21 CFR 864.7525 - Heparin assay.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Heparin assay. 864.7525 Section 864.7525 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7525 Heparin assay. (a) Identification. A...

21 CFR 864.7525 - Heparin assay.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Heparin assay. 864.7525 Section 864.7525 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7525 Heparin assay. (a) Identification. A...

21 CFR 864.7525 - Heparin assay.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Heparin assay. 864.7525 Section 864.7525 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7525 Heparin assay. (a) Identification. A...

21 CFR 864.7525 - Heparin assay.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Heparin assay. 864.7525 Section 864.7525 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7525 Heparin assay. (a) Identification. A...

21 CFR 864.7525 - Heparin assay.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Heparin assay. 864.7525 Section 864.7525 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7525 Heparin assay. (a) Identification. A...

Genotoxicity assessment of propyl thiosulfinate oxide, an organosulfur compound from Allium extract, intended to food active packaging.

PubMed

Mellado-García, P; Maisanaba, S; Puerto, M; Llana-Ruiz-Cabello, M; Prieto, A I; Marcos, R; Pichardo, S; Cameán, A M

2015-12-01

Essential oils from onion (Allium cepa L.), garlic (Allium sativum L.), and their main components, such as propyl thiosulfinate oxide (PTSO) are being intended for active packaging with the purpose of maintaining and extending food product quality and shelf life. The present work aims to assess for the first time the potential mutagenicity/genotoxicity of PTSO (0-50 µM) using the following battery of genotoxicity tests: (1) the bacterial reverse-mutation assay in Salmonella typhimurium (Ames test, OECD 471); (2) the micronucleus test (OECD 487) (MN) and (3) the mouse lymphoma thymidine-kinase assay (OECD 476) (MLA) on L5178YTk(+/-), cells; and (4) the comet assay (with and without Endo III and FPG enzymes) on Caco-2 cells. The results revealed that PTSO was not mutagenic in the Ames test, however it was mutagenic in the MLA assay after 24 h of treatment (2.5-20 µM). The parent compound did not induce MN on mammalian cells; however, its metabolites (in the presence S9) produced positive results (from 15 µM). Data from the comet assay indicated that PTSO did not induce DNA breaks or oxidative DNA damage. Further in vivo genotoxicity tests are needed to confirm its safety before it is used as active additive in food packaging. Copyright © 2015 Elsevier Ltd. All rights reserved.

Comparative assay of antioxidant packages for dimer of estolide esters

USDA-ARS?s Scientific Manuscript database

A series of 26 different antioxidants and commercial antioxidant packages, containing both natural and synthetic-based materials, were evaluated with dimeric coconut-oleic estolide 2-ethylhexyl ester. The different antioxidants were broken down into different classes of materials: phenolic, aminic, ...

Student-Designed Enzyme-Linked Metabolite Assay Kits

ERIC Educational Resources Information Center

Hancock, D.; Johnston, J.; Dimauro, J.; Denyer, G.

2004-01-01

The extensive use of commercial kits in molecular biology and biochemistry has prompted us to design a series of practical sessions to help students become familiar with the uses and limitations of pre-packaged assay systems. To facilitate an understanding of these assay systems and to promote reflection on their appropriate use, students…

21 CFR 864.7490 - Sulfhemoglobin assay.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Sulfhemoglobin assay. 864.7490 Section 864.7490 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7490 Sulfhemoglobin...

21 CFR 864.7490 - Sulfhemoglobin assay.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Sulfhemoglobin assay. 864.7490 Section 864.7490 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7490 Sulfhemoglobin...

21 CFR 864.7425 - Carboxyhemoglobin assay.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Carboxyhemoglobin assay. 864.7425 Section 864.7425 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7425 Carboxyhemoglobin...

21 CFR 864.7490 - Sulfhemoglobin assay.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Sulfhemoglobin assay. 864.7490 Section 864.7490 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7490 Sulfhemoglobin...

21 CFR 864.7425 - Carboxyhemoglobin assay.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Carboxyhemoglobin assay. 864.7425 Section 864.7425 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7425 Carboxyhemoglobin...

21 CFR 864.7490 - Sulfhemoglobin assay.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Sulfhemoglobin assay. 864.7490 Section 864.7490 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7490 Sulfhemoglobin...

21 CFR 864.7425 - Carboxyhemoglobin assay.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Carboxyhemoglobin assay. 864.7425 Section 864.7425 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7425 Carboxyhemoglobin...

21 CFR 864.7490 - Sulfhemoglobin assay.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Sulfhemoglobin assay. 864.7490 Section 864.7490 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7490 Sulfhemoglobin...

21 CFR 864.7425 - Carboxyhemoglobin assay.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Carboxyhemoglobin assay. 864.7425 Section 864.7425 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7425 Carboxyhemoglobin...

SynergyFinder: a web application for analyzing drug combination dose-response matrix data.

PubMed

Ianevski, Aleksandr; He, Liye; Aittokallio, Tero; Tang, Jing

2017-08-01

Rational design of drug combinations has become a promising strategy to tackle the drug sensitivity and resistance problem in cancer treatment. To systematically evaluate the pre-clinical significance of pairwise drug combinations, functional screening assays that probe combination effects in a dose-response matrix assay are commonly used. To facilitate the analysis of such drug combination experiments, we implemented a web application that uses key functions of R-package SynergyFinder, and provides not only the flexibility of using multiple synergy scoring models, but also a user-friendly interface for visualizing the drug combination landscapes in an interactive manner. The SynergyFinder web application is freely accessible at https://synergyfinder.fimm.fi ; The R-package and its source-code are freely available at http://bioconductor.org/packages/release/bioc/html/synergyfinder.html . jing.tang@helsinki.fi. © The Author(s) 2017. Published by Oxford University Press.

Applications Where Snap is BPM for Radioactive Waste Assay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, T.J.

2008-07-01

Historically, the Atomic Weapons Establishment (AWE) at Aldermaston in the United Kingdom (UK), has used a variety of assay techniques to measure the radioactive content of a diverse range of waste packages from decommissioning, operational and legacy sources. The regulator, the Environment Agency in the UK, places conditions and limits on AWE through an authorisation within the Radioactive Substances Act (RSA93). The conditions and limits require Best Practical Means (BPM) measurements to be used to demonstrate compliance with the authorisation. Hence, the assay technique employed needs to achieve a balance between risk of exposure, environmental considerations, technological considerations, health andmore » safety considerations and cost effectiveness, without being grossly disproportionate in terms of money, time or trouble. Recently published work has concluded that the Spectral Non-destructive Assay Platform (SNAP) assay system is BPM for Depleted Uranium (DU) waste assay at AWE (1) and low level plutonium in soft drummed waste, HEPA filters and soils (2-4). The purpose of this paper is to highlight other applications where SNAP represents BPM for radioactive waste assay. This has been done by intercomparison studies of SNAP with other assay techniques, such as Segmented Gamma Scanner (SGS) and Passive Neutron Coincidence Counter (PNCC). It has been concluded that, for a large range of waste packages encountered at AWE, SNAP is BPM. (author)« less

21 CFR 864.7415 - Abnormal hemoglobin assay.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Abnormal hemoglobin assay. 864.7415 Section 864.7415 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7415 Abnormal...

21 CFR 864.7375 - Glutathione reductase assay.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Glutathione reductase assay. 864.7375 Section 864.7375 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7375 Glutathione...

21 CFR 864.7375 - Glutathione reductase assay.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Glutathione reductase assay. 864.7375 Section 864.7375 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7375 Glutathione...

21 CFR 864.7375 - Glutathione reductase assay.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Glutathione reductase assay. 864.7375 Section 864.7375 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7375 Glutathione...

21 CFR 864.7415 - Abnormal hemoglobin assay.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Abnormal hemoglobin assay. 864.7415 Section 864.7415 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7415 Abnormal...

21 CFR 864.7375 - Glutathione reductase assay.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Glutathione reductase assay. 864.7375 Section 864.7375 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7375 Glutathione...

21 CFR 864.7375 - Glutathione reductase assay.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Glutathione reductase assay. 864.7375 Section 864.7375 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7375 Glutathione...

21 CFR 864.7415 - Abnormal hemoglobin assay.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Abnormal hemoglobin assay. 864.7415 Section 864.7415 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7415 Abnormal...

21 CFR 864.7060 - Antithrombin III assay.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Antithrombin III assay. 864.7060 Section 864.7060 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7060 Antithrombin III...

21 CFR 864.7400 - Hemoglobin A 2 assay.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Hemoglobin A 2 assay. 864.7400 Section 864.7400 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7400 Hemoglobin A 2...

21 CFR 864.7060 - Antithrombin III assay.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Antithrombin III assay. 864.7060 Section 864.7060 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7060 Antithrombin III...

21 CFR 864.7060 - Antithrombin III assay.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Antithrombin III assay. 864.7060 Section 864.7060 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7060 Antithrombin III...

21 CFR 864.7400 - Hemoglobin A2 assay.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Hemoglobin A2 assay. 864.7400 Section 864.7400 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7400 Hemoglobin A2...

21 CFR 864.7060 - Antithrombin III assay.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Antithrombin III assay. 864.7060 Section 864.7060 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7060 Antithrombin III...

21 CFR 864.7400 - Hemoglobin A 2 assay.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Hemoglobin A 2 assay. 864.7400 Section 864.7400 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7400 Hemoglobin A 2...

21 CFR 864.7455 - Fetal hemoglobin assay.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Fetal hemoglobin assay. 864.7455 Section 864.7455 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7455 Fetal hemoglobin...

21 CFR 864.7060 - Antithrombin III assay.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Antithrombin III assay. 864.7060 Section 864.7060 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7060 Antithrombin III...

21 CFR 864.7455 - Fetal hemoglobin assay.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Fetal hemoglobin assay. 864.7455 Section 864.7455 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7455 Fetal hemoglobin...

21 CFR 864.7455 - Fetal hemoglobin assay.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Fetal hemoglobin assay. 864.7455 Section 864.7455 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7455 Fetal hemoglobin...

Direct interaction of the bacteriophage SPP1 packaging ATPase with the portal protein.

PubMed

Oliveira, Leonor; Cuervo, Ana; Tavares, Paulo

2010-03-05

DNA packaging in tailed bacteriophages and other viruses requires assembly of a complex molecular machine at a specific vertex of the procapsid. This machine is composed of the portal protein that provides a tunnel for DNA entry, an ATPase that fuels DNA translocation (large terminase subunit), and most frequently, a small terminase subunit. Here we characterized the interaction between the terminase ATPase subunit of bacteriophage SPP1 (gp2) and the procapsid portal vertex. We found, by affinity pulldown assays with purified proteins, that gp2 interacts with the portal protein, gp6, independently of the terminase small subunit gp1, DNA, or ATP. The gp2-procapsid interaction via the portal protein depends on gp2 concentration and requires the presence of divalent cations. Competition experiments showed that isolated gp6 can only inhibit gp2-procapsid interactions and DNA packaging at gp6:procapsid molar ratios above 10-fold. Assays with gp6 carrying mutations in distinct regions of its structure that affect the portal-induced stimulation of ATPase and DNA packaging revealed that none of these mutations impedes gp2-gp6 binding. Our results demonstrate that the SPP1 packaging ATPase binds directly to the portal and that the interaction is stronger with the portal embedded in procapsids. Identification of mutations in gp6 that allow for assembly of the ATPase-portal complex but impair DNA packaging support an intricate cross-talk between the two proteins for activity of the DNA translocation motor.

SLDAssay: A software package and web tool for analyzing limiting dilution assays.

PubMed

Trumble, Ilana M; Allmon, Andrew G; Archin, Nancie M; Rigdon, Joseph; Francis, Owen; Baldoni, Pedro L; Hudgens, Michael G

2017-11-01

Serial limiting dilution (SLD) assays are used in many areas of infectious disease related research. This paper presents SLDAssay, a free and publicly available R software package and web tool for analyzing data from SLD assays. SLDAssay computes the maximum likelihood estimate (MLE) for the concentration of target cells, with corresponding exact and asymptotic confidence intervals. Exact and asymptotic goodness of fit p-values, and a bias-corrected (BC) MLE are also provided. No other publicly available software currently implements the BC MLE or the exact methods. For validation of SLDAssay, results from Myers et al. (1994) are replicated. Simulations demonstrate the BC MLE is less biased than the MLE. Additionally, simulations demonstrate that exact methods tend to give better confidence interval coverage and goodness-of-fit tests with lower type I error than the asymptotic methods. Additional advantages of using exact methods are also discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hensley, D.C.

Nuclear Fuel Services sent more than 800 drums of nuclear waste to Oak Ridge National Laboratory, with the majority of the waste packaged into five different waste matrix types. A thorough and complete assay of the waste was performed at both NFS and at ORNL. A detailed comparing of the two assay sets provides valuable. insights into problems encountered in typical assay campaigns, particularly as there is, for the most part, excellent agreement between these two campaigns.

Telomere Chromatin Condensation Assay (TCCA): a novel approach to study structural telomere integrity.

PubMed

Gonzalez-Vasconcellos, Iria; Alonso-Rodríguez, Silvia; López-Baltar, Isidoro; Fernández, José Luis

2015-01-01

Telomeres, the DNA-protein complexes located at the end of linear eukaryotic chromosomes are essential for genome stability. Improper higher-order chromatin organization at the chromosome ends can give rise to telomeric recombination and genomic instability. We report the development of an assay to quantify differences in the condensation of telomeric chromatin, thereby offering new opportunities to study telomere biology and stability. We have combined a DNA nuclease digestion with a quantitative PCR (qPCR) assay of telomeric DNA, which we term the Telomere Chromatin Condensation Assay (TCCA). By quantifying the relative quantities of telomeric DNA that are progressively digested with the exonuclease Bal 31 the method can discriminate between different levels of telomeric chromatin condensation. The structural chromatin packaging at telomeres shielded against exonuclease digestion delivered an estimate, which we term Chromatin Protection Factor (CPF) that ranged from 1.7 to 2.3 fold greater than that present in unpacked DNA. The CPF was significantly decreased when cell cultures were incubated with the DNA hypomethylating agent 5-azacytidine, demonstrating the ability of the TCCA assay to discriminate between packaging levels of telomeric DNA. Copyright © 2014 Elsevier B.V. All rights reserved.

Disruption of Specific RNA-RNA Interactions in a Double-Stranded RNA Virus Inhibits Genome Packaging and Virus Infectivity

PubMed Central

Fajardo, Teodoro; Sung, Po-Yu; Roy, Polly

2015-01-01

Bluetongue virus (BTV) causes hemorrhagic disease in economically important livestock. The BTV genome is organized into ten discrete double-stranded RNA molecules (S1-S10) which have been suggested to follow a sequential packaging pathway from smallest to largest segment during virus capsid assembly. To substantiate and extend these studies, we have investigated the RNA sorting and packaging mechanisms with a new experimental approach using inhibitory oligonucleotides. Putative packaging signals present in the 3’untranslated regions of BTV segments were targeted by a number of nuclease resistant oligoribonucleotides (ORNs) and their effects on virus replication in cell culture were assessed. ORNs complementary to the 3’ UTR of BTV RNAs significantly inhibited virus replication without affecting protein synthesis. Same ORNs were found to inhibit complex formation when added to a novel RNA-RNA interaction assay which measured the formation of supramolecular complexes between and among different RNA segments. ORNs targeting the 3’UTR of BTV segment 10, the smallest RNA segment, were shown to be the most potent and deletions or substitution mutations of the targeted sequences diminished the RNA complexes and abolished the recovery of viable viruses using reverse genetics. Cell-free capsid assembly/RNA packaging assay also confirmed that the inhibitory ORNs could interfere with RNA packaging and further substitution mutations within the putative RNA packaging sequence have identified the recognition sequence concerned. Exchange of 3’UTR between segments have further demonstrated that RNA recognition was segment specific, most likely acting as part of the secondary structure of the entire genomic segment. Our data confirm that genome packaging in this segmented dsRNA virus occurs via the formation of supramolecular complexes formed by the interaction of specific sequences located in the 3’ UTRs. Additionally, the inhibition of packaging in-trans with inhibitory ORNs suggests this that interaction is a bona fide target for the design of compounds with antiviral activity. PMID:26646790

Disruption of Specific RNA-RNA Interactions in a Double-Stranded RNA Virus Inhibits Genome Packaging and Virus Infectivity.

PubMed

Fajardo, Teodoro; Sung, Po-Yu; Roy, Polly

2015-12-01

Bluetongue virus (BTV) causes hemorrhagic disease in economically important livestock. The BTV genome is organized into ten discrete double-stranded RNA molecules (S1-S10) which have been suggested to follow a sequential packaging pathway from smallest to largest segment during virus capsid assembly. To substantiate and extend these studies, we have investigated the RNA sorting and packaging mechanisms with a new experimental approach using inhibitory oligonucleotides. Putative packaging signals present in the 3'untranslated regions of BTV segments were targeted by a number of nuclease resistant oligoribonucleotides (ORNs) and their effects on virus replication in cell culture were assessed. ORNs complementary to the 3' UTR of BTV RNAs significantly inhibited virus replication without affecting protein synthesis. Same ORNs were found to inhibit complex formation when added to a novel RNA-RNA interaction assay which measured the formation of supramolecular complexes between and among different RNA segments. ORNs targeting the 3'UTR of BTV segment 10, the smallest RNA segment, were shown to be the most potent and deletions or substitution mutations of the targeted sequences diminished the RNA complexes and abolished the recovery of viable viruses using reverse genetics. Cell-free capsid assembly/RNA packaging assay also confirmed that the inhibitory ORNs could interfere with RNA packaging and further substitution mutations within the putative RNA packaging sequence have identified the recognition sequence concerned. Exchange of 3'UTR between segments have further demonstrated that RNA recognition was segment specific, most likely acting as part of the secondary structure of the entire genomic segment. Our data confirm that genome packaging in this segmented dsRNA virus occurs via the formation of supramolecular complexes formed by the interaction of specific sequences located in the 3' UTRs. Additionally, the inhibition of packaging in-trans with inhibitory ORNs suggests this that interaction is a bona fide target for the design of compounds with antiviral activity.

Cytotoxicity and mutagenicity studies on migration extracts from nanocomposites with potential use in food packaging.

PubMed

Maisanaba, Sara; Pichardo, Silvia; Jordá-Beneyto, María; Aucejo, Susana; Cameán, Ana M; Jos, Ángeles

2014-04-01

Clays are used in the food packaging industry to obtain nanocomposites. The use of these new materials is a concern, because they could reach consumers by oral exposure through possible migration, and potential toxic effects could be derived. In the present study, several in vitro basal cytotoxicity and mutagenicity tests on migration extracts obtained from a nanocomposite material with poly (lactic) acid (PLA) and two modified clays, Clay1 and Clay2, are shown. Migration extracts in distilled water showed values of 0.1 ± 0.2mg/dm(2) in all samples. Also, the content of characteristic metals of the clays structure (Al, Ca, Mg, Fe, Si) was studied and no statistical differences were observed. For the cytotoxicity assays, the human intestinal Caco-2 and human liver HepG2 cells were selected. Cells were exposed to concentrations between 2.5% and 100% extracts determining three different biomarkers of cellular viability. No significant differences were observed in the cytotoxicity assays. Finally, mutagenicity was evaluated by the Ames test and resulted in the absence of mutagenic response at all the concentrations assayed. Taking in account all above mentioned, these new materials show a good profile for their use in food packaging although further research is still needed. Copyright © 2014 Elsevier Ltd. All rights reserved.

RNA secondary structures of the bacteriophage phi6 packaging regions.

PubMed

Pirttimaa, M J; Bamford, D H

2000-06-01

Bacteriophage phi6 genome consists of three segments of double-stranded RNA. During maturation, single-stranded copies of these segments are packaged into preformed polymerase complex particles. Only phi6 RNA is packaged, and each particle contains only one copy of each segment. An in vitro packaging and replication assay has been developed for phi6, and the packaging signals (pac sites) have been mapped to the 5' ends of the RNA segments. In this study, we propose secondary structure models for the pac sites of phi6 single-stranded RNA segments. Our models accommodate data from structure-specific chemical modifications, free energy minimizations, and phylogenetic comparisons. Previously reported pac site deletion studies are also discussed. Each pac site possesses a unique architecture, that, however, contains common structural elements.

Structural constraints in the packaging of bluetongue virus genomic segments

PubMed Central

Burkhardt, Christiane; Sung, Po-Yu; Celma, Cristina C.

2014-01-01

The mechanism used by bluetongue virus (BTV) to ensure the sorting and packaging of its 10 genomic segments is still poorly understood. In this study, we investigated the packaging constraints for two BTV genomic segments from two different serotypes. Segment 4 (S4) of BTV serotype 9 was mutated sequentially and packaging of mutant ssRNAs was investigated by two newly developed RNA packaging assay systems, one in vivo and the other in vitro. Modelling of the mutated ssRNA followed by biochemical data analysis suggested that a conformational motif formed by interaction of the 5′ and 3′ ends of the molecule was necessary and sufficient for packaging. A similar structural signal was also identified in S8 of BTV serotype 1. Furthermore, the same conformational analysis of secondary structures for positive-sense ssRNAs was used to generate a chimeric segment that maintained the putative packaging motif but contained unrelated internal sequences. This chimeric segment was packaged successfully, confirming that the motif identified directs the correct packaging of the segment. PMID:24980574

The combined effects of storage temperature and packaging on the sensory, chemical, and physical properties of a Cabernet Sauvignon wine.

PubMed

Hopfer, Helene; Buffon, Peter A; Ebeler, Susan E; Heymann, Hildegarde

2013-04-03

A Californian Cabernet Sauvignon was stored for 6 months at three different constant temperatures to study the combined effects of storage temperature and packaging configuration. Glass bottles with natural cork, synthetic cork, and screw cap closure, as well as two Bag-in-Box treatments, were used in the experiment. A trained sensory panel was able to detect significant changes in aroma, flavor, taste, mouthfeel, and color attributes among the samples, differences that were found also with various chemical and physical measurements (volatile profile, polyphenol pattern, enological parameters, color space). Additionally, two commonly used polyphenol assays were compared to each other in terms of their ability to detect the changes in the polyphenol profile. Generally, sample changes were more pronounced due to the different storage temperatures, with 30 sensory attributes differing significantly among the three different storage temperatures, while only 17 sensory attributes showed a significant packaging effect. With increasing storage temperature the packaging effect became more pronounced, resulting in the largest changes in the Bag-in-Box samples stored at the highest temperature of 40 °C. At the highest storage temperature, all wines showed oxidized characters, independent of the wine packaging configurations, but to a varying degree. Generally, wines that received highest oxygen amounts and storage temperatures were much lighter, less red, and more brown-yellow at the end of the 6-month storage period, compared to their counterparts stored at 10 °C. These changes in color and polyphenols, respectively, were also detected with the two spectrophotometric assays. With increasing storage temperature both assays measured reduced concentrations in total phenols and total anthocyanins, while total tannins, degree of ionized anthocyanins, and color density increased. Various volatile compounds differed significantly among the samples, with largest relative concentration changes in acetates, organic acids, and alcohols, in good agreement with previous literature reports, with some being well correlated to specific sensory attributes too; for example, various acetates correlated to cherry and fruit aromas and flavors. The study shows that storage at elevated temperatures could be a valuable tool for wine packaging screening and testing new and improved wine packaging types under the worst conditions, which are unfortunately not unrealistic.

Botulism challenge studies of a modified atmosphere package for fresh mussels: inoculated pack studies.

PubMed

Newell, C R; Ma, Li; Doyle, Michael

2012-06-01

A series of botulism challenge studies were performed to determine the possibility of production of botulinum toxin in mussels (Mytilus edulis) held under a commercial high-oxygen (60 to 65% O(2)), modified atmosphere packaging (MAP) condition. Spore mixtures of six strains of nonproteolytic Clostridium botulinum were introduced into mussel MAP packages receiving different packaging buffers with or without the addition of lactic acid bacteria. Dye studies and package flipping trials were conducted to ensure internalization of spores by packed mussels. Inoculated mussel packages were stored at normal (4°C) and abusive (12°C) temperatures for 21 and 13 days, respectively, which were beyond the packaged mussels' intended shelf life. Microbiological and chemical analyses were conducted at predetermined intervals (a total of five sampling times at each temperature), including total aerobic plate counts, C. botulinum counts, lactic acid bacterial counts, package headspace gas composition, pH of packaging buffer and mussel meat, and botulinum toxin assays of packaging buffer and mussel meat. Results revealed that C. botulinum inoculated in fresh mussels packed under MAP packaging did not produce toxin, even at an abusive storage temperature and when held beyond their shelf life. No evidence was found that packaging buffers or gas composition influenced the lack of botulinum toxin production in packed mussels.

LDRD final report on microencapsulated immunoreagents for development of one-step ELISA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henderson, C.C.; Singh, A.K.

1997-08-01

Microencapsulation of biological macromolecules was investigated as a method for incorporating the necessary immunoreagents into an improved enzyme-linked immunosorbant assay (ELISA) package that would self-develop. This self-contained ELISA package would eliminate the need for a trained technician to perform multiple additions of immunoreagent to the assay. Microencapsulation by insolution drying was selected from the many available microencapsulation methods, and two satisfactory procedures for microencapsulation of proteins were established. The stability and potential for rapid release of protein from these microencapsulates was then evaluated. The results suggest that the chosen method for protein entrapment produces microcapsules with a considerable amount ofmore » protein in the walls making these particular microcapsules unsuitable for their intended use.« less

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.

PubMed

Ou, Jianhong; Liu, Haibo; Yu, Jun; Kelliher, Michelle A; Castilla, Lucio H; Lawson, Nathan D; Zhu, Lihua Julie

2018-03-01

ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. While several tools have been developed or adopted for assessing read quality, identifying nucleosome occupancy and accessible regions from ATAC-seq data, none of the tools provide a comprehensive set of functionalities for preprocessing and quality assessment of aligned ATAC-seq datasets. We have developed a Bioconductor package, ATACseqQC, for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq data. In addition, this package contains functions to preprocess aligned ATAC-seq data for subsequent peak calling. Here we demonstrate the utilities of our package using 25 publicly available ATAC-seq datasets from four studies. We also provide guidelines on what the diagnostic plots should look like for an ideal ATAC-seq dataset. This software package has been used successfully for preprocessing and assessing several in-house and public ATAC-seq datasets. Diagnostic plots generated by this package will facilitate the quality assessment of ATAC-seq data, and help researchers to evaluate their own ATAC-seq experiments as well as select high-quality ATAC-seq datasets from public repositories such as GEO to avoid generating hypotheses or drawing conclusions from low-quality ATAC-seq experiments. The software, source code, and documentation are freely available as a Bioconductor package at https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html .

Software for the Integration of Multiomics Experiments in Bioconductor.

PubMed

Ramos, Marcel; Schiffer, Lucas; Re, Angela; Azhar, Rimsha; Basunia, Azfar; Rodriguez, Carmen; Chan, Tiffany; Chapman, Phil; Davis, Sean R; Gomez-Cabrero, David; Culhane, Aedin C; Haibe-Kains, Benjamin; Hansen, Kasper D; Kodali, Hanish; Louis, Marie S; Mer, Arvind S; Riester, Markus; Morgan, Martin; Carey, Vince; Waldron, Levi

2017-11-01

Multiomics experiments are increasingly commonplace in biomedical research and add layers of complexity to experimental design, data integration, and analysis. R and Bioconductor provide a generic framework for statistical analysis and visualization, as well as specialized data classes for a variety of high-throughput data types, but methods are lacking for integrative analysis of multiomics experiments. The MultiAssayExperiment software package, implemented in R and leveraging Bioconductor software and design principles, provides for the coordinated representation of, storage of, and operation on multiple diverse genomics data. We provide the unrestricted multiple 'omics data for each cancer tissue in The Cancer Genome Atlas as ready-to-analyze MultiAssayExperiment objects and demonstrate in these and other datasets how the software simplifies data representation, statistical analysis, and visualization. The MultiAssayExperiment Bioconductor package reduces major obstacles to efficient, scalable, and reproducible statistical analysis of multiomics data and enhances data science applications of multiple omics datasets. Cancer Res; 77(21); e39-42. ©2017 AACR . ©2017 American Association for Cancer Research.

Development of an iron chelating polyethylene film for active packaging applications.

PubMed

Tian, Fang; Decker, Eric A; Goddard, Julie M

2012-02-29

Metal-promoted oxidation reactions are a major cause of food quality deterioration. Active packaging offers novel approaches to controlling such oxidation for the purpose of extending shelf life. Herein, we report modification of the surface of polyethylene (PE) films to possess metal chelating activity. Metal chelating carboxylic acids were introduced to the film surface using cross-linking agents [polyethylenimine (PEI) or ethylenediamine (ED)] to increase the number of available carboxylic acids. ATR-FTIR, contact angle, dye assay, and iron chelating assay were used to characterize changes in surface chemistry after each functionalization step. The chelator poly(acrylic acid) (PAA) was attached to the surface at a density of 9.12 ± 0.71 nmol carboxyl groups/cm², and exhibited an iron chelating activity. The results indicate that PAA-modified PE films might have a higher affinity to Fe³⁺ than Fe²⁺ with the optimum binding pH at 5.0. Such inexpensive active packaging materials are promising in food industry for the preservation of liquid and semiliquid food products and have application in heavy metal chelation therapy for biomedical materials as well.

MIRA: An R package for DNA methylation-based inference of regulatory activity.

PubMed

Lawson, John T; Tomazou, Eleni M; Bock, Christoph; Sheffield, Nathan C

2018-03-01

DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for independent region sets with shared biological annotation. Using this profile, MIRA infers and scores the collective regulatory activity for each region set. MIRA facilitates regulatory analysis in situations where classical regulatory assays would be difficult and allows public sources of open chromatin and protein binding regions to be leveraged for novel insight into the regulatory state of DNA methylation datasets. R package available on Bioconductor: http://bioconductor.org/packages/release/bioc/html/MIRA.html. nsheffield@virginia.edu.

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types

PubMed Central

Pagès, Hervé

2018-01-01

Biological experiments involving genomics or other high-throughput assays typically yield a data matrix that can be explored and analyzed using the R programming language with packages from the Bioconductor project. Improvements in the throughput of these assays have resulted in an explosion of data even from routine experiments, which poses a challenge to the existing computational infrastructure for statistical data analysis. For example, single-cell RNA sequencing (scRNA-seq) experiments frequently generate large matrices containing expression values for each gene in each cell, requiring sparse or file-backed representations for memory-efficient manipulation in R. These alternative representations are not easily compatible with high-performance C++ code used for computationally intensive tasks in existing R/Bioconductor packages. Here, we describe a C++ interface named beachmat, which enables agnostic data access from various matrix representations. This allows package developers to write efficient C++ code that is interoperable with dense, sparse and file-backed matrices, amongst others. We evaluated the performance of beachmat for accessing data from each matrix representation using both simulated and real scRNA-seq data, and defined a clear memory/speed trade-off to motivate the choice of an appropriate representation. We also demonstrate how beachmat can be incorporated into the code of other packages to drive analyses of a very large scRNA-seq data set. PMID:29723188

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types.

PubMed

Lun, Aaron T L; Pagès, Hervé; Smith, Mike L

2018-05-01

Biological experiments involving genomics or other high-throughput assays typically yield a data matrix that can be explored and analyzed using the R programming language with packages from the Bioconductor project. Improvements in the throughput of these assays have resulted in an explosion of data even from routine experiments, which poses a challenge to the existing computational infrastructure for statistical data analysis. For example, single-cell RNA sequencing (scRNA-seq) experiments frequently generate large matrices containing expression values for each gene in each cell, requiring sparse or file-backed representations for memory-efficient manipulation in R. These alternative representations are not easily compatible with high-performance C++ code used for computationally intensive tasks in existing R/Bioconductor packages. Here, we describe a C++ interface named beachmat, which enables agnostic data access from various matrix representations. This allows package developers to write efficient C++ code that is interoperable with dense, sparse and file-backed matrices, amongst others. We evaluated the performance of beachmat for accessing data from each matrix representation using both simulated and real scRNA-seq data, and defined a clear memory/speed trade-off to motivate the choice of an appropriate representation. We also demonstrate how beachmat can be incorporated into the code of other packages to drive analyses of a very large scRNA-seq data set.

Applications of nanotechnology in food packaging and food safety: barrier materials, antimicrobials and sensors.

PubMed

Duncan, Timothy V

2011-11-01

In this article, several applications of nanomaterials in food packaging and food safety are reviewed, including: polymer/clay nanocomposites as high barrier packaging materials, silver nanoparticles as potent antimicrobial agents, and nanosensors and nanomaterial-based assays for the detection of food-relevant analytes (gasses, small organic molecules and food-borne pathogens). In addition to covering the technical aspects of these topics, the current commercial status and understanding of health implications of these technologies are also discussed. These applications were chosen because they do not involve direct addition of nanoparticles to consumed foods, and thus are more likely to be marketed to the public in the short term. Published by Elsevier Inc.

Control of lipid oxidation by nonmigratory active packaging films prepared by photoinitiated graft polymerization.

PubMed

Tian, Fang; Decker, Eric A; Goddard, Julie M

2012-08-08

Transition metal-promoted oxidation impacts the quality, shelf life, and nutrition of many packaged foods. Metal-chelating active packaging therefore offers a means to protect foods against oxidation. Herein, we report the development and characterization of nonmigratory metal-chelating active packaging. To prepare the films, carboxylic acids were grafted onto the surfaces of polypropylene films by photoinitiated graft polymerization of acrylic acid. Attenuated total reflectance/Fourier transform infrared spectroscopy, contact angle, scanning electron microscopy, and iron-chelating assay were used to characterize film properties. Graft polymerization yielded a carboxylic acid density of 68.67 ± 9.99 nmol per cm(2) film, with ferrous iron-chelating activity of 71.07 ± 12.95 nmol per cm(2). The functionalized films extended the lag phase of lipid oxidation in a soybean oil-in-water emulsion system from 2 to 9 days. The application of such nonmigratory active packaging films represents a promising approach to reduce additive use while maintaining food quality.

BoolFilter: an R package for estimation and identification of partially-observed Boolean dynamical systems.

PubMed

Mcclenny, Levi D; Imani, Mahdi; Braga-Neto, Ulisses M

2017-11-25

Gene regulatory networks govern the function of key cellular processes, such as control of the cell cycle, response to stress, DNA repair mechanisms, and more. Boolean networks have been used successfully in modeling gene regulatory networks. In the Boolean network model, the transcriptional state of each gene is represented by 0 (inactive) or 1 (active), and the relationship among genes is represented by logical gates updated at discrete time points. However, the Boolean gene states are never observed directly, but only indirectly and incompletely through noisy measurements based on expression technologies such as cDNA microarrays, RNA-Seq, and cell imaging-based assays. The Partially-Observed Boolean Dynamical System (POBDS) signal model is distinct from other deterministic and stochastic Boolean network models in removing the requirement of a directly observable Boolean state vector and allowing uncertainty in the measurement process, addressing the scenario encountered in practice in transcriptomic analysis. BoolFilter is an R package that implements the POBDS model and associated algorithms for state and parameter estimation. It allows the user to estimate the Boolean states, network topology, and measurement parameters from time series of transcriptomic data using exact and approximated (particle) filters, as well as simulate the transcriptomic data for a given Boolean network model. Some of its infrastructure, such as the network interface, is the same as in the previously published R package for Boolean Networks BoolNet, which enhances compatibility and user accessibility to the new package. We introduce the R package BoolFilter for Partially-Observed Boolean Dynamical Systems (POBDS). The BoolFilter package provides a useful toolbox for the bioinformatics community, with state-of-the-art algorithms for simulation of time series transcriptomic data as well as the inverse process of system identification from data obtained with various expression technologies such as cDNA microarrays, RNA-Seq, and cell imaging-based assays.

Antimicrobial effectiveness of bioactive packaging materials from edible chitosan and casein polymers: assessment on carrot, cheese, and salami.

PubMed

Moreira, Maria del Rosario; Pereda, Mariana; Marcovich, Norma E; Roura, Sara I

2011-01-01

Antimicrobial packaging is one of the most promising active packaging systems for controlling spoilage and pathogenic microorganisms. In this work, the intrinsic antimicrobial properties of chitosan (CH) were combined with the excellent thermoplastic and film-forming properties of sodium caseinate (SC) to prepare SC/CH film-forming solutions and films. The antimicrobial effectiveness of SC, CH, and SC/CH coatings on the native microfloras of cheese, salami, and carrots was evaluated. In vitro assays through the test tube assay indicated that the most significant antimicrobial effect was achieved by CH and SC/CH solutions on carrot and cheese native microfloras. SC film-forming solutions did not exert antimicrobial activity on any of the native microflora studied. SC, CH, and SC/CH films stored in controlled environments showed that the retention of the antimicrobial action was observed until 5-d storage, at 65% relative humidity in both temperatures (10 °C and 20 °C). In vivo assays were also performed with SC, CH, and SC/CH applied as coatings or wrappers on the 3 food substrates. CH and SC/CH applied at both immersion and wrapper exerted a significant bactericidal action on mesophilic, psychrotrophic, and yeasts and molds counts, showing the 3 microbial populations analyzed a significant reduction (2.0 to 4.5 log CFU/g). An improvement of the bactericidal properties of the CH/SC blend respect to those of the neat CH film is reported. The ionic interaction between both macromolecules enhances its antimicrobial properties. Practical Application: The continuous consumer interest in high quality and food safety, combined with environmental concerns has stimulated the development and study of biodegradable coatings that avoid the use of synthetic materials. Among them, edible coatings, obtained from generally recognized as safe (GRAS) materials, have the potential to reduce weight loss, respiration rate, and improve food appearance and integrity. They can be used in combination with other food preservation techniques in order to extend the effectiveness of the food preservation chain. Moreover, antimicrobial films and coatings have innovated the concept of active packaging and have been developed to reduce, inhibit, or delay the growth of microorganisms on the surface of food in contact with the package. The use of antimicrobials packaging films to control the growth of microorganisms in food can have a significant impact on shelf-life extension and food safety. In addition, antimicrobial films can be prepared by the combination of inherent antimicrobial materials (that is, CH), with good film-forming protein-based ones (that is, SC). Therefore, the objective of this work is to study the performance of 2 biodegradable and edible biopolymers and their combination as natural packages for selected food products.

ROBOCAL: Gamma-ray isotopic hardware/software interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hurd, J.R.; Bonner, C.A.; Ostenak, C.A.

1989-01-01

ROBOCAL, presently being developed at the Los Alamos National Laboratory, is a full-scale prototypical robotic system for remotely performing calorimetric and gamma-ray isotopics measurements of nuclear materials. It features a fully automated vertical stacker-retriever for storing and retrieving packaged nuclear materials from a multi-drawer system, and a fully automated, uniquely integrated gantry robot for programmable selection and transfer of nuclear materials to calorimetric and gamma-ray isotopic measurement stations. Since ROBOCAL is to require almost no operator intervention, a mechanical control system is required in addition to a totally automated assay system. The assay system must be a completely integrated datamore » acquisition and isotopic analysis package fully capable of performing state-of-the-art homogeneous and heterogeneous analyses on many varied matrices. The TRIFID assay system being discussed at this conference by J. G. Fleissner of the Rocky Flats Plant has been adopted because of its many automated features. These include: MCA/ADC setup and acquisition; spectral storage and analysis utilizing an expert system formalism; report generation with internal measurement control printout; user friendly screens and menus. The mechanical control portion consists primarily of two detector platforms and a sample platform, each with independent movement. Some minor modifications and additions are needed with TRIFID to interface the assay and mechanical portions with the CimRoc 4000 software controlling the robot. 6 refs., 5 figs., 3 tabs.« less

Microplitis demolitor bracovirus genome segments vary in abundance and are individually packaged in virions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beck, Markus H.; Inman, Ross B.; Strand, Michael R.

2007-03-01

Polydnaviruses (PDVs) are distinguished by their unique association with parasitoid wasps and their segmented, double-stranded (ds) DNA genomes that are non-equimolar in abundance. Relatively little is actually known, however, about genome packaging or segment abundance of these viruses. Here, we conducted electron microscopy (EM) and real-time polymerase chain reaction (PCR) studies to characterize packaging and segment abundance of Microplitis demolitor bracovirus (MdBV). Like other PDVs, MdBV replicates in the ovaries of females where virions accumulate to form a suspension called calyx fluid. Wasps then inject a quantity of calyx fluid when ovipositing into hosts. The MdBV genome consists of 15more » segments that range from 3.6 (segment A) to 34.3 kb (segment O). EM analysis indicated that MdBV virions contain a single nucleocapsid that encapsidates one circular DNA of variable size. We developed a semi-quantitative real-time PCR assay using SYBR Green I. This assay indicated that five (J, O, H, N and B) segments of the MdBV genome accounted for more than 60% of the viral DNAs in calyx fluid. Estimates of relative segment abundance using our real-time PCR assay were also very similar to DNA size distributions determined from micrographs. Analysis of parasitized Pseudoplusia includens larvae indicated that copy number of MdBV segments C, B and J varied between hosts but their relative abundance within a host was virtually identical to their abundance in calyx fluid. Among-tissue assays indicated that each viral segment was most abundant in hemocytes and least abundant in salivary glands. However, the relative abundance of each segment to one another was similar in all tissues. We also found no clear relationship between MdBV segment and transcript abundance in hemocytes and fat body.« less

From Cells to Virus Particles: Quantitative Methods to Monitor RNA Packaging

PubMed Central

Ferrer, Mireia; Henriet, Simon; Chamontin, Célia; Lainé, Sébastien; Mougel, Marylène

2016-01-01

In cells, positive strand RNA viruses, such as Retroviridae, must selectively recognize their full-length RNA genome among abundant cellular RNAs to assemble and release particles. How viruses coordinate the intracellular trafficking of both RNA and protein components to the assembly sites of infectious particles at the cell surface remains a long-standing question. The mechanisms ensuring packaging of genomic RNA are essential for viral infectivity. Since RNA packaging impacts on several essential functions of retroviral replication such as RNA dimerization, translation and recombination events, there are many studies that require the determination of RNA packaging efficiency and/or RNA packaging ability. Studies of RNA encapsidation rely upon techniques for the identification and quantification of RNA species packaged by the virus. This review focuses on the different approaches available to monitor RNA packaging: Northern blot analysis, ribonuclease protection assay and quantitative reverse transcriptase-coupled polymerase chain reaction as well as the most recent RNA imaging and sequencing technologies. Advantages, disadvantages and limitations of these approaches will be discussed in order to help the investigator to choose the most appropriate technique. Although the review was written with the prototypic simple murine leukemia virus (MLV) and complex human immunodeficiency virus type 1 (HIV-1) in mind, the techniques were described in order to benefit to a larger community. PMID:27556480

The effectiveness of triclosan-incorporated plastic against bacteria on beef surfaces.

PubMed

Cutter, C N

1999-05-01

Triclosan is a nonionic, broad-spectrum, antimicrobial agent that has been incorporated into a variety of personal hygiene products, including hand soaps, deodorants, shower gels, mouthwashes, and toothpastes. In this study, plastic containing 1,500 ppm of triclosan was evaluated in plate overlay assays and meat experiments as a means of reducing populations of bacteria. Plate overlay assays indicated that the triclosan-incorporated plastic (TIP) inhibited the following organisms: Brochothrix thermosphacta ATCC 11509, Salmonella Typhimurium ATCC 14028, Staphylococcus aureus ATCC 12598, Bacillus subtilis ATCC 6051, Shigella flexneri ATCC 12022, Escherichia coli ATCC 25922, and several strains of E. coli O157:H7. In meat experiment 1, irradiated, lean beef surfaces inoculated with B. thermosphacta, Salmonella Typhimurium, E. coli O157:H7, or B. subtilis were covered with TIP, vacuum packaged, and stored for 24 h at 4 degrees C. Of the organisms tested, only populations of B. thermosphacta were slightly reduced. In meat experiment 2, prerigor beef surfaces were inoculated with E. coli O157: H7, Salmonella Typhimurium, or B. thermosphacta incubated at 4 degrees C for 24 h, wrapped in TIP or control plastic, vacuum packaged, and stored at 4 degrees C for up to 14 days. There was a slight reduction in the population of the organisms after initial application with TIP. However, bacterial populations following long-term, refrigerated (4 degrees C), vacuum-packaged storage up to 14 days were not statistically (P< or =0.05) or numerically different than controls. In meat experiment 3, even TIP-wrapped, vacuum-packaged beef samples that were temperature abused at 12 degrees C did not exhibit significant (P< or =0.05) or sustainable reductions after 14 days of 4 degrees C storage. Another study indicated that populations of E. coli O157:H7 or B. thermosphacta added directly to TIP were not affected after 2 h of refrigerated storage or that the antimicrobial activity could be extracted from the plastic. Additional experiments suggest that presence of fatty acids or adipose may diminish the antimicrobial activity of TIP on meat surfaces. This study demonstrates that while antimicrobial activity is detected against bacterial cultures in antimicrobial plate assays, plastic containing 1,500 ppm of triclosan does not effectively reduce bacterial populations on refrigerated, vacuum-packaged meat surfaces.

viRome: an R package for the visualization and analysis of viral small RNA sequence datasets.

PubMed

Watson, Mick; Schnettler, Esther; Kohl, Alain

2013-08-01

RNA interference (RNAi) is known to play an important part in defence against viruses in a range of species. Second-generation sequencing technologies allow us to assay these systems and the small RNAs that play a key role with unprecedented depth. However, scientists need access to tools that can condense, analyse and display the resulting data. Here, we present viRome, a package for R that takes aligned sequence data and produces a range of essential plots and reports. viRome is released under the BSD license as a package for R available for both Windows and Linux http://virome.sf.net. Additional information and a tutorial is available on the ARK-Genomics website: http://www.ark-genomics.org/bioinformatics/virome. mick.watson@roslin.ed.ac.uk.

An Immunoassay for Quantification of Contamination by Raw Meat Juice on Food Contact Surfaces.

PubMed

Chen, Fur-Chi; Godwin, Sandria; Chambers, Edgar

2016-11-01

Raw chicken products often are contaminated with Salmonella and Campylobacter , which can be transmitted from packages to contact surfaces. Raw meat juices from these packages also provide potential media for cross-contamination. There are limited quantitative data on the levels of consumer exposure to raw meat juice during shopping for and handling of chicken products. An exposure assessment is needed to quantify the levels of transmission and to assess the risk. An enzyme-linked immunosorbent assay (ELISA) was developed and validated for quantitative detection of raw meat juice on hands and various food contact surfaces. Analytical procedures were designed to maximize the recovery of raw meat juice from various surfaces: hands, plastic, wood, stainless steel, laminated countertops, glass, and ceramics. The ELISA was based on the detection of a soluble muscle protein, troponin I (TnI), in the raw meat juice. The assay can detect levels as low as 1.25 ng of TnI, which is equivalent to less than 1 μl of the raw meat juice. The concentrations of TnI in the raw meat juices from 10 retail chicken packages, as determined by ELISA, were between 0.46 and 3.56 ng/μl, with an average of 1.69 ng/μl. The analytical procedures, which include swabbing, extraction, and concentration, enable the detection of TnI from various surfaces. The recoveries of raw meat juice from surfaces of hands were 92%, and recoveries from other tested surfaces were from 55% on plastic cutting boards to 75% on laminated countertops. The ELISA developed has been used for monitoring the transfer of raw meat juice during shopping for and handling of raw chicken products in our studies. The assay also can be applied to other raw meat products, such as pork and beef.

R classes and methods for SNP array data.

PubMed

Scharpf, Robert B; Ruczinski, Ingo

2010-01-01

The Bioconductor project is an "open source and open development software project for the analysis and comprehension of genomic data" (1), primarily based on the R programming language. Infrastructure packages, such as Biobase, are maintained by Bioconductor core developers and serve several key roles to the broader community of Bioconductor software developers and users. In particular, Biobase introduces an S4 class, the eSet, for high-dimensional assay data. Encapsulating the assay data as well as meta-data on the samples, features, and experiment in the eSet class definition ensures propagation of the relevant sample and feature meta-data throughout an analysis. Extending the eSet class promotes code reuse through inheritance as well as interoperability with other R packages and is less error-prone. Recently proposed class definitions for high-throughput SNP arrays extend the eSet class. This chapter highlights the advantages of adopting and extending Biobase class definitions through a working example of one implementation of classes for the analysis of high-throughput SNP arrays.

Image analysis to evaluate the browning degree of banana (Musa spp.) peel.

PubMed

Cho, Jeong-Seok; Lee, Hyeon-Jeong; Park, Jung-Hoon; Sung, Jun-Hyung; Choi, Ji-Young; Moon, Kwang-Deog

2016-03-01

Image analysis was applied to examine banana peel browning. The banana samples were divided into 3 treatment groups: no treatment and normal packaging (Cont); CO2 gas exchange packaging (CO); normal packaging with an ethylene generator (ET). We confirmed that the browning of banana peels developed more quickly in the CO group than the other groups based on sensory test and enzyme assay. The G (green) and CIE L(∗), a(∗), and b(∗) values obtained from the image analysis sharply increased or decreased in the CO group. And these colour values showed high correlation coefficients (>0.9) with the sensory test results. CIE L(∗)a(∗)b(∗) values using a colorimeter also showed high correlation coefficients but comparatively lower than those of image analysis. Based on this analysis, browning of the banana occurred more quickly for CO2 gas exchange packaging, and image analysis can be used to evaluate the browning of banana peels. Copyright © 2015 Elsevier Ltd. All rights reserved.

Three-step Channel Conformational Changes Common to DNA Packaging Motors of Bacterial Viruses T3, T4, SPP1, and Phi29

PubMed Central

Wang, Shaoying; Ji, Zhouxiang; Yan, Erfu; Haque, Farzin; Guo, Peixuan

2016-01-01

The DNA packaging motor of dsDNA bacterial viruses contains a head-tail connector with a channel for genome to enter during assembly and to exit during host infection. The DNA packaging motor of bacterial virus phi29 was recently reported to use the “One-way Revolution” mechanism for DNA packaging. This raises a question of how dsDNA is ejected during infection if the channel acts as a one-way inward valve. Here we report a three step conformational change of the portal channel that is common among DNA translocation motors of bacterial viruses T3, T4, SPP1, and phi29. The channels of these motors exercise three discrete steps of gating, as revealed by electrophysiological assays. It is proposed that the three step channel conformational changes occur during DNA entry process, resulting in a structural transition in preparation of DNA movement in the reverse direction during ejection. PMID:27181501

Nuclease-resistant double-stranded DNA controls or standards for hepatitis B virus nucleic acid amplification assays

PubMed Central

2009-01-01

Background Identical blood samples tested using different kits can give markedly different hepatitis B virus (HBV) DNA levels, which can cause difficulty in the interpretation of viral load. A universal double-stranded DNA control or standard that can be used in all commercial HBV DNA nucleic acid amplification assay kits is urgently needed. By aligning all HBV genotypes (A-H), we found that the surface antigen gene and precore-core gene regions of HBV are the most conserved regions among the different HBV genotypes. We constructed a chimeric fragment by overlapping extension polymerase chain reaction and obtained a 1,349-bp HBVC+S fragment. We then packaged the fragment into lambda phages using a traditional lambda phage cloning procedure. Results The obtained armored DNA was resistant to DNase I digestion and was stable, noninfectious to humans, and could be easily extracted using commercial kits. More importantly, the armored DNA may be used with all HBV DNA nucleic acid amplification assay kits. Conclusions The lambda phage packaging system can be used as an excellent expression platform for armored DNA. The obtained armored DNA possessed all characteristics of an excellent positive control or standard. In addition, this armored DNA is likely to be appropriate for all commercial HBV DNA nucleic acid amplification detection kits. Thus, the constructed armored DNA can probably be used as a universal positive control or standard in HBV DNA assays. PMID:20025781

AOP: An R Package For Sufficient Causal Analysis in Pathway ...

EPA Pesticide Factsheets

Summary: How can I quickly find the key events in a pathway that I need to monitor to predict that a/an beneficial/adverse event/outcome will occur? This is a key question when using signaling pathways for drug/chemical screening in pharma-cology, toxicology and risk assessment. By identifying these sufficient causal key events, we have fewer events to monitor for a pathway, thereby decreasing assay costs and time, while maximizing the value of the information. I have developed the “aop” package which uses backdoor analysis of causal net-works to identify these minimal sets of key events that are suf-ficient for making causal predictions. Availability and Implementation: The source and binary are available online through the Bioconductor project (http://www.bioconductor.org/) as an R package titled “aop”. The R/Bioconductor package runs within the R statistical envi-ronment. The package has functions that can take pathways (as directed graphs) formatted as a Cytoscape JSON file as input, or pathways can be represented as directed graphs us-ing the R/Bioconductor “graph” package. The “aop” package has functions that can perform backdoor analysis to identify the minimal set of key events for making causal predictions.Contact: burgoon.lyle@epa.gov This paper describes an R/Bioconductor package that was developed to facilitate the identification of key events within an AOP that are the minimal set of sufficient key events that need to be tested/monit

Commercial processed food may have endocrine-disrupting potential: soy-based ingredients making the difference.

PubMed

Omoruyi, Iyekhoetin Matthew; Kabiersch, Grit; Pohjanvirta, Raimo

2013-01-01

Processed and packaged food items as well as ready-to-eat snacks are neglected and poorly characterised sources of human exposure to endocrine-disrupting chemicals (EDCs). In this study we investigated the presence of xenoestrogens in commercially processed and packaged Finnish foods, arising from substances deliberately added or inadvertently contaminating the food, substances formed as a result of food processing, or substances leaching from food packaging materials. Samples were obtained in three separate batches of equivalent products from both a supermarket and a local representative of a global chain of hamburger restaurants and extracted by a solid-phase extraction method. Their endocrine-disrupting potential was determined by yeast bioluminescent assay, using two recombinant yeast strains Saccharomyces cerevisiae BMAEREluc/ERα and S. cerevisiae BMA64/luc. In this test system, the majority of samples (both foodstuffs and wrappers) analysed proved negative. However, all batches of industrially prepared hamburgers (but not those obtained from a hamburger restaurant) as well as pepper salami significantly induced luciferase activity in the BMAEREluc/ERα yeast strain indicating the presence of xenoestrogens, with estradiol equivalents of these products ranging from 0.2 to 443 pg g(-1). All three products contained soy-based ingredients, which apparently accounted for, or at least contributed to, their high estrogenic activity, since no signal in the assay was observed with extracts of the packaging material, while two different soy sauces tested yielded an intense signal (28 and 54 pg ml(-1) estradiol-equivalent). These findings imply that by and large chemicals arising in the processing or packaging of foodstuffs in Finland constitute an insignificant source of xenoestrogens to consumers. However, soy-derived ingredients in certain food items might render the entire products highly estrogenic. The estrogenic activity of soy is attributed to isoflavones whose health effects - though widely considered beneficial - are controversial. As hamburgers are a popular type of food among children, the findings are noteworthy and possibly of concern.

RNA packaging device of double-stranded RNA bacteriophages, possibly as simple as hexamer of P4 protein.

PubMed

Kainov, Denis E; Pirttimaa, Markus; Tuma, Roman; Butcher, Sarah J; Thomas, George J; Bamford, Dennis H; Makeyev, Eugene V

2003-11-28

Genomes of complex viruses have been demonstrated, in many cases, to be packaged into preformed empty capsids (procapsids). This reaction is performed by molecular motors translocating nucleic acid against the concentration gradient at the expense of NTP hydrolysis. At present, the molecular mechanisms of packaging remain elusive due to the complex nature of packaging motors. In the case of the double-stranded RNA bacteriophage phi 6 from the Cystoviridae family, packaging of single-stranded genomic precursors requires a hexameric NTPase, P4. In the present study, the purified P4 proteins from two other cystoviruses, phi 8 and phi 13, were characterized and compared with phi 6 P4. All three proteins are hexameric, single-stranded RNA-stimulated NTPases with alpha/beta folds. Using a direct motor assay, we found that phi 8 and phi 13 P4 hexamers translocate 5' to 3' along ssRNA, whereas the analogous activity of phi 6 P4 requires association with the procapsid. This difference is explained by the intrinsically high affinity of phi 8 and phi 13 P4s for nucleic acids. The unidirectional translocation results in RNA helicase activity. Thus, P4 proteins of Cystoviridae exhibit extensive similarity to hexameric helicases and are simple models for studying viral packaging motor mechanisms.

Herpes simplex virus DNA packaging sequences adopt novel structures that are specifically recognized by a component of the cleavage and packaging machinery.

PubMed

Adelman, K; Salmon, B; Baines, J D

2001-03-13

The product of the herpes simplex virus type 1 U(L)28 gene is essential for cleavage of concatemeric viral DNA into genome-length units and packaging of this DNA into viral procapsids. To address the role of U(L)28 in this process, purified U(L)28 protein was assayed for the ability to recognize conserved herpesvirus DNA packaging sequences. We report that DNA fragments containing the pac1 DNA packaging motif can be induced by heat treatment to adopt novel DNA conformations that migrate faster than the corresponding duplex in nondenaturing gels. Surprisingly, these novel DNA structures are high-affinity substrates for U(L)28 protein binding, whereas double-stranded DNA of identical sequence composition is not recognized by U(L)28 protein. We demonstrate that only one strand of the pac1 motif is responsible for the formation of novel DNA structures that are bound tightly and specifically by U(L)28 protein. To determine the relevance of the observed U(L)28 protein-pac1 interaction to the cleavage and packaging process, we have analyzed the binding affinity of U(L)28 protein for pac1 mutants previously shown to be deficient in cleavage and packaging in vivo. Each of the pac1 mutants exhibited a decrease in DNA binding by U(L)28 protein that correlated directly with the reported reduction in cleavage and packaging efficiency, thereby supporting a role for the U(L)28 protein-pac1 interaction in vivo. These data therefore suggest that the formation of novel DNA structures by the pac1 motif confers added specificity on recognition of DNA packaging sequences by the U(L)28-encoded component of the herpesvirus cleavage and packaging machinery.

PrimerSuite: A High-Throughput Web-Based Primer Design Program for Multiplex Bisulfite PCR.

PubMed

Lu, Jennifer; Johnston, Andrew; Berichon, Philippe; Ru, Ke-Lin; Korbie, Darren; Trau, Matt

2017-01-24

The analysis of DNA methylation at CpG dinucleotides has become a major research focus due to its regulatory role in numerous biological processes, but the requisite need for assays which amplify bisulfite-converted DNA represents a major bottleneck due to the unique design constraints imposed on bisulfite-PCR primers. Moreover, a review of the literature indicated no available software solutions which accommodated both high-throughput primer design, support for multiplex amplification assays, and primer-dimer prediction. In response, the tri-modular software package PrimerSuite was developed to support bisulfite multiplex PCR applications. This software was constructed to (i) design bisulfite primers against multiple regions simultaneously (PrimerSuite), (ii) screen for primer-primer dimerizing artefacts (PrimerDimer), and (iii) support multiplex PCR assays (PrimerPlex). Moreover, a major focus in the development of this software package was the emphasis on extensive empirical validation, and over 1300 unique primer pairs have been successfully designed and screened, with over 94% of them producing amplicons of the expected size, and an average mapping efficiency of 93% when screened using bisulfite multiplex resequencing. The potential use of the software in other bisulfite-based applications such as methylation-specific PCR is under consideration for future updates. This resource is freely available for use at PrimerSuite website (www.primer-suite.com).

Single-pipetting microfluidic assay device for rapid detection of Salmonella from poultry package.

PubMed

Fronczek, Christopher F; You, David J; Yoon, Jeong-Yeol

2013-02-15

A direct, sensitive, near-real-time, handheld optical immunoassay device was developed to detect Salmonella typhimurium in the naturally occurring liquid from fresh poultry packages (hereafter "chicken matrix"), with just single pipetting of sample (i.e., no filtration, culturing and/or isolation, thus reducing the assay time and the error associated with them). Carboxylated, polystyrene microparticles were covalently conjugated with anti-Salmonella, and the immunoagglutination due to the presence of Salmonella was detected by reading the Mie scatter signals from the microfluidic channels using a handheld device. The presence of chicken matrix did not affect the light scatter signal, since the optical parameters (particle size d, wavelength of incident light λ and scatter angle θ) were optimized to minimize the effect of sample matrix (animal tissues and blood proteins, etc.). The sample was loaded into a microfluidic chip that was split into two channels, one pre-loaded with vacuum-dried, antibody-conjugated particles and the other with vacuum-dried, bovine serum albumin-conjugated particles. This eliminated the need for a separate negative control, effectively minimizing chip-to-chip and sample-to-sample variations. Particles and the sample were diffused in-channel through chemical agitation by Tween 80, also vacuum-dried within the microchannels. Sequential mixing of the sample to the reagents under a strict laminar flow condition synergistically improved the reproducibility and linearity of the assay. In addition, dried particles were shown to successfully detect lower Salmonella concentrations for up to 8 weeks. The handheld device contains simplified circuitry eliminating unnecessary adjustment stages, providing a stable signal, thus maximizing sensitivity. Total assay time was 10 min, and the detection limit 10 CFU mL(-1) was observed in all matrices, demonstrating the suitability of this device for field assays. Copyright © 2012 Elsevier B.V. All rights reserved.

Computational methods for evaluation of cell-based data assessment--Bioconductor.

PubMed

Le Meur, Nolwenn

2013-02-01

Recent advances in miniaturization and automation of technologies have enabled cell-based assay high-throughput screening, bringing along new challenges in data analysis. Automation, standardization, reproducibility have become requirements for qualitative research. The Bioconductor community has worked in that direction proposing several R packages to handle high-throughput data including flow cytometry (FCM) experiment. Altogether, these packages cover the main steps of a FCM analysis workflow, that is, data management, quality assessment, normalization, outlier detection, automated gating, cluster labeling, and feature extraction. Additionally, the open-source philosophy of R and Bioconductor, which offers room for new development, continuously drives research and improvement of theses analysis methods, especially in the field of clustering and data mining. This review presents the principal FCM packages currently available in R and Bioconductor, their advantages and their limits. Copyright © 2012 Elsevier Ltd. All rights reserved.

Development of antioxidant food packaging materials containing eugenol for extending display life of fresh beef.

PubMed

Navikaite-Snipaitiene, Vesta; Ivanauskas, Liudas; Jakstas, Valdas; Rüegg, Nadine; Rutkaite, Ramune; Wolfram, Evelyn; Yildirim, Selçuk

2018-05-23

In this study, clove essential oil (CL) or eugenol (EU) containing cellulose acetate (CA) or acrylic component/hydrophobically modified starch (AC/S) coatings on corona treated oriented polypropylene film (OPP) were designed and investigated for their possible applications as antioxidant packaging materials for fresh meat. The antioxidant properties of the coatings were investigated by Vapour Phase-DPPH (2,2-diphenyl-1-picrylhydrazyl) assay. The CA coatings containing CL or EU showed 43-92% and 43-94% inhibition against DPPH free radicals through the vapour phase, respectively, whereas AC/S/CL and AC/S/EU coatings resulted in DPPH inhibition of 21-65% and 25-84%, respectively. AC/S/EU and CA/EU coatings on OPP containing from 0.32 ± 0.03 to 6.40 ± 0.14 g/m 2 of EU were used to prepare packaging for fresh beef (Longissimus thoracis). After 14 days, the lipid oxidation in beef steaks kept in control and antioxidant packages was 3.33 and 1.00-1.22 mg of malondialdehyde per kilogram of meat, respectively. Moreover, red colour of beef in antioxidant packages was retained. Copyright © 2018 Elsevier Ltd. All rights reserved.

ProbeDesigner: for the design of probesets for branched DNA (bDNA) signal amplification assays.

PubMed

Bushnell, S; Budde, J; Catino, T; Cole, J; Derti, A; Kelso, R; Collins, M L; Molino, G; Sheridan, P; Monahan, J; Urdea, M

1999-05-01

The sensitivity and specificity of branched DNA (bDNA) assays are derived in part through the judicious design of the capture and label extender probes. To minimize non-specific hybridization (NSH) events, which elevate assay background, candidate probes must be computer screened for complementarity with generic sequences present in the assay. We present a software application which allows for rapid and flexible design of bDNA probesets for novel targets. It includes an algorithm for estimating the magnitude of NSH contribution to background, a mechanism for removing probes with elevated contributions, a methodology for the simultaneous design of probesets for multiple targets, and a graphical user interface which guides the user through the design steps. The program is available as a commercial package through the Pharmaceutical Drug Discovery program at Chiron Diagnostics.

TaqMan 5′-Nuclease Human Immunodeficiency Virus Type 1 PCR Assay with Phage-Packaged Competitive Internal Control for High-Throughput Blood Donor Screening

PubMed Central

Drosten, C.; Seifried, E.; Roth, W. K.

2001-01-01

Screening of blood donors for human immunodeficiency virus type 1 (HIV-1) infection by PCR permits the earlier diagnosis of HIV-1 infection compared with that by serologic assays. We have established a high-throughput reverse transcription (RT)-PCR assay based on 5′-nuclease PCR. By in-tube detection of HIV-1 RNA with a fluorogenic probe, the 5′-nuclease PCR technology (TaqMan PCR) eliminates the risk of carryover contamination, a major problem in PCR testing. We outline the development and evaluation of the PCR assay from a technical point of view. A one-step RT-PCR that targets the gag genes of all known HIV-1 group M isolates was developed. An internal control RNA detectable with a heterologous 5′-nuclease probe was derived from the viral target cDNA and was packaged into MS2 coliphages (Armored RNA). Because the RNA was protected against digestion with RNase, it could be spiked into patient plasma to control the complete sample preparation and amplification process. The assay detected 831 HIV-1 type B genome equivalents per ml of native plasma (95% confidence interval [CI], 759 to 936 HIV-1 B genome equivalents per ml) with a ≥95% probability of a positive result, as determined by probit regression analysis. A detection limit of 1,195 genome equivalents per ml of (individual) donor plasma (95% CI, 1,014 to 1,470 genome equivalents per ml of plasma pooled from individuals) was achieved when 96 samples were pooled and enriched by centrifugation. Up to 4,000 plasma samples per PCR run were tested in a 3-month trial period. Although data from the present pilot feasibility study will have to be complemented by a large clinical validation study, the assay is a promising approach to the high-throughput screening of blood donors and is the first noncommercial test for high-throughput screening for HIV-1. PMID:11724836

MS2 bacteriophage as a delivery vessel of porphyrins for photodynamic therapy

NASA Astrophysics Data System (ADS)

Cohen, Brian A.; Kaloyeros, Alain E.; Bergkvist, Magnus

2011-02-01

Challenges associated with photodynamic therapy (PDT) include the packaging and site-specific delivery of therapeutic agents to the tissue of interest. Nanoscale encapsulation of PDT agents inside targeted virus capsids is a novel concept for packaging and site-specific targeting. The icosahedral MS2 bacteriophage is one potential candidate for such a packaging-system. MS2 has a porous capsid with an exterior diameter of ~28 nm where the pores allow small molecules access to the capsid interior. Furthermore, MS2 presents suitable residues on the exterior capsid for conjugation of targeting ligands. Initial work by the present investigators has successfully demonstrated RNA-based self-packaging of a heterocyclic PDT agent (meso-tetrakis(para-N-trimethylanilinium)porphine, TMAP) into the MS2 capsid. Packaging photoactive compounds in confined spaces could result in energy transfer between the molecules upon photoactivation, which could in turn reduce the production of radical oxygen species (ROS). ROS are key components in photodynamic therapy, and a reduced production could negatively impact the efficacy of PDT treatment. Here, findings are presented from an investigation of ROS generation of TMAP encapsulated within the MS2 capsid compared to free TMAP in solution. Monitoring of ROS production upon photoactivation via a specific singlet oxygen assay revealed the impact on ROS generation between packaged porphyrins as compared to free porphyrin in an aqueous solution. Follow on work will study the ability of MS2-packaged porphyrins to generate ROS in vitro and subsequent cytotoxic effects on cells in culture.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Serwer, Philip, E-mail: serwer@uthscsa.edu; Wright, Elena T.; Liu, Zheng

DNA packaging of phages phi29, T3 and T7 sometimes produces incompletely packaged DNA with quantized lengths, based on gel electrophoretic band formation. We discover here a packaging ATPase-free, in vitro model for packaged DNA length quantization. We use directed evolution to isolate a five-site T3 point mutant that hyper-produces tail-free capsids with mature DNA (heads). Three tail gene mutations, but no head gene mutations, are present. A variable-length DNA segment leaks from some mutant heads, based on DNase I-protection assay and electron microscopy. The protected DNA segment has quantized lengths, based on restriction endonuclease analysis: six sharp bands of DNAmore » missing 3.7–12.3% of the last end packaged. Native gel electrophoresis confirms quantized DNA expulsion and, after removal of external DNA, provides evidence that capsid radius is the quantization-ruler. Capsid-based DNA length quantization possibly evolved via selection for stalling that provides time for feedback control during DNA packaging and injection. - Graphical abstract: Highlights: • We implement directed evolution- and DNA-sequencing-based phage assembly genetics. • We purify stable, mutant phage heads with a partially leaked mature DNA molecule. • Native gels and DNase-protection show leaked DNA segments to have quantized lengths. • Native gels after DNase I-removal of leaked DNA reveal the capsids to vary in radius. • Thus, we hypothesize leaked DNA quantization via variably quantized capsid radius.« less

[Efficient packaging retrovirus and construction of transgenic chicken technical platform].

PubMed

Man, Chaolai; Zhang, Qing; Chen, Yan; Zhu, Dahai

2007-10-01

Transgenic chicken and oviduct bioreactor are growing to be one of the hotspot of scientific study in the field of biology. The most successful method of producing transgenic chicken is pseudotyped retrovirus vector system, but no one has reported the production of transgenic chicken by retrovirus system recently in our country. In order to accelerate our study in this field, we introduced the relevant technical methods such as packaging retrovirus and vesicular stomatitis virus G glycoprotein (VSV-G) pseudotyped retrovirus, optimizing the conditions of packaging retrovirus, concentrating VSV-G pseudotyped retrovirus, helper virus assays, and microinjection of retrovirus. Furthermore, we successfully conducted in vivo study for detecting the marker gene EGFP of chicken embryo as well as in vitro study for detecting that gene of chicken embryo myoblast (CFM), thus we have provided an applied technical platform for studies of transgenic chicken in the future.

Detection of bisphenol A in food packaging based on fluorescent conjugated polymer PPESO3 and enzyme system.

PubMed

Huang, Hui; Li, Yongxin; Liu, Jintong; Tong, Jin; Su, Xingguang

2015-10-15

Bisphenol A (BPA) is a kind of carcinogen, which can interfere with the body's endocrine system. In this paper, a new kind of fluorescent sensor for BPA detection was established based on the fluorescent conjugated polymer PPESO3. The oxidative product of BPA is able to quench PPESO3 in the presence of HRP and H2O2, and the quenched PL intensity of PPESO3 was proportionally to the concentration of BPA in the range of 1-100 μmol/L with a detection limit of 4 × 10(-7) mol/L. The proposed method has been applied to detect BPA in eight food packaging samples with satisfactory results. The proposed method has the potential for the assay of BPA in food or food packaging samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

Packaging of Human Chromosome 19-Specific Adeno-Associated Virus (AAV) Integration Sites in AAV Virions during AAV Wild-Type and Recombinant AAV Vector Production

PubMed Central

Hüser, Daniela; Weger, Stefan; Heilbronn, Regine

2003-01-01

Adeno-associated virus type 2 (AAV-2) establishes latency by site-specific integration into a unique locus on human chromosome 19, called AAVS1. During the development of a sensitive real-time PCR assay for site-specific integration, AAV-AAVS1 junctions were reproducibly detected in highly purified AAV wild-type and recombinant AAV vector stocks. A series of controls documented that the junctions were packaged in AAV capsids and were newly generated during a single round of AAV production. Cloned junctions displayed variable AAV sequences fused to AAVS1. These data suggest that packaged junctions represent footprints of AAV integration during productive infection. Apparently, AAV latency established by site-specific integration and the helper virus-dependent, productive AAV cycle are more closely related than previously thought. PMID:12663794

The comet moment as a measure of DNA damage in the comet assay.

PubMed

Kent, C R; Eady, J J; Ross, G M; Steel, G G

1995-06-01

The development of rapid assays of radiation-induced DNA damage requires the definition of reliable parameters for the evaluation of dose-response relationships to compare with cellular endpoints. We have used the single-cell gel electrophoresis (SCGE) or 'comet' assay to measure DNA damage in individual cells after irradiation. Both the alkaline and neutral protocols were used. In both cases, DNA was stained with ethidium bromide and viewed using a fluorescence microscope at 516-560 nm. Images of comets were stored as 512 x 512 pixel images using OPTIMAS, an image analysis software package. Using this software we tested various parameters for measuring DNA damage. We have developed a method of analysis that rigorously conforms to the mathematical definition of the moment of inertia of a plane figure. This parameter does not require the identification of separate head and tail regions, but rather calculates a moment of the whole comet image. We have termed this parameter 'comet moment'. This method is simple to calculate and can be performed using most image analysis software packages that support macro facilities. In experiments on CHO-K1 cells, tail length was found to increase linearly with dose, but plateaued at higher doses. Comet moment also increased linearly with dose, but over a larger dose range than tail length and had no tendency to plateau.

An RNA-binding compound that stabilizes the HIV-1 gRNA packaging signal structure and specifically blocks HIV-1 RNA encapsidation.

PubMed

Ingemarsdotter, Carin K; Zeng, Jingwei; Long, Ziqi; Lever, Andrew M L; Kenyon, Julia C

2018-03-14

NSC260594, a quinolinium derivative from the NCI diversity set II compound library, was previously identified in a target-based assay as an inhibitor of the interaction between the HIV-1 (ψ) stem-loop 3 (SL3) RNA and Gag. This compound was shown to exhibit potent antiviral activity. Here, the effects of this compound on individual stages of the viral lifecycle were examined by qRT-PCR, ELISA and Western blot, to see if its actions were specific to the viral packaging stage. The structural effects of NSC260594 binding to the HIV-1 gRNA were also examined by SHAPE and dimerization assays. Treatment of cells with NSC260594 did not reduce the number of integration events of incoming virus, and treatment of virus producing cells did not affect the level of intracellular Gag protein or viral particle release as determined by immunoblot. However, NSC260594 reduced the incorporation of gRNA into virions by up to 82%, without affecting levels of gRNA inside the cell. This reduction in packaging correlated closely with the reduction in infectivity of the released viral particles. To establish the structural effects of NSC260594 on the HIV-1 gRNA, we performed SHAPE analyses to pinpoint RNA structural changes. NSC260594 had a stabilizing effect on the wild type RNA that was not confined to SL3, but that was propagated across the structure. A packaging mutant lacking SL3 did not show this effect. NSC260594 acts as a specific inhibitor of HIV-1 RNA packaging. No other viral functions are affected. Its action involves preventing the interaction of Gag with SL3 by stabilizing this small RNA stem-loop which then leads to stabilization of the global packaging signal region (psi or ψ). This confirms data, previously only shown in analyses of isolated SL3 oligonucleotides, that SL3 is structurally labile in the presence of Gag and that this is critical for the complete psi region to be able to adopt different conformations. Since replication is otherwise unaffected by NSC260594 the flexibility of SL3 appears to be a unique requirement for genome encapsidation and identifies this process as a highly specific drug target. This study is proof of principle that development of a new class of antiretroviral drugs that specifically target viral packaging by binding to the viral genomic RNA is achievable.

msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data.

PubMed

Mayne, Benjamin T; Leemaqz, Shalem Y; Buckberry, Sam; Rodriguez Lopez, Carlos M; Roberts, Claire T; Bianco-Miotto, Tina; Breen, James

2018-02-01

Genotyping-by-sequencing (GBS) or restriction-site associated DNA marker sequencing (RAD-seq) is a practical and cost-effective method for analysing large genomes from high diversity species. This method of sequencing, coupled with methylation-sensitive enzymes (often referred to as methylation-sensitive restriction enzyme sequencing or MRE-seq), is an effective tool to study DNA methylation in parts of the genome that are inaccessible in other sequencing techniques or are not annotated in microarray technologies. Current software tools do not fulfil all methylation-sensitive restriction sequencing assays for determining differences in DNA methylation between samples. To fill this computational need, we present msgbsR, an R package that contains tools for the analysis of methylation-sensitive restriction enzyme sequencing experiments. msgbsR can be used to identify and quantify read counts at methylated sites directly from alignment files (BAM files) and enables verification of restriction enzyme cut sites with the correct recognition sequence of the individual enzyme. In addition, msgbsR assesses DNA methylation based on read coverage, similar to RNA sequencing experiments, rather than methylation proportion and is a useful tool in analysing differential methylation on large populations. The package is fully documented and available freely online as a Bioconductor package ( https://bioconductor.org/packages/release/bioc/html/msgbsR.html ).

Packaging of Mason-Pfizer monkey virus (MPMV) genomic RNA depends upon conserved long-range interactions (LRIs) between U5 and gag sequences

PubMed Central

Kalloush, Rawan M.; Vivet-Boudou, Valérie; Ali, Lizna M.; Mustafa, Farah; Marquet, Roland; Rizvi, Tahir A.

2016-01-01

MPMV has great potential for development as a vector for gene therapy. In this respect, precisely defining the sequences and structural motifs that are important for dimerization and packaging of its genomic RNA (gRNA) are of utmost importance. A distinguishing feature of the MPMV gRNA packaging signal is two phylogenetically conserved long-range interactions (LRIs) between U5 and gag complementary sequences, LRI-I and LRI-II. To test their biological significance in the MPMV life cycle, we introduced mutations into these structural motifs and tested their effects on MPMV gRNA packaging and propagation. Furthermore, we probed the structure of key mutants using SHAPE (selective 2′hydroxyl acylation analyzed by primer extension). Disrupting base-pairing of the LRIs affected gRNA packaging and propagation, demonstrating their significance to the MPMV life cycle. A double mutant restoring a heterologous LRI-I was fully functional, whereas a similar LRI-II mutant failed to restore gRNA packaging and propagation. These results demonstrate that while LRI-I acts at the structural level, maintaining base-pairing is not sufficient for LRI-II function. In addition, in vitro RNA dimerization assays indicated that the loss of RNA packaging in LRI mutants could not be attributed to the defects in dimerization. Our findings suggest that U5-gag LRIs play an important architectural role in maintaining the structure of the 5′ region of the MPMV gRNA, expanding the crucial role of LRIs to the nonlentiviral group of retroviruses. PMID:27095024

A high-throughput assay format for determination of nitrate reductase and nitrite reductase enzyme activities

DOE Office of Scientific and Technical Information (OSTI.GOV)

McNally, N.; Liu, Xiang Yang; Choudary, P.V.

1997-01-01

The authors describe a microplate-based high-throughput procedure for rapid assay of the enzyme activities of nitrate reductase and nitrite reductase, using extremely small volumes of reagents. The new procedure offers the advantages of rapidity, small sample size-nanoliter volumes, low cost, and a dramatic increase in the throughput sample number that can be analyzed simultaneously. Additional advantages can be accessed by using microplate reader application software packages that permit assigning a group type to the wells, recording of the data on exportable data files and exercising the option of using the kinetic or endpoint reading modes. The assay can also bemore » used independently for detecting nitrite residues/contamination in environmental/food samples. 10 refs., 2 figs.« less

Measurement of radionuclides in waste packages

DOEpatents

Brodzinski, R.L.; Perkins, R.W.; Rieck, H.G.; Wogman, N.A.

1984-09-12

A method is described for non-destructively assaying the radionuclide content of solid waste in a sealed container by analysis of the waste's gamma-ray spectrum and neutron emissions. Some radionuclides are measured by characteristic photopeaks in the gamma-ray spectrum; transuranic nuclides are measured by neutron emission rate; other radionuclides are measured by correlation with those already measured.

Measurement of radionuclides in waste packages

DOEpatents

Brodzinski, Ronald L.; Perkins, Richard W.; Rieck, Henry G.; Wogman, Ned A.

1986-01-01

A method is described for non-destructively assaying the radionuclide content of solid waste in a sealed container by analysis of the waste's gamma-ray spectrum and neutron emissions. Some radionuclides are measured by characteristic photopeaks in the gamma-ray spectrum; transuranic nuclides are measured by neutron emission rate; other radionuclides are measured by correlation with those already measured.

A physical interaction between viral replicase and capsid protein is required for genome-packaging specificity in an RNA virus.

PubMed

Seo, Jang-Kyun; Kwon, Sun-Jung; Rao, A L N

2012-06-01

Genome packaging is functionally coupled to replication in RNA viruses pathogenic to humans (Poliovirus), insects (Flock house virus [FHV]), and plants (Brome mosaic virus [BMV]). However, the underlying mechanism is not fully understood. We have observed previously that in FHV and BMV, unlike ectopically expressed capsid protein (CP), packaging specificity results from RNA encapsidation by CP that has been translated from mRNA produced from replicating genomic RNA. Consequently, we hypothesize that a physical interaction with replicase increases the CP specificity for packaging viral RNAs. We tested this hypothesis by evaluating the molecular interaction between replicase protein and CP using a FHV-Nicotiana benthamiana system. Bimolecular fluorescence complementation in conjunction with fluorescent cellular protein markers and coimmunoprecipitation assays demonstrated that FHV replicase (protein A) and CP physically interact at the mitochondrial site of replication and that this interaction requires the N-proximal region from either amino acids 1 to 31 or amino acids 32 to 50 of the CP. In contrast to the mitochondrial localization of CP derived from FHV replication, ectopic expression displayed a characteristic punctate pattern on the endoplasmic reticulum (ER). This pattern was altered to relocalize the CP throughout the cytoplasm when the C-proximal hydrophobic domain was deleted. Analysis of the packaging phenotypes of the CP mutants defective either in protein A-CP interactions or ER localization suggested that synchronization between protein A-CP interaction and its subcellular localization is imperative to confer packaging specificity.

A Physical Interaction between Viral Replicase and Capsid Protein Is Required for Genome-Packaging Specificity in an RNA Virus

PubMed Central

Seo, Jang-Kyun; Kwon, Sun-Jung

2012-01-01

Genome packaging is functionally coupled to replication in RNA viruses pathogenic to humans (Poliovirus), insects (Flock house virus [FHV]), and plants (Brome mosaic virus [BMV]). However, the underlying mechanism is not fully understood. We have observed previously that in FHV and BMV, unlike ectopically expressed capsid protein (CP), packaging specificity results from RNA encapsidation by CP that has been translated from mRNA produced from replicating genomic RNA. Consequently, we hypothesize that a physical interaction with replicase increases the CP specificity for packaging viral RNAs. We tested this hypothesis by evaluating the molecular interaction between replicase protein and CP using a FHV-Nicotiana benthamiana system. Bimolecular fluorescence complementation in conjunction with fluorescent cellular protein markers and coimmunoprecipitation assays demonstrated that FHV replicase (protein A) and CP physically interact at the mitochondrial site of replication and that this interaction requires the N-proximal region from either amino acids 1 to 31 or amino acids 32 to 50 of the CP. In contrast to the mitochondrial localization of CP derived from FHV replication, ectopic expression displayed a characteristic punctate pattern on the endoplasmic reticulum (ER). This pattern was altered to relocalize the CP throughout the cytoplasm when the C-proximal hydrophobic domain was deleted. Analysis of the packaging phenotypes of the CP mutants defective either in protein A-CP interactions or ER localization suggested that synchronization between protein A-CP interaction and its subcellular localization is imperative to confer packaging specificity. PMID:22438552

Stochastic approach for radionuclides quantification

NASA Astrophysics Data System (ADS)

Clement, A.; Saurel, N.; Perrin, G.

2018-01-01

Gamma spectrometry is a passive non-destructive assay used to quantify radionuclides present in more or less complex objects. Basic methods using empirical calibration with a standard in order to quantify the activity of nuclear materials by determining the calibration coefficient are useless on non-reproducible, complex and single nuclear objects such as waste packages. Package specifications as composition or geometry change from one package to another and involve a high variability of objects. Current quantification process uses numerical modelling of the measured scene with few available data such as geometry or composition. These data are density, material, screen, geometric shape, matrix composition, matrix and source distribution. Some of them are strongly dependent on package data knowledge and operator backgrounds. The French Commissariat à l'Energie Atomique (CEA) is developing a new methodology to quantify nuclear materials in waste packages and waste drums without operator adjustment and internal package configuration knowledge. This method suggests combining a global stochastic approach which uses, among others, surrogate models available to simulate the gamma attenuation behaviour, a Bayesian approach which considers conditional probability densities of problem inputs, and Markov Chains Monte Carlo algorithms (MCMC) which solve inverse problems, with gamma ray emission radionuclide spectrum, and outside dimensions of interest objects. The methodology is testing to quantify actinide activity in different kind of matrix, composition, and configuration of sources standard in terms of actinide masses, locations and distributions. Activity uncertainties are taken into account by this adjustment methodology.

High-Voltage Leak Detection of a Parenteral Proteinaceous Solution Product Packaged in Form-Fill-Seal Plastic Laminate Bags. Part 3. Chemical Stability and Visual Appearance of a Protein-Based Aqueous Solution for Injection as a Function of HVLD Exposure.

PubMed

Rasmussen, Mats; Damgaard, Rasmus; Buus, Peter; Guazzo, Dana Morton

2013-01-01

This Part 3 of this three-part research series reports the impact of high-voltage leak detection (HVLD) exposure on the physico-chemical stability of the packaged product. The product, intended for human administration by injection, is an aqueous solution formulation of the rapid acting insulin analogue, insulin aspart (NovoRapid®/NovoLog®) by Novo Nordisk A/S, Bagsværd, Denmark. The package is a small-volume form-fill-seal plastic laminate bag. Product-packages exposed to HVLD were compared to unexposed product after storage for 9 months at recommended storage conditions of 5 ± 3 °C. No differences in active ingredient or degradation products assays were noted. No changes in any other stability indicating parameter results were observed. This report concludes this three-part series. Part 1 documented HVLD method development and validation work. Part 2 explored the impact of various package material, package temperature, and package storage conditions on HVLD test results. Detection of leaks in the bag seal area was investigated. In conclusion, HVLD is reported to be a validatable leak test method suitable for rapid, nondestructive container-closure integrity evaluation of the subject product-package. In Part 1 of this three-part series, a leak test method based on electrical conductivity and capacitance, also called high-voltage leak detection (HVLD), was proven to find hole leaks in small plastic bags filled with a solution of insulin aspart intended for human injection (NovoRapid®/NovoLog® by Novo Nordisk A/S, Bagsværd, Denmark). In Part 2, the ability of the HVLD method to find other types of package leaks was tested, and the impact of package material and product storage temperature on HVLD results was explored. This final Part 3 checked how well the packaged protein drug solution maintained its potency after HVLD exposure over 9 months of storage under long-term stability conditions. Results showed that HVLD caused no harm to the product.

Experiences with the in vivo and in vitro comet assay in regulatory testing.

PubMed

Frötschl, Roland

2015-01-01

The in vivo comet assay has recently been implemented into regulatory genotoxicity testing of pharmaceuticals with inclusion into the ICH S2R1 guidance. Regulatory genotoxicity testing aims to detect DNA alterations in form of gene mutations, larger scale chromosomal damage and recombination and aneuploidy. The ICH S2R1 guideline offers two options of standard batteries of tests for the detection of these endpoints. Both options start with an AMES assay and option 1 includes an in vitro mammalian cell assay and an in vivo micronucleus assay in rodent, whereas option 2 includes an in vivo micronucleus assay in bone marrow in rodent and a second in vivo assay in a second tissue with a second endpoint. The test recommended as second in vivo test is the comet assay in rat liver. The in vivo comet assay is considered as mature enough to ensure reliable detection of relevant in vivo genotoxicants in combination with the micronucleus test in bone marrow and the AMES assay. Although lots of research papers have been published using the in vitro comet assay, the in vitro version has not been implemented into official regulatory testing guidelines. A survey of the years 1999-2014 revealed 27 in vivo comet assays submitted to BfArM with market authorisation procedures, European and national advice procedures and clinical trial applications. In three procedures, in vitro comet assays had been submitted within the genetic toxicology packages. © The Author 2014. Published by Oxford University Press on behalf of the Mutagenesis Society. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Development of an in vitro PIG-A gene mutation assay in human cells

PubMed Central

Rees, Benjamin J; Tate, Matthew; Lynch, Anthony M; Thornton, Catherine A; Jenkins, Gareth J; Walmsley, Richard M; Johnson, George E

2017-01-01

Abstract Mutagens can be carcinogens, and traditionally, they have been identified in vitro using the Salmonella ‘Ames’ reverse mutation assay. However, prokaryotic DNA packaging, replication and repair systems are mechanistically very different to those in the humans we inevitably seek to protect. Therefore, for many years, mammalian cell line genotoxicity assays that can detect eukaryotic mutagens as well as clastogens and aneugens have been used. The apparent lack of specificity in these largely rodent systems, due partly to their mutant p53 status, has contributed to the use of animal studies to resolve data conflicts. Recently, silencing mutations at the PIG-A locus have been demonstrated to prevent glycophosphatidylinositol (GPI) anchor synthesis and consequentially result in loss of GPI-anchored proteins from the cell’s extracellular surface. The successful exploitation of this mutant phenotype in animal studies has triggered interest in the development of an analogous in vitro PIG-A mutation screening assay. This article describes the development of a robust assay design using metabolically active human cells. The assay includes viability and cell membrane integrity assessment and conforms to the future ideas of the 21st-century toxicology testing. PMID:28057708

Retrovirus-specific differences in matrix and nucleocapsid protein-nucleic acid interactions: implications for genomic RNA packaging.

PubMed

Sun, Meng; Grigsby, Iwen F; Gorelick, Robert J; Mansky, Louis M; Musier-Forsyth, Karin

2014-01-01

Retroviral RNA encapsidation involves a recognition event between genomic RNA (gRNA) and one or more domains in Gag. In HIV-1, the nucleocapsid (NC) domain is involved in gRNA packaging and displays robust nucleic acid (NA) binding and chaperone functions. In comparison, NC of human T-cell leukemia virus type 1 (HTLV-1), a deltaretrovirus, displays weaker NA binding and chaperone activity. Mutation of conserved charged residues in the deltaretrovirus bovine leukemia virus (BLV) matrix (MA) and NC domains affects virus replication and gRNA packaging efficiency. Based on these observations, we hypothesized that the MA domain may generally contribute to NA binding and genome encapsidation in deltaretroviruses. Here, we examined the interaction between HTLV-2 and HIV-1 MA proteins and various NAs in vitro. HTLV-2 MA displays higher NA binding affinity and better chaperone activity than HIV-1 MA. HTLV-2 MA also binds NAs with higher affinity than HTLV-2 NC and displays more robust chaperone function. Mutation of two basic residues in HTLV-2 MA α-helix II, previously implicated in BLV gRNA packaging, reduces NA binding affinity. HTLV-2 MA binds with high affinity and specificity to RNA derived from the putative packaging signal of HTLV-2 relative to nonspecific NA. Furthermore, an HIV-1 MA triple mutant designed to mimic the basic character of HTLV-2 MA α-helix II dramatically improves binding affinity and chaperone activity of HIV-1 MA in vitro and restores RNA packaging to a ΔNC HIV-1 variant in cell-based assays. Taken together, these results are consistent with a role for deltaretrovirus MA proteins in viral RNA packaging.

Packaging of Mason-Pfizer monkey virus (MPMV) genomic RNA depends upon conserved long-range interactions (LRIs) between U5 and gag sequences.

PubMed

Kalloush, Rawan M; Vivet-Boudou, Valérie; Ali, Lizna M; Mustafa, Farah; Marquet, Roland; Rizvi, Tahir A

2016-06-01

MPMV has great potential for development as a vector for gene therapy. In this respect, precisely defining the sequences and structural motifs that are important for dimerization and packaging of its genomic RNA (gRNA) are of utmost importance. A distinguishing feature of the MPMV gRNA packaging signal is two phylogenetically conserved long-range interactions (LRIs) between U5 and gag complementary sequences, LRI-I and LRI-II. To test their biological significance in the MPMV life cycle, we introduced mutations into these structural motifs and tested their effects on MPMV gRNA packaging and propagation. Furthermore, we probed the structure of key mutants using SHAPE (selective 2'hydroxyl acylation analyzed by primer extension). Disrupting base-pairing of the LRIs affected gRNA packaging and propagation, demonstrating their significance to the MPMV life cycle. A double mutant restoring a heterologous LRI-I was fully functional, whereas a similar LRI-II mutant failed to restore gRNA packaging and propagation. These results demonstrate that while LRI-I acts at the structural level, maintaining base-pairing is not sufficient for LRI-II function. In addition, in vitro RNA dimerization assays indicated that the loss of RNA packaging in LRI mutants could not be attributed to the defects in dimerization. Our findings suggest that U5-gag LRIs play an important architectural role in maintaining the structure of the 5' region of the MPMV gRNA, expanding the crucial role of LRIs to the nonlentiviral group of retroviruses. © 2016 Kalloush et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

A review of digital microfluidics as portable platforms for lab-on a-chip applications.

PubMed

Samiei, Ehsan; Tabrizian, Maryam; Hoorfar, Mina

2016-07-07

Following the development of microfluidic systems, there has been a high tendency towards developing lab-on-a-chip devices for biochemical applications. A great deal of effort has been devoted to improve and advance these devices with the goal of performing complete sets of biochemical assays on the device and possibly developing portable platforms for point of care applications. Among the different microfluidic systems used for such a purpose, digital microfluidics (DMF) shows high flexibility and capability of performing multiplex and parallel biochemical operations, and hence, has been considered as a suitable candidate for lab-on-a-chip applications. In this review, we discuss the most recent advances in the DMF platforms, and evaluate the feasibility of developing multifunctional packages for performing complete sets of processes of biochemical assays, particularly for point-of-care applications. The progress in the development of DMF systems is reviewed from eight different aspects, including device fabrication, basic fluidic operations, automation, manipulation of biological samples, advanced operations, detection, biological applications, and finally, packaging and portability of the DMF devices. Success in developing the lab-on-a-chip DMF devices will be concluded based on the advances achieved in each of these aspects.

Detection of M. tuberculosis using DNA chips combined with an image analysis system.

PubMed

Huang, T-S; Liu, Y-C; Bair, C-H; Sy, C-L; Chen, Y-S; Tu, H-Z; Chen, B-C

2008-01-01

To develop a packaged DNA chip assay (the DR. MTBC Screen assay) for direct detection of the Mycobacterium tuberculosis complex. We described a DNA chip assay based on the IS6110 gene that can be used for the detection of M. tuberculosis complex. Probes were spotted onto the polystyrene strips in the wells of 96-well microtitre plates and used for hybridisation with biotin-labelled amplicon to yield a pattern of visualised positive spots. The plate image was scanned, analysed and interpreted automatically. The results corresponded well with those obtained by conventional culture as well as clinical diagnosis, with sensitivity and specificity rates of respectively 83.8% and 94.2%, and 84.6% and 96.3%. We conclude that the DR. MTBC Screen assay can detect M. tuberculosis complex rapidly in respiratory specimens, readily adapts to routine work and provides a flexible choice to meet different cost-effectiveness and automation needs in TB-endemic countries. The cost for reagents is around US$10 per sample.

A multiparametric assay for quantitative nerve regeneration evaluation.

PubMed

Weyn, B; van Remoortere, M; Nuydens, R; Meert, T; van de Wouwer, G

2005-08-01

We introduce an assay for the semi-automated quantification of nerve regeneration by image analysis. Digital images of histological sections of regenerated nerves are recorded using an automated inverted microscope and merged into high-resolution mosaic images representing the entire nerve. These are analysed by a dedicated image-processing package that computes nerve-specific features (e.g. nerve area, fibre count, myelinated area) and fibre-specific features (area, perimeter, myelin sheet thickness). The assay's performance and correlation of the automatically computed data with visually obtained data are determined on a set of 140 semithin sections from the distal part of a rat tibial nerve from four different experimental treatment groups (control, sham, sutured, cut) taken at seven different time points after surgery. Results show a high correlation between the manually and automatically derived data, and a high discriminative power towards treatment. Extra value is added by the large feature set. In conclusion, the assay is fast and offers data that currently can be obtained only by a combination of laborious and time-consuming tests.

Corneal epithelial cell biocompatibility to silicone hydrogel and conventional hydrogel contact lens packaging solutions

PubMed Central

Tanti, N.C.; Jones, L.; Sheardown, H.

2010-01-01

Purpose Although all contact lenses (CLs) are applied initially to the eye directly from a packaging solution, little is known about the effects of these solutions on human corneal epithelial cells (HCECs). Due to the porous nature of CL materials, they have the potential to sorb components of the packaging solution during storage, which could then be subsequently released upon insertion of the CL on the eye. The purpose of this study was to investigate the effect of various packaging solutions on HCECs, using an in vitro model. Methods An in vitro assay was developed whereby various silicone hydrogels and conventional, poly-2-hydroxyethylmethacrylate  (polyHEMA)-based lens materials were removed directly from their packaging and then incubated for up to 24 h with HCECs. The effect of the retained and released packaging solution components on HCECs was assessed by measuring cell viability, adhesion phenotype, and apoptosis. Results Incubation of HCECs with CLs stored in borate-buffered packaging solutions resulted in a significant reduction in cell viability. Adherent cells incubated with these CLs also exhibited reduced levels of β1 and α3 integrin. Soaking borate-buffered packaged CLs in PBS before cell incubation resolved viability and integrin expression in all cases, with the exception of galyfilcon A and balafilcon A, from which a 20% reduction in cell viability was still observed. In comparison, CLs stored in phosphate-buffered packaging solutions had cellular viability and expression of integrins similar to control cells (cells incubated in the absence of a lens). When incubated with cells at a 10% concentration in serum-free medium, borate-buffered packaging solutions and borate-containing saline (Unisol 4) significantly reduced cell viability and integrin expression. Neither caspase activation nor annexin V binding was observed on cells following exposure to borate buffer solution. However, a significant decrease in reactive oxygen species was observed at 24 h. These latter results suggest that in vitro exposure to low concentration of borate/boric acid results in cell dysfunction, leading to necrosis rather than apoptosis. Conclusions Borate-buffered packaging solutions were shown to adversely affect the viability and integrin expression of HCECs in vitro. When used in ophthalmic packaging solutions, the antimicrobial properties of borate buffer may be outweighed by its relatively cytotoxic effects on cells. PMID:20169012

Corneal epithelial cell biocompatibility to silicone hydrogel and conventional hydrogel contact lens packaging solutions.

PubMed

Gorbet, M B; Tanti, N C; Jones, L; Sheardown, H

2010-02-19

Although all contact lenses (CLs) are applied initially to the eye directly from a packaging solution, little is known about the effects of these solutions on human corneal epithelial cells (HCECs). Due to the porous nature of CL materials, they have the potential to sorb components of the packaging solution during storage, which could then be subsequently released upon insertion of the CL on the eye. The purpose of this study was to investigate the effect of various packaging solutions on HCECs, using an in vitro model. An in vitro assay was developed whereby various silicone hydrogels and conventional, poly-2-hydroxyethylmethacrylate (polyHEMA)-based lens materials were removed directly from their packaging and then incubated for up to 24 h with HCECs. The effect of the retained and released packaging solution components on HCECs was assessed by measuring cell viability, adhesion phenotype, and apoptosis. Incubation of HCECs with CLs stored in borate-buffered packaging solutions resulted in a significant reduction in cell viability. Adherent cells incubated with these CLs also exhibited reduced levels of beta(1) and alpha(3) integrin. Soaking borate-buffered packaged CLs in PBS before cell incubation resolved viability and integrin expression in all cases, with the exception of galyfilcon A and balafilcon A, from which a 20% reduction in cell viability was still observed. In comparison, CLs stored in phosphate-buffered packaging solutions had cellular viability and expression of integrins similar to control cells (cells incubated in the absence of a lens). When incubated with cells at a 10% concentration in serum-free medium, borate-buffered packaging solutions and borate-containing saline (Unisol 4) significantly reduced cell viability and integrin expression. Neither caspase activation nor annexin V binding was observed on cells following exposure to borate buffer solution. However, a significant decrease in reactive oxygen species was observed at 24 h. These latter results suggest that in vitro exposure to low concentration of borate/boric acid results in cell dysfunction, leading to necrosis rather than apoptosis. Borate-buffered packaging solutions were shown to adversely affect the viability and integrin expression of HCECs in vitro. When used in ophthalmic packaging solutions, the antimicrobial properties of borate buffer may be outweighed by its relatively cytotoxic effects on cells.

Optimal packaging of FIV genomic RNA depends upon a conserved long-range interaction and a palindromic sequence within gag.

PubMed

Rizvi, Tahir A; Kenyon, Julia C; Ali, Jahabar; Aktar, Suriya J; Phillip, Pretty S; Ghazawi, Akela; Mustafa, Farah; Lever, Andrew M L

2010-10-15

The feline immunodeficiency virus (FIV) is a lentivirus that is related to human immunodeficiency virus (HIV), causing a similar pathology in cats. It is a potential small animal model for AIDS and the FIV-based vectors are also being pursued for human gene therapy. Previous studies have mapped the FIV packaging signal (ψ) to two or more discontinuous regions within the 5' 511 nt of the genomic RNA and structural analyses have determined its secondary structure. The 5' and 3' sequences within ψ region interact through extensive long-range interactions (LRIs), including a conserved heptanucleotide interaction between R/U5 and gag. Other secondary structural elements identified include a conserved 150 nt stem-loop (SL2) and a small palindromic stem-loop within gag open reading frame that might act as a viral dimerization initiation site. We have performed extensive mutational analysis of these sequences and structures and ascertained their importance in FIV packaging using a trans-complementation assay. Disrupting the conserved heptanucleotide LRI to prevent base pairing between R/U5 and gag reduced packaging by 2.8-5.5 fold. Restoration of pairing using an alternative, non-wild type (wt) LRI sequence restored RNA packaging and propagation to wt levels, suggesting that it is the structure of the LRI, rather than its sequence, that is important for FIV packaging. Disrupting the palindrome within gag reduced packaging by 1.5-3-fold, but substitution with a different palindromic sequence did not restore packaging completely, suggesting that the sequence of this region as well as its palindromic nature is important. Mutation of individual regions of SL2 did not have a pronounced effect on FIV packaging, suggesting that either it is the structure of SL2 as a whole that is necessary for optimal packaging, or that there is redundancy within this structure. The mutational analysis presented here has further validated the previously predicted RNA secondary structure of FIV ψ. Copyright © 2010 Elsevier Ltd. All rights reserved.

A Vignette (User’s Guide) for “An R Package for Statistical Analysis of Chemistry, Histopathology, and Reproduction Endpoints Including Repeated Measures and Multi-Generation Studies (StatCharrms).”

EPA Science Inventory

StatCharrms is a graphical user front-end for ease of use in analyzing data generated from OCSPP 890.2200, Medaka Extended One Generation Reproduction Test (MEOGRT) and OCSPP 890.2300, Larval Amphibian Gonad Development Assay (LAGDA). The analyses StatCharrms is capable of perfor...

Structure-Based Mutagenesis of Sulfolobus Turreted Icosahedral Virus B204 Reveals Essential Residues in the Virion-Associated DNA-Packaging ATPase.

PubMed

Dellas, Nikki; Snyder, Jamie C; Dills, Michael; Nicolay, Sheena J; Kerchner, Keshia M; Brumfield, Susan K; Lawrence, C Martin; Young, Mark J

2015-12-23

Sulfolobus turreted icosahedral virus (STIV), an archaeal virus that infects the hyperthermoacidophile Sulfolobus solfataricus, is one of the most well-studied viruses of the domain Archaea. STIV shares structural, morphological, and sequence similarities with viruses from other domains of life, all of which are thought to belong to the same viral lineage. Several of these common features include a conserved coat protein fold, an internal lipid membrane, and a DNA-packaging ATPase. B204 is the ATPase encoded by STIV and is thought to drive packaging of viral DNA during the replication process. Here, we report the crystal structure of B204 along with the biochemical analysis of B204 mutants chosen based on structural information and sequence conservation patterns observed among members of the same viral lineage and the larger FtsK/HerA superfamily to which B204 belongs. Both in vitro ATPase activity assays and transfection assays with mutant forms of B204 confirmed the essentiality of conserved and nonconserved positions. We also have identified two distinct particle morphologies during an STIV infection that differ in the presence or absence of the B204 protein. The biochemical and structural data presented here are not only informative for the STIV replication process but also can be useful in deciphering DNA-packaging mechanisms for other viruses belonging to this lineage. STIV is a virus that infects a host from the domain Archaea that replicates in high-temperature, acidic environments. While STIV has many unique features, there exist several striking similarities between this virus and others that replicate in different environments and infect a broad range of hosts from Bacteria and Eukarya. Aside from structural features shared by viruses from this lineage, there exists a significant level of sequence similarity between the ATPase genes carried by these different viruses; this gene encodes an enzyme thought to provide energy that drives DNA packaging into the virion during infection. The experiments described here highlight the elements of this enzyme that are essential for proper function and also provide supporting evidence that B204 is present in the mature STIV virion. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

An RNA Domain Imparts Specificity and Selectivity to a Viral DNA Packaging Motor

PubMed Central

Zhao, Wei; Jardine, Paul J.

2015-01-01

ABSTRACT During assembly, double-stranded DNA viruses, including bacteriophages and herpesviruses, utilize a powerful molecular motor to package their genomic DNA into a preformed viral capsid. An integral component of the packaging motor in the Bacillus subtilis bacteriophage ϕ29 is a viral genome-encoded pentameric ring of RNA (prohead RNA [pRNA]). pRNA is a 174-base transcript comprised of two domains, domains I and II. Early studies initially isolated a 120-base form (domain I only) that retains high biological activity in vitro; hence, no function could be assigned to domain II. Here we define a role for this domain in the packaging process. DNA packaging using restriction digests of ϕ29 DNA showed that motors with the 174-base pRNA supported the correct polarity of DNA packaging, selectively packaging the DNA left end. In contrast, motors containing the 120-base pRNA had compromised specificity, packaging both left- and right-end fragments. The presence of domain II also provides selectivity in competition assays with genomes from related phages. Furthermore, motors with the 174-base pRNA were restrictive, in that they packaged only one DNA fragment into the head, whereas motors with the 120-base pRNA packaged several fragments into the head, indicating multiple initiation events. These results show that domain II imparts specificity and stringency to the motor during the packaging initiation events that precede DNA translocation. Heteromeric rings of pRNA demonstrated that one or two copies of domain II were sufficient to impart this selectivity/stringency. Although ϕ29 differs from other double-stranded DNA phages in having an RNA motor component, the function provided by pRNA is carried on the motor protein components in other phages. IMPORTANCE During virus assembly, genome packaging involves the delivery of newly synthesized viral nucleic acid into a protein shell. In the double-stranded DNA phages and herpesviruses, this is accomplished by a powerful molecular motor that translocates the viral DNA into a preformed viral shell. A key event in DNA packaging is recognition of the viral DNA among other nucleic acids in the host cell. Commonly, a DNA-binding protein mediates the interaction of viral DNA with the motor/head shell. Here we show that for the bacteriophage ϕ29, this essential step of genome recognition is mediated by a viral genome-encoded RNA rather than a protein. A domain of the prohead RNA (pRNA) imparts specificity and stringency to the motor by ensuring the correct orientation of DNA packaging and restricting initiation to a single event. Since this assembly step is unique to the virus, DNA packaging is a novel target for the development of antiviral drugs. PMID:26423956

An RNA Domain Imparts Specificity and Selectivity to a Viral DNA Packaging Motor.

PubMed

Zhao, Wei; Jardine, Paul J; Grimes, Shelley

2015-12-01

During assembly, double-stranded DNA viruses, including bacteriophages and herpesviruses, utilize a powerful molecular motor to package their genomic DNA into a preformed viral capsid. An integral component of the packaging motor in the Bacillus subtilis bacteriophage ϕ29 is a viral genome-encoded pentameric ring of RNA (prohead RNA [pRNA]). pRNA is a 174-base transcript comprised of two domains, domains I and II. Early studies initially isolated a 120-base form (domain I only) that retains high biological activity in vitro; hence, no function could be assigned to domain II. Here we define a role for this domain in the packaging process. DNA packaging using restriction digests of ϕ29 DNA showed that motors with the 174-base pRNA supported the correct polarity of DNA packaging, selectively packaging the DNA left end. In contrast, motors containing the 120-base pRNA had compromised specificity, packaging both left- and right-end fragments. The presence of domain II also provides selectivity in competition assays with genomes from related phages. Furthermore, motors with the 174-base pRNA were restrictive, in that they packaged only one DNA fragment into the head, whereas motors with the 120-base pRNA packaged several fragments into the head, indicating multiple initiation events. These results show that domain II imparts specificity and stringency to the motor during the packaging initiation events that precede DNA translocation. Heteromeric rings of pRNA demonstrated that one or two copies of domain II were sufficient to impart this selectivity/stringency. Although ϕ29 differs from other double-stranded DNA phages in having an RNA motor component, the function provided by pRNA is carried on the motor protein components in other phages. During virus assembly, genome packaging involves the delivery of newly synthesized viral nucleic acid into a protein shell. In the double-stranded DNA phages and herpesviruses, this is accomplished by a powerful molecular motor that translocates the viral DNA into a preformed viral shell. A key event in DNA packaging is recognition of the viral DNA among other nucleic acids in the host cell. Commonly, a DNA-binding protein mediates the interaction of viral DNA with the motor/head shell. Here we show that for the bacteriophage ϕ29, this essential step of genome recognition is mediated by a viral genome-encoded RNA rather than a protein. A domain of the prohead RNA (pRNA) imparts specificity and stringency to the motor by ensuring the correct orientation of DNA packaging and restricting initiation to a single event. Since this assembly step is unique to the virus, DNA packaging is a novel target for the development of antiviral drugs. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging.

PubMed

Smyth, Redmond P; Smith, Maureen R; Jousset, Anne-Caroline; Despons, Laurence; Laumond, Géraldine; Decoville, Thomas; Cattenoz, Pierre; Moog, Christiane; Jossinet, Fabrice; Mougel, Marylène; Paillart, Jean-Christophe; von Kleist, Max; Marquet, Roland

2018-05-18

Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell MIME) as a way to define RNA regulatory landscapes at single nucleotide resolution under native conditions. In cell MIME is based on (i) random mutation of an RNA target, (ii) expression of mutated RNA in cells, (iii) physical separation of RNA into functional and non-functional populations, and (iv) high-throughput sequencing to identify mutations affecting function. We used in cell MIME to define RNA elements within the 5' region of the HIV-1 genomic RNA (gRNA) that are important for viral replication in cells. We identified three distinct RNA motifs controlling intracellular gRNA production, and two distinct motifs required for gRNA packaging into virions. Our analysis reveals the 73AAUAAA78 polyadenylation motif within the 5' PolyA domain as a dual regulator of gRNA production and gRNA packaging, and demonstrates that a functional polyadenylation signal is required for viral packaging even though it negatively affects gRNA production.

Characterization and antimicrobial properties of food packaging methylcellulose films containing stem extract of Ginja cherry.

PubMed

Campos, Débora; Piccirillo, Clara; Pullar, Robert C; Castro, Paula Ml; Pintado, Maria M E

2014-08-01

Food contamination and spoilage is a problem causing growing concern. To avoid it, the use of food packaging with appropriate characteristics is essential; ideally, the packaging should protect food from external contamination and exhibit antibacterial properties. With this aim, methylcellulose (MC) films containing natural extracts from the stems of Ginja cherry, an agricultural by-product, were developed and characterized. The antibacterial activity of films was screened by the disc diffusion method and quantified using the viable cell count assay. The films inhibited the growth of both Gram-positive and Gram-negative strains (Listeria innocua, methicillin-sensitive Staphylococcus aureus, methicillin-resistant S. aureus, Salmonella Enteritidis, Escherichia coli). For the films with lower extract content, effectiveness against the microorganisms depended on the inoculum concentration. Scanning electron microscope images of the films showed that those containing the extracts had a smooth and continuous structure. UV-visible spectroscopy showed that these materials do not transmit light in the UV. This study shows that MC films containing agricultural by-products, in this case Ginja cherry stem extract, could be used to prevent food contamination by relevant bacterial strains and degradation by UV light. Using such materials in food packaging, the shelf life of food products could be extended while utilizing an otherwise wasted by-product. © 2013 Society of Chemical Industry.

In cell mutational interference mapping experiment (in cell MIME) identifies the 5′ polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging

PubMed Central

Smith, Maureen R; Jousset, Anne-Caroline; Despons, Laurence; Laumond, Géraldine; Decoville, Thomas; Cattenoz, Pierre; Moog, Christiane; Jossinet, Fabrice; Mougel, Marylène; Paillart, Jean-Christophe

2018-01-01

Abstract Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell MIME) as a way to define RNA regulatory landscapes at single nucleotide resolution under native conditions. In cell MIME is based on (i) random mutation of an RNA target, (ii) expression of mutated RNA in cells, (iii) physical separation of RNA into functional and non-functional populations, and (iv) high-throughput sequencing to identify mutations affecting function. We used in cell MIME to define RNA elements within the 5′ region of the HIV-1 genomic RNA (gRNA) that are important for viral replication in cells. We identified three distinct RNA motifs controlling intracellular gRNA production, and two distinct motifs required for gRNA packaging into virions. Our analysis reveals the 73AAUAAA78 polyadenylation motif within the 5′ PolyA domain as a dual regulator of gRNA production and gRNA packaging, and demonstrates that a functional polyadenylation signal is required for viral packaging even though it negatively affects gRNA production. PMID:29514260

Further characterisation of rotavirus cores: Ss(+)RNAs can be packaged in vitro but packaging lacks sequence specificity☆

PubMed Central

Desselberger, Ulrich; Richards, James; Tchertanov, Luba; Lepault, Jean; Lever, Andrew; Burrone, Oscar; Cohen, Jean

2013-01-01

Rotavirus (RV) cores were released from double-layered particles (DLPs) by high concentrations of CaCl2, purified and ‘opened’ by treatment with EDTA or EGTA. Under appropriate in vitro conditions DLPs have been shown to have transcriptase and ‘open cores’ replicase activity. Furthermore, it has been demonstrated that transcriptase activity and infectivity of native cores can be restored by transcapsidation with VP6, VP7 and VP4. The missing link for particle reconstitution in vitro has been the manipulation of ‘open cores’ to become functionally active cores again. The experiments described here were undertaken with the aim of exploring packaging of RV RNAs into opened cores in vitro. Rotavirus cores were opened by approximately 200 μM EGTA, leading to the release of genomic dsRNA. Conversely, RV cores were found to be stable in the presence of minimum concentrations of Ca2+, Mg2+, spermidine3+ and cobalthexamine3+ of between 40 and 300 μM. Aggregates of purified cores were resolved in the presence of 0.3 mM deoxycholate (minimum concentration). Core shells opened with EGTA were reconstituted by the addition of di- or trivalent cations within 2 min of the opening procedure. Addition of purified, baculovirus recombinant-expressed VP6 to native and reconstituted cores led to the formation of DLPs or DLP-like particles, which upon transfection into MA104 cells were infectious. The rescued infectivity likely originated in part from unopened and in part from reconstituted cores. Radiolabelled RV (+) ssRNAs could be packaged into reconstituted cores and DLPs, as indicated by resistance to RNase I digestion. The packaging reaction was, however, not RV RNA sequence-specific, since unrelated ssRNAs, such as those transcribed from HIV-2 cDNAs, were also packaged. The kinetics of packaging of homologous and heterologous RNAs were similar, as evidenced by competitive packaging assays. None of the packaged in vitro engineered RNA segments has so far been rescued into infectious virus. PMID:24091366

OpenComet: An automated tool for comet assay image analysis

PubMed Central

Gyori, Benjamin M.; Venkatachalam, Gireedhar; Thiagarajan, P.S.; Hsu, David; Clement, Marie-Veronique

2014-01-01

Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time. PMID:24624335

OpenComet: an automated tool for comet assay image analysis.

PubMed

Gyori, Benjamin M; Venkatachalam, Gireedhar; Thiagarajan, P S; Hsu, David; Clement, Marie-Veronique

2014-01-01

Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time.

Real Time Sensing and Discrimination of Single Chemicals Using Channel of Phi29 DNA Packaging Nanomotor

PubMed Central

Haque, Farzin; Lunn, Jennifer; Fang, Huaming; Smithrud, David; Guo, Peixuan

2012-01-01

A highly sensitive and reliable method to sense and identify a single chemical at extremely low concentrations and high contamination is important for environmental surveillance, homeland security, athlete drug monitoring, toxin/drug screening, and earlier disease diagnosis. This manuscript reports a method for precise detection of single chemicals. The hub of the bacteriophage phi29 DNA packaging motor is a connector consisting of twelve protein subunits encircled into a 3.6-nm channel as a path for dsDNA to enter during packaging and to exit during infection. The connector has previously been inserted into a lipid bilayer to serve as a membrane-embedded channel. Herein we report the modification of the phi29 channel to develop a class of sensors to detect single chemicals. The Lysine-234 of each protein subunit was mutated to cysteine, generating 12-SH ring lining the channel wall. Chemicals passing through this robust channel and interactions with the SH-group generated extremely reliable, precise, and sensitive current signatures as revealed by single channel conductance assays. Ethane (57 Daltons), thymine (167 Daltons), and benzene (105 Daltons) with reactive thioester moieties were clearly discriminated upon interaction with the available set of cysteine residues. The covalent attachment of each analyte induced discrete step-wise blockage in current signature with a corresponding decrease in conductance due to the physical blocking of the channel. Transient binding of the chemicals also produced characteristic fingerprints that were deduced from the unique blockage amplitude and pattern of the signals. This study shows that the phi29 connector can be used to sense chemicals with reactive thioesters or maleimide using single channel conduction assays based on their distinct fingerprints. The results demonstrated that this channel system could be further developed into very sensitive sensing devices. PMID:22458779

Real-time sensing and discrimination of single chemicals using the channel of phi29 DNA packaging nanomotor.

PubMed

Haque, Farzin; Lunn, Jennifer; Fang, Huaming; Smithrud, David; Guo, Peixuan

2012-04-24

A highly sensitive and reliable method to sense and identify a single chemical at extremely low concentrations and high contamination is important for environmental surveillance, homeland security, athlete drug monitoring, toxin/drug screening, and earlier disease diagnosis. This article reports a method for precise detection of single chemicals. The hub of the bacteriophage phi29 DNA packaging motor is a connector consisting of 12 protein subunits encircled into a 3.6 nm channel as a path for dsDNA to enter during packaging and to exit during infection. The connector has previously been inserted into a lipid bilayer to serve as a membrane-embedded channel. Herein we report the modification of the phi29 channel to develop a class of sensors to detect single chemicals. The lysine-234 of each protein subunit was mutated to cysteine, generating 12-SH ring lining the channel wall. Chemicals passing through this robust channel and interactions with the SH group generated extremely reliable, precise, and sensitive current signatures as revealed by single channel conductance assays. Ethane (57 Da), thymine (167 Da), and benzene (105 Da) with reactive thioester moieties were clearly discriminated upon interaction with the available set of cysteine residues. The covalent attachment of each analyte induced discrete stepwise blockage in current signature with a corresponding decrease in conductance due to the physical blocking of the channel. Transient binding of the chemicals also produced characteristic fingerprints that were deduced from the unique blockage amplitude and pattern of the signals. This study shows that the phi29 connector can be used to sense chemicals with reactive thioesters or maleimide using single channel conduction assays based on their distinct fingerprints. The results demonstrated that this channel system could be further developed into very sensitive sensing devices.

Contamination of injectable solutions with 2-mercaptobenzothiazole leached from rubber closures.

PubMed

Reepmeyer, J C; Juhl, Y H

1983-11-01

An impurity, discovered in a sample of digoxin injectable solution commercially packaged in a syringe for single-dose delivery, was found to originate from the rubber closure of the syringe and was identified as 2-mercaptobenzothiazole, a common accelerator for rubber vulcanization. Several similarly packaged injectable solutions of a variety of drugs from various manufacturers were examined and over half contained 2-mercaptobenzothiazole. The compound was identified by UV spectrophotometry (including a pH-dependent shift in its absorbance maximum), by mass spectrometry, and by comparison with standard 2-mercaptobenzothiazole using silica gel and reverse-phase high-performance liquid chromatography (HPLC). The presence of this impurity in injectable solutions may have implications with regard to toxicity and may interfere with the assay of digoxin injectable solution by HPLC.

Ferric plasmonic nanoparticles, aptamers, and magnetofluidic chips: toward the development of diagnostic surface-enhanced Raman spectroscopy assays

NASA Astrophysics Data System (ADS)

Marks, Haley; Huang, Po-Jung; Mabbott, Samuel; Graham, Duncan; Kameoka, Jun; Coté, Gerard

2016-12-01

Conjugation of aptamers and their corresponding analytes onto plasmonic nanoparticles mediates the formation of nanoparticle assemblies: molecularly bound nanoclusters that cause a measurable change in the colloid's optical properties. The optimization of a surface-enhanced Raman spectroscopy (SERS) competitive binding assay utilizing plasmonic "target" and magnetic "probe" nanoparticles for the detection of the toxin bisphenol-A (BPA) is presented. These assay nanoclusters were housed inside three types of optofluidic chips patterned with magnetically activated nickel pads, in either a straight or array pattern. Both Fe2O3 and Fe2CoO4 were compared as potential magnetic cores for the silver-coated probe nanoparticles. We found that the Ag@Fe2O3 particles were, on average, more uniform in size and more stable than Ag@Fe2CoO4, whereas the addition of cobalt significantly improved the collection time of particles. Using Raman mapping of the assay housed within the magnetofluidic chips, it was determined that a 1×5 array of 50 μm square nickel pads provided the most uniform SERS enhancement of the assay (coefficient of variation ˜25%) within the magnetofluidic chip. Additionally, the packaged assay demonstrated the desired response to BPA, verifying the technology's potential to translate magnetic nanoparticle assays into a user-free optical analysis platform.

Ferric plasmonic nanoparticles, aptamers, and magnetofluidic chips: toward the development of diagnostic surface-enhanced Raman spectroscopy assays

PubMed Central

Marks, Haley; Huang, Po-Jung; Mabbott, Samuel; Graham, Duncan; Kameoka, Jun; Coté, Gerard

2016-01-01

Abstract. Conjugation of aptamers and their corresponding analytes onto plasmonic nanoparticles mediates the formation of nanoparticle assemblies: molecularly bound nanoclusters that cause a measurable change in the colloid’s optical properties. The optimization of a surface-enhanced Raman spectroscopy (SERS) competitive binding assay utilizing plasmonic “target” and magnetic “probe” nanoparticles for the detection of the toxin bisphenol-A (BPA) is presented. These assay nanoclusters were housed inside three types of optofluidic chips patterned with magnetically activated nickel pads, in either a straight or array pattern. Both Fe2O3 and Fe2CoO4 were compared as potential magnetic cores for the silver-coated probe nanoparticles. We found that the Ag@Fe2O3 particles were, on average, more uniform in size and more stable than Ag@Fe2CoO4, whereas the addition of cobalt significantly improved the collection time of particles. Using Raman mapping of the assay housed within the magnetofluidic chips, it was determined that a 1×5 array of 50  μm square nickel pads provided the most uniform SERS enhancement of the assay (coefficient of variation ∼25%) within the magnetofluidic chip. Additionally, the packaged assay demonstrated the desired response to BPA, verifying the technology’s potential to translate magnetic nanoparticle assays into a user-free optical analysis platform. PMID:27997017

integIRTy: a method to identify genes altered in cancer by accounting for multiple mechanisms of regulation using item response theory.

PubMed

Tong, Pan; Coombes, Kevin R

2012-11-15

Identifying genes altered in cancer plays a crucial role in both understanding the mechanism of carcinogenesis and developing novel therapeutics. It is known that there are various mechanisms of regulation that can lead to gene dysfunction, including copy number change, methylation, abnormal expression, mutation and so on. Nowadays, all these types of alterations can be simultaneously interrogated by different types of assays. Although many methods have been proposed to identify altered genes from a single assay, there is no method that can deal with multiple assays accounting for different alteration types systematically. In this article, we propose a novel method, integration using item response theory (integIRTy), to identify altered genes by using item response theory that allows integrated analysis of multiple high-throughput assays. When applied to a single assay, the proposed method is more robust and reliable than conventional methods such as Student's t-test or the Wilcoxon rank-sum test. When used to integrate multiple assays, integIRTy can identify novel-altered genes that cannot be found by looking at individual assay separately. We applied integIRTy to three public cancer datasets (ovarian carcinoma, breast cancer, glioblastoma) for cross-assay type integration which all show encouraging results. The R package integIRTy is available at the web site http://bioinformatics.mdanderson.org/main/OOMPA:Overview. kcoombes@mdanderson.org. Supplementary data are available at Bioinformatics online.

Development and characterization of bioactive edible films from spider crab (Maja crispata) chitosan incorporated with Spirulina extract.

PubMed

Balti, Rafik; Mansour, Mohamed Ben; Sayari, Nadhem; Yacoubi, Lamia; Rabaoui, Lotfi; Brodu, Nicolas; Massé, Anthony

2017-12-01

Active food packaging films based on crab chitosan and Spirulina extract (SE) were developed. The effects of the SE incorporation at different levels on physical (color, opacity water vapor and oxygen permeability) and mechanical (tensile strength and elongation at break) properties of chitosan films were investigated. FTIR was carried out to observe the potential modifications of the chitosan films when incorporated with SE. The obtained results suggested that incorporation of SE into chitosan films improved mechanical and barrier properties. The antioxidant activity of the chitosan/SE films was characterized by means of three different analytical assays (DPPH, FRAP and FIC). Crab chitosan edible films containing SE showed higher antioxidant activity, regardless concentrations and methods assayed. Furthermore, the antioxidant activity occurred in a concentration-dependent manner. The agar disc diffusion method was used to determine the antibacterial activities of chitosan edible films against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Listeria monocytogenes, Salmonella typhimurium, Bacillus subtilis and Bacillus cereus. The chitosan/SE films were more effective (p<0.05) against five of the seven tested bacteria. The obtained crab chitosan edible films incorporated with SE showed great potential to be used for active food packaging due to its excellent antioxidant and antibacterial activities. Copyright © 2017 Elsevier B.V. All rights reserved.

Anti-listerial activity of a polymeric film coated with hybrid coatings doped with Enterocin 416K1 for use as bioactive food packaging.

PubMed

Iseppi, Ramona; Pilati, Francesco; Marini, Michele; Toselli, Maurizio; de Niederhäusern, Simona; Guerrieri, Elisa; Messi, Patrizia; Sabia, Carla; Manicardi, Giuliano; Anacarso, Immacolata; Bondi, Moreno

2008-04-30

In this study, Enterocin 416K1, a bacteriocin produced by Enterococcus casseliflavus IM 416K1, was entrapped in an organic-inorganic hybrid coating applied to a LDPE (low-density polyethylene) film for its potential use in the active food packaging field. The antibacterial activity of the coated film was evaluated against Listeria monocytogenes NCTC 10888 by qualitative modified agar diffusion assay, quantitative determination in listeria saline solution suspension and direct contact with artificially contaminated food samples (frankfurters and fresh cheeses) stored at room and refrigeration temperatures. All investigations demonstrated that enterocin-activated coatings have a good anti-listeria activity. Qualitative tests showed a clear zone of inhibition in the indicator lawn in contact with and around the coated film. During the quantitative antibacterial evaluation the L. monocytogenes viable counts decreased to 1.5 log units compared to the control. The inhibitory capability was confirmed also in food-contact assays. In all food samples packed with coated films we observed a significant decrease in L. monocytogenes viable counts in the first 24 h compared to the control. This difference was generally maintained up to the seventh day and then decreased, with the exception of the cheese samples stored at refrigeration temperature.

Kinetics of apoptotic markers in exogeneously induced apoptosis of EL4 cells.

PubMed

Jessel, Robert; Haertel, Steffen; Socaciu, Carmen; Tykhonova, Svetlana; Diehl, Horst A

2002-01-01

We investigated the time-dependence of apoptotic events in EL4 cells by monitoring plasma membrane changes in correlation to DNA fragmentation and cell shrinkage. We applied three apoptosis inducers (staurosporine, tubericidine and X-rays) and we looked at various markers to follow the early-to-late apoptotic events: phospholipid translocation (identified through annexin V-fluorescein assay and propidium iodide), lipid package (via merocyanine assay), membrane fluidity and anisotropy (via fluorescent measurements), DNA fragmentation by the fluorescence-labeling test and cell size measurements. The different apoptotic inducers caused different reactions of the cells: staurosporine induced apoptosis most rapidly in a high number of cells, tubercidine triggered apoptosis only in the S phase cells, while X-rays caused a G2/M arrest and subsequently apoptosis. Loss of lipid asymmetry is promptly detectable after one hour of incubation time. The phosphatidylserine translocation, decrease of lipid package and anisotropy, and the increase of membrane fluidity appeared to be based on the same process of lipid asymmetry loss. Therefore, the DNA fragmentation and the cell shrinkage appear to be parallel and independent processes running on different time scales but which are kinetically inter-related. The results indicate different signal steps to apoptosis dependent on inducer characteristics but the kinetics of "early-to-late" apoptosis appears to be a fixed program.

A subchronic 90-day oral toxicity study of Origanum vulgare essential oil in rats.

PubMed

Llana-Ruiz-Cabello, M; Maisanaba, S; Puerto, M; Pichardo, S; Jos, A; Moyano, R; Cameán, A M

2017-03-01

Oregano essential oil (Origanum vulgare L. virens) (OEO) is being used in the food industry due to its useful properties to develop new active packaging systems. In this concern, the safety assessment of this natural extract is of great interest before being commercialized. The European Food Safety Authority requests different in vivo assays to ensure the safety of food contact materials. One of these studies is a 90 days repeated-dose oral assay in rodents. In the present work, 40 male and 40 female Wistar rats were orally exposed to 50, 100 and 200 mg/kg body weight (b.w.) OEO during 90 days following the OECD guideline 408. Data revealed no mortality and no treatment-related adverse effects of the OEO in food/water consumption, body weight, haematology, biochemistry, necropsy, organ weight and histopathology. These findings suggest that the oral no-observed-adverse-effect level (NOAEL) of this OEO is 200 mg/kg b.w. in Wistar rats, the highest dose tested. In conclusion, the use of this OEO in food packaging appears to be safe based on the lack of toxicity during the subchronic study at doses 330-fold higher than those expected to be in contact consumers in the worst scenario of exposure. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again.

PubMed

González-Beltrán, Alejandra; Neumann, Steffen; Maguire, Eamonn; Sansone, Susanna-Assunta; Rocca-Serra, Philippe

2014-01-01

The ISA-Tab format and software suite have been developed to break the silo effect induced by technology-specific formats for a variety of data types and to better support experimental metadata tracking. Experimentalists seldom use a single technique to monitor biological signals. Providing a multi-purpose, pragmatic and accessible format that abstracts away common constructs for describing Investigations, Studies and Assays, ISA is increasingly popular. To attract further interest towards the format and extend support to ensure reproducible research and reusable data, we present the Risa package, which delivers a central component to support the ISA format by enabling effortless integration with R, the popular, open source data crunching environment. The Risa package bridges the gap between the metadata collection and curation in an ISA-compliant way and the data analysis using the widely used statistical computing environment R. The package offers functionality for: i) parsing ISA-Tab datasets into R objects, ii) augmenting annotation with extra metadata not explicitly stated in the ISA syntax; iii) interfacing with domain specific R packages iv) suggesting potentially useful R packages available in Bioconductor for subsequent processing of the experimental data described in the ISA format; and finally v) saving back to ISA-Tab files augmented with analysis specific metadata from R. We demonstrate these features by presenting use cases for mass spectrometry data and DNA microarray data. The Risa package is open source (with LGPL license) and freely available through Bioconductor. By making Risa available, we aim to facilitate the task of processing experimental data, encouraging a uniform representation of experimental information and results while delivering tools for ensuring traceability and provenance tracking. The Risa package is available since Bioconductor 2.11 (version 1.0.0) and version 1.2.1 appeared in Bioconductor 2.12, both along with documentation and examples. The latest version of the code is at the development branch in Bioconductor and can also be accessed from GitHub https://github.com/ISA-tools/Risa, where the issue tracker allows users to report bugs or feature requests.

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again

PubMed Central

2014-01-01

Background The ISA-Tab format and software suite have been developed to break the silo effect induced by technology-specific formats for a variety of data types and to better support experimental metadata tracking. Experimentalists seldom use a single technique to monitor biological signals. Providing a multi-purpose, pragmatic and accessible format that abstracts away common constructs for describing Investigations, Studies and Assays, ISA is increasingly popular. To attract further interest towards the format and extend support to ensure reproducible research and reusable data, we present the Risa package, which delivers a central component to support the ISA format by enabling effortless integration with R, the popular, open source data crunching environment. Results The Risa package bridges the gap between the metadata collection and curation in an ISA-compliant way and the data analysis using the widely used statistical computing environment R. The package offers functionality for: i) parsing ISA-Tab datasets into R objects, ii) augmenting annotation with extra metadata not explicitly stated in the ISA syntax; iii) interfacing with domain specific R packages iv) suggesting potentially useful R packages available in Bioconductor for subsequent processing of the experimental data described in the ISA format; and finally v) saving back to ISA-Tab files augmented with analysis specific metadata from R. We demonstrate these features by presenting use cases for mass spectrometry data and DNA microarray data. Conclusions The Risa package is open source (with LGPL license) and freely available through Bioconductor. By making Risa available, we aim to facilitate the task of processing experimental data, encouraging a uniform representation of experimental information and results while delivering tools for ensuring traceability and provenance tracking. Software availability The Risa package is available since Bioconductor 2.11 (version 1.0.0) and version 1.2.1 appeared in Bioconductor 2.12, both along with documentation and examples. The latest version of the code is at the development branch in Bioconductor and can also be accessed from GitHub https://github.com/ISA-tools/Risa, where the issue tracker allows users to report bugs or feature requests. PMID:24564732

Randomization and In Vivo Selection Reveal a GGRG Motif Essential for Packaging Human Immunodeficiency Virus Type 2 RNA ▿ †

PubMed Central

Baig, Tayyba T.; Lanchy, Jean-Marc; Lodmell, J. Stephen

2009-01-01

The packaging signal (ψ) of human immunodeficiency virus type 2 (HIV-2) is present in the 5′ noncoding region of RNA and contains a 10-nucleotide palindrome (pal; 5′-392-GGAGUGCUCC) located upstream of the dimerization signal stem-loop 1 (SL1). pal has been shown to be functionally important in vitro and in vivo. We previously showed that the 3′ side of pal (GCUCC-3′) is involved in base-pairing interactions with a sequence downstream of SL1 to make an extended SL1, which is important for replication in vivo and the regulation of dimerization in vitro. However, the role of the 5′ side of pal (5′-GGAGU) was less clear. Here, we characterized this role using an in vivo SELEX approach. We produced a population of HIV-2 DNA genomes with random sequences within the 5′ side of pal and transfected these into COS-7 cells. Viruses from COS-7 cells were used to infect C8166 permissive cells. After several weeks of serial passage in C8166 cells, surviving viruses were sequenced. On the 5′ side of pal there was a striking convergence toward a GGRGN consensus sequence. Individual clones with consensus and nonconsensus sequences were tested in infectivity and packaging assays. Analysis of individuals that diverged from the consensus sequence showed normal viral RNA and protein synthesis but had replication defects and impaired RNA packaging. These findings clearly indicate that the GGRG motif is essential for viral replication and genomic RNA packaging. PMID:18971263

Comparison of Hybrid Capture 2 Assay with Real-time-PCR for Detection and Quantitation of Hepatitis B Virus DNA.

PubMed

Majid, Farjana; Jahan, Munira; Lutful Moben, Ahmed; Tabassum, Shahina

2014-01-01

Both real-time-polymerase chain reaction (PCR) and hybrid capture 2 (HC2) assay can detect and quantify hepatitis B virus (HBV) DNA. However, real-time-PCR can detect a wide range of HBV DNA, while HC2 assay could not detect lower levels of viremia. The present study was designed to detect and quantify HBV DNA by real-time-PCR and HC2 assay and compare the quantitative data of these two assays. A cross-sectional study was conducted in between July 2010 and June 2011. A total of 66 serologically diagnosed chronic hepatitis B (CHB) patients were selected for the study. Real-time-PCR and HC2 assay was done to detect HBV DNA. Data were analyzed by statistical Package for the social sciences (SPSS). Among 66 serologically diagnosed chronic hepatitis B patients 40 (60.61%) patients had detectable and 26 (39.39%) had undetectable HBV DNA by HC2 assay. Concordant results were obtained for 40 (60.61%) out of these 66 patients by real-time-PCR and HC2 assay with mean viral load of 7.06 ± 1.13 log 10 copies/ml and 6.95 ± 1.08 log 10 copies/ml, respectively. In the remaining 26 patients, HBV DNA was detectable by real-time-PCR in 20 patients (mean HBV DNA level was 3.67 ± 0.72 log 10 copies/ml. However, HBV DNA could not be detectable in six cases by the both assays. The study showed strong correlation (r = 0.915) between real-time-PCR and HC2 assay for the detection and quantification of HBV DNA. HC2 assay may be used as an alternative to real-time-PCR for CHB patients. How to cite this article: Majid F, Jahan M, Moben AL, Tabassum S. Comparison of Hybrid Capture 2 Assay with Real-time-PCR for Detection and Quantitation of Hepatitis B Virus DNA. Euroasian J Hepato-Gastroenterol 2014;4(1):31-35.

Live cell imaging of interactions between replicase and capsid protein of Brome mosaic virus using Bimolecular Fluorescence Complementation: implications for replication and genome packaging.

PubMed

Chaturvedi, Sonali; Rao, A L N

2014-09-01

In Brome mosaic virus, it was hypothesized that a physical interaction between viral replicase and capsid protein (CP) is obligatory to confer genome packaging specificity. Here we tested this hypothesis by employing Bimolecular Fluorescent Complementation (BiFC) as a tool for evaluating protein-protein interactions in living cells. The efficacy of BiFC was validated by a known interaction between replicase protein 1a (p1a) and protein 2a (p2a) at the endoplasmic reticulum (ER) site of viral replication. Additionally, co-expression in planta of a bona fide pair of interacting protein partners of p1a and p2a had resulted in the assembly of a functional replicase. Subsequent BiFC assays in conjunction with mCherry labeled ER as a fluorescent cellular marker revealed that CP physically interacts with p2a, but not p1a, and this CP:p2a interaction occurs at the cytoplasmic phase of the ER. The significance of the CP:p2a interaction in BMV replication and genome packaging is discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

Review of Software Tools for Design and Analysis of Large scale MRM Proteomic Datasets

PubMed Central

Colangelo, Christopher M.; Chung, Lisa; Bruce, Can; Cheung, Kei-Hoi

2013-01-01

Selective or Multiple Reaction monitoring (SRM/MRM) is a liquid-chromatography (LC)/tandem-mass spectrometry (MS/MS) method that enables the quantitation of specific proteins in a sample by analyzing precursor ions and the fragment ions of their selected tryptic peptides. Instrumentation software has advanced to the point that thousands of transitions (pairs of primary and secondary m/z values) can be measured in a triple quadrupole instrument coupled to an LC, by a well-designed scheduling and selection of m/z windows. The design of a good MRM assay relies on the availability of peptide spectra from previous discovery-phase LC-MS/MS studies. The tedious aspect of manually developing and processing MRM assays involving thousands of transitions has spurred to development of software tools to automate this process. Software packages have been developed for project management, assay development, assay validation, data export, peak integration, quality assessment, and biostatistical analysis. No single tool provides a complete end-to-end solution, thus this article reviews the current state and discusses future directions of these software tools in order to enable researchers to combine these tools for a comprehensive targeted proteomics workflow. PMID:23702368

Differential sensitivity of porcine endogenous retrovirus to APOBEC3-mediated inhibition.

PubMed

Park, Sung-Han; Kim, Jin Ha; Jung, Yong-Tae

2015-08-01

Pigs are considered to be suitable xenotransplantation organ donors. However, the risk of pathogen transmission from pigs to humans is a major concern in the transplantation of porcine tissues. The porcine endogenous retroviruses (PERVs) PERV-A, PERV-A/C, and PERV-B can infect human cells, but PERV-C is an ecotropic virus infecting only pig cells. Thus, several strategies have been proposed to reduce PERV transmission in xenograft recipients. Human APOBEC3G (huA3G) is a single-strand DNA cytosine deaminase, which inactivates the coding capacity of the virus by deamination of cDNA cytosines to uracils. This reaction occurs within the (-) DNA strand during reverse transcription, resulting in a G-to-A mutation in the (+) strand. While recent data have shown that PERV-B is severely inhibited by huA3G and porcine A3Z2-Z3 (poA3F) in a pseudotype assay, little is known about PERV-C. Here, we compare the antiretroviral activities of huA3G, huA3F and poA3Z2-Z3 against PERV-C. Our data show that APOBEC3 was packaged into PERV-C particles and inhibited PERV-C replication in a dose-dependent manner. PERV-C infectivity was strongly inhibited by poA3Z2-Z3, but it did not markedly reduce PERV-B infectivity. This suggests that PERV-C Gag interacts efficiently with poA3Z2-Z3. In addition, we constructed stably huA3G- and poA3Z2-Z3-expressing 293-PERV-PK-CIRCE cells (human 293 cells infected with PK15-derived PERVs) to examine whether PERV is resistant to poA3Z2-Z3 in a virus-spreading assay. The stably expressed huA3G and poA3Z2-Z3 were more packaging-competent than transiently expressed APOBEC3 proteins. These results suggest that poA3Z2-Z3 can inhibit PERV replication in a pseudotype assay as well as in a virus-spreading assay.

Nano selenium as antioxidant agent in a multilayer food packaging material.

PubMed

Vera, Paula; Echegoyen, Yolanda; Canellas, Elena; Nerín, Cristina; Palomo, María; Madrid, Yolanda; Cámara, Carmen

2016-09-01

Selenium nanoparticles (SeNPs) were incorporated in a flexible multilayer plastic material using a water-base adhesive as vehicle for SeNPs. The antioxidant performance of the original solutions containing spherical SeNPs of 50-60 nm diameter, the adhesive containing these SeNPs, and the final multilayer plastic material to be used as food packaging were quantitatively measured. The radical scavenging capacity due to SeNPs was quantified by a free radical assay developed in the laboratory and by the diphenyl-1-picrylhydrazyl (DPPH) method. DPPH was not efficient to measure the scavenging capacity in the multilayer when the free radical scavenger is not in the surface in contact with it. Several multilayer laminated structures composed by [PET (20 m)-adhesive-LDPE (with variable thickness from 35 to 90 μm)] were prepared and measured, demonstrating for the first time that free radicals derived from oxygen (OH·, O2·, and O2H) cross the PE layer and arrive at the adhesive. SeNPs remain as such after manufacture and the final laminate is stable after 3 months of storage. The antioxidant multilayer is a non-migrating efficient free radical scavenger, able to protect the packaged product versus oxidation and extending the shelf life without being in direct contact with the product. Migration tests of both Se and SeNPs to simulants and hazelnuts demonstrated the non-migrating performance of this new active packaging. Graphical abstract ᅟ.

MethylMix 2.0: an R package for identifying DNA methylation genes. | Office of Cancer Genomics

Cancer.gov

DNA methylation is an important mechanism regulating gene transcription, and its role in carcinogenesis has been extensively studied. Hyper and hypomethylation of genes is a major mechanism of gene expression deregulation in a wide range of diseases. At the same time, high-throughput DNA methylation assays have been developed generating vast amounts of genome wide DNA methylation measurements. We developed MethylMix, an algorithm implemented in R to identify disease specific hyper and hypomethylated genes.

Bioconvective Assay As Alternative To Draize Test

NASA Technical Reports Server (NTRS)

Noever, David A.; Matsos, Helen C.

1993-01-01

Protocol to determine toxicities of chemicals implemented relatively cheaply by use of equipment and materials packaged in convenient kit form. Tests involve observation of macroscopic patterns formed at high concentrations of free-swimming protozoan species Tetrahymena pyriformis in liquid media. Provides more-sensitive indication of toxicity and costs less. Given that there are no data on toxicities of 70 to 80 percent of commercial chemicals, high cost of, and current opposition to, testing on higher animals, new protocol helps meet pressing need.

Genotoxicity evaluation of carvacrol in rats using a combined micronucleus and comet assay.

PubMed

Llana-Ruiz-Cabello, María; Maisanaba, Sara; Puerto, María; Prieto, Ana I; Pichardo, Silvia; Moyano, Rosario; González-Pérez, José A; Cameán, Ana M

2016-12-01

Genotoxic data of substances which could be incorporated into food packaging are required by the European Food Safety Authority. Due to its antioxidant and antibacterial properties carvacrol is one of these compounds. This work aims to study for the first time the in vivo genotoxic effects produced in rats orally exposed to 81, 256 or 810 mg cavacrol/kg body weight (bw) at 0, 24 and 45 h. A combination of the micronucleus assay (OECD 474) in bone marrow and the standard (OECD 489) and enzyme-modified comet assay was used to determine the genotoxicity on cells isolated from stomach and liver of exposed animals. In addition, a histopathological study was performed on the assayed tissues, and also in the lungs due to the volatility of carvacrol. Direct analytical pyrolysis was used to search for carvacrol in viscera and to ensure that the compound reaches stomach and liver cells. Results from MN-comet assay revealed that carvacrol (81-810 mg/kg bw) did not induce in vivo genotoxicity or oxidative DNA damage in any of the tissues investigated. Moreover, no histopathological changes were observed. Altogether, these results suggest lack of genotoxicity of carvacrol and therefore its good profile for its potential application as food preservative. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparison of Hybrid Capture 2 Assay with Real-time-PCR for Detection and Quantitation of Hepatitis B Virus DNA

PubMed Central

Jahan, Munira; Lutful Moben, Ahmed; Tabassum, Shahina

2014-01-01

ABSTRACT Background Both real-time-polymerase chain reaction (PCR) and hybrid capture 2 (HC2) assay can detect and quantify hepatitis B virus (HBV) DNA. However, real-time-PCR can detect a wide range of HBV DNA, while HC2 assay could not detect lower levels of viremia. The present study was designed to detect and quantify HBV DNA by real-time-PCR and HC2 assay and compare the quantitative data of these two assays. Materials and methods A cross-sectional study was conducted in between July 2010 and June 2011. A total of 66 serologically diagnosed chronic hepatitis B (CHB) patients were selected for the study. Real-time-PCR and HC2 assay was done to detect HBV DNA. Data were analyzed by statistical Package for the social sciences (SPSS). Results Among 66 serologically diagnosed chronic hepatitis B patients 40 (60.61%) patients had detectable and 26 (39.39%) had undetectable HBV DNA by HC2 assay. Concordant results were obtained for 40 (60.61%) out of these 66 patients by real-time-PCR and HC2 assay with mean viral load of 7.06 ± 1.13 log10 copies/ml and 6.95 ± 1.08 log10 copies/ml, respectively. In the remaining 26 patients, HBV DNA was detectable by real-time-PCR in 20 patients (mean HBV DNA level was 3.67 ± 0.72 log10 copies/ml. However, HBV DNA could not be detectable in six cases by the both assays. The study showed strong correlation (r = 0.915) between real-time-PCR and HC2 assay for the detection and quantification of HBV DNA. Conclusion HC2 assay may be used as an alternative to real-time-PCR for CHB patients. How to cite this article: Majid F, Jahan M, Moben AL, Tabassum S. Comparison of Hybrid Capture 2 Assay with Real-time-PCR for Detection and Quantitation of Hepatitis B Virus DNA. Euroasian J Hepato-Gastroenterol 2014;4(1):31-35. PMID:29264316

Economic evaluation of the 70-gene prognosis-signature (MammaPrint®) in hormone receptor-positive, lymph node-negative, human epidermal growth factor receptor type 2-negative early stage breast cancer in Japan.

PubMed

Kondo, Masahide; Hoshi, Shu-Ling; Ishiguro, Hiroshi; Toi, Masakazu

2012-06-01

The 70-gene prognosis-signature is validated as a good predictor of recurrence for hormone receptor-positive (ER+), lymph node-negative (LN-), human epidermal growth factor receptor type 2-negative (HER2-) early stage breast cancer (ESBC) in Japanese patient population. Its high cost and potential in avoiding unnecessary adjuvant chemotherapy arouse interest in its economic impact. This study evaluates the cost-effectiveness of including the assay into Japan's social health insurance benefit package. An economic decision tree and Markov model under Japan's health system from the societal perspective is constructed with clinical evidence from the pool analysis of validation studies. One-way sensitivity analyses are also performed. Incremental cost-effectiveness ratio is estimated as ¥3,873,922/quality adjusted life year (QALY) (US$43,044/QALY), which is not more than the suggested social willingness-to-pay for one QALY gain from an innovative medical intervention in Japan, ¥5,000,000/QALY (US$55,556/QALY). However, sensitivity analyses show the instability of this estimation. The introduction of the assay into Japanese practice of ER+, LN-, HER2- ESBC treatment by including it to Japan's social health insurance benefit package has a reasonable chance to be judged as cost-effective and may be justified as an efficient deployment of finite health care resources.

Inhibition of foodborne bacteria by antibacterial coatings printed onto food packaging films.

PubMed

Widsten, P; Mesic, B B; Cruz, C D; Fletcher, G C; Chycka, M A

2017-07-01

Films containing antibacterial compounds could be used for packaging perishable foods such as fresh fish and meat for sea freighting over long distances. However, existing commercialised options (films with nanosilver zeolites or wasabi extract) are only permitted for food contact in certain regions and films containing alternative antibacterial ingredients are required e.g. for exports to Europe. Certain non-volatile phenolic plant extracts have shown promising antibacterial activity against a wide range of foodborne bacteria in in vitro assays and when integrated in coatings for perishable foods such as fish and meat. Extracts rich in gallotannins tend to show stronger antibacterial effects than other phenols such as flavonoids. Such extracts could be coated onto commercial barrier films by means of flexographic printing-a more industrially feasible option than rod coating or solvent casting typically used in antibacterial coating research. The goal of the present work was to investigate the antibacterial effect of printed latex coatings containing extracts rich in gallotannins and other types of phenolic compounds against 16 common spoilage and pathogenic bacteria of fish and meat. The largest zones of inhibition in disk diffusion assays were obtained with plastic films with coatings containing tannic acid alone, followed by tannic acid with phenolic-rich extracts of feijoa skin or mango seed. Significant inhibition was seen for all bacteria. This study shows that coatings with gallotannins as the main active ingredient can be printed onto commercial barrier films to control the bacteria that limit the shelf-life of fresh fish and meat.

Review of software tools for design and analysis of large scale MRM proteomic datasets.

PubMed

Colangelo, Christopher M; Chung, Lisa; Bruce, Can; Cheung, Kei-Hoi

2013-06-15

Selective or Multiple Reaction monitoring (SRM/MRM) is a liquid-chromatography (LC)/tandem-mass spectrometry (MS/MS) method that enables the quantitation of specific proteins in a sample by analyzing precursor ions and the fragment ions of their selected tryptic peptides. Instrumentation software has advanced to the point that thousands of transitions (pairs of primary and secondary m/z values) can be measured in a triple quadrupole instrument coupled to an LC, by a well-designed scheduling and selection of m/z windows. The design of a good MRM assay relies on the availability of peptide spectra from previous discovery-phase LC-MS/MS studies. The tedious aspect of manually developing and processing MRM assays involving thousands of transitions has spurred to development of software tools to automate this process. Software packages have been developed for project management, assay development, assay validation, data export, peak integration, quality assessment, and biostatistical analysis. No single tool provides a complete end-to-end solution, thus this article reviews the current state and discusses future directions of these software tools in order to enable researchers to combine these tools for a comprehensive targeted proteomics workflow. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Evaluation of a microarray-based genotyping assay for the rapid detection of cytochrome P450 2C19 *2 and *3 polymorphisms from whole blood using nanoparticle probes.

PubMed

Buchan, Blake W; Peterson, Jess F; Cogbill, Christopher H; Anderson, Dennis K; Ledford, Joellen S; White, Mary N; Quigley, Neil B; Jannetto, Paul J; Ledeboer, Nathan A

2011-10-01

Numerous drugs such as clopidogrel have been developed to reduce coagulation or inhibit platelet function. The hepatic cytochrome P450 (CYP) pathway is involved in the conversion of clopidogrel to its active metabolite. A recent black-box warning was included in the clopidogrel package insert indicating a significant clinical link between specific CYP2C19 genetic variants and poor metabolism of clopidogrel. Of these variants, *2 and *3 are the most common and are associated with complete loss of enzyme activity. In patients who are carriers of a CYP2C19 *2 or *3 allele, the conversion of clopidogrel to its active metabolite may be reduced, which can lead to ischemic events and negative consequence for the patient. We examined the ability of the Verigene CLO assay (Nanosphere, Northbrook, IL) to identify CYP2C19 *2 and *3 polymorphisms in 1,286 unique whole blood samples. The Verigene CLO assay accurately identified homozygous and heterozygous *2 and *3 phenotypes with a specificity of 100% and a final call rate of 99.7%. The assay is fully automated and can produce a result in approximately 3.5 hours.

Mediate gamma radiation effects on some packaged food items

NASA Astrophysics Data System (ADS)

Inamura, Patricia Y.; Uehara, Vanessa B.; Teixeira, Christian A. H. M.; del Mastro, Nelida L.

2012-08-01

For most of prepackaged foods a 10 kGy radiation dose is considered the maximum dose needed; however, the commercially available and practically accepted packaging materials must be suitable for such application. This work describes the application of ionizing radiation on several packaged food items, using 5 dehydrated food items, 5 ready-to-eat meals and 5 ready-to-eat food items irradiated in a 60Co gamma source with a 3 kGy dose. The quality evaluation of the irradiated samples was performed 2 and 8 months after irradiation. Microbiological analysis (bacteria, fungus and yeast load) was performed. The sensory characteristics were established for appearance, aroma, texture and flavor attributes were also established. From these data, the acceptability of all irradiated items was obtained. All ready-to-eat food items assayed like manioc flour, some pâtés and blocks of raw brown sugar and most of ready-to-eat meals like sausages and chicken with legumes were considered acceptable for microbial and sensory characteristics. On the other hand, the dehydrated food items chosen for this study, such as dehydrated bacon potatoes or pea soups were not accepted by the sensory analysis. A careful dose choice and special irradiation conditions must be used in order to achieve sensory acceptability needed for the commercialization of specific irradiated food items.

iScreen: Image-Based High-Content RNAi Screening Analysis Tools.

PubMed

Zhong, Rui; Dong, Xiaonan; Levine, Beth; Xie, Yang; Xiao, Guanghua

2015-09-01

High-throughput RNA interference (RNAi) screening has opened up a path to investigating functional genomics in a genome-wide pattern. However, such studies are often restricted to assays that have a single readout format. Recently, advanced image technologies have been coupled with high-throughput RNAi screening to develop high-content screening, in which one or more cell image(s), instead of a single readout, were generated from each well. This image-based high-content screening technology has led to genome-wide functional annotation in a wider spectrum of biological research studies, as well as in drug and target discovery, so that complex cellular phenotypes can be measured in a multiparametric format. Despite these advances, data analysis and visualization tools are still largely lacking for these types of experiments. Therefore, we developed iScreen (image-Based High-content RNAi Screening Analysis Tool), an R package for the statistical modeling and visualization of image-based high-content RNAi screening. Two case studies were used to demonstrate the capability and efficiency of the iScreen package. iScreen is available for download on CRAN (http://cran.cnr.berkeley.edu/web/packages/iScreen/index.html). The user manual is also available as a supplementary document. © 2014 Society for Laboratory Automation and Screening.

Armored Long RNA Controls or Standards for Branched DNA Assay for Detection of Human Immunodeficiency Virus Type 1▿

PubMed Central

Zhan, Sien; Li, Jinming; Xu, Ruihuan; Wang, Lunan; Zhang, Kuo; Zhang, Rui

2009-01-01

The branched DNA (bDNA) assay is a reliable method for quantifying the RNA of human immunodeficiency virus type 1 (HIV-1). The positive controls and standards for this assay for the detection of HIV-1 consist of naked RNA, which is susceptible to degradation by RNase. Armored RNA is a good candidate for an RNase-resistant positive control or standard. However, its use has been limited by the maximal length of the exogenous RNA packaged into virus-like particles by routine armored RNA technology. In the present study, we produced armored long RNA (armored L-RNA) controls or standards (AR-HIV-pol-3034b) for a bDNA assay of HIV-1 by increasing the amount and affinity of the pac sites (the pac site is a specific 19-nucleotide stem-loop region located at the 5′ terminus of the MS2 bacteriophage replicase gene) by a one-plasmid double-expression system. AR-HIV-pol-3034b was completely resistant to DNase and RNase, was stable in normal human EDTA-preserved plasma at 4°C for at least 6 months, and produced reproducible, linear results in the Versant HIV-1 RNA 3.0 assay. In conclusion, AR-HIV-pol-3034b could act as a positive control or standard in a bDNA assay for the detection of HIV-1. In addition, the one-plasmid double-expression system can be used as a better platform than the one-plasmid expression system and the two-plasmid coexpression system for expressing armored L-RNA. PMID:19494069

Armored long RNA controls or standards for branched DNA assay for detection of human immunodeficiency virus type 1.

PubMed

Zhan, Sien; Li, Jinming; Xu, Ruihuan; Wang, Lunan; Zhang, Kuo; Zhang, Rui

2009-08-01

The branched DNA (bDNA) assay is a reliable method for quantifying the RNA of human immunodeficiency virus type 1 (HIV-1). The positive controls and standards for this assay for the detection of HIV-1 consist of naked RNA, which is susceptible to degradation by RNase. Armored RNA is a good candidate for an RNase-resistant positive control or standard. However, its use has been limited by the maximal length of the exogenous RNA packaged into virus-like particles by routine armored RNA technology. In the present study, we produced armored long RNA (armored L-RNA) controls or standards (AR-HIV-pol-3034b) for a bDNA assay of HIV-1 by increasing the amount and affinity of the pac sites (the pac site is a specific 19-nucleotide stem-loop region located at the 5' terminus of the MS2 bacteriophage replicase gene) by a one-plasmid double-expression system. AR-HIV-pol-3034b was completely resistant to DNase and RNase, was stable in normal human EDTA-preserved plasma at 4 degrees C for at least 6 months, and produced reproducible, linear results in the Versant HIV-1 RNA 3.0 assay. In conclusion, AR-HIV-pol-3034b could act as a positive control or standard in a bDNA assay for the detection of HIV-1. In addition, the one-plasmid double-expression system can be used as a better platform than the one-plasmid expression system and the two-plasmid coexpression system for expressing armored L-RNA.

AssayR: A Simple Mass Spectrometry Software Tool for Targeted Metabolic and Stable Isotope Tracer Analyses.

PubMed

Wills, Jimi; Edwards-Hicks, Joy; Finch, Andrew J

2017-09-19

Metabolic analyses generally fall into two classes: unbiased metabolomic analyses and analyses that are targeted toward specific metabolites. Both techniques have been revolutionized by the advent of mass spectrometers with detectors that afford high mass accuracy and resolution, such as time-of-flights (TOFs) and Orbitraps. One particular area where this technology is key is in the field of metabolic flux analysis because the resolution of these spectrometers allows for discrimination between 13 C-containing isotopologues and those containing 15 N or other isotopes. While XCMS-based software is freely available for untargeted analysis of mass spectrometric data sets, it does not always identify metabolites of interest in a targeted assay. Furthermore, there is a paucity of vendor-independent software that deals with targeted analyses of metabolites and of isotopologues in particular. Here, we present AssayR, an R package that takes high resolution wide-scan liquid chromatography-mass spectrometry (LC-MS) data sets and tailors peak detection for each metabolite through a simple, iterative user interface. It automatically integrates peak areas for all isotopologues and outputs extracted ion chromatograms (EICs), absolute and relative stacked bar charts for all isotopologues, and a .csv data file. We demonstrate several examples where AssayR provides more accurate and robust quantitation than XCMS, and we propose that tailored peak detection should be the preferred approach for targeted assays. In summary, AssayR provides easy and robust targeted metabolite and stable isotope analyses on wide-scan data sets from high resolution mass spectrometers.

AssayR: A Simple Mass Spectrometry Software Tool for Targeted Metabolic and Stable Isotope Tracer Analyses

PubMed Central

2017-01-01

Metabolic analyses generally fall into two classes: unbiased metabolomic analyses and analyses that are targeted toward specific metabolites. Both techniques have been revolutionized by the advent of mass spectrometers with detectors that afford high mass accuracy and resolution, such as time-of-flights (TOFs) and Orbitraps. One particular area where this technology is key is in the field of metabolic flux analysis because the resolution of these spectrometers allows for discrimination between 13C-containing isotopologues and those containing 15N or other isotopes. While XCMS-based software is freely available for untargeted analysis of mass spectrometric data sets, it does not always identify metabolites of interest in a targeted assay. Furthermore, there is a paucity of vendor-independent software that deals with targeted analyses of metabolites and of isotopologues in particular. Here, we present AssayR, an R package that takes high resolution wide-scan liquid chromatography–mass spectrometry (LC-MS) data sets and tailors peak detection for each metabolite through a simple, iterative user interface. It automatically integrates peak areas for all isotopologues and outputs extracted ion chromatograms (EICs), absolute and relative stacked bar charts for all isotopologues, and a .csv data file. We demonstrate several examples where AssayR provides more accurate and robust quantitation than XCMS, and we propose that tailored peak detection should be the preferred approach for targeted assays. In summary, AssayR provides easy and robust targeted metabolite and stable isotope analyses on wide-scan data sets from high resolution mass spectrometers. PMID:28850215

Sodium lactate addition on the quality and shelf life of refrigerated sliced poultry sausage packaged in air or nitrogen atmosphere.

PubMed

Cegielska-Radziejewska, Renata; Pikul, Jan

2004-03-01

The aim of this study was to determine the effect of sodium lactate addition on shelf-life extension of sliced poultry sausage packaged both in air and nitrogen atmospheres and stored in refrigerated conditions. Basic chemical composition, pH, and malonaldehyde content were assayed and color measurement using the reflection method was carried out. Microbiological examination consisted of determination of total number of aerobic psychrotrophic bacteria and number of lactic acid bacteria. Sensory evaluation of products was performed. Microbiological and sensory quality of sliced poultry meat sausage was dependent on the addition during production of sodium lactate and the composition of gases (air or nitrogen) used in packaging. Slices of poultry sausage with 1% as well as 2% of sodium lactate maintained their initial quality of evaluated sensory attributes longer, irrespective of the applied gases. Sodium lactate inhibited growth of aerobic psychrotrophic bacteria and lactic acid bacteria during refrigerated storage. Sodium lactate also inhibited the formation of malonaldehyde in sliced poultry sausage during refrigerated storage. The effectiveness of this process depended on the concentration of sodium lactate addition. It was concluded that 1% as well as 2% addition of sodium lactate could extend the shelf life of sliced poultry sausage packaged in air atmosphere and stored at 5 to 7 degrees C by 3 or 4 times, respectively. Sliced poultry sausage treated with 2% sodium lactate packed in nitrogen had the longest (35-day) shelf life. This was a sevenfold increase in the shelf life of sliced poultry sausage compared with the control.

Effect of Packaging Materials on Orthosiphon Stamineus Dried-Leaf Quality During Storage

NASA Astrophysics Data System (ADS)

Norawanis, A. R.; Shaari, A. R.; Leng, L. Y.

2018-03-01

The experiment was conducted to determine the effects on the total phenolic content, antioxidant capacity, moisture content and total different color (ΔE) when the O. stamineus dried whole-leaf were packed in different packaging materials (plastic bag, paper bag and glass container) and stored under room temperature (±25 °C) and relative humidity (±65 %RH) for 8 weeks. The total phenolic compounds and antioxidant activity were measured using the Folin-Ciocalteu method and 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging activity assay respectively, and analyzed using UV/VIS Spectrophotometer. The moisture content changes were examined using a moisture analyzer and the color changes were analyzed using colorimeter. The results showed that packing O. stamineus dried whole-leaf in different packaging materials significantly affected the herbal leaves quality. After 8 weeks of storage period, the total phenolic content and antioxidant capacity exhibited the increase values during storage. Meanwhile, the moisture content of the samples decreased by storage period for the samples packed in plastic bag and glass container. The moisture content of the samples packed in the paper bag fluctuated along the 8 weeks of storage period. The total different color (ΔE) of the O. stamineus dried whole-leaf increased by storage period. The highest changes of ΔE belonged to the samples packed in the glass container, followed by paper and plastic bags. The selection of the packaging materials can be considered as an important element to control the quality of raw herbal materials for further processing and the herbal finished products.

Targeting RNA–Protein Interactions within the Human Immunodeficiency Virus Type 1 Lifecycle

PubMed Central

2013-01-01

RNA–protein interactions are vital throughout the HIV-1 life cycle for the successful production of infectious virus particles. One such essential RNA–protein interaction occurs between the full-length genomic viral RNA and the major structural protein of the virus. The initial interaction is between the Gag polyprotein and the viral RNA packaging signal (psi or Ψ), a highly conserved RNA structural element within the 5′-UTR of the HIV-1 genome, which has gained attention as a potential therapeutic target. Here, we report the application of a target-based assay to identify small molecules, which modulate the interaction between Gag and Ψ. We then demonstrate that one such molecule exhibits potent inhibitory activity in a viral replication assay. The mode of binding of the lead molecules to the RNA target was characterized by 1H NMR spectroscopy. PMID:24358934

Gelatine-Based Antioxidant Packaging Containing Caesalpinia decapetala and Tara as a Coating for Ground Beef Patties

PubMed Central

Gallego, María Gabriela; Gordon, Michael H.; Segovia, Francisco; Almajano Pablos, María Pilar

2016-01-01

The development of antioxidant-active packaging has numerous advantages, such as the reduction of synthetic additives in food, the reduction of plastic waste and food protection against oxidation reactions. Different concentrations of extracts of the plants Caesalpinia decapetala (CD) and Caesalpinia spinosa “Tara” (CS) were incorporated into gelatine films as natural antioxidants. The physical, mechanical and antioxidant properties of these films were studied. Films containing plant extracts at a high concentration had lower tensile strength with higher elongation at break points, compared to the control film (p < 0.05). Films exhibited antioxidant activity in the oxygen radical absorbance capacity (ORAC) and Trolox equivalence antioxidant capacity (TEAC) assays when added at 0.2%. The application of gelatine film containing CD and CS was found to be effective in delaying lipid oxidation and deterioration of beef patty quality during storage. Therefore, the films prepared in this study offered an alternative edible coating for the preservation of fresh food. PMID:27043638

Glyceraldehyde 3-phosphate dehydrogenase negatively regulates human immunodeficiency virus type 1 infection

PubMed Central

2012-01-01

Background Host proteins are incorporated inside human immunodeficiency virus type 1 (HIV-1) virions during assembly and can either positively or negatively regulate HIV-1 infection. Although the identification efficiency of host proteins is improved by mass spectrometry, how those host proteins affect HIV-1 replication has not yet been fully clarified. Results In this study, we show that virion-associated glyceraldehyde 3-phosphate dehydrogenase (GAPDH) does not allosterically inactivate HIV-1 reverse transcriptase (RT) but decreases the efficiency of reverse transcription reactions by decreasing the packaging efficiency of lysyl-tRNA synthetase (LysRS) and tRNALys3 into HIV-1 virions. Two-dimensional (2D) gel electrophoresis demonstrated that some isozymes of GAPDH with different isoelectric points were expressed in HIV-1-producing CEM/LAV-1 cells, and a proportion of GAPDH was selectively incorporated into the virions. Suppression of GAPDH expression by RNA interference in CEM/LAV-1 cells resulted in decreased GAPDH packaging inside the virions, and the GAPDH-packaging-defective virus maintained at least control levels of viral production but increased the infectivity. Quantitative analysis of reverse transcription products indicated that the levels of early cDNA products of the GAPDH-packaging-defective virus were higher than those of the control virus owing to the higher packaging efficiencies of LysRS and tRNALys3 into the virions rather than the GAPDH-dependent negative allosteric modulation for RT. Furthermore, immunoprecipitation assay using an anti-GAPDH antibody showed that GAPDH directly interacted with Pr55gag and p160gag-pol and the overexpression of LysRS in HIV-1-producing cells resulted in a decrease in the efficiency of GAPDH packaging in HIV particles. In contrast, the viruses produced from cells expressing a high level of GAPDH showed decreased infectivity in TZM-bl cells and reverse transcription efficiency in TZM-bl cells and peripheral blood mononuclear cells (PBMCs). Conclusions These findings indicate that GAPDH negatively regulates HIV-1 infection and provide insights into a novel function of GAPDH in the HIV-1 life cycle and a new host defense mechanism against HIV-1 infection. PMID:23237566

Effect of modified atmosphere packaging on the course of physical and chemical changes in chilled muscle tissue of silver carp (Hypophthalmichthys molitrix, V.).

PubMed

Jezek, F; Buchtová, H

2012-01-01

The effect of two types of modified atmosphere (MA1: 69% N2, 25% CO2, 5% O2, 1% CO; MA2: 70% N2, 30% CO2) on changes in physical and chemical parameters (pH, a(w)--water activity, TVBN - total volatile basic nitrogen, TMA - trimethylamine, FFA - free fatty acids, PV - peroxide value, TBA--thiobarbituric acid) in muscle tissues of the silver carp was monitored in the study. The samples were stored at temperatures +2 +/- 2 degrees C for 18 days. Changes in gas volumes (CO2 and O2) in MAs were also monitored. CO2 levels increased in MA1 but decreased in MA2. At the end of 18 days of storage, a significantly (P < 0.01) lower water activity (a(w)) levels were found in samples packaged under MA1, in contrast to samples packaged under MA2 where water activity values showed considerable fluctuation. Variations in pH values in the two types of MA showed similar trends. Sample pH gradually decreased until day 9 of storage. On day 11, muscle tissue pH increased markedly and then began to decrease again. The overall decrease in pH values was more profound in samples packaged under MA1. TVBN and TMA levels in samples packaged under the two types of MAs remained almost identical until day 9 of the experiment. Later, however, significantly (P < 0.01) higher levels of both parameters were found in muscle tissues packaged under MA1. FFA concentrations in silver carp samples in MA1 were significantly lower (P < 0.01) throughout the experiment. The PV increased significantly in both muscle samples tested. Greater fluctuations in this parameter's values throughout the experiment were observed in samples packaged under MA2. Faster rates of oxidation (P < 0.01) were found in samples packaged under MA1 starting on day 9. Maximum TBA values in MA1 and MA2 were observed on days 14 and 18 of the experiment, respectively. From the course of proteolytic and oxidative changes point of view, the more appropriate combination of gases for silver carp storage seems to be the mixture of 70% N2 and 30% CO2 (MA2), which allows for muscle storage of up to 9 days. We recommend TVBN as a suitable indicator of freshness, and TBA assay as a suitable indicator of the extent of oxidative processes.

Interaction and interdependent packaging of tegument protein UL11 and glycoprotein e of herpes simplex virus.

PubMed

Han, Jun; Chadha, Pooja; Meckes, David G; Baird, Nicholas L; Wills, John W

2011-09-01

The UL11 tegument protein of herpes simplex virus plays a critical role in the secondary envelopment; however, the mechanistic details remain elusive. Here, we report a new function of UL11 in the budding process in which it directs efficient acquisition of glycoprotein E (gE) via a direct interaction. In vitro binding assays showed that the interaction required only the first 28, membrane-proximal residues of the cytoplasmic tail of gE, and the C-terminal 26 residues of UL11. A second, weaker binding site was also found in the N-terminal half of UL11. The significance of the gE-UL11 interaction was subsequently investigated with viral deletion mutants. In the absence of the gE tail, virion packaging of UL11, but not other tegument proteins such as VP22 and VP16, was reduced by at least 80%. Reciprocally, wild-type gE packaging was also drastically reduced by about 87% in the absence of UL11, and this defect could be rescued in trans by expressing U(L)11 at the U(L)35 locus. Surprisingly, a mutant that lacks the C-terminal gE-binding site of UL11 packaged nearly normal amounts of gE despite its strong interaction with the gE tail in vitro, indicating that the interaction with the UL11 N terminus may be important. Mutagenesis studies of the UL11 N terminus revealed that the association of UL11 with membrane was not required for this function. In contrast, the UL11 acidic cluster motif was found to be critical for gE packaging and was not replaceable with foreign acidic clusters. Together, these results highlight an important role of UL11 in the acquisition of glycoprotein-enriched lipid bilayers, and the findings may also have important implications for the role of UL11 in gE-mediated cell-to-cell spread.

Reference Gene Validation for RT-qPCR, a Note on Different Available Software Packages

PubMed Central

De Spiegelaere, Ward; Dern-Wieloch, Jutta; Weigel, Roswitha; Schumacher, Valérie; Schorle, Hubert; Nettersheim, Daniel; Bergmann, Martin; Brehm, Ralph; Kliesch, Sabine; Vandekerckhove, Linos; Fink, Cornelia

2015-01-01

Background An appropriate normalization strategy is crucial for data analysis from real time reverse transcription polymerase chain reactions (RT-qPCR). It is widely supported to identify and validate stable reference genes, since no single biological gene is stably expressed between cell types or within cells under different conditions. Different algorithms exist to validate optimal reference genes for normalization. Applying human cells, we here compare the three main methods to the online available RefFinder tool that integrates these algorithms along with R-based software packages which include the NormFinder and GeNorm algorithms. Results 14 candidate reference genes were assessed by RT-qPCR in two sample sets, i.e. a set of samples of human testicular tissue containing carcinoma in situ (CIS), and a set of samples from the human adult Sertoli cell line (FS1) either cultured alone or in co-culture with the seminoma like cell line (TCam-2) or with equine bone marrow derived mesenchymal stem cells (eBM-MSC). Expression stabilities of the reference genes were evaluated using geNorm, NormFinder, and BestKeeper. Similar results were obtained by the three approaches for the most and least stably expressed genes. The R-based packages NormqPCR, SLqPCR and the NormFinder for R script gave identical gene rankings. Interestingly, different outputs were obtained between the original software packages and the RefFinder tool, which is based on raw Cq values for input. When the raw data were reanalysed assuming 100% efficiency for all genes, then the outputs of the original software packages were similar to the RefFinder software, indicating that RefFinder outputs may be biased because PCR efficiencies are not taken into account. Conclusions This report shows that assay efficiency is an important parameter for reference gene validation. New software tools that incorporate these algorithms should be carefully validated prior to use. PMID:25825906

Reference gene validation for RT-qPCR, a note on different available software packages.

PubMed

De Spiegelaere, Ward; Dern-Wieloch, Jutta; Weigel, Roswitha; Schumacher, Valérie; Schorle, Hubert; Nettersheim, Daniel; Bergmann, Martin; Brehm, Ralph; Kliesch, Sabine; Vandekerckhove, Linos; Fink, Cornelia

2015-01-01

An appropriate normalization strategy is crucial for data analysis from real time reverse transcription polymerase chain reactions (RT-qPCR). It is widely supported to identify and validate stable reference genes, since no single biological gene is stably expressed between cell types or within cells under different conditions. Different algorithms exist to validate optimal reference genes for normalization. Applying human cells, we here compare the three main methods to the online available RefFinder tool that integrates these algorithms along with R-based software packages which include the NormFinder and GeNorm algorithms. 14 candidate reference genes were assessed by RT-qPCR in two sample sets, i.e. a set of samples of human testicular tissue containing carcinoma in situ (CIS), and a set of samples from the human adult Sertoli cell line (FS1) either cultured alone or in co-culture with the seminoma like cell line (TCam-2) or with equine bone marrow derived mesenchymal stem cells (eBM-MSC). Expression stabilities of the reference genes were evaluated using geNorm, NormFinder, and BestKeeper. Similar results were obtained by the three approaches for the most and least stably expressed genes. The R-based packages NormqPCR, SLqPCR and the NormFinder for R script gave identical gene rankings. Interestingly, different outputs were obtained between the original software packages and the RefFinder tool, which is based on raw Cq values for input. When the raw data were reanalysed assuming 100% efficiency for all genes, then the outputs of the original software packages were similar to the RefFinder software, indicating that RefFinder outputs may be biased because PCR efficiencies are not taken into account. This report shows that assay efficiency is an important parameter for reference gene validation. New software tools that incorporate these algorithms should be carefully validated prior to use.

Delayed Gamma-Ray Spectroscopy for Non-Destructive Assay of Nuclear Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ludewigt, Bernhard; Mozin, Vladimir; Campbell, Luke

2015-06-01

High-­energy, beta-delayed gamma-­ray spectroscopy is a potential, non-­destructive assay techniques for the independent verification of declared quantities of special nuclear materials at key stages of the fuel cycle and for directly assaying nuclear material inventories for spent fuel handling, interim storage, reprocessing facilities, repository sites, and final disposal. Other potential applications include determination of MOX fuel composition, characterization of nuclear waste packages, and challenges in homeland security and arms control verification. Experimental measurements were performed to evaluate fission fragment yields, to test methods for determining isotopic fractions, and to benchmark the modeling code package. Experimental measurement campaigns were carried outmore » at the IAC using a photo-­neutron source and at OSU using a thermal neutron beam from the TRIGA reactor to characterize the emission of high-­energy delayed gamma rays from 235U, 239Pu, and 241Pu targets following neutron induced fission. Data were collected for pure and combined targets for several irradiation/spectroscopy cycle times ranging from 10/10 seconds to 15/30 minutes.The delayed gamma-ray signature of 241Pu, a significant fissile constituent in spent fuel, was measured and compared to 239Pu. The 241Pu/ 239Pu ratios varied between 0.5 and 1.2 for ten prominent lines in the 2700-­3600 keV energy range. Such significant differences in relative peak intensities make it possible to determine relative fractions of these isotopes in a mixed sample. A method for determining fission product yields by fitting the energy and time dependence of the delayed gamma-­ray emission was developed and demonstrated on a limited 235U data set. De-­convolution methods for determining fissile fractions were developed and tested on the experimental data. The use of high count-­rate LaBr 3 detectors was investigated as a potential alternative to HPGe detectors. Modeling capabilities were added to an existing framework and codes were adapted as needed for analyzing experiments and assessing application-­specific assay concepts. A de-­convolution analysis of the delayed gamma-­ray response spectra modeled for spent fuel assemblies was performed using the same method that was applied to the experimental spectra.« less

Analysis of HIV using a high resolution melting (HRM) diversity assay: automation of HRM data analysis enhances the utility of the assay for analysis of HIV incidence.

PubMed

Cousins, Matthew M; Swan, David; Magaret, Craig A; Hoover, Donald R; Eshleman, Susan H

2012-01-01

HIV diversity may be a useful biomarker for discriminating between recent and non-recent HIV infection. The high resolution melting (HRM) diversity assay was developed to quantify HIV diversity in viral populations without sequencing. In this assay, HIV diversity is expressed as a single numeric HRM score that represents the width of a melting peak. HRM scores are highly associated with diversity measures obtained with next generation sequencing. In this report, a software package, the HRM Diversity Assay Analysis Tool (DivMelt), was developed to automate calculation of HRM scores from melting curve data. DivMelt uses computational algorithms to calculate HRM scores by identifying the start (T1) and end (T2) melting temperatures for a DNA sample and subtracting them (T2 - T1 =  HRM score). DivMelt contains many user-supplied analysis parameters to allow analyses to be tailored to different contexts. DivMelt analysis options were optimized to discriminate between recent and non-recent HIV infection and to maximize HRM score reproducibility. HRM scores calculated using DivMelt were compared to HRM scores obtained using a manual method that is based on visual inspection of DNA melting curves. HRM scores generated with DivMelt agreed with manually generated HRM scores obtained from the same DNA melting data. Optimal parameters for discriminating between recent and non-recent HIV infection were identified. DivMelt provided greater discrimination between recent and non-recent HIV infection than the manual method. DivMelt provides a rapid, accurate method of determining HRM scores from melting curve data, facilitating use of the HRM diversity assay for large-scale studies.

Analysis of HIV Using a High Resolution Melting (HRM) Diversity Assay: Automation of HRM Data Analysis Enhances the Utility of the Assay for Analysis of HIV Incidence

PubMed Central

Cousins, Matthew M.; Swan, David; Magaret, Craig A.; Hoover, Donald R.; Eshleman, Susan H.

2012-01-01

Background HIV diversity may be a useful biomarker for discriminating between recent and non-recent HIV infection. The high resolution melting (HRM) diversity assay was developed to quantify HIV diversity in viral populations without sequencing. In this assay, HIV diversity is expressed as a single numeric HRM score that represents the width of a melting peak. HRM scores are highly associated with diversity measures obtained with next generation sequencing. In this report, a software package, the HRM Diversity Assay Analysis Tool (DivMelt), was developed to automate calculation of HRM scores from melting curve data. Methods DivMelt uses computational algorithms to calculate HRM scores by identifying the start (T1) and end (T2) melting temperatures for a DNA sample and subtracting them (T2–T1 = HRM score). DivMelt contains many user-supplied analysis parameters to allow analyses to be tailored to different contexts. DivMelt analysis options were optimized to discriminate between recent and non-recent HIV infection and to maximize HRM score reproducibility. HRM scores calculated using DivMelt were compared to HRM scores obtained using a manual method that is based on visual inspection of DNA melting curves. Results HRM scores generated with DivMelt agreed with manually generated HRM scores obtained from the same DNA melting data. Optimal parameters for discriminating between recent and non-recent HIV infection were identified. DivMelt provided greater discrimination between recent and non-recent HIV infection than the manual method. Conclusion DivMelt provides a rapid, accurate method of determining HRM scores from melting curve data, facilitating use of the HRM diversity assay for large-scale studies. PMID:23240016

Novel functional hepatitis C virus glycoprotein isolates identified using an optimized viral pseudotype entry assay.

PubMed

Urbanowicz, Richard A; McClure, C Patrick; King, Barnabas; Mason, Christopher P; Ball, Jonathan K; Tarr, Alexander W

2016-09-01

Retrovirus pseudotypes are a highly tractable model used to study the entry pathways of enveloped viruses. This model has been extensively applied to the study of the hepatitis C virus (HCV) entry pathway, preclinical screening of antiviral antibodies and for assessing the phenotype of patient-derived viruses using HCV pseudoparticles (HCVpp) possessing the HCV E1 and E2 glycoproteins. However, not all patient-isolated clones produce particles that are infectious in this model. This study investigated factors that might limit phenotyping of patient-isolated HCV glycoproteins. Genetically related HCV glycoproteins from quasispecies in individual patients were discovered to behave very differently in this entry model. Empirical optimization of the ratio of packaging construct and glycoprotein-encoding plasmid was required for successful HCVpp genesis for different clones. The selection of retroviral packaging construct also influenced the function of HCV pseudoparticles. Some glycoprotein constructs tolerated a wide range of assay parameters, while others were much more sensitive to alterations. Furthermore, glycoproteins previously characterized as unable to mediate entry were found to be functional. These findings were validated using chimeric cell-cultured HCV bearing these glycoproteins. Using the same empirical approach we demonstrated that generation of infectious ebolavirus pseudoviruses (EBOVpv) was also sensitive to the amount and ratio of plasmids used, and that protocols for optimal production of these pseudoviruses are dependent on the exact virus glycoprotein construct. These findings demonstrate that it is crucial for studies utilizing pseudoviruses to conduct empirical optimization of pseudotype production for each specific glycoprotein sequence to achieve optimal titres and facilitate accurate phenotyping.

Optimization and proficiency testing of a pseudovirus-based assay for detection of HIV-1 neutralizing antibody in China.

PubMed

Nie, Jianhui; Wang, Wenbo; Wen, Zhiheng; Song, Aijing; Hong, Kunxue; Lu, Shan; Zhong, Ping; Xu, Jianqing; Kong, Wei; Li, Jingyun; Shang, Hong; Ling, Hong; Ruan, Li; Wang, Youchun

2012-11-01

Among the neutralizing antibody evaluation assays, the single-cycle pseudovirus infection assay is high-throughput and can provide rapid, sensitive and reproducible measurements after a single cycle of infection. Cell counts, pseudovirus inoculation levels, amount of diethylaminoethyl-dextran (DEAE-dextran), and the nonspecific effects of serum and plasma were tested to identify the optimal conditions for a neutralizing antibody assay based on pseudoviruses. Optimal conditions for cell counts, pseudovirus inoculation, and amount of DEAE-dextran were 1 × 10(4)cells/well, 200TCID(50)/well, and 15 μg/ml, respectively. Compared with serum samples, high-concentration anticoagulants reduced the relative light unit (RLU) value. The RLU value increased sharply initially but then decreased slowly with dilution of the plasma sample. Test kits containing 10 HIV-1 CRF07/08_BC pseudovirus strains and 10 plasma samples from individuals infected with HIV-1 CRF07/08_BC were assembled into two packages and distributed to nine laboratories with a standard operating procedure included. For the 10 laboratories that evaluated the test, 17 of 44 (37%) laboratory pairs were considered equivalent. A statistical qualification rule was developed based on the testing results from 5 experienced laboratories, where a laboratory qualified if at least 83% of values lied within the acceptable range. Copyright © 2012 Elsevier B.V. All rights reserved.

Endotoxin Detection in Pharmaceuticals and Medical Devices with Kinetic-QCL, a Kinetic-Quantitative Chromogenic Limulus Amebocyte Lysate Assay.

PubMed

Berzofsky, Ronald N.

1995-01-01

The observation that endotoxin caused gelation in extracts of Limulus amebocytes has been expanded to the development of an in vitro kinetic, quantitative chromogenic LAL assay (Kinetic-QCL) for the detection of endotoxin in aqueous fluids. Within the last 15 years, the use of Limulus amebocyte lysate to detect and control the presence of pyrogenic substances in pharmaceuticals and medical devices has gained wide international acceptance. Both the United States and European Pharmacopoeias contain descriptions of and requirements for the LAL Bacterial Endotoxin Test. Both pharmacopoeias have begun to remove the rabbit pyrogen test requirement in a majority of drug monographs and have substituted endotoxin limits to be determined by LAL. The use of LAL has proved invaluable in controlling the level of endotoxin in finished product. The endotoxin contribution of raw materials and packaging material can be monitored as well. In-process testing at critical production steps can identify additional sources of endotoxin contamination, and depyrogenation processes can be validated by quantitating the degradation of endotoxin challenges. The speed, reproducibility, sensitivity, and economics of the Kinetic-QCL assay, in conjunction with the ppropriate equipment and software, over both the in vivo rabbit pyrogen test and the more traditional LAL gel-clot assay allow a more in-depth approach to the control of endotoxin in pharmaceuticals and medical devices.

The in-plant evaluation of a uranium NDA system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sprinkle, J.K. Jr.; Baxman, H.R.; Langner, D.G.

1979-12-31

The Los Alamos Scientific Laboratory has an unirradiated enriched uranium reprocessing facility. Various types of solutions are generated in this facility, including distillates and raffinates containing ppm of uranium and concentrated solutions with up to 400 grams U/t. In addition to uranyl nitrate and HNO{sub 3}, the solutions may also contain zirconium, niobium, fluoride, and small amounts of many metals. A uranium solution assay system (USAS) has been installed to allow accurate and more timely process control, accountability, and criticality data to be obtained. The USAS assays are made by a variety of techniques that depend upon state-of-the-art high-resolution Ge(Li)more » gamma-ray spectroscopy integrated with an interactive, user-oriented computer software package. Tight control of the system`s performance is maintained by constantly monitoring the USAS status. Daily measurement control sequences are required, and the user is forced by the software to perform these sequences. Routine assays require 400 or 1000 seconds for a precision of 0.5% over the concentration range of 5--400 g/t. A comparison of the USAS precision and accuracy with that obtained by traditional destructive analytical chemistry techniques (colorimetric and volumetric) is presented.« less

The in-plant evaluation of a uranium NDA system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sprinkle, J.K. Jr.; Baxman, H.R.; Langner, D.G.

1979-01-01

The Los Alamos Scientific Laboratory has an unirradiated enriched uranium reprocessing facility. Various types of solutions are generated in this facility, including distillates and raffinates containing ppm of uranium and concentrated solutions with up to 400 grams U/t. In addition to uranyl nitrate and HNO{sub 3}, the solutions may also contain zirconium, niobium, fluoride, and small amounts of many metals. A uranium solution assay system (USAS) has been installed to allow accurate and more timely process control, accountability, and criticality data to be obtained. The USAS assays are made by a variety of techniques that depend upon state-of-the-art high-resolution Ge(Li)more » gamma-ray spectroscopy integrated with an interactive, user-oriented computer software package. Tight control of the system's performance is maintained by constantly monitoring the USAS status. Daily measurement control sequences are required, and the user is forced by the software to perform these sequences. Routine assays require 400 or 1000 seconds for a precision of 0.5% over the concentration range of 5--400 g/t. A comparison of the USAS precision and accuracy with that obtained by traditional destructive analytical chemistry techniques (colorimetric and volumetric) is presented.« less

Control of Escherichia coli and Listeria monocytogenes in suckling-lamb meat evaluated using microbial challenge tests.

PubMed

Osés, S M; Diez, A M; Gómez, E M; Wilches-Pérez, D; Luning, P A; Jaime, I; Rovira, J

2015-12-01

Escherichia coli and Listeria monocytogenes microbial challenge tests were performed on fresh suckling-lamb meat. Hind leg slices were chilly stored under two modified atmosphere packaging (MAP) environments (A: 15%O2/60%CO2/25%N2, B: 15%O2/30%CO2/55%N2) and vacuum packaging (V). Only E. coli was reduced between 0.72-1.25 log cfu/g from day 1 to day 4 by the combined use of MAP/V, chilling storage and the growth of native lactic acid bacteria. However, L. monocytogenes was not inhibited by the application of V or MAP. Even do, in inoculated samples, this pathogen increased between 1.2-2.7 log cfu/g throughout the study. Consequently, a second experiment that combined the effects of MAP/V and a protective culture (Leuconostoc pseudomesenteroides PCK 18) against L. monocytogenes was designed. Two different levels of protective cultures were assayed (4 and 6 log cfu/g). Lc. pseudomesenteroides PCK 18 was able to control the growth of L. monocytogenes when the differences between them are higher than 2 log cfu/g. Moreover, when high level of protective culture was used a significant reduction of L. monocytogenes counts were noticed in samples packaged in 60% of CO2 along the storage period, although sensory properties were also affected. Copyright © 2015 Elsevier Ltd. All rights reserved.

Experimental validation of the DARWIN2.3 package for fuel cycle applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

San-Felice, L.; Eschbach, R.; Bourdot, P.

2012-07-01

The DARWIN package, developed by the CEA and its French partners (AREVA and EDF) provides the required parameters for fuel cycle applications: fuel inventory, decay heat, activity, neutron, {gamma}, {alpha}, {beta} sources and spectrum, radiotoxicity. This paper presents the DARWIN2.3 experimental validation for fuel inventory and decay heat calculations on Pressurized Water Reactor (PWR). In order to validate this code system for spent fuel inventory a large program has been undertaken, based on spent fuel chemical assays. This paper deals with the experimental validation of DARWIN2.3 for the Pressurized Water Reactor (PWR) Uranium Oxide (UOX) and Mixed Oxide (MOX) fuelmore » inventory calculation, focused on the isotopes involved in Burn-Up Credit (BUC) applications and decay heat computations. The calculation - experiment (C/E-1) discrepancies are calculated with the latest European evaluation file JEFF-3.1.1 associated with the SHEM energy mesh. An overview of the tendencies is obtained on a complete range of burn-up from 10 to 85 GWd/t (10 to 60 GWcVt for MOX fuel). The experimental validation of the DARWIN2.3 package for decay heat calculation is performed using calorimetric measurements carried out at the Swedish Interim Spent Fuel Storage Facility for Pressurized Water Reactor (PWR) assemblies, covering a large burn-up (20 to 50 GWd/t) and cooling time range (10 to 30 years). (authors)« less

Evidence that viral RNAs have evolved for efficient, two-stage packaging.

PubMed

Borodavka, Alexander; Tuma, Roman; Stockley, Peter G

2012-09-25

Genome packaging is an essential step in virus replication and a potential drug target. Single-stranded RNA viruses have been thought to encapsidate their genomes by gradual co-assembly with capsid subunits. In contrast, using a single molecule fluorescence assay to monitor RNA conformation and virus assembly in real time, with two viruses from differing structural families, we have discovered that packaging is a two-stage process. Initially, the genomic RNAs undergo rapid and dramatic (approximately 20-30%) collapse of their solution conformations upon addition of cognate coat proteins. The collapse occurs with a substoichiometric ratio of coat protein subunits and is followed by a gradual increase in particle size, consistent with the recruitment of additional subunits to complete a growing capsid. Equivalently sized nonviral RNAs, including high copy potential in vivo competitor mRNAs, do not collapse. They do support particle assembly, however, but yield many aberrant structures in contrast to viral RNAs that make only capsids of the correct size. The collapse is specific to viral RNA fragments, implying that it depends on a series of specific RNA-protein interactions. For bacteriophage MS2, we have shown that collapse is driven by subsequent protein-protein interactions, consistent with the RNA-protein contacts occurring in defined spatial locations. Conformational collapse appears to be a distinct feature of viral RNA that has evolved to facilitate assembly. Aspects of this process mimic those seen in ribosome assembly.

Comparison of the Solubilization Properties of Polysorbate 80 and Isopropanol/Water Solvent Systems for Organic Compounds Extracted from Three Pharmaceutical Packaging Configurations.

PubMed

Zdravkovic, Steven A

2016-10-10

It has been reported that the presence of polysorbate 80 in a pharmaceutical product's formulation may increase the number and/or amount of impurities leached from materials used during its manufacture, storage, and/or administration. However, it is uncertain if/how the solubilization properties of this surfactant compare to non-surfactant solvent systems. The goal of this study is to provide insight into this area of uncertainty by comparing the solubilization properties of polysorbate 80 to those of isopropanol/water solutions while in contact with a plasticized polyvinylchloride parenteral delivery bag, a single-use type manufacturing bag, and a polypropylene bottle. These properties were determined via a binding experiment, in which a set of model compounds was introduced into the solutions, and via an extraction experiment, in which compounds were extracted from the packaging material by the solutions. In both experiments, the amount of each compound present at equilibrium was assayed to determine the extent they were solubilized by the solution from the packaging material. Results from these experiments illustrate differences in the magnitude of solubilization obtained from solutions containing polysorbate 80 as compared to those composed of isopropanol/water. However, it was also demonstrated that their solubilization properties can be linked via a mathematical model. Copyright © 2016 Elsevier B.V. All rights reserved.

Fluorinated alkyl substances and technical mixtures used in food paper-packaging exhibit endocrine-related activity in vitro.

PubMed

Rosenmai, A K; Taxvig, C; Svingen, T; Trier, X; van Vugt-Lussenburg, B M A; Pedersen, M; Lesné, L; Jégou, B; Vinggaard, A M

2016-07-01

Migration of chemicals from packaging materials to foods may lead to human exposure. Polyfluoroalkyl substances (PFAS) can be used in technical mixtures (TMs) for use in food packaging of paper and board, and PFAS have been detected in human serum and umbilical cord blood. The specific structures of the PFAS in TMs are often unknown, but polyfluorinated alkyl phosphate esters (PAPs) have been characterized in TMs, food packaging, and in food. PAPs can be metabolized into fluorotelomer alcohols (FTOHs) and perfluoroalkyl carboxylic acids (PFCAs). Some PFAS have endocrine activities, highlighting the need to investigate these effects. Herein, we studied the endocrine activity of less characterized PFAS, including short-chain PFCAs and FTOHs, PAPs, and TMs of unknown chemical composition. Long-chain PFCAs were also included. We applied seven assays covering effects on estrogen, glucocorticoid, androgen, and peroxisome proliferator-activated receptor (PPAR) activity, as well as steroidogenesis in vitro and ex vivo. In general, PAPs, FTOHs, TMs, and long-chain PFCAs showed estrogenic activity through receptor activation and/or increasing 17β-estradiol levels. Furthermore, short- and long-chain PFCAs activated PPARα and PPARγ. Collectively, this means that (i) PAPs, FTOHs, and PFCAs exhibit endocrine activity through distinct and sometimes different mechanisms, (ii) two out of three tested TMs exhibited estrogenic activity, and (iii) short-chain FTOHs showed estrogenic activity and short-chain PFCAs generally activate both PPARα and PPARγ with similar potency and efficacy as long-chain PFCAs. In conclusion, several new and divergent toxicological targets were identified for different groups of PFAS. © 2016 American Society of Andrology and European Academy of Andrology.

Defining the Transfer Functions of the PCAD Model in North Atlantic Right Whales (Eubalaena glacialis) - Retrospective Analyses of Existing Data

DTIC Science & Technology

2012-09-30

potentially providing information on nutritional state and chronic stress ( Wasser et al., 2010). We tested both T3 and T4 assays for parallelism.The...EconPapers.RePEc.org/RePEc:inn:wpaper:2011-20 Hunt K.E., Rolland R.M., Kraus S.D., Wasser S.K. 2006. Analysis of fecal glucocorticoids in the North Atlantic right...version 1.2.5. http://CRAN.R-project.org/package=doMC Rolland R.M., Hunt K.E., Kraus S.D., Wasser S.K. 2005. Assessing reproductive status of right

Description of the plasma diagnostics package (PDP) for the OSS-1 Shuttle mission and JSC plasma chamber test in conjunction with the fast pulse electron gun (FPEG)

NASA Technical Reports Server (NTRS)

Shawhan, S. D.

1982-01-01

The objectives, equipment, and techniques for the plasma diagnostics package (PDP) carried by the OSS-1 instrument payload of the STS-4 and scheduled for the Spacelab-2 mission are described. The goals of the first flight were to examine the Orbiter-magnetoplasma interactions by measuring the electric and magnetic field strengths, the ionized particle wakes, and the generated waves. The RMS was employed to lift the unit out of the bay in order to allow characterization of the fields, EM interference, and plasma contamination within 15 m of the Orbiter. The PDP will also be used to examine plasma depletion, chemical reaction rates, waves, and energized plasma produced by firing of the Orbiter thrusters. Operation of the PDP was carried out in the NASA Space Environment Simulation Laboratory test chamber, where the PDP was used to assay the fields, fluxes, wave amplitudes, and particle energy spectra. The PDP instrumentation is also capable of detecting thermal ions, thermal electrons suprathermal particles, VHF/UHF EMI levels, and the S-band field strength.

Tannins and extracts of fruit byproducts: antibacterial activity against foodborne bacteria and antioxidant capacity.

PubMed

Widsten, Petri; Cruz, Cristina D; Fletcher, Graham C; Pajak, Marta A; McGhie, Tony K

2014-11-19

The shelf life of fresh fish and meat transported over long distances could be extended by using plant-based extracts to control spoilage bacteria. The goals of the present study were to identify plant-based extracts that effectively suppress the main spoilage bacteria of chilled fish and lamb and to assess their antioxidant capacity. The phenolic compounds in wood-based tannins and extracts isolated from byproducts of the fruit processing industry were identified and/or quantified. The total phenol content, but not the flavonoid to total phenol ratio, was strongly associated with higher antibacterial activity against several fish and lamb spoilage bacteria in zone of inhibition and minimum inhibitory concentration assays as well as greater antioxidant capacity in the DPPH (2,2-diphenyl-1-picrylhydrazyl) radical assay. The most promising compounds in both cases, and thus good candidates for antibacterial packaging or antioxidant dietary supplements, were mango seed extract and tannic acid containing mostly polygalloyl glucose type phenols.

Performance analysis of automated evaluation of Crithidia luciliae-based indirect immunofluorescence tests in a routine setting - strengths and weaknesses.

PubMed

Hormann, Wymke; Hahn, Melanie; Gerlach, Stefan; Hochstrate, Nicola; Affeldt, Kai; Giesen, Joyce; Fechner, Kai; Damoiseaux, Jan G M C

2017-11-27

Antibodies directed against dsDNA are a highly specific diagnostic marker for the presence of systemic lupus erythematosus and of particular importance in its diagnosis. To assess anti-dsDNA antibodies, the Crithidia luciliae-based indirect immunofluorescence test (CLIFT) is one of the assays considered to be the best choice. To overcome the drawback of subjective result interpretation that inheres indirect immunofluorescence assays in general, automated systems have been introduced into the market during the last years. Among these systems is the EUROPattern Suite, an advanced automated fluorescence microscope equipped with different software packages, capable of automated pattern interpretation and result suggestion for ANA, ANCA and CLIFT analysis. We analyzed the performance of the EUROPattern Suite with its automated fluorescence interpretation for CLIFT in a routine setting, reflecting the everyday life of a diagnostic laboratory. Three hundred and twelve consecutive samples were collected, sent to the Central Diagnostic Laboratory of the Maastricht University Medical Centre with a request for anti-dsDNA analysis over a period of 7 months. Agreement between EUROPattern assay analysis and the visual read was 93.3%. Sensitivity and specificity were 94.1% and 93.2%, respectively. The EUROPattern Suite performed reliably and greatly supported result interpretation. Automated image acquisition is readily performed and automated image classification gives a reliable recommendation for assay evaluation to the operator. The EUROPattern Suite optimizes workflow and contributes to standardization between different operators or laboratories.

Biological profiling and dose-response modeling tools ...

EPA Pesticide Factsheets

Through its ToxCast project, the U.S. EPA has developed a battery of in vitro high throughput screening (HTS) assays designed to assess the potential toxicity of environmental chemicals. At present, over 1800 chemicals have been tested in up to 600 assays, yielding a large number of concentration-response data sets. Standard processing of these data sets involves finding a best fitting mathematical model and set of model parameters that specify this model. The model parameters include quantities such as the half-maximal activity concentration (or “AC50”) that have biological significance and can be used to inform the efficacy or potency of a given chemical with respect to a given assay. All of this data is processed and stored in an online-accessible database and website: http://actor.epa.gov/dashboard2. Results from these in vitro assays are used in a multitude of ways. New pathways and targets can be identified and incorporated into new or existing adverse outcome pathways (AOPs). Pharmacokinetic models such as those implemented EPA’s HTTK R package can be used to translate an in vitro concentration into an in vivo dose; i.e., one can predict the oral equivalent dose that might be expected to activate a specific biological pathway. Such predicted values can then be compared with estimated actual human exposures prioritize chemicals for further testing.Any quantitative examination should be accompanied by estimation of uncertainty. We are developing met

Development of Iron-Chelating Poly(ethylene terephthalate) Packaging for Inhibiting Lipid Oxidation in Oil-in-Water Emulsions.

PubMed

Johnson, David R; Tian, Fang; Roman, Maxine J; Decker, Eric A; Goddard, Julie M

2015-05-27

Foods such as bulk oils, salad dressings, and nutritionally fortified beverages that are susceptible to oxidative degradation are often packaged in poly(ethylene terephthalate) (PET) bottles with metal chelators added to the food to maintain product quality. In the present work, a metal-chelating active packaging material is designed and characterized, in which poly(hydroxamic acid) (PHA) metal-chelating moieties were grafted from the surface of PET. Biomimetic PHA groups were grafted in a two-step UV-initiated process without the use of a photoinitiator. Surface characterization of the films by attenuated total reflective Fourier transform infrared spectroscopy (ATR-FTIR) and scanning electron microscopy (SEM) suggested successful grafting and conversion of poly(hydroxyethyl acrylate) (PHEA) to PHA chelating moieties from the surface of PET. Colorimetric (ferrozine) and inductively coupled plasma mass spectroscopy (ICP-MS) assays demonstrated the ability of PET-g-PHA to chelate iron in a low-pH (3.0) environment containing a competitive metal chelator (citric acid). Lipid oxidation studies demonstrated the antioxidant activity of PET-g-PHA films in inhibiting iron-promoted oxidation in an acidified oil-in-water (O/W) emulsion model system (pH 3.0). Particle size and ζ-potential analysis indicated that the addition of PET-g-PHA films did not affect the physical stability of the emulsion system. This work suggests that biomimetic chelating moieties can be grafted from PET and effectively inhibit iron-promoted degradation reactions, enabling removal of metal-chelating additives from product formulations.

RNA-Dependent Oligomerization of APOBEC3G Is Required for Restriction of HIV-1

PubMed Central

Huthoff, Hendrik; Autore, Flavia; Gallois-Montbrun, Sarah; Fraternali, Franca; Malim, Michael H.

2009-01-01

The human cytidine deaminase APOBEC3G (A3G) is a potent inhibitor of retroviruses and transposable elements and is able to deaminate cytidines to uridines in single-stranded DNA replication intermediates. A3G contains two canonical cytidine deaminase domains (CDAs), of which only the C-terminal one is known to mediate cytidine deamination. By exploiting the crystal structure of the related tetrameric APOBEC2 (A2) protein, we identified residues within A3G that have the potential to mediate oligomerization of the protein. Using yeast two-hybrid assays, co-immunoprecipitation, and chemical crosslinking, we show that tyrosine-124 and tryptophan-127 within the enzymatically inactive N-terminal CDA domain mediate A3G oligomerization, and this coincides with packaging into HIV-1 virions. In addition to the importance of specific residues in A3G, oligomerization is also shown to be RNA-dependent. Homology modelling of A3G onto the A2 template structure indicates an accumulation of positive charge in a pocket formed by a putative dimer interface. Substitution of arginine residues at positions 24, 30, and 136 within this pocket resulted in reduced virus inhibition, virion packaging, and oligomerization. Consistent with RNA serving a central role in all these activities, the oligomerization-deficient A3G proteins associated less efficiently with several cellular RNA molecules. Accordingly, we propose that occupation of the positively charged pocket by RNA promotes A3G oligomerization, packaging into virions and antiviral function. PMID:19266078

An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators.

PubMed

Gautier, Laurent

2010-12-21

Computer languages can be domain-related, and in the case of multidisciplinary projects, knowledge of several languages will be needed in order to quickly implements ideas. Moreover, each computer language has relative strong points, making some languages better suited than others for a given task to be implemented. The Bioconductor project, based on the R language, has become a reference for the numerical processing and statistical analysis of data coming from high-throughput biological assays, providing a rich selection of methods and algorithms to the research community. At the same time, Python has matured as a rich and reliable language for the agile development of prototypes or final implementations, as well as for handling large data sets. The data structures and functions from Bioconductor can be exposed to Python as a regular library. This allows a fully transparent and native use of Bioconductor from Python, without one having to know the R language and with only a small community of translators required to know both. To demonstrate this, we have implemented such Python representations for key infrastructure packages in Bioconductor, letting a Python programmer handle annotation data, microarray data, and next-generation sequencing data. Bioconductor is now not solely reserved to R users. Building a Python application using Bioconductor functionality can be done just like if Bioconductor was a Python package. Moreover, similar principles can be applied to other languages and libraries. Our Python package is available at: http://pypi.python.org/pypi/rpy2-bioconductor-extensions/.

Armored RNA as Virus Surrogate in a Real-Time Reverse Transcriptase PCR Assay Proficiency Panel

PubMed Central

Hietala, S. K.; Crossley, B. M.

2006-01-01

In recent years testing responsibilities for high-consequence pathogens have been expanded from national reference laboratories into networks of local and regional laboratories in order to support enhanced disease surveillance and to test for surge capacity. This movement of testing of select agents and high-consequence pathogens beyond reference laboratories introduces a critical need for standardized, noninfectious surrogates of disease agents for use as training and proficiency test samples. In this study, reverse transcription-PCR assay RNA targets were developed and packaged as armored RNA for use as a noninfectious, quantifiable synthetic substitute for four high-consequence animal pathogens: classical swine fever virus; foot-and-mouth disease virus; vesicular stomatitis virus, New Jersey serogroup; and vesicular stomatitis virus, Indiana serogroup. Armored RNA spiked into oral swab fluid specimens mimicked virus-positive clinical material through all stages of the reverse transcription-PCR testing process, including RNA recovery by four different commercial extraction procedures, reverse transcription, PCR amplification, and real-time detection at target concentrations consistent with the dynamic ranges of the existing real-time PCR assays. The armored RNA concentrations spiked into the oral swab fluid specimens were stable under storage conditions selected to approximate the extremes of time and temperature expected for shipping and handling of proficiency panel samples, including 24 h at 37°C and 2 weeks at temperatures ranging from ambient room temperature to −70°C. The analytic test performance, including the reproducibility over the dynamic range of the assays, indicates that armored RNA can provide a noninfectious, quantifiable, and stable virus surrogate for specific assay training and proficiency test purposes. PMID:16390950

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barrett, Christopher A.; Martinez, Alonzo; McNamara, Bruce K.

International Atom Energy Agency (IAEA) safeguard verification measures in gaseous centrifuge enrichment plants (GCEPs) rely on environmental sampling, non-destructive assay (NDA), and destructive assay (DA) sampling and analysis to determine uranium enrichment. UF6 bias defect measurements are made by DA sampling and analysis to assure that enrichment is consistent with declarations. DA samples are collected from a limited number of cylinders for high precision, offsite mass spectrometer analysis. Samples are typically drawn from a sampling tap into a UF6 sample bottle, then packaged, sealed, and shipped under IAEA chain of custody to an offsite analytical laboratory. Future DA safeguard measuresmore » may require improvements in efficiency and effectiveness as GCEP capacities increase and UF6 shipping regulations become increasingly more restrictive. The Pacific Northwest National Laboratory (PNNL) DA sampler concept and Laser Ablation Absorption Ratio Spectrometry (LAARS) assay method are under development to potentially provide DA safeguard tools that increase inspection effectiveness and reduce sample shipping constraints. The PNNL DA sampler concept uses a handheld sampler to collect DA samples for either onsite LAARS assay or offsite laboratory analysis. The DA sampler design will use a small sampling planchet that is coated with an adsorptive film to collect controlled quantities of UF6 gas directly from a cylinder or process sampling tap. Development efforts are currently underway at PNNL to enhance LAARS assay performance to allow high-precision onsite bias defect measurements. In this paper, we report on the experimental investigation to develop adsorptive films for the PNNL DA sampler concept. These films are intended to efficiently capture UF6 and then stabilize the collected DA sample prior to onsite LAARS or offsite laboratory analysis. Several porous material composite films were investigated, including a film designed to maximize the chemical adsorption and binding of gaseous UF6 onto the sampling planchet.« less

Toward low-cost affinity reagents: lyophilized yeast-scFv probes specific for pathogen antigens.

PubMed

Gray, Sean A; Weigel, Kris M; Ali, Ibne K M; Lakey, Annie A; Capalungan, Jeremy; Domingo, Gonzalo J; Cangelosi, Gerard A

2012-01-01

The generation of affinity reagents, usually monoclonal antibodies, remains a critical bottleneck in biomedical research and diagnostic test development. Recombinant antibody-like proteins such as scFv have yet to replace traditional monoclonal antibodies in antigen detection applications, in large part because of poor performance of scFv in solution. To address this limitation, we have developed assays that use whole yeast cells expressing scFv on their surfaces (yeast-scFv) in place of soluble purified scFv or traditional monoclonal antibodies. In this study, a nonimmune library of human scFv displayed on the surfaces of yeast cells was screened for clones that bind to recombinant cyst proteins of Entamoeba histolytica, an enteric pathogen of humans. Selected yeast-scFv clones were stabilized by lyophilization and used in detection assay formats in which the yeast-scFv served as solid support-bound monoclonal antibodies. Specific binding of antigen to the yeast-scFv was detected by staining with rabbit polyclonal antibodies. In flow cytometry-based assays, lyophilized yeast-scFv reagents retained full binding activity and specificity for their cognate antigens after 4 weeks of storage at room temperature in the absence of desiccants or stabilizers. Because flow cytometry is not available to all potential assay users, an immunofluorescence assay was also developed that detects antigen with similar sensitivity and specificity. Antigen-specific whole-cell yeast-scFv reagents can be selected from nonimmune libraries in 2-3 weeks, produced in vast quantities, and packaged in lyophilized form for extended shelf life. Lyophilized yeast-scFv show promise as low cost, renewable alternatives to monoclonal antibodies for diagnosis and research.

A comprehensive toxicological evaluation of three adhesives using experimental cigarettes.

PubMed

Coggins, Christopher R E; Jerome, Ann M; Lilly, Patrick D; McKinney, Willie J; Oldham, Michael J

2013-01-01

Adhesives are used in several different manufacturing operations in the production of cigarettes. The use of new, "high-speed-manufacture" adhesives (e.g. vinyl acetate based) could affect the smoke chemistry and toxicology of cigarettes, compared with older "low-speed-manufacture" adhesives (e.g. starch based). This study was conducted to determine whether the inclusion of different levels of three adhesives (ethylene vinyl acetate, polyvinyl acetate and starch) in experimental cigarettes results in different smoke chemistry and toxicological responses in in vitro and in vivo assays. A battery of tests (analytical chemistry, in vitro and in vivo assays) was used to compare the chemistry and toxicology of smoke from experimental cigarettes made with different combinations of the three adhesives. Varying levels of the different side-seam adhesives, as well as the transfer of adhesives from packaging materials, were tested. There were differences in some mainstream cigarette smoke constituents as a function of the level of adhesive added to experimental cigarettes and between the tested adhesives. None of these differences translated into statistically significant differences in the in vitro or in vivo assays. The use of newer "high-speed-manufacture" vinyl acetate-based adhesives in cigarettes does not produce toxicological profiles that prevent the adhesives from replacing the older "low-speed-manufacture" adhesives (such as starch).

Structure and Function Study of Phi29 DNA packaging motor

NASA Astrophysics Data System (ADS)

Fang, Huaming

A powerful nanomotor is employed by the tailed dsDNA virus to package the genome into a preformed protein shell during the process of replication. The bacteriophage phi29 is an excellent model for investigating the viral DNA packaging mechanism. The phi29 DNA packaging motor is composed of three ring structures: the dodecameric connector ring, the hexameric pRNA ring and the hexameric ATPase gp16 ring. The connector is the central hub for the DNA to enter and to exit. There are four positively charged lysine rings scattered inside the highly negatively charged connector channel. It is speculated that these positive charged lysine rings may play active roles during DNA packaging in many models. To test this prevalent view, the basic lysine residues were mutated to neutral alanines and the pH environment was altered. Amazingly, the results were beyond expectation. Neither the DNA translocation nor the one-way traffic property of the channel were measurably influenced by the alteration of the charge of lysine residues when the basic lysine residues mutated to neutral alanines or the pH environment changed to acid or basic. The ATPase or the terminase is the central part of the viral DNA packaging motor. The phi29 ATPase is highly hydrophobic and tends to aggregate in solution. A green fluorescent protein tag (eGFP) fused to the N-terminus of gp16 enhanced its solubility and stability. The eGFP-gp16 showed similar activity to wild type gp16 and was easily detected by fluorescent instruments. The interaction between eGFP-gp16 and DNA in the various conditions were investigated by electrophoretic mobility shift assay, FRET and sucrose gradient. gamma-S-ATP dramatically increased gp16 binding affinity to DNA and ATP, ADP, phosphate could release gp16 from gp16-DNA-gamma-S-ATP complex. The sliding of gp16 out of the gp16-DNA-gamma-S-ATP complex could be blocked by addition of Steptavidin to ends of dsDNA which is conjugated with biotins. Also, we found that six eGFP-gp16 molecules were required to bind to one short dsDNA molecule. The inhibitive curve of Walker B mutant gp16 analyzed by binomial distribution model showed that one inactive mutant gp16 in the gp16 ring could block the function of the motor and the stoichiometry of gp16 was six. These findings facilitate our understanding of the molecular mechanism of viral DNA packaging: a novel viral DNA packaging model "push through a one-way valve" was proposed. In this model, the connector functioned as a valve to allow DNA to enter but prevented it from sliding out during DNA packaging; the six subunits in the gp16 ring acted sequentially to push DNA into the connector channel. ATP binding of gp16 induced a conformation change with a high affinity for dsDNA. Then, the ATP was hydrolyzed which resulted in the movement of subdomains in this individual gp16 subunit and DNA was pushed forward, followed by the double helix of dsDNA being brought forward to the adjacent subunit in the gp16 ring. The elucidation of the viral DNA packaging mechanism holds great potential for developing artificial motors for delivering drugs and other molecular cargos.

Effects of holding time during cooling and of type of package on plasma membrane integrity, motility and in vitro oocyte penetration ability of frozen-thawed boar spermatozoa.

PubMed

Eriksson, B M; Vazquez, J M; Martinez, E A; Roca, J; Lucas, X; Rodriguez-Martinez, H

2001-05-01

The effect of a prolonged holding time (HT) during cooling on plasma membrane integrity (PMI), motility and in vitro oocyte penetration ability of boar spermatozoa frozen-thawed in different types of package was investigated. Boar semen was frozen in a split-sample design using 3 different HTs (3, 10 and 20 h) during cooling and three different types of freezing package: Maxi-straws, Medium-straws and FlatPacks. Assessment of PMI (SYBR-14 and propidium iodide, fluorescence microscopy) and sperm motility (visually and with CASA) was done during cooling (at 32 degrees C, 15 degrees C, 5 degrees C) and post-thaw (PT). The in vitro oocyte penetration ability of the spermatozoa was tested only PT, using a homologous in vitro penetration assay (hIVP). During cooling the HTs used had no significant (p<0.05) effect on either PMI or percentage of motile spermatozoa Post-thaw PMI was significantly higher (p<0.05) for 10 h and 20 h HT compared with 3 h, and the percentage of motile spermatozoa decreased significantly with 20 h HT as opposed to 3 h and 10 h. Regarding the freezing packages, the FlatPacks and Maxi-straws yielded significantly more PMI than did the Medium-straws (p<0.05). Post-thaw motility was significantly higher for FlatPacks than for straws, in terms of both percentage motile spermatozoa, and sperm velocity and lateral head displacement (LHD). The hIVP did not show any significant differences among the HTs, although FlatPacks yielded a significantly higher penetration rate and more spermatozoa per penetrated oocyte (p<0.05) than did the straws. Changes in motility patterns, toward a more circular motility during cooling and PT, could be noticed where individual spermatozoa showed a capacitation-like motility pattern. The changes were more obvious with 10-h and 20-h HTs than with 3-h HT.

The assessment of potentially interfering metabolites and dietary components in blood using an osmotic glucose sensor based on the concanavalin A-dextran affinity assay.

PubMed

Krushinitskaya, Olga; Tønnessen, Tor Inge; Jakobsen, Henrik; Johannessen, Erik

2011-10-15

Continuous surveillance of blood glucose is a prerogative of maintaining a tight glycaemic control in people suffering from diabetes mellitus. Implantable sensor technology offers the potential of conducting direct long term continuous glucose measurements, but current size restrictions and operational challenges have limited their applications. The osmotic sensor utilises diffusion to create a hydrostatic pressure that is independent of sensor operation and power consumption. This permits ultra-low power architectures to be realized with a minimal start-up time in a package suitable for miniaturization. In contrast, osmotic sensors suffer from the inability of their membranes to discriminate between different constituents in blood or the interstitial fluid that are of comparable size to glucose. By implementing an affinity assay based on the competitive bonding between concanavalin A and dextran, the selectivity of the membrane can be transferred to the glucose specific recognition of the affinity assay. The osmotic effect from the physiological levels of several key metabolites and nutritional components has been addressed identifying in particular ethanol, lactate and amino acids as potential interfering constituents. Both ascorbic acid and mannose would have a normal physiological concentration that is too low to be detected. The studies shows that an osmotic glucose sensor equipped with the con A-dextran affinity assay, is able to filter out potential interfering constituents present in blood, plasma and the interstitial fluid yet retaining a pressure that is proportional to glucose only. Copyright © 2011 Elsevier B.V. All rights reserved.

Evaluation of the butter flavoring chemical diacetyl and a fluorochemical paper additive for mutagenicity and toxicity using the mammalian cell gene mutation assay in L5178Y mouse lymphoma cells.

PubMed

Whittaker, Paul; Clarke, Jane J; San, Richard H C; Begley, Timothy H; Dunkel, Virginia C

2008-08-01

Diacetyl (2,3-butanedione) is a yellowish liquid that is usually mixed with other ingredients to produce butter flavor or other flavors in a variety of food products. Inhalation of butter flavoring vapors was first associated with clinical bronchiolitis obliterans among workers in microwave popcorn production. Recent findings have shown irreversible obstructive lung disease among workers not only in the microwave popcorn industry, but also in flavoring manufacture, and in chemical synthesis of diacetyl, a predominant chemical for butter flavoring. It has been reported that perfluorochemicals utilized in food packaging are migrating into foods and may be sources of oral exposure. Relatively small quantities of perfluorochemicals are used in the manufacturing of paper or paperboard that is in direct contact with food to repel oil or grease and water. Because of recent concerns about perfluorochemicals such as those found on microwave popcorn bags (e.g. Lodyne P208E) and diacetyl in foods, we evaluated both compounds for mutagenicity using the mammalian cell gene mutation assay in L5178Y mouse lymphoma cells. Lodyne P208E was less toxic than diacetyl and did not induce a mutagenic response. Diacetyl induced a highly mutagenic response in the L5178Y mouse lymphoma mutation assay in the presence of human liver S9 for activation. The increase in the frequency of small colonies in the assay with diacetyl indicates that diacetyl causes damage to multiple loci on chromosome 11 in addition to functional loss of the thymidine kinase locus.

High content analysis of phagocytic activity and cell morphology with PuntoMorph.

PubMed

Al-Ali, Hassan; Gao, Han; Dalby-Hansen, Camilla; Peters, Vanessa Ann; Shi, Yan; Brambilla, Roberta

2017-11-01

Phagocytosis is essential for maintenance of normal homeostasis and healthy tissue. As such, it is a therapeutic target for a wide range of clinical applications. The development of phenotypic screens targeting phagocytosis has lagged behind, however, due to the difficulties associated with image-based quantification of phagocytic activity. We present a robust algorithm and cell-based assay system for high content analysis of phagocytic activity. The method utilizes fluorescently labeled beads as a phagocytic substrate with defined physical properties. The algorithm employs statistical modeling to determine the mean fluorescence of individual beads within each image, and uses the information to conduct an accurate count of phagocytosed beads. In addition, the algorithm conducts detailed and sophisticated analysis of cellular morphology, making it a standalone tool for high content screening. We tested our assay system using microglial cultures. Our results recapitulated previous findings on the effects of microglial stimulation on cell morphology and phagocytic activity. Moreover, our cell-level analysis revealed that the two phenotypes associated with microglial activation, specifically cell body hypertrophy and increased phagocytic activity, are not highly correlated. This novel finding suggests the two phenotypes may be under the control of distinct signaling pathways. We demonstrate that our assay system outperforms preexisting methods for quantifying phagocytic activity in multiple dimensions including speed, accuracy, and resolution. We provide a framework to facilitate the development of high content assays suitable for drug screening. For convenience, we implemented our algorithm in a standalone software package, PuntoMorph. Copyright © 2017 Elsevier B.V. All rights reserved.

Influence of Internal DNA Pressure on Stability and Infectivity of Phage λ

PubMed Central

Bauer, D. W.; Evilevitch, A.

2016-01-01

Viruses must remain infectious while in harsh extracellular environments. An important aspect of viral particle stability for double-stranded DNA viruses is the energetically unfavorable state of the tightly confined DNA chain within the virus capsid creating pressures of tens of atmospheres. Here we study the influence of internal genome pressure on the thermal stability of viral particles. Using differential scanning calorimetry (DSC) to monitor genome loss upon heating, we find that internal pressure destabilizes the virion, resulting in a smaller activation energy barrier to trigger DNA release. These experiments are complemented by plaque assay and electron microscopy measurements to determine the influence of intra-capsid DNA pressure on the rates of viral infectivity loss. At higher temperatures (65 – 75 °C), failure to retain the packaged genome is the dominant mechanism of viral inactivation. Conversely, at lower temperatures (40 – 55 ºC), a separate inactivation mechanism dominates, which results in non-infectious particles that still retain their packaged DNA. Most significantly, both mechanisms of infectivity loss are directly influenced by internal DNA pressure, with higher pressure resulting in a more rapid rate of inactivation at all temperatures. PMID:26254570

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

PubMed Central

Aryee, Martin J.; Jaffe, Andrew E.; Corrada-Bravo, Hector; Ladd-Acosta, Christine; Feinberg, Andrew P.; Hansen, Kasper D.; Irizarry, Rafael A.

2014-01-01

Motivation: The recently released Infinium HumanMethylation450 array (the ‘450k’ array) provides a high-throughput assay to quantify DNA methylation (DNAm) at ∼450 000 loci across a range of genomic features. Although less comprehensive than high-throughput sequencing-based techniques, this product is more cost-effective and promises to be the most widely used DNAm high-throughput measurement technology over the next several years. Results: Here we describe a suite of computational tools that incorporate state-of-the-art statistical techniques for the analysis of DNAm data. The software is structured to easily adapt to future versions of the technology. We include methods for preprocessing, quality assessment and detection of differentially methylated regions from the kilobase to the megabase scale. We show how our software provides a powerful and flexible development platform for future methods. We also illustrate how our methods empower the technology to make discoveries previously thought to be possible only with sequencing-based methods. Availability and implementation: http://bioconductor.org/packages/release/bioc/html/minfi.html. Contact: khansen@jhsph.edu; rafa@jimmy.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24478339

Differential Expression of HERV-K (HML-2) Proviruses in Cells and Virions of the Teratocarcinoma Cell Line Tera-1

PubMed Central

Bhardwaj, Neeru; Montesion, Meagan; Roy, Farrah; Coffin, John M.

2015-01-01

Human endogenous retrovirus (HERV-K (HML-2)) proviruses are among the few endogenous retroviral elements in the human genome that retain coding sequence. HML-2 expression has been widely associated with human disease states, including different types of cancers as well as with HIV-1 infection. Understanding of the potential impact of this expression requires that it be annotated at the proviral level. Here, we utilized the high throughput capabilities of next-generation sequencing to profile HML-2 expression at the level of individual proviruses and secreted virions in the teratocarcinoma cell line Tera-1. We identified well-defined expression patterns, with transcripts emanating primarily from two proviruses located on chromosome 22, only one of which was efficiently packaged. Interestingly, there was a preference for transcripts of recently integrated proviruses, over those from other highly expressed but older elements, to be packaged into virions. We also assessed the promoter competence of the 5’ long terminal repeats (LTRs) of expressed proviruses via a luciferase assay following transfection of Tera-1 cells. Consistent with the RNASeq results, we found that the activity of most LTRs corresponded to their transcript levels. PMID:25746218

Effect of specific silencing of EMMPRIN on the growth and cell cycle distribution of MCF-7 breast cancer cells.

PubMed

Yang, X Q; Yang, J; Wang, R; Zhang, S; Tan, Q W; Lv, Q; Meng, W T; Mo, X M; Li, H J

2015-12-02

The extracellular matrix metalloproteinase inducer (EMMPRIN, CD147) is a member of the immunoglobulin family and shows increased expression in tumor cells. We examined the effect of RNAi-mediated EMMPRIN gene silencing induced by lentiviral on the growth and cycle distribution of MCF-7 breast cancer cells. Lentiviral expressing EMMPRIN-short hairpin RNA were packaged to infect MCF-7 cells. The inhibition efficiency of EMMPRIN was validated by real-time fluorescent quantitation polymerase chain reaction and western blotting. The effect of EMMPRIN on cell proliferation ability was detected using the MTT assay and clone formation experiments. Changes in cell cycle were detected by flow cytometry. EMMPRIN-short hairpin RNA-packaged lentiviral significantly down-regulated EMMPRIN mRNA and protein expression, significantly inhibited cell proliferation and in vitro tumorigenicity, and induced cell cycle abnormalities. Cells in the G0/G1 and G2/M phases were increased, while cells in the S phase were decreased after infection of MCF-7 cells for 3 days. The EMMPRIN gene facilitates breast cancer cell malignant proliferation by regulating cell cycle distribution and may be a molecular target for breast cancer gene therapy.

Quality of fresh-cut baby spinach grown under a floating trays system as affected by nitrogen fertilisation and innovative packaging treatments.

PubMed

Rodríguez-Hidalgo, Stephanie; Artés-Hernández, Francisco; Gómez, Perla A; Fernández, Juan Antonio; Artés, Francisco

2010-04-30

Alternative techniques for cultivation of leafy vegetables such as a floating tray system and unconventional gas mixtures for post-harvest active modified atmosphere packaging (MAP) could be of interest in the minimally processed vegetable industry. The combined effect of three pre-harvest fertilisation doses (8, 12 or 16 mmol N L(-1)) and three post-harvest MAP conditions (passive, super-atmospheric or N2O-enriched) on the main quality attributes of fresh-cut baby spinach leaves throughout 10 days at 5 degrees C was studied. After 8 days of shelf life, spinach leaves fertilised with 8 and 16 mmol N L(-1) and stored under N2O-enriched MAP showed the lowest microbial growth, with good sensory quality. Such combined treatments also preserved the total antioxidant capacity sampled at harvest (8 g ascorbic acid equivalent antioxidant capacity kg(-1) f.w.). A decrease of 10-20% in total vitamin C content regardless of N fertilisation and packaging treatment was found during shelf life. Total phenolics content at harvest was 2 g gallic acid equivalents kg(-1) f.w., which was slightly decreased or preserved during shelf life while total chlorophylls were preserved for all treatments assayed around 550 mg kg(-1) f.w. No clear effect of fertilisation doses was observed during post-harvest storage on overall quality of fresh-cut baby spinach leaves, while N2O-enriched atmospheres seems to be a promising alternative to passive MAP for extending shelf life.

Preparation and characterization of biocomposite film based on chitosan and kombucha tea as active food packaging.

PubMed

Ashrafi, Azam; Jokar, Maryam; Mohammadi Nafchi, Abdorreza

2018-03-01

An active film composed of chitosan and kombucha tea (KT) was successfully prepared using the solvent casting technique. The effect of incorporation of KT at the levels 1%-3% w/w on the physical and functional properties of chitosan film was investigated. The antimicrobial activity of chitosan/KT film against Escherichia coli and Staphylococcus aureus was evaluated using agar diffusion test, and its antioxidant activity was determined using DPpH assay. The results revealed that incorporation of KT into chitosan films improved the water vapor permeability (from 256.7 to 132.1gcm -2 h -1 KPa -1 mm) and enhanced the antioxidant activity of the latter up to 59% DPpH scavenging activity. Moreover, the incorporation of KT into the chitosan film increased the protective effect of the film against ultra violet (UV). Fourier transform infrared spectroscopic analysis revealed the chemical interactions between chitosan and the polyphenol groups of KT. In a minced beef model, chitosan/KT film effectively served as an active packaging and extended the shelf life of the minced beef as manifested in the retardation of lipid oxidation and microbial growth from 5.36 to 2.11logcfugr -1 in 4days storage. The present work demonstrates that the chitosan/KT film not only maintains the quality of the minced beef but also, retards microbial growth significantly, extending the shelf life of the minced beef meat up to 3days; thus, chitosan/KT film is a potential material for active food packaging. Copyright © 2017 Elsevier B.V. All rights reserved.

Development and analytical characterization of vitamin(s)-loaded chitosan nanoparticles for potential food packaging applications

NASA Astrophysics Data System (ADS)

Aresta, Antonella; Calvano, Cosima Damiana; Trapani, Adriana; Cellamare, Saverio; Zambonin, Carlo Giorgio; De Giglio, Elvira

2013-04-01

Most vitamins are well-known natural antioxidant agents which can be usefully employed for foods preservation to increase their shelf life. In the present study, we aimed to investigate the potential of vitamin-based chitosan nanoparticles (CSNPs) for novel food packaging application. In particular, Vitamin C- and/or E-loaded CSNPs were formulated following the ionic gelation technique and using sulfobutylether-β-cyclodextrin as cross-linking agent. The obtained CSNPs were characterized in terms of size and zeta potential measurements, leading to size range of 375-503 nm and zeta range values from +16.0 to +33.8 mV. At the solid-state, the same particles were subjected to X-ray photoelectron spectroscopy, differential scanning calorimetry and Fourier transform infrared spectroscopy. Then, the antioxidant potential of the produced vitamin(s) nanoparticulate formulations has been evaluated through 1,1-diphenyl-2-picrylhydrazyl test, a rapid spectrophotometric assay. The standardized procedure was used on vitamin(s)-modified CSNPs systems to determine both the amount of active vitamin(s) loaded in CSNPs and their release performances by in vitro release studies. Of all, high vitamins association efficiency along with an improvement of their shelf life (also under light exposure up to 7 days) were achieved. Altogether, the results suggest that Vitamin E is available in a hydrophilic delivery system able to replace organic solvents usually used for the solubilization of this antioxidant agent. In conclusion, these nanocarriers represent a promising strategy for the co-administration of Vitamin E and Vitamin C in packaging materials intended for a better storage of hydrophilic and/or lipophilic food.

Live cell imaging of interactions between replicase and capsid protein of Brome mosaic virus using Bimolecular Fluorescence Complementation: Implications for replication and genome packaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chaturvedi, Sonali; Rao, A.L.N., E-mail: arao@ucr.edu

2014-09-15

In Brome mosaic virus, it was hypothesized that a physical interaction between viral replicase and capsid protein (CP) is obligatory to confer genome packaging specificity. Here we tested this hypothesis by employing Bimolecular Fluorescent Complementation (BiFC) as a tool for evaluating protein–protein interactions in living cells. The efficacy of BiFC was validated by a known interaction between replicase protein 1a (p1a) and protein 2a (p2a) at the endoplasmic reticulum (ER) site of viral replication. Additionally, co-expression in planta of a bona fide pair of interacting protein partners of p1a and p2a had resulted in the assembly of a functional replicase.more » Subsequent BiFC assays in conjunction with mCherry labeled ER as a fluorescent cellular marker revealed that CP physically interacts with p2a, but not p1a, and this CP:p2a interaction occurs at the cytoplasmic phase of the ER. The significance of the CP:p2a interaction in BMV replication and genome packaging is discussed. - Highlights: • YFP fusion proteins of BMV p1a and p2a are biologically active. • Self-interaction was observed for p1a, p2a and CP. • CP interacts with p2a but not p1a. • Majority of reconstituted YFP resulting from bona fide fusion protein partners localized on ER.« less

Magnetoresistive immunosensor for the detection of Escherichia coli O157:H7 including a microfluidic network.

PubMed

Mujika, M; Arana, S; Castaño, E; Tijero, M; Vilares, R; Ruano-López, J M; Cruz, A; Sainz, L; Berganza, J

2009-01-01

A hand held device has been designed for the immunomagnetic detection and quantification of the pathogen Escherichia coli O157:H7 in food and clinical samples. In this work, a technology to manufacture a Lab on a Chip that integrates a 3D microfluidic network with a microfabricated biosensor has been developed. With this aim, the sensing film optimization, the design of the microfluidic circuitry, the development of the biological protocols involved in the measurements and, finally, the packaging needed to carry out the assays in a safe and straightforward way have been completed. The biosensor is designed to be capable to detect and quantify small magnetic field variations caused by the presence of superparamagnetic beads bound to the antigens previously immobilized on the sensor surface via an antibody-antigen reaction. The giant magnetoresistive multilayer structure implemented as sensing film consists of 20[Cu(5.10nm)/Co(2.47 nm)] with a magnetoresistance of 3.20% at 235Oe and a sensitivity up to 0.06 Omega/Oe between 150Oe and 230Oe. Silicon nitride has been selected as optimum sensor surface coating due to its suitability for antibody immobilization. In order to guide the biological samples towards the sensing area, a microfluidic network made of SU-8 photoresist has been included. Finally, a novel packaging design has been fabricated employing 3D stereolithographic techniques. The microchannels are connected to the outside using standard tubing. Hence, this packaging allows an easy replacement of the used devices.

An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators

PubMed Central

2010-01-01

Background Computer languages can be domain-related, and in the case of multidisciplinary projects, knowledge of several languages will be needed in order to quickly implements ideas. Moreover, each computer language has relative strong points, making some languages better suited than others for a given task to be implemented. The Bioconductor project, based on the R language, has become a reference for the numerical processing and statistical analysis of data coming from high-throughput biological assays, providing a rich selection of methods and algorithms to the research community. At the same time, Python has matured as a rich and reliable language for the agile development of prototypes or final implementations, as well as for handling large data sets. Results The data structures and functions from Bioconductor can be exposed to Python as a regular library. This allows a fully transparent and native use of Bioconductor from Python, without one having to know the R language and with only a small community of translators required to know both. To demonstrate this, we have implemented such Python representations for key infrastructure packages in Bioconductor, letting a Python programmer handle annotation data, microarray data, and next-generation sequencing data. Conclusions Bioconductor is now not solely reserved to R users. Building a Python application using Bioconductor functionality can be done just like if Bioconductor was a Python package. Moreover, similar principles can be applied to other languages and libraries. Our Python package is available at: http://pypi.python.org/pypi/rpy2-bioconductor-extensions/ PMID:21210978

Armored RNA Technology for Production of Ribonuclease-Resistant Viral RNA Controls and Standards

PubMed Central

Pasloske, Brittan L.; Walkerpeach, Cindy R.; Obermoeller, R. Dawn; Winkler, Matthew; DuBois, Dwight B.

1998-01-01

The widespread use of sensitive assays for the detection of viral and cellular RNA sequences has created a need for stable, well-characterized controls and standards. We describe the development of a versatile, novel system for creating RNase-resistant RNA. “Armored RNA” is a complex of MS2 bacteriophage coat protein and RNA produced in Escherichia coli by the induction of an expression plasmid that encodes the coat protein and an RNA standard sequence. The RNA sequences are completely protected from RNase digestion within the bacteriophage-like complexes. As a prototype, a 172-base consensus sequence from a portion of the human immunodeficiency virus type 1 (HIV-1) gag gene was synthesized and cloned into the packaging vector used to produce the bacteriophage-like particles. After production and purification, the resulting HIV-1 Armored RNA particles were shown to be resistant to degradation in human plasma and produced reproducible results in the Amplicor HIV-1 Monitor assay for 180 days when stored at −20°C or for 60 days at 4°C. Additionally, Armored RNA preparations are homogeneous and noninfectious. PMID:9817878

Performance testing accountability measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oldham, R.D.; Mitchell, W.G.; Spaletto, M.I.

The New Brunswick Laboratory (NBL) provides assessment support to the DOE Operations Offices in the area of Material Control and Accountability (MC and A). During surveys of facilities, the Operations Offices have begun to request from NBL either assistance in providing materials for performance testing of accountability measurements or both materials and personnel to do performance testing. To meet these needs, NBL has developed measurement and measurement control performance test procedures and materials. The present NBL repertoire of performance tests include the following: (1) mass measurement performance testing procedures using calibrated and traceable test weights, (2) uranium elemental concentration (assay)more » measurement performance tests which use ampulated solutions of normal uranyl nitrate containing approximately 7 milligrams of uranium per gram of solution, and (3) uranium isotopic measurement performance tests which use ampulated uranyl nitrate solutions with enrichments ranging from 4% to 90% U-235. The preparation, characterization, and packaging of the uranium isotopic and assay performance test materials were done in cooperation with the NBL Safeguards Measurements Evaluation Program since these materials can be used for both purposes.« less

Application of ToxCast to evaluate potential biological effects ...

EPA Pesticide Factsheets

With the development of “high throughput” in-vitro biological assays, screening-level information on potential adverse biological effects is available for a rapidly increasing number of chemicals. The U.S. EPA ToxCast program has now evaluated several thousand chemicals with more than 800 assays. The original intent of this data was to evaluate potential for human health effects, but it is now being extended to environmental health evaluations. The R package ToxEval was developed as a screening tool to use ToxCast results for evaluation of potential adverse biological effects from trace organic chemicals in water samples. Using ToxEval, trace organic chemical data from water samples and passive samplers collected at 57 Great Lakes tributaries from 2010-2013 were examined to determine the tributaries with the greatest potential for adverse biological effects with prioritization of the most influential contaminants. Results are being used as part of the Great Lakes Restoration Initiative to focus current and future investigations that will help understand likely adverse outcome pathways in biological organisms, and to formulate possible remediation strategies. not applicable

Distinct features of multivesicular body-lysosome fusion revealed by a new cell-free content-mixing assay.

PubMed

Karim, Mahmoud Abdul; Samyn, Dieter Ronny; Mattie, Sevan; Brett, Christopher Leonard

2018-02-01

When marked for degradation, surface receptor and transporter proteins are internalized and delivered to endosomes where they are packaged into intralumenal vesicles (ILVs). Many rounds of ILV formation create multivesicular bodies (MVBs) that fuse with lysosomes exposing ILVs to hydrolases for catabolism. Despite being critical for protein degradation, the molecular underpinnings of MVB-lysosome fusion remain unclear, although machinery underlying other lysosome fusion events is implicated. But how then is specificity conferred? And how is MVB maturation and fusion coordinated for efficient protein degradation? To address these questions, we developed a cell-free MVB-lysosome fusion assay using Saccharomyces cerevisiae as a model. After confirming that the Rab7 ortholog Ypt7 and the multisubunit tethering complex HOPS (homotypic fusion and vacuole protein sorting complex) are required, we found that the Qa-SNARE Pep12 distinguishes this event from homotypic lysosome fusion. Mutations that impair MVB maturation block fusion by preventing Ypt7 activation, confirming that a Rab-cascade mechanism harmonizes MVB maturation with lysosome fusion. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

SFCOMPO-2.0: An OECD NEA database of spent nuclear fuel isotopic assays, reactor design specifications, and operating data

DOE PAGES

Michel-Sendis, F.; Gauld, I.; Martinez, J. S.; ...

2017-08-02

SFCOMPO-2.0 is the new release of the Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) database of experimental assay measurements. These measurements are isotopic concentrations from destructive radiochemical analyses of spent nuclear fuel (SNF) samples. We supplement the measurements with design information for the fuel assembly and fuel rod from which each sample was taken, as well as with relevant information on operating conditions and characteristics of the host reactors. These data are necessary for modeling and simulation of the isotopic evolution of the fuel during irradiation. SFCOMPO-2.0 has been developed and is maintained by the OECDmore » NEA under the guidance of the Expert Group on Assay Data of Spent Nuclear Fuel (EGADSNF), which is part of the NEA Working Party on Nuclear Criticality Safety (WPNCS). Significant efforts aimed at establishing a thorough, reliable, publicly available resource for code validation and safety applications have led to the capture and standardization of experimental data from 750 SNF samples from more than 40 reactors. These efforts have resulted in the creation of the SFCOMPO-2.0 database, which is publicly available from the NEA Data Bank. Our paper describes the new database, and applications of SFCOMPO-2.0 for computer code validation, integral nuclear data benchmarking, and uncertainty analysis in nuclear waste package analysis are briefly illustrated.« less

The analysis of novel microRNA mimic sequences in cancer cells reveals lack of specificity in stem-loop RT-qPCR-based microRNA detection.

PubMed

Winata, Patrick; Williams, Marissa; McGowan, Eileen; Nassif, Najah; van Zandwijk, Nico; Reid, Glen

2017-11-17

MicroRNAs are frequently downregulated in cancer, and restoring expression has tumour suppressive activity in tumour cells. Our recent phase I clinical trial investigated microRNA-based therapy in patients with malignant pleural mesothelioma. Treatment with TargomiRs, microRNA mimics with novel sequence packaged in EGFR antibody-targeted bacterial minicells, revealed clear signs of clinical activity. In order to detect delivery of microRNA mimics to tumour cells in future clinical trials, we tested hydrolysis probe-based assays specific for the sequence of the novel mimics in transfected mesothelioma cell lines using RT-qPCR. The custom assays efficiently and specifically amplified the consensus mimics. However, we found that these assays gave a signal when total RNA from untransfected and control mimic-transfected cells were used as templates. Further investigation revealed that the reverse transcription step using stem-loop primers appeared to introduce substantial non-specific amplification with either total RNA or synthetic RNA templates. This suggests that reverse transcription using stem-loop primers suffers from an intrinsic lack of specificity for the detection of highly similar microRNAs in the same family, especially when analysing total RNA. These results suggest that RT-qPCR is unlikely to be an effective means to detect delivery of microRNA mimic-based drugs to tumour cells in patients.

SFCOMPO-2.0: An OECD NEA database of spent nuclear fuel isotopic assays, reactor design specifications, and operating data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Michel-Sendis, F.; Gauld, I.; Martinez, J. S.

SFCOMPO-2.0 is the new release of the Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) database of experimental assay measurements. These measurements are isotopic concentrations from destructive radiochemical analyses of spent nuclear fuel (SNF) samples. We supplement the measurements with design information for the fuel assembly and fuel rod from which each sample was taken, as well as with relevant information on operating conditions and characteristics of the host reactors. These data are necessary for modeling and simulation of the isotopic evolution of the fuel during irradiation. SFCOMPO-2.0 has been developed and is maintained by the OECDmore » NEA under the guidance of the Expert Group on Assay Data of Spent Nuclear Fuel (EGADSNF), which is part of the NEA Working Party on Nuclear Criticality Safety (WPNCS). Significant efforts aimed at establishing a thorough, reliable, publicly available resource for code validation and safety applications have led to the capture and standardization of experimental data from 750 SNF samples from more than 40 reactors. These efforts have resulted in the creation of the SFCOMPO-2.0 database, which is publicly available from the NEA Data Bank. Our paper describes the new database, and applications of SFCOMPO-2.0 for computer code validation, integral nuclear data benchmarking, and uncertainty analysis in nuclear waste package analysis are briefly illustrated.« less

Adaptation of the ORAC assay to the common laboratory equipment and subsequent application to antioxidant plastic films.

PubMed

Bentayeb, K; Vera, P; Rubio, C; Nerin, C

2009-06-01

The oxygen radical absorbance capacity (ORAC) method has been adapted to the instrumental laboratory and optimized for the determination of the antioxidant capacity of a novel active packaging. As the ORAC assay requires the monitorization of a reaction at controlled temperature by means of the fluorescence signal decrease over time, specific instrumental is usually necessary. In this work, a common liquid chromatographic device has been adapted to perform the ORAC assay, leaving it accessible to any laboratory. Using this adaptation, five different essential oils have been determined resulting in the following antioxidant order: clove (2.66 g Trolox per gram of essential oil), oregano (2.25), cinnamon (1.93), rosemary (1.66), and ginger (1.47). After incorporating the essential oils to the film, its antioxidant capacity has also been checked and related to the concentration of essential oil as well as the thickness of the active film. The results point out that for the same amount of essential oil incorporated measured as grams per square meter, thicker films have more antioxidant capacity than the thinner and more concentrated ones. Furthermore, the antioxidant capacity found in the films was always higher than expected taking into account the amount of essential oil incorporated. Some likely explanations have been proposed, leading to the improvement of the antioxidant film under development.

Pharmacophore modeling, docking, and principal component analysis based clustering: combined computer-assisted approaches to identify new inhibitors of the human rhinovirus coat protein.

PubMed

Steindl, Theodora M; Crump, Carolyn E; Hayden, Frederick G; Langer, Thierry

2005-10-06

The development and application of a sophisticated virtual screening and selection protocol to identify potential, novel inhibitors of the human rhinovirus coat protein employing various computer-assisted strategies are described. A large commercially available database of compounds was screened using a highly selective, structure-based pharmacophore model generated with the program Catalyst. A docking study and a principal component analysis were carried out within the software package Cerius and served to validate and further refine the obtained results. These combined efforts led to the selection of six candidate structures, for which in vitro anti-rhinoviral activity could be shown in a biological assay.

Intracellular Crosslinking of Filoviral Nucleoproteins with Xintrabodies Restricts Viral Packaging

PubMed Central

Darling, Tamarand Lee; Sherwood, Laura Jo; Hayhurst, Andrew

2017-01-01

Viruses assemble large macromolecular repeat structures that become part of the infectious particles or virions. Ribonucleocapsids (RNCs) of negative strand RNA viruses are a prime example where repetition of nucleoprotein (NP) along the genome creates a core polymeric helical scaffold that accommodates other nucleocapsid proteins including viral polymerase. The RNCs are transported through the cytosol for packaging into virions through association with viral matrix proteins at cell membranes. We hypothesized that RNC would be ideal targets for crosslinkers engineered to promote aberrant protein–protein interactions, thereby blocking their orderly transport and packaging. Previously, we had generated single-domain antibodies (sdAbs) against Filoviruses that have all targeted highly conserved C-terminal regions of NP known to be repetitively exposed along the length of the RNCs of Marburgvirus (MARV) and Ebolavirus (EBOV). Our crosslinker design consisted of dimeric sdAb expressed intracellularly, which we call Xintrabodies (X- for crosslinking). Electron microscopy of purified NP polymers incubated with purified sdAb constructs showed NP aggregation occurred in a genus-specific manner with dimeric and not monomeric sdAb. A virus-like particle (VLP) assay was used for initial evaluation where we found that dimeric sdAb inhibited NP incorporation into VP40-based VLPs whereas monomeric sdAb did not. Inhibition of NP packaging was genus specific. Confocal microscopy revealed dimeric sdAb was diffuse when expressed alone but focused on pools of NP when the two were coexpressed, while monomeric sdAb showed ambivalent partition. Infection of stable Vero cell lines expressing dimeric sdAb specific for either MARV or EBOV NP resulted in smaller plaques and reduced progeny of cognate virus relative to wild-type Vero cells. Though the impact was marginal at later time-points, the collective data suggest that viral replication can be reduced by crosslinking intracellular NP using relatively small amounts of dimeric sdAb to restrict NP packaging. The stoichiometry and ease of application of the approach would likely benefit from transitioning away from intracellular expression of crosslinking sdAb to exogenous delivery of antibody. By retuning sdAb specificity, the approach of crosslinking highly conserved regions of assembly critical proteins may well be applicable to inhibiting replication processes of a broad spectrum of viruses. PMID:29021793

Packaging and Prefusion Stabilization Separately and Additively Increase the Quantity and Quality of Respiratory Syncytial Virus (RSV)-Neutralizing Antibodies Induced by an RSV Fusion Protein Expressed by a Parainfluenza Virus Vector.

PubMed

Liang, Bo; Ngwuta, Joan O; Herbert, Richard; Swerczek, Joanna; Dorward, David W; Amaro-Carambot, Emerito; Mackow, Natalie; Kabatova, Barbora; Lingemann, Matthias; Surman, Sonja; Yang, Lijuan; Chen, Man; Moin, Syed M; Kumar, Azad; McLellan, Jason S; Kwong, Peter D; Graham, Barney S; Schaap-Nutt, Anne; Collins, Peter L; Munir, Shirin

2016-11-01

Human respiratory syncytial virus (RSV) and human parainfluenza virus type 3 (HPIV3) are major pediatric respiratory pathogens that lack vaccines. A chimeric bovine/human PIV3 (rB/HPIV3) virus expressing the unmodified, wild-type (wt) RSV fusion (F) protein from an added gene was previously evaluated in seronegative children as a bivalent intranasal RSV/HPIV3 vaccine, and it was well tolerated but insufficiently immunogenic for RSV F. We recently showed that rB/HPIV3 expressing a partially stabilized prefusion form (pre-F) of RSV F efficiently induced "high-quality" RSV-neutralizing antibodies, defined as antibodies that neutralize RSV in vitro without added complement (B. Liang et al., J Virol 89:9499-9510, 2015, doi:10.1128/JVI.01373-15). In the present study, we modified RSV F by replacing its cytoplasmic tail (CT) domain or its CT and transmembrane (TM) domains (TMCT) with counterparts from BPIV3 F, with or without pre-F stabilization. This resulted in RSV F being packaged in the rB/HPIV3 particle with an efficiency similar to that of RSV particles. Enhanced packaging was substantially attenuating in hamsters (10- to 100-fold) and rhesus monkeys (100- to 1,000-fold). Nonetheless, TMCT-directed packaging substantially increased the titers of high-quality RSV-neutralizing serum antibodies in hamsters. In rhesus monkeys, a strongly additive immunogenic effect of packaging and pre-F stabilization was observed, as demonstrated by 8- and 30-fold increases of RSV-neutralizing serum antibody titers in the presence and absence of added complement, respectively, compared to pre-F stabilization alone. Analysis of vaccine-induced F-specific antibodies by binding assays indicated that packaging conferred substantial stabilization of RSV F in the pre-F conformation. This provides an improved version of this well-tolerated RSV/HPIV3 vaccine candidate, with potently improved immunogenicity, which can be returned to clinical trials. Human respiratory syncytial virus (RSV) and human parainfluenza virus type 3 (HPIV3) are major viral agents of acute pediatric bronchiolitis and pneumonia worldwide that lack vaccines. A bivalent intranasal RSV/HPIV3 vaccine candidate consisting of a chimeric bovine/human PIV3 (rB/HPIV3) strain expressing the RSV fusion (F) protein was previously shown to be well tolerated by seronegative children but was insufficiently immunogenic for RSV F. In the present study, the RSV F protein was engineered to be packaged efficiently into vaccine virus particles. This resulted in a significantly enhanced quantity and quality of RSV-neutralizing antibodies in hamsters and nonhuman primates. In nonhuman primates, this effect was strongly additive to the previously described stabilization of the prefusion conformation of the F protein. The improved immunogenicity of RSV F by packaging appeared to involve prefusion stabilization. These findings provide a potently more immunogenic version of this well-tolerated vaccine candidate and should be applicable to other vectored vaccines. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Packaging and Prefusion Stabilization Separately and Additively Increase the Quantity and Quality of Respiratory Syncytial Virus (RSV)-Neutralizing Antibodies Induced by an RSV Fusion Protein Expressed by a Parainfluenza Virus Vector

PubMed Central

Liang, Bo; Ngwuta, Joan O.; Herbert, Richard; Swerczek, Joanna; Dorward, David W.; Amaro-Carambot, Emerito; Mackow, Natalie; Kabatova, Barbora; Lingemann, Matthias; Surman, Sonja; Yang, Lijuan; Chen, Man; Moin, Syed M.; Kumar, Azad; McLellan, Jason S.; Kwong, Peter D.; Graham, Barney S.; Schaap-Nutt, Anne; Collins, Peter L.

2016-01-01

ABSTRACT Human respiratory syncytial virus (RSV) and human parainfluenza virus type 3 (HPIV3) are major pediatric respiratory pathogens that lack vaccines. A chimeric bovine/human PIV3 (rB/HPIV3) virus expressing the unmodified, wild-type (wt) RSV fusion (F) protein from an added gene was previously evaluated in seronegative children as a bivalent intranasal RSV/HPIV3 vaccine, and it was well tolerated but insufficiently immunogenic for RSV F. We recently showed that rB/HPIV3 expressing a partially stabilized prefusion form (pre-F) of RSV F efficiently induced “high-quality” RSV-neutralizing antibodies, defined as antibodies that neutralize RSV in vitro without added complement (B. Liang et al., J Virol 89:9499–9510, 2015, doi:10.1128/JVI.01373-15). In the present study, we modified RSV F by replacing its cytoplasmic tail (CT) domain or its CT and transmembrane (TM) domains (TMCT) with counterparts from BPIV3 F, with or without pre-F stabilization. This resulted in RSV F being packaged in the rB/HPIV3 particle with an efficiency similar to that of RSV particles. Enhanced packaging was substantially attenuating in hamsters (10- to 100-fold) and rhesus monkeys (100- to 1,000-fold). Nonetheless, TMCT-directed packaging substantially increased the titers of high-quality RSV-neutralizing serum antibodies in hamsters. In rhesus monkeys, a strongly additive immunogenic effect of packaging and pre-F stabilization was observed, as demonstrated by 8- and 30-fold increases of RSV-neutralizing serum antibody titers in the presence and absence of added complement, respectively, compared to pre-F stabilization alone. Analysis of vaccine-induced F-specific antibodies by binding assays indicated that packaging conferred substantial stabilization of RSV F in the pre-F conformation. This provides an improved version of this well-tolerated RSV/HPIV3 vaccine candidate, with potently improved immunogenicity, which can be returned to clinical trials. IMPORTANCE Human respiratory syncytial virus (RSV) and human parainfluenza virus type 3 (HPIV3) are major viral agents of acute pediatric bronchiolitis and pneumonia worldwide that lack vaccines. A bivalent intranasal RSV/HPIV3 vaccine candidate consisting of a chimeric bovine/human PIV3 (rB/HPIV3) strain expressing the RSV fusion (F) protein was previously shown to be well tolerated by seronegative children but was insufficiently immunogenic for RSV F. In the present study, the RSV F protein was engineered to be packaged efficiently into vaccine virus particles. This resulted in a significantly enhanced quantity and quality of RSV-neutralizing antibodies in hamsters and nonhuman primates. In nonhuman primates, this effect was strongly additive to the previously described stabilization of the prefusion conformation of the F protein. The improved immunogenicity of RSV F by packaging appeared to involve prefusion stabilization. These findings provide a potently more immunogenic version of this well-tolerated vaccine candidate and should be applicable to other vectored vaccines. PMID:27581977

Multidimensional Normalization to Minimize Plate Effects of Suspension Bead Array Data.

PubMed

Hong, Mun-Gwan; Lee, Woojoo; Nilsson, Peter; Pawitan, Yudi; Schwenk, Jochen M

2016-10-07

Enhanced by the growing number of biobanks, biomarker studies can now be performed with reasonable statistical power by using large sets of samples. Antibody-based proteomics by means of suspension bead arrays offers one attractive approach to analyze serum, plasma, or CSF samples for such studies in microtiter plates. To expand measurements beyond single batches, with either 96 or 384 samples per plate, suitable normalization methods are required to minimize the variation between plates. Here we propose two normalization approaches utilizing MA coordinates. The multidimensional MA (multi-MA) and MA-loess both consider all samples of a microtiter plate per suspension bead array assay and thus do not require any external reference samples. We demonstrate the performance of the two MA normalization methods with data obtained from the analysis of 384 samples including both serum and plasma. Samples were randomized across 96-well sample plates, processed, and analyzed in assay plates, respectively. Using principal component analysis (PCA), we could show that plate-wise clusters found in the first two components were eliminated by multi-MA normalization as compared with other normalization methods. Furthermore, we studied the correlation profiles between random pairs of antibodies and found that both MA normalization methods substantially reduced the inflated correlation introduced by plate effects. Normalization approaches using multi-MA and MA-loess minimized batch effects arising from the analysis of several assay plates with antibody suspension bead arrays. In a simulated biomarker study, multi-MA restored associations lost due to plate effects. Our normalization approaches, which are available as R package MDimNormn, could also be useful in studies using other types of high-throughput assay data.

European multicenter analytical evaluation of the Abbott ARCHITECT STAT high sensitive troponin I immunoassay.

PubMed

Krintus, Magdalena; Kozinski, Marek; Boudry, Pascal; Capell, Nuria Estañ; Köller, Ursula; Lackner, Karl; Lefèvre, Guillaume; Lennartz, Lieselotte; Lotz, Johannes; Herranz, Antonio Mora; Nybo, Mads; Plebani, Mario; Sandberg, Maria B; Schratzberger, Wolfgang; Shih, Jessie; Skadberg, Øyvind; Chargui, Ahmed Taoufik; Zaninotto, Martina; Sypniewska, Grazyna

2014-11-01

International recommendations highlight the superior value of cardiac troponins (cTns) for early diagnosis of myocardial infarction along with analytical requirements of improved precision and detectability. In this multicenter study, we investigated the analytical performance of a new high sensitive cardiac troponin I (hs-cTnI) assay and its 99th percentile upper reference limit (URL). Laboratories from nine European countries evaluated the ARCHITECT STAT high sensitive troponin I (hs-TnI) immunoassay on the ARCHITECT i2000SR/i1000SR immunoanalyzers. Imprecision, limit of blank (LoB), limit of detection (LoD), limit of quantitation (LoQ) linearity of dilution, interferences, sample type, method comparisons, and 99th percentile URLs were evaluated in this study. Total imprecision of 3.3%-8.9%, 2.0%-3.5% and 1.5%-5.2% was determined for the low, medium and high controls, respectively. The lowest cTnI concentration corresponding to a total CV of 10% was 5.6 ng/L. Common interferences, sample dilution and carryover did not affect the hs-cTnI results. Slight, but statistically significant, differences with sample type were found. Concordance between the investigated hs-cTnI assay and contemporary cTnI assay at 99th percentile cut-off was found to be 95%. TnI was detectable in 75% and 57% of the apparently healthy population using the lower (1.1 ng/L) and upper (1.9 ng/L) limit of the LoD range provided by the ARCHITECT STAT hs-TnI package insert, respectively. The 99th percentile values were gender dependent. The new ARCHITECT STAT hs-TnI assay with improved analytical features meets the criteria of high sensitive Tn test and will be a valuable diagnostic tool.

Investigating a multigene prognostic assay based on significant pathways for Luminal A breast cancer through gene expression profile analysis.

PubMed

Gao, Haiyan; Yang, Mei; Zhang, Xiaolan

2018-04-01

The present study aimed to investigate potential recurrence-risk biomarkers based on significant pathways for Luminal A breast cancer through gene expression profile analysis. Initially, the gene expression profiles of Luminal A breast cancer patients were downloaded from The Cancer Genome Atlas database. The differentially expressed genes (DEGs) were identified using a Limma package and the hierarchical clustering analysis was conducted for the DEGs. In addition, the functional pathways were screened using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses and rank ratio calculation. The multigene prognostic assay was exploited based on the statistically significant pathways and its prognostic function was tested using train set and verified using the gene expression data and survival data of Luminal A breast cancer patients downloaded from the Gene Expression Omnibus. A total of 300 DEGs were identified between good and poor outcome groups, including 176 upregulated genes and 124 downregulated genes. The DEGs may be used to effectively distinguish Luminal A samples with different prognoses verified by hierarchical clustering analysis. There were 9 pathways screened as significant pathways and a total of 18 DEGs involved in these 9 pathways were identified as prognostic biomarkers. According to the survival analysis and receiver operating characteristic curve, the obtained 18-gene prognostic assay exhibited good prognostic function with high sensitivity and specificity to both the train and test samples. In conclusion the 18-gene prognostic assay including the key genes, transcription factor 7-like 2, anterior parietal cortex and lymphocyte enhancer factor-1 may provide a new method for predicting outcomes and may be conducive to the promotion of precision medicine for Luminal A breast cancer.

Smartphone spectroscopy: three unique modalities for point-of-care testing

NASA Astrophysics Data System (ADS)

Long, Kenneth D.; Yu, Hojeong; Cunningham, Brian T.

2015-06-01

Here we demonstrate three principle modalities for a smartphone-based spectrometer: absorption, fluorescence, and photonic crystal (PC)-based label-free detection. When combined with some simple optical components, the rear-facing CMOS camera in a mobile device can provide spectrometric data that rivals that of laboratory instruments, but at a fraction of the cost. The use of a smartphone-based platform poses significant advantages based upon the rise of smartphone apps, which allow for user-interface and data-processing algorithms to be packaged and distributed within environments that are externally maintained with potential for integration with services such as cloud storage, GIS-tagging, and remote expert analysis. We demonstrate the absorption modality of our device by performing an enzyme-linked immunosorbent assay (ELISA) on both a cancer biomarker and a peanut allergen, demonstrating clinically relevant limits of detection (LOD). Second, we demonstrate the success of a molecular beacon (MB)-based assay on the smartphone platform, achieving an LOD of 1.3 pM for a specific RNA sequence, less than that of a commercial benchtop instrument. Finally, we use a PC biosensor to perform label-free detection of a representative biological interaction: Protein A and human immunoglobulin G (IgG) in the nanomolar regime. Our work represents the first demonstration of smartphone-based spectroscopy for biological assays, and the first mobile-device-enabled detection instrument that serves to measure three distinct sensing modalities (label-free biosensing, absorption spectroscopy, and fluorescence spectroscopy). The smartphone platform has the potential to expand the use of spectrometric analysis to environments assay from the laboratory, which may include rural or remote locations, low-resource settings, and consumer markets.

Inhibition of apoptosis by knockdown of caspase-3 with siRNA in rat bone marrow mesenchymal stem cells.

PubMed

Hua, Ping; Liu, Li-Bao; Liu, Jia-Liang; Wang, Meng; Jiang, Hui-Qi; Zeng, Kuan; Yang, Yan-Qi; Yang, Song-Ran

2013-09-01

Transplantation of bone marrow mesenchymal stem cells is a promising new strategy for the repair of infarcted cardiac tissue. However, the majority of transplanted bone marrow mesenchymal stem cells (BMSCs) die soon after transplantation, due in part to oxidative stress in the ischemic region. Oxidative stress is known to induce apoptosis through the activation of caspase-3. The aim of this study is to determine whether small interfering RNA targeting caspase-3 can inhibit the apoptosis of rat BMSCs in vitro. Caspase-3 siRNA expression vectors were prepared and transfected into rat BMSCs in the presence of liposomes. Western blot assay and real-time polymerase chain reaction (RT-PCR) were performed to detect caspase-3 expression. A retrovirus packaging system was employed to package 293FT cells producing caspase-3 siRNA virus, which were transfected into rat BMSCs. Those stably expressing caspase-3 siRNA were screened by Western blot assay and RT-PCR to determine caspase-3 expression levels. Stable transfection of caspase-3 siRNA significantly decreased caspase-3 protein (0.26 ± 0.001 vs. 0.42 ± 0.004, P < 0.05) and mRNA expression (0.19 ± 0.002 vs. 1, P < 0.05) in BMSCs compared to non-transfected BMSCs. Cells were incubated in H2O2 to induce apoptosis, which was detected by TUNEL staining, and BMSC morphology was not altered by either transient or stable transfection of caspase-3 siRNA. H2O2-induced apoptosis of BMSCs stably transfected with caspase-3 siRNA was dramatically reduced compared to that of normal BMSCs (11.0 ± 3.2 vs. 25.8 ± 4.2, P < 0.05). Caspase-3 knockdown BMSCs are thus more resistant to apoptosis than normal BMSCs, potentially increasing their survival rates under conditions that cause oxidative stress.

Antimicrobial activity of lauric arginate-coated polylactic acid films against Listeria monocytogenes and Salmonella typhimurium on cooked sliced ham.

PubMed

Theinsathid, Pornpun; Visessanguan, Wonnop; Kruenate, Jittiporn; Kingcha, Yutthana; Keeratipibul, Suwimon

2012-02-01

A novel type of environmentally friendly packaging with antibacterial activity was developed from lauric arginate (LAE)-coating of polylactic acid (PLA) films after surface activation using a corona discharge. Scanning electron microscopy (SEM)-based analysis of the LAE/PLA films confirmed the successful coating of LAE on the PLA surface. The mechanical properties of the LAE/PLA films with different levels of LAE-coating (0% to 2.6%[w/w]) were essentially the same as those of the neat PLA film. The antibacterial activity of the LAE/PLA films against Listeria monocytogenes and Salmonella enterica Serovar Typhimurium (S. Typhimurium) was confirmed by a qualitative modified agar diffusion assay and quantitative JIS Z 2801:2000 method. Using the LAE/PLA film as a food-contact antimicrobial packaging for cooked cured ham, as a model system, suggested a potential application to inhibit L. monocytogenes and S. Typhimurium on ham with a 0.07% (w/w) LAE coating on the PLA when high transparency is required, as evidenced from the 2 to 3 log CFU/tested film lower pathogen growth after 7 d storage but even greater antibacterial activity is obtained with a LAE coating level of 2.6% (w/w) but at the cost of a reduced transparency of the finished product. This article shows how we can simply develop functional green packaging of PLA for food with effective and efficient antimicrobial activity by use of LAE coating on the surface via corona discharge. The effectiveness of an innovative antimicrobial LAE-coated PLA film against foodborne pathogens was demonstrated. Importantly, the application of the LAE to form the LAE-coated PLA film can be customized within current film manufacturing lines. © 2012 Institute of Food Technologists®

Production of biogenic amines by lactic acid bacteria and enterobacteria isolated from fresh pork sausages packaged in different atmospheres and kept under refrigeration.

PubMed

Curiel, J A; Ruiz-Capillas, C; de Las Rivas, B; Carrascosa, A V; Jiménez-Colmenero, F; Muñoz, R

2011-07-01

The occurrence of in vitro amino acid activity in bacterial strains associated with fresh pork sausages packaged in different atmospheres and kept in refrigeration was studied. The presence of biogenic amines in decarboxylase broth was confirmed by ion-exchange chromatography and by the presence of the corresponding decarboxylase genes by PCR. From the 93 lactic acid bacteria and 100 enterobacteria strains analysed, the decarboxylase medium underestimates the number of biogenic amine-producer strains. 28% of the lactic acid bacteria produced tyramine and presented the tdc gene. All the tyramine-producer strains were molecularly identified as Carnobacterium divergens. Differences on the relative abundance of C. divergens were observed among the different packaging atmospheres assayed. After 28 days of storage, the presence of argon seems to inhibit C. divergens growth, while packing under vacuum seems to favour it. Among enterobacteria, putrescine was the amine more frequently produced (87%), followed by cadaverine (85%); agmatine and tyramine were only produced by 13 and 1%, respectively, of the strains analysed. Packing under vacuum or in an atmosphere containing nitrogen seems to inhibit the growth of enterobacteria which produce simultaneously putrescine, cadaverine, and agmatine. Contrarily, over-wrapping or packing in an atmosphere containing argon seems to favour the growth of agmatine producer-enterobacteria. The production of putrescine and cadaverine was associated with the presence of the corresponding amino acid decarboxylase genes. The biogenic amine-producer strains were included in a wide range of enterobacterial species, including Kluyvera intermedia, Enterobacter aerogenes, Yersinia kristensenii, Serratia grimesii, Serratia ficaria, Yersinia rodhei, Providencia vermicola and Obesumbacterium proteus. Copyright © 2011 Elsevier Ltd. All rights reserved.

Large-scale Clinical-grade Retroviral Vector Production in a Fixed-Bed Bioreactor

PubMed Central

Wang, Xiuyan; Olszewska, Malgorzata; Qu, Jinrong; Wasielewska, Teresa; Bartido, Shirley; Hermetet, Gregory; Sadelain, Michel

2015-01-01

The successful genetic engineering of patient T cells with γ-retroviral vectors expressing chimeric antigen receptors or T-cell receptors for phase II clinical trials and beyond requires the large-scale manufacture of high-titer vector stocks. The production of retroviral vectors from stable packaging cell lines using roller bottles or 10- to 40-layer cell factories is limited by a narrow harvest window, labor intensity, open-system operations, and the requirement for significant incubator space. To circumvent these shortcomings, we optimized the production of vector stocks in a disposable fixed-bed bioreactor using good manufacturing practice–grade packaging cell lines. High-titer vector stocks were harvested over 10 days, representing a much broader harvest window than the 3-day harvest afforded by cell factories. For PG13 and 293Vec packaging cells, the average vector titer and the vector stocks’ yield in the bioreactor were higher by 3.2- to 7.3-fold, and 5.6- to 13.1-fold, respectively, than those obtained in cell factories. The vector production was 10.4 and 18.6 times more efficient than in cell factories for PG13 and 293Vec cells, respectively. Furthermore, the vectors produced from the fixed-bed bioreactors passed the release test assays for clinical applications. Therefore, a single vector lot derived from 293Vec is suitable to transduce up to 500 patients cell doses in the context of large clinical trials using chimeric antigen receptors or T-cell receptors. These findings demonstrate for the first time that a robust fixed-bed bioreactor process can be used to produce γ-retroviral vector stocks scalable up to the commercialization phase. PMID:25751502

The impact of primary packaging on the quality of parenteral products.

PubMed

Solomun, Ljiljana; Ibric, Svetlana; Boltic, Zorana; Djuric, Zorica; Stupar, Biljana

2008-11-04

The unique approach in manufacturing of pharmaceutical dosage forms of active substances known to be unstable in aqueous solution is the introduction of lyophilization process. Nevertheless, these products must be reconstituted using the diluent from a separate container before application. The possible solution for this problem is the application of dual chamber vials comprising the freeze-dried product in a lower compartment of the vial and the solution for reconstitution in the upper chamber. The main issue in development of such product is the choice of contact packaging (rubber closures, glass vials and the container closure system as a whole). The most important parameter used for evaluation of the influence of contact material on product quality was the pH value. The results have shown that the type of vials (moulded or tubular glass) has no impact on pH shift of the solution for reconstitution (tested solution-TS), while significant differences in pH value of the TS were observed depending on the rubber closures formulation used (with some formulations, the pH shift during the test was 6.5-9.14). Benzyl alcohol assay during the tests remained unchanged. Integrity tests of the container closure system (CCS) have demonstrated the adequacy of the selected packaging system. The quality of the CCS of choice was confirmed in the course of stability studies, only parameters directly influenced by CCS being presented in this work: loss on drying and pH value. On the basis of these results, no changes in loss on drying were connected to CCS, and the pH value of the reconstituted solution remains unchanged in samples tested both ex-tempore and after in-use period of 48 h.

Melanin-templated rapid synthesis of silver nanostructures

PubMed Central

2014-01-01

Background As a potent antimicrobial agent, silver nanostructures have been used in nanosensors and nanomaterial-based assays for the detection of food relevant analytes such as organic molecules, aroma, chemical contaminants, gases and food borne pathogens. In addition silver based nanocomposites act as an antimicrobial for food packaging materials. In this prospective, the food grade melanin pigment extracted from sponge associated actinobacterium Nocardiopsis alba MSA10 and melanin mediated synthesis of silver nanostructures were studied. Based on the present findings, antimicrobial nanostructures can be developed against food pathogens for food industrial applications. Results Briefly, the sponge associated actinobacterium N. alba MSA10 was screened and fermentation conditions were optimized for the production of melanin pigment. The Plackett-Burman design followed by a Box-Behnken design was developed to optimize the concentration of most significant factors for improved melanin yield. The antioxidant potential, reductive capabilities and physiochemical properties of Nocardiopsis melanin was characterized. The optimum production of melanin was attained with pH 7.5, temperature 35°C, salinity 2.5%, sucrose 25 g/L and tyrosine 12.5 g/L under submerged fermentation conditions. A highest melanin production of 3.4 mg/ml was reached with the optimization using Box-Behnken design. The purified melanin showed rapid reduction and stabilization of silver nanostructures. The melanin mediated process produced uniform and stable silver nanostructures with broad spectrum antimicrobial activity against food pathogens. Conclusions The melanin pigment produced by N. alba MSA10 can be used for environmentally benign synthesis of silver nanostructures and can be useful for food packaging materials. The characteristics of broad spectrum of activity against food pathogens of silver nanostructures gives an insight for their potential applicability in incorporation of food packaging materials and antimicrobials for stored fruits and foods. PMID:24885756

Analysis of a vesicular glutamate transporter (VGLUT2) supports a cell-leakage mode in addition to vesicular packaging.

PubMed

Mackenzie, Bryan; Illing, Anthony C; Morris, Marie E K; Varoqui, Hélène; Erickson, Jeffrey D

2008-02-01

VGLUT2 is one of three vesicular glutamate transporters that play crucial roles in glutamatergic excitatory neurotransmission. We explored the functional properties of the rat VGLUT2 by heterologous expression of VGLUT2 in Xenopus oocytes. Immunocytochemical analysis indicated that most VGLUT2 protein was expressed in intracellular compartments but that some expression occurred also on the plasma membrane. Functional analysis revealed VGLUT2 to be active in two independent modes, namely, uptake into intracellular organelles and efflux at the plasma membrane. VGLUT-specific transport was identified based on the strong preference for glutamate over aspartate--in contrast to plasma-membrane or mitochondrial glutamate transporters--and sensitivity to known VGLUT blockers. VGLUT2 expression in oocytes (1) stimulated the influx of L-[(3)H]glutamate, but not D-[(3)H]aspartate, into digitonin-permeabilized oocytes and (2) stimulated efflux of L-glutamate, but not L-aspartate, from intact oocytes preinjected with (3)H-labeled amino acids. In the latter assay, cellular efflux of glutamate (which was blocked by rose bengal and trypan blue) may be analogous to vesicular packaging of glutamate. Our data are consistent with VGLUT2-mediated H(+)/L-glutamate antiport, but not antiport with chloride. Expression of mammalian VGLUT1 and VGLUT3 also stimulated L-[(3)H]glutamate efflux from Xenopus oocytes, suggesting that this phenomenon is a general feature of vesicular glutamate transporters. Our findings support the idea that vesicular glutamate transporters, when transiently expressed on the neuronal plasma membrane, may mediate Ca(2+)-independent glutamate leakage in addition to their traditional role of packaging glutamate into synaptic vesicles for Ca(2+)-dependent exocytosis.

Single Pore Translocation of Folded, Double-Stranded, and Tetra-stranded DNA through Channel of Bacteriophage Phi29 DNA Packaging Motor

PubMed Central

Haque, Farzin; Wang, Shaoying; Stites, Chris; Chen, Li; Wang, Chi; Guo, Peixuan

2015-01-01

The elegant architecture of the channel of bacteriophage phi29 DNA packaging motor has inspired the development of biomimetics for biophysical and nanobiomedical applications. The reengineered channel inserted into a lipid membrane exhibits robust electrophysiological properties ideal for precise sensing and fingerprinting of dsDNA at the single-molecule level. Herein, we used single channel conduction assays to quantitatively evaluate the translocation dynamics of dsDNA as a function of the length and conformation of dsDNA. We extracted the speed of dsDNA translocation from the dwell time distribution and estimated the various forces involved in the translocation process. A ~35-fold slower speed of translocation per base pair was observed for long dsDNA, a significant contrast to the speed of dsDNA crossing synthetic pores. It was found that the channel could translocate both dsDNA with ~32% of channel current blockage and ~64% for tetra-stranded DNA (two parallel dsDNA). The calculation of both cross-sectional areas of the dsDNA and tetra-stranded DNA suggested that the blockage was purely proportional to the physical space of the channel lumen and the size of the DNA substrate. Folded dsDNA configuration was clearly reflected in their characteristic current signatures. The finding of translocation of tetra-stranded DNA with 64% blockage is in consent with the recently elucidated mechanism of viral DNA packaging via a revolution mode that requires a channel larger than the dsDNA diameter of 2 nm to provide room for viral DNA revolving without rotation. The understanding of the dynamics of dsDNA translocation in the phi29 system will enable us to design more sophisticated single pore DNA translocation devices for future applications in nanotechnology and personal medicine. PMID:25890769

Cross-reactivity of steroid hormone immunoassays: clinical significance and two-dimensional molecular similarity prediction

PubMed Central

2014-01-01

Background Immunoassays are widely used in clinical laboratories for measurement of plasma/serum concentrations of steroid hormones such as cortisol and testosterone. Immunoassays can be performed on a variety of standard clinical chemistry analyzers, thus allowing even small clinical laboratories to do analysis on-site. One limitation of steroid hormone immunoassays is interference caused by compounds with structural similarity to the target steroid of the assay. Interfering molecules include structurally related endogenous compounds and their metabolites as well as drugs such as anabolic steroids and synthetic glucocorticoids. Methods Cross-reactivity of a structurally diverse set of compounds were determined for the Roche Diagnostics Elecsys assays for cortisol, dehydroepiandrosterone (DHEA) sulfate, estradiol, progesterone, and testosterone. These data were compared and contrasted to package insert data and published cross-reactivity studies for other marketed steroid hormone immunoassays. Cross-reactivity was computationally predicted using the technique of two-dimensional molecular similarity. Results The Roche Elecsys Cortisol and Testosterone II assays showed a wider range of cross-reactivity than the DHEA sulfate, Estradiol II, and Progesterone II assays. 6-Methylprednisolone and prednisolone showed high cross-reactivity for the cortisol assay, with high likelihood of clinically significant effect for patients administered these drugs. In addition, 21-deoxycortisol likely produces clinically relevant cross-reactivity for cortisol in patients with 21-hydroxylase deficiency, while 11-deoxycortisol may produce clinically relevant cross-reactivity in 11β-hydroxylase deficiency or following metyrapone challenge. Several anabolic steroids may produce clinically significant false positives on the testosterone assay, although interpretation is limited by sparse pharmacokinetic data for some of these drugs. Norethindrone therapy may impact immunoassay measurement of testosterone in women. Using two-dimensional similarity calculations, all compounds with high cross-reactivity also showed a high degree of similarity to the target molecule of the immunoassay. Conclusions Compounds producing cross-reactivity in steroid hormone immunoassays generally have a high degree of structural similarity to the target hormone. Clinically significant interactions can occur with structurally similar drugs (e.g., prednisolone and cortisol immunoassays; methyltestosterone and testosterone immunoassays) or with endogenous compounds such as 21-deoxycortisol that can accumulate to very high concentrations in certain disease conditions. Simple similarity calculations can help triage compounds for future testing of assay cross-reactivity. PMID:25071417

Refined liquid smoke: a potential antilisterial additive to cold-smoked sockeye salmon (Oncorhynchus nerka).

PubMed

Montazeri, Naim; Himelbloom, Brian H; Oliveira, Alexandra C M; Leigh, Mary Beth; Crapo, Charles A

2013-05-01

Cold-smoked salmon (CSS) is a potentially hazardous ready-to-eat food product due to the high risk of contamination with Listeria monocytogenes and lack of a listericidal step. We investigated the antilisterial property of liquid smokes (LS) against Listeria innocua ATCC 33090 (surrogate to L. monocytogenes) as a potential supplement to vacuum-packaged CSS. A full-strength LS (Code 10-Poly), and three commercially refined fractions (AM-3, AM-10, and 1291) having less color and flavor (lower content of phenols and carbonyl-containing compounds) were tested. In vitro assays showed strong inhibition for all LS except for 1291. The CSS strips were surface coated with AM-3 and AM-10 at 1% LS (vol/wt) with an L-shaped glass rod and then inoculated with L. innocua at 3.5 log CFU/g, vacuum packaged, and stored at 4°C. The LS did not completely eliminate L. innocua but provided a 2-log reduction by day 14, with no growth up to 35 days of refrigerated storage. A simple difference sensory test by 180 untrained panelists showed the application of AM-3 did not significantly influence the overall sensorial quality of CSS. In essence, the application of the refined LS as an antilisterial additive to CSS is recommended.

Multi-compartment medication devices and patient compliance.

PubMed

McGraw, Caroline

2004-07-01

Multi-compartment medication compliance devices are widely used in primary care. The aim of this review is to reveal whether they are effective in promoting adherence among non-adherent adults living at home. Searches were undertaken using two electronic databases (Medline (1966-2003) and International Pharmaceutical Abstracts (1970-2002)). Only randomized controlled trials (including crossover studies) were included in the review. Participants had to be non-institutionalized adults receiving one or more prescription medicines each day and displaying problems with adherence. Studies had to compare multi-compartment medication compliance devices to standard packaging and outcome measures and to include either pill counts, biological assays and/or clinical response. Articles were selected if they described a follow up period of at least three months and demonstrated that over 80% of participants had completed the trial. Two studies were identified that met the criteria, reporting data on a total of 148 patients. The findings from the first study found diabetic patients receiving medication in a compliance device demonstrated better glucose control than patients receiving medication in standard packaging. The second study found compliance devices had no impact on blood pressure control in hypertensive patients. Further research needs to be conducted to assess the effectiveness of multi-compartment medication compliance devices in promoting adherence among non-adherent adults living at home.

Thyme Oil Encapsulated in Halloysite Nanotubes for Antimicrobial Packaging System.

PubMed

Lee, Min Hyeock; Seo, Hyun-Sun; Park, Hyun Jin

2017-04-01

An antimicrobial capsule releasing thyme oil was developed using modified halloysite nanotubes (HNTs). In order to increase the pore volume, HNTs were treated with 5.0 mol/L NaOH solution, which resulted in the encapsulation of more thyme oil molecules inside the HNTs. The morphology of the raw HNTs and NaOH-treated HNTs (N-HNTs) was characterized using transmission electron microscopy and nitrogen adsorption-desorption analysis. The loading capacity increased from 180.7 ± 12.7 to 256.4 ± 16.7 mg thyme oil/g HNT after the NaOH treatment. The aerial release characteristics of thyme oil from both the HNT capsules were investigated in a closed-package atmosphere system at 4, 25, and 40 °C. The antimicrobial activity of the capsule against Escherichia coli O157:H7 was determined using the vapor phase assay. Moreover, the antimicrobial effects of the capsule against E. coli O157:H7, total mesophilic aerobic bacteria (MAB), and molds and yeasts (MY) on the surfaces of cherry tomatoes were investigated at 4 and 25 °C for 5 d. When the cherry tomatoes were exposed to the thyme oil-loaded N-HNT capsule, the number of E. coli O157:H7, MAB, and MY significantly reduced during storage. © 2017 Institute of Food Technologists®.

RNA structural constraints in the evolution of the influenza A virus genome NP segment

PubMed Central

Gultyaev, Alexander P; Tsyganov-Bodounov, Anton; Spronken, Monique IJ; van der Kooij, Sander; Fouchier, Ron AM; Olsthoorn, René CL

2014-01-01

Conserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length, including protein-coding regions. Calculations of mutual information values at the paired nucleotide positions demonstrate that these structures impose considerable constraints on the virus genome evolution. Functional importance of a pseudoknot structure, predicted in the NP packaging signal region, was confirmed by plaque assays of the mutant viruses with disrupted structure and those with restored folding using compensatory substitutions. Possible functions of the conserved RNA folding patterns in the influenza A virus genome are discussed. PMID:25180940

A theoretical insight for solvent effect on myoglobin assay of W(CO)4L2 type novel complexes with DFT/TDDFT

NASA Astrophysics Data System (ADS)

Üstün, Elvan; Demi˙r, Serpil; Coşkun, Feyzullah; Kaloğlu, Murat; Şahi˙n, Onur; Büyükgüngör, Orhan; Özdemi˙r, İsmail

2016-11-01

Novel tetracarbonyl complexes of type W(CO)4L2 (L: 4-chlorobenzylimidazoline; 4-methylbenzylimidazoline; 3,5-dimethylbenzylimidazoline; 2,4,6-trimethylbenzylimidazoline; 2,3,5,6- tetramethylbenzylimidazoline) were synthesized. Then newly synthesized novel compounds were characterized by IR, 1H NMR, 13C NMR and LC-MS. The characterizations of two of the complexes have also been confirmed with single crystal X-Ray diffraction and DFT optimization results of these complexes have been compared with single crystal results. We have investigated the solvent effect on the structure and metal-to-ligand charge transfer (MLCT) transitions with DFT/TDDFT calculations with ORCA package program with BP86 functional.

Stability of gabapentin in extemporaneously compounded oral suspensions.

PubMed

Friciu, Mihaela; Roullin, V Gaëlle; Leclair, Grégoire

2017-01-01

This study reports the stability of extemporaneously prepared gabapentin oral suspensions prepared at 100 mg/mL from bulk drug and capsules in either Oral Mix or Oral Mix SF suspending vehicles. Suspensions were packaged in amber plastic bottles and amber plastic syringes at 25°C / 60%RH for up to 90 days. Throughout the study period, the following tests were performed to evaluate the stability of the preparations: organoleptic inspection to detect homogeneity, color or odor changes; pH measurements; and gabapentin assay using a stability-indicating HPLC-UV method. As crystallization was observed at 5°C, storage at this temperature condition is not recommended. All preparations stored at 25°C / 60%RH remained stable for the whole study duration of 90 days.

Quantitative Assessment of Antimicrobial Activity of PLGA Films Loaded with 4-Hexylresorcinol

PubMed Central

Kemme, Michael; Heinzel-Wieland, Regina

2018-01-01

Profound screening and evaluation methods for biocide-releasing polymer films are crucial for predicting applicability and therapeutic outcome of these drug delivery systems. For this purpose, we developed an agar overlay assay embedding biopolymer composite films in a seeded microbial lawn. By combining this approach with model-dependent analysis for agar diffusion, antimicrobial potency of the entrapped drug can be calculated in terms of minimum inhibitory concentrations (MICs). Thus, the topical antiseptic 4-hexylresorcinol (4-HR) was incorporated into poly(lactic-co-glycolic acid) (PLGA) films at different loadings up to 3.7 mg/cm2 surface area through a solvent casting technique. The antimicrobial activity of 4-HR released from these composite films was assessed against a panel of Gram-negative and Gram–positive bacteria, yeasts and filamentous fungi by the proposed assay. All the microbial strains tested were susceptible to PLGA-4-HR films with MIC values down to 0.4% (w/w). The presented approach serves as a reliable method in screening and quantifying the antimicrobial activity of polymer composite films. Moreover, 4-HR-loaded PLGA films are a promising biomaterial that may find future application in the biomedical and packaging sector. PMID:29324696

Enhanced Stability of Inactivated Influenza Vaccine Encapsulated in Dissolving Microneedle Patches

PubMed Central

Chu, Leonard Y.; Ye, Ling; Dong, Ke; Compans, Richard W.; Yang, Chinglai; Prausnitz, Mark R.

2015-01-01

Purpose This study tested the hypothesis that encapsulation of influenza vaccine in microneedle patches increases vaccine stability during storage at elevated temperature. Methods Whole inactivated influenza virus vaccine (A/Puerto Rico/8/34) was formulated into dissolving microneedle patches and vaccine stability was evaluated by in vitro and in vivo assays of antigenicity and immunogenicity after storage for up to 3 months at 4, 25, 37 and 45°C. Results While liquid vaccine completely lost potency as determined by hemagglutination (HA) activity within 1–2 weeks outside of refrigeration, vaccine in microneedle patches lost 40–50% HA activity during or shortly after fabrication, but then had no significant additional loss of activity over 3 months of storage, independent of temperature. This level of stability required reduced humidity by packaging with desiccant, but was not affected by presence of oxygen. This finding was consistent with additional stability assays, including antigenicity of the vaccine measured by ELISA, virus particle morphological structure captured by transmission electron microscopy and protective immune responses by immunization of mice in vivo. Conclusions These data show that inactivated influenza vaccine encapsulated in dissolving microneedle patches has enhanced stability during extended storage at elevated temperatures. PMID:26620313

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.

PubMed

Waszak, Sebastian M; Kilpinen, Helena; Gschwind, Andreas R; Orioli, Andrea; Raghav, Sunil K; Witwicki, Robert M; Migliavacca, Eugenia; Yurovsky, Alisa; Lappalainen, Tuuli; Hernandez, Nouria; Reymond, Alexandre; Dermitzakis, Emmanouil T; Deplancke, Bart

2014-01-15

High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifacts. We investigated the impact of library amplification bias on the identification of allele-specific (AS) molecular events from high-throughput sequencing data derived from chromatin immunoprecipitation assays (ChIP-seq). Putative AS DNA binding activity for RNA polymerase II was determined using ChIP-seq data derived from lymphoblastoid cell lines of two parent-daughter trios. We found that, at high-sequencing depth, many significant AS binding sites suffered from an amplification bias, as evidenced by a larger number of clonal reads representing one of the two alleles. To alleviate this bias, we devised an amplification bias detection strategy, which filters out sites with low read complexity and sites featuring a significant excess of clonal reads. This method will be useful for AS analyses involving ChIP-seq and other functional sequencing assays. The R package abs filter for library clonality simulations and detection of amplification-biased sites is available from http://updepla1srv1.epfl.ch/waszaks/absfilter

The higher structure of chromatin in the LCR of the beta-globin locus changes during development.

PubMed

Fang, Xiangdong; Yin, Wenxuan; Xiang, Ping; Han, Hemei; Stamatoyannopoulos, George; Li, Qiliang

2009-11-27

The beta-globin locus control region (LCR) is able to enhance the expression of all globin genes throughout the course of development. However, the chromatin structure of the LCR at the different developmental stages is not well defined. We report DNase I and micrococcal nuclease hypersensitivity, chromatin immunoprecipitation analyses for histones H2A, H2B, H3, and H4, and 3C (chromatin conformation capture) assays of the normal and mutant beta-globin loci, which demonstrate that nucleosomes at the DNase I hypersensitive sites of the LCR could be either depleted or retained depending on the stages of development. Furthermore, MNase sensitivity and 3C assays suggest that the LCR chromatin is more open in embryonic erythroblasts than in definitive erythroblasts at the primary- and secondary-structure levels; however, the LCR chromatin is packaged more tightly in embryonic erythroblasts than in definitive erythroblasts at the tertiary chromatin level. Our study provides the first evidence that the occupancy of nucleosomes at a DNase I hypersensitive site is a developmental stage-related event and that embryonic and adult cells possess distinct chromatin structures of the LCR.

Stability of gabapentin in extemporaneously compounded oral suspensions

PubMed Central

Friciu, Mihaela; Roullin, V. Gaëlle

2017-01-01

This study reports the stability of extemporaneously prepared gabapentin oral suspensions prepared at 100 mg/mL from bulk drug and capsules in either Oral Mix or Oral Mix SF suspending vehicles. Suspensions were packaged in amber plastic bottles and amber plastic syringes at 25°C / 60%RH for up to 90 days. Throughout the study period, the following tests were performed to evaluate the stability of the preparations: organoleptic inspection to detect homogeneity, color or odor changes; pH measurements; and gabapentin assay using a stability-indicating HPLC-UV method. As crystallization was observed at 5°C, storage at this temperature condition is not recommended. All preparations stored at 25°C / 60%RH remained stable for the whole study duration of 90 days. PMID:28414771

Absolute determination of single-stranded and self-complementary adeno-associated viral vector genome titers by droplet digital PCR.

PubMed

Lock, Martin; Alvira, Mauricio R; Chen, Shu-Jen; Wilson, James M

2014-04-01

Accurate titration of adeno-associated viral (AAV) vector genome copies is critical for ensuring correct and reproducible dosing in both preclinical and clinical settings. Quantitative PCR (qPCR) is the current method of choice for titrating AAV genomes because of the simplicity, accuracy, and robustness of the assay. However, issues with qPCR-based determination of self-complementary AAV vector genome titers, due to primer-probe exclusion through genome self-annealing or through packaging of prematurely terminated defective interfering (DI) genomes, have been reported. Alternative qPCR, gel-based, or Southern blotting titering methods have been designed to overcome these issues but may represent a backward step from standard qPCR methods in terms of simplicity, robustness, and precision. Droplet digital PCR (ddPCR) is a new PCR technique that directly quantifies DNA copies with an unparalleled degree of precision and without the need for a standard curve or for a high degree of amplification efficiency; all properties that lend themselves to the accurate quantification of both single-stranded and self-complementary AAV genomes. Here we compare a ddPCR-based AAV genome titer assay with a standard and an optimized qPCR assay for the titration of both single-stranded and self-complementary AAV genomes. We demonstrate absolute quantification of single-stranded AAV vector genomes by ddPCR with up to 4-fold increases in titer over a standard qPCR titration but with equivalent readout to an optimized qPCR assay. In the case of self-complementary vectors, ddPCR titers were on average 5-, 1.9-, and 2.3-fold higher than those determined by standard qPCR, optimized qPCR, and agarose gel assays, respectively. Droplet digital PCR-based genome titering was superior to qPCR in terms of both intra- and interassay precision and is more resistant to PCR inhibitors, a desirable feature for in-process monitoring of early-stage vector production and for vector genome biodistribution analysis in inhibitory tissues.

PRISE2: software for designing sequence-selective PCR primers and probes.

PubMed

Huang, Yu-Ting; Yang, Jiue-in; Chrobak, Marek; Borneman, James

2014-09-25

PRISE2 is a new software tool for designing sequence-selective PCR primers and probes. To achieve high level of selectivity, PRISE2 allows the user to specify a collection of target sequences that the primers are supposed to amplify, as well as non-target sequences that should not be amplified. The program emphasizes primer selectivity on the 3' end, which is crucial for selective amplification of conserved sequences such as rRNA genes. In PRISE2, users can specify desired properties of primers, including length, GC content, and others. They can interactively manipulate the list of candidate primers, to choose primer pairs that are best suited for their needs. A similar process is used to add probes to selected primer pairs. More advanced features include, for example, the capability to define a custom mismatch penalty function. PRISE2 is equipped with a graphical, user-friendly interface, and it runs on Windows, Macintosh or Linux machines. PRISE2 has been tested on two very similar strains of the fungus Dactylella oviparasitica, and it was able to create highly selective primers and probes for each of them, demonstrating the ability to create useful sequence-selective assays. PRISE2 is a user-friendly, interactive software package that can be used to design high-quality selective primers for PCR experiments. In addition to choosing primers, users have an option to add a probe to any selected primer pair, enabling design of Taqman and other primer-probe based assays. PRISE2 can also be used to design probes for FISH and other hybridization-based assays.

Massively parallel cis-regulatory analysis in the mammalian central nervous system

PubMed Central

Shen, Susan Q.; Myers, Connie A.; Hughes, Andrew E.O.; Byrne, Leah C.; Flannery, John G.; Corbo, Joseph C.

2016-01-01

Cis-regulatory elements (CREs, e.g., promoters and enhancers) regulate gene expression, and variants within CREs can modulate disease risk. Next-generation sequencing has enabled the rapid generation of genomic data that predict the locations of CREs, but a bottleneck lies in functionally interpreting these data. To address this issue, massively parallel reporter assays (MPRAs) have emerged, in which barcoded reporter libraries are introduced into cells, and the resulting barcoded transcripts are quantified by next-generation sequencing. Thus far, MPRAs have been largely restricted to assaying short CREs in a limited repertoire of cultured cell types. Here, we present two advances that extend the biological relevance and applicability of MPRAs. First, we adapt exome capture technology to instead capture candidate CREs, thereby tiling across the targeted regions and markedly increasing the length of CREs that can be readily assayed. Second, we package the library into adeno-associated virus (AAV), thereby allowing delivery to target organs in vivo. As a proof of concept, we introduce a capture library of about 46,000 constructs, corresponding to roughly 3500 DNase I hypersensitive (DHS) sites, into the mouse retina by ex vivo plasmid electroporation and into the mouse cerebral cortex by in vivo AAV injection. We demonstrate tissue-specific cis-regulatory activity of DHSs and provide examples of high-resolution truncation mutation analysis for multiplex parsing of CREs. Our approach should enable massively parallel functional analysis of a wide range of CREs in any organ or species that can be infected by AAV, such as nonhuman primates and human stem cell–derived organoids. PMID:26576614

Toward Serotonin Fluorescent False Neurotransmitters: Development of Fluorescent Dual Serotonin and Vesicular Monoamine Transporter Substrates for Visualizing Serotonin Neurons.

PubMed

Henke, Adam; Kovalyova, Yekaterina; Dunn, Matthew; Dreier, Dominik; Gubernator, Niko G; Dincheva, Iva; Hwu, Christopher; Šebej, Peter; Ansorge, Mark S; Sulzer, David; Sames, Dalibor

2018-05-16

Ongoing efforts in our laboratories focus on design of optical reporters known as fluorescent false neurotransmitters (FFNs) that enable the visualization of uptake into, packaging within, and release from individual monoaminergic neurons and presynaptic sites in the brain. Here, we introduce the molecular probe FFN246 as an expansion of the FFN platform to the serotonergic system. Combining the acridone fluorophore with the ethylamine recognition element of serotonin, we identified FFN54 and FFN246 as substrates for both the serotonin transporter and the vesicular monoamine transporter 2 (VMAT2). A systematic structure-activity study revealed the basic structural chemotype of aminoalkyl acridones required for serotonin transporter (SERT) activity and enabled lowering the background labeling of these probes while maintaining SERT activity, which proved essential for obtaining sufficient signal in the brain tissue (FFN246). We demonstrate the utility of FFN246 for direct examination of SERT activity and SERT inhibitors in 96-well cell culture assays, as well as specific labeling of serotonergic neurons of the dorsal raphe nucleus in the living tissue of acute mouse brain slices. While we found only minor FFN246 accumulation in serotonergic axons in murine brain tissue, FFN246 effectively traces serotonin uptake and packaging in the soma of serotonergic neurons with improved photophysical properties and loading parameters compared to known serotonin-based fluorescent tracers.

Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data.

PubMed

Lepre, Jorge; Rice, J Jeremy; Tu, Yuhai; Stolovitzky, Gustavo

2004-05-01

Despite the growing literature devoted to finding differentially expressed genes in assays probing different tissues types, little attention has been paid to the combinatorial nature of feature selection inherent to large, high-dimensional gene expression datasets. New flexible data analysis approaches capable of searching relevant subgroups of genes and experiments are needed to understand multivariate associations of gene expression patterns with observed phenotypes. We present in detail a deterministic algorithm to discover patterns of multivariate gene associations in gene expression data. The patterns discovered are differential with respect to a control dataset. The algorithm is exhaustive and efficient, reporting all existent patterns that fit a given input parameter set while avoiding enumeration of the entire pattern space. The value of the pattern discovery approach is demonstrated by finding a set of genes that differentiate between two types of lymphoma. Moreover, these genes are found to behave consistently in an independent dataset produced in a different laboratory using different arrays, thus validating the genes selected using our algorithm. We show that the genes deemed significant in terms of their multivariate statistics will be missed using other methods. Our set of pattern discovery algorithms including a user interface is distributed as a package called Genes@Work. This package is freely available to non-commercial users and can be downloaded from our website (http://www.research.ibm.com/FunGen).

Estimating Likelihood of Fetal In Vivo Interactions Using In ...

EPA Pesticide Factsheets

Tox21/ToxCast efforts provide in vitro concentration-response data for thousands of compounds. Predicting whether chemical-biological interactions observed in vitro will occur in vivo is challenging. We hypothesize that using a modified model from the FDA guidance for drug interaction studies, Cmax/AC50 (i.e., maximal in vivo blood concentration over the half-maximal in in vitro activity concentration), will give a useful approximation for concentrations where in vivo interactions are likely. Further, for doses where maternal blood concentrations are likely to elicit an interaction (Cmax/AC50>0.1), where do the compounds accumulate in fetal tissues? In order to estimate these doses based on Tox21 data, in silico parameters of chemical fraction unbound in plasma and intrinsic hepatic clearance were estimated from ADMET predictor (Simulations-Plus Inc.) and used in the HTTK R-package to obtain Cmax values from a physiologically-based toxicokinetics model. In silico estimated Cmax values predicted in vivo human Cmax with median absolute error of 0.81 for 93 chemicals, giving confidence in the R-package and in silico estimates. A case example evaluating Cmax/AC50 values for peroxisome proliferator-activated receptor gamma (PPARγ) and glucocorticoid receptor revealed known compounds (glitazones and corticosteroids, respectively) highest on the list at pharmacological doses. Doses required to elicit likely interactions across all Tox21/ToxCast assays were compared to

Application of the lymphocyte Cytokinesis-Block Micronucleus Assay to populations exposed to petroleum and its derivatives: Results from a systematic review and meta-analysis.

PubMed

Angelini, Sabrina; Bermejo, Justo Lorenzo; Ravegnini, Gloria; Sammarini, Giulia; Hrelia, Patrizia

The lymphocyte cytokinesis-block micronucleus (CBMN) assay is applied in many different in vivo biomonitoring studies of human exposure to genotoxic chemicals. Among extensively chemicals investigated, we identified petroleum and its derivatives, in particular benzene and the most common mixture of benzene, toluene, and xylene. Although conflicting results have been reported on the effects of benzene exposure, the number of positive findings in independent studies suggests that occupational exposure to benzene causes DNA damage in peripheral blood lymphocytes. To assess current evidence on this hypothesis, we conducted a meta-analysis. Our aim was to evaluate the effect of benzene exposure on genetic damage, quantified using the CBMN assay on individuals occupationally exposed to petroleum and its derivatives. Statistical analyses were conducted using the rmeta package from the free Software Environment for Statistical Computing R. Combined study results indicated that benzene exposure is associated with an increased level of genetic damage in peripheral blood lymphocytes, as reflected by an increased MN frequency. The summary mean difference in MN frequency between exposed and unexposed individuals was 1.64 (95% CI: 0.80-2.47). Overall, this finding points to MN frequency as a sensitive biomarker which could be used to evaluate genetic damage induced by occupational - industrial or environmental - exposure to benzene. This review also identified some important knowledge gaps as well as the need of large, well-designed studies. In particular, it is fundamental to accurately characterize the investigated population, including dietary habits and genetic variability which could modulate MN frequency in both exposed individuals and unexposed controls. In conclusion, according to present findings the use of the CBMN assay in biomonitoring studies could provide objective evidence to guide prioritization of preventive interventions in subjects occupationally exposed to petroleum derivatives, and in particular benzene. Copyright © 2016 Elsevier B.V. All rights reserved.

Innovations in the Assay of Un-Segregated Multi-Isotopic Grade TRU Waste Boxes with SuperHENC and FRAM Technology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simpson, A. P.; Barber, S.; Abdurrahman, N. M.

2006-07-01

The Super High Efficiency Neutron Coincidence Counter (SuperHENC) was originally developed by BIL Solutions Inc., Los Alamos National Laboratory (LANL) and Rocky Flats Environmental Technology Site (RFETS) for assay of transuranic (TRU) waste in Standard Waste Boxes (SWB) at Rocky Flats. This mobile system was a key component in the shipment of over 4,000 SWBs to the Waste Isolation Pilot Plant (WIPP) in Carlsbad, New Mexico. The system was WIPP certified in 2001 and operated at the site for four years. The success of this system, a passive neutron coincidence counter combined with high resolution gamma spectroscopy, led to themore » order of two new units, delivered to Hanford in 2004. Several new challenges were faced at Hanford: For example, the original RFETS system was calibrated for segregated waste streams such that metals, plastics, wet combustibles and dry combustibles were separated by 'Item Description Codes' prior to assay. Furthermore, the RFETS mission of handling only weapons grade plutonium, enabled the original SuperHENC to benefit from the use of known Pu isotopics. Operations at Hanford, as with most other DOE sites, generate un-segregated waste streams, with a wide diversity of Pu isotopics. Consequently, the new SuperHENCs are required to deal with new technical challenges. The neutron system's software and calibration methodology have been modified to encompass these new requirements. In addition, PC-FRAM software has been added to the gamma system, providing a robust isotopic measurement capability. Finally a new software package has been developed that integrates the neutron and gamma data to provide a final assay results and analysis report. The new system's performance has been rigorously tested and validated against WIPP quality requirements. These modifications, together with the mobile platform, make the new SuperHENC far more versatile in handling diverse waste streams and allow for rapid redeployment around the DOE complex. (authors)« less

CellAnimation: an open source MATLAB framework for microscopy assays.

PubMed

Georgescu, Walter; Wikswo, John P; Quaranta, Vito

2012-01-01

Advances in microscopy technology have led to the creation of high-throughput microscopes that are capable of generating several hundred gigabytes of images in a few days. Analyzing such wealth of data manually is nearly impossible and requires an automated approach. There are at present a number of open-source and commercial software packages that allow the user to apply algorithms of different degrees of sophistication to the images and extract desired metrics. However, the types of metrics that can be extracted are severely limited by the specific image processing algorithms that the application implements, and by the expertise of the user. In most commercial software, code unavailability prevents implementation by the end user of newly developed algorithms better suited for a particular type of imaging assay. While it is possible to implement new algorithms in open-source software, rewiring an image processing application requires a high degree of expertise. To obviate these limitations, we have developed an open-source high-throughput application that allows implementation of different biological assays such as cell tracking or ancestry recording, through the use of small, relatively simple image processing modules connected into sophisticated imaging pipelines. By connecting modules, non-expert users can apply the particular combination of well-established and novel algorithms developed by us and others that are best suited for each individual assay type. In addition, our data exploration and visualization modules make it easy to discover or select specific cell phenotypes from a heterogeneous population. CellAnimation is distributed under the Creative Commons Attribution-NonCommercial 3.0 Unported license (http://creativecommons.org/licenses/by-nc/3.0/). CellAnimationsource code and documentation may be downloaded from www.vanderbilt.edu/viibre/software/documents/CellAnimation.zip. Sample data are available at www.vanderbilt.edu/viibre/software/documents/movies.zip. walter.georgescu@vanderbilt.edu Supplementary data available at Bioinformatics online.

A “Coiled-Coil” Motif Is Important for Oligomerization and DNA Binding Properties of Human Cytomegalovirus Protein UL77

PubMed Central

Dittmer, Alexandra; Lapp, Sara; Bogner, Elke

2011-01-01

Human cytomegalovirus (HCMV) UL77 gene encodes the essential protein UL77, its function is characterized in the present study. Immunoprecipitation identified monomeric and oligomeric pUL77 in HCMV infected cells. Immunostaining of purified virions and subviral fractions showed that pUL77 is a structural protein associated with capsids. In silico analysis revealed the presence of a coiled-coil motif (CCM) at the N-terminus of pUL77. Chemical cross-linking of either wild-type pUL77 or CCM deletion mutant (pUL77ΔCCM) implicated that CCM is critical for oligomerization of pUL77. Furthermore, co-immunoprecipitations of infected and transfected cells demonstrated that pUL77 interacts with the capsid-associated DNA packaging motor components, pUL56 and pUL104, as well as the major capsid protein. The ability of pUL77 to bind dsDNA was shown by an in vitro assay. Binding to certain DNA was further confirmed by an assay using biotinylated 36-, 250-, 500-, 1000-meric dsDNA and 966-meric HCMV-specific dsDNA designed for this study. The binding efficiency (BE) was determined by image processing program defining values above 1.0 as positive. While the BE of the pUL56 binding to the 36-mer bio-pac1 containing a packaging signal was 10.0±0.63, the one for pUL77 was only 0.2±0.03. In contrast to this observation the BE of pUL77 binding to bio-500 bp or bio-1000 bp was 2.2±0.41 and 4.9±0.71, respectively. By using pUL77ΔCCM it was demonstrated that this protein could not bind to dsDNA. These data indicated that pUL77 (i) could form homodimers, (ii) CCM of pUL77 is crucial for oligomerization and (iii) could bind to dsDNA in a sequence independent manner. PMID:21998635

[Determination of physicochemical characteristics and evaluation of decontaminating efficacy and in vitro safety of cleaning products for contact lenses].

PubMed

Simon, M; Coiffard, L J; Rivalland, P; De Roeck-Holtzhauer, Y

1996-01-01

This work aims to characterize products designed for cleaning contact lenses and particularly their physicochemical properties, their efficiency and their ocular irritancy potential compared to the main requirements of eye-washes. The physicochemical controls include pH determination, viscosity and freezing point depression. In addition, we carried out the hydrogen peroxide assay for products containing this active substance. A microbiological control was performed when opening the product and after simulation of a 21-day aging. We determined the decontaminating efficacy of the products on four bacterial strains and a fungal strain. Finally, we tested their ocular allowance by an in vitro test. The pH values obtained ranged from 3.2 (oxygenated water solutions) to 7.6. The viscosity was close to a water solution one (about 1 centipoise). The different assays showed hydrogen peroxide content similar to that stated on the package: rate averaged to 3% and was negligible after neutralization. At opening and after simulation the bacteriological quality was excellent. Finally, decontaminating efficiency against germs was very good for the products tested. The products were classified as non-irritant by the ocular irritancy test. The results obtained show that the products tested met the reference criteria, particularly eye-wash criteria.

In vivo genotoxicity assessment of acrylamide and glycidyl methacrylate.

PubMed

Dobrovolsky, Vasily N; Pacheco-Martinez, M Monserrat; McDaniel, L Patrice; Pearce, Mason G; Ding, Wei

2016-01-01

Acrylamide (ACR) and glycidyl methacrylate (GMA) are structurally related compounds used for making polymers with various properties. Both chemicals can be present in food either as a byproduct of processing or a constituent of packaging. We performed a comprehensive evaluation of ACR and GMA genotoxicity in Fisher 344 rats using repeated gavage administrations. Clastogenicity was measured by scoring micronucleated (MN) erythrocytes from peripheral blood, DNA damage in liver, bone marrow and kidneys was measured using the Comet assay, and gene mutation was measured using the red blood cell (RBC) and reticulocyte Pig-a assay. A limited histopathology evaluation was performed in order to determine levels of cytotoxicity. Doses of up to 20 mg/kg/day of ACR and up to 250 mg/kg/day of GMA were used. ACR treatment resulted in DNA damage in the liver, but not in the bone marrow. While ACR was not a clastogen, it was a weak (equivocal) mutagen in the cells of bone marrow. GMA caused DNA damage in the cells of bone marrow, liver and kidney, and induced MN reticulocytes and Pig-a mutant RBCs in a dose-dependent manner. Collectively, our data suggest that both compounds are in vivo genotoxins, but the genotoxicity of ACR is tissue specific. Published by Elsevier Ltd.

Rapid High-Throughput Assessment of Aerobic Bacteria in Complex Samples by Fluorescence-Based Oxygen Respirometry

PubMed Central

O'Mahony, Fiach C.; Papkovsky, Dmitri B.

2006-01-01

A simple method has been developed for the analysis of aerobic bacteria in complex samples such as broth and food homogenates. It employs commercial phosphorescent oxygen-sensitive probes to monitor oxygen consumption of samples containing bacteria using standard microtiter plates and fluorescence plate readers. As bacteria grow in aqueous medium, at certain points they begin to deplete dissolved oxygen, which is seen as an increase in probe fluorescence above baseline signal. The time required to reach threshold signal is used to either enumerate bacteria based on a predetermined calibration or to assess the effects of various effectors on the growth of test bacteria by comparison with an untreated control. This method allows for the sensitive (down to a single cell), rapid (0.5 to 12 h) enumeration of aerobic bacteria without the need to conduct lengthy (48 to 72 h) and tedious colony counts on agar plates. It also allows for screening a wide range of chemical and environmental samples for their toxicity. These assays have been validated with different bacteria, including Escherichia coli, Micrococcus luteus, and Pseudomonas fluorescens, with the enumeration of total viable counts in broth and industrial food samples (packaged ham, chicken, and mince meat), and comparison with established agar plating and optical-density-at-600-nm assays has been given. PMID:16461677

Neuraminidase Subtyping of Avian Influenza Viruses with PrimerHunter-Designed Primers and Quadruplicate Primer Pools

PubMed Central

Huang, Yanyan; Khan, Mazhar; Măndoiu, Ion I.

2013-01-01

We have previously developed a software package called PrimerHunter to design primers for PCR-based virus subtyping. In this study, 9 pairs of primers were designed with PrimerHunter and successfully used to differentiate the 9 neuraminidase (NA) genes of avian influenza viruses (AIVs) in multiple PCR-based assays. Furthermore, primer pools were designed and successfully used to decrease the number of reactions needed for NA subtyping from 9 to 4. The quadruplicate primer-pool method is cost-saving, and was shown to be suitable for the NA subtyping of both cultured AIVs and uncultured AIV swab samples. The primers selected for this study showed excellent sensitivity and specificity in NA subtyping by RT-PCR, SYBR green-based Real-time PCR and Real-time RT-PCR methods. AIV RNA of 2 to 200 copies (varied by NA subtypes) could be detected by these reactions. No unspecific amplification was displayed when detecting RNAs of other avian infectious viruses such as Infectious bronchitis virus, Infectious bursal disease virus and Newcastle disease virus. In summary, this study introduced several sensitive and specific PCR-based assays for NA subtyping of AIVs and also validated again the effectiveness of the PrimerHunter tool for the design of subtyping primers. PMID:24312367

In vivo mutagenicity of conazole fungicides correlates with tumorigenicity.

PubMed

Ross, Jeffrey A; Moore, Tanya; Leavitt, Sharon A

2009-03-01

Triadimefon, propiconazole and myclobutanil are conazoles, an important class of agricultural and therapeutic fungicides. Triadimefon and propiconazole are mouse liver tumorigens, while myclobutanil is not. All three conazoles are generally inactive in short-term genotoxicity tests. We studied the in vivo mutagenicity of these three conazoles using the Big Blue mouse assay system. Groups of mice were fed either control diet or diet containing 1800 p.p.m. triadimefon, 2500 p.p.m. propiconazole or 2000 p.p.m. myclobutanil. After 4 days of feeding, mice were immediately euthanized, livers were removed, DNA isolated and lacI genes recovered into infectious bacteriophage lambda particles by in vitro packaging. Bacteriophage with mutations in the lacI gene was detected by infecting into Escherichia coli, and mutant frequencies were determined using a colorimetric plaque assay. Propiconazole induced a 1.97-fold increase in mutant frequency compared to concurrent controls (P = 0.018) and triadimefon induced a 1.94-fold increase compared to concurrent controls (P = 0.009). Myclobutanil did not induce any change in mutant frequency (P = 0.548). These results provide the first evidence that the hepatotumorigenic conazoles are capable of inducing mutations in liver in vivo while the non-tumorigen myclobutanil is not, suggesting that mutagenicity may represent a key event in conazoles tumorigenic mode of action.

49 CFR 173.24a - Additional general requirements for non-bulk packagings and packages.

Code of Federal Regulations, 2010 CFR

2010-10-01

... subchapter. (b) Non-bulk packaging filling limits. (1) A single or composite non-bulk packaging may be filled... gross mass marked on the packaging. (3) A single or composite non-bulk packaging which is tested and... marked on the packaging, or 1.2 if not marked. In addition: (i) A single or composite non-bulk packaging...

49 CFR 173.24a - Additional general requirements for non-bulk packagings and packages.

Code of Federal Regulations, 2012 CFR

2012-10-01

... subchapter. (b) Non-bulk packaging filling limits. (1) A single or composite non-bulk packaging may be filled... gross mass marked on the packaging. (3) A single or composite non-bulk packaging which is tested and... marked on the packaging, or 1.2 if not marked. In addition: (i) A single or composite non-bulk packaging...

49 CFR 173.24a - Additional general requirements for non-bulk packagings and packages.

Code of Federal Regulations, 2013 CFR

2013-10-01

... subchapter. (b) Non-bulk packaging filling limits. (1) A single or composite non-bulk packaging may be filled... gross mass marked on the packaging. (3) A single or composite non-bulk packaging which is tested and... marked on the packaging, or 1.2 if not marked. In addition: (i) A single or composite non-bulk packaging...

Detecting small holes in packages

DOEpatents

Kronberg, James W.; Cadieux, James R.

1996-01-01

A package containing a tracer gas, and a method for determining the presence of a hole in the package by sensing the presence of the gas outside the package. The preferred tracer gas, especially for food packaging, is sulfur hexafluoride. A quantity of the gas is added to the package and the package is closed. The concentration of the gas in the atmosphere outside the package is measured and compared to a predetermined value of the concentration of the gas in the absence of the package. A measured concentration greater than the predetermined value indicates the presence of a hole in the package. Measuring may be done in a chamber having a lower pressure than that in the package.

Green Packaging Management of Logistics Enterprises

NASA Astrophysics Data System (ADS)

Zhang, Guirong; Zhao, Zongjian

From the connotation of green logistics management, we discuss the principles of green packaging, and from the two levels of government and enterprises, we put forward a specific management strategy. The management of green packaging can be directly and indirectly promoted by laws, regulations, taxation, institutional and other measures. The government can also promote new investment to the development of green packaging materials, and establish specialized institutions to identify new packaging materials, standardization of packaging must also be accomplished through the power of the government. Business units of large scale through the packaging and container-based to reduce the use of packaging materials, develop and use green packaging materials and easy recycling packaging materials for proper packaging.

DFP: a Bioconductor package for fuzzy profile identification and gene reduction of microarray data

PubMed Central

Glez-Peña, Daniel; Álvarez, Rodrigo; Díaz, Fernando; Fdez-Riverola, Florentino

2009-01-01

Background Expression profiling assays done by using DNA microarray technology generate enormous data sets that are not amenable to simple analysis. The greatest challenge in maximizing the use of this huge amount of data is to develop algorithms to interpret and interconnect results from different genes under different conditions. In this context, fuzzy logic can provide a systematic and unbiased way to both (i) find biologically significant insights relating to meaningful genes, thereby removing the need for expert knowledge in preliminary steps of microarray data analyses and (ii) reduce the cost and complexity of later applied machine learning techniques being able to achieve interpretable models. Results DFP is a new Bioconductor R package that implements a method for discretizing and selecting differentially expressed genes based on the application of fuzzy logic. DFP takes advantage of fuzzy membership functions to assign linguistic labels to gene expression levels. The technique builds a reduced set of relevant genes (FP, Fuzzy Pattern) able to summarize and represent each underlying class (pathology). A last step constructs a biased set of genes (DFP, Discriminant Fuzzy Pattern) by intersecting existing fuzzy patterns in order to detect discriminative elements. In addition, the software provides new functions and visualisation tools that summarize achieved results and aid in the interpretation of differentially expressed genes from multiple microarray experiments. Conclusion DFP integrates with other packages of the Bioconductor project, uses common data structures and is accompanied by ample documentation. It has the advantage that its parameters are highly configurable, facilitating the discovery of biologically relevant connections between sets of genes belonging to different pathologies. This information makes it possible to automatically filter irrelevant genes thereby reducing the large volume of data supplied by microarray experiments. Based on these contributions GENECBR, a successful tool for cancer diagnosis using microarray datasets, has recently been released. PMID:19178723

DFP: a Bioconductor package for fuzzy profile identification and gene reduction of microarray data.

PubMed

Glez-Peña, Daniel; Alvarez, Rodrigo; Díaz, Fernando; Fdez-Riverola, Florentino

2009-01-29

Expression profiling assays done by using DNA microarray technology generate enormous data sets that are not amenable to simple analysis. The greatest challenge in maximizing the use of this huge amount of data is to develop algorithms to interpret and interconnect results from different genes under different conditions. In this context, fuzzy logic can provide a systematic and unbiased way to both (i) find biologically significant insights relating to meaningful genes, thereby removing the need for expert knowledge in preliminary steps of microarray data analyses and (ii) reduce the cost and complexity of later applied machine learning techniques being able to achieve interpretable models. DFP is a new Bioconductor R package that implements a method for discretizing and selecting differentially expressed genes based on the application of fuzzy logic. DFP takes advantage of fuzzy membership functions to assign linguistic labels to gene expression levels. The technique builds a reduced set of relevant genes (FP, Fuzzy Pattern) able to summarize and represent each underlying class (pathology). A last step constructs a biased set of genes (DFP, Discriminant Fuzzy Pattern) by intersecting existing fuzzy patterns in order to detect discriminative elements. In addition, the software provides new functions and visualisation tools that summarize achieved results and aid in the interpretation of differentially expressed genes from multiple microarray experiments. DFP integrates with other packages of the Bioconductor project, uses common data structures and is accompanied by ample documentation. It has the advantage that its parameters are highly configurable, facilitating the discovery of biologically relevant connections between sets of genes belonging to different pathologies. This information makes it possible to automatically filter irrelevant genes thereby reducing the large volume of data supplied by microarray experiments. Based on these contributions GENECBR, a successful tool for cancer diagnosis using microarray datasets, has recently been released.

Human apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G (APOBEC3G) is incorporated into HIV-1 virions through interactions with viral and nonviral RNAs.

PubMed

Svarovskaia, Evguenia S; Xu, Hongzhan; Mbisa, Jean L; Barr, Rebekah; Gorelick, Robert J; Ono, Akira; Freed, Eric O; Hu, Wei-Shau; Pathak, Vinay K

2004-08-20

Apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G (APOBEC3G) is a host cytidine deaminase that is packaged into virions and confers resistance to retroviral infection. APOBEC3G deaminates deoxycytidines in minus strand DNA to deoxyuridines, resulting in G to A hypermutation and viral inactivation. Human immunodeficiency virus type 1 (HIV-1) virion infectivity factor counteracts the antiviral activity of APOBEC3G by inducing its proteosomal degradation and preventing virion incorporation. To elucidate the mechanism of viral suppression by APOBEC3G, we developed a sensitive cytidine deamination assay and analyzed APOBEC3G virion incorporation in a series of HIV-1 deletion mutants. Virus-like particles derived from constructs in which pol, env, and most of gag were deleted still contained high levels of cytidine deaminase activity; in addition, coimmunoprecipitation of APOBEC3G and HIV-1 Gag in the presence and absence of RNase A indicated that the two proteins do not interact directly but form an RNase-sensitive complex. Viral particles lacking HIV-1 genomic RNA which were generated from the gag-pol expression constructs pC-Help and pSYNGP packaged APOBEC3G at 30-40% of the wild-type level, indicating that interactions with viral RNA are not necessary for incorporation. In addition, viral particles produced from an nucleocapsid zinc finger mutant contained approximately 1% of the viral genomic RNA but approximately 30% of the cytidine deaminase activity. The reduction in APOBEC3G incorporation was equivalent to the reduction in the total RNA present in the nucleocapsid mutant virions. These results indicate that interactions with viral proteins or viral genomic RNA are not essential for APOBEC3G incorporation and suggest that APOBEC3G interactions with viral and nonviral RNAs that are packaged into viral particles are sufficient for APOBEC3G virion incorporation.

Assessment of Quality Assurance Measures for Radioactive Material Transport Packages not Requiring Competent Authority Design Approval - 13282

DOE Office of Scientific and Technical Information (OSTI.GOV)

Komann, Steffen; Groeke, Carsten; Droste, Bernhard

The majority of transports of radioactive materials are carried out in packages which don't need a package design approval by a competent authority. Low-active radioactive materials are transported in such packages e.g. in the medical and pharmaceutical industry and in the nuclear industry as well. Decommissioning of NPP's leads to a strong demand for packages to transport low and middle active radioactive waste. According to IAEA regulations the 'non-competent authority approved package types' are the Excepted Packages and the Industrial Packages of Type IP-1, IP-2 and IP-3 and packages of Type A. For these types of packages an assessment bymore » the competent authority is required for the quality assurance measures for the design, manufacture, testing, documentation, use, maintenance and inspection (IAEA SSR 6, Chap. 306). In general a compliance audit of the manufacturer of the packaging is required during this assessment procedure. Their regulatory level in the IAEA regulations is not comparable with the 'regulatory density' for packages requiring competent authority package design approval. Practices in different countries lead to different approaches within the assessment of the quality assurance measures in the management system as well as in the quality assurance program of a special package design. To use the package or packaging in a safe manner and in compliance with the regulations a management system for each phase of the life of the package or packaging is necessary. The relevant IAEA-SSR6 chap. 801 requires documentary verification by the consignor concerning package compliance with the requirements. (authors)« less

Smart packaging systems for food applications: a review.

PubMed

Biji, K B; Ravishankar, C N; Mohan, C O; Srinivasa Gopal, T K

2015-10-01

Changes in consumer preference for safe food have led to innovations in packaging technologies. This article reviews about different smart packaging systems and their applications in food packaging, packaging research with latest innovations. Active and intelligent packing are such packaging technologies which offer to deliver safer and quality products. Active packaging refers to the incorporation of additives into the package with the aim of maintaining or extending the product quality and shelf life. The intelligent systems are those that monitor the condition of packaged food to give information regarding the quality of the packaged food during transportation and storage. These technologies are designed to the increasing demand for safer foods with better shelf life. The market for active and intelligent packaging systems is expected to have a promising future by their integration into packaging materials or systems.

Detecting small holes in packages

DOEpatents

Kronberg, J.W.; Cadieux, J.R.

1996-03-19

A package containing a tracer gas, and a method for determining the presence of a hole in the package by sensing the presence of the gas outside the package are disclosed. The preferred tracer gas, especially for food packaging, is sulfur hexafluoride. A quantity of the gas is added to the package and the package is closed. The concentration of the gas in the atmosphere outside the package is measured and compared to a predetermined value of the concentration of the gas in the absence of the package. A measured concentration greater than the predetermined value indicates the presence of a hole in the package. Measuring may be done in a chamber having a lower pressure than that in the package. 3 figs.

A Review of Patents for the Smart Packaging of Meat and Muscle-based Food Products.

PubMed

Holman, Benjamin; Kerry, Joseph P; Hopkins, David L

2017-10-31

Meat packaging once acted primarily as an inert barrier to protect its contents against contamination and this function has shifted. Packaging now includes complementary functions that improve product quality, longevity and customer/retail appeal. The devices and methods applied to achieve these functions may be categorised as smart packaging, which includes intelligent packaging, devised to monitor and communicate packaged content status, and active packaging, to provide passive adjustment of in-pack conditions from its interactions with the packaged meat. Smart packaging examples already available from recent patents include antimicrobial and antioxidant packaging coatings and inserts; sensors or indicators that identify spoilage and freshness; functional engineering customisations; improvements to packaging integrity; leak or tamper detectors; and, environmentally sustainable options. Together, these inventions respond to industry and customer demands for meat packaging and are therefore the focus of this review, in which we discuss their applications and limitations in meat packaging. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Active and intelligent packaging systems for a modern society.

PubMed

Realini, Carolina E; Marcos, Begonya

2014-11-01

Active and intelligent packaging systems are continuously evolving in response to growing challenges from a modern society. This article reviews: (1) the different categories of active and intelligent packaging concepts and currently available commercial applications, (2) latest packaging research trends and innovations, and (3) the growth perspectives of the active and intelligent packaging market. Active packaging aiming at extending shelf life or improving safety while maintaining quality is progressing towards the incorporation of natural active agents into more sustainable packaging materials. Intelligent packaging systems which monitor the condition of the packed food or its environment are progressing towards more cost-effective, convenient and integrated systems to provide innovative packaging solutions. Market growth is expected for active packaging with leading shares for moisture absorbers, oxygen scavengers, microwave susceptors and antimicrobial packaging. The market for intelligent packaging is also promising with strong gains for time-temperature indicator labels and advancements in the integration of intelligent concepts into packaging materials. Copyright © 2014 Elsevier Ltd. All rights reserved.

A magnetic induction heating system with multi-cascaded coils and adjustable magnetic circuit for hyperthermia.

PubMed

Huang, Chi-Fang; Chao, Hsuan-Yi; Chang, Hsun-Hao; Lin, Xi-Zhang

2016-01-01

Based on the characteristics of cancer cells that cannot survive in an environment with temperature over 42 °C, a magnetic induction heating system for cancer treatment is developed in this work. First, the methods and analyses for designing the multi-cascaded coils magnetic induction hyperthermia system are proposed, such as internal impedance measurement of power generator, impedance matching of coils, and analysis of the system. Besides, characteristics of the system are simulated by a full-wave package for engineering optimization. Furthermore, by considering the safety factor of patients, a two-sectional needle is designed for hyperthermia. Finally, this system is employed to test the liver of swine in ex-vivo experiments, and through Hematoxylin and Eosin (H&E) stain and NADPH oxidase activity assay, the feasibility of this system is verified.

CRAVE: a database, middleware and visualization system for phenotype ontologies.

PubMed

Gkoutos, Georgios V; Green, Eain C J; Greenaway, Simon; Blake, Andrew; Mallon, Ann-Marie; Hancock, John M

2005-04-01

A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies. CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches.

Packaging and Embedded Electronics for the Next Generation

NASA Technical Reports Server (NTRS)

Sampson, Michael J.

2010-01-01

This viewgraph presentation describes examples of electronic packaging that protects an electronic element from handling, contamination, shock, vibration and light penetration. The use of Hermetic and non-hermetic packaging is also discussed. The topics include: 1) What is Electronic Packaging? 2) Why Package Electronic Parts? 3) Evolution of Packaging; 4) General Packaging Discussion; 5) Advanced non-hermetic packages; 6) Discussion of Hermeticity; 7) The Class Y Concept and Possible Extensions; 8) Embedded Technologies; and 9) NEPP Activities.

Packaging Your Training Materials

ERIC Educational Resources Information Center

Espeland, Pamela

1977-01-01

The types of packaging and packaging materials to use for training materials should be determined during the planning of the training programs, according to the packaging market. Five steps to follow in shopping for packaging are presented, along with a list of packaging manufacturers. (MF)

Current topics in active and intelligent food packaging for preservation of fresh foods.

PubMed

Lee, Seung Yuan; Lee, Seung Jae; Choi, Dong Soo; Hur, Sun Jin

2015-11-01

The purpose of this review is to provide an overview of current packaging systems, e.g. active packaging and intelligent packaging, for various foods. Active packaging, such as modified atmosphere packaging (MAP), extends the shelf life of fresh produce, provides a high-quality product, reduces economic losses, including those caused by delay of ripening, and improves appearance. However, in active packaging, several variables must be considered, such as temperature control and different gas formulations with different product types and microorganisms. Active packaging refers to the incorporation of additive agents into packaging materials with the purpose of maintaining or extending food product quality and shelf life. Intelligent packaging is emerging as a potential advantage in food processing and is an especially useful tool for tracking product information and monitoring product conditions. Moreover, intelligent packaging facilitates data access and information exchange by altering conditions inside or outside the packaging and product. In spite of these advantages, few of these packaging systems are commercialized because of high cost, strict safety and hygiene regulations or limited consumer acceptance. Therefore more research is needed to develop cheaper, more easily applicable and effective packaging systems for various foods. © 2015 Society of Chemical Industry.

Color stability of ground beef packaged in a low carbon monoxide atmosphere or vacuum.

PubMed

Jeong, Jong Youn; Claus, James R

2011-01-01

Ground beef was either packaged in an atmosphere of 0.4% CO, 30% CO₂, and 69.6% N₂ (CO-MAP) or vacuum. After storage (48 h, 2-3°C), packages of CO-MAP and vacuum were opened and overwrapped with polyvinyl chloride. Other CO-MAP and vacuum packages were left intact. Packages were initially displayed for 7 days (2-3°C). Intact packages were further displayed up to 35 days before being opened and displayed (1 or 3 days). Intact CO-MAP packaged ground beef was always more red than intact vacuum-packaged ground beef. Color was relatively stable for both types of intact packages over 35 days of display. Upon opening CO-MAP packaged ground beef, the red color decreased slower than in ground beef from vacuum packages. Published by Elsevier Ltd.

Packaging Concerns and Techniques for Large Devices: Challenges for Complex Electronics

NASA Technical Reports Server (NTRS)

LaBel, Kenneth A.; Sampson, Michael J.

2010-01-01

NASA is going to have to accept the use of non-hermetic packages for complex devices. There are a large number of packaging options available. Space application subjects the packages to stresses that they were probably not designed for (vacuum for instance). NASA has to find a way of having assurance in the integrity of the packages. There are manufacturers interested in qualifying non-hermetic packages to MIL-PRF-38535 Class V. Government space users are agreed that Class V should be for hermetic packages only. NASA is working on a new Class for non-hermetic packages for M38535 Appendix B, "Class Y". Testing for package integrity will be required but can be package specific as described by a Package Integrity Test Plan. The plan is developed by the manufacturer and approved by DSCC and government space.

Molecular Characterization and Development of Real-Time PCR Assay for Pine-Wood Nematode Bursaphelenchus xylophilus (Nematoda: Parasitaphelenchidae)

PubMed Central

Ye, Weimin; Giblin-Davis, Robin M.

2013-01-01

Bursaphelenchus xylophilus, the pine-wood nematode (PWN), is the causal agent of pine wilt disease, one of the most damaging emerging pest problems to forests around the world. It is native to North America where it causes relatively minor damage to native conifers but is labeled an EPPO-A-2 pest and a quarantine nematode for many countries outside of the United States because of its potential for destruction to their native conifers. Exports of wood logs and commodities involving softwood packaging materials now require a lab test for the presence/absence of this regulated nematode species. We characterized the DNA sequences on the ribosomal DNA small subunit, large subunit D2/D3, internal transcribed spacer (ITS) and mitochondrial DNA cytochrome oxidase subunit one on the aphelenchid species and described the development of a real-time-PCR method for rapid and accurate identification of PWN targeting the ITS-1. A total of 97 nematode populations were used to evaluate the specificity and sensitivity of this assay, including 45 populations of B. xylophilus and 36 populations of 21 other species of Bursaphelenchus which belong to the abietinus, cocophilus, eggersi, fungivorus, hofmanni, kevini, leoni, sexdentati, and xylophilus groups and one unassigned group from a total of 13 groups in the genus Bursaphelenchus; 15 populations of Aphelenchoides besseyi, A. fragariae, Aphelenchoides species and Aphelenchus avenae; and one population of mixed nematode species from a soil sample. This assay proved to be specific to B. xylophilus only and was sensitive to a single nematode specimen regardless of the life stages present. This approach provides rapid species identification necessary to comply with the zero-tolerance export regulations. PMID:24244367

19 CFR 191.13 - Packaging materials.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 19 Customs Duties 2 2010-04-01 2010-04-01 false Packaging materials. 191.13 Section 191.13 Customs... (CONTINUED) DRAWBACK General Provisions § 191.13 Packaging materials. (a) Imported packaging material... packaging material when used to package or repackage merchandise or articles exported or destroyed pursuant...

49 CFR 178.905 - Large Packaging identification codes.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Large Packaging identification codes. 178.905... FOR PACKAGINGS Large Packagings Standards § 178.905 Large Packaging identification codes. Large packaging code designations consist of: two numerals specified in paragraph (a) of this section; followed by...

Advancements in meat packaging.

PubMed

McMillin, Kenneth W

2017-10-01

Packaging of meat provides the same or similar benefits for raw chilled and processed meats as other types of food packaging. Although air-permeable packaging is most prevalent for raw chilled red meat, vacuum and modified atmosphere packaging offer longer shelf life. The major advancements in meat packaging have been in the widely used plastic polymers while biobased materials and their integration into composite packaging are receiving much attention for functionality and sustainability. At this time, active and intelligent packaging are not widely used for antioxidant, antimicrobial, and other functions to stabilize and enhance meat properties although many options are being developed and investigated. The advances being made in nanotechnology will be incorporated into food packaging and presumably into meat packaging when appropriate and useful. Intelligent packaging using sensors for transmission of desired information and prompting of subsequent changes in packaging materials, environments or the products to maintain safety and quality are still in developmental stages. Copyright © 2017 Elsevier Ltd. All rights reserved.

Packaging Concerns/Techniques for Large Devices

NASA Technical Reports Server (NTRS)

Sampson, Michael J.

2009-01-01

This slide presentation reviews packaging challenges and options for electronic parts. The presentation includes information about non-hermetic packages, space challenges for packaging and complex package variations.

Stability Studies of a Freeze-Dried Recombinant Human Epidermal Growth Factor Formulation for Wound Healing.

PubMed

Santana, Héctor; García, Gerardo; Vega, Maribel; Beldarraín, Alejandro; Páez, Rolando

2015-01-01

We report on the stability assessment of a recombinant human epidermal growth factor (rhEGF) freeze-dried formulation for wound healing by intra-lesional injections. The suitability of packaging material for the light protection of finished dried powder was evaluated after stressed exposure conditions. Degradation kinetics of powder for injection was investigated at concentrations of 25-250 μg/vial and temperatures of 45, 60, and 70 °C. The long-term stability was evaluated after storage at 25 ± 2 °C/60 ± 5% relative humidity (6 months) and 2-8 °C (24 months) in the dark and analyzed at several time points. The stability after reconstitution with various diluents was also assessed after 24 h storage at 2-8 °C. The rhEGF samples were analyzed for structural integrity by reversed-phase high-performance liquid chromatography (RP-HPLC), size-exclusion HPLC, and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Biological activity was investigated by measuring the cell proliferation in a murine fibroblast cell line. Results show that freeze-dried rhEGF in primary packaging only was photosensitive, as degradation by RP-HPLC that was completely suppressed by the secondary carton package was revealed. An increase in freeze-dried rhEGF stability was observed with the increase in protein concentration from 25 to 250 μg/vial. The long-term stability study showed no significant rhEGF degradation or physical change within the freeze-dried formulations containing 25 or 250 μg/vial of rhEGF. No physical, chemical or biological changes were observed for rhEGF after reconstitution in water for injection or 0.9% sodium chloride during the storage conditions studied. The stability of a recombinant human epidermal growth factor (rhEGF) freeze-dried formulation for wound healing by intra-lesional injections was assessed. The suitability of packaging material for the light protection of finished dried powder was evaluated after stressed exposure conditions. Degradation kinetics of powder for injection was investigated at concentrations of 25-250 μg/vial and temperatures of 45, 60, and 70 °C. The accelerated, long-term, and reconstitution stabilities were examined according to ICH guidelines for their utility time. The stability of rhEGF samples was analyzed by different chemical, physical, and biological activity assays. Results show that freeze-dried rhEGF in primary packaging only was photosensitive, as degradation by reversed-phase high performance liquid chromatography that was completely suppressed by the secondary carton package was revealed. An increase in freeze-dried rhEGF stability was observed with the increase in protein concentration. No significant rhEGF degradation or physical changes were observed within the freeze-dried formulations after 6 months storage at 25 ± 2 °C/60 ± 5% relative humidity or 24 months storage at 2-8 °C. No physical, chemical, or biological changes were observed for rhEGF after reconstitution in water for injection or 0.9% sodium chloride after 24 h storage at 2-8 °C. © PDA, Inc. 2015.

Transformation of food packaging from passive to innovative via nanotechnology: concepts and critiques.

PubMed

Mlalila, Nichrous; Kadam, Dattatreya M; Swai, Hulda; Hilonga, Askwar

2016-09-01

In recent decades, there is a global advancement in manufacturing industry due to increased applications of nanotechnology. Food industry also has been tremendously changing from passive packaging to innovative packaging, to cope with global trends, technological advancements, and consumer preferences. Active research is taking place in food industry and other scientific fields to develop innovative packages including smart, intelligent and active food packaging for more effective and efficient packaging materials with balanced environmental issues. However, in food industry the features behind smart packaging are narrowly defined to be distinguished from intelligent packaging as in other scientific fields, where smart materials are under critical investigations. This review presents some scientific concepts and features pertaining innovative food packaging. The review opens new research window in innovative food packaging to cover the existing disparities for further precise research and development of food packaging industry.

IFT Scientific Status Summary 2008: Innovative Food Packaging Solutions

USDA-ARS?s Scientific Manuscript database

Food and beverage packaging comprises 55-65% of the $110 billion value of packaging in the United States. This review provides a summary of innovative technology developments in food packaging. The expanded role of food and beverage packaging is reviewed. Active and intelligent food packaging, ba...

49 CFR 178.920 - Standards for metal Large Packagings.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 3 2011-10-01 2011-10-01 false Standards for metal Large Packagings. 178.920... PACKAGINGS Large Packagings Standards § 178.920 Standards for metal Large Packagings. (a) The provisions in this section apply to metal Large Packagings intended to contain liquids and solids. Metal Large...

49 CFR 178.920 - Standards for metal Large Packagings.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Standards for metal Large Packagings. 178.920... FOR PACKAGINGS Large Packagings Standards § 178.920 Standards for metal Large Packagings. (a) The provisions in this section apply to metal Large Packagings intended to contain liquids and solids. Metal...

78 FR 17890 - Energy Efficiency Program for Commercial and Industrial Equipment: Public Meeting and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-25

... Document for Packaged Terminal Air Conditioners and Packaged Terminal Heat Pumps AGENCY: Office of Energy... must identify the framework document for packaged terminal air conditioners and packaged terminal heat... packaged terminal air conditioners and packaged terminal heat pumps. 78 FR 12252. The document provided for...

49 CFR 178.925 - Standards for rigid plastic Large Packagings.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 3 2011-10-01 2011-10-01 false Standards for rigid plastic Large Packagings. 178... FOR PACKAGINGS Large Packagings Standards § 178.925 Standards for rigid plastic Large Packagings. (a) The provisions in this section apply to rigid plastic Large Packagings intended to contain liquids and...

49 CFR 178.925 - Standards for rigid plastic Large Packagings.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 3 2012-10-01 2012-10-01 false Standards for rigid plastic Large Packagings. 178... FOR PACKAGINGS Large Packagings Standards § 178.925 Standards for rigid plastic Large Packagings. (a) The provisions in this section apply to rigid plastic Large Packagings intended to contain liquids and...

49 CFR 178.925 - Standards for rigid plastic Large Packagings.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 3 2014-10-01 2014-10-01 false Standards for rigid plastic Large Packagings. 178... FOR PACKAGINGS Large Packagings Standards § 178.925 Standards for rigid plastic Large Packagings. (a) The provisions in this section apply to rigid plastic Large Packagings intended to contain liquids and...

49 CFR 178.925 - Standards for rigid plastic Large Packagings.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 3 2013-10-01 2013-10-01 false Standards for rigid plastic Large Packagings. 178... FOR PACKAGINGS Large Packagings Standards § 178.925 Standards for rigid plastic Large Packagings. (a) The provisions in this section apply to rigid plastic Large Packagings intended to contain liquids and...

49 CFR 178.350 - Specification 7A; general packaging, Type A.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Specification 7A; general packaging, Type A. 178... FOR PACKAGINGS Specifications for Packagings for Class 7 (Radioactive) Materials § 178.350 Specification 7A; general packaging, Type A. (a) Each packaging must meet all applicable requirements of subpart...

Package for integrated optic circuit and method

DOEpatents

Kravitz, Stanley H.; Hadley, G. Ronald; Warren, Mial E.; Carson, Richard F.; Armendariz, Marcelino G.

1998-01-01

A structure and method for packaging an integrated optic circuit. The package comprises a first wall having a plurality of microlenses formed therein to establish channels of optical communication with an integrated optic circuit within the package. A first registration pattern is provided on an inside surface of one of the walls of the package for alignment and attachment of the integrated optic circuit. The package in one embodiment may further comprise a fiber holder for aligning and attaching a plurality of optical fibers to the package and extending the channels of optical communication to the fibers outside the package. In another embodiment, a fiber holder may be used to hold the fibers and align the fibers to the package. The fiber holder may be detachably connected to the package.

Package for integrated optic circuit and method

DOEpatents

Kravitz, S.H.; Hadley, G.R.; Warren, M.E.; Carson, R.F.; Armendariz, M.G.

1998-08-04

A structure and method are disclosed for packaging an integrated optic circuit. The package comprises a first wall having a plurality of microlenses formed therein to establish channels of optical communication with an integrated optic circuit within the package. A first registration pattern is provided on an inside surface of one of the walls of the package for alignment and attachment of the integrated optic circuit. The package in one embodiment may further comprise a fiber holder for aligning and attaching a plurality of optical fibers to the package and extending the channels of optical communication to the fibers outside the package. In another embodiment, a fiber holder may be used to hold the fibers and align the fibers to the package. The fiber holder may be detachably connected to the package. 6 figs.

Technical Review Report for the Model 9978-96 Package Safety Analysis Report for Packaging (S-SARP-G-00002, Revision 1, March 2009)

DOE Office of Scientific and Technical Information (OSTI.GOV)

West, M

2009-03-06

This Technical Review Report (TRR) documents the review, performed by Lawrence Livermore National Laboratory (LLNL) Staff, at the request of the Department of Energy (DOE), on the 'Safety Analysis Report for Packaging (SARP), Model 9978 B(M)F-96', Revision 1, March 2009 (S-SARP-G-00002). The Model 9978 Package complies with 10 CFR 71, and with 'Regulations for the Safe Transport of Radioactive Material-1996 Edition (As Amended, 2000)-Safety Requirements', International Atomic Energy Agency (IAEA) Safety Standards Series No. TS-R-1. The Model 9978 Packaging is designed, analyzed, fabricated, and tested in accordance with Section III of the American Society of Mechanical Engineers Boiler and Pressuremore » Vessel Code (ASME B&PVC). The review presented in this TRR was performed using the methods outlined in Revision 3 of the DOE's 'Packaging Review Guide (PRG) for Reviewing Safety Analysis Reports for Packages'. The format of the SARP follows that specified in Revision 2 of the Nuclear Regulatory Commission's Regulatory Guide 7.9, i.e., 'Standard Format and Content of Part 71 Applications for Approval of Packages for Radioactive Material'. Although the two documents are similar in their content, they are not identical. Formatting differences have been noted in this TRR, where appropriate. The Model 9978 Packaging is a single containment package, using a 5-inch containment vessel (5CV). It uses a nominal 35-gallon drum package design. In comparison, the Model 9977 Packaging uses a 6-inch containment vessel (6CV). The Model 9977 and Model 9978 Packagings were developed concurrently, and they were referred to as the General Purpose Fissile Material Package, Version 1 (GPFP). Both packagings use General Plastics FR-3716 polyurethane foam as insulation and as impact limiters. The 5CV is used as the Primary Containment Vessel (PCV) in the Model 9975-96 Packaging. The Model 9975-96 Packaging also has the 6CV as its Secondary Containment Vessel (SCV). In comparison, the Model 9975 Packagings use Celotex{trademark} for insulation and as impact limiters. To provide a historical perspective, it is noted that the Model 9975-96 Packaging is a 35-gallon drum package design that has evolved from a family of packages designed by DOE contractors at the Savannah River Site. Earlier package designs, i.e., the Model 9965, the Model 9966, the Model 9967, and the Model 9968 Packagings, were originally designed and certified in the early 1980s. In the 1990s, updated package designs that incorporated design features consistent with the then-newer safety requirements were proposed. The updated package designs at the time were the Model 9972, the Model 9973, the Model 9974, and the Model 9975 Packagings, respectively. The Model 9975 Package was certified by the Packaging Certification Program, under the Office of Safety Management and Operations. The Model 9978 Package has six Content Envelopes: C.1 ({sup 238}Pu Heat Sources), C.2 ( Pu/U Metals), C.3 (Pu/U Oxides, Reserved), C.4 (U Metal or Alloy), C.5 (U Compounds), and C.6 (Samples and Sources). Per 10 CFR 71.59 (Code of Federal Regulations), the value of N is 50 for the Model 9978 Package leading to a Criticality Safety Index (CSI) of 1.0. The Transport Index (TI), based on dose rate, is calculated to be a maximum of 4.1.« less

49 CFR 173.24 - General requirements for packagings and packages.

Code of Federal Regulations, 2011 CFR

2011-10-01

...) New packagings and packagings which are reused; and (3) Specification and non-specification packagings..., sufficient ullage (outage) must be left to ensure that neither leakage nor permanent distortion of the...

mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data

PubMed Central

Larralde, Martin; Lawson, Thomas N.; Weber, Ralf J. M.; Moreno, Pablo; Haug, Kenneth; Rocca-Serra, Philippe; Viant, Mark R.; Steinbeck, Christoph; Salek, Reza M.

2017-01-01

Abstract Summary Submission to the MetaboLights repository for metabolomics data currently places the burden of reporting instrument and acquisition parameters in ISA-Tab format on users, who have to do it manually, a process that is time consuming and prone to user input error. Since the large majority of these parameters are embedded in instrument raw data files, an opportunity exists to capture this metadata more accurately. Here we report a set of Python packages that can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files. The parsing packages are separated into mzML2ISA (encompassing mzML and imzML formats) and nmrML2ISA (nmrML format only). Overall, the use of mzML2ISA & nmrML2ISA reduces the time needed to capture metadata substantially (capturing 90% of metadata on assay and sample levels), is much less prone to user input errors, improves compliance with minimum information reporting guidelines and facilitates more finely grained data exploration and querying of datasets. Availability and Implementation mzML2ISA & nmrML2ISA are available under version 3 of the GNU General Public Licence at https://github.com/ISA-tools. Documentation is available from http://2isa.readthedocs.io/en/latest/. Contact reza.salek@ebi.ac.uk or isatools@googlegroups.com Supplementary information Supplementary data are available at Bioinformatics online. PMID:28402395

mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.

PubMed

Larralde, Martin; Lawson, Thomas N; Weber, Ralf J M; Moreno, Pablo; Haug, Kenneth; Rocca-Serra, Philippe; Viant, Mark R; Steinbeck, Christoph; Salek, Reza M

2017-08-15

Submission to the MetaboLights repository for metabolomics data currently places the burden of reporting instrument and acquisition parameters in ISA-Tab format on users, who have to do it manually, a process that is time consuming and prone to user input error. Since the large majority of these parameters are embedded in instrument raw data files, an opportunity exists to capture this metadata more accurately. Here we report a set of Python packages that can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files. The parsing packages are separated into mzML2ISA (encompassing mzML and imzML formats) and nmrML2ISA (nmrML format only). Overall, the use of mzML2ISA & nmrML2ISA reduces the time needed to capture metadata substantially (capturing 90% of metadata on assay and sample levels), is much less prone to user input errors, improves compliance with minimum information reporting guidelines and facilitates more finely grained data exploration and querying of datasets. mzML2ISA & nmrML2ISA are available under version 3 of the GNU General Public Licence at https://github.com/ISA-tools. Documentation is available from http://2isa.readthedocs.io/en/latest/. reza.salek@ebi.ac.uk or isatools@googlegroups.com. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Rapid Reconstitution Packages (RRPs) implemented by integration of computational fluid dynamics (CFD) and 3D printed microfluidics.

PubMed

Chi, Albert; Curi, Sebastian; Clayton, Kevin; Luciano, David; Klauber, Kameron; Alexander-Katz, Alfredo; D'hers, Sebastian; Elman, Noel M

2014-08-01

Rapid Reconstitution Packages (RRPs) are portable platforms that integrate microfluidics for rapid reconstitution of lyophilized drugs. Rapid reconstitution of lyophilized drugs using standard vials and syringes is an error-prone process. RRPs were designed using computational fluid dynamics (CFD) techniques to optimize fluidic structures for rapid mixing and integrating physical properties of targeted drugs and diluents. Devices were manufactured using stereo lithography 3D printing for micrometer structural precision and rapid prototyping. Tissue plasminogen activator (tPA) was selected as the initial model drug to test the RRPs as it is unstable in solution. tPA is a thrombolytic drug, stored in lyophilized form, required in emergency settings for which rapid reconstitution is of critical importance. RRP performance and drug stability were evaluated by high-performance liquid chromatography (HPLC) to characterize release kinetics. In addition, enzyme-linked immunosorbent assays (ELISAs) were performed to test for drug activity after the RRPs were exposed to various controlled temperature conditions. Experimental results showed that RRPs provided effective reconstitution of tPA that strongly correlated with CFD results. Simulation and experimental results show that release kinetics can be adjusted by tuning the device structural dimensions and diluent drug physical parameters. The design of RRPs can be tailored for a number of applications by taking into account physical parameters of the active pharmaceutical ingredients (APIs), excipients, and diluents. RRPs are portable platforms that can be utilized for reconstitution of emergency drugs in time-critical therapies.

Clinical grade adult stem cell banking

PubMed Central

Thirumala, Sreedhar; Goebel, W Scott

2009-01-01

There has been a great deal of scientific interest recently generated by the potential therapeutic applications of adult stem cells in human care but there are several challenges regarding quality and safety in clinical applications and a number of these challenges relate to the processing and banking of these cells ex-vivo. As the number of clinical trials and the variety of adult cells used in regenerative therapy increases, safety remains a primary concern. This has inspired many nations to formulate guidelines and standards for the quality of stem cell collection, processing, testing, banking, packaging and distribution. Clinically applicable cryopreservation and banking of adult stem cells offers unique opportunities to advance the potential uses and widespread implementation of these cells in clinical applications. Most current cryopreservation protocols include animal serum proteins and potentially toxic cryoprotectant additives (CPAs) that prevent direct use of these cells in human therapeutic applications. Long term cryopreservation of adult stem cells under good manufacturing conditions using animal product free solutions is critical to the widespread clinical implementation of ex-vivo adult stem cell therapies. Furthermore, to avoid any potential cryoprotectant related complications, reduced CPA concentrations and efficient post-thaw washing to remove CPA are also desirable. The present review focuses on the current strategies and important aspects of adult stem cell banking for clinical applications. These include current good manufacturing practices (cGMPs), animal protein free freezing solutions, cryoprotectants, freezing & thawing protocols, viability assays, packaging and distribution. The importance and benefits of banking clinical grade adult stem cells are also discussed. PMID:20046678

Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data.

PubMed

Li, Wenyuan; Gong, Ke; Li, Qingjiao; Alber, Frank; Zhou, Xianghong Jasmine

2015-03-15

Genome-wide proximity ligation assays, e.g. Hi-C and its variant TCC, have recently become important tools to study spatial genome organization. Removing biases from chromatin contact matrices generated by such techniques is a critical preprocessing step of subsequent analyses. The continuing decline of sequencing costs has led to an ever-improving resolution of the Hi-C data, resulting in very large matrices of chromatin contacts. Such large-size matrices, however, pose a great challenge on the memory usage and speed of its normalization. Therefore, there is an urgent need for fast and memory-efficient methods for normalization of Hi-C data. We developed Hi-Corrector, an easy-to-use, open source implementation of the Hi-C data normalization algorithm. Its salient features are (i) scalability-the software is capable of normalizing Hi-C data of any size in reasonable times; (ii) memory efficiency-the sequential version can run on any single computer with very limited memory, no matter how little; (iii) fast speed-the parallel version can run very fast on multiple computing nodes with limited local memory. The sequential version is implemented in ANSI C and can be easily compiled on any system; the parallel version is implemented in ANSI C with the MPI library (a standardized and portable parallel environment designed for solving large-scale scientific problems). The package is freely available at http://zhoulab.usc.edu/Hi-Corrector/. © The Author 2014. Published by Oxford University Press.

Curcumin inhibits in vitro and in vivo chronic myelogenous leukemia cells growth: a possible role for exosomal disposal of miR-21

PubMed Central

Taverna, Simona; Giallombardo, Marco; Pucci, Marzia; Flugy, Anna; Manno, Mauro; Raccosta, Samuele; Rolfo, Christian; De Leo, Giacomo; Alessandro, Riccardo

2015-01-01

Exosomes are nanosize vesicles released from cancer cells containing microRNAs that can influence gene expression in target cells. Curcumin has been shown to exhibit antitumor activities in a wide spectrum of human cancer. The addition of Curcumin, to Chronic Myelogenous Leukemia (CML) cells, caused a dose-dependent increase of PTEN, target of miR-21. Curcumin treatment also decreased AKT phosphorylation and VEGF expression and release. Colony formation assays indicated that Curcumin affects the survival of CML cells. Some observation suggest a possible cellular disposal of miRNAs by exosomes. To elucidate if Curcumin caused a decrease of miR-21 in CML cells and its packaging in exosomes, we analyzed miR-21 content in K562 and LAMA84 cells and exosomes, after treatment with Curcumin. Furthermore, we showed that addition of Curcumin to CML cells caused a downregulation of Bcr-Abl expression through the cellular increase of miR-196b. The effects of Curcumin was then investigated on a CML xenograft in SCID mice. We observed that animals treated with Curcumin, developed smaller tumors compared to mice control. Real time PCR analysis showed that exosomes, released in the plasma of the Curcumin-treated mice, were enriched in miR-21 with respect control. Taken together, our results suggested that a selective packaging of miR-21 in exosomes may contribute to the antileukemic effect of Curcumin in CML. PMID:26116834

On the Rocks: Microbiological Quality and Microbial Diversity of Packaged Ice in Southern California.

PubMed

Lee, Kun Ho; Ab Samad, Liana S; Lwin, Phillip M; Riedel, Stefan F; Magin, Ashley; Bashir, Mina; Vaishampayan, Parag A; Lin, Wei-Jen

2017-06-01

Ice is defined as a food and is frequently used in direct contact with food and beverages. Packaged ice is commercially produced and can be easily found in grocery and convenience stores. However, the quality and safety of packaged ice products is not consistent. The Packaged Ice Quality Control Standards manual (PIQCS) published by the International Packaged Ice Association provides the quality and processing standards for packaged ice produced by its members. Packaged ice produced on the premise of stores (on-site packaged ice) is not required to be in compliance with these standards. In this study, packaged ice produced by manufacturing plants or by in-store bagger (ISB) machines and on-site packaged ice were compared for their microbiological quality and microbial diversity. Our results revealed that 19% of the 120 on-site packaged ice samples did not meet the PIQCS microbial limit of 500 CFU/mL (or g) and also the absence of coliforms and Escherichia coli . Staphylococci were found in 34% of the on-site packaged ice samples, most likely through contamination from the packaging workers. None of the ISB and manufactured packaged ice samples had unacceptable microbial levels, and all were devoid of staphylococci. Salmonella was absent in all samples analyzed in this study. Microbial community analysis of ice based on 16S/18S rRNA targeted sequencing revealed a much higher microbial diversity and abundance in the on-site packaged ice than in the ISB ice. Proteobacteria, especially Alphaproteobacteria and Betaproteobacteria, were the dominant bacterial groups in all samples tested. Most of these bacteria were oligotrophic; however, a few opportunistic or potential pathogens were found at low levels in the on-site packaged ice but not in the ISB packaged ice. The types of microbes identified may provide information needed to investigate potential sources of contamination. Our data also suggest a need for enforcement of processing standards during the on-site packaging of ice.

Food packages for Space Shuttle

NASA Technical Reports Server (NTRS)

Fohey, M. F.; Sauer, R. L.; Westover, J. B.; Rockafeller, E. F.

1978-01-01

The paper reviews food packaging techniques used in space flight missions and describes the system developed for the Space Shuttle. Attention is directed to bite-size food cubes used in Gemini, Gemini rehydratable food packages, Apollo spoon-bowl rehydratable packages, thermostabilized flex pouch for Apollo, tear-top commercial food cans used in Skylab, polyethylene beverage containers, Skylab rehydratable food package, Space Shuttle food package configuration, duck-bill septum rehydration device, and a drinking/dispensing nozzle for Space Shuttle liquids. Constraints and testing of packaging is considered, a comparison of food package materials is presented, and typical Shuttle foods and beverages are listed.

Re-design of apple pia packaging using quality function deployment method

NASA Astrophysics Data System (ADS)

Pulungan, M. H.; Nadira, N.; Dewi, I. A.

2018-03-01

This study was aimed to identify the attributes for premium apple pia packaging, to determine the technical response to be carried out by Permata Agro Mandiri Small and Medium Enterprise (SME) and to design a new apple pie packaging acceptable by the SME. The Quality Function Deployment (QFD) method was employed to improve the apple pia packaging design, which consisted of seven stages in data analysis. The results indicated that whats attribute required by the costumers include graphic design, dimensions, capacity, shape, strength, and resistance of packaging. While, the technical responses to be conducted by the SMEs were as follows: attractive visual packaging designs, attractive colors, clear images and information, packaging size dimensions, a larger capacity packaging (more product content), ergonomic premium packaging, not easily torn, and impact resistant packaging materials. The findings further confirmed that the design of premium apple pia packaging accepted by the SMES was the one with the capacity of ten apple pia or 200 g weight, and with rectangular or beam shape form. The packaging material used was a duplex carton with 400 grammage (g/m2), the outer part of the packaging was coated with plastic and the inside was added with duplex carton. The acceptable packaging dimension was 30 cm x 5 cm x 3 cm (L x W x H) with a mix of black and yellow color in the graphical design.

Child-resistant and tamper-resistant packaging: A systematic review to inform tobacco packaging regulation.

PubMed

Jo, Catherine L; Ambs, Anita; Dresler, Carolyn M; Backinger, Cathy L

2017-02-01

We aimed to investigate the effects of special packaging (child-resistant, adult-friendly) and tamper-resistant packaging on health and behavioral outcomes in order to identify research gaps and implications for packaging standards for tobacco products. We searched seven databases for keywords related to special and tamper-resistant packaging, consulted experts, and reviewed citations of potentially relevant studies. 733 unique papers were identified. Two coders independently screened each title and abstract for eligibility. They then reviewed the full text of the remaining papers for a second round of eligibility screening. Included studies investigated a causal relationship between type of packaging or packaging regulation and behavioral or health outcomes and had a study population composed of consumers. Studies were excluded on the basis of publication type, if they were not peer-reviewed, and if they had low external validity. Two reviewers independently coded each paper for study and methodological characteristics and limitations. Discrepancies were discussed and resolved. The review included eight studies: four assessing people's ability to access the contents of different packaging types and four evaluating the impact of packaging requirements on health-related outcomes. Child-resistant packaging was generally more difficult to open than non-child-resistant packaging. Child-resistant packaging requirements have been associated with reductions in child mortality. Child-resistant packaging holds the expectation to reduce tobacco product poisonings among children under six. Published by Elsevier Inc.

Child-resistant and tamper-resistant packaging: A systematic review to inform tobacco packaging regulation

PubMed Central

Jo, Catherine L.; Ambs, Anita; Dresler, Carolyn M.; Backinger, Cathy L.

2017-01-01

Objective We aimed to investigate the effects of special packaging (child-resistant, adult-friendly) and tamper-resistant packaging on health and behavioral outcomes in order to identify research gaps and implications for packaging standards for tobacco products. Methods We searched seven databases for keywords related to special and tamper-resistant packaging, consulted experts, and reviewed citations of potentially relevant studies. 733 unique papers were identified. Two coders independently screened each title and abstract for eligibility. They then reviewed the full text of the remaining papers for a second round of eligibility screening. Included studies investigated a causal relationship between type of packaging or packaging regulation and behavioral or health outcomes and had a study population composed of consumers. Studies were excluded on the basis of publication type, if they were not peer-reviewed, and if they had low external validity. Two reviewers independently coded each paper for study and methodological characteristics and limitations. Discrepancies were discussed and resolved. Results The review included eight studies: four assessing people’s ability to access the contents of different packaging types and four evaluating the impact of packaging requirements on health-related outcomes. Child-resistant packaging was generally more difficult to open than non-child-resistant packaging. Child-resistant packaging requirements have been associated with reductions in child mortality. Conclusions Child-resistant packaging holds the expectation to reduce tobacco product poisonings among children under six. PMID:27939602

49 CFR 173.459 - Mixing of fissile material packages with non-fissile or fissile-excepted material packages.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 2 2012-10-01 2012-10-01 false Mixing of fissile material packages with non... (Radioactive) Materials § 173.459 Mixing of fissile material packages with non-fissile or fissile-excepted material packages. Mixing of fissile material packages with other types of Class 7 (radioactive) materials...

49 CFR 173.459 - Mixing of fissile material packages with non-fissile or fissile-excepted material packages.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 2 2013-10-01 2013-10-01 false Mixing of fissile material packages with non... (Radioactive) Materials § 173.459 Mixing of fissile material packages with non-fissile or fissile-excepted material packages. Mixing of fissile material packages with other types of Class 7 (radioactive) materials...

49 CFR 173.459 - Mixing of fissile material packages with non-fissile or fissile-excepted material packages.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 2 2011-10-01 2011-10-01 false Mixing of fissile material packages with non... (Radioactive) Materials § 173.459 Mixing of fissile material packages with non-fissile or fissile-excepted material packages. Mixing of fissile material packages with other types of Class 7 (radioactive) materials...

49 CFR 173.459 - Mixing of fissile material packages with non-fissile or fissile-excepted material packages.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Mixing of fissile material packages with non... (Radioactive) Materials § 173.459 Mixing of fissile material packages with non-fissile or fissile-excepted material packages. Mixing of fissile material packages with other types of Class 7 (radioactive) materials...

49 CFR 173.459 - Mixing of fissile material packages with non-fissile or fissile-excepted material packages.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 2 2014-10-01 2014-10-01 false Mixing of fissile material packages with non... (Radioactive) Materials § 173.459 Mixing of fissile material packages with non-fissile or fissile-excepted material packages. Mixing of fissile material packages with other types of Class 7 (radioactive) materials...

77 FR 70198 - Self-Regulatory Organizations; The NASDAQ Stock Market LLC; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-23

....com Trading and Compliance Data Package service (``Data Package'').\\5\\ The Data Package service... reports provided by the Data Package. The equity trade journal report of the Data Package provides trade... the Data Package report, but requires further segregation and arrangement of the data so that it is...

Integrated Approach to Industrial Packaging Design

NASA Astrophysics Data System (ADS)

Vorobeva, O.

2017-11-01

The article reviews studies in the field of industrial packaging design. The major factors which influence technological, ergonomic, economic and ecological features of packaging are established. The main modern trends in packaging design are defined, the principles of marketing communications and their influence on consumers’ consciousness are indicated, and the function of packaging as a transmitter of brand values is specified. Peculiarities of packaging technology and printing techniques in modern printing industry are considered. The role of designers in the stage-by-stage development of the construction, form and graphic design concept of packaging is defined. The examples of authentic packaging are given and the mention of the tetrahedron packaging history is made. At the end of the article, conclusions on the key research aspects are made.

Transmissible Gastroenteritis Coronavirus Genome Packaging Signal Is Located at the 5′ End of the Genome and Promotes Viral RNA Incorporation into Virions in a Replication-Independent Process

PubMed Central

Morales, Lucia; Mateos-Gomez, Pedro A.; Capiscol, Carmen; del Palacio, Lorena; Sola, Isabel

2013-01-01

Preferential RNA packaging in coronaviruses involves the recognition of viral genomic RNA, a crucial process for viral particle morphogenesis mediated by RNA-specific sequences, known as packaging signals. An essential packaging signal component of transmissible gastroenteritis coronavirus (TGEV) has been further delimited to the first 598 nucleotides (nt) from the 5′ end of its RNA genome, by using recombinant viruses transcribing subgenomic mRNA that included potential packaging signals. The integrity of the entire sequence domain was necessary because deletion of any of the five structural motifs defined within this region abrogated specific packaging of this viral RNA. One of these RNA motifs was the stem-loop SL5, a highly conserved motif in coronaviruses located at nucleotide positions 106 to 136. Partial deletion or point mutations within this motif also abrogated packaging. Using TGEV-derived defective minigenomes replicated in trans by a helper virus, we have shown that TGEV RNA packaging is a replication-independent process. Furthermore, the last 494 nt of the genomic 3′ end were not essential for packaging, although this region increased packaging efficiency. TGEV RNA sequences identified as necessary for viral genome packaging were not sufficient to direct packaging of a heterologous sequence derived from the green fluorescent protein gene. These results indicated that TGEV genome packaging is a complex process involving many factors in addition to the identified RNA packaging signal. The identification of well-defined RNA motifs within the TGEV RNA genome that are essential for packaging will be useful for designing packaging-deficient biosafe coronavirus-derived vectors and providing new targets for antiviral therapies. PMID:23966403

Influence of gag and RRE Sequences on HIV-1 RNA Packaging Signal Structure and Function.

PubMed

Kharytonchyk, Siarhei; Brown, Joshua D; Stilger, Krista; Yasin, Saif; Iyer, Aishwarya S; Collins, John; Summers, Michael F; Telesnitsky, Alice

2018-07-06

The packaging signal (Ψ) and Rev-responsive element (RRE) enable unspliced HIV-1 RNAs' export from the nucleus and packaging into virions. For some retroviruses, engrafting Ψ onto a heterologous RNA is sufficient to direct encapsidation. In contrast, HIV-1 RNA packaging requires 5' leader Ψ elements plus poorly defined additional features. We previously defined minimal 5' leader sequences competitive with intact Ψ for HIV-1 packaging, and here examined the potential roles of additional downstream elements. The findings confirmed that together, HIV-1 5' leader Ψ sequences plus a nuclear export element are sufficient to specify packaging. However, RNAs trafficked using a heterologous export element did not compete well with RNAs using HIV-1's RRE. Furthermore, some RNA additions to well-packaged minimal vectors rendered them packaging-defective. These defects were rescued by extending gag sequences in their native context. To understand these packaging defects' causes, in vitro dimerization properties of RNAs containing minimal packaging elements were compared to RNAs with sequence extensions that were or were not compatible with packaging. In vitro dimerization was found to correlate with packaging phenotypes, suggesting that HIV-1 evolved to prevent 5' leader residues' base pairing with downstream residues and misfolding of the packaging signal. Our findings explain why gag sequences have been implicated in packaging and show that RRE's packaging contributions appear more specific than nuclear export alone. Paired with recent work showing that sequences upstream of Ψ can dictate RNA folds, the current work explains how genetic context of minimal packaging elements contributes to HIV-1 RNA fate determination. Copyright © 2018 Elsevier Ltd. All rights reserved.

Tearing as a test for mechanical characterization of thin adhesive films

NASA Astrophysics Data System (ADS)

Hamm, Eugenio; Reis, Pedro; Leblanc, Michael; Roman, Benoit; Cerda, Enrique

2008-05-01

Thin adhesive films have become increasingly important in applications involving packaging, coating or for advertising. Once a film is adhered to a substrate, flaps can be detached by tearing and peeling, but they narrow and collapse in pointy shapes. Similar geometries are observed when peeling ultrathin films grown or deposited on a solid substrate, or skinning the natural protective cover of a ripe fruit. Here, we show that the detached flaps have perfect triangular shapes with a well-defined vertex angle; this is a signature of the conversion of bending energy into surface energy of fracture and adhesion. In particular, this triangular shape of the tear encodes the mechanical parameters related to these three forms of energy and could form the basis of a quantitative assay for the mechanical characterization of thin adhesive films, nanofilms deposited on substrates or fruit skin.

Tearing as a test for mechanical characterization of thin adhesive films.

PubMed

Hamm, Eugenio; Reis, Pedro; LeBlanc, Michael; Roman, Benoit; Cerda, Enrique

2008-05-01

Thin adhesive films have become increasingly important in applications involving packaging, coating or for advertising. Once a film is adhered to a substrate, flaps can be detached by tearing and peeling, but they narrow and collapse in pointy shapes. Similar geometries are observed when peeling ultrathin films grown or deposited on a solid substrate, or skinning the natural protective cover of a ripe fruit. Here, we show that the detached flaps have perfect triangular shapes with a well-defined vertex angle; this is a signature of the conversion of bending energy into surface energy of fracture and adhesion. In particular, this triangular shape of the tear encodes the mechanical parameters related to these three forms of energy and could form the basis of a quantitative assay for the mechanical characterization of thin adhesive films, nanofilms deposited on substrates or fruit skin.

Synthesis and characterization of zinc oxide-neem oil-chitosan bionanocomposite for food packaging application.

PubMed

Sanuja, S; Agalya, A; Umapathy, M J

2015-03-01

Nano zinc oxide at different concentrations (0.1, 0.3 and 0.5%) and neem essential oil were incorporated into the chitosan polymer by solution cast method to enhance the properties of the bionanocomposite film. The functional groups, crystalline particle size, thermal stability and morphology were determined using FTIR, XRD, TGA and SEM, respectively. The results showed that 0.5% nano zinc oxide incorporated composite film have improved tensile strength, elongation, film thickness, film transparency and decreased water solubility, swelling and barrier properties due to the presence of neem oil and nano zinc oxide in the polymer matrix. Further antibacterial activity by well diffusion assay method was followed against Escherichia coli which were found to have good inhibition effect. In addition to this food quality application were carried against carrot and compared with the commercial film. Copyright © 2014. Published by Elsevier B.V.

Investigation of a thiolated polymer in gene delivery

NASA Astrophysics Data System (ADS)

Bacalocostantis, Irene

Thiol-containing bioreducible polymers show significant potential as delivery vectors in gene therapy, a rapidly growing field which seeks to treat genetic-based disorders by delivering functional synthetic genes to diseased cells. Studies have shown that thiolated polymers exhibit improved biodegradability and prolonged in vivo circulation times over non-thiolated polymers. However, the extent to which thiol concentrations impact the carrier's delivery potential has not been well explored. The aim of this dissertation is to investigate how relative concentrations of free thiols and disulfide crosslinks impact a polymeric carriers delivery performance with respect to DNA packaging, complex stability, cargo protection, gene release, internalization efficiency and cytotoxicity. To accomplish this goal, several fluorescent polymers containing varying concentrations of thiol groups were synthesized by conjugating thiol-pendant chains onto the primary amines of cationic poly(allylamine). In vitro delivery assays and characterization techniques were employed to assess the effect of thiols in gene delivery.

Pinosylvin-Based Polymers: Biodegradable Poly(Anhydride-Esters) for Extended Release of Antibacterial Pinosylvin.

PubMed

Bien-Aime, Stephan; Yu, Weiling; Uhrich, Kathryn E

2016-07-01

Pinosylvin is a natural stilbenoid known to exhibit antibacterial bioactivity against foodborne bacteria. In this work, pinosylvin is chemically incorporated into a poly(anhydride-ester) (PAE) backbone via melt-condensation polymerization, and characterized with respect to its physicochemical and thermal properties. In vitro release studies demonstrate that pinosylvin-based PAEs hydrolytically degrade over 40 d to release pinosylvin. Pseudo-first order kinetic experiments on model compounds, butyric anhydride and 3-butylstilbene ester, indicate that the anhydride linkages hydrolyze first, followed by the ester bonds to ultimately release pinosylvin. An antibacterial assay shows that the released pinosylvin exhibit bioactivity, while in vitro cytocompatibility studies demonstrate that the polymer is noncytotoxic toward fibroblasts. These preliminary findings suggest that the pinosylvin-based PAEs can serve as food preservatives in food packaging materials by safely providing antibacterial bioactivity over extended time periods. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Penalized Ordinal Regression Methods for Predicting Stage of Cancer in High-Dimensional Covariate Spaces.

PubMed

Gentry, Amanda Elswick; Jackson-Cook, Colleen K; Lyon, Debra E; Archer, Kellie J

2015-01-01

The pathological description of the stage of a tumor is an important clinical designation and is considered, like many other forms of biomedical data, an ordinal outcome. Currently, statistical methods for predicting an ordinal outcome using clinical, demographic, and high-dimensional correlated features are lacking. In this paper, we propose a method that fits an ordinal response model to predict an ordinal outcome for high-dimensional covariate spaces. Our method penalizes some covariates (high-throughput genomic features) without penalizing others (such as demographic and/or clinical covariates). We demonstrate the application of our method to predict the stage of breast cancer. In our model, breast cancer subtype is a nonpenalized predictor, and CpG site methylation values from the Illumina Human Methylation 450K assay are penalized predictors. The method has been made available in the ordinalgmifs package in the R programming environment.

Evaluation of the intercept oral specimen collection device with HIV assays versus paired serum/plasma specimens.

PubMed

Beelaert, G; Van Heddegem, L; Van Frankenhuijsen, M; Vandewalle, G; Compernolle, V; Florence, E; Fransen, K

2016-08-01

Oral fluid has many advantages over blood-based techniques: it is less invasive, eliminates the occupational risk associated with needle stick accidents and collection can be self-administrated. Each individual test is packaged with a corresponding collection device. This study tested the suitability of the Intercept Oral Specimen Collection Device for different HIV diagnostic tests: three different rapid HIV tests and two adapted ELISAs, which were evaluated and compared with a gold standard on blood. In addition a total IgG quantification was performed to demonstrate the quality of the specimen. HIV antibodies were detected with a sensitivity of 100%, 99.3%, 98.6%, 100% and 95.7% for, DPP, OraQuick, Aware, Genscreen and Vironostika respectively using the Intercept Collection Device. Respective specificities were 100%, 100%, 99.3%, 97.3% and 100%. Copyright © 2016 Elsevier B.V. All rights reserved.

Quality control of anti-tuberculosis FDC formulations in the global market: part II-accelerated stability studies.

PubMed

Ashokraj, Y; Kohli, G; Kaul, C L; Panchagnula, R

2005-11-01

To determine the quality and performance of rifampicin (RMP) containing fixed-dose combination (FDC) formulations of anti-tuberculosis drugs sourced from the international market with respect to physical, chemical and dissolution properties after storage at accelerated stability conditions (40 degrees C/75% relative humidity) and to identify appropriate storage specifications. Formulations across different companies and combinations were subjected to 6-month accelerated stability testing in packaging conditions recommended by the manufacturer. Various pharmacopeial and nonpharmacopeial tests for tablets were performed for 3- and 6-month samples. All the formulations were found to be stable, where extent of dissolution was within +/- 10% of that of the initial value, and all formulations passed the pharmacopeial limits for assay and content uniformity of 90-110% and +/- 15% of average drug content, respectively. Good quality RMP-containing FDCs that remain stable after 6-month accelerated stability testing are available in the marketplace.

Components of Adenovirus Genome Packaging

PubMed Central

Ahi, Yadvinder S.; Mittal, Suresh K.

2016-01-01

Adenoviruses (AdVs) are icosahedral viruses with double-stranded DNA (dsDNA) genomes. Genome packaging in AdV is thought to be similar to that seen in dsDNA containing icosahedral bacteriophages and herpesviruses. Specific recognition of the AdV genome is mediated by a packaging domain located close to the left end of the viral genome and is mediated by the viral packaging machinery. Our understanding of the role of various components of the viral packaging machinery in AdV genome packaging has greatly advanced in recent years. Characterization of empty capsids assembled in the absence of one or more components involved in packaging, identification of the unique vertex, and demonstration of the role of IVa2, the putative packaging ATPase, in genome packaging have provided compelling evidence that AdVs follow a sequential assembly pathway. This review provides a detailed discussion on the functions of the various viral and cellular factors involved in AdV genome packaging. We conclude by briefly discussing the roles of the empty capsids, assembly intermediates, scaffolding proteins, portal vertex and DNA encapsidating enzymes in AdV assembly and packaging. PMID:27721809

Eradication of high viable loads of Listeria monocytogenes contaminating food-contact surfaces

PubMed Central

de Candia, Silvia; Morea, Maria; Baruzzi, Federico

2015-01-01

This study demonstrates the efficacy of cold gaseous ozone treatments at low concentrations in the eradication of high Listeria monocytogenes viable cell loads from glass, polypropylene, stainless steel, and expanded polystyrene food-contact surfaces. Using a step by step approach, involving the selection of the most resistant strain-surface combinations, 11 Listeria sp. strains resulted inactivated by a continuous ozone flow at 1.07 mg m-3 after 24 or 48 h of cold incubation, depending on both strain and surface evaluated. Increasing the inoculum level to 9 log CFU coupon-1, the best inactivation rate was obtained after 48 h of treatment at 3.21 mg m-3 ozone concentration when cells were deposited onto stainless steel and expanded polystyrene coupons, resulted the most resistant food-contact surfaces in the previous assays. The addition of naturally contaminated meat extract to a high load of L. monocytogenes LMG 23775 cells, the most resistant strain out of the 11 assayed Listeria sp. strains, led to its complete inactivation after 4 days of treatment. To the best of our knowledge, this is the first report describing the survival of L. monocytogenes and the effect of ozone treatment under cold storage conditions on expanded polystyrene, a commonly used material in food packaging. The results of this study could be useful for reducing pathogen cross-contamination phenomena during cold food storage. PMID:26236306

Geometric approach to segmentation and protein localization in cell culture assays.

PubMed

Raman, S; Maxwell, C A; Barcellos-Hoff, M H; Parvin, B

2007-01-01

Cell-based fluorescence imaging assays are heterogeneous and require the collection of a large number of images for detailed quantitative analysis. Complexities arise as a result of variation in spatial nonuniformity, shape, overlapping compartments and scale (size). A new technique and methodology has been developed and tested for delineating subcellular morphology and partitioning overlapping compartments at multiple scales. This system is packaged as an integrated software platform for quantifying images that are obtained through fluorescence microscopy. Proposed methods are model based, leveraging geometric shape properties of subcellular compartments and corresponding protein localization. From the morphological perspective, convexity constraint is imposed to delineate and partition nuclear compartments. From the protein localization perspective, radial symmetry is imposed to localize punctate protein events at submicron resolution. Convexity constraint is imposed against boundary information, which are extracted through a combination of zero-crossing and gradient operator. If the convexity constraint fails for the boundary then positive curvature maxima are localized along the contour and the entire blob is partitioned into disjointed convex objects representing individual nuclear compartment, by enforcing geometric constraints. Nuclear compartments provide the context for protein localization, which may be diffuse or punctate. Punctate signal are localized through iterative voting and radial symmetries for improved reliability and robustness. The technique has been tested against 196 images that were generated to study centrosome abnormalities. Corresponding computed representations are compared against manual counts for validation.

SMM-system: A mining tool to identify specific markers in Salmonella enterica.

PubMed

Yu, Shuijing; Liu, Weibing; Shi, Chunlei; Wang, Dapeng; Dan, Xianlong; Li, Xiao; Shi, Xianming

2011-03-01

This report presents SMM-system, a software package that implements various personalized pre- and post-BLASTN tasks for mining specific markers of microbial pathogens. The main functionalities of SMM-system are summarized as follows: (i) converting multi-FASTA file, (ii) cutting interesting genomic sequence, (iii) automatic high-throughput BLASTN searches, and (iv) screening target sequences. The utility of SMM-system was demonstrated by using it to identify 214 Salmonella enterica-specific protein-coding sequences (CDSs). Eighteen primer pairs were designed based on eighteen S. enterica-specific CDSs, respectively. Seven of these primer pairs were validated with PCR assay, which showed 100% inclusivity for the 101 S. enterica genomes and 100% exclusivity of 30 non-S. enterica genomes. Three specific primer pairs were chosen to develop a multiplex PCR assay, which generated specific amplicons with a size of 180bp (SC1286), 238bp (SC1598) and 405bp (SC4361), respectively. This study demonstrates that SMM-system is a high-throughput specific marker generation tool that can be used to identify genus-, species-, serogroup- and even serovar-specific DNA sequences of microbial pathogens, which has a potential to be applied in food industries, diagnostics and taxonomic studies. SMM-system is freely available and can be downloaded from http://foodsafety.sjtu.edu.cn/SMM-system.html. Copyright © 2011 Elsevier B.V. All rights reserved.

16 CFR 1700.15 - Poison prevention packaging standards.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 16 Commercial Practices 2 2012-01-01 2012-01-01 false Poison prevention packaging standards. 1700.15 Section 1700.15 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION POISON PREVENTION PACKAGING ACT OF 1970 REGULATIONS POISON PREVENTION PACKAGING § 1700.15 Poison prevention packaging...

16 CFR 1700.15 - Poison prevention packaging standards.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 16 Commercial Practices 2 2014-01-01 2014-01-01 false Poison prevention packaging standards. 1700.15 Section 1700.15 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION POISON PREVENTION PACKAGING ACT OF 1970 REGULATIONS POISON PREVENTION PACKAGING § 1700.15 Poison prevention packaging...

16 CFR 1700.15 - Poison prevention packaging standards.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Poison prevention packaging standards. 1700.15 Section 1700.15 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION POISON PREVENTION PACKAGING ACT OF 1970 REGULATIONS POISON PREVENTION PACKAGING § 1700.15 Poison prevention packaging...

16 CFR 1700.15 - Poison prevention packaging standards.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Poison prevention packaging standards. 1700.15 Section 1700.15 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION POISON PREVENTION PACKAGING ACT OF 1970 REGULATIONS POISON PREVENTION PACKAGING § 1700.15 Poison prevention packaging...

16 CFR 1700.3 - Establishment of standards for special packaging.

Code of Federal Regulations, 2011 CFR

2011-01-01

... standard; (2) Available scientific, medical, and engineering data concerning special packaging and... such standards, the Commission shall not prescribe specific packaging designs, product content, package... such substance in a package which the Commission determines is unnecessarily attractive to children. (e...

16 CFR 1700.3 - Establishment of standards for special packaging.

Code of Federal Regulations, 2010 CFR

2010-01-01

... standard; (2) Available scientific, medical, and engineering data concerning special packaging and... such standards, the Commission shall not prescribe specific packaging designs, product content, package... such substance in a package which the Commission determines is unnecessarily attractive to children. (e...

16 CFR 1700.3 - Establishment of standards for special packaging.

Code of Federal Regulations, 2012 CFR

2012-01-01

... standard; (2) Available scientific, medical, and engineering data concerning special packaging and... such standards, the Commission shall not prescribe specific packaging designs, product content, package... such substance in a package which the Commission determines is unnecessarily attractive to children. (e...

16 CFR 1700.3 - Establishment of standards for special packaging.

Code of Federal Regulations, 2014 CFR

2014-01-01

... standard; (2) Available scientific, medical, and engineering data concerning special packaging and... such standards, the Commission shall not prescribe specific packaging designs, product content, package... such substance in a package which the Commission determines is unnecessarily attractive to children. (e...

49 CFR 173.25 - Authorized packagings and overpacks.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Authorized packagings and overpacks. 173.25...-GENERAL REQUIREMENTS FOR SHIPMENTS AND PACKAGINGS Preparation of Hazardous Materials for Transportation § 173.25 Authorized packagings and overpacks. (a) Authorized packages containing hazardous materials may...

40 CFR 157.27 - Unit packaging.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Unit packaging. 157.27 Section 157.27 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS PACKAGING REQUIREMENTS FOR PESTICIDES AND DEVICES Child-Resistant Packaging § 157.27 Unit packaging. Pesticide products...

49 CFR 173.23 - Previously authorized packaging.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Previously authorized packaging. 173.23 Section... REQUIREMENTS FOR SHIPMENTS AND PACKAGINGS Preparation of Hazardous Materials for Transportation § 173.23 Previously authorized packaging. (a) When the regulations specify a packaging with a specification marking...

High-performance packaging for monolithic microwave and millimeter-wave integrated circuits

NASA Technical Reports Server (NTRS)

Shalkhauser, K. A.; Li, K.; Shih, Y. C.

1992-01-01

Packaging schemes are developed that provide low-loss, hermetic enclosure for enhanced monolithic microwave and millimeter-wave integrated circuits. These package schemes are based on a fused quartz substrate material offering improved RF performance through 44 GHz. The small size and weight of the packages make them useful for a number of applications, including phased array antenna systems. As part of the packaging effort, a test fixture was developed to interface the single chip packages to conventional laboratory instrumentation for characterization of the packaged devices.

Reliability of high I/O high density CCGA interconnect electronic packages under extreme thermal environments

NASA Astrophysics Data System (ADS)

Ramesham, Rajeshuni

2012-03-01

Ceramic column grid array (CCGA) packages have been increasing in use based on their advantages such as high interconnect density, very good thermal and electrical performances, compatibility with standard surfacemount packaging assembly processes, and so on. CCGA packages are used in space applications such as in logic and microprocessor functions, telecommunications, payload electronics, and flight avionics. As these packages tend to have less solder joint strain relief than leaded packages or more strain relief over lead-less chip carrier packages, the reliability of CCGA packages is very important for short-term and long-term deep space missions. We have employed high density CCGA 1152 and 1272 daisy chained electronic packages in this preliminary reliability study. Each package is divided into several daisy-chained sections. The physical dimensions of CCGA1152 package is 35 mm x 35 mm with a 34 x 34 array of columns with a 1 mm pitch. The dimension of the CCGA1272 package is 37.5 mm x 37.5 mm with a 36 x 36 array with a 1 mm pitch. The columns are made up of 80% Pb/20%Sn material. CCGA interconnect electronic package printed wiring polyimide boards have been assembled and inspected using non-destructive x-ray imaging techniques. The assembled CCGA boards were subjected to extreme temperature thermal atmospheric cycling to assess their reliability for future deep space missions. The resistance of daisy-chained interconnect sections were monitored continuously during thermal cycling. This paper provides the experimental test results of advanced CCGA packages tested in extreme temperature thermal environments. Standard optical inspection and x-ray non-destructive inspection tools were used to assess the reliability of high density CCGA packages for deep space extreme temperature missions.

Polymer dispensing and embossing technology for the lens type LED packaging

NASA Astrophysics Data System (ADS)

Chien, Chien-Lin Chang; Huang, Yu-Che; Hu, Syue-Fong; Chang, Chung-Min; Yip, Ming-Chuen; Fang, Weileun

2013-06-01

This study presents a ring-type micro-structure design on the substrate and its corresponding micro fabrication processes for a lens-type light-emitting diode (LED) package. The dome-type or crater-type silicone lenses are achieved by a dispensing and embossing process rather than a molding process. Silicone with a high viscosity and thixotropy index is used as the encapsulant material. The ring-type micro structure is adopted to confine the dispensed silicone encapsulant so as to form the packaged lens. With the architecture and process described, this LED package technology herein has three merits: (1) the flexibility of lens-type LED package designs is enhanced; (2) a dome-type package design is used to enhance the intensity; (3) a crater-type package design is used to enhance the view angle. Measurement results show the ratio between the lens height and lens radius can vary from 0.4 to 1 by changing the volume of dispensed silicone. The view angles of dome-type and crater-type packages can reach 155° ± 5° and 175° ± 5°, respectively. As compared with the commercial plastic leaded chip carrier-type package, the luminous flux of a monochromatic blue light LED is improved by 15% by the dome-type package (improved by 7% by the crater-type package) and the luminous flux of a white light LED is improved by 25% by the dome-type package (improved by 13% by the crater-type package). The luminous flux of monochromatic blue light LED and white light LED are respectively improved by 8% and 12% by the dome-type package as compare with the crater-type package.

Method of fabricating a microelectronic device package with an integral window

DOEpatents

Peterson, Kenneth A.; Watson, Robert D.

2003-01-01

A method of fabricating a microelectronic device package with an integral window for providing optical access through an aperture in the package. The package is made of a multilayered insulating material, e.g., a low-temperature cofired ceramic (LTCC) or high-temperature cofired ceramic (HTCC). The window is inserted in-between personalized layers of ceramic green tape during stackup and registration. Then, during baking and firing, the integral window is simultaneously bonded to the sintered ceramic layers of the densified package. Next, the microelectronic device is flip-chip bonded to cofired thick-film metallized traces on the package, where the light-sensitive side is optically accessible through the window. Finally, a cover lid is attached to the opposite side of the package. The result is a compact, low-profile package, flip-chip bonded, hermetically-sealed package having an integral window.

Sensory impacts of food-packaging interactions.

PubMed

Duncan, Susan E; Webster, Janet B

2009-01-01

Sensory changes in food products result from intentional or unintentional interactions with packaging materials and from failure of materials to protect product integrity or quality. Resolving sensory issues related to plastic food packaging involves knowledge provided by sensory scientists, materials scientists, packaging manufacturers, food processors, and consumers. Effective communication among scientists and engineers from different disciplines and industries can help scientists understand package-product interactions. Very limited published literature describes sensory perceptions associated with food-package interactions. This article discusses sensory impacts, with emphasis on oxidation reactions, associated with the interaction of food and materials, including taints, scalping, changes in food quality as a function of packaging, and examples of material innovations for smart packaging that can improve sensory quality of foods and beverages. Sensory evaluation is an important tool for improved package selection and development of new materials.

Efficacy of Antimicrobial Agents for Food Contact Applications: Biological Activity, Incorporation into Packaging, and Assessment Methods: A Review.

PubMed

Mousavi Khaneghah, Amin; Hashemi, Seyed Mohammad Bagher; Eş, Ismail; Fracassetti, Daniela; Limbo, Sara

2018-07-01

Interest in the utilization of antimicrobial active packaging for food products has increased in recent years. Antimicrobial active packaging involves the incorporation of antimicrobial compounds into packaging materials, with the aim of maintaining or extending food quality and shelf life. Plant extracts, essential oils, organic acids, bacteriocins, inorganic substances, enzymes, and proteins are used as antimicrobial agents in active packaging. Evaluation of the antimicrobial activity of packaging materials using different methods has become a critical issue for both food safety and the commercial utilization of such packaging technology. This article reviews the different types of antimicrobial agents used for active food packaging materials, the main incorporation techniques, and the assessment methods used to examine the antimicrobial activity of packaging materials, taking into account their safety as food contact materials.

78 FR 1101 - Hazardous Materials: Harmonization With the United Nations Recommendations on the Transport of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-07

... packaging maintains an equivalent level of performance to the originally tested packaging design must be... material, packing group assignments, special provisions, packaging authorizations, packaging sections, air... responsibilities related to packaging design variation, manufacturer notification, and recordkeeping requirements...

16 CFR § 1700.3 - Establishment of standards for special packaging.

Code of Federal Regulations, 2013 CFR

2013-01-01

... such standard; (2) Available scientific, medical, and engineering data concerning special packaging and... such standards, the Commission shall not prescribe specific packaging designs, product content, package... such substance in a package which the Commission determines is unnecessarily attractive to children. (e...

Packaging Technologies for 500C SiC Electronics and Sensors

NASA Technical Reports Server (NTRS)

Chen, Liang-Yu

2013-01-01

Various SiC electronics and sensors are currently under development for applications in 500C high temperature environments such as hot sections of aerospace engines and the surface of Venus. In order to conduct long-term test and eventually commercialize these SiC devices, compatible packaging technologies for the SiC electronics and sensors are required. This presentation reviews packaging technologies developed for 500C SiC electronics and sensors to address both component and subsystem level packaging needs for high temperature environments. The packaging system for high temperature SiC electronics includes ceramic chip-level packages, ceramic printed circuit boards (PCBs), and edge-connectors. High temperature durable die-attach and precious metal wire-bonding are used in the chip-level packaging process. A high temperature sensor package is specifically designed to address high temperature micro-fabricated capacitive pressure sensors for high differential pressure environments. This presentation describes development of these electronics and sensor packaging technologies, including some testing results of SiC electronics and capacitive pressure sensors using these packaging technologies.

Effect of Various Packaging Methods on Small-Scale Hanwoo (Korean Native Cattle) during Refrigerated Storage

PubMed Central

Yu, Hwan Hee; Song, Myung Wook; Kim, Tae-Kyung; Choi, Yun-Sang; Cho, Gyu Yong; Lee, Na-Kyoung; Paik, Hyun-Dong

2018-01-01

Abstract The objective of this study was to investigate comparison of physicochemical, microbiological, and sensory characteristics of Hanwoo eye of round by various packaging methods [wrapped packaging (WP), modified atmosphere packaging (MAP), vacuum packaging (VP) with three different vacuum films, and vacuum skin packaging (VSP)] at a small scale. Packaged Hanwoo beef samples were stored in refrigerated conditions (4±1°C) for 28 days. Packaged beef was sampled on days 0, 7, 14, 21, and 28. Physicochemical [pH, surface color, thiobarbituric acid reactive substances (TBARS), and volatile basic nitrogen (VBN) values], microbiological, and sensory analysis of packaged beef samples were performed. VP and VSP samples showed low TBARS and VBN values, and pH and surface color did not change substantially during the 28-day period. For VSP, total viable bacteria, psychrotrophic bacteria, lactic acid bacteria, and coliform counts were lower than those for other packaging systems. Salmonella spp. and Escherichia coli O157:H7 were not detected in any packaged beef samples. A sensory analysis showed that the scores for appearance, flavor, color, and overall acceptability did not change significantly until day 7. In total, VSP was effective with respect to significantly higher a* values, physicochemical stability, and microbial safety in Hanwoo packaging (p<0.05). PMID:29805283

Natural biopolimers in organic food packaging

NASA Astrophysics Data System (ADS)

Wieczynska, Justyna; Cavoski, Ivana; Chami, Ziad Al; Mondelli, Donato; Di Donato, Paola; Di Terlizzi, Biagio

2014-05-01

Concerns on environmental and waste problems caused by use of non-biodegradable and non-renewable based plastic packaging have caused an increase interest in developing biodegradable packaging using renewable natural biopolymers. Recently, different types of biopolymers like starch, cellulose, chitosan, casein, whey protein, collagen, egg white, soybean protein, corn zein, gelatin and wheat gluten have attracted considerable attention as potential food packaging materials. Recyclable or biodegradable packaging material in organic processing standards is preferable where possible but specific principles of packaging are not precisely defined and standards have to be assessed. There is evidence that consumers of organic products have specific expectations not only with respect to quality characteristics of processed food but also in social and environmental aspects of food production. Growing consumer sophistication is leading to a proliferation in food eco-label like carbon footprint. Biopolymers based packaging for organic products can help to create a green industry. Moreover, biopolymers can be appropriate materials for the development of an active surfaces designed to deliver incorporated natural antimicrobials into environment surrounding packaged food. Active packaging is an innovative mode of packaging in which the product and the environment interact to prolong shelf life or enhance safety or sensory properties, while maintaining the quality of the product. The work will discuss the various techniques that have been used for development of an active antimicrobial biodegradable packaging materials focusing on a recent findings in research studies. With the current focus on exploring a new generation of biopolymer-based food packaging materials with possible applications in organic food packaging. Keywords: organic food, active packaging, biopolymers , green technology

Evaluating Penetration Ability of Plodia interpunctella (Hübner) (Lepidoptera: Pyralidae) Larvae into Multilayer Polypropylene Packages.

PubMed

Scheff, Deanna S; Sehgal, Blossom; Subramanyam, Bhadriraju

2018-04-18

The larvae of the Indian meal moth, Plodia interpunctella (Hübner), can invade or penetrate packaging materials and infest food products. Energy bars with three polypropylene packaging types were challenged with eggs (first instars), third instars, and fifth instars of P. interpunctella to determine package resistance at 28 °C and 65% r.h. The packing types were also challenged with two male and two female pupae of P. interpunctella under similar conditions in order to determine which package provided the greatest protection against larval penetration. Samples infested with eggs, third instars, and pupae were evaluated after 21 days and 42 days to count the number of larvae, pupae, and adults found inside the packages. Packages challenged with fifth instars were observed after 21 days to count the number of larvae, pupae, and adults inside each package. The number and diameter of the holes were determined in each package, followed by the amount of damage sustained to the energy bar. Third and fifth instars showed a higher tendency to penetrate all of the packaging types. First instars showed a reduction in package penetration ability compared with third and fifth instars. The increase in exposure time resulted in an increase in the damage sustained to the energy bars. Among packaging types, the thickest package (Test A) was most resilient to penetration by all of the larval stages. In conclusion, energy bar manufacturers need to invest more effort into improving packaging designs, creating thicker gauge films, or advancing odor barrier technology, in order to prevent penetration and infestation by P. interpunctella larvae.

77 FR 22504 - Hazardous Materials; Packages Intended for Transport by Aircraft

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-16

... material to absorb the entire contents of the inner packaging, before being placed in its outer package... combination packaging intended for the air transportation of liquid hazardous materials is capable of..., leakproof receptacle or intermediate packaging containing sufficient absorbent material to absorb the entire...

40 CFR 157.30 - Voluntary use of child-resistant packaging.

Code of Federal Regulations, 2010 CFR

2010-07-01

... packaging. 157.30 Section 157.30 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS PACKAGING REQUIREMENTS FOR PESTICIDES AND DEVICES Child-Resistant Packaging § 157.30 Voluntary use of child-resistant packaging. A registrant whose product is not required to be in child...

49 CFR 173.428 - Empty Class 7 (radioactive) materials packaging.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Empty Class 7 (radioactive) materials packaging... SHIPPERS-GENERAL REQUIREMENTS FOR SHIPMENTS AND PACKAGINGS Class 7 (Radioactive) Materials § 173.428 Empty Class 7 (radioactive) materials packaging. A packaging which previously contained Class 7 (radioactive...

49 CFR 173.29 - Empty packagings.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Empty packagings. 173.29 Section 173.29... SHIPMENTS AND PACKAGINGS Preparation of Hazardous Materials for Transportation § 173.29 Empty packagings. (a) General. Except as otherwise provided in this section, an empty packaging containing only the residue of a...

Sex-specific 99th percentiles derived from the AACC Universal Sample Bank for the Roche Gen 5 cTnT assay: Comorbidities and statistical methods influence derivation of reference limits.

PubMed

Gunsolus, Ian L; Jaffe, Allan S; Sexter, Anne; Schulz, Karen; Ler, Ranka; Lindgren, Brittany; Saenger, Amy K; Love, Sara A; Apple, Fred S

2017-12-01

Our purpose was to determine a) overall and sex-specific 99th percentile upper reference limits (URL) and b) influences of statistical methods and comorbidities on the URLs. Heparin plasma from 838 normal subjects (423 men, 415 women) were obtained from the AACC (Universal Sample Bank). The cobas e602 measured cTnT (Roche Gen 5 assay); limit of detection (LoD), 3ng/L. Hemoglobin A1c (URL 6.5%), NT-proBNP (URL 125ng/L) and eGFR (60mL/min/1.73m 2 ) were measured, along with identification of statin use, to better define normality. 99th percentile URLs were determined by the non-parametric (NP), Harrell-Davis Estimator (HDE) and Robust (R) methods. 355 men and 339 women remained after exclusions. Overall<50% of subjects had measureable concentrations ≥ LoD: 45.6% no exclusion, 43.5% after exclusion; compared to men: 68.1% no exclusion, 65.1% post exclusion; women: 22.7% no exclusion, 20.9% post exclusion. The statistical method used influenced URLs as follows: pre/post exclusion overall, NP 16/16ng/L, HDE 17/17ng/L, R not available; men NP 18/16ng/L, HDE 21/19ng/L, R 16/11ng/L; women NP 13/10ng/L, HDE 14/14ng/L, R not available. We demonstrated that a) the Gen 5 cTnT assay does not meet the IFCC guideline for high-sensitivity assays, b) surrogate biomarkers significantly lowers the URLs and c) statistical methods used impact URLs. Our data suggest lower sex-specific cTnT 99th percentiles than reported in the FDA approved package insert. We emphasize the importance of detailing the criteria used to include and exclude subjects for defining a healthy population and the statistical method used to calculate 99th percentiles and identify outliers. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Application of a unique server-based oligonucleotide probe selection tool toward a novel biosensor for the detection of Streptococcus pyogenes.

PubMed

Nugen, Sam R; Leonard, Barbara; Baeumner, Antje J

2007-05-15

We developed a software program for the rapid selection of detection probes to be used in nucleic acid-based assays. In comparison to commercially available software packages, our program allows the addition of oligotags as required by nucleic acid sequence-based amplification (NASBA) as well as automatic BLAST searches for all probe/primer pairs. We then demonstrated the usefulness of the program by designing a novel lateral flow biosensor for Streptococcus pyogenes that does not rely on amplification methods such as the polymerase chain reaction (PCR) or NASBA to obtain low limits of detection, but instead uses multiple reporter and capture probes per target sequence and an instantaneous amplification via dye-encapsulating liposomes. These assays will decrease the detection time to just a 20 min hybridization reaction and avoid costly enzymatic gene amplification reactions. The lateral flow assay was developed quantifying the 16S rRNA from S. pyogenes by designing reporter and capture probes that specifically hybridize with the RNA and form a sandwich. DNA reporter probes were tagged with dye-encapsulating liposomes, biotinylated DNA oligonucleotides were used as capture probes. From the initial number of capture and reporter probes chosen, a combination of two capture and three reporter probes were found to provide optimal signal generation and significant enhancement over single capture/reporter probe combinations. The selectivity of the biosensor was proven by analyzing organisms closely related to S. pyogenes, such as other Streptococcus and Enterococcus species. All probes had been selected by the software program within minutes and no iterative optimization and re-design of the oligonucleotides was required which enabled a very rapid biosensor prototyping. While the sensitivity obtained with the biosensor was only 135 ng, future experiments will decrease this significantly by the addition of more reporter and capture probes for either the same rRNA or a different nucleic acid target molecule. This will lead to the possibility of detecting S. pyogenes with a rugged assay that does not require a cell culturing or gene amplification step and will therefore enable rapid, specific and sensitive onsite testing.

Analytical method for the identification and assay of 12 phthalates in cosmetic products: application of the ISO 12787 international standard "Cosmetics-Analytical methods-Validation criteria for analytical results using chromatographic techniques".

PubMed

Gimeno, Pascal; Maggio, Annie-Françoise; Bousquet, Claudine; Quoirez, Audrey; Civade, Corinne; Bonnet, Pierre-Antoine

2012-08-31

Esters of phthalic acid, more commonly named phthalates, may be present in cosmetic products as ingredients or contaminants. Their presence as contaminant can be due to the manufacturing process, to raw materials used or to the migration of phthalates from packaging when plastic (polyvinyl chloride--PVC) is used. 8 phthalates (DBP, DEHP, BBP, DMEP, DnPP, DiPP, DPP, and DiBP), classified H360 or H361, are forbidden in cosmetics according to the European regulation on cosmetics 1223/2009. A GC/MS method was developed for the assay of 12 phthalates in cosmetics, including the 8 phthalates regulated. Analyses are carried out on a GC/MS system with electron impact ionization mode (EI). The separation of phthalates is obtained on a cross-linked 5%-phenyl/95%-dimethylpolysiloxane capillary column 30 m × 0.25 mm (i.d.) × 0.25 mm film thickness using a temperature gradient. Phthalate quantification is performed by external calibration using an internal standard. Validation elements obtained on standard solutions, highlight a satisfactory system conformity (resolution>1.5), a common quantification limit at 0.25 ng injected, an acceptable linearity between 0.5 μg mL⁻¹ and 5.0 μg mL⁻¹ as well as a precision and an accuracy in agreement with in-house specifications. Cosmetic samples ready for analytical injection are analyzed after a dilution in ethanol whereas more complex cosmetic matrices, like milks and creams, are assayed after a liquid/liquid extraction using ter-butyl methyl ether (TBME). Depending on the type of cosmetics analyzed, the common limits of quantification for the 12 phthalates were set at 0.5 or 2.5 μg g⁻¹. All samples were assayed using the analytical approach described in the ISO 12787 international standard "Cosmetics-Analytical methods-Validation criteria for analytical results using chromatographic techniques". This analytical protocol is particularly adapted when it is not possible to make reconstituted sample matrices. Copyright © 2012 Elsevier B.V. All rights reserved.

49 CFR 173.162 - Gallium.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 2 2014-10-01 2014-10-01 false Gallium. 173.162 Section 173.162 Transportation... PACKAGINGS Non-bulk Packaging for Hazardous Materials Other Than Class 1 and Class 7 § 173.162 Gallium. (a) Except when packaged in cylinders or steel flasks, gallium must be packaged in packagings which meet the...

49 CFR 173.162 - Gallium.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 2 2012-10-01 2012-10-01 false Gallium. 173.162 Section 173.162 Transportation... PACKAGINGS Non-bulk Packaging for Hazardous Materials Other Than Class 1 and Class 7 § 173.162 Gallium. (a) Except when packaged in cylinders or steel flasks, gallium must be packaged in packagings which meet the...

49 CFR 173.162 - Gallium.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 2 2013-10-01 2013-10-01 false Gallium. 173.162 Section 173.162 Transportation... PACKAGINGS Non-bulk Packaging for Hazardous Materials Other Than Class 1 and Class 7 § 173.162 Gallium. (a) Except when packaged in cylinders or steel flasks, gallium must be packaged in packagings which meet the...

10 CFR 60.135 - Criteria for the waste package and its components.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Section 60.135 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES... for the waste package and its components. (a) High-level-waste package design in general. (1) Packages... package's permanent written records. (c) Waste form criteria for HLW. High-level radioactive waste that is...

16 CFR § 1700.15 - Poison prevention packaging standards.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 16 Commercial Practices 2 2013-01-01 2013-01-01 false Poison prevention packaging standards. § 1700.15 Section § 1700.15 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION POISON PREVENTION PACKAGING ACT OF 1970 REGULATIONS POISON PREVENTION PACKAGING § 1700.15 Poison prevention packaging...

19 CFR 10.2022 - Retail packaging materials and containers.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 19 Customs Duties 1 2014-04-01 2014-04-01 false Retail packaging materials and containers. 10.2022... Trade Promotion Agreement Rules of Origin § 10.2022 Retail packaging materials and containers. (a) Effect on tariff shift rule. Packaging materials and containers in which a good is packaged for retail...

49 CFR 173.36 - Hazardous materials in Large Packagings.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Packagings (e.g., 51H) are only authorized for use with flexible inner packagings. (3) Friction. The nature and thickness of the outer packaging must be such that friction during transportation is not likely to... transportation in inner packagings appropriately resistant to an increase of internal pressure likely to develop...

16 CFR 305.15 - Labeling for lighting products.

Code of Federal Regulations, 2011 CFR

2011-01-01

...) Package labeling. For purposes of labeling under this section, packaging for such fluorescent lamp... individually or in small numbers. The encircled capital letter “E” on packages containing fluorescent lamp... ink, on the surface of the package on which printing or a label normally appears. If the package...

21 CFR 801.437 - User labeling for devices that contain natural rubber.

Code of Federal Regulations, 2014 CFR

2014-04-01

... User labeling for devices that contain natural rubber. (a) Data in the Medical Device Reporting System... of the device packaging, the outside package, container or wrapper, and the immediate device package... panel of the device packaging, the outside package, container or wrapper, and the immediate device...

21 CFR 801.437 - User labeling for devices that contain natural rubber.

Code of Federal Regulations, 2011 CFR

2011-04-01

... User labeling for devices that contain natural rubber. (a) Data in the Medical Device Reporting System... of the device packaging, the outside package, container or wrapper, and the immediate device package... panel of the device packaging, the outside package, container or wrapper, and the immediate device...

49 CFR 173.415 - Authorized Type A packages.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 2 2011-10-01 2011-10-01 false Authorized Type A packages. 173.415 Section 173... REQUIREMENTS FOR SHIPMENTS AND PACKAGINGS Class 7 (Radioactive) Materials § 173.415 Authorized Type A packages. The following packages are authorized for shipment if they do not contain quantities exceeding A1 or...

49 CFR 173.415 - Authorized Type A packages.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 2 2013-10-01 2013-10-01 false Authorized Type A packages. 173.415 Section 173... REQUIREMENTS FOR SHIPMENTS AND PACKAGINGS Class 7 (Radioactive) Materials § 173.415 Authorized Type A packages. The following packages are authorized for shipment if they do not contain quantities exceeding A1 or...

21 CFR 801.437 - User labeling for devices that contain natural rubber.

Code of Federal Regulations, 2013 CFR

2013-04-01

... User labeling for devices that contain natural rubber. (a) Data in the Medical Device Reporting System... of the device packaging, the outside package, container or wrapper, and the immediate device package... panel of the device packaging, the outside package, container or wrapper, and the immediate device...

49 CFR 173.415 - Authorized Type A packages.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Authorized Type A packages. 173.415 Section 173... REQUIREMENTS FOR SHIPMENTS AND PACKAGINGS Class 7 (Radioactive) Materials § 173.415 Authorized Type A packages. The following packages are authorized for shipment if they do not contain quantities exceeding A1 or...

21 CFR 801.437 - User labeling for devices that contain natural rubber.

Code of Federal Regulations, 2012 CFR

2012-04-01

... User labeling for devices that contain natural rubber. (a) Data in the Medical Device Reporting System... of the device packaging, the outside package, container or wrapper, and the immediate device package... panel of the device packaging, the outside package, container or wrapper, and the immediate device...

21 CFR 801.437 - User labeling for devices that contain natural rubber.

Code of Federal Regulations, 2010 CFR

2010-04-01

... User labeling for devices that contain natural rubber. (a) Data in the Medical Device Reporting System... of the device packaging, the outside package, container or wrapper, and the immediate device package... panel of the device packaging, the outside package, container or wrapper, and the immediate device...

49 CFR 173.415 - Authorized Type A packages.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 2 2012-10-01 2012-10-01 false Authorized Type A packages. 173.415 Section 173... REQUIREMENTS FOR SHIPMENTS AND PACKAGINGS Class 7 (Radioactive) Materials § 173.415 Authorized Type A packages. The following packages are authorized for shipment if they do not contain quantities exceeding A1 or...

7 CFR 58.340 - Printing and packaging.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Printing and packaging. 58.340 Section 58.340... Procedures § 58.340 Printing and packaging. Printing and packaging of consumer size containers of butter... packaging equipment should be provided. The outside cartons should be removed from bulk butter in a room...

9 CFR 112.10 - Special packaging and labeling.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Special packaging and labeling. 112.10... AGRICULTURE VIRUSES, SERUMS, TOXINS, AND ANALOGOUS PRODUCTS; ORGANISMS AND VECTORS PACKAGING AND LABELING § 112.10 Special packaging and labeling. A biological product, which requires special packaging and/or...

21 CFR 820.130 - Device packaging.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Device packaging. 820.130 Section 820.130 Food and... QUALITY SYSTEM REGULATION Labeling and Packaging Control § 820.130 Device packaging. Each manufacturer shall ensure that device packaging and shipping containers are designed and constructed to protect the...

7 CFR 58.151 - Packaging and repackaging.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Packaging and repackaging. 58.151 Section 58.151... Specifications for Dairy Plants Approved for USDA Inspection and Grading Service 1 Packaging and General Identification § 58.151 Packaging and repackaging. (a) Packaging dairy products or cutting and repackaging all...

49 CFR 173.206 - Packaging requirements for chlorosilanes.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Packaging requirements for chlorosilanes. 173.206...-GENERAL REQUIREMENTS FOR SHIPMENTS AND PACKAGINGS Non-bulk Packaging for Hazardous Materials Other Than Class 1 and Class 7 § 173.206 Packaging requirements for chlorosilanes. (a) When § 172.101 of this...

7 CFR 58.444 - Packaging and repackaging.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Packaging and repackaging. 58.444 Section 58.444... Procedures § 58.444 Packaging and repackaging. (a) Packaging rindless cheese or cutting and repackaging all styles of bulk cheese shall be conducted under rigid sanitary conditions. The atmosphere of the packaging...

19 CFR 10.461 - Retail packaging materials and containers.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 19 Customs Duties 1 2010-04-01 2010-04-01 false Retail packaging materials and containers. 10.461... Free Trade Agreement Rules of Origin § 10.461 Retail packaging materials and containers. Packaging... requirement, the value of such packaging materials and containers will be taken into account as originating or...

7 CFR 58.53 - Supervisor of packaging required.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Supervisor of packaging required. 58.53 Section 58.53... Packaging Products with Official Identification § 58.53 Supervisor of packaging required. The official....54 through 58.57, shall be done only under the supervision of a supervisor of packaging. The...

21 CFR 310.515 - Patient package inserts for estrogens.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 5 2011-04-01 2011-04-01 false Patient package inserts for estrogens. 310.515... package inserts for estrogens. (a) Requirement for a patient package insert. FDA concludes that the safe... patient package insert containing information concerning the drug's benefits and risks. An estrogen drug...

Packaging for Food Service

NASA Technical Reports Server (NTRS)

Stilwell, E. J.

1985-01-01

Most of the key areas of concern in packaging the three principle food forms for the space station were covered. It can be generally concluded that there are no significant voids in packaging materials availability or in current packaging technology. However, it must also be concluded that the process by which packaging decisions are made for the space station feeding program will be very synergistic. Packaging selection will depend heavily on the preparation mechanics, the preferred presentation and the achievable disposal systems. It will be important that packaging be considered as an integral part of each decision as these systems are developed.

Environmental Assessment of Packaging: The Consumer Point of View

PubMed

Van Dam YK

1996-09-01

When marketing environmentally responsible packaged products, the producer is confronted with consumer beliefs concerning the environmental friendliness of packaging materials. When making environmentally conscious packaging decisions, these consumer beliefs should be taken into account alongside the technical guidelines. Dutch consumer perceptions of the environmental friendliness of packaged products are reported and compared with the results of a life-cycle analysis assessment. It is shown that consumers judge environmental friendliness mainly from material and returnability. Furthermore, the consumer perception of the environmental friendliness of packaging material is based on the postconsumption waste, whereas the environmental effects of production are ignored. From the consumer beliefs concerning environmental friendliness implications are deduced for packaging policy and for environmental policy.KEY WORDS: Consumer behavior; Environment; Food; Packaging; Perception; Waste

Bi-level microelectronic device package with an integral window

DOEpatents

Peterson, Kenneth A.; Watson, Robert D.

2004-01-06

A package with an integral window for housing a microelectronic device. The integral window is bonded directly to the package without having a separate layer of adhesive material disposed in-between the window and the package. The device can be a semiconductor chip, CCD chip, CMOS chip, VCSEL chip, laser diode, MEMS device, or IMEMS device. The multilayered package can be formed of a LTCC or HTCC cofired ceramic material, with the integral window being simultaneously joined to the package during LTCC or HTCC processing. The microelectronic device can be flip-chip bonded so that the light-sensitive side is optically accessible through the window. The package has at least two levels of circuits for making electrical interconnections to a pair of microelectronic devices. The result is a compact, low-profile package having an integral window that is hermetically sealed to the package prior to mounting and interconnecting the microelectronic device(s).

Why Packaging Is Commercially Vital for Tobacco Corporations.

PubMed

Barraclough, Simon; Gleeson, Deborah

2017-03-01

This study analyses what British American Tobacco (BAT) and its 4 publicly listed Asian subsidiary companies have told their shareholders about the commercial value of tobacco packaging. The discourse on packaging in BAT annual reports was analyzed, revealing themes of modernization, rejuvenation, internationalism, heritage, innovation, value for money, and competitive edge. Packaging was credited with providing existing brands with a competitive edge and enabling the successful "launch" of new ones. Since advertising, sponsorship, and free samples were prohibited in many countries, packaging has become more important for advertising. New brands and brand variants have proliferated. BAT companies have allocated considerable resources to regularly altering packaging for marketing purposes. Clearly, restrictions on packaging will substantially detract from the promotion of the company's brands. The findings provide further evidence from industry sources of the vital function of packaging and further justify plain packaging as an essential part of any comprehensive tobacco control policy.

Food packaging history and innovations.

PubMed

Risch, Sara J

2009-09-23

Food packaging has evolved from simply a container to hold food to something today that can play an active role in food quality. Many packages are still simply containers, but they have properties that have been developed to protect the food. These include barriers to oxygen, moisture, and flavors. Active packaging, or that which plays an active role in food quality, includes some microwave packaging as well as packaging that has absorbers built in to remove oxygen from the atmosphere surrounding the product or to provide antimicrobials to the surface of the food. Packaging has allowed access to many foods year-round that otherwise could not be preserved. It is interesting to note that some packages have actually allowed the creation of new categories in the supermarket. Examples include microwave popcorn and fresh-cut produce, which owe their existence to the unique packaging that has been developed.

The comparison of antimicrobial packaging properties with different applications incorporation method of active material

NASA Astrophysics Data System (ADS)

Anwar, R. W.; Sugiarto; Warsiki, E.

2018-03-01

Contamination after the processing of products during storage, distribution and marketing is one of the main causes of food safety issues. Handling of food products after processing can be done during the packaging process. Antimicrobial (AM) active packaging is one of the concept of packaging product development by utilize the interaction between the product and the packaging environment that can delay the bacterial damage by killing or reducing bacterial growth. The active system is formed by incorporating an antimicrobial agent against a packaging matrix that will function as a carrier. Many incorporation methods have been developed in this packaging-making concept which were direct mixing, polishing, and encapsulation. The aims of this research were to examine the different of the AM packaging performances including its stability and effectiveness of its function that would be produced by three different methods. The stability of the packaging function was analyzed by looking at the diffusivity of the active ingredient to the matrix using SEM. The effectiveness was analyzed by the ability of the packaging to prevent the growing of the microbial. The results showed that different incorporation methods resulted on different characteristics of the AM packaging.

Application of Au-Sn eutectic bonding in hermetic radio-frequency microelectromechanical system wafer level packaging

NASA Astrophysics Data System (ADS)

Wang, Qian; Choa, Sung-Hoon; Kim, Woonbae; Hwang, Junsik; Ham, Sukjin; Moon, Changyoul

2006-03-01

Development of packaging is one of the critical issues toward realizing commercialization of radio-frequency-microelectromechanical system (RF-MEMS) devices. The RF-MEMS package should be designed to have small size, hermetic protection, good RF performance, and high reliability. In addition, packaging should be conducted at sufficiently low temperature. In this paper, a low-temperature hermetic wafer level packaging scheme for the RF-MEMS devices is presented. For hermetic sealing, Au-Sn eutectic bonding technology at temperatures below 300°C is used. Au-Sn multilayer metallization with a square loop of 70 µm in width is performed. The electrical feed-through is achieved by the vertical through-hole via filling with electroplated Cu. The size of the MEMS package is 1 mm × 1 mm × 700 µm. The shear strength and hermeticity of the package satisfies the requirements of MIL-STD-883F. Any organic gases or contamination are not observed inside the package. The total insertion loss for the packaging is 0.075 dB at 2 GHz. Furthermore, the robustness of the package is demonstrated by observing no performance degradation and physical damage of the package after several reliability tests.

Development of low cost, high reliability sealing techniques for hybrid microcircuit packages. Phase 2, supplement 1: Moisture permeation of adhesive-sealed hybrid microcircuit packages

NASA Technical Reports Server (NTRS)

Perkins, K. L.; Licari, J. J.

1978-01-01

The susceptibility of adhesive-sealed ceramic packages to moisture permeation was investigated. The two adhesives, Ablebond 789-1 and Epo-Tek H77, were evaluated as package sealants. These adhesives were previously selected as the most promising candidates for this application from a group of ten adhesives. Ceramic packages sealed with these adhesives were exposed to temperature-humidity conditions of 25 C/98 percent RH, 50 C/60 percent RH, 50 C/98 percent RH, and 85 C/85 percent RH and their moisture contents using were monitored solid state moisture sensors sealed inside them. Five packages were tested at each of these exposures - two ceramic packages sealed with each of the two adhesives and one seam-sealed gold-plated Kovar package. This latter package was included to serve as a control. The results showed that the adhesive-sealed packages were not hermetic to moisture. The rates at which moisture entered the packages increased with the severity of the exposure environments (i.e., higher temperatures and higher moisture vapor pressures) with greater dependence on temperature than on moisture vapor pressure.

High-performance packaging for monolithic microwave and millimeter-wave integrated circuits

NASA Technical Reports Server (NTRS)

Shalkhauser, K. A.; Li, K.; Shih, Y. C.

1992-01-01

Packaging schemes were developed that provide low-loss, hermetic enclosure for advanced monolithic microwave and millimeter-wave integrated circuits (MMICs). The package designs are based on a fused quartz substrate material that offers improved radio frequency (RF) performance through 44 gigahertz (GHz). The small size and weight of the packages make them appropriate for a variety of applications, including phased array antenna systems. Packages were designed in two forms; one for housing a single MMIC chip, the second in the form of a multi-chip phased array module. The single chip array module was developed in three separate sizes, for chips of different geometry and frequency requirements. The phased array module was developed to address packaging directly for antenna applications, and includes transmission line and interconnect structures to support multi-element operation. All packages are fabricated using fused quartz substrate materials. As part of the packaging effort, a test fixture was developed to interface the single chip packages to conventional laboratory instrumentation for characterization of the packaged devices. The package and test fixture designs were both developed in a generic sense, optimizing performance for a wide range of possible applications and devices.

Essential interventions: implementation strategies and proposed packages of care

PubMed Central

2014-01-01

In an effort to accelerate progress towards achieving Millennium Development Goal (MDG) 4 and 5, provision of essential reproductive, maternal, newborn and child health (RMNCH) interventions is being considered. Not only should a state-of-the-art approach be taken for services delivered to the mother, neonate and to the child, but services must also be deployed across the household to hospital continuum of care approach and in the form of packages. The paper proposed several packages for improved maternal, newborn and child health that can be delivered across RMNCH continuum of care. These packages include: supportive care package for women to promote awareness related to healthy pre-pregnancy and pregnancy interventions; nutritional support package for mother to improve supplementation of essential nutrients and micronutrients; antenatal care package to detect, treat and manage infectious and noninfectious diseases and promote immunization; high risk care package to manage preeclampsia and eclampsia in pregnancy; childbirth package to promote support during labor and importance of skilled birth attendance during labor; essential newborn care package to support healthy newborn care practices; and child health care package to prevent and manage infections. This paper further discussed the implementation strategies for employing these interventions at scale. PMID:25178110

Healthy choice?: Exploring how children evaluate the healthfulness of packaged foods.

PubMed

Elliott, Charlene; Brierley, Meaghan

2012-11-06

Today's supermarket contains hundreds of packaged foods specifically targeted at children. Yet research has shown that children are confused by the various visual messages found on packaged food products. This study explores children's nutrition knowledge with regard to packaged food products, to uncover strengths and difficulties they have in evaluating the healthfulness of these foods. Focus groups were conducted with children (grades 1-6). Particular attention was paid to the ways children made use of what they know about nutrition when faced with the visual elements and appeals presented on food packaging. Children relied heavily on packages' written and visual aspects--including colour, images, spokes-characters, front-of-package claims--to assess the healthfulness of a food product. These elements interfere with children's ability to make healthy choices when it comes to packaged foods. Choosing healthy packaged foods is challenging for children due to competing sets of knowledge: one pertains to their understanding of visual, associational cues; the other, to translating their understanding of nutrition to packaged foods. Canada's Food Guide, along with the curriculum taught to Canadian children at schools, does not appear to provide children with the tools necessary to navigate a food environment dominated by packaged foods.

Fabrication and Performance of MEMS-Based Pressure Sensor Packages Using Patterned Ultra-Thick Photoresists

PubMed Central

Chen, Lung-Tai; Chang, Jin-Sheng; Hsu, Chung-Yi; Cheng, Wood-Hi

2009-01-01

A novel plastic packaging of a piezoresistive pressure sensor using a patterned ultra-thick photoresist is experimentally and theoretically investigated. Two pressure sensor packages of the sacrifice-replacement and dam-ring type were used in this study. The characteristics of the packaged pressure sensors were investigated by using a finite-element (FE) model and experimental measurements. The results show that the thermal signal drift of the packaged pressure sensor with a small sensing-channel opening or with a thin silicon membrane for the dam-ring approach had a high packaging induced thermal stress, leading to a high temperature coefficient of span (TCO) response of −0.19% span/°C. The results also show that the thermal signal drift of the packaged pressure sensors with a large sensing-channel opening for sacrifice-replacement approach significantly reduced packaging induced thermal stress, and hence a low TCO response of −0.065% span/°C. However, the packaged pressure sensors of both the sacrifice-replacement and dam-ring type still met the specification −0.2% span/°C of the unpackaged pressure sensor. In addition, the size of proposed packages was 4 × 4 × 1.5 mm3 which was about seven times less than the commercialized packages. With the same packaging requirement, the proposed packaging approaches may provide an adequate solution for use in other open-cavity sensors, such as gas sensors, image sensors, and humidity sensors. PMID:22454580

Which community care for patients with schizophrenic disorders? Packages of care provided by Departments of Mental Health in Lombardy (Italy).

PubMed

Lora, Antonio; Cosentino, Ugo; Gandini, Anna; Zocchetti, Carlo

2007-01-01

The treatment of schizophrenic disorders is the most important challenge for community care. The analysis focuses on packages of care provided to 23.602 patients with a ICD-10 diagnosis of schizophrenic disorder and treated in 2001 by the Departments of Mental Health in Lombardy, Italy. Packages of care refer to a mix of treatments provided to each patient during the year by different settings. Direct costs of the packages were calculated. Linear Discriminant Analysis has been used to link socio-demographic and diagnostic sub-groups of the patients to packages of care. People with schizophrenic disorders received relatively few care packages: only four packages involved more than 5%. Two thirds of the patients received only care provided by Community Mental Health Centres. In the other two packages with a percentage over 5%, the activity was provided by CMHCs, jointly with General Hospitals or Day Care Facilities. Complex care packages were rare (only 6%). As well as the intensity, also the variety of care provided by CMHCs increased with the complexity of care packages. In Lombardy more than half of the resources were spent for schizophrenia. The range of the costs per package was very wide. LDA failed to link characteristics of the patients to packages of care. Care packages are useful tools to understand better how mental health system works, how resources have been spent and to point out problems in the quality of care.

GENERAL PURPOSE ADA PACKAGES

NASA Technical Reports Server (NTRS)

Klumpp, A. R.

1994-01-01

Ten families of subprograms are bundled together for the General-Purpose Ada Packages. The families bring to Ada many features from HAL/S, PL/I, FORTRAN, and other languages. These families are: string subprograms (INDEX, TRIM, LOAD, etc.); scalar subprograms (MAX, MIN, REM, etc.); array subprograms (MAX, MIN, PROD, SUM, GET, and PUT); numerical subprograms (EXP, CUBIC, etc.); service subprograms (DATE_TIME function, etc.); Linear Algebra II; Runge-Kutta integrators; and three text I/O families of packages. In two cases, a family consists of a single non-generic package. In all other cases, a family comprises a generic package and its instances for a selected group of scalar types. All generic packages are designed to be easily instantiated for the types declared in the user facility. The linear algebra package is LINRAG2. This package includes subprograms supplementing those in NPO-17985, An Ada Linear Algebra Package Modeled After HAL/S (LINRAG). Please note that LINRAG2 cannot be compiled without LINRAG. Most packages have widespread applicability, although some are oriented for avionics applications. All are designed to facilitate writing new software in Ada. Several of the packages use conventions introduced by other programming languages. A package of string subprograms is based on HAL/S (a language designed for the avionics software in the Space Shuttle) and PL/I. Packages of scalar and array subprograms are taken from HAL/S or generalized current Ada subprograms. A package of Runge-Kutta integrators is patterned after a built-in MAC (MIT Algebraic Compiler) integrator. Those packages modeled after HAL/S make it easy to translate existing HAL/S software to Ada. The General-Purpose Ada Packages program source code is available on two 360K 5.25" MS-DOS format diskettes. The software was developed using VAX Ada v1.5 under DEC VMS v4.5. It should be portable to any validated Ada compiler and it should execute either interactively or in batch. The largest package requires 205K of main memory on a DEC VAX running VMS. The software was developed in 1989, and is a copyrighted work with all copyright vested in NASA.

Reliability of High I/O High Density CCGA Interconnect Electronic Packages under Extreme Thermal Environment

NASA Technical Reports Server (NTRS)

Ramesham, Rajeshuni

2012-01-01

This paper provides the experimental test results of advanced CCGA packages tested in extreme temperature thermal environments. Standard optical inspection and x-ray non-destructive inspection tools were used to assess the reliability of high density CCGA packages for deep space extreme temperature missions. Ceramic column grid array (CCGA) packages have been increasing in use based on their advantages such as high interconnect density, very good thermal and electrical performances, compatibility with standard surface-mount packaging assembly processes, and so on. CCGA packages are used in space applications such as in logic and microprocessor functions, telecommunications, payload electronics, and flight avionics. As these packages tend to have less solder joint strain relief than leaded packages or more strain relief over lead-less chip carrier packages, the reliability of CCGA packages is very important for short-term and long-term deep space missions. We have employed high density CCGA 1152 and 1272 daisy chained electronic packages in this preliminary reliability study. Each package is divided into several daisy-chained sections. The physical dimensions of CCGA1152 package is 35 mm x 35 mm with a 34 x 34 array of columns with a 1 mm pitch. The dimension of the CCGA1272 package is 37.5 mm x 37.5 mm with a 36 x 36 array with a 1 mm pitch. The columns are made up of 80% Pb/20%Sn material. CCGA interconnect electronic package printed wiring polyimide boards have been assembled and inspected using non-destructive x-ray imaging techniques. The assembled CCGA boards were subjected to extreme temperature thermal atmospheric cycling to assess their reliability for future deep space missions. The resistance of daisy-chained interconnect sections were monitored continuously during thermal cycling. This paper provides the experimental test results of advanced CCGA packages tested in extreme temperature thermal environments. Standard optical inspection and x-ray non-destructive inspection tools were used to assess the reliability of high density CCGA packages for deep space extreme temperature missions. Keywords: Extreme temperatures, High density CCGA qualification, CCGA reliability, solder joint failures, optical inspection, and x-ray inspection.

Packaging Technologies for High Temperature Electronics and Sensors

NASA Technical Reports Server (NTRS)

Chen, Liang-Yu; Hunter, Gary W.; Neudeck, Philip G.; Beheim, Glenn M.; Spry, David J.; Meredith, Roger D.

2013-01-01

This paper reviews ceramic substrates and thick-film metallization based packaging technologies in development for 500 C silicon carbide (SiC) electronics and sensors. Prototype high temperature ceramic chip-level packages and printed circuit boards (PCBs) based on ceramic substrates of aluminum oxide (Al2O3) and aluminum nitride (AlN) have been designed and fabricated. These ceramic substrate-based chip-level packages with gold (Au) thick-film metallization have been electrically characterized at temperatures up to 550 C. A 96% alumina based edge connector for a PCB level subsystem interconnection has also been demonstrated recently. The 96% alumina packaging system composed of chip-level packages and PCBs has been tested with high temperature SiC devices at 500 C for over 10,000 hours. In addition to tests in a laboratory environment, a SiC JFET with a packaging system composed of a 96% alumina chip-level package and an alumina printed circuit board mounted on a data acquisition circuit board was launched as a part of the MISSE-7 suite to the International Space Station via a Shuttle mission. This packaged SiC transistor was successfully tested in orbit for eighteen months. A spark-plug type sensor package designed for high temperature SiC capacitive pressure sensors was developed. This sensor package combines the high temperature interconnection system with a commercial high temperature high pressure stainless steel seal gland (electrical feed-through). Test results of a packaged high temperature capacitive pressure sensor at 500 C are also discussed. In addition to the pressure sensor package, efforts for packaging high temperature SiC diode-based gas chemical sensors are in process.

Packaging Technologies for High Temperature Electronics and Sensors

NASA Technical Reports Server (NTRS)

Chen, Liangyu; Hunter, Gary W.; Neudeck, Philip G.; Beheim, Glenn M.; Spry, David J.; Meredith, Roger D.

2013-01-01

This paper reviews ceramic substrates and thick-film metallization based packaging technologies in development for 500degC silicon carbide (SiC) electronics and sensors. Prototype high temperature ceramic chip-level packages and printed circuit boards (PCBs) based on ceramic substrates of aluminum oxide (Al2O3) and aluminum nitride (AlN) have been designed and fabricated. These ceramic substrate-based chiplevel packages with gold (Au) thick-film metallization have been electrically characterized at temperatures up to 550degC. A 96% alumina based edge connector for a PCB level subsystem interconnection has also been demonstrated recently. The 96% alumina packaging system composed of chip-level packages and PCBs has been tested with high temperature SiC devices at 500degC for over 10,000 hours. In addition to tests in a laboratory environment, a SiC JFET with a packaging system composed of a 96% alumina chip-level package and an alumina printed circuit board mounted on a data acquisition circuit board was launched as a part of the MISSE-7 suite to the International Space Station via a Shuttle mission. This packaged SiC transistor was successfully tested in orbit for eighteen months. A spark-plug type sensor package designed for high temperature SiC capacitive pressure sensors was developed. This sensor package combines the high temperature interconnection system with a commercial high temperature high pressure stainless steel seal gland (electrical feed-through). Test results of a packaged high temperature capacitive pressure sensor at 500degC are also discussed. In addition to the pressure sensor package, efforts for packaging high temperature SiC diode-based gas chemical sensors are in process.

Multilayered microelectronic device package with an integral window

DOEpatents

Peterson, Kenneth A.; Watson, Robert D.

2003-01-01

An apparatus for packaging of microelectronic devices is disclosed, wherein the package includes an integral window. The microelectronic device can be a semiconductor chip, a CCD chip, a CMOS chip, a VCSEL chip, a laser diode, a MEMS device, or a IMEMS device. The package can comprise, for example, a cofired ceramic frame or body. The package has an internal stepped structure made of a plurality of plates, with apertures, which are patterned with metallized conductive circuit traces. The microelectronic device can be flip-chip bonded on the plate to these traces, and oriented so that the light-sensitive side is optically accessible through the window. A cover lid can be attached to the opposite side of the package. The result is a compact, low-profile package, having an integral window that can be hermetically-sealed. The package body can be formed by low-temperature cofired ceramic (LTCC) or high-temperature cofired ceramic (HTCC) multilayer processes with the window being simultaneously joined (e.g. cofired) to the package body during LTCC or HTCC processing. Multiple chips can be located within a single package, according to some embodiments. The cover lid can include a window. The apparatus is particularly suited for packaging of MEMS devices, since the number of handling steps is greatly reduced, thereby reducing the potential for contamination. The integral window can further include a lens for optically transforming light passing through the window. The package can include an array of binary optic lenslets made integral with the window. The package can include an electrically-switched optical modulator, such as a lithium niobate window attached to the package, for providing a very fast electrically-operated shutter.

Short communication: Effect of active food packaging materials on fluid milk quality and shelf life.

PubMed

Wong, Dana E; Goddard, Julie M

2014-01-01

Active packaging, in which active agents are embedded into or on the surface of food packaging materials, can enhance the nutritive value, economics, and stability of food, as well as enable in-package processing. In one embodiment of active food packaging, lactase was covalently immobilized onto packaging films for in-package lactose hydrolysis. In prior work, lactase was covalently bound to low-density polyethylene using polyethyleneimine and glutaraldehyde cross-linkers to form the packaging film. Because of the potential contaminants of proteases, lipases, and spoilage organisms in typical enzyme preparations, the goal of the current work was to determine the effect of immobilized-lactase active packaging technology on unanticipated side effects, such as shortened shelf-life and reduced product quality. Results suggested no evidence of lipase or protease activity on the active packaging films, indicating that such active packaging films could enable in-package lactose hydrolysis without adversely affecting product quality in terms of dairy protein or lipid stability. Storage stability studies indicated that lactase did not migrate from the film over a 49-d period, and that dry storage resulted in 13.41% retained activity, whereas wet storage conditions enabled retention of 62.52% activity. Results of a standard plate count indicated that the film modification reagents introduced minor microbial contamination; however, the microbial population remained under the 20,000 cfu/mL limit through the manufacturer's suggested 14-d storage period for all film samples. This suggests that commercially produced immobilized lactase active packaging should use purified cross-linkers and enzymes. Characterization of unanticipated effects of active packaging on food quality reported here is important in demonstrating the commercial potential of such technologies. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Common Ada (tradename) Missile Package (CAMP) Project. Missile Software Parts. Volume 8. Detail Design Document

DTIC Science & Technology

1988-03-01

PACKAGE BODY ) TLCSC P661 (CATALOG #P106-0) This package contains the CAMP parts required to do the vaypoint steering portion of navigation. The...3.3.4.1.6 PROCESSING The following describes the processing performed by this part: package body WaypointSteering is package body ...Steering_Vector_Operations is separate; package body Steering_Vector_Operations_with_Arcsin is separate; procedure Compute Turn_Angle_and Direction (UnitNormal C

Function Package for Computing Quantum Resource Measures

NASA Astrophysics Data System (ADS)

Huang, Zhiming

2018-05-01

In this paper, we present a function package for to calculate quantum resource measures and dynamics of open systems. Our package includes common operators and operator lists, frequently-used functions for computing quantum entanglement, quantum correlation, quantum coherence, quantum Fisher information and dynamics in noisy environments. We briefly explain the functions of the package and illustrate how to use the package with several typical examples. We expect that this package is a useful tool for future research and education.

19 CFR 11.3 - Package and notice requirements for cigars and cigarettes; package requirements for cigarette...

Code of Federal Regulations, 2013 CFR

2013-04-01

... cigarettes; package requirements for cigarette papers and tubes. 11.3 Section 11.3 Customs Duties U.S... STAMPING; MARKING Packing and Stamping § 11.3 Package and notice requirements for cigars and cigarettes; package requirements for cigarette papers and tubes. Exemptions from tax on cigars, cigarettes, and...

19 CFR 11.3 - Package and notice requirements for cigars and cigarettes; package requirements for cigarette...

Code of Federal Regulations, 2011 CFR

2011-04-01

... cigarettes; package requirements for cigarette papers and tubes. 11.3 Section 11.3 Customs Duties U.S... STAMPING; MARKING Packing and Stamping § 11.3 Package and notice requirements for cigars and cigarettes; package requirements for cigarette papers and tubes. Exemptions from tax on cigars, cigarettes, and...

49 CFR 173.474 - Quality control for construction of packaging.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 2 2011-10-01 2011-10-01 false Quality control for construction of packaging. 173...-GENERAL REQUIREMENTS FOR SHIPMENTS AND PACKAGINGS Class 7 (Radioactive) Materials § 173.474 Quality control for construction of packaging. Prior to the first use of any packaging for the shipment of Class 7...

49 CFR 173.474 - Quality control for construction of packaging.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Quality control for construction of packaging. 173...-GENERAL REQUIREMENTS FOR SHIPMENTS AND PACKAGINGS Class 7 (Radioactive) Materials § 173.474 Quality control for construction of packaging. Prior to the first use of any packaging for the shipment of Class 7...

49 CFR 178.935 - Standards for wooden Large Packagings.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Packagings. (i) Natural wood used in the construction of Large Packagings must be well-seasoned, commercially...) Reconstituted wood used in the construction of Large Packagings must be water resistant reconstituted wood such... Packaging types are designated: (1) 50C natural wood. (2) 50D plywood. (3) 50F reconstituted wood. (b...

9 CFR 381.144 - Packaging materials.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 2 2011-01-01 2011-01-01 false Packaging materials. 381.144 Section... Packaging materials. (a) Edible products may not be packaged in a container which is composed in whole or in... to health. All packaging materials must be safe for the intended use within the meaning of section...

49 CFR 178.523 - Standards for composite packagings with inner glass, porcelain, or stoneware receptacles.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Standards for composite packagings with inner... Packaging Standards § 178.523 Standards for composite packagings with inner glass, porcelain, or stoneware receptacles. (a) The following are identification codes for composite packagings with inner receptacles of...

19 CFR 11.3 - Package and notice requirements for cigars and cigarettes; package requirements for cigarette...

Code of Federal Regulations, 2014 CFR

2014-04-01

... cigarettes; package requirements for cigarette papers and tubes. 11.3 Section 11.3 Customs Duties U.S... STAMPING; MARKING Packing and Stamping § 11.3 Package and notice requirements for cigars and cigarettes; package requirements for cigarette papers and tubes. Exemptions from tax on cigars, cigarettes, and...

19 CFR 11.3 - Package and notice requirements for cigars and cigarettes; package requirements for cigarette...

Code of Federal Regulations, 2010 CFR

2010-04-01

... cigarettes; package requirements for cigarette papers and tubes. 11.3 Section 11.3 Customs Duties U.S... STAMPING; MARKING Packing and Stamping § 11.3 Package and notice requirements for cigars and cigarettes; package requirements for cigarette papers and tubes. Exemptions from tax on cigars, cigarettes, and...

19 CFR 11.3 - Package and notice requirements for cigars and cigarettes; package requirements for cigarette...

Code of Federal Regulations, 2012 CFR

2012-04-01

... cigarettes; package requirements for cigarette papers and tubes. 11.3 Section 11.3 Customs Duties U.S... STAMPING; MARKING Packing and Stamping § 11.3 Package and notice requirements for cigars and cigarettes; package requirements for cigarette papers and tubes. Exemptions from tax on cigars, cigarettes, and...

19 CFR 10.922 - Retail packaging materials and containers.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 19 Customs Duties 1 2014-04-01 2014-04-01 false Retail packaging materials and containers. 10.922... Trade Promotion Agreement Rules of Origin § 10.922 Retail packaging materials and containers. (a) Effect on tariff shift rule. Packaging materials and containers in which a good is packaged for retail sale...

19 CFR 10.922 - Retail packaging materials and containers.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 19 Customs Duties 1 2013-04-01 2013-04-01 false Retail packaging materials and containers. 10.922... Trade Promotion Agreement Rules of Origin § 10.922 Retail packaging materials and containers. (a) Effect on tariff shift rule. Packaging materials and containers in which a good is packaged for retail sale...

19 CFR 10.461 - Retail packaging materials and containers.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 19 Customs Duties 1 2011-04-01 2011-04-01 false Retail packaging materials and containers. 10.461... Free Trade Agreement Rules of Origin § 10.461 Retail packaging materials and containers. Packaging materials and containers in which a good is packaged for retail sale, if classified with the good for which...

19 CFR 10.922 - Retail packaging materials and containers.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 19 Customs Duties 1 2012-04-01 2012-04-01 false Retail packaging materials and containers. 10.922... Trade Promotion Agreement Rules of Origin § 10.922 Retail packaging materials and containers. (a) Effect on tariff shift rule. Packaging materials and containers in which a good is packaged for retail sale...

19 CFR 10.1022 - Retail packaging materials and containers.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 19 Customs Duties 1 2012-04-01 2012-04-01 false Retail packaging materials and containers. 10.1022... Free Trade Agreement Rules of Origin § 10.1022 Retail packaging materials and containers. (a) Effect on tariff shift rule. Packaging materials and containers in which a good is packaged for retail sale, if...

19 CFR 10.3022 - Retail packaging materials and containers.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 19 Customs Duties 1 2013-04-01 2013-04-01 false Retail packaging materials and containers. 10.3022...-Colombia Trade Promotion Agreement Rules of Origin § 10.3022 Retail packaging materials and containers. (a) Effect on tariff shift rule. Packaging materials and containers in which a good is packaged for retail...

19 CFR 10.461 - Retail packaging materials and containers.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 19 Customs Duties 1 2013-04-01 2013-04-01 false Retail packaging materials and containers. 10.461... Free Trade Agreement Rules of Origin § 10.461 Retail packaging materials and containers. Packaging materials and containers in which a good is packaged for retail sale, if classified with the good for which...

19 CFR 10.3022 - Retail packaging materials and containers.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 19 Customs Duties 1 2014-04-01 2014-04-01 false Retail packaging materials and containers. 10.3022...-Colombia Trade Promotion Agreement Rules of Origin § 10.3022 Retail packaging materials and containers. (a) Effect on tariff shift rule. Packaging materials and containers in which a good is packaged for retail...

19 CFR 10.461 - Retail packaging materials and containers.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 19 Customs Duties 1 2014-04-01 2014-04-01 false Retail packaging materials and containers. 10.461... Free Trade Agreement Rules of Origin § 10.461 Retail packaging materials and containers. Packaging materials and containers in which a good is packaged for retail sale, if classified with the good for which...

19 CFR 10.539 - Retail packaging materials and containers.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 19 Customs Duties 1 2013-04-01 2013-04-01 false Retail packaging materials and containers. 10.539...-Singapore Free Trade Agreement Rules of Origin § 10.539 Retail packaging materials and containers. Packaging materials and containers in which a good is packaged for retail sale, if classified with the good for which...

19 CFR 10.1022 - Retail packaging materials and containers.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 19 Customs Duties 1 2014-04-01 2014-04-01 false Retail packaging materials and containers. 10.1022... Free Trade Agreement Rules of Origin § 10.1022 Retail packaging materials and containers. (a) Effect on tariff shift rule. Packaging materials and containers in which a good is packaged for retail sale, if...

19 CFR 10.461 - Retail packaging materials and containers.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 19 Customs Duties 1 2012-04-01 2012-04-01 false Retail packaging materials and containers. 10.461... Free Trade Agreement Rules of Origin § 10.461 Retail packaging materials and containers. Packaging materials and containers in which a good is packaged for retail sale, if classified with the good for which...

19 CFR 10.539 - Retail packaging materials and containers.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 19 Customs Duties 1 2014-04-01 2014-04-01 false Retail packaging materials and containers. 10.539...-Singapore Free Trade Agreement Rules of Origin § 10.539 Retail packaging materials and containers. Packaging materials and containers in which a good is packaged for retail sale, if classified with the good for which...

19 CFR 10.539 - Retail packaging materials and containers.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 19 Customs Duties 1 2011-04-01 2011-04-01 false Retail packaging materials and containers. 10.539...-Singapore Free Trade Agreement Rules of Origin § 10.539 Retail packaging materials and containers. Packaging materials and containers in which a good is packaged for retail sale, if classified with the good for which...

19 CFR 10.539 - Retail packaging materials and containers.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 19 Customs Duties 1 2012-04-01 2012-04-01 false Retail packaging materials and containers. 10.539...-Singapore Free Trade Agreement Rules of Origin § 10.539 Retail packaging materials and containers. Packaging materials and containers in which a good is packaged for retail sale, if classified with the good for which...

19 CFR 10.1022 - Retail packaging materials and containers.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 19 Customs Duties 1 2013-04-01 2013-04-01 false Retail packaging materials and containers. 10.1022... Free Trade Agreement Rules of Origin § 10.1022 Retail packaging materials and containers. (a) Effect on tariff shift rule. Packaging materials and containers in which a good is packaged for retail sale, if...

49 CFR 373.105 - Low value packages.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 5 2010-10-01 2010-10-01 false Low value packages. 373.105 Section 373.105... Carrier Receipts and Bills § 373.105 Low value packages. The carrier and shipper may elect to waive the... “low value” packages. This includes the option of shipping such packages under the provisions of 49 U.S...

10 CFR 60.135 - Criteria for the waste package and its components.

Code of Federal Regulations, 2011 CFR

2011-01-01

... IN GEOLOGIC REPOSITORIES Technical Criteria Design Criteria for the Waste Package § 60.135 Criteria for the waste package and its components. (a) High-level-waste package design in general. (1) Packages for HLW shall be designed so that the in situ chemical, physical, and nuclear properties of the waste...

10 CFR 60.135 - Criteria for the waste package and its components.

Code of Federal Regulations, 2013 CFR

2013-01-01

... IN GEOLOGIC REPOSITORIES Technical Criteria Design Criteria for the Waste Package § 60.135 Criteria for the waste package and its components. (a) High-level-waste package design in general. (1) Packages for HLW shall be designed so that the in situ chemical, physical, and nuclear properties of the waste...

10 CFR 60.135 - Criteria for the waste package and its components.

Code of Federal Regulations, 2014 CFR

2014-01-01

... IN GEOLOGIC REPOSITORIES Technical Criteria Design Criteria for the Waste Package § 60.135 Criteria for the waste package and its components. (a) High-level-waste package design in general. (1) Packages for HLW shall be designed so that the in situ chemical, physical, and nuclear properties of the waste...

10 CFR 60.135 - Criteria for the waste package and its components.

Code of Federal Regulations, 2012 CFR

2012-01-01

... IN GEOLOGIC REPOSITORIES Technical Criteria Design Criteria for the Waste Package § 60.135 Criteria for the waste package and its components. (a) High-level-waste package design in general. (1) Packages for HLW shall be designed so that the in situ chemical, physical, and nuclear properties of the waste...

7 CFR 993.501 - Consumer package of prunes.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 8 2011-01-01 2011-01-01 false Consumer package of prunes. 993.501 Section 993.501... CALIFORNIA Pack Specification as to Size Definitions § 993.501 Consumer package of prunes. Consumer package of prunes means consumer package as defined in § 993.22. Effective Date Note: At 70 FR 30613, May 27...

"Plain packaging" regulations for tobacco products: the impact of standardizing the color and design of cigarette packs.

PubMed

Hammond, David

2010-01-01

Tobacco packaging and labeling policies have emerged as prominent and cost-effective tobacco control measures. Although packaging policies have primarily focused on health warnings, there is growing recognition of the importance of packaging as a marketing tool for the tobacco industry. The current paper reviews evidence on the potential impact of standardizing the color and design of tobacco packages -so called "plain" packaging. The evidence indicates three primary benefits of plain packaging: increasing the effectiveness of health warnings, reducing false health beliefs about cigarettes, and reducing brand appeal especially among youth and young adults. Overall, the research to date suggests that "plain" packaging regulations would be an effective tobacco control measure, particularly in jurisdictions with comprehensive restrictions on other forms of marketing.

Quality and safety aspects of meat products as affected by various physical manipulations of packaging materials.

PubMed

Lee, Keun Taik

2010-09-01

This article explores the effects of physically manipulated packaging materials on the quality and safety of meat products. Recently, innovative measures for improving quality and extending the shelf-life of packaged meat products have been developed, utilizing technologies including barrier film, active packaging, nanotechnology, microperforation, irradiation, plasma and far-infrared ray (FIR) treatments. Despite these developments, each technology has peculiar drawbacks which will need to be addressed by meat scientists in the future. To develop successful meat packaging systems, key product characteristics affecting stability, environmental conditions during storage until consumption, and consumers' packaging expectations must all be taken into consideration. Furthermore, the safety issues related to packaging materials must also be taken into account when processing, packaging and storing meat products.

Packaging films for electronic and space-related hardware

NASA Astrophysics Data System (ADS)

Shon, E. M.; Hamberg, O.

1985-08-01

Flexible packaging films are used to bag and/or wrap precision cleaned electronic or space hardware to protect them from environmental degradation during shipping and storage. Selection of packaging films depends on a knowledge of product requirements and packaging film characteristics. The literature presently available on protective packaging films has been updated to include new materials and to amplify space-related applications. Presently available packaging film materials are compared for their various characteristics: electrostatic discharge (ESD) control, flame retardancy, water vapor transmission rate, particulate shedding, molecular contamination, and transparency. The tradeoff between product requirements and the characteristics of the packaging films available are discussed. Selection considerations are given for the application of specific materials of space hardware-related applications. Applications for intimate, environmental, and electrostatic protective packaging are discussed.

Definition of Small Gram Quantity Contents for Type B Radioactive Material Transportation Packages: Activity-Based Content Limitations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sitaraman, S; Kim, S; Biswas, D

2010-10-27

Since the 1960's, the Department of Transportation Specification (DOT Spec) 6M packages have been used extensively for transportation of Type B quantities of radioactive materials between Department of Energy (DOE) facilities, laboratories, and productions sites. However, due to the advancement of packaging technology, the aging of the 6M packages, and variability in the quality of the packages, the DOT implemented a phased elimination of the 6M specification packages (and other DOT Spec packages) in favor of packages certified to meet federal performance requirements. DOT issued the final rule in the Federal Register on October 1, 2004 requiring that use ofmore » the DOT Specification 6M be discontinued as of October 1, 2008. A main driver for the change was the fact that the 6M specification packagings were not supported by a Safety Analysis Report for Packaging (SARP) that was compliant with Title 10 of the Code of Federal Regulations part 71 (10 CFR 71). Therefore, materials that would have historically been shipped in 6M packages are being identified as contents in Type B (and sometimes Type A fissile) package applications and addenda that are to be certified under the requirements of 10 CFR 71. The requirements in 10 CFR 71 include that the Safety Analysis Report for Packaging (SARP) must identify the maximum radioactivity of radioactive constituents and maximum quantities of fissile constituents (10 CFR 71.33(b)(1) and 10 CFR 71.33(b)(2)), and that the application (i.e., SARP submittal or SARP addendum) demonstrates that the external dose rate (due to the maximum radioactivity of radioactive constituents and maximum quantities of fissile constituents) on the surface of the packaging (i.e., package and contents) not exceed 200 mrem/hr (10 CFR 71.35(a), 10 CFR 71.47(a)). It has been proposed that a 'Small Gram Quantity' of radioactive material be defined, such that, when loaded in a transportation package, the dose rates at external points of an unshielded packaging not exceed the regulatory limits prescribed by 10 CFR 71 for non-exclusive shipments. The mass of each radioisotope presented in this paper is limited by the radiation dose rate on the external surface of the package, which per the regulatory limit should not exceed 200 mrem/hr. The results presented are a compendium of allowable masses of a variety of different isotopes (with varying impurity levels of beryllium in some of the actinide isotopes) that, when loaded in an unshielded packaging, do not result in an external dose rate on the surface of the package that exceeds 190 mrem/hr (190 mrem/hr was chosen to provide 5% conservatism relative to the regulatory limit). These mass limits define the term 'Small Gram Quantity' (SGQ) contents in the context of radioactive material transportation packages. The term SGQ is isotope-specific and pertains to contents in radioactive material transportation packages that do not require shielding and still satisfy the external dose rate requirements. Since these calculated mass limits are for contents without shielding, they are conservative for packaging materials that provide some limited shielding or if the contents are placed into a shielded package. The isotopes presented in this paper were chosen as the isotopes that Department of Energy (DOE) sites most likely need to ship. Other more rarely shipped isotopes, along with industrial and medical isotopes, are planned to be included in subsequent extensions of this work.« less

Data from fitting Gaussian process models to various data sets using eight Gaussian process software packages.

PubMed

Erickson, Collin B; Ankenman, Bruce E; Sanchez, Susan M

2018-06-01

This data article provides the summary data from tests comparing various Gaussian process software packages. Each spreadsheet represents a single function or type of function using a particular input sample size. In each spreadsheet, a row gives the results for a particular replication using a single package. Within each spreadsheet there are the results from eight Gaussian process model-fitting packages on five replicates of the surface. There is also one spreadsheet comparing the results from two packages performing stochastic kriging. These data enable comparisons between the packages to determine which package will give users the best results.

Packaging Technologies for 500 C SiC Electronics and Sensors: Challenges in Material Science and Technology

NASA Technical Reports Server (NTRS)

Chen, Liang-Yu; Neudeck, Philip G.; Behelm, Glenn M.; Spry, David J.; Meredith, Roger D.; Hunter, Gary W.

2015-01-01

This paper presents ceramic substrates and thick-film metallization based packaging technologies in development for 500C silicon carbide (SiC) electronics and sensors. Prototype high temperature ceramic chip-level packages and printed circuit boards (PCBs) based on ceramic substrates of aluminum oxide (Al2O3) and aluminum nitride (AlN) have been designed and fabricated. These ceramic substrate-based chip-level packages with gold (Au) thick-film metallization have been electrically characterized at temperatures up to 550C. The 96 alumina packaging system composed of chip-level packages and PCBs has been successfully tested with high temperature SiC discrete transistor devices at 500C for over 10,000 hours. In addition to tests in a laboratory environment, a SiC junction field-effect-transistor (JFET) with a packaging system composed of a 96 alumina chip-level package and an alumina printed circuit board was tested on low earth orbit for eighteen months via a NASA International Space Station experiment. In addition to packaging systems for electronics, a spark-plug type sensor package based on this high temperature interconnection system for high temperature SiC capacitive pressure sensors was also developed and tested. In order to further significantly improve the performance of packaging system for higher packaging density, higher operation frequency, power rating, and even higher temperatures, some fundamental material challenges must be addressed. This presentation will discuss previous development and some of the challenges in material science (technology) to improve high temperature dielectrics for packaging applications.

Effect on moisture permeability of typewriting on unit dose package surfaces.

PubMed

Rackson, J T; Zellhofer, M J; Birmingham, P H

1984-10-01

The effects of typewriting on labels of two unit dose packages with respect to moisture permeability were examined. Using an electric typewriter, a standard label format was imprinted on two different types of class A unit dose packages: (1) a heat-sealed paper-backed foil and cellofilm strip pouch, and (2) a copolyester and polyethylene multiple-cup blister with a heat-sealed paper-backed foil and cellofilm cover. The labels were typed at various typing-element impact settings. The official USP test for water permeation was then performed on typed packages and untyped control packages. The original untyped packages were confirmed to be USP class A quality. The packages for which successively harder impact settings were used showed a corresponding increase in moisture permeability. This resulted in a lowering of USP package ratings from class A to class B and D, some of which would be unsuitable for use in any unit dose system under current FDA repackaging standards. Typing directly onto the label of a unit dose package before it is sealed will most likely damage the package and possibly make it unfit for use. Pharmacists who must type labels for the unit dose packages studied should use the lowest possible typewriter impact setting and test for damage using the USP moisture-permeation test.

Hidden costs of antiretroviral treatment: the public health efficiency of drug packaging.

PubMed

Andreu-Crespo, Àngels; Llibre, Josep M; Cardona-Peitx, Glòria; Sala-Piñol, Ferran; Clotet, Bonaventura; Bonafont-Pujol, Xavier

2015-01-01

While the overall percentage of unused antiretroviral medicines returned to the hospital pharmacy is low, their cost is quite high. Adverse events, treatment failure, pharmacokinetic interactions, pregnancy, or treatment simplification are common reasons for unplanned treatment changes. Socially inefficient antiretroviral packages prevent the reuse of drugs returned to the hospital pharmacy. We defined antiretroviral package categories based on the excellence of drug packaging and analyzed the number of pills and costs of drugs returned during a period of 1 year in a hospital-based HIV unit attending to 2,413 treated individuals. A total of 6,090 pills (34% of all returned antiretrovirals) - with a cost of 47,139.91 € - would be totally lost, mainly due to being packed up in the lowest efficiency packages. Newer treatments are packaged in low-excellence categories of packages, thus favoring the maintenance of these hidden costs in the near future. Therefore, costs of this low-efficiency drug packaging, where medication packages are started but not completed, in high-cost medications are substantial and should be properly addressed. Any improvement in the packaging by the manufacturer, and favoring the choice of drugs supplied through efficient packages (when efficacy, toxicity, and convenience are similar), should minimize the treatment expenditures paid by national health budgets.

Hidden costs of antiretroviral treatment: the public health efficiency of drug packaging

PubMed Central

Andreu-Crespo, Àngels; Llibre, Josep M; Cardona-Peitx, Glòria; Sala-Piñol, Ferran; Clotet, Bonaventura; Bonafont-Pujol, Xavier

2015-01-01

While the overall percentage of unused antiretroviral medicines returned to the hospital pharmacy is low, their cost is quite high. Adverse events, treatment failure, pharmacokinetic interactions, pregnancy, or treatment simplification are common reasons for unplanned treatment changes. Socially inefficient antiretroviral packages prevent the reuse of drugs returned to the hospital pharmacy. We defined antiretroviral package categories based on the excellence of drug packaging and analyzed the number of pills and costs of drugs returned during a period of 1 year in a hospital-based HIV unit attending to 2,413 treated individuals. A total of 6,090 pills (34% of all returned antiretrovirals) – with a cost of 47,139.91€ – would be totally lost, mainly due to being packed up in the lowest efficiency packages. Newer treatments are packaged in low-excellence categories of packages, thus favoring the maintenance of these hidden costs in the near future. Therefore, costs of this low-efficiency drug packaging, where medication packages are started but not completed, in high-cost medications are substantial and should be properly addressed. Any improvement in the packaging by the manufacturer, and favoring the choice of drugs supplied through efficient packages (when efficacy, toxicity, and convenience are similar), should minimize the treatment expenditures paid by national health budgets. PMID:26273190

MEMS packaging: state of the art and future trends

NASA Astrophysics Data System (ADS)

Bossche, Andre; Cotofana, Carmen V. B.; Mollinger, Jeff R.

1998-07-01

Now that the technology for Integrated sensor and MEMS devices has become sufficiently mature to allow mass production, it is expected that the prices of bare chips will drop dramatically. This means that the package prices will become a limiting factor in market penetration, unless low cost packaging solutions become available. This paper will discuss the developments in packaging technology. Both single-chip and multi-chip packaging solutions will be addressed. It first starts with a discussion on the different requirements that have to be met; both from a device point of view (open access paths to the environment, vacuum cavities, etc.) and from the application point of view (e.g. environmental hostility). Subsequently current technologies are judged on their applicability for MEMS and sensor packaging and a forecast is given for future trends. It is expected that the large majority of sensing devices will be applied in relative friendly environments for which plastic packages would suffice. Therefore, on the short term an important role is foreseen for recently developed plastic packaging techniques such as precision molding and precision dispensing. Just like in standard electronic packaging, complete wafer level packaging methods for sensing devices still have a long way to go before they can compete with the highly optimized and automated plastic packaging processes.

Savannah River Site Eastern Transportation Hub: A Concept For a DOE Eastern Packaging, Staging and Maintenance Center - 13143

DOE Office of Scientific and Technical Information (OSTI.GOV)

England, Jeffery L.; Adams, Karen; Maxted, Maxcine

2013-07-01

The Department of Energy (DOE) is working to de-inventory sites and consolidate hazardous materials for processing and disposal. The DOE administers a wide range of certified shipping packages for the transport of hazardous materials to include Special Nuclear Material (SNM), radioactive materials, sealed sources and radioactive wastes. A critical element to successful and safe transportation of these materials is the availability of certified shipping packages. There are over seven thousand certified packagings (i.e., Type B/Type AF) utilized within the DOE for current missions. The synergistic effects of consolidated maintenance, refurbishment, testing, certification, and costing of these services would allow formore » efficient management of the packagings inventory and to support anticipated future in-commerce shipping needs. The Savannah River Site (SRS) receives and ships radioactive materials (including SNM) and waste on a regular basis for critical missions such as consolidated storage, stabilization, purification, or disposition using H-Canyon and HB-Line. The Savannah River National Laboratory (SRNL) has the technical capability and equipment for all aspects of packaging management. SRS has the only active material processing facility in the DOE complex and is one of the sites of choice for nuclear material consolidation. SRS is a logical location to perform maintenance and periodic testing of the DOE fleet of certified packagings. This initiative envisions a DOE Eastern Packaging Staging and Maintenance Center (PSMC) at the SRS and a western hub at the Nevada National Security Site (NNSS), an active DOE Regional Disposal Site. The PSMC's would be the first place DOE would go to meet their radioactive packaging needs and the primary locations projects would go to disposition excess packaging for beneficial reuse. These two hubs would provide the centralized management of a packaging fleet rather than the current approach to design, procure, maintain and dispose of packagings on a project-by-project basis. This initiative provides significant savings in packaging costs and acceleration of project schedules. In addition to certified packaging, the PSMC would be well suited for select designs of 7A Type A packaging and Industrial Packaging. (authors)« less

Youth Work Training Package Review: More of the Same or Radical Rationalisation?

ERIC Educational Resources Information Center

Corney, Tim; Broadbent, Robyn

2007-01-01

The development of a national youth work training package in Australia began over 15 years ago. The current package sits under the umbrella of the general Community Services Industry Training Package. The first stage of a review of this package has been completed and the subsequent report not only confirms the recent trend towards the…

Think INSIDE the Box: Package Engineering

ERIC Educational Resources Information Center

Snyder, Mark; Painter, Donna

2014-01-01

Most products people purchase, keep in their homes, and often discard, are typically packaged in some way. Packaging is so prevalent in daily lives that many of take it for granted. That is by design-the expectation of good packaging is that it exists for the sake of the product. The primary purposes of any package (to contain, inform, display,…

75 FR 33637 - United States v. Bemis Company, Inc., et al.; Public Comments and Response on Proposed Final...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-14

... shredded natural cheese packaged for retail sale and flexible-packaging shrink bags for fresh meat in the..., production, and sale of flexible-packaging rollstock for chunk, sliced, and shredded natural cheese packaged..., sliced, and shredded natural cheese packaged for retail sale from two to one, would have eliminated...

19 CFR 158.4 - Liability of carrier for lost or missing packages.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 19 Customs Duties 2 2012-04-01 2012-04-01 false Liability of carrier for lost or missing packages... EXPORTED Lost or Missing Packages and Deficiencies in Contents of Packages § 158.4 Liability of carrier for lost or missing packages. Upon a joint determination or independent determination of quantity as set...

19 CFR 158.4 - Liability of carrier for lost or missing packages.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 19 Customs Duties 2 2013-04-01 2013-04-01 false Liability of carrier for lost or missing packages... EXPORTED Lost or Missing Packages and Deficiencies in Contents of Packages § 158.4 Liability of carrier for lost or missing packages. Upon a joint determination or independent determination of quantity as set...

19 CFR 158.4 - Liability of carrier for lost or missing packages.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 19 Customs Duties 2 2011-04-01 2011-04-01 false Liability of carrier for lost or missing packages... EXPORTED Lost or Missing Packages and Deficiencies in Contents of Packages § 158.4 Liability of carrier for lost or missing packages. Upon a joint determination or independent determination of quantity as set...

19 CFR 158.4 - Liability of carrier for lost or missing packages.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 19 Customs Duties 2 2014-04-01 2014-04-01 false Liability of carrier for lost or missing packages... EXPORTED Lost or Missing Packages and Deficiencies in Contents of Packages § 158.4 Liability of carrier for lost or missing packages. Upon a joint determination or independent determination of quantity as set...

19 CFR 158.4 - Liability of carrier for lost or missing packages.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 19 Customs Duties 2 2010-04-01 2010-04-01 false Liability of carrier for lost or missing packages... EXPORTED Lost or Missing Packages and Deficiencies in Contents of Packages § 158.4 Liability of carrier for lost or missing packages. Upon a joint determination or independent determination of quantity as set...

A Description and Analysis of the German Packaging Take-Back System

ERIC Educational Resources Information Center

Nakajima, Nina; Vanderburg, Willem H.

2006-01-01

The German packaging ordinance is an example of legislated extended producer responsibility (also known as product take-back). Consumers can leave packaging with retailers, and packagers are required to pay for their recycling and disposal. It can be considered to be successful in reducing waste, spurring the redesign of packaging to be more…

49 CFR Appendix B to Part 173 - Procedure for Testing Chemical Compatibility and Rate of Permeation in Plastic Packaging and...

Code of Federal Regulations, 2011 CFR

2011-10-01

... Rate of Permeation in Plastic Packaging and Receptacles B Appendix B to Part 173 Transportation Other... Plastic Packaging and Receptacles 1. The purpose of this procedure is to determine the chemical compatibility and permeability of liquid hazardous materials packaged in plastic packaging and receptacles...

49 CFR 173.28 - Reuse, reconditioning and remanufacture of packagings.

Code of Federal Regulations, 2012 CFR

2012-10-01

... non-bulk packaging. A non-bulk packaging used more than once must conform to the following provisions and limitations: (1) A non-bulk packaging which, upon inspection, shows evidence of a reduction in... thickness of 1.0 mm (0.039 inch). (6) A previously used non-bulk packaging may be reused for the shipment of...

49 CFR 173.28 - Reuse, reconditioning and remanufacture of packagings.

Code of Federal Regulations, 2011 CFR

2011-10-01

... non-bulk packaging. A non-bulk packaging used more than once must conform to the following provisions and limitations: (1) A non-bulk packaging which, upon inspection, shows evidence of a reduction in... thickness of 1.0 mm (0.039 inch). (6) A previously used non-bulk packaging may be reused for the shipment of...

49 CFR 173.28 - Reuse, reconditioning and remanufacture of packagings.

Code of Federal Regulations, 2013 CFR

2013-10-01

... non-bulk packaging. A non-bulk packaging used more than once must conform to the following provisions and limitations: (1) A non-bulk packaging which, upon inspection, shows evidence of a reduction in... thickness of 1.0 mm (0.039 inch). (6) A previously used non-bulk packaging may be reused for the shipment of...

49 CFR 173.28 - Reuse, reconditioning and remanufacture of packagings.

Code of Federal Regulations, 2014 CFR

2014-10-01

... non-bulk packaging. A non-bulk packaging used more than once must conform to the following provisions and limitations: (1) A non-bulk packaging which, upon inspection, shows evidence of a reduction in... thickness of 1.0 mm (0.039 inch). (6) A previously used non-bulk packaging may be reused for the shipment of...

49 CFR 173.28 - Reuse, reconditioning and remanufacture of packagings.

Code of Federal Regulations, 2010 CFR

2010-10-01

... non-bulk packaging. A non-bulk packaging used more than once must conform to the following provisions and limitations: (1) A non-bulk packaging which, upon inspection, shows evidence of a reduction in... thickness of 1.0 mm (0.039 inch). (6) A previously used non-bulk packaging may be reused for the shipment of...

49 CFR Appendix B to Part 173 - Procedure for Testing Chemical Compatibility and Rate of Permeation in Plastic Packaging and...

Code of Federal Regulations, 2010 CFR

2010-10-01

... Rate of Permeation in Plastic Packaging and Receptacles B Appendix B to Part 173 Transportation Other... Plastic Packaging and Receptacles 1. The purpose of this procedure is to determine the chemical compatibility and permeability of liquid hazardous materials packaged in plastic packaging and receptacles...

49 CFR Appendix B to Part 173 - Procedure for Testing Chemical Compatibility and Rate of Permeation in Plastic Packaging and...

Code of Federal Regulations, 2012 CFR

2012-10-01

... Rate of Permeation in Plastic Packaging and Receptacles B Appendix B to Part 173 Transportation Other... Plastic Packaging and Receptacles 1. The purpose of this procedure is to determine the chemical compatibility and permeability of liquid hazardous materials packaged in plastic packaging and receptacles...

49 CFR Appendix B to Part 173 - Procedure for Testing Chemical Compatibility and Rate of Permeation in Plastic Packaging and...

Code of Federal Regulations, 2013 CFR

2013-10-01

... Rate of Permeation in Plastic Packaging and Receptacles B Appendix B to Part 173 Transportation Other... Plastic Packaging and Receptacles 1. The purpose of this procedure is to determine the chemical compatibility and permeability of liquid hazardous materials packaged in plastic packaging and receptacles...

21 CFR 800.12 - Contact lens solutions and tablets; tamper-resistant packaging.

Code of Federal Regulations, 2010 CFR

2010-04-01

...-resistant retail packages, there is the opportunity for the malicious adulteration of these products with... confidence in the security of the packages of over-the-counter (OTC) health care products. The Food and Drug... used to make such a solution for retail sale that is not packaged in a tamper-resistant package and...

21 CFR 800.12 - Contact lens solutions and tablets; tamper-resistant packaging.

Code of Federal Regulations, 2011 CFR

2011-04-01

...-resistant retail packages, there is the opportunity for the malicious adulteration of these products with... confidence in the security of the packages of over-the-counter (OTC) health care products. The Food and Drug... used to make such a solution for retail sale that is not packaged in a tamper-resistant package and...

21 CFR 800.12 - Contact lens solutions and tablets; tamper-resistant packaging.

Code of Federal Regulations, 2012 CFR

2012-04-01

...-resistant retail packages, there is the opportunity for the malicious adulteration of these products with... confidence in the security of the packages of over-the-counter (OTC) health care products. The Food and Drug... used to make such a solution for retail sale that is not packaged in a tamper-resistant package and...

21 CFR 800.12 - Contact lens solutions and tablets; tamper-resistant packaging.

Code of Federal Regulations, 2013 CFR

2013-04-01

...-resistant retail packages, there is the opportunity for the malicious adulteration of these products with... confidence in the security of the packages of over-the-counter (OTC) health care products. The Food and Drug... used to make such a solution for retail sale that is not packaged in a tamper-resistant package and...

21 CFR 800.12 - Contact lens solutions and tablets; tamper-resistant packaging.

Code of Federal Regulations, 2014 CFR

2014-04-01

...-resistant retail packages, there is the opportunity for the malicious adulteration of these products with... confidence in the security of the packages of over-the-counter (OTC) health care products. The Food and Drug... used to make such a solution for retail sale that is not packaged in a tamper-resistant package and...

Fluorochemicals used in food packaging inhibit male sex hormone synthesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosenmai, A.K., E-mail: akjro@food.dtu.dk; Nielsen, F.K.; Pedersen, M.

Polyfluoroalkyl phosphate surfactants (PAPS) are widely used in food contact materials (FCMs) of paper and board and have recently been detected in 57% of investigated materials. Human exposure occurs as PAPS have been measured in blood; however knowledge is lacking on the toxicology of PAPS. The aim of this study was to elucidate the effects of six fluorochemicals on sex hormone synthesis and androgen receptor (AR) activation in vitro. Four PAPS and two metabolites, perfluorooctanoic acid (PFOA) and 8:2 fluorotelomer alcohol (8:2 FTOH) were tested. Hormone profiles, including eight steroid hormones, generally showed that 8:2 diPAPS, 8:2 monoPAPS and 8:2more » FTOH led to decreases in androgens (testosterone, dehydroepiandrosterone, and androstenedione) in the H295R steroidogenesis assay. Decreases were observed for progesterone and 17-OH-progesterone as well. These observations indicated that a step prior to progestagen and androgen synthesis had been affected. Gene expression analysis of StAR, Bzrp, CYP11A, CYP17, CYP21 and CYP19 mRNA showed a decrease in Bzrp mRNA levels for 8:2 monoPAPS and 8:2 FTOH indicating interference with cholesterol transport to the inner mitochondria. Cortisol, estrone and 17β-estradiol levels were in several cases increased with exposure. In accordance with these data CYP19 gene expression increased with 8:2 diPAPS, 8:2 monoPAPS and 8:2 FTOH exposures indicating that this is a contributing factor to the decreased androgen and the increased estrogen levels. Overall, these results demonstrate that fluorochemicals present in food packaging materials and their metabolites can affect steroidogenesis through decreased Bzrp and increased CYP19 gene expression leading to lower androgen and higher estrogen levels. -- Highlights: ► Fluorochemicals found in 57% of paper and board food packaging were tested. ► Collectively six fluorochemicals were tested for antiandrogenic potential in vitro. ► Three out of six tested fluorochemicals inhibited synthesis of male sex hormones. ► Generally, levels of estrogens and cortisol stayed unaffected or increased. ► The effect on steroid synthesis was specific on gene expression of Bzrp and CYP19.« less

Protection of Grain Products from Sitophilus oryzae (L.) Contamination by Anti-Insect Pest Repellent Sachet Containing Allyl Mercaptan Microcapsule.

PubMed

Chang, Yoonjee; Lee, Soo-Hyun; Na, Ja Hyun; Chang, Pahn-Shick; Han, Jaejoon

2017-11-01

The purpose of this study was to develop an anti-insect pest repellent sachet to prevent Sitophilus oryzae (L.) (Coleoptera: Curculionidae) contamination in grain packaging. The anti-insect pest activities of essential oils (EOs) from garlic (Allium Sativum), ginger (Zingiber Officinalis), black pepper (Piper nigrum), onion (Allium cepa), and fennel (Foeniculum vulgare) as well as major compounds (allyl disulfide, AD; allyl mercaptan, AM) isolated from of garlic and onion (AD and AM) were measured against S. oryzae. The results revealed that garlic EO, onion EO, AD, and AM showed strong fumigant insecticidal activities. Among these, AM showed the highest acetylcholinesterase (AChE) inhibition rate, indicating that the fumigation insecticidal efficacy of AM is related with its AChE inhibition ability. Subsequently, the microcapsules were produced with a high efficiency (80.02%) by using AM as a core material and rice flour as a wall material. Finally, sachet composed of rice flour microcapsule containing 2% AM (RAM) was produced. Repellent assay was performed to measure anti-insect pest ability of the RAM sachet, showed remarkable repelling effect within 48 h both in the presence or absence of attractant. In a release profile of RAM sachet, it was expected to last over 20 mo during the distribution period of brown rice. Moreover, RAM sachet showed no undesirable changes to the sensory properties of the rice both before and after cooking. Taken together, these results suggest that the newly developed RAM sachet could be used as a packaging material to protect grain products from S. oryzae contamination. The rice weevil, Sitophilus oryzae (L.) (Coleoptera: Curculionidae), causes damages to stored products and its contamination in grain products has become a major problem in cereal market. To preserve brown rice, an anti-insect pest repellent sachet containing 2% allyl mercaptan was newly developed and it showed remarkable repellent abilities against S. oryzae. It could be used as an active food packaging system to protect grain products from insect pest contamination. © 2017 Institute of Food Technologists®.

R software package based statistical optimization of process components to simultaneously enhance the bacterial growth, laccase production and textile dye decolorization with cytotoxicity study

PubMed Central

Dudhagara, Pravin; Tank, Shantilal

2018-01-01

The thermophilic bacterium, Bacillus licheniformis U1 is used for the optimization of bacterial growth (R1), laccase production (R2) and synthetic disperse blue DBR textile dye decolorization (R3) in the present study. Preliminary optimization has been performed by one variable at time (OVAT) approach using four media components viz., dye concentration, copper sulphate concentration, pH, and inoculum size. Based on OVAT result further statistical optimization of R1, R2 and R3 performed by Box–Behnken design (BBD) using response surface methodology (RSM) in R software with R Commander package. The total 29 experimental runs conducted in the experimental design study towards the construction of a quadratic model. The model indicated that dye concentration 110 ppm, copper sulphate 0.2 mM, pH 7.5 and inoculum size 6% v/v were found to be optimum to maximize the laccase production and bacterial growth. Whereas, maximum dye decolorization achieved in media containing dye concentration 110 ppm, copper sulphate 0.6 mM, pH 6 and inoculum size 6% v/v. R package predicted R2 of R1, R2 and R3 were 0.9917, 0.9831 and 0.9703 respectively; likened to Design-Expert (Stat-Ease) (DOE) predicted R2 of R1, R2, and R3 were 0.9893, 0.9822 and 0.8442 respectively. The values obtained by R software were more precise, reliable and reproducible, compared to the DOE model. The laccase production was 1.80 fold increased, and 2.24 fold enhancement in dye decolorization was achieved using optimized medium than initial experiments. Moreover, the laccase-treated sample demonstrated the less cytotoxic effect on L132 and MCF-7 cell lines compared to untreated sample using MTT assay. Higher cell viability and lower cytotoxicity observed in a laccase-treated sample suggest the impending application of bacterial laccase in the reduction of toxicity of dye to design rapid biodegradation process. PMID:29718934

Container system for enabling commercial production of cryopreserved cell therapy products.

PubMed

Woods, Erik J; Bagchi, Aniruddha; Goebel, W Scott; Vilivalam, Vinod D; Vilivalam, Vinod D

2010-07-01

The expansion of cellular therapeutics will require large-scale manufacturing processes to expand and package cell products, which may not be feasible with current blood-banking bag technology. This study investigated the potential for freezing, storing and shipping cell therapy products using novel pharmaceutical-grade Crystal Zenith((R)) (CZ) plastic vials. CZ vials (0.5, 5 and 30 ml volume) with several closure systems were filled with mesenchymal stem cells and stored at either -85 or -196 degrees C for 6 months. Vials were tested for their ability to maintain cell viability, proliferative and differentiation capacity, as well as durability and integrity utilizing a 1-m drop test. As controls, 2 ml polypropylene vials were investigated under the same conditions. Post-thaw viability utilizing a dye exclusion assay was over 95% in all samples. Stored cells exhibited rapid recovery 2 h post-thaw and cultures were approximately 70% confluent within 5-7 days, consistent with nonfrozen controls and indicative of functional recovery. Doubling times were consistent over all vials. The doubling rate for cells from CZ vials were 2.14 + or - 0.83 days (1 week), 1.84 + or - 0.68 days (1 month) and 1.79 + or - 0.71 days (6 months), which were not significantly different compared with frozen and fresh controls. Cells recovered from the vials exhibited trilineage differentiation consistent with controls. As part of vial integrity via drop testing, no evidence of external damage was found on vial surfaces or on closure systems. Furthermore, the filled vials stored for 6 months were tested for container closure integrity. Vials removed from freezer conditions were transported to the test laboratory on dry ice and tested using pharmaceutical packaging tests, including dye ingress and microbial challenge. The results of all stoppered vials indicated container closure integrity with no failures. Pharmaceutical-grade plastic CZ vials, which are commercially used to package pharmaceutical products, are suitable for low-temperature storage and transport of mesenchymal stem cells, and are a scalable container system for commercial manufacturing and fill-finish operation of cell therapy products.

Packaging's Contribution for the Effectiveness of the Space Station's Food Service Operation

NASA Technical Reports Server (NTRS)

Rausch, B. A.

1985-01-01

Storage limitations will have a major effect on space station food service. For example: foods with low bulk density such as ice cream, bread, cake, standard type potato chips and other low density snacks, flaked cereals, etc., will exacerbate the problem of space limitations; package containers are inherently volume consuming and refuse creating; and the useful observation that the optimum package is no package at all leads to the tentative conclusion that the least amount of packaging per unit of food, consistent with storage, aesthetics, preservation, cleanliness, cost and disposal criteria, is the most practical food package for the space station. A series of trade offs may have to be made to arrive at the most appropriate package design for a particular type of food taking all the criteria into account. Some of these trade offs are: single serve vs. bulk; conventional oven vs. microwave oven; nonmetallic aseptically vs. non-aseptically packaged foods; and comparison of aseptic vs. nonaseptic food packages. The advantages and disadvantages are discussed.

Practical fundamentals of glass, rubber, and plastic sterile packaging systems.

PubMed

Sacha, Gregory A; Saffell-Clemmer, Wendy; Abram, Karen; Akers, Michael J

2010-01-01

Sterile product packaging systems consist of glass, rubber, and plastic materials that are in intimate contact with the formulation. These materials can significantly affect the stability of the formulation. The interaction between the packaging materials and the formulation can also affect the appropriate delivery of the product. Therefore, a parenteral formulation actually consists of the packaging system as well as the product that it contains. However, the majority of formulation development time only considers the product that is contained in the packaging system. Little time is spent studying the interaction of the packaging materials with the contents. Interaction between the packaging and the contents only becomes a concern when problems are encountered. For this reason, there are few scientific publications that describe the available packaging materials, their advantages and disadvantages, and their important product attributes. This article was created as a reference for product development and describes some of the packaging materials and systems that are available for parenteral products.

The Importance of Take-Out Food Packaging Attributes: Conjoint Analysis and Quality Function Deployment Approach

NASA Astrophysics Data System (ADS)

Lestari Widaningrum, Dyah

2014-03-01

This research aims to investigate the importance of take-out food packaging attributes, using conjoint analysis and QFD approach among consumers of take-out food products in Jakarta, Indonesia. The conjoint results indicate that perception about packaging material (such as paper, plastic, and polystyrene foam) plays the most important role overall in consumer perception. The clustering results that there is strong segmentation in which take-out food packaging material consumer consider most important. Some consumers are mostly oriented toward the colour of packaging, while another segment of customers concerns on packaging shape and packaging information. Segmentation variables based on packaging response can provide very useful information to maximize image of products through the package's impact. The results of House of Quality development described that Conjoint Analysis - QFD is a useful combination of the two methodologies in product development, market segmentation, and the trade off between customers' requirements in the early stages of HOQ process

Natural biopolymer-based nanocomposite films for packaging applications.

PubMed

Rhim, Jong-Whan; Ng, Perry K W

2007-01-01

Concerns on environmental waste problems caused by non-biodegradable petrochemical-based plastic packaging materials as well as the consumer's demand for high quality food products has caused an increasing interest in developing biodegradable packaging materials using annually renewable natural biopolymers such as polysaccharides and proteins. Inherent shortcomings of natural polymer-based packaging materials such as low mechanical properties and low water resistance can be recovered by applying a nanocomposite technology. Polymer nanocomposites, especially natural biopolymer-layered silicate nanocomposites, exhibit markedly improved packaging properties due to their nanometer size dispersion. These improvements include increased modulus and strength, decreased gas permeability, and increased water resistance. Additionally, biologically active ingredients can be added to impart the desired functional properties to the resulting packaging materials. Consequently, natural biopolymer-based nanocomposite packaging materials with bio-functional properties have a huge potential for application in the active food packaging industry. In this review, recent advances in the preparation of natural biopolymer-based films and their nanocomposites, and their potential use in packaging applications are addressed.

Signalling product healthiness through symbolic package cues: Effects of package shape and goal congruence on consumer behaviour.

PubMed

van Ooijen, Iris; Fransen, Marieke L; Verlegh, Peeter W J; Smit, Edith G

2017-02-01

Three studies show that product packaging shape serves as a cue that communicates healthiness of food products. Inspired by embodiment accounts, we show that packaging that simulates a slim body shape acts as a symbolic cue for product healthiness (e.g., low in calories), as opposed to packaging that simulates a wide body shape. Furthermore, we show that the effect of slim package shape on consumer behaviour is goal dependent. Whereas simulation of a slim (vs. wide) body shape increases choice likelihood and product attitude when consumers have a health-relevant shopping goal, packaging shape does not affect these outcomes when consumers have a hedonic shopping goal. In Study 3, we adopt a realistic shopping paradigm using a shelf with authentic products, and find that a slim (as opposed to wide) package shape increases on-shelf product recognition and increases product attitude for healthy products. We discuss results and implications regarding product positioning and the packaging design process. Copyright © 2016 Elsevier Ltd. All rights reserved.

49 CFR 173.36 - Hazardous materials in Large Packagings.

Code of Federal Regulations, 2013 CFR

2013-10-01

... an inner packaging is constructed of paper or flexible plastic, the inner packaging must be replaced...) The Large Packaging is free from corrosion, contamination, cracks, cuts, or other damage which would...

49 CFR 173.36 - Hazardous materials in Large Packagings.

Code of Federal Regulations, 2014 CFR

2014-10-01

... an inner packaging is constructed of paper or flexible plastic, the inner packaging must be replaced...) The Large Packaging is free from corrosion, contamination, cracks, cuts, or other damage which would...

Reviews.

ERIC Educational Resources Information Center

Radcliffe, George; And Others

1988-01-01

Reviews three software packages: 1) a package containing 68 programs covering general topics in chemistry; 2) a package dealing with acid-base titration curves and allows for variables to be changed; 3) a chemistry tutorial and drill package. (MVL)

14 CFR 417.1 - General information.

Code of Federal Regulations, 2014 CFR

2014-01-01

... package, (3) Preliminary and final flight data packages, (4) A tailored version of EWR 127-1, (5) Range...) Missile system pre-launch safety package, (3) Preliminary and final flight data packages, (4) A tailored...

14 CFR 417.1 - General information.

Code of Federal Regulations, 2013 CFR

2013-01-01

... package, (3) Preliminary and final flight data packages, (4) A tailored version of EWR 127-1, (5) Range...) Missile system pre-launch safety package, (3) Preliminary and final flight data packages, (4) A tailored...

14 CFR 417.1 - General information.

Code of Federal Regulations, 2011 CFR

2011-01-01

... package, (3) Preliminary and final flight data packages, (4) A tailored version of EWR 127-1, (5) Range...) Missile system pre-launch safety package, (3) Preliminary and final flight data packages, (4) A tailored...

14 CFR 417.1 - General information.

Code of Federal Regulations, 2012 CFR

2012-01-01

... package, (3) Preliminary and final flight data packages, (4) A tailored version of EWR 127-1, (5) Range...) Missile system pre-launch safety package, (3) Preliminary and final flight data packages, (4) A tailored...

Migration and sorption phenomena in packaged foods.

PubMed

Gnanasekharan, V; Floros, J D

1997-10-01

Rapidly developing analytical capabilities and continuously evolving stringent regulations have made food/package interactions a subject of intense research. This article focuses on: (1) the migration of package components such as oligomers and monomers, processing aids, additives, and residual reactants in to packaged foods, and (2) sorption of food components such as flavors, lipids, and moisture into packages. Principles of diffusion and thermodynamics are utilized to describe the mathematics of migration and sorption. Mathematical models are developed from first principles, and their applicability is illustrated using numerical simulations and published data. Simulations indicate that available models are system (polymer-penetrant) specific. Furthermore, some models best describe the early stages of migration/sorption, whereas others should be used for the late stages of these phenomena. Migration- and/or sorption-related problems with respect to glass, metal, paper-based and polymeric packaging materials are discussed, and their importance is illustrated using published examples. The effects of migrating and absorbed components on food safety, quality, and the environment are presented for various foods and packaging materials. The impact of currently popular packaging techniques such as microwavable, ovenable, and retortable packaging on migration and sorption are discussed with examples. Analytical techniques for investigating migration and sorption phenomena in food packaging are critically reviewed, with special emphasis on the use and characteristics of food-simulating liquids (FSLs). Finally, domestic and international regulations concerning migration in packaged foods, and their impact on food packaging is briefly presented.