Interdomain contacts control folding of transcription factor RfaH

Escherichia coli RfaH activates gene expression by tethering the elongating RNA polymerase to the ribosome. This bridging action requires a complete refolding of the RfaH C-terminal domain (CTD) from an α-helical hairpin, which binds to the N-terminal domain (NTD) in the free protein, to a β-barrel, which interacts with the ribosomal protein S10 following RfaH recruitment to its target operons. The CTD forms a β-barrel when expressed alone or proteolytically separated from the NTD, indicating that the α-helical state is trapped by the NTD, perhaps co-translationally. Alternatively, the interdomain contacts may be sufficient to drive the formation of the α-helical form. Here, we use functional and NMR analyses to show that the denatured RfaH refolds into the native state and that RfaH in which the order of the domains is reversed is fully functional in vitro and in vivo. Our results indicate that all information necessary to determine its fold is encoded within RfaH itself, whereas accessory factors or sequential folding of NTD and CTD during translation are dispensable. These findings suggest that universally conserved RfaH homologs may change folds to accommodate diverse interaction partners and that context-dependent protein refolding may be widespread in nature.     

Sino-Canadian Collaborations in Stem Cell Research: A Scientometric Analysis

Background

International collaboration (IC) is essential for the advance of stem cell research, a field characterized by marked asymmetries in knowledge and capacity between nations. China is emerging as a global leader in the stem cell field. However, knowledge on the extent and characteristics of IC in stem cell science, particularly China’s collaboration with developed economies, is lacking.

Methods and Findings

We provide a scientometric analysis of the China–Canada collaboration in stem cell research, placing this in the context of other leading producers in the field. We analyze stem cell research published from 2006 to 2010 from the Scopus database, using co-authored papers as a proxy for collaboration. We examine IC levels, collaboration preferences, scientific impact, the collaborating institutions in China and Canada, areas of mutual interest, and funding sources. Our analysis shows rapid global expansion of the field with 48% increase in papers from 2006 to 2010. China now ranks second globally after the United States. China has the lowest IC rate of countries examined, while Canada has one of the highest. China–Canada collaboration is rising steadily, more than doubling during 2006–2010. China–Canada collaboration enhances impact compared to papers authored solely by China-based researchers This difference remained significant even when comparing only papers published in English.

Conclusions

While China is increasingly courted in IC by developed countries as a partner in stem cell research, it is clear that it has reached its status in the field largely through domestic publications. Nevertheless, IC enhances the impact of stem cell research in China, and in the field in general. This study establishes an objective baseline for comparison with future studies, setting the stage for in-depth exploration of the dynamics and genesis of IC in stem cell research.     

Mechanoluminescence,thermoluminescence, photoluminescence studies on Ca3Y2Si3O12:RE3+ (RE3+ = Dy3+and Eu3+) phosphors

Dy³⁺ and Eu³⁺ activated Ca₃Y₂Si₃O₁₂ phosphors were synthesized by the solid‐state synthesis method. The phosphors were characterized by X‐ray diffraction (XRD), mechanoluminescence (ML), thermoluminescence (TL) and photoluminescence (PL) to determine structure and luminescence. For ML glow curves, only one peak was observed, as only one type of luminescence centre was formed during irradiation. The Ca₃Y₂Si₃O₁₂:Dy³⁺ TL glow curve showed a single peak at 151.55°C and the Ca₃Y₂Si₃O₁₂:Eu³⁺ TL glow curve peaked at 323°C with a small peak at 192°C, indicating that two types of traps were activated. The trapping parameters for both the samples were calculated using Chen's peak shape method. Dy³⁺‐activated Ca₃Y₂Si₃O₁₂ showed emission at 482 and 574 nm when excited by a 351 nm excitation wavelength, whereas the Eu³⁺‐activated Ca₃Y₂Si₃O₁₂ phosphor PL emission spectra showed emission peaks at 613 nm, 591 nm, 580 nm when excited at 395 nm wavelength. When excited at 466 nm, prominent emission peaks were observed at their respective positions with very slight shifts. Copyright © 2015 John Wiley & Sons, Ltd.     

Green enzymatic production of glyceryl monoundecylenate using immobilized Candida antarctica lipase B

Enzymatic synthesis of glyceryl monoundecylenate (GMU) was performed using indigenously immobilized Candida anatarctica lipase B preparation (named as PyCal) using glycerol and undecylenic acid as substrates. The effect of molar ratio, enzyme load, reaction time, and organic solvent on the reaction conversion was determined. Both batch and continuous processes for GMU synthesis with shortened reaction time were developed. Under optimized batch reaction conditions such as 1:5 molar ratio of undecylenic acid and glycerol, 2?h of reaction time at 30% substrate concentration in tert-butyl alcohol, conversion of 82% in the absence of molecular sieve, and conversion of 93% in the presence of molecular sieve were achieved. Packed bed reactor studies resulted in high conversion of 86% in 10-min residence time. Characterization of formed GMU was performed by FTIR, MS/MS. Enzymatic process resulted in GMU as a predominant product in high yield and shorter reaction time periods with GMU content of 92% and DAG content of 8%. Optimized GMU synthesis in the present study can be used as a useful reference for industrial synthesis of fatty acid esters of glycerol by the enzymatic route.     

Biodegradation of aromatic compounds byRhodopseudomonas gelatinosa

A few photosynthetic bacteria have been isolated from a biological treatment system treating producer gas plant effluent. One of them was identified asRhodopseudomonas gelatinosa on the basis of physiological and morphological characteristics. Biodegradation of aromatic compounds byR. gelatinosa appears not to have been reported in the literature. The culture was found to degrade benzoic acid,p-hydroxybenzoic acid, cinnamic acid, andp-coumaric acid. The doubling time for this culture was found to be 18, 19, 23, and 31 h for benzoic acid, p-hydroxybenzoic acid, cinnamic acid, andp-coumaric acid respectively.     

Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis

Roots are the primary site of interaction between plants and microorganisms. To meet food demands in changing climates, improved yields and stress resistance are increasingly important, stimulating efforts to identify factors that affect plant productivity. The role of bacterial endophytes that reside inside plants remains largely unexplored, because analysis of their specific functions is impeded by difficulties in cultivating most prokaryotes. Here, we present the first metagenomic approach to analyze an endophytic bacterial community resident inside roots of rice, one of the most important staple foods. Metagenome sequences were obtained from endophyte cells extracted from roots of field-grown plants. Putative functions were deduced from protein domains or similarity analyses of protein-encoding gene fragments, and allowed insights into the capacities of endophyte cells. This allowed us to predict traits and metabolic processes important for the endophytic lifestyle, suggesting that the endorhizosphere is an exclusive microhabitat requiring numerous adaptations. Prominent features included flagella, plant-polymer-degrading enzymes, protein secretion systems, iron acquisition and storage, quorum sensing, and detoxification of reactive oxygen species. Surprisingly, endophytes might be involved in the entire nitrogen cycle, as protein domains involved in N(2)-fixation, denitrification, and nitrification were detected and selected genes expressed. Our data suggest a high potential of the endophyte community for plant-growth promotion, improvement of plant stress resistance, biocontrol against pathogens, and bioremediation, regardless of their culturability.