The Role of Semidisorder in Temperature Adaptation of Bacterial FlgM Proteins

Probabilities of disorder for FlgM proteins of 39 species whose optimal growth temperature ranges from 273 K (0°C) to 368 K (95°C) were predicted by a newly developed method called Sequence-based Prediction with Integrated NEural networks for Disorder (SPINE-D). We showed that the temperature-dependent behavior of FlgM proteins could be separated into two subgroups according to their sequence lengths. Only shorter sequences evolved to adapt to high temperatures (>318 K or 45°C). Their ability to adapt to high temperatures was achieved through a transition from a fully disordered state with little secondary structure to a semidisordered state with high predicted helical probability at the N-terminal region. The predicted results are consistent with available experimental data. An analysis of all orthologous protein families in 39 species suggests that such a transition from a fully disordered state to semidisordered and/or ordered states is one of the strategies employed by nature for adaptation to high temperatures.     

Ultrahigh frequency lensless ultrasonic transducers for acoustic tweezers application

Similar to optical tweezers, a tightly focused ultrasound microbeam is needed to manipulate microparticles in acoustic tweezers. The development of highly sensitive ultrahigh frequency ultrasonic transducers is crucial for trapping particles or cells with a size of a few microns. As an extra lens would cause excessive attenuation at ultrahigh frequencies, two types of 200‐MHz lensless transducer design were developed as an ultrasound microbeam device for acoustic tweezers application. Lithium niobate single crystal press‐focused (PF) transducer and zinc oxide self‐focused transducer were designed, fabricated and characterized. Tightly focused acoustic beams produced by these transducers were shown to be capable of manipulating single microspheres as small as 5 µm two‐dimensionally within a range of hundreds of micrometers in distilled water. The size of the trapped microspheres is the smallest ever reported in the literature of acoustic PF devices. These results suggest that these lensless ultrahigh frequency ultrasonic transducers are capable of manipulating particles at the cellular level and that acoustic tweezers may be a useful tool to manipulate a single cell or molecule for a wide range of biomedical applications. Biotechnol. Bioeng. 2013; 110: 881–886. © 2012 Wiley Periodicals, Inc.     

Tethered Spectroscopic Probes Estimate Dynamic Distances with Subnanometer Resolution in Voltage-Dependent Potassium Channels

Measurements of inter- and intramolecular distances are important for monitoring structural changes and understanding protein interaction networks. Fluorescence resonance energy transfer and functionalized chemical spacers are the two predominantly used strategies to map short-range distances in living cells. Here, we describe the development of a hybrid approach that combines the key advantages of spectroscopic and chemical methods to estimate dynamic distance information from labeled proteins. Bifunctional spectroscopic probes were designed to make use of adaptable-anchor and length-varied spacers to estimate molecular distances by exploiting short-range collisional electron transfer. The spacers were calibrated using labeled polyproline peptides of defined lengths and validated by molecular simulations. This approach was extended to estimate distance restraints that enable us to evaluate the resting-state model of the Shaker potassium channel.     

A biofilm model to understand the onset of sulfate reduction in denitrifying membrane biofilm reactors

This work presents a multispecies biofilm model that describes the co‐existence of nitrate‐ and sulfate‐reducing bacteria in the H₂‐based membrane biofilm reactor (MBfR). The new model adapts the framework of a biofilm model for simultaneous nitrate and perchlorate removal by considering the unique metabolic and physiological characteristics of autotrophic sulfate‐reducing bacteria that use H₂ as their electron donor. To evaluate the model, the simulated effluent H₂, UAP (substrate‐utilization‐associated products), and BAP (biomass‐associated products) concentrations are compared to experimental results, and the simulated biomass distributions are compared to real‐time quantitative polymerase chain reaction (qPCR) data in the experiments for parameter optimization. Model outputs and experimental results match for all major trends and explain when sulfate reduction does or does not occur in parallel with denitrification. The onset of sulfate reduction occurs only when the nitrate concentration at the fiber's outer surface is low enough so that the growth rate of the denitrifying bacteria is equal to that of the sulfate‐reducing bacteria. An example shows how to use the model to design an MBfR that achieves satisfactory nitrate reduction, but suppresses sulfate reduction. Biotechnol. Bioeng. 2013; 110: 763–772. © 2012 Wiley Periodicals, Inc.     

New Insights into the Interdependence between Amino Acid Stereochemistry and Protein Structure

To successfully design new proteins and understand the effects of mutations in natural proteins, we must understand the geometric and physicochemical principles underlying protein structure. The side chains of amino acids in peptides and proteins adopt specific dihedral angle combinations; however, we still do not have a fundamental quantitative understanding of why some side-chain dihedral angle combinations are highly populated and others are not. Here we employ a hard-sphere plus stereochemical constraint model of dipeptide mimetics to enumerate the side-chain dihedral angles of leucine (Leu) and isoleucine (Ile), and identify those conformations that are sterically allowed versus those that are not as a function of the backbone dihedral angles ? and ψ. We compare our results with the observed distributions of side-chain dihedral angles in proteins of known structure. With the hard-sphere plus stereochemical constraint model, we obtain agreement between the model predictions and the observed side-chain dihedral angle distributions for Leu and Ile. These results quantify the extent to which local, geometrical constraints determine protein side-chain conformations.     

Overwintering strategy of endoparasitoids in Chilo suppressalis: a perspective from the cold hardiness of a host

Although parasitoids ultimately kill their host, koinobiont parasitoids must protect not only themselves but also their hosts against extreme environments. In this study, the parasitism rate of Chilo suppressalis Walker (Lepidoptera: Pyralidae) was investigated, and the average body weights, supercooling points, and concentrations of glycerol (acting as a cryoprotectant) in the hemolymph were compared between parasitized and non‐parasitized larvae. Five species of koinobiont endoparasitoids parasitized the overwintering C. suppressalis larvae and the total parasitism rate was 47.6% (n = 1 537). Average body weight of parasitized larvae was significantly lower than that of non‐parasitized larvae, and the parasitism rate of the lighter group (20–30 mg) was highest. The supercooling point of parasitized C. suppressalis larvae (?15.7 ± 0.3 °C) was significantly lower than that of the non‐parasitized larvae (?14.3 ± 0.2 °C). In addition, supercooling points were not correlated with body weights between parasitized and non‐parasitized larvae, indicating that cold hardiness of parasitized larvae was enhanced by endoparasitoids. Furthermore, the concentration of glycerol in the hemolymph was significantly higher in parasitized larvae (205.0 ± 7.1 μmol ml^?1) than in non‐parasitized larvae (169.8 ± 14.4 μmol ml^?1), which suggests that the mechanism that decreases the supercooling point of parasitized larvae was associated with glycerol. All these results indicated that the cold hardiness of parasitized C. suppressalis larvae was enhanced by their endoparasitoids, which benefitted overwintering endoparasitoids.     

桑疫病病原拮抗菌的分离、鉴定及发酵条件优化北大核心CSCD

【目的】从健康桑树内生菌中分离获得对桑疫病病原菌(Pseudomonas syringae pv.mori)具有显著拮抗作用的菌株,优化其产生抑菌活性物质的发酵条件,为其生防利用奠定基础。【方法】从严格表面消毒的桑树根茎中分离内生菌,采用平板划线法纯化内生菌,用抑菌圈法筛选拮抗菌;根据菌株的形态与培养特征、生理生化特性、16S rDNA序列分析对其进行鉴定。通过单因素试验和正交设计试验优化培养基组分及发酵条件。【结果】从健康桑树中分离获得内生菌77株,其中,编号为SWg2的菌株对桑疫病病原菌具有强而稳定的抑制作用。菌株SWg2的形态与培养特征、生理生化特性和泛菌属(Pantoea sp.)相符,而16S rDNA序列分析结果显示它与成团泛菌(P.agglomerans)的亲缘关系接近。研究表明其最佳发酵配方和培养条件为:甘油(2.00%)、硝酸铵(2.00%)、KH2PO4(0.10%)和MgSO4·7H2O(0.15%),起始pH为7.5,装瓶量20 mL/100 mL,最适培养温度为28℃,转速为170 r/min,种子液接种量为4%,摇瓶培养5 d。【结论】经鉴定,对桑疫病病原具拮抗作用的桑树内生菌SWg2为成团泛菌(P.agglomerans),命名为成团泛菌SWg2。对其发酵条件进行优化后对桑疫病病原菌显示出更强的拮抗作用。     

Tenuibacillus halotolerans sp. nov., a novel bacterium isolated from a soil sample from a salt lake in Xinjiang, China and emended description of the genus Tenuibacillus

A Gram-positive, moderately halotolerant, rod-shaped bacterium, designated YIM 94025^T, was isolated from a soil sample from a salt lake in Xinjiang province, north-west China. Strain YIM 94025^T was observed to grow at 25–45 °C (optimum 37 °C), 0–22 % NaCl (optimum 2–10 %) and pH 6.0–9.0 (optimum pH 8.0). Phylogenetic analyses based on 16S rRNA gene sequences revealed that the organism belongs to the genus Tenuibacillus and exhibited sequence similarity of 98.0 % to the closest type strain, Tenuibacillus multivorans AS 1.3442^T. The predominant menaquinone was found to be MK-7; the cell-wall peptidoglycan diamino acid was meso-diaminopimelic acid; the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid and an unknown lipid; and the major fatty acids were found to contain iso-C_15:0, anteiso-C_15:0 and iso-C_16:0. The chemotaxonomic characteristics of strain YIM 94025^T are consistent with those of the genus Tenuibacillus. The level of DNA–DNA relatedness value between YIM 94025^T and T. multivorans AS 1.3442^T was 36.6 ± 4.5 %. The G+C content of the strain YIM 94025^T was determined to be 38.5 %. Based on the comparative analysis of physiological, biochemical and chemotaxonomic data, as well as DNA–DNA hybridization results, the isolate is considered to represent a novel species of the genus Tenuibacillus, for which the name Tenuibacillus halotolerans sp. nov., is proposed, with the type strain of YIM 94025^T (=CCTCC AB 2012860^T = KCTC 33046^T).