Investigation on bioactive protection of the amino acids derived from LEA protein on insulin by molecular simulation

Nowadays heat-sensitive protein medicines are increasingly showing their importance in the treatment of various diseases. Their popularisation and application are meeting a great challenge because of their heat lability. In this study, human insulin as a heat-sensitive protein medicine and 66 amino acids derived from a Group 3 late embryogenesis abundant protein fragment as a complex bioactive protectant, were chosen to be investigated to determine whether these amino acids can be used to protect the insulin from denaturation due to drying. The experiments were carried out by using a replica exchange molecular dynamics (REMD) simulation and GROMACS software with Gromos96 (53a6) force field. The REMD results indicate that those amino acids can effectively prevent the reversal between hydrophilic and hydrophobic surface. Both the configurations and secondary structures of the protected insulin were preserved very well. The H-bonding and electrostatic interactions between the insulin and the protectant play key roles in the bioactive protection of insulin. These results agree well with the water replacement hypothesis. All the results prove that these amino acids are a perfect bioactive protectant for heat-sensitive protein medicines.     

Anti-neuroinflammatory Effect of a Novel Caffeamide Derivative, KS370G, in Microglial cells

Accumulating evidence suggests that inflammatory processes in the central nervous system that are mediated by microglial activation play important roles in several neurodegenerative disorders. Therefore, development of methods for microglial inhibition is considered an important strategy in the search for neuroprotective agents. Caffeic acid phenethyl ester (CAPE) is distributed wildly in nature, but rapid decomposition by esterase leads to its low bioavailability. In this study, we investigated the effects of KS370G, a novel caffeic acid phenylethyl amide, on microglial activation. KS370G significantly inhibited the release of nitric oxide (NO) and the expressions of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). Treatment with KS370G also induced heme oxygenase (HO)-1 and suppressors of cytokine signaling (SOCS)-3 expression in the microglia. Furthermore, the anti-inflammatory effects of KS370G were found to be regulated by phosphorylated adenosine monophosphate-activated protein kinase-α (AMPK-α) translocated to the nucleus. Moreover, KS370G showed significant anti-neuroinflammatory effects on microglial activation in vivo and on motor behavior as well. The protective effect of KS370G was weakened by an AMPK inhibitor Compound C. This study focuses on the importance of key molecular determinants of inflammatory homeostasis, AMPK, HO-1, and SOCS-3, and their possible involvement in anti-neuroinflammatory responses.     

Evolutionary transition from C3 to C4 photosynthesis and the route to C4 rice

Compared with C₃ plants, C₄ plants possess a mechanism to concentrate CO₂ around the ribulose-1,5-bisphosphate carboxylase/oxygenase in chloroplasts of bundle sheath cells so that the carboxylation reaction work at a much more efficient rate, thereby substantially eliminate the oxygenation reaction and the resulting photorespiration. It is observed that C₄ photosynthesis is more efficient than C₃ photosynthesis under conditions of low atmospheric CO₂, heat, drought and salinity, suggesting that these factors are the important drivers to promote C₄ evolution. Although C₄ evolution took over 66 times independently, it is hypothesized that it shared the following evolutionary trajectory: 1) gene duplication followed by neofunctionalization; 2) anatomical and ultrastructral changes of leaf architecture to improve the hydraulic systems; 3) establishment of two-celled photorespiratory pump; 4) addition of transport system; 5) co-option of the duplicated genes into C₄ pathway and adaptive changes of C₄ enzymes. Based on our current understanding on C₄ evolution, several strategies for engineering C₄ rice have been proposed to increase both photosynthetic efficiency and yield significantly in order to avoid international food crisis in the future, especially in the developing countries. Here we summarize the latest progresses on the studies of C₄ evolution and discuss the strategies to introduce two-celled C₄ pathway into rice.     

Single-Molecule Force Spectroscopy Study on the Mechanism of RNA Disassembly in Tobacco Mosaic Virus

To explore the disassembly mechanism of tobacco mosaic virus (TMV), a model system for virus study, during infection, we have used single-molecule force spectroscopy to mimic and follow the process of RNA disassembly from the protein coat of TMV by the replisome (molecular motor) in vivo, under different pH and Ca²⁺ concentrations. Dynamic force spectroscopy revealed the unbinding free-energy landscapes as that at pH 4.7 the disassembly process is dominated by one free-energy barrier, whereas at pH 7.0 the process is dominated by one barrier and that there exists a second barrier. The additional free-energy barrier at longer distance has been attributed to the hindrance of disordered loops within the inner channel of TMV, and the biological function of those protein loops was discussed. The combination of pH increase and Ca²⁺ concentration drop could weaken RNA-protein interactions so much that the molecular motor replisome would be able to pull and disassemble the rest of the genetic RNA from the protein coat in vivo. All these facts provide supporting evidence at the single-molecule level, to our knowledge for the first time, for the cotranslational disassembly mechanism during TMV infection under physiological conditions.     

Inherent Relationships among Different Biophysical Prediction Methods for Intrinsically Disordered Proteins

Intrinsically disordered proteins do not have stable secondary and/or tertiary structures but still function. More than 50 prediction methods have been developed and inherent relationships may be expected to exist among them. To investigate this, we conducted molecular simulations and algorithmic analyses on a minimal coarse-grained polypeptide model and discovered a common basis for the charge-hydropathy plot and packing-density algorithms that was verified by correlation analysis. The correlation analysis approach was applied to realistic datasets, which revealed correlations among some physical-chemical properties (charge-hydropathy plot, packing density, pairwise energy). The correlations indicated that these biophysical methods find a projected direction to discriminate ordered and disordered proteins. The optimized projection was determined and the ultimate accuracy limit of the existing algorithms is discussed.     

Development of a high-efficient transformation system of Bacillus pumilus strain DX01 to facilitate gene isolation via gfp-tagged insertional mutagenesis and visualize bacterial colonization of rice roots

A Tn5 transposition vector, pMOD-tet-egfp, was constructed and used for the random insertional mutagenesis of Bacillus pumilus. Various parameters were investigated to increase the transformation efficiency B. pumilus DX01 via Tn5 transposition complexes (transposome): bacterial growth phase, type of electroporation buffer, electric field strength, and recovery medium. Transformation efficiency was up to 3?×?10⁴?transformants/μg of DNA under the optimized electroporation conditions, and a total of 1,467 gfp-tagged transformants were obtained. Fluorescence-activated cell sorting analysis showed that all gfp-tagged bacterial cells expressed GFP, indicating that foreign DNA has been successfully integrated into the genome of B. pumilus and expressed. Finally, flanking DNA sequences were isolated from several transformants and colonization of rice roots by B. pumilus DX01 was also studied. The method developed here will be useful for creating an insertion mutant library of gram-positive bacteria, thus facilitating their molecular genetic and cytological studies.     

Actinoplanes hulinensis sp. nov., a novel actinomycete isolated from soybean root (Glycine max (L.) Merr)

A novel actinomycete, designated strain NEAU-M9^T, was isolated from soybean root (Glycine max (L.) Merr) and characterized using a polyphasic approach. 16S rRNA gene sequence similarity studies showed that strain NEAU-M9^T belonged to the genus Actinoplanes, being most closely related to Actinoplanes campanulatus DSM 43148^T (98.85 %), Actinoplanes capillaceus DSM 44859^T (98.70 %), Actinoplanes lobatus DSM 43150^T (98.30 %), Actinoplanes auranticolor DSM 43031^T (98.23 %) and Actinoplanes sichuanensis 03-723^T (98.06 %); similarity to other type strains of the genus Actinoplanes ranged from 95.87 to 97.56 %. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that the isolate formed a distinct phyletic line with A. campanulatus DSM 43148^T and A. capillaceus DSM 44859^T. This branching pattern was also supported by the tree constructed with the maximum-likelihood method. However, the low level of DNA–DNA relatedness allowed the isolate to be differentiated from the above-mentioned two Actinoplanes species. Moreover, strain NEAU-M9^T could also be distinguished from the most closely related species by morphological, physiological and characteristics. Therefore, it is proposed that strain NEAU-M9^T represents a novel Actinoplanes species, Actinoplanes hulinensis sp. nov. The type strain of Actinoplanes hulinensis is NEAU-M9^T (= CGMCC 4.7036^T = DSM 45728^T).     

Restoration of a subtropical eutrophic shallow lake in China: effects on nutrient concentrations and biological communities

Disturbances caused by rainfall are common in streams with the impact on stream inhabitants determined by the frequency, intensity, and predictability of the event. Here, we examine the response of winter-emerging Chironomidae (Diptera) to extreme flooding disturbance. In August of 2007, a severe flood impacted southeastern Minnesota, imparting stress on aquatic communities. Chironomid pupal exuviae collections were obtained biweekly from 18 southeast Minnesota streams during the following winter to assess resistance and resilience of winter-active chironomids to flooding. Streams examined were divided into moderate (2.5–10 cm), heavy (10–20 cm), or extreme (20+ cm) rainfall categories with rainfall amounts in each category representing total precipitation during the 3-day storm. Post-flood samples were compared to samples obtained from the same localities during prior winters. Our findings contradict studies of responses by Chironomidae to flooding during warmer-water conditions and show that winter-emerging Chironomidae are resistant to stress imposed by summer spates. Significantly more taxa emerged during winter after flooding as compared to historic collections, and the number of species emerging in winter was positively correlated with rainfall severity, indicating that 15 species responded opportunistically to disturbance. This indicates that winter-active Chironomidae may be resistant to increased severity of summer spates associated with climate change predictions.