Identification of DNA-binding proteins by incorporating evolutionary information into pseudo amino acid composition via the top-n-gram approach

DNA-binding proteins are crucial for various cellular processes and hence have become an important target for both basic research and drug development. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to establish an automated method for rapidly and accurately identifying DNA-binding proteins based on their sequence information alone. Owing to the fact that all biological species have developed beginning from a very limited number of ancestral species, it is important to take into account the evolutionary information in developing such a high-throughput tool. In view of this, a new predictor was proposed by incorporating the evolutionary information into the general form of pseudo amino acid composition via the top-n-gram approach. It was observed by comparing the new predictor with the existing methods via both jackknife test and independent data-set test that the new predictor outperformed its counterparts. It is anticipated that the new predictor may become a useful vehicle for identifying DNA-binding proteins. It has not escaped our notice that the novel approach to extract evolutionary information into the formulation of statistical samples can be used to identify many other protein attributes as well.     

5-Aminolevulinic Acid Ameliorates the Growth, Photosynthetic Gas Exchange Capacity, and Ultrastructural Changes Under Cadmium Stress in Brassica napus L.

Heavy-metal toxicity in soil is one of the major constraints for oilseed rape (Brassica napus L.) production. One of the best ways to overcome this constraint is the use of growth regulators to induce plant tolerance. Response to cadmium (Cd) toxicity in combination with a growth regulator, 5-aminolevulinic acid (ALA), was investigated in oilseed rape grown hydroponically in greenhouse conditions under three levels of Cd (0, 100, and 500 μM) and three levels of foliar application of ALA (0, 12.5, and 25 mg l^?1). Cd decreased plant growth and the chlorophyll concentration in leaves. Foliar application of ALA improved plant growth and increased the chlorophyll concentration in the leaves of Cd-stressed plants. Significant reductions in photosynthetic parameters were observed by the addition of Cd alone. Application of ALA improved the net photosynthetic and gas exchange capacity of plants under Cd stress. ALA also reduced the Cd content in shoots and roots, which was elevated by high concentrations of Cd. The microscopic studies of leaf mesophyll cells under different Cd and ALA concentrations showed that foliar application of ALA significantly ameliorated the Cd effect and improved the structure of leaf mesophyll cells. However, the higher Cd concentration (500 μM) could totally damage leaf structure, and at this level the nucleus and intercellular spaces were not established as well; the cell membrane and cell wall were fused to each other. Chloroplasts were totally damaged and contained starch grains. However, foliar application of ALA improved cell structure under Cd stress and the visible cell structure had a nucleus, cell wall, and cell membrane. These results suggest that under 15-day Cd-induced stress, application of ALA helped improve plant growth, chlorophyll content, photosynthetic gas exchange capacity, and ultrastructural changes in leaf mesophyll cells of the rape plant.     

The critical soil P levels for crop yield, soil fertility and environmental safety in different soil types

Background and aims

Sufficient soil phosphorus (P) is important for achieving optimal crop production, but excessive soil P levels may create a risk of P losses and associated eutrophication of surface waters. The aim of this study was to determine critical soil P levels for achieving optimal crop yields and minimal P losses in common soil types and dominant cropping systems in China.

Methods

Four long-term experiment sites were selected in China. The critical level of soil Olsen-P for crop yield was determined using the linear-plateau model. The relationships between the soil total P, Olsen-P and CaCl₂-P were evaluated using two-segment linear model to determine the soil P fertility rate and leaching change-point.

Results

The critical levels of soil Olsen-P for optimal crop yield ranged from 10.9 mg kg^?1 to 21.4 mg kg^?1, above which crop yield response less to the increasing of soil Olsen-P. The P leaching change-points of Olsen-P ranged from 39.9 mg kg^?1 to 90.2 mg kg^?1, above which soil CaCl₂-P greatly increasing with increasing soil Olsen-P. Similar change-point was found between soil total P and Olsen-P. Overall, the change-point ranged from 4.6 mg kg^?1 to 71.8 mg kg^?1 among all the four sites. These change-points were highly affected by crop specie, soil type, pH and soil organic matter content.

Conclusions

The three response curves could be used to access the soil Olsen-P status for crop yield, soil P fertility rate and soil P leaching risk for a sustainable soil P management in field.     

Effect of aboveground intervention on fine root mass, production, and turnover rate in a Chinese cork oak (Quercus variabilis Blume) forest

Aims

Fine root is an important part of the forest carbon cycle. The growth of fine roots is usually affected by forest intervention. This study aims to investigate the fine root mass, production, and turnover in the disturbed forest.

Methods

The seasonal and vertical distributions of fine root (diameter ≤2 mm) were measured in a Chinese cork oak (Quercus variabilis Blume) forest. The biomass and necromass of roots with diameters ≤1 mm and 1-2 mm in 0-40 cm soil profiles were sampled by using a sequential soil coring method in the stands after clear cutting for 3 years, with the stands of the remaining intact trees as the control.

Results

The fine root biomass (FRB) and fine root necromass (FRN) varied during the growing season and reached their peak in August. Lower FRB and higher FRN were found in the clear cutting stands. The ratio between FRN and FRB increased after forest clear cutting compared with the control and was the highest in June. The root mass with diameter ≤1 mm was affected proportionately more than that of diameter 1-2 mm root. Clear cutting reduced FRB and increased FRN of roots both ≤1 mm and 1-2 mm in diameter along the soil depths. Compared with the control, the annual fine root production and the average turnover rate decreased by 30.7 % and 20.7 %, respectively, after clear cutting for 3 years. The decline of canopy cover contributed to the dramatic fluctuation of soil temperature and moisture from April to October. With redundancy discriminate analysis (RDA) analysis, the first axis was explained by soil temperature (positive) and moisture (negative) in the control stands. Aboveground stand structure, including canopy cover, sprout height, and basal area, influenced FRB and FRN primarily after forest clear cutting.

Conclusions

This study suggested that the reduction of fine root biomass, production, and turnover rate can be attributed to the complex changes that occur after forest intervention, including canopy damage, increased soil temperature, and degressive soil moisture.     

Fusaric acid induction of programmed cell death modulated through nitric oxide signalling in tobacco suspension cells

Fusaric acid (FA) is a nonhost-selective toxin mainly produced by Fusarium oxysporum, the causal agent of plant wilt diseases. We demonstrate that FA can induce programmed cell death (PCD) in tobacco suspension cells and the FA-induced PCD is modulated by nitric oxide (NO) signalling. Cells undergoing cell death induced by FA treatment exhibited typical characteristics of PCD including cytoplasmic shrinkage, chromatin condensation, DNA fragmentation, membrane plasmolysis, and formation of small cytoplasmic vacuoles. In addition, caspase-3-like activity was activated upon the FA treatment. The process of FA-induced PCD was accompanied by a rapid accumulation of NO in a FA dose-dependent manner. Pre-treatment of cells with NO scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO) or NO synthase inhibitor N ^G-monomethyl-arginine monoacetate (L-NMMA) significantly reduced the rate of FA-induced cell death. Furthermore, the caspase-3-like activity and the expression of PAL and Hsr203J genes were alleviated by application of cPTIO or L-NMMA to FA-treated tobacco cells. This indicates that NO is an important factor involved in the FA-induced PCD. Our results also show that pre-treatment of tobacco cells with a caspase-3-specific inhibitor, Ac-DEVD-CHO, can reduce the rate of FA-induced cell death. These results demonstrate that the FA-induced cell death is a PCD and is modulated by NO signalling through caspase-3-like activation.     

Converting paddy fields to Lei bamboo (Phyllostachys praecox) stands affected soil nutrient concentrations, labile organic carbon pools, and organic carbon chemical compositions

Background and aims

Land-use change often markedly alters soil carbon (C) and nitrogen (N) pool sizes with implications for climate change and soil sustainability. The objective of this research was to study the effect of converting paddy fields to Lei bamboo (Phyllostachys praecox) stands on soil C and N and other nutrient pools as well as the chemical structure of soil organic C (SOC) in the soil profile.

Methods

Soils (Anthrosols) from four adjacent paddy field–bamboo forest pairs with a known land-use history were sampled from Lin’an County, Zhejiang Province. Soil water soluble organic C (WSOC), hot water soluble organic C (HWSOC), microbial biomass C (MBC), readily oxidizable C (ROC), water soluble organic N (WSON), and other soil chemical and physical properties were determined. Soil organic C functional group compositions were determined by ¹³C-nuclear magnetic resonance (NMR).

Results

Concentrations of soil available P, available K, and different N forms increased (P?<?0.05) by the land-use conversion. Higher concentrations of SOC and total N (TN) were observed in the subsoil (20–40 and 40–60 cm soil layers) but not in the topsoil (0–20 cm layer) in the bamboo stands than in the paddy fields. The storage of SOC and TN in the entire soil profile (0–60 cm) increased by 56.7 and 70.7 %, respectively, after the land-use change. The increases in the SOC stock of the three soil layers were 11.0, 14.3, and 9.5 Mg C ha^?1, respectively. The conversion decreased WSOC concentrations in the subsoil but increased the ROC concentration in the topsoil. Solid-state NMR spectroscopy of soil samples showed that the conversion increased (P?<?0.05) the O-alkyl C content while decreased the aromatic C content, alkyl C to O-alkyl C ratio (A/O-A), and aromaticity of SOC.

Conclusions

Conversion of paddy fields to bamboo stands increased soil nutrient availability, and SOC and TN stocks. Effects of land-use change on C pools and C chemistry of SOC varied among different soil layers in the profile. The impact of the land-use conversion on soil organic C pools was not restricted to the topsoil, but changes in the subsoil were equally large and should be accounted for.     

Hemagglutinin Stalk-Based Universal Vaccine Constructs Protect against Group 2 Influenza A Viruses

Current influenza virus vaccines contain H1N1 (phylogenetic group 1 hemagglutinin), H3N2 (phylogenetic group 2 hemagglutinin), and influenza B virus components. These vaccines induce good protection against closely matched strains by predominantly eliciting antibodies against the membrane distal globular head domain of their respective viral hemagglutinins. This domain, however, undergoes rapid antigenic drift, allowing the virus to escape neutralizing antibody responses. The membrane proximal stalk domain of the hemagglutinin is much more conserved compared to the head domain. In recent years, a growing collection of antibodies that neutralize a broad range of influenza virus strains and subtypes by binding to this domain has been isolated. Here, we demonstrate that a vaccination strategy based on the stalk domain of the H3 hemagglutinin (group 2) induces in mice broadly neutralizing anti-stalk antibodies that are highly cross-reactive to heterologous H3, H10, H14, H15, and H7 (derived from the novel Chinese H7N9 virus) hemagglutinins. Furthermore, we demonstrate that these antibodies confer broad protection against influenza viruses expressing various group 2 hemagglutinins, including an H7 subtype. Through passive transfer experiments, we show that the protection is mediated mainly by neutralizing antibodies against the stalk domain. Our data suggest that, in mice, a vaccine strategy based on the hemagglutinin stalk domain can protect against viruses expressing divergent group 2 hemagglutinins.     

Human Parainfluenza Virus Type 2 V Protein Inhibits TRAF6-Mediated Ubiquitination of IRF7 To Prevent TLR7- and TLR9-Dependent Interferon Induction

Paramyxovirus V proteins block Toll-like receptor 7 (TLR7)- and TLR9-dependent signaling leading to alpha interferon production. Our recent study has provided evidence that interaction of the V proteins with IRF7 is important for the blockade. However, the detailed mechanisms still remain unclear. Here we reexamined the interaction of the human parainfluenza virus type 2 (HPIV2) V protein with signaling molecules involved in TLR7/9-dependent signaling. Immunoprecipitation experiments in HEK293T cells transfected with V protein and one of the signaling molecules revealed that the V protein interacted with not only IRF7 but also TRAF6, IKKα, and MyD88. Whereas overexpression of TRAF6 markedly enhanced the level of V protein associating with IRF7, IKKα, and MyD88 in HEK293T cells, the level of V protein associating with TRAF6 was little affected by overexpression of IRF7, IKKα, and MyD88. Moreover, knockdown or knockout of endogenous TRAF6 in HEK293T or mouse embryonic fibroblast cells resulted in dissociation of the V protein from IRF7, IKKα, and MyD88. These results demonstrate that binding of the V protein to IRF7, IKKα, and MyD88 is largely indirect and mediated by endogenous TRAF6. It was found that the V protein inhibited TRAF6-mediated lysine 63 (K63)-linked polyubiquitination of IRF7, which is prerequisite for IRF7 activation. Disruption of the tryptophan-rich motif of the V protein significantly affected its TRAF6-binding efficiency, which correlated well with the magnitude of inhibition of K63-linked polyubiquitination and the resultant activation of IRF7. Taken together, these results suggest that the HPIV2 V protein prevents TLR7/9-dependent interferon induction by inhibiting TRAF6-mediated K63-linked polyubiquitination of IRF7.