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Soil sampling and analysis plan for the 3718-F Alkali Metal Treatment and Storage Facility closure activities
Amendment V.13.B.b to the approved closure plan (DOE-RL 1995a) requires that a soil sampling and analysis plan be prepared and submitted to the Washington State Department of Ecology (Ecology) for review and approval. Amendment V.13.B.c requires that a diagram of the 3718-F Alkali Metal Treatment and Storage Facility unit (the treatment, storage, and disposal [TSD] unit) boundary that is to be closed, including the maximum extent of operation, be prepared and submitted as part is of the soil sampling and analysis plan. This document describes the sampling and analysis that is to be performed in response to these requirements and amends the closure plan. Specifically, this document supersedes Section 6.2, lines 43--46, and Section 7.3.6 of the closure plan. Results from the analysis will be compared to cleanup levels identified in the closure plan. These cleanup levels will be established using residential exposure assumptions in accordance with the Model Toxics Control Act (MTCA) Cleanup Regulation (Washington Administrative Code [WAC] 173-340) as required in Amendment V.13.B.I. Results of all sampling, including the raw analytical data, a summary of analytical results, a data validation package, and a narrative summary with conclusions will be provided to Ecology as specified in Amendment V.13.B.e. The results and process used to collect and analyze the soil samples will be certified by a licensed professional engineer. These results and a certificate of closure for the balance of the TSD unit, as outlined in Chapter 7.0 of the approved closure plan (storage shed, concrete pad, burn building, scrubber, and reaction tanks), will provide the basis for a closure determination
Spatial Modulation Microscopy for Real-Time Imaging of Plasmonic Nanoparticles and Cells
Spatial modulation microscopy is a technique originally developed for
quantitative spectroscopy of individual nano-objects. Here, a parallel
implementation of the spatial modulation microscopy technique is demonstrated
based on a line detector capable of demodulation at kHz frequencies. The
capabilities of the imaging system are shown using an array of plasmonic
nanoantennas and dendritic cells incubated with gold nanoparticles.Comment: 3 pages, 4 figure
Gold nanoparticles delivery in mammalian live cells: a critical review
Functional nanomaterials have recently attracted strong interest from the biology community, not only as potential drug delivery vehicles or diagnostic tools, but also as optical nanomaterials. This is illustrated by the explosion of publications in the field with more than 2,000 publications in the last 2 years (4,000 papers since 2000; from ISI Web of Knowledge, ‘nanoparticle and cell’ hit). Such a publication boom in this novel interdisciplinary field has resulted in papers of unequal standard, partly because it is challenging to assemble the required expertise in chemistry, physics, and biology in a single team. As an extreme example, several papers published in physical chemistry journals claim intracellular delivery of nanoparticles, but show pictures of cells that are, to the expert biologist, evidently dead (and therefore permeable). To attain proper cellular applications using nanomaterials, it is critical not only to achieve efficient delivery in healthy cells, but also to control the intracellular availability and the fate of the nanomaterial. This is still an open challenge that will only be met by innovative delivery methods combined with rigorous and quantitative characterization of the uptake and the fate of the nanoparticles. This review mainly focuses on gold nanoparticles and discusses the various approaches to nanoparticle delivery, including surface chemical modifications and several methods used to facilitate cellular uptake and endosomal escape. We will also review the main detection methods and how their optimum use can inform about intracellular localization, efficiency of delivery, and integrity of the surface capping
Plasmon oscillations in ellipsoid nanoparticles: beyond dipole approximation
The plasmon oscillations of a metallic triaxial ellipsoid nanoparticle have
been studied within the framework of the quasistatic approximation. A general
method has been proposed for finding the analytical expressions describing the
potential and frequencies of the plasmon oscillations of an arbitrary
multipolarity order. The analytical expressions have been derived for an
electric potential and plasmon oscillation frequencies of the first 24 modes.
Other higher orders plasmon modes are investigated numerically.Comment: 33 pages, 12 figure
An in vivo genetic screen for genes involved in spliced leader trans-splicing indicates a crucial role for continuous de novo spliced leader RNP assembly
ACKNOWLEDGEMENTS Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). We would also like to thank Prof. Shohei Mitani,at the National Bioresource Project for the Experimental Animal ‘Nematode C. elegans’, Japan, for FX3079. We are grateful to Prof. Tom Blumenthal (University of Colorado, Boulder) for suggestions and support of this work; and to Kathrine Wood for her contribution to the initial stages of part of this work. Author contributions. L.P., G.P., R.F., N.H., J.P. and B.M. performed experiments; B.M., J.P. and B.C. designed and lead the study; B.M. and J.P. drafted the manuscript. All authors reviewed the manuscript. FUNDING Biotechnology and Biological Sciences Research Council (BBSRC) [Project grant BB/J007137/1]; Medical Research Council (MRC) Confidence in Concept 2014 - University of Aberdeen Award(MC PC 14114v.2); University of Aberdeen Elphinstone Scholarship (to R.F.) and TET Fund support through Adekunle Ajasin University, Nigeria (to R.F.). Funding for open access charge: Biotechnology and Biological Sciences Research Council and Medical Research Council.Peer reviewedPublisher PD
PEG Branched Polymer for Functionalization of Nanomaterials with Ultralong Blood Circulation
Nanomaterials have been actively pursued for biological and medical
applications in recent years. Here, we report the synthesis of several new
poly(ethylene glycol) grafted branched-polymers for functionalization of
various nanomaterials including carbon nanotubes, gold nanoparticles (NP) and
gold nanorods (NRs), affording high aqueous solubility and stability for these
materials. We synthesize different surfactant polymers based upon
poly-(g-glutamic acid) (gPGA) and poly(maleic anhydride-alt-1-octadecene)
(PMHC18). We use the abundant free carboxylic acid groups of gPGA for attaching
lipophilic species such as pyrene or phospholipid, which bind to nanomaterials
via robust physisorption. Additionally, the remaining carboxylic acids on gPGA
or the amine-reactive anhydrides of PMHC18 are then PEGylated, providing
extended hydrophilic groups, affording polymeric amphiphiles. We show that
single-walled carbon nanotubes (SWNTs), Au NPs and NRs functionalized by the
polymers exhibit high stability in aqueous solutions at different pHs, at
elevated temperatures and in serum. Morever, the polymer-coated SWNTs exhibit
remarkably long blood circulation (t1/2 22.1 h) upon intravenous injection into
mice, far exceeding the previous record of 5.4 h. The ultra-long blood
circulation time suggests greatly delayed clearance of nanomaterials by the
reticuloendothelial system (RES) of mice, a highly desired property for in vivo
applications of nanomaterials, including imaging and drug delivery
Genomic-Bioinformatic Analysis of Transcripts Enriched in the Third-Stage Larva of the Parasitic Nematode Ascaris suum
Differential transcription in Ascaris suum was investigated using a genomic-bioinformatic approach. A cDNA archive enriched for molecules in the infective third-stage larva (L3) of A. suum was constructed by suppressive-subtractive hybridization (SSH), and a subset of cDNAs from 3075 clones subjected to microarray analysis using cDNA probes derived from RNA from different developmental stages of A. suum. The cDNAs (n = 498) shown by microarray analysis to be enriched in the L3 were sequenced and subjected to bioinformatic analyses using a semi-automated pipeline (ESTExplorer). Using gene ontology (GO), 235 of these molecules were assigned to ‘biological process’ (n = 68), ‘cellular component’ (n = 50), or ‘molecular function’ (n = 117). Of the 91 clusters assembled, 56 molecules (61.5%) had homologues/orthologues in the free-living nematodes Caenorhabditis elegans and C. briggsae and/or other organisms, whereas 35 (38.5%) had no significant similarity to any sequences available in current gene databases. Transcripts encoding protein kinases, protein phosphatases (and their precursors), and enolases were abundantly represented in the L3 of A. suum, as were molecules involved in cellular processes, such as ubiquitination and proteasome function, gene transcription, protein–protein interactions, and function. In silico analyses inferred the C. elegans orthologues/homologues (n = 50) to be involved in apoptosis and insulin signaling (2%), ATP synthesis (2%), carbon metabolism (6%), fatty acid biosynthesis (2%), gap junction (2%), glucose metabolism (6%), or porphyrin metabolism (2%), although 34 (68%) of them could not be mapped to a specific metabolic pathway. Small numbers of these 50 molecules were predicted to be secreted (10%), anchored (2%), and/or transmembrane (12%) proteins. Functionally, 17 (34%) of them were predicted to be associated with (non-wild-type) RNAi phenotypes in C. elegans, the majority being embryonic lethality (Emb) (13 types; 58.8%), larval arrest (Lva) (23.5%) and larval lethality (Lvl) (47%). A genetic interaction network was predicted for these 17 C. elegans orthologues, revealing highly significant interactions for nine molecules associated with embryonic and larval development (66.9%), information storage and processing (5.1%), cellular processing and signaling (15.2%), metabolism (6.1%), and unknown function (6.7%). The potential roles of these molecules in development are discussed in relation to the known roles of their homologues/orthologues in C. elegans and some other nematodes. The results of the present study provide a basis for future functional genomic studies to elucidate molecular aspects governing larval developmental processes in A. suum and/or the transition to parasitism
CellCognition : time-resolved phenotype annotation in high-throughput live cell imaging
Author Posting. © The Authors, 2010. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature Methods 7 (2010): 747-754, doi:10.1038/nmeth.1486.Fluorescence time-lapse imaging has become a powerful tool to investigate complex
dynamic processes such as cell division or intracellular trafficking. Automated
microscopes generate time-resolved imaging data at high throughput, yet tools for
quantification of large-scale movie data are largely missing. Here, we present
CellCognition, a computational framework to annotate complex cellular dynamics.
We developed a machine learning method that combines state-of-the-art classification
with hidden Markov modeling for annotation of the progression through
morphologically distinct biological states. The incorporation of time information into
the annotation scheme was essential to suppress classification noise at state
transitions, and confusion between different functional states with similar
morphology. We demonstrate generic applicability in a set of different assays and
perturbation conditions, including a candidate-based RNAi screen for mitotic exit
regulators in human cells. CellCognition is published as open source software,
enabling live imaging-based screening with assays that directly score cellular
dynamics.Work in the Gerlich
laboratory is supported by Swiss National Science Foundation (SNF) research grant
3100A0-114120, SNF ProDoc grant PDFMP3_124904, a European Young
Investigator (EURYI) award of the European Science Foundation, an EMBO YIP
fellowship, and a MBL Summer Research Fellowship to D.W.G., an ETH TH grant, a
grant by the UBS foundation, a Roche Ph.D. fellowship to M.H.A.S, and a Mueller
fellowship of the Molecular Life Sciences Ph.D. program Zurich to M.H. M.H. and
M.H.A.S are fellows of the Zurich Ph.D. Program in Molecular Life Sciences. B.F.
was supported by European Commission’s seventh framework program project
Cancer Pathways. Work in the Ellenberg laboratory is supported by a European
Commission grant within the Mitocheck consortium (LSHG-CT-2004-503464). Work
in the Peter laboratory is supported by the ETHZ, Oncosuisse, SystemsX.ch (LiverX)
and the SNF
The Ternary Rab27a–Myrip–Myosin VIIa Complex Regulates Melanosome Motility in the Retinal Pigment Epithelium
The retinal pigment epithelium (RPE) contains melanosomes similar to those found in the skin melanocytes, which undergo dramatic light-dependent movements in fish and amphibians. In mammals, those movements are more subtle and appear to be regulated by the Rab27a GTPase and the unconventional myosin, Myosin VIIa (MyoVIIa). Here we address the hypothesis that a recently identified Rab27a- and MyoVIIa-interacting protein, Myrip, promotes the formation of a functional tripartite complex. In heterologous cultured cells, all three proteins co-immunoprecipitated following overexpression. Rab27a and Myrip localize to the peripheral membrane of RPE melanosomes as observed by immunofluorescence and immunoelectron microscopy. Melanosome dynamics were studied using live-cell imaging of mouse RPE primary cultures. Wild-type RPE melanosomes exhibited either stationary or slow movement interrupted by bursts of fast movement, with a peripheral directionality trend. Nocodazole treatment led to melanosome paralysis, suggesting that movement requires microtubule motors. Significant and similar alterations in melanosome dynamics were observed when any one of the three components of the complex was missing, as studied in ashen- (Rab27a defective) and shaker-1 (MyoVIIa mutant)-derived RPE cells, and in wild-type RPE cells transduced with adenovirus carrying specific sequences to knockdown Myrip expression. We observed a significant increase in the number of motile melanosomes, exhibiting more frequent and prolonged bursts of fast movement, and inversion of directionality. Similar alterations were observed upon cytochalasin D treatment, suggesting that the Rab27a–Myrip–MyoVIIa complex regulates tethering of melanosomes onto actin filaments, a process that ensures melanosome movement towards the cell periphery
Systematic Analysis of Pleiotropy in C. elegans Early Embryogenesis
Pleiotropy refers to the phenomenon in which a single gene controls several distinct, and seemingly unrelated, phenotypic effects. We use C. elegans early embryogenesis as a model to conduct systematic studies of pleiotropy. We analyze high-throughput RNA interference (RNAi) data from C. elegans and identify “phenotypic signatures”, which are sets of cellular defects indicative of certain biological functions. By matching phenotypic profiles to our identified signatures, we assign genes with complex phenotypic profiles to multiple functional classes. Overall, we observe that pleiotropy occurs extensively among genes involved in early embryogenesis, and a small proportion of these genes are highly pleiotropic. We hypothesize that genes involved in early embryogenesis are organized into partially overlapping functional modules, and that pleiotropic genes represent “connectors” between these modules. In support of this hypothesis, we find that highly pleiotropic genes tend to reside in central positions in protein-protein interaction networks, suggesting that pleiotropic genes act as connecting points between different protein complexes or pathways
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