Alleviation of salt stress by low dose γ-irradiation in rice

The effects of salt stress on the growth, photosynthesis, and antioxidative ability of the rice (Oryza sativa L.) plants raising from -irradiated seeds were investigated using two cultivars, Ilpumbyeo and Sanghaehyanghyella. The 50 and 100 mM NaCl solutions caused a remarkable decrease of the early germination rate and seedling growth. However, the salt stress-induced inhibition of the growth was significantly alleviated in the -irradiated plants. The chlorophyll contents and the effective quantum yield of photosystem 2 ( _{PS 2}) were lower in the NaCl-treated plants than in the control ones, while the non-photochemical quenching was higher in the former ones. Activities of the antioxidant enzymes such as superoxide dismutase (SOD) and ascorbate peroxidase (APX) increased with increasing NaCl concentrations, and the irradiated groups had even higher SOD and APX activities than the non-irradiated ones. These alleviation effects were observed similarly in both the cultivars tested.     

Functional Unfolding of ��1-Antitrypsin Probed by Hydrogen-Deuterium Exchange Coupled with Mass Spectrometry

The native state of α₁-antitrypsin (α₁AT), a member of the serine protease inhibitor (serpin) family, is considered a kinetically trapped folding intermediate that converts to a more stable form upon complex formation with a target protease. Although previous structural and mutational studies of α₁AT revealed the structural basis of the native strain and the kinetic trap, the mechanism of how the native molecule overcomes the kinetic barrier to reach the final stable conformation during complex formation remains unknown. We hypothesized that during complex formation, a substantial portion of the molecule undergoes unfolding, which we dubbed functional unfolding. Hydrogen-deuterium exchange coupled with ESI-MS was used to analyze this serpin in three forms: native, complexing, and complexed with bovine β-trypsin. Comparing the deuterium content at the corresponding regions of these three samples, we probed the unfolding of α₁AT during complex formation. A substantial portion of the α₁AT molecule unfolded transiently during complex formation, including not only the regions expected from previous structural studies, such as the reactive site loop, helix F, and the following loop, but also regions not predicted previously, such as helix A, strand 6 of β-sheet B, and the N terminus. Such unfolding of the native interactions may elevate the free energy level of the kinetically trapped native serpin sufficiently to cross the transition state during complex formation. In the current study, we provide evidence that protein unfolding has to accompany functional execution of the protein molecule.The native strain of serine protease inhibitors (serpins)¹ is considered to be crucial to their biological functions, such as plasma protease inhibition (1, 2) and hormone delivery (3). Functional execution of serpins is accompanied by the conversion of the strained native structure into a more stable conformation (4). Because some of the strained native serpin structures are spontaneously converted into a more relaxed stable latent form under physiological conditions (5–7), the native structure is not the thermodynamically most stable conformation but is a kinetically trapped conformation. Upon binding a target protease, the scissile bond of the reactive site loop (RSL) is cleaved while the protease is covalently attached to the N-terminal part of the RSL (8, 9). During the conversion of the strained structure into the stable complex conformation (Fig. 1), RSL is inserted into the central β-sheet (A sheet) between strands 3 and 5 (s3A and s5A) to form strand 4 (s4A), and the covalently attached protease is concomitantly translocated to the opposite pole (10). Serpin inhibition occurs via a suicide substrate mechanism (4, 11, 12) in which serpins, upon binding proteases, partition between cleaved serpins and stable serpin-enzyme complexes.Open in a separate windowFig. 1.Structures of native α₁AT and α₁AT-trypsin complex. Left, structure of native α₁AT (Protein Data Bank code 1QLP) illustrated with secondary structural elements (1). Right, structure of α₁AT-trypsin complex (Protein Data Bank code 1EZX). The nine α-helices are colored dark gray, and the 16 β-strands are colored light gray.As a member of the serpin family, α₁-antitrypsin (α₁AT), which serves to modulate the activity of human leukocyte elastase in the lung, has been most extensively studied with regard to both structure and inhibition mechanism. Our previous studies with stabilizing mutations of α₁AT showed that the native strain is distributed throughout the molecule and that various unfavorable structural motifs, such as hydrophobic packing, cavity in the core, and surface hydrophobic patch, appear to maintain the native strain (13, 14). Indeed stabilizing mutations localized in the region of RSL insertion during complex formation affected the inhibitory function individually by retarding the loop insertion (15). Mutations in other regions did not affect the inhibitory function individually, but collectively these mutations affected the inhibitory function when the stabilization effect reached a certain threshold (16). Maintaining the kinetic trap appears to require sustaining RSL at the hydrophobic β-barrel composed of sheet B and sheet C (B/C β-barrel) because the conversion into the stable latent conformation occurs by destabilization of the B/C β-barrel (6) as well as by the extension of RSL length (17). Thus, upon binding a target protease, RSL cleavage appears to induce a conformational conversion, and the resultant strain throughout the molecule facilitates the opening of β-sheet A and the insertion of the RSL, which is critical for the inhibitory pathway as opposed to the substrate pathway (10).Although these structural and mutational studies revealed the structural basis for maintaining the kinetic trap and its relation to the inhibitory mechanism, several questions still remain. For example, what structural changes does the native serpin molecule undergo to overcome the kinetic barrier and reach the final stable conformation during the complex formation? In the present study, to probe the structural process of overcoming the kinetic barrier during complex formation with a target protease, amide hydrogen exchange (hydrogen-deuterium exchange (H/D-EX)) was explored during the conversion of the native α₁AT to the stable complex. H/D-EX coupled with ESI-MS is a powerful analytical tool for observing protein dynamics, transient conformational changes, and protein-protein interactions (18–22). These experiments demonstrated that transient structural unfolding occurred in many regions in the α₁AT molecule during formation of the complex with β-trypsin, and some of this unfolding was unpredicted from previous structural studies.     

Mitochondrial NADH-cytochrome b(5) reductase plays a crucial role in the reduction of D-erythroascorbyl free radical in Saccharomyces cerevisiae.

The relevance of NADH-cytochrome b(5) reductase to the NADH-dependent reduction of D-erythroascorbyl free radical was investigated in Saccharomyces cerevisiae. MCR1, which is known to encode NADH-cytochrome b(5) reductase in S. cerevisiae, was disrupted by the insertion of URA3 gene into the gene of MCR1. In the mcr1 disruptant cells, the activity of NADH-D-erythroascorbyl free radical reductase almost disappeared and the intracellular level of D-erythroascorbic acid was about 11% of that of the congenic wild-type strain. In the transformant cells carrying MCR1 in multicopy plasmid, the intracellular level of D-erythroascorbic acid and the activity of NADH-D-erythroascorbyl free radical reductase increased up to 1.7-fold and 2.1-fold, respectively. Therefore, it indicated that the MCR1 product, mitochondrial NADH-cytochrome b(5) reductase, plays a key role in the NADH-dependent reduction of D-erythroascorbyl free radical in S. cerevisiae. On the other hand, the mcr1 disruptant cells were hypersensitive to hydrogen peroxide and menadione, and overexpression of MCR1 made the cells more resistant against oxidative stress. These results suggested that the mitochondrial NADH-cytochrome b(5) reductase functions as NADH-D-erythroascorbyl free radical reductase and plays an important role in the response to oxidative damage in S. cerevisiae.     

Possible role of macrophage-derived soluble mediators in the pathogenesis of encephalomyocarditis virus-induced diabetes in mice.

Pancreatic islets from DBA/2 mice infected with the D variant of encephalomyocarditis (EMC-D) virus revealed lymphocytic infiltration with moderate to severe destruction of pancreatic beta cells. Our previous studies showed that the major population of infiltrating cells at the early stages of infection is macrophages. The inactivation of macrophages prior to viral infection resulted in the prevention of diabetes, whereas activation of macrophages prior to viral infection resulted in the enhancement of beta-cell destruction. This investigation was initiated to determine whether macrophage-produced soluble mediators play a role in the destruction of pancreatic beta cells in mice infected with a low dose of EMC-D virus. When we examined the expression of the soluble mediators interleukin-1 beta (IL-1beta), tumor necrosis factor alpha (TNF-alpha), and inducible nitric oxide synthase (iNOS) in the pancreatic islets, we found that these mediators were clearly expressed at an early stage of insulitis and that this expression was evident until the development of diabetes. We confirmed the expression of these mediators by in situ hybridization with digoxigenin-labelled RNA probes or immunohistochemistry in the pancreatic islets. Mice treated with antibody against IL-1beta or TNF-alpha or with the iNOS inhibitor aminoguanidine exhibited a significant decrease in the incidence of diabetes. Mice treated with a combination of anti-IL-1beta antibody, anti-TNF-alpha antibody, and aminoguanidine exhibited a greater decrease in the incidence of disease than did mice treated with one of the antibodies or aminoguanidine. On the basis of these observations, we conclude that macrophage-produced soluble mediators play an important role in the destruction of pancreatic beta cells, resulting in the development of diabetes in mice infected with a low dose of EMC-D virus.     

Effects of endocytosis inhibitory drugs on rubella virus entry into VeroE6 cells

It has been suggested that infectious entry of rubella virus (RV) is conducted by receptor mediated endocytosis. To explore the cellular entry mechanism of RV, inhibitory effects of drugs affecting various endocytic pathways on RV entry into VeroE6 cells were analyzed. Results showed that RV infectious entry into VeroE6 cells is mediated by clathrin-dependent endocytosis and not by caveolae-mediated endocytosis. Moreover, chemical inhibition of macropinocytosis such as treatments of amiloride, actin and microtubule-disrupting drug significantly reduced RV infection. Considering that macropinocytosis is inducible endocytosis by cellular stimulations, clathrin-mediated endocytosis is likely to be a major route of RV infectious entry.     

Five hepatopancreatic and one epidermal chitinases from a pandalid shrimp (Pandalopsis japonica): cloning and effects of eyestalk ablation on gene expression

Six cDNAs encoding chitinase proteins in Pandalopsis japonica were isolated by using polymerase chain reaction (PCR) cloning methods and bioinformatic analysis of expressed sequence tags (ESTs). The cDNAs, designated Pj-Cht1, 2, 3A, 3B, 3C, and 4, encoded proteins ranging from 388 to 607 amino acid residues in length (43.61-67.62 kDa) and displayed a common structural organization: an N-terminal catalytic domain, a Thr/Pro-rich linker region, and either 0 (Pj-Cht2, 3A), 1 (Pj-Cht1, 3B, and 3C), or 2 (Pj-Cht4) C-terminal chitin-binding domain(s) (CBD). Pj-Cht1 and 2 lacked the 5′ end of the open reading frame (ORF); the other Pj-Chts contained the complete ORF. All known decapod crustacean chitinases were segregated into at least four groups based on phylogenetic analysis and domain organization. Group 1 chitinases, represented by Pj-Cht1, were most closely related to insect group I chitinases and may function in the digestion of the peritrophic membrane. Group 2 chitinases including Pj-Cht2 show different domain organizations and pI value from other chitinases and appear to function in degradation of the old exoskeleton during the premolt period. Group 3 chitinases, represented by Pj-Cht3A, 3B, and 3C, may function in digestion of chitin-containing food and defense against pathogens. Group 4 chitinases, represented by Pj-Cht4, have two CBDs and their functions are unknown. Five Pj-Chts (Pj-Cht1, 3A, 3B, 3C, and 4) are expressed in the hepatopancreas and intestine, whereas Pj-Cht2 is expressed in epidermis and SG/XO complex suggesting crustacean chitinases can be classified into two groups (hepatopancreatic and epidermal) based on the expression profile. Eyestalk ablation (ESA) down-regulated the hepatopancreatic chitinase expression (Pj-Cht1, 3A, and 3C); Pj-Cht3B expression was not significantly affected by ESA. By contrast, mRNA levels of Pj-Cht2 were significantly upregulated in 7 days post-ESA. Pj-Cht4 mRNA levels were too low for measurement with quantitative polymerase chain reaction. ESA had no significant effect on chitinase expression in the intestine. These data indicate that Pj-Cht1, 3A, 3B, 3C, and 4 are hepatopancreatic chitinases that may function in the digestion of ingested chitin and the modification of peritrophic membrane in the intestine. By contrast, epidermal chitinase, Pj-Cht2 may play a role in chitin metabolism during molt cycle as shown in other crustacean group 2 chitinases.     

Functional genomic approaches using the nematode Caenorhabditis elegans as a model system

Since the completion of the genome project of the nematode C. elegans in 1998, functional genomic approaches have been applied to elucidate the gene and protein networks in this model organism. The recent completion of the whole genome of C. briggsae, a close sister species of C. elegans, now makes it possible to employ the comparative genomic approaches for identifying regulatory mechanisms that are conserved in these species and to make more precise annotation of the predicted genes. RNA interference (RNAi) screenings in C. elegans have been performed to screen the whole genome for the genes whose mutations give rise to specific phenotypes of interest. RNAi screens can also be used to identify genes that act genetically together with a gene of interest. Microarray experiments have been very useful in identifying genes that exhibit co-regulated expression profiles in given genetic or environmental conditions. Proteomic approaches also can be applied to the nematode, just as in other species whose genomes are known. With all these functional genomic tools, genetics will still remain an important tool for gene function studies in the post genome era. New breakthroughs in C. elegans biology, such as establishing a feasible gene knockout method, immortalized cell lines, or identifying viruses that can be used as vectors for introducing exogenous gene constructs into the worms, will augment the usage of this small organism for genome-wide biology.     

Mathematical model for simultaneous nitrification and denitrification (SND) in membrane bioreactor (MBR) under Low Dissolved Oxygen (DO) concentrations

Activated Sludge Model no. 1 (ASM1) was modified and applied to Simultaneous Nitrification and Denitrification (SND) in oxygen-limited MBR. In order to calibrate the model correctly, the parametric sensitivity was performed using AQUASIM 2.0 to find the most important coefficients. The most sensitive coefficients in the model of oxygen-limited MBR were related to the growth of heterotrophic biomass. While the total autotrophic biomass concentration (X_BA) was decreased by decreasing DO concentration, there was an increase in the nitrite-oxidizing biomass concentration by a small amount. This model also showed that over 97% of permeate Soluble Chemical Oxygen Demand (S_COD) was the Soluble Inert (S_I). The model showed the change in the ammonia-oxidizing and nitrite-oxidizing biomass was decreased by decreasing DO concentration. However, there was an increase in the nitrite-oxidizing biomass concentration by a small amount due to the biomass retained in the bioreactor with membrane. It is contradictory to the reported observations for conventional activated sludge process.