64 research outputs found
The distribution and history of nuclear weapons related contamination in sediments from the Ob River, Siberia as determined by isotopic ratios of Plutonium, Neptunium, and Cesium
Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2002This thesis addresses the sources and transport of nuclear weapons related
contamination in the Ob River region, Siberia. In addition to being one of the largest
rivers flowing into the Arctic Ocean, the bulk of the former Soviet Union's nuclear fuel
reprocessing and weapons testing facilities (i.e. Mayak, Tomsk-7, and Semipalitinsk) are
located within the Ob drainage basin. The atom ratios 240Pu/239Pu, 237Np/239Pu, and
13Cs/240Pu, measured by magnetic-sector ICP-MS, are used to distinguish between
contamination derived from global fallout and contamination derived from local sources.
Deposition chronologies estimated for sediment cores are used to construct a record of
weapons related contamination at the sites sampled. Contaminant records indicate that in
addition to debris from atmospheric weapons tests, materials derived from local sources
have also played a role in nuclear weapons related contamination of the Ob region.
Isotopic data presented in this study clearly demonstrate that non-fallout contamination
has been transported the full length of the Tobol, Irysh, and Ob Rivers (i.e. the tributaries
draining Mayak, Semipalitinsk, and Tomsk-7, respectively).
In several instances, unique isotopic compositions are observed in sediments
collected from tributaries draining each of the suspected non-fallout sources. In such
cases, these materials and their deposition ages have been used to link contamination in
the Ob delta to Mayak, Tomsk-7, or Semipalitinsk. Linear transport rate estimates (km
yr-1) indicate that contaminated sediments transit between source tributaries and the Ob
delta on time-scales of ≤ l year. These estimates suggest that a catastrophic release of
contamination due to dam failure at one of the many reservoirs located at both Mayak
and Tomsk-7 that contain high levels of radioactive waste would result in measurable
levels of contamination in the delta within as little as 1 year.
Isotopic concentrations in sequentially extracted sediments containing weapons
related contamination reveal that the majority of plutonium and neptunium (80 to 90
percent) behaves in a similar fashion regardless of the source and is removed by treating
the sediments with citrate-dithionite. This indicates that plutonium and neptunium are
not truly refractory and likely associate with redox sensitive sedimentary components.
Isotopic ratios measured in extracted fractions suggest that only a minor fraction of
contamination is associated with acid leachable or acid digestible sedimentary phases.Funding for this research was provided by the Office of Naval Research under
Grants N00014-93-1-1139, and NOOOI4-1-95), and the National Science Foundation
under Grant EAR-98-07590
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A history of vegetation, sediment and nutrient dynamics at Tivoli North Bay, Hudson Estuary, New York
We conduct a stratigraphic paleoecological investigation at a Hudson River National Estuarine Research Reserve (HRNERR) site, Tivoli Bays, spanning the past 1100 years. Marsh sediment cores were analyzed for ecosystem changes using multiple proxies, including pollen, spores, macrofossils, charcoal, sediment bulk chemistry, and stable carbon and nitrogen isotopes. The results reveal climatic shifts such as the warm and dry Medieval Warm Period (MWP) followed by the cooler Little Ice Age (LIA), along with significant anthropogenic influence on the watershed ecosystem. A five-fold expansion of invasive species, including Typha angustifolia and Phragmites australis, is documented along with marked changes in sediment composition and nutrient input. During the last century, a ten-fold sedimentation rate increase due to land-use changes is observed. The large magnitude of shifts in vegetation, sedimentation, and nutrients during the last few centuries suggest that human activities have made the greatest impact to the marshes of the Hudson Estuary during the last millennium. Climate variability and ecosystem changes similar to those observed at other marshes in northeastern and mid-Atlantic estuaries, attest to the widespread regional signature recorded at Tivoli Bays
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Integrative Acoustic Mapping Reveals Hudson River Sediment Processes and Habitats
Rivers and estuaries around the world are the focus of human settlements and activities. Needs for clean water, ecosystem preservation, commercial navigation, industrial development, and recreational access compete for the use of estuaries, and management of these resources requires a detailed understanding of estuarine morphology and sediment dynamics. This article presents an overview of the first estuary-wide study of a heavily used estuary, the Hudson River, based on high-resolution acoustic mapping of the river bottom. The integration of three high-resolution acoustic methods with extensive sampling reveals an unexpected complexity of bottom features and allows detailed classification of the benthic environment in terms of riverbed morphology, sediment type, and sedimentary processes
Ensuring confidence in radionuclide-based sediment chronologies and bioturbation rates
Author Posting. © The Author(s), 2006. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Estuarine, Coastal and Shelf Science 71 (2007): 537-544, doi:10.1016/j.ecss.2006.09.006.Sedimentary records of naturally occurring and fallout-derived radionuclides are widely
used as tools for estimating both the ages of recent sediments and rates of sedimentation
and bioturbation. Developing these records to the point of data interpretation requires
careful sample collection, processing, analysis and data modeling. In this work, we
document a number of potential pitfalls that can impact sediment core records and their
interpretation. This paper is not intended as an exhaustive treatment of these potential
problems. Rather, the emphasis is on potential problems that are not well documented in
the literature, as follows: 1) The mere sampling of sediment cores at a resolution that is
too coarse can result in an apparent diffusive mixing of the sedimentary record at rates
comparable to diffusive bioturbation rates observed in many locations; 2) 210Pb profiles in
slowly accumulating sediments can easily be misinterpreted to be driven by
sedimentation, when in fact bioturbation is the dominant control. Multiple isotopes of
different half lives and/or origin may help to distinguish between these two possible
interpretations; 3) Apparent mixing can occur due simply to numerical artifacts inherent
in the finite difference approximations of the advection diffusion equation used to model
sedimentation and bioturbation. Model users need to be aware of this potential problem.
Solutions to each of these potential pitfalls are offered to ensure the best possible
sediment age estimates and/or sedimentation and bioturbation rates can be obtained.Thanks to the U.S. Geological Survey Coastal and Marine Geology Program, the Andrew F.
Mellon Foundation, the Earth Institute Postdoctoral Fellowship Program at Columbia
University, and the National Science Foundation for funding
Trapping \u3ci\u3ePhyllophaga \u3c/i\u3espp. (Coleoptera: Scarabaeidae: Melolonthinae) in the United States and Canada using sex attractants.
The sex pheromone of the scarab beetle, Phyllophaga anxia, is a blend of the methyl esters of two amino acids, L-valine and L-isoleucine. A field trapping study was conducted, deploying different blends of the two compounds at 59 locations in the United States and Canada. More than 57,000 males of 61 Phyllophaga species (Coleoptera: Scarabaeidae: Melolonthinae) were captured and identified. Three major findings included: (1) widespread use of the two compounds [of the 147 Phyllophaga (sensu stricto) species found in the United States and Canada, males of nearly 40% were captured]; (2) in most species intraspecific male response to the pheromone blends was stable between years and over geography; and (3) an unusual pheromone polymorphism was described from P. anxia. Populations at some locations were captured with L-valine methyl ester alone, whereas populations at other locations were captured with L-isoleucine methyl ester alone. At additional locations, the L-valine methyl ester-responding populations and the L-isoleucine methyl ester-responding populations were both present, producing a bimodal capture curve. In southeastern Massachusetts and in Rhode Island, in the United States, P. anxia males were captured with blends of L-valine methyl ester and L-isoleucine methyl ester
Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium
The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium Database (http://ipcd.ibis.ulaval.ca/). Here, we present our strategy and the results that emerged from the analysis of the first 389 genomes. With as yet unmatched resolution, our results confirm that P. aeruginosa strains can be divided into three major groups that are further divided into subgroups, some not previously reported in the literature. We also provide the first snapshot of P. aeruginosa strain diversity with respect to antibiotic resistance. Our approach will allow us to draw potential links between environmental strains and those implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care
Genome-wide Analyses Identify KIF5A as a Novel ALS Gene
To identify novel genes associated with ALS, we undertook two lines of investigation. We carried out a genome-wide association study comparing 20,806 ALS cases and 59,804 controls. Independently, we performed a rare variant burden analysis comparing 1,138 index familial ALS cases and 19,494 controls. Through both approaches, we identified kinesin family member 5A (KIF5A) as a novel gene associated with ALS. Interestingly, mutations predominantly in the N-terminal motor domain of KIF5A are causative for two neurodegenerative diseases: hereditary spastic paraplegia (SPG10) and Charcot-Marie-Tooth type 2 (CMT2). In contrast, ALS-associated mutations are primarily located at the C-terminal cargo-binding tail domain and patients harboring loss-of-function mutations displayed an extended survival relative to typical ALS cases. Taken together, these results broaden the phenotype spectrum resulting from mutations in KIF5A and strengthen the role of cytoskeletal defects in the pathogenesis of ALS.Peer reviewe
Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma
SummaryWe describe a comprehensive genomic characterization of adrenocortical carcinoma (ACC). Using this dataset, we expand the catalogue of known ACC driver genes to include PRKAR1A, RPL22, TERF2, CCNE1, and NF1. Genome wide DNA copy-number analysis revealed frequent occurrence of massive DNA loss followed by whole-genome doubling (WGD), which was associated with aggressive clinical course, suggesting WGD is a hallmark of disease progression. Corroborating this hypothesis were increased TERT expression, decreased telomere length, and activation of cell-cycle programs. Integrated subtype analysis identified three ACC subtypes with distinct clinical outcome and molecular alterations which could be captured by a 68-CpG probe DNA-methylation signature, proposing a strategy for clinical stratification of patients based on molecular markers
Integrated genomic characterization of pancreatic ductal adenocarcinoma
We performed integrated genomic, transcriptomic, and proteomic profiling of 150 pancreatic ductal adenocarcinoma (PDAC) specimens, including samples with characteristic low neoplastic cellularity. Deep whole-exome sequencing revealed recurrent somatic mutations in KRAS, TP53, CDKN2A, SMAD4, RNF43, ARID1A, TGFβR2, GNAS, RREB1, and PBRM1. KRAS wild-type tumors harbored alterations in other oncogenic drivers, including GNAS, BRAF, CTNNB1, and additional RAS pathway genes. A subset of tumors harbored multiple KRAS mutations, with some showing evidence of biallelic mutations. Protein profiling identified a favorable prognosis subset with low epithelial-mesenchymal transition and high MTOR pathway scores. Associations of non-coding RNAs with tumor-specific mRNA subtypes were also identified. Our integrated multi-platform analysis reveals a complex molecular landscape of PDAC and provides a roadmap for precision medicine
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Comprehensive molecular characterization of gastric adenocarcinoma
Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein–Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also knownasPD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies
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