Minimization of Hypoglycemia as an Adverse Event During Insulin Infusion: Further Refinement of the Yale Protocol.

PubMed

Marvin, Michael R; Inzucchi, Silvio E; Besterman, Brian J

2016-08-01

The management of hyperglycemia in the intensive care unit has been a controversial topic for more than a decade, with target ranges varying from 80-110 mg/dL to <200 mg/dL. Multiple insulin infusion protocols exist, including several computerized protocols, which have attempted to achieve these targets. Importantly, compliance with these protocols has not been a focus of clinical studies. GlucoCare™, a Food and Drug Administration (FDA)-cleared insulin-dosing calculator, was originally designed based on the Yale Insulin Infusion Protocol to target 100-140 mg/dL and has undergone several modifications to reduce hypoglycemia. The original Yale protocol was modified from 100-140 mg/dL to a range of 120-140 mg/dL (GlucoCare 120-140) and then to 140 mg/dL (GlucoCare 140, not a range but a single blood glucose [BG] level target) in an iterative and evidence-based manner to eliminate hypoglycemia <70 mg/dL. The final modification [GlucoCare 140(B)] includes the addition of bolus insulin "midprotocol" during an insulin infusion to reduce peak insulin rates for insulin-resistant patients. This study examined the results of these protocol modifications and evaluated the role of compliance with the protocol in the incidence of hypoglycemia <70 mg/dL. Protocol modifications resulted in mean BG levels of 133.4, 136.4, 143.8, and 146.4 mg/dL and hypoglycemic BG readings <70 mg/dL of 0.998%, 0.367%, 0.256%, and 0.04% for the 100-140, 120-140, 140, and 140(B) protocols, respectively (P < 0.001). Adherence to the glucose check interval significantly reduced the incidence of hypoglycemia (P < 0.001). Protocol modifications led to a reduction in peak insulin infusion rates (P < 0.001) and the need for dextrose-containing boluses (P < 0.001). This study demonstrates that refinements in protocol design can improve glucose control in critically ill patients and that the use of GlucoCare 140(B) can eliminate all significant hypoglycemia while achieving mean glucose levels between 140 and 150 mg/dL. In addition, attention to the timely performance of glucose levels can also reduce hypoglycemic events.

A step-by-step protocol for assaying protein carbonylation in biological samples.

PubMed

Colombo, Graziano; Clerici, Marco; Garavaglia, Maria Elisa; Giustarini, Daniela; Rossi, Ranieri; Milzani, Aldo; Dalle-Donne, Isabella

2016-04-15

Protein carbonylation represents the most frequent and usually irreversible oxidative modification affecting proteins. This modification is chemically stable and this feature is particularly important for storage and detection of carbonylated proteins. Many biochemical and analytical methods have been developed during the last thirty years to assay protein carbonylation. The most successful method consists on protein carbonyl (PCO) derivatization with 2,4-dinitrophenylhydrazine (DNPH) and consequent spectrophotometric assay. This assay allows a global quantification of PCO content due to the ability of DNPH to react with carbonyl giving rise to an adduct able to absorb at 366 nm. Similar approaches were also developed employing chromatographic separation, in particular HPLC, and parallel detection of absorbing adducts. Subsequently, immunological techniques, such as Western immunoblot or ELISA, have been developed leading to an increase of sensitivity in protein carbonylation detection. Currently, they are widely employed to evaluate change in total protein carbonylation and eventually to highlight the specific proteins undergoing selective oxidation. In the last decade, many mass spectrometry (MS) approaches have been developed for the identification of the carbonylated proteins and the relative amino acid residues modified to carbonyl derivatives. Although these MS methods are much more focused and detailed due to their ability to identify the amino acid residues undergoing carbonylation, they still require too expensive equipments and, therefore, are limited in distribution. In this protocol paper, we summarise and comment on the most diffuse protocols that a standard laboratory can employ to assess protein carbonylation; in particular, we describe step-by-step the different protocols, adding suggestions coming from our on-bench experience. Copyright © 2015 Elsevier B.V. All rights reserved.

Sequential ChIP Protocol for Profiling Bivalent Epigenetic Modifications (ReChIP).

PubMed

Desvoyes, Bénédicte; Sequeira-Mendes, Joana; Vergara, Zaida; Madeira, Sofia; Gutierrez, Crisanto

2018-01-01

Identification of chromatin modifications, e.g., histone acetylation and methylation, among others, is widely carried out by using a chromatin immunoprecipitation (ChIP) strategy. The information obtained with these procedures is useful to gain an overall picture of modifications present in all cells of the population under study. It also serves as a basis to figure out the mechanisms of chromatin organization and gene regulation at the population level. However, the ultimate goal is to understand gene regulation at the level of single chromatin fibers. This requires the identification of chromatin modifications that occur at a given genomic location and within the same chromatin fiber. This is achieved by following a sequential ChIP strategy using two antibodies to distinguish different chromatin modifications. Here, we describe a sequential ChIP protocol (Re-ChIP), paying special attention to the controls needed and the required steps to obtain meaningful and reproducible results. The protocol is developed for young Arabidopsis seedlings but could be adapted to other plant materials.

Chemical Modification in the Design of Immobilized Enzyme Biocatalysts: Drawbacks and Opportunities.

PubMed

Rueda, Nazzoly; Dos Santos, Jose C S; Ortiz, Claudia; Torres, Rodrigo; Barbosa, Oveimar; Rodrigues, Rafael C; Berenguer-Murcia, Ángel; Fernandez-Lafuente, Roberto

2016-06-01

Chemical modification of enzymes and immobilization used to be considered as separate ways to improve enzyme properties. This review shows how the coupled use of both tools may greatly improve the final biocatalyst performance. Chemical modification of a previously immobilized enzyme is far simpler and easier to control than the modification of the free enzyme. Moreover, if protein modification is performed to improve its immobilization (enriching the enzyme in reactive groups), the final features of the immobilized enzyme may be greatly improved. Chemical modification may be directed to improve enzyme stability, but also to improve selectivity, specificity, activity, and even cell penetrability. Coupling of immobilization and chemical modification with site-directed mutagenesis is a powerful instrument to obtain fully controlled modification. Some new ideas such as photoreceptive enzyme modifiers that change their physical properties under UV exposition are discussed. © 2016 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spacelab system analysis: The modified free access protocol: An access protocol for communication systems with periodic and Poisson traffic

NASA Technical Reports Server (NTRS)

Ingels, Frank; Owens, John; Daniel, Steven

1989-01-01

The protocol definition and terminal hardware for the modified free access protocol, a communications protocol similar to Ethernet, are developed. A MFA protocol simulator and a CSMA/CD math model are also developed. The protocol is tailored to communication systems where the total traffic may be divided into scheduled traffic and Poisson traffic. The scheduled traffic should occur on a periodic basis but may occur after a given event such as a request for data from a large number of stations. The Poisson traffic will include alarms and other random traffic. The purpose of the protocol is to guarantee that scheduled packets will be delivered without collision. This is required in many control and data collection systems. The protocol uses standard Ethernet hardware and software requiring minimum modifications to an existing system. The modification to the protocol only affects the Ethernet transmission privileges and does not effect the Ethernet receiver.

Reverse engineering the ancient ceramic technology based on X-ray fluorescence spectromicroscopy

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

Sciau, Philippe; Leon, Yoanna; Goudeau, Philippe

2011-07-06

We present results of X-ray fluorescence (XRF) microprobe analyses of ancient ceramic cross-sections aiming at deciphering the different firing protocols used for their production. Micro-focused XRF elemental mapping, Fe chemical mapping and Fe K-edge X-ray absorption near edge structure spectroscopy were performed on pre-sigillata ceramics from southern Gaul, and terra Sigillata vessels from Italy and southern Gaul. Pieces from the different workshops and regions showed significant difference in the starting clay material, clay conditioning and kiln firing condition. By contrast, sherds from the same workshop exhibited more subtle differences and possible misfirings. Understanding the precise firing conditions and protocols wouldmore » allow recreation of kilns for various productions. Furthermore, evolution and modification of kiln design would shed some light on how ancient potters devised solutions to diverse technological problems they encountered.« less

A method for acetylcholinesterase staining of brain sections previously processed for receptor autoradiography.

PubMed

Lim, M M; Hammock, E A D; Young, L J

2004-02-01

Receptor autoradiography using selective radiolabeled ligands allows visualization of brain receptor distribution and density on film. The resolution of specific brain regions on the film often can be difficult to discern owing to the general spread of the radioactive label and the lack of neuroanatomical landmarks on film. Receptor binding is a chemically harsh protocol that can render the tissue virtually unstainable by Nissl and other conventional stains used to delineate neuroanatomical boundaries of brain regions. We describe a method for acetylcholinesterase (AChE) staining of slides previously processed for receptor binding. AChE staining is a useful tool for delineating major brain nuclei and tracts. AChE staining on sections that have been processed for receptor autoradiography provides a direct comparison of brain regions for more precise neuroanatomical description. We report a detailed thiocholine protocol that is a modification of the Koelle-Friedenwald method to amplify the AChE signal in brain sections previously processed for autoradiography. We also describe several temporal and experimental factors that can affect the density and clarity of the AChE signal when using this protocol.

Enhancing the Properties of Carbon and Gold Substrates by Surface Modification

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

Harnisch, Jennifer Anne

2001-01-01

The properties of both carbon and gold substrates are easily affected by the judicious choice of a surface modification protocol. Several such processes for altering surface composition have been published in literature. The research presented in this thesis primarily focuses on the development of on-column methods to modify carbon stationary phases used in electrochemically modulated liquid chromatography (EMLC). To this end, both porous graphitic carbon (PGC) and glassy carbon (GC) particles have been modified on-column by the electroreduction of arenediazonium salts and the oxidation of arylacetate anions (the Kolbe reaction). Once modified, the carbon stationary phases show enhanced chromatographic performancemore » both in conventional liquid chromatographic columns and EMLC columns. Additionally, one may also exploit the creation of aryl films to by electroreduction of arenediazonium salts in the creation of nanostructured materials. The formation of mercaptobenzene film on the surface of a GC electrode provides a linking platform for the chemisorption of gold nanoparticles. After deposition of nanoparticles, the surface chemistry of the gold can be further altered by self-assembled monolayer (SAM) formation via the chemisorption of a second thiol species. Finally, the properties of gold films can be altered such that they display carbon-like behavior through the formation of benzenehexathiol (BHT) SAMs. BHT chemisorbs to the gold surface in a previously unprecedented planar fashion. Carbon and gold substrates can be chemically altered by several methodologies resulting in new surface properties. The development of modification protocols and their application in the analytical arena is considered herein.« less

PLGA microspheres encapsulating siRNA.

PubMed

De Rosa, Giuseppe; Salzano, Giuseppina

2015-01-01

The therapeutic use of small interfering RNA (siRNA) represents a new and powerful approach to suppress the expression of pathologically genes. However, biopharmaceutical drawbacks, such as short half-life, poor cellular uptake, and unspecific distribution into the body, hamper the development of siRNA-based therapeutics. Poly(lactide-co-glycolide), (PLGA) microspheres can be a useful tool to overcome these issues. siRNA can be encapsulated into the PLGA microspheres, which protects the loaded nucleic acid against the enzymatic degradation. Moreover, PLGA microspheres can be injected directly into the action site, where the siRNA can be released in controlled manner, thus avoiding the need of frequent invasive administrations. The complete biodegradability of PLGA to monomers easily metabolized by the body, and its approval by FDA and EMA for parenteral administration, assure the safety of this copolymer and do not require the removal of the device after the complete drug release. In chapter, a basic protocol for the preparation of PLGA microspheres encapsulating siRNA is described. This protocol is based on a double emulsion/solvent evaporation technique, a well known and easy to reproduce method. This specific protocol has been developed to encapsulate a siRNA anti-TNFα in PLGA microspheres, and it has been designed and optimized to achieve high siRNA encapsulation efficiency and slow siRNA release in vitro. However, it can be extended also to other siRNA as well as other RNA or DNA-based oligonucleotides (miRNA, antisense, decoy, etc.). Depending on the applications, chemical modifications of the backbone and site-specific modification within the siRNA sequences could be required.

Blytheville AFB, Arkansas. Water quality management survey. Final report 11-14 Apr 83

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

New, G.R.; Gibson, D.P. Jr.

1983-05-01

The USAF OEHL conducted an on site water quality management survey at Blytheville AFB. Main areas of interest were (1) the wastewater treatment plant effluent fecal coliform count, and residual chlorine content, and (2) the stream sampling protocol. The drinking water plant, landfill and industrial shops were also included in the survey. Results of the survey indicated that the low residual chlorine content caused high fecal coliform counts in the wastewater effluent. The chemical parameters sampled in the stream monitoring program did not coincide with the requirements of the State of Arkansas and required modification. Recommendations were made to increasemore » the residual chlorine content of the wastewater effluent and to increase the mixing of the chlorine contact chamber. A list of the chemical parameters was included in the report for stream monitoring.« less

Empirical Examinations of Modifications and Adaptations to Evidence-Based Psychotherapies: Methodologies, Impact, and Future Directions.

PubMed

Stirman, Shannon Wiltsey; Gamarra, Jennifer; Bartlett, Brooke; Calloway, Amber; Gutner, Cassidy

2017-12-01

This review describes methods used to examine the modifications and adaptations to evidence-based psychological treatments (EBPTs), assesses what is known about the impact of modifications and adaptations to EBPTs, and makes recommendations for future research and clinical care. One hundred eight primary studies and three meta-analyses were identified. All studies examined planned adaptations, and many simultaneously investigated multiple types of adaptations. With the exception of studies on adding or removing specific EBPT elements, few studies compared adapted EBPTs to the original protocols. There was little evidence that adaptations in the studies were detrimental, but there was also limited consistent evidence that adapted protocols outperformed the original protocols, with the exception of adding components to EBPTs. Implications for EBPT delivery and future research are discussed.

Regulatory ecotoxicity testing of nanomaterials - proposed modifications of OECD test guidelines based on laboratory experience with silver and titanium dioxide nanoparticles.

PubMed

Hund-Rinke, Kerstin; Baun, Anders; Cupi, Denisa; Fernandes, Teresa F; Handy, Richard; Kinross, John H; Navas, José M; Peijnenburg, Willie; Schlich, Karsten; Shaw, Benjamin J; Scott-Fordsmand, Janeck J

2016-12-01

Regulatory ecotoxicity testing of chemicals is of societal importance and a large effort is undertaken at the OECD to ensure that OECD test guidelines (TGs) for nanomaterials (NMs) are available. Significant progress to support the adaptation of selected TGs to NMs was achieved in the context of the project MARINA ( http://www.marina-fp7.eu/ ) funded within the 7th European Framework Program. Eight OECD TGs were adapted based on the testing of at least one ion-releasing NM (Ag) and two inert NMs (TiO 2 ). With the materials applied, two main variants of NMs (ion releasing vs. inert NMs) were addressed. As the modifications of the test guidelines refer to general test topics (e.g. test duration or measuring principle), we assume that the described approaches and modifications will be suitable for the testing of further NMs with other chemical compositions. Firm proposals for modification of protocols with scientific justification(s) are presented for the following tests: growth inhibition using the green algae Raphidocelis subcapitata (formerly: Pseudokirchneriella subcapitata; TG 201), acute toxicity with the crustacean Daphnia magna (TG 202), development toxicity with the fish Danio rerio (TG 210), reproduction of the sediment-living worm Lumbriculus variegatus (TG 225), activity of soil microflora (TGs 216, 217), and reproduction of the invertebrates (Enchytraeus crypticus, Eisenia fetida, TGs 220, 222). Additionally, test descriptions for two further test systems (root elongation of plants in hydroponic culture; test on fish cells) are presented. Ecotoxicological data obtained with the modified test guidelines for TiO 2 NMs and Ag NM and detailed method descriptions are available.

Oxidative Modulation of Voltage-Gated Potassium Channels

PubMed Central

Sahoo, Nirakar; Hoshi, Toshinori

2014-01-01

Abstract Significance: Voltage-gated K+ channels are a large family of K+-selective ion channel protein complexes that open on membrane depolarization. These K+ channels are expressed in diverse tissues and their function is vital for numerous physiological processes, in particular of neurons and muscle cells. Potentially reversible oxidative regulation of voltage-gated K+ channels by reactive species such as reactive oxygen species (ROS) represents a contributing mechanism of normal cellular plasticity and may play important roles in diverse pathologies including neurodegenerative diseases. Recent Advances: Studies using various protocols of oxidative modification, site-directed mutagenesis, and structural and kinetic modeling provide a broader phenomenology and emerging mechanistic insights. Critical Issues: Physicochemical mechanisms of the functional consequences of oxidative modifications of voltage-gated K+ channels are only beginning to be revealed. In vivo documentation of oxidative modifications of specific amino-acid residues of various voltage-gated K+ channel proteins, including the target specificity issue, is largely absent. Future Directions: High-resolution chemical and proteomic analysis of ion channel proteins with respect to oxidative modification combined with ongoing studies on channel structure and function will provide a better understanding of how the function of voltage-gated K+ channels is tuned by ROS and the corresponding reducing enzymes to meet cellular needs. Antioxid. Redox Signal. 21, 933–952. PMID:24040918

Additional considerations are required when preparing a protocol for a systematic review with multiple interventions.

PubMed

Chaimani, Anna; Caldwell, Deborah M; Li, Tianjing; Higgins, Julian P T; Salanti, Georgia

2017-03-01

The number of systematic reviews that aim to compare multiple interventions using network meta-analysis is increasing. In this study, we highlight aspects of a standard systematic review protocol that may need modification when multiple interventions are to be compared. We take the protocol format suggested by Cochrane for a standard systematic review as our reference and compare the considerations for a pairwise review with those required for a valid comparison of multiple interventions. We suggest new sections for protocols of systematic reviews including network meta-analyses with a focus on how to evaluate their assumptions. We provide example text from published protocols to exemplify the considerations. Standard systematic review protocols for pairwise meta-analyses need extensions to accommodate the increased complexity of network meta-analysis. Our suggested modifications are widely applicable to both Cochrane and non-Cochrane systematic reviews involving network meta-analyses. Copyright © 2017 Elsevier Inc. All rights reserved.

Comparison of protocols measuring diffusion and partition coefficients in the stratum corneum

PubMed Central

Rothe, H.; Obringer, C.; Manwaring, J.; Avci, C.; Wargniez, W.; Eilstein, J.; Hewitt, N.; Cubberley, R.; Duplan, H.; Lange, D.; Jacques‐Jamin, C.; Klaric, M.; Schepky, A.

2017-01-01

Abstract Partition (K) and diffusion (D) coefficients are important to measure for the modelling of skin penetration of chemicals through the stratum corneum (SC). We compared the feasibility of three protocols for the testing of 50 chemicals in our main studies, using three cosmetics‐relevant model chemicals with a wide range of logP values. Protocol 1: SC concentration‐depth profile using tape‐stripping (measures KSC/v and DSC/HSC 2, where HSC is the SC thickness); Protocol 2A: incubation of isolated SC with chemical (direct measurement of KSC/v only) and Protocol 2B: diffusion through isolated SC mounted on a Franz cell (measures KSC/v and DSC/HSC 2, and is based on Fick's laws). KSC/v values for caffeine and resorcinol using Protocol 1 and 2B were within 30% of each other, values using Protocol 2A were ~two‐fold higher, and all values were within 10‐fold of each other. Only indirect determination of KSC/v by Protocol 2B was different from the direct measurement of KSC/v by Protocol 2A and Protocol 1 for 7‐EC. The variability of KSC/v for all three chemicals using Protocol 2B was higher compared to Protocol 1 and 2A. DSC/HSC 2 values for the three chemicals were of the same order of magnitude using all three protocols. Additionally, using Protocol 1, there was very little difference between parameters measured in pig and human SC. In conclusion, KSC/v, and DSC values were comparable using different methods. Pig skin might be a good surrogate for human skin for the three chemicals tested. Copyright © 2017 The Authors Journal of Applied Toxicology published by John Wiley & Sons Ltd. PMID:28139006

Quantum direct communication protocol strengthening against Pavičić’s attack

NASA Astrophysics Data System (ADS)

Zhang, Bo; Shi, Wei-Xu; Wang, Jian; Tang, Chao-Jing

2015-12-01

A quantum circuit providing an undetectable eavesdropping of information in message mode, which compromises all two-state ψ-ϕ quantum direct communication (QDC) protocols, has been recently proposed by Pavičić [Phys. Rev. A 87 (2013) 042326]. A modification of the protocol’s control mode is proposed, which improves users’ 25% detection probability of Eve to 50% at best, as that in ping-pong protocol. The modification also improves the detection probability of Wójcik’s attack [Phys. Rev. Lett 90 (2003) 157901] to 75% at best. The resistance against man-in-the-middle (MITM) attack as well as the discussion of security for four Bell state protocols is presented. As a result, the protocol security is strengthened both theoretically and practically, and quantum advantage of superdense coding is restored.

Determining Functional Aptamer-Protein Interaction by Biolayer Interferometry.

PubMed

Lou, Xinhui; Egli, Martin; Yang, Xianbin

2016-12-01

Short single-stranded nucleic acids called aptamers are widely being explored as recognition molecules of high affinity and specificity for binding a wide range of target molecules, particularly protein targets. In biolayer interferometry (BLI), a simple Dip-and-Read approach in which the aptamer-coated biosensors are dipped into microplate wells is used to study the interactions between an aptamer and its target protein. Here we describe the protocol for the analysis of the interaction between a well-characterized anti-thrombin RNA aptamer with thrombin (Basic Protocol). We also report on the protocol for the affinity screening of a panel of anti-thrombin RNA aptamers with a single phosphorodithioate (PS2) modification, whereby the position of the modification along the RNA backbone is varied systematically (Support Protocol). The PS2 modification uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphodiester backbone linkage. The PS2-modified RNAs are nuclease resistant and several in vitro and in vivo assays have demonstrated their biological activity. For example, combining the PS2 with the 2'-OMe modification affords increased loading of modified small interfering RNA (siRNA) duplexes into the RNA-induced silencing complex (RISC) as well as enhanced gene-silencing antitumor activity. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Cumulative effects of prenatal-exposure to exogenous chemicals and psychosocial stress on fetal growth: Systematic-review of the human and animal evidence

PubMed Central

Morello-Frosch, Rachel; Sen, Saunak; Zeise, Lauren; Woodruff, Tracey J.

2017-01-01

Background Adverse effects of prenatal stress or environmental chemical exposures on fetal growth are well described, yet their combined effect remains unclear. Objectives To conduct a systematic review on the combined impact and interaction of prenatal exposure to stress and chemicals on developmental outcomes. Methods We used the first three steps of the Navigation Guide systematic review. We wrote a protocol, performed a robust literature search to identify relevant animal and human studies and extracted data on developmental outcomes. For the most common outcome (fetal growth), we evaluated risk of bias, calculated effect sizes for main effects of individual and combined exposures, and performed a random effects meta-analysis of those studies reporting on odds of low birthweight (LBW) by smoking and socioeconomic status (SES). Results We identified 17 human- and 22 animal-studies of combined chemical and stress exposures and fetal growth. Human studies tended to have a lower risk of bias across nine domains. Generally, we found stronger effects for chemicals than stress, and these exposures were associated with reduced fetal growth in the low-stress group and the association was often greater in high stress groups, with limited evidence of effect modification. We found smoking associated with significantly increased odds of LBW, with a greater effect for high stress (low SES; OR 4.75 (2.46–9.16)) compared to low stress (high SES; OR 1.95 (95% CI 1.53–2.48)). Animal studies generally had a high risk of bias with no significant combined effect or effect modification. Conclusions We found that despite concern for the combined effects of environmental chemicals and stress, this is still an under-studied topic, though limited available human studies indicate chemical exposures exert stronger effects than stress, and this effect is generally larger in the presence of stress. PMID:28700705

Cumulative effects of prenatal-exposure to exogenous chemicals and psychosocial stress on fetal growth: Systematic-review of the human and animal evidence.

PubMed

Vesterinen, Hanna M; Morello-Frosch, Rachel; Sen, Saunak; Zeise, Lauren; Woodruff, Tracey J

2017-01-01

Adverse effects of prenatal stress or environmental chemical exposures on fetal growth are well described, yet their combined effect remains unclear. To conduct a systematic review on the combined impact and interaction of prenatal exposure to stress and chemicals on developmental outcomes. We used the first three steps of the Navigation Guide systematic review. We wrote a protocol, performed a robust literature search to identify relevant animal and human studies and extracted data on developmental outcomes. For the most common outcome (fetal growth), we evaluated risk of bias, calculated effect sizes for main effects of individual and combined exposures, and performed a random effects meta-analysis of those studies reporting on odds of low birthweight (LBW) by smoking and socioeconomic status (SES). We identified 17 human- and 22 animal-studies of combined chemical and stress exposures and fetal growth. Human studies tended to have a lower risk of bias across nine domains. Generally, we found stronger effects for chemicals than stress, and these exposures were associated with reduced fetal growth in the low-stress group and the association was often greater in high stress groups, with limited evidence of effect modification. We found smoking associated with significantly increased odds of LBW, with a greater effect for high stress (low SES; OR 4.75 (2.46-9.16)) compared to low stress (high SES; OR 1.95 (95% CI 1.53-2.48)). Animal studies generally had a high risk of bias with no significant combined effect or effect modification. We found that despite concern for the combined effects of environmental chemicals and stress, this is still an under-studied topic, though limited available human studies indicate chemical exposures exert stronger effects than stress, and this effect is generally larger in the presence of stress.

Proteomic analysis of adducted butyrylcholinesterase for biomonitoring organophosphorus exposures

PubMed Central

Marsillach, Judit; Hsieh, Edward J.; Richter, Rebecca J.; MacCoss, Michael J.; Furlong, Clement E.

2014-01-01

Organophosphorus (OP) compounds include a broad group of toxic chemicals such as insecticides, chemical warfare agents and antiwear agents. The liver cytochromes P450 bioactivate many OPs to potent inhibitors of serine hydrolases. Cholinesterases were the first OP targets discovered and are the most studied. They are used to monitor human exposures to OP compounds. However, the assay that is currently used has limitations. The mechanism of action of OP compounds is the inhibition of serine hydrolases by covalently modifying their active-site serine. After structural rearrangement, the complex OP inhibitor-enzyme is irreversible and will remain in circulation until the modified enzyme is degraded. Mass spectrometry is a sensitive technology for analyzing protein modifications, such as OP-adducted enzymes. These analyses also provide some information about the nature of the OP adduct. Our aim is to develop high-throughput protocols for monitoring OP exposures using mass spectrometry. PMID:23123252

Protocols for self-assembly and imaging of DNA nanostructures.

PubMed

Sobey, Thomas L; Simmel, Friedrich C

2011-01-01

Programed molecular structures allow us to research and make use of physical, chemical, and biological effects at the nanoscale. They are an example of the "bottom-up" approach to nanotechnology, with structures forming through self-assembly. DNA is a particularly useful molecule for this purpose, and some of its advantages include parallel (as opposed to serial) assembly, naturally occurring "tools," such as enzymes and proteins for making modifications and attachments, and structural dependence on base sequence. This allows us to develop one, two, and three dimensional structures that are interesting for their fundamental physical and chemical behavior, and for potential applications such as biosensors, medical diagnostics, molecular electronics, and efficient light-harvesting systems. We describe five techniques that allow one to assemble and image such structures: concentration measurement by ultraviolet absorption, titration gel electrophoresis, thermal annealing, fluorescence microscopy, and atomic force microscopy in fluids.

Modification of Semiconductor Surfaces through Si-N Linkages by Wet-Chemistry Approaches and Modular Functionalization of Zinc Oxide Surfaces for Chemical Protection of Material Morphology

NASA Astrophysics Data System (ADS)

Gao, Fei

Semiconductor substrates are widely used in many applications. Multiple practical uses involving these materials require the ability to tune their physical and chemical properties to adjust those to a specific application. In recent years, surface and interface reactions have affected dramatically device fabrication and material design. Novel surface functionalization techniques with diverse chemical approaches make the desired physical, thermal, electrical, and mechanical properties attainable. Meanwhile, the modified surface can serve as one of the most important key steps for further assembly process in order to make novel devices and materials. In the following chapters, novel chemical approaches to the functionalization of silicon and zinc oxide substrates will be reviewed and discussed. The specific functionalities including amines, azides, and alkynes on surfaces of different materials will be applied to address subsequent attachment of large molecules and assembly processes. This research is aimed to develop new strategies for manipulating the surface properties of semiconductor materials in a controlled way. The findings of these investigations will be relevant for future applications in molecular and nanoelectronics, sensing, and solar energy conversion. The ultimate goals of the projects are: 1) Preparation of an oxygen-and carbon-free silicon surface based exclusively on Si-N linkages for further modification protocols.. This project involves designing the surface reaction of hydrazine on chlorine-terminated silicon surface, introduction of additional functional group through dehydrohalogenation condensation reaction and direct covalent attachment of C60. 2) Demonstrating alternative method to anchor carbon nanotubes to solid substrates directly through the carbon cage.. This project targets surface modification of silicon and gold substrates with amine-terminated organic monolayers and the covalent attachment of nonfunctionalized and carboxylic acid-functionalized carbon nanotubes. 3) Designing a universal method for the modular functionalization of zinc oxide surface for the chemical protection of material morphology.. This project involves surface modification of zinc oxide nanopowder under vacuum condition with propiolic acid, followed by "click" reaction. A combination of spectroscopy and microscopy techniques was utilized to study the surface functionalization and assembly processes. Fourier-transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS) and time of fight secondary ion mass spectroscopy (ToF-SIMS) were employed to elucidate the chemical structure of the modified surface. Atomic force microscopy (AFM), transmission electron microscopy (TEM) and scanning electron microscopy (SEM) were combined to obtain the surface morphological information. Density functional theory (DFT) calculations were applied to confirm the experimental results and to suggest plausible reaction mechanisms. Other complementary techniques for these projects also include nuclear magnetic resonance (NMR) spectroscopy to identify the chemical species on the surface and charge-carrier lifetime measurements to evaluate the electronic property of C60-modified silicon surface.

Effect of pH on the chemical modification of quercetin and structurally related flavonoids characterized by optical (UV-visible and Raman) spectroscopy.

PubMed

Jurasekova, Z; Domingo, C; Garcia-Ramos, J V; Sanchez-Cortes, S

2014-07-07

In this work we report the study of the chemical modifications undergone by flavonoids, especially by quercetin (QUC), under alkaline conditions by UV-visible absorption, Raman and surface-enhanced Raman scattering (SERS) spectroscopy, the study was performed in aqueous solution and also on Ag nanoparticles (AgNPs). Several processes are involved in the effect of alkaline pH both in solution and on AgNPs: autoxidation affecting mainly the C-ring of the molecule and giving rise to the molecular fragmentation leading to simpler molecular products, and/or the dimerization and further polymerization leading to species with a higher molecular weight. In addition, there exists a clear structure-instability correlation concerning mainly particular groups in the molecule: the C3-OH group in the C-ring, the catechol moiety in the B-ring and the C2=C3 bond also existing in the C-ring. QUC possesses all these groups and exhibits high instability in alkaline solution. The SERS spectra registered at different pH revealed a change in the dimerization protocol of QUC going from the A- and C-rings-like-condensation to B-ring-like-condensation. Increasing the knowledge of the chemical properties of these compounds and determining the structure-activity relationship under specific environmental factors allow us to improve their beneficial properties for health as well as the preservation of Cultural Heritage objects, for example, by preventing their degradation.

Comparison of protocols measuring diffusion and partition coefficients in the stratum corneum.

PubMed

Rothe, H; Obringer, C; Manwaring, J; Avci, C; Wargniez, W; Eilstein, J; Hewitt, N; Cubberley, R; Duplan, H; Lange, D; Jacques-Jamin, C; Klaric, M; Schepky, A; Grégoire, S

2017-07-01

Partition (K) and diffusion (D) coefficients are important to measure for the modelling of skin penetration of chemicals through the stratum corneum (SC). We compared the feasibility of three protocols for the testing of 50 chemicals in our main studies, using three cosmetics-relevant model chemicals with a wide range of logP values. Protocol 1: SC concentration-depth profile using tape-stripping (measures K SC/v and D SC /H SC 2 , where H SC is the SC thickness); Protocol 2A: incubation of isolated SC with chemical (direct measurement of K SC/v only) and Protocol 2B: diffusion through isolated SC mounted on a Franz cell (measures K SC/v and D SC /H SC 2 , and is based on Fick's laws). K SC/v values for caffeine and resorcinol using Protocol 1 and 2B were within 30% of each other, values using Protocol 2A were ~two-fold higher, and all values were within 10-fold of each other. Only indirect determination of K SC/v by Protocol 2B was different from the direct measurement of K SC/v by Protocol 2A and Protocol 1 for 7-EC. The variability of K SC/v for all three chemicals using Protocol 2B was higher compared to Protocol 1 and 2A. D SC /H SC 2 values for the three chemicals were of the same order of magnitude using all three protocols. Additionally, using Protocol 1, there was very little difference between parameters measured in pig and human SC. In conclusion, K SC/v, and D SC values were comparable using different methods. Pig skin might be a good surrogate for human skin for the three chemicals tested. Copyright © 2017 The Authors Journal of Applied Toxicology published by John Wiley & Sons Ltd. Copyright © 2017 The Authors Journal of Applied Toxicology published by John Wiley & Sons Ltd.

Chemical methods for encoding and decoding of posttranslational modifications

PubMed Central

Chuh, Kelly N.; Batt, Anna R.; Pratt, Matthew R.

2016-01-01

A large array of posttranslational modifications can dramatically change the properties of proteins and influence different aspects of their biological function such as enzymatic activity, binding interactions, and proteostasis. Despite the significant knowledge that has been gained about the function of posttranslational modifications using traditional biological techniques, the analysis of the site-specific effects of a particular modification, the identification of the full compliment of modified proteins in the proteome, and the detection of new types of modifications remains challenging. Over the years, chemical methods have contributed significantly in both of these areas of research. This review highlights several posttranslational modifications where chemistry-based approaches have made significant contributions to our ability to both prepare homogeneously modified proteins and identify and characterize particular modifications in complex biological settings. As the number and chemical diversity of documented posttranslational modifications continues to rise, we believe that chemical strategies will be essential to advance the field in years to come. PMID:26933738

Evaluation of a High Throughput Starch Analysis Optimised for Wood

PubMed Central

Bellasio, Chandra; Fini, Alessio; Ferrini, Francesco

2014-01-01

Starch is the most important long-term reserve in trees, and the analysis of starch is therefore useful source of physiological information. Currently published protocols for wood starch analysis impose several limitations, such as long procedures and a neutralization step. The high-throughput standard protocols for starch analysis in food and feed represent a valuable alternative. However, they have not been optimised or tested with woody samples. These have particular chemical and structural characteristics, including the presence of interfering secondary metabolites, low reactivity of starch, and low starch content. In this study, a standard method for starch analysis used for food and feed (AOAC standard method 996.11) was optimised to improve precision and accuracy for the analysis of starch in wood. Key modifications were introduced in the digestion conditions and in the glucose assay. The optimised protocol was then evaluated through 430 starch analyses of standards at known starch content, matrix polysaccharides, and wood collected from three organs (roots, twigs, mature wood) of four species (coniferous and flowering plants). The optimised protocol proved to be remarkably precise and accurate (3%), suitable for a high throughput routine analysis (35 samples a day) of specimens with a starch content between 40 mg and 21 µg. Samples may include lignified organs of coniferous and flowering plants and non-lignified organs, such as leaves, fruits and rhizomes. PMID:24523863

Nucleic acid-based aptamers: applications, development and clinical trials.

PubMed

Kanwar, Jagat R; Roy, Kislay; Maremanda, Nihal G; Subramanian, Krishnakumar; Veedu, Rakesh N; Bawa, Raj; Kanwar, Rupinder K

2015-01-01

Short single-stranded oligonucleotides called aptamers, often termed as chemical antibodies, have been developed as powerful alternatives to traditional antibodies with respect to their obvious advantages like high specificity and affinity, longer shelf-life, easier manufacturing protocol, freedom to introduce chemical modifications for further improvement, etc. Reiterative selection process of aptamers over 10-15 cycles starting from a large initial pool of random nucleotide sequences renders them with high binding affinity, thereby making them extremely specific for their targets. Aptamer-based detection systems are well investigated and likely to displace primitive detection systems. Aptamer chimeras (combination of aptamers with another aptamer or biomacromolecule or chemical moiety) have the potential activity of both the parent molecules, and thus hold the capability to perform diverse functions at the same time. Owing to their extremely high specificity and lack of immunogenicity or pathogenicity, a number of other aptamers have recently entered clinical trials and have garnered favorable attention from pharmaceutical companies. Promising results from the clinical trials provide new hope to change the conventional style of therapy. Aptamers have attained high therapeutic relevance in a short time as compared to synthetic drugs and/or other modes of therapy. This review follows the various trends in aptamer technology including production, selection, modifications and success in clinical fields. It focusses largely on the various applications of aptamers which mainly depend upon their selection procedures. The review also sheds light on various modifications and chimerizations that have been implemented in order to improve the stability and functioning of the aptamers, including introduction of locked nucleic acids (LNAs). The application of various aptamers in detection systems has been discussed elaborately in order to stress on their role as efficient diagnostic agents. The key aspect of this review is focused on success of aptamers on the basis of their performance in clinical trials for various diseases.

Modifications in trypsin digestion protocol for increasing the efficiency and coverage.

PubMed

Syal, Kirtimaan; Tadala, Raghu

2015-01-01

Standard trypsin digestion protocol of proteins followed by MALDI-MS analysis has been realized as an important tool for the identification and characterization of proteins. In this article, we proposed the elimination of the step of 'staining/de-staining of gel pieces' in in-gel digestion protocol in order to improve the efficiency of trypsin digestion. Coomassie dye is known to interfere with digestion of proteins by trypsin and the procedure of staining-de-staining could result in loss of photoaffinity probe, post translational modifications and catalytic activities of enzymes. Further, we studied parameters like hydrophobicity and isoelectric point, and attempted to quantitatively relate it to the efficiency of trypsin digestion. We suggest that properties of proteins should be considered and trypsin digestion protocol should be appropriately modified as per sequence and other information.

General Characteristics of the Changes in the Thermal Stability of Proteins and Enzymes After the Chemical Modification of Their Functional Groups

NASA Astrophysics Data System (ADS)

Kutuzova, G. D.; Ugarova, N. N.; Berezin, Ilya V.

1984-11-01

The principal structural and physicochemical factors determining the stability of protein macromolecules in solution and the characteristics of the structure of the proteins from thermophilic microorganisms are examined. The mechanism of the changes in the thermal stability of proteins and enzymes after the chemical modification of their functional side groups and the experimental data concerning the influence of chemical modification on the thermal stability of proteins are analysed. The dependence of the stabilisation effect and of the changes in the structure of protein macromolecules on the degree of modification and on the nature of the modified groups and the groups introduced into proteins in the course of modification (their charge and hydrophobic properties) is demonstrated. The great practical value of the method of chemical modification for the preparation of stabilised forms of biocatalysts is shown in relation to specific examples. The bibliography includes 178 references.

Advances in chemical synthesis of structurally modified bioactive RNAs.

PubMed

Li, Ziyuan; Zhou, Haipin; Wu, Xiaoming; Yao, Hequan

2013-01-01

Methods for the chemical synthesis of RNA have been available for almost half century, and presently, RNA could be chemically synthesized by automated synthesizers, using protected ribonucleosides preactivated as phosphoramidites, which has already been covered by many reviews. In addition to advancement on synthetic methods, a variety of modifications have also been made on the synthesized oligonucleotides, and previous reviews on the general synthesis of RNAs have not covered this area. In this tutorial review, three types of modifications have been summarized standing at the viewpoint of medicinal chemistry: (1) modifications on nucleobase, comprising substituent introduction and replacement with pseudobase; (2) modifications on ribose, consisting of modifications on the 2', 3' or 5'-position, alternation of configuration, and conformational restriction on ribose; (3) modifications on internucleoside linkages, including amide, formacetal, sulfide, sulfone, ether, phosphorothiolate and phosphorothioate linkages. Synthetic methods achieving these modifications along with the functions or values of these modifications have also been discussed and commented on.

RNA isolation from mouse pancreas: a ribonuclease-rich tissue.

PubMed

Azevedo-Pouly, Ana Clara P; Elgamal, Ola A; Schmittgen, Thomas D

2014-08-02

Isolation of high-quality RNA from ribonuclease-rich tissue such as mouse pancreas presents a challenge. As a primary function of the pancreas is to aid in digestion, mouse pancreas may contain as much a 75 mg of ribonuclease. We report modifications of standard phenol/guanidine thiocyanate lysis reagent protocols to isolate RNA from mouse pancreas. Guanidine thiocyanate is a strong protein denaturant and will effectively disrupt the activity of ribonuclease under most conditions. However, critical modifications to standard protocols are necessary to successfully isolate RNA from ribonuclease-rich tissues. Key steps include a high lysis reagent to tissue ratio, removal of undigested tissue prior to phase separation and inclusion of a ribonuclease inhibitor to the RNA solution. Using these and other modifications, we routinely isolate RNA with RNA Integrity Number (RIN) greater than 7. The isolated RNA is of suitable quality for routine gene expression analysis. Adaptation of this protocol to isolate RNA from ribonuclease rich tissues besides the pancreas should be readily achievable.

A Balanced Protocol for Return to School for Children and Youth Following Concussive Injury.

PubMed

DeMatteo, Carol; Stazyk, Kathy; Giglia, Lucy; Mahoney, William; Singh, Sheila K; Hollenberg, Robert; Harper, Jessica A; Missiuna, Cheryl; Law, Mary; McCauley, Dayle; Randall, Sarah

2015-07-01

Few protocols exist for returning children/youth to school after concussion. Childhood concussion can significantly affect school performance, which is vital to social development, academic learning, and preparation for future roles. The goal of this knowledge translation research was to develop evidence based materials to inform physicians about pediatric concussion. The Return to School (RTS) concussion protocol was developed following the National Institute for Health and Care Excellence procedures. Based on a scoping review, and stakeholder opinions, an RTS protocol was developed for children/youth. This unique protocol focuses on school adaptation in 4 main areas: (a) timetable/attendance, (b) curriculum, (c) environmental modifications, and (d) activity modifications. A balance of cognitive rest and timely return to school need to be considered for returning any student to school after a concussion. Implementation of these new recommendations may be an important tool in prevention of prolonged absence from school and academic failure while supporting brain recovery. © The Author(s) 2015.

The use of high-fidelity human patient simulation as an evaluative tool in the development of clinical research protocols and procedures.

PubMed

Wright, Melanie C; Taekman, Jeffrey M; Barber, Linda; Hobbs, Gene; Newman, Mark F; Stafford-Smith, Mark

2005-12-01

Errors in clinical research can be costly, in terms of patient safety, data integrity, and data collection. Data inaccuracy in early subjects of a clinical study may be associated with problems in the design of the protocol, procedures, and data collection tools. High-fidelity patient simulation centers provide an ideal environment to apply human-centered design to clinical trial development. A draft of a complex clinical protocol was designed, evaluated and modified using a high-fidelity human patient simulator in the Duke University Human Simulation and Patient Safety Center. The process included walk-throughs, detailed modifications of the protocol and development of procedural aids. Training of monitors and coordinators provided an opportunity for observation of performance that was used to identify further improvements to the protocol. Evaluative steps were used to design the research protocol and procedures. Iterative modifications were made to the protocol and data collection tools. The success in use of human simulation in the preparation of a complex clinical drug trial suggests the benefits of human patient simulation extend beyond training and medical equipment evaluation. Human patient simulation can provide a context for informal expert evaluation of clinical protocol design and for formal "rehearsal" to evaluate the efficacy of procedures and support tools.

Statistical controversies in clinical research: comparison of primary outcomes in protocols, public clinical-trial registries and publications: the example of oncology trials.

PubMed

Perlmutter, A S; Tran, V-T; Dechartres, A; Ravaud, P

2017-04-01

Protocols are often unavailable to peer-reviewers and readers. To detect outcome reporting bias (ORB), readers usually have to resort to publicly available descriptions of study design such as public clinical trial registries. We compared primary outcomes in protocols, ClinicalTrials.gov and publications of oncology trials and evaluated the use of ClinicalTrials.gov as compared with protocols in detecting discrepancies between planned and published outcomes. We searched for phase III oncology trials registered in ClinicalTrials.gov and published in the Journal of Clinical Oncology and New England Journal of Medicine between January 2014 and June 2015. We extracted primary outcomes reported in the protocol, ClinicalTrials.gov and the publication. First, we assessed the quality of primary outcome descriptions by using a published framework. Second, we evaluated modifications of primary outcomes between each source. Finally, we evaluated the agreement, specificity and sensitivity of detecting modifications between planned and published outcomes by using protocols or ClinicalTrials.gov. We included 65 trials, with 81 primary outcomes common among the 3 sources. The proportion of primary outcomes reporting all items from the framework was 73%, 22%, and 75% for protocols, ClinicalTrials.gov and publications, respectively. Eight (12%) trials presented a discrepancy between primary outcomes reported in the protocol and in the publication. Twelve (18.5%) trials presented a discrepancy between primary outcomes registered at ClinicalTrials.gov and in publications. We found a moderate agreement in detecting discrepant reporting of outcomes by using protocols or ClinicalTrials.gov [κ = 0.53, 95% confidence interval (0.25-0.81)]. Using ClinicalTrials.gov to detect discrepant reporting of outcomes showed high specificity (89.5%) but lacked sensitivity (75%) as compared with use of protocols. In oncology trials, primary outcome descriptions in ClinicalTrials.gov are often of low quality and may not reflect what is in the protocol, thus limiting the detection of modifications between planned and published outcomes. © The Author 2016. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Designing Endocrine Disruption Out of the Next Generation of Chemicals.

PubMed

Schug, T T; Abagyan, R; Blumberg, B; Collins, T J; Crews, D; DeFur, P L; Dickerson, S M; Edwards, T M; Gore, A C; Guillette, L J; Hayes, T; Heindel, J J; Moores, A; Patisaul, H B; Tal, T L; Thayer, K A; Vandenberg, L N; Warner, J; Watson, C S; Saal, F S Vom; Zoeller, R T; O'Brien, K P; Myers, J P

2013-01-01

A central goal of green chemistry is to avoid hazard in the design of new chemicals. This objective is best achieved when information about a chemical's potential hazardous effects is obtained as early in the design process as feasible. Endocrine disruption is a type of hazard that to date has been inadequately addressed by both industrial and regulatory science. To aid chemists in avoiding this hazard, we propose an endocrine disruption testing protocol for use by chemists in the design of new chemicals. The Tiered Protocol for Endocrine Disruption (TiPED) has been created under the oversight of a scientific advisory committee composed of leading representatives from both green chemistry and the environmental health sciences. TiPED is conceived as a tool for new chemical design, thus it starts with a chemist theoretically at "the drawing board." It consists of five testing tiers ranging from broad in silico evaluation up through specific cell- and whole organism-based assays. To be effective at detecting endocrine disruption, a testing protocol must be able to measure potential hormone-like or hormone-inhibiting effects of chemicals, as well as the many possible interactions and signaling sequellae such chemicals may have with cell-based receptors. Accordingly, we have designed this protocol to broadly interrogate the endocrine system. The proposed protocol will not detect all possible mechanisms of endocrine disruption, because scientific understanding of these phenomena is advancing rapidly. To ensure that the protocol remains current, we have established a plan for incorporating new assays into the protocol as the science advances. In this paper we present the principles that should guide the science of testing new chemicals for endocrine disruption, as well as principles by which to evaluate individual assays for applicability, and laboratories for reliability. In a 'proof-of-principle' test, we ran 6 endocrine disrupting chemicals (EDCs) that act via different endocrinological mechanisms through the protocol using published literature. Each was identified as endocrine active by one or more tiers. We believe that this voluntary testing protocol will be a dynamic tool to facilitate efficient and early identification of potentially problematic chemicals, while ultimately reducing the risks to public health.

Protocol for HER2 FISH Using a Non-cross-linking, Formalin-free Tissue Fixative to Combine Advantages of Cryo-preservation and Formalin Fixation

PubMed Central

Loibner, Martina; Oberauner-Wappis, Lisa; Viertler, Christian; Groelz, Daniel; Zatloukal, Kurt

2017-01-01

Morphologic assessment of formalin-fixed, paraffin-embedded (FFPE) tissue samples has been the gold standard for cancer diagnostics for decades due to its excellent preservation of morphology. Personalized medicine increasingly provides individually adapted and targeted therapies for characterized individual diseases enabled by combined morphological and molecular analytical technologies and diagnostics. Performance of morphologic and molecular assays from the same FFPE specimen is challenging because of the negative impact of formalin due to chemical modification and cross-linking of nucleic acids and proteins. A non-cross-linking, formalin-free tissue fixative has been recently developed to fulfil both requirements, i.e., to preserve morphology like FFPE and biomolecules like cryo-preservation. Since FISH is often required in combination with histopathology and molecular diagnostics, we tested the applicability of FISH protocols on tissues treated with this new fixative. We found that formalin post-fixation of histological sections of non-cross-linking, formalin-free and paraffin-embedded (NCFPE) breast cancer tissue generated equivalent results to those with FFPE tissue in human epidermal growth factor receptor 2 (HER2) FISH analysis. This protocol describes how a FISH assay originally developed and validated for FFPE tissue can be used for NCFPE tissues by a simple post-fixation step of histological sections. PMID:29364207

Online attention modification for social anxiety disorder: replication of a randomized controlled trial.

PubMed

Carleton, R Nicholas; Teale Sapach, Michelle J N; Oriet, Chris; LeBouthillier, Daniel M

2017-01-01

Social anxiety disorder (SAD) models posit vigilance for external social threat cues and exacerbated self-focused attention as key in disorder development and maintenance. Evidence indicates a modified dot-probe protocol may reduce symptoms of SAD; however, the efficacy when compared to a standard protocol and long-term maintenance of treatment gains remains unclear. Furthermore, the efficacy of such protocols on SAD-related constructs remains relatively unknown. The current investigation clarified these associations using a randomized control trial replicating and extending previous research. Participants with SAD (n = 113; 71% women) were randomized to complete a standard (i.e. control) or modified (i.e. active) dot-probe protocol consisting of 15-min sessions twice weekly for four weeks. Self-reported symptoms were measured at baseline, post-treatment, and 4-month and 8-month follow-ups. Hierarchical linear modeling indicated significant self-reported reductions in symptoms of social anxiety, fear of negative evaluation, trait anxiety, and depression, but no such reductions in fear of positive evaluation. Symptom changes did not differ based on condition and were maintained at 8-month follow-up. Attentional biases during the dot-probe task were not related to symptom change. Overall, our results replicate support for the efficacy of both protocols in reducing symptoms of SAD and specific related constructs, and suggest a role of exposure, expectancy, or practice effects, rather than attention modification, in effecting such reductions. The current results also support distinct relationships between fears of negative and positive evaluation and social anxiety. Further research focused on identifying the mechanisms of change in attention modification protocols appears warranted.

PCR-based detection of a rare linear DNA in cell culture.

PubMed

Saveliev, Sergei V.

2002-11-11

The described method allows for detection of rare linear DNA fragments generated during genomic deletions. The predicted limit of the detection is one DNA molecule per 10(7) or more cells. The method is based on anchor PCR and involves gel separation of the linear DNA fragment and chromosomal DNA before amplification. The detailed chemical structure of the ends of the linear DNA can be defined with the use of additional PCR-based protocols. The method was applied to study the short-lived linear DNA generated during programmed genomic deletions in a ciliate. It can be useful in studies of spontaneous DNA deletions in cell culture or for tracking intracellular modifications at the ends of transfected DNA during gene therapy trials.

PCR-based detection of a rare linear DNA in cell culture

PubMed Central

2002-01-01

The described method allows for detection of rare linear DNA fragments generated during genomic deletions. The predicted limit of the detection is one DNA molecule per 107 or more cells. The method is based on anchor PCR and involves gel separation of the linear DNA fragment and chromosomal DNA before amplification. The detailed chemical structure of the ends of the linear DNA can be defined with the use of additional PCR-based protocols. The method was applied to study the short-lived linear DNA generated during programmed genomic deletions in a ciliate. It can be useful in studies of spontaneous DNA deletions in cell culture or for tracking intracellular modifications at the ends of transfected DNA during gene therapy trials. PMID:12734566

Halloysite Nanotubes for Cleaning, Consolidation and Protection.

PubMed

Cavallaro, Giuseppe; Lazzara, Giuseppe; Milioto, Stefana; Parisi, Filippo

2018-01-10

Herein, we report our recent research concerning the development of halloysite based protocols for cleaning, consolidation and protection purposes. Surface modification of halloysite cavity by anionic surfactants was explored to fabricate inorganic micelles able to solubilize hydrophobic contaminants. Hybrid dispersions based on halloysite and ecocompatible polymers were tested as consolidants for paper and waterlogged archaeological woods. Encapsulation of deacidifying and flame retardant agents within the halloysite lumen was conducted with aim to obtain nanofiller with a long-term protection ability. The results prove the suitability and versatility of halloysite nanotubes, which are perspective inorganic nanoparticles within materials science, remedation and conservation of cultural heritage fields. © 2018 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Surface-engineered substrates for improved human pluripotent stem cell culture under fully defined conditions.

PubMed

Saha, Krishanu; Mei, Ying; Reisterer, Colin M; Pyzocha, Neena Kenton; Yang, Jing; Muffat, Julien; Davies, Martyn C; Alexander, Morgan R; Langer, Robert; Anderson, Daniel G; Jaenisch, Rudolf

2011-11-15

The current gold standard for the culture of human pluripotent stem cells requires the use of a feeder layer of cells. Here, we develop a spatially defined culture system based on UV/ozone radiation modification of typical cell culture plastics to define a favorable surface environment for human pluripotent stem cell culture. Chemical and geometrical optimization of the surfaces enables control of early cell aggregation from fully dissociated cells, as predicted from a numerical model of cell migration, and results in significant increases in cell growth of undifferentiated cells. These chemically defined xeno-free substrates generate more than three times the number of cells than feeder-containing substrates per surface area. Further, reprogramming and typical gene-targeting protocols can be readily performed on these engineered surfaces. These substrates provide an attractive cell culture platform for the production of clinically relevant factor-free reprogrammed cells from patient tissue samples and facilitate the definition of standardized scale-up friendly methods for disease modeling and cell therapeutic applications.

Recent studies of laser science in paintings conservation and research.

PubMed

Pouli, Paraskevi; Selimis, Alexandros; Georgiou, Savas; Fotakis, Costas

2010-06-15

The removal of aged and deteriorated molecular overlayers from the surface of paintings is a delicate and critical intervention in Cultural Heritage (CH) conservation. This irreversible action gets particularly complicated given the multitude of materials that may be present within a painted work of art (often in ultrathin layers or traces), as well as the exceptional sensitivity of the original surfaces to environmental conditions such as heat, light, and so on. Lasers hold an important role among the available cleaning methodologies, as they enable high control and accuracy, material selectivity, and immediate feedback. Still, prior to their implementation, it is imperative to optimize the cleaning parameters, so to ensure that any potential implications to the remaining materials are minimal and well understood. Toward this aim, research at IESL-FORTH is focused on both refining and continuously updating the laser-cleaning protocols (by introducing novel laser technologies into the field, i.e., ultrashort laser pulses), as well as on investigating and studying the nature and extent of laser-induced physicochemical alterations to the involved materials. In this Account, extended work for the understanding of ultraviolet (UV) laser ablation of polymers is presented. Emphasis is placed on the use of model systems (polymers doped with chromophores of known photochemistry) to examine the in-depth laser-induced modifications at the processed surfaces and thus to illustrate the dependence of their nature and extent on laser parameters and material properties. Furthermore, studies for the potential use of femtosecond UV pulses to overcome certain limitations involved with the nanosecond ablation of molecular overlayers from CH surfaces are highlighted. In particular, it is demonstrated that in the femtosecond regime any chemical modifications are, qualitatively and quantitatively, highly defined, limited and nearly independent of the material properties, such as the absorptivity and the degree of polymerization/molecular weight. Thus, they can be highly potent in the treatment of molecular substrates, enabling new material processing schemes that have not been possible with nanosecond laser technology, as for example, processing of ultrathin varnish layers. Finally, a sensitive indicator is introduced to elucidate the extent of any photochemical or structural modification induced at the substrate on the process of the laser-assisted removal of overpaints. A realistic scenario of an overlayered modern painting is simulated by a sensitive polymer film covered with acrylic paint. The indicator is doped with photosensitizers of known photochemistry and strong fluorescence emission, which allow the employment of laser induced fluorescence (LIF) for the detection of any chemical modifications generated into the substrate during laser cleaning. In addition, nonlinear microscopy techniques are successfully employed to examine the extent of these modifications. The suggested methodology is proven to reliably and accurately detect potential changes, and thus, it can serve as a monitoring tool to fine-tune the cleaning protocol and safeguard the original painting.

PCR on yeast colonies: an improved method for glyco-engineered Saccharomyces cerevisiae

PubMed Central

2013-01-01

Background Saccharomyces cerevisiae is extensively used in bio-industries. However, its genetic engineering to introduce new metabolism pathways can cause unexpected phenotypic alterations. For example, humanisation of the glycosylation pathways is a high priority pharmaceutical industry goal for production of therapeutic glycoproteins in yeast. Genomic modifications can lead to several described physiological changes: biomass yields decrease, temperature sensitivity or cell wall structure modifications. We have observed that deletion of several N-mannosyltransferases in Saccharomyces cerevisiae, results in strains that can no longer be analyzed by classical PCR on yeast colonies. Findings In order to validate our glyco-engineered Saccharomyces cerevisiae strains, we developed a new protocol to carry out PCR directly on genetically modified yeast colonies. A liquid culture phase, combined with the use of a Hot Start DNA polymerase, allows a 3-fold improvement of PCR efficiency. The results obtained are repeatable and independent of the targeted sequence; as such the protocol is well adapted for intensive screening applications. Conclusions The developed protocol enables by-passing of many of the difficulties associated with PCR caused by phenotypic modifications brought about by humanisation of the glycosylation in yeast and allows rapid validation of glyco-engineered Saccharomyces cerevisiae cells. It has the potential to be extended to other yeast strains presenting cell wall structure modifications. PMID:23688076

Designing Endocrine Disruption Out of the Next Generation of Chemicals

PubMed Central

Schug, T.T; Abagyan, R.; Blumberg, B.; Collins, T.J.; Crews, D.; DeFur, P.L.; Dickerson, S.M.; Edwards, T.M.; Gore, A.C.; Guillette, L.J.; Hayes, T.; Heindel, J.J.; Moores, A.; Patisaul, H.B.; Tal, T.L.; Thayer, K.A.; Vandenberg, L.N.; Warner, J.; Watson, C.S.; Saal, F.S. vom; Zoeller, R.T.; O’Brien, K.P.; Myers, J.P.

2013-01-01

A central goal of green chemistry is to avoid hazard in the design of new chemicals. This objective is best achieved when information about a chemical’s potential hazardous effects is obtained as early in the design process as feasible. Endocrine disruption is a type of hazard that to date has been inadequately addressed by both industrial and regulatory science. To aid chemists in avoiding this hazard, we propose an endocrine disruption testing protocol for use by chemists in the design of new chemicals. The Tiered Protocol for Endocrine Disruption (TiPED) has been created under the oversight of a scientific advisory committee composed of leading representatives from both green chemistry and the environmental health sciences. TiPED is conceived as a tool for new chemical design, thus it starts with a chemist theoretically at “the drawing board.” It consists of five testing tiers ranging from broad in silico evaluation up through specific cell- and whole organism-based assays. To be effective at detecting endocrine disruption, a testing protocol must be able to measure potential hormone-like or hormone-inhibiting effects of chemicals, as well as the many possible interactions and signaling sequellae such chemicals may have with cell-based receptors. Accordingly, we have designed this protocol to broadly interrogate the endocrine system. The proposed protocol will not detect all possible mechanisms of endocrine disruption, because scientific understanding of these phenomena is advancing rapidly. To ensure that the protocol remains current, we have established a plan for incorporating new assays into the protocol as the science advances. In this paper we present the principles that should guide the science of testing new chemicals for endocrine disruption, as well as principles by which to evaluate individual assays for applicability, and laboratories for reliability. In a ‘proof-of-principle’ test, we ran 6 endocrine disrupting chemicals (EDCs) that act via different endocrinological mechanisms through the protocol using published literature. Each was identified as endocrine active by one or more tiers. We believe that this voluntary testing protocol will be a dynamic tool to facilitate efficient and early identification of potentially problematic chemicals, while ultimately reducing the risks to public health. PMID:25110461

Quick Fluorescent In Situ Hybridization Protocol for Xist RNA Combined with Immunofluorescence of Histone Modification in X-chromosome Inactivation

PubMed Central

Yamada, Norishige; Ogawa, Akiyo; Ogawa, Yuya

2014-01-01

Combining RNA fluorescent in situ hybridization (FISH) with immunofluorescence (immuno-FISH) creates a technique that can be employed at the single cell level to detect the spatial dynamics of RNA localization with simultaneous insight into the localization of proteins, epigenetic modifications and other details which can be highlighted by immunofluorescence. X-chromosome inactivation is a paradigm for long non-coding RNA (lncRNA)-mediated gene silencing. X-inactive specific transcript (Xist) lncRNA accumulation (called an Xist cloud) on one of the two X-chromosomes in mammalian females is a critical step to initiate X-chromosome inactivation. Xist RNA directly or indirectly interacts with various chromatin-modifying enzymes and introduces distinct epigenetic landscapes to the inactive X-chromosome (Xi). One known epigenetic hallmark of the Xi is the Histone H3 trimethyl-lysine 27 (H3K27me3) modification. Here, we describe a simple and quick immuno-FISH protocol for detecting Xist RNA using RNA FISH with multiple oligonucleotide probes coupled with immunofluorescence of H3K27me3 to examine the localization of Xist RNA and associated epigenetic modifications. Using oligonucleotide probes results in a shorter incubation time and more sensitive detection of Xist RNA compared to in vitro transcribed RNA probes (riboprobes). This protocol provides a powerful tool for understanding the dynamics of lncRNAs and its associated epigenetic modification, chromatin structure, nuclear organization and transcriptional regulation. PMID:25489864

Real Time Detection of Protein Trafficking with High Throughput Flow Cytometry (HTFC) and Fluorogen Activating Protein (FAP) Base Biosensor

PubMed Central

Wu, Yang; Tapia, Phillip H.; Jarvik, Jonathan; Waggoner, Alan S.; Sklar, Larry A.

2014-01-01

We combined fluorogen activating protein (FAP) technology with high-throughput flow cytometry to detect real-time protein trafficking to and from the plasma membrane in living cells. The hybrid platform allows drug discovery for trafficking receptors, such as G-protein coupled receptors, receptor tyrosine kinases and ion channels, that were previously not suitable for high throughput screening by flow cytometry.. The system has been validated using the β2-adrenergic receptor (β2AR) system and extended to other GPCRs. When a chemical library containing ~1,200 off-patent drugs was screened against cells expressing FAP tagged β2AR, all known β2AR active ligands in the library were successfully identified, together with a few compounds that were later confirmed to regulate receptor internalization in a non-traditional manner. The unexpected discovery of new ligands by this approach indicates the potential of using this protocol for GPCR de-orphanization. In addition, screens of multiplexed targets promise improved efficiency with minor protocol modification. PMID:24510772

Optimized methods of chromatin immunoprecipitation for profiling histone modifications in industrial microalgae Nannochloropsis spp.

PubMed

Wei, Li; Xu, Jian

2018-06-01

Epigenetic factors such as histone modifications play integral roles in plant development and stress response, yet their implications in algae remain poorly understood. In the industrial oleaginous microalgae Nannochloropsis spp., the lack of an efficient methodology for chromatin immunoprecipitation (ChIP), which determines the specific genomic location of various histone modifications, has hindered probing the epigenetic basis of their photosynthetic carbon conversion and storage as oil. Here, a detailed ChIP protocol was developed for Nannochloropsis oceanica, which represents a reliable approach for the analysis of histone modifications, chromatin state, and transcription factor-binding sites at the epigenetic level. Using ChIP-qPCR, genes related to photosynthetic carbon fixation in this microalga were systematically assessed. Furthermore, a ChIP-Seq protocol was established and optimized, which generated a genome-wide profile of histone modification events, using histone mark H3K9Ac as an example. These results are the first step for appreciation of the chromatin landscape in industrial oleaginous microalgae and for epigenetics-based microalgal feedstock development. © 2018 Phycological Society of America.

Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank.

PubMed

Park, Sang-Jun; Lee, Jumin; Patel, Dhilon S; Ma, Hongjing; Lee, Hui Sun; Jo, Sunhwan; Im, Wonpil

2017-10-01

Glycans play a central role in many essential biological processes. Glycan Reader was originally developed to simplify the reading of Protein Data Bank (PDB) files containing glycans through the automatic detection and annotation of sugars and glycosidic linkages between sugar units and to proteins, all based on atomic coordinates and connectivity information. Carbohydrates can have various chemical modifications at different positions, making their chemical space much diverse. Unfortunately, current PDB files do not provide exact annotations for most carbohydrate derivatives and more than 50% of PDB glycan chains have at least one carbohydrate derivative that could not be correctly recognized by the original Glycan Reader. Glycan Reader has been improved and now identifies most sugar types and chemical modifications (including various glycolipids) in the PDB, and both PDB and PDBx/mmCIF formats are supported. CHARMM-GUI Glycan Reader is updated to generate the simulation system and input of various glycoconjugates with most sugar types and chemical modifications. It also offers a new functionality to edit the glycan structures through addition/deletion/modification of glycosylation types, sugar types, chemical modifications, glycosidic linkages, and anomeric states. The simulation system and input files can be used for CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Glycan Fragment Database in GlycanStructure.Org is also updated to provide an intuitive glycan sequence search tool for complex glycan structures with various chemical modifications in the PDB. http://www.charmm-gui.org/input/glycan and http://www.glycanstructure.org. wonpil@lehigh.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Method of Performance-Aware Security of Unicast Communication in Hybrid Satellite Networks

NASA Technical Reports Server (NTRS)

Baras, John S. (Inventor); Roy-Chowdhury, Ayan (Inventor)

2014-01-01

A method and apparatus utilizes Layered IPSEC (LES) protocol as an alternative to IPSEC for network-layer security including a modification to the Internet Key Exchange protocol. For application-level security of web browsing with acceptable end-to-end delay, the Dual-mode SSL protocol (DSSL) is used instead of SSL. The LES and DSSL protocols achieve desired end-to-end communication security while allowing the TCP and HTTP proxy servers to function correctly.

Security of modified Ping-Pong protocol in noisy and lossy channel

PubMed Central

Han, Yun-Guang; Yin, Zhen-Qiang; Li, Hong-Wei; Chen, Wei; Wang, Shuang; Guo, Guang-Can; Han, Zheng-Fu

2014-01-01

The “Ping-Pong” (PP) protocol is a two-way quantum key protocol based on entanglement. In this protocol, Bob prepares one maximally entangled pair of qubits, and sends one qubit to Alice. Then, Alice performs some necessary operations on this qubit and sends it back to Bob. Although this protocol was proposed in 2002, its security in the noisy and lossy channel has not been proven. In this report, we add a simple and experimentally feasible modification to the original PP protocol, and prove the security of this modified PP protocol against collective attacks when the noisy and lossy channel is taken into account. Simulation results show that our protocol is practical. PMID:24816899

Security of modified Ping-Pong protocol in noisy and lossy channel.

PubMed

Han, Yun-Guang; Yin, Zhen-Qiang; Li, Hong-Wei; Chen, Wei; Wang, Shuang; Guo, Guang-Can; Han, Zheng-Fu

2014-05-12

The "Ping-Pong" (PP) protocol is a two-way quantum key protocol based on entanglement. In this protocol, Bob prepares one maximally entangled pair of qubits, and sends one qubit to Alice. Then, Alice performs some necessary operations on this qubit and sends it back to Bob. Although this protocol was proposed in 2002, its security in the noisy and lossy channel has not been proven. In this report, we add a simple and experimentally feasible modification to the original PP protocol, and prove the security of this modified PP protocol against collective attacks when the noisy and lossy channel is taken into account. Simulation results show that our protocol is practical.

Apoptosis evaluation in epithelial cells exposed to different chemicals: relevance of floating cells.

PubMed

Turco, L; De Angelis, I; Stammati, A; Zucco, F

2000-01-01

The recent increase in understanding of cell death has promoted new approaches in toxicological studies, mainly those dealing with in vitro systems where the evaluation of cell death has been the most widely adopted end-point in measuring the effects of chemical toxicants. The aim of this study was to investigate the possibility of improving the traditional cytotoxicity test protocols in order to produce more specific information on the type of cell death induced by exposure to toxicants. In particular, we characterized the mode of cell death in an established epithelial cell line, HEp-2 cells, which is frequently used in cytotoxicity testing owing to its easy handling and standardization of culture conditions. Reference chemicals for apoptosis and necrosis were selected as controls, together with other molecules that have been shown, in preliminary studies, to induce various morphological and structural modifications in relation to cell death. The results obtained show that: (a) the floating fraction of treated cells gives the clearest picture of the necrotic/apoptotic distribution; (b) morphological analysis is crucial for characterization of apoptosis; (c) more than one cytotoxic end-point is necessary to clearly identify the type of cell death.

Detecting Chemically Modified DNA Bases Using Surface Enhanced Raman Spectroscopy

PubMed Central

Barhoumi, Aoune; Halas, Naomi J.

2013-01-01

Post-translational modifications of DNA- changes in the chemical structure of individual bases that occur without changes in the DNA sequence- are known to alter gene expression. They are believed to result in frequently deleterious phenotypic changes, such as cancer. Methylation of adenine, methylation and hydroxymethylation of cytosine, and guanine oxidation are the primary DNA base modifications identified to date. Here we show it is possible to use surface enhanced Raman spectroscopy (SERS) to detect these primary DNA base modifications. SERS detection of modified DNA bases is label-free and requires minimal additional sample preparation, reducing the possibility of additional chemical modifications induced prior to measurement. This approach shows the feasibility of DNA base modification assessment as a potentially routine analysis that may be further developed for clinical diagnostics. PMID:24427449

Detecting Chemically Modified DNA Bases Using Surface Enhanced Raman Spectroscopy.

PubMed

Barhoumi, Aoune; Halas, Naomi J

2011-12-15

Post-translational modifications of DNA- changes in the chemical structure of individual bases that occur without changes in the DNA sequence- are known to alter gene expression. They are believed to result in frequently deleterious phenotypic changes, such as cancer. Methylation of adenine, methylation and hydroxymethylation of cytosine, and guanine oxidation are the primary DNA base modifications identified to date. Here we show it is possible to use surface enhanced Raman spectroscopy (SERS) to detect these primary DNA base modifications. SERS detection of modified DNA bases is label-free and requires minimal additional sample preparation, reducing the possibility of additional chemical modifications induced prior to measurement. This approach shows the feasibility of DNA base modification assessment as a potentially routine analysis that may be further developed for clinical diagnostics.

Modification degrees at specific sites on heparan sulphate: an approach to measure chemical modifications on biological molecules with stable isotope labelling

PubMed Central

Wu, Zhengliang L.; Lech, Miroslaw

2005-01-01

Chemical modification of biological molecules is a general mechanism for cellular regulation. A quantitative approach has been developed to measure the extent of modification on HS (heparan sulphates). Sulphation on HS by sulphotransferases leads to variable sulphation levels, which allows cells to tune their affinities to various extracellular proteins, including growth factors. With stable isotope labelling and HPLC-coupled MS, modification degrees at various O-sulphation sites could be determined. A bovine kidney HS sample was first saturated in vitro with 34S by an OST (O-sulphotransferase), then digested with nitrous acid and analysed with HPLC-coupled MS. The 34S-labelled oligosaccharides were identified based on their unique isotope clusters. The modification degrees at the sulphotransferase recognition sites were obtained by calculating the intensities of isotopic peaks in the isotope clusters. The modification degrees at 3-OST-1 and 6-OST-1 sites were examined in detail. This approach can also be used to study other types of chemical modifications on biological molecules. PMID:15743272

40 CFR 455.47 - Pretreatment standards for new sources (PSNS).

Code of Federal Regulations, 2012 CFR

2012-07-01

...) EFFLUENT GUIDELINES AND STANDARDS (CONTINUED) PESTICIDE CHEMICALS Pesticide Chemicals Formulating and... received a modification by Best Engineering Judgement for modifications not listed in Table 8 to this part...

40 CFR 455.47 - Pretreatment standards for new sources (PSNS).

Code of Federal Regulations, 2014 CFR

2014-07-01

...) EFFLUENT GUIDELINES AND STANDARDS (CONTINUED) PESTICIDE CHEMICALS Pesticide Chemicals Formulating and... received a modification by Best Engineering Judgement for modifications not listed in Table 8 to this part...

Transformation assay in Bhas 42 cells: a model using initiated cells to study mechanisms of carcinogenesis and predict carcinogenic potential of chemicals.

PubMed

Sasaki, Kiyoshi; Umeda, Makoto; Sakai, Ayako; Yamazaki, Shojiro; Tanaka, Noriho

2015-01-01

Transformation assays using cultured cells have been applied to the study of carcinogenesis. Although various cell systems exist, few cell types such as BALB/c 3T3 subclones and Syrian hamster embryo cells have been used to study chemically induced two-stage carcinogenesis. Bhas 42 cells were established as a clone by the transfection with the v-Ha-ras gene into mouse BALB/c 3T3 A31-1-1 cells and their subsequent selection based on their sensitivity to 12-O-tetradecanoylphorbol-13-acetate. Using Bhas 42 cells, transformed foci were induced by the treatment with nongenotoxic carcinogens, most of which act as tumor promoters. Therefore, Bhas 42 cells were considered to be a model of initiated cells. Subsequently, not only nongenotoxic carcinogens but also genotoxic carcinogens, most of which act as tumor initiators, were found to induce transformed foci by the modification of the protocol. Furthermore, transformation of Bhas 42 cells was induced by the transfection with genes of oncogenic potential. We interpret this high sensitivity of Bhas 42 cells to various types of carcinogenic stimuli to be related to the multistage model of carcinogenesis, as the transfection of v-Ha-ras gene further advances the parental BALB/c 3T3 A31-1-1 cells toward higher transforming potential. Thus, we propose that Bhas 42 cells are a novel and sensitive cell line for the analysis of carcinogenesis and can be used for the detection of not only carcinogenic substances but also gene alterations related to oncogenesis. This review will address characteristics of Bhas 42 cells, the transformation assay protocol, validation studies, and the various chemicals tested in this assay.

40 CFR 766.28 - Expert review of protocols.

Code of Federal Regulations, 2013 CFR

2013-07-01

... CONTROL ACT DIBENZO-PARA-DIOXINS/DIBENZOFURANS Specific Chemical Testing/Reporting Requirements § 766.28 Expert review of protocols. EPA will gather a panel of experts in analysis of chemical matrices for HDDs... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Expert review of protocols. 766.28...

40 CFR 766.28 - Expert review of protocols.

Code of Federal Regulations, 2014 CFR

2014-07-01

... CONTROL ACT DIBENZO-PARA-DIOXINS/DIBENZOFURANS Specific Chemical Testing/Reporting Requirements § 766.28 Expert review of protocols. EPA will gather a panel of experts in analysis of chemical matrices for HDDs... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Expert review of protocols. 766.28...

40 CFR 766.28 - Expert review of protocols.

Code of Federal Regulations, 2011 CFR

2011-07-01

... CONTROL ACT DIBENZO-PARA-DIOXINS/DIBENZOFURANS Specific Chemical Testing/Reporting Requirements § 766.28 Expert review of protocols. EPA will gather a panel of experts in analysis of chemical matrices for HDDs... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Expert review of protocols. 766.28...

40 CFR 766.28 - Expert review of protocols.

Code of Federal Regulations, 2012 CFR

2012-07-01

... CONTROL ACT DIBENZO-PARA-DIOXINS/DIBENZOFURANS Specific Chemical Testing/Reporting Requirements § 766.28 Expert review of protocols. EPA will gather a panel of experts in analysis of chemical matrices for HDDs... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Expert review of protocols. 766.28...

40 CFR 766.35 - Reporting requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... protocol for the test as follows: (A) The protocols for each chlorinated chemical substance produced by... be submitted 12 months after manufacture or importation begins for chlorinated chemical substances... exclusion for chlorinated chemical substances, and 24 months after expiration of the exemption, waiver or...

40 CFR 766.35 - Reporting requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... protocol for the test as follows: (A) The protocols for each chlorinated chemical substance produced by... be submitted 12 months after manufacture or importation begins for chlorinated chemical substances... exclusion for chlorinated chemical substances, and 24 months after expiration of the exemption, waiver or...

Analysis of Proximity-1 Space Link Interleaved Time Synchronization (PITS) Protocol

NASA Technical Reports Server (NTRS)

Woo, Simon S.

2011-01-01

To synchronize clocks between spacecraft in proximity, the Proximity-1 Space Link Interleaved Time Synchronization (PITS) Protocol has been proposed. PITS is based on the NTP Interleaved On-Wire Protocol and is capable of being adapted and integrated into CCSDS Proximity-1 Space Link Protocol with minimal modifications. In this work, we will discuss the correctness and liveness of PITS. Further, we analyze and evaluate the performance of time synchronization latency with various channel error rates in different PITS operational modes.

Impact of home modification services on ability in everyday life for people ageing with disabilities.

PubMed

Petersson, Ingela; Lilja, Margareta; Hammel, Joy; Kottorp, Anders

2008-04-01

To examine the impact of home modifications on self-rated ability in everyday life from various aspects for people ageing with disabilities. The study sample was recruited from an agency providing home modification services in Sweden and comprised 73 subjects whose referrals had been approved and who were scheduled to receive home modifications (intervention group) and 41 subjects waiting for their applications to be assessed for approval (comparison group). The subjects rated their ability in everyday life using the Client-Clinician Assessment Protocol Part I on 2 occasions: at baseline and follow-up. The Client-Clinician Assessment Protocol Part I provides data on the clients' self-rated independence, difficulty and safety in everyday life. The data were first subjected to Rasch analysis in order to convert the raw scores into interval measures. Further analyses to investigate changes in self-rated ability were conducted with parametric statistics. Subjects who had received home modifications reported a statistically significant improvement in their self-rated ability in everyday life compared with those in the comparison group. Subjects who had received home modifications reported less difficulty and increased safety, especially in tasks related to self-care in the bathroom and transfers, such as getting in and out of the home. Home modifications have a positive impact on self-rated ability in everyday life, especially on decreasing the level of difficulty and increasing safety.

Posttranscriptional RNA Modifications: playing metabolic games in a cell's chemical Legoland.

PubMed

Helm, Mark; Alfonzo, Juan D

2014-02-20

Nature combines existing biochemical building blocks, at times with subtlety of purpose. RNA modifications are a prime example of this, where standard RNA nucleosides are decorated with chemical groups and building blocks that we recall from our basic biochemistry lectures. The result: a wealth of chemical diversity whose full biological relevance has remained elusive despite being public knowledge for some time. Here, we highlight several modifications that, because of their chemical intricacy, rely on seemingly unrelated pathways to provide cofactors for their synthesis. Besides their immediate role in affecting RNA function, modifications may act as sensors and transducers of information that connect a cell's metabolic state to its translational output, carefully orchestrating a delicate balance between metabolic rate and protein synthesis at a system's level. Copyright © 2014 Elsevier Ltd. All rights reserved.

DNA-magnetic Particle Binding Analysis by Dynamic and Electrophoretic Light Scattering.

PubMed

Haddad, Yazan; Dostalova, Simona; Kudr, Jiri; Zitka, Ondrej; Heger, Zbynek; Adam, Vojtech

2017-11-09

Isolation of DNA using magnetic particles is a field of high importance in biotechnology and molecular biology research. This protocol describes the evaluation of DNA-magnetic particles binding via dynamic light scattering (DLS) and electrophoretic light scattering (ELS). Analysis by DLS provides valuable information on the physicochemical properties of particles including particle size, polydispersity, and zeta potential. The latter describes the surface charge of the particle which plays major role in electrostatic binding of materials such as DNA. Here, a comparative analysis exploits three chemical modifications of nanoparticles and microparticles and their effects on DNA binding and elution. Chemical modifications by branched polyethylenimine, tetraethyl orthosilicate and (3-aminopropyl)triethoxysilane are investigated. Since DNA exhibits a negative charge, it is expected that zeta potential of particle surface will decrease upon binding of DNA. Forming of clusters should also affect particle size. In order to investigate the efficiency of these particles in isolation and elution of DNA, the particles are mixed with DNA in low pH (~6), high ionic strength and dehydration environment. Particles are washed on magnet and then DNA is eluted by Tris-HCl buffer (pH = 8). DNA copy number is estimated using quantitative polymerase chain reaction (PCR). Zeta potential, particle size, polydispersity and quantitative PCR data are evaluated and compared. DLS is an insightful and supporting method of analysis that adds a new perspective to the process of screening of particles for DNA isolation.

MicroSEQ® Salmonella spp. Detection Kit Using the Pathatrix® 10-Pooling Salmonella spp. Kit Linked Protocol Method Modification.

PubMed

Wall, Jason; Conrad, Rick; Latham, Kathy; Liu, Eric

2014-03-01

Real-time PCR methods for detecting foodborne pathogens offer the advantages of simplicity and quick time to results compared to traditional culture methods. The addition of a recirculating pooled immunomagnetic separation method prior to real-time PCR analysis increases processing output while reducing both cost and labor. This AOAC Research Institute method modification study validates the MicroSEQ® Salmonella spp. Detection Kit [AOAC Performance Tested Method (PTM) 031001] linked with the Pathatrix® 10-Pooling Salmonella spp. Kit (AOAC PTM 090203C) in diced tomatoes, chocolate, and deli ham. The Pathatrix 10-Pooling protocol represents a method modification of the enrichment portion of the MicroSEQ Salmonella spp. The results of the method modification were compared to standard cultural reference methods for diced tomatoes, chocolate, and deli ham. All three matrixes were analyzed in a paired study design. An additional set of chocolate test portions was analyzed using an alternative enrichment medium in an unpaired study design. For all matrixes tested, there were no statistically significant differences in the number of positive test portions detected by the modified candidate method compared to the appropriate reference method. The MicroSEQ Salmonella spp. protocol linked with the Pathatrix individual or 10-Pooling procedure demonstrated reliability as a rapid, simplified, method for the preparation of samples and subsequent detection of Salmonella in diced tomatoes, chocolate, and deli ham.

The use of a photoionization detector to detect harmful volatile chemicals by emergency personnel

PubMed Central

Patel, Neil D; Fales, William D; Farrell, Robert N

2009-01-01

Objective The objective of this investigation was to determine if a photoionization detector (PID) could be used to detect the presence of a simulated harmful chemical on simulated casualties of a chemical release. Methods A screening protocol, based on existing radiation screening protocols, was developed for the purposes of the investigation. Three simulated casualties were contaminated with a simulated chemical agent and two groups of emergency responders were involved in the trials. The success–failure ratio of the participants was used to judge the performance of the PID in this application. Results A high success rate was observed when the screening protocol was properly adhered to (97.67%). Conversely, the success rate suffered when participants deviated from the protocol (86.31%). With one exception, all failures were noted to have been the result of a failure to correctly observe the established screening protocol. Conclusions The results of this investigation indicate that the PID may be an effective screening tool for emergency responders. However, additional study is necessary to both confirm the effectiveness of the PID and refine the screening protocol if necessary. PMID:27147829

Physical and chemical modification of starches: A review.

PubMed

Zia-Ud-Din; Xiong, Hanguo; Fei, Peng

2017-08-13

The development of green material in the last decade has been increased, which tends to reduce the impact of humans on the environment. Starch as an agro-sourced polymer has become very popular recently due to its characteristics, such as wide availability, low cost, and total compostability without toxic residues. Starch is the most abundant organic compound found in nature after cellulose. Starches are inherently unsuitable for most applications and, therefore, must be modified physically and/or chemically to enhance their positive attributes and/or to minimize their defects. Modification of starches is generally carried out by using physical methods that are simple and inexpensive due to the absence of chemical agents. However, chemical modification involves the exploitation of hydroxyl group present in the starches that brings about the desired results for the utilization of starches for specific applications. All these techniques have the tendency to produce starches with altered physicochemical properties and modified structural attributes for various food and nonfood applications. This paper reviews the recent knowledge and developments using physical modification methods, some chemical modification methods, and a combination of both to produce a novel molecule with substantial applications, in food industry along with future perspectives.

Proteomic analyses of the environmental toxicity of carcinogenic chemicals

EPA Science Inventory

Protein expression and posttranslational modifications consistently change in response to the exposure to environmental chemicals. Recent technological advances in proteomics provide new tools for more efficient characterization of protein expression and posttranslational modific...

siRNAmod: A database of experimentally validated chemically modified siRNAs.

PubMed

Dar, Showkat Ahmad; Thakur, Anamika; Qureshi, Abid; Kumar, Manoj

2016-01-28

Small interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod.

ChIP-Seq Analysis for Identifying Genome-Wide Histone Modifications Associated with Stress-Responsive Genes in Plants.

PubMed

Li, Guosheng; Jagadeeswaran, Guru; Mort, Andrew; Sunkar, Ramanjulu

2017-01-01

Histone modifications represent the crux of epigenetic gene regulation essential for most biological processes including abiotic stress responses in plants. Thus, identification of histone modifications at the genome-scale can provide clues for how some genes are 'turned-on' while some others are "turned-off" in response to stress. This chapter details a step-by-step protocol for identifying genome-wide histone modifications associated with stress-responsive gene regulation using chromatin immunoprecipitation (ChIP) followed by sequencing of the DNA (ChIP-seq).

Chemical Modification of Boron-Doped Diamond Electrodes for Applications to Biosensors and Biosensing.

PubMed

Svítková, Jana; Ignat, Teodora; Švorc, Ľubomír; Labuda, Ján; Barek, Jiří

2016-05-03

Boron-doped diamond (BDD) is a prospective electrode material that possesses many exceptional properties including wide potential window, low noise, low and stable background current, chemical and mechanical stability, good biocompatibility, and last but not least exceptional resistance to passivation. These characteristics extend its usability in various areas of electrochemistry as evidenced by increasing number of published articles over the past two decades. The idea of chemically modifying BDD electrodes with molecular species attached to the surface for the purpose of creating a rational design has found promising applications in the past few years. BDD electrodes have appeared to be excellent substrate materials for various chemical modifications and subsequent application to biosensors and biosensing. Hence, this article presents modification strategies that have extended applications of BDD electrodes in electroanalytical chemistry. Different methods and steps of surface modification of this electrode material for biosensing and construction of biosensors are discussed.

Pelvic Muscle Rehabilitation: A Standardized Protocol for Pelvic Floor Dysfunction

PubMed Central

Pedraza, Rodrigo; Nieto, Javier; Ibarra, Sergio; Haas, Eric M.

2014-01-01

Introduction. Pelvic floor dysfunction syndromes present with voiding, sexual, and anorectal disturbances, which may be associated with one another, resulting in complex presentation. Thus, an integrated diagnosis and management approach may be required. Pelvic muscle rehabilitation (PMR) is a noninvasive modality involving cognitive reeducation, modification, and retraining of the pelvic floor and associated musculature. We describe our standardized PMR protocol for the management of pelvic floor dysfunction syndromes. Pelvic Muscle Rehabilitation Program. The diagnostic assessment includes electromyography and manometry analyzed in 4 phases: (1) initial baseline phase; (2) rapid contraction phase; (3) tonic contraction and endurance phase; and (4) late baseline phase. This evaluation is performed at the onset of every session. PMR management consists of 6 possible therapeutic modalities, employed depending on the diagnostic evaluation: (1) down-training; (2) accessory muscle isolation; (3) discrimination training; (4) muscle strengthening; (5) endurance training; and (6) electrical stimulation. Eight to ten sessions are performed at one-week intervals with integration of home exercises and lifestyle modifications. Conclusions. The PMR protocol offers a standardized approach to diagnose and manage pelvic floor dysfunction syndromes with potential advantages over traditional biofeedback, involving additional interventions and a continuous pelvic floor assessment with management modifications over the clinical course. PMID:25006337

Chemical modification of wood : a short review

Treesearch

Roger M. Rowell

2006-01-01

For most markets for wood, it is used without any treatments or modifications. When wood is used in adverse environments, it may be treated with chemicals to help prevent decay, improve water resistance, reduce the effects of ultraviolet radiation or increase fire retardancy. Many of these treatments involve the use of toxic or corrosive chemicals that can harm the...

Chemical modification of protein a chromatography ligands with polyethylene glycol. II: Effects on resin robustness and process selectivity.

PubMed

Weinberg, Justin; Zhang, Shaojie; Kirkby, Allison; Shachar, Enosh; Carta, Giorgio; Przybycien, Todd

2018-04-20

We have proposed chemical modification of Protein A (ProA) chromatography ligands with polyethylene glycol (PEGylation) as a strategy to increase the resin selectivity and robustness by providing the ligand with a steric repulsion barrier against non-specific binding. Here, we report on robustness and selectivity benefits for Repligen CaptivA PriMAB resin with ligands modified with 5.2 kDa and 21.5 kDa PEG chains, respectively. PEGylation of ProA ligands allowed the resin to retain a higher percentage of static binding capacity relative to the unmodified resin upon digestion with chymotrypsin, a representative serine protease. The level of protection against digestion was independent of the PEG molecular weight or modification extent for the PEGylation chemistry used. Additionally, PEGylation of the ligands was found to decrease the level of non-specific binding of fluorescently labeled bovine serum albumin (BSA) aggregates to the surface of the resin particles as visualized via confocal laser scanning microscopy (CLSM). The level of aggregate binding decreased as the PEG molecular weight increased, but increasing the extent of modification with 5.2 kDa PEG chains had no effect. Further examination of resin particles via CLSM confirmed that the PEG chains on the modified ligands were capable of blocking the "hitchhiking" association of BSA, a mock contaminant, to an adsorbed mAb that is prone to BSA binding. Ligands modified with 21.5 kDa PEG chains were effective at blocking the association, while ligands modified with 5.2 kDa PEG chains were not. Finally, ligands with 21.5 kDa PEG chains increased the selectivity of the resin against host cell proteins (HCPs) produced by Chinese Hamster Ovary (CHO) cells by up to 37% during purification of a monoclonal antibody (mAb) from harvested cell culture fluid (HCCF) using a standard ProA chromatography protocol. The combined work suggests that PEGylating ProA chromatography media is a viable pathway for increasing both resin lifetime and host cell impurity clearance in downstream bioprocessing. Copyright © 2018 Elsevier B.V. All rights reserved.

Minimal 2'-O-methyl phosphorothioate linkage modification pattern of synthetic guide RNAs for increased stability and efficient CRISPR-Cas9 gene editing avoiding cellular toxicity

PubMed Central

Basila, Megan; Kelley, Melissa L.

2017-01-01

Since its initial application in mammalian cells, CRISPR-Cas9 has rapidly become a preferred method for genome engineering experiments. The Cas9 nuclease is targeted to genomic DNA using guide RNAs (gRNA), either as the native dual RNA system consisting of a DNA-targeting CRISPR RNA (crRNA) and a trans-activating crRNA (tracrRNA), or as a chimeric single guide RNA (sgRNA). Entirely DNA-free CRISPR-Cas9 systems using either Cas9 protein or Cas9 mRNA and chemically synthesized gRNAs allow for transient expression of CRISPR-Cas9 components, thereby reducing the potential for off-targeting, which is a significant advantage in therapeutic applications. In addition, the use of synthetic gRNA allows for the incorporation of chemical modifications for enhanced properties including improved stability. Previous studies have demonstrated the utility of chemically modified gRNAs, but have focused on one pattern with multiple modifications in co-electroporation with Cas9 mRNA or multiple modifications and patterns with Cas9 plasmid lipid co-transfections. Here we present gene editing results using a series of chemically modified synthetic sgRNA molecules and chemically modified crRNA:tracrRNA molecules in both electroporation and lipid transfection assessing indel formation and/or phenotypic gene knockout. We show that while modifications are required for co-electroporation with Cas9 mRNA, some modification patterns of the gRNA are toxic to cells compared to the unmodified gRNA and most modification patterns do not significantly improve gene editing efficiency. We also present modification patterns of the gRNA that can modestly improve Cas9 gene editing efficiency when co-transfected with Cas9 mRNA or Cas9 protein (> 1.5-fold difference). These results indicate that for certain applications, including those relevant to primary cells, the incorporation of some, but not all chemical modification patterns on synthetic crRNA:tracrRNA or sgRNA can be beneficial to CRISPR-Cas9 gene editing. PMID:29176845

Minimal 2'-O-methyl phosphorothioate linkage modification pattern of synthetic guide RNAs for increased stability and efficient CRISPR-Cas9 gene editing avoiding cellular toxicity.

PubMed

Basila, Megan; Kelley, Melissa L; Smith, Anja van Brabant

2017-01-01

Since its initial application in mammalian cells, CRISPR-Cas9 has rapidly become a preferred method for genome engineering experiments. The Cas9 nuclease is targeted to genomic DNA using guide RNAs (gRNA), either as the native dual RNA system consisting of a DNA-targeting CRISPR RNA (crRNA) and a trans-activating crRNA (tracrRNA), or as a chimeric single guide RNA (sgRNA). Entirely DNA-free CRISPR-Cas9 systems using either Cas9 protein or Cas9 mRNA and chemically synthesized gRNAs allow for transient expression of CRISPR-Cas9 components, thereby reducing the potential for off-targeting, which is a significant advantage in therapeutic applications. In addition, the use of synthetic gRNA allows for the incorporation of chemical modifications for enhanced properties including improved stability. Previous studies have demonstrated the utility of chemically modified gRNAs, but have focused on one pattern with multiple modifications in co-electroporation with Cas9 mRNA or multiple modifications and patterns with Cas9 plasmid lipid co-transfections. Here we present gene editing results using a series of chemically modified synthetic sgRNA molecules and chemically modified crRNA:tracrRNA molecules in both electroporation and lipid transfection assessing indel formation and/or phenotypic gene knockout. We show that while modifications are required for co-electroporation with Cas9 mRNA, some modification patterns of the gRNA are toxic to cells compared to the unmodified gRNA and most modification patterns do not significantly improve gene editing efficiency. We also present modification patterns of the gRNA that can modestly improve Cas9 gene editing efficiency when co-transfected with Cas9 mRNA or Cas9 protein (> 1.5-fold difference). These results indicate that for certain applications, including those relevant to primary cells, the incorporation of some, but not all chemical modification patterns on synthetic crRNA:tracrRNA or sgRNA can be beneficial to CRISPR-Cas9 gene editing.

Efficiency and security problems of anonymous key agreement protocol based on chaotic maps

NASA Astrophysics Data System (ADS)

Yoon, Eun-Jun

2012-07-01

In 2011, Niu-Wang proposed an anonymous key agreement protocol based on chaotic maps in [Niu Y, Wang X. An anonymous key agreement protocol based on chaotic maps. Commun Nonlinear Sci Simulat 2011;16(4):1986-92]. Niu-Wang's protocol not only achieves session key agreement between a server and a user, but also allows the user to anonymously interact with the server. Nevertheless, this paper points out that Niu-Wang's protocol has the following efficiency and security problems: (1) The protocol has computational efficiency problem when a trusted third party decrypts the user sending message. (2) The protocol is vulnerable to Denial of Service (DoS) attack based on illegal message modification by an attacker.

Conditionally controlling nuclear trafficking in yeast by chemical-induced protein dimerization

PubMed Central

Xu, Tao; Johnson, Cole A; Gestwicki, Jason E; Kumar, Anuj

2016-01-01

We present here a protocol to conditionally control the nuclear trafficking of target proteins in yeast. In this system, rapamycin is used to heterodimerize two chimeric proteins. one chimera consists of a FK506-binding protein (FKBp12) fused to a cellular ‘address’ (nuclear localization signal or nuclear export sequence). the second chimera consists of a target protein fused to a fluorescent protein and the FKBp12-rapamycin-binding (FrB) domain from FKBp-12-rapamycin associated protein 1 (Frap1, also known as mtor). rapamycin induces dimerization of the FKBp12- and FrB-containing chimeras; these interactions selectively place the target protein under control of the cell address, thereby directing the protein into or out of the nucleus. By chemical-induced dimerization, protein mislocalization is reversible and enables the identification of conditional loss-of-function and gain-of-function phenotypes, in contrast to other systems that require permanent modification of the targeted protein. Yeast strains for this analysis can be constructed in 1 week, and the technique allows protein mislocalization within 15 min after drug treatment. PMID:21030958

Conditionally controlling nuclear trafficking in yeast by chemical-induced protein dimerization.

PubMed

Xu, Tao; Johnson, Cole A; Gestwicki, Jason E; Kumar, Anuj

2010-11-01

We present here a protocol to conditionally control the nuclear trafficking of target proteins in yeast. In this system, rapamycin is used to heterodimerize two chimeric proteins. One chimera consists of a FK506-binding protein (FKBP12) fused to a cellular 'address' (nuclear localization signal or nuclear export sequence). The second chimera consists of a target protein fused to a fluorescent protein and the FKBP12-rapamycin-binding (FRB) domain from FKBP-12-rapamycin associated protein 1 (FRAP1, also known as mTor). Rapamycin induces dimerization of the FKBP12- and FRB-containing chimeras; these interactions selectively place the target protein under control of the cell address, thereby directing the protein into or out of the nucleus. By chemical-induced dimerization, protein mislocalization is reversible and enables the identification of conditional loss-of-function and gain-of-function phenotypes, in contrast to other systems that require permanent modification of the targeted protein. Yeast strains for this analysis can be constructed in 1 week, and the technique allows protein mislocalization within 15 min after drug treatment.

75 FR 69505 - Self-Regulatory Organizations; Notice of Filing and Immediate Effectiveness of Proposed Rule...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-12

... routing standardized equity and index options. Specifically, the Exchange proposes to adopt a tiered fee... in connection with the use of other trading telecommunication protocols: [ $500 per month for each... is a protocol used by NOM market participants for order entry, modification and cancellation and...

Chemical modification of citrus pectin: Structural, physical and rheologial implications.

PubMed

Fracasso, Aline Francielle; Perussello, Camila Augusto; Carpiné, Danielle; Petkowicz, Carmen Lúcia de Oliveira; Haminiuk, Charles Windson Isidoro

2018-04-01

The present study aimed to investigate the physical, structural and rheological modifications caused by the chemical modification process of citrus pectin. Therefore, three commercial citrus pectins with different degree of esterification were chemically modified by sequential alkali and acidic hydrolytic process to produce modified citrus pectins (MCP) with special properties. The molar mass (M w ), degree of esterification (DE), monosaccharide composition, 13 C NMR spectra, homogeneity, morphology (SEM) and rheological behavior of both native and modified citrus pectins (MCP) were investigated. The chemical modification reduced the acid uronic content (up to 28.3%) and molar mass (up to 29.98%), however, showed little influence on the degree of esterification of native pectins. Modified citrus pectins presented higher amounts of neutral monosaccharides, mainly galactose, arabinose and rhamnose, typical of the Ramnogalacturonana-I (RG-I) region. Rheological tests indicated that the native and modified citrus pectins presented pseudoplastic behavior, however, the MCP samples were less viscous, compared to the native ones. Modified samples presented better dissolution in water and less strong gels, with good stability during oscillatory shearing at 25°C. This study aims to better understand the implications that chemical modifications may impose on the structure of citrus pectins. Copyright © 2017 Elsevier B.V. All rights reserved.

Chemical modification of semiconductor surfaces

NASA Technical Reports Server (NTRS)

Finklea, H. O.

1981-01-01

Results of research on the chemical modification of TiO2 powders in the gas phase and the examination of the modified powders by infrared absorption spectroscopy are comprehensively summarized. The range of information obtainable by IR spectroscopy of chemically modified semiconductors, and a definition of the optimum reaction conditions for synthesizing a monolayer of methylsilanes using vapor phase reaction conditions were considered.

Crab shell chitin whiskers reinforced natural rubber nanocomposites. 3. Effect of chemical modification of chitin whiskers.

PubMed

Gopalan Nair, Kalaprasad; Dufresne, Alain; Gandini, Alessandro; Belgacem, Mohamed Naceur

2003-01-01

The purpose of this study was to chemically modify the surface of chitin whiskers and to investigate the effect of the incorporation of these modified whiskers into a natural rubber (NR) matrix on the properties of the ensuing nanocomposite. Different chemical coupling agents were tested, namely, phenyl isocyanate (PI), alkenyl succinic anhydride (ASA) (Accosize 18 from American Cyanamid), and 3-isopropenyl-alpha,alpha'-dimethylbenzyl isocyanate (TMI). The extent of chemical modification was evaluated by Fourier transform infrared (FTIR) spectroscopy, transmission electron microscopy (TEM), and surface energy analysis. After chemical modification, nanocomposite films were obtained using a toluene natural rubber solution in which the whiskers were dispersed. Their mechanical properties were found to be inferior to those of unmodified chitin/NR composites presented in our previous study. In fact, even though there is an increase in filler-matrix interaction as a result of chemical modification of the chitin whiskers, this does not contribute to the improvement in the mechanical properties of the resulting nanocomposite. It is concluded that this loss of performance is due to the partial destruction of the three-dimensional network of chitin whiskers assumed to be present in the unmodified composites.

Constantly evolving safety assessment protocols for GM foods.

PubMed

Sesikeran, B; Vasanthi, Siruguri

2008-01-01

he introduction of GM foods has led to the evolution of a food safety assessment paradigm that establishes safety of the GM food relative to its conventional counterpart. The GM foods currently approved and marketed in several countries have undergone extensive safety testing under a structured safety assessment framework evolved by international organizations like FAO, WHO, Codex and OECD. The major elements of safety assessment include molecular characterization of inserted genes and stability of the trait, toxicity and allergenicity potential of the expressed substances, compositional analysis, potential for gene transfer to gut microflora and unintentional effects of the genetic modification. As more number and type of food crops are being brought under the genetic modification regime, the adequacy of existing safety assessment protocols for establishing safety of these foods has been questioned. Such crops comprise GM crops with higher agronomic vigour, nutritional or health benefit/ by modification of plant metabolic pathways and those expressing bioactive substances and pharmaceuticals. The safety assessment challenges of these foods are the potential of the methods to detect unintentional effects with higher sensitivity and rigor. Development of databases on food compositions, toxicants and allergens is currently seen as an important aid to development of safety protocols. With the changing global trends in genetic modification technology future challenge would be to develop GM crops with minimum amount of inserted foreign DNA so as to reduce the burden of complex safety assessments while ensuring safety and utility of the technology.

Satellite Communications Using Commercial Protocols

NASA Technical Reports Server (NTRS)

Ivancic, William D.; Griner, James H.; Dimond, Robert; Frantz, Brian D.; Kachmar, Brian; Shell, Dan

2000-01-01

NASA Glenn Research Center has been working with industry, academia, and other government agencies in assessing commercial communications protocols for satellite and space-based applications. In addition, NASA Glenn has been developing and advocating new satellite-friendly modifications to existing communications protocol standards. This paper summarizes recent research into the applicability of various commercial standard protocols for use over satellite and space- based communications networks as well as expectations for future protocol development. It serves as a reference point from which the detailed work can be readily accessed. Areas that will be addressed include asynchronous-transfer-mode quality of service; completed and ongoing work of the Internet Engineering Task Force; data-link-layer protocol development for unidirectional link routing; and protocols for aeronautical applications, including mobile Internet protocol routing for wireless/mobile hosts and the aeronautical telecommunications network protocol.

The nuclear matrix prepared by amine modification

PubMed Central

Wan, Katherine M.; Nickerson, Jeffrey A.; Krockmalnic, Gabriela; Penman, Sheldon

1999-01-01

The nucleus is spatially ordered by attachments to a nonchromatin nuclear structure, the nuclear matrix. The nuclear matrix and chromatin are intimately connected and integrated structures, and so a major technical challenge in nuclear matrix research has been to remove chromatin while retaining a native nuclear matrix. Most methods for removing chromatin require first a nuclease digestion and then a salt extraction to remove cut chromatin. We have hypothesized that cut chromatin is held in place by charge interactions involving nucleosomal amino groups. We have tested this hypothesis by chemically modifying amino groups after nuclease digestion. By using this protocol, chromatin could be effectively removed at physiological ionic strength. We compared the ultrastructure and composition of this nuclear matrix preparation with the traditional high-salt nuclear matrix and with the third nuclear matrix preparation that we have developed from which chromatin is removed after extensive crosslinking. All three matrix preparations reveal internal nuclear matrix structures that are built on a network of branched filaments of about 10 nm diameter. That such different chromatin-removal protocols reveal similar principles of nuclear matrix construction increases our confidence that we are observing important architectural elements of the native structure in the living cell. PMID:9927671

[The characterization of biosolids produced by the San Fernando wastewater treatment plant in Itagui, Antioquia, Colombia].

PubMed

Bedoya-Urrego, Katherine; Acevedo-Ruíz, José M; Peláez-Jaramillo, Carlos A; Agudelo-López, Sonia Del Pilar

2013-01-01

ABSTRACT Objective This study was aimed at evaluating pertinent physicochemical and microbiological (bacteria and parasites) parameters regarding the biosolids produced by the San Fernando wastewater treatment plant (WWTP) in Itagui, Antioquia, Colombia. Methods Twelve samples were collected and evaluated every month from January to December during 2010. The chemical, physical and microbiological tests followed the protocol described in Colombian technical guideline 5167. The protocol described in Mexican official Norm 004 (with some modifications) was used for identifying helminth ova and assessing their viability. Results All samples proved positive for Ascarislumbricoides, viable ova count ranging from 4 to 22 eggs/2gTS. Both Salmonella and Enterobacteriawere detected in all samples evaluated, the latter having 3,000 colony forming unit (CFU)/g minimum concentration. Biosolid sample values met the heavy metal concentration requirement established by national guidelines. There was no statistical association between rainfall and the pathogen's presence in the biosolids. Conclusion Our results suggested that the biosolids being produced by the San Fernando wastewater treatment plant (WWTP) could be used as organic fertilizer; however they should be treated/sanitized to meet the stipulations in Colombian technical guideline 5167.

Ecotoxicological impact of MSW landfills: assessment of teratogenic effects by means of an adapted FETAX assay.

PubMed

de Lapuente, J; González-Linares, J; Pique, E; Borràs, M

2014-01-01

The introduction of chemical products into the environment can cause long-term effects on the ecosystems. Increasing efforts are being made to determine the extent of contamination in particularly affected areas using diverse methods to assess the ecotoxicological impact. We used a modified Frog Embrio Toxicity Assay-Xenopus method to determine the extent of toxicological load in different sample soils obtained near three municipal solid waste landfills in Catalonia (Spain). The results show that the Garraf landfill facility produces more embryotoxic damage to the surroundings, than the others ones: Can Mata landfill and Montferrer-Castellbó landfill. The aim of this work is to demonstrate how different management of complex sources of contamination as the controlled dumping sites can modulate the presence of toxics in the environment and their effects and through this, help determine the safer way to treat these wastes. To this effect some conceptual modifications have been made on the established American Society for Testing and Materials protocol. The validity of the new model, both as to model of calculation as to protocol, has been demonstrated in three different sites with complex sources of contamination.

Redirecting adenovirus tropism by genetic, chemical, and mechanical modification of the adenovirus surface for cancer gene therapy.

PubMed

Yoon, A-Rum; Hong, Jinwoo; Kim, Sung Wan; Yun, Chae-Ok

2016-06-01

Despite remarkable advancements, clinical evaluations of adenovirus (Ad)-mediated cancer gene therapies have highlighted the need for improved delivery and targeting. Genetic modification of Ad capsid proteins has been extensively attempted. Although genetic modification enhances the therapeutic potential of Ad, it is difficult to successfully incorporate extraneous moieties into the capsid and the engineering process is laborious. Recently, chemical modification of the Ad surface with nanomaterials and targeting moieties has been found to enhance Ad internalization into the target by both passive and active mechanisms. Alternatively, external stimulus-mediated targeting can result in selective accumulation of Ad in the tumor and prevent dissemination of Ad into surrounding nontarget tissues. In the present review, we discuss various genetic, chemical, and mechanical engineering strategies for overcoming the challenges that hinder the therapeutic efficacy of Ad-based approaches. Surface modification of Ad by genetic, chemical, or mechanical engineering strategies enables Ad to overcome the shortcomings of conventional Ad and enhances delivery efficiency through distinct and unique mechanisms that unmodified Ad cannot mimic. However, although the therapeutic potential of Ad-mediated gene therapy has been enhanced by various surface modification strategies, each strategy still possesses innate limitations that must be addressed, requiring innovative ideas and designs.

Key advances in the chemical modification of nanocelluloses.

PubMed

Habibi, Youssef

2014-03-07

Nanocelluloses, including nanocrystalline cellulose, nanofibrillated cellulose and bacterial cellulose nanofibers, have become fascinating building blocks for the design of new biomaterials. Derived from the must abundant and renewable biopolymer, they are drawing a tremendous level of attention, which certainly will continue to grow in the future driven by the sustainability trend. This growing interest is related to their unsurpassed quintessential physical and chemical properties. Yet, owing to their hydrophilic nature, their utilization is restricted to applications involving hydrophilic or polar media, which limits their exploitation. With the presence of a large number of chemical functionalities within their structure, these building blocks provide a unique platform for significant surface modification through various chemistries. These chemical modifications are prerequisite, sometimes unavoidable, to adapt the interfacial properties of nanocellulose substrates or adjust their hydrophilic-hydrophobic balance. Therefore, various chemistries have been developed aiming to surface-modify these nano-sized substrates in order to confer to them specific properties, extending therefore their use to highly sophisticated applications. This review collocates current knowledge in the research and development of nanocelluloses and emphasizes more particularly on the chemical modification routes developed so far for their functionalization.

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

Coburn, Natalie, E-mail: natalie.coburn@swahs.health.nsw.gov.au; Beldham-Collins, Rachael; Radiation Oncology Network, Westmead Cancer Care Centre, University of Sydney, Sydney, New South Wales

Protocols commonly implemented in radiotherapy work areas may be classified as being either rigid (class solution) or flexible. Because formal evaluation of these protocol types has not occurred within the literature, we evaluated the efficiency of a rigid compared with flexible prostate planning protocol by assessing a series of completed 3D conformal prostate plans. Twenty prostate cancer patients with an average age of 70 years (range, 52-77) and sizes comprising 8 small, 10 medium, and 2 large were planned on the Phillips Pinnacle treatment planning system 6 times by radiation therapists with <2 years, 2-5 years, and >5 years ofmore » experience using a rigid and flexible protocol. Plans were critiqued using critical organ doses, confirmation numbers, and conformity index. Plans were then classified as being acceptable or not. Plans produced with the flexible protocol were 53% less likely to require modification (OR 0.47, 95% CI: 0.26, 0.84, p = 0.01). Planners with >5 years of experience were 78% more likely to produce plans requiring modification (OR 1.78, 95% CI: 1.12, 2.83, P = 0.02). Plans according to the flexible protocol took longer (112 min) compared with the time taken using a rigid protocol (68 min) (p < 0.001). The results suggest that further studies are needed; however, we propose that all radiation therapy planners should start with the same limitations, and if an acceptable plan is not reached, then flexibility should be given to improve the plan to meet the desired results.« less

Development and validation of a remote home safety protocol.

PubMed

Romero, Sergio; Lee, Mi Jung; Simic, Ivana; Levy, Charles; Sanford, Jon

2018-02-01

Environmental assessments and subsequent modifications conducted by healthcare professionals can enhance home safety and promote independent living. However, travel time, expense and the availability of qualified professionals can limit the broad application of this intervention. Remote technology has the potential to increase access to home safety evaluations. This study describes the development and validation of a remote home safety protocol that can be used by a caregiver of an elderly person to video-record their home environment for later viewing and evaluation by a trained professional. The protocol was developed based on literature reviews and evaluations from clinical and content experts. Cognitive interviews were conducted with a group of six caregivers to validate the protocol. The final protocol included step-by-step directions to record indoor and outdoor areas of the home. The validation process resulted in modifications related to safety, clarity of the protocol, readability, visual appearance, technical descriptions and usability. Our final protocol includes detailed instructions that a caregiver should be able to follow to record a home environment for subsequent evaluation by a home safety professional. Implications for Rehabilitation The results of this study have several implications for rehabilitation practice The remote home safety evaluation protocol can potentially improve access to rehabilitation services for clients in remote areas and prevent unnecessary delays for needed care. Using our protocol, a patient's caregiver can partner with therapists to quickly and efficiently evaluate a patient's home before they are released from the hospital. Caregiver narration, which reflects a caregiver's own perspective, is critical to evaluating home safety. In-home safety evaluations, currently not available to all who need them due to access barriers, can enhance a patient's independence and provide a safer home environment.

Hydrofluoric Acid-Based Derivatization Strategy To Profile PARP-1 ADP-Ribosylation by LC-MS/MS.

PubMed

Gagné, Jean-Philippe; Langelier, Marie-France; Pascal, John M; Poirier, Guy G

2018-06-11

Despite significant advances in the development of mass spectrometry-based methods for the identification of protein ADP-ribosylation, current protocols suffer from several drawbacks that preclude their widespread applicability. Given the intrinsic heterogeneous nature of poly(ADP-ribose), a number of strategies have been developed to generate simple derivatives for effective interrogation of protein databases and site-specific localization of the modified residues. Currently, the generation of spectral signatures indicative of ADP-ribosylation rely on chemical or enzymatic conversion of the modification to a single mass increment. Still, limitations arise from the lability of the poly(ADP-ribose) remnant during tandem mass spectrometry, the varying susceptibilities of different ADP-ribose-protein bonds to chemical hydrolysis, or the context dependence of enzyme-catalyzed reactions. Here, we present a chemical-based derivatization method applicable to the confident identification of site-specific ADP-ribosylation by conventional mass spectrometry on any targeted amino acid residue. Using PARP-1 as a model protein, we report that treatment of ADP-ribosylated peptides with hydrofluoric acid generates a specific +132 Da mass signature that corresponds to the decomposition of mono- and poly(ADP-ribosylated) peptides into ribose adducts as a consequence of the cleavage of the phosphorus-oxygen bonds.

Prediction of ocular irritancy of 26 chemicals and 26 cosmetic products with isolated rabbit eye (IRE) test.

PubMed

Guo, Xiang; Yang, Xing Fen; Yang, Ying; Hans, Raabe; Cai, Jing Heng; Xue, Jin Yu; Tan, Xiao Hua; Xie, Xiao Ping; Xiong, Xi Kun; Huang, Jun Ming

2012-06-01

This study aims to establish and evaluate the methodology of isolated rabbit eye (IRE) test. IRE test was performed according to modifications of the in vitro toxicology (INVITTOX) Protocol No.85: Rabbit enucleated eye test by European Centre for the Validation of Alternative Methods (ECVAM), and then 26 chemicals and 26 cosmetic products were tested in both in vitro IRE and in vivo Draize tests. A statistical analysis was conducted to determine the relevance of the IRE test to the data generated in the Draize test. IRE test was established successfully in our laboratory. It was shown that ranking correlation and class concordance were fairly well between the IRE test and the Draize test for 26 reference chemicals (Fisher's Exact Test χ(2)=51.314, P<0.001; McNemar P=0.261; Gamma=0.960, P<0.001; Kappa=0.843, P<0.001) and 26 cosmetic products (Fisher's Exact Test χ(2)=15.522, P<0.001; McNemar P=0.311; Gamma=0.967, P<0.001; Kappa=0.611, P<0.001). IRE test was established successfully for in vitro testing of eye irritation as an alternative to Draize test. Copyright © 2012 The Editorial Board of Biomedical and Environmental Sciences. Published by Elsevier B.V. All rights reserved.

Towards an alternative for the acute fish LC(50) test in chemical assessment: the fish embryo toxicity test goes multi-species -- an update.

PubMed

Braunbeck, Thomas; Boettcher, Melanie; Hollert, Henner; Kosmehl, Thomas; Lammer, Eva; Leist, Erik; Rudolf, Mark; Seitz, Nadja

2005-01-01

After its standardisation at the national level in Germany (DIN 38415-6, 2001, 2001), the 48 h sewage testing assay with zebrafish (Danio rerio) embryos has been submitted for standardisation to ISO. As an alternative to the conventional acute (96 h) fish test, a modified fish embryo test will be submitted to the OECD for chemical testing in late 2005. For this, a protocol originally designed for zebrafish was adapted to fit also the requirements of other OECD species, namely medaka (Oryzias latipes) and fathead minnow (Pimephales promelas). Results document that the transfer of the protocol is possible with only minor modifications. Data obtained from embryo tests with the three species are comparable. Statistical analysis of existing zebrafish embryo toxicity data resulted in the conclusions (1) that there is a reliable correlation between the fish embryo test and the acute fish test, (2) that the confidence belt of the regression line was relatively small, but that the prediction range was relatively wide. The regression thus seems appropriate to describe the relationship between acute fish and embryo LC(50) with good confidence, but is less appropriate as a prediction model. Investigations into oxygen requirements of zebrafish embryos reveal that they adapt to a broad range of oxygen levels and survive at concentrations of 2 mg/l without malformations. Zebrafish embryos can thus be exposed in very small toxicant volumes (100 microl), which is of particular interest for the testing of metabolites. Dechorionation studies with 48 h old zebrafish embryos indicate that the barrier function of the chorion increases with the lipophilicity of the test compound. Finally, examples are given as to how additional endpoints can be incorporated into the fish embryo test protocol to extend its scope, e.g. to sediment toxicity assessment or genotoxicity and mutagenicity testing.

Heat-induced Irreversible Denaturation of the Camelid Single Domain VHH Antibody Is Governed by Chemical Modifications

PubMed Central

Akazawa-Ogawa, Yoko; Takashima, Mizuki; Lee, Young-Ho; Ikegami, Takahisa; Goto, Yuji; Uegaki, Koichi; Hagihara, Yoshihisa

2014-01-01

The variable domain of camelid heavy chain antibody (VHH) is highly heat-resistant and is therefore ideal for many applications. Although understanding the process of heat-induced irreversible denaturation is essential to improve the efficacy of VHH, its inactivation mechanism remains unclear. Here, we showed that chemical modifications predominantly governed the irreversible denaturation of VHH at high temperatures. After heat treatment, the activity of VHH was dependent only on the incubation time at 90 °C and was insensitive to the number of heating (90 °C)-cooling (20 °C) cycles, indicating a negligible role for folding/unfolding intermediates on permanent denaturation. The residual activity was independent of concentration; therefore, VHH lost its activity in a unimolecular manner, not by aggregation. A VHH mutant lacking Asn, which is susceptible to chemical modifications, had significantly higher heat resistance than did the wild-type protein, indicating the importance of chemical modifications to VHH denaturation. PMID:24739391

Visual modifications on the P300 speller BCI paradigm

NASA Astrophysics Data System (ADS)

Salvaris, M.; Sepulveda, F.

2009-08-01

The best known P300 speller brain-computer interface (BCI) paradigm is the Farwell and Donchin paradigm. In this paper, various changes to the visual aspects of this protocol are explored as well as their effects on classification. Changes to the dimensions of the symbols, the distance between the symbols and the colours used were tested. The purpose of the present work was not to achieve the highest possible accuracy results, but to ascertain whether these simple modifications to the visual protocol will provide classification differences between them and what these differences will be. Eight subjects were used, with each subject carrying out a total of six different experiments. In each experiment, the user spelt a total of 39 characters. Two types of classifiers were trained and tested to determine whether the results were classifier dependant. These were a support vector machine (SVM) with a radial basis function (RBF) kernel and Fisher's linear discriminant (FLD). The single-trial classification results and multiple-trial classification results were recorded and compared. Although no visual protocol was the best for all subjects, the best performances, across both classifiers, were obtained with the white background (WB) visual protocol. The worst performance was obtained with the small symbol size (SSS) visual protocol.

Enhancing the functional properties of thermophilic enzymes by chemical modification and immobilization.

PubMed

Cowan, Don A; Fernandez-Lafuente, Roberto

2011-09-10

The immobilization of proteins (mostly typically enzymes) onto solid supports is mature technology and has been used successfully to enhance biocatalytic processes in a wide range of industrial applications. However, continued developments in immobilization technology have led to more sophisticated and specialized applications of the process. A combination of targeted chemistries, for both the support and the protein, sometimes in combination with additional chemical and/or genetic engineering, has led to the development of methods for the modification of protein functional properties, for enhancing protein stability and for the recovery of specific proteins from complex mixtures. In particular, the development of effective methods for immobilizing large multi-subunit proteins with multiple covalent linkages (multi-point immobilization) has been effective in stabilizing proteins where subunit dissociation is the initial step in enzyme inactivation. In some instances, multiple benefits are achievable in a single process. Here we comprehensively review the literature pertaining to immobilization and chemical modification of different enzyme classes from thermophiles, with emphasis on the chemistries involved and their implications for modification of the enzyme functional properties. We also highlight the potential for synergies in the combined use of immobilization and other chemical modifications. Copyright © 2011 Elsevier Inc. All rights reserved.

An Efficient Electroporation Protocol for the Genetic Modification of Mammalian Cells

PubMed Central

Chicaybam, Leonardo; Barcelos, Camila; Peixoto, Barbara; Carneiro, Mayra; Limia, Cintia Gomez; Redondo, Patrícia; Lira, Carla; Paraguassú-Braga, Flávio; Vasconcelos, Zilton Farias Meira De; Barros, Luciana; Bonamino, Martin Hernán

2017-01-01

Genetic modification of cell lines and primary cells is an expensive and cumbersome approach, often involving the use of viral vectors. Electroporation using square-wave generating devices, like Lonza’s Nucleofector, is a widely used option, but the costs associated with the acquisition of electroporation kits and the transient transgene expression might hamper the utility of this methodology. In the present work, we show that our in-house developed buffers, termed Chicabuffers, can be efficiently used to electroporate cell lines and primary cells from murine and human origin. Using the Nucleofector II device, we electroporated 14 different cell lines and also primary cells, like mesenchymal stem cells and cord blood CD34+, providing optimized protocols for each of them. Moreover, when combined with sleeping beauty-based transposon system, long-term transgene expression could be achieved in all types of cells tested. Transgene expression was stable and did not interfere with CD34+ differentiation to committed progenitors. We also show that these buffers can be used in CRISPR-mediated editing of PDCD1 gene locus in 293T and human peripheral blood mononuclear cells. The optimized protocols reported in this study provide a suitable and cost-effective platform for the genetic modification of cells, facilitating the widespread adoption of this technology. PMID:28168187

Preparation of BAC libraries from marine microbial populations.

PubMed

Sabehi, Gazalah; Béjà, Oded

2013-01-01

A protocol is presented here for the construction of BAC (bacterial artificial chromosome) libraries from planktonic microbial communities collected in marine environments. The protocol describes the collection and preparation of the planktonic microbial cells, high molecular weight DNA purification from those cells, the preparation of the BAC vector, and the special ligation and electrotransformation procedures required for successful library preparation. With small modifications, this protocol can be applied to microbes collected from other environments. © 2013 Elsevier Inc. All rights reserved.

Modification of wheat starch with succinic acid/acetanhydride and azelaic acid/acetanhydride mixtures. II. Chemical and physical properties.

PubMed

Ačkar, Durđica; Subarić, Drago; Babić, Jurislav; Miličević, Borislav; Jozinović, Antun

2014-08-01

The aim of this research was to investigate the influence of modification with succinic acid/acetanhydride and azelaic acid/acetanhydride mixtures on chemical and physical properties of wheat starch. Starch was isolated from two wheat varieties and modified with mixtures of succinic acid and acetanhydride and azelaic acid and acetanhydride in 4, 6 and 8% (w/w). Total starch content, resistant starch content, degree of modification, changes in FT-IR spectra, colour, gel texture and freeze-thaw stability were determined. Results showed that resistant starch content increased by both investigated modifications, and degree of modification increased proportionally to amount of reagents used. FT-IR analysis of modified starches showed peak around 1,740 cm(-1), characteristic for carbonyl group of ester. Total colour difference caused by modifications was detectable by trained people. Adhesiveness significantly increased, while freeze-thaw stability decreased by both investigated modifications.

Dechorionation as a tool to improve the fish embryo toxicity test (FET) with the zebrafish (Danio rerio).

PubMed

Henn, Kirsten; Braunbeck, Thomas

2011-01-01

Prior to hatching, the zebrafish embryo is surrounded by an acellular envelope, the chorion. Despite repeated speculations, it could not be clarified unequivocally whether the chorion represents an effective barrier and, thus, protects the embryo from exposure to distinct chemicals. Potentially, there is a risk of generating false negative results in developmental toxicity studies due to limited permeability of the chorion for some compounds. The simplest way to exclude this is to remove the chorion and expose the "naked" embryo. In the context of ecotoxicity testing, standardized protocols do not exist for fish embryo dechorionation, and survival rates of dechorionated embryos have usually not been subjected to statistical analysis. Since reproducibly high survival rates are of fundamental importance for chemical toxicity assessment, the present study was designed to develop and optimize a dechorionation procedure. With appropriate modifications of the fish embryo test protocol, embryos can be dechorionated at 24h post-fertilization (hpf) with survival rates of ≥90%. However, for fish embryo tests with dechorionated embryos, the standard positive control test substance, 3,4-dichloroaniline, should be replaced by another compound, e.g., acetone, since 3,4-dichloroaniline exerts its effects during the first 24h of development. Dechorionation of younger stages (<24 hpf) is generally possible, however with lower survival rates. The effect of dechorionation was demonstrated with the cationic polymer Luviquat HM 552, which is blocked by the chorion non-dechorionated embryos due to its molecular weight of ~400,000 Dalton, but becomes strongly toxic after dechorionation. Copyright © 2010 Elsevier Inc. All rights reserved.

The Effect of Postmastectomy Radiation Therapy on Breast Implants: Material Analysis on Silicone and Polyurethane Prosthesis.

PubMed

Lo Torto, Federico; Relucenti, Michela; Familiari, Giuseppe; Vaia, Nicola; Casella, Donato; Matassa, Roberto; Miglietta, Selenia; Marinozzi, Franco; Bini, Fabiano; Fratoddi, Ilaria; Sciubba, Fabio; Cassese, Raffaele; Tombolini, Vincenzo; Ribuffo, Diego

2018-05-17

The pathogenic mechanism underlying capsular contracture is still unknown. It is certainly a multifactorial process, resulting from human body reaction, biofilm activation, bacteremic seeding, or silicone exposure. The scope of the present article is to investigate the effect of hypofractionated radiotherapy protocol (2.66 Gy × 16 sessions) both on silicone and polyurethane breast implants. Silicone implants and polyurethane underwent irradiation according to a hypofractionated radiotherapy protocol for the treatment of breast cancer. After irradiation implant shells underwent mechanical, chemical, and microstructural evaluation by means of tensile testing, infrared spectra in attenuated total reflectance mode, nuclear magnetic resonance, and field emission scanning electron microscopy. At superficial analysis, irradiated silicone samples show several visible secondary and tertiary blebs. Polyurethane implants showed an open cell structure, which closely resembles a sponge. Morphological observation of struts from treated polyurethane sample shows a more compact structure, with significantly shorter and thicker struts compared with untreated sample. The infrared spectra in attenuated total reflectance mode spectra of irradiated and control samples were compared either for silicon and polyurethane samples. In the case of silicone-based membranes, treated and control specimens showed similar bands, with little differences in the treated one. Nuclear magnetic resonance spectra on the fraction soluble in CDCl3 support these observations. Tensile tests on silicone samples showed a softer behavior of the treated ones. Tensile tests on Polyurethane samples showed no significant differences. Polyurethane implants seem to be more resistant to radiotherapy damage, whereas silicone prosthesis showed more structural, mechanical, and chemical modifications.

Automated Solid-Phase Protein Modification with Integrated Enzymatic Digest for Reaction Validation: Application of a Compartmented Microfluidic Reactor for Rapid Optimization and Analysis of Protein Biotinylation

PubMed Central

Fraas, Regina; Diehm, Juliane; Franzreb, Matthias

2017-01-01

Protein modification by covalent coupling of small ligands or markers is an important prerequisite for the use of proteins in many applications. Well-known examples are the use of proteins with fluorescent markers in many in vivo experiments or the binding of biotinylated antibodies via biotin–streptavidin coupling in the frame of numerous bioassays. Multiple protocols were established for the coupling of the respective molecules, e.g., via the C and N-terminus, or via cysteines and lysines exposed at the protein surface. Still, in most cases the conditions of these standard protocols are only an initial guess. Optimization of the coupling parameters like reagent concentrations, pH, or temperature may strongly increase coupling yield and the biological activity of the modified protein. In order to facilitate the process of optimizing coupling conditions, a method was developed which uses a compartmented microfluidic reactor for the rapid screening of different coupling conditions. In addition, the system allows for the integration of an enzymatic digest of the modified protein directly after modification. In combination with a subsequent MALDI-TOF analysis of the resulting fragments, this gives a fast and detailed picture not only of the number and extent of the generated modifications but also of their position within the protein sequence. The described process was demonstrated for biotinylation of green fluorescent protein. Different biotin-excesses and different pH-values were tested in order to elucidate the influence on the modification extent and pattern. In addition, the results of solid-phase based modifications within the microfluidic reactor were compared to modification patterns resulting from coupling trials with unbound protein. As expected, modification patterns of immobilized proteins showed clear differences to the ones of dissolved proteins. PMID:29181376

Evaluation of modifications of the traditional patch test in assessing the chemical irritation potential of feminine hygiene products.

PubMed

Farage, Miranda A; Meyer, Sandy; Walter, Dave

2004-05-01

The first main objective of the work presented in this paper was to investigate ways of optimizing the current arm patch test protocol by (1) increasing the sensitivity of the test in order to evaluate more effectively the products that are inherently non-irritating, and/or (2) reducing the costs of these types of studies by shortening the protocol. The second main objective was to use the results of these studies and the results of the parallel studies conducted using the behind-the-knee method to better understand the contribution of mechanical irritation to the skin effects produced by these types of products. In addition, we were interested in continuing the evaluation of sensory effects and their relationship to objective measures of irritation. Test materials were prepared from three, currently marketed feminine protection pads. Wet and dry samples were applied to the upper arm using the standard 24-h patch test. Applications were repeated daily for 4 consecutive days. The test sites were scored for irritation prior to the first patch application, and 30-60 min after removal of each patch. Some test sites were treated by tape stripping the skin prior to the initial patch application. In addition, in one experiment, panelists were asked to keep a daily diary describing any sensory skin effects they noticed at each test site. All protocol variations ([intact skin/dry samples], [compromised skin/dry samples], [intact skin/wet samples], and [compromised skin/wet samples]) gave similar results for the products tested. When compared to the behind-the-knee test method, the standard upper arm patch test gave consistently lower levels of irritation when the test sites were scored shortly after patch removal, even though the sample application was longer (24 vs. 6 h) in the standard patch test. The higher level of irritation in the behind-the-knee method was likely due to mechanical irritation. The sensory skin effects did not appear to be related to a particular test product or a particular protocol variation. However, the mean irritation scores at those sites where a sensory effect was reported were higher than the mean irritation scores at those sites were no sensory effects were reported. All four protocol variations of the standard upper arm patch test can be used to assess the inherent chemical irritant properties of feminine protection products. For these products, which are inherently non-irritating, tape stripping and/or applying wet samples does not increase the sensitivity of the patch test method. Differences in irritation potential were apparent after one to three 24-h applications. Therefore, the standard patch test protocol can be shortened to three applications without compromising our ability to detect differences in the chemical irritation produced by the test materials. The patch test can be used to evaluate effectively the inherent chemical irritation potential of these types of products. However, this method is not suitable for testing the mechanical irritation due to friction that occurs during product use. There is no relationship between specific test conditions, i.e., compromised skin and/or testing wet samples and reports of perceived sensory reactions. However, there seems to be a clear relationship between sensory reactions and objective irritation scores.

Demonstration/Validation of Environmentally-Preferable Coatings for Launch Facilities

NASA Technical Reports Server (NTRS)

Lewis, Pattie

2011-01-01

Kennedy Space Center (KSC) is responsible for a number of facilities/structures with metallic structural and non-structural components in a highly corrosive environment. Metals require periodic maintenance activity to guard against the insidious effects of corrosion and thus ensure that structures meet or exceed design or performance life. The standard practice for protecting metallic substrates in atmospheric environments is the application of an applied coating system. Applied coating systems work via a variety of methods (barrier, galvanic and/or inhibitor) and adhere to the substrate through a combination of chemical and physical bonds. Maintenance at KSC and other NASA Centers is governed by NASA-STD-50088 (Protective Coating of Carbon Steel, Stainless Steel, and Aluminum on Launch Structures, Facilities, and Ground Support Equipment) which establishes practices for the protective coating of ground support equipment and related facilities used by or for NASA programs and projects. The Standard is for the design of non-flight hardware used to support the operations of receiving, transportation, handling, assembly, inspection, test, checkout, service, and launch of space vehicles and payloads at NASA launch, landing, or retrieval sites. These criteria and practices contained within the Standard may be used for items used at the manufacturing, development, and test sites upstream of the launch, landing, or retrieval sites. The objective of this effort is to demonstrate and validate environmentally-preferable alternatives in accordance with NASA-STD-50088 and KSC requirements which can then be added to the Approved Products List. This Test Protocol contains the critical requirements and tests necessary to qualify alternatives for structural steel applications. These tests were derived from engineering, performance, and operational impact (supportability) requirements defined by a consensus of KSC participants. A Test Report will document the results of the testing as well as any test modifications made during the execution of the testing. Users of this Test Protocol should check the project's Test Report for additional test details or minor modifications that may have been necessary in the execution of the testing. The technical stakeholders will have agreed upon test procedures modifications documented in the Test Report.

An efficient immunodetection method for histone modifications in plants.

PubMed

Nic-Can, Geovanny; Hernández-Castellano, Sara; Kú-González, Angela; Loyola-Vargas, Víctor M; De-la-Peña, Clelia

2013-12-16

Epigenetic mechanisms can be highly dynamic, but the cross-talk among them and with the genome is still poorly understood. Many of these mechanisms work at different places in the cell and at different times of organism development. Covalent histone modifications are one of the most complex and studied epigenetic mechanisms involved in cellular reprogramming and development in plants. Therefore, the knowledge of the spatial distribution of histone methylation in different tissues is important to understand their behavior on specific cells. Based on the importance of epigenetic marks for biology, we present a simplified, inexpensive and efficient protocol for in situ immunolocalization on different tissues such as flowers, buds, callus, somatic embryo and meristematic tissue from several plants of agronomical and biological importance. Here, we fully describe all the steps to perform the localization of histone modifications. Using this method, we were able to visualize the distribution of H3K4me3 and H3K9me2 without loss of histological integrity of tissues from several plants, including Agave tequilana, Capsicum chinense, Coffea canephora and Cedrela odorata, as well as Arabidopsis thaliana. There are many protocols to study chromatin modifications; however, most of them are expensive, difficult and require sophisticated equipment. Here, we provide an efficient protocol for in situ localization of histone methylation that dispenses with the use of expensive and sensitive enzymes. The present method can be used to investigate the cellular distribution and localization of a wide array of proteins, which could help to clarify the biological role that they play at specific times and places in different tissues of various plant species.

Obtaining 3D Chemical Maps by Energy Filtered Transmission Electron Microscopy Tomography.

PubMed

Roiban, Lucian; Sorbier, Loïc; Hirlimann, Charles; Ersen, Ovidiu

2018-06-09

Energy filtered transmission electron microscopy tomography (EFTEM tomography) can provide three-dimensional (3D) chemical maps of materials at a nanometric scale. EFTEM tomography can separate chemical elements that are very difficult to distinguish using other imaging techniques. The experimental protocol described here shows how to create 3D chemical maps to understand the chemical distribution and morphology of a material. Sample preparation steps for data segmentation are presented. This protocol permits the 3D distribution analysis of chemical elements in a nanometric sample. However, it should be noted that currently, the 3D chemical maps can only be generated for samples that are not beam sensitive, since the recording of filtered images requires long exposure times to an intense electron beam. The protocol was applied to quantify the chemical distribution of the components of two different heterogeneous catalyst supports. In the first study, the chemical distribution of aluminum and titanium in titania-alumina supports was analyzed. The samples were prepared using the swing-pH method. In the second, the chemical distribution of aluminum and silicon in silica-alumina supports that were prepared using the sol-powder and mechanical mixture methods was examined.

Protocol for Uniformly Measuring and Expressing the Performance of Energy Storage Systems

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

Conover, David R.; Crawford, Aladsair J.; Viswanathan, Vilayanur V.

2014-06-01

The Protocol for Uniformly Measuring and Expressing the Performance of Energy Storage Systems (PNNL-22010) was first issued in November 2012 as a first step toward providing a foundational basis for developing an initial standard for the uniform measurement and expression of energy storage system (ESS) performance. Its subsequent use in the field and review by the protocol working group and most importantly the users’ subgroup and the thermal subgroup has led to the fundamental modifications reflected in this update of the 2012 Protocol. As an update of the 2012 Protocol, this document (the June 2014 Protocol) is intended to supersedemore » its predecessor and be used as the basis for measuring and expressing ESS performance. The foreword provides general and specific details about what additions, revisions, and enhancements have been made to the 2012 Protocol and the rationale for them in arriving at the June 2014 Protocol.« less

A modification of the trans-oesophageal echocardiography protocol can reduce post-operative dysphagia following cardiac surgery.

PubMed

Chin, J-H; Lee, E-H; Choi, D-K; Choi, I-C

2011-01-01

Use of intra-operative trans-oesophageal echocardiography (TEE) is an independent risk factor for post-operative dysphagia. This study investigated whether modifying the TEE probe-placement protocol could reduce the incidence of post-operative dysphagia. In group I (n = 100), the TEE probe was inserted after anaesthetic induction and remained in place until the completion of surgery. In group II (n = 100), the TEE probe was inserted after anaesthetic induction, the heart was examined, then the probe was removed. The probe was inserted again before weaning from cardiopulmonary bypass and then immediately removed after examination. The incidence of dysphagia was significantly higher in group I than in group II patients (51.1% versus 28.6%). Multivariate regression analysis showed that the length of time that the TEE probe was in the oesophagus was an independent predictor of dysphagia. Modification of the TEE protocol in this way can reduce the incidence of post-operative dysphagia in cardiac surgery patients.

Elementary Teachers' Ideas about, Planning for and Implementation of Learner-Directed and Teacher-Directed Inquiry: A Mixed Methods Study

ERIC Educational Resources Information Center

Biggers, Mandy Sue

2013-01-01

Using a framework for variations of classroom inquiry (National Research Council [NRC], 2000, p. 29), this study explored 40 inservice elementary teachers' planning, modification, and enactment of kit-based science curriculum materials. As part of the study, a new observation protocol was modified from an existing protocol (Practices of…

Chemical Modification of Cyclodextrin and Amylose by Click Reaction and Its Application to the Synthesis of Poly-alkylamine-Modified Antibacterial Sugars.

PubMed

Yamamura, Hatsuo

2017-01-01

Cyclodextrin (CD) can be chemically modified into desired and sophisticated functional molecules. However, poly-modification often produces complicated mixtures, resulting in a low yield of the desired product. As the most promising procedure to solve such problems and to achieve poly-modification of the CD molecule, we present here the Huisgen 1,3-dipolar cycloaddition, known as a click reaction. This review will describe the results of our microwave-assisted click reaction for the poly-modification of CD and amylose molecules, and its application to the study of synthetic membrane active antibacterial derivatives.

Thio-amide functionalized polymers via polymerization or post-polymerization modification

NASA Astrophysics Data System (ADS)

Ozcam, Ali; Henke, Adam; Stibingerova, Iva; Srogl, Jiri; Genzer, Jan

2011-03-01

Decreasing supplies of fresh water and increasing population necessitates development of advanced water cleaning technologies, which would facilitate the removal of water pollutants. Amongst the worst of such contaminants are heavy metals and cyanides, infamous for their high toxicity. To assist the water purification processes, we aim to synthesize functionalized macromolecules that would contribute in the decontamination processes by scavenging detrimental chemicals. Epitomizing this role thio-amide unit features remarkable chemical flexibility that facilitates reversible catch-release of the ions, where the behavior controlled by subtle red-ox changes in the environment. Chemical tunability of the thio-amide moiety enables synthesis of thio-amide based monomers and post-polymerization modification agents. Two distinct synthetic pathways, polymerization and post-polymerization modification, have been exploited, leading to functional thioamide-based macromolecules: thioamide-monomers were copolymerized with N-isopropylacrylamide and post-polymerization modifications of poly(dimethylaminoethyl methacrylate) and poly(propargyl methacrylate) were accomplished via quarternization and ``click'' reactions, respectively.

Enzyme Technology of Peroxidases: Immobilization, Chemical and Genetic Modification

NASA Astrophysics Data System (ADS)

Longoria, Adriana; Tinoco, Raunel; Torres, Eduardo

An overview of enzyme technology applied to peroxidases is made. Immobilization on organic, inorganic, and hybrid supports; chemical modification of amino acids and heme group; and genetic modification by site-directed and random mutagenesis are included. Different strategies that were carried out to improve peroxidase performance in terms of stability, selectivity, and catalytic activity are analyzed. Immobilization of peroxidases on inorganic and organic materials enhances the tolerance of peroxidases toward the conditions normally found in many industrial processes, such as the presence of an organic solvent and high temperature. In addition, it is shown that immobilization helps to increase the Total Turnover Number at levels high enough to justify the use of a peroxidase-based biocatalyst in a synthesis process. Chemical modification of peroxidases produces modified enzymes with higher thermostability and wider substrate variability. Finally, through mutagenesis approaches, it is possible to produce modified peroxidases capable of oxidizing nonnatural substrates with high catalytic activity and affinity.

Modified CTAB and TRIzol protocols improve RNA extraction from chemically complex Embryophyta1

PubMed Central

Jordon-Thaden, Ingrid E.; Chanderbali, Andre S.; Gitzendanner, Matthew A.; Soltis, Douglas E.

2015-01-01

Premise of the study: Here we present a series of protocols for RNA extraction across a diverse array of plants; we focus on woody, aromatic, aquatic, and other chemically complex taxa. Methods and Results: Ninety-one taxa were subjected to RNA extraction with three methods presented here: (1) TRIzol/TURBO DNA-free kits using the manufacturer’s protocol with the addition of sarkosyl; (2) a combination method using cetyltrimethylammonium bromide (CTAB) and TRIzol/sarkosyl/TURBO DNA-free; and (3) a combination of CTAB and QIAGEN RNeasy Plant Mini Kit. Bench-ready protocols are given. Conclusions: After an iterative process of working with chemically complex taxa, we conclude that the use of TRIzol supplemented with sarkosyl and the TURBO DNA-free kit is an effective, efficient, and robust method for obtaining RNA from 100 mg of leaf tissue of land plant species (Embryophyta) examined. Our protocols can be used to provide RNA of suitable stability, quantity, and quality for transcriptome sequencing. PMID:25995975

Marine exposure of preservative-treated small wood panels

Treesearch

B. R. Johnson; D. I. Gutzmer

1984-01-01

Small wood panels treated with many different chemicals have been exposed to limnorian and teredine marine borers in the sea at Key West, Florida. These preservatives and treatments include creosotes with and without modification, waterborne salts, salt-creosote dual treatments, chemical modifications of wood, and modified polymers. In spite of the accelerated nature...

Chemical and Biological Tools for the Preparation of Modified Histone Proteins

PubMed Central

Howard, Cecil J.; Yu, Ruixuan R.; Gardner, Miranda L.; Shimko, John C.; Ottesen, Jennifer J.

2016-01-01

Eukaryotic chromatin is a complex and dynamic system in which the DNA double helix is organized and protected by interactions with histone proteins. This system is regulated through, a large network of dynamic post-translational modifications (PTMs) exists to ensure proper gene transcription, DNA repair, and other processes involving DNA. Homogenous protein samples with precisely characterized modification sites are necessary to better understand the functions of modified histone proteins. Here, we discuss sets of chemical and biological tools that have been developed for the preparation of modified histones, with a focus on the appropriate choice of tool for a given target. We start with genetic approaches for the creation of modified histones, including the incorporation of genetic mimics of histone modifications, chemical installation of modification analogs, and the use of the expanded genetic code to incorporate modified amino acids. Additionally, we will cover the chemical ligation techniques that have been invaluable in the generation of complex modified histones that are indistinguishable from the natural counterparts. Finally, we will end with a prospectus on future directions of synthetic chromatin in living systems. PMID:25863817

Sulfenic acid chemistry, detection and cellular lifetime☆

PubMed Central

Gupta, Vinayak; Carroll, Kate S.

2014-01-01

Background Reactive oxygen species-mediated cysteine sulfenic acid modification has emerged as an important regulatory mechanism in cell signaling. The stability of sulfenic acid in proteins is dictated by the local microenvironment and ability of antioxidants to reduce this modification. Several techniques for detecting this cysteine modification have been developed, including direct and in situ methods. Scope of review This review presents a historical discussion of sulfenic acid chemistry and highlights key examples of this modification in proteins. A comprehensive survey of available detection techniques with advantages and limitations is discussed. Finally, issues pertaining to rates of sulfenic acid formation, reduction, and chemical trapping methods are also covered. Major conclusions Early chemical models of sulfenic acid yielded important insights into the unique reactivity of this species. Subsequent pioneering studies led to the characterization of sulfenic acid formation in proteins. In parallel, the discovery of oxidant-mediated cell signaling pathways and pathological oxidative stress has led to significant interest in methods to detect these modifications. Advanced methods allow for direct chemical trapping of protein sulfenic acids directly in cells and tissues. At the same time, many sulfenic acids are short-lived and the reactivity of current probes must be improved to sample these species, while at the same time, preserving their chemical selectivity. Inhibitors with binding scaffolds can be rationally designed to target sulfenic acid modifications in specific proteins. General significance Ever increasing roles for protein sulfenic acids have been uncovered in physiology and pathology. A more complete understanding of sulfenic acid-mediated regulatory mechanisms will continue to require rigorous and new chemical insights. This article is part of a Special Issue entitled Current methods to study reactive oxygen species - pros and cons and biophysics of membrane proteins. Guest Editor: Christine Winterbourn. PMID:23748139

Reliable method for generating double-stranded DNA vectors containing site-specific base modifications.

PubMed

Brégeon, Damien; Doetsch, Paul W

2004-11-01

Cells of all living organisms are continuously exposed to physical and chemical agents that damage DNA and alter the integrity of their genomes. Despite the relatively high efficiency of the different repair pathways, some lesions remain in DNA when it is replicated or transcribed. Lesion bypass by DNA and RNA polymerases has been the subject of numerous investigations. However, knowledge of the in vivo mechanism of transcription lesion bypass is very limited because no robust methodology is available. Here we describe a protocol based on the synthesis of a complementary strand of a circular, single-stranded DNA molecule, which allows for the production of large amounts of double-stranded DNA containing a lesion at a specific position in a transcribed sequence. Such constructs can subsequently be used for lesion bypass studies in vivo by RNA polymerase and to ascertain how these events can be affected by the genetic background of the cells.

Reduced dimensionality tailored HN(C)N experiments for facile backbone resonance assignment of proteins through unambiguous identification of sequential HSQC peaks

NASA Astrophysics Data System (ADS)

Kumar, Dinesh

2013-12-01

Two novel reduced dimensionality (RD) tailored HN(C)N [S.C. Panchal, N.S. Bhavesh, R.V. Hosur, Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: application to unfolded proteins, J. Biomol. NMR 20 (2001) 135-147] experiments are proposed to facilitate the backbone resonance assignment of proteins both in terms of its accuracy and speed. These experiments - referred here as (4,3)D-hNCOcaNH and (4,3)D-hNcoCANH - exploit the linear combination of backbone 15N and 13C‧/13Cα chemical shifts simultaneously to achieve higher peak dispersion and randomness along their respective F1 dimensions. Simply, this has been achieved by modulating the backbone 15N(i) chemical shifts with that of 13C‧ (i - 1)/13Cα (i - 1) spins following the established reduced dimensionality NMR approach [T. Szyperski, D.C. Yeh, D.K. Sukumaran, H.N. Moseley, G.T. Montelione, Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment, Proc. Natl. Acad. Sci. USA 99 (2002) 8009-8014]. Though the modification is simple it has resulted an ingenious improvement of HN(C)N both in terms of peak dispersion and easiness of establishing the sequential connectivities. The increased dispersion along F1 dimension solves two purposes here: (i) resolves the ambiguities arising because of degenerate 15N chemical shifts and (ii) reduces the signal overlap in F2(15N)-F3(1H) planes (an important requisite in HN(C)N based assignment protocol for facile and unambiguous identification of sequentially connected HSQC peaks). The performance of both these experiments and the assignment protocol has been demonstrated using bovine apo Calbindin-d9k (75 aa) and urea denatured UNC60B (a 152 amino acid ADF/cofilin family protein of Caenorhabditis elegans), as representatives of folded and unfolded protein systems, respectively.

Effect of Reduction of Redox Modifications of Cys-Residues in the Na,K-ATPase α1-Subunit on Its Activity

PubMed Central

Dergousova, Elena A.; Petrushanko, Irina Yu.; Klimanova, Elizaveta A.; Mitkevich, Vladimir A.; Ziganshin, Rustam H.; Lopina, Olga D.; Makarov, Alexander A.

2017-01-01

Sodium-potassium adenosine triphosphatase (Na,K-ATPase) creates a gradient of sodium and potassium ions necessary for the viability of animal cells, and it is extremely sensitive to intracellular redox status. Earlier we found that regulatory glutathionylation determines Na,K-ATPase redox sensitivity but the role of basal glutathionylation and other redox modifications of cysteine residues is not clear. The purpose of this study was to detect oxidized, nitrosylated, or glutathionylated cysteine residues in Na,K-ATPase, evaluate the possibility of removing these modifications and assess their influence on the enzyme activity. To this aim, we have detected such modifications in the Na,K-ATPase α1-subunit purified from duck salt glands and tried to eliminate them by chemical reducing agents and the glutaredoxin1/glutathione reductase enzyme system. Detection of cysteine modifications was performed using mass spectrometry and Western blot analysis. We have found that purified Na,K-ATPase α1-subunit contains glutathionylated, nitrosylated, and oxidized cysteines. Chemical reducing agents partially eliminate these modifications that leads to the slight increase of the enzyme activity. Enzyme system glutaredoxin/glutathione reductase, unlike chemical reducing agents, produces significant increase of the enzyme activity. At the same time, the enzyme system deglutathionylates native Na,K-ATPase to a lesser degree than chemical reducing agents. This suggests that the enzymatic reducing system glutaredoxin/glutathione reductase specifically affects glutathionylation of the regulatory cysteine residues of Na,K-ATPase α1-subunit. PMID:28230807

Aryl-modified graphene quantum dots with enhanced photoluminescence and improved pH tolerance

NASA Astrophysics Data System (ADS)

Luo, Peihui; Ji, Zhe; Li, Chun; Shi, Gaoquan

2013-07-01

Chemical modification is an important technique to modulate the chemical and optical properties of graphene quantum dots (GQDs). In this paper, we report a versatile diazonium chemistry method to graft aryl groups including phenyl, 4-carboxyphenyl, 4-sulfophenyl and 5-sulfonaphthyl to GQDs via Gomberg-Bachmann reaction. The aryl-modified GQDs are nanocrystals with lateral dimensions in the range of 2-4 nm and an average thickness lower than 1 nm. Upon chemical modification with aryl groups, the photoluminescence (PL) bands of GQDs were tuned in the range of 418 and 447 nm, and their fluorescence quantum yields (QYs) were increased for up to about 6 times. Furthermore, the aryl-modified GQDs exhibited stable PL (both intensity and peak position) in a wide pH window of 1-11. The mechanism of improving the PL properties of GQDs by aryl-modification was also discussed.Chemical modification is an important technique to modulate the chemical and optical properties of graphene quantum dots (GQDs). In this paper, we report a versatile diazonium chemistry method to graft aryl groups including phenyl, 4-carboxyphenyl, 4-sulfophenyl and 5-sulfonaphthyl to GQDs via Gomberg-Bachmann reaction. The aryl-modified GQDs are nanocrystals with lateral dimensions in the range of 2-4 nm and an average thickness lower than 1 nm. Upon chemical modification with aryl groups, the photoluminescence (PL) bands of GQDs were tuned in the range of 418 and 447 nm, and their fluorescence quantum yields (QYs) were increased for up to about 6 times. Furthermore, the aryl-modified GQDs exhibited stable PL (both intensity and peak position) in a wide pH window of 1-11. The mechanism of improving the PL properties of GQDs by aryl-modification was also discussed. Electronic supplementary information (ESI) available: Fluorescence quantum yield measurements, estimation of grafting ratio, TEM images, FTIR spectra, PL spectra and zeta potentials. See DOI: 10.1039/c3nr02156d

CON4EI: CONsortium for in vitro Eye Irritation testing strategy - EpiOcular™ time-to-toxicity (EpiOcular ET-50) protocols for hazard identification and labelling of eye irritating chemicals.

PubMed

Kandarova, Helena; Letasiova, Silvia; Adriaens, Els; Guest, Robert; Willoughby, Jamin A; Drzewiecka, Agnieszka; Gruszka, Katarzyna; Alépée, Nathalie; Verstraelen, Sandra; Van Rompay, An R

2018-06-01

Assessment of acute eye irritation potential is part of the international regulatory requirements for testing of chemicals. The objective of the CON4EI (CONsortium for in vitro Eye Irritation testing strategy) project was to develop tiered testing strategies for eye irritation assessment for all drivers of classification. A set of 80 reference chemicals (38 liquids and 42 solids) was tested with eight different alternative methods. Here, the results obtained with reconstructed human cornea-like epithelium (RhCE) EpiOcular™ in the EpiOcular time-to-toxicity Tests (Neat and Dilution ET-50 protocols) are presented. The primary aim of this study was to evaluate whether test methods can discriminate chemicals not requiring classification for serious eye damage/eye irritancy (No Category) from chemicals requiring classification and labelling for Category 1 and Category 2. In addition, the predictive capacity in terms of in vivo drivers of classification was investigated. The chemicals were tested in two independent runs by MatTek In Vitro Life Science Laboratories. Results of this study demonstrate very high specificity of both test protocols. With the existing prediction models described in the SOPs, the specificity of the Neat and Dilution method was 87% and 100%, respectively. The Dilution method was able to correctly predicting 66% of GHS Cat 2 chemicals, however, prediction of GHS Cat 1 chemicals was only 47%-55% using the current protocols. In order to achieve optimal prediction for all three classes, a testing strategy was developed which combines the most predictive time-points of both protocols and for tests liquids and solids separately. Using this new testing strategy, the sensitivity for predicting GHS Cat 1 and GHS Cat 2 chemicals was 73% and 64%, respectively and the very high specificity of 97% was maintained. None of the Cat 1 chemicals was underpredicted as GHS No Category. Further combination of the EpiOcular time-to-toxicity protocols with other validated in vitro systems evaluated in this project, should enable significant reduction and even possible replacement of the animal tests for the final assessment of the irritation potential in all of the GHS classes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mobile Phone Cognitive Bias Modification Research Platform for Substance Use Disorders: Protocol for a Feasibility Study.

PubMed

Zhang, Melvyn; Ying, JiangBo; Song, Guo; Fung, Daniel Ss; Smith, Helen

2018-06-12

Cognitive biases refer to automatic attentional and interpretational tendencies, which could be retained by cognitive bias modification interventions. Cristea et al and Jones et al have published reviews (in 2016 and 2017 respectively) on the effectiveness of such interventions. The advancement of technologies such as electronic health (eHealth) and mobile health (mHealth) has led to them being harnessed for the delivery of cognitive bias modification. To date, at least eight studies have demonstrated the feasibility of mobile technologies for the delivery of cognitive bias modification. Most of the studies are limited to a description of the conventional cognitive bias modification methodology that has been adopted. None of the studies shared the developmental process for the methodology involved, such that future studies could adopt it in the cost-effective replication of such interventions. It is important to have a common platform that could facilitate the design and customization of cognitive bias modification interventions for a variety of psychiatric and addictive disorders. It is the aim of the current research protocol to describe the design of a research platform that allows for customization of cognitive bias modification interventions for addictive disorders. A multidisciplinary team of 2 addiction psychiatrists, a psychologist with expertise in cognitive bias modification, and a computer engineer, were involved in the development of the intervention. The proposed platform would comprise of a mobile phone version of the cognitive bias task which is controlled by a server that could customize the algorithm for the tasks and collate the reaction-time data in realtime. The server would also allow the researcher to program the specific set of images that will be present in the task. The mobile phone app would synchronize with the backend server in real-time. An open-sourced cross-platform gaming software from React Native was used in the current development. Multimedia Appendix 1 contains a video demonstrating the operation of the app, as well as a sample dataset of the reaction times (used for the computation of attentional biases) captured by the app. The current design can be utilized for cognitive bias modification across a spectrum of disorders and is not limited to one disorder. It will be of value for future research to utilize the above platform and compare the efficacy of mHealth approaches, such as the one described in this study, with conventional Web-based approaches in the delivery of attentional bias modification interventions. RR1-10.2196/9740. ©Melvyn Zhang, JiangBo Ying, Guo Song, Daniel SS Fung, Helen Smith. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 12.06.2018.

78 FR 26786 - 510(k) Device Modifications: Deciding When To Submit a 510(k) for a Change to an Existing Device...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-08

... test protocols that will be used to examine those specifications pre- and post-modification, within the... information after May 31, 2013. If you have never attended a Connect Pro event before, test your connection at https://collaboration.fda.gov/common/help/en/support/meeting_test.htm . To get a quick overview of the...

The Unexpected and Exceptionally Facile Chemical Modification of the Phenolic Hydroxyl Group of Tyrosine by Polyhalogenated Quinones under Physiological Conditions.

PubMed

Qu, Na; Li, Feng; Shao, Bo; Shao, Jie; Zhai, Guijin; Wang, Fuyi; Zhu, Ben-Zhan

2016-10-17

The phenolic hydroxyl group of tyrosine residue plays a crucial role in the structure and function of many proteins. However, little study has been reported about its modification by chemical agents under physiological conditions. In this study, we found, unexpectedly, that the phenolic hydroxyl group of tyrosine can be rapidly and efficiently modified by tetrafluoro-1,4-benzoquinone and other polyhalogenated quinones, which are the major genotoxic and carcinogenic quinoid metabolites of polyhalogenated aromatic compounds. The modification was found to be mainly due to the formation of a variety of fluoroquinone-O-tyrosine conjugates and their hydroxylated derivatives via nucleophilic substitution pathway. Analogous modifications were observed for tyrosine-containing peptides. Further studies showed that the blockade of the reactive phenolic hydroxyl group of tyrosine in the substrate peptide, even by very low concentration of tetrafluoro-1,4-benzoquinone, can prevent the kinase catalyzed tyrosine phosphorylation. This is the first report showing the exceptionally facile chemical modification of the phenolic hydroxyl group of tyrosine by polyhalogenated quinones under normal physiological conditions, which may have potential biological and toxicological implications.

Environmental Technology Verification Program Materials Management and Remediation Center Generic Protocol for Verification of In Situ Chemical Oxidation

EPA Science Inventory

The protocol provides generic procedures for implementing a verification test for the performance of in situ chemical oxidation (ISCO), focused specifically to expand the application of ISCO at manufactured gas plants with polyaromatic hydrocarbon (PAH) contamination (MGP/PAH) an...

Network Upgrade for the SLC: Control System Modifications

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

Crane, M.; Mackenzie, R.; Sass, R.

2011-09-09

Current communications between the SLAC Linear Collider control system central host and the SLCmicros is built upon the SLAC developed SLCNET communication hardware and protocols. We will describe how the Internet Suite of protocols (TCP/IP) are used to replace the SLCNET protocol interface. The major communication pathways and their individual requirements are described. A proxy server is used to reduce the number of total system TCP/IP connections. The SLCmicros were upgraded to use Ethernet and TCP/IP as well as SLCNET. Design choices and implementation experiences are addressed.

Impact of the excess sludge modification with selected chemical reagents on the increase of dissolved organic substances concentration compounds transformations in activated sludge.

PubMed

Zawieja, Iwona; Lidia, Wolny; Marta, Próba

2017-07-01

Submission of excess sludge initial disintegration process significantly affects the efficiency of anaerobic stabilization process. Expression of increasing the concentration of organic matter in dissolved form is to increase sludge disintegration. As a result of chemical modification is an increase of the chemical oxygen demand and the concentration of volatile fatty acids. The aim of this study was to determine the impact of the disintegration process with selected chemical reagents to increase the concentration of organic substances in dissolved form. The process of chemical disintegration of excess sludge was treated using the following reagents: Mg(OH) 2 , Ca(OH) 2 , HCl, H 2 SO 4 , H 2 O 2 . The modification was carried out at ambient temperature for 2, 6 and 24h. During sludge disintegration it was noticed the growth of indicators values that confirmed the susceptibility of prepared sludge to biodegradation. Copyright © 2017 Elsevier Inc. All rights reserved.

Stable-isotope-labeled Histone Peptide Library for Histone Post-translational Modification and Variant Quantification by Mass Spectrometry *

PubMed Central

Lin, Shu; Wein, Samuel; Gonzales-Cope, Michelle; Otte, Gabriel L.; Yuan, Zuo-Fei; Afjehi-Sadat, Leila; Maile, Tobias; Berger, Shelley L.; Rush, John; Lill, Jennie R.; Arnott, David; Garcia, Benjamin A.

2014-01-01

To facilitate accurate histone variant and post-translational modification (PTM) quantification via mass spectrometry, we present a library of 93 synthetic peptides using Protein-Aqua™ technology. The library contains 55 peptides representing different modified forms from histone H3 peptides, 23 peptides representing H4 peptides, 5 peptides representing canonical H2A peptides, 8 peptides representing H2A.Z peptides, and peptides for both macroH2A and H2A.X. The PTMs on these peptides include lysine mono- (me1), di- (me2), and tri-methylation (me3); lysine acetylation; arginine me1; serine/threonine phosphorylation; and N-terminal acetylation. The library was subjected to chemical derivatization with propionic anhydride, a widely employed protocol for histone peptide quantification. Subsequently, the detection efficiencies were quantified using mass spectrometry extracted ion chromatograms. The library yields a wide spectrum of detection efficiencies, with more than 1700-fold difference between the peptides with the lowest and highest efficiencies. In this paper, we describe the impact of different modifications on peptide detection efficiencies and provide a resource to correct for detection biases among the 93 histone peptides. In brief, there is no correlation between detection efficiency and molecular weight, hydrophobicity, basicity, or modification type. The same types of modifications may have very different effects on detection efficiencies depending on their positions within a peptide. We also observed antagonistic effects between modifications. In a study of mouse trophoblast stem cells, we utilized the detection efficiencies of the peptide library to correct for histone PTM/variant quantification. For most histone peptides examined, the corrected data did not change the biological conclusions but did alter the relative abundance of these peptides. For a low-abundant histone H2A variant, macroH2A, the corrected data led to a different conclusion than the uncorrected data. The peptide library and detection efficiencies presented here may serve as a resource to facilitate studies in the epigenetics and proteomics fields. PMID:25000943

Effects of channel modifications on the hydrology of Chicod Creek basin, North Carolina, 1975-87

USGS Publications Warehouse

Mason, R.R.; Simmons, C.E.; Watkins, S.A.

1990-01-01

Drainage modifications in this Coastal Plain basin from 1978 to 1981 consisted of channel excavation and clearing of blockages. A study was begun in 1975 to define hydrologic conditions of the basin before, during, and after modifications and to determine what changes were attributed to modifications. Surface-water conditions were altered during and following modifications. Minimum flow at Juniper Branch was increased from less than 0.1 cu ft/sec to 0.4 cu ft/second;streamflow variability was reduced from an index of 0.87 to 0.49. In-channel velocity at Chicod Creek was increased from a mean of 0.4 ft/sec to 1.5 ft/sec. Substantial groundwater level declines were observed in wells 180 and 250 ft from Juniper Branch during the modifications phase;these were 0.4 and 0.2 ft, respectively. However, most surface-water and groundwater conditions returned nearly to premodification levels by 1987. Water-quality characteristics monitored during the investigation included physical, chemical, and bacteriological characteristics. Physical characteristics monitored were suspended sediment, temperature, dissolved oxygen, and pH. Of these physical characteristics, only sediment concentrations increased substantially during channel modifications. Chemical characteristics studied were major dissolved constituents, nutrients, trace metals, and pesticides. Substantial changes ranged from a decline in total iron concentrations of 77% to an increase in total nitrite concentrations of 130%. Changes in many chemical characteristics persisted following channel modifications. Bacterial counts did not change substantially.

Modification of Rat Lung Decellularization Protocol Based on Dynamic Conductometry of Working Solution.

PubMed

Kuevda, E V; Gubareva, E A; Gumenyuk, I S; Sotnichenko, A S; Gilevich, I V; Nakokhov, R Z; Rusinova, T V; Yudina, T G; Red'ko, A N; Alekseenko, S N

2017-03-01

We modified the protocol of obtaining of biological scaffolds of rat lungs based on dynamic recording of specific resistivity of working detergent solution (conductometry) during perfusion decellularization. Termination of sodium deoxycholate exposure after attaining ionic equilibrium plateau did not impair the quality of decellularization and preserved structural matrix components, which was confirmed by morphological analysis and quantitative assay of residual DNA.

Prior to Conception: The Role of an Acupuncture Protocol in Improving Women's Reproductive Functioning Assessed by a Pilot Pragmatic Randomised Controlled Trial

PubMed Central

Cochrane, Suzanne; Smith, Caroline A.; Possamai-Inesedy, Alphia; Bensoussan, Alan

2016-01-01

The global average of couples with fertility problems is 9%. Assisted reproductive technologies are often inaccessible. Evidence points to acupuncture offering an opportunity to promote natural fertility. This study asked whether providing a multiphasic fertility acupuncture protocol to women with sub/infertility would increase their awareness of fertility and achieve normalisation of their menstrual cycle compared with a lifestyle control. In a pragmatic randomised controlled trial sub/infertile women were offered an intervention of acupuncture and lifestyle modification or lifestyle modification only. There was a statistically significant increase in fertility awareness in the acupuncture group (86.4%, 19) compared to 40% (n = 8) of the lifestyle only participants (Relative Risk (RR) 2.38, 95% confidence interval (CI) of 1.25, 4.50), with an adjusted p value of 0.011. Changes in menstrual regularity were not statistically significant. There was no statistical difference in the pregnancy rate with seven women (adjusted p = 0.992) achieving pregnancy during the course of the study intervention. Those receiving the acupuncture conceived within an average of 5.5 weeks compared to 10.67 weeks for the lifestyle only group (p = 0.422). The acupuncture protocol tested influenced women who received it compared to women who used lifestyle modification alone: their fertility awareness and wellbeing increased, and those who conceived did so in half the time. PMID:27242910

Improvements to the Kunkel mutagenesis protocol for constructing primary and secondary phage-display libraries.

PubMed

Huang, Renhua; Fang, Pete; Kay, Brian K

2012-09-01

Site-directed mutagenesis is routinely performed in protein engineering experiments. One method, termed Kunkel mutagenesis, is frequently used for constructing libraries of peptide or protein variants in M13 bacteriophage, followed by affinity selection of phage particles. To make this method more efficient, the following two modifications were introduced: culture was incubated at 25°C for phage replication, which yielded two- to sevenfold more single-stranded DNA template compared to growth at 37°C, and restriction endonuclease recognition sites were used to remove non-recombinants. With both of the improvements, we could construct primary libraries of high complexity and that were 99-100% recombinant. Finally, with a third modification to the standard protocol of Kunkel mutagenesis, two secondary (mutagenic) libraries of a fibronectin type III (FN3) monobody were constructed with DNA segments that were amplified by error-prone and asymmetric PCR. Two advantages of this modification are that it bypasses the lengthy steps of restriction enzyme digestion and ligation, and that the pool of phage clones, recovered after affinity selection, can be used directly to generate a secondary library. Screening one of the two mutagenic libraries yielded variants that bound two- to fourfold tighter to human Pak1 kinase than the starting clone. The protocols described in this study should accelerate the discovery of phage-displayed recombinant affinity reagents. Copyright © 2012 Elsevier Inc. All rights reserved.

Effects of chemically modified wood on bond durability

Treesearch

Rishawn Brandon; Rebecca E. Ibach; Charles R. Frihart

2005-01-01

Chemical modification of wood can improve its dimensional stability and resistance to biological degradation and moisture, but modification can also create a new surface for bonding. Acetylation of wood results in the loss of hydroxyl groups, making the wood more hydrophobic and reduces its ability to hydrogen-bond with the adhesive. In contrast, reacting wood with...

Ultrasonic modification of carbon materials for electrochemical capacitors

NASA Astrophysics Data System (ADS)

Rachiy, Bogdan I.; Nykoliuk, Marian O.; Budzulyak, Ivan M.; Kachmar, Andrii I.

2017-01-01

The paper is devoted to study the ultrasonic impact on the biomass of natural raw materials, which were used for the creation a nanoporous carbon material (NCM), which was used as electrode material for electrochemical capacitors (EC). The dry shells of apricot seeds were a feedstock, which were modified by the chemical treatment in the phosphoric acid and part of them were impacted by ultrasonic waves for 25 minutes. The NCM, which were obtained by carbonization at 550 °C, were modified by chemical treatment in the nitric acid. Thus, the different of modification NCM was obtained to compare their capacitance characteristics for EC. From experimental data we can do a conclusion, that ultrasonic modification and chemical treatment in nitric acidare improvecapacitance characteristics of NCM for EC.

Recent advances in the chemical modification of unsaturated polymers

NASA Technical Reports Server (NTRS)

Schulz, D. N.; Turner, S. R.; Golub, M. A.

1982-01-01

The present discussion has the objective to update the most comprehensive reviews on the considered subject and to fill in the gaps of less complete, but more modern treatments. Only simple chemical functionalization or structural modification of unsaturated polymers are covered, and the literature of diene polymer modification since 1974 is emphasized. Attention is given to hydrogenation, halogenation and hydrohalogenation, cyclization, cis-trans isomerization, epoxidation, ene and other cycloaddition reactions, sulfonation, carboxylation, phosphonylation, sulfenyl chloride addition, carbene addition, metalation, and silylation. It is pointed out that modern synthetic reagents and catalysts have been advantageously employed to improve process and/or product quality. Synthetic techniques have been refined to allow the selective modification of specific polymer microstructures or blocks.

Ionospheric chemical releases

NASA Technical Reports Server (NTRS)

Bernhardt, Paul A.; Scales, W. A.

1990-01-01

Ionospheric plasma density irregularities can be produced by chemical releases into the upper atmosphere. F-region plasma modification occurs by: (1) chemically enhancing the electron number density; (2) chemically reducing the electron population; or (3) physically convecting the plasma from one region to another. The three processes (production, loss, and transport) determine the effectiveness of ionospheric chemical releases in subtle and surprising ways. Initially, a chemical release produces a localized change in plasma density. Subsequent processes, however, can lead to enhanced transport in chemically modified regions. Ionospheric modifications by chemical releases excites artificial enhancements in airglow intensities by exothermic chemical reactions between the newly created plasma species. Numerical models were developed to describe the creation and evolution of large scale density irregularities and airglow clouds generated by artificial means. Experimental data compares favorably with theses models. It was found that chemical releases produce transient, large amplitude perturbations in electron density which can evolve into fine scale irregularities via nonlinear transport properties.

Diazo Compounds: Versatile Tools for Chemical Biology.

PubMed

Mix, Kalie A; Aronoff, Matthew R; Raines, Ronald T

2016-12-16

Diazo groups have broad and tunable reactivity. That and other attributes endow diazo compounds with the potential to be valuable reagents for chemical biologists. The presence of diazo groups in natural products underscores their metabolic stability and anticipates their utility in a biological context. The chemoselectivity of diazo groups, even in the presence of azido groups, presents many opportunities. Already, diazo compounds have served as chemical probes and elicited novel modifications of proteins and nucleic acids. Here, we review advances that have facilitated the chemical synthesis of diazo compounds, and we highlight applications of diazo compounds in the detection and modification of biomolecules.

Epigenome analysis of pluripotent stem cells

PubMed Central

Ricupero, Christopher L.; Swerdel, Mavis R.; Hart, Ronald P.

2015-01-01

Summary Mis-regulation of gene expression due to epigenetic abnormalities has been linked with complex genetic disorders, psychiatric illness and cancer. In addition, the dynamic epigenetic changes that occur in pluripotent stem cells are believed to impact regulatory networks essential for proper lineage development. Chromatin immunoprecipitation (ChIP) is a technique used to isolate and enrich chromatin fragments using antibodies against specific chromatin modifications, such as DNA binding proteins or covalent histone modifications. Until recently, many ChIP protocols required millions of cells for each immunoprecipitation. This severely limited analysis of rare cell populations or post-mitotic, differentiated cell lines. Here, we describe a low cell number ChIP protocol with next generation sequencing and analysis, that has the potential to uncover novel epigenetic regulatory pathways that were previously difficult or impossible to obtain. PMID:23546758

Chemical fields during Southeast Nexus (SENEX) field experiment and design of verification metrics for efficacy of capturing wild fire emissions

NASA Astrophysics Data System (ADS)

Lee, P.

2016-12-01

Wildfires are commonplace in North America. Air pollution resulted from wildfires pose a significant risk for human health and crop damage. The pollutants alter the vertical distribution of many atmospheric constituents including O3 and many fine particulate (PM) species. Compared to anthropogenic emissions of air pollutants, emissions from wildfires are largely uncontrolled and unpredictable. Therefore, quantitatively describing wildfire emissions and their contributions to air pollution remains a substantial challenge for atmospheric modeler and air quality forecasters. In this study, we investigated the modification and redistribution of atmospheric composition within the Conterminous U.S (CONUS) by wild fire plumes originated within and outside of the CONUS. We used the National Air Quality Forecasting Capability (NAQFC) to conduct the investigation. NAQFC uses dynamic lateral chemical boundary conditions derived from the National Weather Service experimental global aerosol tracer model accounting for intrusion of fire-associated aerosol species. Within CONUS, the NAQFC derives both gaseous and aerosol wildfire associated species from the National Environmental Satellite, Data, and Information Service (NESDIS) hazard mapping system (HMS) hot-spot detection, and US Forestry Service Blue-sky protocol for quantifying fire characteristics, and the US EPA Sparse Matrix Object Kernel Emission (SMOKE) calculation for plume rise. Attributions of both of these wildfire influences inherently reflect the aged plumes intruded into the CONUS through the model boundaries as well as the fresher emissions from sources within the CONUS. Both emission sources contribute significantly to the vertical structure modification of the atmosphere. We conducted case studies within the fire active seasons to demonstrate some possible impacts on the vertical structures of O3 and PM species by the wildfire activities.

Effect of Crumb Rubber and Warm Mix Additives on Asphalt Aging, Rheological, and Failure Properties

NASA Astrophysics Data System (ADS)

Agrawal, Prashant

Asphalt-rubber mixtures have been shown to have useful properties with respect to distresses observed in asphalt concrete pavements. The most notable change in properties is a large increase in viscosity and improved low-temperature cracking resistance. Warm mix additives can lower production and compaction temperatures. Lower temperatures reduce harmful emissions and lower energy consumption, and thus provide environmental benefits and cut costs. In this study, the effects of crumb rubber modification on various asphalts such as California Valley, Boscan, Alaska North Slope, Laguna and Cold Lake were also studied. The materials used for warm mix modification were obtained from various commercial sources. The RAF binder was produced by Imperial Oil in their Nanticoke, Ontario, refinery on Lake Erie. A second commercial PG 52-34 (hereafter denoted as NER) was obtained/sampled during the construction of a northern Ontario MTO contract. Some regular tests such as Dynamic Shear Rheometer (DSR) and Bending Beam Rheometer (BBR), Multiple Stress Creep Recovery (MSCR) and some modified new protocols such as the extended BBR test (LS-308) and the Double-Edge Notched Tension (DENT) test (LS-299) are used to study, the effect of warm mix and a host of other additives on rheological, aging and failure properties. A comparison in the properties of RAF and NER asphalts has also been made as RAF is good quality asphalt and NER is bad quality asphalt. From the studies the effect of additives on chemical and physical hardening tendencies was found to be significant. The asphalt samples tested in this study showed a range of tendencies for chemical and physical hardening.

Harnessing epigenome modifications for better crops

USDA-ARS?s Scientific Manuscript database

Chemical DNA modifications such as methylation influence translation of the DNA code to specific genetic outcomes. While such modifications can be heritable, others are transient, and their overall contribution to plant genetic diversity remains intriguing but uncertain. The focus of this article is...

Embedding and Chemical Reactivation of Green Fluorescent Protein in the Whole Mouse Brain for Optical Micro-Imaging

PubMed Central

Gang, Yadong; Zhou, Hongfu; Jia, Yao; Liu, Ling; Liu, Xiuli; Rao, Gong; Li, Longhui; Wang, Xiaojun; Lv, Xiaohua; Xiong, Hanqing; Yang, Zhongqin; Luo, Qingming; Gong, Hui; Zeng, Shaoqun

2017-01-01

Resin embedding has been widely applied to fixing biological tissues for sectioning and imaging, but has long been regarded as incompatible with green fluorescent protein (GFP) labeled sample because it reduces fluorescence. Recently, it has been reported that resin-embedded GFP-labeled brain tissue can be imaged with high resolution. In this protocol, we describe an optimized protocol for resin embedding and chemical reactivation of fluorescent protein labeled mouse brain, we have used mice as experiment model, but the protocol should be applied to other species. This method involves whole brain embedding and chemical reactivation of the fluorescent signal in resin-embedded tissue. The whole brain embedding process takes a total of 7 days. The duration of chemical reactivation is ~2 min for penetrating 4 μm below the surface in the resin-embedded brain. This protocol provides an efficient way to prepare fluorescent protein labeled sample for high-resolution optical imaging. This kind of sample was demonstrated to be imaged by various optical micro-imaging methods. Fine structures labeled with GFP across a whole brain can be detected. PMID:28352214

Structure-based design of novel chemical modification of the 3'-overhang for optimization of short interfering RNA performance.

PubMed

Xu, Lexing; Wang, Xin; He, Hongwei; Zhou, Jinming; Li, Xiaoyu; Ma, Hongtao; Li, Zelin; Zeng, Yi; Shao, Rongguang; Cen, Shan; Wang, Yucheng

2015-02-10

Short interfering RNAs (siRNAs) are broadly used to manipulate gene expression in mammalian cells. Although chemical modification is useful for increasing the potency of siRNAs in vivo, rational optimization of siRNA performance through chemical modification is still a challenge. In this work, we designed and synthesized a set of siRNAs containing modified two-nucleotide 3'-overhangs with the aim of strengthening the interaction between the 3'-end of the siRNA strand and the PAZ domain of Ago2. Their efficiency of binding to the PAZ domain was calculated using a computer modeling program, followed by measurement of RNA-Ago2 interaction in a surface plasmon resonance biochemical assay. The results suggest that increasing the level of binding of the 3'-end of the guiding strand with the PAZ domain, and/or reducing the level of binding of the sense strand through modifying the two-nucleotide 3'-overhangs, affects preferential strand selection and improves siRNA activity, while we cannot exclude the possibility that the modifications at the 3'-end of the sense strand may also affect the recognition of the 5'-end of the guiding strand by the MID domain. Taken together, our work presents a strategy for optimizing siRNA performance through asymmetric chemical modification of 3'-overhangs and also helps to develop the computer modeling method for rational siRNA design.

Surface modification of protein enhances encapsulation in chitosan nanoparticles

NASA Astrophysics Data System (ADS)

Koyani, Rina D.; Andrade, Mariana; Quester, Katrin; Gaytán, Paul; Huerta-Saquero, Alejandro; Vazquez-Duhalt, Rafael

2018-04-01

Chitosan nanoparticles have a huge potential as nanocarriers for environmental and biomedical purposes. Protein encapsulation in nano-sized chitosan provides protection against inactivation, proteolysis, and other alterations due to environmental conditions, as well as the possibility to be targeted to specific tissues by ligand functionalization. In this work, we demonstrate that the chemical modification of the protein surface enhances the protein loading in chitosan nanocarriers. Encapsulation of green fluorescent protein and the cytochrome P450 was studied. The increase of electrostatic interactions between the free amino groups of chitosan and the increased number of free carboxylic groups in the protein surface enhance the protein loading, protein retention, and, thus, the enzymatic activity of chitosan nanoparticles. The chemical modification of protein surface with malonic acid moieties reduced drastically the protein isoelectric point increasing the protein interaction with the polycationic biomaterial and chitosan. The chemical modification of protein does not alter the morphology of chitosan nanoparticles that showed an average diameter of 18 nm, spheroidal in shape, and smooth surfaced. The strategy of chemical modification of protein surface, shown here, is a simple and efficient technique to enhance the protein loading in chitosan nanoparticles. This technique could be used for other nanoparticles based on polycationic or polyanionic materials. The increase of protein loading improves, doubtless, the performance of protein-loaded chitosan nanoparticles for biotechnological and biomedical applications.

Chemically Patterned Inverse Opal Created by a Selective Photolysis Modification Process.

PubMed

Tian, Tian; Gao, Ning; Gu, Chen; Li, Jian; Wang, Hui; Lan, Yue; Yin, Xianpeng; Li, Guangtao

2015-09-02

Anisotropic photonic crystal materials have long been pursued for their broad applications. A novel method for creating chemically patterned inverse opals is proposed here. The patterning technique is based on selective photolysis of a photolabile polymer together with postmodification on released amine groups. The patterning method allows regioselective modification within an inverse opal structure, taking advantage of selective chemical reaction. Moreover, combined with the unique signal self-reporting feature of the photonic crystal, the fabricated structure is capable of various applications, including gradient photonic bandgap and dynamic chemical patterns. The proposed method provides the ability to extend the structural and chemical complexity of the photonic crystal, as well as its potential applications.

Preparation of visible-light-activated metal complexes and their use in photoredox/nickel dual catalysis.

PubMed

Kelly, Christopher B; Patel, Niki R; Primer, David N; Jouffroy, Matthieu; Tellis, John C; Molander, Gary A

2017-03-01

Visible-light-activated photoredox catalysts provide synthetic chemists with the unprecedented capability to harness reactive radicals through discrete, single-electron transfer (SET) events. This protocol describes the synthesis of two transition metal complexes, [Ir{dF(CF 3 ) 2 ppy} 2 (bpy)]PF 6 (1a) and [Ru(bpy) 3 ](PF 6 ) 2 (2a), that are activated by visible light. These photoredox catalysts are SET agents that can be used to facilitate transformations ranging from proton-coupled electron-transfer-mediated cyclizations to C-C bond constructions, dehalogenations, and H-atom abstractions. These photocatalysts have been used in the synthesis of medicinally relevant compounds for drug discovery, as well as the degradation of biological polymers to access fine chemicals. These catalysts are prepared from IrCl 3 and RuCl 3 , respectively, in three chemical steps. These steps can be described as a series of two ligand modifications followed by an anion metathesis. Using the cost-effective, scalable procedures described here, the ruthenium-based photocatalyst 2a can be synthesized in a 78% overall yield (∼8.1 g), and the iridium-based photocatalyst 1a can be prepared in a 56% overall yield (∼4.4 g). The total time necessary for the complete protocols ranges from ∼2 d for 2a to 5-7 d for 1a. Procedures for applying each catalyst in representative photoredox/Ni cross-coupling to form C sp 3-C sp 2 bonds using the appropriate radical precursor-organotrifluoroborates with 1a and bis(catecholato)alkylsilicates with 2a-are described. In addition, more traditional photoredox-mediated transformations are included as diagnostic tests for catalytic activity.

Research into alternative network approaches for space operations

NASA Technical Reports Server (NTRS)

Kusmanoff, Antone L.; Barton, Timothy J.

1990-01-01

The main goal is to resolve the interoperability problem of applications employing DOD TCP/IP (Department of Defence Transmission Control Protocol/Internet Protocol) family of protocols on a CCITT/ISO based network. The objective is to allow them to communicate over the CCITT/ISO protocol GPLAN (General Purpose Local Area Network) network without modification to the user's application programs. There were two primary assumptions associated with the solution that was actually realized. The first is that the solution had to allow for future movement to the exclusive use of the CCITT/ISO standards. The second is that the solution had to be software transparent to the currently installed TCP/IP and CCITT/ISO user application programs.

A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects

PubMed Central

Bramsen, Jesper B.; Pakula, Malgorzata M.; Hansen, Thomas B.; Bus, Claus; Langkjær, Niels; Odadzic, Dalibor; Smicius, Romualdas; Wengel, Suzy L.; Chattopadhyaya, Jyoti; Engels, Joachim W.; Herdewijn, Piet; Wengel, Jesper; Kjems, Jørgen

2010-01-01

Small interfering RNAs (siRNAs) are now established as the preferred tool to inhibit gene function in mammalian cells yet trigger unintended gene silencing due to their inherent miRNA-like behavior. Such off-target effects are primarily mediated by the sequence-specific interaction between the siRNA seed regions (position 2–8 of either siRNA strand counting from the 5′-end) and complementary sequences in the 3′UTR of (off-) targets. It was previously shown that chemical modification of siRNAs can reduce off-targeting but only very few modifications have been tested leaving more to be identified. Here we developed a luciferase reporter-based assay suitable to monitor siRNA off-targeting in a high throughput manner using stable cell lines. We investigated the impact of chemically modifying single nucleotide positions within the siRNA seed on siRNA function and off-targeting using 10 different types of chemical modifications, three different target sequences and three siRNA concentrations. We found several differently modified siRNAs to exercise reduced off-targeting yet incorporation of the strongly destabilizing unlocked nucleic acid (UNA) modification into position 7 of the siRNA most potently reduced off-targeting for all tested sequences. Notably, such position-specific destabilization of siRNA–target interactions did not significantly reduce siRNA potency and is therefore well suited for future siRNA designs especially for applications in vivo where siRNA concentrations, expectedly, will be low. PMID:20453030

Chemically Derivatized Semiconductor Photoelectrodes.

ERIC Educational Resources Information Center

Wrighton, Mark S.

1983-01-01

Deliberate modification of semiconductor photoelectrodes to improve durability and enhance rate of desirable interfacial redox processes is discussed for a variety of systems. Modification with molecular-based systems or with metals/metal oxides yields results indicating an important role for surface modification in devices for fundamental study…

Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement.

PubMed

Moher, David; Shamseer, Larissa; Clarke, Mike; Ghersi, Davina; Liberati, Alessandro; Petticrew, Mark; Shekelle, Paul; Stewart, Lesley A

2015-01-01

Systematic reviews should build on a protocol that describes the rationale, hypothesis, and planned methods of the review; few reviews report whether a protocol exists. Detailed, well-described protocols can facilitate the understanding and appraisal of the review methods, as well as the detection of modifications to methods and selective reporting in completed reviews. We describe the development of a reporting guideline, the Preferred Reporting Items for Systematic reviews and Meta-Analyses for Protocols 2015 (PRISMA-P 2015). PRISMA-P consists of a 17-item checklist intended to facilitate the preparation and reporting of a robust protocol for the systematic review. Funders and those commissioning reviews might consider mandating the use of the checklist to facilitate the submission of relevant protocol information in funding applications. Similarly, peer reviewers and editors can use the guidance to gauge the completeness and transparency of a systematic review protocol submitted for publication in a journal or other medium.

Stormwater filtration of toxic heavy metal ions using lignocellulosic materials selection process, fiberization, chemical modification, and mat formation

Treesearch

James S. Han

1999-01-01

Lignocellulosic materials were evaluated for their effectiveness in filtering toxic heavy metals from stormwater. Kenaf, alfalfa, juniper, and aspen fibers were used as models to evaluate the effectiveness and limitations of chemical modification and the extent of fiber degradation. Individual and mixed aqueous solutions of nickel, copper, zinc, and cadmium in various...

Automation of data acquisition in electron crystallography.

PubMed

Cheng, Anchi

2013-01-01

General considerations for using automation software for acquiring high-resolution images of 2D crystals under low-dose conditions are presented. Protocol modifications specific to this application in Leginon are provided.

Ultrasonic modification of carbon materials for electrochemical capacitors.

PubMed

Rachiy, Bogdan I; Nykoliuk, Marian O; Budzulyak, Ivan M; Kachmar, Andrii I

2017-12-01

The paper is devoted to study the ultrasonic impact on the biomass of natural raw materials, which were used for the creation a nanoporous carbon material (NCM), which was used as electrode material for electrochemical capacitors (EC). The dry shells of apricot seeds were a feedstock, which were modified by the chemical treatment in the phosphoric acid and part of them were impacted by ultrasonic waves for 25 minutes. The NCM, which were obtained by carbonization at 550 °C, were modified by chemical treatment in the nitric acid. Thus, the different of modification NCM was obtained to compare their capacitance characteristics for EC. From experimental data we can do a conclusion, that ultrasonic modification and chemical treatment in nitric acidare improvecapacitance characteristics of NCM for EC.

Selective Modification of Chitin and Chitosan: En Route to Tailored Oligosaccharides.

PubMed

Carvalho, Luísa C R; Queda, Fausto; Santos, Cátia V Almeida; Marques, M Manuel B

2016-12-19

Chitin and chitosan are attractive biopolymers with enormous structural possibilities for chemical modification, creating platforms for new chemical entities with a broad scope of applications, ranging from material science to medicine. During the last few years, incredible efforts have been dedicated to the regioselective modification of these biopolymers paving the way for improved properties and tailored activities. Herein, the most recent advances in chitin/chitosan regioselective modification, reaction conditions, selectivity, and the impact on its applications are highlighted. Moreover, the recent focus on chitooligosaccharides, their regioselective and chemoselective functionalization, as well as their role in biological studies, including molecular recognition with several biological targets are also covered. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Source term evaluation for combustion modeling

NASA Technical Reports Server (NTRS)

Sussman, Myles A.

1993-01-01

A modification is developed for application to the source terms used in combustion modeling. The modification accounts for the error of the finite difference scheme in regions where chain-branching chemical reactions produce exponential growth of species densities. The modification is first applied to a one-dimensional scalar model problem. It is then generalized to multiple chemical species, and used in quasi-one-dimensional computations of shock-induced combustion in a channel. Grid refinement studies demonstrate the improved accuracy of the method using this modification. The algorithm is applied in two spatial dimensions and used in simulations of steady and unsteady shock-induced combustion. Comparisons with ballistic range experiments give confidence in the numerical technique and the 9-species hydrogen-air chemistry model.

A Vastly Increased Chemical Variety of RNA Modifications Containing a Thioacetal Structure.

PubMed

Dal Magro, Christina; Keller, Patrick; Kotter, Annika; Werner, Stephan; Duarte, Victor; Marchand, Virginie; Ignarski, Michael; Freiwald, Anja; Müller, Roman-Ulrich; Dieterich, Christoph; Motorin, Yuri; Butter, Falk; Atta, Mohamed; Helm, Mark

2018-06-25

Recently discovered new chemical entities in RNA modifications have involved surprising functional groups that enlarge the chemical space of RNA. Using LC-MS, we found over 100 signals of RNA constituents that contained a ribose moiety in tRNAs from E. coli. Feeding experiments with variegated stable isotope labeled compounds identified 37 compounds that are new structures of RNA modifications. One structure was elucidated by deuterium exchange and high-resolution mass spectrometry. The structure of msms 2 i 6 A (2-methylthiomethylenethio-N6-isopentenyl-adenosine) was confirmed by methione-D3 feeding experiments and by synthesis of the nucleobase. The msms 2 i 6 A contains a thioacetal, shown in vitro to be biosynthetically derived from ms 2 i 6 A by the radical-SAM enzyme MiaB. This enzyme performs thiomethylation, forming ms 2 i 6 A from i 6 A in a first turnover. The new thioacetal is formed by a second turnover. Along with the pool of 36 new modifications, this work describes a new layer of RNA modification chemistry. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coatings with controlled porosity and chemical properties

DOEpatents

Frye, Gregory C.; Brinker, C. Jeffrey; Doughty, Daniel H.; Bein, Thomas; Moller, Karin

1996-01-01

Coatings and sensors having both steric and chemical selectivity. Controlled porosity provides the steric selectivity, whereas chemically tailored film properties, using controlled composition or modification by coupling agents, chemical species replacement, or chemical species within pores, provide the chemical selectivity. Single or multiple layers may be provided.

Coatings with controlled porosity and chemical properties

DOEpatents

Frye, Gregory C.; Brinker, C. Jeffrey; Doughty, Daniel H.; Bein, Thomas; Moller, Karin

1993-01-01

Coatings and sensors having both steric and chemical selectivity. Controlled porosity provides the steric selectivity, whereas chemically tailored film properties, using controlled composition or modification by coupling agents, chemical species replacement, or chemical species within pores, provide the chemical selectivity. Single or multiple layers may be provided.

The Control of Chemical and Biological Weapons.

ERIC Educational Resources Information Center

Alexander, Archibald S.; And Others

This book is composed of four papers prepared to illuminate the problem areas which might arise if the policies of the 1925 Geneva Protocol and other measures to limit chemical and biological weapons are ratified by the United States Senate. The papers included are: Legal Aspects of the Geneva Protocol of 1925; The Use of Herbicides in War: A…

Influence of major-groove chemical modifications of DNA on transcription by bacterial RNA polymerases

PubMed Central

Raindlová, Veronika; Janoušková, Martina; Slavíčková, Michaela; Perlíková, Pavla; Boháčová, Soňa; Milisavljevič, Nemanja; Šanderová, Hana; Benda, Martin; Barvík, Ivan; Krásný, Libor; Hocek, Michal

2016-01-01

DNA templates containing a set of base modifications in the major groove (5-substituted pyrimidines or 7-substituted 7-deazapurines bearing H, methyl, vinyl, ethynyl or phenyl groups) were prepared by PCR using the corresponding base-modified 2′-deoxyribonucleoside triphosphates (dNTPs). The modified templates were used in an in vitro transcription assay using RNA polymerase from Bacillus subtilis and Escherichia coli. Some modified nucleobases bearing smaller modifications (H, Me in 7-deazapurines) were perfectly tolerated by both enzymes, whereas bulky modifications (Ph at any nucleobase) and, surprisingly, uracil blocked transcription. Some middle-sized modifications (vinyl or ethynyl) were partly tolerated mostly by the E. coli enzyme. In all cases where the transcription proceeded, full length RNA product with correct sequence was obtained indicating that the modifications of the template are not mutagenic and the inhibition is probably at the stage of initiation. The results are promising for the development of bioorthogonal reactions for artificial chemical switching of the transcription. PMID:27001521

Artificial specific binders directly recovered from chemically modified nucleic acid libraries.

PubMed

Kasahara, Yuuya; Kuwahara, Masayasu

2012-01-01

Specific binders comprised of nucleic acids, that is, RNA/DNA aptamers, are attractive functional biopolymers owing to their potential broad application in medicine, food hygiene, environmental analysis, and biological research. Despite the large number of reports on selection of natural DNA/RNA aptamers, there are not many examples of direct screening of chemically modified nucleic acid aptamers. This is because of (i) the inferior efficiency and accuracy of polymerase reactions involving transcription/reverse-transcription of modified nucleotides compared with those of natural nucleotides, (ii) technical difficulties and additional time and effort required when using modified nucleic acid libraries, and (iii) ambiguous efficacies of chemical modifications in binding properties until recently; in contrast, the effects of chemical modifications on biostability are well studied using various nucleotide analogs. Although reports on the direct screening of a modified nucleic acid library remain in the minority, chemical modifications would be essential when further functional expansion of nucleic acid aptamers, in particular for medical and biological uses, is considered. This paper focuses on enzymatic production of chemically modified nucleic acids and their application to random screenings. In addition, recent advances and possible future research are also described.

Microwave plasma induced surface modification of diamond-like carbon films

NASA Astrophysics Data System (ADS)

Rao Polaki, Shyamala; Kumar, Niranjan; Gopala Krishna, Nanda; Madapu, Kishore; Kamruddin, Mohamed; Dash, Sitaram; Tyagi, Ashok Kumar

2017-12-01

Tailoring the surface of diamond-like carbon (DLC) film is technically relevant for altering the physical and chemical properties, desirable for useful applications. A physically smooth and sp3 dominated DLC film with tetrahedral coordination was prepared by plasma-enhanced chemical vapor deposition technique. The surface of the DLC film was exposed to hydrogen, oxygen and nitrogen plasma for physical and chemical modifications. The surface modification was based on the concept of adsorption-desorption of plasma species and surface entities of films. Energetic chemical species of microwave plasma are adsorbed, leading to desorbtion of the surface carbon atoms due to energy and momentum exchange. The interaction of such reactive species with DLC films enhanced the roughness, surface defects and dangling bonds of carbon atoms. Adsorbed hydrogen, oxygen and nitrogen formed a covalent network while saturating the dangling carbon bonds around the tetrahedral sp3 valency. The modified surface chemical affinity depends upon the charge carriers and electron covalency of the adsorbed atoms. The contact angle of chemically reconstructed surface increases when a water droplet interacts either through hydrogen or van dear Waals bonding. These weak interactions influenced the wetting property of the DLC surface to a great extent.

Chemical Modification of Waste Cotton Linters for Oil Spill Cleanup Application

NASA Astrophysics Data System (ADS)

Chattopadhyay, Debapriya; Umrigar, Keval

2017-12-01

The possibility of use of waste cotton linters as oil sorbents by chemical modification such as acetylation and cyanoethylation was studied. The acetylation process was carried out in presence of acetic anhydride using either H2SO4 or HClO4 as catalyst. The acetylation treatment time was 30, 60 and 120 min and treatment temperature was room temperature, 50 and 70 °C. For cyanoethylation, the waste cotton linters were pre-treated with 2, 5 and 10% NaOH. The treatment temperature for cyanoethylation was room temperature, 50 and 70 °C and treatment time was 30, 60 and 120 min. Both the chemical modification processes were optimized on the basis of oil absorption capacity of the chemically modified cotton fibre with the help of MATLAB software. The modified samples were tested for its oleophilicity in terms of oil absorption capacity, oil retention capacity, oil recovery capacity, reusability of sample and water uptake and buoyancy as oil sorbent. Chemically modified fibres were characterized by Fourier transform infra red spectrophotometer, scanning electron microscope and degree of substitutions.

Decontamination and management of human remains following incidents of hazardous chemical release.

PubMed

Hauschild, Veronique D; Watson, Annetta; Bock, Robert

2012-01-01

To provide specific guidance and resources for systematic and orderly decontamination of human remains resulting from a chemical terrorist attack or accidental chemical release. A detailed review and health-based decision criteria protocol is summarized. Protocol basis and logic are derived from analyses of compound-specific toxicological data and chemical/physical characteristics. Guidance is suitable for civilian or military settings where human remains potentially contaminated with hazardous chemicals may be present, such as sites of transportation accidents, terrorist operations, or medical examiner processing points. Guidance is developed from data-characterizing controlled experiments with laboratory animals, fabrics, and materiel. Logic and specific procedures for decontamination and management of remains, protection of mortuary affairs personnel, and decision criteria to determine when remains are sufficiently decontaminated are presented. Established procedures as well as existing materiel and available equipment for decontamination and verification provide reasonable means to mitigate chemical hazards from chemically exposed remains. Unique scenarios such as those involving supralethal concentrations of certain liquid chemical warfare agents may prove difficult to decontaminate but can be resolved in a timely manner by application of the characterized systematic approaches. Decision criteria and protocols to "clear" decontaminated remains for transport and processing are also provided. Once appropriate decontamination and verification have been accomplished, normal procedures for management of remains and release can be followed.

Coatings with controlled porosity and chemical properties

DOEpatents

Frye, G.C.; Brinker, C.J.; Doughty, D.H.; Bein, T.; Moller, K.

1996-12-31

Coatings and sensors are disclosed having both steric and chemical selectivity. Controlled porosity provides the steric selectivity, whereas chemically tailored film properties, using controlled composition or modification by coupling agents, chemical species replacement, or chemical species within pores, provide the chemical selectivity. Single or multiple layers may be provided. 7 figs.

Coatings with controlled porosity and chemical properties

DOEpatents

Frye, G.C.; Brinker, C.J.; Doughty, D.H.; Bein, T.; Moller, K.

1993-07-06

Coatings and sensors are described having both steric and chemical selectivity. Controlled porosity provides the steric selectivity, whereas chemically tailored film properties, using controlled composition or modification by coupling agents, chemical species replacement, or chemical species within pores, provide the chemical selectivity. Single or multiple layers may be provided.

CFDP for Interplanetary Overlay Network

NASA Technical Reports Server (NTRS)

Burleigh, Scott C.

2011-01-01

The CCSDS (Consultative Committee for Space Data Systems) File Delivery Protocol for Interplanetary Overlay Network (CFDP-ION) is an implementation of CFDP that uses IO' s DTN (delay tolerant networking) implementation as its UT (unit-data transfer) layer. Because the DTN protocols effect automatic, reliable transmission via multiple relays, CFDP-ION need only satisfy the requirements for Class 1 ("unacknowledged") CFDP. This keeps the implementation small, but without loss of capability. This innovation minimizes processing resources by using zero-copy objects for file data transmission. It runs without modification in VxWorks, Linux, Solaris, and OS/X. As such, this innovation can be used without modification in both flight and ground systems. Integration with DTN enables the CFDP implementation itself to be very simple; therefore, very small. Use of ION infrastructure minimizes consumption of storage and processing resources while maximizing safety.

Discovery of a Chemical Modification by Citric Acid in a Recombinant Monoclonal Antibody

PubMed Central

2015-01-01

Recombinant therapeutic monoclonal antibodies exhibit a high degree of heterogeneity that can arise from various post-translational modifications. The formulation for a protein product is to maintain a specific pH and to minimize further modifications. Generally Recognized as Safe (GRAS), citric acid is commonly used for formulation to maintain a pH at a range between 3 and 6 and is generally considered chemically inert. However, as we reported herein, citric acid covalently modified a recombinant monoclonal antibody (IgG1) in a phosphate/citrate-buffered formulation at pH 5.2 and led to the formation of so-called “acidic species” that showed mass increases of 174 and 156 Da, respectively. Peptide mapping revealed that the modification occurred at the N-terminus of the light chain. Three additional antibodies also showed the same modification but displayed different susceptibilities of the N-termini of the light chain, heavy chain, or both. Thus, ostensibly unreactive excipients under certain conditions may increase heterogeneity and acidic species in formulated recombinant monoclonal antibodies. By analogy, other molecules (e.g., succinic acid) with two or more carboxylic acid groups and capable of forming an anhydride may exhibit similar reactivities. Altogether, our findings again reminded us that it is prudent to consider formulations as a potential source for chemical modifications and product heterogeneity. PMID:25136741

Improving CRISPR-Cas specificity with chemical modifications in single-guide RNAs.

PubMed

Ryan, Daniel E; Taussig, David; Steinfeld, Israel; Phadnis, Smruti M; Lunstad, Benjamin D; Singh, Madhurima; Vuong, Xuan; Okochi, Kenji D; McCaffrey, Ryan; Olesiak, Magdalena; Roy, Subhadeep; Yung, Chong Wing; Curry, Bo; Sampson, Jeffrey R; Bruhn, Laurakay; Dellinger, Douglas J

2018-01-25

CRISPR systems have emerged as transformative tools for altering genomes in living cells with unprecedented ease, inspiring keen interest in increasing their specificity for perfectly matched targets. We have developed a novel approach for improving specificity by incorporating chemical modifications in guide RNAs (gRNAs) at specific sites in their DNA recognition sequence ('guide sequence') and systematically evaluating their on-target and off-target activities in biochemical DNA cleavage assays and cell-based assays. Our results show that a chemical modification (2'-O-methyl-3'-phosphonoacetate, or 'MP') incorporated at select sites in the ribose-phosphate backbone of gRNAs can dramatically reduce off-target cleavage activities while maintaining high on-target performance, as demonstrated in clinically relevant genes. These findings reveal a unique method for enhancing specificity by chemically modifying the guide sequence in gRNAs. Our approach introduces a versatile tool for augmenting the performance of CRISPR systems for research, industrial and therapeutic applications. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Improving CRISPR–Cas specificity with chemical modifications in single-guide RNAs

PubMed Central

Ryan, Daniel E; Taussig, David; Steinfeld, Israel; Phadnis, Smruti M; Lunstad, Benjamin D; Singh, Madhurima; Vuong, Xuan; Okochi, Kenji D; McCaffrey, Ryan; Olesiak, Magdalena; Roy, Subhadeep; Yung, Chong Wing; Curry, Bo; Sampson, Jeffrey R; Dellinger, Douglas J

2018-01-01

Abstract CRISPR systems have emerged as transformative tools for altering genomes in living cells with unprecedented ease, inspiring keen interest in increasing their specificity for perfectly matched targets. We have developed a novel approach for improving specificity by incorporating chemical modifications in guide RNAs (gRNAs) at specific sites in their DNA recognition sequence (‘guide sequence’) and systematically evaluating their on-target and off-target activities in biochemical DNA cleavage assays and cell-based assays. Our results show that a chemical modification (2′-O-methyl-3′-phosphonoacetate, or ‘MP’) incorporated at select sites in the ribose-phosphate backbone of gRNAs can dramatically reduce off-target cleavage activities while maintaining high on-target performance, as demonstrated in clinically relevant genes. These findings reveal a unique method for enhancing specificity by chemically modifying the guide sequence in gRNAs. Our approach introduces a versatile tool for augmenting the performance of CRISPR systems for research, industrial and therapeutic applications. PMID:29216382

Chemical Structure and Surface Modification of Dendritic Nanomaterials Tailored for Therapeutic and Diagnostic Applications.

PubMed

Myung, Ja Hye; Hsu, Hao-Jui; Bugno, Jason; Tam, Kevin A; Hong, Seungpyo

2017-01-01

Dendritic nanomaterials have attracted a great deal of scientific interest due to their high capacity for multifunctionalization and potential in various biomedical applications, such as drug/gene delivery and diagnostic systems. Depending on the molecular structure and starting monomers, several different types of dendrimers have been developed, including poly(amidoamine) (PAMAM), poly(propylenimine) (PPI), and poly(L-lysine) (PLL) dendrimers, in addition to modified dendritic nanomaterials, such as Janus dendrimers and dendritic block copolymers. The chemical structure and surface modification of dendritic nanomaterials have been found to play a critical role in governing their biological behaviors. In this review, we present a comprehensive overview focusing on the synthesis and chemical structures of dendrimers and modified dendritic nanomaterials that are currently being investigated for drug delivery, gene delivery, and diagnostic applications. In addition, the impact of chemical surface modification and functionalization to the dendritic nanomaterials on their therapeutic and diagnostic applications are highlighted. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Evaluation of the University of Florida lomustine, vincristine, procarbazine, and prednisone chemotherapy protocol for the treatment of relapsed lymphoma in dogs: 33 cases (2003-2009).

PubMed

Fahey, Christine E; Milner, Rowan J; Barabas, Karri; Lurie, David; Kow, Kelvin; Parfitt, Shannon; Lyles, Sarah; Clemente, Monica

2011-07-15

To evaluate the toxicity and efficacy of a modification of a previously evaluated combination of lomustine, vincristine, procarbazine, and prednisone (LOPP) as a rescue protocol for refractory lymphoma in dogs. Retrospective case series. Animals-33 dogs with a cytologic or histologic diagnosis of lymphoma that developed resistance to their induction chemotherapy protocol. Lomustine was administered on day 0 of the protocol. Vincristine was administered on day 0 and again 1 time on day 14. Procarbazine and prednisone were administered on days 0 through 13 of the protocol. This cycle was repeated every 28 days. Median time from initiation to discontinuation of the University of Florida LOPP protocol was 84 days (range, 10 to 308 days). Overall median survival time was 290 days (range, 51 to 762 days). Overall response rate with this protocol was 61% (20/33), with 36% (12) having a complete response and 24% (8) having a partial response. Toxicosis rates were lower than for the previously published LOPP protocol. The University of Florida LOPP protocol may be an acceptable alternative to the mechlorethamine, vincristine, procarbazine, and prednisone protocol as a rescue protocol for dogs with lymphoma.

A Taxonomy of Attacks on the DNP3 Protocol

NASA Astrophysics Data System (ADS)

East, Samuel; Butts, Jonathan; Papa, Mauricio; Shenoi, Sujeet

Distributed Network Protocol (DNP3) is the predominant SCADA protocol in the energy sector - more than 75% of North American electric utilities currently use DNP3 for industrial control applications. This paper presents a taxonomy of attacks on the protocol. The attacks are classified based on targets (control center, outstation devices and network/communication paths) and threat categories (interception, interruption, modification and fabrication). To facilitate risk analysis and mitigation strategies, the attacks are associated with the specific DNP3 protocol layers they exploit. Also, the operational impact of the attacks is categorized in terms of three key SCADA objectives: process confi- dentiality, process awareness and process control. The attack taxonomy clarifies the nature and scope of the threats to DNP3 systems, and can provide insights into the relative costs and benefits of implementing mitigation strategies.

The use of new, aqueous chemical wood modifications to improve the durability of wood-plastic composites

Treesearch

Rebecca E. Ibach; Craig M. Clemons; George C. Chen

2017-01-01

The wood flour used in wood-plastic composites (WPCs) can biologically deteriorate and thus the overall mechanical performance of WPCs decrease when exposed to moisture and fungal decay. Protecting the wood flour by chemical modification can improve the durability of the wood in a nontoxic way so it is not harmful to the environment. WPCs were made with modified wood...

Chemical modification: the key to clinical application of RNA interference?

PubMed Central

Corey, David R.

2007-01-01

RNA interference provides a potent and specific method for controlling gene expression in human cells. To translate this potential into a broad new family of therapeutics, it is necessary to optimize the efficacy of the RNA-based drugs. As discussed in this Review, it might be possible to achieve this optimization using chemical modifications that improve their in vivo stability, cellular delivery, biodistribution, pharmacokinetics, potency, and specificity. PMID:18060019

Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry

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

Zhou, Mowei; Wu, Si; Stenoien, David L.

Top-down mass spectrometry is a valuable tool for charactering post-translational modifications on histones for understanding of gene control and expression. In this protocol, we describe a top-down workflow using liquid chromatography coupled to mass spectrometry for fast global profiling of changes in histone proteoforms between a wild-type and a mutant of a fungal species. The proteoforms exhibiting different abundances can be subjected to further targeted studies by other mass spectrometric or biochemical assays. This method can be generally adapted for preliminary screening for changes in histone modifications between samples such as wild-type vs. mutant, and control vs. disease.

Thermo-chemical pretreatment of rice straw for further processing for levulinic acid production.

PubMed

Elumalai, Sasikumar; Agarwal, Bhumica; Sangwan, Rajender S

2016-10-01

A variety of pretreatment protocols for rice straw fiber reconstruction were evaluated under mild conditions (upto 0.2%wt. and 121°C) with the object of improving polymer susceptibility to chemical attack while preserving carbohydrate sugars for levulinic acid (LA) production. Each of the protocols tested significantly enhanced pretreatment recoveries of carbohydrate sugars and lignin, and a NaOH protocol showed the most promise, with enhanced carbohydrate preservation (upto 20% relative to the other protocols) and more effective lignin dissolution (upto 60%). Consequently, post-pretreatment fibers were evaluated for LA preparation using an existing co-solvent system consisting of HCl and THF, in addition supplementation of DMSO was attempted, in order to improve final product recovery. In contrast to pretreatment response, H2SO4 protocol fibers yielded highest LA conc. (21%wt. with 36% carbohydrate conversion efficiency) under the modest reaction conditions. Apparent spectroscopic analysis witnessed for fiber destruction and delocalization of inherent constituents during pretreatment protocols. Copyright © 2016 Elsevier Ltd. All rights reserved.

75 FR 26049 - Regulation of Fuels and Fuel Additives: Modifications to Renewable Fuel Standard Program

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-10

... conducted by ``a licensed professional engineer or foreign equivalent who works in the chemical engineering... chemical engineering field. EPA views renewable fuel production to fall generally within the chemical... basic organic chemical manufacturers. Industry 424690 5169 Chemical and allied products merchant...

Recent Advances in Chemical Modification of Peptide Nucleic Acids

PubMed Central

Rozners, Eriks

2012-01-01

Peptide nucleic acid (PNA) has become an extremely powerful tool in chemistry and biology. Although PNA recognizes single-stranded nucleic acids with exceptionally high affinity and sequence selectivity, there is considerable ongoing effort to further improve properties of PNA for both fundamental science and practical applications. The present paper discusses selected recent studies that improve on cellular uptake and binding of PNA to double-stranded DNA and RNA. The focus is on chemical modifications of PNA's backbone and heterocyclic nucleobases. The paper selects representative recent studies and does not attempt to provide comprehensive coverage of the broad and vibrant field of PNA modification. PMID:22991652

Functionalization of chitosan by click chemistry

NASA Astrophysics Data System (ADS)

Cheaburu-Yilmaz, Catalina Natalia; Karavana, Sinem Yaprak; Yilmaz, Onur

2017-12-01

Chitosan modification represents a challenge nowadays. The variety of compounds which can be obtained with various architectures and different functionalities made it attractive to be used in fields like pharmacy and material science. Presents study deals with the chemical modification of chitosan by using click chemistry technique. The study adopted the approach of clicking azidated chitosan with a synthesized alkyne terminated polymer i.e. poly N isopropylacrylamide with thermoresponsive properties. Structures were confirmed by the FT-IR and HNMR spectra. Thermal characterization was performed showing different thermal behaviour with the chemical modification. The final synthesized graft copolymer can play important role within pharmaceutical formulations carrying drugs for topical or oral treatments.

Development of pig welfare assessment protocol integrating animal-, environment-, and management-based measures.

PubMed

Renggaman, Anriansyah; Choi, Hong L; Sudiarto, Sartika Ia; Alasaarela, Laura; Nam, Ok S

2015-01-01

Due to increased interest in animal welfare, there is now a need for a comprehensive assessment protocol to be used in intensive pig farming systems. There are two current welfare assessment protocols for pigs: Welfare Quality® Assessment Protocols (applicable in the Europe Union), that mostly focuses on animal-based measures, and the Swine Welfare Assurance Program (applicable in the United States), that mostly focuses on management- and environment-based measures. In certain cases, however, animal-based measures might not be adequate for properly assessing pig welfare status. Similarly, welfare assessment that relies only on environment- and management-based measures might not represent the actual welfare status of pigs. Therefore, the objective of this paper was to develop a new welfare protocol by integrating animal-, environment-, and management-based measures. The background for selection of certain welfare criteria and modification of the scoring systems from existing welfare assessment protocols are described. The developed pig welfare assessment protocol consists of 17 criteria that are related to four main principles of welfare (good feeding, good housing, good health, and appropriate behavior). Good feeding, good housing, and good health were assessed using a 3-point scale: 0 (good welfare), 1 (moderate welfare), and 2 (poor welfare). In certain cases, only a 2-point scale was used: 0 (certain condition is present) or 2 (certain condition is absent). Appropriate behavior was assessed by scan sampling of positive and negative social behaviors based on qualitative behavior assessment and human-animal relationship tests. Modification of the body condition score into a 3-point scale revealed pigs with a moderate body condition (score 1). Moreover, additional criteria such as feed quality confirmed that farms had moderate (score 1) or poor feed quality (score 2), especially those farms located in a high relative humidity region. The developed protocol can be utilized to assess welfare status in an intensive pig farming system. Although further improvements are still needed, this study is a first step in developing a pig welfare assessment protocol that combines animal-, environment-, and management-based measures.

Scalability enhancement of AODV using local link repairing

NASA Astrophysics Data System (ADS)

Jain, Jyoti; Gupta, Roopam; Bandhopadhyay, T. K.

2014-09-01

Dynamic change in the topology of an ad hoc network makes it difficult to design an efficient routing protocol. Scalability of an ad hoc network is also one of the important criteria of research in this field. Most of the research works in ad hoc network focus on routing and medium access protocols and produce simulation results for limited-size networks. Ad hoc on-demand distance vector (AODV) is one of the best reactive routing protocols. In this article, modified routing protocols based on local link repairing of AODV are proposed. Method of finding alternate routes for next-to-next node is proposed in case of link failure. These protocols are beacon-less, means periodic hello message is removed from the basic AODV to improve scalability. Few control packet formats have been changed to accommodate suggested modification. Proposed protocols are simulated to investigate scalability performance and compared with basic AODV protocol. This also proves that local link repairing of proposed protocol improves scalability of the network. From simulation results, it is clear that scalability performance of routing protocol is improved because of link repairing method. We have tested protocols for different terrain area with approximate constant node densities and different traffic load.

A sensitive mass spectrometric method for hypothesis-driven detection of peptide post-translational modifications: multiple reaction monitoring-initiated detection and sequencing (MIDAS).

PubMed

Unwin, Richard D; Griffiths, John R; Whetton, Anthony D

2009-01-01

The application of a targeted mass spectrometric workflow to the sensitive identification of post-translational modifications is described. This protocol employs multiple reaction monitoring (MRM) to search for all putative peptides specifically modified in a target protein. Positive MRMs trigger an MS/MS experiment to confirm the nature and site of the modification. This approach, termed MIDAS (MRM-initiated detection and sequencing), is more sensitive than approaches using neutral loss scanning or precursor ion scanning methodologies, due to a more efficient use of duty cycle along with a decreased background signal associated with MRM. We describe the use of MIDAS for the identification of phosphorylation, with a typical experiment taking just a couple of hours from obtaining a peptide sample. With minor modifications, the MIDAS method can be applied to other protein modifications or unmodified peptides can be used as a MIDAS target.

Ready-to-Use Tissue Construct for Military Bone and Cartilage Trauma

DTIC Science & Technology

2012-10-01

times. We hypothesize that our Ready-to-Use constructs can successfully restore 3 cm critical size segmental defects in dog tibiae. We will examine the...defects) of the grant. The approved IACUC protocol permits 3 pilot dogs for Aim 1 and 3 pilot dogs for Aim 2. Several minor modifications to the...original IACUC protocol were required which are provided in the Appendix. All the pilot dogs were to receive scaffolds composed of 90% poly-caprolactone

Three Dimensional (3D) Printing: A Straightforward, User-Friendly Protocol to Convert Virtual Chemical Models to Real-Life Objects

ERIC Educational Resources Information Center

Rossi, Sergio; Benaglia, Maurizio; Brenna, Davide; Porta, Riccardo; Orlandi, Manuel

2015-01-01

A simple procedure to convert protein data bank files (.pdb) into a stereolithography file (.stl) using VMD software (Virtual Molecular Dynamic) is reported. This tutorial allows generating, with a very simple protocol, three-dimensional customized structures that can be printed by a low-cost 3D-printer, and used for teaching chemical education…

Influence of major-groove chemical modifications of DNA on transcription by bacterial RNA polymerases.

PubMed

Raindlová, Veronika; Janoušková, Martina; Slavíčková, Michaela; Perlíková, Pavla; Boháčová, Soňa; Milisavljevič, Nemanja; Šanderová, Hana; Benda, Martin; Barvík, Ivan; Krásný, Libor; Hocek, Michal

2016-04-20

DNA templates containing a set of base modifications in the major groove (5-substituted pyrimidines or 7-substituted 7-deazapurines bearing H, methyl, vinyl, ethynyl or phenyl groups) were prepared by PCR using the corresponding base-modified 2'-deoxyribonucleoside triphosphates (dNTPs). The modified templates were used in an in vitro transcription assay using RNA polymerase from Bacillus subtilis and Escherichia coli Some modified nucleobases bearing smaller modifications (H, Me in 7-deazapurines) were perfectly tolerated by both enzymes, whereas bulky modifications (Ph at any nucleobase) and, surprisingly, uracil blocked transcription. Some middle-sized modifications (vinyl or ethynyl) were partly tolerated mostly by the E. colienzyme. In all cases where the transcription proceeded, full length RNA product with correct sequence was obtained indicating that the modifications of the template are not mutagenic and the inhibition is probably at the stage of initiation. The results are promising for the development of bioorthogonal reactions for artificial chemical switching of the transcription. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Base modifications affecting RNA polymerase and reverse transcriptase fidelity.

PubMed

Potapov, Vladimir; Fu, Xiaoqing; Dai, Nan; Corrêa, Ivan R; Tanner, Nathan A; Ong, Jennifer L

2018-06-20

Ribonucleic acid (RNA) is capable of hosting a variety of chemically diverse modifications, in both naturally-occurring post-transcriptional modifications and artificial chemical modifications used to expand the functionality of RNA. However, few studies have addressed how base modifications affect RNA polymerase and reverse transcriptase activity and fidelity. Here, we describe the fidelity of RNA synthesis and reverse transcription of modified ribonucleotides using an assay based on Pacific Biosciences Single Molecule Real-Time sequencing. Several modified bases, including methylated (m6A, m5C and m5U), hydroxymethylated (hm5U) and isomeric bases (pseudouridine), were examined. By comparing each modified base to the equivalent unmodified RNA base, we can determine how the modification affected cumulative RNA polymerase and reverse transcriptase fidelity. 5-hydroxymethyluridine and N6-methyladenosine both increased the combined error rate of T7 RNA polymerase and reverse transcriptases, while pseudouridine specifically increased the error rate of RNA synthesis by T7 RNA polymerase. In addition, we examined the frequency, mutational spectrum and sequence context of reverse transcription errors on DNA templates from an analysis of second strand DNA synthesis.

The Geneva Protocol of 1925: Past and Present.

ERIC Educational Resources Information Center

Harbison, John L.

1982-01-01

Presents a position paper for use in high school social studies class debates on the Geneva Protocol of 1925. The Protocol was an international agreement to restrict chemical and biological warfare (CBW). The author traces the history of U.S. policies dealing with CBW since 1925. (AM)

Systematic Review Protocol for the IRIS Chloroform Assessment (Inhalation) (Preliminary Assessment Materials)

EPA Science Inventory

In January 2018, EPA released the Systematic Review Protocol for the IRIS Chloroform Assessment (Inhalation). As part of developing a draft IRIS assessment, EPA presents a methods document, referred to as the protocol, for conducting a chemical-specific systematic revie...

Genetic engineering and chemical conjugation of potato virus X.

PubMed

Lee, Karin L; Uhde-Holzem, Kerstin; Fischer, Rainer; Commandeur, Ulrich; Steinmetz, Nicole F

2014-01-01

Here we report the genetic engineering and chemical modification of potato virus X (PVX) for the presentation of various peptides, proteins, and fluorescent dyes, or other chemical modifiers. Three different ways of genetic engineering are described and by these means, peptides are successfully expressed not only when the foot and mouth disease virus (FMDV) 2A sequence or a flexible glycine-serine linker is included, but also when the peptide is fused directly to the PVX coat protein. When larger proteins or unfavorable peptide sequences are presented, a partial fusion via the FMDV 2A sequence is preferable. When these PVX chimeras retain the ability to assemble into viral particles and are thus able to infect plants systemically, they can be utilized to inoculate susceptible plants for isolation of sufficient amounts of virus particles for subsequent chemical modification. Chemical modification is required for the display of nonbiological ligands such as fluorophores, polymers, and small drug compounds. We present three methods of chemical bioconjugation. For direct conjugation of small chemical modifiers to solvent exposed lysines, N-hydroxysuccinimide chemistry can be applied. Bio-orthogonal reactions such as copper-catalyzed azide-alkyne cycloaddition or hydrazone ligation are alternatives to achieve more efficient conjugation (e.g., when working with high molecular weight or insoluble ligands). Furthermore, hydrazone ligation offers an attractive route for the introduction of pH-cleavable cargos (e.g., therapeutic molecules).

Causes of genome instability: the effect of low dose chemical exposures in modern society

PubMed Central

Langie, Sabine A.S.; Koppen, Gudrun; Desaulniers, Daniel; Al-Mulla, Fahd; Al-Temaimi, Rabeah; Amedei, Amedeo; Azqueta, Amaya; Bisson, William H.; Brown, Dustin; Brunborg, Gunnar; Charles, Amelia K.; Chen, Tao; Colacci, Annamaria; Darroudi, Firouz; Forte, Stefano; Gonzalez, Laetitia; Hamid, Roslida A.; Knudsen, Lisbeth E.; Leyns, Luc; Lopez de Cerain Salsamendi, Adela; Memeo, Lorenzo; Mondello, Chiara; Mothersill, Carmel; Olsen, Ann-Karin; Pavanello, Sofia; Raju, Jayadev; Rojas, Emilio; Roy, Rabindra; Ryan, Elizabeth; Ostrosky-Wegman, Patricia; Salem, Hosni K.; Scovassi, Ivana; Singh, Neetu; Vaccari, Monica; Van Schooten, Frederik J.; Valverde, Mahara; Woodrick, Jordan; Zhang, Luoping; van Larebeke, Nik; Kirsch-Volders, Micheline; Collins, Andrew R.

2015-01-01

Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome’s integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus, genome instability can be defined as an enhanced tendency for the genome to acquire mutations; ranging from changes to the nucleotide sequence to chromosomal gain, rearrangements or loss. This review raises the hypothesis that in addition to known human carcinogens, exposure to low dose of other chemicals present in our modern society could contribute to carcinogenesis by indirectly affecting genome stability. The selected chemicals with their mechanisms of action proposed to indirectly contribute to genome instability are: heavy metals (DNA repair, epigenetic modification, DNA damage signaling, telomere length), acrylamide (DNA repair, chromosome segregation), bisphenol A (epigenetic modification, DNA damage signaling, mitochondrial function, chromosome segregation), benomyl (chromosome segregation), quinones (epigenetic modification) and nano-sized particles (epigenetic pathways, mitochondrial function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make scientists aware of the increasing need to unravel the underlying mechanisms via which chemicals at low doses can induce genome instability and thus promote carcinogenesis. PMID:26106144

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens.

PubMed

Saeidi, Saman; McKain, Michael R; Kellogg, Elizabeth A

2018-03-08

Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with a number of challenges including sample preservation quality, degraded DNA, and destructive sampling of rare specimens. In order to more effectively use herbarium material in large sequencing projects, a dependable and scalable method of DNA isolation and library preparation is needed. This paper demonstrates a robust, beginning-to-end protocol for DNA isolation and high-throughput library construction from herbarium specimens that does not require modification for individual samples. This protocol is tailored for low quality dried plant material and takes advantage of existing methods by optimizing tissue grinding, modifying library size selection, and introducing an optional reamplification step for low yield libraries. Reamplification of low yield DNA libraries can rescue samples derived from irreplaceable and potentially valuable herbarium specimens, negating the need for additional destructive sampling and without introducing discernible sequencing bias for common phylogenetic applications. The protocol has been tested on hundreds of grass species, but is expected to be adaptable for use in other plant lineages after verification. This protocol can be limited by extremely degraded DNA, where fragments do not exist in the desired size range, and by secondary metabolites present in some plant material that inhibit clean DNA isolation. Overall, this protocol introduces a fast and comprehensive method that allows for DNA isolation and library preparation of 24 samples in less than 13 h, with only 8 h of active hands-on time with minimal modifications.

The Effects of Training Contingency Awareness During Attention Bias Modification on Learning and Stress Reactivity.

PubMed

Lazarov, Amit; Abend, Rany; Seidner, Shiran; Pine, Daniel S; Bar-Haim, Yair

2017-09-01

Current attention bias modification (ABM) procedures are designed to implicitly train attention away from threatening stimuli with the hope of reducing stress reactivity and anxiety symptoms. However, the mechanisms underlying effective ABM delivery are not well understood, with awareness of the training contingency suggested as one possible factor contributing to ABM efficacy. Here, 45 high-anxious participants were trained to divert attention away from threat in two ABM sessions. They were randomly assigned to one of three training protocols: an implicit protocol, comprising two standard implicit ABM training sessions; an explicit protocol, comprising two sessions with explicit instruction as to the attention training contingency; and an implicit-explicit protocol, in which participants were not informed of the training contingency in the first ABM session and informed of it at the start of the second session. We examined learning processes and stress reactivity following a stress-induction task. Results indicate that relative to implicit instructions, explicit instructions led to stronger learning during the first training session. Following rest, the explicit and implicit groups exhibited consolidation-related improvement in performance, whereas no such improvement was noted for the implicit-explicit group. Finally, although stress reactivity was reduced after training, contingency awareness did not yield a differential effect on stress reactivity measured using both self-reports and skin conductance, within and across sessions. These results suggest that explicit ABM administration leads to greater initial learning during the training protocol while not differing from standard implicit administration in terms of off-line learning and stress reactivity. Copyright © 2017. Published by Elsevier Ltd.

A new setup for the investigation of swift heavy ion induced particle emission and surface modifications

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

Meinerzhagen, F.; Breuer, L.; Bukowska, H.

2016-01-15

The irradiation with fast ions with kinetic energies of >10 MeV leads to the deposition of a high amount of energy along their trajectory (up to several ten keV/nm). The energy is mainly transferred to the electronic subsystem and induces different secondary processes of excitations, which result in significant material modifications. A new setup to study these ion induced effects on surfaces will be described in this paper. The setup combines a variable irradiation chamber with different techniques of surface characterizations like scanning probe microscopy, time-of-flight secondary ion, and neutral mass spectrometry, as well as low energy electron diffraction undermore » ultra high vacuum conditions, and is mounted at a beamline of the universal linear accelerator (UNILAC) of the GSI facility in Darmstadt, Germany. Here, samples can be irradiated with high-energy ions with a total kinetic energy up to several GeVs under different angles of incidence. Our setup enables the preparation and in situ analysis of different types of sample systems ranging from metals to insulators. Time-of-flight secondary ion mass spectrometry enables us to study the chemical composition of the surface, while scanning probe microscopy allows a detailed view into the local electrical and morphological conditions of the sample surface down to atomic scales. With the new setup, particle emission during irradiation as well as persistent modifications of the surface after irradiation can thus be studied. We present first data obtained with the new setup, including a novel measuring protocol for time-of-flight mass spectrometry with the GSI UNILAC accelerator.« less

FEDEF: A High Level Architecture Federate Development Framework

DTIC Science & Technology

2010-09-01

require code changes for operability between HLA specifications. Configuration of federate requirements such as publications, subscriptions, time ... management , and management protocol should occur outside of federate source code, allowing for federate reusability without code modification and re

Chemically Modified Polyvinyl Chloride for Removal of Thionine Dye (Lauth’s Violet)

PubMed Central

Silva, Cleuzilene V.; Royer, Betina; Rodrigues Filho, Guimes; Cerqueira, Daniel A.; Assunção, Rosana M. N.

2017-01-01

The chemical modification of hydrophobic polymer matrices is an alternative way to elchange their surface properties. The introduction of sulfonic groups in the polymer changes the surface properties such as adhesion, wettability, catalytic ability, and adsorption capacity. This work describes the production and application of chemically modified polyvinyl chloride (PVC) as adsorbent for dyes removal. Chemical modification of PVC was evaluated by infrared spectroscopy and elemental analysis, which indicated the presence of sulfonic groups on PVC. The chemically modified PVC (PVCDS) showed an ion exchange capacity of 1.03 mmol−1, and efficiently removed the thionine dye (Lauth’s violet) from aqueous solutions, reaching equilibrium in 30 min. The adsorption kinetics was better adjusted for a pseudo second order model. This result indicates that the adsorption of thionine onto PVCDS occurs by chemisorption. Among the models for the state of equilibrium, SIPS and Langmuir exhibited the best fit to the experimental results and PVCDS showed high adsorption capacities (370 mg−1). Thus, it is assumed that the system presents homogeneous characteristics to the distribution of active sites. The modification promoted the formation of surface characteristics favorable to the dye adsorption by the polymer. PMID:29137158

Plant Sterols: Chemical and Enzymatic Structural Modifications and Effects on Their Cholesterol-Lowering Activity.

PubMed

He, Wen-Sen; Zhu, Hanyue; Chen, Zhen-Yu

2018-03-28

Plant sterols have attracted increasing attention due to their excellent cholesterol-lowering activity. However, free plant sterols have some characteristics of low oil solubility, water insolubility, high melting point, and low bioavailability, which greatly limit their application in foods. Numerous studies have been undertaken to modify their chemical structures to improve their chemical and physical properties in meeting the needs of various applications. The present review is to summarize the literature and update the progress on structural modifications of plant sterols in the following aspects: (i) synthesis of plant sterol esters by esterification and transesterification with hydrophobic fatty acids and triacylglycerols to improve their oil solubility, (ii) synthesis of plant sterol derivatives by coupling with various hydrophilic moieties to enhance their water solubility, and (iii) mechanisms by which plant sterols reduce plasma cholesterol and the effect of structural modifications on plasma cholesterol-lowering activity of plant sterols.

Modification of chemical reactivity of enzymatic hydrolysis lignin by ultrasound treatment in dilute alkaline solutions.

PubMed

Ma, Zhuoming; Li, Shujun; Fang, Guizhen; Patil, Nikhil; Yan, Ning

2016-12-01

In this study, we have explored various ultrasound treatment conditions for structural modification of enzymatic hydrolysis lignin (EHL) for enhanced chemical reactivity. The key structural modifications were characterized by using a combination of analytical methods, including, Fourier Transform-Infrared spectroscopy (FTIR), Proton Nuclear Magnetic Resonance ( 1 H NMR), Gel permeation chromatography (GPC), X-ray photoelectron spectroscopy (XPS), and Folin-Ciocalteu (F-C) method. Chemical reactivity of the modified EHL samples was determined by both 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging activity and their reactivity towards formaldehyde. It was observed that the modified EHL had a higher phenolic hydroxyl group content, a lower molecular weight, a higher reactivity towards formaldehyde, and a greater antioxidant property. The higher reactivity demonstrated by the samples after treatment suggesting that ultrasound is a promising method for modifying enzymatic hydrolysis lignin for value-added applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Protective activity of Cynara scolymus L. leaf extract against chemically induced complex genomic alterations in CHO cells.

PubMed

Jacociunas, Laura Vicedo; de Andrade, Heloisa Helena Rodrigues; Lehmann, Mauricio; Pedersini, Larissa Wölfle; Ferraz, Alexandre de Barros Falcão; da Silva, Juliana; Dihl, Rafael Rodrigues

2013-09-15

Cynara scolymus L., popularly known as artichoke, has been widely used in traditional medicine as an herbal medicament for therapeutic purposes. The study aimed at assessing the protective activity of Cynara scolymus leaf extract (LE) against DNA lesions induced by the alkylating agent ethylmethnesulphonate (EMS) in Chinese hamster ovary cells (CHO). The ability of C. scolymus L. LE to modulate the mutagenicity of EMS was examined using the cytokinesis block micronucleus (CBMN) cytome assay in three antigenotoxic protocols, pre- post- and simultaneous treatments. In the pre-treatment, C. scolymus L. LE reduced the frequencies of MNi and NBUDs induced by EMS in the lower concentration. In contrast, at the highest concentration (5 mg/ml) artichoke enhanced the frequency of MNi, potentiating EMS genotoxicity. In the simultaneous treatment only the induction of MNi was repressed by the exposure of cells to C. scolymus L. LE. No modification in genotoxicity was observed in LE post-treatment. The results obtained in this study suggest that lower concentrations of artichoke prevent chemically induced genomic damage in mammalian cells. In this context, the protective activity of C. scolymus L. could be associated to its constitutive antioxidants compounds. Copyright © 2013 Elsevier GmbH. All rights reserved.

Site-directed introduction of disulfide groups on antibodies for highly sensitive immunosensors.

PubMed

Acero Sánchez, Josep Ll; Fragoso, Alex; Joda, Hamdi; Suárez, Guillaume; McNeil, Calum J; O'Sullivan, Ciara K

2016-07-01

The interface between the sample and the transducer surface is critical to the performance of a biosensor. In this work, we compared different strategies for covalent self-assembly of antibodies onto bare gold substrates by introducing disulfide groups into the immunoglobulin structure, which acted as anchor molecules able to chemisorb spontaneously onto clean gold surfaces. The disulfide moieties were chemically introduced to the antibody via the primary amines, carboxylic acids, and carbohydrates present in its structure. The site-directed modification via the carbohydrate chains exhibited the best performance in terms of analyte response using a model system for the detection of the stroke marker neuron-specific enolase. SPR measurements clearly showed the potential for creating biologically active densely packed self-assembled monolayers (SAMs) in a one-step protocol compared to both mixed SAMs of alkanethiol compounds and commercial immobilization layers. The ability of the carbohydrate strategy to construct an electrochemical immunosensor was investigated using electrochemical impedance spectroscopy (EIS) and differential pulse voltammetry (DPV) transduction. Graphical Abstract Left: Functionalization strategies of bare gold substrates via direct bio-SAM using disulfide-containing antibody chemically modified via their primary amines (A), carbohydrates (B) and carboxylic acids (C). Right: Dependence of the peak height with NSE concentration at NSE21-CHO modified electrochemical immunosensor. Inset: Logarithmic calibration plot.

Generating gene knockout rats by homologous recombination in embryonic stem cells

PubMed Central

Tong, Chang; Huang, Guanyi; Ashton, Charles; Li, Ping; Ying, Qi-Long

2013-01-01

We describe here a detailed protocol for generating gene knockout rats by homologous recombination in embryonic stem (ES) cells. This protocol comprises the following procedures: derivation and expansion of rat ES cells, construction of gene-targeting vectors, generation of gene-targeted rat ES cells and, finally, production of gene-targeted rats. The major differences between this protocol and the classical mouse gene-targeting protocol include ES cell culture methods, drug selection scheme, colony picking and screening strategies. This ES cell–based gene-targeting technique allows sophisticated genetic modifications to be performed in the rat, as many laboratories have been doing in the mouse for the past two decades. Recently we used this protocol to generate Tp53 (also known as p53) gene knockout rats. The entire process requires ~1 year to complete, from derivation of ES cells to generation of knockout rats. PMID:21637202

Novel protocol for highly efficient gas-phase chemical derivatization of surface amine groups using trifluoroacetic anhydride

NASA Astrophysics Data System (ADS)

Duchoslav, Jiri; Kehrer, Matthias; Hinterreiter, Andreas; Duchoslav, Vojtech; Unterweger, Christoph; Fürst, Christian; Steinberger, Roland; Stifter, David

2018-06-01

In the current work, chemical derivatization of amine (NH2) groups with trifluoroacetic anhydride (TFAA) as an analytical method to improve the information scope of X-ray photoelectron spectroscopy (XPS) is investigated. TFAA is known to successfully label hydroxyl (OH) groups. With the introduction of a newly developed gas-phase derivatization protocol conducted at ambient pressure and using a catalyst also NH2 groups can now efficiently be labelled with a high yield and without the formation of unwanted by-products. By establishing a comprehensive and self-consistent database of reference binding energies for XPS a promising approach for distinguishing hydroxyl from amine groups is presented. The protocol was verified on different polymers, including poly(allylamine), poly(ethyleneimine), poly(vinylalcohol) and chitosan, the latter one containing both types of addressed chemical groups.

Design and Control of Chemical Grouting : Volume 3 - Engineering Practice

DOT National Transportation Integrated Search

1983-04-01

Recent improvements in the engineering practice of chemical grouting have provided increased confidence in this method of ground modification. Designers can significantly improve the success of chemical grouting by defining their grouting program obj...

Chemical Data Reporting - Previously Collected Data

EPA Pesticide Factsheets

EPA now refers to the Inventory Update Reporting (IUR) rule as the Chemical Data Reporting (CDR) Rule. This change was effective with the publication of the Inventory Update Reporting Modifications; Chemical Data Reporting Final Rule in August 2011.

Non-aqueous homogenous biocatalytic conversion of polysaccharides in ionic liquids using chemically modified glucosidase.

PubMed

Brogan, Alex P S; Bui-Le, Liem; Hallett, Jason P

2018-06-25

The increasing requirement to produce platform chemicals and fuels from renewable sources means advances in biocatalysis are rapidly becoming a necessity. Biomass is widely used in nature as a source of energy and as chemical building blocks. However, recalcitrance towards traditional chemical processes and solvents provides a significant barrier to widespread utility. Here, by optimizing enzyme solubility in ionic liquids, we have discovered solvent-induced substrate promiscuity of glucosidase, demonstrating an unprecedented example of homogeneous enzyme bioprocessing of cellulose. Specifically, chemical modification of glucosidase for solubilization in ionic liquids can increase thermal stability to up to 137 °C, allowing for enzymatic activity 30 times greater than is possible in aqueous media. These results establish that through a synergistic combination of chemical biology (enzyme modification) and reaction engineering (solvent choice), the biocatalytic capability of enzymes can be intensified: a key step towards the full-scale deployment of industrial biocatalysis.

The development and application of composite complexity models and a relative complexity metric in a software maintenance environment

NASA Technical Reports Server (NTRS)

Hops, J. M.; Sherif, J. S.

1994-01-01

A great deal of effort is now being devoted to the study, analysis, prediction, and minimization of software maintenance expected cost, long before software is delivered to users or customers. It has been estimated that, on the average, the effort spent on software maintenance is as costly as the effort spent on all other software costs. Software design methods should be the starting point to aid in alleviating the problems of software maintenance complexity and high costs. Two aspects of maintenance deserve attention: (1) protocols for locating and rectifying defects, and for ensuring that noe new defects are introduced in the development phase of the software process; and (2) protocols for modification, enhancement, and upgrading. This article focuses primarily on the second aspect, the development of protocols to help increase the quality and reduce the costs associated with modifications, enhancements, and upgrades of existing software. This study developed parsimonious models and a relative complexity metric for complexity measurement of software that were used to rank the modules in the system relative to one another. Some success was achieved in using the models and the relative metric to identify maintenance-prone modules.

Exploring the Arabidopsis proteome: influence of protein solubilization buffers on proteome coverage.

PubMed

Marondedze, Claudius; Wong, Aloysius; Groen, Arnoud; Serrano, Natalia; Jankovic, Boris; Lilley, Kathryn; Gehring, Christoph; Thomas, Ludivine

2014-12-31

The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

PubMed Central

Marondedze, Claudius; Wong, Aloysius; Groen, Arnoud; Serrano, Natalia; Jankovic, Boris; Lilley, Kathryn; Gehring, Christoph; Thomas, Ludivine

2014-01-01

The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins. PMID:25561235

Remote C-H Activation of Quinolines through Copper-Catalyzed Radical Cross-Coupling.

PubMed

Xu, Jun; Shen, Chao; Zhu, Xiaolei; Zhang, Pengfei; Ajitha, Manjaly J; Huang, Kuo-Wei; An, Zhongfu; Liu, Xiaogang

2016-03-18

Achieving site selectivity in carbon-hydrogen (C-H) functionalization reactions is a formidable challenge in organic chemistry. Herein, we report a novel approach to activating remote C-H bonds at the C5 position of 8-aminoquinoline through copper-catalyzed sulfonylation under mild conditions. Our strategy shows high conversion efficiency, a broad substrate scope, and good toleration with different functional groups. Furthermore, our mechanistic investigations suggest that a single-electron-transfer process plays a vital role in generating sulfonyl radicals and subsequently initiating C-S cross-coupling. Importantly, our copper-catalyzed remote functionalization protocol can be expanded for the construction of a variety of chemical bonds, including C-O, C-Br, C-N, C-C, and C-I. These findings provide a fundamental insight into the activation of remote C-H bonds, while offering new possibilities for rational design of drug molecules and optoelectronic materials requiring specific modification of functional groups. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation.

PubMed

Shore, Sabrina; Henderson, Jordana M; Lebedev, Alexandre; Salcedo, Michelle P; Zon, Gerald; McCaffrey, Anton P; Paul, Natasha; Hogrefe, Richard I

2016-01-01

For most sample types, the automation of RNA and DNA sample preparation workflows enables high throughput next-generation sequencing (NGS) library preparation. Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products formed during library preparation. These side products, known as adapter dimer, are very similar in size to the tagged library. Most sRNA library preparation strategies thus employ a gel purification step to isolate tagged library from adapter dimer contaminants. At very low sample inputs, adapter dimer side products dominate the reaction and limit the sensitivity of this technique. Here we address the need for improved specificity of sRNA library preparation workflows with a novel library preparation approach that uses modified adapters to suppress adapter dimer formation. This workflow allows for lower sample inputs and elimination of the gel purification step, which in turn allows for an automatable sRNA library preparation protocol.

Cell Membrane Electropulsation: Chemical Analysis of Cell Membrane Modifications and Associated Transport Mechanisms.

PubMed

Azan, Antoine; Gailliègue, Florian; Mir, Lluis M; Breton, Marie

2017-01-01

The transport of substances across the cell membrane is complex because the main physiological role of the membrane is the control of the substances that would enter or exit the cells. Life would not be possible without this control. Cell electropulsation corresponds to the delivery of electric pulses to the cells and comprises cell electroporation and cell electropermeabilization. Cell electropulsation allows for the transport of non-permeant molecules across the membrane, bypassing the physiological limitations. In this chapter we discuss the changes occurring in the cell membrane during electroporation or electropermeabilization as they allow to understand which molecules can be transported as well as when and how their transport can occur. Electrophoretic or diffusive transports across the cell membrane can be distinguished. This understanding has a clear impact on the choice of the electrical parameters to be applied to the cells as well as on other aspects of the experimental protocols that have to be set to load the cells with non-permeant molecules.

Investigating the effects of proton exchange membrane fuel cell conditions on carbon supported platinum electrocatalyst composition and performance

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

Patel, Anant; Artyushkova, Kateryna; Atanassov, Plamen

2011-12-01

Changes that carbon-supported platinum electrocatalysts undergo in a proton exchange membrane fuel cell environment were simulated by ex situ heat treatment of catalyst powder samples at 150 C and 100% relative humidity. In order to study modifications that are introduced to chemistry, morphology, and performance of electrocatalysts, XPS, HREELS and three-electrode rotating disk electrode experiments were performed. Before heat treatment, graphitic content varied by 20% among samples with different types of carbon supports, with distinct differences between bulk and surface compositions within each sample. Following the aging protocol, the bulk and surface chemistry of the samples were similar, with graphitemore » content increasing or remaining constant and Pt-carbide decreasing for all samples. From the correlation of changes in chemical composition and losses in performance of the electrocatalysts, we conclude that relative distribution of Pt particles on graphitic and amorphous carbon is as important for electrocatalytic activity as the absolute amount of graphitic carbon present« less

A synergistic approach to protein crystallization: Combination of a fixed-arm carrier with surface entropy reduction

PubMed Central

Moon, Andrea F; Mueller, Geoffrey A; Zhong, Xuejun; Pedersen, Lars C

2010-01-01

Protein crystallographers are often confronted with recalcitrant proteins not readily crystallizable, or which crystallize in problematic forms. A variety of techniques have been used to surmount such obstacles: crystallization using carrier proteins or antibody complexes, chemical modification, surface entropy reduction, proteolytic digestion, and additive screening. Here we present a synergistic approach for successful crystallization of proteins that do not form diffraction quality crystals using conventional methods. This approach combines favorable aspects of carrier-driven crystallization with surface entropy reduction. We have generated a series of maltose binding protein (MBP) fusion constructs containing different surface mutations designed to reduce surface entropy and encourage crystal lattice formation. The MBP advantageously increases protein expression and solubility, and provides a streamlined purification protocol. Using this technique, we have successfully solved the structures of three unrelated proteins that were previously unattainable. This crystallization technique represents a valuable rescue strategy for protein structure solution when conventional methods fail. PMID:20196072

Synthesis of Protein Bioconjugates via Cysteine-maleimide Chemistry.

PubMed

Mason, Alexander F; Thordarson, Pall

2016-07-20

The chemical linking or bioconjugation of proteins to fluorescent dyes, drugs, polymers and other proteins has a broad range of applications, such as the development of antibody drug conjugates (ADCs) and nanomedicine, fluorescent microscopy and systems chemistry. For many of these applications, specificity of the bioconjugation method used is of prime concern. The Michael addition of maleimides with cysteine(s) on the target proteins is highly selective and proceeds rapidly under mild conditions, making it one of the most popular methods for protein bioconjugation. We demonstrate here the modification of the only surface-accessible cysteine residue on yeast cytochrome c with a ruthenium(II) bisterpyridine maleimide. The protein bioconjugation is verified by gel electrophoresis and purified by aqueous-based fast protein liquid chromatography in 27% yield of isolated protein material. Structural characterization with MALDI-TOF MS and UV-Vis is then used to verify that the bioconjugation is successful. The protocol shown here is easily applicable to other cysteine - maleimide coupling of proteins to other proteins, dyes, drugs or polymers.

Gut microbiota in toxicological risk assessment of drugs and chemicals: The need of hour.

PubMed

Velmurugan, Ganesan

2018-03-06

The advent of industrial revolution caused a large inflow of synthetic chemicals for medical, agricultural, industrial and other purposes in the world. In general, these chemicals were subjected to toxicological risk assessment for human health and ecology before release for public use. But today we are witnessing a negative impact of some of these chemicals on human health and environment indicating an underestimation of toxic effects by current risk assessment protocol. Recent studies established gut microbiota as one of the key player in intercession of toxicity of drugs and synthetic chemicals. Hence, the need of the hour is to include the assessment for microbiota specifically gut microbiota in human toxicological risk assessment protocol. Herewith we are proposing a framework for assessment of gut microbiota upon exposure to drugs or chemicals.

An optimized immunohistochemistry protocol for detecting the guidance cue Netrin-1 in neural tissue.

PubMed

Salameh, Samer; Nouel, Dominique; Flores, Cecilia; Hoops, Daniel

2018-01-01

Netrin-1, an axon guidance protein, is difficult to detect using immunohistochemistry. We performed a multi-step, blinded, and controlled protocol optimization procedure to establish an efficient and effective fluorescent immunohistochemistry protocol for characterizing Netrin-1 expression. Coronal mouse brain sections were used to test numerous antigen retrieval methods and combinations thereof in order to optimize the stain quality of a commercially available Netrin-1 antibody. Stain quality was evaluated by experienced neuroanatomists for two criteria: signal intensity and signal-to-noise ratio. After five rounds of testing protocol variants, we established a modified immunohistochemistry protocol that produced a Netrin-1 signal with good signal intensity and a high signal-to-noise ratio. The key protocol modifications are as follows: •Use phosphate buffer (PB) as the blocking solution solvent.•Use 1% sodium dodecyl sulfate (SDS) treatment for antigen retrieval. The original protocol was optimized for use with the Netrin-1 antibody produced by Novus Biologicals. However, we subsequently further modified the protocol to work with the antibody produced by Abcam. The Abcam protocol uses PBS as the blocking solution solvent and adds a citrate buffer antigen retrieval step.

A Simple Method for High Throughput Chemical Screening in Caenorhabditis Elegans

PubMed Central

Lucanic, Mark; Garrett, Theo; Gill, Matthew S.; Lithgow, Gordon J.

2018-01-01

Caenorhabditis elegans is a useful organism for testing chemical effects on physiology. Whole organism small molecule screens offer significant advantages for identifying biologically active chemical structures that can modify complex phenotypes such as lifespan. Described here is a simple protocol for producing hundreds of 96-well culture plates with fairly consistent numbers of C. elegans in each well. Next, we specified how to use these cultures to screen thousands of chemicals for effects on the lifespan of the nematode C. elegans. This protocol makes use of temperature sensitive sterile strains, agar plate conditions, and simple animal handling to facilitate the rapid and high throughput production of synchronized animal cultures for screening. PMID:29630057

Chemical modification of cellulose-rich fibres to clarify the influence of the chemical structure on the physical and mechanical properties of cellulose fibres and thereof made sheets.

PubMed

López Durán, Verónica; Larsson, Per A; Wågberg, Lars

2018-02-15

Despite the different chemical approaches used earlier to increase the ductility of fibre-based materials, it has not been possible to link the chemical modification to their mechanical performance. In this study, cellulose fibres have been modified by periodate oxidation, alone or followed either by borohydride reduction, reductive amination or chlorite oxidation. In addition, TEMPO oxidation, and TEMPO oxidation in combination with periodate oxidation and further reduction with sodium borohydride have also been studied. The objective was to gain understanding of the influence of different functional groups on the mechanical and structural properties of handsheets made from the modified fibres. It was found that the modifications studied improved the tensile strength of the fibres to different extents, but that only periodate oxidation followed by borohydride reduction provided more ductile fibre materials. Changes in density, water-holding capacity and mechanical performance were also quantified and all are dependent on the functional group introduced. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluation of modified titanium surfaces physical and chemical characteristics

NASA Astrophysics Data System (ADS)

Lukaszewska-Kuska, Magdalena; Leda, Bartosz; Gajdus, Przemyslaw; Hedzelek, Wieslaw

2017-11-01

Development of dental implantology is focused, among other things, on devising active surface of the implant, conditioning acceleration of the implant's integration with the bone. Increased roughness, characteristic for group of implants with developed surface, altered topography and chemically modified implant's surface determines increased implants stability. In this study four different titanium surfaces modifications: turned (TS); aluminium oxide-blasted (Al2O3); resorbable material blasted (RBM); sandblast and then etched with a mixture of acids (SAE), were evaluated in terms of surfaces topography and chemical composition prior to in vivo analysis. Topography analysis revealed two groups: one with smooth, anisotropic, undeveloped TS surface and the second group with remaining surfaces presenting rough, isotropic, developed surfaces with added during blasting procedure aluminium for Al2O3 and calcium and phosphorus for RBM. Physical and chemical modifications of titanium surface change its microstructure (typical for SAE) and increase its roughness (highest for Al2O3-blasted and RBM surfaces). The introduced modifications develop titanium surface - 10 times for SAE surfaces, 16 times for Al2O3-blasted surfaces, and 20 times for RBM surfaces.

Lyceum: A Multi-Protocol Digital Library Gateway

NASA Technical Reports Server (NTRS)

Maa, Ming-Hokng; Nelson, Michael L.; Esler, Sandra L.

1997-01-01

Lyceum is a prototype scalable query gateway that provides a logically central interface to multi-protocol and physically distributed, digital libraries of scientific and technical information. Lyceum processes queries to multiple syntactically distinct search engines used by various distributed information servers from a single logically central interface without modification of the remote search engines. A working prototype (http://www.larc.nasa.gov/lyceum/) demonstrates the capabilities, potentials, and advantages of this type of meta-search engine by providing access to over 50 servers covering over 20 disciplines.

Packet Controller For Wireless Headset

NASA Technical Reports Server (NTRS)

Christensen, Kurt K.; Swanson, Richard J.

1993-01-01

Packet-message controller implements communications protocol of network of wireless headsets. Designed for headset application, readily adapted to other uses; slight modification enables controller to implement Integrated Services Digital Network (ISDN) X.25 protocol, giving far-reaching applications in telecommunications. Circuit converts continuous voice signals into digital packets of data and vice versa. Operates in master or slave mode. Controller reduced to single complementary metal oxide/semiconductor integrated-circuit chip. Occupies minimal space in headset and consumes little power, extending life of headset battery.

Double C-NOT attack and counterattack on `Three-step semi-quantum secure direct communication protocol'

NASA Astrophysics Data System (ADS)

Gu, Jun; Lin, Po-hua; Hwang, Tzonelih

2018-07-01

Recently, Zou and Qiu (Sci China Phys Mech Astron 57:1696-1702, 2014) proposed a three-step semi-quantum secure direct communication protocol allowing a classical participant who does not have a quantum register to securely send his/her secret message to a quantum participant. However, this study points out that an eavesdropper can use the double C-NOT attack to obtain the secret message. To solve this problem, a modification is proposed.

Authenticated communication from quantum readout of PUFs

NASA Astrophysics Data System (ADS)

Škorić, Boris; Pinkse, Pepijn W. H.; Mosk, Allard P.

2017-08-01

Quantum readout of physical unclonable functions (PUFs) is a recently introduced method for remote authentication of objects. We present an extension of the protocol to enable the authentication of data: A verifier can check if received classical data were sent by the PUF holder. We call this modification QR-d or, in the case of the optical-PUF implementation, QSA-d. We discuss how QSA-d can be operated in a parallel way. We also present a protocol for authenticating quantum states.

Identification and characterization of ana o 3 modifications on arginine-111 residue in heated cashew nuts

USDA-ARS?s Scientific Manuscript database

Heating foods can alter the physical, chemical, and biological characteristics of the proteins we consume. Raw and roasted cashew nut extracts were evaluated for allergen modifications by mass-spectrometry. We did not identify modifications on Ana o 1 or Ana o 2, but we observed two independent mo...

Efficacy of scalp hair decontamination following exposure to vapours of sulphur mustard simulants 2-chloroethyl ethyl sulphide and methyl salicylate.

PubMed

Spiandore, Marie; Piram, Anne; Lacoste, Alexandre; Prevost, Philippe; Maloni, Pascal; Torre, Franck; Asia, Laurence; Josse, Denis; Doumenq, Pierre

2017-04-01

Chemical warfare agents are an actual threat and victims' decontamination is a main concern when mass exposure occurs. Skin decontamination with current protocols has been widely documented, as well as surface decontamination. However, considering hair ability to trap chemicals in vapour phase, we investigated hair decontamination after exposure to sulphur mustard simulants methyl salicylate and 2-chloroethyl ethyl sulphide. Four decontamination protocols were tested on hair, combining showering and emergency decontamination (use of Fuller's earth or Reactive Skin Decontamination Lotion RSDL ® ). Both simulants were recovered from hair after treatment, but contents were significantly reduced (42-85% content allowance). Showering alone was the least efficient protocol. Concerning 2-chloroethyl ethyl sulphide, protocols did not display significant differences in decontamination efficacy. For MeS, use of emergency decontaminants significantly increased showering efficacy (10-20% rise), underlining their usefulness before thorough decontamination. Our results highlighted the need to extensively decontaminate hair after chemical exposure. Residual amounts after decontamination are challenging, as their release from hair could lead to health issues. Copyright © 2016. Published by Elsevier B.V.

A covalent modification for graphene by adamantane groups through two-step chlorination-Grignard reactions

NASA Astrophysics Data System (ADS)

Sun, Xuzhuo; Li, Bo; Lu, Mingxia

2017-07-01

Chemical modification of graphene is a promising approach to manipulate its properties for its end applications. Herein we designed a two-step route through chlorination-Grignard reactions to covalently decorate the surface of graphene with adamantane groups. The chemically modified graphene was characterized by Raman spectroscopy, atomic force microscopy, and X-ray photoelectron spectroscopy. Chlorination of graphene occurred rapidly, and the substitution of chlorine atoms on chlorinated graphene by adamantane Grignard reagent afforded adamantane graphene in almost quantitative yield. Adamantane groups were found to be covalently bonded to the graphene carbons. The present two-step procedure may provide an effective and facile route for graphene modification with varieties of organic functional groups.

A Chemical-Adsorption Strategy to Enhance the Reaction Kinetics of Lithium-Rich Layered Cathodes via Double-Shell Surface Modification.

PubMed

Guo, Lichao; Li, Jiajun; Cao, Tingting; Wang, Huayu; Zhao, Naiqin; He, Fang; Shi, Chunsheng; He, Chunnian; Liu, Enzuo

2016-09-21

Sluggish surface reaction kinetics hinders the power density of Li-ion battery. Thus, various surface modification techniques have been applied to enhance the electronic/ionic transfer kinetics. However, it is challenging to obtain a continuous and uniform surface modification layer on the prime particles with structure integration at the interface. Instead of classic physical-adsorption/deposition techniques, we propose a novel chemical-adsorption strategy to synthesize double-shell modified lithium-rich layered cathodes with enhanced mass transfer kinetics. On the basis of experimental measurement and first-principles calculation, MoO2S2 ions are proved to joint the layered phase via chemical bonding. Specifically, the Mo-O or Mo-S bonds can flexibly rotate to bond with the cations in the layered phase, leading to the good compatibility between the thiomolybdate adsorption layer and layered cathode. Followed by annealing treatment, the lithium-excess-spinel inner shell forms under the thiomolybdate adsorption layer and functions as favorable pathways for lithium and electron. Meanwhile, the nanothick MoO3-x(SO4)x outer shell protects the transition metal from dissolution and restrains electrolyte decomposition. The double-shell modified sample delivers an enhanced discharge capacity almost twice as much as that of the unmodified one at 1 A g(-1) after 100 cycles, demonstrating the superiority of the surface modification based on chemical adsorption.

Drug development and manufacturing

DOEpatents

Warner, Benjamin P.; McCleskey, T. Mark; Burrell, Anthony K.

2015-10-13

X-ray fluorescence (XRF) spectrometry has been used for detecting binding events and measuring binding selectivities between chemicals and receptors. XRF may also be used for estimating the therapeutic index of a chemical, for estimating the binding selectivity of a chemical versus chemical analogs, for measuring post-translational modifications of proteins, and for drug manufacturing.

Protein chemical synthesis by α-ketoacid-hydroxylamine ligation.

PubMed

Harmand, Thibault J; Murar, Claudia E; Bode, Jeffrey W

2016-06-01

Total chemical synthesis of proteins allows researchers to custom design proteins without the complex molecular biology that is required to insert non-natural amino acids or the biocontamination that arises from methods relying on overexpression in cells. We describe a detailed procedure for the chemical synthesis of proteins with the α-ketoacid-hydroxylamine (KAHA ligation), using (S)-5-oxaproline (Opr) as a key building block. This protocol comprises two main parts: (i) the synthesis of peptide fragments by standard fluorenylmethoxycarbonyl (Fmoc) chemistry and (ii) the KAHA ligation between fragments containing Opr and a C-terminal peptide α-ketoacid. This procedure provides an alternative to native chemical ligation (NCL) that could be valuable for the synthesis of proteins, particularly targets that do not contain cysteine residues. The ligation conditions-acidic DMSO/H2O or N-methyl-2-pyrrolidinone (NMP)/H2O-are ideally suited for solubilizing peptide segments, including many hydrophobic examples. The utility and efficiency of the protocol is demonstrated by the total chemical synthesis of the mature betatrophin (also called ANGPTL8), a 177-residue protein that contains no cysteine residues. With this protocol, the total synthesis of the betatrophin protein has been achieved in around 35 working days on a multimilligram scale.

A multigear protocol for sampling crayfish assemblages in Gulf of Mexico coastal streams

Treesearch

William R. Budnick; William E. Kelso; Susan B. Adams; Michael D. Kaller

2018-01-01

Identifying an effective protocol for sampling crayfish in streams that vary in habitat and physical/chemical characteristics has proven problematic. We evaluated an active, combined-gear (backpack electrofishing and dipnetting) sampling protocol in 20 Coastal Plain streams in Louisiana. Using generalized linear models and rarefaction curves, we evaluated environmental...

10 CFR 963.17 - Postclosure suitability criteria.

Code of Federal Regulations, 2014 CFR

2014-01-01

...) Near field geochemical environment—for example, the chemical reactions and products resulting from... probability and potential consequences of a self-sustaining nuclear reaction as a result of chemical or..., drip shields, backfill, coatings, or chemical modifications, and (ii) Waste package degradation—for...

10 CFR 963.17 - Postclosure suitability criteria.

Code of Federal Regulations, 2012 CFR

2012-01-01

...) Near field geochemical environment—for example, the chemical reactions and products resulting from... probability and potential consequences of a self-sustaining nuclear reaction as a result of chemical or..., drip shields, backfill, coatings, or chemical modifications, and (ii) Waste package degradation—for...

10 CFR 963.17 - Postclosure suitability criteria.

Code of Federal Regulations, 2010 CFR

2010-01-01

...) Near field geochemical environment—for example, the chemical reactions and products resulting from... probability and potential consequences of a self-sustaining nuclear reaction as a result of chemical or..., drip shields, backfill, coatings, or chemical modifications, and (ii) Waste package degradation—for...

10 CFR 963.17 - Postclosure suitability criteria.

Code of Federal Regulations, 2013 CFR

2013-01-01

...) Near field geochemical environment—for example, the chemical reactions and products resulting from... probability and potential consequences of a self-sustaining nuclear reaction as a result of chemical or..., drip shields, backfill, coatings, or chemical modifications, and (ii) Waste package degradation—for...

10 CFR 963.17 - Postclosure suitability criteria.

Code of Federal Regulations, 2011 CFR

2011-01-01

...) Near field geochemical environment—for example, the chemical reactions and products resulting from... probability and potential consequences of a self-sustaining nuclear reaction as a result of chemical or..., drip shields, backfill, coatings, or chemical modifications, and (ii) Waste package degradation—for...

Towards Enhanced Performance Thin-film Composite Membranes via Surface Plasma Modification

PubMed Central

Reis, Rackel; Dumée, Ludovic F.; Tardy, Blaise L.; Dagastine, Raymond; Orbell, John D.; Schutz, Jürg A.; Duke, Mikel C.

2016-01-01

Advancing the design of thin-film composite membrane surfaces is one of the most promising pathways to deal with treating varying water qualities and increase their long-term stability and permeability. Although plasma technologies have been explored for surface modification of bulk micro and ultrafiltration membrane materials, the modification of thin film composite membranes is yet to be systematically investigated. Here, the performance of commercial thin-film composite desalination membranes has been significantly enhanced by rapid and facile, low pressure, argon plasma activation. Pressure driven water desalination tests showed that at low power density, flux was improved by 22% without compromising salt rejection. Various plasma durations and excitation powers have been systematically evaluated to assess the impact of plasma glow reactions on the physico-chemical properties of these materials associated with permeability. With increasing power density, plasma treatment enhanced the hydrophilicity of the surfaces, where water contact angles decreasing by 70% were strongly correlated with increased negative charge and smooth uniform surface morphology. These results highlight a versatile chemical modification technique for post-treatment of commercial membrane products that provides uniform morphology and chemically altered surface properties. PMID:27363670

[Construction of chemical information database based on optical structure recognition technique].

PubMed

Lv, C Y; Li, M N; Zhang, L R; Liu, Z M

2018-04-18

To create a protocol that could be used to construct chemical information database from scientific literature quickly and automatically. Scientific literature, patents and technical reports from different chemical disciplines were collected and stored in PDF format as fundamental datasets. Chemical structures were transformed from published documents and images to machine-readable data by using the name conversion technology and optical structure recognition tool CLiDE. In the process of molecular structure information extraction, Markush structures were enumerated into well-defined monomer molecules by means of QueryTools in molecule editor ChemDraw. Document management software EndNote X8 was applied to acquire bibliographical references involving title, author, journal and year of publication. Text mining toolkit ChemDataExtractor was adopted to retrieve information that could be used to populate structured chemical database from figures, tables, and textual paragraphs. After this step, detailed manual revision and annotation were conducted in order to ensure the accuracy and completeness of the data. In addition to the literature data, computing simulation platform Pipeline Pilot 7.5 was utilized to calculate the physical and chemical properties and predict molecular attributes. Furthermore, open database ChEMBL was linked to fetch known bioactivities, such as indications and targets. After information extraction and data expansion, five separate metadata files were generated, including molecular structure data file, molecular information, bibliographical references, predictable attributes and known bioactivities. Canonical simplified molecular input line entry specification as primary key, metadata files were associated through common key nodes including molecular number and PDF number to construct an integrated chemical information database. A reasonable construction protocol of chemical information database was created successfully. A total of 174 research articles and 25 reviews published in Marine Drugs from January 2015 to June 2016 collected as essential data source, and an elementary marine natural product database named PKU-MNPD was built in accordance with this protocol, which contained 3 262 molecules and 19 821 records. This data aggregation protocol is of great help for the chemical information database construction in accuracy, comprehensiveness and efficiency based on original documents. The structured chemical information database can facilitate the access to medical intelligence and accelerate the transformation of scientific research achievements.

The influence of chemical methods (acid modification) on elephant foot yam flour to improve physical and chemical quality on processed food

NASA Astrophysics Data System (ADS)

Paramita, Octavianti; Wahyuningsih, Ansori, Muhammad

2018-03-01

This study was aimed at improving the physicochemical quality of elephant foot yam flour in Gunungpati, Semarang by acid modification. The utilization of elephant foot yam flour in several processed food was also discussed in this study. The flour of the experimental result discussed in this study was expected to become a reference for the manufacturers of elephant foot yam flour and its processed food in Gunungpati. This study modified the elephant foot yam flour using acid modification method. The physical and chemical quality of each elephant foot yam flour of the experimental result sample were assessed using proximate analysis. The resulting tuber flour weighed 50 grams and the soaked in acid solution with various concentrations 5 %, 10 % and 15 % with soaking duration 30, 60 and 90 minutes at temperature 35 °C. The resulting suspension was washed 3 times, filtered and then dried by cabinet dryer using 46 °C for 2 days. The dried flour was sifted with a 80 mesh sieve. Chemical test was conducted after elephant foot yam was acid modification to determine changes in the quality flour: test levels of protein, fat, crude fiber content, moisture content, ash content and starch content. In addition, color tests and granular test on elephant foot yam flour were also conducted. The acid modification as chemical treatment on elephant foot yam flour in this study was able to change the functional properties of elephant foot yam flour towards a better processing characterized by a brighter color (L = 80, a = 8 and b = 12), the hydrolysis of polysaccharides flour into shorter chain (flour content decreased to 72%), the expansion of granules in elephant foot yam resulting in a process - ready flour, and better monolayer water content of 11%. The content of protein and fiber on the elephant foot yam flour also can be maintained at a level of 8% and 1.9% levels.

The Use of Molecular Techniques at Hazardous Waste Sites

EPA Science Inventory

It is clear that typical protocols used for soil analysis would certainly fail to adequately interrogate ground-water treatment systems unless they were substantially modified. The modifications found necessary to compensate for the low biomass include molecular tools and techniq...

Data Acquisition for a Patient-directed Intervention Protocol in the Dynamic Intensive Care Unit Setting

PubMed Central

Chlan, Linda; Patterson, Robert P.; Heiderscheit, Annie

2011-01-01

Methods to easily, accurately, and efficiently obtain data in an ICU-based clinical trial can be challenging in this high-tech setting. Patient medical status and the dynamic nature of this clinical setting further complicates data collection. The purpose of this paper is to describe the modifications of commercially available headphones and the application of a data logging device to capture frequency and length of protocol use (music listening or headphones only for noise cancellation) without burdening participants or busy ICU nurses. With the automatic capture of protocol use by research participants, there have been no instances of lost data for this clinical trial. PMID:21382515

Two-party secret key distribution via a modified quantum secret sharing protocol.

PubMed

Grice, W P; Evans, P G; Lawrie, B; Legré, M; Lougovski, P; Ray, W; Williams, B P; Qi, B; Smith, A M

2015-03-23

We present and demonstrate a novel protocol for distributing secret keys between two and only two parties based on N-party single-qubit Quantum Secret Sharing (QSS). We demonstrate our new protocol with N = 3 parties using phase-encoded photons. We show that any two out of N parties can build a secret key based on partial information from each other and with collaboration from the remaining N - 2 parties. Our implementation allows for an accessible transition between N-party QSS and arbitrary two party QKD without modification of hardware. In addition, our approach significantly reduces the number of resources such as single photon detectors, lasers and dark fiber connections needed to implement QKD.

Data acquisition for a patient-directed intervention protocol in the dynamic intensive care unit setting.

PubMed

Chlan, Linda; Patterson, Robert P; Heiderscheit, Annie

2011-07-01

Methods to easily, accurately, and efficiently obtain data in an ICU-based clinical trial can be challenging in this high-tech setting. Patient medical status and the dynamic nature of this clinical setting further complicate data collection. The purpose of this paper is to describe the modifications of commercially available headphones and the application of a data logging device to capture frequency and length of protocol use (music listening or headphones only for noise cancellation) without burdening participants or busy ICU nurses. With the automatic capture of protocol use by research participants, there have been no instances of lost data for this clinical trial. Copyright © 2011 Elsevier Inc. All rights reserved.

[Study on surface modification and biocompatibility of NiTi alloy intravascular stents].

PubMed

Shen, Yang; Wang, Gui-xue; Quan, Xue-jun; Yu, Qing-song

2006-01-01

This paper introduces the surface modification of NiTi alloy intravascular stents for roughness by chemical erosion and plasma deposition technology. The stent which had been granulated with chemical erosion was treated with TiO2 film prepared with Gel-sol. The study on the biocompatibility of the modified stent by the above two ways shows that the modified stent is rougher, and its anticoagulation and hydrophilicity are improved. However, the capability of erosion resistance is not enhanced significantly.

21 CFR 1313.53 - Waiver of modification of rules.

Code of Federal Regulations, 2010 CFR

2010-04-01

... EXPORTATION OF LIST I AND LIST II CHEMICALS Hearings § 1313.53 Waiver of modification of rules. The... in this part by notice in advance of the hearing, if he determines that no party in the hearing will...

40 CFR 60.489a - List of chemicals produced by affected facilities.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 7 2014-07-01 2014-07-01 false List of chemicals produced by affected... Equipment Leaks of VOC in the Synthetic Organic Chemicals Manufacturing Industry for Which Construction, Reconstruction, or Modification Commenced After November 7, 2006 § 60.489a List of chemicals produced by affected...

Chemical treatment of the intra-canal dentin surface: a new approach to modify dentin hydrophobicity

PubMed Central

GAITAN-FONSECA, Cesar; COLLART-DUTILLEUL, Pierre-Yves; SEMETEY, Vincent; ROMIEU, Olivier; CRUZ, Roel; FLORES, Hector; CUISINIER, Frédéric; PÉREZ, Elías; POZOS-GUILLEN, Amaury

2013-01-01

Objective: This study evaluated the hydrophobicity of dentin surfaces that were modified through chemical silanization with octadecyltrichlorosilane (OTS). Material and Methods: An in vitro experimental study was performed using 40 human permanent incisors that were divided into the following two groups: non-silanized and silanized. The specimens were pretreated and chemically modified with OTS. After the chemical modification, the dentin hydrophobicity was examined using a water contact angle measurement (WCA). The effectiveness of the modification of hydrophobicity was verified by the fluid permeability test (FPT). Results and Conclusions: Statistically significant differences were found in the values of WCA and FPT between the two groups. After silanization, the hydrophobic intraradicular dentin surface exhibited in vitro properties that limit fluid penetration into the sealed root canal. This chemical treatment is a new approach for improving the sealing of the root canal system. PMID:23559114

ERLN Activities Details

EPA Pesticide Factsheets

Environmental Response Laboratory Network activities include the All Hazard Receipt Facility and Screening Protocol, standardizing chemical methods, Chemical Warfare Agent Fixed Laboratory Pilot Project, microbial efforts, and WLA response plan.

40 CFR 455.47 - Pretreatment standards for new sources (PSNS).

Code of Federal Regulations, 2011 CFR

2011-07-01

...) EFFLUENT GUIDELINES AND STANDARDS PESTICIDE CHEMICALS Pesticide Chemicals Formulating and Packaging... Best Engineering Judgement for modifications not listed in Table 8 to this part 455); (2) The...

40 CFR 455.47 - Pretreatment standards for new sources (PSNS).

Code of Federal Regulations, 2010 CFR

2010-07-01

...) EFFLUENT GUIDELINES AND STANDARDS PESTICIDE CHEMICALS Pesticide Chemicals Formulating and Packaging... Best Engineering Judgement for modifications not listed in Table 8 to this part 455); (2) The...

Are child-centric aspects in newborn and child health systematic review and meta-analysis protocols and reports adequately reported?-two systematic reviews.

PubMed

Farid-Kapadia, Mufiza; Joachim, Kariym C; Balasingham, Chrinna; Clyburne-Sherin, April; Offringa, Martin

2017-03-06

Evidence suggests that newborn and child health systematic reviews and meta-analyses exhibit poor quality in reporting. The "Preferred Reporting Items in Systematic Review and Meta-Analysis" (PRISMA) and PRISMA-Protocols (PRISMA-P) checklists have been developed to improve the reporting of systematic review results and protocols, respectively. We aimed to evaluate the clarity and transparency in reporting of child-centric items in child health systematic reviews (SRs) and SR protocols and to identify areas where reporting could be strengthened. Two preliminary lists of potential child-centric reporting items were used to examine current reporting. The Cochrane, DARE, MEDLINE, and EMBASE libraries were searched from 2010 to 2014 for systematic reviews that included children. Each report and protocol that met the inclusion criteria had their quality of reporting assessed by their reporting of child-centric items. Quality of reporting was assessed per whether one third, one to two thirds, or more than two thirds of papers complied with potential child-centric potential modifications/extensions to PRISMA and were analyzed by the following: (i) paper type (i.e., report vs. protocol), (ii) publication type (i.e., Cochrane vs. non-Cochrane), and (iii) population type (i.e., child-only vs. mixed populations vs. family/maternal). Of the 414 eligible articles, 248 reports and 76 protocols were included. In 21 of 24 potential SR reporting items and 13 of 14 potential SR protocol reporting items, less than two thirds of papers met the child-centric reporting item requirements. Mixed population studies displayed significantly poorer reporting in comparison to child-only and family/maternal intervention studies for 11 potential SR reporting items (p < 0.05) and five potential SR protocol items (p < 0.05). When comparing non-Cochrane to Cochrane reports and protocols, five items in both lists were found to perform significantly poorer in non-Cochrane reports (p < 0.05). Significant differences in reporting quality were found in three of 14 items shared between the potential SR reporting items and potential SR protocol reporting items (p < 0.05). Newborn and child health systematic reviews and meta-analyses exhibit incomplete reporting, thereby hindering prudent decision-making by healthcare providers and policy makers. These results provide a rationale for the implementation of child-centric extensions and modifications to current PRISMA and PRISMA-P, such as to improve reporting in this population.

ASSESSMENT OF DE-71, A COMMERCIAL POLYBROMINATED DIPHENYL ETHER (PBDE) MIXTURE, IN THE EDSP MALE AND FEMALE PUBERTAL PROTOCOLS

EPA Science Inventory

DE-71, a commercial mixture, was used to test the sensitivity of the female and male pubertal protocol to detect thyroid active chemicals. These protocols are being evaluated for the U.S. EPA's Endocrine Disruptor Screening Program as part of a Tier I Screening Battery. To exa...

Mass spectrometry-based carboxyl footprinting of proteins: Method evaluation

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

Zhang, Hao; Wen, Jianzhong; Huang, Richard Y-C.

2012-02-01

Protein structure determines function in biology, and a variety of approaches have been employed to obtain structural information about proteins. Mass spectrometry-based protein footprinting is one fast-growing approach. One labeling-based footprinting approach is the use of a water-soluble carbodiimide, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and glycine ethyl ester (GEE) to modify solvent-accessible carboxyl groups on glutamate (E) and aspartate (D). This paper describes method development of carboxyl-group modification in protein footprinting. The modification protocol was evaluated by using the protein calmodulin as a model. Because carboxyl-group modification is a slow reaction relative to protein folding and unfolding, there is an issue that modificationsmore » at certain sites may induce protein unfolding and lead to additional modification at sites that are not solvent-accessible in the wild-type protein. We investigated this possibility by using hydrogen deuterium amide exchange (H/DX). The study demonstrated that application of carboxyl group modification in probing conformational changes in calmodulin induced by Ca{sup 2+} binding provides useful information that is not compromised by modification-induced protein unfolding.« less

Polydopamine-mediated surface modification of scaffold materials for human neural stem cell engineering.

PubMed

Yang, Kisuk; Lee, Jung Seung; Kim, Jin; Lee, Yu Bin; Shin, Heungsoo; Um, Soong Ho; Kim, Jeong Beom; Park, Kook In; Lee, Haeshin; Cho, Seung-Woo

2012-10-01

Surface modification of tissue engineering scaffolds and substrates is required for improving the efficacy of stem cell therapy by generating physicochemical stimulation promoting proliferation and differentiation of stem cells. However, typical surface modification methods including chemical conjugation or physical absorption have several limitations such as multistep, complicated procedures, surface denaturation, batch-to-batch inconsistencies, and low surface conjugation efficiency. In this study, we report a mussel-inspired, biomimetic approach to surface modification for efficient and reliable manipulation of human neural stem cell (NSC) differentiation and proliferation. Our study demonstrates that polydopamine coating facilitates highly efficient, simple immobilization of neurotrophic growth factors and adhesion peptides onto polymer substrates. The growth factor or peptide-immobilized substrates greatly enhance differentiation and proliferation of human NSCs (human fetal brain-derived NSCs and human induced pluripotent stem cell-derived NSCs) at a level comparable or greater than currently available animal-derived coating materials (Matrigel) with safety issues. Therefore, polydopamine-mediated surface modification can provide a versatile platform technology for developing chemically defined, safe, functional substrates and scaffolds for therapeutic applications of human NSCs. Copyright © 2012 Elsevier Ltd. All rights reserved.

Comparison of some effects of modification of a polylactide surface layer by chemical, plasma, and laser methods

NASA Astrophysics Data System (ADS)

Moraczewski, Krzysztof; Rytlewski, Piotr; Malinowski, Rafał; Żenkiewicz, Marian

2015-08-01

The article presents the results of studies and comparison of selected properties of the modified PLA surface layer. The modification was carried out with three methods. In the chemical method, a 0.25 M solution of sodium hydroxide in water and ethanol was utilized. In the plasma method, a 50 W generator was used, which produced plasma in the air atmosphere under reduced pressure. In the laser method, a pulsed ArF excimer laser with fluency of 60 mJ/cm2 was applied. Polylactide samples were examined by using the following techniques: scanning electron microscopy (SEM), atomic force microscopy (AFM), goniometry and X-ray photoelectron spectroscopy (XPS). Images of surfaces of the modified samples were recorded, contact angles were measured, and surface free energy was calculated. Qualitative and quantitative analyses of chemical composition of the PLA surface layer were performed as well. Based on the survey it was found that the best modification results are obtained using the plasma method.

Expanding the Bioactive Chemical Space of Anthrabenzoxocinones through Engineering the Highly Promiscuous Biosynthetic Modification Steps.

PubMed

Mei, Xianyi; Yan, Xiaoli; Zhang, Hui; Yu, Mingjia; Shen, Guangqing; Zhou, Linjun; Deng, Zixin; Lei, Chun; Qu, Xudong

2018-01-19

Anthrabenzoxocinones (ABXs) including (-)-ABXs and (+)-ABXs are a group of bacterial FabF-specific inhibitors with potent antimicrobial activity of resistant strains. Optimization of their chemical structures is a promising method to develop potent antibiotics. Through biosynthetic investigation, we herein identified and characterized two highly promiscuous enzymes involved in the (-)-ABX structural modification. The promiscuous halogenase and methyltransferase can respectively introduce halogen-modifications into various positions of the ABX scaffolds and methylation to highly diverse substrates. Manipulation of their activity in both of the (-)-ABXs and (+)-ABXs biosyntheses led to the generation of 14 novel ABX analogues of both enantiomers. Bioactivity assessment revealed that a few of the analogues showed significantly improved antimicrobial activity, with the C3-hydroxyl and chlorine substitutions critical for their activity. This study enormously expands the bioactive chemical space of the ABX family and FabF-specific inhibitors. The disclosed broad-selective biosynthetic machineries and structure-activity relationship provide a solid basis for further generation of potent antimicrobial agents.

Control of peptide nanotube diameter by chemical modifications of an aromatic residue involved in a single close contact

PubMed Central

Tarabout, Christophe; Roux, Stéphane; Gobeaux, Frédéric; Fay, Nicolas; Pouget, Emilie; Meriadec, Cristelle; Ligeti, Melinda; Thomas, Daniel; IJsselstijn, Maarten; Besselievre, François; Buisson, David-Alexandre; Verbavatz, Jean-Marc; Petitjean, Michel; Valéry, Céline; Perrin, Lionel; Rousseau, Bernard; Artzner, Franck; Paternostre, Maité; Cintrat, Jean-Christophe

2011-01-01

Supramolecular self-assembly is an attractive pathway for bottom-up synthesis of novel nanomaterials. In particular, this approach allows the spontaneous formation of structures of well-defined shapes and monodisperse characteristic sizes. Because nanotechnology mainly relies on size-dependent physical phenomena, the control of monodispersity is required, but the possibility of tuning the size is also essential. For self-assembling systems, shape, size, and monodispersity are mainly settled by the chemical structure of the building block. Attempts to change the size notably by chemical modification usually end up with the loss of self-assembly. Here, we generated a library of 17 peptides forming nanotubes of monodisperse diameter ranging from 10 to 36 nm. A structural model taking into account close contacts explains how a modification of a few Å of a single aromatic residue induces a fourfold increase in nanotube diameter. The application of such a strategy is demonstrated by the formation of silica nanotubes of various diameters. PMID:21518895

The Integrated Safety-Critical Advanced Avionics Communication and Control (ISAACC) System Concept: Infrastructure for ISHM

NASA Technical Reports Server (NTRS)

Gwaltney, David A.; Briscoe, Jeri M.

2005-01-01

Integrated System Health Management (ISHM) architectures for spacecraft will include hard real-time, critical subsystems and soft real-time monitoring subsystems. Interaction between these subsystems will be necessary and an architecture supporting multiple criticality levels will be required. Demonstration hardware for the Integrated Safety-Critical Advanced Avionics Communication & Control (ISAACC) system has been developed at NASA Marshall Space Flight Center. It is a modular system using a commercially available time-triggered protocol, ?Tp/C, that supports hard real-time distributed control systems independent of the data transmission medium. The protocol is implemented in hardware and provides guaranteed low-latency messaging with inherent fault-tolerance and fault-containment. Interoperability between modules and systems of modules using the TTP/C is guaranteed through definition of messages and the precise message schedule implemented by the master-less Time Division Multiple Access (TDMA) communications protocol. "Plug-and-play" capability for sensors and actuators provides automatically configurable modules supporting sensor recalibration and control algorithm re-tuning without software modification. Modular components of controlled physical system(s) critical to control algorithm tuning, such as pumps or valve components in an engine, can be replaced or upgraded as "plug and play" components without modification to the ISAACC module hardware or software. ISAACC modules can communicate with other vehicle subsystems through time-triggered protocols or other communications protocols implemented over Ethernet, MIL-STD- 1553 and RS-485/422. Other communication bus physical layers and protocols can be included as required. In this way, the ISAACC modules can be part of a system-of-systems in a vehicle with multi-tier subsystems of varying criticality. The goal of the ISAACC architecture development is control and monitoring of safety critical systems of a manned spacecraft. These systems include spacecraft navigation and attitude control, propulsion, automated docking, vehicle health management and life support. ISAACC can integrate local critical subsystem health management with subsystems performing long term health monitoring. The ISAACC system and its relationship to ISHM will be presented.

Chemical modification of uniform soils and soils with high/low plasticity index.

DOT National Transportation Integrated Search

2016-08-01

The addition of chemicals into the subgrade has been widely used during construction to improve the soil properties. The chemicals, often Lime Kiln Dust (LKD) and Portland cement, are added to the soil to improve its workability, compactability and e...

Evaluating Pharmacokinetic and Pharmacodynamic Interactions with Computational Models in Cumulative Risk Assessment

EPA Science Inventory

Simultaneous or sequential exposure to multiple chemicals may cause interactions in the pharmacokinetics (PK) and/or pharmacodynamics (PD) of the individual chemicals. Such interactions can cause modification of the internal or target dose/response of one chemical in the mixture ...

Radiotherapy quality assurance report from children's oncology group AHOD0031

PubMed Central

Dharmarajan, Kavita V.; Friedman, Debra L.; FitzGerald, T.J.; McCarten, Kathleen M.; Constine, Louis S.; Chen, Lu; Kessel, Sandy K.; Iandoli, Matt; Laurie, Fran; Schwartz, Cindy L.; Wolden, Suzanne L.

2016-01-01

Purpose A phase III trial assessing response-based therapy in intermediate-risk Hodgkin lymphoma, mandated real-time central review of involved field radiotherapy and imaging records by a centralized review center to maximize protocol compliance. We report the impact of centralized radiotherapy review upon protocol compliance. Methods Review of simulation films, port films, and dosimetry records was required pre-treatment and after treatment completion. Records were reviewed by study-affiliated or review center-affiliated radiation oncologists. A 6–10% deviation from protocol-specified dose was scored as “minor”; >10% was “major”. A volume deviation was scored as “minor” if margins were less than specified, or “major” if fields transected disease-bearing areas. Interventional review and final compliance review scores were assigned to each radiotherapy case and compared. Results Of 1712 patients enrolled, 1173 underwent IFRT at 256 institutions in 7 countries. An interventional review was performed in 88% and a final review in 98%. Overall, minor and major deviations were found in 12% and 6%, respectively. Among the cases for which ≥ 1 pre-IFRT modification was requested by QARC and subsequently made by the treating institution, 100% were made compliant on final review. In contrast, among the cases for which ≥ 1 modification was requested but not made by the treating institution, 10% were deemed compliant on final review. Conclusion In a large trial with complex treatment pathways and heterogeneous radiotherapy fields, central review was performed in a large percentage of cases pre-IFRT and identified frequent potential deviations in a timely manner. When suggested modifications were performed by the institutions, deviations were almost eliminated. PMID:25670539

40 CFR 455.46 - Pretreatment standards for existing sources (PSES).

Code of Federal Regulations, 2014 CFR

2014-07-01

...) EFFLUENT GUIDELINES AND STANDARDS (CONTINUED) PESTICIDE CHEMICALS Pesticide Chemicals Formulating and... listed in Table 8 to this part 455 (or received a modification by Best Engineering Judgement for...

40 CFR 455.46 - Pretreatment standards for existing sources (PSES).

Code of Federal Regulations, 2011 CFR

2011-07-01

...) EFFLUENT GUIDELINES AND STANDARDS PESTICIDE CHEMICALS Pesticide Chemicals Formulating and Packaging... listed in Table 8 to this part 455 (or received a modification by Best Engineering Judgement for...

40 CFR 455.46 - Pretreatment standards for existing sources (PSES).

Code of Federal Regulations, 2012 CFR

2012-07-01

...) EFFLUENT GUIDELINES AND STANDARDS (CONTINUED) PESTICIDE CHEMICALS Pesticide Chemicals Formulating and... listed in Table 8 to this part 455 (or received a modification by Best Engineering Judgement for...

40 CFR 455.46 - Pretreatment standards for existing sources (PSES).

Code of Federal Regulations, 2010 CFR

2010-07-01

...) EFFLUENT GUIDELINES AND STANDARDS PESTICIDE CHEMICALS Pesticide Chemicals Formulating and Packaging... listed in Table 8 to this part 455 (or received a modification by Best Engineering Judgement for...

Identification of Phosphorylated Proteins on a Global Scale.

PubMed

Iliuk, Anton

2018-05-31

Liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) has enabled researchers to analyze complex biological samples with unprecedented depth. It facilitates the identification and quantification of modifications within thousands of proteins in a single large-scale proteomic experiment. Analysis of phosphorylation, one of the most common and important post-translational modifications, has particularly benefited from such progress in the field. Here, detailed protocols are provided for a few well-regarded, common sample preparation methods for an effective phosphoproteomic experiment. © 2018 by John Wiley & Sons, Inc. Copyright © 2018 John Wiley & Sons, Inc.

The Influence of Chemical Modification on Linker Rotational Dynamics in Metal-Organic Frameworks.

PubMed

Damron, Joshua T; Ma, Jialiu; Kurz, Ricardo; Saalwächter, Kay; Matzger, Adam J; Ramamoorthy, Ayyalusamy

2018-05-21

The robust synthetic flexibility of metal-organic frameworks (MOFs) offers a promising class of tailorable materials, for which the ability to tune specific physicochemical properties is highly desired. This is achievable only through a thorough description of the consequences for chemical manipulations both in structure and dynamics. Magic angle spinning solid-state NMR spectroscopy offers many modalities in this pursuit, particularly for dynamic studies. Herein, we employ a separated-local-field NMR approach to show how specific intraframework chemical modifications to MOF UiO-66 heavily modulate the dynamic evolution of the organic ring moiety over several orders of magnitude. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A quantitative strategy to detect changes in accessibility of protein regions to chemical modification on heterodimerization

PubMed Central

Dreger, Mathias; Leung, Bo Wah; Brownlee, George G; Deng, Tao

2009-01-01

We describe a method for studying quantitative changes in accessibility of surface lysine residues of the PB1 subunit of the influenza RNA polymerase as a result of association with the PA subunit to form a PB1-PA heterodimer. Our method combines two established methods: (i) the chemical modification of surface lysine residues of native proteins by N-hydroxysuccinimidobiotin (NHS-biotin) and (ii) the stable isotope labeling of amino acids in cell culture (SILAC) followed by tryptic digestion and mass spectrometry. By linking the chemical modification with the SILAC methodology for the first time, we obtain quantitative data on chemical modification allowing subtle changes in accessibility to be described. Five regions in the PB1 monomer showed altered reactivity to NHS-biotin when compared with the [PB1-PA] heterodimer. Mutational analysis of residues in two such regions—at K265 and K481 of PB1, which were about three- and twofold, respectively, less accessible to biotinylation in the PB1-PA heterodimer compared with the PB1 monomer, demonstrated that both K265 and K481 were crucial for polymerase function. This novel assay of quantitative profiling of biotinylation patterns (Q-POP assay) highlights likely conformational changes at important functional sites, as observed here for PB1, and may provide information on protein–protein interaction interfaces. The Q-POP assay should be a generally applicable approach and may detect novel functional sites suitable for targeting by drugs. PMID:19517532

Apparatus and methods for detecting chemical permeation

DOEpatents

Vo-Dinh, Tuan

1994-01-01

Apparatus and methods for detecting the permeation of hazardous or toxic chemicals through protective clothing are disclosed. The hazardous or toxic chemicals of interest do not possess the spectral characteristic of luminescence. The apparatus and methods utilize a spectrochemical modification technique to detect the luminescence quenching of an indicator compound which upon permeation of the chemical through the protective clothing, the indicator is exposed to the chemical, thus indicating chemical permeation.

Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function.

PubMed

Väre, Ville Y P; Eruysal, Emily R; Narendran, Amithi; Sarachan, Kathryn L; Agris, Paul F

2017-03-16

RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability of RNAs to play multiple roles in cellular metabolism is made possible by extensive variation in length, conformational dynamics, and the over 100 post-transcriptional modifications. There are several reviews of the biochemical pathways leading to RNA modification, but the physicochemical nature of modified nucleosides and how they facilitate RNA function is of keen interest, particularly with regard to the contributions of modified nucleosides. Transfer RNAs (tRNAs) are the most extensively modified RNAs. The diversity of modifications provide versatility to the chemical and structural environments. The added chemistry, conformation and dynamics of modified nucleosides occurring at the termini of stems in tRNA's cloverleaf secondary structure affect the global three-dimensional conformation, produce unique recognition determinants for macromolecules to recognize tRNAs, and affect the accurate and efficient decoding ability of tRNAs. This review will discuss the impact of specific chemical moieties on the structure, stability, electrochemical properties, and function of tRNAs.

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

Fitzpatrick, L.C.; Goven, A.J.; Muratti-Ortiz, J.F.

Earthworms are ideal soil organisms for use in terrestrial ecotoxicology. As such, several earthworm protocols have been developed for testing toxic potential of chemicals and contaminated soils. Of these, the 48-h filter paper contact (FP) and the 14-d artificial soil exposure (AS) protocols, using mortality (LC50) as the toxic endpoint and Eisenia fetida as the test species, have received the most attention, with the latter being adopted by both OECD and EEC in Europe and the Environmental Protection Agency (USEPA) in the United States. Although the FP technique, adopted by EEC, provides for inexpensive reproducible toxicity screening for chemicals (i.e.more » establishing relative toxicities), it has been criticized for lacking the ecotoxicological relevance of the AS protocol. Choice of earthworm species for laboratory testing also has been controversial. The manure worm, E. fetida, is criticized for not being sufficiently sensitive to chemicals or representative of {open_quotes}typical{close_quotes} earthworms. Lumbricus terrestris and Apporectodea caliginosa have been suggested as more sensitive and ecologically relevant earthworms by Dean-Ross and Martin, respectively. This paper compares the AS and FP protocols in assessing toxicity of cadminum to L. terrestris and E. fetida using LC50s and LC50s. 19 refs., 2 tabs.« less

Strong attachment of circadian pacemaker neurons on modified ultrananocrystalline diamond surfaces.

PubMed

Voss, Alexandra; Wei, HongYing; Zhang, Yi; Turner, Stuart; Ceccone, Giacomo; Reithmaier, Johann Peter; Stengl, Monika; Popov, Cyril

2016-07-01

Diamond is a promising material for a number of bio-applications, including the fabrication of platforms for attachment and investigation of neurons and of neuroprostheses, such as retinal implants. In the current work ultrananocrystalline diamond (UNCD) films were deposited by microwave plasma chemical vapor deposition, modified by UV/O3 treatment or NH3 plasma, and comprehensively characterized with respect to their bulk and surface properties, such as crystallinity, topography, composition and chemical bonding nature. The interactions of insect circadian pacemaker neurons with UNCD surfaces with H-, O- and NH2-terminations were investigated with respect to cell density and viability. The fast and strong attachment achieved without application of adhesion proteins allowed for advantageous modification of dispersion protocols for the preparation of primary cell cultures. Centrifugation steps, which are employed for pelletizing dispersed cells to separate them from dispersing enzymes, easily damage neurons. Now centrifugation can be avoided since dispersed neurons quickly and strongly attach to the UNCD surfaces. Enzyme solutions can be easily washed off without losing many of the dispersed cells. No adverse effects on the cell viability and physiological responses were observed as revealed by calcium imaging. Furthermore, the enhanced attachment of the neurons, especially on the modified UNCD surfaces, was especially advantageous for the immunocytochemical procedures with the cell cultures. The cell losses during washing steps were significantly reduced by one order of magnitude in comparison to controls. In addition, the integration of a titanium grid structure under the UNCD films allowed for individual assignment of physiologically characterized neurons to immunocytochemically stained cells. Thus, employing UNCD surfaces free of foreign proteins improves cell culture protocols and immunocytochemistry with cultured cells. The fast and strong attachment of neurons was attributed to a favorable combination of topography, surface chemistry and wettability. Copyright © 2016 Elsevier B.V. All rights reserved.

Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry.

PubMed

Zhou, Mowei; Wu, Si; Stenoien, David L; Zhang, Zhaorui; Connolly, Lanelle; Freitag, Michael; Paša-Tolić, Ljiljana

2017-01-01

Top-down mass spectrometry is a valuable tool for understanding gene expression through characterization of combinatorial histone post-translational modifications (i.e., histone code). In this protocol, we describe a top-down workflow that employs liquid chromatography (LC) coupled to mass spectrometry (MS), for fast global profiling of changes in histone proteoforms, and apply LCMS top-down approach for comparative analysis of a wild-type and a mutant fungal species. The proteoforms exhibiting differential abundances can be subjected to further targeted studies by other MS or orthogonal (e.g., biochemical) assays. This method can be generally adapted for screening of changes in histone modifications between samples such as wild type vs. mutant or healthy vs. diseased.

Detection and quantification of RNA 2′-O-methylation and pseudouridylation

PubMed Central

Karijolich, John

2016-01-01

RNA-guided RNA modification is a naturally occurring process that introduces 2′-O-methylation and pseudouridylation into rRNA, spliceosomal snRNA and several other types of RNA. The Box C/D ribonucleoproteins (RNP) and Box H/ACA RNP, each containing one unique guide RNA (Box C/D RNA or Box H/ACA RNA) and a set of core proteins, are responsible for 2′-O-methylation and pseudouridylation respectively. Box C/D RNA and Box H/ACA RNA provide the modification specificity through base pairing with their RNA substrate. These post-transcriptional modifications could profoundly alter the properties and functions of substrate RNAs. Thus it is desirable to establish reliable and standardized modification methods to study biological functions of modified nucleotides in RNAs. Here, we present several sensitive and efficient methods and protocols for detecting and quantifying post-transcriptional 2′-O-methylation and pseudouridylation. PMID:26853326

Tools for phospho- and glycoproteomics of plasma membranes.

PubMed

Wiśniewski, Jacek R

2011-07-01

Analysis of plasma membrane proteins and their posttranslational modifications is considered as important for identification of disease markers and targets for drug treatment. Due to their insolubility in water, studying of plasma membrane proteins using mass spectrometry has been difficult for a long time. Recent technological developments in sample preparation together with important improvements in mass spectrometric analysis have facilitated analysis of these proteins and their posttranslational modifications. Now, large scale proteomic analyses allow identification of thousands of membrane proteins from minute amounts of sample. Optimized protocols for affinity enrichment of phosphorylated and glycosylated peptides have set new dimensions in the depth of characterization of these posttranslational modifications of plasma membrane proteins. Here, I summarize recent advances in proteomic technology for the characterization of the cell surface proteins and their modifications. In the focus are approaches allowing large scale mapping rather than analytical methods suitable for studying individual proteins or non-complex mixtures.

Optimization of Native and Formaldehyde iPOND Techniques for Use in Suspension Cells.

PubMed

Wiest, Nathaniel E; Tomkinson, Alan E

2017-01-01

The isolation of proteins on nascent DNA (iPOND) technique developed by the Cortez laboratory allows a previously unparalleled ability to examine proteins associated with replicating and newly synthesized DNA in mammalian cells. Both the original, formaldehyde-based iPOND technique and a more recent derivative, accelerated native iPOND (aniPOND), have mostly been performed in adherent cell lines. Here, we describe modifications to both protocols for use with suspension cell lines. These include cell culture, pulse, and chase conditions that optimize sample recovery in both protocols using suspension cells and several key improvements to the published aniPOND technique that reduce sample loss, increase signal to noise, and maximize sample recovery. Additionally, we directly and quantitatively compare the iPOND and aniPOND protocols to test the strengths and limitations of both. Finally, we present a detailed protocol to perform the optimized aniPOND protocol in suspension cell lines. © 2017 Elsevier Inc. All rights reserved.

Bio-Inspired Nanomaterials: Protein Cage Nano-Architectures

DTIC Science & Technology

2008-04-01

chemical modification of protein cage materials and controlled chemical synthesis under mild biological conditions. High- resolution structural...properties based on a combination of controlled mobility and metal ligand interactions. Using the exterior surface of the CCMV viral cage we have chemically ...follows: Patterning by microplotter was achieved by depositing a preselected antibody solution directly onto chemically activated silicon or gold

Organic synthesis via magnetic attraction: benign and sustainable protocols using magnetic nanoferrites

EPA Science Inventory

Magnetic nano-catalysts have been prepared using simple modification of iron ferrites wherein their quasi-homogeneous state, because of nm size range, facilitates the catalysis process as increased surface is available for reaction; the easy separation of the catalysts by externa...

The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry

PubMed Central

Gaston, Kirk W; Limbach, Patrick A

2014-01-01

The analysis of ribonucleic acids (RNA) by mass spectrometry has been a valuable analytical approach for more than 25 years. In fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from RNA isolated out of biological samples. This review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. Applications of mass spectrometry in the identification, characterization and quantification of modified nucleosides are discussed. At the oligonucleotide level, advances in modern mass spectrometry approaches combined with the standard RNA modification mapping protocol enable the characterization of RNAs of varying lengths ranging from low molecular weight short interfering RNAs (siRNAs) to the extremely large 23 S rRNAs. New variations and improvements to this protocol are reviewed, including top-down strategies, as these developments now enable qualitative and quantitative measurements of RNA modification patterns in a variety of biological systems. PMID:25616408

The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry.

PubMed

Gaston, Kirk W; Limbach, Patrick A

2014-01-01

The analysis of ribonucleic acids (RNA) by mass spectrometry has been a valuable analytical approach for more than 25 years. In fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from RNA isolated out of biological samples. This review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. Applications of mass spectrometry in the identification, characterization and quantification of modified nucleosides are discussed. At the oligonucleotide level, advances in modern mass spectrometry approaches combined with the standard RNA modification mapping protocol enable the characterization of RNAs of varying lengths ranging from low molecular weight short interfering RNAs (siRNAs) to the extremely large 23 S rRNAs. New variations and improvements to this protocol are reviewed, including top-down strategies, as these developments now enable qualitative and quantitative measurements of RNA modification patterns in a variety of biological systems.

Non-Gradient Blue Native Polyacrylamide Gel Electrophoresis.

PubMed

Luo, Xiaoting; Wu, Jinzi; Jin, Zhen; Yan, Liang-Jun

2017-02-02

Gradient blue native polyacrylamide gel electrophoresis (BN-PAGE) is a well established and widely used technique for activity analysis of high-molecular-weight proteins, protein complexes, and protein-protein interactions. Since its inception in the early 1990s, a variety of minor modifications have been made to this gradient gel analytical method. Here we provide a major modification of the method, which we call non-gradient BN-PAGE. The procedure, similar to that of non-gradient SDS-PAGE, is simple because there is no expensive gradient maker involved. The non-gradient BN-PAGE protocols presented herein provide guidelines on the analysis of mitochondrial protein complexes, in particular, dihydrolipoamide dehydrogenase (DLDH) and those in the electron transport chain. Protocols for the analysis of blood esterases or mitochondrial esterases are also presented. The non-gradient BN-PAGE method may be tailored for analysis of specific proteins according to their molecular weight regardless of whether the target proteins are hydrophobic or hydrophilic. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Pull-down Assay to Characterize Ca2+/Calmodulin Binding to Plant Receptor Kinases.

PubMed

Kaufmann, Christine; Sauter, Margret

2017-01-01

Plant receptor-like kinases (RLKs) are regulated by posttranscriptional modification and by interaction with regulatory proteins. A common modification of RLKs is (auto)phosphorylation, and a common regulatory protein is the calcium sensor calmodulin (CaM). We have developed protocols to detect the interaction of an RLK with CaM. The interaction with CaM was shown by bimolecular fluorescence complementation (BiFC) (see Chapter 14) and pull-down assay (this chapter). Both methods offer unique advantages. BiFC is useful in showing interaction of soluble as well as of membrane-bound proteins in planta. Pull-down assays are restricted to soluble proteins and provide in vitro data. The pull-down assay provides the advantage that proteins can be modified prior to binding and that experimental conditions such as the concentration of Ca 2+ or other divalent cations can be controlled. This chapter provides a pull-down protocol to study RLK-CaM interaction with optional steps to investigate the impact of RLK phosphorylation or of Ca 2+ .

Biophysical analysis of the effect of chemical modification by 4-oxononenal on the structure, stability, and function of binding immunoglobulin protein (BiP)

PubMed Central

Shah, Dinen D.; Singh, Surinder M.; Dzieciatkowska, Monika

2017-01-01

Binding immunoglobulin protein (BiP) is a molecular chaperone important for the folding of numerous proteins, which include millions of immunoglobulins in human body. It also plays a key role in the unfolded protein response (UPR) in the endoplasmic reticulum. Free radical generation is a common phenomenon that occurs in cells under healthy as well as under stress conditions such as ageing, inflammation, alcohol consumption, and smoking. These free radicals attack the cell membranes and generate highly reactive lipid peroxidation products such as 4-oxononenal (4-ONE). BiP is a key protein that is modified by 4-ONE. In this study, we probed how such chemical modification affects the biophysical properties of BiP. Upon modification, BiP shows significant tertiary structural changes with no changes in its secondary structure. The protein loses its thermodynamic stability, particularly, that of the nucleotide binding domain (NBD) where ATP binds. In terms of function, the modified BiP completely loses its ATPase activity with decreased ATP binding affinity. However, modified BiP retains its immunoglobulin binding function and its chaperone activity of suppressing non-specific protein aggregation. These results indicate that 4-ONE modification can significantly affect the structure-function of key proteins such as BiP involved in cellular pathways, and provide a molecular basis for how chemical modifications can result in the failure of quality control mechanisms inside the cell. PMID:28886061

40 CFR 766.1 - Scope and purpose.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ascertain whether certain specified chemical substances may be contaminated with halogenated dibenzodioxins... TSCA, 15 U.S.C. 2607. (b) Section 766.35(b) requires manufacturers and processors of chemical... chemical substances for concentrations of HDDs/HDFs, applicable protocols, and the results of the analysis...

Assuring the Safety of Chemicals through Improved Exposure Science

EPA Science Inventory

Thousands of chemicals are currently in commercial use and hundreds more are introduced each year. Of these, only a small fraction has been assessed adequately for potential risks. Existing chemical testing and exposure measurement protocols are expensive and time consuming. Fu...

Causes of genome instability: the effect of low dose chemical exposures in modern society.

PubMed

Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel; Al-Mulla, Fahd; Al-Temaimi, Rabeah; Amedei, Amedeo; Azqueta, Amaya; Bisson, William H; Brown, Dustin G; Brunborg, Gunnar; Charles, Amelia K; Chen, Tao; Colacci, Annamaria; Darroudi, Firouz; Forte, Stefano; Gonzalez, Laetitia; Hamid, Roslida A; Knudsen, Lisbeth E; Leyns, Luc; Lopez de Cerain Salsamendi, Adela; Memeo, Lorenzo; Mondello, Chiara; Mothersill, Carmel; Olsen, Ann-Karin; Pavanello, Sofia; Raju, Jayadev; Rojas, Emilio; Roy, Rabindra; Ryan, Elizabeth P; Ostrosky-Wegman, Patricia; Salem, Hosni K; Scovassi, A Ivana; Singh, Neetu; Vaccari, Monica; Van Schooten, Frederik J; Valverde, Mahara; Woodrick, Jordan; Zhang, Luoping; van Larebeke, Nik; Kirsch-Volders, Micheline; Collins, Andrew R

2015-06-01

Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus, genome instability can be defined as an enhanced tendency for the genome to acquire mutations; ranging from changes to the nucleotide sequence to chromosomal gain, rearrangements or loss. This review raises the hypothesis that in addition to known human carcinogens, exposure to low dose of other chemicals present in our modern society could contribute to carcinogenesis by indirectly affecting genome stability. The selected chemicals with their mechanisms of action proposed to indirectly contribute to genome instability are: heavy metals (DNA repair, epigenetic modification, DNA damage signaling, telomere length), acrylamide (DNA repair, chromosome segregation), bisphenol A (epigenetic modification, DNA damage signaling, mitochondrial function, chromosome segregation), benomyl (chromosome segregation), quinones (epigenetic modification) and nano-sized particles (epigenetic pathways, mitochondrial function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make scientists aware of the increasing need to unravel the underlying mechanisms via which chemicals at low doses can induce genome instability and thus promote carcinogenesis. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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.

Review of laboratory-based terrestrial bioaccumulation assessment approaches for organic chemicals: Current status and future possibilities.

PubMed

Hoke, Robert; Huggett, Duane; Brasfield, Sandra; Brown, Becky; Embry, Michelle; Fairbrother, Anne; Kivi, Michelle; Paumen, Miriam Leon; Prosser, Ryan; Salvito, Dan; Scroggins, Rick

2016-01-01

In the last decade, interest has been renewed in approaches for the assessment of the bioaccumulation potential of chemicals, principally driven by the need to evaluate large numbers of chemicals as part of new chemical legislation, while reducing vertebrate test organism use called for in animal welfare legislation. This renewed interest has inspired research activities and advances in bioaccumulation science for neutral organic chemicals in aquatic environments. In January 2013, ILSI Health and Environmental Sciences Institute convened experts to identify the state of the science and existing shortcomings in terrestrial bioaccumulation assessment of neutral organic chemicals. Potential modifications to existing laboratory methods were identified, including areas in which new laboratory approaches or test methods could be developed to address terrestrial bioaccumulation. The utility of "non-ecotoxicity" data (e.g., mammalian laboratory data) was also discussed. The highlights of the workshop discussions are presented along with potential modifications in laboratory approaches and new test guidelines that could be used for assessing the bioaccumulation of chemicals in terrestrial organisms. © 2015 SETAC.

Transport Protocols for Wireless Mesh Networks

NASA Astrophysics Data System (ADS)

Eddie Law, K. L.

Transmission control protocol (TCP) provides reliable connection-oriented services between any two end systems on the Internet. With TCP congestion control algorithm, multiple TCP connections can share network and link resources simultaneously. These TCP congestion control mechanisms have been operating effectively in wired networks. However, performance of TCP connections degrades rapidly in wireless and lossy networks. To sustain the throughput performance of TCP connections in wireless networks, design modifications may be required accordingly in the TCP flow control algorithm, and potentially, in association with other protocols in other layers for proper adaptations. In this chapter, we explain the limitations of the latest TCP congestion control algorithm, and then review some popular designs for TCP connections to operate effectively in wireless mesh network infrastructure.

Novel approach for classifying chemicals according to skin sensitizing potency by non-radioisotopic modification of the local lymph node assay.

PubMed

Takeyoshi, Masahiro; Iida, Kenji; Shiraishi, Keiji; Hoshuyama, Satsuki

2005-01-01

The murine local lymph node assay (LLNA) is currently recognized as a stand-alone sensitization test for determining the sensitizing potential of chemicals, and it has the advantage of yielding a quantitative endpoint that can be used to predict the sensitization potency of chemicals. The EC3 has been proposed as a parameter for classifying chemicals according to the sensitization potency. We previously developed a non-radioisotopic endpoint for the LLNA based on 5-bromo-2'-deoxyuridine (BrdU) incorporation (non-RI LLNA), and we are proposing a new procedure to predict the sensitization potency of chemicals based on comparisons with known human contact allergens. Nine chemicals (i.e. diphencyclopropenone, p-phenylenediamine, glutaraldehyde, cinnamicaldehyde, citral, eugenol, isopropyl myristate, propyleneglycol and hexane) categorized as human contact allergen classes 1-5 were tested by the non-RI LLNA with the following reference allergens: 2,4-dinitrochlorobenzene (DNCB) as a class 1 human contact allergen, isoeugenol as a class 2 human contact allergen and alpha-hexylcinnamic aldehyde (HCA) as a class 3 human contact allergen. Consequently, nine test chemicals were almost assigned to their correct allergen class. The results suggested that the new procedure for non-RI LLNA can provide correct sensitization potency data. Sensitization potency data are useful for evaluating the sensitization risk to humans of exposure to new chemical products. Accordingly, this approach would be an effective modification of LLNA with regard to its experimental design. Moreover, this procedure can be applied also to the standard LLNA with radioisotopes and to other modifications of the LLNA. Copyright 2005 John Wiley & Sons, Ltd.

Self-Delivering RNAi Targeting PD-1 Improves Tumor-Specific T Cell Functionality for Adoptive Cell Therapy of Malignant Melanoma.

PubMed

Ligtenberg, Maarten A; Pico de Coaña, Yago; Shmushkovich, Taisia; Yoshimoto, Yuya; Truxova, Iva; Yang, Yuan; Betancur-Boissel, Monica; Eliseev, Alexey V; Wolfson, Alexey D; Kiessling, Rolf

2018-06-06

Adoptive cell therapy (ACT) is becoming a prominent alternative therapeutic treatment for cancer patients relapsing on traditional therapies. In parallel, antibodies targeting immune checkpoint molecules, such as cytotoxic-T-lymphocyte-associated antigen 4 (CTLA-4) and cell death protein 1 pathway (PD-1), are rapidly being approved for multiple cancer types, including as first line therapy for PD-L1-expressing non-small-cell lung cancer. The combination of ACT and checkpoint blockade could substantially boost the efficacy of ACT. In this study, we generated a novel self-delivering small interfering RNA (siRNA) (sdRNA) that knocked down PD-1 expression on healthy donor T cells as well as patient-derived tumor-infiltrating lymphocytes (TIL). We have developed an alternative chemical modification of RNA backbone for improved stability and increased efficacy. Our results show that T cells treated with sdRNA specific for PD-1 had increased interferon γ (IFN-γ) secreting capacity and that this modality of gene expression interference could be utilized in our rapid expansion protocol for production of TIL for therapy. TIL expanded in the presence of PD-1-specific sdRNA performed with increased functionality against autologous tumor as compared to control TIL. This method of introducing RNAi into T cells to modify the expression of proteins could easily be adopted into any ACT protocol and will lead to the exploration of new combination therapies. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Physical modification of palm kernel meal improved available carbohydrate, physicochemical properties and in vitro digestibility in economic freshwater fish.

PubMed

Thongprajukaew, Karun; Yawang, Pinya; Dudae, Lateepah; Bilanglod, Husna; Dumrongrittamatt, Terdtoon; Tantikitti, Chutima; Kovitvadhi, Uthaiwan

2013-12-01

Unavailable carbohydrates are an important limiting factor for utilization of palm kernel meal (PKM) as aquafeed ingredients. The aim of this study was to improve available carbohydrate from PKM. Different physical modifications including water soaking, microwave irradiation, gamma irradiation and electron beam, were investigated in relation to chemical composition, physicochemical properties and in vitro carbohydrate digestibility using digestive enzymes from economic freshwater fish. Modified methods had significant (P < 0.05) effects on chemical composition by decreasing crude fiber and increasing available carbohydrates. Improvements in physicochemical properties of PKM, such as water solubility, microstructure, relative crystallinity and lignocellulosic spectra, were mainly achieved by soaking and microwave irradiation. Carbohydrate digestibility varied among the physical modifications tested (P < 0.05) and three fish species had different abilities to digest PKM. Soaking was the appropriate modification for increasing carbohydrate digestion specifically in Nile tilapia (Oreochromis niloticus), whereas either soaking or microwave irradiation was effective for striped snakehead (Channa striata). For walking catfish (Clarias batrachus), carbohydrate digestibility was similar among raw, soaked and microwave-irradiated PKM. These findings suggest that soaking and microwave irradiation could be practical methods for altering appropriate physicochemical properties of PKM as well as increasing carbohydrate digestibility in select economic freshwater fish. © 2013 Society of Chemical Industry.

Traffic placement policies for a multi-band network

NASA Technical Reports Server (NTRS)

Maly, Kurt J.; Foudriat, E. C.; Game, David; Mukkamala, R.; Overstreet, C. Michael

1990-01-01

Recently protocols were introduced that enable the integration of synchronous traffic (voice or video) and asynchronous traffic (data) and extend the size of local area networks without loss in speed or capacity. One of these is DRAMA, a multiband protocol based on broadband technology. It provides dynamic allocation of bandwidth among clusters of nodes in the total network. A number of traffic placement policies for such networks are proposed and evaluated. Metrics used for performance evaluation include average network access delay, degree of fairness of access among the nodes, and network throughput. The feasibility of the DRAMA protocol is established through simulation studies. DRAMA provides effective integration of synchronous and asychronous traffic due to its ability to separate traffic types. Under the suggested traffic placement policies, the DRAMA protocol is shown to handle diverse loads, mixes of traffic types, and numbers of nodes, as well as modifications to the network structure and momentary traffic overloads.

Articles of protective clothing adapted for deflecting chemical permeation and methods therefor

DOEpatents

Vo-Dinh, Tuan

1996-01-01

Apparatus and methods for detecting the permeation of hazardous or toxic chemicals through protective clothing are disclosed. The hazardous or toxic chemicals of interest do not possess the spectral characteristic of luminescence. The apparatus and methods utilize a spectrochemical modification technique to detect the luminescence quenching of an indicator compound which upon permeation of the chemical through the protective clothing, the indicator is exposed to the chemical, thus indicating chemical permeation.

Chemical Modifications that Affect Nutritional and Functional Properties of Proteins.

ERIC Educational Resources Information Center

Richardson, T.; Kester, J. J.

1984-01-01

Discusses chemical alterations of selected amino acids resulting from environmental effects (photooxidations, pH extremes, thermally induced effects). Also dicusses use of intentional chemical derivatizations of various functional groups in amino acid residue side chains and how recombinant DNA techniques might be useful in structure/function…

Triacetic acid lactone production from Saccharomyces cerevisiae

USDA-ARS?s Scientific Manuscript database

Triacetic acid lactone (TAL) is a potential platform chemical produced from acetyl-CoA and malonyl-CoA by the Gerbera hybrida 2-pyrone synthase (2PS) gene. Studies are ongoing to optimize production, purification, and chemical modification of TAL, which can be used to create the commercial chemicals...

Chemical modification of nanocellulose with canola oil fatty acid methyl ester

Treesearch

Liqing Wei; Umesh P. Agarwal; Kolby C. Hirth; Laurent M. Matuana; Ronald C. Sabo; Nicole M. Stark

2017-01-01

Cellulose nanocrystals (CNCs), produced from dissolving wood pulp, were chemically functionalized by transesterification with canola oil fatty acid methyl ester (CME). CME performs as both the reaction reagent and solvent. Transesterified CNC (CNCFE) was characterized for their chemical structure, morphology, crystalline structure, thermal stability, and hydrophobicity...

Determining the Location of DNA Modification and Mutation Caused by UVB Light in Skin Cancer

DTIC Science & Technology

2013-09-01

we obtain cleavage patterns consistent with the administered UV dosage and that sequencing libraries generated for both yeast and human cells show...understanding the mutations they cause. 15. SUBJECT TERMS UV DNA modification, HeLa cells, Skin Cancer 16. SECURITY CLASSIFICATION OF: 17...of mutations that are caused by UV light in cells and correlate them to modification frequencies. Understanding the initial chemical changes

Effects of covalent modification by 4-hydroxy-2-nonenal on the noncovalent oligomerization of ubiquitin.

PubMed

Grasso, Giuseppe; Axelsen, Paul H

2017-01-01

When lipid membranes containing ω-6 polyunsaturated fatty acyl chains are subjected to oxidative stress, one of the reaction products is 4-hydroxy-2-nonenal (HNE)-a chemically reactive short chain alkenal that can covalently modify proteins. The ubiquitin proteasome system is involved in the clearing of proteins modified by oxidation products such as HNE, but the chemical structure, stability and function of ubiquitin may be impaired by HNE modification. To evaluate this possibility, the susceptibility of ubiquitin to modification by HNE has been characterized over a range of concentrations where ubiquitin forms non-covalent oligomers. Results indicate that HNE modifies ubiquitin at only two of the many possible sites, and that HNE modification at these two sites alters the ubiquitin oligomerization equilibrium. These results suggest that any role ubiquitin may have in clearing proteins damaged by oxidative stress may itself be impaired by oxidative lipid degradation products. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Toxicological features of maleilated polyflavonoids from Pinus radiata (D. Don.) as potential functional additives for biomaterials design.

PubMed

García, Danny E; Medina, Paulina A; Zúñiga, Valentina I

2017-11-01

Polyflavonoids from Pinus radiata (D. Don.) are an abundant natural oligomers highly desirable as renewable chemicals. However, structural modification of polyflavonoids is a viable strategy in order to use such polyphenols as macrobuilding-blocks for biomaterial design. Polyflavonoids were esterified with three five-member cyclic anhydrides (maleic, itaconic, and citraconic) at 20 °C during 24 h in order to diversify physicochemical-, and biological-properties for agricultural, and food-packaging applications. In addition, the influence of the chemical modification, as well as the chemical structure of the grafting on toxicological features was evaluated. Structural features of derivatives were analyzed by spectroscopy (FT-IR and 1 H-NMR), and the degree of substitution was calculated. Toxicological profile was assessed by using three target species in a wide range of concentration (0.01-100 mgL - 1 ). Effect of polyflavonoids on the growth rate (Selenastrum capricornutum), mortality (Daphnia magna), and germination and radicle length (Lactuca sativa) was determined. Chemical modification affects the toxicological profile on the derivatives in a high extent. Results described remarkable differences in function of the target specie. The bioassays indicate differences of the polyflavonoids toxicological profile associated to the chemical structure of the grafting. Results allowed conclude that polyflavonoids from pine bark show slight toxic properties. Copyright © 2017 Elsevier Ltd. All rights reserved.

Isolation and characterization of new lignin streams derived from extractive-ammonia (EA) pretreatment

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

da Costa Sousa, Leonardo; Foston, Marcus; Bokade, Vijay

One of the key challenges facing lignin conversion to fuels and chemicals is related to the level of carbohydrate and ash impurities found in extracted lignin. Structural modifications of lignin may also occur as a result of biomass pretreatment and harsh lignin extraction protocols. Extractive-Ammonia (EA) is a new pretreatment technology that uses liquid ammonia to cleave lignin–carbohydrate complexes, decrystallize cellulose, solubilize lignin, and selectively extract lignin from lignocellulosic biomass, enabling better utilization of both lignin and carbohydrate components in a biorefinery. The EA-based biorefinery produces two different lignin-rich streams, with different properties, that could potentially be upgraded to fuelsmore » and chemicals using green processes. Here, a water/ethanol-based fractionation method was developed to enrich the ammonia-soluble extractives, resulting in a major product stream containing 92% lignin. Detailed characterization of the various streams resulting from EA treatment, including compositional analysis, structural characterization by nuclear magnetic resonance (NMR) spectrometry, elemental analysis, molecular weight analysis, and thermo-gravimetric analysis provides a broad evaluation of the EA-derived lignin product stream structures and properties, assessing their potential for commercial applications. In conclusion, EA-derived lignins preserve much of lignin's functionality, including the sensitive β-aryl ether units. Furthermore, we observed nitrogen incorporation in the lignin-rich streams, notably due to the presence of hydroxycinnamoyl amides formed during ammonia pretreatment.« less

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

Vogt

This report describes a U.S. Department of Energy, (DOE) Chemical and Biological National Security Program project that sought to establish what is known about decontamination of structures, objects, and people following an exposure to chemical or biological materials. Specifically we sought to identify the procedures and protocols used to determine when and how people or buildings are considered ''clean'' following decontamination. To fulfill this objective, the study systematically examined reported decontamination experiences to determine what procedures and protocols are currently employed for decontamination, the timeframe involved to initiate and complete the decontamination process, how the contaminants were identified, the factorsmore » determining when people were (or were not) decontaminated, the problems encountered during the decontamination process, how response efforts of agencies were coordinated, and the perceived social psychological effects on people who were decontaminated or who participated in the decontamination process. Findings and recommendations from the study are intended to aid decision-making and to improve the basis for determining appropriate decontamination protocols for recovery planners and policy makers for responding to chemical and biological events.« less

Effects of air speed and liquid temperature on droplet size

USDA-ARS?s Scientific Manuscript database

Advancements in both application hardware (e.g. nozzles and spray assist devices) and spray modification products have led to a number of products that are specifically designed to maximize the spray deposition and minimize off-target. Testing protocols are being developed to objectively measure sp...

Spray drift reduction evaluations of spray nozzles using a standardized testing protocol

USDA-ARS?s Scientific Manuscript database

The development and testing of drift reduction technologies has come to the forefront of application research in the past few years in the United States. Drift reduction technologies (DRTs) can be spray nozzles, sprayer modifications, spray delivery assistance, spray property modifiers (adjuvants),...

Heterostructures Prepared by Surface Modification of Nanocrystals

ERIC Educational Resources Information Center

Lee, Bo Hyun

2009-01-01

Inorganic nanocrystals (NCs) have drawn the attention from many researchers due to their promising potentials for next generation technologies, from photovoltaics to biological applications. Various types of NCs have become available by synthetic protocols developed in the last two decades. In addition, multicomponent hybrid NCs which can be…

75 FR 10818 - Proposed Modifications to the Harmonized Tariff Schedule of the United States

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-09

... international Harmonized System nomenclature. The Recommendation--the fourth in a series--is part of the WCO's... amendments to the international Convention on the Harmonized Commodity Description and Coding System (Harmonized System), and the Protocol thereto, are recommended by [[Page 10819

Gestational diabetes insipidus, HELLP syndrome and eclampsia in a twin pregnancy: a case report.

PubMed

Woelk, J L; Dombroski, R A; Brezina, P R

2010-02-01

We report a case of eclampsia in a twin pregnancy complicated by HELLP syndrome and diabetes insipidus. This confluence of disease processes suggests that a modification of common magnesium sulfate treatment protocols may be appropriate in a certain subset of patients.

An implementation of the SNR high speed network communication protocol (Receiver part)

NASA Astrophysics Data System (ADS)

Wan, Wen-Jyh

1995-03-01

This thesis work is to implement the receiver pan of the SNR high speed network transport protocol. The approach was to use the Systems of Communicating Machines (SCM) as the formal definition of the protocol. Programs were developed on top of the Unix system using C programming language. The Unix system features that were adopted for this implementation were multitasking, signals, shared memory, semaphores, sockets, timers and process control. The problems encountered, and solved, were signal loss, shared memory conflicts, process synchronization, scheduling, data alignment and errors in the SCM specification itself. The result was a correctly functioning program which implemented the SNR protocol. The system was tested using different connection modes, lost packets, duplicate packets and large data transfers. The contributions of this thesis are: (1) implementation of the receiver part of the SNR high speed transport protocol; (2) testing and integration with the transmitter part of the SNR transport protocol on an FDDI data link layered network; (3) demonstration of the functions of the SNR transport protocol such as connection management, sequenced delivery, flow control and error recovery using selective repeat methods of retransmission; and (4) modifications to the SNR transport protocol specification such as corrections for incorrect predicate conditions, defining of additional packet types formats, solutions for signal lost and processes contention problems etc.

EXPERIMENTAL PROTOCOL FOR DETERMINING PROTOLYSIS REACTION RATE CONSTANTS

EPA Science Inventory

An experimental protocol to determine photolysis rates of chemicals which photolyze relatively rapidly in the gas phase has been developed. This procedure provides a basis for evaluating the relative importance of one atmospheric reaction pathway (i.e., photolysis) for organic su...

Enhanced understanding of the relationship between chemical modification and mechanical properties of wood

Treesearch

Charles R. Frihart; Daniel J. Yelle; John Ralph; Robert J. Moon; Donald S. Stone; Joseph E. Jakes

2008-01-01

Chemical additions to wood often change its bulk properties, which can be determined using conventional macroscopic mechanical tests. However, the controlling interactions between chemicals and wood take place at and below the scale of individual cells and cell walls. To better understand the effects of chemical additions to wood, we have adapted and extended two...

Criteria to assess human oocyte quality after cryopreservation.

PubMed

Coticchio, G; Bonu, M A; Bianchi, V; Flamigni, C; Borini, A

2005-10-01

Oocyte cryopreservation certainly represents one of the most attractive developments in the field of assisted reproduction, with the aim of preserving female fertility and circumventing the ethical and legal drawbacks associated with embryo freezing. Despite the achievement of the first pregnancy from frozen oocytes dating back as early as 1987, since then fewer than 150 pregnancies have been reported. Over a long period of time, application of oocyte storage on a large scale has been prevented by various factors, namely poor post-thaw survival. Fertilization rates remained low even after the introduction of intracytoplasmic sperm injection. Modifications of slow-freezing protocols, mainly based on the increase of the concentration of sucrose used as non-penetrating cryoprotectant (CPA) and the replacement of sodium with choline, appear to have decisively improved survival rates to over 80%. Investigations at the cellular level on thawed oocytes are largely lacking. Fertilization rates have also benefited from protocol modifications, reaching values indistinguishable from those normally obtained with fresh material. Vitrification protocols have also been tested, giving rise to improvements whose reproducibility is still uncertain. Data on the dynamics of fertilization and preimplantation development of embryos derived from frozen oocytes are extremely scarce. At the moment, clinical efficiency of oocyte cryopreservation cannot be precisely assessed because of the lack of controlled studies, although it appears to be considerably lower than that achieved with embryo freezing. In summary, encouraging advances have been made in the field of oocyte cryopreservation, but presently no protocol can ensure standards of success and safety comparable to those guaranteed by embryo storage.

The effect of polymerization mode on monomer conversion, free radical entrapment, and interaction with hydroxyapatite of commercial self-adhesive cements.

PubMed

D'Alpino, Paulo Henrique Perlatti; Silva, Marília Santos; Vismara, Marcus Vinícius Gonçalves; Di Hipólito, Vinicius; Miranda González, Alejandra Hortencia; de Oliveira Graeff, Carlos Frederico

2015-06-01

This study evaluated the degree of conversion, the free radical entrapment, and the chemical interaction of self-adhesive resin cements mixed with pure hydroxyapatite, as a function of the polymerization activation mode among a variety of commercial self-adhesive cements. Four cements (Embrace WetBond, MaxCem Elite, Bifix SE, and RelyX U200) were mixed, combined with hydroxyapatite, dispensed into molds, and distributed into three groups, according to polymerization protocols: IP (photoactivation for 40s); DP (delayed photoactivation, 10 min self-curing plus 40s light-activated); and CA (chemical activation, no light exposure). Infrared (IR) spectra were obtained and monomer conversion (%) was calculated by comparing the aliphatic-to-aromatic IR absorption peak ratio before and after polymerization (n=10). The free radical entrapment values of the resin cements were characterized using Electron Paramagnetic Resonance (EPR) and the concentration of spins (number of spins/mass) calculated (n=3). Values were compared using two-way ANOVA and Tukey's post-hoc test (α=5%). X-ray diffraction (XRD) characterized the crystallinity of hydroxyapatite as a function of the chemical interactions with the resin cements. The tested parameters varied as a function of resin cement and polymerization protocol. Embrace WetBond and RelyX U200 demonstrated dependence on photoactivation (immediate or delayed), whereas MaxCem Elite exhibited dependence on the chemical activation mode. Bifix SE presented the best balance based on the parameters analyzed, irrespective of the activation protocol. Choice of polymerization protocol affects the degree of conversion, free radical entrapment, and the chemical interaction between hydroxyapatite and self-adhesive resin cement mixtures. Copyright © 2015 Elsevier Ltd. All rights reserved.

Periradicular Infiltration of the Cervical Spine: How New CT Scanner Techniques and Protocol Modifications Contribute to the Achievement of Low-Dose Interventions.

PubMed

Elsholtz, Fabian Henry Jürgen; Kamp, Julia Evi-Katrin; Vahldiek, Janis Lucas; Hamm, Bernd; Niehues, Stefan Markus

2018-06-18

 CT-guided periradicular infiltration of the cervical spine is an effective symptomatic treatment in patients with radiculopathy-associated pain syndromes. This study evaluates the robustness and safety of a low-dose protocol on a CT scanner with iterative reconstruction software.  A total of 183 patients who underwent periradicular infiltration therapy of the cervical spine were included in this study. 82 interventions were performed on a new CT scanner with a new intervention protocol using an iterative reconstruction algorithm. Spot scanning was implemented for planning and a basic low-dose setup of 80 kVp and 5 mAs was established during intermittent fluoroscopy. The comparison group included 101 prior interventions on a scanner without iterative reconstruction. The dose-length product (DLP), number of acquisitions, pain reduction on a numeric analog scale, and protocol changes to achieve a safe intervention were recorded.  The median DLP for the whole intervention was 24.3 mGy*cm in the comparison group and 1.8 mGy*cm in the study group. The median pain reduction was -3 in the study group and -2 in the comparison group. A 5 mAs increase in the tube current-time product was required in 5 patients of the study group.  Implementation of a new scanner and intervention protocol resulted in a 92.6 % dose reduction without a compromise in safety and pain relief. The dose needed here is more than 75 % lower than doses used for similar interventions in published studies. An increase of the tube current-time product was needed in only 6 % of interventions.   · The presented ultra-low-dose protocol allows for a significant dose reduction without compromising outcome.. · The protocol includes spot scanning for planning purposes and a basic setup of 80 kVp and 5 mAs.. · The iterative reconstruction algorithm is activated during fluoroscopy.. · Elsholtz FH, Kamp JE, Vahldiek JL et al. Periradicular Infiltration of the Cervical Spine: How New CT Scanner Techniques and Protocol Modifications Contribute to the Achievement of Low-Dose Interventions. Fortschr Röntgenstr 2018; DOI: 10.1055/a-0632-3930. © Georg Thieme Verlag KG Stuttgart · New York.

75 FR 74773 - Mandatory Reporting of Greenhouse Gases: Additional Sources of Fluorinated GHGs

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-01

..., Methods for Estimating Air Emissions from Chemical Manufacturing Facilities; Protocol for Equipment Leak... chemical vapor deposition process (CVD) or other manufacturing processes use N 2 O. Production processes.... N 2 O emissions from chemical vapor deposition and other electronics manufacturing processes...

Identification of Maillard reaction induced chemical modifications on Ara h 1

USDA-ARS?s Scientific Manuscript database

The Maillard reaction is a non-enzymatic glycation reaction between proteins and reducing sugars that can modify nut allergens during thermal processing. These modifications can alter the structural and immunological properties of these allergens, and may result in increased IgE binding. Here, we ...

Encoded libraries of chemically modified peptides.

PubMed

Heinis, Christian; Winter, Greg

2015-06-01

The use of powerful technologies for generating and screening DNA-encoded protein libraries has helped drive the development of proteins as pharmaceutical ligands. However the development of peptides as pharmaceutical ligands has been more limited. Although encoded peptide libraries are typically several orders of magnitude larger than classical chemical libraries, can be more readily screened, and can give rise to higher affinity ligands, their use as pharmaceutical ligands is limited by their intrinsic properties. Two of the intrinsic limitations include the rotational flexibility of the peptide backbone and the limited number (20) of natural amino acids. However these limitations can be overcome by use of chemical modification. For example, the libraries can be modified to introduce topological constraints such as cyclization linkers, or to introduce new chemical entities such as small molecule ligands, fluorophores and photo-switchable compounds. This article reviews the chemistry involved, the properties of the peptide ligands, and the new opportunities offered by chemical modification of DNA-encoded peptide libraries. Copyright © 2015. Published by Elsevier Ltd.

Articles of protective clothing adapted for deflecting chemical permeation and methods there for

DOEpatents

Vo-Dinh, T.

1996-02-27

Apparatus and methods for detecting the permeation of hazardous or toxic chemicals through protective clothing are disclosed. The hazardous or toxic chemicals of interest do not possess the spectral characteristic of luminescence. The apparatus and methods utilize a spectrochemical modification technique to detect the luminescence quenching of an indicator compound which upon permeation of the chemical through the protective clothing, the indicator is exposed to the chemical, thus indicating chemical permeation. 12 figs.

Surface modification of polymers for biocompatibility via exposure to extreme ultraviolet radiation.

PubMed

Inam Ul Ahad; Bartnik, Andrzej; Fiedorowicz, Henryk; Kostecki, Jerzy; Korczyc, Barbara; Ciach, Tomasz; Brabazon, Dermot

2014-09-01

Polymeric biomaterials are being widely used for the treatment of various traumata, diseases and defects in human beings due to ease in their synthesis. As biomaterials have direct interaction with the extracellular environment in the biological world, biocompatibility is a topic of great significance. The introduction or enhancement of biocompatibility in certain polymers is still a challenge to overcome. Polymer biocompatibility can be controlled by surface modification. Various physical and chemical methods (e.g., chemical and plasma treatment, ion implantation, and ultraviolet irradiation etc.) are in use or being developed for the modification of polymer surfaces. However an important limitation in their employment is the alteration of bulk material. Different surface and bulk properties of biomaterials are often desirable for biomedical applications. Because extreme ultraviolet (EUV) radiation penetration is quite limited even in low density mediums, it could be possible to use it for surface modification without influencing the bulk material. This article reviews the degree of biocompatibility of different polymeric biomaterials being currently employed in various biomedical applications, the surface properties required to be modified for biocompatibility control, plasma and laser ablation based surface modification techniques, and research studies indicating possible use of EUV for enhancing biocompatibility. © 2013 Wiley Periodicals, Inc.

Sol–gel synthesis of MCM-41 silicas and selective vapor-phase modification of their surface

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

Roik, N.V., E-mail: roik_nadya@ukr.net; Belyakova, L.A.

2013-11-15

Silica particles with uniform hexagonal mesopore architecture were synthesized by template directed sol–gel condensation of tetraethoxysilane or mixture of tetraethoxysilane and (3-chloropropyl)triethoxysilane in a water–ethanol–ammonia solution. Selective functionalization of exterior surface of parent materials was carried out by postsynthetic treatment of template-filled MCM-41 and Cl-MCM-41 with vapors of (3-chloropropyl)triethoxysilane and 1,2-ethylenediamine in vacuum. The chemical composition of obtained mesoporous silicas was estimated by IR spectroscopy and chemical analysis of surface products of reactions. Characteristics of porous structure of resulting materials were determined from the data of X-ray, low-temperature nitrogen ad-desorption and transmission electron microscopy measurements. Obtained results confirm invariability ofmore » highly ordered mesoporous structure of MCM-41 and Cl-MCM-41 after their selective postsynthetic modification in vapor phase. It was proved that proposed method of vapor-phase functionalization of template-filled starting materials is not accompanied by dissolution of the template and chemical modification of pores surface. This provides preferential localization of grafted functional groups onto the exterior surface of mesoporous silicas. - Graphical abstract: Sol–gel synthesis and postsynthetic chemical modification of template-filled MCM-41 and Cl-MCM-41 with (3-chloropropyl)triethoxysilane and 1,2-ethylenediamine in vapor phase. Display Omitted - Highlights: • Synthesis of MCM-41 silica by template directed sol–gel condensation. • Selective vapor-phase functionalization of template-filled silica particles. • Preferential localization of grafted groups onto the exterior surface of mesoporous silicas.« less

Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective

NASA Technical Reports Server (NTRS)

Gutell, R. R.; Larsen, N.; Woese, C. R.

1994-01-01

The 16S and 23S rRNA higher-order structures inferred from comparative analysis are now quite refined. The models presented here differ from their immediate predecessors only in minor detail. Thus, it is safe to assert that all of the standard secondary-structure elements in (prokaryotic) rRNAs have been identified, with approximately 90% of the individual base pairs in each molecule having independent comparative support, and that at least some of the tertiary interactions have been revealed. It is interesting to compare the rRNAs in this respect with tRNA, whose higher-order structure is known in detail from its crystal structure (36) (Table 2). It can be seen that rRNAs have as great a fraction of their sequence in established secondary-structure elements as does tRNA. However, the fact that the former show a much lower fraction of identified tertiary interactions and a greater fraction of unpaired nucleotides than the latter implies that many of the rRNA tertiary interactions remain to be located. (Alternatively, the ribosome might involve protein-rRNA rather than intramolecular rRNA interactions to stabilize three-dimensional structure.) Experimental studies on rRNA are consistent to a first approximation with the structures proposed here, confirming the basic assumption of comparative analysis, i.e., that bases whose compositions strictly covary are physically interacting. In the exhaustive study of Moazed et al. (45) on protection of the bases in the small-subunit rRNA against chemical modification, the vast majority of bases inferred to pair by covariation are found to be protected from chemical modification, both in isolated small-subunit rRNA and in the 30S subunit. The majority of the tertiary interactions are reflected in the chemical protection data as well (45). On the other hand, many of the bases not shown as paired in Fig. 1 are accessible to chemical attack (45). However, in this case a sizeable fraction of them are also protected against chemical modification (in the isolated rRNA), which suggests that considerable higher-order structure remains to be found (although all of it may not involve base-base interactions and so may not be detectable by comparative analysis). The agreement between the higher-order structure of the small-subunit rRNA and protection against chemical modification is not perfect, however; some bases shown to covary canonically are accessible to chemical modification (45).(ABSTRACT TRUNCATED AT 400 WORDS).

Two Decades into the LCR: What We Do and Still Don’t Know to Solve Lead Problems

EPA Science Inventory

Site selection and sampling protocol biases in LCR samplingunderestimate peak lead and copper concentrations whilemissing erratic lead release episodes resulting from distributionsystem chemical and physical disturbances. Possible sitetargeting and sampling protocol changes could...

Two Decades into the LCR: What We Do and Still Don’t Know to Solve Lead Problems - abstract

EPA Science Inventory

Site selection and sampling protocol biases in LCR samplingunderestimate peak lead and copper concentrations whilemissing erratic lead release episodes resulting from distributionsystem chemical and physical disturbances. Possible sitetargeting and sampling protocol changes could...

Chapter 15: Preparations of entomopathogens and diseased specimens for more detailed study using microscopy

USDA-ARS?s Scientific Manuscript database

The science of Insect Pathology encompasses a diverse assemblage of pathogens from a large and varied group of hosts. Microscopy techniques and protocols for these organisms are complex and varied and often require modifications and adaptations of standard procedures. The objective of this chapter...

Changing feedbacks in the climate-biosphere system

Treesearch

F. Stuart Chapin; James T. Randerson; A. David McGuire; Jonathan A. Foley; Christopher B. Field

2008-01-01

Ecosystems influence climate through multiple pathways, primarily by changing the energy, water, and greenhouse-gas balance of the atmosphere. Consequently, efforts to mitigate climate change through modification of one pathway, as with carbon in the Kyoto Protocol, only partially address the issue of ecosystem-climate interactions. For example, the cooling of climate...

Usability and Instructional Design Heuristics for E-Learning Evaluation.

ERIC Educational Resources Information Center

Reeves, Thomas C.; Benson, Lisa; Elliott, Dean; Grant, Michael; Holschuh, Doug; Kim, Beaumie; Kim, Hyeonjin; Lauber, Erick; Loh, Sebastian

Heuristic evaluation is a methodology for investigating the usability of software originally developed by Nielsen (1993, 2000). Nielsen's protocol was modified and refined for evaluating e-learning programs by participants in a doctoral seminar held at the University of Georgia in 2001. The modifications primarily involved expanding Nielsen's…

76 FR 38457 - Petition for Waiver of Compliance

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-30

...) conducts freight operations on 23 miles of this 33-mile rail line; and presently the only common track use... modifications requested above would follow the existing protocols such as good communication between HVRM and... is under Yard Limit Rules with good visibility conditions. The new petition states that HVRM operates...

Chemical modification

Treesearch

R. M. Rowell

2004-01-01

Wood is a hygroscopic resource that was designed to perform, in nature, in a wet environment. Nature is programmed to recycle wood in a timely way through biological, thermal, aqueous, photochemical, chemical, and mechanical degradations. In simple terms, nature builds wood from carbon dioxide and water and has all the tools to recycle it back to the starting chemicals...

76 FR 76674 - Receipt of Several Pesticide Petitions Filed for Residues of Pesticide Chemicals in or on Various...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-08

... Several Pesticide Petitions Filed for Residues of Pesticide Chemicals in or on Various Commodities AGENCY...: This document announces the Agency's receipt of several initial filings of pesticide petitions requesting the establishment or modification of regulations for residues of pesticide chemicals in or on...

Properties Characterization of Chemically Modified Hemp Hurds

PubMed Central

Stevulova, Nadezda; Cigasova, Julia; Estokova, Adriana; Terpakova, Eva; Geffert, Anton; Kacik, Frantisek; Singovszka, Eva; Holub, Marian

2014-01-01

The effect of chemical treatment of hemp hurds slices in three solutions (EDTA (Ethylenediaminetetraacetic acid), NaOH and Ca(OH)2) on the properties of natural material was discussed in this paper. Changes in the morphology, chemical composition and structure as well as thermal stability of hemp hurds before and after their modification were investigated by using FTIR (Fourier transform infrared spectroscopy), XRD (X-ray powder diffraction analysis) and TG (thermogravimetry)/DSC (differential scanning calorimetry). Size exclusion chromatography (SEC) measurements were used for determination of degree of cellulose polymerization of hemp hurd samples. Chemical modification is related to the partial removal of non-cellulosic components of lignin, hemicellulose and pectin as well as waxes from the surface of hemp hurd slices. Another effect of the chemical treatment applied is connected with increasing the crystallinity index of cellulose determined by FTIR and XRD methods. Decrease in degree of cellulose polymerization and polydispersity index in chemically modified hemp hurds compared to the original sample was observed. Increase in thermal stability of treated hemp hurd was found. The most significant changes were observed in alkaline treated hemp hurds by NaOH. PMID:28788294

Microchemical Pen: An Open Microreactor for Region-Selective Surface Modification.

PubMed

Mao, Sifeng; Sato, Chiho; Suzuki, Yuma; Yang, Jianmin; Zeng, Hulie; Nakajima, Hizuru; Yang, Ming; Lin, Jin-Ming; Uchiyama, Katsumi

2016-10-18

Various micro surface-modification approaches including photolithography, dip-pen lithography and ink-jet systems have been developed and used to extend the functionalities of solid surfaces. While those approaches work in the "open space", push-pull systems which work in solutions have recently drawn considerable attention. However, the confining flows performed by push-pull systems have realized only the dispense process, while microscale, region-selective chemical reactions have remained unattainable. This study reports a microchemical pen that enables region-selective chemical reactions for the micro surface modification/patterning. The chemical pen is based on the principle of microfluidic laminar flows and the resulting mixing of reagents by the mutual diffusion. The tiny diffusion layer performs as the working region. This report represents the first demonstration of an open microreactor in which two different reagents react on a real solid sample. The multifunctional characteristics of the microchemical pen are confirmed by different types of reactions in many research areas, including inorganic chemistry, polymer science, electrochemistry and biological sample treatment. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Extensive Chemical Modifications in the Primary Protein Structure of IgG1 Subvisible Particles Are Necessary for Breaking Immune Tolerance.

PubMed

Boll, Björn; Bessa, Juliana; Folzer, Emilien; Ríos Quiroz, Anacelia; Schmidt, Roland; Bulau, Patrick; Finkler, Christof; Mahler, Hanns-Christian; Huwyler, Jörg; Iglesias, Antonio; Koulov, Atanas V

2017-04-03

A current concern with the use of therapeutic proteins is the likely presence of aggregates and submicrometer, subvisible, and visible particles. It has been proposed that aggregates and particles may lead to unwanted increases in the immune response with a possible impact on safety or efficacy. The aim of this study was thus to evaluate the ability of subvisible particles of a therapeutic antibody to break immune tolerance in an IgG1 transgenic mouse model and to understand the particle attributes that might play a role in this process. We investigated the immunogenic properties of subvisible particles (unfractionated, mixed populations, and well-defined particle size fractions) using a transgenic mouse model expressing a mini-repertoire of human IgG1 (hIgG1 tg). Immunization with proteinaceous subvisible particles generated by artificial stress conditions demonstrated that only subvisible particles bearing very extensive chemical modifications within the primary amino acid structure could break immune tolerance in the hIgG1 transgenic mouse model. Protein particles exhibiting low levels of chemical modification were not immunogenic in this model.

CHEMICAL REMOVAL OF BIOMASS FROM WASTE AIR BIOTRICKLING FILTERS: SCREENING CHEMICALS OF POTENTIAL INTEREST. (R825392)

EPA Science Inventory

A protocol was developed to rapidly assess the efficiency of chemical washing for the removal of excess biomass from biotrickling filters for waste air treatment. Although the experiment was performed on a small scale, conditions were chosen to simulate application in full-scale ...

40 CFR 160.135 - Physical and chemical characterization studies.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Physical and chemical characterization...) PESTICIDE PROGRAMS GOOD LABORATORY PRACTICE STANDARDS Protocol for and Conduct of a Study § 160.135 Physical and chemical characterization studies. (a) All provisions of the GLP standards shall apply to physical...

40 CFR 160.135 - Physical and chemical characterization studies.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Physical and chemical characterization...) PESTICIDE PROGRAMS GOOD LABORATORY PRACTICE STANDARDS Protocol for and Conduct of a Study § 160.135 Physical and chemical characterization studies. (a) All provisions of the GLP standards shall apply to physical...

40 CFR 160.135 - Physical and chemical characterization studies.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Physical and chemical characterization...) PESTICIDE PROGRAMS GOOD LABORATORY PRACTICE STANDARDS Protocol for and Conduct of a Study § 160.135 Physical and chemical characterization studies. (a) All provisions of the GLP standards shall apply to physical...

40 CFR 160.135 - Physical and chemical characterization studies.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Physical and chemical characterization...) PESTICIDE PROGRAMS GOOD LABORATORY PRACTICE STANDARDS Protocol for and Conduct of a Study § 160.135 Physical and chemical characterization studies. (a) All provisions of the GLP standards shall apply to physical...

Evaluating Chemical Dispersant Efficacy In An Experimental Wave Tank: 1, Dispersant Effectiveness As A Function Of Energy Dissipation Rate

EPA Science Inventory

Numerous laboratory test systems have been developed for the comparison of efficacy between various chemical oil dispersant formulations. However, for the assessment of chemical dispersant effectiveness under realistic sea state, test protocols are required to produce hydrodynam...

Chemical modifications and bioconjugate reactions of nanomaterials for sensing, imaging, drug delivery and therapy.

PubMed

Biju, Vasudevanpillai

2014-02-07

As prepared nanomaterials of metals, semiconductors, polymers and carbon often need surface modifications such as ligand exchange, and chemical and bioconjugate reactions for various biosensor, bioanalytical, bioimaging, drug delivery and therapeutic applications. Such surface modifications help us to control the physico-chemical, toxicological and pharmacological properties of nanomaterials. Furthermore, introduction of various reactive functional groups on the surface of nanomaterials allows us to conjugate a spectrum of contrast agents, antibodies, peptides, ligands, drugs and genes, and construct multifunctional and hybrid nanomaterials for the targeted imaging and treatment of cancers. This tutorial review is intended to provide an introduction to newcomers about how chemical and bioconjugate reactions transform the surface of nanomaterials such as silica nanoparticles, gold nanoparticles, gold quantum clusters, semiconductor quantum dots, carbon nanotubes, fullerene and graphene, and accordingly formulate them for applications such as biosensing, bioimaging, drug and gene delivery, chemotherapy, photodynamic therapy and photothermal therapy. Nonetheless, controversial reports and our growing concerns about toxicity and pharmacokinetics of nanomaterials suggest the need for not only rigorous in vivo experiments in animal models but also novel nanomaterials for practical applications in the clinical settings. Further reading of original and review articles cited herein is necessary to buildup in-depth knowledge about the chemistry, bioconjugate chemistry and biological applications of individual nanomaterials.

Fixation Strategies For Retinal Immunohistochemistry

PubMed Central

Stradleigh, Tyler W.; Ishida, Andrew T.

2015-01-01

Immunohistochemical and ex vivo anatomical studies have provided many glimpses of the variety, distribution, and signaling components of vertebrate retinal neurons. The beauty of numerous images published to date, and the qualitative and quantitative information they provide, indicate that these approaches are fundamentally useful. However, obtaining these images entailed tissue handling and exposure to chemical solutions that differ from normal extracellular fluid in composition, temperature, and osmolarity. Because the differences are large enough to alter intercellular and intracellular signaling in neurons, and because retinae are susceptible to crush, shear, and fray, it is natural to wonder if immunohistochemical and anatomical methods disturb or damage the cells they are designed to examine. Tissue fixation is typically incorporated to guard against this damage and is therefore critically important to the quality and significance of the harvested data. Here, we describe mechanisms of fixation; advantages and disadvantages of using formaldehyde and glutaraldehyde as fixatives during immunohistochemistry; and modifications of widely used protocols that have recently been found to improve cell shape preservation and immunostaining patterns, especially in proximal retinal neurons. PMID:25892361

Study of sporadical properties of crosslinked polyelectrolyte multilayers

NASA Astrophysics Data System (ADS)

Balu, Deebika

Polyelectrolyte multilayers (PEM) have become a highly studied class of materials due to the range of their applicability in many areas of research, including biology, chemistry and materials science. Recent advances in surface coatings have enabled modification of PEM surfaces to provide desirable properties such as controlled release, super-hydrophobicity, biocompatibility, antifouling and antibacterial properties. In the past decade, antimicrobial PEM coatings have been investigated as a safer alternative to the traditional disinfection methods that usually involve application of hazardous chemicals onto the surface to be cleaned. These antimicrobial coatings could be applied to common surfaces prone to colonization of bacteria (such as bench tops, faucet handles, etc) to supplement routine sanitization protocols by providing sustained antimicrobial activity. Vegetative bacteria (such as Escherichia coli) are more susceptible to antimicrobial agents than bacterial species that form spores. Hence, the antimicrobial activity of PEM coatings fabricated using Layer by Layer (LbL) technique were assayed using Bacillus anthracis spores (Sterne strain). In this thesis, the sporicidal effect of various polyelectrolyte multilayer coatings containing cross-linked polymers immersed in bleach have been evaluated as potential augmentation to existing disinfection methods.

9-Fluorenylmethyl (Fm) Disulfides: Biomimetic Precursors for Persulfides

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

Park, Chung-Min; Johnson, Brett A.; Duan, Jicheng

Protein S-sulfhydration has been recognized as an important post-translational modification that regulates H2S signals. However, the reactivity and biological implications of the products of S-sulfhydration, i.e. persulfides, are still unclear. This is mainly due to the instability of persulfides and difficulty to access these molecules. Under physiological conditions persulfides mainly exist in anionic forms because of their low pKa values. However, current methods do not allow for the direct generation of persulfide anions under biomimetic and non-H2S conditions. Herein we report the development of a functional disulfide, FmSSPy-A (Fm =9-fluorenylmethyl; Py = pyridinyl). This reagent can effectively convert both smallmore » molecule and protein thiols (-SH) to form –S-SFm adducts under mild conditions. It allows for a H2S-free and biomimetic protocol to generate highly reactive persulfides (in their anionic forms). We also demonstrated the high nucleophilicity of persulfides toward a number of thiol-blocking reagents. This method holds promise for further understanding the chemical biology of persulfides and S-sulfhydration.« less

Design of S-Allylcysteine in Situ Production and Incorporation Based on a Novel Pyrrolysyl-tRNA Synthetase Variant.

PubMed

Exner, Matthias P; Kuenzl, Tilmann; To, Tuyet Mai T; Ouyang, Zhaofei; Schwagerus, Sergej; Hoesl, Michael G; Hackenberger, Christian P R; Lensen, Marga C; Panke, Sven; Budisa, Nediljko

2017-01-03

The noncanonical amino acid S-allyl cysteine (Sac) is one of the major compounds of garlic extract and exhibits a range of biological activities. It is also a small bioorthogonal alkene tag capable of undergoing controlled chemical modifications, such as photoinduced thiol-ene coupling or Pd-mediated deprotection. Its small size guarantees minimal interference with protein structure and function. Here, we report a simple protocol efficiently to couple in-situ semisynthetic biosynthesis of Sac and its incorporation into proteins in response to amber (UAG) stop codons. We exploited the exceptional malleability of pyrrolysyl-tRNA synthetase (PylRS) and evolved an S-allylcysteinyl-tRNA synthetase (SacRS) capable of specifically accepting the small, polar amino acid instead of its long and bulky aliphatic natural substrate. We succeeded in generating a novel and inexpensive strategy for the incorporation of a functionally versatile amino acid. This will help in the conversion of orthogonal translation from a standard technique in academic research to industrial biotechnology. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biogenic unmodified gold nanoparticles for selective and quantitative detection of cerium using UV-vis spectroscopy and photon correlation spectroscopy (DLS).

PubMed

Priyadarshini, E; Pradhan, N; Panda, P K; Mishra, B K

2015-06-15

The ability of self-functionalized biogenic GNPs towards highly selective colorimetric detection of rare earth element cerium is being reported for the first time. GNPs underwent rapid aggregation on addition of cerium indicated by red shift of SPR peak followed by complete precipitation. Hereby, this concept of co-ordination of cerium ions onto the GNP surface has been utilized for detection of cerium. The remarkable capacity of GNPs to sensitively detect Ce without proves beneficial compared to previous reports of colorimetric sensing. MDL was 15 and 35 ppm by DLS and UV-vis spectroscopy respectively, suggesting DLS to be highly sensitive and a practical alternative in ultrasensitive detection studies. The sensing system showed a good linear fit favouring feasible detection of cerium in range of 2-50 ppm. Similar studies further showed the superior selectivity of biogenic GNPs compared to chemically synthesized counterparts. The sensing system favours on-site analysis as it overcomes need of complex instrumentation, lengthy protocols and surface modification of GNP. Copyright © 2015 Elsevier B.V. All rights reserved.

In vitro evaluation of digestive and endolysosomal enzymes to cleave CML-modified Ara h 1 peptides

USDA-ARS?s Scientific Manuscript database

The sensory, biological, chemical, and immunological characteristics of foods can be modified non-enzymatically during processing. Notably, these modifications may modulate the allergenic potency of food allergens, such as the Ara h 1 peanut allergen. Carboxymethyl-lysine (CML) modification is a p...

Chemical Modification of Papain and Subtilisin: An Active Site Comparison

ERIC Educational Resources Information Center

St-Vincent, Mireille; Dickman, Michael

2004-01-01

An experiment using methyle methanethiosulfonate (MMTS) and phenylmethylsulfonyl flouride (PMSF) to specifically modify the cysteine and serine residues in the active sites of papain and subtilism respectively is demonstrated. The covalent modification of these enzymes and subsequent rescue of papain shows the beginning biochemist that proteins…

Improvement of activity and stability of chloroperoxidase by chemical modification

PubMed Central

Liu, Jian-Zhong; Wang, Min

2007-01-01

Background Enzymes show relative instability in solvents or at elevated temperature and lower activity in organic solvent than in water. These limit the industrial applications of enzymes. Results In order to improve the activity and stability of chloroperoxidase, chloroperoxidase was modified by citraconic anhydride, maleic anhydride or phthalic anhydride. The catalytic activities, thermostabilities and organic solvent tolerances of native and modified enzymes were compared. In aqueous buffer, modified chloroperoxidases showed similar Km values and greater catalytic efficiencies kcat/Km for both sulfoxidation and oxidation of phenol compared to native chloroperoxidase. Of these modified chloroperoxidases, citraconic anhydride-modified chloroperoxidase showed the greatest catalytic efficiency in aqueous buffer. These modifications of chloroperoxidase increased their catalytic efficiencies for sulfoxidation by 12%~26% and catalytic efficiencies for phenol oxidation by 7%~53% in aqueous buffer. However, in organic solvent (DMF), modified chloroperoxidases had lower Km values and higher catalytic efficiencies kcat/Km than native chloroperoxidase. These modifications also improved their thermostabilities by 1~2-fold and solvent tolerances of DMF. CD studies show that these modifications did not change the secondary structure of chloroperoxidase. Fluorescence spectra proved that these modifications changed the environment of tryptophan. Conclusion Chemical modification of epsilon-amino groups of lysine residues of chloroperoxidase using citraconic anhydride, maleic anhydride or phthalic anhydride is a simple and powerful method to enhance catalytic properties of enzyme. The improvements of the activity and stability of chloroperoxidase are related to side chain reorientations of aromatics upon both modifications. PMID:17511866

Base modification strategies to modulate immune stimulation by an siRNA.

PubMed

Valenzuela, Rachel Anne P; Suter, Scott R; Ball-Jones, Alexi A; Ibarra-Soza, José M; Zheng, Yuxuan; Beal, Peter A

2015-01-19

Immune stimulation triggered by siRNAs is one of the major challenges in the development of safe RNAi-based therapeutics. Within an immunostimulatory siRNA sequence, this hurdle is commonly addressed by using ribose modifications (e.g., 2'-OMe or 2'-F), which results in decreased cytokine production. However, as immune stimulation by siRNAs is a sequence-dependent phenomenon, recognition of the nucleobases by the trigger receptor(s) is also likely. Here, we use the recently published crystal structures of Toll-like receptor 8 (TLR8) bound to small-molecule agonists to generate computational models for ribonucleotide binding by this immune receptor. Our modeling suggested that modification of either the Watson-Crick or Hoogsteen face of adenosine would disrupt nucleotide/TLR8 interactions. We employed chemical synthesis to alter either the Watson-Crick or Hoogsteen face of adenosine and evaluated the effect of these modifications in an siRNA guide strand by measuring the immunostimulatory and RNA interference properties. For the siRNA guide strand tested, we found that modifying the Watson-Crick face is generally more effective at blocking TNFα production in human peripheral blood mononuclear cells (PBMCs) than modification at the Hoogsteen edge. We also observed that modifications near the 5'-end were more effective at blocking cytokine production than those placed at the 3'-end. This work advances our understanding of how chemical modifications can be used to optimize siRNA performance. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical modification of chitosan for efficient gene therapy.

PubMed

Jiang, Hu-Lin; Cui, Peng-Fei; Xie, Rong-Lin; Cho, Chong-Su

2014-01-01

Gene therapy involves the introduction of foreign genetic material into cells in order to exert a therapeutic effect. Successful gene therapy relies on effective vector system. Viral vectors are highly efficient in transfecting cells, but the undesirable complications limit their therapeutic applications. As a natural biopolymer, chitosan has been considered to be a good gene carrier candidate due to its ideal character which combines biocompatibility, low toxicity with high cationic density together. However, the low cell specificity and low transfection efficiency of chitosan as a gene carrier need to be overcome before undertaking clinical trials. This chapter is principally on those endeavors such as chemical modifications using cell-specific ligands and stimuli-response groups as well as penetrating modifications that have been done to increase the performances of chitosan in gene therapy. © 2014 Elsevier Inc. All rights reserved.

Manipulating surface wettability and oil absorbency of diatomite depending on processing and ambient conditions

NASA Astrophysics Data System (ADS)

Özen, İlhan; Şimşek, Süleyman; Okyay, Gamze

2015-03-01

In this study, a diatomite sample, which is a natural inorganic mineral with inherently high water and oil absorption capacity, was subjected to grinding before surface modification. Afterwards, the diatomite surface was modified via facile methods using a fluorocarbon (FC) chemical and stearic acid (SA) in addition to the sol-gel fluorosilanization (FS) process. The water and oil wettability, and oil absorbency properties of the unmodified and modified diatomites were investigated in addition to diatomite characterizations such as chemical content, surface area, particle size distribution, morphology, and modification efficiency. It was revealed that the wettability was changed completely depending on the surface modification agent and the media used, while the oil absorbency property surprisingly did not change. On the other hand, the oil absorbency was worsened by the grinding process, whereas the wettability was not affected.

Chemical modification of the cocoa shell surface using diazonium salts.

PubMed

Fioresi, Flavia; Vieillard, Julien; Bargougui, Radhouane; Bouazizi, Nabil; Fotsing, Patrick Nkuigue; Woumfo, Emmanuel Djoufac; Brun, Nicolas; Mofaddel, Nadine; Le Derf, Franck

2017-05-15

The outer portion of the cocoa bean, also known as cocoa husk or cocoa shell (CS), is an agrowaste material from the cocoa industry. Even though raw CS is used as food additive, garden mulch, and soil conditioner or even burnt for fuel, this biomass material has hardly ever been investigated for further modification. This article proposes a strategy of chemical modification of cocoa shell to add value to this natural material. The study investigates the grafting of aryl diazonium salt on cocoa shell. Different diazonium salts were grafted on the shell surface and characterized by infrared spectroscopy and scanning electronic microscopy imaging. Strategies were developed to demonstrate the spontaneous grafting of aryl diazonium salt on cocoa shell and to elucidate that lignin is mainly involved in immobilizing the phenyl layer. Copyright © 2017 Elsevier Inc. All rights reserved.

Impact of a lung transplantation donor-management protocol on lung donation and recipient outcomes.

PubMed

Angel, Luis F; Levine, Deborah J; Restrepo, Marcos I; Johnson, Scott; Sako, Edward; Carpenter, Andrea; Calhoon, John; Cornell, John E; Adams, Sandra G; Chisholm, Gary B; Nespral, Joe; Roberson, Ann; Levine, Stephanie M

2006-09-15

One of the limitations associated with lung transplantation is the lack of available organs. To determine whether a lung donor-management protocol could increase the number of lungs for transplantation without affecting the survival rates of the recipients. We implemented the San Antonio Lung Transplant protocol for managing potential lung donors according to modifications of standard criteria for donor selection and strategies for donor management. We then compared information gathered during a 4-yr period, during which the protocol was used with information gathered during a 4-yr period before protocol implementation. Primary outcome measures were the procurement rate of lungs and the 30-d and 1-yr survival rates of recipients. We reviewed data from 711 potential lung donors. The mean rate of lung procurement was significantly higher (p < 0.0001) during the protocol period (25.5%) than during the pre-protocol period (11.5%), with an estimated risk ratio of 2.2 in favor of the protocol period. More patients received transplants during the protocol period (n = 121) than during the pre-protocol period (n = 53; p < 0.0001). Of 98 actual lung donors during the protocol period, 53 (54%) had initially been considered poor donors; these donors provided 64 (53%) of the 121 lung transplants. The type of donor was not associated with significant differences in recipients' 30-d and 1-yr survival rates or any clinical measures of adequate graft function. The protocol was associated with a significant increase in the number of lung donors and transplant procedures without compromising pulmonary function, length of stay, or survival of the recipients.

Protocol Design Challenges in the Detection of Awareness in Aware Subjects Using EEG Signals.

PubMed

Henriques, J; Gabriel, D; Grigoryeva, L; Haffen, E; Moulin, T; Aubry, R; Pazart, L; Ortega, J-P

2016-10-01

Recent studies have evidenced serious difficulties in detecting covert awareness with electroencephalography-based techniques both in unresponsive patients and in healthy control subjects. This work reproduces the protocol design in two recent mental imagery studies with a larger group comprising 20 healthy volunteers. The main goal is assessing if modifications in the signal extraction techniques, training-testing/cross-validation routines, and hypotheses evoked in the statistical analysis, can provide solutions to the serious difficulties documented in the literature. The lack of robustness in the results advises for further search of alternative protocols more suitable for machine learning classification and of better performing signal treatment techniques. Specific recommendations are made using the findings in this work. © EEG and Clinical Neuroscience Society (ECNS) 2014.

Progress Toward Standards for the Seamless Interoperability of Broadband Satellite Communication Networks

NASA Technical Reports Server (NTRS)

Ivancic, William D.; Glover, Daniel R.; vonDeak, Thomas C.; Bhasin, Kul B.

1998-01-01

The realization of the full potential of the National Information Infrastructure (NH) and Global Information Infrastructure (GII) requires seamless interoperability of emerging satellite networks with terrestrial networks. This requires a cooperative effort between industry, academia and government agencies to develop and advocate new, satellite-friendly communication protocols and modifications to existing communication protocol standards. These groups have recently come together to actively participating in a number of standards making bodies including: the Internet Engineering Task Force (IETF), the Asynchronous Transfer Mode (ATM) Forum, the International Telecommunication Union (ITU) and the Telecommunication Industry Association MA) to ensure that issues regarding efficient use of these protocols over satellite links are not overlooked. This paper will summarize the progress made toward standards development to achieve seamless integration and accelerate the deployment of multimedia applications.

Reply to ``Comment II on `Quantum secret sharing based on reusable Greenberger-Horne-Zeilinger states as secure carriers' ''

NASA Astrophysics Data System (ADS)

Karimipour, V.

2006-07-01

In the preceding Comment [Jian-Zhong Du, Su-Juan Qin, Qiao-Yan Wen, and Fu-Chen Zhu, Phys. Rev. A 74, 016301 (2006)], it has been shown that in a quantum secret sharing protocol proposed in [S. Bagherinezhad and V. Karimipour, Phys. Rev. A 67, 044302 (2003)], one of the receivers can cheat by splitting the entanglement of the carrier and intercepting the secret, without being detected. In this reply we show that a simple modification of the protocol prevents the receivers from this kind of cheating.

Balancing quality and cost for Adult Tobacco Telephone Surveys.

PubMed

Fernandez, Barbara M; Hannah, Kristie M; Wallack, Randal S Zu; Hicks, Jennifer K D; Gorrigan, Anne M; Mariolis, Peter

2007-01-01

To demonstrate the ability to cost-effectively coordinate Adult Tobacco Survey stakeholder interests while reducing the risk of potential bias. Key smoking indicators were compared across 2 surveys and analyzed based on modifications to calling protocols. Mixed results were found when comparing smoking rates across 2 surveys, by early, mid, and late respondents, and by the number of rufusals. Significant cost sayings can be obtained by reducing the number of telephone call attempts. Few significant differences may encourage reductions in protocol, but this must be weighed against the possibility of cost-saving measures resulting in biased estimates.

Risks and benefits of citrate anticoagulation for continuous renal replacement therapy.

PubMed

Shum, H P; Yan, W W; Chan, T M

2015-04-01

Heparin, despite its significant side-effects, is the most commonly used anticoagulant for continuous renal replacement therapy in critical care setting. In recent years, citrate has gained much popularity by improving continuous renal replacement therapy circuit survival and decreasing blood transfusion requirements. However, its complex metabolic consequences warrant modification in the design of the citrate-based continuous renal replacement therapy protocol. With thorough understanding of the therapeutic mechanism of citrate, a simple and practicable protocol can be devised. Citrate-based continuous renal replacement therapy can be safely and widely used in the clinical setting with appropriate clinical staff training.

A Modified Protocol for High-Quality RNA Extraction from Oleoresin-Producing Adult Pines.

PubMed

de Lima, Júlio César; Füller, Thanise Nogueira; de Costa, Fernanda; Rodrigues-Corrêa, Kelly C S; Fett-Neto, Arthur G

2016-01-01

RNA extraction resulting in good yields and quality is a fundamental step for the analyses of transcriptomes through high-throughput sequencing technologies, microarray, and also northern blots, RT-PCR, and RTqPCR. Even though many specific protocols designed for plants with high content of secondary metabolites have been developed, these are often expensive, time consuming, and not suitable for a wide range of tissues. Here we present a modification of the method previously described using the commercially available Concert™ Plant RNA Reagent (Invitrogen) buffer for field-grown adult pine trees with high oleoresin content.

[Giant hernias with loss of domain: what is the best way to prepare patients?].

PubMed

Balaphas, Alexandre; Morel, Philippe; Breguet, Romain; Assalino, Michela

2016-06-15

Giant hernias with loss of domain induce physiological modifications that impair quality of life and make more complex their surgical management. A good preparation of patients before surgery is the key to an eventless postoperative course. The progressive pre-operative pneumoperitoneum (PPP) is one of the described abdominal augmentation protocols which can help patients to tolerate hernia content reintegration and avoid components separation technique during hernia repair. This article describes the management of these complex patients. We also report the case of a patient who follows successfully a PPP protocol.

Immunocytochemical detection of astrocytes in brain slices in combination with Nissl staining.

PubMed

Korzhevskii, D E; Otellin, V A

2005-07-01

The present study was performed to develop a simple and reliable method for the combined staining of specimens to allow the advantages of immunocytochemical detection of astrocytes and assessment of the functional state of neurons by the Nissl method to be assessed simultaneously. The protocol suggested for processing paraffin sections allows preservation of tissue structure at high quality and allows the selective identification of astrocytes with counterstaining of neurons by the Nissl method. The protocol can be used without modification for processing brain specimens from humans and various mammals--except mice and rabbits.

Modification of Keap1 Cysteine Residues by Sulforaphane

PubMed Central

Hu, Chenqi; Eggler, Aimee L.; Mesecar, Andrew D.; van Breemen, Richard B.

2011-01-01

Activation of the transcription factor NF-E2-related factor-2 (Nrf2) through modification of Kelch-like ECH-associated protein 1 (Keap1) cysteines, leading to up-regulation of the antioxidant response element (ARE), is an important mechanism of cellular defense against reactive oxygen species and xenobiotic electrophiles. Sulforaphane, occurring in cruciferous vegetables such as broccoli, is a potent natural ARE activator that functions by modifying Keap1 cysteine residues, but there are conflicting in vitro and in vivo data regarding which of these cysteine residues react. Although most biological data indicate that modification of C151 is essential for sulforaphane action, some recent studies using mass spectrometry have failed to identify C151 as a site of Keap1 sulforaphane reaction. We have reconciled these conflicting data using mass spectrometry with a revised sample preparation protocol and confirmed that C151 is indeed among the most readily modified cysteines of Keap1 by sulforaphane. Previous mass spectrometry-based studies used iodoacetamide during sample preparation to derivatize free cysteine sulfhydryl groups causing loss of sulforaphane from highly reactive and reversible cysteine residues on Keap1 including C151. By omitting iodoacetamide from the protocol and reducing sample preparation time, our mass spectrometry-based studies now confirm previous cell-based studies which showed that sulforaphane reacts with at least four cysteine residues of Keap1 including C151. PMID:21391649

Using Chromatin Immunoprecipitation in Toxicology: A Step-by-Step Guide to Increasing Efficiency, Reducing Variability, and Expanding Applications.

PubMed

McCullough, Shaun D; On, Doan M; Bowers, Emma C

2017-05-02

Histone modifications work in concert with DNA methylation to regulate cellular structure, function, and response to environmental stimuli. More than 130 unique histone modifications have been described to date, and chromatin immunoprecipitation (ChIP) allows for the exploration of their associations with the regulatory regions of target genes and other DNA/chromatin-associated proteins across the genome. Many variations of ChIP have been developed in the 30 years since its earliest version came into use, which makes it challenging for users to integrate the procedure into their research programs. Furthermore, the differences in ChIP protocols can confound efforts to increase reproducibility across studies. The streamlined ChIP procedure presented here can be readily applied to samples from a wide range of in vitro studies (cell lines and primary cells) and clinical samples (peripheral leukocytes) in toxicology. We also provide detailed guidance on the optimization of critical protocol parameters, such as chromatin fixation, fragmentation, and immunoprecipitation, to increase efficiency and improve reproducibility. Expanding toxicoepigenetic studies to more readily include histone modifications will facilitate a more comprehensive understanding of the role of the epigenome in environmental exposure effects and the integration of epigenetic data in mechanistic toxicology, adverse outcome pathways, and risk assessment. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

In situ hybridization protocol for enhanced detection of gene expression in the planarian Schmidtea mediterranea

PubMed Central

2013-01-01

Background The freshwater planarian Schmidtea mediterranea has emerged as a powerful model for studies of regenerative, stem cell, and germ cell biology. Whole-mount in situ hybridization (WISH) and whole-mount fluorescent in situ hybridization (FISH) are critical methods for determining gene expression patterns in planarians. While expression patterns for a number of genes have been elucidated using established protocols, determining the expression patterns for particularly low-abundance transcripts remains a challenge. Results We show here that a short bleaching step in formamide dramatically enhances signal intensity of WISH and FISH. To further improve signal sensitivity we optimized blocking conditions for multiple anti-hapten antibodies, developed a copper sulfate quenching step that virtually eliminates autofluorescence, and enhanced signal intensity through iterative rounds of tyramide signal amplification. For FISH on regenerating planarians, we employed a heat-induced antigen retrieval step that provides a better balance between permeabilization of mature tissues and preservation of regenerating tissues. We also show that azide most effectively quenches peroxidase activity between rounds of development for multicolor FISH experiments. Finally, we apply these modifications to elucidate the expression patterns of a few low-abundance transcripts. Conclusion The modifications we present here provide significant improvements in signal intensity and signal sensitivity for WISH and FISH in planarians. Additionally, these modifications might be of widespread utility for whole-mount FISH in other model organisms. PMID:23497040

Slow histidine H/D exchange protocol for thermodynamic analysis of protein folding and stability using mass spectrometry.

PubMed

Tran, Duc T; Banerjee, Sambuddha; Alayash, Abdu I; Crumbliss, Alvin L; Fitzgerald, Michael C

2012-02-07

Described here is a mass spectrometry-based protocol to study the thermodynamic stability of proteins and protein-ligand complexes using the chemical denaturant dependence of the slow H/D exchange reaction of the imidazole C(2) proton in histidine side chains. The protocol is developed using several model protein systems including: ribonuclease (Rnase) A, myoglobin, bovine carbonic anhydrase (BCA) II, hemoglobin (Hb), and the hemoglobin-haptoglobin (Hb-Hp) protein complex. Folding free energies consistent with those previously determined by other more conventional techniques were obtained for the two-state folding proteins, Rnase A and myoglobin. The protocol successfully detected a previously observed partially unfolded intermediate stabilized in the BCA II folding/unfolding reaction, and it could be used to generate a K(d) value of 0.24 nM for the Hb-Hp complex. The compatibility of the protocol with conventional mass spectrometry-based proteomic sample preparation and analysis methods was also demonstrated in an experiment in which the protocol was used to detect the binding of zinc to superoxide dismutase in the yeast cell lysate sample. The yeast cell sample analyses also helped define the scope of the technique, which requires the presence of globally protected histidine residues in a protein's three-dimensional structure for successful application. © 2011 American Chemical Society

40 CFR 766.28 - Expert review of protocols.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Expert review of protocols. 766.28 Section 766.28 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT DIBENZO-PARA-DIOXINS/DIBENZOFURANS Specific Chemical Testing/Reporting Requirements § 766.28...

Protocol for Microplastics Sampling on the Sea Surface and Sample Analysis

PubMed Central

Kovač Viršek, Manca; Palatinus, Andreja; Koren, Špela; Peterlin, Monika; Horvat, Petra; Kržan, Andrej

2016-01-01

Microplastic pollution in the marine environment is a scientific topic that has received increasing attention over the last decade. The majority of scientific publications address microplastic pollution of the sea surface. The protocol below describes the methodology for sampling, sample preparation, separation and chemical identification of microplastic particles. A manta net fixed on an »A frame« attached to the side of the vessel was used for sampling. Microplastic particles caught in the cod end of the net were separated from samples by visual identification and use of stereomicroscopes. Particles were analyzed for their size using an image analysis program and for their chemical structure using ATR-FTIR and micro FTIR spectroscopy. The described protocol is in line with recommendations for microplastics monitoring published by the Marine Strategy Framework Directive (MSFD) Technical Subgroup on Marine Litter. This written protocol with video guide will support the work of researchers that deal with microplastics monitoring all over the world. PMID:28060297

Protocol for Microplastics Sampling on the Sea Surface and Sample Analysis.

PubMed

Kovač Viršek, Manca; Palatinus, Andreja; Koren, Špela; Peterlin, Monika; Horvat, Petra; Kržan, Andrej

2016-12-16

Microplastic pollution in the marine environment is a scientific topic that has received increasing attention over the last decade. The majority of scientific publications address microplastic pollution of the sea surface. The protocol below describes the methodology for sampling, sample preparation, separation and chemical identification of microplastic particles. A manta net fixed on an »A frame« attached to the side of the vessel was used for sampling. Microplastic particles caught in the cod end of the net were separated from samples by visual identification and use of stereomicroscopes. Particles were analyzed for their size using an image analysis program and for their chemical structure using ATR-FTIR and micro FTIR spectroscopy. The described protocol is in line with recommendations for microplastics monitoring published by the Marine Strategy Framework Directive (MSFD) Technical Subgroup on Marine Litter. This written protocol with video guide will support the work of researchers that deal with microplastics monitoring all over the world.

Apparatus and methods for detecting chemical permeation

DOEpatents

Vo-Dinh, T.

1994-12-27

Apparatus and methods for detecting the permeation of hazardous or toxic chemicals through protective clothing are disclosed. The hazardous or toxic chemicals of interest do not possess the spectral characteristic of luminescence. The apparatus and methods utilize a spectrochemical modification technique to detect the luminescence quenching of an indicator compound which upon permeation of the chemical through the protective clothing, the indicator is exposed to the chemical, thus indicating chemical permeation. The invention also relates to the fabrication of protective clothing materials. 13 figures.

Supramolecular engineering through temperature-induced chemical modification of 2H-tetraphenylporphyrin on Ag(111): flat phenyl conformation and possible dehydrogenation reactions.

PubMed

Di Santo, Giovanni; Blankenburg, Stephan; Castellarin-Cudia, Carla; Fanetti, Mattia; Borghetti, Patrizia; Sangaletti, Luigi; Floreano, Luca; Verdini, Alberto; Magnano, Elena; Bondino, Federica; Pignedoli, Carlo A; Nguyen, Manh-Thuong; Gaspari, Roberto; Passerone, Daniele; Goldoni, Andrea

2011-12-16

Scratching the surface: Formation of a monolayer of 2H-tetraphenylporphyrins (2H-TPP) on Ag(111), either by sublimation of a multilayer in the range 525-600 K or by annealing (at the same temperature) a monolayer deposited at room temperature, induces a chemical modification of the molecules. Rotation of the phenyl rings into a flat conformation is observed and tentatively explained, by using DFT calculations, as a peculiar reaction due to molecular dehydrogenation. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structures, properties, modifications, and uses of oat starch.

PubMed

Zhu, Fan

2017-08-15

There has been increasing interest to utilise oats and their components to formulate healthy food products. Starch is the major component of oat kernels and may account up to 60% of the dry weight. Starch properties may greatly determine the product quality. As a by-product of oat processing and fractionation, the starch may also be utilised for food and non-food applications. This mini-review updates the recent advances in the isolation, chemical and granular structures, physicochemical properties, chemical and physical modifications, and food and non-food uses of oat starch. Copyright © 2017 Elsevier Ltd. All rights reserved.

cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.

PubMed

Martin-Herranz, Daniel E; Ribeiro, António J M; Krueger, Felix; Thornton, Janet M; Reik, Wolf; Stubbs, Thomas M

2017-11-16

DNA methylation is an important epigenetic modification in many species that is critical for development, and implicated in ageing and many complex diseases, such as cancer. Many cost-effective genome-wide analyses of DNA modifications rely on restriction enzymes capable of digesting genomic DNA at defined sequence motifs. There are hundreds of restriction enzyme families but few are used to date, because no tool is available for the systematic evaluation of restriction enzyme combinations that can enrich for certain sites of interest in a genome. Herein, we present customised Reduced Representation Bisulfite Sequencing (cuRRBS), a novel and easy-to-use computational method that solves this problem. By computing the optimal enzymatic digestions and size selection steps required, cuRRBS generalises the traditional MspI-based Reduced Representation Bisulfite Sequencing (RRBS) protocol to all restriction enzyme combinations. In addition, cuRRBS estimates the fold-reduction in sequencing costs and provides a robustness value for the personalised RRBS protocol, allowing users to tailor the protocol to their experimental needs. Moreover, we show in silico that cuRRBS-defined restriction enzymes consistently out-perform MspI digestion in many biological systems, considering both CpG and CHG contexts. Finally, we have validated the accuracy of cuRRBS predictions for single and double enzyme digestions using two independent experimental datasets. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

A comparison of methods for counting viruses in aquatic systems.

PubMed

Bettarel, Y; Sime-Ngando, T; Amblard, C; Laveran, H

2000-06-01

In this study, we compared different methods-including transmission electron microscopy-and various nucleic acid labeling methods in which we used the fluorochromes 4',6'-diamidino-2-phenylindole (DAPI), 4-[3-methyl-2,3-dihydro-(benzo-1, 3-oxazole)-2-methylmethyledene]-1-(3'-trimethyl ammoniumpropyl)-quinilinium diioide (YOPRO-1), and SYBR Green I, which can be detected by epifluorescence microscopy (EM), for counting viruses in samples obtained from freshwater ecosystems whose trophic status varied and from a culture of T7 phages. From a quantitative and qualitative viewpoint, our results showed that the greatest efficiency for all ecosystems was obtained when we used the EM counting protocol in which YOPRO-1 was the label, as this fluorochrome exhibited strong and very stable fluorescence. A modification of the original protocol in which YOPRO-1 was used is recommended, because this modification makes the protocol faster and allows it to be used for routine analysis of fixed samples. Because SYBR Green I fades very quickly, the use of this fluorochrome is not recommended for systems in which the viral content is very high (>10(8) particles/ml), such as treated domestic sewage effluents. Experiments in which we used DNase and RNase revealed that the number of viruses determined by EM was slightly overestimated (by approximately 15%) because of interference caused by the presence of free nucleic acids.

Designing a pain management protocol for craniotomy: A narrative review and consideration of promising practices

PubMed Central

Vacas, Susana; Van de Wiele, Barbara

2017-01-01

Background: Craniotomy is a relatively common surgical procedure with a high incidence of postoperative pain. Development of standardized pain management and enhanced recovery after surgery (ERAS) protocols are necessary and crucial to optimize outcomes and patient satisfaction and reduce health care costs. Methods: This work is based upon a literature search of published manuscripts (between 1996 and 2017) from Pubmed, Cochrane Central Register, and Google Scholar. It seeks to both synthesize and review our current scientific understanding of postcraniotomy pain and its part in neurosurgical ERAS protocols. Results: Strategies to ameliorate craniotomy pain demand interventions during all phases of patient care: preoperative, intraoperative, and postoperative interventions. Pain management should begin in the perioperative period with risk assessment, patient education, and premedication. In the intraoperative period, modifications in anesthesia technique, choice of opioids, acetaminophen and nonsteroidal anti-inflammatory drugs (NSAIDs), regional techniques, dexmedetomidine, ketamine, lidocaine, corticosteroids, and interdisciplinary communication are all strategies to consider and possibly deploy. Opioids remain the mainstay for pain relief, but patient-controlled analgesia, NSAIDs, standardization of pain management, bio/behavioral interventions, modification of head dressings as well as patient-centric management are useful opportunities that potentially improve patient care. Conclusions: Future research on mechanisms, predictors, treatments, and pain management pathways will help define the combinations of interventions that optimize pain outcomes. PMID:29285407

A Comparison of Methods for Counting Viruses in Aquatic Systems

PubMed Central

Bettarel, Yvan; Sime-Ngando, Telesphore; Amblard, Christian; Laveran, Henri

2000-01-01

In this study, we compared different methods—including transmission electron microscopy—and various nucleic acid labeling methods in which we used the fluorochromes 4′,6′-diamidino-2-phenylindole (DAPI), 4-[3-methyl-2,3-dihydro-(benzo-1,3-oxazole)-2-methylmethyledene]-1-(3′-trimethyl ammoniumpropyl)-quinilinium diioide (YOPRO-1), and SYBR Green I, which can be detected by epifluorescence microscopy (EM), for counting viruses in samples obtained from freshwater ecosystems whose trophic status varied and from a culture of T7 phages. From a quantitative and qualitative viewpoint, our results showed that the greatest efficiency for all ecosystems was obtained when we used the EM counting protocol in which YOPRO-1 was the label, as this fluorochrome exhibited strong and very stable fluorescence. A modification of the original protocol in which YOPRO-1 was used is recommended, because this modification makes the protocol faster and allows it to be used for routine analysis of fixed samples. Because SYBR Green I fades very quickly, the use of this fluorochrome is not recommended for systems in which the viral content is very high (>108 particles/ml), such as treated domestic sewage effluents. Experiments in which we used DNase and RNase revealed that the number of viruses determined by EM was slightly overestimated (by approximately 15%) because of interference caused by the presence of free nucleic acids. PMID:10831400

Proposed Modifications of Environmental Protection Agency Method 1601 for Detection of Coliphages in Drinking Water, with Same-Day Fluorescence-Based Detection and Evaluation by the Performance-Based Measurement System and Alternative Test Protocol Validation Approaches▿

PubMed Central

Salter, Robert S.; Durbin, Gregory W.; Conklin, Ernestine; Rosen, Jeff; Clancy, Jennifer

2010-01-01

Coliphages are microbial indicators specified in the Ground Water Rule that can be used to monitor for potential fecal contamination of drinking water. The Total Coliform Rule specifies coliform and Escherichia coli indicators for municipal water quality testing; thus, coliphage indicator use is less common and advances in detection methodology are less frequent. Coliphages are viral structures and, compared to bacterial indicators, are more resistant to disinfection and diffuse further distances from pollution sources. Therefore, coliphage presence may serve as a better predictor of groundwater quality. This study describes Fast Phage, a 16- to 24-h presence/absence modification of U.S. Environmental Protection Agency (EPA) Method 1601 for detection of coliphages in 100 ml water. The objective of the study is to demonstrate that the somatic and male-specific coliphage modifications provide results equivalent to those of Method 1601. Five laboratories compared the modifications, featuring same-day fluorescence-based prediction, to Method 1601 by using the performance-based measurement system (PBMS) criterion. This requires a minimum 50% positive response in 10 replicates of 100-ml water samples at coliphage contamination levels of 1.3 to 1.5 PFU/100 ml. The laboratories showed that Fast Phage meets PBMS criteria with 83.5 to 92.1% correlation of the same-day rapid fluorescence-based prediction with the next-day result. Somatic coliphage PBMS data are compared to manufacturer development data that followed the EPA alternative test protocol (ATP) validation approach. Statistical analysis of the data sets indicates that PBMS utilizes fewer samples than does the ATP approach but with similar conclusions. Results support testing the coliphage modifications by using an EPA-approved national PBMS approach with collaboratively shared samples. PMID:20935123

Proposed modifications of Environmental Protection Agency Method 1601 for detection of coliphages in drinking water, with same-day fluorescence-based detection and evaluation by the performance-based measurement system and alternative test protocol validation approaches.

PubMed

Salter, Robert S; Durbin, Gregory W; Conklin, Ernestine; Rosen, Jeff; Clancy, Jennifer

2010-12-01

Coliphages are microbial indicators specified in the Ground Water Rule that can be used to monitor for potential fecal contamination of drinking water. The Total Coliform Rule specifies coliform and Escherichia coli indicators for municipal water quality testing; thus, coliphage indicator use is less common and advances in detection methodology are less frequent. Coliphages are viral structures and, compared to bacterial indicators, are more resistant to disinfection and diffuse further distances from pollution sources. Therefore, coliphage presence may serve as a better predictor of groundwater quality. This study describes Fast Phage, a 16- to 24-h presence/absence modification of U.S. Environmental Protection Agency (EPA) Method 1601 for detection of coliphages in 100 ml water. The objective of the study is to demonstrate that the somatic and male-specific coliphage modifications provide results equivalent to those of Method 1601. Five laboratories compared the modifications, featuring same-day fluorescence-based prediction, to Method 1601 by using the performance-based measurement system (PBMS) criterion. This requires a minimum 50% positive response in 10 replicates of 100-ml water samples at coliphage contamination levels of 1.3 to 1.5 PFU/100 ml. The laboratories showed that Fast Phage meets PBMS criteria with 83.5 to 92.1% correlation of the same-day rapid fluorescence-based prediction with the next-day result. Somatic coliphage PBMS data are compared to manufacturer development data that followed the EPA alternative test protocol (ATP) validation approach. Statistical analysis of the data sets indicates that PBMS utilizes fewer samples than does the ATP approach but with similar conclusions. Results support testing the coliphage modifications by using an EPA-approved national PBMS approach with collaboratively shared samples.

Dopamine Polymerization in Liquid Marbles: A General Route to Janus Particle Synthesis.

PubMed

Sheng, Yifeng; Sun, Guanqing; Ngai, To

2016-04-05

Coating a liquid with a particle shell not only renders a droplet superhydrophobic but also isolates a well-confined microenvironment for miniaturized chemical processes. Previously, we have demonstrated that particles at the liquid marble interface provide an ideal platform for the site-selective modification of superhydrophobic particles. However, the need for a special chemical reaction limits their potential use for the fabrication of Janus particles with various properties. Herein, we combine the employment of liquid marbles as microreactors with the remarkable adhesive ability of polydopamine to develop a general route for the synthesis of Janus particles from micrometer-sized superhydrophobic particles. We demonstrate that dopamine polymerization and deposition inside liquid marbles could be used for the selective surface modification of microsized silica particles, resulting in the formation of Janus particles. Moreover, it is possible to manipulate the Janus balance of the particles via the addition of surfactants and/or organic solvents to tune the interfacial energy. More importantly, owing to the many functional groups in polydopamine, we show that versatile strategies could be introduced to use these partially polydopamine-coated silica particles as platforms for further modification, including nanoparticle immobilization, metal ion chelation and reduction, as well as for chemical reactions. Given the flexibility in the choice of cores and the modification strategies, this developed method is distinctive in its high universality, good controllability, and great practicability.

Protocols for Late Maxillary Protraction in Cleft Lip and Palate Patients at Childrens Hospital Los Angeles

PubMed Central

Yen, Stephen L-K

2011-01-01

This paper describes the protocols used at Childrens Hospital Los Angeles (CHLA) to protract the maxilla during early adolescence. It is a modification of techniques introduced by Eric Liou with his Alternate Rapid Maxillary Expansion and Constriction (ALT-RAMEC) technique. The main differences between the CHLA protocol and previous maxillary protraction protocols are the age the protraction is attempted, the sutural loosening by alternating weekly expansion with constriction and the use of Class III elastics to support and redirect the protraction by nightly facemask wear. The CHLA protocol entirely depends on patient compliance and must be carefully taught and monitored. In a cooperative patient, the technique can correct a Class III malocclusion that previously would have been treated with LeFort 1 maxillary advancement surgery. Thus, it is not appropriate for patients requiring 2 jaw surgeries to correct mandibular prognathism, occlusal cants or facial asymmetry. The maxillary protraction appears to work by a combination of skeletal advancement, dental compensation and rotation of the occlusal planes. Microscrew/microimplant/temporary anchorage devices have been used with these maxillary protraction protocols to assist in expanding the maxilla, increasing skeletal anchorage during protraction, limiting dental compensations and reducing skeletal relapse. PMID:21765629

Investigation of surface halide modification of nitrile butadiene rubber

NASA Astrophysics Data System (ADS)

Sukhareva, K. V.; Mikhailov, I. A.; Andriasyan, Yu O.; Mastalygina, E. E.; Popov, A. A.

2017-12-01

The investigation is devoted to the novel technology of surface halide modification of rubber samples based on nitrile butadiene rubber (NBR). 1,1,2-trifluoro-1,2,2-trichlorethane was used as halide modifier. The developed technology is characterized by production stages reduction to one by means of treating the rubber compound with a halide modifier. The surface halide modification of compounds based on nitrile butadiene rubber (NBR) was determined to result in increase of resistance to thermal oxidation and aggressive media. The conducted research revealed the influence of modification time on chemical resistance and physical-mechanical properties of rubbers under investigation.

Influence of pyrolysis temperature on lead immobilization by chemically modified coconut fiber-derived biochars in aqueous environments.

PubMed

Wu, Weidong; Li, Jianhong; Niazi, Nabeel Khan; Müller, Karin; Chu, Yingchao; Zhang, Lingling; Yuan, Guodong; Lu, Kouping; Song, Zhaoliang; Wang, Hailong

2016-11-01

Biochar has received widespread attention as an eco-friendly and efficient material for immobilization of toxic heavy metals in aqueous environments. In the present study, three types of coconut fiber-derived biochars were obtained by pyrolyzing at three temperatures, i.e., 300, 500, and 700 °C. In addition, nine types of biochars were prepared by chemical modification with ammonia, hydrogen peroxide, and nitric acid, respectively, which were used to investigate changes in physico-chemical properties by inter alia, Fourier transformation infrared spectrophotometry (FTIR), scanning electron microscope (SEM), and BET specific surface area analysis. Batch sorption experiments were carried out to determine the sorption capacity of the biochars for lead (Pb) in aqueous solutions. Results showed that the cation exchange capacity of biochar pyrolyzed at 300 °C and modified with nitric acid increased threefold compared to the control. Loosely corrugated carbon surface and uneven carbon surface of the biochar pyrolyzed at 300 °C were produced during ammonia and nitric acid modifications. Removal rate of Pb by the coconut biochar pyrolyzed at 300 °C and modified with ammonia was increased from 71.8 to 99.6 % compared to the untreated biochar in aqueous solutions containing 100 mg L -1 Pb. However, chemical modification did not enhance adsorption of Pb of the biochars pyrolyzed at higher temperatures (e.g., 500 or 700 °C), indicating that resistance of biochars to chemical treatment increased with pyrolysis temperature.

Optimized protocols for Mycobacterium leprae strain management: frozen stock preservation and maintenance in athymic nude mice.

PubMed

Trombone, Ana Paula Fávaro; Pedrini, Sílvia Cristina Barbosa; Diório, Suzana Madeira; Belone, Andréa de Faria Fernandes; Fachin, Luciana Raquel Vicenzi; do Nascimento, Dejair Caitano; Rosa, Patricia Sammarco

2014-03-23

Leprosy, caused by Mycobacterium leprae, is an important infectious disease that is still endemic in many countries around the world, including Brazil. There are currently no known methods for growing M. leprae in vitro, presenting a major obstacle in the study of this pathogen in the laboratory. Therefore, the maintenance and growth of M. leprae strains are preferably performed in athymic nude mice (NU-Foxn1(nu)). The laboratory conditions for using mice are readily available, easy to perform, and allow standardization and development of protocols for achieving reproducible results. In the present report, we describe a simple protocol for purification of bacilli from nude mouse footpads using trypsin, which yields a suspension with minimum cell debris and with high bacterial viability index, as determined by fluorescent microscopy. A modification to the standard method for bacillary counting by Ziehl-Neelsen staining and light microscopy is also demonstrated. Additionally, we describe a protocol for freezing and thawing bacillary stocks as an alternative protocol for maintenance and storage of M. leprae strains.

Evaluation of different protein extraction methods for banana (Musa spp.) root proteome analysis by two-dimensional electrophoresis.

PubMed

Vaganan, M Mayil; Sarumathi, S; Nandakumar, A; Ravi, I; Mustaffa, M M

2015-02-01

Four protocols viz., the trichloroacetic acid-acetone (TCA), phenol-ammonium acetate (PAA), phenol/SDS-ammonium acetate (PSA) and trisbase-acetone (TBA) were evaluated with modifications for protein extraction from banana (Grand Naine) roots, considered as recalcitrant tissues for proteomic analysis. The two-dimensional electrophoresis (2-DE) separated proteins were compared based on protein yield, number of resolved proteins, sum of spot quantity, average spot intensity and proteins resolved in 4-7 pI range. The PAA protocol yielded more proteins (0.89 mg/g of tissues) and protein spots (584) in 2-DE gel than TCA and other protocols. Also, the PAA protocol was superior in terms of sum of total spot quantity and average spot intensity than TCA and other protocols, suggesting phenol as extractant and ammonium acetate as precipitant of proteins were the most suitable for banana rooteomics analysis by 2-DE. In addition, 1:3 ratios of root tissue to extraction buffer and overnight protein precipitation were most efficient to obtain maximum protein yield.

Practical quantum private query of blocks based on unbalanced-state Bennett-Brassard-1984 quantum-key-distribution protocol

NASA Astrophysics Data System (ADS)

Wei, Chun-Yan; Gao, Fei; Wen, Qiao-Yan; Wang, Tian-Yin

2014-12-01

Until now, the only kind of practical quantum private query (QPQ), quantum-key-distribution (QKD)-based QPQ, focuses on the retrieval of a single bit. In fact, meaningful message is generally composed of multiple adjacent bits (i.e., a multi-bit block). To obtain a message from database, the user Alice has to query l times to get each ai. In this condition, the server Bob could gain Alice's privacy once he obtains the address she queried in any of the l queries, since each ai contributes to the message Alice retrieves. Apparently, the longer the retrieved message is, the worse the user privacy becomes. To solve this problem, via an unbalanced-state technique and based on a variant of multi-level BB84 protocol, we present a protocol for QPQ of blocks, which allows the user to retrieve a multi-bit block from database in one query. Our protocol is somewhat like the high-dimension version of the first QKD-based QPQ protocol proposed by Jacobi et al., but some nontrivial modifications are necessary.

Practical quantum private query of blocks based on unbalanced-state Bennett-Brassard-1984 quantum-key-distribution protocol

PubMed Central

Wei, Chun-Yan; Gao, Fei; Wen, Qiao-Yan; Wang, Tian-Yin

2014-01-01

Until now, the only kind of practical quantum private query (QPQ), quantum-key-distribution (QKD)-based QPQ, focuses on the retrieval of a single bit. In fact, meaningful message is generally composed of multiple adjacent bits (i.e., a multi-bit block). To obtain a message from database, the user Alice has to query l times to get each ai. In this condition, the server Bob could gain Alice's privacy once he obtains the address she queried in any of the l queries, since each ai contributes to the message Alice retrieves. Apparently, the longer the retrieved message is, the worse the user privacy becomes. To solve this problem, via an unbalanced-state technique and based on a variant of multi-level BB84 protocol, we present a protocol for QPQ of blocks, which allows the user to retrieve a multi-bit block from database in one query. Our protocol is somewhat like the high-dimension version of the first QKD-based QPQ protocol proposed by Jacobi et al., but some nontrivial modifications are necessary. PMID:25518810

Zinc Oxide—From Synthesis to Application: A Review

PubMed Central

Kołodziejczak-Radzimska, Agnieszka; Jesionowski, Teofil

2014-01-01

Zinc oxide can be called a multifunctional material thanks to its unique physical and chemical properties. The first part of this paper presents the most important methods of preparation of ZnO divided into metallurgical and chemical methods. The mechanochemical process, controlled precipitation, sol-gel method, solvothermal and hydrothermal method, method using emulsion and microemulsion enviroment and other methods of obtaining zinc oxide were classified as chemical methods. In the next part of this review, the modification methods of ZnO were characterized. The modification with organic (carboxylic acid, silanes) and inroganic (metal oxides) compounds, and polymer matrices were mainly described. Finally, we present possible applications in various branches of industry: rubber, pharmaceutical, cosmetics, textile, electronic and electrotechnology, photocatalysis were introduced. This review provides useful information for specialist dealings with zinc oxide. PMID:28788596

THE DEVELOPMENT AND INTER-LABORATORY VERIFICATION OF LC-MS LIBRARIES FOR ORGANIC CHEMICALS OF ENVIRONMENTAL CONCERN

EPA Science Inventory

The development, verification, and comparison study between LC-MS libraries for two manufacturers’ instruments and a verified protocol are discussed. The LC-MS library protocol was verified through an inter-laboratory study that involved Federal, State, and private laboratories. ...

Chemical modification : a non-toxic approach to wood preservation

Treesearch

Roger M. Rowell

2006-01-01

Wood can be chemically modified to reduce the moisture content of the cell wall and increases decay resistance. As the level of bonded chemical increases, the cell wall equilibrium moisture content decreases and the resistance to attack by white-and brown-rot fungi increases. There is a direct relationship between the decrease in cell wall moisture Content and...

Chemical modifications of renewable cellulosic materials

USDA-ARS?s Scientific Manuscript database

In agriculture, there is a fair amount of byproducts and waste materials. These materials typically contain significant portions of cellulose and hemicellulose. A good opportunity is to take advantage of these relatively cheap renewable materials, carry out chemical reactions, and increase their v...

Technical modification of the Balb/c 3T3 cell transformation assay: the use of serum-reduced medium to optimise the practicability of the protocol.

PubMed

Hayashi, Kumiko; Sasaki, Kiyoshi; Asada, Shin; Tsuchiya, Toshiyuki; Hayashi, Makoto; Yoshimura, Isao; Tanaka, Noriho; Umeda, Makoto

2008-12-01

The two-stage Balb/c 3T3 model of cell transformation can mimic the two-stage carcinogenicity bioassay, and has been recognised as a screening method for detecting potential tumour initiators and promoters. A technical modification to the original protocol (which involved the use of M10F medium, consisting of MEM plus 10% fetal bovine serum [FBS]) has been previously proposed, in order to increase its efficacy, namely: the introduction of enriched, serum-reduced medium (DF2F medium, comprising DMEM/F12 plus 2% FBS and other supplements). The aim of this study was to further modify the protocol, so as to attain higher practicability for the assay. The protocol was further optimised by: a) reducing the number of plates required, through the use of larger plates; b) reducing the cost of the assay by retaining the reduced serum concentration and by using 2microg/ml insulin, rather than the more-complex insulin-transferrin-ethanolamine-sodium selenite (ITES) supplement (i.e. DF2F2I medium); and c) extending the culture period from 24-25 days to 31-32 days, resulting in clearer foci (the number of medium changes did not increase, as less-frequent medium changes were performed during the extended culture period). Growth curve construction revealed that variations in the saturation densities of the parental Balb/c 3T3 cell line and its three transformed clones were highest when M10F medium was replaced with DF2F2I medium just before cells reached confluence. We applied this newly-optimised protocol to the assessment of: a) the tumour initiating activity of 3-methylcholanthrene (MCA), N-methyl-N'-nitro-N-nitrosoguanidine, mitomycin C, methylmethane sulphonate, CdCl(2) and phenacetin, combining a post-treatment of 100ng/ml 12-O-tetradecanoylphorbol-13-acetate at the promotion stage; and b) the tumour promoting activity of insulin, lithocholic acid, CdCl(2) and phenobarbital, with pre-treatment of 0.2microg/ml MCA at the initiation stage. In the present study, only phenobarbital was negative when tested by using the modified protocol. 2008 FRAME.

Patient-Specific Induced Pluripotent Stem Cell Models: Generation and Characterization of Cardiac Cells.

PubMed

Zanella, Fabian; Sheikh, Farah

2016-01-01

The generation of human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes has been of utmost interest for the study of cardiac development, cardiac disease modeling, and evaluation of cardiotoxic effects of novel candidate drugs. Several protocols have been developed to guide human stem cells toward the cardiogenic path. Pioneering work used serum to promote cardiogenesis; however, low cardiogenic throughputs, lack of chemical definition, and batch-to-batch variability of serum lots constituted a considerable impediment to the implementation of those protocols to large-scale cell biology. Further work focused on the manipulation of pathways that mouse genetics indicated to be fundamental in cardiac development to promote cardiac differentiation in stem cells. Although extremely elegant, those serum-free protocols involved the use of human recombinant cytokines that tend to be quite costly and which can also be variable between lots. The latest generation of cardiogenic protocols aimed for a more cost-effective and reproducible definition of the conditions driving cardiac differentiation, using small molecules to manipulate cardiogenic pathways overriding the need for cytokines. This chapter details methods based on currently available cardiac differentiation protocols for the generation and characterization of robust numbers of hiPSC-derived cardiomyocytes under chemically defined conditions.

Moving away from methyl bromide: political economy of pesticide transition for California strawberries since 2004.

PubMed

Mayfield, Erin N; Norman, Catherine Shelley

2012-09-15

We examine the progress of the phaseout of the use of the pesticide methyl bromide in the production of California field strawberries. This phaseout is required under the Montreal Protocol and has been contentious in this sector, which receives exemptions from the schedule initially agreed under the treaty, and in international negotiations over the future of the Protocol. We examine the various ex-ante predictions of the impacts on growers, consumers and trade patterns in light of several years of declining allocations under the Critical Use provisions of the Protocol and the 2010 approval of iodomethane for use in California and subsequent 2012 withdrawal of this alternative from the US market. We find that, contrary to ex-ante industry claims, the years of declining methyl bromide use have been years of rising yields, acreage, exports, revenues and market share for California growers, even when faced with a global recession and increased imports from Mexican growers who retain the right to use the chemical under the Protocol. This has implications for the Protocol as a whole and for the remainder of the US phaseout of this chemical in particular. Copyright © 2012 Elsevier Ltd. All rights reserved.

Quantitative proteomic characterization of redox-dependent post-translational modifications on protein cysteines

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

Duan, Jicheng; Gaffrey, Matthew J.; Qian, Wei-Jun

Protein cysteine thiols play a crucial role in redox signaling, regulation of enzymatic activity and protein function, and maintaining redox homeostasis in living systems. The unique chemical reactivity of thiol groups makes cysteine susceptible to oxidative modifications by reactive oxygen and nitrogen species to form a broad array of reversible and irreversible protein post-translational modifications (PTMs). The reversible modifications in particular are one of the major components of redox signaling and are involved in regulation of various cellular processes under physiological and pathological conditions. The biological significance of these redox PTMs in health and diseases has been increasingly recognized. Herein,more » we review the recent advances of quantitative proteomic approaches for investigating redox PTMs in complex biological systems, including the general considerations of sample processing, various chemical or affinity enrichment strategies, and quantitative approaches. We also highlight a number of redox proteomic approaches that enable effective profiling of redox PTMs for addressing specific biological questions. Although some technological limitations remain, redox proteomics is paving the way towards a better understanding of redox signaling and regulation in human health and diseases.« less

Incorporation of post-translational modified amino acids as an approach to increase both chemical and biological diversity of conotoxins and conopeptides.

PubMed

Espiritu, Michael J; Cabalteja, Chino C; Sugai, Christopher K; Bingham, Jon-Paul

2014-01-01

Bioactive peptides from Conus venom contain a natural abundance of post-translational modifications that affect their chemical diversity, structural stability, and neuroactive properties. These modifications have continually presented hurdles in their identification and characterization. Early endeavors in their analysis relied on classical biochemical techniques that have led to the progressive development and use of novel proteomic-based approaches. The critical importance of these post-translationally modified amino acids and their specific assignment cannot be understated, having impact on their folding, pharmacological selectivity, and potency. Such modifications at an amino acid level may also provide additional insight into the advancement of conopeptide drugs in the quest for precise pharmacological targeting. To achieve this end, a concerted effort between the classical and novel approaches is needed to completely elucidate the role of post-translational modifications in conopeptide structure and dynamics. This paper provides a reflection in the advancements observed in dealing with numerous and multiple post-translationally modified amino acids within conotoxins and conopeptides and provides a summary of the current techniques used in their identification.

On the Electrodeposition of Ca-P Coatings on Nitinol Alloy: A Comparison Between Different Surface Modification Methods

NASA Astrophysics Data System (ADS)

Etminanfar, M. R.; Khalil-Allafi, J.

2016-02-01

In this study, a combination of surface modification process and the electrochemical deposition of Ca-P coatings was used for the modification of the Nitinol shape memory alloy. DSC, SEM, GIB-XRD, FT-Raman, XPS, and FTIR measurements were performed for the characterization of the samples. Results indicated that chemical etching and boiling of the samples in distilled water formed TiO film on the surface. After the chemical modification, subsequent aging of the sample, at 470 °C for 30 min, converted the oxide film to a stable structure of titanium dioxide. In that case, the treated substrate indicated a superelastic behavior. At the same electrochemical condition, the treated substrate revealed more stable and uniform Ca-P coatings in comparison with the abraded Nitinol substrate. This difference was attributed to the presence of hydroxyl groups on the titanium dioxide surface. Also, after soaking the sample in SBF, the needle-like coating on the treated substrate was completely covered with the hydroxyapatite phase which shows a good bioactivity of the coating.

Role of low density lipoprotein in the activation of plasma lysolecithin acyltransferase activity. Effect of chemical and enzymatic modifications of the lipoprotein on enzyme activity.

PubMed

Subbaiah, P V; Chen, C H; Bagdade, J D; Albers, J J

1985-01-01

The effect of various chemical and enzymatic modifications of low density lipoprotein (LDL) on its ability to activate the isolated human plasma lysolecithin acyltransferase (LAT) was studied. Removal of all lipids from LDL resulted in the complete loss of LAT activation. Removal of only neutral lipids by extraction with heptane retained up to 50% of the original activity, which was not increased further by reconstitution of the LDL with the extracted lipids. Hydrolysis of the diacylphosphoglycerides of the LDL with phospholipases resulted in complete loss of LAT activation which was partially restored by the addition of egg lecithin. Hydrolysis of more than 4% of LDL protein by trypsin led to a linear decrease in activity with complete loss of activity occurring when about 25% of the LDL protein is hydrolyzed. Modification of the arginine groups of LDL reversibly inhibited the activation of LAT. Modification of lysine residues of LDL by acetylation, acetoacetylation or succinylation also abolished its ability to activate lysolecithin acylation.

Structural modifications of polymethacrylates: impact on thermal behavior and release characteristics of glassy solid solutions.

PubMed

Claeys, Bart; De Coen, Ruben; De Geest, Bruno G; de la Rosa, Victor R; Hoogenboom, Richard; Carleer, Robert; Adriaensens, Peter; Remon, Jean Paul; Vervaet, Chris

2013-11-01

Polymethacrylates such as Eudragit® polymers are well established as drug delivery matrix. Here, we synthesize several Eudragit E PO (n-butyl-, dimethylaminoethyl-, methyl-methacrylate-terpolymer) analogues via free radical polymerization. These polymers are processed via hot melt extrusion, followed by injection molding and evaluated as carriers to produce immediate release solid solution tablets. Three chemical modifications increased the glass transition temperature of the polymer: (a) substitution of n-butyl by t-butyl groups, (b) reduction of the dimethylaminoethyl methacrylate (DMAEMA) content, and (c) incorporation of a bulky isobornyl repeating unit. These structural modifications revealed the possibility to increase the mechanical stability of the tablets via altering the polymer Tg without influencing the drug release characteristics and glassy solid solution forming properties. The presence of DMAEMA units proved to be crucial with respect to API/polymer interaction (essential in creating glassy solid solutions) and drug release characteristics. Moreover, these chemical modifications accentuate the need for a more rational design of (methacrylate) polymer matrix excipients for drug formulation via hot melt extrusion and injection molding. Copyright © 2013 Elsevier B.V. All rights reserved.

Chemical Functionalization of Plasmonic Surface Biosensors: A Tutorial Review on Issues, Strategies, and Costs

PubMed Central

2017-01-01

In an ideal plasmonic surface sensor, the bioactive area, where analytes are recognized by specific biomolecules, is surrounded by an area that is generally composed of a different material. The latter, often the surface of the supporting chip, is generally hard to be selectively functionalized, with respect to the active area. As a result, cross talks between the active area and the surrounding one may occur. In designing a plasmonic sensor, various issues must be addressed: the specificity of analyte recognition, the orientation of the immobilized biomolecule that acts as the analyte receptor, and the selectivity of surface coverage. The objective of this tutorial review is to introduce the main rational tools required for a correct and complete approach to chemically functionalize plasmonic surface biosensors. After a short introduction, the review discusses, in detail, the most common strategies for achieving effective surface functionalization. The most important issues, such as the orientation of active molecules and spatial and chemical selectivity, are considered. A list of well-defined protocols is suggested for the most common practical situations. Importantly, for the reported protocols, we also present direct comparisons in term of costs, labor demand, and risk vs benefit balance. In addition, a survey of the most used characterization techniques necessary to validate the chemical protocols is reported. PMID:28796479

Silver nanoparticles with planar twinned defects: effect of halides for precise tuning of plasmon resonance maxima from 400 to >900 nm.

PubMed

Cathcart, Nicole; Frank, Andrew J; Kitaev, Vladimir

2009-12-14

We studied effects of halides on morphology of planar twinned silver nanoparticles and demonstrated application of these effects to precisely tune silver surface plasmon resonance maxima in a broad vis-NIR range using a reliable two-stage modification protocol.

Quantification of protein carbonylation.

PubMed

Wehr, Nancy B; Levine, Rodney L

2013-01-01

Protein carbonylation is the most commonly used measure of oxidative modification of proteins. It is most often measured spectrophotometrically or immunochemically by derivatizing proteins with the classical carbonyl reagent 2,4 dinitrophenylhydrazine (DNPH). We present protocols for the derivatization and quantification of protein carbonylation with these two methods, including a newly described dot blot with greatly increased sensitivity.

Training Anxious Children to Disengage Attention from Threat: A Randomized Controlled Trial

ERIC Educational Resources Information Center

Bar-Haim, Yair; Morag, Inbar; Glickman, Shlomit

2011-01-01

Background: Threat-related attention biases have been implicated in the etiology and maintenance of anxiety disorders. As a result, attention bias modification (ABM) protocols have been employed as treatments for anxious adults. However, they have yet to emerge for children. A randomized, double-blind placebo-controlled trial was conducted to…

Domestic Implementation of a Chemical Weapons Treaty

DTIC Science & Technology

1989-10-01

regulations can be used for treaty comliance; identify producers of certain treaty chemicals and present case studies on two such chemicals; review and...discuss the protocol limitations of using existing statutes for the reporting requirements through case studies of two chemicals for which reporting...requirements or requ.lations can be used to facilitate domestic implementation, studies the domestic implmentation procedures and experience gained fron the

Assessment of the human epidermal model LabCyte EPI-MODEL for In vitro skin corrosion testing according to the OECD test guideline 431.

PubMed

Katoh, Masakazu; Hamajima, Fumiyasu; Ogasawara, Takahiro; Hata, Ken-Ichiro

2010-06-01

A new OECD test guideline 431 (TG431) for in vitro skin corrosion tests using human reconstructed skin models was adopted by OECD in 2004. TG431 defines the criteria for the general function and performance of applicable skin models. In order to confirm that the new reconstructed human epidermal model, LabCyte EPI-MODEL is applicable for the skin corrosion test according to TG431, the predictability and repeatability of the model for the skin corrosion test was evaluated. The test was performed according to the test protocol described in TG431. Based on the knowledge that LabCyte EPI-MODEL is an epidermal model as well as EpiDerm, we decided to adopt the the Epiderm prediction model of skin corrosion for the LabCyte EPI-MODEL, using twenty test chemicals (10 corrosive chemicals and 10 non-corrosive chemicals) in the 1(st) stage. The prediction model results showed that the distinction of non-corrosion to corrosion corresponded perfectly. Therefore, it was judged that the prediction model of EpiDerm could be applied to the LabCyte EPI-MODEL. In the 2(nd) stage, the repeatability of this test protocol with the LabCyte EPI-MODEL was examined using twelve chemicals (6 corrosive chemicals and 6 non-corrosive chemicals) that are described in TG431, and these results recognized a high repeatability and accurate predictability. It was concluded that LabCyte EPI-MODEL is applicable for the skin corrosive test protocol according to TG431.

Connecting Levels of Representation: Emergent versus Submergent Perspective

ERIC Educational Resources Information Center

Rappoport, Lana T.; Ashkenazi, Guy

2008-01-01

Chemical phenomena can be described using three representation modes: macro, submicro, and symbolic. The way students use and connect these modes when solving conceptual problems was studied, using a think-aloud interview protocol. The protocol was validated through interviews with six faculty members, and then applied to four graduate and six…

Chemical modification of coating of Pinus halepensis pollen by ozone exposure.

PubMed

Naas, Oumsaad; Mendez, Maxence; Quijada, Melesio; Gosselin, Sylvie; Farah, Jinane; Choukri, Ali; Visez, Nicolas

2016-07-01

Pollen coating, located on the exine, includes an extractible lipid fraction. The modification of the pollen coating by air pollutants may have implications on the interactions of pollen with plant stigmas and human cells. Pinus halepensis pollen was exposed to ozone in vitro and the pollen coating was extracted with organic solvent and analyzed by GC-MS. Ozone has induced chemical changes in the coating as observed with an increase in dicarboxylic acids, short-chain fatty acids and aldehydes. 4-Hydroxybenzaldehyde was identified as the main reaction product and its formation was shown to occur both on native pollen and on defatted pollen. 4-Hydroxybenzaldehyde is very likely formed via the ozonolysis of acid coumaric-like monomers constitutive of the sporopollenin. Modification of pollen coating by air pollutants should be accounted for in further studies on effect of pollution on germination and on allergenicity. Copyright © 2016 Elsevier Ltd. All rights reserved.

Higher sensitivity secondary ion mass spectrometry of biological molecules for high resolution, chemically specific imaging.

PubMed

McDonnell, Liam A; Heeren, Ron M A; de Lange, Robert P J; Fletcher, Ian W

2006-09-01

To expand the role of high spatial resolution secondary ion mass spectrometry (SIMS) in biological studies, numerous developments have been reported in recent years for enhancing the molecular ion yield of high mass molecules. These include both surface modification, including matrix-enhanced SIMS and metal-assisted SIMS, and polyatomic primary ions. Using rat brain tissue sections and a bismuth primary ion gun able to produce atomic and polyatomic primary ions, we report here how the sensitivity enhancements provided by these developments are additive. Combined surface modification and polyatomic primary ions provided approximately 15.8 times more signal than using atomic primary ions on the raw sample, whereas surface modification and polyatomic primary ions yield approximately 3.8 and approximately 8.4 times more signal. This higher sensitivity is used to generate chemically specific images of higher mass biomolecules using a single molecular ion peak.

Multiphoton microscopy guides neurotrophin modification with poly(ethylene glycol) to enhance interstitial diffusion

NASA Astrophysics Data System (ADS)

Stroh, Mark; Zipfel, Warren R.; Williams, Rebecca M.; Ma, Shu Chin; Webb, Watt W.; Saltzman, W. Mark

2004-07-01

Brain-derived neurotrophic factor (BDNF) is a promising therapeutic agent for the treatment of neurodegenerative diseases. However, the limited distribution of this molecule after administration into the brain tissue considerably hampers its efficacy. Here, we show how multiphoton microscopy of fluorescently tagged BDNF in brain-tissue slices provides a useful and rapid screening method for examining the diffusion of large molecules in tissues, and for studying the effects of chemical modifications-for example, conjugating with polyethylene glycol (PEG)-on the diffusion constant. This single variable, obtained by monitoring short-term diffusion in real time, can be effectively used for rational drug design. In this study on fluorescently tagged BDNF and BDNF-PEG, we identify slow diffusion as a major contributing factor to the limited penetration of BDNF, and demonstrate how chemical modification can be used to overcome this barrier.

Cell signaling, post-translational protein modifications and NMR spectroscopy

PubMed Central

Theillet, Francois-Xavier; Smet-Nocca, Caroline; Liokatis, Stamatios; Thongwichian, Rossukon; Kosten, Jonas; Yoon, Mi-Kyung; Kriwacki, Richard W.; Landrieu, Isabelle; Lippens, Guy

2016-01-01

Post-translationally modified proteins make up the majority of the proteome and establish, to a large part, the impressive level of functional diversity in higher, multi-cellular organisms. Most eukaryotic post-translational protein modifications (PTMs) denote reversible, covalent additions of small chemical entities such as phosphate-, acyl-, alkyl- and glycosyl-groups onto selected subsets of modifiable amino acids. In turn, these modifications induce highly specific changes in the chemical environments of individual protein residues, which are readily detected by high-resolution NMR spectroscopy. In the following, we provide a concise compendium of NMR characteristics of the main types of eukaryotic PTMs: serine, threonine, tyrosine and histidine phosphorylation, lysine acetylation, lysine and arginine methylation, and serine, threonine O-glycosylation. We further delineate the previously uncharacterized NMR properties of lysine propionylation, butyrylation, succinylation, malonylation and crotonylation, which, altogether, define an initial reference frame for comprehensive PTM studies by high-resolution NMR spectroscopy. PMID:23011410

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

Low, K.S.; Lee, C.K.; Lee, P.L.

The use of low-cost biological materials for the removal and recovery of heavy metals from solution has been investigated extensively in recent times. To enhance their sorption capacities various chemical modifications on the sorbents were attempted. Freer et al. showed that bark from the Pinus radiata (D. Don) had a greater sorption capacity for metals after treatment with both inorganic acid and formaldehyde. Apple wastes treated with phosphorus oxychloride improved the efficiency of removing metal ions. Ethylenediamine tetraacetic acid (EDTA)-modified groundnut, Arachis hypogea, was reported to improve the sorption of cadmium and lead ions. Modifications with the aid of dyesmore » also enhanced metal sorption. Moss and coconut husk (CH) are readily obtainable in Malaysia. Their sorption potential for metals has been reported. This paper reports on the metal sorption enhancement of these two biosorbents after chemical modification with nitrilotriacetic acid (NTA). 13 refs., 5 figs., 2 tabs.« less

Physical, Chemical and Biochemical Modifications of Protein-Based Films and Coatings: An Extensive Review

PubMed Central

Zink, Joël; Wyrobnik, Tom; Prinz, Tobias; Schmid, Markus

2016-01-01

Protein-based films and coatings are an interesting alternative to traditional petroleum-based materials. However, their mechanical and barrier properties need to be enhanced in order to match those of the latter. Physical, chemical, and biochemical methods can be used for this purpose. The aim of this article is to provide an overview of the effects of various treatments on whey, soy, and wheat gluten protein-based films and coatings. These three protein sources have been chosen since they are among the most abundantly used and are well described in the literature. Similar behavior might be expected for other protein sources. Most of the modifications are still not fully understood at a fundamental level, but all the methods discussed change the properties of the proteins and resulting products. Mastering these modifications is an important step towards the industrial implementation of protein-based films. PMID:27563881

Favorable 2'-substitution in the loop region of a thrombin-binding DNA aptamer.

PubMed

Awachat, Ragini; Wagh, Atish A; Aher, Manisha; Fernandes, Moneesha; Kumar, Vaijayanti A

2018-06-01

Simple 2'-OMe-chemical modification in the loop region of the 15mer G-rich DNA sequence GGTTGGTGTGGTTGG is reported. The G-quadruplex structure of this thrombin-binding aptamer (TBA), is stabilized by single modifications (T → 2'-OMe-U), depending on the position of the modification. The structural stability also renders significantly increased inhibition of thrombin-induced fibrin polymerization, a process closely associated with blood-clotting. Copyright © 2018 Elsevier Ltd. All rights reserved.

Patient-centred screening for primary immunodeficiency: a multi-stage diagnostic protocol designed for non-immunologists

PubMed Central

de Vries, E

2006-01-01

Efficient early identification of primary immunodeficiency disease (PID) is important for prognosis, but is not an easy task for non-immunologists. The Clinical Working Party of the European Society for Immunodeficiencies (ESID) has composed a multi-stage diagnostic protocol that is based on expert opinion, in order to increase the awareness of PID among doctors working in different fields. The protocol starts from the clinical presentation of the patient; immunological skills are not needed for its use. The multi-stage design allows cost-effective screening for PID within the large pool of potential cases in all hospitals in the early phases, while more expensive tests are reserved for definitive classification in collaboration with an immunologist at a later stage. Although many PIDs present in childhood, others may present at any age. The protocols presented here are therefore aimed at both adult physicians and paediatricians. While designed for use throughout Europe, there will be national differences which may make modification of this generic algorithm necessary. PMID:16879238

Fast and facile fabrication of antifouling and hemocompatible PVDF membrane tethered with amino-acid modified PEG film

NASA Astrophysics Data System (ADS)

Zhang, Shuyou; Cao, Jingjing; Ma, Na; You, Meng; Wang, Xushan; Meng, Jianqiang

2018-01-01

A fast and facile protocol is reported aiming at improving the antifouling property and hemocompatibility of poly(vinylidene fluoride) (PVDF) membranes by tethering PEG hydrogel and zwitterion immobilization. The coated PEG hydrogel was first prepared by interfacial polymerization and tethered on an alkali treated PVDF membrane (PVDFA) surface via a simultaneous thio-ene and thiol-epoxy reaction. Then, the thiol groups of cysteine reacted with the epoxy groups in PEG hydrogel to fabricate the PVDFA-g-Cys membrane. The membrane fabrication was complete within less than 20 min and was conducted in mild conditions. The successful preparation of PVDFA-g-Cys membrane was confirmed by ATR-FTIR and XPS. Raman spectroscopy showed that the hydrogels covalently bonded to the PVDF membrane surface. The membrane retained its mechanical strength after modification. The SEM measurements suggested that the membrane became denser after hydrogel coating, meanwhile, the EDX test verified that the functional species uniformly distributed in the membrane matrix. Water contact angle (WCA), protein adsorption and protein filtration tests showed significant improvements in hydrophilicity and antifouling properties for the modified membrane. The negativity of the membrane surface measured by the streaming potential method provides a basis for protein resistance and hemocompatibility. Moreover, the suppressed platelet adhesion and prolonged plasma coagulant time show that the PVDFA-g-Cys membrane has ultralow thrombotic potential and better hemocompatibility. The reported surface modification method combing thio-ene and thio-epoxy chemistry not only facilitates fabrication of hemocompatible PVDF membrane but also provide an universal chemical platform for multifunctionalization of porous membranes.

Microwave Technology--Applications in Chemical Synthesis

EPA Science Inventory

Microwave heating, being specific and instantaneous, is unique and has found a place for expeditious chemical syntheses. Specifically, the solvent-free reactions are convenient to perform and have advantages over the conventional heating protocols as summarized in the previous se...

Current Development in Reproductive Toxicity Testing of Pesticides

EPA Science Inventory

A protocol to evaluate the potential developmental and reproductive effects of test chemicals has been developed by the Life Stages Task Force of the International Life Sciences Institute (ILSI)/Health and Environmental Sciences Institute (HESI) Agricultural Chemical Safety Asses...

Rapid End-Group Modification of Polysaccharides for Biomaterial Applications in Regenerative Medicine.

PubMed

Bondalapati, Somasekhar; Ruvinov, Emil; Kryukov, Olga; Cohen, Smadar; Brik, Ashraf

2014-09-15

Polysaccharides have emerged as important functional materials because of their unique properties such as biocompatibility, biodegradability, and availability of reactive sites for chemical modifications to optimize their properties. The overwhelming majority of the methods to modify polysaccharides employ random chemical modifications, which often improve certain properties while compromising others. On the other hand, the employed methods for selective modifications often require excess of coupling partners, long reaction times and are limited in their scope and wide applicability. To circumvent these drawbacks, aniline-catalyzed oxime formation is developed for selective modification of a variety of polysaccharides through their reducing end. Notably, it is found that for efficient oxime formation, different conditions are required depending on the composition of the specific polysaccharide. It is also shown how our strategy can be applied to improve the physical and functional properties of alginate hydrogels, which are widely used in tissue engineering and regenerative medicine applications. While the randomly and selectively modified alginate exhibits similar viscoelastic properties, the latter forms significantly more stable hydrogel and superior cell adhesive and functional properties. Our results show that the developed conjugation reaction is robust and should open new opportunities for preparing polysaccharide-based functional materials with unique properties. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis and physico-chemical characterization of modified starches from banana (Musa AAB) and its biological activities in diabetic rats.

PubMed

Reddy, Chagam Koteswara; Suriya, M; Vidya, P V; Haripriya, Sundaramoorthy

2017-01-01

This study describes a simple method of preparation and physico-chemical properties of modified starches (type-3 resistant starches) from banana (Musa AAB), and the modified starches investigated as functional food with a beneficial effect on type-2 diabetes. RS3 was prepared using a method combined with debranching modification and physical modification; native and modifies starches were characterized by scanning electron microscope (SEM), powder X-ray diffraction (XRD), differential scanning calorimetry (DSC) and rapid visco analyzer (RVA). Use of the enzymatic and physical modification methodology, improved the yield of RS (26.62%) from Musa AAB. A reduced viscosity and swelling power; increased transition temperatures, water absorption capacity and solubility index with B-type crystalline pattern and loss of granular appearance were observed during the debranching modification and physical modification. The modified starches exhibited beneficial health effects in diabetic and HFD rats who consumed it. These results recommend that dietary feeding of RS3 was effective in the regulation of glucose and lipid profile in serum and suppressing the oxidative stress in rats under diabetic and HFD condition. This current study provides new bioactive starches, with potential applications in the food and non-food industries. Copyright © 2016 Elsevier B.V. All rights reserved.

A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding.

PubMed

Lin, Ying-Ting

2013-04-30

A tandem technique of hard equipment is often used for the chemical analysis of a single cell to first isolate and then detect the wanted identities. The first part is the separation of wanted chemicals from the bulk of a cell; the second part is the actual detection of the important identities. To identify the key structural modifications around ligand binding, the present study aims to develop a counterpart of tandem technique for cheminformatics. A statistical regression and its outliers act as a computational technique for separation. A PPARγ (peroxisome proliferator-activated receptor gamma) agonist cellular system was subjected to such an investigation. Results show that this tandem regression-outlier analysis, or the prioritization of the context equations tagged with features of the outliers, is an effective regression technique of cheminformatics to detect key structural modifications, as well as their tendency of impact to ligand binding. The key structural modifications around ligand binding are effectively extracted or characterized out of cellular reactions. This is because molecular binding is the paramount factor in such ligand cellular system and key structural modifications around ligand binding are expected to create outliers. Therefore, such outliers can be captured by this tandem regression-outlier analysis.

Continuous-flow centrifugation to collect suspended sediment for chemical analysis

USGS Publications Warehouse

Conn, Kathleen E.; Dinicola, Richard S.; Black, Robert W.; Cox, Stephen E.; Sheibley, Richard W.; Foreman, James R.; Senter, Craig A.; Peterson, Norman T.

2016-12-22

Recent advances in suspended-sediment monitoring tools and surrogate technologies have greatly improved the ability to quantify suspended-sediment concentrations and to estimate daily, seasonal, and annual suspended-sediment fluxes from rivers to coastal waters. However, little is known about the chemical composition of suspended sediment, and how it may vary spatially between water bodies and temporally within a single system owing to climate, seasonality, land use, and other natural and anthropogenic drivers. Many water-quality contaminants, such as organic and inorganic chemicals, nutrients, and pathogens, preferentially partition in sediment rather than water. Suspended sediment-bound chemical concentrations may be undetected during analysis of unfiltered water samples, owing to small water sample volumes and analytical limitations. Quantification of suspended sediment‑bound chemical concentrations is needed to improve estimates of total chemical concentrations, chemical fluxes, and exposure levels of aquatic organisms and humans in receiving environments. Despite these needs, few studies or monitoring programs measure the chemical composition of suspended sediment, largely owing to the difficulty in consistently obtaining samples of sufficient quality and quantity for laboratory analysis.A field protocol is described here utilizing continuous‑flow centrifugation for the collection of suspended sediment for chemical analysis. The centrifuge used for development of this method is small, lightweight, and portable for the field applications described in this protocol. Project scoping considerations, deployment of equipment and system layout options, and results from various field and laboratory quality control experiments are described. The testing confirmed the applicability of the protocol for the determination of many inorganic and organic chemicals sorbed on suspended sediment, including metals, pesticides, polycyclic aromatic hydrocarbons, and polychlorinated biphenyls. The particle-size distribution of the captured sediment changes to a more fine-grained sample during centrifugation, and the necessity to account for this change when extrapolating chemical concentrations on the centrifuged sediment sample to the environmental water system is discussed.The data produced using this method will help eliminate a data gap of suspended sediment-bound chemical concentrations, and will support management decisions, such as chemical source-control efforts or in-stream restoration activities. When coupled with streamflow and sediment flux data, it will improve estimates of riverine chemical fluxes, and will aid in assessing the importance and impacts of suspended sediment-bound chemicals to downstream freshwater and coastal marine ecosystems.

A soil bioassay using the nematode Caenorhabditis elegans

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

Freeman, M.N.; Peredney, C.L.; Williams, P.L.

1999-07-01

Caenorhabditis elegans is a free-livings soil nematode that is commonly used as a biological model. Recently, much work has been done using the nematode as a toxicological model as well. Much of the work involving C. elegans has been performed in aquatic media, since it lives in the interstitial water of soil. However, testing in soil would be expected to more accurately reproduce the organism's normal environment and may take into consideration other factors not available in an aquatic test, i.e., toxicant availability effects due to sorption, various chemical interactions, etc. This study used a modification of a previous experimentalmore » protocol to determine 24h LC{sub 50} values for Cu in a Cecil series soil mixture, and examined the use of CuCl{sub 2} as a reference toxicant for soil toxicity testing with C. elegans. Three different methods of determining percent lethality were used, each dependent on how the number of worms missing after the recovery process was used in the lethality calculations. Only tests having {ge}80% worm recovery and {ge}90% control survival were used in determining the LC{sub 50}s, by Probit analysis. The replicate LC{sub 50} values generated a control chart for each method of calculating percent lethality. The coefficient of variation (CV) for each of the three methods was {le}14%. The control charts and the protocol outlined in this study are intended to be used to assess test organism health and monitor precision of future soil toxicity tests with C. elegans.« less

Optimization of Nonambulant Mass Casualty Decontamination Protocols as Part of an Initial or Specialist Operational Response to Chemical Incidents.

PubMed

Chilcott, Robert P; Mitchell, Hannah; Matar, Hazem

2018-05-30

The UK's Initial Operational Response (IOR) is a new process for improving the survival of multiple casualties following a chemical, biological, radiological or nuclear incident. Whilst the introduction of IOR represents a patient-focused response for ambulant casualties, there is currently no provision for disrobe and dry decontamination of nonambulant casualties. Moreover, the current specialist operational response (SOR) protocol for nonambulant casualty decontamination (also referred to as "clinical decontamination") has not been subject to rigorous evaluation or development. Therefore, the aim of this study was to confirm the effectiveness of putatively optimized dry (IOR) and wet (SOR) protocols for nonambulant decontamination in human volunteers. Dry and wet decontamination protocols were objectively evaluated using human volunteers. Decontamination effectiveness was quantified by liquid chromatography-mass spectrometry analysis of the recovery of a chemical warfare agent simulant (methylsalicylate) from skin and hair of volunteers, with whole-body fluorescence imaging to quantify the skin distribution of residual simulant. Both the dry and wet decontamination processes were rapid (3 and 4 min, respectively) and were effective in removing simulant from the hair and skin of volunteers, with no observable adverse effects related to skin surface spreading of contaminant. Further studies are required to assess the combined effectiveness of dry and wet decontamination under more realistic conditions and to develop appropriate operational procedures that ensure the safety of first responders.

Chemical Methods for the Direct Detection and Labeling of S-Nitrosothiols

PubMed Central

Bechtold, Erika

2012-01-01

Abstract Significance: Posttranslational modification of proteins through phosphorylation, glycosylation, and oxidation adds complexity to the proteome by reversibly altering the structure and function of target proteins in a highly controlled fashion. Recent Advances: The study of reversible cysteine oxidation highlights a role for this oxidative modification in complex signal transduction pathways. Nitric oxide (NO), and its respective metabolites (including reactive nitrogen species), participates in a variety of these cellular redox processes, including the reversible oxidation of cysteine to S-nitrosothiols (RSNOs). RSNOs act as endogenous transporters of NO, but also possess beneficial effects independent of NO-related signaling, which suggests a complex and versatile biological role. In this review, we highlight the importance of RSNOs as a required posttranslational modification and summarize the current methods available for detecting S-nitrosation. Critical Issues: Given the limitations of these indirect detection methods, the review covers recent developments toward the direct detection of RSNOs by phosphine-based chemical probes. The intrinsic properties that dictate this phosphine/RSNO reactivity are summarized. In general, RSNOs (both small molecule and protein) react with phosphines to yield reactive S-substituted aza-ylides that undergo further reactions leading to stable RSNO-based adducts. Future Directions: This newly explored chemical reactivity forms the basis of a number of exciting potential chemical methods for protein RSNO detection in biological systems. Antioxid. Redox Signal. 17, 981–991. PMID:22356122

Utilization of magnetically responsive cereal by-product for organic dye removal.

PubMed

Baldikova, Eva; Politi, Dorothea; Maderova, Zdenka; Pospiskova, Kristyna; Sidiras, Dimitrios; Safarikova, Mirka; Safarik, Ivo

2016-04-01

Barley straw, an agricultural by-product, can also serve as a low-cost and relatively efficient adsorbent of various harmful compounds. In this case, adsorption of four water-soluble dyes belonging to different dye classes (specifically Bismarck brown Y, representing the azo group; methylene blue, quinone-imine group; safranin O, safranin group; and crystal violet, triphenylmethane group) on native and citric acid-NaOH-modified barley straw, both in magnetic and non-magnetic versions, was studied. The adsorption was characterized using three adsorption models, namely Langmuir, Freundlich and Sips. To compare the maximum adsorption capacities (qmax), the Langmuir model was employed. The qmax values reached 86.5-124.3 mg of dye per g of native non-magnetic straw and 410.8-520.3 mg of dye per g of magnetic chemically modified straw. Performed characterization studies suggested that the substantial increase in qmax values after chemical modification could be caused by rougher surface of adsorbent (observed by scanning electron microscopy) and by the presence of higher amounts of carboxyl groups (detected by Fourier transform infrared spectroscopy). The adsorption processes followed the pseudo-second-order kinetic model and thermodynamic studies indicated spontaneous and endothermic adsorption. The chemical modification of barley straw led to a significant increase in maximum adsorption capacities for all tested dyes, while magnetic modification substantially facilitated the manipulation with adsorbent. © 2015 Society of Chemical Industry.

Environmental chemical exposures and human epigenetics

PubMed Central

Hou, Lifang; Zhang, Xiao; Wang, Dong; Baccarelli, Andrea

2012-01-01

Every year more than 13 million deaths worldwide are due to environmental pollutants, and approximately 24% of diseases are caused by environmental exposures that might be averted through preventive measures. Rapidly growing evidence has linked environmental pollutants with epigenetic variations, including changes in DNA methylation, histone modifications and microRNAs. Environ mental chemicals and epigenetic changes All of these mechanisms are likely to play important roles in disease aetiology, and their modifications due to environmental pollutants might provide further understanding of disease aetiology, as well as biomarkers reflecting exposures to environmental pollutants and/or predicting the risk of future disease. We summarize the findings on epigenetic alterations related to environmental chemical exposures, and propose mechanisms of action by means of which the exposures may cause such epigenetic changes. We discuss opportunities, challenges and future directions for future epidemiology research in environmental epigenomics. Future investigations are needed to solve methodological and practical challenges, including uncertainties about stability over time of epigenomic changes induced by the environment, tissue specificity of epigenetic alterations, validation of laboratory methods, and adaptation of bioinformatic and biostatistical methods to high-throughput epigenomics. In addition, there are numerous reports of epigenetic modifications arising following exposure to environmental toxicants, but most have not been directly linked to disease endpoints. To complete our discussion, we also briefly summarize the diseases that have been linked to environmental chemicals-related epigenetic changes. PMID:22253299

Pipeline of Known Chemical Classes of Antibiotics

PubMed Central

d’Urso de Souza Mendes, Cristina; de Souza Antunes, Adelaide Maria

2013-01-01

Many approaches are used to discover new antibiotic compounds, one of the most widespread being the chemical modification of known antibiotics. This type of discovery has been so important in the development of new antibiotics that most antibiotics used today belong to the same chemical classes as antibiotics discovered in the 1950s and 1960s. Even though the discovery of new classes of antibiotics is urgently needed, the chemical modification of antibiotics in known classes is still widely used to discover new antibiotics, resulting in a great number of compounds in the discovery and clinical pipeline that belong to existing classes. In this scenario, the present article presents an overview of the R&D pipeline of new antibiotics in known classes of antibiotics, from discovery to clinical trial, in order to map out the technological trends in this type of antibiotic R&D, aiming to identify the chemical classes attracting most interest, their spectrum of activity, and the new subclasses under development. The result of the study shows that the new antibiotics in the pipeline belong to the following chemical classes: quinolones, aminoglycosides, macrolides, oxazolidinones, tetracyclines, pleuromutilins, beta-lactams, lipoglycopeptides, polymyxins and cyclic lipopeptides. PMID:27029317

Generating mouse lines for lineage tracing and knockout studies.

PubMed

Kraus, Petra; Sivakamasundari, V; Xing, Xing; Lufkin, Thomas

2014-01-01

In 2007 Capecchi, Evans, and Smithies received the Nobel Prize in recognition for discovering the principles for introducing specific gene modifications in mice via embryonic stem cells, a technology, which has revolutionized the field of biomedical science allowing for the generation of genetically engineered animals. Here we describe detailed protocols based on and developed from these ground-breaking discoveries, allowing for the modification of genes not only to create mutations to study gene function but additionally to modify genes with fluorescent markers, thus permitting the isolation of specific rare wild-type and mutant cell types for further detailed analysis at the biochemical, pathological, and genomic levels.

Maleic anhydride-g-low density polyethylene: Modification of LDPE molecular structure by γ-irradiation

NASA Astrophysics Data System (ADS)

Sheeja, Manaf, O.; Sujith, A.

2017-06-01

Polymer modification by radiation grafting of monomers onto polymers has received much attention recently. In the current study, γ-irradiation technique was used to achieve graft copolymerization of maleic anhydride (MA) onto low-density polyethylene (LDPE). To optimize, the process was performed at different γ-irradiation doses and MA concentration. The microstructure of grafted polymer film has been characterized by Fourier transform infrared spectroscopy, thermogravimetric analysis, differential scanning calorimetry, field emission-scanning electron microscopy, and atomic force microscopy. The studies performed made possible the selection of experimental protocols adequate for the production of new copolymeric materials with high grafting yield.

A Digital Framework to Support Providers and Patients in Diabetes Related Behavior Modification.

PubMed

Abidi, Samina; Vallis, Michael; Piccinini-Vallis, Helena; Imran, Syed Ali; Abidi, Syed Sibte Raza

2017-01-01

We present Diabetes Web-Centric Information and Support Environment (D-WISE) that features: (a) Decision support tool to assist family physicians to administer Behavior Modification (BM) strategies to patients; and (b) Patient BM application that offers BM strategies and motivational interventions to engage patients. We take a knowledge management approach, using semantic web technologies, to model the social cognition theory constructs, Canadian diabetes guidelines and BM protocols used locally, in terms of a BM ontology that drives the BM decision support to physicians and BM strategy adherence monitoring and messaging to patients. We present the qualitative analysis of D-WISE usability by both physicians and patients.

SOURCE APPORTIONMENT OF PM 2.5 AND CARBON IN SEATTLE USING CHEMICAL MASS BALANCE AND POSITIVE MATRIX FACTORIZATION

EPA Science Inventory

Three years of PM2.5 speciated data were collected and chemically analyzed using the IMPROVE protocol at the Beacon Hill site in Seattle. The data were analyzed by the Chemical Mass Balance Version 8 (CMB8) and Positive Matrix Factorization (PMF) source apportionment models. T...

Nanocapillary Atmospheric Pressure Plasma Jet: A Tool for Ultrafine Maskless Surface Modification at Atmospheric Pressure.

PubMed

Motrescu, Iuliana; Nagatsu, Masaaki

2016-05-18

With respect to microsized surface functionalization techniques we proposed the use of a maskless, versatile, simple tool, represented by a nano- or microcapillary atmospheric pressure plasma jet for producing microsized controlled etching, chemical vapor deposition, and chemical modification patterns on polymeric surfaces. In this work we show the possibility of size-controlled surface amination, and we discuss it as a function of different processing parameters. Moreover, we prove the successful connection of labeled sugar chains on the functionalized microscale patterns, indicating the possibility to use ultrafine capillary atmospheric pressure plasma jets as versatile tools for biosensing, tissue engineering, and related biomedical applications.

Engineering specific chemical modification sites into a collagen-like protein from Streptococcus pyogenes.

PubMed

Stoichevska, Violet; Peng, Yong Y; Vashi, Aditya V; Werkmeister, Jerome A; Dumsday, Geoff J; Ramshaw, John A M

2017-03-01

Recombinant bacterial collagens provide a new opportunity for safe biomedical materials. They are readily expressed in Escherichia coli in good yield and can be readily purified by simple approaches. However, recombinant proteins are limited in that direct secondary modification during expression is generally not easily achieved. Thus, inclusion of unusual amino acids, cyclic peptides, sugars, lipids, and other complex functions generally needs to be achieved chemically after synthesis and extraction. In the present study, we have illustrated that bacterial collagens that have had their sequences modified to include cysteine residue(s), which are not normally present in bacterial collagen-like sequences, enable a range of specific chemical modification reactions to be produced. Various model reactions were shown to be effective for modifying the collagens. The ability to include alkyne (or azide) functions allows the extensive range of substitutions that are available via "click" chemistry to be accessed. When bifunctional reagents were used, some crosslinking occurred to give higher molecular weight polymeric proteins, but gels were not formed. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 806-813, 2017. © 2016 Wiley Periodicals, Inc.

Synthesis of inulin derivatives with quaternary phosphonium salts and their antifungal activity.

PubMed

Chen, Yuan; Tan, Wenqiang; Li, Qing; Dong, Fang; Gu, Guodong; Guo, Zhanyong

2018-07-01

Inulin is a kind of renewable and biodegradable carbohydrate with good water solubility and numerous physiological functions. For further utilization of inulin, chemical modification can be applied to improve its bioactivities. In this paper, five novel inulin derivatives were synthesized via chemical modification with quaternary phosphonium salt. Their antifungal activity against three kinds of plant pathogens including Colletotrichum lagenarium, Phomopsis asparagi, and Fusarium oxysporum was assessed with radial growth assay in vitro. Results revealed that all the inulin derivatives exhibited improved antifungal activity compared with inulin. Particularly, inulin modified with triphenylphosphine (TPhPAIL) exhibited the best antifungal activity with inhibitory indices of 80.0%, 78.8%, and 87.4% against Colletotrichum lagenarium, Phomopsis asparagi, and Fusarium oxysporum at 1.0mg/mL respectively. The results clearly showed that chemical modification of inulin with quaternary phosphonium salt could efficiently improve derivatives' antifungal activity. Further analysis of results indicated that the antifungal activity was influenced by alkyl chain length or electron-withdrawing ability of the grafted quaternary phosphonium salts. Longer alkyl chain lengths or the stronger electron-withdrawing groups would lead to enhanced antifungal efficacy. Copyright © 2018 Elsevier B.V. All rights reserved.

Mass Spectrometry of Intact Proteins Reveals +98 u Chemical Artifacts Following Precipitation in Acetone.

PubMed

Güray, Melda Z; Zheng, Shi; Doucette, Alan A

2017-02-03

Protein precipitation in acetone is frequently employed ahead of mass spectrometry for sample preconcentration and purification. Unfortunately, acetone is not chemically inert; mass artifacts have previously been observed on glycine-containing peptides when exposed to acetone under acidic conditions. We herein report a distinct chemical modification occurring at the level of intact proteins when incubated in acetone. This artifact manifests as one or more satellite peaks in the MS spectrum of intact protein, spaced 98 u above the mass of the unmodified protein. Other artifacts (+84, +112 u) also appear upon incubation of proteins or peptides in acetone. The reaction is pH-sensitive, being suppressed when proteins are exposed to acetone under acidic conditions. The +98 u artifact is speculated to originate through an intermediate product of aldol condensation of acetone to form diacetone alcohol and mesityl oxide. A +98 u product could originate from nucleophilic attack on mesityl oxide or through condensation with diacetone alcohol. Given the extent of modification possible upon exposure of proteins to acetone, particularly following overnight solvent exposure or incubation at room temperature, an awareness of the variables influencing this novel modification is valued by proteomics researchers who employ acetone precipitation for protein purification.

Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element.

PubMed Central

Mathews, D H; Banerjee, A R; Luan, D D; Eickbush, T H; Turner, D H

1997-01-01

RNA transcripts corresponding to the 250-nt 3' untranslated region of the R2 non-LTR retrotransposable element are recognized by the R2 reverse transcriptase and are sufficient to serve as templates in the target DNA-primed reverse transcription (TPRT) reaction. The R2 protein encoded by the Bombyx mori R2 can recognize this region from both the B. mori and Drosophila melanogaster R2 elements even though these regions show little nucleotide sequence identity. A model for the RNA secondary structure of the 3' untranslated region of the D. melanogaster R2 retrotransposon was developed by sequence comparison of 10 species aided by free energy minimization. Chemical modification experiments are consistent with this prediction. A secondary structure model for the 3' untranslated region of R2 RNA from the R2 element from B. mori was obtained by a combination of chemical modification data and free energy minimization. These two secondary structure models, found independently, share several common sites. This study shows the utility of combining free energy minimization, sequence comparison, and chemical modification to model an RNA secondary structure. PMID:8990394

Chemical modification of Saccharomycopsis fibuligera R64 α-amylase to improve its stability against thermal, chelator, and proteolytic inactivation.

PubMed

Ismaya, Wangsa Tirta; Hasan, Khomaini; Kardi, Idar; Zainuri, Amalia; Rahmawaty, Rinrin Irma; Permanahadi, Satyawisnu; El Viera, Baiq Vera; Harinanto, Gunawan; Gaffar, Shabarni; Natalia, Dessy; Subroto, Toto; Soemitro, Soetijoso

2013-05-01

α-Amylase catalyzes hydrolysis of starch to oligosaccharides, which are further degraded to simple sugars. The enzyme has been widely used in food and textile industries and recently, in generation of renewable energy. An α-amylase from yeast Saccharomycopsis fibuligera R64 (Sfamy) is active at 50 °C and capable of degrading raw starch, making it attractive for the aforementioned applications. To improve its characteristics as well as to provide information for structural study ab initio, the enzyme was chemically modified by acid anhydrides (nonpolar groups), glyoxylic acid (GA) (polar group), dimethyl adipimidate (DMA) (cross-linking), and polyethylene glycol (PEG) (hydrophilization). Introduction of nonpolar groups increased enzyme stability up to 18 times, while modification by a cross-linking agent resulted in protection of the calcium ion, which is essential for enzyme activity and integrity. The hydrophilization with PEG resulted in protection against tryptic digestion. The chemical modification of Sfamy by various modifiers has thereby resulted in improvement of its characteristics and provided systematic information beneficial for structural study of the enzyme. An in silico structural study of the enzyme improved the interpretation of the results.

Therapeutic charm of quercetin and its derivatives: a review of research and patents.

PubMed

Sharma, Ajay; Kashyap, Dharambir; Sak, Katrin; Tuli, Hardeep Singh; Sharma, Anil K

2018-01-01

Bioactive polyphenolic compounds derived from plants are being utilized for prevention of various chronic diseases including cancer and cardiovascular disorders. Quercetin, a potential poly-phenolic flavonol, found in onions, apples and berries, has been implicated against cancer proliferation, chronic inflammation and various other oxidative manifestations. Evidences suggested that quercetin negatively regulates the numerous crucial signaling pathways associated with life-threatening diseases. Major signaling pathways including NF-κB, MAPK, PI3K-AKT and mTOR are found to be regulated by quercetin. In addition, several patents have reported recently on quercetin derivatives describing wide therapeutic applications such as anticancer/antiproliferatory, antioxidative/antiaging, antiviral, anti-inflammatory, cardioprotective. Present review emphasizes the chemistry and sources of quercetin followed by description of its broad-spectrum therapeutic potential along with proposed mechanisms of action. Furthermore, this review also highlights the important modifications in the basic chemical structure of quercetin in terms of published patents. Insolubility of the bioactive compounds restricts their medicinal importance which could be overcome by modifications in the chemical structure of so-called derivatives. Most of the patents deal with the modifications in chemical structure of quercetin mainly at hydroxyl groups and C-6 and C-7 positions.

78 FR 65570 - Modification of Significant New Uses of 1-Propene, 2,3,3,3-tetrafluoro-

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-01

... include, but are not limited to: Manufacturers or processors of the subject chemical substance (NAICS... by this action. Other types of entities not listed in this unit could also be affected. The North... modification. One of the commenters also noted a potential ambiguity in the proposed regulatory text. Part of...

Ring structure modifications of phenylalanine 19 increase fibrillation kinetics and reduce toxicity of amyloid β (1-40).

PubMed

Korn, Alexander; Surendran, Dayana; Krueger, Martin; Maiti, Sudipta; Huster, Daniel

2018-05-24

We investigated the influence of the chemical structure of the phenylalanine side chain in position 19 of the 40 residue amyloid β peptide. Side chain modifications in this position yielded fibrils of essentially unaltered morphology, structure, and dynamics, but significantly increased fibrillation kinetics and diminished the toxicity of the peptides.

Structural and physico-chemical properties of insoluble rice bran fiber: effect of acid–base induced modifications

USDA-ARS?s Scientific Manuscript database

The structural modifications of insoluble rice bran fiber (IRBF) by sequential regimes of sulphuric acid (H2SO4) and their effects on the physicochemical attributes were studied. The increment of H2SO4 concentration resulted in decreased water holding capacity that ultimately enhanced the oil bindin...

Wetting in Color

NASA Astrophysics Data System (ADS)

Burgess, Ian Bruce

Colorimetric litmus tests such as pH paper have enjoyed wide commercial success due to their inexpensive production and exceptional ease of use. However, expansion of colorimetry to new sensing paradigms is challenging because macroscopic color changes are seldom coupled to arbitrary differences in the physical/chemical properties of a system. In this thesis I present in detail the development of Wetting in Color Technology, focusing primarily on its application as an inexpensive and highly selective colorimetric indicator for organic liquids. The technology exploits chemically-encoded inverse-opal photonic crystals to control the infiltration of fluids to liquid-specific spatial patterns, projecting minute differences in liquids' wettability to macroscopically distinct, easy-to-visualize structural color patterns. It is shown experimentally and corroborated with theoretical modeling using percolation theory that the high selectivity of wetting, upon-which the sensitivity of the indicator relies, is caused by the highly symmetric structure of our large-area, defect-free SiO2 inverse-opals. The regular structure also produces a bright iridescent color, which disappears when infiltrated with liquid - naturally coupling the optical and fluidic responses. Surface modification protocols are developed, requiring only silanization and selective oxidation, to facilitate the deterministic design of an indicator that differentiates a broad range of liquids. The resulting tunable, built-in horizontal and vertical chemistry gradients allow the wettability threshold to be tailored to specific liquids across a continuous range, and make the readout rely only on countable color differences. As wetting is a generic fluidic phenomenon, Wetting in Color technology could be suitable for applications in authentication or identification of unknown liquids across a broad range of industries. However, the generic nature of the response also ensures chemical non-specificity. It is shown that combinatorial measurements from an array of indicators add a degree of chemical specificity to the platform, which can be further improved by monitoring the drying of the inverse-opal films. While colorimetry is the central focus of this thesis, applications of this platform in encryption, fluidics and nanofabrication are also briefly explored.

Amine control for DUV lithography: identifying hidden sources

NASA Astrophysics Data System (ADS)

Kishkovich, Oleg P.; Larson, Carl E.

2000-06-01

The impact of airborne basic molecular contamination (MB) on the performance of chemically amplified (CA) resist systems has been a long standing problem. Low ppb levels of MB may be sufficient for robust 0.25 micrometer lithography with today's advanced CA resist systems combined with adequate chemical air filtration. However, with minimum CD targets heading below 150 nm, the introduction of new resist chemistries for Next Generation Lithography, and the trend towards thinner resists, the impact of MB at low and sub-ppb levels again becomes a critical manufacturing issue. Maximizing process control at aggressive feature sizes requires that the level of MB be maintained below a certain limit, which depends on such parameters as the sensitivity of the CA resist, the type of production tools, product mix, and process characteristics. Three approaches have been identified to reduce the susceptibility of CA resists to MB: effective chemical air filtration, modifications to resist chemistry/processing and cleanroom protocols involving MB monitoring and removal of MB sources from the fab. The final MB concentration depends on the effectiveness of filtration resources and on the total pollution originating from different sources in and out of the cleanroom. There are many well-documented sources of MB. Among these are: ambient air; polluted exhaust from other manufacturing areas re-entering the cleanroom through make-up air handlers; manufacturing process chemicals containing volatile molecular bases; certain cleanroom construction materials, such as paint and ceiling tiles; and volatile, humidifier system boiler additives (corrosion inhibitors), such as morpholine, cyclohexylamine, and dimethylaminoethanol. However, there is also an indeterminate number of other 'hidden' pollution sources, which are neither obvious nor well-documented. None of these sources are new, but they had little impact on earlier semiconductor manufacturing processes because the contamination levels are low enough that they were tolerable. The purpose of this article is to investigate some of these frequently overlooked sources of basic molecular contamination and to thereby increase the reader's awareness of their potential risks.

RNA methylation in nuclear pre-mRNA processing.

PubMed

Covelo-Molares, Helena; Bartosovic, Marek; Vanacova, Stepanka

2018-06-19

Eukaryotic RNA can carry more than 100 different types of chemical modifications. Early studies have been focused on modifications of highly abundant RNA, such as ribosomal RNA and transfer RNA, but recent technical advances have made it possible to also study messenger RNA (mRNA). Subsequently, mRNA modifications, namely methylation, have emerged as key players in eukaryotic gene expression regulation. The most abundant and widely studied internal mRNA modification is N 6 -methyladenosine (m 6 A), but the list of mRNA chemical modifications continues to grow as fast as interest in this field. Over the past decade, transcriptome-wide studies combined with advanced biochemistry and the discovery of methylation writers, readers, and erasers revealed roles for mRNA methylation in the regulation of nearly every aspect of the mRNA life cycle and in diverse cellular, developmental, and disease processes. Although large parts of mRNA function are linked to its cytoplasmic stability and regulation of its translation, a number of studies have begun to provide evidence for methylation-regulated nuclear processes. In this review, we summarize the recent advances in RNA methylation research and highlight how these new findings have contributed to our understanding of methylation-dependent RNA processing in the nucleus. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Processing > Splicing Regulation/Alternative Splicing RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications. © 2018 The Authors. WIREs RNA published by Wiley Periodicals, Inc.

Comparative Study of Surface Chemical Composition and Oxide Layer Modification upon Oxygen Plasma Cleaning and Piranha Etching on a Novel Low Elastic Modulus Ti25Nb21Hf Alloy

NASA Astrophysics Data System (ADS)

Paredes, Virginia; Salvagni, Emiliano; Rodríguez-Castellón, Enrique; Manero, José María

2017-08-01

Metals are widely employed for many biological artificial replacements, and it is known that the quality and the physical/chemical properties of the surface are crucial for the success of the implant. Therefore, control over surface implant materials and their elastic moduli may be crucial to avoid undesired effects. In this study, surface modification upon cleaning and activation of a low elastic modulus Ti alloy (Ti25Hf21Nb) was investigated. Two different methods, oxygen plasma (OP) cleaning and piranha (PI) solution, were studied and compared. Both surface treatments were effective for organic contaminant removal and to increase the Ti-oxide layer thickness rather than other metal-oxides present at the surface, which is beneficial for biocompatibility of the material. Furthermore, both techniques drastically increased hydrophilicity and introduced oxidation and hydroxylation (OH)-functional groups at the surface that may be beneficial for further chemical modifications. However, these treatments did not alter the surface roughness and bulk material properties. The surfaces were fully characterized in terms of surface roughness, wettability, oxide layer composition, and hydroxyl surface density through analytical techniques (interferometry, X-ray photoelectron spectroscopy (XPS), contact angle, and zinc complexation). These findings provide essential information when planning surface modifications for cleanliness, oxide layer thickness, and surface hydroxyl density, as control over these factors is essential for many applications, especially in biomaterials.

Monitoring wilderness stream ecosystems

Treesearch

Jeffrey C. Davis; G. Wayne Minshall; Christopher T. Robinson; Peter Landres

2001-01-01

A protocol and methods for monitoring the major physical, chemical, and biological components of stream ecosystems are presented. The monitoring protocol is organized into four stages. At stage 1 information is obtained on a basic set of parameters that describe stream ecosystems. Each following stage builds upon stage 1 by increasing the number of parameters and the...

Recolonization of the oral cavity by Streptococcus mutans after a combined mechanical/chemical antisepsis protocol.

PubMed

Farina, R; Squarzoni, M A; Calura, G; Trombelli, L

2009-06-01

The bacterial colonization of teeth by Streptococcus mutans (StrepM) represents a major risk factor for the development of dental caries. At present, no clinical studies have explored the effect of a combined mechanical-chemical antisepsis protocol in a periodontally-healthy population and the pattern of recolonization of StrepM in subjects whose StrepM infection was successfully eradicated. The present study was designed in order to 1) determine the salivary and plaque changes in StrepM content after a combined mechanical/chemical antisepsis protocol; and 2) evaluate the pattern of recolonization when StrepM was successfully eradicated from saliva and plaque. Thirty-five periodontally-healthy and caries-susceptible subjects successfully entered and concluded the study. At baseline, non-surgical periodontal therapy was performed according to the principles of full mouth disinfection. Adjunctive home-based rinsing with a 0.2% chlorhexidine mouthrinse was requested for the following week. StrepM concentration was assessed in saliva and plaque at the initial contact appointment, at baseline, and 1-week, 1-month, 3-month and 6-month follow-up. A significant effect of ''time'' on StrepM concentration in saliva and plaque was observed (P<0.000). In subjects with successful eradication of StrepM at 1 week (N=17 plaque samples), StrepM infection recurrence occurred within 3-6 months. The results of the present study demonstrated that 1) the application of the investigated mechanical/chemical antisepsis protocol can effectively reduce StrepM colonies in saliva and plaque of periodontally healthy subjects; and 2) in plaque samples, StrepM infection recurrence tends to occur within 3-6 months.

RNA Isolation from Plant Tissues: A Hands-On Laboratory Experimental Experience for Undergraduates

ERIC Educational Resources Information Center

Zhang, Nianhui; Yu, Dong; Zhu, Xiaofeng

2018-01-01

The practice of RNA isolation in undergraduate experimental courses is rare because of the existence of robust, ubiquitous and stable ribonucleases. We reported here modifications to our original protocol for RNA isolation from plant tissues, including the recovery of nucleic acids by ethanol precipitation at 0 degrees C for 10 min and the…

Comparison of intraocular lens types for cataract surgery in eyes with uveitis

PubMed Central

Ssemanda, Elizabeth; Lindsley, Kristina; Ervin, Ann-Margret; Kempen, John

2013-01-01

This is the protocol for a review and there is no abstract. The objectives are as follows: The aim of this systematic review is to summarize the effects of different IOLs after cataract surgery in uveitis patients. Alternative types of IOLs include PMMA, silicone, acrylic with or without heparin-surface modification. PMID:25013384

Examining the Teaching of Science, and Technology and Engineering Content and Practices: An Instrument Modification Study

ERIC Educational Resources Information Center

Love, Tyler S.; Wells, John G.; Parkes, Kelly A.

2017-01-01

A modified Reformed Teaching Observation Protocol (RTOP) (Piburn & Sawada, 2000) instrument was used to separately examine eight technology and engineering (T&E) educators' teaching of science, and T&E content and practices, as called for by the "Standards for Technological Literacy: Content for the Study of Technology"…

Long-Lasting Modifications of Saccadic Eye Movements Following Adaptation Induced in the Double-Step Target Paradigm

ERIC Educational Resources Information Center

Alahyane, Nadia; Pelisson, Denis

2005-01-01

The adaptation of saccadic eye movements to environmental changes occurring throughout life is a good model of motor learning and motor memory. Numerous studies have analyzed the behavioral properties and neural substrate of oculomotor learning in short-term saccadic adaptation protocols, but to our knowledge, none have tested the persistence of…

Modifications to the Current EPA Endocrine Disruptor Screening Program's Tier 1 Female Pubertal Protocol: A Study on the Effects of the Chlorotriazine Simazine

EPA Science Inventory

Currently the US EPA is implementing a screening program for environmental endocrine disruptors. One of the in vivo assays in the Tier 1 Screen of the Endocrine Disruptors Screening Program (EDSP) is a female pubertal assay. In this study we examined the chlorotriazine simazine, ...

Review of existing terrestrial bioaccumulation models and terrestrial bioaccumulation modeling needs for organic chemicals

EPA Science Inventory

Protocols for terrestrial bioaccumulation assessments are far less-developed than for aquatic systems. This manuscript reviews modeling approaches that can be used to assess the terrestrial bioaccumulation potential of commercial organic chemicals. Models exist for plant, inver...

Using Neural Progenitor Cells in High-Throughput Screens for Developmental Neurotoxicants: Triumphs and Tragedies

EPA Science Inventory

Current protocols for developmental neurotoxicity testing are insufficient to test thousands of commercial chemicals. Thus, development of highthroughput screens (HTS) to detect and prioritize chemicals that may cause developmental neurotoxicity is needed to improve protection of...

AIR DRYING AND PRETREATMENT EFFECTS ON SOIL SULFATE SORPTION

EPA Science Inventory

Drying, freezing, and refrigeration are commonly employed to facilitate the handling and storage of soil samples on which chemical, biological and physical analyses are to be performed. hese laboratory protocol have the potential to alter soil chemical characteristics and may res...

VIRAL PESTICIDES: PRESENT KNOWLEDGE AND POTENTIAL EFFECTS ON PUBLIC AND ENVIRONMENTAL HEALTH (SYMPOSIUM PROCEEDINGS)

EPA Science Inventory

Baculoviruses appear to be effective alternatives to chemical pest control. To date deleterious effects on other components of the ecosystem have not been demonstrated. However, safety testing recommended for registration utilize protocols developed for chemical pesticides. Safet...

Sampling protocol for post-landfall Deepwater Horizon oil release, Gulf of Mexico, 2010

USGS Publications Warehouse

Wilde, F.D.; Skrobialowski, S.C.; Hart, J.S.

2010-01-01

The protocols and procedures described in this report are designed to be used by U.S. Geological Survey (USGS) field teams for the collection of environmental data and samples in coastal areas affected by the 2010 Deepwater Horizon oil spill in the Gulf of Mexico. This sampling protocol focuses specifically on sampling for water, sediments, benthic invertebrates, and microorganisms (ambient bacterial populations) after shoreline arrival of petroleum-associated product on beach, barrier island, and wetland environments of the Gulf of Mexico coastal states. Deployment to sampling sites, site setup, and sample collection in these environments necessitates modifications to standard USGS sampling procedures in order to address the regulatory, logistical, and legal requirements associated with samples collected in oil-impacted coastal areas. This document, therefore, has been written as an addendum to the USGS National Field Manual for the Collection of Water-Quality Data (NFM) (http://pubs.water.usgs.gov/twri9A/), which provides the basis for training personnel in the use of standard USGS sampling protocols. The topics covered in this Gulf of Mexico oil-spill sampling protocol augment NFM protocols for field-deployment preparations, health and safety precautions, sampling and quality-assurance procedures, and decontamination requirements under potentially hazardous environmental conditions. Documentation procedures and maintenance of sample integrity by use of chain-of-custody procedures also are described in this protocol.

Chemical modification of corn fiber with ion-exchanging groups

USDA-ARS?s Scientific Manuscript database

Pretreated corn fiber was chemically modified with quaternary ammonium group or/and sulfonated with 3-chloro-2-hydroxypropanesulfonic acid under vacuum or at ambient pressure. The soluble fraction was dialyzed through 1 kDa MWCO dialysis tubing and the material retained inside the tubing was filtere...

Toward a public toxicogenomics capability for supporting predictive toxicology: survey of current resources and chemical indexing of experiments in GEO and ArrayExpress.

PubMed

Williams-Devane, ClarLynda R; Wolf, Maritja A; Richard, Ann M

2009-06-01

A publicly available toxicogenomics capability for supporting predictive toxicology and meta-analysis depends on availability of gene expression data for chemical treatment scenarios, the ability to locate and aggregate such information by chemical, and broad data coverage within chemical, genomics, and toxicological information domains. This capability also depends on common genomics standards, protocol description, and functional linkages of diverse public Internet data resources. We present a survey of public genomics resources from these vantage points and conclude that, despite progress in many areas, the current state of the majority of public microarray databases is inadequate for supporting these objectives, particularly with regard to chemical indexing. To begin to address these inadequacies, we focus chemical annotation efforts on experimental content contained in the two primary public genomic resources: ArrayExpress and Gene Expression Omnibus. Automated scripts and extensive manual review were employed to transform free-text experiment descriptions into a standardized, chemically indexed inventory of experiments in both resources. These files, which include top-level summary annotations, allow for identification of current chemical-associated experimental content, as well as chemical-exposure-related (or "Treatment") content of greatest potential value to toxicogenomics investigation. With these chemical-index files, it is possible for the first time to assess the breadth and overlap of chemical study space represented in these databases, and to begin to assess the sufficiency of data with shared protocols for chemical similarity inferences. Chemical indexing of public genomics databases is a first important step toward integrating chemical, toxicological and genomics data into predictive toxicology.

Performance evaluation of complete data transfer of physical layer according to IEEE 802.15.4 standard

NASA Astrophysics Data System (ADS)

Raju, Kota Solomon; Merugu, Naresh Babu; Neetu, Babu, E. Ram

2016-03-01

ZigBee is well-accepted industrial standard for wireless sensor networks based on IEEE 802.15.4 standard. Wireless Sensor Networks is the major concern of communication these days. These Wireless Sensor Networks investigate the properties of networks of small battery-powered sensors with wireless communication. The communication between any two wireless nodes of wireless sensor networks is carried out through a protocol stack. This protocol stack has been designed by different vendors in various ways. Every custom vendor possesses his own protocol stack and algorithms especially at the MAC layer. But, many applications require modifications in their algorithms at various layers as per their requirements, especially energy efficient protocols at MAC layer that are simulated in Wireless sensor Network Simulators which are not being tested in real time systems because vendors do not allow the programmability of each layer in their protocol stack. This problem can be quoted as Vendor-Interoperability. The solution is to develop the programmable protocol stack where we can design our own application as required. As a part of the task first we tried implementing physical layer and transmission of data using physical layer. This paper describes about the transmission of the total number of bytes of Frame according to the IEEE 802.15.4 standard using Physical Layer.

Simple algorithm for improved security in the FDDI protocol

NASA Astrophysics Data System (ADS)

Lundy, G. M.; Jones, Benjamin

1993-02-01

We propose a modification to the Fiber Distributed Data Interface (FDDI) protocol based on a simple algorithm which will improve confidential communication capability. This proposed modification provides a simple and reliable system which exploits some of the inherent security properties in a fiber optic ring network. This method differs from conventional methods in that end to end encryption can be facilitated at the media access control sublayer of the data link layer in the OSI network model. Our method is based on a variation of the bit stream cipher method. The transmitting station takes the intended confidential message and uses a simple modulo two addition operation against an initialization vector. The encrypted message is virtually unbreakable without the initialization vector. None of the stations on the ring will have access to both the encrypted message and the initialization vector except the transmitting and receiving stations. The generation of the initialization vector is unique for each confidential transmission and thus provides a unique approach to the key distribution problem. The FDDI protocol is of particular interest to the military in terms of LAN/MAN implementations. Both the Army and the Navy are considering the standard as the basis for future network systems. A simple and reliable security mechanism with the potential to support realtime communications is a necessary consideration in the implementation of these systems. The proposed method offers several advantages over traditional methods in terms of speed, reliability, and standardization.

Effect modification of FADS2 polymorphisms on the association between breastfeeding and intelligence: protocol for a collaborative meta-analysis

PubMed Central

Hartwig, Fernando Pires; Davies, Neil Martin; Horta, Bernardo Lessa; Victora, Cesar Gomes; Davey Smith, George

2016-01-01

Introduction Evidence from observational studies and randomised controlled trials suggests that breastfeeding is positively associated with IQ, possibly because breast milk is a source of long-chain polyunsaturated fatty acids. Different studies have detected gene-breastfeeding interactions involving FADS2 variants and intelligence. However, findings are inconsistent regarding the direction of such effect modification. Methods/design To clarify how FADS2 and breastfeeding interact in their association with IQ, we are conducting a consortium-based meta-analysis of independent studies. Results produced by each individual study using standardised analysis scripts and harmonised data will be used. Inclusion criteria: breastfeeding, IQ and either rs174575 or rs1535 polymorphisms available; and being of European ancestry. Exclusion criteria: twin studies; only poorly imputed genetic data available; or unavailability of proper ethics approval. Studies will be invited based on being known to have at least some of the required data, or suggested by participating studies as potentially eligible. This inclusive approach will favour achieving a larger sample size and be less prone to publication bias. Discussion Improving current understanding of FADS2-breastfeeding interaction may provide important biological insights regarding the importance of long-chain polyunsaturated fatty acids for the breastfeeding-IQ association. This meta-analysis will help to improve such knowledge by replicating earlier studies, conducting additional analysis and evaluating different sources of heterogeneity. Publishing this protocol will minimise the possibility of bias due to post hoc changes to the analysis protocol. PMID:27311901

tRNAmodpred: a computational method for predicting posttranscriptional modifications in tRNAs

PubMed Central

Machnicka, Magdalena A.; Dunin-Horkawicz, Stanislaw; de Crécy-Lagard, Valerie; Bujnicki, Janusz M.

2016-01-01

tRNA molecules contain numerous chemically altered nucleosides, which are formed by enzymatic modification of the primary transcripts during the complex tRNA maturation process. Some of the modifications are introduced by single reactions, while other require complex series of reactions carried out by several different enzymes. The location and distribution of various types of modifications vary greatly between different tRNA molecules, organisms and organelles. We have developed a computational method tRNAmodpred, for predicting modifications in tRNA sequences. Briefly, our method takes as an input one or more unmodified tRNA sequences and a set of protein sequences corresponding to a proteome of a cell. Subsequently it identifies homologs of known tRNA modification enzymes in the proteome, predicts tRNA modification activities and maps them onto known pathways of RNA modification from the MODOMICS database. Thereby, theoretically possible modification pathways are identified, and products of these modification reactions are proposed for query tRNAs. This method allows for predicting modification patterns for newly sequenced genomes as well as for checking tentative modification status of tRNAs from one species treated with enzymes from another source, e.g. to predict the possible modifications of eukaryotic tRNAs expressed in bacteria. tRNAmodpred is freely available as web server at http://genesilico.pl/trnamodpred/. PMID:27016142

Hardware Modifications to the US Army Research Laboratory’s Metalorganic Chemical Vapor Deposition (MOCVD) System for Optimization of Complex Oxide Thin Film Fabrication

DTIC Science & Technology

2015-04-01

studies on flow and thermal fields in MOCVD reactor. Chinese Science Bulletin. 2010;55:560–566. 36. Hampdensmith MJ, Kodas TT. Chemical vapor...Chemistry. 1995;19727–750. 47. Xu CY, Hampdensmith MJ, Kodas TT. Aerosol-assisted chemical-vapor- deposition (AACVD) of binary alloy (AGXPD1-X, CUXPD1-X

The effect on biological and moisture resistance of epichlorohydrin chemically modified wood

Treesearch

Rebecca E. Ibach; Beom-Goo Lee

2002-01-01

Southern pine solid wood and fiber were chemically modified with epichlorohydrin to help in understanding the role of moisture in the mechanism of biological effectiveness of chemically modified wood. The solid wood had weight gains from 11% to 34%, while the fiber had weight gains from 9% to 75%. After modification, part of the specimens were water leached for 2 weeks...

Microplastics in seafood: Benchmark protocol for their extraction and characterization.

PubMed

Dehaut, Alexandre; Cassone, Anne-Laure; Frère, Laura; Hermabessiere, Ludovic; Himber, Charlotte; Rinnert, Emmanuel; Rivière, Gilles; Lambert, Christophe; Soudant, Philippe; Huvet, Arnaud; Duflos, Guillaume; Paul-Pont, Ika

2016-08-01

Pollution of the oceans by microplastics (<5 mm) represents a major environmental problem. To date, a limited number of studies have investigated the level of contamination of marine organisms collected in situ. For extraction and characterization of microplastics in biological samples, the crucial step is the identification of solvent(s) or chemical(s) that efficiently dissolve organic matter without degrading plastic polymers for their identification in a time and cost effective way. Most published papers, as well as OSPAR recommendations for the development of a common monitoring protocol for plastic particles in fish and shellfish at the European level, use protocols containing nitric acid to digest the biological tissues, despite reports of polyamide degradation with this chemical. In the present study, six existing approaches were tested and their effects were compared on up to 15 different plastic polymers, as well as their efficiency in digesting biological matrices. Plastic integrity was evaluated through microscopic inspection, weighing, pyrolysis coupled with gas chromatography and mass spectrometry, and Raman spectrometry before and after digestion. Tissues from mussels, crabs and fish were digested before being filtered on glass fibre filters. Digestion efficiency was evaluated through microscopical inspection of the filters and determination of the relative removal of organic matter content after digestion. Five out of the six tested protocols led to significant degradation of plastic particles and/or insufficient tissue digestion. The protocol using a KOH 10% solution and incubation at 60 °C during a 24 h period led to an efficient digestion of biological tissues with no significant degradation on all tested polymers, except for cellulose acetate. This protocol appeared to be the best compromise for extraction and later identification of microplastics in biological samples and should be implemented in further monitoring studies to ensure relevance and comparison of environmental and seafood product quality studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Optimization of a Sample Processing Protocol for Recovery of ...

EPA Pesticide Factsheets

Journal Article Following a release of Bacillus anthracis spores into the environment, there is a potential for lasting environmental contamination in soils. There is a need for detection protocols for B. anthracis in environmental matrices. However, identification of B. anthracis within a soil is a difficult task. Processing soil samples helps to remove debris, chemical components, and biological impurities that can interfere with microbiological detection. This study aimed to optimize a previously used indirect processing protocol, which included a series of washing and centrifugation steps.

Effect of mouse strain in a model of chemical-induced respiratory allergy.

PubMed

Nishino, Risako; Fukuyama, Tomoki; Watanabe, Yuko; Kurosawa, Yoshimi; Ueda, Hideo; Kosaka, Tadashi

2014-01-01

The inhalation of many types of chemicals is a leading cause of allergic respiratory diseases, and effective protocols are needed for the detection of environmental chemical-related respiratory allergies. In our previous studies, we developed a method for detecting environmental chemical-related respiratory allergens by using a long-term sensitization-challenge protocol involving BALB/c mice. In the current study, we sought to improve our model by characterizing strain-associated differences in respiratory allergic reactions to the well-known chemical respiratory allergen glutaraldehyde (GA). According to our protocol, BALB/c, NC/Nga, C3H/HeN, C57BL/6N, and CBA/J mice were sensitized dermally with GA for 3 weeks and then challenged with intratracheal or inhaled GA at 2 weeks after the last sensitization. The day after the final challenge, all mice were euthanized, and total serum IgE levels were assayed. In addition, immunocyte counts, cytokine production, and chemokine levels in the hilar lymph nodes (LNs) and bronchoalveolar lavage fluids (BALF) were also assessed. In conclusion, BALB/c and NC/Nga mice demonstrated markedly increased IgE reactions. Inflammatory cell counts in BALF were increased in the treated groups of all strains, especially BALB/c, NC/Nga, and CBA/J strains. Cytokine levels in LNs were increased in all treated groups except for C3H/HeN and were particularly high in BALB/c and NC/Nga mice. According to our results, we suggest that BALB/c and NC/Nga are highly susceptible to respiratory allergic responses and therefore are good candidates for use in our model for detecting environmental chemical respiratory allergens.

Surface hydrophobic modification of polyurethanes by diaryl carbene chemistry: Synthesis and characterization

NASA Astrophysics Data System (ADS)

Yang, Pengfei; Wang, Yongqing; Lu, Ling; Yu, Xi; Liu, Lian

2018-03-01

Dodecyl diaryl diazomethane was firstly synthesized from 4,4-dihydroxybenzophenone and 1-bromododecane by a series of reaction steps. Then water-borne polyurethane films with different amount of DMPA were prepared, as well as a type of solvent-borne polyurethane film for comparison. Finally, all these polyurethane films were modified by dodecyl diaryl diazomethane. The dodecyl diaryl carbene was generated from dodecyl diaryl diazomethane by strong solar light, which was very convenient to insert into the Xsbnd H bonds (X = C, N) on the surface of polyurethane films. The contact angle test was used to characterize these films and depict the surface property. DSC analysis and tensile test were used to investigate the physical properties of polyurethane films before and after modification. It was suggested that the hydrophobic modification protocol with carbene insertion was very useful and convenient to prepare water-proof coatings outdoors under direct solar-light exposure.

Porcelain surface conditioning protocols and shear bond strength of orthodontic brackets.

PubMed

Lestrade, Ashley M; Ballard, Richard W; Xu, Xiaoming; Yu, Qingzhao; Kee, Edwin L; Armbruster, Paul C

2016-05-01

The objective of the present study was to determine which of six bonding protocols yielded a clinically acceptable shear bond strength (SBS) of metal orthodontic brackets to CAD/CAM lithium disilicate porcelain restorations. A secondary aim was to determine which bonding protocol produced the least surface damage at debond. Sixty lithium disilicate samples were fabricated to replicate the facial surface of a mandibular first molar using a CEREC CAD/CAM machine. The samples were split into six test groups, each of which received different mechanical/chemical pretreatment protocols to roughen the porcelain surface prior to bonding a molar orthodontic attachment. Shear bond strength testing was conducted using an Instron machine. The mean, maximum, minimal, and standard deviation SBS values for each sample group including an enamel control were calculated. A t-test was used to evaluate the statistical significance between the groups. No significant differences were found in SBS values, with the exception of surface roughening with a green stone prior to HFA and silane treatment. This protocol yielded slightly higher bond strength which was statistically significant. Chemical treatment alone with HFA/silane yielded SBS values within an acceptable clinical range to withstand forces applied by orthodontic treatment and potentially eliminates the need to mechanically roughen the ceramic surface.

Holistic Metrics for Assessment of the Greenness of Chemical Reactions in the Context of Chemical Education

ERIC Educational Resources Information Center

Ribeiro, M. Gabriela T. C.; Machado, Adelio A. S. C.

2013-01-01

Two new semiquantitative green chemistry metrics, the green circle and the green matrix, have been developed for quick assessment of the greenness of a chemical reaction or process, even without performing the experiment from a protocol if enough detail is provided in it. The evaluation is based on the 12 principles of green chemistry. The…

Practical quantum private query of blocks based on unbalanced-state Bennett-Brassard-1984 quantum-key-distribution protocol.

PubMed

Wei, Chun-Yan; Gao, Fei; Wen, Qiao-Yan; Wang, Tian-Yin

2014-12-18

Until now, the only kind of practical quantum private query (QPQ), quantum-key-distribution (QKD)-based QPQ, focuses on the retrieval of a single bit. In fact, meaningful message is generally composed of multiple adjacent bits (i.e., a multi-bit block). To obtain a message a1a2···al from database, the user Alice has to query l times to get each ai. In this condition, the server Bob could gain Alice's privacy once he obtains the address she queried in any of the l queries, since each a(i) contributes to the message Alice retrieves. Apparently, the longer the retrieved message is, the worse the user privacy becomes. To solve this problem, via an unbalanced-state technique and based on a variant of multi-level BB84 protocol, we present a protocol for QPQ of blocks, which allows the user to retrieve a multi-bit block from database in one query. Our protocol is somewhat like the high-dimension version of the first QKD-based QPQ protocol proposed by Jacobi et al., but some nontrivial modifications are necessary.

Fabrication, modification, and application of poly(methyl methacrylate) microfluidic chips.

PubMed

Chen, Yun; Zhang, Luyan; Chen, Gang

2008-05-01

Poly(methyl methacrylate) (PMMA) is particularly useful for microfluidic chips with the features of low price, excellent optic transparency, attractive mechanical and chemical properties, ease of fabrication and modification, biocompatibility, etc. During the past decade, significant progress in the PMMA microfluidic chips has occurred. This review, which contains 120 references, summarizes the recent advances and the key strategies in the fabrication, modification, and application of PMMA microfluidic chips. It is expected that PMMA microchips should find a wide range of applications and will lead to the creation of truly disposable microfluidic devices.

TiO2 induced structural modifications in Cs containing borosilicate glasses: Raman and infrared studies

NASA Astrophysics Data System (ADS)

Pandey, M.; Banerjee, D.; Sudarsan, V.; Kshirsagar, R. J.

2018-04-01

Effect of TiO2 addition in Cs containing Sodium-borosilicate glasses is studied using Raman and infrared spectroscopic techniques. As revealed from infrared and Raman studies, TiO2 does not form segregated phase, but instead enters into the borosilicate network. It is further observed that TiO2 addition results in modifications of the borate and silicate structural units by transforming into tetraborates and metasilicate structural units. These structural modifications are responsible for Cs immobilization, leach rate and chemical durability of these glasses.

Update: Mechanisms underlying N6-methyladenosine modification of eukaryotic mRNA

PubMed Central

Wang, Yang; Zhao, Jing Crystal

2016-01-01

Summary Eukaryotic messenger RNA (mRNA) undergoes chemical modification both at the 5′cap [1, 2] and internally [3–14]. Among internal modifications, m6A, by far the most abundant, is present in all eukaryotes examined, including mammals [3–6], flies [15], plants [16, 17] and yeast [18, 19]. m6A modification plays an essential role in diverse biological processes. Over the past few years, our knowledge relevant to establishment and function of this modification has grown rapidly. This review focuses on technologies that have facilitated m6A detection in mRNAs, identification of m6A methylation enzymes and binding proteins, and potential functions of the modification at the molecular level. Regarding m6A function at cellular or organismal levels or in disease, please refer to other recent reviews [20–23]. PMID:27793360

Protein mass analysis of histones.

PubMed

Galasinski, Scott C; Resing, Katheryn A; Ahn, Natalie G

2003-09-01

Posttranslational modification of chromatin-associated proteins, including histones and high-mobility-group (HMG) proteins, provides an important mechanism to control gene expression, genome integrity, and epigenetic inheritance. Protein mass analysis provides a rapid and unbiased approach to monitor multiple chemical modifications on individual molecules. This review describes methods for acid extraction of histones and HMG proteins, followed by separation by reverse-phase chromatography coupled to electrospray ionization mass spectrometry (LC/ESI-MS). Posttranslational modifications are detected by analysis of full-length protein masses. Confirmation of protein identity and modification state is obtained through enzymatic digestion and peptide sequencing by MS/MS. For differentially modified forms of each protein, the measured intensities are semiquantitative and allow determination of relative abundance and stoichiometry. The method simultaneously detects covalent modifications on multiple proteins and provides a facile assay for comparing chromatin modification states between different cell types and/or cellular responses.

The Expanding Landscape of the Thiol Redox Proteome*

PubMed Central

Yang, Jing; Carroll, Kate S.; Liebler, Daniel C.

2016-01-01

Cysteine occupies a unique place in protein chemistry. The nucleophilic thiol group allows cysteine to undergo a broad range of redox modifications beyond classical thiol-disulfide redox equilibria, including S-sulfenylation (-SOH), S-sulfinylation (-SO2H), S-sulfonylation (-SO3H), S-nitrosylation (-SNO), S-sulfhydration (-SSH), S-glutathionylation (-SSG), and others. Emerging evidence suggests that these post-translational modifications (PTM) are important in cellular redox regulation and protection against oxidative damage. Identification of protein targets of thiol redox modifications is crucial to understanding their roles in biology and disease. However, analysis of these highly labile and dynamic modifications poses challenges. Recent advances in the design of probes for thiol redox forms, together with innovative mass spectrometry based chemoproteomics methods make it possible to perform global, site-specific, and quantitative analyses of thiol redox modifications in complex proteomes. Here, we review chemical proteomic strategies used to expand the landscape of thiol redox modifications. PMID:26518762

Posttranslational Modifications Regulate the Postsynaptic Localization of PSD-95.

PubMed

Vallejo, Daniela; Codocedo, Juan F; Inestrosa, Nibaldo C

2017-04-01

The postsynaptic density (PSD) consists of a lattice-like array of interacting proteins that organizes and stabilizes synaptic receptors, ion channels, structural proteins, and signaling molecules required for normal synaptic transmission and synaptic function. The scaffolding and hub protein postsynaptic density protein-95 (PSD-95) is a major element of central chemical synapses and interacts with glutamate receptors, cell adhesion molecules, and cytoskeletal elements. In fact, PSD-95 can regulate basal synaptic stability as well as the activity-dependent structural plasticity of the PSD and, therefore, of the excitatory chemical synapse. Several studies have shown that PSD-95 is highly enriched at excitatory synapses and have identified multiple protein structural domains and protein-protein interactions that mediate PSD-95 function and trafficking to the postsynaptic region. PSD-95 is also a target of several signaling pathways that induce posttranslational modifications, including palmitoylation, phosphorylation, ubiquitination, nitrosylation, and neddylation; these modifications determine the synaptic stability and function of PSD-95 and thus regulate the fates of individual dendritic spines in the nervous system. In the present work, we review the posttranslational modifications that regulate the synaptic localization of PSD-95 and describe their functional consequences. We also explore the signaling pathways that induce such changes.

Mechanistic understanding of the cysteine capping modifications of antibodies enables selective chemical engineering in live mammalian cells.

PubMed

Zhong, Xiaotian; He, Tao; Prashad, Amar S; Wang, Wenge; Cohen, Justin; Ferguson, Darren; Tam, Amy S; Sousa, Eric; Lin, Laura; Tchistiakova, Lioudmila; Gatto, Scott; D'Antona, Aaron; Luan, Yen-Tung; Ma, Weijun; Zollner, Richard; Zhou, Jing; Arve, Bo; Somers, Will; Kriz, Ronald

2017-04-20

Protein modifications by intricate cellular machineries often redesign the structure and function of existing proteins to impact biological networks. Disulfide bond formation between cysteine (Cys) pairs is one of the most common modifications found in extracellularly-destined proteins, key to maintaining protein structure. Unpaired surface cysteines on secreted mammalian proteins are also frequently found disulfide-bonded with free Cys or glutathione (GSH) in circulation or culture, the mechanism for which remains unknown. Here we report that these so-called Cys-capping modifications take place outside mammalian cells, not in the endoplasmic reticulum (ER) where oxidoreductase-mediated protein disulfide formation occurs. Unpaired surface cysteines of extracellularly-arrived proteins such as antibodies are uncapped upon secretion before undergoing disulfide exchange with cystine or oxidized GSH in culture medium. This observation has led to a feasible way to selectively modify the nucleophilic thiol side-chain of cell-surface or extracellular proteins in live mammalian cells, by applying electrophiles with a chemical handle directly into culture medium. These findings provide potentially an effective approach for improving therapeutic conjugates and probing biological systems. Copyright © 2017 Elsevier B.V. All rights reserved.