25 research outputs found
In Situ Immobilization of Uranium in Structured Porous Media via Biomineralization at the Fracture/Matrix Interface – Subproject to Co-PI Eric E. Roden
No full textAlthough the biogeochemical processes underlying in situ bioremediation technologies are increasingly well understood, field-scale heterogeneity (both physical and biogeochemical) remains a major obstacle to successful field-scale implementation. In particular, slow release of contamination from low-permeability regions (primarily by diffusive/dispersive mass transfer) can hinder the effectiveness of remediation. The research described in this report was conducted in conjunction with a project entitled “In Situ Immobilization of Uranium in Structured Porous Media via Biomineralization at the Fracture/Matrix Interface”, which was funded through the Field Research element of the former NABIR Program (now the Environmental Remediation Sciences Program) within the Office of Biological and Environmental Research. Dr. Timothy Scheibe (Pacific Northwest National Laboratory) was the overall PI/PD for the project, which included Scott Brooks (Oak Ridge National Laboratory) and Eric Roden (formerly at The University of Alabama, now at the University of Wisconsin) as separately-funded co-PIs. The overall goal of the project was to evaluate strategies that target bioremediation at interfaces between high- and low-permeability regions of an aquifer in order to minimize the rate of contaminant transfer into high-permeability/high fluid flow zones. The research was conducted at the Area 2 site of the Field Research Center (FRC) at Oak Ridge National Laboratory (ORNL). Area 2 is a shallow pathway for migration of contaminated groundwater to seeps in the upper reach of Bear Creek at ORNL, mainly through a ca. 1 m thick layer of gravel located 4-5 m below the ground surface. Hydrological tracer studies indicate that the gravel layer receives input of uranium from both upstream sources and from diffusive mass transfer out of highly contaminated fill and saprolite materials above and below the gravel layer. We sought to test the hypothesis that injection of electron donor into this layer would induce formation of a redox barrier in the less conductive materials above and below the gravel, resulting in decreased mass transfer of uranium out these materials and attendant declines in groundwater U(VI) concentration. Details regarding the planning, execution, and results of the in situ biostimulation experiment will be provided in separate peer-reviewed publications by the project PIs and colleagues. This report summarizes research activities conducted at The University of Alabama (2002-2005) and the University of Wisconsin (2005-2007) in support of the field experiment, which included (1) chemical and microbiological characterization of sediment cores from Area 2; (2) sediment slurry experiments with Area 2 materials which evaluated the biogeochemical response to ethanol amendment and the potential for U(VI) reduction; (3) analysis of the response of groundwater microbial communities to in situ biostimulation. In addition, biogeochemical reaction models of microbial metabolism in ethanol-stimulated sediments, developed based on sediment slurry experiments, are described
Suboxic Deposition of Ferric Iron by Bacteria in Opposing Gradients of Fe(II) and Oxygen at Circumneutral pH
No full textAuthor Accepted ManuscriptThe influence of lithotrophic Fe(II)-oxidizing bacteria on patterns of ferric oxide deposition in opposing gradients of Fe(II) and O(2) was examined at submillimeter resolution by use of an O(2) microelectrode and diffusion microprobes for iron. In cultures inoculated with lithotrophic Fe(II)-oxidizing bacteria, the majority of Fe(III) deposition occurred below the depth of O(2) penetration. In contrast, Fe(III) deposition in abiotic control cultures occurred entirely within the aerobic zone. The diffusion microprobes revealed the formation of soluble or colloidal Fe(III) compounds during biological Fe(II) oxidation. The presence of mobile Fe(III) in diffusion probes from live cultures was verified by washing the probes in anoxic water, which removed ca. 70% of the Fe(III) content of probes from live cultures but did not alter the Fe(III) content of probes from abiotic controls. Measurements of the amount of Fe(III) oxide deposited in the medium versus the probes indicated that ca. 90% of the Fe(III) deposited in live cultures was formed biologically. Our findings show that bacterial Fe(II) oxidation is likely to generate reactive Fe(III) compounds that can be immediately available for use as electron acceptors for anaerobic respiration and that biological Fe(II) oxidation may thereby promote rapid microscale Fe redox cycling at aerobic-anaerobic interfaces.This research was supported by grants from the National Science Foundation (DEB 94-7233), the U.S. Department of Energy, Office of Energy Research, Environmental Management Science Program (DE-FG07-96ER62321), and the School of Mines and Energy Development, University of Alabama
Author Correction: Transcript expression-aware annotation improves rare variant interpretation
No full textIn this Article, author Marquis P. Vawter was missing from the Genome Aggregation Database Consortium list. They are associated with the affiliation: ‘Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, CA, USA’, and contributed to the generation of the primary data incorporated into the gnomAD resource. The original Article has been corrected online
Author Correction: The mutational constraint spectrum quantified from variation in 141,456 humanS
No full textIn this Article, author Marquis P. Vawter was missing from the Genome Aggregation Database Consortium list. They are associated with the affiliation: ‘Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, CA, USA’, and contributed to the generation of the primary data incorporated into the gnomAD resource. In addition, in the legend to Fig. 1, ‘ten’ should have been ‘seven’ in the sentence: “a, Uniform manifold approximation and projection (UMAP)46,47 plot depicting the ancestral diversity of all individuals in gnomAD, using seven principal components.” The original Article has been corrected online
FXR1 splicing is important for muscle development and biomolecular condensates in muscle cells
No full text© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Smith, J. A., Curry, E. G., Blue, R. E., Roden, C., Dundon, S. E. R., Rodríguez-Vargas, A., Jordan, D. C., Chen, X., Lyons, S. M., Crutchley, J., Anderson, P., Horb, M. E., Gladfelter, A. S., & Giudice, J. FXR1 splicing is important for muscle development and biomolecular condensates in muscle cells. Journal of Cell Biology, 219(4), (2020): e201911129, doi: 10.1083/jcb.201911129.Fragile-X mental retardation autosomal homologue-1 (FXR1) is a muscle-enriched RNA-binding protein. FXR1 depletion is perinatally lethal in mice, Xenopus, and zebrafish; however, the mechanisms driving these phenotypes remain unclear. The FXR1 gene undergoes alternative splicing, producing multiple protein isoforms and mis-splicing has been implicated in disease. Furthermore, mutations that cause frameshifts in muscle-specific isoforms result in congenital multi-minicore myopathy. We observed that FXR1 alternative splicing is pronounced in the serine- and arginine-rich intrinsically disordered domain; these domains are known to promote biomolecular condensation. Here, we show that tissue-specific splicing of fxr1 is required for Xenopus development and alters the disordered domain of FXR1. FXR1 isoforms vary in the formation of RNA-dependent biomolecular condensates in cells and in vitro. This work shows that regulation of tissue-specific splicing can influence FXR1 condensates in muscle development and how mis-splicing promotes disease.We thank the A.S. Gladfelter and J. Giudice laboratories, Nancy Kedersha, and Silvia Ramos for critical discussions; Eunice Y. Lee for technical help; Dr. Stephanie Gupton (University of North Carolina at Chapel Hill, Chapel Hill, NC) for donation of WT C57BL/6J mouse embryos; and Marcin Wlizla and National Xenopus Resource (RRID:SCR_013731) for their help in maintaining adult frogs and other important technical support.
This work has been funded by a University of North Carolina at Chapel Hill Junior Faculty Development Award (to J. Giudice); a Nutrition and Obesity Research Center, University of North Carolina at Chapel Hill, Pilot & Feasibility Research grant (P30DK056350 to J. Giudice); University of North Carolina at Chapel Hill startup funds (to J. Giudice); the March of Dimes Foundation (5-FY18-36, Basil O’Connor Starter Scholar Award to J. Giudice); and NCTraCs Pilot Grant (550KR181805) from the National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, through Grant Award Number UL1TR002489 (to J. Giudice), National Institutes of Health National Institute of General Medical Sciences grants (R01-GM130866 to J. Giudice, R01-GM081506 to A.S. Gladfelter, R35-GM126901 to P. Anderson, K99-GM124458 to S.M. Lyons, R25-GM089569 and 2R25-GM055336-20 to E.G. Curry); Howard Hughes Medical Institute Faculty Scholars program (A.S. Gladfelter), and National Institute of Health grants R01-HD084409 and P40-OD010997 (to M.E. Horb). The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies.2020-09-1
Coupled dynamics of iron and iron-bound organic carbon in forest soils during anaerobic reduction
No full textThe behavior of iron (Fe)-bound organic carbon (DC) under anoxic conditions in natural soils and sediments represents a critical knowledge gap for understanding the biogeochemical cycles of OC and Fe. In this study, we investigated the dynamics of Fe and OC in four forest soils in the presence of the dissimilatory Fe-reducing bacterium, Shewanella oneidensis MR-1. Over an 8-day reduction period, 3.8-9.9% of total OC was released to solution in conjunction with the reduction of 12.5-37.7% of reactive Fe. The fraction of OC released was correlated with the fraction of Fe reduced, indicating that the reductive release was the controlling factor for the mobilization of OC upon the anaerobic microbial reaction. During the reduction, the fractions of poorly crystalline Fe oxides decreased, coupling with an increase in the relative abundance of crystalline Fe oxides. Lability of OC (as reflected by water-extractable OC content) increased after microbial reduction, indicating the decreased stability of OC because of changes in mineral-OC interactions and the conformation of mineral-OC complexes. The reduction of Fe was closely related to bulk soil electron accepting capacity (0.15-034 mmol e(-)/mol C). Our findings demonstrate that the redox reactions of Fe, modified by the redox reactivity of OC, play an important role in regulating the stability and transformation of OC. (C) 2016 Elsevier B.V. All rights reserved.University of Nevada-Reno Startup fund; DOE [DE-SC0014275]; USDA [2015-67018-23120]; Georgia Institute of Technology; American Chemical Society Petroleum Research Fund [54143-DNI5]; National Science Foundation [CHE-1429768]CPCI-S(ISTP)118-12646
genotypes and Statin‐Associated Musculoskeletal Symptoms
No full textPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/172334/1/cpt2557.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/172334/2/cpt2557_am.pd
Erratum to:A multi-stage genome-wide association study of uterine fibroids in African Americans
No full textThe article “A multi-stage genome-wide association study of uterine fibroids in African Americans”, written by Jacklyn N. Hellwege, was originally published Online First without open access. After publication in volume 136, issue 10, page 1363–1373 the author decided to opt for Open Choice and to make the article an open access publication. Therefore, the copyright of the article has been changed to</p
Author Correction: Inherited causes of clonal haematopoiesis in 97,691 whole genomes
No full textA Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03280-1
