Growth deficiency of a Xanthomonas oryzae pv. oryzae fur mutant in rice leaves is rescued by ascorbic acid supplementation

Xanthomonas oryzae pv. oryzae causes bacterial leaf blight, a serious disease of rice. A mutation was isolated in the ferric uptake regulator (fur) gene of X. oryzae pv. oryzae and it was shown to result in the production of siderophores in a constitutive manner. The fur mutant is hypersensitive to the metallo-antibiotic streptonigrin, a phenotype that is indicative of intracellular free-iron overload, and also exhibits a slow growth phenotype on rich medium. The fur mutant is virulence deficient, hypersensitive to hydrogen peroxide, and exhibits reduced catalase activity. Exogenous supplementation with ascorbic acid (an antioxidant) rescues the growth deficiency of the fur mutant in rice leaves. The virulence deficiency of the X. oryzae pv. oryzae fur mutant is proposed to be due, at least in part, to an impaired ability to cope with the oxidative stress conditions that are encountered during infection.     

Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA

Pus10, a recently identified pseudouridine (Ψ) synthase, does not belong to any of the five commonly identified families of Ψ synthases. Pyrococcus furiosus Pus10 has been shown to produce Ψ55 in tRNAs. However, in vitro studies have identified another mechanism for tRNA Ψ55 production in Archaea, which uses Cbf5 and other core proteins of the H/ACA ribonucleoprotein complex, in a guide RNA-independent manner. Pus10 homologs have been observed in nearly all sequenced archaeal genomes and in some higher eukaryotes, but not in yeast and bacteria. This coincides with the presence of Ψ54 in the tRNAs of Archaea and higher eukaryotes and its absence in yeast and bacteria. No tRNA Ψ54 synthase has been reported so far. Here, using recombinant Methanocaldococcus jannaschii and P. furiosus Pus10, we show that these proteins can function as synthase for both tRNA Ψ54 and Ψ55. The two modifications seem to occur independently. Salt concentration dependent variations in these activities of both proteins are observed. The Ψ54 synthase activity of M. jannaschii protein is robust, while the same activity of P. furiosus protein is weak. Probable reasons for these differences are discussed. Furthermore, unlike bacterial TruB and yeast Pus4, archaeal Pus10 does not require a U54•A58 reverse Hoogstein base pair and pyrimidine at position 56 to convert tRNA U55 to Ψ55. The homology of eukaryal Pus10 with archaeal Pus10 suggests that the former may also have a tRNA Ψ54 synthase activity.     

Seasonal seston stoichiometry: effects on zooplankton in cyanobacteria-dominated lakes

Seasonal dynamics in elemental composition [carbon (C), nitrogenand phosphorus (P)] of seston and zooplankton were studied overseveral years in three hypereutrophic Dutch lakes with persistentdominance and high biomass of cyanobacteria. In all three lakes,there was a strong pattern with decreased P-content and increasedC:P ratio in seston (<150 µm) coinciding with the increasein water temperature. The seston C:P ratios (at:at) were morethan doubled with the rising temperature, i.e. from 200 (at:at)in winter to 500 in summer. Sestonic C:P ratios increased overthe growing season, suggesting that seasonal dynamics amongautotrophs with high P-uptake in winter and support of subsequentphytoplankton growth by consumption of internal cellular P (P-quota)was the main cause of low sestonic P contents in late summer.This could, however, occur in concert with a physiologicallydriven decrease in cell-specific P at higher temperatures insummer. In contrast, the annual variation of C:P ratios of thezooplankton fraction was only 10% of that of seston. The variationsof C:P ratios of the zooplankton were, nevertheless, stronglycorrelated with those of seston. For most of the summer, sestonC:P ratios were far above the threshold ratio for P-limitationin Daphnia and other P-demanding species. This will pose furtherconstraints on growth performance of Daphnia in these lakes,thus adding to the fish predation pressure and the poor foodquality of cyanobacteria per se. The low grazing pressure causesa high biomass of low-quality autotrophs, promoting a stablestate with low trophic transfer efficiency.     

A transiently expressed transposase system to generate <Emphasis Type="Italic">Ds</Emphasis>-tagged mutants for functional genomics in sorghum

Six T-DNA/Ds launch pad lines (T₀) previously generated by Agrobacterium-mediated transformation of M 35-1 genotype of sorghum were confirmed by PCR. T₁ plants of all six lines showed 3:1 segregation when sprayed with 12 ppm Basta herbicide, indicating single copy insertion, which was also confirmed by left border flanking sequence tag. Calli derived from pNU435-T₀(1) primary transformant was co-infected with Agrobacterium-carrying iAc construct for transient expression of transposase to generate stable Ds-tagged mutants in the T₀ generation. All nine regenerants were PCR-positive for Ds. However, four contained intact T-DNA/Ds launch pad, while five plants carried empty launch pad, indicating transposition of the Ds. One of these plants, IDs-T₀(8), was negative for iAc PCR, indicating that it was a stable Ds-tagged mutant. Of the four plants with intact T-DNA/Ds, IDs-T₀(5) carrying iAc was a double transformant and mutagenic, which can generate mutants in the subsequent generation. Hence, the transient expression of transposase system in sorghum reported here can be employed for high throughput mutagenesis.     

Identification of clinically relevant protein targets in prostate cancer with 2D-DIGE coupled mass spectrometry and systems biology network platform

Prostate cancer (PCa) is the most common type of cancer found in men and among the leading causes of cancer death in the western world. In the present study, we compared the individual protein expression patterns from histologically characterized PCa and the surrounding benign tissue obtained by manual micro dissection using highly sensitive two-dimensional differential gel electrophoresis (2D-DIGE) coupled with mass spectrometry. Proteomic data revealed 118 protein spots to be differentially expressed in cancer (n = 24) compared to benign (n = 21) prostate tissue. These spots were analysed by MALDI-TOF-MS/MS and 79 different proteins were identified. Using principal component analysis we could clearly separate tumor and normal tissue and two distinct tumor groups based on the protein expression pattern. By using a systems biology approach, we could map many of these proteins both into major pathways involved in PCa progression as well as into a group of potential diagnostic and/or prognostic markers. Due to complexity of the highly interconnected shortest pathway network, the functional sub networks revealed some of the potential candidate biomarker proteins for further validation. By using a systems biology approach, our study revealed novel proteins and molecular networks with altered expression in PCa. Further functional validation of individual proteins is ongoing and might provide new insights in PCa progression potentially leading to the design of novel diagnostic and therapeutic strategies.     

Stereoselective enzymatic hydrolysis of (exo,exo)-7-oxabicyclo[2.2.1]heptane-2,3-dimethanol diacetate ester in a biphasic system

Summary A key chiral intermediate lactol(3)[3aS (3a,4,7,7a)]-hexahydro-4,7-epoxy-isobenzofuran-1 (3H)-one was prepared for the total synthesis of a new thromboxane antagonist. The stereoselective hydrolysis of (exo,exo)-7-oxabicyclo[2.2.1]heptane-2,3-dimethanol, diacetate ester (1) to the corresponding chiral monoacetate ester (2) was carried out with lipases, among which Amano P-30 lipase from Pseudomonas sp. was most effective since it gave the desired enantiomer of monoacetate ester. A yield of 75 mol% and optical purity of >99% was obtained when the reaction was conducted in a biphasic system with 10% toluene at 5 g/l of the substrate. Lipase P-30 was immobilized on Accurel polypropylene (PP) and the immobilized enzyme was reused (five cycles) without loss of enzyme activity, productivity or optical purity. The reaction process was scaled-up to 80 1 (400 g substrate) and monoacetate (2) was isolated in 80 mol% yield with 99.3% optical purity as determined by chiral HPLC and nuclear magnetic resonance (NMR) analysis. A gas chromatography of 99.5% and specific rotation, []_D of -7.6° was obtained. The chiral monoacetate ester (2) was oxidized to its corresponding aldehyde and subsequently hydrolyzed to give lactol (3).     

Bidirectional electron transfer in photosystem I: accumulation of A0- in A-side or B-side mutants of the axial ligand to chlorophyll A0

Photosystem I contains two potential electron transfer pathways between P(700) and F(X). These branches are made up of the electron transfer chain components A, A(0), and A(1). The primary electron acceptor A(0) is a chlorophyll a monomer that could be one or both of the two chlorophyll molecules, eC-A(3)/eC-B(3), identified in the 2.5 A resolution structure. The eC-A(3)/eC-B(3) chlorophylls are both coordinated by the sulfur atom of a methionine. This coordination is highly unusual, as interactions between the acid Mg(2+) and the soft base sulfur are weak. The eC-A(3)/eC-B(3) chlorophylls also are located close to one of the connecting chlorophylls that may link the antenna and the electron transfer chain chlorophylls. Due to their location in the structure, the eC-A(3)/eC-B(3) chlorophylls may play a role in both excitation energy transfer and electron transfer. To test the role of the eC-A(3)/eC-B(3) chlorophylls in electron transfer, Met-684 of PsaA and Met-664 of PsaB have been changed to His, Ser, and Leu. Replacement of either M(A684) or M(B664) results in a significant alteration in growth phenotype. The His and Leu mutants are very light sensitive in the presence of oxygen. Growth is impaired to a greater extent in the B-side mutants. However, all of the mutants are able to grow anaerobically at comparable rates. The His and Ser mutants all accumulate PSI at a level similar to that of wild type, whereas the Leu mutants have reduced amounts of PSI. Ultrafast transient absorbance measurements show that the (A(0)(-) - A(0)) difference signal accumulates in the MH(A684) and MH(B664) mutants under neutral conditions, demonstrating that electron transfer between A(0)(-) and A(1) is blocked or significantly slowed. The results show that both the A-branch and the B-branch of the ETC are active in PSI from Chlamydomonas reinhardtii.     

Endocytosis by random initiation and stabilization of clathrin-coated pits

Clathrin-coated vesicles carry traffic from the plasma membrane to endosomes. We report here the real-time visualization of cargo sorting and endocytosis by clathrin-coated pits in living cells. We have detected the formation of coats by monitoring incorporation of fluorescently tagged clathrin or its adaptor AP-2; we have also followed clathrin-mediated uptake of transferrin and of single LDL or reovirus particles. The intensity of a cargo-loaded clathrin cluster grows steadily during its lifetime, and the time required to complete assembly is proportional to the size of the cargo particle. These results are consistent with a nucleation-growth mechanism and an approximately constant growth rate. There are no strongly preferred nucleation sites. A proportion of the nucleation events are weak and short lived. Cargo incorporation occurs primarily or exclusively in a newly formed coated pit. Our data lead to a model in which coated pits initiate randomly but collapse unless stabilized, perhaps by cargo capture.     

Comparative study on enzymatic digestibility of switchgrass varieties and harvests processed by leading pretreatment technologies

Feedstock quality of switchgrass for biofuel production depends on many factors such as morphological types, geographic origins, maturity, environmental and cultivation parameters, and storage. We report variability in compositions and enzymatic digestion efficiencies for three cultivars of switchgrass (Alamo, Dacotah and Shawnee), grown and harvested at different locations and seasons. Saccharification yields of switchgrass processed by different pretreatment technologies (AFEX, dilute sulfuric acid, liquid hot water, lime, and soaking in aqueous ammonia) are compared in regards to switchgrass genotypes and harvest seasons. Despite its higher cellulose content per dry mass, Dacotah switchgrass harvested after wintering consistently gave a lower saccharification yield than the other two varieties harvested in the fall. The recalcitrance of upland cultivars and over-wintered switchgrass may require more severe pretreatment conditions. We discuss the key features of different pretreatment technologies and differences in switchgrass cultivars and harvest seasons on hydrolysis performance for the applied pretreatment methods.