The Zymomonas mobilis regulator hfq contributes to tolerance against multiple lignocellulosic pretreatment inhibitors

<p>Abstract</p> <p>Background</p> <p><it>Zymomonas mobilis </it>produces near theoretical yields of ethanol and recombinant strains are candidate industrial microorganisms. To date, few studies have examined its responses to various stresses at the gene level. Hfq is a conserved bacterial member of the Sm-like family of RNA-binding proteins, coordinating a broad array of responses including multiple stress responses. In a previous study, we observed <it>Z. mobilis </it>ZM4 gene ZMO0347 showed higher expression under anaerobic, stationary phase compared to that of aerobic, stationary conditions.</p> <p>Results</p> <p>We generated a <it>Z. mobilis hfq </it>insertion mutant AcRIM0347 in an acetate tolerant strain (AcR) background and investigated its role in model lignocellulosic pretreatment inhibitors including acetate, vanillin, furfural and hydroxymethylfurfural (HMF). <it>Saccharomyces cerevisiae </it>Lsm protein (Hfq homologue) mutants and Lsm protein overexpression strains were also assayed for their inhibitor phenotypes. Our results indicated that all the pretreatment inhibitors tested in this study had a detrimental effect on both <it>Z. mobilis </it>and <it>S. cerevisiae</it>, and vanillin had the most inhibitory effect followed by furfural and then HMF for both <it>Z. mobilis </it>and <it>S. cerevisiae</it>. AcRIM0347 was more sensitive than the parental strain to the inhibitors and had an increased lag phase duration and/or slower growth depending upon the conditions. The <it>hfq </it>mutation in AcRIM0347 was complemented partially by trans-acting <it>hfq </it>gene expression. We also assayed growth phenotypes for <it>S. cerevisiae </it>Lsm protein mutant and overexpression phenotypes. Lsm1, 6, and 7 mutants showed reduced tolerance to acetate and other pretreatment inhibitors. <it>S. cerevisiae </it>Lsm protein overexpression strains showed increased acetate and HMF resistance as compared to the wild-type, while the overexpression strains showed greater inhibition under vanillin stress conditions.</p> <p>Conclusions</p> <p>We have shown the utility of the pKNOCK suicide plasmid for mutant construction in <it>Z. mobilis</it>, and constructed a Gateway compatible expression plasmid for use in <it>Z. mobilis </it>for the first time. We have also used genetics to show <it>Z. mobilis </it>Hfq and <it>S. cerevisiae </it>Lsm proteins play important roles in resisting multiple, important industrially relevant inhibitors. The conserved nature of this global regulator offers the potential to apply insights from these fundamental studies for further industrial strain development.</p

Mortality Awareness: New Directions

Thinking about our own death and its salience in relation to decision making has become a fruitful area of multidisciplinary research across the breadth of psychological science. By bringing together experts from philosophy, cognitive and affective neuroscience, clinical and computational psychiatry we have attempted to set out the current state of the art and point to areas of further enquiry. One stimulus for doing this is the need to engage with policy makers who are now having to consider guidelines on suicide and assisted suicide so that they may be aware of their own as well as the wider populations' cognitive processes when confronted with the ultimate truth of mortality

Data-driven train set crash dynamics simulation

© 2016 Informa UK Limited, trading as Taylor & Francis GroupTraditional finite element (FE) methods are arguably expensive in computation/simulation of the train crash. High computational cost limits their direct applications in investigating dynamic behaviours of an entire train set for crashworthiness design and structural optimisation. On the contrary, multi-body modelling is widely used because of its low computational cost with the trade-off in accuracy. In this study, a data-driven train crash modelling method is proposed to improve the performance of a multi-body dynamics simulation of train set crash without increasing the computational burden. This is achieved by the parallel random forest algorithm, which is a machine learning approach that extracts useful patterns of force–displacement curves and predicts a force–displacement relation in a given collision condition from a collection of offline FE simulation data on various collision conditions, namely different crash velocities in our analysis. Using the FE simulation results as a benchmark, we compared our method with traditional multi-body modelling methods and the result shows that our data-driven method improves the accuracy over traditional multi-body models in train crash simulation and runs at the same level of efficiency

Three-dimensional controlled growth of monodisperse sub-50 nm heterogeneous nanocrystals

The ultimate frontier in nanomaterials engineering is to realize their composition control with atomic scale precision to enable fabrication of nanoparticles with desirable size, shape and surface properties. Such control becomes even more useful when growing hybrid nanocrystals designed to integrate multiple functionalities. Here we report achieving such degree of control in a family of rare-earth-doped nanomaterials. We experimentally verify the co-existence and different roles of oleate anions (OA-) and molecules (OAH) in the crystal formation. We identify that the control over the ratio of OA- to OAH can be used to directionally inhibit, promote or etch the crystallographic facets of the nanoparticles. This control enables selective grafting of shells with complex morphologies grown over nanocrystal cores, thus allowing the fabrication of a diverse library of monodisperse sub-50 nm nanoparticles. With such programmable additive and subtractive engineering a variety of three-dimensional shapes can be implemented using a bottom-up scalable approach

3D sunken relief generation from a single image by feature line enhancement

Sunken relief is an art form whereby the depicted shapes are sunk into a given flat plane with a shallow overall depth. In this paper, we propose an efficient sunken relief generation algorithm based on a single image by the technique of feature line enhancement. Our method starts from a single image. First, we smoothen the image with morphological operations such as opening and closing operations and extract the feature lines by comparing the values of adjacent pixels. Then we apply unsharp masking to sharpen the feature lines. After that, we enhance and smoothen the local information to obtain an image with less burrs and jaggies. Differential operations are applied to produce the perceptive relief-like images. Finally, we construct the sunken relief surface by triangularization which transforms two-dimensional information into a three-dimensional model. The experimental results demonstrate that our method is simple and efficient

Fabrication and Magnetic Properties of Fe65Co35–ZnO Nano-Granular Films

A series of nano-granular films composed of magnetic metal (Fe65Co35) granules with a few nanometers in size and semiconductor oxide (ZnO) have been fabricated by a magnetron sputtering method, and excellent soft magnetic properties have been achieved in a wide metal volume fraction (x) range for as-deposited samples due to the exchange coupling between FeCo granules (a ferromagnetic interaction in nano-scale). In a wide range (0.53 <x < 0.71), the films exhibit coercivity HC not exceeding 15 Oe, along with high resistivity. Especially for the sample with x = 0.67, coercivities in hard and easy axes are 1.43 and 7.08 Oe, respectively, 4πMS = 9.85 kg, and ρ reaches 2.06 × 103 μΩ cm. The dependence of complex permeability μ = μ′ − jμ″ on frequency shows that the real part μ′ is more than 100 below 1.83 GHz and that the ferromagnetic resonance frequency reaches 2.31 GHz, implying the promising for high frequency application. The measured negative temperature coefficient of resistivity reveals that may be the weak localized electrons existing in samples mediate the exchange coupling

Distinct Neurocognitive Strategies for Comprehensions of Human and Artificial Intelligence

Although humans have inevitably interacted with both human and artificial intelligence in real life situations, it is unknown whether the human brain engages homologous neurocognitive strategies to cope with both forms of intelligence. To investigate this, we scanned subjects, using functional MRI, while they inferred the reasoning processes conducted by human agents or by computers. We found that the inference of reasoning processes conducted by human agents but not by computers induced increased activity in the precuneus but decreased activity in the ventral medial prefrontal cortex and enhanced functional connectivity between the two brain areas. The findings provide evidence for distinct neurocognitive strategies of taking others' perspective and inhibiting the process referenced to the self that are specific to the comprehension of human intelligence

Complement and the Alternative Pathway Play an Important Role in LPS/D-GalN-Induced Fulminant Hepatic Failure

Fulminant hepatic failure (FHF) is a clinically severe type of liver injury with an extremely high mortality rate. Although the pathological mechanisms of FHF are not well understood, evidence suggests that the complement system is involved in the pathogenesis of a variety of liver disorders. In the present study, to investigate the role of complement in FHF, we examined groups of mice following intraperitoneal injection of LPS/D-GalN: wild-type C57BL/6 mice, wild-type mice treated with a C3aR antagonist, C5aR monoclonal antibody (C5aRmAb) or CR2-Factor H (CR2-fH, an inhibitor of the alternative pathway), and C3 deficient mice (C3−/− mice). The animals were euthanized and samples analyzed at specific times after LPS/D-GalN injection. The results show that intraperitoneal administration of LPS/D-GalN activated the complement pathway, as evidenced by the hepatic deposition of C3 and C5b-9 and elevated serum levels of the complement activation product C3a, the level of which was associated with the severity of the liver damage. C3a receptor (C3aR) and C5a receptor (C5aR) expression was also upregulated. Compared with wild-type mice, C3−/− mice survived significantly longer and displayed reduced liver inflammation and attenuated pathological damage following LPS/D-GalN injection. Similar levels of protection were seen in mice treated with C3aR antagonist,C5aRmAb or CR2-fH. These data indicate an important role for the C3a and C5a generated by the alternative pathway in LPS/D-GalN-induced FHF. The data further suggest that complement inhibition may be an effective strategy for the adjunctive treatment of fulminant hepatic failure

Phenotype MicroArray Profiling of Zymomonas mobilis ZM4

In this study, we developed a Phenotype MicroArray™ (PM) protocol to profile cellular phenotypes in Zymomonas mobilis, which included a standard set of nearly 2,000 assays for carbon, nitrogen, phosphorus and sulfur source utilization, nutrient stimulation, pH and osmotic stresses, and chemical sensitivities with 240 inhibitory chemicals. We observed two positive assays for C-source utilization (fructose and glucose) using the PM screen, which uses redox chemistry and cell respiration as a universal reporter to profile growth phenotypes in a high-throughput 96-well plate-based format. For nitrogen metabolism, the bacterium showed a positive test results for ammonia, aspartate, asparagine, glutamate, glutamine, and peptides. Z. mobilis appeared to use a diverse array of P-sources with two exceptions being pyrophosphate and tripolyphosphate. The assays suggested that Z. mobilis uses both inorganic and organic compounds as S-sources. No stimulation by nutrients was detected; however, there was evidence of partial inhibition by purines and pyrimidines, NAD, and deferoxamine. Z. mobilis was relatively resistant to acid pH, tolerating a pH down to about 4.0. It also tolerated phosphate, sulfate, and nitrate, but was rather sensitive to chloride and nitrite. Z. mobilis showed resistance to a large number of diverse chemicals that inhibit most bacteria. The information from PM analysis provides an overview of Z. mobilis physiology and a foundation for future comparisons of other wild-type and mutant Z. mobilis strains