Draft Genome Sequence of Aspergillus niger Strain An76.

The filamentous fungus Aspergillus niger has become one of the most important fungi in industrial biotechnology, and it can efficiently secrete both polysaccharide-degrading enzymes and organic acids. We report here the 6,074,961,332-bp draft sequence of A. niger strain An76, and the findings provide important information related to its lignocellulose-degrading ability.

Subsite-specific contributions of different aromatic residues in the active site architecture of glycoside hydrolase family 12.

The active site architecture of glycoside hydrolase (GH) is a contiguous subregion of the enzyme constituted by residues clustered in the three-dimensional space, recognizing the monomeric unit of ligand through hydrogen bonds and hydrophobic interactions. Mutations of the key residues in the active site architecture of the GH12 family exerted different impacts on catalytic efficiency. Binding affinities between the aromatic amino acids and carbohydrate rings were quantitatively determined by isothermal titration calorimetry (ITC) and the quantum mechanical (QM) method, showing that the binding capacity order of Tyr>Trp>His (and Phe) was determined by their side-chain properties.

Substrate-binding specificity of chitinase and chitosanase as revealed by active-site architecture analysis.

Chitinases and chitosanases, referred to as chitinolytic enzymes, are two important categories of glycoside hydrolases (GH) that play a key role in degrading chitin and chitosan, two naturally abundant polysaccharides. Here, we investigate the active site architecture of the major chitosanase (GH8, GH46) and chitinase families (GH18, GH19). Both charged (Glu, His, Arg, Asp) and aromatic amino acids (Tyr, Trp, Phe) are observed with higher frequency within chitinolytic active sites as compared to elsewhere in the enzyme structure, indicating significant roles related to enzyme function.

Comparative Secretome Analysis of Aspergillus niger, Trichoderma reesei, and Penicillium oxalicum During Solid-State Fermentation.

Filamentous fungi such as Aspergillus spp., Trichoderma spp., and Penicillium spp.

Determination of the action modes of cellulases from hydrolytic profiles over a time course using fluorescence-assisted carbohydrate electrophoresis.

Fluorescence-assisted carbohydrate electrophoresis (FACE) is a sensitive and simple method for the separation of oligosaccharides. It relies on labeling the reducing ends of oligosaccharides with a fluorophore, followed by PAGE. Concentration changes of oligosaccharides following hydrolysis of a carbohydrate polymer could be quantitatively measured continuously over time using the FACE method.

Draft Genome Sequence of Cellulose-Digesting Bacterium Sporocytophaga myxococcoides PG-01.

Sporocytophaga myxococcoides, a Gram-negative bacterium isolated from soil, is an efficient hydrolyzer of crystalline cellulose. Here, we report its draft genome sequence, which may provide important genetic information regarding the cellulolytic and hemicellulolytic enzymes that contribute to the cellulose-degrading abilities of this bacterium.

Dynamic changes in xylanases and β-1,4-endoglucanases secreted by Aspergillus niger An-76 in response to hydrolysates of lignocellulose polysaccharide.

Aspergillus niger is an effective secretor of glycoside hydrolases that facilitate the saprophytic lifestyle of the fungus by degrading plant cell wall polysaccharides. In the present study, a series of dynamic zymography assays were applied to quantify the secreted glycoside hydrolases of A. niger cultured in media containing different carbon sources.

Discussion on research methods of bacterial resistant mutation mechanisms under selective culture--uncertainty analysis of data from the Luria-Delbrück fluctuation experiment.

Whether bacterial drug-resistance is drug-induced or results from rapid propagation of random spontaneous mutations in the flora prior to exposure, remains a long-term key issue concerned and debated in both genetics and medicinal fields. In a pioneering study, Luria and Delbrück exposed E. coli to T1 phage, to investigate whether the number of resistant colonies followed the Poisson distribution.

In situ demonstration and quantitative analysis of the intrinsic properties of glycoside hydrolases.

Based on digital image analysis techniques and a series of optimizations in native electrophoresis, a new direct method to simultaneously detect the intrinsic properties of each active component in the enzymatic system of glycoside hydrolase was established. The key technique is that the concentration changes of substrate (or product) on the gel can be determined quantitatively by the gray value changes of the corresponding band after electrophoretic separation. In this manner, the catalytic characteristics of each glycoside hydrolase component were demonstrated in situ and were easily determined after immersing the gel in a series of solutions containing substrates or their derivatives.

Accurate assessment of antibiotic susceptibility and screening resistant strains of a bacterial population by linear gradient plate.

The dynamics of a bacterial population exposed to the minimum inhibitory concentration (MIC) of an antibiotic is an important issue in pharmacological research. Therefore, a novel antibiotic susceptibility test is urgently needed that can both precisely determine the MIC and accurately select antibiotic-resistant strains from clinical bacterial populations. For this purpose, we developed a method based on Fick's laws of diffusion using agar plates containing a linear gradient of antibiotic.

[Effect of continuous temperature change on hydrolytic products of yeast beta-glucan by endo-beta-1,3-glucanase].

In order to explore the influence of reaction temperature on the product composition, the effect of continuous temperature change (22 degrees C-60 degrees C, +/-0.1 degree C) on hydrolysis of yeast beta-glucan by endo-beta-1,3-glucanase was determined by using self-developed Biochem-temperature Characteristic Apparatus. The activation energy of enzymatic hydrolysis of yeast beta-glucan was 84.

[Bactericidal effect of soybean peroxidase-hydrogen peroxide-potassium iodide system].

Objective: To study the bactericidal effect and the possible mechanisms of the three components system [soybean peroxidases (SBP)-hydrogen peroxide (H2O2)-potassium iodide (KI), SBP-H2O2-KI].

Methods: The inhibition and bactericidal effect of SBP-H2O2-KI system to bacteria was detected by OD600 and the number of live bacteria (CFU). The sensitivity was tested by comparing the minimum inhibitory concentration (MIC) of bacterial cultures before and after cultured under sub-lethal dose of SBP-H2O2-KI system.

A novel approach for estimating the relationship between the kinetics and thermodynamics of glycoside hydrolases.

A series of experiments were performed, in which p-nitrophenyl-β-D-cellobioside (PNPC) was hydrolyzed by 1, 4-β-D-glucan-cellobiohydrolase (CBHI: EC 3.2.1.

The Exploration of the Antibacterial Mechanism of FE(3+) against Bacteria.

This study demonstrated that the bacteria could adsorb Fe(3+) and reduce Fe(3+) to Fe(2+). Iron had significant bacteriostatic effects, which were directly proportional to the iron concentration and under the influence of pH and chelator. It presumed that the inhibition of Fe(3+) acts through the formation of hydroxyl free radicals.

The combined effects of amino acid substitutions and indels on the evolution of structure within protein families.

Background: In the process of protein evolution, sequence variations within protein families can cause changes in protein structures and functions. However, structures tend to be more conserved than sequences and functions. This leads to an intriguing question: what is the evolutionary mechanism by which sequence variations produce structural changes? To investigate this question, we focused on the most common types of sequence variations: amino acid substitutions and insertions/deletions (indels).

A novel approach for assessing the susceptibility of Escherichia coli to antibiotics.

The dynamic growth process of Escherichia coli CVCC249 under different concentrations of antibiotics was analyzed. The results suggested that the main reason that definitive results cannot be obtained by antibiotic susceptibility testing (AST) is that the ratio of drug concentration to the population of bacteria and the combined effect of drug concentration and action time cannot be completely determined with the methods used. Based on the analysis of the growth process with a series of concentrations of gentamicin acting for a certain time, and according to the forward difference method, a novel method for AST was proposed.

Impact of indels on the flanking regions in structural domains.

Amino acid substitution and insertions/deletions (indels) are two common events in protein evolution; however, current knowledge on indels is limited. In this study, we investigated the effects of indels on the flanking regions in protein structure superfamilies. Comprehensive analysis of structural classification of proteins superfamilies revealed that indels lead to a series of changes in the flanking regions, including the following: 1) structural shift in the tertiary structure, with a first-order exponential decay relation between structural shift and the distance to indels, 2) instability of the secondary structure elements in which parts of the α helix and β sheet are destroyed, and 3) an increase in the amino acid substitution rate of the primary structure and the nonsimilar amino acid substitution rate.

Mutagenicity of Chinese traditional medicine Semen Armeniacae amarum by two modified Ames tests.

Background: Semen armeniacae amarum (SAA) is a Chinese traditional medicine and has long been used to control acute lower respiratory tract infection and asthma, as a result of its expectorant and antiasthmatic activities. However, its mutagenicity in vitro and in vivo has not yet been reported. The Ames test for mutagenicity is used worldwide.

[Strategy and application of metaproteomics].

Metaproteomics is an emerging proteomics technology to analyze large scale protein expression in environmental microbial ecosystem. It is termed as the large-scale characterization of the entire protein complement of environmental microbial community at a given point in time. This review focuses on the research strategies and the recent applications in this field based on the published reports and in combination with our own research experiences.

[Morphologic changes in the life cycle of Cytophaga hutchinsonii].

Objective: To study the morphological changes of Cytophaga hutchinsonii cell during its life circle.

Methods: Cytophaga hutchinsonii cell was observed under light microscope, fluorescence microscope and scanning electron microscope. The nucleoids in the cell were stained with fluorescent dye Hoechst33342 and examined by fluorescence microscopy.

Immobilization of lignin peroxidase on nanoporous gold: enzymatic properties and in situ release of H2O2 by co-immobilized glucose oxidase.

Immobilization of enzymes on porous inorganic materials is very important for biocatalysis and biotransformation. In this paper, nanoporous gold (NPG) was used as a support for lignin peroxidase (LiP) immobilization. NPG with a pore size of 40-50 nm was prepared by dealloying Au/Ag alloy (50:50 wt%) for 17 h.

Enzyme-modified nanoporous gold-based electrochemical biosensors.

On the basis of the unique physical and chemical properties of nanoporous gold (NPG), which was obtained simply by dealloying Ag from Au/Ag alloy, an attempt was made in the present study to develop NPG-based electrochemical biosensors. The NPG-modified glassy carbon electrode (NPG/GCE) exhibited high-electrocatalytic activity toward the oxidation of nicotinamide adenine dinucleotide (NADH) and hydrogen peroxide (H(2)O(2)), which resulted in a remarkable decrease in the overpotential of NADH and H(2)O(2) electro-oxidation when compared with the gold sheet electrode. The high density of edge-plane-like defective sites and large specific surface area of NPG should be responsible for the electrocatalytic behavior.

A modified suspension test for estimating the mutagenicity of samples containing free and (or) protein-bound histidine.

The Ames test has not been very effective in estimating the mutagenicity of histidine-containing samples because external free and (or) protein-bound histidine in these samples would allow the histidine auxotrophs in such test samples to grow more compared with the negative controls that were used as the reference. This could give rise to a false positive.n this study, a modified suspension mutagenicity assay (MS assay) was developed.

Purification and characterization of a thermostable laccase with unique oxidative characteristics from Trametes hirsuta.

A laccase was purified from Trametes hirsuta. This laccase was classified as a "white" or "yellow" laccase. pH 2.

Comparison of the different types of surfactants for the effect on activity and structure of soybean peroxidase.

In the pH 2.6 and 5.2 systems, soybean peroxidase (SBP) (isoelectric point, pI 3.