SciCombinator

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Concept: Nitrogen

166

Escherichia coli is most widely used prokaryotic expression system for the production of recombinant proteins. Several strategies have been employed for expressing recombinant proteins in E.coli. This includes the development of novel host systems, expression vectors and cost effective media. In this study, we exploit tender coconut water (TCW) as a natural and cheaper growth medium for E.coli and Pichia pastoris.Result: E.coli and P.pastoris were cultivated in TCW and the growth rate was monitored by measuring optical density at 600nm (OD600nm), where 1.55 for E.coli and 8.7 for P.pastoris was obtained after 12 and 60 hours, respectively. However, variation in growth rate was observed among TCW when collected from different localities (0.15-2.5 at OD600nm), which is attributed to the varying chemical profile among samples. In this regard, we attempted the supplementation of TCW with different carbon and nitrogen sources to attain consistency in growth rate. Here, supplementation of TCW with 25mM ammonium sulphate (TCW-S) was noted efficient for the normalization of inconsistency, which further increased the biomass of E.coli by 2 to 10 folds, and 1.5 to 2 fold in P.pastoris. These results indicate that nitrogen source is the major limiting factor for growth. This was supported by total nitrogen and carbon estimation where, nitrogen varies from 20 to 60mg/100ml while carbohydrates showed no considerable variation (2.32 to 3.96 g/100 ml). In this study, we also employed TCW as an expression media for recombinant proteins by demonstrating successful expression of maltose binding protein (MBP), MBP-TEV protease fusion and a photo switchable fluorescent protein (mEos2) using TCW and the expression level was found to be equivalent to Luria Broth (LB).

Concepts: Oxygen, Coconut, Nitrogen, Recombinant DNA, Bacteria, DNA, Protein, Escherichia coli

166

BACKGROUND: The Bacillus subtilis genome-reduced strain MGB874 exhibits enhanced production of exogenous extracellular enzymes under batch fermentation conditions. We predicted that deletion of the gene for RocG, a bi-functional protein that acts as a glutamate dehydrogenase and an indirect repressor of glutamate synthesis, would improve glutamate metabolism, leading to further increased enzyme production. However, deletion of rocG dramatically decreased production of the alkaline cellulase Egl-237 in strain MGB874 (strain 874[increment]rocG). RESULTS: Transcriptome analysis and cultivation profiles suggest that this phenomenon is attributable to impaired secretion of alkaline cellulase Egl-237 and nitrogen starvation, caused by decreased external pH and ammonium depletion, respectively. With NH3-pH auxostat fermentation, production of alkaline cellulase Egl-237 in strain 874[increment]rocG was increased, exceeding that in the wild-type-background strain 168[increment]rocG. Notably, in strain 874[increment]rocG, high enzyme productivity was observed throughout cultivation, possibly due to enhancement of metabolic flux from 2-oxoglutarate to glutamate and generation of metabolic energy through activation of the tricarboxylic acid (TCA) cycle. The level of alkaline cellulase Egl-237 obtained corresponded to about 5.5 g l-1, the highest level reported so far. CONCLUSIONS: We found the highest levels of production of alkaline cellulase Egl-237 with the reduced-genome strain 874[increment]rocG and using the NH3-pH auxostat. Deletion of the glutamate dehydrogenase gene rocG enhanced enzyme production via a prolonged auxostat fermentation, possibly due to improved glutamate synthesis and enhanced generation of metabolism energy.

Concepts: Nitrogen, Cell, Amino acid, Protein, Bacteria, Bacillus subtilis, Enzyme, Metabolism

165

Room temperature operation, low detection limit and fast response time are highly desirable for a wide range of gas sensing applications. However, the available gas sensors suffer mainly from high temperature operation or external stimulation for response/recovery. Here, we report an ultrasensitive-flexible-silver-nanoparticle based nanocomposite resistive sensor for ammonia detection and established the sensing mechanism. We show that the nanocomposite can detect ammonia as low as 500 parts-per-trillion at room temperature in a minute time. Furthermore, the evolution of ammonia from different chemical reactions has been demonstrated using the nanocomposite sensor as an example. Our results demonstrate the proof-of-concept for the new detector to be used in several applications including homeland security, environmental pollution and leak detection in research laboratories and many others.

Concepts: Gas sensors, Ammonia, Hydrogen, Gas leak, Sensor, Nitrogen, Natural gas, Chemical reaction

165

Cyanobacteria-plant symbioses play an important role in many ecosystems due to the fixation of atmospheric nitrogen (N) by the cyanobacterial symbiont. The ubiquitous feather moss Pleurozium schreberi (Brid.) Mitt. is colonized by cyanobacteria in boreal systems with low N deposition. Here, cyanobacteria fix substantial amounts of N2 and represent a potential N source. The feather moss appears to be resistant to decomposition, which could be partly a result of toxins produced by cyanobacteria. To assess how cyanobacteria modulated the toxicity of moss, we measured inhibition of bacterial growth. Moss with varying numbers of cyanobacteria was added to soil bacteria to test the inhibition of their growth using the thymidine incorporation technique. Moss could universally inhibit bacterial growth, but moss toxicity did not increase with N2 fixation rates (numbers of cyanobacteria). Instead, we see evidence for a negative relationship between moss toxicity to bacteria and N2 fixation, which could be related to the ecological mechanisms that govern the cyanobacteria - moss relationship. We conclude that cyanobacteria associated with moss do not contribute to the resistance to decomposition of moss, and from our results emerges the question as to what type of relationship the moss and cyanobacteria share.

Concepts: Oxygen, Plant, Cyanobacteria, Symbiosis, Evolution, Mosses, Nitrogen, Bacteria

163

We report a facile and green method to synthesize a new type of catalyst by coating Pd nanoparticles (NPs) on reduced graphene oxide (rGO)-carbon nanotube (CNT) nanocomposite. An rGO-CNT nanocomposite with three-dimensional microstructures was obtained by hydrothermal treatment of an aqueous dispersion of graphene oxide (GO) and CNTs. After the rGO-CNT composites have been dipped in K2PdCl4 solution, the spontaneous redox reaction between the GO-CNT and PdCl4(2-) led to the formation of nanohybrid materials consisting rGO-CNT decorated with 4 nm Pd NPs, which exhibited excellent and stable catalytic activity: the reduction of 4-nitrophenol to 4-aminophenol using NaBH4 as a catalyst was completed in only 20 s at room temperature, even when the Pd content of the catalyst was 1.12 wt%. This method does not require rigorous conditions or toxic agents and thus is a rapid, efficient, and green approach to the fabrication of highly active catalysts.

Concepts: Catalytic converter, Catalysis, Chemical reaction, Enzyme, Hydrogenation, Hydrogen, Nitrogen, Electrochemistry

161

Phytochrome photoreceptors in plants and microorganisms switch photochromically between two states, controlling numerous important biological processes. Although this phototransformation is generally considered to involve rotation of ring D of the tetrapyrrole chromophore, Ulijasz et al. (2010, Nature 463, 250-254) proposed that the A-ring rotates instead. Here, we apply MAS NMR to the two parent states of following studies of the 23-kDa GAF-domain fragment of phytochrome from Synechococcus OS-B'. Major changes occur at the A-ring covalent linkage to the protein as well as at the protein residue contact of ring D. Conserved contacts associated with the A-ring nitrogen rule out an A-ring photoflip, whereas loss of contact of the D-ring nitrogen to the protein implies movement of ring D. Although none of the methine bridges showed a chemical shift change comparable to those characteristic of the D-ring photoflip in canonical phytochromes, denaturation experiments showed conclusively that the same occurs in Synechococcus OS-B' phytochrome upon photoconversion. The results are consistent with the D-ring being strongly tilted in both states and the C15=C16 double bond undergoing a Z/E isomerization upon light absorption. More subtle changes are associated with the A-ring linkage to the protein. Our findings thus disprove A-ring rotation and are discussed in relation to the position of the D-ring, photoisomerization and photochromicity in the phytochrome family.

Concepts: Absorption, Rotation, Nitrogen, Covalent bond, Metabolism, Group, Oxygen, Protein

160

The effects of microbial iron reduction and oxidation on the immobilization and mobilization of copper was investigated in a high concentration of sulfate with synthesized Fe(III) minerals and red earth soils rich in amorphous Fe (hydr)oxides. Batch microcosm experiments showed that red earth soil inoculated with subsurface sediments had a faster Fe(III) bioreduction rate than pure amorphous Fe(III) minerals and resulted in quicker immobilization of Cu in the aqueous fraction. Coinciding with the decrease of aqueous Cu, SO4(2-) in the inoculated red earth soil decreased acutely after incubation. The shift in the microbial community composite in the inoculated soil was analyzed through denaturing gradient gel electrophoresis. Results revealed the potential cooperative effect of microbial Fe(III) reduction and sulfate reduction on copper immobilization. After exposure to air for 144 h, more than 50% of the immobilized Cu was remobilized from the anaerobic matrices; aqueous sulfate increased significantly. Sequential extraction analysis demonstrated that the organic matter/sulfide-bound Cu increased by 52% after anaerobic incubation relative to the abiotic treatment but decreased by 32% after oxidation, indicating the generation and oxidation of Cu-sulfide co-precipitates in the inoculated red earth soil. These findings suggest that the immobilization of copper could be enhanced by mediating microbial Fe(III) reduction with sulfate reduction under anaerobic conditions. The findings have an important implication for bioremediation in Cu-contaminated and Fe-rich soils, especially in acid mine drainage (AMD)-affected sites.

Concepts: Archaea, Redox, Hydrogen, Bioremediation, Zinc, Nitrogen, Aluminium, Iron

158

Phenolic lipids were isolated from rye grains, cashew nutshell liquid (CNSL) from Anacardium occidentale, and fruit bodies of Merrulius tremellosus, and their effects on the electric eel acetylcholinesterase activity and conformation were studied. The observed effect distinctly depended on the chemical structure of the phenolic lipids that were available for interaction with the enzyme. All of the tested compounds reduced the activity of acetylcholinesterase. The degree of inhibition varied, showing a correlation with changes in the conformation of the enzyme tested by the intrinsic fluorescence of the Trp residues of the protein.

Concepts: Chemical compound, Effect, Eel, Nitrogen, Enzyme, Electricity, Cashew, Electric eel

157

Rapid development of agriculture and fossil fuel combustion greatly increased US reactive nitrogen emissions to the atmosphere in the second half of the 20th century, resulting in excess nitrogen deposition to natural ecosystems. Recent efforts to lower nitrogen oxides emissions have substantially decreased nitrate wet deposition. Levels of wet ammonium deposition, by contrast, have increased in many regions. Together these changes have altered the balance between oxidized and reduced nitrogen deposition. Across most of the United States, wet deposition has transitioned from being nitrate-dominated in the 1980s to ammonium-dominated in recent years. Ammonia has historically not been routinely measured because there are no specific regulatory requirements for its measurement. Recent expansion in ammonia observations, however, along with ongoing measurements of nitric acid and fine particle ammonium and nitrate, permit new insight into the balance of oxidized and reduced nitrogen in the total (wet + dry) US nitrogen deposition budget. Observations from 37 sites reveal that reduced nitrogen contributes, on average, ∼65% of the total inorganic nitrogen deposition budget. Dry deposition of ammonia plays an especially key role in nitrogen deposition, contributing from 19% to 65% in different regions. Future progress toward reducing US nitrogen deposition will be increasingly difficult without a reduction in ammonia emissions.

Concepts: Oxidizing agent, Nitric oxide, Ammonium nitrate, Redox, Carbon dioxide, Hydrogen, Ammonia, Nitrogen

156

The Three Gorges Dam has significantly altered ecological and environmental conditions within the reservoir region, but how these changes affect bacterioplankton structure and function is unknown. Here, three widely accepted metagenomic tools were employed to study the impact of damming on the bacterioplankton community in the Xiangxi River. Our results indicated that bacterioplankton communities were both taxonomically and functionally different between backwater and riverine sites, which represent communities with and without direct dam effects, respectively. There were many more nitrogen cycling Betaproteobacteria (e.g., Limnohabitans), and a higher abundance of functional genes and KEGG orthology (KO) groups involved in nitrogen cycling in the riverine sites, suggesting a higher level of bacterial activity involved in generating more nitrogenous nutrients for the growth of phytoplankton. Additionally, the KO categories involved in carbon and sulfur metabolism, as well as most of the detected functional genes also showed clear backwater and riverine patterns. As expected, these diversity patterns all significantly correlated with environmental characteristics, confirming that the bacterioplankton communities in the Xiangxi River were really affected by environmental changes from the Three Gorges Dam. This study provides a first comparative metagenomic insight for evaluating the impacts of the large dam on microbial function.

Concepts: Three Gorges, Oxygen, River, Nitrogen, Bacteria, Metabolism, Three Gorges Dam, Dam