects were significant for all traits and dominance effects were significant for all traits except 2.5% span length. CS-B25 had additive effects increasing fiber strength and fiber length and decreasing micronaire. CS-B16 and CS-B18 had additive effects related to reduced yields. The results point toward specific chromosomes of G. barbadense 3-79 as the probable locations of the genes that significantly affect quantitative traits of importance. Our results provided a scope to analyze individual chromosomes of the genome in homozygous and heterozygous conditions and thus detected novel effects of alleles controlling important QTL.     

Carbamylated erythropoietin reduces radiosurgically-induced brain injury

Gamma knife radiosurgery is an attractive noninvasive treatment of brain tumors and vascular malformations that minimizes collateral tissue damage. However, exposure of normal tissue to even low-dose radiation triggers a cascade of acute and chronic injury and potentially significant morbidity and mortality. Because many irradiated patients now survive for years, identifying methods to prevent radiotherapy-induced collateral tissue damage is a major focus of current research. Erythropoietin (EPO), a cytokine produced locally by many tissues in response to injury, antagonizes apoptosis, reduces inflammation, and promotes healing. Systemic administration of recombinant EPO, widely used for treatment of anemia, provides robust protection from numerous insults in a variety of tissues, including the brain. Although irradiation injury is likely sensitive to EPO, the hematopoietic activity of EPO is undesirable in this setting, increasing erythrocyte number and predisposing to thrombosis. To avoid these potential adverse effects, we developed carbamylated EPO (CEPO) which does not stimulate the bone marrow. In this study, we show that CEPO (50 microg kg(-1) intraperitoneally) improves functional outcome when administered to adult rats just before, and then once daily for 10 d after, a necrotizing dose of radiation (100 Gy) to the right striatum. Immediately following irradiation, use and reflex movements of the contralateral forelimb to vibrissae stimulation were abnormal but rapidly improved in animals receiving CEPO. Moreover, histological examination revealed that the extent of brain necrosis after 90 days was reduced by approximately 50%. These findings further extend the kinds of injury for which administration of a tissue-protective cytokine provides benefit.     

Thermodynamic basis of selectivity in guide-target-mismatched RNA interference

Silencing in RNAi is strongly affected by guide‐strand/target‐mRNA mismatches. Target nucleation is thought to occur at positions 2–8 of the guide (“seed region”); successful hybridization in this region is the primary determinant of target‐binding affinity and hence target cleavage. To define a molecular basis for the target sequence selectivity in RNAi, we studied all possible distinct single mismatches in seven positions of the seed region—a total of 21 substitutions. We report results from soft‐core thermodynamic integration simulations to determine changes in targeting binding‐free energies to Argonaute due to single mismatches in the guide strand, which arise during binding of an imperfectly matched target mRNA. In agreement with experiment, most mismatches impair target binding, consistent with a prominent role for binding affinity changes in RNAi sequence selectivity. Individual Argonaute residues located near the mismatched base pair are found to contribute significantly to binding affinity changes. We also use this methodology to analyze the mismatch‐dependent free energy changes for dissociation of a DNA?RNA hybrid from Argonaute, as a model for the escape of miRNAs from the silencing pathway. Several mismatched sequences of the miRNA have increased affinity to Argonaute, implying that some mismatches may reduce the probability for escape. Furthermore, calculations of base‐substitution‐dependent free energy changes for binding ssDNA reveal mild sequence sensitivity as expected for guide strand binding to Argonaute. Our findings give a thermodynamic basis for RNAi target sequence selectivity and suggest that miRNA mismatches may increase silencing effectiveness and thus could be evolutionarily advantageous. Proteins 2012; © 2011 Wiley Periodicals, Inc.