Metagenomic sequencing unravels gene fragments with phylogenetic signatures of O2-tolerant NiFe membrane-bound hydrogenases in lacustrine sediment

Many promising hydrogen technologies utilising hydrogenase enzymes have been slowed by the fact that most hydrogenases are extremely sensitive to O2. Within the group 1 membrane-bound NiFe hydrogenase, naturally occurring tolerant enzymes do exist, and O2 tolerance has been largely attributed to changes in iron–sulphur clusters coordinated by different numbers of cysteine residues in the enzyme’s small subunit. Indeed, previous work has provided a robust phylogenetic signature of O2 tolerance [1], which when combined with new sequencing technologies makes bio prospecting in nature a far more viable endeavour. However, making sense of such a vast diversity is still challenging and could be simplified if known species with O2-tolerant enzymes were annotated with information on metabolism and natural environments. Here, we utilised a bioinformatics approach to compare O2-tolerant and sensitive membrane-bound NiFe hydrogenases from 177 bacterial species with fully sequenced genomes for differences in their taxonomy, O2 requirements, and natural environment. Following this, we interrogated a metagenome from lacustrine surface sediment for novel hydrogenases via high-throughput shotgun DNA sequencing using the Illumina™ MiSeq platform. We found 44 new NiFe group 1 membrane-bound hydrogenase sequence fragments, five of which segregated with the tolerant group on the phylogenetic tree of the enzyme’s small subunit, and four with the large subunit, indicating de novo O2-tolerant protein sequences that could help engineer more efficient hydrogenases

Case Study on Remote Diagnostics in Resolving Random Vibration on a Steam Turbine

Case StudyCase Study 7: This case study narrates an incident of random vibration spikes which occurred in year 2014 on one of the steam turbine bearings of a propane refrigeration compressor train. The random vibration spikes caused the turbine high vibration to trip leading to a train shutdown. This case study outlines how the random vibration spikes were successfully diagnosed through remote monitoring center, the root cause for the high vibration trips, and finally how it was mitigated. The case study also discusses lessons learned with respect to the discovery methodology using expert system available at site, and the importance of monitoring key operating parameters

Chemical reaction and heat transfer on boundary layer Maxwell Ferro-fluid flow under magnetic dipole with Soret and suction effects

AbstractIn this article, the influence of chemical reaction and heat transfer analysis of Maxwell saturated Ferro-fluid flow over a stretching sheet under the influence of magnetic dipole with Soret and suction effects are investigated. The sheet is assumed to be permeable in a semi-infinite domain. Firstly, partial differential equations of mass, momentum and concentration for the governing flow problem are modelled and converted into a system of differential equations by utilizing similarity approach. Then the solution of resulting non-linear differential equations is solved by efficient Runge-Kutta technique based on shooting algorithm with the help of MATLAB. Effect of all appropriate parameters like ferromagnetic interaction parameter, chemical reaction parameter, Maxwell parameter, Soret number, suction parameter, Maxwell parameter, Schmidt number, and suction parameter on velocity, temperature and concentration field are confirmed through graphs and table. From the present conclusions, it is examined that by increasing the Maxwell parameter there is a decrease in the fluid velocity and boundary layer thickness. On the other hand, the uprising behaviour is prominent for both temperature and concentration profiles. Also predicted that there is an enhancement in skin friction coefficient and rate of heat transfer by enlarging suction parameter, but opposite trend is noted for Sherwood number. Also noted that the values of Prandtl are taken ranges from 0.72 to 10. The Nusselt number increases from 1.09 to 4.80

A Quadrupole/Time-of-Flight Mass Spectrometry Study of Trp-Cage’s Conformation

Trp-cage is a synthetic 20-residue miniprotein that uses tertiary contacts to stabilize its native conformation. NMR, circular dichroism (CD), and UV-resonance Raman spectroscopy were used to probe its energy landscape. In this quadrupole/time-of-flight study, electrospray ionization charge state distribution (CSD) and solution-phase H/D exchange are used to probe Trp-cage’s tertiary structure. The CSDs of Trp-cage and its mutant provide spectra showing a pH-dependent conformation change. Solution-phase H/D exchange in 30% deuterated trifluoroethanol solution of the wild type shows increased protection of one labile hydrogen in the native state. Together, CSDs and solution-phase H/D exchange are demonstrated to constitute a simple but effective means to follow conformation changes in a small tertiary protein

Enhanced strength and temperature dependence of mechanical properties of Li at small length scales and its implications for Li metal anodes

Most next-generation Li-ion battery chemistries require a functioning lithium metal (Li) anode. However, its application in secondary batteries has been inhibited because of uncontrollable dendrite growth during cycling. Mechanical suppression of dendrite growth through solid polymer electrolytes (SPE) or through robust separators has shown the most potential for alleviating this problem. Studies of the mechanical behavior of Li at any length scale and temperature are virtually non-existent because of its extreme reactivity, which renders sample preparation, transfer, microstructure characterization and mechanical testing prohibitively challenging. We conduct nano-mechanical experiments in an in-situ Scanning Electron Microscope and show that micron-sized Li attains extremely high strengths of 105 MPa at room temperature and of 35MPa at 90$^\circ$C. We demonstrate that single crystalline Li exhibits a power-law size-effect at the micron- and sub-micron length scales, with the strengthening exponent of -0.68 at room temperature and of -1.00 at 90$^\circ$C. We also report the elastic and shear moduli as a function of crystallographic orientation gleaned from experiments and first principles calculations, which show a high level of anisotropy up to the melting point, where the elastic and shear moduli vary by a factor of ~4 between the stiffest and most compliant orientations. The emergence of such high strengths in small-scale Li and sensitivity of this metal's stiffness to crystallographic orientation help explain why the existing methods of dendrite suppression have been mainly unsuccessful and have significant implications for practical design of future-generation batteries.Comment: 43 pages, 4 figures, Supporting Informatio

Relevance of progesterone receptor immunohistochemical staining to Oncotype DX recurrence score

AbstractObjective/BackgroundProgesterone-receptor negativity (PR−) is predictive of adverse outcomes in estrogen receptor-positive (ER+) breast cancer. The Oncotype DX assay provides risk stratification for hormone receptor-positive (HR+) invasive breast cancer; however, the association of PR status and Oncotype DX recurrence scores (RSs) is less clear.MethodsWe designed an analysis to determine whether a significant difference exists in the RS for ER+/PR− tumors when compared with ER+/PR+ breast cancer. Three hundred and fifty patients with HR+ invasive breast cancer who underwent Oncotype DX testing at our institution from December 2006 to October 2013 were included. We also examined the concordance in the HR status reported by immunohistochemical (IHC) and reverse transcriptase-polymerase chain reaction (RT-PCR) analyses. The data were analyzed by analysis of variance, F test, t test, and chi-square tests. Multivariate linear regression was used to determine significant predictors of Oncotype DX RS.ResultsA total of 301 patients had ER+/PR+ tumors and 47 patients had ER+/PR− tumors by IHC. PR− tumors had a significantly higher RS than PR+ tumors (24.7±8.53 vs. 17.3±7.38; p<.001), predicting a greater 10-year risk of distant recurrence. Multivariate linear regression showed PR status and tumor grade to be significant predictors of Oncotype DX RS (p<.0001). A total of 284 patients had HR status reported by Oncotype DX assay. Concordance between IHC and RT-PCR was 99.3% for ER and 88.7% for PR.ConclusionOur study shows that ER+/PR− breast cancer tumors are associated with a significantly higher Oncotype DX scores; this interprets into a higher risk of recurrence. Our data also show that the concordance between IHC and RT-PCR was 99.3% for ER and lower at 88.7% for PR

Plasmodium berghei Kinesin-5 Associates With the Spindle Apparatus During Cell Division and Is Important for Efficient Production of Infectious Sporozoites

Kinesin-5 motors play essential roles in spindle apparatus assembly during cell division, by generating forces to establish and maintain the spindle bipolarity essential for proper chromosome segregation. Kinesin-5 is largely conserved structurally and functionally in model eukaryotes, but its role is unknown in the Plasmodium parasite, an evolutionarily divergent organism with several atypical features of both mitotic and meiotic cell division. We have investigated the function and subcellular location of kinesin-5 during cell division throughout the Plasmodium berghei life cycle. Deletion of kinesin-5 had little visible effect at any proliferative stage except sporozoite production in oocysts, resulting in a significant decrease in the number of motile sporozoites in mosquito salivary glands, which were able to infect a new vertebrate host. Live-cell imaging showed kinesin-5-GFP located on the spindle and at spindle poles during both atypical mitosis and meiosis. Fixed-cell immunofluorescence assays revealed kinesin-5 co-localized with α-tubulin and centrin-2 and a partial overlap with kinetochore marker NDC80 during early blood stage schizogony. Dual-color live-cell imaging showed that kinesin-5 is closely associated with NDC80 during male gametogony, but not with kinesin-8B, a marker of the basal body and axonemes of the forming flagella. Treatment of gametocytes with microtubule-specific inhibitors confirmed kinesin-5 association with nuclear spindles and not cytoplasmic axonemal microtubules. Altogether, our results demonstrate that kinesin-5 is associated with the spindle apparatus, expressed in proliferating parasite stages, and important for efficient production of infectious sporozoites

Stormwater quality and microbial ecology in an urban rain garden system

Rain gardens are an alternative to traditional drainage, able to lower flood risk and reduce environmental contamination from stormwater. Removal of contaminants by rain gardens is driven by both physical processes (such as filtration and sedimentation) and biological metabolic processes by soil microorganisms. To better understand rain garden performance, this study explored the impact of rain gardens on pollution removal and microbial composition and function using rain gardens fed real stormwater from a busy road. Each rain garden had different grain size and hydraulic conductivities as these parameters have been argued to impact pollution removal. All four rain gardens were able to reduce the contaminant load in the stormwaters, reducing the concentration of dissolved metals, suspended solids and chemical oxygen demand. Significantly, road salting in the winter did not cause dissolved metals to be released from the rain gardens, suggesting that rain gardens can continue to reduce contaminant loads during winter salting regimes. Some variation in pollutant removal was seen between the soils tested, but overall no clear trend could be identified based on grain size and hydraulic conductivity with all rain gardens performing broadly similarly. The rain garden soil altered the microbial community in the stormwater, resulting in greater taxonomic evenness and functional richness in the effluent water compared to the influent. Functional richness of the soils was also higher than that of the input waters, indicating that the microbes in the rain gardens were able to perform a wider range of functions than those of the influent. Effluent and soil microbiology was more impacted by sampling date than soil grain size, which may be a result of the soil communities maturing and changing over time. As greater numbers of rain gardens are installed to tackle flooding from climate change, it is important to ensure the environment is protected from urban contaminants in the stormwater. The results in this study further highlight the ability of rain gardens to undertake this important task

The distinct features of microbial 'dysbiosis' of Crohn's disease do not occur to the same extent in their unaffected, genetically linked kindred

Background/Aims: Studying the gut microbiota in unaffected relatives of people with Crohn’s disease (CD) may advance our understanding of the role of bacteria in disease aetiology. Methods: Faecal microbiota composition (16S rRNA gene sequencing), genetic functional capacity (shotgun metagenomics) and faecal short chain fatty acids (SCFA) were compared in unaffected adult relatives of CD children (CDR, n = 17) and adult healthy controls, unrelated to CD patients (HUC, n = 14). The microbiota characteristics of 19 CD children were used as a benchmark of CD ‘dysbiosis’. Results: The CDR microbiota was less diverse (p = 0.044) than that of the HUC group. Local contribution of β-diversity analysis showed no difference in community structure between the CDR and HUC groups. Twenty one of 1,243 (1.8%) operational taxonomic units discriminated CDR from HUC. The metagenomic functional capacity (p = 0.207) and SCFA concentration or pattern were similar between CDR and HUC (p&#62;0.05 for all SCFA). None of the KEGG metabolic pathways were different between these two groups. Both of these groups (HUC and CDR) had a higher microbiota α-diversity (CDR, p = 0.026 and HUC, p&#60;0.001) with a community structure (β-diversity) distinct from that of children with CD. Conclusions: While some alterations were observed, a distinct microbial ‘dysbiosis’, characteristic of CD patients, was not observed in their unaffected, genetically linked kindred