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Aromatic amino acid metabolism and active transport regulation are implicated in microbial persistence in fractured shale reservoirs
Abstract Hydraulic fracturing has unlocked vast amounts of hydrocarbons trapped within unconventional shale formations. This large-scale engineering approach inadvertently introduces microorganisms into the hydrocarbon reservoir, allowing them to inhabit a new physical space and thrive in the unique biogeochemical resources present in the environment. Advancing our fundamental understanding of microbial growth and physiology in this extreme subsurface environment is critical to improving biofouling control efficacy and maximizing opportunities for beneficial natural resource exploitation. Here, we used metaproteomics and exometabolomics to investigate the biochemical mechanisms underpinning the adaptation of model bacterium Halanaerobium congolense WG10 and mixed microbial consortia enriched from shale-produced fluids to hypersalinity and very low reservoir flow rates (metabolic stress). We also queried the metabolic foundation for biofilm formation in this system, a major impediment to subsurface energy exploration. For the first time, we report that H. congolense WG10 accumulates tyrosine for osmoprotection, an indication of the flexible robustness of stress tolerance that enables its long-term persistence in fractured shale environments. We also identified aromatic amino acid synthesis and cell wall maintenance as critical to biofilm formation. Finally, regulation of transmembrane transport is key to metabolic stress adaptation in shale bacteria under very low well flow rates. These results provide unique insights that enable better management of hydraulically fractured shale systems, for more efficient and sustainable energy extraction.
Splicing factor SR34b mutation reduces cadmium tolerance in Arabidopsis by regulating iron-regulated transporter 1 gene
Highlights: • Arabidopsis splicing factor SR34b gene is cadmium-inducible. • SR34b T-DNA insertion mutant is sensitive to cadmium due to high cadmium uptake. • SR34b is a regulator of cadmium transporter IRT1 at the posttranscription level. • These results highlight the roles of splicing factors in cadmium tolerance of plant. - Abstract: Serine/arginine-rich (SR) proteins are important splicing factors. However, the biological functions of plant SR proteins remain unclear especially in abiotic stresses. Cadmium (Cd) is a non-essential element that negatively affects plant growth and development. In this study, we provided clear evidence for SR gene involved in Cd tolerance in planta. Systemic expression analysis of 17 Arabidopsis SR genes revealed that SR34b is the only SR gene upregulated by Cd, suggesting its potential roles in Arabidopsis Cd tolerance. Consistent with this, a SR34b T-DNA insertion mutant (sr34b) was moderately sensitive to Cd, which had higher Cd{sup 2+} uptake rate and accumulated Cd in greater amounts than wild-type. This was due to the altered expression of iron-regulated transporter 1 (IRT1) gene in sr34b mutant. Under normal growth conditions, IRT1 mRNAs highly accumulated in sr34b mutant, which was a result of increased stability of IRT1 mRNA. Under Cd stress, however, sr34b mutant plants had a splicing defect in IRT1 gene, thus reducing the IRT1 mRNA accumulation. Despite of this, sr34b mutant plants still constitutively expressed IRT1 proteins under Cd stress, thereby resulting in Cd stress-sensitive phenotype. We therefore propose the essential roles of SR34b in posttranscriptional regulation of IRT1 expression and identify it as a regulator of Arabidopsis Cd tolerance.
Local conformational dynamics regulating transport properties of a Cl − /H + antiporter
ClC‐ec1 is a Cl − /H + antiporter that exchanges Cl − and H + ions across the membrane. Experiments have demonstrated that several mutations, including I109F, decrease the Cl − and H + transport rates by an order of magnitude. Using reactive molecular dynamics simulations of explicit proton transport across the central region in the I109F mutant, a two‐dimensional free energy profile has been constructed that is consistent with the experimental transport rates. The importance of a phenylalanine gate formed by F109 and F357 and its influence on hydration connectivity through the central proton transport pathway is revealed. This work demonstrates how seemingly subtle changes in local conformational dynamics can dictate hydration changes and thus transport properties. © 2019 Wiley Periodicals, Inc.
Functional mechanisms of neurotransmitter transporters regulated by lipid–protein interactions of their terminal loops
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Tetragonal crystal form of the cyanobacterial bicarbonate-transporter regulator SbtB from Synechocystis sp. PCC 6803
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Suppressed Cosmic-Ray Energy Densities in Molecular Clouds from Streaming Instability-regulated Transport
Abstract Cosmic rays (CRs) are the primary driver of ionization in star-forming molecular clouds (MCs). Despite their potential impacts on gas dynamics and chemistry, no simulations of star cluster formation following the creation of individual stars have included explicit cosmic-ray transport (CRT) to date. We conduct the first numerical simulations following the collapse of a 2000 M ⊙ MC and the subsequent star formation including CRT using the STAR FORmation in Gaseous Environments framework implemented in the GIZMO code. We show that when CRT is streaming-dominated, the CR energy in the cloud is strongly attenuated due to energy losses from the streaming instability. Consequently, in a Milky Way–like environment the median CR ionization rate in the cloud is low ( ζ ≲ 2 × 10 −19 s −1 ) during the main star-forming epoch of the calculation and the impact of CRs on the star formation in the cloud is limited. However, in high-CR environments, the CR distribution in the cloud is elevated ( ζ ≲ 6 × 10 −18 ), and the relatively higher CR pressure outside the cloud causes slightly earlier cloud collapse and increases the star formation efficiency by 50% to ∼13%. The initial mass function is similar in all cases except with possible variations in a high-CR environment. Further studies are needed to explain the range of ionization rates observed in MCs and explore star formation in extreme CR environments.
Conserved ABC Transport System Regulated by the General Stress Response Pathways of Alpha- and Gammaproteobacteria
ABSTRACT Brucella abortus σ E1 is an EcfG family sigma factor that regulates the transcription of dozens of genes in response to diverse stress conditions and is required for maintenance of chronic infection in a mouse model. A putative ATP-binding cassette transporter operon, bab1_0223-bab1_0226 , is among the most highly activated gene sets in the σ E1 regulon. The proteins encoded by the operon resemble quaternary ammonium-compatible solute importers but are most similar in sequence to the broadly conserved YehZYXW system, which remains largely uncharacterized. Transcription of yehZYXW is activated by the general stress sigma factor σ S in Enterobacteriaceae , which suggests a functional role for this transport system in bacterial stress response across the classes Alphaproteobacteria and Gammaproteobacteria . We present evidence that B. abortus YehZYXW does not function as an importer of known compatible solutes under physiological conditions and does not contribute to the virulence defect of a σ E1 -null strain. The sole in vitro phenotype associated with genetic disruption of this putative transport system is reduced growth in the presence of high Li + ion concentrations. A crystal structure of B. abortus YehZ revealed a class II periplasmic binding protein fold with significant structural homology to Archaeoglobus fulgidus ProX, which binds glycine betaine. However, the structure of the YehZ ligand-binding pocket is incompatible with high-affinity binding to glycine betaine. This is consistent with weak measured binding of YehZ to glycine betaine and related compatible solutes. We conclude that YehZYXW is a conserved, stress-regulated transport system that is phylogenetically and functionally distinct from quaternary ammonium-compatible solute importers. IMPORTANCE Brucella abortus σ E1 regulates transcription in response to stressors encountered in its mammalian host and is necessary for maintenance of chronic infection in a mouse model. The functions of the majority of genes regulated by σ E1 remain undefined. We present a functional/structural analysis of a conserved putative membrane transport system (YehZYXW) whose expression is strongly activated by σ E1 . Though annotated as a quaternary ammonium osmolyte uptake system, experimental physiological studies and measured ligand-binding properties of the periplasmic binding protein (PBP), YehZ, are inconsistent with this function. A crystal structure of B. abortus YehZ provides molecular insight into differences between bona fide quaternary ammonium osmolyte importers and YehZ-related proteins, which form a distinct phylogenetic and functional group of PBPs.
A Study on Korea Experience in Regulating the Transport of Low and Intermediate-level Radioactive Wastes - 17182
In the Republic of Korea, the transport of Low and Intermediate-Level Radioactive Wastes (LILW) from nuclear power plants (NPP), nuclear research reactor, and radioactive isotope storage facility to Gyeongju LILW disposal facility has increased since the operation license of facility was approved in December 2014. As a result, there has been an increase in public anxiety and concerns over damage or social disorder with LILW transport. So the necessity of strengthened safety confirmation on LILW has been constantly raised. In August 2016, the Enforcement Regulations of the Nuclear Safety Act were amended in relation to the reporting and inspection of LILW transport. The first section of this paper describes the domestic transport regulations including the recently revised contents. The second section shows that the status of domestic and inspection of LILW transport were introduced and transportation regulatory experience was shared in Korea. (authors)
Path of Disposal for Hazardous and Non-hazardous Waste from Cradle to Grave
Hazardous waste is a threat to human health and the environment and must be managed and disposed of properly. A Solid Waste is defined as any material (solid, liquid, containerized gas) which has been discarded, abandoned (no longer needed), or recycled. The Resource Conservation Recovery Act (RCRA) is a law that creates the framework for the proper management of solid waste. Under RCRA, EPA has developed a program which ensures hazardous waste is managed safely from the moment it is generated to its final disposal (cradle-to-grave)2. To educate about how waste is handled at the Savannah River Research Campus (SRRC) under RCRA, the path it takes from point of generation (cradle) to disposal (grave), and the responsibilities of every person involved in the process. Researcher or other laboratory personnel that generates waste as a result of their work Responsibilities: - Fill out inventory log sheet and corresponding container sheet which includes the constituents of the waste; - Properly label waste container with SAA/WSA ID no., generator's name, what it is, the hazards, and date; - Place waste in designated waste storage area. Laboratory Custodian Responsibilities: - Ensures waste is handled and stored properly; - Ensures inventory is updated; - Ensures all container sheets are completed; - Ensures only authorized personal have access to waste storage areas. Environmental Compliance Authority Responsibilities: - Develops waste procedures; - Provide waste training; - Inspects for improperly handled waste; - Establishes or closes waste storage areas as needed; - Determines if waste can be recycled; - Determines if waste is RCRA hazardous: Is it U or P listed? - Unused commercial chemical products; Is it F listed - Spent solvents; Is it characteristic? - Flammable/Oxidizer, Corrosive, Reactive, Toxic; - Weighs waste to ensure laboratory has not exceeded its monthly or total storage limits; - Maintains waste records; - Determines how waste should be disposed: Trash - Nonhazardous solids; Drain - Nonhazardous Liquids; Labpack; - Prepares waste for shipment with Vendor and Department of Transportation (DOT) personnel. Packages, Transports, and Treats Hazardous Waste Responsibilities: - Must be EPA permitted and approved by the Department of Energy - Picks up hazardous waste for transport to a treatment, storage or disposal facility depending on waste disposal requirements - Must meet all Department of Transportation regulations for transporting hazardous waste - Dispose of waste according to RCRA regulations. Due to the potential risks to human health and the environment, waste must be handled safely through the chain of possession from cradle to grave. To ensure proper handling, there are many safety checks as required by RCRA and DOT regulations. This includes proper labeling, inventory, and characterization to ensure all hazards are known, inspections by the Custodian, ECA, and the state regulator (SCDHEC), and transportation verifications and manifesting. One of the best ways to reduce the risks that waste presents is to minimize or eliminate the creation of waste. This can be accomplished through source reduction which includes: Inventory control, material substitution, process modification, improved housekeeping, and preventative maintenance and recycling.
Transport of French PWR steam generators to very low level waste disposal - 15203
When considering the complexity of IAEA nuclear transport regulations, the transport of a Steam Generator (SG) in one un-packaged block from a dismantling plant to a nuclear waste disposal is a challenge. The choices made, the difficulties encountered and the feedback that has been learnt from it are described. The disposal of decommissioning waste requires taking into account not only the constraints of acceptance of the repository but also the specific constraints of transportation from the dismantling plant to the final disposal site. In France, these criteria and regulations are respectively under the supervision of the French National Radioactive Waste Management Agency (ANDRA) and the French Nuclear Safety Authority (ASN). In the course of the dismantling of the EDF PWR plant Chooz A, the four decontaminated SGs were shipped to the ANDRA Very Low Level Waste (VLLW) repository. After removal, the SGs were decontaminated, allowing them to attain the criteria of VLLW and thus be accepted by the ANDRA. However, to transport these decontaminated SGs as single un-packaged blocks, it was necessary to ensure compliance with the Surface Contaminated Object SCO-I regulation criteria. For this, transport safety files were written and surface contamination and radiation criteria checked. One of the four SGs had to be decontaminated again and another one had to be transported under special arrangement. Due to the exceptional nature of the transportation, specialized means of transport and stowage were also studied. (authors)
Redundant roles of four ZIP family members in zinc homeostasis and seed development in Arabidopsis thaliana
Zinc (Zn) is essential for normal plant growth and development. The Zn-regulated transporter, iron-regulated transporter (IRT)-like protein (ZIP) family members are involved in Zn transport and cellular Zn homeostasis throughout the domains of life. In this study, we have characterized four ZIP transporters from Arabidopsis thaliana (IRT3, ZIP4, ZIP6, and ZIP9) to better understand their functional roles. The four ZIP proteins can restore the growth defect of a yeast Zn uptake mutant and are upregulated under Zn deficiency. Single and double mutants show no phenotypes under Zn-sufficient or Zn-limited growth conditions. In contrast, triple and quadruple mutants show impaired growth irrespective of external Zn supply due to reduced Zn translocation from root to shoot. All four ZIP genes are highly expressed during seed development, and siliques from all single and higher-order mutants exhibited an increased number of abnormal seeds and decreased Zn levels in mature seeds relative to wild type. The seed phenotypes could be reversed by supplementing the soil with Zn. Finally, our data demonstrate that IRT3, ZIP4, ZIP6, and ZIP9 function redundantly in maintaining Zn homeostasis and seed development in A. thaliana.
The Arabidopsis ATP-BINDING CASSETTE Transporter ABCB21 Regulates Auxin Levels in Cotyledons, the Root Pericycle, and Leaves
The phytohormone auxin plays significant roles in regulating plant growth and development. In Arabidopsis, a subset of ATP-BINDING CASSETTE subfamily B (ABCB) transporters participate in polar movement of auxin by exclusion from and prevention of reuptake at the plasma membrane. A previous analysis identified ABCB21 as a conditional auxin uptake/efflux transporter that regulates cellular auxin levels, but clear physiological roles for ABCB21 in planta remain unknown. Here we show that ABCB21 maintains the acropetal auxin transport stream by regulating auxin levels in the pericycle. Loss of ABCB21 reduces rootward auxin transport and delays lateral root emergence. In seedling shoots, ABCB21 regulates mobilization of auxin from the photosynthetic cotyledons that is important for phototropic bending. In rosette leaves ABCB21 contributes to lateral auxin distribution. These results support a primary role for ABCB21 in regulating auxin distribution supplementary to the primary ABCB auxin transporters ABCB1 and 19.
Tradable credits system design and cost savings for a national low carbon fuel standard for road transport
This research examines the economic implications of different designs for a national low carbon fuel standard (NLCFS) for the road transportation sector. A NLCFS based on the average Carbon Intensity (CI) of all fuels sold in the gasoline and diesel markets will generate an incentive for fuel suppliers to reduce the measured CI of their petroleum fuels. The economic impacts of a NLCFS are fundamentally determined by: the availability of low carbon fuels; the compliance path; the reference level CI of the fuel baseline; and the degree of flexibility in the credit system. To quantitatively examine the implications of a NLCFS, we created the Transportation Regulation and Credit Trading (TRACT) Model. With TRACT, we model a NLCFS credit trading system among profit maximizing fuel suppliers for light- and heavy-duty vehicle fuel use for the United States from 2012 - 2030. Given the wide range of cost and availability of biofuels, we find that credit trading across gasoline and diesel fuel markets combined with credit banking can significantly reduce compliance costs and stabilize credit prices. We make policy recommendations on how to combine a NLCFS with other existing regulations for transportation fuels.
Alisol B 23-acetate protects against ANIT-induced hepatotoxity and cholestasis, due to FXR-mediated regulation of transporters and enzymes involved in bile acid homeostasis
Intrahepatic cholestasis is a clinical syndrome with systemic and intrahepatic accumulation of excessive toxic bile acids that ultimately cause hepatobiliary injury. Appropriate regulation of bile acids in hepatocytes is critically important for protection against liver injury. In the present study, we characterized the protective effect of alisol B 23-acetate (AB23A), a natural triterpenoid, on alpha-naphthylisothiocyanate (ANIT)-induced liver injury and intrahepatic cholestasis in mice and further elucidated the mechanisms in vivo and in vitro. AB23A treatment dose-dependently protected against liver injury induced by ANIT through reducing hepatic uptake and increasing efflux of bile acid via down-regulation of hepatic uptake transporters (Ntcp) and up-regulation of efflux transporter (Bsep, Mrp2 and Mdr2) expression. Furthermore, AB23A reduced bile acid synthesis through repressing Cyp7a1 and Cyp8b1, increased bile acid conjugation through inducing Bal, Baat and bile acid metabolism through an induction in gene expression of Sult2a1. We further demonstrate the involvement of farnesoid X receptor (FXR) in the hepatoprotective effect of AB23A. The changes in transporters and enzymes, as well as ameliorative liver histology in AB23A-treated mice were abrogated by FXR antagonist guggulsterone in vivo. In vitro evidences also directly demonstrated the effect of AB23A on FXR activation in a dose-dependent manner using luciferase reporter assay in HepG2 cells. In conclusion, AB23A produces protective effect against ANIT-induced hepatotoxity and cholestasis, due to FXR-mediated regulation of transporters and enzymes. - Highlights: • AB23A has at least three roles in protection against ANIT-induced liver injury. • AB23A decreases Ntcp, and increases Bsep, Mrp2 and Mdr2 expression. • AB23A represses Cyp7a1 and Cyp8b1 through inducing Shp and Fgf15 expression. • AB23A increases bile acid metabolism through inducing Sult2a1 expression. • FXR activation is involved in the hepatoprotective effect of AB23A.
Regulatory Design for Transport Security Regulations of Nuclear and Other Radioactive Material
A cornerstone within a nuclear security regime of a country is a legislative and regulatory framework that both regulates the individuals using radioactive and nuclear materials, but also regulates the regulators for their commitments under International Law. When drafting nuclear law and regulations, both technical and legal expertise is needed to ensure the regulation meets the technical requirements for security, but also is legally enforceable within a country’s jurisdiction. While the Primary Nuclear Law, or Enabling Act provides establishes the Competent Authority and responsibilities for nuclear security, regulatory development is where the proverbial, rubber meets the road for requirements. The regulations provide instruction for inspections, authorizations, and managed activities, such as use storage, and transport. Transport Security regulatory development for radioactive and nuclear material is complex because the regulation maybe multi-jurisdictional, multi-modal, and involve multiple stakeholders. Development of transport security regulations requires coordination with other ministerial stakeholders, transport operators, and alignment to international treaties and conventions outside the nuclear domain. This paper provides a brief discussion of the challenges associated with regulatory development for transport security regulations for nuclear and other radioactive materials in transport. The paper will briefly identify key stakeholders, international law involved, and current efforts by the International Atomic Energy Agency (IAEA) in supporting Member States in regulatory development. While active in that regulations are necessary for a robust nuclear security regime, regulatory development is more a slow-burn than an active activity in nuclear security.
Maximizing the habitat restoration potential of controlled releases at hydropower dams; Understanding impacts of hydrograph form on sediment transport
Regulation of streamflow for hydropower often alters natural hydrographs, commonly reducing peak flows, increasing baseflows, and increasing ramping rates. Simultaneously, reservoirs typically trap sediment, reducing the supply to the reach downstream of the dam. These changes to the flow regime and sediment supply impact channel morphology and sediment transport processes in ways that reduce the diversity and suitability of instream habitat. A variety of restoration approaches have attempted to mitigate for some of these changes and a growing number include releases of high flows designed to mimic key characteristics of the pre-regulation hydrograph. One example is the Trinity River, CA, where the addition of augmentation gravel to the channel has been combined with high flows designed to restore portions of the pre-regulation hydrograph to improve channel conditions for spawning fish on the Trinity River, CA. Another example is the high-flow experiments on the Colorado River through the Grand Canyon that aim to restore eroding sand bars that not only provide habitat but camping for rafting groups. More projects that restore portions of the pre-regulation hydrograph are likely in the future because the Federal Energy Regulatory Commission (FERC) requires habitat mitigation efforts in the relicensing process for hydropower facilities. However, the outcomes of these costly restoration efforts are often hard to predict because little is known about how hydrograph form actually impacts channel morphology and bedload transport in rivers. Here we summarize the results of two flume experiments designed to investigate the impacts of hydrograph form on the morphology of a channel bar and bedload transport processes. The first experiment primarily investigated the impacts of hydrograph recession rate on the morphology of a channel-bar in a sand bed channel. Additional runs examined the combined effects of hydrograph recession and a dense patch of vegetation on bar form. The second flume experiment investigated bedload transport processes in an armored, gravel bed channel during hydrographs with varying form. It documented total bedload flux for a hydrograph, bedload flux rates, persistence of the coarse armor surface, and changes in bed surface structure. Both experiments observed links between hydrograph form and the resulting bar morphology or bedload transport processes, providing insight into ways that high flow hydrographs can be designed to better facilitate restoration goals downstream of hydropower facilities.