Genome Sequence of a Highly Efficient Aerobic Denitrifying Bacterium,Pseudomonas stutzeri T13

Pseudomonas stutzeri T13 is a highly efficient aerobic denitrifying bacterium. Information about the genome of this aerobic denitrifying bacterium has been limited until now. We present the draft genome of P. stutzeri T13. The results could provide further insight into the aerobic denitrification mechanism in strain T13.     

Continuous biosynthesis of abscisic acid (ABA) may be required for maintaining dormancy of isolated embryos and intact seeds of Euonymus alatus

Euonymus alatus (Thunb.) Sieb. is a popular landscape plant in the United States due to its brilliant red fall foliage. It is also an important ornamental plant in many other areas of the world such as China, Japan and Europe. However, E. alatus is considered as a highly invasive plant species in the US. Mutation breeding can be used to create sterile, non-invasive cultivars. Seeds are the most commonly used explants for mutagen treatments, but E. alatus mature seeds possess prolonged dormancy and only a low percentage of them germinate even after 18?months of cold stratification. Here we report an immature embryo culture method for E. alatus ??Compactus?? to circumvent the seed dormancy problem. Also, we have found that activated charcoal, gibberellic acid (GA₃) and 6-benzyladenine (BA) can reduce the dormancy of isolated embryos, which suggests that abscisic acid (ABA) might play a role in controlling seed dormancy. We have further demonstrated that exogenous ABA enhances dormancy of isolated E. alatus embryos while fluridone, an inhibitor for ABA biosynthesis, can effectively break their dormancy. These results, particularly the effect of fluridone, suggest that continuous ABA biosynthesis plays an important role in controlling the dormancy of E. alatus seeds.     

Spectroscopic studies of protein folding: linear and nonlinear methods

Although protein folding is a simple outcome of the underlying thermodynamics, arriving at a quantitative and predictive understanding of how proteins fold nevertheless poses huge challenges. Therefore, both advanced experimental and computational methods are continuously being developed and refined to probe and reveal the atomistic details of protein folding dynamics and mechanisms. Herein, we provide a concise review of recent developments in spectroscopic studies of protein folding, with a focus on new triggering and probing methods. In particular, we describe several laser-based techniques for triggering protein folding/unfolding on the picosecond and/or nanosecond timescales and various linear and nonlinear spectroscopic techniques for interrogating protein conformations, conformational transitions, and dynamics.     

Phosphorylation of Ser-129 is the dominant pathological modification of alpha-synuclein in familial and sporadic Lewy body disease

A comprehensive, unbiased inventory of synuclein forms present in Lewy bodies from patients with dementia with Lewy bodies was carried out using two-dimensional immunoblot analysis, novel sandwich enzyme-linked immunosorbent assays with modification-specific synuclein antibodies, and mass spectroscopy. The predominant modification of alpha-synuclein in Lewy bodies is a single phosphorylation at Ser-129. In addition, there is a set of characteristic modifications that are present to a lesser extent, including ubiquitination at Lys residues 12, 21, and 23 and specific truncations at Asp-115, Asp-119, Asn-122, Tyr-133, and Asp-135. No other modifications are detectable by tandem mass spectrometry mapping, except for a ubiquitous N-terminal acetylation. Small amounts of Ser-129 phosphorylated and Asp-119-truncated alpha-synuclein are present in the soluble fraction of both normal and disease brains, suggesting that these Lewy body-associated forms are produced during normal metabolism of alpha-synuclein. In contrast, ubiquitination is only detected in Lewy bodies and is primarily present on phosphorylated synuclein; it therefore likely occurs after phosphorylated synuclein has deposited into Lewy bodies. This invariant pattern of specific phosphorylation, truncation, and ubiquitination is also present in the detergent-insoluble fraction of brain from patients with familial Parkinson's disease (synuclein A53T mutation) as well as multiple system atrophy, suggesting a common pathogenic pathway for both genetic and sporadic Lewy body diseases. These observations are most consistent with a model in which preferential accumulation of normally produced Ser-129 phosphorylated alpha-synuclein is the key event responsible for the formation of Lewy bodies in various Lewy body diseases.     

Model plants for studying the interaction between Methylobacterium mesophilicum and Xylella fastidiosa

Over the last few years, endophytic bacterial communities associated with citrus have been studied as key components interacting with Xylella fastidiosa. In this study, we investigated the possible interaction between the citrus endophyte Methylobacterium mesophilicum SR1.6/6 and X. fastidiosa in model plants such as Catharanthus roseus (Madagaskar periwinkle) and Nicotiana clevelandii (Clevelands tobacco). The aim of this study was to establish the fate of M. mesophilicum SR1.6/6 after inoculation of C. roseus and N. clevelandii plants, using PCR-DGGE (polymerase chain reaction--denaturing gradient gel electrophoresis) and plating techniques. Shifts in the indigenous endophytic bacterial communities were observed in plants inoculated with strain SR1.6/6, using specific primers targeting alpha- and beta-Proteobacteria. Cells of strain SR1.6/6 were observed in a biofilm structure on the root and hypocotyl surfaces of in vitro seedlings inoculated with M. mesophilicum SR1.6/6. This emphasizes the importance of these tissues as main points of entrance for this organism. The results showed that C. roseus and N. clevelandii could be used as model plants to study the interaction between M. mesophilicum and X. fastidiosa.     

Chemical composition, nutritive value, fatty acid and amino acid contents of Galega officinalis L. during its growth stage and in regrowth

The aim of this study was to determine the chemical composition, nutritive value, fatty acid profile and amino acid concentrations of Galega officinalis L. during its first growth cycle and in regrowth. Herbage samples were collected three times at progressive morphological stages from the vegetative to the budding stage, and during regrowth. The dry matter (DM), organic matter (OM), neutral detergent fibre (NDFom), acid detergent fibre (ADFom), lignin (sa) and gross energy (GE) increased during maturation, while the crude protein (CP), ether extract (EE), ash and OM digestibility (OMD) decreased with increasing stage. During the whole growth cycle, and in regrowth, the NE_L was unchanged. Analyses of fatty acids did not reveal differences among plant stages, but did instead between the first cut and regrowth cut. The fatty acid profiles in the plant during growth was characterised by three dominant fatty acids, being -linolenic acid (C_{18:3n − 3}), palmitic acid (C_16:0), and linoleic acid (C_{18:2n − 6}). The -linolenic acid content was instead lower than in the whole plant during growth. The n − 6/n − 3 polyunsaturated fatty acid ratio of the plant was steady at 0.13 during the growth cycle and in regrowth, while it was 0.78 in the seed. The individual amino acid contents of G. officinalis declined with increasing stage of maturity, as the CP declined, but with the exception of the serine content, there was no change in the relative proportions of the individual amino acids due to stage of maturity. Data shows that the nutritive value of G. officinalis forage did not diminish during its growth cycle and that it can improve the self sufficiency of dairy farms. Autumn regrowth was judged to be a good quality forage with a high nutritive value and a higher level of -linolenic acid than during the first growth cycle.     

A preliminary survey of the arbuscular mycorrhizal status of grassland plants in southern Tibet

We report for the first time the arbuscular mycorrhizal (AM) status of native plant species and AM fungal diversity in the grasslands of southern Tibet. A total of 51 soil samples were collected from the rhizospheres of the dominant plant species, and AM fungal structures were observed in 18 (82%) of 22 plant species examined. Vesicles and aseptate hyphae were the structures most frequently observed in the plant roots. After trap culture for 5 months, 25 AM fungal taxa were identified in the soil samples collected, of which nine belonged to Glomus, ten to Acaulospora, one to Entrophospora and five to Scutellospora. The frequency of occurrence of different genera and species varied greatly. Glomus was the dominant genus, and the most frequent and abundant species was Glomus mosseae. Over the whole sampling area, spore density in the rhizosphere soil of different host plant species ranged from 2 to 66 per 20 g air-dried soil. Overall AM fungal species richness was 2.10 and species diversity was 2.35. AM fungal diversity was also compared among the four different land use types (farmland and normal, disturbed and highly disturbed montane scrub grassland). Spore densities in the farmland and normal grassland were much higher than in the grasslands that had been degraded to varying degrees. The species richness in normal grassland was the highest of the four land use types examined. Species diversity varied from 1.99 to 0.94 and was highest in normal grassland, intermediate in degraded grassland and farmland, and lowest in the highly disturbed grassland.     

Synthesis, characterization and electrocatalysis of diiron propanediselenolate derivatives as the active site models of [FeFe]-hydrogenases

As an extension of our study on the H-cluster model compounds, a series of diiron propanediselenolate (PDS)-type models have been successfully synthesized. Reaction of diselenol HSe(CH₂)₃SeH with Fe₃(CO)₁₂ in THF (tetrahydrofuran) at reflux gave the parent model compound [μ-Se(CH₂)₃Se-μ]Fe₂(CO)₆ (1) in 48% yield. Further reaction of 1 with PPh₃ or PPh₂H in the presence of Me₃NO in MeCN at room temperature afforded the phosphine-monosubstituted model compounds [μ-Se(CH₂)₃Se-μ]Fe₂(CO)₅(L) (2, L = PPh₃; 3, L = PPh₂H) in 76% and 68% yields, respectively. Similarly, the N-heterocyclic carbene I_Mes-monosubstituted model compound [μ-Se(CH₂)₃Se-μ]Fe₂(CO)₅(I_Mes) (4) could be prepared in 46% yield by reaction of imidazolium salt I_Mes · HCl with n-BuLi followed by treatment of the resulting I_Mes ligand with 1 in THF at room temperature. Compounds 1-4 were fully characterized by elemental analysis and various spectroscopic methods. While the structures of 1-4 were further confirmed by X-ray crystallography, the comparative study of 1 and its analog [μ-S(CH₂)₃S-μ]Fe₂(CO)₆ demonstrates that 1 is a better catalyst for TsOH proton reduction to hydrogen under electrochemical conditions.     

Generation and characterization of functional cardiomyocytes using induced pluripotent stem cells derived from human fibroblasts

We have successfully developed both spontaneous and inductive cardiomyocyte differentiation of iPS cells reprogrammed from human foreskin fibroblasts. The reprogrammed iPS cells morphologically resemble human cardiomyocytes which can beat. RT-PCR and immunostaining show that cardiac markers are expressed that are comparable to the differentiation pattern of authentic human embryonic stem cells, indicating the existence of both immature and mature differentiated cardiomyocytes. 5-Azacytidine greatly enhanced the efficiency of cardiomyocyte differentiation, whereas dimethylsulfoxide had no effect. Low serum and bone morphogenetic protein-2 marginally improved differentiation efficiency. iPS cell-derived cardiomyocytes changed their beat frequency in response to cardiac drugs, which included ion channel blockers and α/β adrenergic stimulators. Derived cardiomyocytes look promising as an in vitro system for potential drug screen and/or toxicity, making this system closer to practical use in the near future.