Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6 dehydratase provides insights into the enzyme's catalytic mechanism and regulation by GDP-fucose

Background: GDP-mannose 4,6 dehydratase (GMD) catalyzes the conversion of GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose. This is the first and regulatory step in the de novo biosynthesis of GDP-(L)-fucose. Fucose forms part of a number of glycoconjugates, including the ABO blood groups and the selectin ligand sialyl Lewis X. Defects in GDP-fucose metabolism have been linked to leukocyte adhesion deficiency type II (LADII). Results: The structure of the GDP-mannose 4,6 dehydratase apo enzyme has been determined and refined using data to 2.3 A resolution. GMD is a homodimeric protein with each monomer composed of two domains. The larger N-terminal domain binds the NADP(H) cofactor in a classical Rossmann fold and the C-terminal domain harbors the sugar-nucleotide binding site. We have determined the GMD dissociation constants for NADP, NADPH and GDP-mannose. Each GMD monomer binds one cofactor and one substrate molecule, suggesting that both subunits are catalytically competent. GDP-fucose acts as a competitive inhibitor, suggesting that it binds to the same site as GDP-mannose, providing a mechanism for the feedback inhibition of fucose biosynthesis. Conclusions: The X-ray structure of GMD reveals that it is a member of the short-chain dehydrogenase/reductase (SDR) family of proteins. We have modeled the binding of NADP and GDP-mannose to the enzyme and mutated four of the active-site residues to determine their function. The combined modeling and mutagenesis data suggests that at position 133 threonine substitutes serine as part of the serine-tyrosine-lysine catalytic triad common to the SDR family and Glu 135 functions as an active-site base.     

甲功五项化学发光免疫分析的基质效应对临床测值的影响

目的:探索评价基质效应在化学发光免疫分析中对甲状腺功能五项指标的影响。方法:选取甲状腺功能五项高值血清,用10种基质牛血清、马血清、山羊血清、水解明胶、BSA、PBS、生理盐水、正常人血清、甲减人血清、甲亢人血清分别对T3、T4、FT3、FT4、TSH的高值血清进行倍比稀释,观察基质效应,另将10种基质用考马斯亮兰法检测蛋白含量,分析蛋白含量与基质效应的关系。结果:T3项目牛血清、水解明胶、BSA有明显基质效应;T4和FT3项目牛血清、水解明胶、BSA、PBS、生理盐水有明显基质效应;FT4项目牛血清、马血清、水解明胶、BSA、PBS、生理盐水有明显基质效应;TSH项目没有发现基质效应,正常人血清、甲减人血清和甲亢人血清对甲状腺功能五项无基质效应。检测结果显示蛋白含量多少与基质效应无关。结论:人血清基质是用于稀释样本,基质效应最小的液体,针对个体差异性进行的选择,稀释T3、T4、FT3、FT4高值血清选择甲减人血清,稀释TSH高值血清选择甲亢人血清,可以得到较为满意的结果。     

Seed germination of Pilosocereus arrabidae (Cactaceae) from a semiarid region of south‐east Brazil

We evaluated the effect of temperature regimes (six constant and four alternating temperatures), light qualities (five red : far red ratios) and water potentials (ΨW; seven NaCl and polyethylene glycol 6000 [PEG] solutions) on the percentage and germination rate, as well as the post‐seminal development morphology, that allow Pilosocereus arrabidae seeds to germinate in a hot semiarid climate on the south‐eastern Brazilian coast. The results showed that seeds germinated similarly between constant and alternating temperatures, with an optimal germination at 25/20°C and 20°C. Pilosocereus arrabidae seeds were photoblastic positive and the final germination percentage was inhibited at low red : far red ratios. Maximum germination was obtained in distilled water (0 MPa) and decreases of Ψ_W in the solutions reduced the germination, which was lower in NaCl than in iso‐osmotic PEG solutions. Germination inhibition appears to be osmotic because the recovery response was high when non‐germinated seeds from both iso‐osmotic solutions were transferred to water. Seeds of P. arrabidae are small and germination is phaneroepigeal. Despite the slow growth typically seen in seedlings and adults of Cactaceae, germination in this species depends on the ability of the seeds to appropriately sense and react to environmental cues that correlate with times and places under low‐risk growth conditions.     

Brassinosteroid leaf unrolling QTL mapping in durum wheat

Brassinosteroids are a newly reported class of plant growth phytohormones found in plants throughout the plant kingdom. Functioning at very low concentrations, they play an essential role in improving biomass yield and stress tolerance. There are no reports in the literature of the genetic variability of responsiveness of brassinosteroids in wheat; most studies on brassinosteroids have focused on the physiological effects of exogenous addition of brassinosteroids. Our aim was to study the genetic variation in the responsiveness of a doubled haploid durum wheat population to three brassinosteroid concentrations using the leaf unrolling test, which is a simple bioassay to test brassinosteroid activity. An F₁-derived doubled haploid population of 77 individuals from the cross Strongfield/Blackbird was used to construct a genetic map of 427 molecular marker loci. The leaf unrolling test was performed on the parents and doubled haploid genotypes of the population using 0.2, 2 and 20 nM brassinosteroid concentrations. The results indicated significant differences in leaf unrolling between the two parents, doubled haploid genotypes, treatments and genotype-by-treatment combinations. Transgressive segregation beyond Strongfield of leaf unrolling was observed for all concentrations, with the strongest response at 20 nM. Putative quantitative trait loci were revealed in the intervals Xgwm2–Xbarc45 on chromosome 3A and Xwmc643a–Xwmc625a on chromosome 3B. Additional quantitative trait loci were associated with markers Xwmc48a, Xwmc511, Xwmc89a and Xgwmc692 on chromosome 4B, and Xwmc17 on chromosome 7A. This work should enhance the understanding of the relationship between stress tolerance and productivity, and responsiveness to brassinosteroids.     

NR4A Nuclear Receptors Target Poly-ADP-Ribosylated DNA-PKcs Protein to Promote DNA Repair

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Histone tails and the H3 alphaN helix regulate nucleosome mobility and stability

Nucleosomes fulfill the apparently conflicting roles of compacting DNA within eukaryotic genomes while permitting access to regulatory factors. Central to this is their ability to stably associate with DNA while retaining the ability to undergo rearrangements that increase access to the underlying DNA. Here, we have studied different aspects of nucleosome dynamics including nucleosome sliding, histone dimer exchange, and DNA wrapping within nucleosomes. We find that alterations to histone proteins, especially the histone tails and vicinity of the histone H3 alphaN helix, can affect these processes differently, suggesting that they are mechanistically distinct. This raises the possibility that modifications to histone proteins may provide a means of fine-tuning specific aspects of the dynamic properties of nucleosomes to the context in which they are located.     

A trait-based approach across the native and invaded range to understand plant invasiveness and community impact

Alien plant species invasiveness and impact on diversity (i.e. species richness and composition) can be driven by the altered competitive interactions experienced by the invader in its invaded range compared to its native range. Trait-based competition effects on invasiveness can be mediated through size-asymmetric competition, i.e. a trait suit of the invader that drives competitive dominance, and through ‘niche differences', i.e. trait differentiation and thus minimized competition between invader and the invaded community. In terms of invasion impact, size-asymmetric competition is expected to result in competitive exclusion of co-occurring subordinate species, whereas ‘niche differences' might result in competitive exclusion of the most functionally similar co-occurring species. Although observational work does not allow the full disentanglement of both trait-based effects, it does allow to verify the occurrence of expected theoretical trait patters. In this study, we explored the trait-based competition effects on invasiveness and diversity impact for Rosa rugosa in both its invaded range in Belgium and its native range in Japan, based on seven functional traits across 100 vegetation plots. Following the predictions for enhanced invasiveness, we found much lower functional overlap between R. rugosa and the co-occurring species in the invaded range compared to the native range. This likely also explains the absence of diversity impact in its native range. Despite the absence of changes in species richness in the invaded range, the invader did strongly impact species composition of invaded communities. This impact occurred through strong shade tolerance responses, suggesting size-asymmetric competition effects and cover loss of co-occurring dominant species, next to exclusion of co-occurring species most functionally similar to the invader; suggesting niche difference effects. In conclusion, this case-study illustrates how exploring functional trait patterns across a species native and invaded range can help in understanding how trait-based competition processes can affect invasiveness and community impact.     

Construction of helper plasmid-mediated dual-display phage for autoantibody screening in serum

M13 filamentous bacteriophage has been used in displaying disease-specific antibodies, biomarkers, and peptides. One of the major drawbacks of using phage in diagnostic assays is the aspecific adsorption of proteins leading to a high background signal and decreasing sensitivity. To deal with this, we developed a genetically pure, exchangeable dual-display phage system in which biomarkers and streptavidin-binding protein (SBP) are displayed at opposite ends of the phage. This approach allows for sample purification, using streptavidin-coated magnetic beads resulting in a higher sensitivity of signal detection assays. Our dual-display cassette system approach also allows for easy exchange of both the anchor protein (SBP) and the displayed biomarker. The presented principle is applied for the detection of antibody reactivity against UH-RA.21 which is a good candidate biomarker for rheumatoid arthritis (RA). The applicability of dual-display phage preparation using a helper plasmid system is demonstrated, and its increased sensitivity in phage ELISA assays using patient serum samples is shown.