Separation and purification of a keratinase as pesticide against root-knot nematodes

A new alkaline keratinase, which could kill Meloidogyne incognita (a root-knot nematode) was separated and purified from Bacillus sp. 50-3 in this study. The solid ammonium sulfate was selected to precipitate the enzyme and its proper adding mass was also determined. After solid ammonium sulfate precipitation and liquid chromatography on DEAE-Sephadex-A50 column, there was 17.7-fold purification with a yield of 46.5%, as determined by azokeratin as substrate. The purification effect was determined through SDS-PAGE and the molecular weight of the enzyme was found to be 27,423 Da by the MALDI-TOF-MS. When the second-stage juveniles of Meloidogyne incognita were exposed to 50 μg/ml of keratinase solution, 98.5% of Meloidogyne incognita mortality rates were obtained compared to control after 24 h. Its simple purification step and high yield from the cheap medium affords this keratinase great biotechnological potential, especially in controlling root-knot nematodes such as Meloidogyne incognita. To the best of our knowledge, this study is the first report that uses keratinase as a pesticide.     

A versatile and highly sensitive probe for Hg(II), Pb(II) and Cd(II) detection individually and totally in water samples

The detection of heavy metal ions using enzyme-linked immunosorbent assays (ELISA) has been reported by several research groups. However, highly sensitive and selective detection of total heavy metal ions using ELISA is a major technical limitation. Here we describe the development of a versatile and highly sensitive probe combining goat anti-mice IgG, colloidal gold nanoparticles (AuNPs) and horseradish peroxidase (HRP). We demonstrate the utility of this probe using three kinds of heavy metal complete antigens and three monoclonal antibodies (McAbs) in one ELISA system to establish a high-throughput screening protocol. The procedure was successfully applied to analysis of Hg(II), Pb(II) and Cd(II) individually and totally from different water samples. The sensitivities for the detection of Hg(II), Pb(II) and Cd(II) individually and totally are 27.4, 3.9, 15.8 and 18.2 nM, respectively. And all limit of detection (LODs) are lower than 1.2 nM. The recovery results obtained from the developed technique showed a good correlation (R² = 0.983) with those from ICP-MS. The major advantage of the probe is the versatility and high sensibility. The probe could be potentially used, upon demand, as a sensitive and versatile detector for a broad range of applications.     

Carbon nanoparticle for highly sensitive and selective fluorescent detection of mercury(II) ion in aqueous solution

In this article, carbon nanoparticles (CNPs) were used as a novel fluorescent sensing platform for highly sensitive and selective Hg(2+) detection. To the best of our knowledge, this is the first example of CNPs obtained from candle soot used in this type of sensor. The general concept used in this approach is based on that adsorption of the fluorescently labeled single-stranded DNA (ssDNA) probe by CNP via π-π stacking interactions between DNA bases and CNP leads to substantial dye fluorescence quenching; however, in the presence of Hg(2+), T-Hg(2+)-T induced hairpin structure does not adsorb on CNP and thus retains the dye fluorescence. A detection limit as low as 10nM was achieved. The present CNP-based biosensor for Hg(2+) detection exhibits remarkable specificity against other possible metal ions. Furthermore, superior selectivity performance was observed when Hg(2+) detection was carried out in the presence of a large amount of other interference ions. Finally, in order to evaluate its potential practical application, Hg(2+) detection was conducted with the use of lake water other than pure buffer and it is believed that it holds great promise for real sample analysis upon further development.     

Isolation and alga-inhibiting characterization of Vibrio sp. BS02 against Alexandrium tamarense

The bacterium BS02 which is closely related to the genus Vibrio sp. and capable of inhibiting the toxic dinoflagellate Alexandrium tamarense was isolated from a mangrove area in Zhangjiangkou, Fujian Province, China. The bacterium was not species-specific since it displayed varying degrees of lysing activities against eight of the eighteen algae tested. There was a close interaction between initial bacterial and A. tamarense cell densities, indicating that algal growth was prompted at low bacterial concentrations, while the number of the alga cells was reduced at high concentrations. Alga-lysing characterization of Vibrio sp. BS02 suggested that the alga-lysing substance was extracellularly produced, less than 500 in molecular weight, as well as non proteinaceous, stable under wide range of temperature and pH conditions, UV radiation, repeated freezing and thawing and heavy metal treatments. These findings suggested that BS02 could play an important role in controlling harmful algal blooms.     

RDC derived protein backbone resonance assignment using fragment assembly

Experimental residual dipolar couplings (RDCs) in combination with structural models have the potential for accelerating the protein backbone resonance assignment process because RDCs can be measured accurately and interpreted quantitatively. However, this application has been limited due to the need for very high-resolution structural templates. Here, we introduce a new approach to resonance assignment based on optimal agreement between the experimental and calculated RDCs from a structural template that contains all assignable residues. To overcome the inherent computational complexity of such a global search, we have adopted an efficient two-stage search algorithm and included connectivity data from conventional assignment experiments. In the first stage, a list of strings of resonances (CA-links) is generated via exhaustive searches for short segments of sequentially connected residues in a protein (local templates), and then ranked by the agreement of the experimental ¹³C_α chemical shifts and ¹⁵N-¹H RDCs to the predicted values for each local template. In the second stage, the top CA-links for different local templates in stage I are combinatorially connected to produce CA-links for all assignable residues. The resulting CA-links are ranked for resonance assignment according to their measured RDCs and predicted values from a tertiary structure. Since the final RDC ranking of CA-links includes all assignable residues and the assignment is derived from a “global minimum”, our approach is far less reliant on the quality of experimental data and structural templates. The present approach is validated with the assignments of several proteins, including a 42 kDa maltose binding protein (MBP) using RDCs and structural templates of varying quality. Since backbone resonance assignment is an essential first step for most of biomolecular NMR applications and is often a bottleneck for large systems, we expect that this new approach will improve the efficiency of the assignment process for small and medium size proteins and will extend the size limits assignable by current methods for proteins with structural models.     

General allometric equations and biomass allocation of <Emphasis Type="Italic">Pinus massoniana</Emphasis> trees on a regional scale in southern China

Applying allometric equations in combination with forest inventory data is an effective approach to use when qualifying forest biomass and carbon storage on a regional scale. The objectives of this study were to (1) develop general allometric tree component biomass equations and (2) investigate tree biomass allocation patterns for Pinus massoniana, a principal tree species native to southern China, by applying 197 samples across 20 site locations. The additive allometric equations utilized to compute stem, branch, needle, root, aboveground, and total tree biomass were developed by nonlinear seemingly unrelated regression. Results show that the relative proportion of stem biomass to tree biomass increased while the contribution of canopy biomass to tree biomass decreased as trees continued to grow through time. Total root biomass was a large biomass pool in itself, and its relative proportion to tree biomass exhibited a slight increase with tree growth. Although equations employing stem diameter at breast height (dbh) alone as a predictor could accurately predict stem, aboveground, root, and total tree biomass, they were poorly fitted to predict the canopy biomass component. The inclusion of the tree height (H) variable either slightly improved or did not in any way increase model fitness. Validation results demonstrate that these equations are suitable to estimate stem, aboveground, and total tree biomass across a broad range of P. massoniana stands on a regional scale.     

454 Genome sequencing of Pseudoperonospora cubensis reveals effector proteins with a QXLR translocation motif

Pseudoperonospora cubensis is a biotrophic oomycete pathogen that causes downy mildew of cucurbits, a devastating foliar disease threatening cucurbit production worldwide. We sequenced P. cubensis genomic DNA using 454 pyrosequencing and obtained random genomic sequences covering approximately 14% of the genome, thus providing the first set of useful genomic sequence information for P. cubensis. Using bioinformatics approaches, we identified 32 putative RXLR effector proteins. Interestingly, we also identified 29 secreted peptides with high similarity to RXLR effectors at the N-terminal translocation domain, yet containing an R-to-Q substitution in the first residue of the translocation motif. Among these, a family of QXLR-containing proteins, designated as PcQNE, was confirmed to have a functional signal peptide and was further characterized as being localized in the plant nucleus. Internalization of secreted PcQNE into plant cells requires the QXLR-EER motif. This family has a large number of near-identical copies within the P. cubensis genome, is under diversifying selection at the C-terminal domain, and is upregulated during infection of plants, all of which are common characteristics of characterized oomycete effectors. Taken together, the data suggest that PcQNE are bona fide effector proteins with a QXLR translocation motif, and QXLR effectors are prevalent in P. cubensis. Furthermore, the massive duplication of PcQNE suggests that they might play pivotal roles in pathogen fitness and pathogenicity.     

Postsynaptic TrkC and presynaptic PTPσ function as a bidirectional excitatory synaptic organizing complex

Neurotrophin receptor tyrosine kinases (Trks) have well-defined trophic roles in nervous system development through kinase activation by neurotrophins. Yet Trks have typical cell-adhesion domains and express noncatalytic isoforms, suggesting additional functions. Here we discovered noncatalytic TrkC in an unbiased hippocampal neuron-fibroblast coculture screen for proteins that trigger differentiation of neurotransmitter release sites in axons. All TrkC isoforms, but not TrkA or TrkB, function directly in excitatory glutamatergic synaptic adhesion by neurotrophin-independent high-affinity trans binding to axonal protein tyrosine phosphatase receptor PTPσ. PTPσ triggers and TrkC mediates clustering of postsynaptic molecules in dendrites, indicating bidirectional synaptic organizing functions. Effects of a TrkC-neutralizing antibody that blocks TrkC-PTPσ interaction and TrkC knockdown in culture and in?vivo reveal essential roles of TrkC-PTPσ in glutamatergic synapse formation. Thus, postsynaptic TrkC trans interaction with presynaptic PTPσ generates bidirectional adhesion and recruitment essential for excitatory synapse development and positions these signaling molecules at the center of synaptic pathways.     

Enhancement of methane production from cassava residues by biological pretreatment using a constructed microbial consortium

In the study, a stable thermophilic microbial consortium with high cellulose-degradation ability was successfully constructed. That several species of microbes coexisted in this consortium was proved by DGGE (denaturing gradient gel electrophoresis) and sequence analysis. The cooperation and symbiosis of these microbes in this consortium enhanced their cellulose-degradation ability. The pretreatment of cassava residues mixing with distillery wastewater prior to anaerobic digestion was investigated by using this microbial consortium as inoculums in batch bioreactors at 55 °C. The experimental results showed that the maximum methane yield (259.46 mL/g-VS) of cassava residues was obtained through 12 h of pretreatment by this microbial consortium, which was 96.63% higher than the control (131.95 mL/g-VS). In addition, it was also found that the maximum methane yield is obtained when the highest filter paper cellulase (FPase), carboxymethyl cellulase (CMCase) and xylanase activity and soluble COD (sCOD) are produced.