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Oxidation of NH3 to N2 by pentapyridyl metal complexes via hydrogen atom abstraction was investigated computationally. Quantum chemical analysis reveals insights on orbital symmetry requirements for efficient NH3 oxidation. The most promising complex, [(PY5)Mo(NH3)]2+, was studied experimentally. It shows conversion of NH3 to N2 upon treatment with 2,4,6-tri-tertbutylphenoxyl radical.
The plant-specific translation initiation complex eIFiso4F is encoded by three genes in Arabidopsis ( Arabidopsis thaliana )—genes encoding the cap binding protein eIFiso4E ( eifiso4e ) and two isoforms of the large subunit scaffolding protein eIFiso4G ( i4g1 and i4g2 ). To quantitate phenotypic changes, a phenomics platform was used to grow wild-type and mutant plants ( i4g1 , i4g2 , i4e , i4g1 x i4g2 , and i4g1 x i4g2 x i4e [ i4f ]) under various light conditions. Mutants lacking both eIFiso4G isoforms showed the most obvious phenotypic differences from the wild type. Two-dimensional differential gel electrophoresis and mass spectrometry were used to identify changes in protein levels in plants lacking eIFiso4G. Four of the proteins identified as measurably decreased and validated by immunoblot analysis were two light harvesting complex binding proteins 1 and 3, Rubisco activase, and carbonic anhydrase. The observed decreased levels for these proteins were not the direct result of decreased transcription or protein instability. Chlorophyll fluorescence induction experiments indicated altered quinone reduction kinetics for the double and triple mutant plants with significant differences observed for absorbance, trapping, and electron transport. Transmission electron microscopy analysis of the chloroplasts in mutant plants showed impaired grana stacking and increased accumulation of starch granules consistent with some chloroplast proteins being decreased. Rescue of the i4g1 x i4g2 plant growth phenotype and increased expression of the validated proteins to wild-type levels was obtained by overexpression of eIFiso4G1. These data suggest a direct and specialized role for eIFiso4G in the synthesis of a subset of plant proteins.
Highlights: • On-site biocovers were evaluated to mitigate odors at a Korean sanitary landfill. • The biocover systems achieved above 80% removal of complex odor. • Removal efficiency of sulfur odor as significant contributor was greater than 90%. • The most abundant bacteria had little correlation with odor removability. • Bacteria increased in relative abundance contributed highly to odor removal. Unpleasant odors emitted from landfills have been caused environmental and societal problems. For odor abatement, two pilot-scale biocovers were installed at a sanitary landfill site in South Korea. Biocovers PBC1 and PBC2 comprised a soil mixture with different ratios of earthworm casts as an inoculum source and were operated for 240 days. Their odor removal efficiencies were evaluated, and their bacterial community structures were characterized using pyrosequencing. In addition, the correlation between odor removability and bacterial community dynamics was assessed using network analysis. The removal efficiency of complex odor intensity in the two biocovers ranged from 81.1% to 97.8%. Removal efficiencies of sulfur-containing odors (hydrogen sulfide, methanethiol, dimethyl sulfide, and dimethyl disulfide), which contributed most to complex odor intensity, were greater than 91% in both biocovers. Despite the fluctuations in ambient temperature (−8.2 to 31.3 °C) and inlet complex odor intensity (10,000–42,748 of odor dilution ratio), biocovers PBC1 and PBC2 displayed stable deodorizing performance. A high ratio of earthworm casts as an inoculum source led to high odor removability during the first 25 days of operation, but different mixing ratios of earthworm casts did not significantly affect overall odor removability. A bacterial community analysis showed that Methylobacter, Arthrobacter, Acinetobacter, Rhodanobacter, and Pedobacter were the dominant genera in both biocovers. Network analysis results indicated that Steroidobacter, Cystobacter, Methylosarcina, Solirubrobacter, and Pseudoxanthomonas increased in relative abundance with time and were major contributors to odor removal, although these bacteria had a relatively low abundance compared to the overall bacterial community. These data contribute to a more comprehensive understanding of the relationship between bacterial community dynamics and deodorizing performance in biocovers.
The rhizosphere microbiome plays a crucial role in supporting plant productivity and ecosystem functioning by regulating nutrient cycling, soil integrity, and carbon storage. However, deciphering the intricate interplay between microbial relationships within the rhizosphere is challenging due to the overwhelming taxonomic and functional diversity. Here we present our systematic design framework built on microbial colocalization and microbial interaction, toward successful assembly of multiple rhizosphere-derived Reduced Complexity Consortia (RCC). We enriched co-localized microbes from Brachypodium roots grown in field soil with carbon substrates mimicking Brachypodium root exudates, generating 768 enrichments. By transferring the enrichments every 3 or 7 days for 10 generations, we developed both fast and slow-growing reduced complexity microbial communities. Most carbon substrates led to highly stable RCC just after a few transfers. 16S rRNA gene amplicon analysis revealed distinct community compositions based on inoculum and carbon source, with complex carbon enriching slow growing yet functionally important soil taxa like Acidobacteria and Verrucomicrobia. Network analysis showed that microbial consortia, whether differentiated by growth rate (fast vs. slow) or by succession (across generations), had significantly different network centralities. Besides, the keystone taxa identified within these networks belong to genera with plant growth-promoting traits, underscoring their critical function in shaping rhizospheric microbiome networks. Furthermore, tested consortia demonstrated high stability and reproducibility, assuring successful revival from glycerol stocks for long-term viability and use. Our study represents a significant step toward developing a framework for assembling rhizosphere consortia based on microbial colocalization and interaction, with future implications for sustainable agriculture and environmental management.
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Severe malarial anemia (SMA, Hb < 6.0 g/dL) is a leading cause of childhood morbidity and mortality in holoendemic Plasmodium falciparum transmission zones. This study explored the entire expressed human transcriptome in whole blood from 66 Kenyan children with non-SMA (Hb ≥ 6.0 g/dL, n = 41) and SMA (n = 25), focusing on host immune response networks. RNA-seq analysis revealed 6862 differentially expressed genes, with equally distributed up-and down-regulated genes, indicating a complex host immune response. Deconvolution analyses uncovered leukocytic immune profiles indicative of a diminished antigenic response, reduced immune priming, and polarization toward cellular repair in SMA. Weighted gene co-expression network analysis revealed that immune-regulated processes are central molecular distinctions between non-SMA and SMA. A top dysregulated immune response signaling network in SMA was the HSP60-HSP70-TLR2/4 signaling pathway, indicating altered pathogen recognition, innate immune activation, stress responses, and antigen recognition. Validation with high-throughput gene expression from a separate cohort of Kenyan children (n = 50) with varying severities of malarial anemia (n = 38 non-SMA and n = 12 SMA) confirmed the RNA-seq findings. Proteomic analyses in 35 children with matched transcript and protein abundance (n = 19 non-SMA and n = 16 SMA) confirmed dysregulation in the HSP60-HSP70-TLR2/4 signaling pathway. Additionally, glutamine transporter and glutamine synthetase genes were differentially expressed, indicating altered glutamine metabolism in SMA. This comprehensive analysis underscores complex immune dysregulation and novel pathogenic features in SMA.
The XGAM spectrum-fitting code and associated software were developed specifically to analyze the complex gamma-ray spectra that can result from neutron-induced reactions. The XGAM code is designed to fit a spectrum over the entire available gamma-ray energy range as a single entity, in contrast to the more traditional piecewise approaches. This global-fit philosophy enforces background continuity as well as consistency between local and global behavior throughout the spectrum, and in a natural way. This report presents XGAM and the suite of programs built around it with an emphasis on how they fit into an overall analysis methodology for complex gamma-ray data. An application to the analysis of time-dependent delayed gamma-ray yields from 235 U fission is shown in order to showcase the codes and how they interact.
The geometric constraints imposed by a tetradentate P4N2 ligand play an essential role in stabilizing square planar Fe complexes with changes in metal oxidation state. A combination of high-pressure electrochemistry and variable temperature UV-vis spectroscopy were used to obtain these thermodynamic measurements, while X-ray crystallography, 57Fe Mössbauer spectroscopy, and EPR spectroscopy were used to fully characterize these new compounds. Analysis of Fe0, FeI, and FeII complexes reveals that the free energy of N2 binding across three oxidation states spans more than 37 kcal mol-1. The square pyramidal Fe0(N2)(P4N2) complex catalyzes the conversion of N2 to N(SiR3)3 (R = Me, Et) at room temperature, representing the highest turnover number (TON) of any Fe-based N2 silylation catalyst to date (up to 65 equiv N(SiMe3)3 per Fe center). Elevated N2 pressures (> 1 atm) have a dramatic effect on catalysis, increasing N2 solubility and the thermodynamic N2 binding affinity at Fe0(N2)(P4N2). Acknowledgment. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences. EPR experiments were performed using EMSL, a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for the U.S. DOE. Computational resources were provided by the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. The authors thank Prof. Yisong Alex Guo at Carnegie Mellon University for recording Mössbauer data for some complexes and Emma Wellington and Kaye Kuphal for their assistance with the collection of Mössbauer data at Colgate University, Dr. Katarzyna Grubel for X-ray assistance, and Dr. Rosalie Chu for mass spectrometry assistance. The authors also thank Dr. Aaron Appel and Dr. Alex Kendall for helpful discussions.
Copper is a part of various enzymes and helps them to function properly. It can be effectively used to produce promising anticancer drugs and presently, many studies are being pursued worldwide on the development of copper-based complexes as potential anticancer drugs. Herein, we briefly discuss the importance of reactive oxygen species in biological applications and copper(II) complexes as anticancer drugs. The anti-angiogenic properties of mono-nuclear copper(II) complexes have been demonstrated by in vivo chick embryo angiogenesis analysis. The plausible mechanism behind anticancer activity of these complexes is by the formation of excessive intracellular Reactive Oxygen Species (ROS). ROS is a composite term used for oxygen derivative non-radicals and free radicals of highly reactive components, that enhances the killing response of immune cells to microbial invasion. Previous reports have shown that ROS plays an important role as a messenger in cell cycling and normal cell signal transduction. .
Activation of the oxo bond of uranyl, UO22+, was achieved by collision induced dissociation (CID) of UO2(N3)Cl2– in a quadrupole ion trap mass spectrometer. The gas phase complex UO2(N3)Cl2– was produced by electrospray ionization of solutions of UO2Cl2 and NaN3. CID of UO2(N3)Cl2– resulted in the loss of N2 to form UO(NO)Cl2–, in which the “inert” uranyl oxo bond has been activated. Formation of UO2Cl2– via N3 loss was also observed. Density functional theory computations predict that the UO(NO)Cl2– complex has nonplanar Cs symmetry and a singlet ground state. Analysis of the bonding of the UO(NO)Cl2– complex shows that the side-on bonded NO moiety can be considered as NO3–, suggesting a formal oxidation state of U(VI). Activation of the uranyl oxo bond in UO2(N3)Cl2– to form UO(NO)Cl2– and N2 was computed to be endothermic by 169 kJ/mol, which is energetically more favorable than formation of NUOCl2– and UO2Cl2–. The observation of UO2Cl2– during CID is most likely due to the absence of an energy barrier for neutral ligand loss.
The scientific opportunity offered by the combination of data from LSST, WFIRST and Euclid goes well beyond the science enabled by any one of the data sets alone. The range in wavelength, angular resolution and redshift coverage that these missions jointly span is remarkable. With major investments in LSST and WFIRST, and partnership with ESA in Euclid, the US has an outstanding scientific opportunity to carry out a combined analysis of these data sets. It is imperative for us to seize it and, together with our European colleagues, prepare for the defining cosmological pursuit of the 21st century. The main argument for conducting a single, high-quality reference co-analysis exercise and carefully documenting the results is the complexity and subtlety of systematics that define this co-analysis. Falling back on many small efforts by different teams in selected fields and for narrow goals will be inefficient, leading to significant duplication of effort.
VCAT is a knowledge modeling and analysis tool. It was synthesized from ideas in functional analysis, business process modeling, and complex network science. VCAT discovers synergies by analyzing natural language descriptions. Specifically, it creates visual analytic perspectives that capture intended organization structures, then overlays the serendipitous relationships that point to potential synergies within an organization or across multiple organizations.
We present VIMOS-Very Large Telescope (VLT) spectroscopy of the Frontier Fields cluster MACS J0416.1-2403 ( z = 0.397). Taken as part of the CLASH-VLT survey, the large spectroscopic campaign provided more than 4000 reliable redshifts over ∼600 arcmin{sup 2}, including ∼800 cluster member galaxies. The unprecedented sample of cluster members at this redshift allows us to perform a highly detailed dynamical and structural analysis of the cluster out to ∼2.2 r {sub 200} (∼4 Mpc). Our analysis of substructures reveals a complex system composed of a main massive cluster ( M {sub 200} ∼ 0.9 × 10{sup 15} M {sub ⊙} and σ{sub V,r200} ∼ 1000 km s{sup −1}) presenting two major features: (i) a bimodal velocity distribution, showing two central peaks separated by Δ V {sub rf} ∼ 1100 km s{sup −1} with comparable galaxy content and velocity dispersion, and (ii) a projected elongation of the main substructures along the NE–SW direction, with a prominent sub-clump ∼600 kpc SW of the center and an isolated BCG approximately halfway between the center and the SW clump. We also detect a low-mass structure at z ∼ 0.390, ∼10′ south of the cluster center, projected at ∼3 Mpc, with a relative line-of-sight velocity of Δ V{sub rf} ∼ −1700 km s{sup −1}. The cluster mass profile that we obtain through our dynamical analysis deviates significantly from the “universal” NFW, being best fit by a Softened Isothermal Sphere model instead. The mass profile measured from the galaxy dynamics is found to be in relatively good agreement with those obtained from strong and weak lensing, as well as with that from the X-rays, despite the clearly unrelaxed nature of the cluster. Our results reveal an overall complex dynamical state of this massive cluster and support the hypothesis that the two main subclusters are being observed in a pre-collisional phase, in agreement with recent findings from radio and deep X-ray data. In this article, we also release the entire redshift catalog of 4386 sources in the field of this cluster, which includes 60 identified Chandra X-ray sources and 105 JVLA radio sources.
So far, only a few of the interactions between the {approx}30 nucleoporins comprising the modular structure of the nuclear pore complex have been defined at atomic resolution. Here we report the crystal structure, at 2.6 {angstrom} resolution, of a heterotrimeric complex, composed of fragments of three cytoplasmically oriented nucleoporins of yeast: Nup82, Nup116, and Nup159. Our data show that the Nup82 fragment, representing more than the N-terminal half of the molecule, folds into an extensively decorated, seven-bladed {beta}-propeller that forms the centerpiece of this heterotrimeric complex and anchors both a C-terminal fragment of Nup116 and the C-terminal tail of Nup159. Binding between Nup116 and Nup82 is mutually reinforced via two loops, one emanating from the Nup82 {beta}-propeller and the other one from the {beta}-sandwich fold of Nup116, each contacting binding pockets in their counterparts. The Nup82-Nup159 interaction occurs through an amphipathic {alpha}-helix of Nup159, which is cradled in a large hydrophobic groove that is generated from several large surface decorations of the Nup82 {beta}-propeller. Although Nup159 and Nup116 fragments bind to the Nup82 {beta}-propeller in close vicinity, there are no direct contacts between them, consistent with the noncooperative binding that was detected biochemically. Extensive mutagenesis delineated hot-spot residues for these interactions. We also showed that the Nup82 {beta}-propeller binds to other yeast Nup116 family members, Nup145N, Nup100 and to the mammalian homolog, Nup98. Notably, each of the three nucleoporins contains additional nuclear pore complex binding sites, distinct from those that were defined here in the heterotrimeric Nup82 {center_dot} Nup159 {center_dot} Nup116 complex.
Management of soil biological resources to optimise plant production, efficiency of nutrient inputs, and system sustainability is an emerging opportunity for pastoral agriculture. To attain these goals, suitable tools that can assess the functional state of the soil ecosystem must be developed and standardised approaches to their application adopted. Towards this end, we have undertaken comprehensive, high-density functional-gene microarray analysis (GeoChip5) of environmental DNA (eDNA) extracted from 50 pastoral soils. When combined with soil, environmental and management metadata, the information can be used to provide insights into soil biological processes spanning greenhouse gas emissions, through to natural suppression of plant root diseases. To give an example of a structured workflow of analysis in a pastoral system context, we analysed the GeoChip data using a combination of approaches spanning routine univariate methods through to more complex multivariate and network-based analysis. Analyses were restricted to comparing effects of land-use (dairy or ‘other’ farming systems), and exploring relationships of the GeoChip data with the soil properties from each sample. These exemplar analyses introduce a pathway for the application of eDNA approaches (GeoChip or others) to deliver outcomes for pastoral agricultural in New Zealand.
Environmental management problems associated with contamination of groundwater resources with heavy metals (such as chromium) typically require complex biogeochemical model simulations and analysis of in situ remediation. Frequently, the in situ remediation is the only viable treatment option. In these cases, a three-dimensional reactive transport model of relevant biogeochemical processes is invaluable. Recently, we have developed a novel unique biogeochemical simulator called CHROTRAN (http://chrotran.lanl.gov; Hansen et al. 2017, Vesselinov et al. 2018a) capable to represent the full three-dimensional dynamics of processes associated with in situ biogeochemical remediation of heavy metals in heterogeneous aquifers. CHROTRAN accounts for spatial and temporal transients of (1) the heavy metal to be remediated, (2) introduced amendments (e.g., through well injection), and (3) biomass growth and decay. The introduced amendments can include (1) an electron donor (e.g., molasses), (2) a nontoxic-conservative bio-inhibitor (e.g., ethanol), and (3) a biocide (e.g., dithionite). In addition, direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled in CHROTRAN. Other critical processes, such as donor sorption, bio-fouling and biomass death are also modeled. CHROTRAN can simulate the groundwater flow dynamics introduced due a series of injection and extraction wells and account for reduction of aquifer permeability near the wells due bio clogging. CHROTRAN is based on the existing PFLOTRAN (http://pflotran.org; Lichtner et al, 2017a) code framework, taking advantage of the reaction interface allowing for implementation of complex model features and leverage other facets of PFLOTRAN, such as multi-component geochemistry and high-performance computing. Here, we present numerical simulations and model analyses related to the Los Alamos National Laboratory (LANL) chromium site. The analyses are performed by coupling of CHROTRAN with MADS (Model Analysis and Decision Support; http://mads.lanl.gov; Vesselinov et al., 2018b). We present analyses related to uncertainty quantification of model predictions, sensitivity of model parameters and remedial decision support. (authors)
Solvothermal reactions of Zn(NO{sub 3}){sub 2}·6H{sub 2}O with 3,6-bis(1-imidazolyl)carbazole (3,6-bmcz) and 1,4-benzenedicarboxylic acid (1,4-H{sub 2}bdc), p-phenylenediacetic acid (p-H{sub 2}pda), benzophenone-4,4-dicarboxylic acid (H{sub 2}bpda) afforded three coordination polymers [Zn(1,4-bdc)(3,6-bmcz)]{sub n} (1), {[Zn(p-pda)(3,6-bmcz)]·1.5H_2O}{sub n} (2) and {[Zn(bpda)(3,6-bmcz)]·0.25H_2O}{sub n} (3). Complexes 1–3 were characterized by elemental analysis, IR, powder X-ray diffraction, and single-crystal X-ray diffraction. Complex 1 shows 3D structure with 2D nets inclined polycatenation. Complexes 2 and 3 possess an extended 3D supramolecular architecture based on their respective 2D layers through hydrogen-bonding interactions and the π···π stacking interactions. The solid state luminescent and optical properties of 1–3 at ambient temperature were also investigated. A comparative study on their photocatalytic activity toward the degradation of methylene blue in polluted water was explored. - Graphical abstract: Reactions of Zn(NO{sub 3}){sub 2} and 3,6-(1-imidazolyl)carbazole with 1,4-benzenedicarboxylic acid, p-phenylenediacetic acid or benzophenone-4,4-dicarboxylic acid afforded three coordination polymers with different topologies and photocatalytic activity. - Highlights: • Reactions of 1,4-H{sub 2}bdc, p-H{sub 2}pda or H{sub 2}bpda with 3,6-bmcz and Zn(II) gave three CPs. • Complex 1 is a 3D entanglement. • Complex 2 or 3 is a 3D supramolecular structure based on different 2D layers. • Complex 2 exhibited good catalytic activity of methylene blue photodegradation.
In this study, the solution chemistry of a chelator developed for 227 Th targeted alpha therapy was probed. The compound of interest is an octadentate ligand comprising four N-methyl-3-hydroxy-pyridine-2-one metal-binding units, two tertiary amine groups, and one carboxylate arm appended for bioconjugation. The seven pK a values of the ligand and the stability constants of complexes formed with Th(IV), Hf(IV), Zr(IV), Gd(III), Eu(III), Al(III), and Fe(III) were determined. The ligand exhibits extreme thermodynamic selectivity toward tetravalent metal ions with a ca. 20 orders of magnitude difference between the formation constant of the Th(IV) species formed at physiological pH, namely [ThL] - , and that of its Eu(III) analogue. Likewise, log β 110 values of 41.7 ± 0.3 and 26.9 ± 0.3 (T = 25 °C) were measured for [ThL] - and [Fe III L] 2- , respectively, highlighting the high affinity and selectivity of the ligand for Th ions over potentially competing endogenous metals. Single crystal X-ray analysis of the Fe(III) complex revealed a dinuclear 2:2 metal:chelator complex crystallizing in the space group P1 - . The formation of this dimeric species is likely favored by several intramolecular hydrogen bonds and the protonation state of the chelator in acidic media. L III edge EXAFS data on the Th(IV) complexes of both the ligand and a monoclonal antibody conjugate revealed the expected mononuclear 1:1 metal:chelator coordination environment. This was also confirmed by high resolution mass spectrometry. Lastly, kinetic experiments demonstrated that labeling the bioconjugated ligand with Th(IV) could be achieved and completed after 1 h at room temperature, reinforcing the high suitability of this chelator for 227 Th targeted alpha therapy.