The Rab5 guanine nucleotide exchange factor Rabex-5 binds ubiquitin (Ub) and functions as a Ub ligase through an atypical Ub-interacting motif and a zinc finger domain

Rabex-5, the mammalian orthologue of yeast Vps9p, is a guanine nucleotide exchange factor for Rab5. Rabex-5 forms a tight complex with Rabaptin-5, a multivalent adaptor protein that also binds to Rab4, Rab5, and to domains present in gamma-adaptins and the Golgi-localized, gamma-ear-containing, ARF-binding proteins (GGAs). Rabaptin-5 augments the Rabex-5 exchange activity, thus generating GTP-bound, membrane-associated Rab5 that, in turn, binds Rabaptin-5 and stabilizes the Rabex-5.Rabaptin-5 complex on endosomes. Although the Rabex-5.Rabaptin-5 complex is critical to the regulation of endosomal fusion, the structural determinants of this interaction are unknown. Likewise, the possible binding and covalent attachment of ubiquitin to Rabex-5, two modifications that are critical to the function of yeast Vps9p in endosomal transport, have not been studied. In this study, we identify the 401-462 and 551-661 coiled-coils as the regions in Rabex-5 and Rabaptin-5, respectively, that interact with one another. We also demonstrate that Rabex-5 undergoes ubiquitination and binds ubiquitin, though not via its proposed C-terminal CUE-like domain. Instead, the N-terminal region of Rabex-5 (residues 1-76), comprising an A20-like Cys2/Cys2 zinc finger and an adjacent alpha-helix, is important for ubiquitin binding and ubiquitination. Importantly, we demonstrate that the Rabex-5 zinc finger displays ubiquitin ligase (E3) activity. These observations extend our understanding of the regulation of Rabex-5 by Rabaptin-5. Moreover, the demonstration that Rabex-5 is a ubiquitin ligase that binds ubiquitin and undergoes ubiquitination indicates that its role in endosome fusion may be subject to additional regulation by ubiquitin-dependent modifications.     

Analysis of flagellin perception mediated by flg22 receptor OsFLS2 in rice

Plants have sensitive perception systems that recognize various pathogen-derived molecules. We previously reported that rice detects flagellin from a rice-incompatible strain of gram-negative phytopathogenic bacterium, Acidovorax avenae, which induces subsequent immune responses involving cell death. The mechanism of flagellin perception in rice, however, has remained obscure. In this study, we found that flg22, a peptide derived from the flagellin N-terminus, induced weak immune responses without cell death in cultured rice cells. To elucidate the mechanism by which flg22 induced signaling in rice, we characterized OsFLS2, the rice ortholog of AtFLS2, which mediates flg22 perception. Heterologous expression of OsFLS2 functions in Arabidopsis, showing the conservation of the flg22 signaling pathway across divergent plant taxa. OsFLS2-overexpressing rice cultured cells generated stronger immune responses with the induction of cell death following stimulation with flg22 and flagellin. However, examination of the growth rate of the compatible strain in inoculated OsFLS2-overexpressing rice could not confirm bacterial growth suppression compared with wild-type rice. These results suggest that rice possesses a conserved flagellin perception system utilizing the FLS2 receptor which, when upregulated, hardly affects resistance against compatible A. avenae.     

Prediction of the heterosis of <Emphasis Type="Italic">Laminaria</Emphasis> hybrids with the genetic distance between their parental gametophyte clones

Eighteen microsatellite markers were used to determine the genetic distances between the parental gametophyte clones of 14 Laminaria hybrids, which were then used to establish a linear relationship with the heterosis (hybrid vigor) of economic traits including yield, mean blade try weight, mean blade fresh weight, blade length, blade width and mean blade thickness using regression analysis. Significant regression was found between the genetic distance (x) and the heterosis (y) of yield (y = 115.10x − 77.97, r = 0.8151, p = 0.00038), mean blade dry weight (y = 115.23x  −77.97, r = 0.8154, p = 0.00038), mean blade fresh weight (y = 100.08x − 57.85, r = 0.7306, p = 0.0030) and blade length (y = 204.11x − 46.77, r = 0.6963, p = 0.00566). The prediction of the heterosis of Laminaria hybrids with the genetic distance between parental gametophyte clones will facilitate the selection of elite Laminaria hybrids by avoiding the time-consuming and labor-intensive trait evaluation of a large number of hybridization combinations.     

Effect of HRT on the biological pre-denitrification process for the simultaneous removal of toxic pollutants from cokes wastewater

A lab-scale serial anoxic-aerobic reactor for the pre-denitrification process was continuously operated to efficiently and economically treat actual cokes wastewater containing various pollutants, such as phenol, ammonia, thiocyanate and cyanide compounds. The biodegradation efficiencies of the pollutants were examined by changing hydraulic retention time (HRT) as a main operating variable. The long-term operation of the pre-denitrification process reactor showed that approximately 100% phenol, approximately 100% free cyanide, approximately 100% SCN(-), 97% ammonia, 85% COD, 84% TOC (total organic carbon) and 83% TN (total nitrogen) were removed at HRT above 11.9h. Removal efficiency of total cyanides significantly decreased with a decrease in the HRT. Free cyanide and some of total cyanides were removed in anoxic reactor, whereas thiocyanate was removed in aerobic reactor. Phenol was completely removed under successive anoxic and aerobic conditions. Although actual cokes wastewater contained high concentrations of various toxic pollutants, the pre-denitrification process showed stable and successful performances in both nitrification and denitrification reactions.     

Polyhydroxyalkanoate (PHA) production using waste vegetable oil by Pseudomonas sp. strain DR2

To produce polyhydroxyalkanoate (PHA) from inexpensive substrates by bacteria, vegetable-oil-degrading bacteria were isolated from a rice field using enrichment cultivation. The isolated Pseudomonas sp. strain DR2 showed clear orange or red spots of accumulated PHA granules when grown on phosphate and nitrogen limited medium containing vegetable oil as the sole carbon source and stained with Nile blue A. Up to 37.34% (w/w) of intracellular PHA was produced from corn oil, which consisted of three major 3-hydroxyalkanoates; octanoic (C8:0, 37.75% of the total 3-hydroxyalkanoate content of PHA), decanoic (C10:0, 36.74%), and dodecanoic (C12:0, 11.36%). Pseudomonas sp. strain DR2 accumulated up to 23.52% (w/w) of PHAMCL from waste vegetable oil. The proportion of 3- hydroxyalkanoate of the waste vegetable-oil-derived PHA [hexanoic (5.86%), octanoic (45.67%), decanoic (34.88%), tetradecanoic (8.35%), and hexadecanoic (5.24%)] showed a composition ratio different from that of the corn-oil-derived PHA. Strain DR2 used three major fatty acids in the same ratio, and linoleic acid was the major source of PHA production. Interestingly, the production of PHA in Pseudomonas sp. strain DR2 could not occur in either acetate- or butyrate-amended media. Pseudomonas sp. strain DR2 accumulated a greater amount of PHA than other well-studied strains (Chromobacterium violaceum and Ralstonia eutropha H16) when grown on vegetable oil. The data showed that Pseudomonas sp. strain DR2 was capable of producing PHA from waste vegetable oil.     

Increased damage of exon 5 of p53 gene in workers from an arsenic plant

Mutagenesis is a multistage process. Substitution mutations can be induced by base modified through alteration of pairing property. Mutations of exon 5 and 8 of p53 gene have been found in most arsenicosis patients with precarcinomas and carcinomas, but never in arsenicosis individuals without precarcinomas and carcinomas. This study investigates whether base modification exists in exon 5 and 8 of p53 gene, and explores the dose-effect relationship between damage of exon 5 of p53 gene and urinary arsenic. Concentrations of urinary 8-hydroxydeoxyguanine (8-OHdG) are analyzed to identify the occurrence of DNA damage. The real-time PCR developed by Sikorsky et al. is applied to detect base modification in exon 5 and 8 of p53 gene for apparently healthy participants. Our results show that the mean total arsenic concentrations of two exposed groups from an arsenic plant are significantly elevated compared with the control group, and the damage level of exon 5 of the high-exposed group is significantly higher than that of the control group, but which does not happen in exon 8. The closely correlation between the damage index of exon 5 and urinary organic arsenic concentration are found. Concentration of 8-OHdG of the high-exposed group is significantly higher than that of the control group. These results imply that base modification in exon 5 of p53 gene can be induced by arsenic. In addition, our study suggests that the damage level of exon 5 is a useful biomarker to assess adverse health effect levels caused by chronic exposure to arsenic.     

<Emphasis Type="Italic">Arthrobacter soli</Emphasis> sp. nov., a novel bacterium isolated from wastewater reservoir sediment

A novel Gram-positive bacterium, designated SYB2T, was isolated from wastewater reservoir sediment, and a polyphasic taxonomic study was conducted based on its morphological, physiological, and biochemical features, as well as the analysis of its 16S rRNA gene sequence. During the phylogenetic analysis of the strain SYB2T, results of a 16S rRNA gene sequence analysis placed this bacterium in the genus Arthrobacter within the family Micrococcaceae. SYB2T and Arthrobacter protophormiae ATCC 19271T, the most closely related species, both exhibited a 16S rRNA gene sequence similarity of 98.99%. The genomic DNA G+C content of the novel strain was found to be 62.0 mol%. The predominant fatty acid composition was anteiso-C15:0, anteiso-C17:0, iso-C16:0, and iso-C15:0. Analysis of 16S rRNA gene sequences and DNA-DNA relatedness, as well as physiological and biochemical tests, showed genotypic and phenotypic differences between strain SYB2T and other Arthrobacter species. The type strain of the novel species was identified as SYB2T (= KCTC 19291T= DSM 19449T).     

Formation of Avenacein Y by<Emphasis Type="Italic">Fusarium avenaceum</Emphasis> Fries Sacc. isolates from poland and biological properties of the compound

Eighteen isolates ofFusarium avenaceum Fries Sacc. originating from cereals, potato and carrot from Poland synthesized Avenacein Y in amounts ranging from 0.01 to 2.0 g/kg of wheat grain. The compound was produced in 1 kg of corn kernels by isolate KF-58, isolated, identified and used to test for antibiotic activity against plant pathogenic fungi of 11 genera. Application of Avenacein Y caused slight decrease of mycelium growth in four species only.     

Ca2+ dynamics in a pollen grain and papilla cell during pollination of Arabidopsis

Ca2+ dynamics in the growing pollen tube have been well documented in vitro using germination assays and Ca2+ imaging techniques. However, very few in vivo studies of Ca2+ in the pollen grain and papilla cell during pollination have been performed. We expressed yellow cameleon, a Ca2+ indicator based on green fluorescent protein, in the pollen grains and papilla cells of Arabidopsis (Arabidopsis thaliana) and monitored Ca2+ dynamics during pollination. In the pollen grain, [Ca2+]cyt increased at the potential germination site soon after hydration and remained augmented until germination. As in previous in vitro germination studies, [Ca2+]cyt oscillations were observed in the tip region of the growing pollen tube, but the oscillation frequency was faster and [Ca2+]cyt was higher than had been observed in vitro. In the pollinated papilla cell, remarkable increases in [Ca2+]cyt occurred three times in succession, just under the site of pollen-grain attachment. [Ca2+]cyt increased first soon after pollen hydration, with a second increase occurring after pollen protrusion. The third and most remarkable [Ca2+]cyt increase took place when the pollen tube penetrated into the papilla cell wall.     

Strong evidence for changing fish reproductive phenology under climate warming on the Tibetan Plateau

Phenological responses to climate change have been widely observed and have profound and lasting effects on ecosystems and biodiversity. However, compared to terrestrial ecosystems, the long‐term effects of climate change on species’ phenology are poorly understood in aquatic ecosystems. Understanding the long‐term changes in fish reproductive phenology is essential for predicting population dynamics and for informing management strategies, but is currently hampered by the requirement for intensive field observations and larval identification. In this study, a very low‐frequency sampling of juveniles and adults combined with otolith measurements (long axis length of the first annulus; LAFA) of an endemic Tibetan Plateau fish (Gymnocypris selincuoensis) was used to examine changes in reproductive phenology associated with climate changes from the 1970s to 2000s. Assigning individual fish to their appropriate calendar year class was assisted by dendrochronological methods (crossdating). The results demonstrated that LAFA was significantly and positively associated with temperature and growing season length. To separate the effects of temperature and the growing season length on LAFA growth, measurements of larval otoliths from different sites were conducted and revealed that daily increment additions were the main contributor (46.3%), while temperature contributed less (12.0%). Using constructed water‐air temperature relationships and historical air temperature records, we found that the reproductive phenology of G. selincuoensis was strongly advanced in the spring during the 1970s and 1990s, while the increased growing season length in the 2000s was mainly due to a delayed onset of winter. The reproductive phenology of G. selincuoensis advanced 2.9 days per decade on average from the 1970s to 2000s, and may have effects on recruitment success and population dynamics of this species and other biota in the ecosystem via the food web. The methods used in this study are applicable for studying reproductive phenological changes across a wide range of species and ecosystems.