The relevance of microbial processes in geo-energy applications

The subsurface is a vast reservoir which we exploit in various ways. We extract energy in the form of oil/gas or heat from it. We use it for the storage of energy, e.g., in shallow geothermal applications or for the underground storage of natural gas. A lot of recent research has studied the potential for storing hydrogen (H2) in the subsurface. We also use the subsurface to dispose of energy-related waste, e.g., radioactive materials, carbon dioxide (CO2), and acid gas.For a long time, the subsurface was considered sterile below a few metres, probably stemming from work carried out in the 1950s which suggested that bacteria in Pacific sediments most likely disappeared somewhere just below 8m (Morita and ZoBell, 1955). This observation seems to have been extrapolated to the subsurface in general, but over time, as methods developed and microbiologists probed harder, this view changed, and it is now recognised that microbial communities exist at depths where the subsurface is exploited for most types of geo-energy. This raises questions about what sort of microbial community exists, how active it is, what limits and drives that activity and how this might impact geo-energy operations.Cited as: Ebigbo, A., Gregory, S. P. The relevance of microbial processes in geo-energy applications. Advances in Geo-Energy Research, 2021, 5(1): 5-7, doi: 10.46690/ager.2021.01.0

Customizing the therapeutic response of signaling networks to promote antitumor responses by drug combinations

Drug resistance, de novo and acquired, pervades cellular signaling networks (SNs) from one signaling motif to another as a result of cancer progression and/or drug intervention. This resistance is one of the key determinants of efficacy in targeted anti-cancer drug therapy. Although poorly understood, drug resistance is already being addressed in combination therapy by selecting drug targets where SN sensitivity increases due to combination components or as a result of de novo or acquired mutations. Additionally, successive drug combinations have shown low resistance potential. To promote a rational, systematic development of combination therapies, it is necessary to establish the underlying mechanisms that drive the advantages of combination therapies, and design methods to determine drug targets for combination regimens. Based on a joint systems analysis of cellular SN response and its sensitivity to drug action and oncogenic mutations, we describe an in silico method to analyze the targets of drug combinations. Our method explores mechanisms of sensitizing the SN through a combination of two drugs targeting vertical signaling pathways. We propose a paradigm of SN response customization by one drug to both maximize the effect of another drug in combination and promote a robust therapeutic response against oncogenic mutations. The method was applied to customize the response of the ErbB/PI3K/PTEN/AKT pathway by combination of drugs targeting HER2 receptors and proteins in the down-stream pathway. The results of a computational experiment showed that the modification of the SN response from hyperbolic to smooth sigmoid response by manipulation of two drugs in combination leads to greater robustness in therapeutic response against oncogenic mutations determining cancer heterogeneity. The application of this method in drug combination co-development suggests a combined evaluation of inhibition effects together with the capability of drug combinations to suppress resistance mechanisms before they become clinically manifest

Microbial community analysis of constructed wetlands treating effluent from a land-based marine fish farm.

The use of constructed wetlands to treat wastewater from fish farms has the potential to reduce the environmental impact of the aquaculture industry. In order to gain a greater understanding of the processes occurring within a newly constructed wetland at a commercial marine fish farm, nitrogen removal and bacterial communities were studied in model wetlands and the fish farm wetland. The limits of nitrification capacity in a vertical trickle flow model system were tested by dosing with aquaculture wastewater supplemented with increasing amounts of ammonium chloride. Greater than 97% ammonia removal was observed with ammonia concentrations of up to 358ppm. At higher concentrations of ammonia a lower percentage of ammonia removal occurred, and nitrite accumulation was observed. A decrease in the number of detected bacterial OTUs (as measured by 16s rRNA T-RFLP) was detected concurrent with the reduction in the percent of ammonia removed. T-RFLP analysis of the ammonia mono-oxygenase gene showed a clear successional pattern of three different ammonia oxidizing bacterial OTUs (belonging to the Nitrosomonas Nm143 lineage N.oligotropha/N.ureae lineage and N.aestuarii/N.marina lineage). Lab-scale wetlands were used to investigate the effect of flood/drain cycles on nitrogen removal. When the multiple cycles were used, the concentrations of ammonia and organic nitrogen were lower after treatment in the flood/drain wetlands than in permanently submerged wetlands. However, the concentrations of nitrites and nitrates were higher in the flood/drain wetlands. Elevation of nitrate concentration could be prevented by shortening the drainage period. Subsequent work on the fish farm wetland also showed that flood/drain cycles improved ammonia removal, but reduced nitrate and nitrite removal. The total bacterial communities in the submerged wetlands showed a greater degree of similarity to each other than those in the flood/drain wetlands. The ammonia oxidizing bacterial communities in the flood/drain wetlands were dominated by bacteria belonging to the Nitrosomonas aestuarii/N.marina lineage, and the submerged wetlands were dominated by a bacterial OTU that was unidentified by T-RFLP. Nitrosomonas aestuarii/N.marina was the dominant ammonia oxidizing bacteria during the first 17 months of operation of the fish farm wetland. The abundance of other ammonia oxidizing OTU showed seasonal variation. The total bacterial community did not show clear temporal or spatial patterns of variation. Effective nitrogen removal was seen in the wetlands with the exception of one pair of cells which began to experience elevated ammonia concentrations after about 15 months. It was shown that introducing flood/drain cycles to this wetland could rapidly improve performance and prevent ammonia accumulation

Comparison of heterotrophic bioleaching and ammonium sulfate ion exchange leaching of Rare Earth Elements from a Madagascan Ion-Adsorption Clay

Rare earth elements (REE) are considered to be a critical resource, because of their importance in green energy applications and the overdependence on Chinese imports. REE rich ion-adsorption deposits (IAD) result from tropical weathering of REE enriched igneous rocks. Commercial REE leaching from IAD, using salt solutions occurs via an ion-exchange mechanism. Bioleaching of IAD by Aspergillus or Bacillus, was compared to Uninoculated Control and Salt leaching (0.5 M ammonium sulfate) over 60 days. Salt leaching was most effective, followed by Aspergillus, Bacillus then Uninoculated Control. Most of the REE and major elements released by Salt leaching occurred before day 3. With bioleaching, REE and major elements release increased with time and had a greater heavy to light REE ratio. Similar total heavy REE release was observed in Salt leaching and Aspergillus (73.1% and 70.7% Lu respectively). In bioleaching experiments, pH was inversely correlated with REE release (R2 = 0.947 for Lu) indicating leaching by microbially produced acids. These experiments show the potential for bioleaching of REE from IAD, but dissolution of undesirable elements could cause problems in downstream processing. Further understanding of the bioleaching mechanisms could lead to optimization of REE recover

Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels

Background Inflammatory bowel disease (IBD), is a debilitating group of chronic diseases including Crohn’s Disease (CD) and ulcerative colitis (UC), which causes inflammation of the gut and affects millions of people worldwide. At different taxonomic levels, the structure of the gut microbiota is significantly altered in IBD patients compared to that of healthy individuals. However, it is unclear how these IBD-affected bacterial groups are related to other common bacteria in the gut, and how they are connected across different disease conditions at the global scale. Results In this study, using faecal samples from patients with IBD, we show through diversity analysis of the microbial community structure based on the 16S rRNA gene that the gut microbiome of IBD patients is less diverse compared to healthy individuals. Furthermore, we have identified which bacterial groups change in abundance in both CD and UC compared to healthy controls. A substantial imbalance was observed across four major bacterial phyla including Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria, which together constitute >98% of the gut microbiota. Next, we reconstructed a bacterial family co-abundance network based on the correlation of abundance profiles obtained from the public gut microbiome data of >22000 samples of faecal and gut biopsies taken from both diseased and healthy individuals. The data was compiled using the EBI metagenomics database [1]. By mapping IBD-altered bacterial families to the network, we show that the bacterial families which exhibit an increased abundance in IBD conditions are not well connected to other groups, implying that these families generally do not coexist together with common gut organisms. Whereas, the bacterial families whose abundance is reduced or did not change in IBD conditions compared to healthy conditions are very well connected to other bacterial groups, suggesting they are highly important groups of bacteria in the gut that can coexist with other bacteria across a range of conditions. Conclusions IBD patients exhibited a less diverse gut microbiome compared to healthy individuals. Bacterial groups which changed in IBD patients were found to be groups which do not co-exist well with common commensal gut bacteria, whereas bacterial groups which did not change in patients with IBD were found to commonly co-exist with commensal gut microbiota. This gives a potential insight into the dynamics of the gut microbiota in patients with IBD

Dark-ages reionization & galaxy formation simulation IV: UV luminosity functions of high-redshift galaxies

In this paper we present calculations of the UV luminosity function from the Dark-ages Reionization And Galaxy-formation Observables from Numerical Simulations (DRAGONS) project, which combines N-body, semi-analytic and semi-numerical modelling designed to study galaxy formation during the Epoch of Reionization. Using galaxy formation physics including supernova feedback, the model naturally reproduces the UV LFs for high-redshift star-forming galaxies from $z{\sim}5$ through to $z{\sim}10$. We investigate the luminosity--star formation rate (SFR) relation, finding that variable SFR histories of galaxies result in a scatter around the median relation of $0.1$--$0.3$ dex depending on UV luminosity. We find close agreement between the model and observationally derived SFR functions. We use our calculated luminosities to investigate the luminosity function below current detection limits, and the ionizing photon budget for reionization. We predict that the slope of the UV LF remains steep below current detection limits and becomes flat at $M_\mathrm{UV}{\gtrsim}{-14}$. We find that $48$ ($17$) per cent of the total UV flux at $z{\sim}6$ ($10$) has been detected above an observational limit of $M_\mathrm{UV}{\sim}{-17}$, and that galaxies fainter than $M_\mathrm{UV}{\sim}{-17}$ are the main source of ionizing photons for reionization. We investigate the luminosity--stellar mass relation, and find a correlation for galaxies with $M_\mathrm{UV}{<}{-14}$ that has the form $M_*{\propto}10^{-0.47M_\mathrm{UV}}$, in good agreement with observations, but which flattens for fainter galaxies. We determine the luminosity--halo mass relation to be $M_\mathrm{vir}{\propto}10^{-0.35M_\mathrm{UV}}$, finding that galaxies with $M_\mathrm{UV}{=}{-20}$ reside in host dark matter haloes of $10^{11.0\pm 0.1}\mathrm{M_\odot}$ at $z{\sim}6$, and that this mass decreases towards high redshift.Comment: 17 pages, 14 figures, Accepted for publication in MNRA

Comparison of Three Approaches for Bioleaching of Rare Earth Elements from Bauxite

Approximately 300 million tonnes of bauxite are processed annually, primarily to extract alumina, and can contain moderate rare earth element (REE) concentrations, which are critical to a green energy future. Three bioleaching techniques (organic acid, reductive and oxidative) were tested on three karst bauxites using either Aspergillus sp. (organic acid bioleaching) or Acidithiobacillus ferrooxidans (reductive and oxidative bioleaching). Recovery was highest in relation to middle REE (generally Nd to Gd), with maximum recovery of individual REE between 26.2% and 62.8%, depending on the bauxite sample. REE recovery occurred at low pH (generally < 3), as a result of organic acids produced by Aspergillus sp. or sulphuric acid present in A. ferrooxidans growth media. Acid production was seen when A. ferrooxidans was present. However, a clear increase in REE recovery in the presence of A. ferrooxidans (compared to the control) was only seen with one bauxite sample (clay-rich) and only under oxidative conditions. The complex and varied nature of REE-bearing minerals in bauxite provides multiple targets for bioleaching, and although the majority of recoverable REE can be leached by organic and inorganic acids, there is potential for enhanced recovery by bioleaching

Performance of Multi-Beacon DGPS

Historically, maritime organizations seeking accurate shipboard positioning have relied upon some form of differential GNSS, such as DGPS, WAAS, or EGNOS, to improve the accuracy and integrity of the GPS. Groundbased augmentation systems, such as DGPS, broadcast corrections to the GPS signal from geographically distributed terrestrial stations, often called beacons. Specifically, pseudorange corrections for the GPS L1 C/A signal are computed at each reference site, then broadcast in the nearby geographic area using a medium frequency (approximately 300 kHz) communications link. The user then adds these corrections onto their measured pseudoranges before implementing a position solution algorithm. Within the United States, the U.S. Coast Guard operates 86 DGPS reference beacons. Similar DGPS systems are operated in Europe and elsewhere around the globe. While current DGPS receiver algorithms typically use one set of pseudorange corrections from one DGPS reference site (often the one with the “strongest” signal), many user locations can successfully receive two or more different DGPS broadcasts. This brings to mind obvious questions: “If available, how does one select the corrections to use from multiple sets of corrections?” and “Is it advantageous to combine corrections in some way?” We note that a number of factors might influence the effectiveness of any particular station’s corrections. Some of these refer to the effectiveness of the communications link itself, including concerns about interference from other beacons (skywave interference from far-away beacons on similar frequencies, a notable problem in Europe) and self-interference (skywave fading). Other factors refer to the accuracies of pseudorange corrections. For example, ionospheric storm-enhanced plasma density (SED) events can cause the corrections to have large spatial variation, making them poor choices even for users close to a beacon. Earlier work in the area of DGPS beacon selection has identified several options including choosing the beacon closest to the user or the beacon with the least skywave interference. There have also been suggestions on how to combine corrections when multiple beacons are available. The most common of these is a weighted sum of the corrections, where the weights are typically inversely proportional to the distance from the user to the individual beacon. This paper reexamines the concept of multi-beacon DGPS by evaluating methods of combining beacon corrections based on spatial relativity. Of relevance to this topic is our recent observation that DGPS accuracy performance is biased. The mean of the error scatter with DGPS corrections does not fall on the actual receiver position. We established this both by processing GPS L1 C/A observables from hundreds of CORS (Continuously Operating References Station) sites around the U.S.A. and via simulation using a Spirent GSS8000 GPS simulator. Specifically, we found that the position solution computed using DGPS beacon corrections is typically biased in a direction away from the beacon, and that the size of the bias depends upon the distance from the beacon. This bias grows with a slope of approximately one-third of a meter per 100 km of user-to-beacon distance. This paper compares the performance of several multibeacon algorithms assessed using GPS simulator data. These algorithms include the nearest beacon, a weighted sum based on distances, and a spatial linearly-interpolated correction using the actual locations of the transmitters (distance and angle). We note that as part of this research effort we developed a DGPS receiver using software-defined radio (USRP). A complete description of this system is included in the paper

Braneworld stars and black holes

We look for spherically symmetric star or black hole solutions on a Randall-Sundrum brane from the perspective of the bulk. We take a known bulk solution, and analyse possible braneworld trajectories within it that correspond, from the braneworld point of view, to solutions of the brane Tolman-Oppenheimer-Volkoff equations. Our solutions are therefore embedded consistently into a full bulk solution. We find the full set of static gravitating matter sources on a brane in a range of bulk spacetimes, analyzing which can correspond to physically sensible sources. Finally, we look at time-dependent trajectories in a Schwarzschild--anti de Sitter spacetime as possible descriptions of time-dependent braneworld black holes, highlighting some of the general features one might expect, as well as some of the difficulties involved in getting a full solution to the question.Comment: 39 pages, 15 figure

The non-dipolar magnetic fields of accreting T Tauri stars

Models of magnetospheric accretion on to classical T Tauri stars often assume that stellar magnetic fields are simple dipoles. Recently published surface magnetograms of BP Tau and V2129 Oph have shown, however, that their fields are more complex. The magnetic field of V2129 Oph was found to be predominantly octupolar. For BP Tau the magnetic energy was shared mainly between the dipole and octupole field components, with the dipole component being almost four times as strong as that of V2129 Oph. From the published surface maps of the photospheric magnetic fields we extrapolate the coronal fields of both stars, and compare the resulting field structures with that of a dipole. We consider different models where the disc is truncated at, or well-within, the Keplerian corotation radius. We find that although the structure of the surface magnetic field is particularly complex for both stars, the geometry of the larger scale field, along which accretion is occurring, is somewhat simpler. However, the larger scale field is distorted close to the star by the stronger field regions, with the net effect being that the fractional open flux through the stellar surface is less than would be expected with a dipole magnetic field model. Finally, we estimate the disc truncation radius, assuming that this occurs where the magnetic torque from the stellar magnetosphere is comparable to the viscous torque in the disc.Comment: 14 pages, 8 figures. Figures are reduced resolutio