Formation of the 67-kDa laminin receptor by acylation of the precursor.

PubMed

Butò, S; Tagliabue, E; Ardini, E; Magnifico, A; Ghirelli, C; van den Brûle, F; Castronovo, V; Colnaghi, M I; Sobel, M E; Ménard, S

1998-06-01

Even though the involvement of the 67-kDa laminin receptor (67LR) in tumor invasiveness has been clearly demonstrated, its molecular structure remains an open problem, since only a full-length gene encoding a 37-kDa precursor protein (37LRP) has been isolated so far. A pool of recently obtained monoclonal antibodies directed against the recombinant 37LRP molecule was used to investigate the processing that leads to the formation of the 67-kDa molecule. In soluble extracts of A431 human carcinoma cells, these reagents recognize the precursor molecule as well as the mature 67LR and a 120-kDa molecule. The recovery of these proteins was found to be strikingly dependent upon the cell solubilization conditions: the 67LR is soluble in NP-40-lysis buffer whereas the 37LRP is NP-40-insoluble. Inhibition of 67LR formation by cerulenin indicates that acylation is involved in the processing of the receptor. It is likely a palmitoylation process, as indicated by sensitivity of NP-40-soluble extracts to hydroxylamine treatment. Immunoblotting assays performed with a polyclonal serum directed against galectin3 showed that both the 67- and the 120-kDa proteins carry galectin3 epitopes whereas the 37LRP does not. These data suggest that the 67LR is a heterodimer stabilized by strong intramolecular hydrophobic interactions, carried by fatty acids bound to the 37LRP and to a galectin3 cross-reacting molecule.

Changes in the vascular cell adhesion molecule-1, intercellular adhesion molecule-1 and c-reactive protein following administration of aqueous extract of piper sarmentosum on experimental rabbits fed with cholesterol diet

PubMed Central

2011-01-01

Background Inflammation process plays an important role in the development of atherosclerosis. Hypercholesterolemia is one of the major risk factors for atherosclerosis. The present study aimed to evaluate the effect of aqueous extract of Piper sarmentosum (P.s) on inflammatory markers like vascular cell adhesion molecule-1 (VCAM-1), intercellular adhesion molecule-1 (ICAM-1), and C-reactive protein (CRP). Methods Forty two male New Zealand white rabbits were divided equally into seven groups; (i) C- control group fed normal rabbit chow (ii) CH- cholesterol diet (1%cholesterol) (iii) X1- 1% cholesterol with water extract of P.s (62.5 mg/kg) (iv) X2- 1% cholesterol with water extract of P.s (125 mg/kg (v) X3- 1% cholesterol with water extract of P.s (250 mg/kg) (vi) X4- 1% cholesterol with water extract of P.s (500 mg/kg) and (vii) SMV group fed with 1% cholesterol supplemented with simvistatin drug (1.2 mg/kg). All animals were treated for 10 weeks. Blood serum was taken for observing the inflammatory markers at the beginning and end of the experiment. Results Rabbits fed with 1% cholesterol diet (CH) showed significant increase in the level of VCAM-1, ICAM-1 and CRP compared to the C group. The levels of VCAM-1, ICAM-1 and CRP in the 1% cholesterol group and supplemented with P.s (500 mg/kg) were significantly reduced compared to the cholesterol group. Similar results were also reported with simvistatin group. Conclusion These results suggest that the supplementation of Piper sarmentosum extract could inhibit inflammatory markers which in turn could prevent atherosclerosis. PMID:21214952

Single molecule data under scrutiny. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb & S.K. Sarkar

NASA Astrophysics Data System (ADS)

Wohland, Thorsten

2015-06-01

Single Molecule Detection and Spectroscopy have grown from their first beginnings into mainstream, mature research areas that are widely applied in the biological sciences. However, despite the advances in technology and the application of many single molecule techniques even in in vivo settings, the data analysis of single molecule experiments is complicated by noise, systematic errors, and complex underlying processes that are only incompletely understood. Colomb and Sarkar provide in this issue an overview of single molecule experiments and the accompanying problems in data analysis, which have to be overcome for a proper interpretation of the experiments [1].

Ambient Mass Spectrometry Imaging Using Direct Liquid Extraction Techniques

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

Laskin, Julia; Lanekoff, Ingela

2015-11-13

Mass spectrometry imaging (MSI) is a powerful analytical technique that enables label-free spatial localization and identification of molecules in complex samples.1-4 MSI applications range from forensics5 to clinical research6 and from understanding microbial communication7-8 to imaging biomolecules in tissues.1, 9-10 Recently, MSI protocols have been reviewed.11 Ambient ionization techniques enable direct analysis of complex samples under atmospheric pressure without special sample pretreatment.3, 12-16 In fact, in ambient ionization mass spectrometry, sample processing (e.g., extraction, dilution, preconcentration, or desorption) occurs during the analysis.17 This substantially speeds up analysis and eliminates any possible effects of sample preparation on the localization of moleculesmore » in the sample.3, 8, 12-14, 18-20 Venter and co-workers have classified ambient ionization techniques into three major categories based on the sample processing steps involved: 1) liquid extraction techniques, in which analyte molecules are removed from the sample and extracted into a solvent prior to ionization; 2) desorption techniques capable of generating free ions directly from substrates; and 3) desorption techniques that produce larger particles subsequently captured by an electrospray plume and ionized.17 This review focuses on localized analysis and ambient imaging of complex samples using a subset of ambient ionization methods broadly defined as “liquid extraction techniques” based on the classification introduced by Venter and co-workers.17 Specifically, we include techniques where analyte molecules are desorbed from solid or liquid samples using charged droplet bombardment, liquid extraction, physisorption, chemisorption, mechanical force, laser ablation, or laser capture microdissection. Analyte extraction is followed by soft ionization that generates ions corresponding to intact species. Some of the key advantages of liquid extraction techniques include the ease of operation, ability to analyze samples in their native environments, speed of analysis, and ability to tune the extraction solvent composition to a problem at hand. For example, solvent composition may be optimized for efficient extraction of different classes of analytes from the sample or for quantification or online derivatization through reactive analysis. In this review, we will: 1) introduce individual liquid extraction techniques capable of localized analysis and imaging, 2) describe approaches for quantitative MSI experiments free of matrix effects, 3) discuss advantages of reactive analysis for MSI experiments, and 4) highlight selected applications (published between 2012 and 2015) that focus on imaging and spatial profiling of molecules in complex biological and environmental samples.« less

L1000CDS2: LINCS L1000 characteristic direction signatures search engine.

PubMed

Duan, Qiaonan; Reid, St Patrick; Clark, Neil R; Wang, Zichen; Fernandez, Nicolas F; Rouillard, Andrew D; Readhead, Ben; Tritsch, Sarah R; Hodos, Rachel; Hafner, Marc; Niepel, Mario; Sorger, Peter K; Dudley, Joel T; Bavari, Sina; Panchal, Rekha G; Ma'ayan, Avi

2016-01-01

The library of integrated network-based cellular signatures (LINCS) L1000 data set currently comprises of over a million gene expression profiles of chemically perturbed human cell lines. Through unique several intrinsic and extrinsic benchmarking schemes, we demonstrate that processing the L1000 data with the characteristic direction (CD) method significantly improves signal to noise compared with the MODZ method currently used to compute L1000 signatures. The CD processed L1000 signatures are served through a state-of-the-art web-based search engine application called L1000CDS 2 . The L1000CDS 2 search engine provides prioritization of thousands of small-molecule signatures, and their pairwise combinations, predicted to either mimic or reverse an input gene expression signature using two methods. The L1000CDS 2 search engine also predicts drug targets for all the small molecules profiled by the L1000 assay that we processed. Targets are predicted by computing the cosine similarity between the L1000 small-molecule signatures and a large collection of signatures extracted from the gene expression omnibus (GEO) for single-gene perturbations in mammalian cells. We applied L1000CDS 2 to prioritize small molecules that are predicted to reverse expression in 670 disease signatures also extracted from GEO, and prioritized small molecules that can mimic expression of 22 endogenous ligand signatures profiled by the L1000 assay. As a case study, to further demonstrate the utility of L1000CDS 2 , we collected expression signatures from human cells infected with Ebola virus at 30, 60 and 120 min. Querying these signatures with L1000CDS 2 we identified kenpaullone, a GSK3B/CDK2 inhibitor that we show, in subsequent experiments, has a dose-dependent efficacy in inhibiting Ebola infection in vitro without causing cellular toxicity in human cell lines. In summary, the L1000CDS 2 tool can be applied in many biological and biomedical settings, while improving the extraction of knowledge from the LINCS L1000 resource.

Investigating organic molecules responsible of auxin-like activity of humic acid fraction extracted from vermicompost.

PubMed

Scaglia, Barbara; Nunes, Ramom Rachide; Rezende, Maria Olímpia Oliveira; Tambone, Fulvia; Adani, Fabrizio

2016-08-15

This work studied the auxin-like activity of humic acids (HA) obtained from vermicomposts produced using leather wastes plus cattle dung at different maturation stages (fresh, stable and mature). Bioassays were performed by testing HA concentrations in the range of 100-6000mgcarbonL(-1). (13)C CPMAS-NMR and GC-MS instrumental methods were used to assess the effect of biological processes and starting organic mixtures on HA composition. Not all HAs showed IAA-like activity and in general, IAA-like activity increased with the length of the vermicomposting process. The presence of leather wastes was not necessary to produce the auxin-like activity of HA, since HA extracted from a mix of cattle manure and sawdust, where no leather waste was added, showed IAA-like activity as well. CPMAS (13)CNMR revealed that HAs were similar independently of the mix used and that the humification process involved the increasing concentration of pre-existing alkali soluble fractions in the biomass. GC/MS allowed the identification of the molecules involved in IAA-like effects: carboxylic acids and amino acids. The concentration of active molecules, rather than their simple presence in HA, determined the bio-stimulating effect, and a good linear regression between auxin-like activity and active stimulating molecules concentration was found (R(2)=-0.85; p<0.01, n=6). Copyright © 2016 Elsevier B.V. All rights reserved.

Isothermal dehydration of thin films of water and sugar solutions

NASA Astrophysics Data System (ADS)

Heyd, R.; Rampino, A.; Bellich, B.; Elisei, E.; Cesàro, A.; Saboungi, M.-L.

2014-03-01

The process of quasi-isothermal dehydration of thin films of pure water and aqueous sugar solutions is investigated with a dual experimental and theoretical approach. A nanoporous paper disk with a homogeneous internal structure was used as a substrate. This experimental set-up makes it possible to gather thermodynamic data under well-defined conditions, develop a numerical model, and extract needed information about the dehydration process, in particular the water activity. It is found that the temperature evolution of the pure water film is not strictly isothermal during the drying process, possibly due to the influence of water diffusion through the cellulose web of the substrate. The role of sugar is clearly detectable and its influence on the dehydration process can be identified. At the end of the drying process, trehalose molecules slow down the diffusion of water molecules through the substrate in a more pronounced way than do the glucose molecules.

Isothermal dehydration of thin films of water and sugar solutions

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

Heyd, R.; Rampino, A.; Laboratory of Physical and Macromolecular Chemistry, University of Trieste, Via Giorgieri 1, 34127 Trieste

The process of quasi-isothermal dehydration of thin films of pure water and aqueous sugar solutions is investigated with a dual experimental and theoretical approach. A nanoporous paper disk with a homogeneous internal structure was used as a substrate. This experimental set-up makes it possible to gather thermodynamic data under well-defined conditions, develop a numerical model, and extract needed information about the dehydration process, in particular the water activity. It is found that the temperature evolution of the pure water film is not strictly isothermal during the drying process, possibly due to the influence of water diffusion through the cellulose webmore » of the substrate. The role of sugar is clearly detectable and its influence on the dehydration process can be identified. At the end of the drying process, trehalose molecules slow down the diffusion of water molecules through the substrate in a more pronounced way than do the glucose molecules.« less

Single-Molecule Sensing with Nanopore Confinement: From Chemical Reactions to Biological Interactions.

PubMed

Lin, Yao; Ying, Yi-Lun; Gao, Rui; Long, Yi-Tao

2018-03-25

The nanopore can generate an electrochemical confinement for single-molecule sensing that help understand the fundamental chemical principle in nanoscale dimensions. By observing the generated ionic current, individual bond-making and bond-breaking steps, single biomolecule dynamic conformational changes and electron transfer processes that occur within pore can be monitored with high temporal and current resolution. These single-molecule studies in nanopore confinement are revealing information about the fundamental chemical and biological processes that cannot be extracted from ensemble measurements. In this Concept article, we introduce and discuss the electrochemical confinement effects on single-molecule covalent reactions, conformational dynamics of individual molecules and host-guest interactions in protein nanopores. Then, we extend the concept of nanopore confinement effects to confine electrochemical redox reactions in solid-state nanopores for developing new sensing mechanisms. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Single-Molecule Analysis of Pre-mRNA Splicing with Colocalization Single-Molecule Spectroscopy (CoSMoS).

PubMed

Braun, Joerg E; Serebrov, Victor

2017-01-01

Recent development of single-molecule techniques to study pre-mRNA splicing has provided insights into the dynamic nature of the spliceosome. Colocalization single-molecule spectroscopy (CoSMoS) allows following spliceosome assembly in real time at single-molecule resolution in the full complexity of cellular extracts. A detailed protocol of CoSMoS has been published previously (Anderson and Hoskins, Methods Mol Biol 1126:217-241, 2014). Here, we provide an update on the technical advances since the first CoSMoS studies including slide surface treatment, data processing, and representation. We describe various labeling strategies to generate RNA reporters with multiple dyes (or other moieties) at specific locations.

Plant Extract Synthesized PLA Nanoparticles for Controlled and Sustained Release of Quercetin: A Green Approach

PubMed Central

Yadav, Sudesh Kumar

2012-01-01

Background Green synthesis of metallic nanoparticles (NPs) has been extensively carried out by using plant extracts (PEs) which have property of stabilizers/ emulsifiers. To our knowledge, there is no comprehensive study on applying a green approach using PEs for fabrication of biodegradable PLA NPs. Conventional methods rely on molecules like polyvinyl alcohol, polyethylene glycol, D-alpha-tocopheryl poly(ethylene glycol 1000) succinate as stabilizers/emulsifiers for the synthesis of such biodegradable NPs which are known to be toxic. So, there is urgent need to look for stabilizers which are biogenic and non-toxic. The present study investigated use of PEs as stabilizers/emulsifiers for the fabrication of stable PLA NPs. Synthesized PLA NPs through this green process were explored for controlled release of the well known antioxidant molecule quercetin. Methodology/Principal Findings Stable PLA NPs were synthesized using leaf extracts of medicinally important plants like Syzygium cumini (1), Bauhinia variegata (2), Cedrus deodara (3), Lonicera japonica (4) and Eleaocarpus sphaericus (5). Small and uniformly distributed NPs in the size range 70±30 nm to 143±36 nm were formed with these PEs. To explore such NPs for drugs/ small molecules delivery, we have successfully encapsulated quercetin a lipophilic molecule on a most uniformly distributed PLA-4 NPs synthesized using Lonicera japonica leaf extract. Quercetin loaded PLA-4 NPs were observed for slow and sustained release of quercetin molecule. Conclusions This green approach based on PEs mediated synthesis of stable PLA NPs pave the way for encapsulating drug/small molecules, nutraceuticals and other bioactive ingredients for safer cellular uptake, biodistribution and targeted delivery. Hence, such PEs synthesized PLA NPs would be useful to enhance the therapeutic efficacy of encapsulated small molecules/drugs. Furthermore, different types of plants can be explored for the synthesis of PLA as well as other polymeric NPs of smaller size. PMID:22844443

Imaging ultrafast dynamics of molecules with laser-induced electron diffraction.

PubMed

Lin, C D; Xu, Junliang

2012-10-14

We introduce a laser-induced electron diffraction method (LIED) for imaging ultrafast dynamics of small molecules with femtosecond mid-infrared lasers. When molecules are placed in an intense laser field, both low- and high-energy photoelectrons are generated. According to quantitative rescattering (QRS) theory, high-energy electrons are produced by a rescattering process where electrons born at the early phase of the laser pulse are driven back to rescatter with the parent ion. From the high-energy electron momentum spectra, field-free elastic electron-ion scattering differential cross sections (DCS), or diffraction images, can be extracted. With mid-infrared lasers as the driving pulses, it is further shown that the DCS can be used to extract atomic positions in a molecule with sub-angstrom spatial resolution, in close analogy to the standard electron diffraction method. Since infrared lasers with pulse duration of a few to several tens of femtoseconds are already available, LIED can be used for imaging dynamics of molecules with sub-angstrom spatial and a few-femtosecond temporal resolution. The first experiment with LIED has shown that the bond length of oxygen molecules shortens by 0.1 Å in five femtoseconds after single ionization. The principle behind LIED and its future outlook as a tool for dynamic imaging of molecules are presented.

Use of Laboratory Data to Model Interstellar Chemistry

NASA Technical Reports Server (NTRS)

Vidali, Gianfranco; Roser, J. E.; Manico, G.; Pirronello, V.

2006-01-01

Our laboratory research program is about the formation of molecules on dust grains analogues in conditions mimicking interstellar medium environments. Using surface science techniques, in the last ten years we have investigated the formation of molecular hydrogen and other molecules on different types of dust grain analogues. We analyzed the results to extract quantitative information on the processes of molecule formation on and ejection from dust grain analogues. The usefulness of these data lies in the fact that these results have been employed by theoreticians in models of the chemical evolution of ISM environments.

Bioluminescent Reaction by Immobilized Luciferase

NASA Astrophysics Data System (ADS)

Tanaka, Ryuta; Takahama, Eriko; Iinuma, Masataka; Ikeda, Takeshi; Kadoya, Yutaka; Kuroda, Akio

We have investigated an effect of immobilization of luciferase molecules at the optical fiber end on a bioluminescent reaction. The time dependence of measured count rates of emitted photons has been analyzed by fitting with numerical solution of differential equations including the effect of the product-inhibitor and the deactivation of the luciferase. Through the analysis, we have successfully extracted kinetic constants such as, reaction rate, number of active luciferase molecules, etc. Ratio of active molecules to total luciferase molecules in immobilization was one order of magnitude lower than that in solution. The reaction rate of the bioluminescent process was also different from the one of free luciferase in solution.

Multiplexed Sequence Encoding: A Framework for DNA Communication.

PubMed

Zakeri, Bijan; Carr, Peter A; Lu, Timothy K

2016-01-01

Synthetic DNA has great propensity for efficiently and stably storing non-biological information. With DNA writing and reading technologies rapidly advancing, new applications for synthetic DNA are emerging in data storage and communication. Traditionally, DNA communication has focused on the encoding and transfer of complete sets of information. Here, we explore the use of DNA for the communication of short messages that are fragmented across multiple distinct DNA molecules. We identified three pivotal points in a communication-data encoding, data transfer & data extraction-and developed novel tools to enable communication via molecules of DNA. To address data encoding, we designed DNA-based individualized keyboards (iKeys) to convert plaintext into DNA, while reducing the occurrence of DNA homopolymers to improve synthesis and sequencing processes. To address data transfer, we implemented a secret-sharing system-Multiplexed Sequence Encoding (MuSE)-that conceals messages between multiple distinct DNA molecules, requiring a combination key to reveal messages. To address data extraction, we achieved the first instance of chromatogram patterning through multiplexed sequencing, thereby enabling a new method for data extraction. We envision these approaches will enable more widespread communication of information via DNA.

Automatic differential analysis of NMR experiments in complex samples.

PubMed

Margueritte, Laure; Markov, Petar; Chiron, Lionel; Starck, Jean-Philippe; Vonthron-Sénécheau, Catherine; Bourjot, Mélanie; Delsuc, Marc-André

2018-06-01

Liquid state nuclear magnetic resonance (NMR) is a powerful tool for the analysis of complex mixtures of unknown molecules. This capacity has been used in many analytical approaches: metabolomics, identification of active compounds in natural extracts, and characterization of species, and such studies require the acquisition of many diverse NMR measurements on series of samples. Although acquisition can easily be performed automatically, the number of NMR experiments involved in these studies increases very rapidly, and this data avalanche requires to resort to automatic processing and analysis. We present here a program that allows the autonomous, unsupervised processing of a large corpus of 1D, 2D, and diffusion-ordered spectroscopy experiments from a series of samples acquired in different conditions. The program provides all the signal processing steps, as well as peak-picking and bucketing of 1D and 2D spectra, the program and its components are fully available. In an experiment mimicking the search of a bioactive species in a natural extract, we use it for the automatic detection of small amounts of artemisinin added to a series of plant extracts and for the generation of the spectral fingerprint of this molecule. This program called Plasmodesma is a novel tool that should be useful to decipher complex mixtures, particularly in the discovery of biologically active natural products from plants extracts but can also in drug discovery or metabolomics studies. Copyright © 2017 John Wiley & Sons, Ltd.

Fast kinetics of chromatin assembly revealed by single-molecule videomicroscopy and scanning force microscopy

PubMed Central

Ladoux, Benoit; Quivy, Jean-Pierre; Doyle, Patrick; Roure, Olivia du; Almouzni, Geneviève; Viovy, Jean-Louis

2000-01-01

Fluorescence videomicroscopy and scanning force microscopy were used to follow, in real time, chromatin assembly on individual DNA molecules immersed in cell-free systems competent for physiological chromatin assembly. Within a few seconds, molecules are already compacted into a form exhibiting strong similarities to native chromatin fibers. In these extracts, the compaction rate is more than 100 times faster than expected from standard biochemical assays. Our data provide definite information on the forces involved (a few piconewtons) and on the reaction path. DNA compaction as a function of time revealed unique features of the assembly reaction in these extracts. They imply a sequential process with at least three steps, involving DNA wrapping as the final event. An absolute and quantitative measure of the kinetic parameters of the early steps in chromatin assembly under physiological conditions could thus be obtained. PMID:11114182

Optimization of an extraction protocol for organic matter from soils and sediments using high resolution mass spectrometry: selectivity and biases

NASA Astrophysics Data System (ADS)

Chu, R. K.; Tfaily, M. M.; Tolic, N.; Kyle, J. E.; Robinson, E. R.; Hess, N. J.; Paša-Tolić, L.

2015-12-01

Soil organic matter (SOM) is a complex mixture of above and belowground plant litter and microbial residues, and is a key reservoir for carbon (C) and nutrient biogeochemical cycling in different ecosystems. A limited understanding of the molecular composition of SOM prohibits the ability to routinely decipher chemical processes within soil and predict how terrestrial C fluxes will response to changing climatic conditions. Here, we present that the choice of solvent can be used to selectively extract different compositional fractions from SOM to either target a specific class of compounds or gain a better understanding of the entire composition of the soil sample using 12T Fourier transform ion cyclotron resonance mass spectrometry. Specifically, we found that hexane and chloroform were selective for lipid-like compounds with very low O:C ratios; water was selective for carbohydrates with high O:C ratios; acetonitrile preferentially extracts lignin, condensed structures, and tannin polyphenolic compounds with O:C > 0.5; methanol has higher selectivity towards lignin and lipid compounds characterized with relatively low O:C < 0.5. Hexane, chloroform, methanol, acetonitrile and water increase the number and types of organic molecules extracted from soil for a broader range of chemically diverse soil types. Since each solvent extracts a selective group of compounds, using a suite of solvents with varying polarity for analysis results in more comprehensive representation of the diversity of organic molecules present in soil and a better representation of the whole spectrum of available substrates for microorganisms. Moreover, we have developed a sequential extraction protocol that permits sampling diverse classes of organic compounds while minimizing ionization competition during ESI while increasing sample throughput and decreasing sample volume. This allowed us to hypothesize about possible chemical reactions relating classes of organic molecules that reflect abiotic and biotic processes impacting SOM composition.

Fractionation of yeast extract by nanofiltration process to assess key compounds involved in CHO cell culture improvement.

PubMed

Mosser, Mathilde; Kapel, Romain; Chevalot, Isabelle; Olmos, Eric; Marc, Ivan; Marc, Annie; Oriol, Eric

2015-01-01

Yeast extract (YE) is known to greatly enhance mammalian cell culture performances, but its undefined composition decreases process reliability. Accordingly, in the present study, the nature of YE compounds involved in the improvement of recombinant CHO cell growth and IgG production was investigated. First, the benefits of YE were verified, revealing that it increased maximal concentrations of viable cells and IgG up to 73 and 60%, respectively compared to a reference culture. Then, the analyses of YE composition highlighted the presence of molecules such as amino acids, vitamins, salts, nucleobase, and glucose that were contained in reference medium, while others including peptides, trehalose, polysaccharides, and nucleic acids were not. Consequently, YE was fractionated by a nanofiltration process to deeper evaluate its effects on CHO cell cultures. The YE molecules already contained in reference medium were mainly isolated in the permeate fraction together with trehalose and short peptides, while other molecules were concentrated in the retentate. Permeate, which was free of macromolecules, exhibited a similar positive effect than raw YE on maximal concentrations. Additional studies on cell energetic metabolism underlined that dipeptides and tripeptides in permeate were used as an efficient source of nitrogenous substrates. © 2015 American Institute of Chemical Engineers.

Mechanism of bio molecule stabilized selenium nanoparticles against oxidation process and Clostridium Botulinum.

PubMed

Tareq, Foysal Kabir; Fayzunnesa, Mst; Kabir, Md Shahariar; Nuzat, Musrat

2018-02-01

The bio molecules from plant leaf extract utilized in the preparation of selenium material at the nano scale. The selenium ion was reduced to selenium nanoparticles in the presence of molecule residue of the plant leaf extract. The bio molecule stabilized selenium nanoparticles were grown gradually in the reaction mixture. The selenium nanoparticles were characterized using atomic absorption spectroscopy, fourier transform inferred spectroscopy, X-ray diffraction, scanning electronic microscope and transmission electronic microscope. The selenium nanoparticles were synthesized successfully as the nano-crystalline pure hexagonal phase and the size range of 26-41 nm with spherical in shape. The activity and mechanism of nanoparticles suggested that the selenium nanoparticles are causes of leakage of reducing sugars and protein of pathogens membrane cell. The selenium nano are responsible for death and fully inhibited the microbial growth of pathogen. The bio molecule stabilized selenium nanoparticles were also investigated for the antioxidant agent. Selenium nanoparticles showed scavenging activity up to 94.48%. These results recommended that the advantages of using this method for synthesis of selenium nanoparticles with excellent antioxidant and antimicrobial mechanism and activity, which can be used as the antioxidant and antibiotic agent. Copyright © 2017 Elsevier Ltd. All rights reserved.

Complementary experimental-simulational study of surfactant micellar phase in the extraction process of metallic ions: Effects of temperature and salt concentration

NASA Astrophysics Data System (ADS)

Soto-Ángeles, Alan Gustavo; Rodríguez-Hidalgo, María del Rosario; Soto-Figueroa, César; Vicente, Luis

2018-02-01

The thermoresponsive micellar phase behaviour that exhibits the Triton-X-100 micelles by temperature effect and addition of salt in the extraction process of metallic ions was explored from mesoscopic and experimental points. In the theoretical study, we analyse the formation of Triton-X-100 micelles, load and stabilization of dithizone molecules and metallic ions extraction inside the micellar core at room temperature; finally, a thermal analysis is presented. In the experimental study, the spectrophotometric outcomes confirm the solubility of the copper-dithizone complex in the micellar core, as well as the extraction of metallic ions of aqueous environment via a cloud-point at 332.2 K. The micellar solutions with salt present a low absorbance value compared with the micellar solutions without salt. The decrease in the absorbance value is attributed to a change in the size of hydrophobic region of colloidal micelles. All transitory stages of extraction process are discussed and analysed in this document.

An RF-Powered Micro-Reactor for Efficient Extraction and Hydrolysis

NASA Astrophysics Data System (ADS)

Scott, V.

2014-12-01

An RF sample-processing micro-reactor that was developed as part of potential in situ Exploration Missions to inner- and outer-planetary bodies was designed to utilize aqueous solutions subjected to 60 GHz radiation at 730 mW of input power to extract target organic compounds and molecular and inorganic ions as well as to hydrolyze complex polymeric materials. Successful identification and characterization of these molecules relies on the sample-processing techniques utilized alongside state-of-the-art detection and analysis. For mass and power restrictions put on space exploration missions, smaller and more efficient instruments are highly desirable. The RF micro-reactor potentially offers a simplified alternative to the typical gold-standard extractions that often use solvents, chemicals, and conditions that can vary wildly and depend on the targeted molecules. Instead, this instrument uses a single solvent ­— water — that can be "tuned" under the different experimental conditions, leveraging the operating principles of the Sub-Critical Water Extractor. Proof-of-concept experiments examining the hydrolysis of glycosidic and peptide bonds were successful in demonstrating the RF micro-reactor's capabilities. Progress toward coupling the reactor with a micro-scale sample-handling system enabling slurry delivery has been made and preliminary results on heterogeneous reactions and extractions will be presented.

L1000CDS2: LINCS L1000 characteristic direction signatures search engine

PubMed Central

Duan, Qiaonan; Reid, St Patrick; Clark, Neil R; Wang, Zichen; Fernandez, Nicolas F; Rouillard, Andrew D; Readhead, Ben; Tritsch, Sarah R; Hodos, Rachel; Hafner, Marc; Niepel, Mario; Sorger, Peter K; Dudley, Joel T; Bavari, Sina; Panchal, Rekha G; Ma’ayan, Avi

2016-01-01

The library of integrated network-based cellular signatures (LINCS) L1000 data set currently comprises of over a million gene expression profiles of chemically perturbed human cell lines. Through unique several intrinsic and extrinsic benchmarking schemes, we demonstrate that processing the L1000 data with the characteristic direction (CD) method significantly improves signal to noise compared with the MODZ method currently used to compute L1000 signatures. The CD processed L1000 signatures are served through a state-of-the-art web-based search engine application called L1000CDS2. The L1000CDS2 search engine provides prioritization of thousands of small-molecule signatures, and their pairwise combinations, predicted to either mimic or reverse an input gene expression signature using two methods. The L1000CDS2 search engine also predicts drug targets for all the small molecules profiled by the L1000 assay that we processed. Targets are predicted by computing the cosine similarity between the L1000 small-molecule signatures and a large collection of signatures extracted from the gene expression omnibus (GEO) for single-gene perturbations in mammalian cells. We applied L1000CDS2 to prioritize small molecules that are predicted to reverse expression in 670 disease signatures also extracted from GEO, and prioritized small molecules that can mimic expression of 22 endogenous ligand signatures profiled by the L1000 assay. As a case study, to further demonstrate the utility of L1000CDS2, we collected expression signatures from human cells infected with Ebola virus at 30, 60 and 120 min. Querying these signatures with L1000CDS2 we identified kenpaullone, a GSK3B/CDK2 inhibitor that we show, in subsequent experiments, has a dose-dependent efficacy in inhibiting Ebola infection in vitro without causing cellular toxicity in human cell lines. In summary, the L1000CDS2 tool can be applied in many biological and biomedical settings, while improving the extraction of knowledge from the LINCS L1000 resource. PMID:28413689

Metal Cationization Extractive Electrospray Ionization Mass Spectrometry of Compounds Containing Multiple Oxygens

NASA Astrophysics Data System (ADS)

Swanson, Kenneth D.; Spencer, Sandra E.; Glish, Gary L.

2017-06-01

Extractive electrospray ionization is an ambient ionization technique that allows real-time sampling of liquid samples, including organic aerosols. Similar to electrospray ionization, the composition of the electrospray solvent used in extractive electrospray ionization can easily be altered to form metal cationized molecules during ionization simply by adding a metal salt to the electrospray solvent. An increase in sensitivity is observed for some molecules that are lithium, sodium, or silver cationized compared with the protonated molecule formed in extractive electrospray ionization with an acid additive. Tandem mass spectrometry of metal cationized molecules can also significantly improve the ability to identify a compound. Tandem mass spectrometry of lithium and silver cationized molecules can result in an increase in the number and uniqueness of dissociation pathways relative to [M + H]+. These results highlight the potential for extractive electrospray ionization with metal cationization in analyzing complex aerosol mixtures. [Figure not available: see fulltext.

Analyzing Single-Molecule Time Series via Nonparametric Bayesian Inference

PubMed Central

Hines, Keegan E.; Bankston, John R.; Aldrich, Richard W.

2015-01-01

The ability to measure the properties of proteins at the single-molecule level offers an unparalleled glimpse into biological systems at the molecular scale. The interpretation of single-molecule time series has often been rooted in statistical mechanics and the theory of Markov processes. While existing analysis methods have been useful, they are not without significant limitations including problems of model selection and parameter nonidentifiability. To address these challenges, we introduce the use of nonparametric Bayesian inference for the analysis of single-molecule time series. These methods provide a flexible way to extract structure from data instead of assuming models beforehand. We demonstrate these methods with applications to several diverse settings in single-molecule biophysics. This approach provides a well-constrained and rigorously grounded method for determining the number of biophysical states underlying single-molecule data. PMID:25650922

Single-molecule studies of oligomer extraction and uptake of dyes in poly(dimethylsiloxane) films.

PubMed

Lange, Jeffrey J; Collinson, Maryanne M; Culbertson, Christopher T; Higgins, Daniel A

2009-12-15

Single-molecule microscopic methods were used to probe the uptake, mobility, and entrapment of dye molecules in cured poly(dimethylsiloxane) (PDMS) films as a function of oligomer extraction. The results are relevant to the use of PDMS in microfluidic separations, pervaporation, solid-phase microextraction, and nanofiltration. PDMS films were prepared by spin-casting dilute solutions of Sylgard 184 onto glass coverslips, yielding approximately 1.4 microm thick films after curing. Residual oligomers were subsequently extracted from the films by "spin extraction". In this procedure, 200 microL aliquots of isopropyl alcohol were repeatedly dropped onto the film surface and spun off at 2000 rpm. Samples extracted 5, 10, 20, and 40 times were investigated. Dye molecules were loaded into these films by spin-casting nanomolar dye solutions onto the films. Both neutral perylene diimide (N,N'-bis(butoxypropyl)perylene-3,4,9,10-tetracarboxylic diimide) and cationic rhodamine 6G (R6G) dyes were employed. The films were imaged by confocal fluorescence microscopy. The images obtained depict nonzero populations of fixed and mobile molecules in all films. Cross-correlation methods were used to quantitatively determine the population of fixed molecules in a given region, while a Bayesian burst analysis was used to obtain the total population of molecules. The results show that the total amount of dye loaded increases with increased oligomer extraction, while the relative populations of fixed and mobile molecules decrease and increase, respectively. Bulk R6G data also show greater dye loading with increased oligomer extraction.

Proglobulin processing enzyme in vacuoles isolated from developing pumpkin cotyledons

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

Hara-Nishimura, I.; Nishimura, M.

1987-10-01

The enzymic conversion of proglobulin to globulin catalyzed by the extracts of vacuoles isolated from developing pumpkin (Cucurbita sp. cv Kurokawa Amakuri Nankin) cotyledons was investigated. The endoplasmic reticulum fraction isolated from the developing cotyledons pulse-labeled with (/sup 35/S)methionine was shown to contain mainly the radiolabeled proglobulin, which was used as a substrate for assaying the proteolytic processing in vitro. The vacuolar extracts catalyzed the proteolytic processing of the proglobulin molecule to produce globulin containing two kinds of polypeptide chains, ..gamma.. and delta. The pH optimum for the vacuole-mediated conversion was at pH 5.0. The proteolytic processing of proglobulin bymore » the vacuolar extracts was inhibited in the presence of various thiol reagents, e.g. p-chloromercuribenzoate, N-ethylmaleimide, iodoacetic acid, Hg/sup 2 +/, and Cu/sup 2 +/, but not phenylmethylsulfonyl fluoride, EDTA, o-phenanthroline, leupeptin, antipain, pepstatin, chymostatin, or pumpkin trypsin inhibitor, and was activated in the presence of dithiothreitol and cysteine, indicating that the processing enzyme is a thiol protease. The suborganellar fractionation of the vacuoles showed that the processing activity was localized in the matrix fraction, but not in the membrane or crystalloid fractions. During the seed development, the enzyme was shown to increase, exhibiting the maximal activity at the late developmental stage. The matrix fraction of the protein bodies isolated from the dry castor bean (Ricinus communis) exhibited the processing activity toward the pumpkin proglobulin molecules in the same manner as that by the matrix fraction of pumpkin vacuoles.« less

A comparison study on microwave-assisted extraction of Artemisia sphaerocephala polysaccharides with conventional method: Molecule structure and antioxidant activities evaluation.

PubMed

Wang, Junlong; Zhang, Ji; Wang, Xiaofang; Zhao, Baotang; Wu, Yiqian; Yao, Jian

2009-12-01

The conventional extraction methods for polysaccharides were time-consuming, laborious and energy-consuming. Microwave-assisted extraction (MAE) technique was employed for the extraction of Artemisia sphaerocephala polysaccharides (ASP), which is a traditional Chinese food. The extracting parameters were optimized by Box-Behnken design. In microwave heating process, a decrease in molecular weight (M(w)) was detected in SEC-LLS measurement. A d(f) value of 2.85 indicated ASP using MAE exhibited as a sphere conformation of branched clusters in aqueous solution. Furthermore, it showed stronger antioxidant activities compared with hot water extraction. The data obtained showed that the molecular weights played a more important role in antioxidant activities.

Thermal Degradation of Small Molecules: A Global Metabolomic Investigation.

PubMed

Fang, Mingliang; Ivanisevic, Julijana; Benton, H Paul; Johnson, Caroline H; Patti, Gary J; Hoang, Linh T; Uritboonthai, Winnie; Kurczy, Michael E; Siuzdak, Gary

2015-11-03

Thermal processes are widely used in small molecule chemical analysis and metabolomics for derivatization, vaporization, chromatography, and ionization, especially in gas chromatography mass spectrometry (GC/MS). In this study the effect of heating was examined on a set of 64 small molecule standards and, separately, on human plasma metabolite extracts. The samples, either derivatized or underivatized, were heated at three different temperatures (60, 100, and 250 °C) at different exposure times (30 s, 60 s, and 300 s). All the samples were analyzed by liquid chromatography coupled to electrospray ionization mass spectrometry (LC/MS) and the data processed by XCMS Online ( xcmsonline.scripps.edu ). The results showed that heating at an elevated temperature of 100 °C had an appreciable effect on both the underivatized and derivatized molecules, and heating at 250 °C created substantial changes in the profile. For example, over 40% of the molecular peaks were altered in the plasma metabolite analysis after heating (250 °C, 300s) with a significant formation of degradation and transformation products. The analysis of 64 small molecule standards validated the temperature-induced changes observed on the plasma metabolites, where most of the small molecules degraded at elevated temperatures even after minimal exposure times (30 s). For example, tri- and diorganophosphates (e.g., adenosine triphosphate and adenosine diphosphate) were readily degraded into a mono-organophosphate (e.g., adenosine monophosphate) during heating. Nucleosides and nucleotides (e.g., inosine and inosine monophosphate) were also found to be transformed into purine derivatives (e.g., hypoxanthine). A newly formed transformation product, oleoyl ethyl amide, was identified in both the underivatized and derivatized forms of the plasma extracts and small molecule standard mixture, and was likely generated from oleic acid. Overall these analyses show that small molecules and metabolites undergo significant time-sensitive alterations when exposed to elevated temperatures, especially those conditions that mimic sample preparation and analysis in GC/MS experiments.

In situ product removal in fermentation systems: improved process performance and rational extractant selection.

PubMed

Dafoe, Julian T; Daugulis, Andrew J

2014-03-01

The separation of inhibitory compounds as they are produced in biotransformation and fermentation systems is termed in situ product removal (ISPR). This review examines recent ISPR strategies employing several classes of extractants including liquids, solids, gases, and combined extraction systems. Improvement through the simple application of an auxiliary phase are tabulated and summarized to indicate the breadth of recent ISPR activities. Studies within the past 5 years that have highlighted and have discussed "second phase" properties, and that have an effect on fermentation performance, are particular focus of this review. ISPR, as a demonstrably effective processing strategy, continues to be widely adopted as more applications are explored; however, focus on the properties of extractants and their rational selection based on first principle considerations will likely be key to successfully applying ISPR to more challenging target molecules.

A Method for Extracting the Free Energy Surface and Conformational Dynamics of Fast-Folding Proteins from Single Molecule Photon Trajectories

PubMed Central

2015-01-01

Single molecule fluorescence spectroscopy holds the promise of providing direct measurements of protein folding free energy landscapes and conformational motions. However, fulfilling this promise has been prevented by technical limitations, most notably, the difficulty in analyzing the small packets of photons per millisecond that are typically recorded from individual biomolecules. Such limitation impairs the ability to accurately determine conformational distributions and resolve sub-millisecond processes. Here we develop an analytical procedure for extracting the conformational distribution and dynamics of fast-folding proteins directly from time-stamped photon arrival trajectories produced by single molecule FRET experiments. Our procedure combines the maximum likelihood analysis originally developed by Gopich and Szabo with a statistical mechanical model that describes protein folding as diffusion on a one-dimensional free energy surface. Using stochastic kinetic simulations, we thoroughly tested the performance of the method in identifying diverse fast-folding scenarios, ranging from two-state to one-state downhill folding, as a function of relevant experimental variables such as photon count rate, amount of input data, and background noise. The tests demonstrate that the analysis can accurately retrieve the original one-dimensional free energy surface and microsecond folding dynamics in spite of the sub-megahertz photon count rates and significant background noise levels of current single molecule fluorescence experiments. Therefore, our approach provides a powerful tool for the quantitative analysis of single molecule FRET experiments of fast protein folding that is also potentially extensible to the analysis of any other biomolecular process governed by sub-millisecond conformational dynamics. PMID:25988351

A Method for Extracting the Free Energy Surface and Conformational Dynamics of Fast-Folding Proteins from Single Molecule Photon Trajectories.

PubMed

Ramanathan, Ravishankar; Muñoz, Victor

2015-06-25

Single molecule fluorescence spectroscopy holds the promise of providing direct measurements of protein folding free energy landscapes and conformational motions. However, fulfilling this promise has been prevented by technical limitations, most notably, the difficulty in analyzing the small packets of photons per millisecond that are typically recorded from individual biomolecules. Such limitation impairs the ability to accurately determine conformational distributions and resolve sub-millisecond processes. Here we develop an analytical procedure for extracting the conformational distribution and dynamics of fast-folding proteins directly from time-stamped photon arrival trajectories produced by single molecule FRET experiments. Our procedure combines the maximum likelihood analysis originally developed by Gopich and Szabo with a statistical mechanical model that describes protein folding as diffusion on a one-dimensional free energy surface. Using stochastic kinetic simulations, we thoroughly tested the performance of the method in identifying diverse fast-folding scenarios, ranging from two-state to one-state downhill folding, as a function of relevant experimental variables such as photon count rate, amount of input data, and background noise. The tests demonstrate that the analysis can accurately retrieve the original one-dimensional free energy surface and microsecond folding dynamics in spite of the sub-megahertz photon count rates and significant background noise levels of current single molecule fluorescence experiments. Therefore, our approach provides a powerful tool for the quantitative analysis of single molecule FRET experiments of fast protein folding that is also potentially extensible to the analysis of any other biomolecular process governed by sub-millisecond conformational dynamics.

Fluorous tagging strategy for solution-phase synthesis of small molecules, peptides and oligosaccharides

PubMed Central

Zhang, Wei

2005-01-01

The purification of reaction mixtures is a slow process in organic synthesis, especially during the production of large numbers of analogs and compound libraries. Phase-tag methods such as solid-phase synthesis and fluorous synthesis, provide efficient ways of addressing the separation issue. Fluorous synthesis employs functionalized perfluoroalkyl groups attached to substrates or reagents. The separation of the resulting fluorous molecules can be achieved using strong and selective fluorous liquid-liquid extraction, fluorous silica gel-based solid-phase extraction or high-performance liquid chromatography. Fluorous technology is a novel solution-phase method, which has the advantages of fast reaction times in homogeneous environments, being readily adaptable to literature conditions, having easy intermediate analysis, and having flexibility in reaction scale and scope. In principle, any synthetic methods that use a solid-support could be conducted in solution-phase by replacing the polymer linker with a corresponding fluorous tag. This review summarizes the progress of fluorous tags in solution-phase synthesis of small molecules, peptides and oligosaccharides. PMID:15595439

In situ temperature monitoring in single-molecule FRET experiments

NASA Astrophysics Data System (ADS)

Hartmann, Andreas; Berndt, Frederic; Ollmann, Simon; Krainer, Georg; Schlierf, Michael

2018-03-01

Thermodynamic properties of single molecules including enthalpic and entropic contributions are often determined from experiments by a direct control and precise measurement of the local temperature. However, common temperature monitoring techniques using, for example, ultrafine temperature probes can lead to uncertainties as the probe cannot be placed in the vicinity of the molecule of interest. Here, we devised an approach to measure the local temperature in freely diffusing confocal single-molecule Förster Resonance Energy Transfer (smFRET) experiments in situ by directly adding the temperature-sensitive fluorescent dye Rhodamine B, whose fluorescence lifetime serves as a probe of the local temperature in the confocal volume. We demonstrate that the temperature and FRET efficiencies of static and dynamic molecules can be extracted within one measurement simultaneously, without the need of a reference chamber. We anticipate this technique to be particularly useful in the physicochemical analyses of temperature-dependent biomolecular processes from single-molecule measurements.

Unifying diffusion and seepage for nonlinear gas transport in multiscale porous media

NASA Astrophysics Data System (ADS)

Song, Hongqing; Wang, Yuhe; Wang, Jiulong; Li, Zhengyi

2016-09-01

We unify the diffusion and seepage process for nonlinear gas transport in multiscale porous media via a proposed new general transport equation. A coherent theoretical derivation indicates the wall-molecule and molecule-molecule collisions drive the Knudsen and collective diffusive fluxes, and constitute the system pressure across the porous media. A new terminology, nominal diffusion coefficient can summarize Knudsen and collective diffusion coefficients. Physical and numerical experiments show the support of the new formulation and provide approaches to obtain the diffusion coefficient and permeability simultaneously. This work has important implication for natural gas extraction and greenhouse gases sequestration in geological formations.

Xanthium strumarium extract inhibits mammalian cell proliferation through mitotic spindle disruption mediated by xanthatin.

PubMed

Sánchez-Lamar, Angel; Piloto-Ferrer, Janet; Fiore, Mario; Stano, Pasquale; Cozzi, Renata; Tofani, Daniela; Cundari, Enrico; Francisco, Marbelis; Romero, Aylema; González, Maria L; Degrassi, Francesca

2016-12-24

Xanthium strumarium L. is a member of the Asteraceae family popularly used with multiple therapeutic purposes. Whole extracts of this plant have shown anti-mitotic activity in vitro suggesting that some components could induce mitotic arrest in proliferating cells. Aim of the present work was to characterize the anti-mitotic properties of the X. strumarium whole extract and to isolate and purify active molecule(s). The capacity of the whole extract to inhibit mitotic progression in mammalian cultured cells was investigated to identify its anti-mitotic activity. Isolation of active component(s) was performed using a bioassay-guided multistep separation procedure in which whole extract was submitted to a progressive process of fractionation and fractions were challenged for their anti-mitotic activity. Our results show for the first time that X. strumarium whole extract inhibits assembly of the mitotic spindle and spindle-pole separation, thereby heavily affecting mitosis, impairing the metaphase to anaphase transition and inducing apoptosis. The purification procedure led to a fraction with an anti-mitotic activity comparable to that of the whole extract. Chemical analysis of this fraction showed that its major component was xanthatin. The present work shows a new activity of X. strumarium extract, i.e. the alteration of the mitotic apparatus in cultured cells that may be responsible for the anti-proliferative activity of the extract. Anti-mitotic activity is shown to be mainly exerted by xanthatin. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Self-Sealing Wet Chemistry Cell for Field Analysis

NASA Technical Reports Server (NTRS)

Beegle, Luther W.; Soto, Juancarlos; Lasnik, James; Roark, Shane

2012-01-01

In most analytical investigations, there is a need to process complex field samples for the unique detection of analytes, especially when detecting low concentration organic molecules that may identify extraterrestrial life. Wet chemistry based instruments are the techniques of choice for most laboratory- based analysis of organic molecules due to several factors including less fragmentation of fragile biomarkers, and ability to concentrate target species resulting in much lower limits of detection. Development of an automated wet chemistry preparation system that can operate autonomously on Earth and is also designed to operate under Martian ambient conditions will demonstrate the technical feasibility of including wet chemistry on future missions. An Automated Sample Processing System (ASPS) has recently been developed that receives fines, extracts organics through solvent extraction, processes the extract by removing non-organic soluble species, and delivers sample to multiple instruments for analysis (including for non-organic soluble species). The key to this system is a sample cell that can autonomously function under field conditions. As a result, a self-sealing sample cell was developed that can autonomously hermetically seal fines and powder into a container, regardless of orientation of the apparatus. The cap is designed with a beveled edge, which allows the cap to be self-righted as the capping motor engages. Each cap consists of a C-clip lock ring below a crucible O-ring that is placed into a groove cut into the sample cap.

Different Conformations of Surface Cellulose Molecules in Native Cellulose Microfibrils Revealed by Layer-by-Layer Peeling.

PubMed

Funahashi, Ryunosuke; Okita, Yusuke; Hondo, Hiromasa; Zhao, Mengchen; Saito, Tsuguyuki; Isogai, Akira

2017-11-13

Layer-by-layer peeling of surface molecules of native cellulose microfibrils was performed using a repeated sequential process of 2,2,6,6-tetramethylpiperidine-1-oxyl radical-mediated oxidation followed by hot alkali extraction. Both highly crystalline algal and tunicate celluloses and low-crystalline cotton and wood celluloses were investigated. Initially, the C6-hydroxy groups of the outermost surface molecules of each algal cellulose microfibril facing the exterior had the gauche-gauche (gg) conformation, whereas those facing the interior had the gauche-trans (gt) conformation. All the other C6-hydroxy groups of the cellulose molecules inside the microfibrils contributing to crystalline cellulose I had the trans-gauche (tg) conformation. After surface peeling, the originally second-layer molecules from the microfibril surface became the outermost surface molecules, and the original tg conformation changed to gg and gt conformations. The plant cellulose microfibrils likely had disordered structures for both the outermost surface and second-layer molecules, as demonstrated using the same layer-by-layer peeling technique.

Antimicrobial and anti-Quorum Sensing activities of selected medicinal plants of Ethiopia: Implication for development of potent antimicrobial agents.

PubMed

Bacha, Ketema; Tariku, Yinebeb; Gebreyesus, Fisseha; Zerihun, Shibru; Mohammed, Ali; Weiland-Bräuer, Nancy; Schmitz, Ruth A; Mulat, Mulugeta

2016-07-11

Traditional medicinal plants have been used as an alternative medicine in many parts of the world, including Ethiopia. There are many documented scientific reports on antimicrobial activities of the same. To our knowledge, however, there is no report on the anti-Quorum Sensing (Quorum Quenching, QQ) potential of traditional Ethiopian medicinal plants. As many of the opportunistic pathogenic bacteria depend on Quorum Sensing (QS) systems to coordinate their virulence expression, interference with QS could be a novel approach to control bacterial infections. Thus, the aim of this study was to evaluate selected medicinal plants from Ethiopia for their antimicrobial activities against bacterial and fungal pathogens; and to assess the interference of these plant extracts with QS of bacteria. Antimicrobial activities of plant extracts (oil, resins and crude extracts) were evaluated following standard agar diffusion technique. The minimum inhibitory concentrations (MIC) of potent extracts were determined using 96 well micro-titer plates and optical densities were measured using an ELISA Microplate reader. Interference with Quorum Sensing activities of extracts was determined using the recently established E. coli based reporter strain AI1-QQ.1 and signaling molecule N-(ß-ketocaproyl)-L-homoserine lactone (3-oxo-C6-HSL). Petroleum ether extract of seed of Nigella sativa exhibited the highest activity against both the laboratory isolated Bacillus cereus [inhibition zone (IZ), 44 ± 0.31 mm] and B. cereus ATCC 10987 (IZ, 40 ± 2.33 mm). Similarly, oil extract from mature ripe fruit husk of Aframomum corrorima and mature unripe fruit of A. corrorima revealed promising activities against Candida albicans ATCC 90028 (IZ, 35 ± 1.52 mm) and Staphylococcus aureus DSM 346 (IZ, 25 ± 1.32 mm), respectively. Antimicrobial activities of oil extract from husk of A. corrorima and petroleum ether extract of seed of N. sativa were significantly higher than that of the control antibiotic [Gentamycin sulfate, (IZ, 25-30 mm)]. The lowest MIC value (12.5 mg/mL) was recorded for oil from husk of A. corrorima against Pseudomonas aeruginosa. Of the total eighteen extracts evaluated, two of the extracts [Methanol extract of root of Albiza schimperiana (ASRM) and petroleum ether extract of seed of Justica schimperiana (JSSP)] interfered with cell-cell communication most likely by interacting with the signaling molecules. Traditional medicinal plants from Ethiopia are potential source of alternative medicine for the local community and scientific research in search for alternative drugs to halt challenges associated with the emerging antimicrobial resistance. Furthermore, the Quorum Quenching activities observed in two of the plant extracts calls for more comprehensive evaluation of medicinal plants for the control of many bacterial processes and phenotypic behaviors such as pathogenicity, swarming, and biofilm formation. Being the first assessment of its kind on the potential application of Ethiopian traditional medicinal plants for interference in microbial cell-cell communication (anti-Quorum Sensing activities), the detailed chemistry of the active compounds and possible mechanism(s) of actions of the bio-molecules responsible for the observed interference were not addressed in the current study. Thus, further evaluation for the nature of those active compounds (bio-molecules) and detailed mechanism(s) of their interaction with microbial processes are recommended.

[Effect of total hypothermia on the fatty acid composition of blood phospholipids of rats and sousliks and light irradiation on chemical processes in lipid extract].

PubMed

Zabelinskiĭ, S A; Chebotareva, M A; Kalandarov, A M; Feĭzulaev, B A; Klichkhanov, N K; Krivchenko, A I; Kazennov, A M

2011-01-01

Effect of hypothermia on the fatty acid composition of rat and souslik blood phospholipids is studied. Different reaction of these animals to cooling is revealed: in rats no changes were observed in the fatty acid composition of blood phospholipids, whereas in the hibernating there were significant changes in the content of individual fatty acids (FA). The content of monoenic acids in sousliks decreased almost by 50%, while the content of saturated acid (C18) and of polyenic acids C18 : 2omega6 and C20 : 4omega6 rose significantly. Such changes seem to be the mechanism that promotes maintenance of the organism viability under conditions of a decreased level of metabolism, heart rhythm, and body temperature and is evolutionarily acquired. At the same time, the observed changes in the content of individual FA do not lead to sharp changes in such integrative parameters as the total non-saturation of phospholipids, which determines liquid properties of chylomicrons and other lipolipoprotein transport particles of the souslik blood. There are studied absorption spectra of blood lipid extracts of rats and sousliks under effect of light as well as effect of light upon the FA composition of lipid extracts of these animals. The FA composition of lipid extracts has been established to remain practically constant, whereas the character of changes of spectra under action of light indicates the presence in the extracts of oxidation-reduction reactions. The obtained data allow suggesting that in the lipid extract there occurs cooperation both of the phospholipid molecules themselves and of them with other organic molecules, which makes it possible for fatty acids to participate in processes of transport both of electrons and of protons. This novel role of FA as a participant of the electron transfer might probably be extrapolated to chemical reactions (processes) occurring inside the membrane.

Development of new natural extracts.

PubMed

Lavoine-Hanneguelle, Sophie; Périchet, Christine; Schnaebele, Nicolas; Humbert, Marina

2014-11-01

For over the past 20 years, a remarkable development in the study and search of natural products has been observed. This is linked to a new market trend towards ecology and also due to new regulations. This could be a rupture, but also a real booster for creativity. Usually, in the flavor and fragrance field, creativity was boosted by the arrival of new synthetic molecules. Naturals remained the traditional, century-old products, protected by secrecy and specific know-how from each company. Regulatory restrictions or eco-friendly certification constraints like hexane-free processes triggered an important brainstorming in the industry. As a result, we developed new eco-friendly processes including supercritical CO2 extraction, allowing fresh plants to be used to obtain industrial flower extracts (Jasmine Grandiflorum, Jasmine Sambac, Orange blossom). These extracts are analyzed by GC, GC/MS, GCO, and HPTLC techniques. New or unusual raw materials can also be explored, but the resulting extracts have to be tested for safety reasons. Some examples are described. Copyright © 2014 Verlag Helvetica Chimica Acta AG, Zürich.

Lipid extraction methods from microalgal biomass harvested by two different paths: screening studies toward biodiesel production.

PubMed

Ríos, Sergio D; Castañeda, Joandiet; Torras, Carles; Farriol, Xavier; Salvadó, Joan

2013-04-01

Microalgae can grow rapidly and capture CO2 from the atmosphere to convert it into complex organic molecules such as lipids (biodiesel feedstock). High scale economically feasible microalgae based oil depends on optimizing the entire process production. This process can be divided in three very different but directly related steps (production, concentration, lipid extraction and transesterification). The aim of this study is to identify the best method of lipid extraction to undergo the potentiality of some microalgal biomass obtained from two different harvesting paths. The first path used all physicals concentration steps, and the second path was a combination of chemical and physical concentration steps. Three microalgae species were tested: Phaeodactylum tricornutum, Nannochloropsis gaditana, and Chaetoceros calcitrans One step lipid extraction-transesterification reached the same fatty acid methyl ester yield as the Bligh and Dyer and soxhlet extraction with n-hexane methods with the corresponding time, cost and solvent saving. Copyright © 2013 Elsevier Ltd. All rights reserved.

A multiplexed microfluidic toolbox for the rapid optimization of affinity-driven partition in aqueous two phase systems.

PubMed

Bras, Eduardo J S; Soares, Ruben R G; Azevedo, Ana M; Fernandes, Pedro; Arévalo-Rodríguez, Miguel; Chu, Virginia; Conde, João P; Aires-Barros, M Raquel

2017-09-15

Antibodies and other protein products such as interferons and cytokines are biopharmaceuticals of critical importance which, in order to be safely administered, have to be thoroughly purified in a cost effective and efficient manner. The use of aqueous two-phase extraction (ATPE) is a viable option for this purification, but these systems are difficult to model and optimization procedures require lengthy and expensive screening processes. Here, a methodology for the rapid screening of antibody extraction conditions using a microfluidic channel-based toolbox is presented. A first microfluidic structure allows a simple negative-pressure driven rapid screening of up to 8 extraction conditions simultaneously, using less than 20μL of each phase-forming solution per experiment, while a second microfluidic structure allows the integration of multi-step extraction protocols based on the results obtained with the first device. In this paper, this microfluidic toolbox was used to demonstrate the potential of LYTAG fusion proteins used as affinity tags to optimize the partitioning of antibodies in ATPE processes, where a maximum partition coefficient (K) of 9.2 in a PEG 3350/phosphate system was obtained for the antibody extraction in the presence of the LYTAG-Z dual ligand. This represents an increase of approx. 3.7 fold when compared with the same conditions without the affinity molecule (K=2.5). Overall, this miniaturized and versatile approach allowed the rapid optimization of molecule partition followed by a proof-of-concept demonstration of an integrated back extraction procedure, both of which are critical procedures towards obtaining high purity biopharmaceuticals using ATPE. Copyright © 2017 Elsevier B.V. All rights reserved.

Untargeted metabolomics analysis reveals dynamic changes in azelaic acid- and salicylic acid derivatives in LPS-treated Nicotiana tabacum cells.

PubMed

Mhlongo, M I; Tugizimana, F; Piater, L A; Steenkamp, P A; Madala, N E; Dubery, I A

2017-01-22

To counteract biotic stress factors, plants employ multilayered defense mechanisms responsive to pathogen-derived elicitor molecules, and regulated by different phytohormones and signaling molecules. Here, lipopolysaccharide (LPS), a microbe-associated molecular pattern (MAMP) molecule, was used to induce defense responses in Nicotiana tabacum cell suspensions. Intracellular metabolites were extracted with methanol and analyzed using a liquid chromatography-mass spectrometry (UHPLC-qTOF-MS/MS) platform. The generated data were processed and examined with multivariate and univariate statistical tools. The results show time-dependent dynamic changes and accumulation of glycosylated signaling molecules, specifically those of azelaic acid, salicylic acid and methyl-salicylate as contributors to the altered metabolomic state in LPS-treated cells. Copyright © 2016 Elsevier Inc. All rights reserved.

Investigation of flavonoid influence on peroxidation processes intensity in the blood

NASA Astrophysics Data System (ADS)

Navolokin, N. A.; Mudrak, D. A.; Plastun, I. L.; Bucharskaya, A. B.; Agandeeva, K. E.; Ivlichev, A. V.; Tychina, S. A.; Afanasyeva, G. A.; Polukonova, N. V.; Maslyakova, G. N.

2017-03-01

Influence of flavonoids on the intensity of peroxidation processes in the blood is investigated by numerical modeling and by experiment in vivo. As an example we consider the effects of flavonoid-containing extract of Helichrysum arenarium L. with antitumor activity on serum of rats with transplanted liver cancer PC-1. It was found that the content of malondialdehyde, lipid hydroperoxides and average mass molecules were decreased in animals with transplanted liver cancer after intramuscular and oral administration of Helichrysum arenarium L extract in a dose of 1000 mg/mL. The extract reduces the intensity of lipid peroxidation processes in animals. The compound formation possibility of flavonoids and products of lipid peroxidation is investigated by numerical simulations. Using the density functional theory method of molecular modeling, we analyze hydrogen bonds formation and their influence on IR - spectra and structure of molecular complex which is formed due to interaction between flavonoids and products of lipid peroxidation processes on example of naringine and malondialdehyde. We have found that naringine can form a steady molecular complex with malondialdehyde by hydrogen bonds formation. Thus, the application of Helichrysum arenarium L. extract for suppression processes of lipid peroxidation and activation of enzymatic and non-enzymatic antioxidant systems is promising.

Optimization of ultrasound-assisted extraction to obtain mycosterols from Agaricus bisporus L. by response surface methodology and comparison with conventional Soxhlet extraction.

PubMed

Heleno, Sandrina A; Diz, Patrícia; Prieto, M A; Barros, Lillian; Rodrigues, Alírio; Barreiro, Maria Filomena; Ferreira, Isabel C F R

2016-04-15

Ergosterol, a molecule with high commercial value, is the most abundant mycosterol in Agaricus bisporus L. To replace common conventional extraction techniques (e.g. Soxhlet), the present study reports the optimal ultrasound-assisted extraction conditions for ergosterol. After preliminary tests, the results showed that solvents, time and ultrasound power altered the extraction efficiency. Using response surface methodology, models were developed to investigate the favourable experimental conditions that maximize the extraction efficiency. All statistical criteria demonstrated the validity of the proposed models. Overall, ultrasound-assisted extraction with ethanol at 375 W during 15 min proved to be as efficient as the Soxhlet extraction, yielding 671.5 ± 0.5mg ergosterol/100 g dw. However, with n-hexane extracts with higher purity (mg ergosterol/g extract) were obtained. Finally, it was proposed for the removal of the saponification step, which simplifies the extraction process and makes it more feasible for its industrial transference. Copyright © 2015 Elsevier Ltd. All rights reserved.

Processing of waste material of radix physochlainae for preparation of fine chemicals after extraction

NASA Astrophysics Data System (ADS)

He, A.; Yohannes, A.; Feng, X. T.; Yao, S.

2017-02-01

Waste residues of Chinese traditional medicine radix physochlainae (Huashanshen) contain a large amount of hemicelluloses after extraction. After the removal of the cellulose and lignin, main components of the solution are different degree of hydrolysis products of hemicelluloses. In the degradation process, hemicelluloses firstly become pentose, and then pentose loses 3 molecules of water and turns into furfural. This study explored a series of conditions of the method; finally the yield of furfural can reach 8.5% (calculated with the weight of raw residues) under the condition of pH of 0.2-0.3, temperature of 104-106°C, hydrolysis duration for 10 minutes. Furfural can be further processed to be resin materials.

Cellulose Nanofibril Based-Aerogel Microreactors: A High Efficiency and Easy Recoverable W/O/W Membrane Separation System

PubMed Central

Zhang, Fang; Ren, Hao; Dou, Jing; Tong, Guolin; Deng, Yulin

2017-01-01

Hereby we report a novel cellulose nanofirbril aerogel-based W/O/W microreactor system that can be used for fast and high efficient molecule or ions extraction and separation. The ultra-light cellulose nanofibril based aerogel microspheres with high porous structure and water storage capacity were prepared. The aerogel microspheres that were saturated with stripping solution were dispersed in an oil phase to form a stable water-in-oil (W/O) suspension. This suspension was then dispersed in large amount of external waste water to form W/O/W microreactor system. Similar to a conventional emulsion liquid membrane (ELM), the molecules or ions in external water can quickly transport to the internal water phase. However, the microreactor is also significantly different from traditional ELM: the water saturated nanocellulose cellulose aerogel microspheres can be easily removed by filtration or centrifugation after extraction reaction. The condensed materials in the filtrated aerogel particles can be squeezed and washed out and aerogel microspheres can be reused. This novel process overcomes the key barrier step of demulsification in traditional ELM process. Our experimental indicates the novel microreactor was able to extract 93% phenol and 82% Cu2+ from external water phase in a few minutes, suggesting its great potential for industrial applications. PMID:28059153

Cellulose Nanofibril Based-Aerogel Microreactors: A High Efficiency and Easy Recoverable W/O/W Membrane Separation System

NASA Astrophysics Data System (ADS)

Zhang, Fang; Ren, Hao; Dou, Jing; Tong, Guolin; Deng, Yulin

2017-01-01

Hereby we report a novel cellulose nanofirbril aerogel-based W/O/W microreactor system that can be used for fast and high efficient molecule or ions extraction and separation. The ultra-light cellulose nanofibril based aerogel microspheres with high porous structure and water storage capacity were prepared. The aerogel microspheres that were saturated with stripping solution were dispersed in an oil phase to form a stable water-in-oil (W/O) suspension. This suspension was then dispersed in large amount of external waste water to form W/O/W microreactor system. Similar to a conventional emulsion liquid membrane (ELM), the molecules or ions in external water can quickly transport to the internal water phase. However, the microreactor is also significantly different from traditional ELM: the water saturated nanocellulose cellulose aerogel microspheres can be easily removed by filtration or centrifugation after extraction reaction. The condensed materials in the filtrated aerogel particles can be squeezed and washed out and aerogel microspheres can be reused. This novel process overcomes the key barrier step of demulsification in traditional ELM process. Our experimental indicates the novel microreactor was able to extract 93% phenol and 82% Cu2+ from external water phase in a few minutes, suggesting its great potential for industrial applications.

Single-molecule electronics: Cooling individual vibrational modes by the tunneling current.

PubMed

Lykkebo, Jacob; Romano, Giuseppe; Gagliardi, Alessio; Pecchia, Alessandro; Solomon, Gemma C

2016-03-21

Electronic devices composed of single molecules constitute the ultimate limit in the continued downscaling of electronic components. A key challenge for single-molecule electronics is to control the temperature of these junctions. Controlling heating and cooling effects in individual vibrational modes can, in principle, be utilized to increase stability of single-molecule junctions under bias, to pump energy into particular vibrational modes to perform current-induced reactions, or to increase the resolution in inelastic electron tunneling spectroscopy by controlling the life-times of phonons in a molecule by suppressing absorption and external dissipation processes. Under bias the current and the molecule exchange energy, which typically results in heating of the molecule. However, the opposite process is also possible, where energy is extracted from the molecule by the tunneling current. Designing a molecular "heat sink" where a particular vibrational mode funnels heat out of the molecule and into the leads would be very desirable. It is even possible to imagine how the vibrational energy of the other vibrational modes could be funneled into the "cooling mode," given the right molecular design. Previous efforts to understand heating and cooling mechanisms in single molecule junctions have primarily been concerned with small models, where it is unclear which molecular systems they correspond to. In this paper, our focus is on suppressing heating and obtaining current-induced cooling in certain vibrational modes. Strategies for cooling vibrational modes in single-molecule junctions are presented, together with atomistic calculations based on those strategies. Cooling and reduced heating are observed for two different cooling schemes in calculations of atomistic single-molecule junctions.

Complex admixtures of clathrate hydrates in a water desalination method

DOEpatents

Simmons, Blake A [San Francisco, CA; Bradshaw, Robert W [Livermore, CA; Dedrick, Daniel E [Berkeley, CA; Anderson, David W [Riverbank, CA

2009-07-14

Disclosed is a method that achieves water desalination by utilizing and optimizing clathrate hydrate phenomena. Clathrate hydrates are crystalline compounds of gas and water that desalinate water by excluding salt molecules during crystallization. Contacting a hydrate forming gaseous species with water will spontaneously form hydrates at specific temperatures and pressures through the extraction of water molecules from the bulk phase followed by crystallite nucleation. Subsequent dissociation of pure hydrates yields fresh water and, if operated correctly, allows the hydrate-forming gas to be efficiently recycled into the process stream.

The use of analytical sedimentation velocity to extract thermodynamic linkage.

PubMed

Cole, James L; Correia, John J; Stafford, Walter F

2011-11-01

For 25 years, the Gibbs Conference on Biothermodynamics has focused on the use of thermodynamics to extract information about the mechanism and regulation of biological processes. This includes the determination of equilibrium constants for macromolecular interactions by high precision physical measurements. These approaches further reveal thermodynamic linkages to ligand binding events. Analytical ultracentrifugation has been a fundamental technique in the determination of macromolecular reaction stoichiometry and energetics for 85 years. This approach is highly amenable to the extraction of thermodynamic couplings to small molecule binding in the overall reaction pathway. In the 1980s this approach was extended to the use of sedimentation velocity techniques, primarily by the analysis of tubulin-drug interactions by Na and Timasheff. This transport method necessarily incorporates the complexity of both hydrodynamic and thermodynamic nonideality. The advent of modern computational methods in the last 20 years has subsequently made the analysis of sedimentation velocity data for interacting systems more robust and rigorous. Here we review three examples where sedimentation velocity has been useful at extracting thermodynamic information about reaction stoichiometry and energetics. Approaches to extract linkage to small molecule binding and the influence of hydrodynamic nonideality are emphasized. These methods are shown to also apply to the collection of fluorescence data with the new Aviv FDS. Copyright © 2011 Elsevier B.V. All rights reserved.

The use of analytical sedimentation velocity to extract thermodynamic linkage

PubMed Central

Cole, James L.; Correia, John J.; Stafford, Walter F.

2011-01-01

For 25 years, the Gibbs Conference on Biothermodynamics has focused on the use of thermodynamics to extract information about the mechanism and regulation of biological processes. This includes the determination of equilibrium constants for macromolecular interactions by high precision physical measurements. These approaches further reveal thermodynamic linkages to ligand binding events. Analytical ultracentrifugation has been a fundamental technique in the determination of macromolecular reaction stoichiometry and energetics for 85 years. This approach is highly amenable to the extraction of thermodynamic couplings to small molecule binding in the overall reaction pathway. In the 1980’s this approach was extended to the use of sedimentation velocity techniques, primarily by the analysis of tubulin-drug interactions by Na and Timasheff. This transport method necessarily incorporates the complexity of both hydrodynamic and thermodynamic nonideality. The advent of modern computational methods in the last 20 years has subsequently made the analysis of sedimentation velocity data for interacting systems more robust and rigorous. Here we review three examples where sedimentation velocity has been useful at extracting thermodynamic information about reaction stoichiometry and energetics. Approaches to extract linkage to small molecule binding and the influence of hydrodynamic nonideality are emphasized. These methods are shown to also apply to the collection of fluorescence data with the new Aviv FDS. PMID:21703752

Separation of time scales in one-dimensional directed nucleation-growth processes

NASA Astrophysics Data System (ADS)

Pierobon, Paolo; Miné-Hattab, Judith; Cappello, Giovanni; Viovy, Jean-Louis; Lagomarsino, Marco Cosentino

2010-12-01

Proteins involved in homologous recombination such as RecA and hRad51 polymerize on single- and double-stranded DNA according to a nucleation-growth kinetics, which can be monitored by single-molecule in vitro assays. The basic models currently used to extract biochemical rates rely on ensemble averages and are typically based on an underlying process of bidirectional polymerization, in contrast with the often observed anisotropic polymerization of similar proteins. For these reasons, if one considers single-molecule experiments, the available models are useful to understand observations only in some regimes. In particular, recent experiments have highlighted a steplike polymerization kinetics. The classical model of one-dimensional nucleation growth, the Kolmogorov-Avrami-Mehl-Johnson (KAMJ) model, predicts the correct polymerization kinetics only in some regimes and fails to predict the steplike behavior. This work illustrates by simulations and analytical arguments the limitation of applicability of the KAMJ description and proposes a minimal model for the statistics of the steps based on the so-called stick-breaking stochastic process. We argue that this insight might be useful to extract information on the time and length scales involved in the polymerization kinetics.

Analysis of additivity and synergism in the anti-plasmodial effect of purified compounds from plant extracts.

PubMed

Deharo, Eric; Ginsburg, Hagai

2011-03-15

In the search for antimalarials from ethnobotanical origin, plant extracts are chemically fractionated and biological tests guide the isolation of pure active compounds. To establish the responsibility of isolated active compound(s) to the whole antiplasmodial activity of a crude extract, the literature in this field was scanned and results were analysed quantitatively to find the contribution of the pure compound to the activity of the whole extract. It was found that, generally, the activity of isolated molecules could not account on their own for the activity of the crude extract. It is suggested that future research should take into account the "drugs beside the drug", looking for those products (otherwise discarded along the fractionation process) able to boost the activity of isolated active compounds.

Mesoporous-silica nanofluidic channels for quick enrichment/extraction of trace pesticide molecules

NASA Astrophysics Data System (ADS)

Xu, Pengcheng; Chen, Chuanzhao; Li, Xinxin

2015-11-01

As nanofluidic channels, uniaxially oriented mesoporous-silica is, for the first time, in-situ self-assembled in a microfluidic chip for quick enrichment/extraction of ng L-1(ppt)-level organo-phosphorous (OP) pesticide residue from aqueous solution to ethanol. This micro/nano combined pre-treatment chip is essential for following gas chromatography-mass spectrometry (GC-MS) quantitative analysis. Featuring huge surface area and dense silanol groups at the inwall surface, the mesoporous-silica is uniaxially self-assembled in a micro-reservoir to form a pile of nanofluidic channels (diameter = 2.1 nm). The captured/enriched pesticide molecules in the nanochannels can be efficiently extracted by much smaller volume of ethanol due to its much higher solubility to OP. In our affirming experiment, three mixed OP pesticides of dichlorvos, paraoxon and chlorpyrifos (in water) are captured/enriched by the nano-channels and eluted/extracted by only 0.6 mL ethanol. The whole process only takes 16 min. The GC-MS quantitative results for the extracted three pesticides indicate that the extraction recovery achieves 80%. The achieved limit of quantification (LOQ) and the limit of detection (LOD) are 100 ng L-1 and 30 ng L-1, respectively. The nanofluidic-channel pre-treatment technique is promising in various application fields like agriculture and food safety security.

Extracting Models in Single Molecule Experiments

NASA Astrophysics Data System (ADS)

Presse, Steve

2013-03-01

Single molecule experiments can now monitor the journey of a protein from its assembly near a ribosome to its proteolytic demise. Ideally all single molecule data should be self-explanatory. However data originating from single molecule experiments is particularly challenging to interpret on account of fluctuations and noise at such small scales. Realistically, basic understanding comes from models carefully extracted from the noisy data. Statistical mechanics, and maximum entropy in particular, provide a powerful framework for accomplishing this task in a principled fashion. Here I will discuss our work in extracting conformational memory from single molecule force spectroscopy experiments on large biomolecules. One clear advantage of this method is that we let the data tend towards the correct model, we do not fit the data. I will show that the dynamical model of the single molecule dynamics which emerges from this analysis is often more textured and complex than could otherwise come from fitting the data to a pre-conceived model.

A combined Cyanex-923/HEH[EHP]/Dodecane solvent for recovery of transuranic elements from used nuclear fuel

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

Johnson, A.; Nash, K.L.

2013-07-01

The separation of minor actinides from fission product lanthanides remains a primary challenge for enabling the recycle of used nuclear fuel. To minimize the complexity of materials handling, combining extractant processes has become an increasingly attractive option. Unfortunately, combined processes sometimes suffer reduced utility due to strong dipole-dipole interactions between the extractants. The results reported here describe a system based on a combination of commercially available extractants Cyanex-923 and HEH[EHP]. In contrast to other combined extractant systems, these extractant molecules exhibit comparatively weak interactions, reducing the impact of secondary interactions. In this process, mixtures containing equal ratios of Cyanex-923 andmore » HEH[EHP] were seen to co-extract americium and the lanthanides from nitric acid solutions. Stripping of An(III) was effectively achieved through contact with an aqueous phase comprised of glycine (for pH control) and a polyamino-poly-carboxylate stripping reagent that selectively removes An(III) from the extractant phase. The lanthanides can then be stripped from the loaded organic phase contacting with high nitric acid concentrations. Extraction of fission products zirconium and molybdenum was also investigated and potential strategies for their management have been identified. The work presented demonstrates the feasibility of combining Cyanex-923 and HEH[EHP] for separating and recovering the transuranic elements from the Ln(III). (authors)« less

Metathesis depolymerizable surfactants

DOEpatents

Jamison, Gregory M [Albuquerque, NM; Wheeler, David R [Albuquerque, NM; Loy, Douglas A [Tucson, AZ; Simmons, Blake A [San Francisco, CA; Long, Timothy M [Evanston, IL; McElhanon, James R [Manteca, CA; Rahimian, Kamyar [Albuquerque, NM; Staiger, Chad L [Albuquerque, NM

2008-04-15

A class of surfactant molecules whose structure includes regularly spaced unsaturation in the tail group and thus, can be readily decomposed by ring-closing metathesis, and particularly by the action of a transition metal catalyst, to form small molecule products. These small molecules are designed to have increased volatility and/or enhanced solubility as compared to the original surfactant molecule and are thus easily removed by solvent extraction or vacuum extraction at low temperature. By producing easily removable decomposition products, the surfactant molecules become particularly desirable as template structures for preparing meso- and microstructural materials with tailored properties.

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

Lykkebo, Jacob; Solomon, Gemma C., E-mail: gsolomon@nano.ku.dk; Romano, Giuseppe

Electronic devices composed of single molecules constitute the ultimate limit in the continued downscaling of electronic components. A key challenge for single-molecule electronics is to control the temperature of these junctions. Controlling heating and cooling effects in individual vibrational modes can, in principle, be utilized to increase stability of single-molecule junctions under bias, to pump energy into particular vibrational modes to perform current-induced reactions, or to increase the resolution in inelastic electron tunneling spectroscopy by controlling the life-times of phonons in a molecule by suppressing absorption and external dissipation processes. Under bias the current and the molecule exchange energy, whichmore » typically results in heating of the molecule. However, the opposite process is also possible, where energy is extracted from the molecule by the tunneling current. Designing a molecular “heat sink” where a particular vibrational mode funnels heat out of the molecule and into the leads would be very desirable. It is even possible to imagine how the vibrational energy of the other vibrational modes could be funneled into the “cooling mode,” given the right molecular design. Previous efforts to understand heating and cooling mechanisms in single molecule junctions have primarily been concerned with small models, where it is unclear which molecular systems they correspond to. In this paper, our focus is on suppressing heating and obtaining current-induced cooling in certain vibrational modes. Strategies for cooling vibrational modes in single-molecule junctions are presented, together with atomistic calculations based on those strategies. Cooling and reduced heating are observed for two different cooling schemes in calculations of atomistic single-molecule junctions.« less

The role of dissolved cations in coffee extraction.

PubMed

Hendon, Christopher H; Colonna-Dashwood, Lesley; Colonna-Dashwood, Maxwell

2014-05-28

The flavorsome compounds in coffee beans exist in the form of aprotic charge neutral species, as well as a collection of acids and conjugate salts. The dissolution and extraction of these organic molecules is a process dependent on the dissolved mineral content of the water. It is known that different rates and compositions of coffee extraction are achieved through the control of the water "impurities", Na(+), Mg(2+), and Ca(2+), which coordinate to nucleophilic motifs in coffee. Using density functional theory, we quantify the thermodynamic binding energies of five familiar coffee-contained acids, caffeine, and a representative flavor component, eugenol. From this, we provide insight into the mechanism and ideal mineral composition of water for extraction of flavorsome compounds in coffee.

Multidimensional biochemical information processing of dynamical patterns

NASA Astrophysics Data System (ADS)

Hasegawa, Yoshihiko

2018-02-01

Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multidimensional information from dynamical concentration patterns of signaling molecules. We herein study how biochemical systems can process multidimensional information embedded in dynamical patterns. We model the decoding networks by linear response functions, and optimize the functions with the calculus of variations to maximize the mutual information between patterns and output. We find that, when the noise intensity is lower, decoders with different linear response functions, i.e., distinct decoders, can extract much information. However, when the noise intensity is higher, distinct decoders do not provide the maximum amount of information. This indicates that, when transmitting information by dynamical patterns, embedding information in multiple patterns is not optimal when the noise intensity is very large. Furthermore, we explore the biochemical implementations of these decoders using control theory and demonstrate that these decoders can be implemented biochemically through the modification of cascade-type networks, which are prevalent in actual signaling pathways.

Multidimensional biochemical information processing of dynamical patterns.

PubMed

Hasegawa, Yoshihiko

2018-02-01

Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multidimensional information from dynamical concentration patterns of signaling molecules. We herein study how biochemical systems can process multidimensional information embedded in dynamical patterns. We model the decoding networks by linear response functions, and optimize the functions with the calculus of variations to maximize the mutual information between patterns and output. We find that, when the noise intensity is lower, decoders with different linear response functions, i.e., distinct decoders, can extract much information. However, when the noise intensity is higher, distinct decoders do not provide the maximum amount of information. This indicates that, when transmitting information by dynamical patterns, embedding information in multiple patterns is not optimal when the noise intensity is very large. Furthermore, we explore the biochemical implementations of these decoders using control theory and demonstrate that these decoders can be implemented biochemically through the modification of cascade-type networks, which are prevalent in actual signaling pathways.

AJIPHASE®: A Highly Efficient Synthetic Method for One-Pot Peptide Elongation in the Solution Phase by an Fmoc Strategy.

PubMed

Takahashi, Daisuke; Inomata, Tatsuji; Fukui, Tatsuya

2017-06-26

We previously reported an efficient peptide synthesis method, AJIPHASE®, that comprises repeated reactions and isolations by precipitation. This method utilizes an anchor molecule with long-chain alkyl groups as a protecting group for the C-terminus. To further improve this method, we developed a one-pot synthesis of a peptide sequence wherein the synthetic intermediates were isolated by solvent extraction instead of precipitation. A branched-chain anchor molecule was used in the new process, significantly enhancing the solubility of long peptides and the operational efficiency compared with the previous method, which employed precipitation for isolation and a straight-chain aliphatic group. Another prerequisite for this solvent-extraction-based strategy was the use of thiomalic acid and DBU for Fmoc deprotection, which facilitates the removal of byproducts, such as the fulvene adduct. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sample Processing technique onboard ExoMars (MOMA) to analyze organic compounds by Gas Chromatography-Mass Spectrometry

NASA Astrophysics Data System (ADS)

Buch, A.; Freissinet, C.; Sternberg, R.; Szopa, C.; Coll, P. J.; Brault, A.; Pinnick, V.; Siljeström, S.; Raulin, F.; Steininger, H.; Goesmann, F.; MOMA Team

2011-12-01

With the aim of separating and detecting organic compounds from Martian soil onboard the Mars Organic Molecule Analyzer (MOMA) experiment of the ExoMars 2018 upcoming joint ESA/NASA mission, we have developed three different space compatible sample preparation techniques compatible with space missions, able to extract and analyze by GC-MS a wide range of volatile and refractory compounds, including chirality analysis. Then, a sample processing utilizing three derivatization/extraction reactions has been carried out. The first reaction is based on a silyl reagent N-Methyl-N- (Tert-Butyldimethylsilyl)trifluoroacetamide (MTBSTFA) [1], the second one, N,N-Dimethylformamide Dimethylacetal (DMF-DMA) [2,3] is dedicated to the chirality detection and the third one is a thermochemolysis based on the use of tetramethylammoniumhydroxide (TMAH). The sample processing system is performed in an oven, dedicated to the MOMA experiment containing the solid sample (50-100mg). The internal temperature of the oven ranges from 20 to 900 °C. The extraction step is achieved by using thermodesorption in the range of 100 to 300°C for 5 to 20 min. Then, the chemical derivatization of the extracted compounds is performed directly on the soil sample by using a derivatyization capsule which contains a mixture of MTBSTFA-DMF or DMF-DMA solution when enantiomeric separation is required. By decreasing the polarity of the targeted molecules, this step allows their volatilization at a temperature below 250°C without any thermal degradation. Once derivatized, the volatile target molecules are trapped in a chemical trap and promptly desorbed into the gas chromatograph coupled to a mass spectrometer. Thermochemolysis is directly performed in the oven at 400°C during 5 min with a 25% (w/w) methanol solution of tetramethylammonium hydroxide (TMAH). Then, pyrolysis in the presence of TMAH allows both an efficient cleavage of polar bonds and the subsequent methylation of COOH, OH and NH2 groups, hence the release of less polar, GC-amenable compounds. By using thermochemolysis several families of biological molecules were detected such as fatty acids, n-alkenes and n-alkanols [4]. [1] A. Buch et al., Development of a gas chromatography compatible Sample Processing System (SPS) for the in-situ analysis of refractory organic matter in martian soil: preliminary result. Advances in Space Research 43, 143-151, 2009. [2] C. Freissinet et al., Journal of Chromatography A.1217 (5), 731-740, 2010. [3] U. Meierhenrich et al., Journal of Analytical and Applied Pyrolysis 60, 13-26, 2001. [4] C. Geffroy-Rodier et al., Journal of Analytical and Applied Pyrolysis, 85, 2009.

Synthesis of Surface-Modified Iron Oxides for the Solvent-Free Recovery of Bacterial Bioactive Compound Prodigiosin and Its Algicidal Activity.

PubMed

Arivizhivendhan, K V; Mahesh, M; Boopathy, R; Patchaimurugan, K; Maharaja, P; Swarnalatha, S; Regina Mary, R; Sekaran, G

2016-09-15

Prodigiosin (PG) is a bioactive compound produced by several bacterial species. Currently, many technologies are being developed for the production of PG by fermentation processes. However, new challenges are being faced with regard to the production of PG in terms of the recovery and purification steps, owing to the labile nature of PG molecules and the cost of the purification steps. Conventional methods have limitations due to high cost, low reusability, and health hazards. Hence, the present investigation was focused on the development of surface-functionalized magnetic iron oxide ([Fe3O4]F) for solvent-free extraction of bioactive PG from the bacterial fermented medium. Fe3O4 was functionalized with diethanolamine and characterized by FT-IR, diffuse reflectance spectroscopy, thermogravimetric analysis, scanning electron microscopy, and confocal microscopy. The various process parameters, such as contact time, temperature, pH, and mass of Fe3O4, were optimized for the extraction of PG using functionalized Fe3O4. Instrumental analyses confirmed that the PG molecules were cross-linked with functional groups on [Fe3O4]F through van der Waals forces of attraction. PG extracted through Fe3O4 or [Fe3O4]F was separated from the fermentation medium by applying an external electromagnetic field and regenerated for successive reuse cycles. The purity of the extracted PG was characterized by high-performance liquid chromatography, FT-IR, and UV-visible spectroscopy. The iron oxide-diethanolamine-PG cross-linked ([Fe3O4]F-PG) composite matrix effectively deactivates harmful fouling by cyanobacterial growth in water-treatment plants. The present investigation provides the possibility of solvent-free extraction of bacterial bioactive PG from a fermented medium using functionalized magnetic iron oxide.

Microfluidic Extraction of Biomarkers using Water as Solvent

NASA Technical Reports Server (NTRS)

Amashukeli, Xenia; Manohara, Harish; Chattopadhyay, Goutam; Mehdi, Imran

2009-01-01

A proposed device, denoted a miniature microfluidic biomarker extractor (mu-EX), would extract trace amounts of chemicals of interest from samples, such as soils and rocks. Traditionally, such extractions are performed on a large scale with hazardous organic solvents; each solvent capable of dissolving only those molecules lying within narrow ranges of specific chemical and physical characteristics that notably include volatility, electric charge, and polarity. In contrast, in the mu-EX, extractions could be performed by use of small amounts (typically between 0.1 and 100 L) of water as a universal solvent. As a rule of thumb, in order to enable solvation and extraction of molecules, it is necessary to use solvents that have polarity sufficiently close to the polarity of the target molecules. The mu-EX would make selection of specific organic solvents unnecessary, because mu-EX would exploit a unique property of liquid water: the possibility of tuning its polarity to match the polarity of organic solvents appropriate for extraction of molecules of interest. The change of the permittivity of water would be achieved by exploiting interactions between the translational states of water molecules and an imposed electromagnetic field in the frequency range of 300 to 600 GHz. On a molecular level, these interactions would result in disruption of the three-dimensional hydrogen-bonding network among liquid-water molecules and subsequent solvation and hydrolysis of target molecules. The mu-EX is expected to be an efficient means of hydrolyzing chemical bonds in complex macromolecules as well and, thus, enabling analysis of the building blocks of these complex chemical systems. The mu-EX device would include a microfluidic channel, part of which would lie within a waveguide coupled to an electronically tuned source of broad-band electromagnetic radiation in the frequency range from 300 to 600 GHz (see figure). The part of the microfluidic channel lying in the waveguide would constitute an interaction volume. The dimensions of the interaction volume would be chosen in accordance with the anticipated amount of solid sample material needed to ensure extraction of sufficient amount of target molecules for detection and analysis. By means that were not specified at the time of reporting the information for this article, the solid sample material would be placed in the interaction volume. Then the electromagnetic field would be imposed within the waveguide and water would be pumped through the interaction volume to effect the extraction.

Natural Gas Evolution in a Gas Hydrate Melt: Effect of Thermodynamic Hydrate Inhibitors.

PubMed

Sujith, K S; Ramachandran, C N

2017-01-12

Natural gas extraction from gas hydrate sediments by injection of hydrate inhibitors involves the decomposition of hydrates. The evolution of dissolved gas from the hydrate melt is an important step in the extraction process. Using classical molecular dynamics simulations, we study the evolution of dissolved methane from its hydrate melt in the presence of two thermodynamic hydrate inhibitors, NaCl and CH 3 OH. An increase in the concentration of hydrate inhibitors is found to promote the nucleation of methane nanobubbles in the hydrate melt. Whereas NaCl promotes bubble formation by enhancing the hydrophobic interaction between aqueous CH 4 molecules, CH 3 OH molecules assist bubble formation by stabilizing CH 4 bubble nuclei formed in the solution. The CH 3 OH molecules accumulate around the nuclei leading to a decrease in the surface tension at their interface with water. The nanobubbles formed are found to be highly dynamic with frequent exchange of CH 4 molecules between the bubble and the surrounding liquid. A quantitative analysis of the dynamic behavior of the bubble is performed by introducing a unit step function whose value depends on the location of CH 4 molecules with respect to the bubble. It is observed that an increase in the concentration of thermodynamic hydrate inhibitors reduces the exchange process, making the bubble less dynamic. It is also found that for a given concentration of the inhibitor, larger bubbles are less dynamic compared to smaller ones. The dependence of the dynamic nature of nanobubbles on bubble size and inhibitor concentration is correlated with the solubility of CH 4 and the Laplace pressure within the bubble. The effect of CO 2 on the formation of nanobubble in the CH 4 -CO 2 mixed gas hydrate melt in the presence of inhibitors is also examined. The simulations show that the presence of CO 2 molecules significantly reduces the induction time for methane nanobubble nucleation. The role of CO 2 in the early nucleation of bubble is explained based on the interaction between the bubble and the dissolved CO 2 molecules.

Silicon technology compatible photonic molecules for compact optical signal processing

NASA Astrophysics Data System (ADS)

Barea, Luis A. M.; Vallini, Felipe; Jarschel, Paulo F.; Frateschi, Newton C.

2013-11-01

Photonic molecules (PMs) based on multiple inner coupled microring resonators allow to surpass the fundamental constraint between the total quality factor (QT), free spectral range (FSR), and resonator size. In this work, we use a PM that presents doublets and triplets resonance splitting, all with high QT. We demonstrate the use of the doublet splitting for 34.2 GHz signal extraction by filtering the sidebands of a modulated optical signal. We also demonstrate that very compact optical modulators operating 2.75 times beyond its resonator linewidth limit may be obtained using the PM triplet splitting, with separation of ˜55 GHz.

Novel method for the rapid and specific extraction of multiple β2 -agonist residues in food by tailor-made Monolith-MIPs extraction disks and detection by gas chromatography with mass spectrometry.

PubMed

Liu, Haibo; Gan, Ning; Chen, Yinji; Ding, Qingqing; Huang, Jie; Lin, Saichai; Cao, Yuting; Li, Tianhua

2016-09-01

A quick and specific pretreatment method based on a series of extraction clean-up disks, consisting of molecularly imprinted polymer monoliths and C18 adsorbent, was developed for the specific enrichment of salbutamol and clenbuterol residues in food. The molecularly imprinted monolithic polymer disk was synthesized using salbutamol as a template through a one-step synthesis process. It can simultaneously and specifically recognize salbutamol and clenbuterol. The monolithic polymer disk and series of C18 disks were assembled with a syringe to form a set of tailor-made devices for the extraction of target molecules. In a single run, salbutamol and clenbuterol can be specifically extracted, cleaned, and eluted by methanol/acetic acid/H2 O. The target molecules, after a silylation derivatization reaction were detected by gas chromatography-mass spectrometry. The parameters including solvent desorption, sample pH, and the cycles of reloading were investigated and discussed. Under the optimized extraction and clean-up conditions, the limits of detection and quantitation were determined as 0.018-0.022 and 0.042-0.049 ng/g for salbutamol and clenbuterol, respectively. The assay described was convenient, rapid, and specific; thereby potentially efficient in the high-throughput analysis of β2 -agonists residues in real food samples. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Degradation of rotenone in yam bean seeds ( Pachyrhizus sp.) through food processing.

PubMed

Catteau, Lucy; Lautié, Emmanuelle; Koné, Oumou; Coppée, Marie; Hell, Kerstin; Pomalegni, Charles Bertrand; Quetin-Leclercq, Joëlle

2013-11-20

The purpose of this research is to screen different processes that could potentially decrease or even eliminate rotenone, a toxic isoflavonoid, from Pachyrhizus seeds. Yam bean seeds have very interesting nutritional characteristics, especially their high protein and lipid contents, and could potentially increase food security in under-nourished populations. However, they contain rotenone, a natural molecule previously used as an insecticide inhibiting the respiratory mitochondrial chain. It was also proven to be toxic to mammals as chronic exposure leads to the development of Parkinson-like symptoms in rats. As the thermosensitivity of rotenone had been reported, this study tested different processes (drying, roasting, boiling, frying, alcohol extraction), tegument removal, and traditional Beninese culinary recipes. Rotenone was then quantified in end-products by a validated method, associating microwave extraction, solid phase extraction (SPE), and HPLC-UV. With these processes a rotenone removal of up to 80% was obtained. The most effective methods were the drying and roasting of the seeds and the maceration of their flour in local alcohol. Rotenone degradation and elimination were confirmed by cytotoxic assays, effectively inducing a decrease in sample toxicity.

Molecular characteristics of continuously released DOM during one year of root and leaf litter decomposition

NASA Astrophysics Data System (ADS)

Altmann, Jens; Jansen, Boris; Kalbitz, Karsten; Filley, Timothy

2013-04-01

Dissolved organic matter (DOM) is one of the most dynamic carbon pools linking the terrestrial with the aquatic carbon cycle. Besides the insecure contribution of terrestrial DOM to the greenhouse effect, DOM also plays an important role for the mobility and availability of heavy metals and organic pollutants in soils. These processes depend very much on the molecular characteristics of the DOM. Surprisingly the processes that determine the molecular composition of DOM are only poorly understood. DOM can originate from various sources, which influence its molecular composition. It has been recognized that DOM formation is not a static process and DOM characteristics vary not only between different carbon sources. However, molecular characteristics of DOM extracts have scarcely been studied continuously over a longer period of time. Due to constant molecular changes of the parent litter material or soil organic matter during microbial degradation, we assumed that also the molecular characteristics of litter derived DOM varies at different stages during root and needle decomposition. For this study we analyzed the chemical composition of root and leaf samples of 6 temperate tree species during one year of litter decomposition in a laboratory incubation. During this long-term experiment we measured continuously carbon and nitrogen contents of the water extracts and the remaining residues, C mineralization rates, and the chemical composition of water extracts and residues by Curie-point pyrolysis mass spectrometry with TMAH We focused on the following questions: (I) How mobile are molecules derived from plant polymers like tannin, lignin, suberin and cutin? (II) How does the composition of root and leaf derived DOM change over time in dependence on the stage of decomposition and species? Litter derived DOM was generally dominated by aromatic compounds. Substituded fatty acids as typically cutin or suberin derived were not detected in the water extracts. Fresh leaf and needle samples released a much higher amount of tannins than fresh root samples. At later litter decomposition stages the influence of tannins decreased and lignin derived phenols dominated the extracts. With ongoing litter degradation the degree of oxidation for the litter material increased, which was also reflected by the water extracted molecules.

Photothermal stress triggered by near-infrared-irradiated carbon nanotubes up-regulates osteogenesis and mineral deposition in tooth-extracted sockets.

PubMed

Kajiya, Hiroshi; Katsumata, Yuri; Sasaki, Mina; Tsutsumi, Takashi; Kawaguchi, Minoru; Fukushima, Tadao

2015-01-01

The bone regenerative healing process is often prolonged, with a high risk of infection particularly in elderly and diseased patients. A reduction in healing process time usually requires mechanical stress devices, chemical cues, or laser/thermal therapies. Although these approaches have been used extensively for the reduction of bone healing time, the exact mechanisms involved in thermal stress-induced bone regeneration remain unclear. Photothermal stress (PTS) stimulation was carried out using a novel photothermal device, composed of an alginate gel (AG) including carbon nanotubes (CNT-AGs) and their irradiator with near-infrared (NIR) light. We investigated the effects of optimal hyperthermia on osteogenesis, its signalling pathway in vitro and mineral deposition in tooth-extracted sockets in vivo. The PTS (10 min at 42 °C, every day), triggered by NIR-induced CNT, increased the activity of alkaline phosphatase (ALP) in mouse osteoblast MC3T3-E1 cells in a time-dependent manner compared with the non-thermal stress control. PTS significantly induced the expression of osteogenic-related molecules such as ALP, RUNX2 and Osterix in a time-dependent manner with phosphorylated mitogen-activated protein kinases (MAPK). PTS increased the expression of heat shock factor (HSF) 2, but not HSF1, resulting in activation of heat shock protein 27. PTS significantly up-regulated mineral deposition in tooth-extracted sockets in normal and ovariectomised osteoporotic model mice in vivo. Our novel CNT-based PTS up-regulated osteogenesis via activation of heat shock-related molecules, resulting in promotion of mineral deposition in enhanced tooth-extracted sockets.

A Fragment-Based Method of Creating Small-Molecule Libraries to Target the Aggregation of Intrinsically Disordered Proteins.

PubMed

Joshi, Priyanka; Chia, Sean; Habchi, Johnny; Knowles, Tuomas P J; Dobson, Christopher M; Vendruscolo, Michele

2016-03-14

The aggregation process of intrinsically disordered proteins (IDPs) has been associated with a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Currently, however, no drug in clinical use targets IDP aggregation. To facilitate drug discovery programs in this important and challenging area, we describe a fragment-based approach of generating small-molecule libraries that target specific IDPs. The method is based on the use of molecular fragments extracted from compounds reported in the literature to inhibit of the aggregation of IDPs. These fragments are used to screen existing large generic libraries of small molecules to form smaller libraries specific for given IDPs. We illustrate this approach by describing three distinct small-molecule libraries to target, Aβ, tau, and α-synuclein, which are three IDPs implicated in Alzheimer's and Parkinson's diseases. The strategy described here offers novel opportunities for the identification of effective molecular scaffolds for drug discovery for neurodegenerative disorders and to provide insights into the mechanism of small-molecule binding to IDPs.

Evaluation of terrestrial plants extracts for uranium sorption and characterization of potent phytoconstituents.

PubMed

Sharma, Sunita; Singh, Bikram; Thulasidas, S K; Kulkarni, Madhuri J; Natarajan, V; Manchanda, Vijay K

2016-01-01

Sorption capacity of four plants (Funaria hygrometrica, Musa acuminata, Brassica juncea and Helianthus annuus) extracts/fractions for uranium, a radionuclide was investigated by EDXRF and tracer studies. The maximum sorption capacity, i.e., 100% (complete sorption) was observed in case of Musa acuminata extract and fractions. Carbohydrate, proteins, phenolics and flavonoids contents in the active fraction (having maximum sorption capacity) were also determined. Further purification of the most active fraction provided three pure molecules, mannitol, sorbitol and oxo-linked potassium oxalate. The characterization of isolated molecules was achieved by using FTIR, NMR, GC-MS, MS-MS, and by single crystal-XRD analysis. Of three molecules, oxo-linked potassium oxalate was observed to have 100% sorption activity. Possible binding mechanism of active molecule with the uranyl cation has been purposed.

Extending the analytical window for water-soluble organic matter in sediments by aqueous Soxhlet extraction

NASA Astrophysics Data System (ADS)

Schmidt, Frauke; Koch, Boris P.; Witt, Matthias; Hinrichs, Kai-Uwe

2014-09-01

Dissolved organic matter (DOM) in marine sediments is a complex mixture of thousands of individual constituents that participate in biogeochemical reactions and serve as substrates for benthic microbes. Knowledge of the molecular composition of DOM is a prerequisite for a comprehensive understanding of the biogeochemical processes in sediments. In this study, interstitial water DOM was extracted with Rhizon samplers from a sediment core from the Black Sea and compared to the corresponding water-extractable organic matter fraction (<0.4 μm) obtained by Soxhlet extraction, which mobilizes labile particulate organic matter and DOM. After solid phase extraction (SPE) of DOM, samples were analyzed for the molecular composition by Fourier Transform Ion-Cyclotron Resonance Mass Spectrometry (FT-ICR MS) with electrospray ionization in negative ion mode. The average SPE extraction yield of the dissolved organic carbon (DOC) in interstitial water was 63%, whereas less than 30% of the DOC in Soxhlet-extracted organic matter was recovered. Nevertheless, Soxhlet extraction yielded up to 4.35% of the total sedimentary organic carbon, which is more than 30-times the organic carbon content of the interstitial water. While interstitial water DOM consisted primarily of carbon-, hydrogen- and oxygen-bearing compounds, Soxhlet extracts yielded more complex FT-ICR mass spectra with more peaks and higher abundances of nitrogen- and sulfur-bearing compounds. The molecular composition of both sample types was affected by the geochemical conditions in the sediment; elevated concentrations of HS- promoted the early diagenetic sulfurization of organic matter. The Soxhlet extracts from shallow sediment contained specific three- and four-nitrogen-bearing molecular formulas that were also detected in bacterial cell extracts and presumably represent proteinaceous molecules. These compounds decreased with increasing sediment depth while one- and two-nitrogen-bearing molecules increased, resulting in a higher similarity of both sample types in the deep sediment. In summary, Soxhlet extraction of sediments accessed a larger and more complex pool of organic matter than present in interstitial water DOM.

Bioactive molecules in Kalanchoe pinnata leaves: extraction, purification, and identification.

PubMed

El Abdellaoui, Saïda; Destandau, Emilie; Toribio, Alix; Elfakir, Claire; Lafosse, Michel; Renimel, Isabelle; André, Patrice; Cancellieri, Perrine; Landemarre, Ludovic

2010-10-01

Kalanchoe pinnata (Lam.) Pers. (syn. Bryophyllum pinnatum; family Crassulaceae) is a popular plant used in traditional medicine in many temperate regions of the world and particularly in South America. In Guyana, the leaves are traditionally used as an anti-inflammatory and antiseptic to treat coughs, ulcers, and sores. The purpose of this study was to implement a method for targeting and identifying molecules with antimicrobial activity, which could replace chemical preservatives in cosmetic applications. The leaves were extracted by a method based on pressurized liquid extraction (PLE), using different solvents. A study of antimicrobial activity and cytotoxicity tests were performed to select the most interesting extract. To isolate one or more active molecules, the selected crude extract was fractionated by centrifugal partition chromatography (CPC) and then antimicrobial activity and cytotoxicity of each fraction were tested under the same procedure. The last step consisted of identifying the main compounds in the most active fraction by LC-MS/MS.

Single-molecule pull-down (SiMPull) for new-age biochemistry: methodology and biochemical applications of single-molecule pull-down (SiMPull) for probing biomolecular interactions in crude cell extracts.

PubMed

Aggarwal, Vasudha; Ha, Taekjip

2014-11-01

Macromolecular interactions play a central role in many biological processes. Protein-protein interactions have mostly been studied by co-immunoprecipitation, which cannot provide quantitative information on all possible molecular connections present in the complex. We will review a new approach that allows cellular proteins and biomolecular complexes to be studied in real-time at the single-molecule level. This technique is called single-molecule pull-down (SiMPull), because it integrates principles of conventional immunoprecipitation with the powerful single-molecule fluorescence microscopy. SiMPull is used to count how many of each protein is present in the physiological complexes found in cytosol and membranes. Concurrently, it serves as a single-molecule biochemical tool to perform functional studies on the pulled-down proteins. In this review, we will focus on the detailed methodology of SiMPull, its salient features and a wide range of biological applications in comparison with other biosensing tools. © 2014 WILEY Periodicals, Inc.

Modern extraction techniques and their impact on the pharmacological profile of Serenoa repens extracts for the treatment of lower urinary tract symptoms

PubMed Central

2014-01-01

Background Bioactive compounds from plants (i.e., Serenoa repens) are often used in medicine in the treatment of several pathologies, among which benign prostatic hyperplasia (BPH) associated to lower urinary tract symptoms (LUTS). Discussion There are different techniques of extraction, also used in combination, with the aim of enhancing the amount of the target molecules, gaining time and reducing waste of solvents. However, the qualitative and quantitative composition of the bioactives depends on the extractive process, and so the brands of the recovered products from the same plant are different in terms of clinical efficacy (no product interchangeability among different commercial brands). Summary In this review, we report on several and recent extraction techniques and their impact on the composition/biological activity of S. repens-based available products. PMID:25112532

Multiplexed Sequence Encoding: A Framework for DNA Communication

PubMed Central

Zakeri, Bijan; Carr, Peter A.; Lu, Timothy K.

2016-01-01

Synthetic DNA has great propensity for efficiently and stably storing non-biological information. With DNA writing and reading technologies rapidly advancing, new applications for synthetic DNA are emerging in data storage and communication. Traditionally, DNA communication has focused on the encoding and transfer of complete sets of information. Here, we explore the use of DNA for the communication of short messages that are fragmented across multiple distinct DNA molecules. We identified three pivotal points in a communication—data encoding, data transfer & data extraction—and developed novel tools to enable communication via molecules of DNA. To address data encoding, we designed DNA-based individualized keyboards (iKeys) to convert plaintext into DNA, while reducing the occurrence of DNA homopolymers to improve synthesis and sequencing processes. To address data transfer, we implemented a secret-sharing system—Multiplexed Sequence Encoding (MuSE)—that conceals messages between multiple distinct DNA molecules, requiring a combination key to reveal messages. To address data extraction, we achieved the first instance of chromatogram patterning through multiplexed sequencing, thereby enabling a new method for data extraction. We envision these approaches will enable more widespread communication of information via DNA. PMID:27050646

Application of bacterial cytological profiling to crude natural product extracts reveals the antibacterial arsenal of Bacillus subtilis.

PubMed

Nonejuie, Poochit; Trial, Rachelle M; Newton, Gerald L; Lamsa, Anne; Ranmali Perera, Varahenage; Aguilar, Julieta; Liu, Wei-Ting; Dorrestein, Pieter C; Pogliano, Joe; Pogliano, Kit

2016-05-01

Although most clinically used antibiotics are derived from natural products, identifying new antibacterial molecules from natural product extracts is difficult due to the complexity of these extracts and the limited tools to correlate biological activity with specific molecules. Here, we show that bacterial cytological profiling (BCP) provides a rapid method for mechanism of action determination on plates and in complex natural product extracts and for activity-guided purification. We prepared an extract from Bacillus subtilis 3610 that killed the Escherichia coli lptD mutant and used BCP to observe two types of bioactivities in the unfractionated extract: inhibition of translation and permeablization of the cytoplasmic membrane. We used BCP to guide purification of the molecules responsible for each activity, identifying the translation inhibitors bacillaene and bacillaene B (glycosylated bacillaene) and demonstrating that two molecules contribute to cell permeabilitization, the bacteriocin subtilosin and the cyclic peptide sporulation killing factor. Our results suggest that bacillaene mediates translational arrest, and show that bacillaene B has a minimum inhibitory concentration 10 × higher than unmodified bacillaene. Finally, we show that BCP can be used to screen strains on an agar plate without the need for extract preparation, greatly saving time and improving throughput. Thus, BCP simplifies the isolation of novel natural products, by identifying strains, crude extracts and fractions with interesting bioactivities even when multiple activities are present, allowing investigators to focus labor-intensive steps on those with desired activities.

Application of bacterial cytological profiling to crude natural product extracts reveals the antibacterial arsenal of Bacillus subtilis

PubMed Central

Nonejuie, Poochit; Trial, Rachelle M.; Newton, Gerald L.; Lamsa, Anne; Perera, Varahenage Ranmali; Aguilar, Julieta; Liu, Wei-Ting; Dorrestein, Pieter C.; Pogliano, Joe; Pogliano, Kit

2016-01-01

Although most clinically used antibiotics are derived from natural products, identifying new antibacterial molecules from natural product extracts is difficult due to the complexity of these extracts and the limited tools to correlate biological activity with specific molecules. Here, we show that bacterial cytological profiling (BCP) provides a rapid method for mechanism of action determination on plates and in complex natural product extracts and for activity-guided purification. We prepared an extract from Bacillus subtilis 3610 that killed the Escherichia coli lptD mutant and used BCP to observe two types of bioactivities in the unfractionated extract: inhibition of translation and permeablization of the cytoplasmic membrane. We used BCP to guide purification of the molecules responsible for each activity, identifying the translation inhibitors bacillaene and bacillaene B (glycosylated bacillaene) and demonstrating that two molecules contribute to cell permeabilitization, the bacteriocin subtilosin and the cyclic peptide sporulation killing factor. Our results suggest that bacillaene mediates translational arrest, and show that bacillaene B has a minimum inhibitory concentration 10 × higher than unmodified bacillaene. Finally, we show that BCP can be used to screen strains on an agar plate without the need for extract preparation, greatly saving time and improving throughput. Thus, BCP simplifies the isolation of novel natural products, by identifying strains, crude extracts and fractions with interesting bioactivities even when multiple activities are present, allowing investigators to focus labor-intensive steps on those with desired activities. PMID:26648120

Current at Metal-Organic Interfaces

NASA Astrophysics Data System (ADS)

Kern, Klaus

2012-02-01

Charge transport through atomic and molecular constrictions greatly affects the operation and performance of organic electronic devices. Much of our understanding of the charge injection and extraction processes in these systems relays on our knowledge of the electronic structure at the metal-organic interface. Despite significant experimental and theoretical advances in studying charge transport in nanoscale junctions, a microscopic understanding at the single atom/molecule level is missing. In the present talk I will present our recent results to probe directly the nanocontact between single molecules and a metal electrode using scanning probe microscopy and spectroscopy. The experiments provide unprecedented microscopic details of single molecule and atom junctions and open new avenues to study quantum critical and many body phenomena at the atomic scale. Implications for energy conversion devices and carbon based nanoelectronics will also be discussed.

Sodium metabisulfite–induced polymerization of sickle cell hemoglobin incubated in the extracts of three medicinal plants (Anacardium occidentale, Psidium guajava, and Terminalia catappa)

PubMed Central

Chikezie, Paul Chidoka

2011-01-01

Background: The exploitation and utilization of vast varieties of herbal extracts may serve as alternative measures to deter aggregation of deoxygenated sickle cell hemoglobin (deoxyHbS) molecules. Objective: The present in vitro study ascertained the capacity of three medicinal plants, namely, Anacardium occidentale, Psidium guajava, and Terminalia catappa, to alter polymerization of HbS. Materials and Methods: Spectrophotometric method was used to monitor the level of polymerization of hemolysate HbS molecules treated with sodium metabisulfite (Na2 S2 O5) at a regular interval of 30 s for a period of 180 s in the presence of separate aqueous extracts of A. occidentale, P. guajava, and T. catappa. At time intervals of 30 s, the level of polymerization was expressed as percentage of absorbance relative to the control sample at the 180th s. Results: Although extracts of the three medicinal plants caused significant (P < 0.05) reduction in polymerization of deoxyHbS molecules, the corresponding capacity in this regard diminished with increase in incubation time. Aqueous extract of P. guajava exhibited the highest capacity to reduced polymerization of deoxyHbS molecules. Whereas at t > 60 s, extract concentration of 400 mg% of A. occidentale activated polymerization of deoxyHbS molecules by 6.23±1.34, 14.53±1.67, 21.15±1.89, and 24.42±1.09%, 800 mg% of T. catappa at t > 30 s gave values of 2.50±1.93, 5.09±1.96, 10.00±0.99, 15.38±1.33, and 17.31±0.97%. Conclusion: The capacity of the three medicinal plants to interfere with polymerization of deoxyHbS molecules depended on the duration of incubation and concentration of the extracts. PMID:21716622

Supercritical fluid extraction of the non-polar organic compounds in meteorites

NASA Astrophysics Data System (ADS)

Sephton, M. A.; Pillinger, C. T.; Gilmour, I.

2001-01-01

The carbonaceous chondrite meteorites contain a variety of extraterrestrial organic molecules. These organic components provide a valuable insight into the formation and evolution of the solar system. Attempts at obtaining and interpreting this information source are hampered by the small sample sizes available for study and the interferences from terrestrial contamination. Supercritical fluid extraction represents an efficient and contamination-free means of isolating extraterrestrial molecules. Gas chromatography-mass spectrometry analyses of extracts from Orgueil and Cold Bokkeveld reveal a complex mixture of free non-polar organic molecules which include normal alkanes, isoprenoid alkanes, tetrahydronaphthalenes and aromatic hydrocarbons. These organic assemblages imply contributions from both terrestrial and extraterrestrial sources.

Gp63-like molecules in Phytomonas serpens: possible role in the insect interaction.

PubMed

d'Avila-Levy, Claudia M; Santos, Lívia O; Marinho, Fernanda A; Dias, Felipe A; Lopes, Angela H; Santos, André L S; Branquinha, Marta H

2006-06-01

In this study, we demonstrated that metallopeptidase inhibitors (EDTA, EGTA, and 1,10-phenanthroline) were able to arrest Phytomonas serpens growth in distinct patterns. This parasite released exclusively metallopeptidases to the extracellular environment, whereas in cellular extracts only cysteine peptidases were detected. In addition, an extracellular polypeptide of 60 kDa reacted in Western blotting probed with polyclonal antibody raised against gp63 of Leishmania amazonensis. In the cellular parasite extract, this antibody recognized bands migrating at 63 and 52 kDa, which partitioned on both aqueous and membrane-rich fractions. Flow cytometry and fluorescence microscopy analyses showed that the gp63-like molecules have a surface location. Moreover, phospholipase C (PLC)-treated parasites reduced the number of gp63-positive cells. The anti-cross-reacting determinant (CRD) and anti-gp63 antibodies recognized the 60-kDa band in the supernatant from PLC-treated cells, suggesting that this protein is glycosylphosphatidylinositol-anchored to the plasma membrane. This is the first report on the presence of gp63-like molecules in members of the Phytomonas genus. The pretreatment of the parasites with anti-gp63 antibody significantly diminished their adhesion index to explanted salivary glands of the phytophagous insect Oncopeltus fasciatus, suggesting a potential involvement of the gp63-like molecules in the adhesive process of this plant trypanosomatid.

Method for performing site-specific affinity fractionation for use in DNA sequencing

DOEpatents

Mirzabekov, Andrei Darievich; Lysov, Yuri Petrovich; Dubley, Svetlana A.

1999-01-01

A method for fractionating and sequencing DNA via affinity interaction is provided comprising contacting cleaved DNA to a first array of oligonucleotide molecules to facilitate hybridization between said cleaved DNA and the molecules; extracting the hybridized DNA from the molecules; contacting said extracted hybridized DNA with a second array of oligonucleotide molecules, wherein the oligonucleotide molecules in the second array have specified base sequences that are complementary to said extracted hybridized DNA; and attaching labeled DNA to the second array of oligonucleotide molecules, wherein the labeled re-hybridized DNA have sequences that are complementary to the oligomers. The invention further provides a method for performing multi-step conversions of the chemical structure of compounds comprising supplying an array of polyacrylamide vessels separated by hydrophobic surfaces; immobilizing a plurality of reactants, such as enzymes, in the vessels so that each vessel contains one reactant; contacting the compounds to each of the vessels in a predetermined sequence and for a sufficient time to convert the compounds to a desired state; and isolating the converted compounds from said array.

Miniaturized reaction vessel system, method for performing site-specific biochemical reactions and affinity fractionation for use in DNA sequencing

DOEpatents

Mirzabekov, Andrei Darievich; Lysov, Yuri Petrovich; Dubley, Svetlana A.

2000-01-01

A method for fractionating and sequencing DNA via affinity interaction is provided comprising contacting cleaved DNA to a first array of oligonucleotide molecules to facilitate hybridization between said cleaved DNA and the molecules; extracting the hybridized DNA from the molecules; contacting said extracted hybridized DNA with a second array of oligonucleotide molecules, wherein the oligonucleotide molecules in the second array have specified base sequences that are complementary to said extracted hybridized DNA; and attaching labeled DNA to the second array of oligonucleotide molecules, wherein the labeled re-hybridized DNA have sequences that are complementary to the oligomers. The invention further provides a method for performing multi-step conversions of the chemical structure of compounds comprising supplying an array of polyacrylamide vessels separated by hydrophobic surfaces; immobilizing a plurality of reactants, such as enzymes, in the vessels so that each vessel contains one reactant; contacting the compounds to each of the vessels in a predetermined sequence and for a sufficient time to convert the compounds to a desired state; and isolating the converted compounds from said array.

Method for performing site-specific affinity fractionation for use in DNA sequencing

DOEpatents

Mirzabekov, A.D.; Lysov, Y.P.; Dubley, S.A.

1999-05-18

A method for fractionating and sequencing DNA via affinity interaction is provided comprising contacting cleaved DNA to a first array of oligonucleotide molecules to facilitate hybridization between the cleaved DNA and the molecules; extracting the hybridized DNA from the molecules; contacting the extracted hybridized DNA with a second array of oligonucleotide molecules, wherein the oligonucleotide molecules in the second array have specified base sequences that are complementary to the extracted hybridized DNA; and attaching labeled DNA to the second array of oligonucleotide molecules, wherein the labeled re-hybridized DNA have sequences that are complementary to the oligomers. The invention further provides a method for performing multi-step conversions of the chemical structure of compounds comprising supplying an array of polyacrylamide vessels separated by hydrophobic surfaces; immobilizing a plurality of reactants, such as enzymes, in the vessels so that each vessel contains one reactant; contacting the compounds to each of the vessels in a predetermined sequence and for a sufficient time to convert the compounds to a desired state; and isolating the converted compounds from the array. 14 figs.

Essential oils: from extraction to encapsulation.

PubMed

El Asbahani, A; Miladi, K; Badri, W; Sala, M; Aït Addi, E H; Casabianca, H; El Mousadik, A; Hartmann, D; Jilale, A; Renaud, F N R; Elaissari, A

2015-04-10

Essential oils are natural products which have many interesting applications. Extraction of essential oils from plants is performed by classical and innovative methods. Numerous encapsulation processes have been developed and reported in the literature in order to encapsulate biomolecules, active molecules, nanocrystals, oils and also essential oils for various applications such as in vitro diagnosis, therapy, cosmetic, textile, food etc. Essential oils encapsulation led to numerous new formulations with new applications. This insures the protection of the fragile oil and controlled release. The most commonly prepared carriers are polymer particles, liposomes and solid lipid nanoparticles. Copyright © 2015 Elsevier B.V. All rights reserved.

[Mechanism of gold solid extraction from aurocyanide solution using D3520 resin impregnated with TRPO].

PubMed

Yang, Xiang-Jun; Wang, Shi-Xiong; Zou, An-Qin; Chen, Jing; Guo, Hong

2014-02-01

Trialkyphosphine oxides (TRPO) was successfully used for the impregnation of D3520 resin to prepare an extractant-impregnated resin (EIR). Solid extraction of Au(I) from alkaline cyanide solution was studied using this extractant-impregnated resin (EIR), with addition of cetyltrimethylammonium bromide (CTMAB), directly into the aurous aqueous phase in advance. The mechanism of solid extraction was further investigated by means of FTIR, XPS and SEM. The column separation studies have shown that cationic surfactant CTMAB played a key role in the solid phase extraction, and the resin containing TRPO were effective for the extraction of gold when the molar ratio of CTMAB: Au( I ) reached 1:1. FTIR spectroscopy of gold loaded EIR showed that the frequency of C[triple bond]N stretching vibration was at 2144 cm(-1), and the frequency of P=O stretching vibration shifted to lower frequency from 1153 to 1150 cm(-1). The XPS spectrum of N(1s), Au(4f7/2) and Au(4f5/2) sugges- ted that the coordination environment of gold did not change before and after extraction, and gold was still as the form of Au (CN)2(-) anion exiting in the loaded resin; O(1s) spectrum showed that the chemically combined water significantly increased after solid extraction from 30.74% to 42.34%; Comparing to the P(2p) spectrum before and after extraction, the binding energy increased from 132. 15 to 132. 45 eV, indicating there maybe existing hydrogen-bond interaction between P=O and water molecule, such as P=O...H-O-H. The above results obtained established that in the solid extraction process, the hydrophobic ion association [CTMA+ x Au(CN)] diffused from the bulk solution into the pores of the EIR, and then be solvated by TRPO adsorbed in the pores through hydrogen bonding bridged by the water molecules.

Sarcoptes scabiei (Acari: Sarcoptidae) Mite Extract Modulates Expression of Cytokines and Adhesion Molecules by Human Dermal Microvascular Endothelial Cells.

PubMed Central

Elder, B. Laurel; Arlian, Larry G.; Morgan, Marjorie S.

2007-01-01

The inflammatory and immune responses seen with the worldwide disease scabies (caused by the mite Sarcoptes scabiei) are complex. Clinical symptoms are delayed for weeks in patients when they are infested with scabies for the first time. This study was undertaken to elucidate the role of the human dermal microvascular endothelial cell (HMVEC-D) in modulating the inflammatory and immune responses in the skin to S. scabiei. Extracts of S. scabiei were incubated with HMVEC-D and the expression of adhesion molecules and chemokine receptors on the cells and the secretion of selected cytokines were determined by ELISA. S. scabiei extract was found to inhibit HMVEC-D expression of E-selectin and vascular cell adhesion molecule-1 (VCAM-1) although not intercellular adhesion molecule-1 (ICAM-1). The secretion of interleukin-8 (IL-8) was also inhibited by S. scabiei extract. S. scabiei extract increased expression of the chemokine receptor CXCR-1, and both down-regulated and up-regulated expression of CXCR-2 depending on the concentration tested. These findings help explain the delayed inflammatory reaction to infestation with S. scabiei. PMID:17017228

A combined model of heat and mass transfer for the in situ extraction of volatile water from lunar regolith

NASA Astrophysics Data System (ADS)

Reiss, P.

2018-05-01

Chemical analysis of lunar soil samples often involves thermal processing to extract their volatile constituents, such as loosely adsorbed water. For the characterization of volatiles and their bonding mechanisms it is important to determine their desorption temperature. However, due to the low thermal diffusivity of lunar regolith, it might be difficult to reach a uniform heat distribution in a sample that is larger than only a few particles. Furthermore, the mass transport through such a sample is restricted, which might lead to a significant delay between actual desorption and measurable outgassing of volatiles from the sample. The entire volatiles extraction process depends on the dynamically changing heat and mass transfer within the sample, and is influenced by physical parameters such as porosity, tortuosity, gas density, temperature and pressure. To correctly interpret measurements of the extracted volatiles, it is important to understand the interaction between heat transfer, sorption, and gas transfer through the sample. The present paper discusses the molecular kinetics and mechanisms that are involved in the thermal extraction process and presents a combined parametrical computation model to simulate this process. The influence of water content on the gas diffusivity and thermal diffusivity is discussed and the issue of possible resorption of desorbed molecules within the sample is addressed. Based on the multi-physical computation model, a case study for the ProSPA instrument for in situ analysis of lunar volatiles is presented, which predicts relevant dynamic process parameters, such as gas pressure and process duration.

Quantifying Dimer and Trimer Formation by Tri- n -butyl Phosphates in n -Dodecane: Molecular Dynamics Simulations

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

Vo, Quynh N.; Dang, Liem X.; Nilsson, Mikael

2016-07-21

Tri-n-butyl phosphate (TBP), a representative of neutral organophosphorous ligands, is an important extractant used in solvent extraction process for the recovery of uranium and plutonium from spent nuclear fuel. Microscopic pictures of TBP isomerism and its behavior in n-dodecane diluent were investigated utilizing MD simulations with previously optimized force field parameters for TBP and n-dodecane. Potential Mean Force (PMF) calculations on a single TBP molecule show seven probable TBP isomers. Radial Distribution Functions (RDF) of TBP suggests the existence of TBP trimers at high TBP concentrations in addition to dimers. 2D PMF calculations were performed to determine the angle andmore » distance criteria for TBP trimers. The dimerization and trimerization constants of TBP in n-dodecane were obtained and match our own experimental values using FTIR technique. The new insights into the conformational behaviors of TBP molecule as a monomer and as part of an aggregate could greatly aid the understanding of the complexation between TBP and metal ions in solvent extraction system. The U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences funded the work performed by LXD.« less

Identification of extracellular miRNA in archived serum samples by next-generation sequencing from RNA extracted using multiple methods.

PubMed

Gautam, Aarti; Kumar, Raina; Dimitrov, George; Hoke, Allison; Hammamieh, Rasha; Jett, Marti

2016-10-01

miRNAs act as important regulators of gene expression by promoting mRNA degradation or by attenuating protein translation. Since miRNAs are stably expressed in bodily fluids, there is growing interest in profiling these miRNAs, as it is minimally invasive and cost-effective as a diagnostic matrix. A technical hurdle in studying miRNA dynamics is the ability to reliably extract miRNA as small sample volumes and low RNA abundance create challenges for extraction and downstream applications. The purpose of this study was to develop a pipeline for the recovery of miRNA using small volumes of archived serum samples. The RNA was extracted employing several widely utilized RNA isolation kits/methods with and without addition of a carrier. The small RNA library preparation was carried out using Illumina TruSeq small RNA kit and sequencing was carried out using Illumina platform. A fraction of five microliters of total RNA was used for library preparation as quantification is below the detection limit. We were able to profile miRNA levels in serum from all the methods tested. We found out that addition of nucleic acid based carrier molecules had higher numbers of processed reads but it did not enhance the mapping of any miRBase annotated sequences. However, some of the extraction procedures offer certain advantages: RNA extracted by TRIzol seemed to align to the miRBase best; extractions using TRIzol with carrier yielded higher miRNA-to-small RNA ratios. Nuclease free glycogen can be carrier of choice for miRNA sequencing. Our findings illustrate that miRNA extraction and quantification is influenced by the choice of methodologies. Addition of nucleic acid- based carrier molecules during extraction procedure is not a good choice when assaying miRNA using sequencing. The careful selection of an extraction method permits the archived serum samples to become valuable resources for high-throughput applications.

ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files.

PubMed

Karthikeyan, Muthukumarasamy; Vyas, Renu

2016-01-01

Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular information, generally from a PDF document format is a daunting task. Here we present an approach to harvest 3D molecular data from the supporting information of scientific research articles that are normally available from publisher's resources. In order to demonstrate the feasibility of extracting truly computable molecules from PDF file formats in a fast and efficient manner, we have developed a Java based application, namely ChemEngine. This program recognizes textual patterns from the supplementary data and generates standard molecular structure data (bond matrix, atomic coordinates) that can be subjected to a multitude of computational processes automatically. The methodology has been demonstrated via several case studies on different formats of coordinates data stored in supplementary information files, wherein ChemEngine selectively harvested the atomic coordinates and interpreted them as molecules with high accuracy. The reusability of extracted molecular coordinate data was demonstrated by computing Single Point Energies that were in close agreement with the original computed data provided with the articles. It is envisaged that the methodology will enable large scale conversion of molecular information from supplementary files available in the PDF format into a collection of ready- to- compute molecular data to create an automated workflow for advanced computational processes. Software along with source codes and instructions available at https://sourceforge.net/projects/chemengine/files/?source=navbar.Graphical abstract.

Three chamber negative ion source

DOEpatents

Leung, Ka-Ngo; Ehlers, Kenneth W.; Hiskes, John R.

1985-01-01

A negative ion vessel is divided into an excitation chamber, a negative ionization chamber and an extraction chamber by two magnetic filters. Input means introduces neutral molecules into a first chamber where a first electron discharge means vibrationally excites the molecules which migrate to a second chamber. In the second chamber a second electron discharge means ionizes the molecules, producing negative ions which are extracted into or by a third chamber. A first magnetic filter prevents high energy electrons from entering the negative ionization chamber from the excitation chamber. A second magnetic filter prevents high energy electrons from entering the extraction chamber from the negative ionizing chamber. An extraction grid at the end of the negative ion vessel attracts negative ions into the third chamber and accelerates them. Another grid, located adjacent to the extraction grid, carries a small positive voltage in order to inhibit positive ions from migrating into the extraction chamber and contour the plasma potential. Additional electrons can be suppressed from the output flux using ExB forces provided by magnetic field means and the extractor grid electric potential.

The effect of bean origin and temperature on grinding roasted coffee

NASA Astrophysics Data System (ADS)

Uman, Erol; Colonna-Dashwood, Maxwell; Colonna-Dashwood, Lesley; Perger, Matthew; Klatt, Christian; Leighton, Stephen; Miller, Brian; Butler, Keith T.; Melot, Brent C.; Speirs, Rory W.; Hendon, Christopher H.

2016-04-01

Coffee is prepared by the extraction of a complex array of organic molecules from the roasted bean, which has been ground into fine particulates. The extraction depends on temperature, water chemistry and also the accessible surface area of the coffee. Here we investigate whether variations in the production processes of single origin coffee beans affects the particle size distribution upon grinding. We find that the particle size distribution is independent of the bean origin and processing method. Furthermore, we elucidate the influence of bean temperature on particle size distribution, concluding that grinding cold results in a narrower particle size distribution, and reduced mean particle size. We anticipate these results will influence the production of coffee industrially, as well as contribute to how we store and use coffee daily.

The effect of bean origin and temperature on grinding roasted coffee.

PubMed

Uman, Erol; Colonna-Dashwood, Maxwell; Colonna-Dashwood, Lesley; Perger, Matthew; Klatt, Christian; Leighton, Stephen; Miller, Brian; Butler, Keith T; Melot, Brent C; Speirs, Rory W; Hendon, Christopher H

2016-04-18

Coffee is prepared by the extraction of a complex array of organic molecules from the roasted bean, which has been ground into fine particulates. The extraction depends on temperature, water chemistry and also the accessible surface area of the coffee. Here we investigate whether variations in the production processes of single origin coffee beans affects the particle size distribution upon grinding. We find that the particle size distribution is independent of the bean origin and processing method. Furthermore, we elucidate the influence of bean temperature on particle size distribution, concluding that grinding cold results in a narrower particle size distribution, and reduced mean particle size. We anticipate these results will influence the production of coffee industrially, as well as contribute to how we store and use coffee daily.

The effect of bean origin and temperature on grinding roasted coffee

PubMed Central

Uman, Erol; Colonna-Dashwood, Maxwell; Colonna-Dashwood, Lesley; Perger, Matthew; Klatt, Christian; Leighton, Stephen; Miller, Brian; Butler, Keith T.; Melot, Brent C.; Speirs, Rory W.; Hendon, Christopher H.

2016-01-01

Coffee is prepared by the extraction of a complex array of organic molecules from the roasted bean, which has been ground into fine particulates. The extraction depends on temperature, water chemistry and also the accessible surface area of the coffee. Here we investigate whether variations in the production processes of single origin coffee beans affects the particle size distribution upon grinding. We find that the particle size distribution is independent of the bean origin and processing method. Furthermore, we elucidate the influence of bean temperature on particle size distribution, concluding that grinding cold results in a narrower particle size distribution, and reduced mean particle size. We anticipate these results will influence the production of coffee industrially, as well as contribute to how we store and use coffee daily. PMID:27086837

Bioavailability of Bioactive Molecules from Olive Leaf Extracts and its Functional Value.

PubMed

Martín-Vertedor, Daniel; Garrido, María; Pariente, José Antonio; Espino, Javier; Delgado-Adámez, Jonathan

2016-07-01

Olive leaves are an important low-cost source of bioactive compounds. The present study aimed to examine the effect of in vitro digestibility of an olive leaf aqueous extract so as to prove the availability of its phenolic compounds as well as its antioxidant, antimicrobial, and anticancer activity after a simulated digestion process. The total phenolic content was significantly higher in the pure lyophilized extract. Phenolic compounds, however, decreased by 60% and 90% in simulated gastric fluid (SGF) and simulated intestinal fluid (SIF), respectively. Regarding antioxidant activity, it was reduced by 10% and 50% after gastric and intestinal digestion, respectively; despite this fact, high antioxidant capacity was found in both SGF and SIF. Moreover, the olive leaf extract showed an unusual combined antimicrobial action at low concentration, which suggested their great potential as nutraceuticals, particularly as a source of phenolic compounds. Finally, olive leaf extracts produced a general dose-dependent cytotoxic effect against U937 cells. To sum up, these findings suggest that the olive leaf aqueous extract maintains its beneficial properties after a simulated digestion process, and therefore its regular consumption could be helpful in the management and the prevention of oxidative stress-related chronic disease, bacterial infection, or even cancer. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Molecularly imprinted polymers with synthetic dummy template for simultaneously selective removal and enrichment of ginkgolic acids from Ginkgo biloba L. leaves extracts.

PubMed

Ji, Wenhua; Ma, Xiuli; Xie, Hongkai; Chen, Lingxiao; Wang, Xiao; Zhao, Hengqiang; Huang, Luqi

2014-11-14

Dummy molecularly imprinted polymers (DMIPs) for simultaneously selective removal and enrichment of ginkgolic acids (GAs) during the processing of Ginkgo biloba leaves have been prepared. Two dummy template molecule with similar structural skeleton to GAs, 6-methoxysalicylic acid (MOSA, DT-1) and 6-hexadecyloxysalicylic acid (HOSA, DT-2), have been designed and synthesized. The performance of the DMIPs and NIPs were evaluated including selective recognition capacity, adsorption isotherm, and adsorption kinetics. The selective recognition capacity of the three GAs with four analogues on the sorbents illustrated that the DMIPs sorbents have high specificity for GAs. An efficient method based on DMIP-HOSA coupled with solid-phase extraction (SPE) was developed for simultaneously selective removal and enrichment of ginkgolic acids (GAs) during the processing of Ginkgo biloba leaves. The method showed excellent recoveries (82.5-88.7%) and precision (RSD 0.5-2.6%, n=5) for licorice extracts, Gastrodia elata extracts and pepper extracts spiked at three concentration levels each (50, 100, 200 μg mL(-1)). The results indicated that GAs and standardized Ginkgo biloba leaves extracts could be obtained simultaneously through the DMIP-SPE. Copyright © 2014 Elsevier B.V. All rights reserved.

Predicting drug side-effect profiles: a chemical fragment-based approach

PubMed Central

2011-01-01

Background Drug side-effects, or adverse drug reactions, have become a major public health concern. It is one of the main causes of failure in the process of drug development, and of drug withdrawal once they have reached the market. Therefore, in silico prediction of potential side-effects early in the drug discovery process, before reaching the clinical stages, is of great interest to improve this long and expensive process and to provide new efficient and safe therapies for patients. Results In the present work, we propose a new method to predict potential side-effects of drug candidate molecules based on their chemical structures, applicable on large molecular databanks. A unique feature of the proposed method is its ability to extract correlated sets of chemical substructures (or chemical fragments) and side-effects. This is made possible using sparse canonical correlation analysis (SCCA). In the results, we show the usefulness of the proposed method by predicting 1385 side-effects in the SIDER database from the chemical structures of 888 approved drugs. These predictions are performed with simultaneous extraction of correlated ensembles formed by a set of chemical substructures shared by drugs that are likely to have a set of side-effects. We also conduct a comprehensive side-effect prediction for many uncharacterized drug molecules stored in DrugBank, and were able to confirm interesting predictions using independent source of information. Conclusions The proposed method is expected to be useful in various stages of the drug development process. PMID:21586169

High-throughput bioluminescence screening of ubiquitin-proteasome pathway inhibitors from chemical and natural sources.

PubMed

Ausseil, Frederic; Samson, Arnaud; Aussagues, Yannick; Vandenberghe, Isabelle; Creancier, Laurent; Pouny, Isabelle; Kruczynski, Anna; Massiot, Georges; Bailly, Christian

2007-02-01

To discover original inhibitors of the ubiquitin-proteasome pathway, the authors have developed a cell-based bioluminescent assay and used it to screen collections of plant extracts and chemical compounds. They first established a DLD-1 human colon cancer cell line that stably expresses a 4Ubiquitin-Luciferase (4Ub-Luc) reporter protein, efficiently targeted to the ubiquitin-proteasome degradation pathway. The assay was then adapted to 96- and 384-well plate formats and calibrated with reference proteasome inhibitors. Assay robustness was carefully assessed, particularly cell toxicity, and the statistical Z factor value was calculated to 0.83, demonstrating a good performance level of the assay. A total of 18,239 molecules and 15,744 plant extracts and fractions thereof were screened for their capacity to increase the luciferase activity in DLD-1 4Ub-Luc cells, and 21 molecules and 66 extracts inhibiting the ubiquitin-proteasome pathway were identified. The fractionation of an active methanol extract of Physalis angulata L. aerial parts was performed to isolate 2 secosteroids known as physalin B and C. In a cell-based Western blot assay, the ubiquitinated protein accumulation was confirmed after a physalin treatment confirming the accuracy of the screening process. The method reported here thus provides a robust approach to identify novel ubiquitin-proteasome pathway inhibitors in large collections of chemical compounds and natural products.

Universal Temporal Profile of Replication Origin Activation in Eukaryotes

NASA Astrophysics Data System (ADS)

Goldar, Arach

2011-03-01

The complete and faithful transmission of eukaryotic genome to daughter cells involves the timely duplication of mother cell's DNA. DNA replication starts at multiple chromosomal positions called replication origin. From each activated replication origin two replication forks progress in opposite direction and duplicate the mother cell's DNA. While it is widely accepted that in eukaryotic organisms replication origins are activated in a stochastic manner, little is known on the sources of the observed stochasticity. It is often associated to the population variability to enter S phase. We extract from a growing Saccharomyces cerevisiae population the average rate of origin activation in a single cell by combining single molecule measurements and a numerical deconvolution technique. We show that the temporal profile of the rate of origin activation in a single cell is similar to the one extracted from a replicating cell population. Taking into account this observation we exclude the population variability as the origin of observed stochasticity in origin activation. We confirm that the rate of origin activation increases in the early stage of S phase and decreases at the latter stage. The population average activation rate extracted from single molecule analysis is in prefect accordance with the activation rate extracted from published micro-array data, confirming therefore the homogeneity and genome scale invariance of dynamic of replication process. All these observations point toward a possible role of replication fork to control the rate of origin activation.

Identification of Novel Human Dipeptidyl Peptidase-IV Inhibitors of Natural Origin (Part II): In Silico Prediction in Antidiabetic Extracts

PubMed Central

Guasch, Laura; Sala, Esther; Ojeda, María José; Valls, Cristina; Bladé, Cinta; Mulero, Miquel; Blay, Mayte; Ardévol, Anna; Garcia-Vallvé, Santiago; Pujadas, Gerard

2012-01-01

Background Natural extracts play an important role in traditional medicines for the treatment of diabetes mellitus and are also an essential resource for new drug discovery. Dipeptidyl peptidase IV (DPP-IV) inhibitors are potential candidates for the treatment of type 2 diabetes mellitus, and the effectiveness of certain antidiabetic extracts of natural origin could be, at least partially, explained by the inhibition of DPP-IV. Methodology/Principal Findings Using an initial set of 29,779 natural products that are annotated with their natural source and an experimentally validated virtual screening procedure previously developed in our lab (Guasch et al.; 2012) [1], we have predicted 12 potential DPP-IV inhibitors from 12 different plant extracts that are known to have antidiabetic activity. Seven of these molecules are identical or similar to molecules with described antidiabetic activity (although their role as DPP-IV inhibitors has not been suggested as an explanation for their bioactivity). Therefore, it is plausible that these 12 molecules could be responsible, at least in part, for the antidiabetic activity of these extracts through their inhibitory effect on DPP-IV. In addition, we also identified as potential DPP-IV inhibitors 6 molecules from 6 different plants with no described antidiabetic activity but that share the same genus as plants with known antidiabetic properties. Moreover, none of the 18 molecules that we predicted as DPP-IV inhibitors exhibits chemical similarity with a group of 2,342 known DPP-IV inhibitors. Conclusions/Significance Our study identified 18 potential DPP-IV inhibitors in 18 different plant extracts (12 of these plants have known antidiabetic properties, whereas, for the remaining 6, antidiabetic activity has been reported for other plant species from the same genus). Moreover, none of the 18 molecules exhibits chemical similarity with a large group of known DPP-IV inhibitors. PMID:23028712

Anti-inflammatory and angiogenic activity of polysaccharide extract obtained from Tibetan kefir.

PubMed

Prado, Maria Rosa Machado; Boller, Christian; Zibetti, Rosiane Guetter Mello; de Souza, Daiany; Pedroso, Luciana Lopes; Soccol, Carlos Ricardo

2016-11-01

The search for new bioactive molecules is a driving force for research pharmaceutical industries, especially those molecules obtained from fermentation. The molecules possessing angiogenic and anti-inflammatory attributes have attracted attention and are the focus of this study. Angiogenic activity from kefir polysaccharide extract, via chorioallantoic membrane assay, exhibited a pro-angiogenic effect compared with vascular endothelial factor (pro-angiogenic) and hydrocortisone (anti-angiogenic) activity as standards with an EC50 of 192ng/mL. In terms of anti-inflammatory activity determined via hyaluronidase enzyme assay, kefir polysaccharide extract inhibited the enzyme with a minimal activity of 2.08mg/mL and a maximum activity of 2.57mg/mL. For pharmaceutical purposes, kefir polysaccharide extract is considered to be safe because it does not inhibit VERO cells in cytotoxicity assays. Copyright © 2016 Elsevier Inc. All rights reserved.

High-Throughput Screening of Australian Marine Organism Extracts for Bioactive Molecules Affecting the Cellular Storage of Neutral Lipids

PubMed Central

Rae, James; Fontaine, Frank; Salim, Angela A.; Lo, Harriet P.; Capon, Robert J.; Parton, Robert G.; Martin, Sally

2011-01-01

Mammalian cells store excess fatty acids as neutral lipids in specialised organelles called lipid droplets (LDs). Using a simple cell-based assay and open-source software we established a high throughput screen for LD formation in A431 cells in order to identify small bioactive molecules affecting lipid storage. Screening an n-butanol extract library from Australian marine organisms we identified 114 extracts that produced either an increase or a decrease in LD formation in fatty acid-treated A431 cells with varying degrees of cytotoxicity. We selected for further analysis a non-cytotoxic extract derived from the genus Spongia (Heterofibria). Solvent partitioning, HPLC fractionation and spectroscopic analysis (NMR, MS) identified a family of related molecules within this extract with unique structural features, a subset of which reduced LD formation. We selected one of these molecules, heterofibrin A1, for more detailed cellular analysis. Inhibition of LD biogenesis by heterofibrin A1 was observed in both A431 cells and AML12 hepatocytes. The activity of heterofibrin A1 was dose dependent with 20 µM inhibiting LD formation and triglyceride accumulation by ∼50% in the presence of 50 µM oleic acid. Using a fluorescent fatty acid analogue we found that heterofibrin A1 significantly reduces the intracellular accumulation of fatty acids and results in the formation of distinct fatty acid metabolites in both cultured cells and in embryos of the zebrafish Danio rerio. In summary we have shown using readily accessible software and a relatively simple assay system that we can identify and isolate bioactive molecules from marine extracts, which affect the formation of LDs and the metabolism of fatty acids both in vitro and in vivo. PMID:21857959

IMS - MS Data Extractor

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

2015-10-20

An automated drift time extraction and computed associated collision cross section software tool for small molecule analysis with ion mobility spectrometry-mass spectrometry (IMS-MS). The software automatically extracts drift times and computes associated collision cross sections for small molecules analyzed using ion mobility spectrometry-mass spectrometry (IMS-MS) based on a target list of expected ions provided by the user.

High-throughput screening of small molecules in miniaturized mammalian cell-based assays involving post-translational modifications.

PubMed

Stockwell, B R; Haggarty, S J; Schreiber, S L

1999-02-01

Fully adapting a forward genetic approach to mammalian systems requires efficient methods to alter systematically gene products without prior knowledge of gene sequences, while allowing for the subsequent characterization of these alterations. Ideally, these methods would also allow function to be altered in a temporally controlled manner. We report the development of a miniaturized cell-based assay format that enables a genetic-like approach to understanding cellular pathways in mammalian systems using small molecules, rather than mutations, as the source of gene-product alterations. This whole-cell immunodetection assay can sensitively detect changes in specific cellular macromolecules in high-density arrays of mammalian cells. Furthermore, it is compatible with screening large numbers of small molecules in nanoliter to microliter culture volumes. We refer to this assay format as a 'cytoblot', and demonstrate the use of cytoblotting to monitor biosynthetic processes such as DNA synthesis, and post-translational processes such as acetylation and phosphorylation. Finally, we demonstrate the applicability of these assays to natural-product screening through the identification of marine sponge extracts exhibiting genotype-specific inhibition of 5-bromodeoxyuridine incorporation and suppression of the anti-proliferative effect of rapamycin. We show that cytoblots can be used for high-throughput screening of small molecules in cell-based assays. Together with small-molecule libraries, the cytoblot assay can be used to perform chemical genetic screens analogous to those used in classical genetics and thus should be applicable to understanding a wide variety of cellular processes, especially those involving post-transitional modifications.

Single-molecule dynamics in nanofabricated traps

NASA Astrophysics Data System (ADS)

Cohen, Adam

2009-03-01

The Anti-Brownian Electrokinetic trap (ABEL trap) provides a means to immobilize a single fluorescent molecule in solution, without surface attachment chemistry. The ABEL trap works by tracking the Brownian motion of a single molecule, and applying feedback electric fields to induce an electrokinetic motion that approximately cancels the Brownian motion. We present a new design for the ABEL trap that allows smaller molecules to be trapped and more information to be extracted from the dynamics of a single molecule than was previously possible. In particular, we present strategies for extracting dynamically fluctuating mobilities and diffusion coefficients, as a means to probe dynamic changes in molecular charge and shape. If one trapped molecule is good, many trapped molecules are better. An array of single molecules in solution, each immobilized without surface attachment chemistry, provides an ideal test-bed for single-molecule analyses of intramolecular dynamics and intermolecular interactions. We present a technology for creating such an array, using a fused silica plate with nanofabricated dimples and a removable cover for sealing single molecules within the dimples. With this device one can watch the shape fluctuations of single molecules of DNA or study cooperative interactions in weakly associating protein complexes.

Magnetic Separator Enhances Treatment Possibilities

NASA Technical Reports Server (NTRS)

2008-01-01

Since the earliest missions in space, NASA specialists have performed experiments in low gravity. Protein crystal growth, cell and tissue cultures, and separation technologies such as electrophoresis and magnetophoresis have been studied on Apollo 14, Apollo 16, STS-107, and many other missions. Electrophoresis and magnetophoresis, respectively, are processes that separate substances based on the electrical charge and magnetic field of a molecule or particle. Electrophoresis has been studied on over a dozen space shuttle flights, leading to developments in electrokinetics, which analyzes the effects of electric fields on mass transport (atoms, molecules, and particles) in fluids. Further studies in microgravity will continue to improve these techniques, which researchers use to extract cells for various medical treatments and research.

Advanced solvent based methods for molecular characterization of soil organic matter by high-resolution mass spectrometry

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

Tfaily, Malak M.; Chu, Rosalie K.; Tolic, Nikola

2015-05-19

Soil organic matter (SOM) a complex, heterogeneous mixture of above and belowground plant litter and animal and microbial residues at various degrees of decomposition, is a key reservoir for carbon (C) and nutrient biogeochemical cycling in soil based ecosystems. A limited understanding of the molecular composition of SOM limits the ability to routinely decipher chemical processes within soil and predict accurately how terrestrial carbon fluxes will response to changing climatic conditions and land use. To elucidate the molecular-level structure of SOM, we selectively extracted a broad range of intact SOM compounds by a combination of different organic solvents from soilsmore » with a wide range of C content. Our use of Electrospray ionization (ESI) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and a suite of solvents with varying polarity significantly expands the inventory of the types of organic molecules present in soils. Specifically, we found that hexane is selective for lipid-like compounds with very low O:C ratios; water was selective for carbohydrates with high O:C ratios; acetonitrile preferentially extracts lignin, condensed structures, and tannin poly phenolic compounds with O:C > 0.5; methanol has higher selectivity towards compounds characterized with low O:C < 0.5; and hexane, MeOH, ACN and water solvents increase the number and types of organic molecules extracted from soil for a broader range of chemically diverse soil types. Our study of SOM molecules by ESI-FTICR MS revealed new insight into the molecular-level complexity of organics contained in soils.« less

Effect of the Drying Process on the Intensification of Phenolic Compounds Recovery from Grape Pomace Using Accelerated Solvent Extraction

PubMed Central

Rajha, Hiba N.; Ziegler, Walter; Louka, Nicolas; Hobaika, Zeina; Vorobiev, Eugene; Boechzelt, Herbert G.; Maroun, Richard G.

2014-01-01

In light of their environmental and economic interests, food byproducts have been increasingly exploited and valorized for their richness in dietary fibers and antioxidants. Phenolic compounds are antioxidant bioactive molecules highly present in grape byproducts. Herein, the accelerated solvent extraction (ASE) of phenolic compounds from wet and dried grape pomace, at 45 °C, was conducted and the highest phenolic compounds yield (PCY) for wet (16.2 g GAE/100 g DM) and dry (7.28 g GAE/100 g DM) grape pomace extracts were obtained with 70% ethanol/water solvent at 140 °C. The PCY obtained from wet pomace was up to two times better compared to the dry byproduct and up to 15 times better compared to the same food matrices treated with conventional methods. With regard to Resveratrol, the corresponding dry pomace extract had a better free radical scavenging activity (49.12%) than the wet extract (39.8%). The drying pretreatment process seems to ameliorate the antiradical activity, especially when the extraction by ASE is performed at temperatures above 100 °C. HPLC-DAD analysis showed that the diversity of the flavonoid and the non-flavonoid compounds found in the extracts was seriously affected by the extraction temperature and the pretreatment of the raw material. This diversity seems to play a key role in the scavenging activity demonstrated by the extracts. Our results emphasize on ASE usage as a promising method for the preparation of highly concentrated and bioactive phenolic extracts that could be used in several industrial applications. PMID:25322155

Effect of the drying process on the intensification of phenolic compounds recovery from grape pomace using accelerated solvent extraction.

PubMed

Rajha, Hiba N; Ziegler, Walter; Louka, Nicolas; Hobaika, Zeina; Vorobiev, Eugene; Boechzelt, Herbert G; Maroun, Richard G

2014-10-15

In light of their environmental and economic interests, food byproducts have been increasingly exploited and valorized for their richness in dietary fibers and antioxidants. Phenolic compounds are antioxidant bioactive molecules highly present in grape byproducts. Herein, the accelerated solvent extraction (ASE) of phenolic compounds from wet and dried grape pomace, at 45 °C, was conducted and the highest phenolic compounds yield (PCY) for wet (16.2 g GAE/100 g DM) and dry (7.28 g GAE/100 g DM) grape pomace extracts were obtained with 70% ethanol/water solvent at 140 °C. The PCY obtained from wet pomace was up to two times better compared to the dry byproduct and up to 15 times better compared to the same food matrices treated with conventional methods. With regard to Resveratrol, the corresponding dry pomace extract had a better free radical scavenging activity (49.12%) than the wet extract (39.8%). The drying pretreatment process seems to ameliorate the antiradical activity, especially when the extraction by ASE is performed at temperatures above 100 °C. HPLC-DAD analysis showed that the diversity of the flavonoid and the non-flavonoid compounds found in the extracts was seriously affected by the extraction temperature and the pretreatment of the raw material. This diversity seems to play a key role in the scavenging activity demonstrated by the extracts. Our results emphasize on ASE usage as a promising method for the preparation of highly concentrated and bioactive phenolic extracts that could be used in several industrial applications.

Tackling saponin diversity in marine animals by mass spectrometry: data acquisition and integration.

PubMed

Decroo, Corentin; Colson, Emmanuel; Demeyer, Marie; Lemaur, Vincent; Caulier, Guillaume; Eeckhaut, Igor; Cornil, Jérôme; Flammang, Patrick; Gerbaux, Pascal

2017-05-01

Saponin analysis by mass spectrometry methods is nowadays progressively supplementing other analytical methods such as nuclear magnetic resonance (NMR). Indeed, saponin extracts from plant or marine animals are often constituted by a complex mixture of (slightly) different saponin molecules that requires extensive purification and separation steps to meet the requirement for NMR spectroscopy measurements. Based on its intrinsic features, mass spectrometry represents an inescapable tool to access the structures of saponins within extracts by using LC-MS, MALDI-MS, and tandem mass spectrometry experiments. The combination of different MS methods nowadays allows for a nice description of saponin structures, without extensive purification. However, the structural characterization process is based on low kinetic energy CID which cannot afford a total structure elucidation as far as stereochemistry is concerned. Moreover, the structural difference between saponins in a same extract is often so small that coelution upon LC-MS analysis is unavoidable, rendering the isomeric distinction and characterization by CID challenging or impossible. In the present paper, we introduce ion mobility in combination with liquid chromatography to better tackle the structural complexity of saponin congeners. When analyzing saponin extracts with MS-based methods, handling the data remains problematic for the comprehensive report of the results, but also for their efficient comparison. We here introduce an original schematic representation using sector diagrams that are constructed from mass spectrometry data. We strongly believe that the proposed data integration could be useful for data interpretation since it allows for a direct and fast comparison, both in terms of composition and relative proportion of the saponin contents in different extracts. Graphical Abstract A combination of state-of-the-art mass spectrometry methods, including ion mobility spectroscopy, is developed to afford a complete description of the saponin molecules in natural extracts.

A novel approach to the simultaneous extraction and non-targeted analysis of the small molecules metabolome and lipidome using 96-well solid phase extraction plates with column-switching technology.

PubMed

Li, Yubo; Zhang, Zhenzhu; Liu, Xinyu; Li, Aizhu; Hou, Zhiguo; Wang, Yuming; Zhang, Yanjun

2015-08-28

This study combines solid phase extraction (SPE) using 96-well plates with column-switching technology to construct a rapid and high-throughput method for the simultaneous extraction and non-targeted analysis of small molecules metabolome and lipidome based on ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry. This study first investigated the columns and analytical conditions for small molecules metabolome and lipidome, separated by an HSS T3 and BEH C18 columns, respectively. Next, the loading capacity and actuation duration of SPE were further optimized. Subsequently, SPE and column switching were used together to rapidly and comprehensively analyze the biological samples. The experimental results showed that the new analytical procedure had good precision and maintained sample stability (RSD<15%). The method was then satisfactorily applied to more widely analyze the small molecules metabolome and lipidome to test the throughput. The resulting method represents a new analytical approach for biological samples, and a highly useful tool for researches in metabolomics and lipidomics. Copyright © 2015 Elsevier B.V. All rights reserved.

Dark-field-based observation of single-nanoparticle dynamics on a supported lipid bilayer for in situ analysis of interacting molecules and nanoparticles.

PubMed

Lee, Young Kwang; Kim, Sungi; Nam, Jwa-Min

2015-01-12

Observation of single plasmonic nanoparticles in reconstituted biological systems allows us to obtain snapshots of dynamic processes between molecules and nanoparticles with unprecedented spatiotemporal resolution and single-molecule/single-particle-level data acquisition. This Concept is intended to introduce nanoparticle-tethered supported lipid bilayer platforms that allow for the dynamic confinement of nanoparticles on a two-dimensional fluidic surface. The dark-field-based long-term, stable, real-time observation of freely diffusing plasmonic nanoparticles on a lipid bilayer enables one to extract a broad range of information about interparticle and molecular interactions throughout the entire reaction period. Herein, we highlight important developments in this context to provide ideas on how molecular interactions can be interpreted by monitoring dynamic behaviors and optical signals of laterally mobile nanoparticles. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Application of double-hybrid density functionals to charge transfer in N-substituted pentacenequinones.

PubMed

Sancho-García, J C

2012-05-07

A set of N-heteroquinones, deriving from oligoacenes, have been recently proposed as n-type organic semiconductors with high electron mobilities in thin-film transistors. Generally speaking, this class of compounds self-assembles in neighboring π-stacks linked by weak hydrogen bonds. We aim at theoretically characterizing here the sequential charge transport (hopping) process expected to take place across these arrays of molecules. To do so, we need to accurately address the preferred packing of these materials simultaneously to single-molecule properties related to charge-transfer events, carefully employing dispersion-corrected density functional theory methods to accurately extract the key molecular parameters governing this phenomenon at the nanoscale. This study confirms the great deal of interest around these compounds, since controlled functionalization of model molecules (i.e., pentacene) allows to efficiently tune the corresponding charge mobilities, and the capacity of modern quantum-chemical methods to predict it after rationalizing the underlying structure-property relationships.

Novel PDE4 Inhibitors Derived from Chinese Medicine Forsythia

PubMed Central

Coon, Tiffany A.; McKelvey, Alison C.; Weathington, Nate M.; Birru, Rahel L.; Lear, Travis; Leikauf, George D.; Chen, Bill B.

2014-01-01

Cyclic adenosine monophosphate (cAMP) is a crucial intracellular second messenger molecule that converts extracellular molecules to intracellular signal transduction pathways generating cell- and stimulus-specific effects. Importantly, specific phosphodiesterase (PDE) subtypes control the amplitude and duration of cAMP-induced physiological processes and are therefore a prominent pharmacological target currently used in a variety of fields. Here we tested the extracts from traditional Chinese medicine, Forsythia suspense seeds, which have been used for more than 2000 years to relieve respiratory symptoms. Using structural-functional analysis we found its major lignin, Forsynthin, acted as an immunosuppressant by inhibiting PDE4 in inflammatory and immune cell. Moreover, several novel, selective small molecule derivatives of Forsythin were tested in vitro and in murine models of viral and bacterial pneumonia, sepsis and cytokine-driven systemic inflammation. Thus, pharmacological targeting of PDE4 may be a promising strategy for immune-related disorders characterized by amplified host inflammatory response. PMID:25549252

House dust mite induces expression of intercellular adhesion molecule-1 in EoL-1 human eosinophilic leukemic cells.

PubMed

Kwon, Byoung Chul; Sohn, Myung Hyun; Kim, Kyung Won; Kim, Eun Soo; Kim, Kyu-Earn; Shin, Myeong Heon

2007-10-01

The house dust mite (HDM) is considered to be the most common indoor allergen associated with bronchial asthma. In this study, we investigated whether crude extract of the HDM Dermatophagoides farinae could activate human eosinophilic leukemic cells (EoL-1) to induce upregulation of cell-surface adhesion molecules. When EoL-1 cells were incubated with D. farinae extract, expression of intercellular adhesion molecule-1 (ICAM-1) significantly increased on the cell surfaces compared to cells incubated with medium alone. In contrast, surface expression of CD11b and CD49d in EoL-1 cells was not affected by D. farinae extract. In addition, pretreatment of cells with NF-kappaB inhibitor (MG-132) or JNK inhibitor (SP600125) significantly inhibited ICAM-1 expression promoted by HDM extract. However, neither p38 MAP kinase inhibitor nor MEK inhibitor prevented HDM-induced ICAM-1 expression in EoL-1 cells. These results suggest that crude extract of D. farinae induces ICAM-1 expression in EoL-1 cells through signaling pathways involving both NF-kappaB and JNK.

House Dust Mite Induces Expression of Intercellular Adhesion Molecule-1 in EoL-1 Human Eosinophilic Leukemic Cells

PubMed Central

Kwon, Byoung Chul; Sohn, Myung Hyun; Kim, Kyung Won; Kim, Eun Soo; Kim, Kyu-Earn

2007-01-01

The house dust mite (HDM) is considered to be the most common indoor allergen associated with bronchial asthma. In this study, we investigated whether crude extract of the HDM Dermatophagoides farinae could activate human eosinophilic leukemic cells (EoL-1) to induce upregulation of cell-surface adhesion molecules. When EoL-1 cells were incubated with D. farinae extract, expression of intercellular adhesion molecule-1 (ICAM-1) significantly increased on the cell surfaces compared to cells incubated with medium alone. In contrast, surface expression of CD11b and CD49d in EoL-1 cells was not affected by D. farinae extract. In addition, pretreatment of cells with NF-κB inhibitor (MG-132) or JNK inhibitor (SP600125) significantly inhibited ICAM-1 expression promoted by HDM extract. However, neither p38 MAP kinase inhibitor nor MEK inhibitor prevented HDM-induced ICAM-1 expression in EoL-1 cells. These results suggest that crude extract of D. farinae induces ICAM-1 expression in EoL-1 cells through signaling pathways involving both NF-κB and JNK. PMID:17982228

Taraxacum officinale and Urtica dioica extracts inhibit dengue virus serotype 2 replication in vitro.

PubMed

Flores-Ocelotl, María R; Rosas-Murrieta, Nora H; Moreno, Diego A; Vallejo-Ruiz, Verónica; Reyes-Leyva, Julio; Domínguez, Fabiola; Santos-López, Gerardo

2018-03-16

Urtica dioica, Taraxacum officinale, Calea integrifolia and Caesalpinia pulcherrima are widely used all over the world for treatment of different illnesses. In Mexico, these plants are traditionally used to alleviate or counteract rheumatism and inflammatory muscle diseases. In the present study we evaluated the activity of aqueous and methanolic extracts of these four plants, on the replication of dengue virus serotype 2 (DENV2). Extraction process was carried out in a Soxtherm® system at 60, 85 and 120 °C; a chemical fractionation in silica gel chromatography was performed and compounds present in the active fractions were identified by HPLC-DAD-ESI/MSn. The cytotoxic concentration and the inhibitory effect of extracts or fractions on the DENV2 replication were analyzed in the BHK-21 cell line (plaque forming assay). The half maximal inhibitory concentration (IC 50 ) and the selectivity index (SI) were calculated for the extracts and fractions. The methanolic extracts at 60 °C of T. officinale and U. dioica showed the higher inhibitory effects on DENV2 replication. After the chemical fractionation, the higher activity fraction was found for U. dioica and T. officinale, presenting IC 50 values of 165.7 ± 3.85 and 126.1 ± 2.80 μg/ml, respectively; SI values were 5.59 and 6.01 for each fraction. The compounds present in T. officinale, were luteolin and caffeoylquinic acids derivatives and quercertin diclycosides. The compounds in the active fraction of U. dioica, were, chlorogenic acid, quercertin derivatives and flavonol glycosides (quercetin and kaempferol). Two fractions from U. dioica and T. officinale methanolic extracts with anti-dengue activity were found. The compounds present in both fractions were identified, several recognized molecules have demonstrated activity against other viral species. Subsequent biological analysis of the molecules, alone or in combination, contained in the extracts will be carried out to develop therapeutics against DENV2.

Preparation of translationally cold neutral molecules.

PubMed

Di Domenicantonio, Giulia; Bertsche, Benjamin; Osterwalder, Andreas

2011-01-01

Efforts at EPFL to obtain translationally cold neutral molecules are described. Active deceleration of polar molecules is performed by confining the molecules in moving three-dimensional electrostatic traps, and by appropriately choosing the velocity of those traps. Alternatively, cold molecules can be obtained by velocity filtering. Here, the velocity of the molecules is not changed, but instead the cold molecules are extracted from a thermal sample by using the competition between the electrostatic force and the centrifugal force inside a bent electrostatic guide for polar molecules.

Molecular dynamics: deciphering the data.

PubMed

Dauber-Osguthorpe, P; Maunder, C M; Osguthorpe, D J

1996-06-01

The dynamic behaviour of molecules is important in determining their activity. Molecular dynamics (MD) simulations give a detailed description of motion, from small fluctuations to conformational transitions, and can include solvent effects. However, extracting useful information about conformational motion from a trajectory is not trivial. We have used digital signal-processing techniques to characterise the motion in MD simulations, including: calculating the frequency distribution, applying filtering functions, and extraction of vectors defining the characteristic motion for each frequency in an MD simulation. We describe here some typical results obtained for peptides and proteins. The nature of the low-frequency modes of motion, as obtained from MD and normal mode (NM) analysis, of Ace-(Ala)31-Nma and of a proline mutant is discussed. Low-frequency modes extracted from the MD trajectories of Rop protein and phospholipase A2 reveal characteristic motions of secondary structure elements, as well as concerned motions that are of significance to the protein's biological activity. MD simulations are also used frequently as a tool for conformational searches and for investigating protein folding/unfolding. We have developed a novel method that uses time-domain filtering to channel energy into conformational motion and thus enhance conformational transitions. The selectively enhanced molecular dynamics method is tested on the small molecule hexane.

Molecular dynamics: Deciphering the data

NASA Astrophysics Data System (ADS)

Dauber-Osguthorpe, Pnina; Maunder, Colette M.; Osguthorpe, David J.

1996-06-01

The dynamic behaviour of molecules is important in determining their activity. Molecular dynamics (MD) simulations give a detailed description of motion, from small fluctuations to conformational transitions, and can include solvent effects. However, extracting useful information about conformational motion from a trajectory is not trivial. We have used digital signal-processing techniques to characterise the motion in MD simulations, including: calculating the frequency distribution, applying filtering functions, and extraction of vectors defining the characteristic motion for each frequency in an MD simulation. We describe here some typical results obtained for peptides and proteins. The nature of the low-frequency modes of motion, as obtained from MD and normal mode (NM) analysis, of Ace-(Ala)31-Nma and of a proline mutant is discussed. Low-frequency modes extracted from the MD trajectories of Rop protein and phospholipase A2 reveal characteristic motions of secondary structure elements, as well as concerted motions that are of significance to the protein's biological activity. MD simulations are also used frequently as a tool for conformational searches and for investigating protein folding/unfolding. We have developed a novel method that uses time-domain filtering to channel energy into conformational motion and thus enhance conformational transitions. The selectively enhanced molecular dynamics method is tested on the small molecule hexane.

Extraction of Organic Molecules from Terrestrial Material: Quantitative Yields from Heat and Water Extractions

NASA Technical Reports Server (NTRS)

Beegle, L. W.; Abbey, W. A.; Tsapin, A. T.; Dragoi, D.; Kanik, I.

2004-01-01

In the robotic search for life on Mars, different proposed missions will analyze the chemical and biological signatures of life using different platforms. The analysis of samples via analytical instrumentation on the surface of Mars has thus far only been attempted by the two Viking missions. Robotic arms scooped relogith material into a pyrolysis oven attached to a GC/MS. No trace of organic material was found on any of the two different samples at either of the two different landing sites. This null result puts an upper limit on the amount of organics that might be present in Martian soil/rocks, although the level of detection for each individual molecular species is still debated. Determining the absolute limit of detection for each analytical instrument is essential so that null results can be understood. This includes investigating the trade off of using pyrolysis versus liquid solvent extraction to release organic materials (in terms of extraction efficiencies and the complexity of the sample extraction process.) Extraction of organics from field samples can be accomplished by a variety of methods such utilizing various solvents including HCl, pure water, supercritical fluid and Soxhelt extraction. Utilizing 6N HCl is one of the most commonly used method and frequently utilized for extraction of organics from meteorites but it is probably infeasible for robotic exploration due to difficulty of storage and transport. Extraction utilizing H2O is promising, but it could be less efficient than 6N HCl. Both supercritical fluid and Soxhelt extraction methods require bulky hardware and require complex steps, inappropriate for inclusion on rover spacecraft. This investigation reports the efficiencies of pyrolysis and solvent extraction methods for amino acids for different terrestrial samples. The samples studied here, initially created in aqueous environments, are sedimentary in nature. These particular samples were chosen because they possibly represent one of the best terrestrial analogs of Mars and they represent one of the absolute best case scenarios for finding organic molecules on the Martian surface.

Magnetic amphiphilic hybrid carbon nanotubes containing N-doped and undoped sections: powerful tensioactive nanostructures

NASA Astrophysics Data System (ADS)

Purceno, Aluir D.; Machado, Bruno F.; Teixeira, Ana Paula C.; Medeiros, Tayline V.; Benyounes, Anas; Beausoleil, Julien; Menezes, Helvecio C.; Cardeal, Zenilda L.; Lago, Rochel M.; Serp, Philippe

2014-11-01

In this work, unique amphiphilic magnetic hybrid carbon nanotubes (CNTs) are synthesized and used as tensioactive nanostructures in different applications. These CNTs interact very well with aqueous media due to the hydrophilic N-doped section, whereas the undoped hydrophobic one has strong affinity for organic molecules. The amphiphilic character combined with the magnetic properties of these CNTs opens the door to completely new and exciting applications in adsorption science and catalysis. These amphiphilic N-doped CNTs can also be used as powerful tensioactive emulsification structures. They can emulsify water/organic mixtures and by a simple magnetic separation the emulsion can be easily broken. We demonstrate the application of these CNTs in the efficient adsorption of various molecules, in addition to promoting biphasic processes in three different reactions, i.e. transesterification of soybean oil, quinoline extractive oxidation with H2O2 and a metal-catalyzed aqueous oxidation of heptanol with molecular oxygen.In this work, unique amphiphilic magnetic hybrid carbon nanotubes (CNTs) are synthesized and used as tensioactive nanostructures in different applications. These CNTs interact very well with aqueous media due to the hydrophilic N-doped section, whereas the undoped hydrophobic one has strong affinity for organic molecules. The amphiphilic character combined with the magnetic properties of these CNTs opens the door to completely new and exciting applications in adsorption science and catalysis. These amphiphilic N-doped CNTs can also be used as powerful tensioactive emulsification structures. They can emulsify water/organic mixtures and by a simple magnetic separation the emulsion can be easily broken. We demonstrate the application of these CNTs in the efficient adsorption of various molecules, in addition to promoting biphasic processes in three different reactions, i.e. transesterification of soybean oil, quinoline extractive oxidation with H2O2 and a metal-catalyzed aqueous oxidation of heptanol with molecular oxygen. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr04005h

Chloride channel inhibition by a red wine extract and a synthetic small molecule prevents rotaviral secretory diarrhoea in neonatal mice

PubMed Central

Ko, Eun-A; Jin, Byung-Ju; Namkung, Wan; Ma, Tonghui; Thiagarajah, Jay R.; Verkman, A. S.

2014-01-01

Background Rotavirus is the most common cause of severe secretory diarrhoea in infants and young children globally. The rotaviral enterotoxin, NSP4, has been proposed to stimulate calcium-activated chloride channels (CaCC) on the apical plasma membrane of intestinal epithelial cells. We previously identified red wine and small molecule CaCC inhibitors. Objective To investigate the efficacy of a red wine extract and a synthetic small molecule, CaCCinh-A01, in inhibiting intestinal CaCCs and rotaviral diarrhoea. Design Inhibition of CaCC-dependent current was measured in T84 cells and mouse ileum. The effectiveness of an orally administered wine extract and CaCCinh-A01 in inhibiting diarrhoea in vivo was determined in a neonatal mouse model of rotaviral infection. Results Screening of ~150 red wines revealed a Cabernet Sauvignon that inhibited CaCC current in T84 cells with IC50 at a ~1:200 dilution, and higher concentrations producing 100% inhibition. A >1 kdalton wine extract prepared by dialysis, which retained full inhibition activity, blocked CaCC current in T84 cells and mouse intestine. In rotavirus-inoculated mice, oral administration of the wine extract prevented diarrhoea by inhibition of intestinal fluid secretion without affecting rotaviral infection. The wine extract did not inhibit the cystic fibrosis chloride channel (CFTR) in cell cultures, nor did it prevent watery stools in neonatal mice administered cholera toxin, which activates CFTR-dependent fluid secretion. CaCCinh-A01 also inhibited rotaviral diarrhoea. Conclusions Our results support a pathogenic role for enterocyte CaCCs in rotaviral diarrhoea and demonstrate the antidiarrhoeal action of CaCC inhibition by an alcohol-free, red wine extract and by a synthetic small molecule. PMID:24052273

Organic extract of diesel exhaust particles stimulates expression of Ia and costimulatory molecules associated with antigen presentation in rat peripheral blood monocytes but not in alveolar macrophages

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

Koike, Eiko; Kobayashi, Takahiro

2005-12-15

We hypothesized that diesel exhaust particles (DEP) induce the activation of antigen-presenting cells (APC) in lung. The present study was designed to clarify the following about DEP: (1) whether it affects the expression of Ia and B7 molecules in alveolar macrophages (AM) as a mature cell or in peripheral blood monocytes (PBM) as an immature cell (2) if it affects the antigen-presenting (AP) activity of PBM (3) what component of DEP is responsible for the effects, and (4) whether the effect of DEP is related to oxidative stress. DEP was extracted with methylene chloride. Cells were exposed to whole DEP,more » organic extract, or residual particles for 24 h. Cell-surface molecules were measured by flow cytometry. AP activity was assessed by antigen-specific T cell proliferation. Whole DEP or organic extract significantly increased the expression of Ia and B7 molecules on PBM but not on AM. No significant effect of residual particles was observed. A low concentration of organic extract also increased the AP activity of PBM. When the induction of an antioxidative enzyme was assessed, heme oxygenase-1 protein was found to be significantly increased by exposure to whole DEP, and the organic extract was more effective than the residual particles. Furthermore, the organic extract-induced expression of Ia antigen on PBM was reduced by the addition of an antioxidative agent. These results suggest that DEP may act on immature APC and enhance their AP activity and that the action contributing to oxidative stress may be mediated by organic compounds of DEP.« less

Extraction of cellulose microcrystalline from galam wood for biopolymer

NASA Astrophysics Data System (ADS)

Ismail, Ika; Sa'adiyah, Devy; Rahajeng, Putri; Suprayitno, Abdi; Andiana, Rocky

2018-04-01

Consumption of plastic raw materials tends to increase, but until now the meet of the consumption of plastic raw are still low, even some are still imported. Nowadays, Indonesia's plastic needs are supported by petrochemicals where raw materials are still dependent abroad and petropolymer raw materials are derived from petroleum which will soon be depleted due to rising petroleum needs. Therefore, various studies have been conducted to develop natural fiber-based polymers that are biodegradable and abundant in nature. It is because the natural polymer production process is very efficient and very environmentally friendly. There have been many studies of biopolymers especially natural fiber-based polymers from plants, due to plants containing cellulose, hemicellulose and lignin. However, cellulose is the only one who has crystalline structures. Cellulose has a high crystality compared to amorphous lignin and hemicellulose. In this study, extracted cellulose as biopolymer and amplifier on composite. The cellulose is extracted from galam wood from East Kalimantan. Cellulose extraction will be obtained in nano / micro form through chemical and mechanical treatment processes. The chemical treatment of cellulose extraction is alkalinization process using NaOH solution, bleaching using NaClO2 and acid hydrolysis using sulfuric acid. After chemical treatment, ultrasonic mechanical treatment is made to make cellulose fibers into micro or nano size. Besides, cellulose results will be characterized. Characterization was performed to analyze molecules of cellulose compounds extracted from plants using Fourier Transformation Infra Red (FTIR) testing. XRD testing to analyze cellulose crystallinity. Scanning Electron Microscope (SEM) test to analyze morphology and fiber size.

Trivalent Ions under Charged Langmuir Monolayers: Nanoscale Mechanisms for Charge Inversion and Liquid-Liquid Extraction

NASA Astrophysics Data System (ADS)

Miller, Mitchell

Ions dissolved in solution are known to interact in remarkable ways with charged Langmuir monolayers. The organic monolayer can be used as a molecular template for ordered nucleation of inorganic crystals (biomineralization) and functional nanoparticles. However, the clear majority of experiments demonstrating these behaviors have been performed with divalent ions. Trivalent ions are present in several important processes that are unique from previously studied divalent systems. We will demonstrate that trivalent ions under floating monolayers can model two important systems: charge inversion and liquid-liquid solvent extraction. Using in situ synchrotron x-ray scattering and emission methods, we can make direct, nanoscale observations of the interactions between ion and monolayer. Charge inversion is a fascinating phenomenon in which small ions of an opposite charge to some large object (colloidal particle, DNA molecule, etc.) will attach to and reverse the object's charge, rather than simply neutralizing it. There are many experimental systems demonstrating this behavior and an enormous body of theoretical work to explain it. Two classes of explanation exist for how charge inversion may occur, "chemical" and "physical" mechanism. Using grazing incidence diffraction (GID), we have found that ions can form an ordered lattice which is incommensurate to a floating, charged monolayer. Because the ions are incommensurate, they cannot be specifically attached to molecules in the monolayer and must be, therefore, held in place by "physical" means. Solvent extraction can be an extremely complex procedure, so our approach to studying it is to simplify the system into a basic model. Ordinarily, two immiscible liquids--an aqueous phase containing some desired species and other impurities and an organic phase, which sometimes contains extractant molecules that improve efficiency--are mixed together and allowed to separate again. While the liquids are being mixed together, the target species from the aqueous phase is pulled across the interface into the organic phase. The mechanism by which the transfer occurs is very poorly understood and very difficult to study directly since it is a very dynamic process and obscured by the bulk of the liquids. Here we propose that the air-water interface is a model of the liquid-liquid interface; in our model, the hydrophobic "organic" phase is the air above the water. This lets us make direct observations of the interactions between ions dissolved in the aqueous phase and the extractant molecules in the organic phase with x-rays, something which would be impossible in an ordinary solvent extraction experiment. We observed a sharp transition in ordering as the atomic weight of the ion dissolved in solution is increased. One would expect a continuous variation, since the size of the ions varies continuously. Second, using x-ray fluorescence, we find that heavier lanthanides are much more strongly attracted to the monolayer than light ones. The unexpected nature of our results emphasizes the need for bottom-up approaches to understanding these systems rather than the top-down method used for the last century. In addition, our results demonstrate that it is, indeed, possible to overcome the experimental difficulties and make the types of measurements necessary for this approach.

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

Ma, Jian; Casey, Cameron P.; Zheng, Xueyun

Motivation: Drift tube ion mobility spectrometry (DTIMS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS coupled with mass spectrometry and compute their associated collisional cross sections (CCS) we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of information necessary to create a reference library containing accu-rate masses, DTIMS arrival times and CCSs for use in high throughput omics analyses. Results: We demonstrate the utility of this approach bymore » automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were identical to those calculated by hand and within error of those calcu-lated using commercially available instrument vendor software.« less

Expedient preparative isolation and tandem mass spectrometric characterization of C-seco triterpenoids from Neem oil.

PubMed

Haldar, Saikat; Mulani, Fayaj A; Aarthy, Thiagarayaselvam; Dandekar, Devdutta S; Thulasiram, Hirekodathakallu V

2014-10-31

C-seco triterpenoids are widely bioactive class of natural products with high structural complexity and diversity. The preparative isolation of these molecules with high purity is greatly desirable, although restricted due to the complexity of natural extracts. In this article we have demonstrated a Medium Pressure Liquid Chromatography (MPLC) based protocol for the isolation of eight major C-seco triterpenoids of salannin skeleton from Neem (Azadirachta indica) oil. Successive application of normal phase pre-packed silica-gel columns for the fractionation followed by reverse phase in automated MPLC system expedited the process and furnished highly pure metabolites. Furthermore, eight isolated triterpenoids along with five semi-synthesized derivatives were characterized using ultra performance liquid chromatography-electrospray ionization-quadrupole/orbitrap-MS/MS spectrometry as a rapid and sensitive identification technique. The structure-fragment relationships were established on the basis of plausible mechanistic pathway for the generation of daughter ions. The MS/MS spectral information of the triterpenoids was further utilized for the identification of studied molecules in the complex extract of stem and bark tissues from Neem. Copyright © 2014 Elsevier B.V. All rights reserved.

The influence of natural deep eutectic solvents on bioactive natural products: studying interactions between a hydrogel model and Schisandra chinensis metabolites.

PubMed

Liu, Yang; Zhang, Yu; Chen, Shao-Nong; Friesen, J Brent; Nikolić, Dejan; Choules, Mary P; McAlpine, James B; Lankin, David C; Gemeinhart, Richard A; Pauli, Guido F

2018-06-01

Natural Deep Eutectic Solvent (NADES) species can exhibit unexpected solubilizing power for lipophilic molecules despite their simple composition: hydrophilic organic molecules and water. In the present study, the unique properties of NADES species were applied in combination with a model polymer system: a hydrophilic chitosan/alginate hydrogel. Briefly, NADES species (e.g., mannose-dimethylurea-water, 2:5:5, mole/mole) formed matrices to 1) dissolve lipophilic molecules (e.g., curcumin), 2) load lipophilic molecule(s) into the hydrogel, and 3) spontaneously vacate from the system. NADES species ubiquitously occur in natural sources, and a crude extract is a mixture of the NADES species and bioactive metabolites. Based on these ideas, we hypothesized that the crude extract may also allow the loading of natural bioactive molecules from a natural NADES species into (bio)hydrogel systems. To evaluate this hypothesis in vitro, Schisandra chinensis fruit extract was chosen as a representative mixture of lipophilic botanical molecules and hydrophilic NADES species. The results showed that the NADES matrix of S. chinensis was capable of loading at least three bioactive lignans (i.e., gomisin A, gomisin J, and angeloylgomisin H) into the polymer system. The lipophilic metabolites can subsequently be released from the hydrogel. The outcomes suggest that a unique drug delivery mechanism may exist in nature, thereby potentially improving the bioavailability of lipophilic metabolites through physicochemical interactions with the NADES. Copyright © 2018 Elsevier B.V. All rights reserved.

Insecticidal effect of plant extracts on Phlebotomus argentipes (Diptera: Psychodidae) in Bihar, India.

PubMed

Dinesh, Diwakar Singh; Kumari, Seema; Pandit, Vibhishan; Kumar, Jainendra; Kumari, Nisha; Kumar, Prahlad; Hassan, Faizan; Kumar, Vijay; Das, Pradeep

2015-12-01

Phlebotomus argentipes (Diptera: Psychodidae), the established vector for kala-azar is presently being controlled by indoor residual spray of DDT in kala-azar endemic areas in India. Search for non-hazardous and non-toxic biodegradable active molecules from botanicals may provide cost-effective and eco-friendly alternatives to synthetic insecticides. The present study was aimed at evaluating various plant extracts from endemic and non-endemic areas of Bihar for their insecticidal activity against sandfly to identify the most effective plant extract. Bio-assay test was conducted with larvae and adult of P. argentipes with different plant extracts collected in distilled water, hexane, ethyl acetate, acetone and methanol. Thin layer chromatography (TLC), column chromatography and high performance liquid chromatography (HPLC) were conducted for detection of active molecules. Adults and larvae of sandflies exposed to the aqueous extract of Nicotiana tabacum resulted in 100 per cent mortality. The hexane extract of Clerodendrum infortunatum was found to kill 77 per cent adults but was ineffective against larvae. Bio-assay test of the ninth fraction (hexane extract-methanol phase) separated by column chromatography was found to be 63 per cent effective. The purple spot on the TLC of this fraction indicated the presence of a diterpenoid. HPLC of this fraction detected nine compounds with two peaks covering 20.44 and 56.52 per cent areas with retention time of 2.439 and 5.182 min, respectively supporting the TLC results. The column separated 9 [th] fraction of C. infortunatum extract was found to be effective in killing 63 per cent of adult P. argentipes. Compounds of this fraction need to be evaluated further for identification and characterization of the active molecule by conducting individual bio-assay tests followed by further fractionation and HPLC. Once the structure of the active molecule is identified and validated, it may be synthesized and formulated as a product.

Insecticidal effect of plant extracts on Phlebotomus argentipes (Diptera: Psychodidae) in Bihar, India

PubMed Central

Dinesh, Diwakar Singh; Kumari, Seema; Pandit, Vibhishan; Kumar, Jainendra; Kumari, Nisha; Kumar, Prahlad; Hassan, Faizan; Kumar, Vijay; Das, Pradeep

2015-01-01

Background & objectives: Phlebotomus argentipes (Diptera: Psychodidae), the established vector for kala-azar is presently being controlled by indoor residual spray of DDT in kala-azar endemic areas in India. Search for non-hazardous and non-toxic biodegradable active molecules from botanicals may provide cost-effective and eco-friendly alternatives to synthetic insecticides. The present study was aimed at evaluating various plant extracts from endemic and non-endemic areas of Bihar for their insecticidal activity against sandfly to identify the most effective plant extract. Methods: Bio-assay test was conducted with larvae and adult of P. argentipes with different plant extracts collected in distilled water, hexane, ethyl acetate, acetone and methanol. Thin layer chromatography (TLC), column chromatography and high performance liquid chromatography (HPLC) were conducted for detection of active molecules. Results: Adults and larvae of sandflies exposed to the aqueous extract of Nicotiana tabacum resulted in 100 per cent mortality. The hexane extract of Clerodendrum infortunatum was found to kill 77 per cent adults but was ineffective against larvae. Bio-assay test of the ninth fraction (hexane extract-methanol phase) separated by column chromatography was found to be 63 per cent effective. The purple spot on the TLC of this fraction indicated the presence of a diterpenoid. HPLC of this fraction detected nine compounds with two peaks covering 20.44 and 56.52 per cent areas with retention time of 2.439 and 5.182 min, respectively supporting the TLC results. Interpretation & conclusions: The column separated 9th fraction of C. infortunatum extract was found to be effective in killing 63 per cent of adult P. argentipes. Compounds of this fraction need to be evaluated further for identification and characterization of the active molecule by conducting individual bio-assay tests followed by further fractionation and HPLC. Once the structure of the active molecule is identified and validated, it may be synthesized and formulated as a product. PMID:26905249

Advanced solvent based methods for molecular characterization of soil organic matter by high-resolution mass spectrometry.

PubMed

Tfaily, Malak M; Chu, Rosalie K; Tolić, Nikola; Roscioli, Kristyn M; Anderton, Christopher R; Paša-Tolić, Ljiljana; Robinson, Errol W; Hess, Nancy J

2015-01-01

Soil organic matter (SOM), a complex, heterogeneous mixture of above and belowground plant litter and animal and microbial residues at various degrees of decomposition, is a key reservoir for carbon (C) and nutrient biogeochemical cycling in soil based ecosystems. A limited understanding of the molecular composition of SOM limits the ability to routinely decipher chemical processes within soil and accurately predict how terrestrial carbon fluxes will respond to changing climatic conditions and land use. To elucidate the molecular-level structure of SOM, we selectively extracted a broad range of intact SOM compounds by a combination of different organic solvents from soils with a wide range of C content. Our use of electrospray ionization (ESI) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and a suite of solvents with varying polarity significantly expands the inventory of the types of organic molecules present in soils. Specifically, we found that hexane is selective for lipid-like compounds with very low O/C ratios (<0.1); water (H2O) was selective for carbohydrates with high O/C ratios; acetonitrile (ACN) preferentially extracts lignin, condensed structures, and tannin polyphenolic compounds with O/C > 0.5; methanol (MeOH) has higher selectivity toward compounds characterized with low O/C < 0.5; and hexane, MeOH, ACN, and H2O solvents increase the number and types of organic molecules extracted from soil for a broader range of chemically diverse soil types. Our study of SOM molecules by ESI FTICR MS revealed new insight into the molecular-level complexity of organics contained in soils. We present the first comparative study of the molecular composition of SOM from different ecosystems using ultra high-resolution mass spectrometry.

Multiscale Modeling of Diffusion in a Crowded Environment.

PubMed

Meinecke, Lina

2017-11-01

We present a multiscale approach to model diffusion in a crowded environment and its effect on the reaction rates. Diffusion in biological systems is often modeled by a discrete space jump process in order to capture the inherent noise of biological systems, which becomes important in the low copy number regime. To model diffusion in the crowded cell environment efficiently, we compute the jump rates in this mesoscopic model from local first exit times, which account for the microscopic positions of the crowding molecules, while the diffusing molecules jump on a coarser Cartesian grid. We then extract a macroscopic description from the resulting jump rates, where the excluded volume effect is modeled by a diffusion equation with space-dependent diffusion coefficient. The crowding molecules can be of arbitrary shape and size, and numerical experiments demonstrate that those factors together with the size of the diffusing molecule play a crucial role on the magnitude of the decrease in diffusive motion. When correcting the reaction rates for the altered diffusion we can show that molecular crowding either enhances or inhibits chemical reactions depending on local fluctuations of the obstacle density.

Rediscovering natural products as a source of new drugs.

PubMed

Koehn, Frank E; Carter, Guy T

2005-04-01

Extract: Since the very beginnings of human medicine, physicians have relied on chemical compounds produced by animals, plants and microorganisms, so-called natural products, to treat diseases. Natural products are directly or indirectly responsible for roughly one-half of all drugs currently in use. Of the 877 small-molecule new drug molecules introduced between 1981 and 2002, 49% were natural products or natural product analogs. Despite the great success of the 70s and 80s, the pharmaceutical industry de-emphasized natural products research during the following decade. In this article, we examine the underlying reasons for the decline, and assess future prospects for natural products research in drug discovery. In the 1990s, major pharmaceutical companies moved to a lead-finding strategy based on High Throughput Screening (HTS) of very large collections (libraries) of synthetic compounds. The move arose from the belief that techniques such as combinatorial chemistry could produce larger, more cost-effective libraries with improved hit rates and quality. Additionally, advances in molecular biology, cellular biology and genomics dramatically increased the number of molecular targets, prompting shorter drug discovery timelines. In today's drug discovery environment, rapid screening and identification of potential drug molecules is essential for success. This puts traditional natural products-based programs, with their reliance on the lengthy processes of the screening of extracts library, bioassay-guided isolation of the active components, structure elucidation and subsequent production scale-up, at a competitive disadvantage.

3beta-taraxerol of Mangifera indica, a PI3K dependent dual activator of glucose transport and glycogen synthesis in 3T3-L1 adipocytes.

PubMed

Sangeetha, Kadapakkam Nandabalan; Sujatha, Sundaresan; Muthusamy, Velusamy Shanmuganathan; Anand, Singaravel; Nithya, Nirmal; Velmurugan, Devadasan; Balakrishnan, Arun; Lakshmi, Baddireddi Subhadra

2010-03-01

The present study focuses on identifying and developing an anti-diabetic molecule from plant sources that would effectively combat insulin resistance through proper channeling of glucose metabolism involving glucose transport and storage. Insulin-stimulated glucose uptake formed the basis for isolation of a bioactive molecule through column chromatography followed by its characterization using NMR and mass spectroscopic analysis. Mechanism of glucose transport and storage was evaluated based on the expression profiling of signaling molecules involved in the process. The study reports (i) the isolation of a bioactive compound 3beta-taraxerol from the ethyl acetate extract (EAE) of the leaves of Mangifera indica (ii) the bioactive compound exhibited insulin-stimulated glucose uptake through translocation and activation of the glucose transporter (GLUT4) in an IRTK and PI3K dependent fashion. (iii) the fate of glucose following insulin-stimulated glucose uptake was ascertained through glycogen synthesis assay that involved the activation of PKB and suppression of GSK3beta. This study demonstrates the dual activity of 3beta-taraxerol and the ethyl acetate extract of Mangifera indica as a glucose transport activator and stimulator of glycogen synthesis. 3beta-taraxerol can be validated as a potent candidate for managing the hyperglycemic state. Copyright (c) 2009 Elsevier B.V. All rights reserved.

Recovery of bioactive molecules from chestnut (Castanea sativa Mill.) by-products through extraction by different solvents.

PubMed

Vella, Filomena Monica; Laratta, Bruna; La Cara, Francesco; Morana, Alessandra

2018-05-01

The underutilised forest and industrial biomass of Castanea sativa (Mill.) is generally discarded during post-harvest and food processing, with high impact on environmental quality. The searching on alternative sources of natural antioxidants from low-cost supplies, by methods involving environment-friendly techniques, has become a major goal of numerous researches in recent times. The aim of the present study was the set-up of a biomolecules extraction procedure from chestnut leaves, burs and shells and the assessing of their potential antioxidant activity. Boiling water was the best extraction solvent referring to polyphenols from chestnut shells and burs, whereas the most efficient for leaves resulted 60% ethanol at room temperature. Greatest polyphenol contents were 90.35, 60.01 and 17.68 mg gallic acid equivalents g -1 in leaves, burs and shells, respectively. Moreover, flavonoids, tannins and antioxidant activity were assessed on the best extract obtained from each chestnut by-product.

In situ analysis of dynamic laminar flow extraction using surface-enhanced Raman spectroscopy

NASA Astrophysics Data System (ADS)

Wang, Fei; Wang, Hua-Lin; Qiu, Yang; Chang, Yu-Long; Long, Yi-Tao

2015-12-01

In this study, we performed micro-scale dynamic laminar flow extraction and site-specific in situ chloride concentration measurements. Surface-enhanced Raman spectroscopy was utilized to investigate the diffusion process of chloride ions from an oil phase to a water phase under laminar flow. In contrast to common logic, we used SERS intensity gradients of Rhodamine 6G to quantitatively calculate the concentration of chloride ions at specific positions on a microfluidic chip. By varying the fluid flow rates, we achieved different extraction times and therefore different chloride concentrations at specific positions along the microchannel. SERS spectra from the water phase were recorded at these different positions, and the spatial distribution of the SERS signals was used to map the degree of nanoparticle aggregation. The concentration of chloride ions in the channel could therefore be obtained. We conclude that this method can be used to explore the extraction behaviour and efficiency of some ions or molecules that enhance the SERS intensity in water or oil by inducing nanoparticle aggregation.

Bioherbicidal activity of a germacranolide sesquiterpene dilactone from Ambrosia artemisiifolia L.

PubMed

Molinaro, Francesco; Monterumici, Chiara Mozzetti; Ferrero, Aldo; Tabasso, Silvia; Negre, Michèle

2016-12-01

Ambrosia artemisiifolia L. (common ragweed) is an invasive plant whose allelopathic properties have been suggested by its field behaviour and demonstrated through phytotoxicity bioassays. However, the nature of the molecules responsible for the allelopathic activity of common ragweed has not been explored. The main objective of this study was to identify the phytotoxic molecules produced by A. artemisiifolia. A preliminary investigation has indicated that a methanol extract of A. artemisiifolia completely inhibited the germination of cress and radish. Semi-preparative fractionation of the methanol extract allowed separating of phytotoxic fraction which contained a single compound. The structure of this compound was elucidated by liquid chromatography-mass spectrometry (LC-MS)/MS, high-resolution mass spectral, nuclear magnetic resonance, and Fourier transform infrared spectra as sesquiterpene lactone isabelin (C 15 H 16 O 4 ). The effect of pure isabelin was tested on four different weed species, confirming the inhibitory activity of molecule. The results indicate directions for the future studies about herbicidal specific activity of isabelin, as pure molecule or in the crude extract, as a potential candidate for biological weed control.

MARS: bringing the automation of small-molecule bioanalytical sample preparations to a new frontier.

PubMed

Li, Ming; Chou, Judy; Jing, Jing; Xu, Hui; Costa, Aldo; Caputo, Robin; Mikkilineni, Rajesh; Flannelly-King, Shane; Rohde, Ellen; Gan, Lawrence; Klunk, Lewis; Yang, Liyu

2012-06-01

In recent years, there has been a growing interest in automating small-molecule bioanalytical sample preparations specifically using the Hamilton MicroLab(®) STAR liquid-handling platform. In the most extensive work reported thus far, multiple small-molecule sample preparation assay types (protein precipitation extraction, SPE and liquid-liquid extraction) have been integrated into a suite that is composed of graphical user interfaces and Hamilton scripts. Using that suite, bioanalytical scientists have been able to automate various sample preparation methods to a great extent. However, there are still areas that could benefit from further automation, specifically, the full integration of analytical standard and QC sample preparation with study sample extraction in one continuous run, real-time 2D barcode scanning on the Hamilton deck and direct Laboratory Information Management System database connectivity. We developed a new small-molecule sample-preparation automation system that improves in all of the aforementioned areas. The improved system presented herein further streamlines the bioanalytical workflow, simplifies batch run design, reduces analyst intervention and eliminates sample-handling error.

Application of a multivariate normal distribution methodology to the dissociation of doubly ionized molecules: The DMDS (CH3 -SS-CH3 ) case.

PubMed

Varas, Lautaro R; Pontes, F C; Santos, A C F; Coutinho, L H; de Souza, G G B

2015-09-15

The ion-ion-coincidence mass spectroscopy technique brings useful information about the fragmentation dynamics of doubly and multiply charged ionic species. We advocate the use of a matrix-parameter methodology in order to represent and interpret the entire ion-ion spectra associated with the ionic dissociation of doubly charged molecules. This method makes it possible, among other things, to infer fragmentation processes and to extract information about overlapped ion-ion coincidences. This important piece of information is difficult to obtain from other previously described methodologies. A Wiley-McLaren time-of-flight mass spectrometer was used to discriminate the positively charged fragment ions resulting from the sample ionization by a pulsed 800 eV electron beam. We exemplify the application of this methodology by analyzing the fragmentation and ionic dissociation of the dimethyl disulfide (DMDS) molecule as induced by fast electrons. The doubly charged dissociation was analyzed using the Multivariate Normal Distribution. The ion-ion spectrum of the DMDS molecule was obtained at an incident electron energy of 800 eV and was matrix represented using the Multivariate Distribution theory. The proposed methodology allows us to distinguish information among [CH n SH n ] + /[CH 3 ] + (n = 1-3) fragment ions in the ion-ion coincidence spectra using ion-ion coincidence data. Using the momenta balance methodology for the inferred parameters, a secondary decay mechanism is proposed for the [CHS] + ion formation. As an additional check on the methodology, previously published data on the SiF 4 molecule was re-analyzed with the present methodology and the results were shown to be statistically equivalent. The use of a Multivariate Normal Distribution allows for the representation of the whole ion-ion mass spectrum of doubly or multiply ionized molecules as a combination of parameters and the extraction of information among overlapped data. We have successfully applied this methodology to the analysis of the fragmentation of the DMDS molecule. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Simultaneous separation and purification of (-)-epigallocatechin gallate and caffeine from tea extract by size exclusion effect on modified porous adsorption material.

PubMed

Zhang, Xiaofeng; Xu, Yi; Zhang, Qing; Cao, Kun; Mu, Xiuni

2016-09-15

A dual-task method for the simultaneous separation and purification of (-)-epigallocatechin gallate (EGCG) and caffeine (CAF) from crude extract of green tea was established by size exclusion effect onto hydroquinone modified porous adsorbents. The results showed that hydroquinone modified porous adsorbents P4 provided the best separation power due to it has more porous structure and phenolic hydroxyl group. The adsorption-desorption behaviors of EGCG and CAF onto P4 adsorbents were investigated. Adsorption kinetics of EGCG and CAF results showed that the adsorption followed the pseudo-second-order kinetic model. The results also indicated that the equilibrium adsorption data best fit the Langmuir model. Meanwhile, EGCG and CAF were separated successfully onto P4 adsorbents packed columns in a gradient eluent process, and P4 adsorbents exhibited the size exclusion effect for small molecules CAF. Based on the phenolic hydroxyl group and size exclusion effect of P4 adsorbents, the high purity EGCG and CAF were obtained with 40% (v/v) ethanol eluent successively. The process fulfilled the task of simultaneous separation and purification of EGCG and CAF, and proved to be a promising basis for preparations of difficult to obtain active components that have similar polarity and different sizes of molecules and derived from the same natural products. Copyright © 2016 Elsevier B.V. All rights reserved.

Microwave-assisted extraction of herbacetin diglucoside from flax (Linum usitatissimum L.) seed cakes and its quantification using an RP-HPLC-UV system.

PubMed

Fliniaux, Ophélie; Corbin, Cyrielle; Ramsay, Aina; Renouard, Sullivan; Beejmohun, Vickram; Doussot, Joël; Falguières, Annie; Ferroud, Clotilde; Lamblin, Frédéric; Lainé, Eric; Roscher, Albrecht; Grand, Eric; Mesnard, François; Hano, Christophe

2014-03-10

Flax (Linum usitatissimum L.) seeds are widely used for oil extraction and the cold-pressed flaxseed (or linseed) cakes obtained during this process constitute a valuable by-product. The flavonol herbacetin diglucoside (HDG) has been previously reported as a constituent of the flaxseed lignan macromolecule linked through ester bonds to the linker molecule hydroxymethylglutaric acid. In this context, the development and validation of a new approach using microwave-assisted extraction (MAE) of HDG from flaxseed cakes followed by quantification with a reverse-phase HPLC system with UV detection was purposed. The experimental parameters affecting the HDG extraction yield, such as microwave power, extraction time and sodium hydroxide concentration, from the lignan macromolecule were optimized. A maximum HDG concentration of 5.76 mg/g DW in flaxseed cakes was measured following an irradiation time of 6 min, for a microwave power of 150 W using a direct extraction in 0.1 M NaOH in 70% (v/v) aqueous methanol. The optimized method was proven to be rapid and reliable in terms of precision, repeatability, stability and accuracy for the extraction of HDG. Comparison with a conventional extraction method demonstrated that MAE is more effective and less time-consuming.

Mining marine shellfish wastes for bioactive molecules: chitin and chitosan--Part A: extraction methods.

PubMed

Hayes, Maria; Carney, Brian; Slater, John; Brück, Wolfram

2008-07-01

Legal restrictions, high costs and environmental problems regarding the disposal of marine processing wastes have led to amplified interest in biotechnology research concerning the identification and extraction of additional high grade, low-volume by-products produced from shellfish waste treatments. Shellfish waste consisting of crustacean exoskeletons is currently the main source of biomass for chitin production. Chitin is a polysaccharide composed of N-acetyl-D-glucosamine units and the multidimensional utilization of chitin derivatives including chitosan, a deacetylated derivative of chitin, is due to a number of characteristics including: their polyelectrolyte and cationic nature, the presence of reactive groups, high adsorption capacities, bacteriostatic and fungistatic influences, making them very versatile biomolecules. Part A of this review aims to consolidate useful information concerning the methods used to extract and characterize chitin, chitosan and glucosamine obtained through industrial, microbial and enzymatic hydrolysis of shellfish waste.

Comparison of Timothy grass pollen extract- and single major allergen-induced gene expression and mediator release in airway epithelial cells: a meta-analysis.

PubMed

Röschmann, K I L; van Kuijen, A-M; Luiten, S; Jonker, M J; Breit, T M; Fokkens, W J; Petersen, A; van Drunen, C M

2012-10-01

Seasonal allergic rhinitis (AR) is a global health problem and its prevalence has increased considerably in the last decades. As the allergic response with its clinical manifestations is triggered by only a few proteins within natural extracts, there is an increasing tendency for single-component-resolved diagnosis and immunotherapy. As natural exposure is not to single proteins, but to complex mixtures of molecules, we were interested in comparing the activation of respiratory epithelial cells induced by the purified major allergen Phl p 1 with the induction caused by a complete extract of Timothy grass pollen (GPE). NCI-H292 cells were exposed to GPE or Ph1 p 1 for 24 h, isolated RNA and cell culture supernatants were used for microarray analysis, multiplex enzyme-linked immunosorbant assay (ELISA) and subsequent analysis. We found 262 genes that showed a GPE-induced change of at least 3-fold, whereas Ph1 p 1-stimulation resulted in 71 genes with a fold induction of more than 3-fold. Besides genes that were regulated by both stimuli, we also detected genes displaying an opposite response after stimulation, suggesting that GPE might be more than purified major allergens with regard to induced immune responses. Additional components within GPE and the resulting modulation of general processes affecting gene transcription and signalling pathways might be crucial to maintain/overcome the diseased phenotype and to induce the influx of cells contributing to late-phase allergic responses. When the initial process of sensitization is the matter of interest or late-phase allergic responses, one might miss important immune modulatory molecules and their interaction with allergens by applying single components only. © 2012 Blackwell Publishing Ltd.

Isolation and structure elucidation of avocado seed (Persea americana) lipid derivatives that inhibit Clostridium sporogenes endospore germination.

PubMed

Rodríguez-Sánchez, Dariana Graciela; Pacheco, Adriana; García-Cruz, María Isabel; Gutiérrez-Uribe, Janet Alejandra; Benavides-Lozano, Jorge Alejandro; Hernández-Brenes, Carmen

2013-07-31

Avocado fruit extracts are known to exhibit antimicrobial properties. However, the effects on bacterial endospores and the identity of antimicrobial compounds have not been fully elucidated. In this study, avocado seed extracts were tested against Clostridium sporogenes vegetative cells and active endospores. Bioassay-guided purification of a crude extract based on inhibitory properties linked antimicrobial action to six lipid derivatives from the family of acetogenin compounds. Two new structures and four compounds known to exist in nature were identified as responsible for the activity. Structurally, most potent molecules shared features of an acetyl moiety and a trans-enone group. All extracts produced inhibition zones on vegetative cells and active endospores. Minimum inhibitory concentrations (MIC) of isolated molecules ranged from 7.8 to 15.6 μg/mL, and bactericidal effects were observed for an enriched fraction at 19.5 μg/mL. Identified molecules showed potential as natural alternatives to additives and antibiotics used by the food and pharmaceutical industries to inhibit Gram-positive spore-forming bacteria.

Molecular docking and ex vivo and in vitro anticholinesterase activity studies of Salvia sp. and highlighted rosmarinic acid.

PubMed

Demirezer, Lütfiye Ömür; Gürbüz, Perihan; Kelicen Uğur, Emine Pelin; Bodur, Mine; Özenver, Nadire; Uz, Ayse; Güvenalp, Zühal

2015-01-01

To evaluate acetylcholinesterase (AChE) inhibitory activity and antioxidant capacity of the major molecule from Salvia sp., rosmarinic acid, as a drug candidate molecule for treatment of Alzheimer disease (AD). The AChE inhibitory activity of different extracts from Salvia trichoclada, Salvia verticillata, and Salvia fruticosa was determined by the Ellman and isolated guinea pig ileum methods, and the antioxidant capacity was determined with DPPH. The AChE inhibitory activity of the major molecule rosmarinic acid was determined by in silico docking and isolated guinea pig ileum methods. The methanol extract of Salvia trichoclada showed the highest inhibition on AChE. The same extract and rosmarinic acid showed significant contraction responses on isolated guinea pig ileum. All the extracts and rosmarinic acid showed high radical scavenging capacities. Docking results of rosmarinic acid showed high affinity to the selected target, AChE. In this study in vitro and ex vivo studies and in silico docking research of rosmarinic acid were used simultaneously for the first time. Rosmarinic acid showed promising results in all the methods tested.

Mutagenicity and clastogenicity of extracts of Helicobacter pylori detected by the Ames test and in the micronucleus test using human lymphoblastoid cells.

PubMed

Arimoto-Kobayashi, Sakae; Ohta, Kaori; Yuhara, Yuta; Ayabe, Yuka; Negishi, Tomoe; Okamoto, Keinosuke; Nakajima, Yoshihiro; Ishikawa, Takeshi; Oguma, Keiji; Otsuka, Takanao

2015-07-01

Epidemiological studies have demonstrated a close association between infection with Helicobacter pylori (H.pylori) and the development of gastric carcinoma. Chronic H.pylori infection increases the frequency of mutation in gastric epithelial cells. However, the mechanism by which infection of H.pylori leads to mutation in gastric epithelial cells is unclear. We suspected that components in H.pylori may be related to the mutagenic response associated with DNA alkylation, and could be detected with the Ames test using a more sensitive strain for alkylating agents. Our investigation revealed that an extract of H.pylori was mutagenic in the Ames test with Salmonella typhimurium YG7108, which is deficient in the DNA repair of O(6)-methylguanine. The extract of H.pylori may contain methylating or alkylating agents, which might induce O (6)-alkylguanine in DNA. Mutagenicity of the alkylating agents N-methyl-N-nitrosourea (MNU) and N-methyl-N'-nitro-N-nitrosoguanidine in the Ames test with S.typhimurium TA1535 was enhanced significantly in the presence of the extract of H.pylori. The tested extracts of H.pylori resulted in a significant induction of micronuclei in human-derived lymphoblastoid cells. Heat instability and dialysis resistance of the extracts of H.pylori suggest that the mutagenic component in the extracts of H.pylori is a heat-unstable large molecule or a heat-labile small molecule strongly attached or adsorbed to a large molecule. Proteins in the extracts of H.pylori were subsequently fractionated using ammonium sulphate precipitation. However, all fractions expressed enhancing effects toward MNU mutagenicity. These results suggest the mutagenic component is a small molecule that is absorbed into proteins in the extract of H.pylori, which resist dialysis. Continuous and chronic exposure of gastric epithelial cells to the alkylative mutagenic component from H.pylori chronically infected in the stomach might be a causal factor in the gastric carcinogenesis associated with H.pylori. © The Author 2015. Published by Oxford University Press on behalf of the UK Environmental Mutagen Society. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

FT-IR Spectroscopic Evidence Of Phase Transition For NaA-ROH-Kerosine-H2O Microemulsion System Containing Nd3+ Ions

NASA Astrophysics Data System (ADS)

Liao, Hua; Xu, Zhen-Hua; Shi, Nai; Wu, Jin-Guang; Xu, Guang-Xian

1989-12-01

In the previous investigation, the saponification of naphthenic acid extractant system has been proved to be a process of the formation of a microemulsion of 14/0 type, and its full extraction of rare earths is a process of destruction of the W/O microemulsion[1]. When NdCl3 is partially extracted with NaA (sodium naphthenate) secoctylalcohol-- kerosine-- water microemulsion system (ME), both the NdA3 and the NaA co-exist in the same organic phase. However,the formation mechanism of microemulsion containing neodymium has not been much studied. In this paper, 10 aliquots of fully saponificated extractants were equilibrated with various amounts of NdC13 solutions respectively, then ten organic phases with different extraction efficiencies of neodymium from 094 to 9094 were obtained. After extraction,the volume of neodymium containing organic phase increased by 5 to 4594, because of the transfer of water molecules. The appearance of these organic phase still remained clear and transparent. The average hydrodynamic radius of the drops were found to be 100-300 Angstrom by using light scattering techniques. The results give a direct evidence of the microemulsion formation in the organic phase. Their FT-IR spectra were measured with CaFa liquid cells utilizing a Nicolet 7199B FT-IR spectrometer. The presence of various amounts of water in the organic phases was clearly detected from the relative intensity changes of 1644 cm-I, which is assigned to the bending mode of 1110 molecules. Fig.1 shows the change of water contents to the percent extraction of neodymium. Comparsion with the FT-IR spectra, it is seen that the 1560 cm-1 peak of the full saponificated extractant is attributed to the asym. stretching vibration of COO''' group, it shifted to 1536 for 100% extration of Nd ions, indicating the formation of neodymium naphthenate (NdA ) from ionic sodium naphthenate. The sym. strethching vibration of COO''' located at 1406 cm-1, it shifted to 1408 cm in 45% Nd extration. and disappeared when the percentage extration of Nd3+ was larger than 50%, at the same time, the water content dropped sharply (Fig.1).These results suggested that a series of microemulsion containing Nd ions formed in these organic phases, at the transition region ( more than 50 percentage extration of neodymium), a morphological change of the W/0 dispersion system might occur.

Optimized extraction by cetyl trimethyl ammonium bromide reversed micelles of xylose reductase and xylitol dehydrogenase from Candida guilliermondii homogenate.

PubMed

Cortez, Ely Vieira; Pessoa, Adalberto; das Graças de Almeida Felipe, Maria; Roberto, Inês Conceição; Vitolo, Michele

2004-07-25

The intracellular enzymes xylose reductase (XR, EC 1.1.1.21) and xylitol dehydrogenase (XD, EC 1.1.1.9) from Candida guilliermondii, grown in sugar cane bagasse hydrolysate, were separated by reversed micelles of cetyl trimethyl ammonium bromide (CTAB) cationic surfactant. An experimental design was employed to optimize the extraction conditions of both enzymes. Under these conditions (temperature = 5 degree C, hexanol: isooctane proportion = 5% (v/v), 22 %, surfactant concentration = 0.15M, pH = 7.0 and electrical conductivity = 14 mScm(-1)) recovery values of about 100 and 80% were achieved for the enzymes XR and XD, respectively. The purity of XR and XD increased 5.6- and 1.8-fold, respectively. The extraction process caused some structural modifications in the enzymes molecules, as evidenced by the alteration of K(M) values determined before and after extraction, either in regard to the substrate (up 35% for XR and down 48% for XD) or cofactor (down 29% for XR and up 11% for XD). However, the average variation of V(max) values for both enzymes was not higher than 7%, indicating that the modified affinity of enzymes for their respective substrates and cofactors, as consequence of structural modifications suffered by them during the extraction, are compensated in some extension. This study demonstrated that liquid-liquid extraction by CTAB reversed micelles is an efficient process to separate the enzymes XR and XD present in the cell extract, and simultaneously increase the enzymatic activity and the purity of both enzymes produced by C. guilliermondii.

Biomimetic air sampling for detection of low concentrations of molecules and bioagents : LDRD 52744 final report.

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

Hughes, Robert Clark

2003-12-01

Present methods of air sampling for low concentrations of chemicals like explosives and bioagents involve noisy and power hungry collectors with mechanical parts for moving large volumes of air. However there are biological systems that are capable of detecting very low concentrations of molecules with no mechanical moving parts. An example is the silkworm moth antenna which is a highly branched structure where each of 100 branches contains about 200 sensory 'hairs' which have dimensions of 2 microns wide by 100 microns long. The hairs contain about 3000 pores which is where the gas phase molecules enter the aqueous (lymph)more » phase for detection. Simulations of diffusion of molecules indicate that this 'forest' of hairs is 'designed' to maximize the extraction of the vapor phase molecules. Since typical molecules lose about 4 decades in diffusion constant upon entering the liquid phase, it is important to allow air diffusion to bring the molecule as close to the 'sensor' as possible. The moth acts on concentrations as low as 1000 molecules per cubic cm. (one part in 1e16). A 3-D collection system of these dimensions could be fabricated by micromachining techniques available at Sandia. This LDRD addresses the issues involved with extracting molecules from air onto micromachined structures and then delivering those molecules to microsensors for detection.« less

RNA isolation from mammalian cells using porous polymer monoliths: an approach for high-throughput automation.

PubMed

Chatterjee, Anirban; Mirer, Paul L; Zaldivar Santamaria, Elvira; Klapperich, Catherine; Sharon, Andre; Sauer-Budge, Alexis F

2010-06-01

The life science and healthcare communities have been redefining the importance of ribonucleic acid (RNA) through the study of small molecule RNA (in RNAi/siRNA technologies), micro RNA (in cancer research and stem cell research), and mRNA (gene expression analysis for biologic drug targets). Research in this field increasingly requires efficient and high-throughput isolation techniques for RNA. Currently, several commercial kits are available for isolating RNA from cells. Although the quality and quantity of RNA yielded from these kits is sufficiently good for many purposes, limitations exist in terms of extraction efficiency from small cell populations and the ability to automate the extraction process. Traditionally, automating a process decreases the cost and personnel time while simultaneously increasing the throughput and reproducibility. As the RNA field matures, new methods for automating its extraction, especially from low cell numbers and in high throughput, are needed to achieve these improvements. The technology presented in this article is a step toward this goal. The method is based on a solid-phase extraction technology using a porous polymer monolith (PPM). A novel cell lysis approach and a larger binding surface throughout the PPM extraction column ensure a high yield from small starting samples, increasing sensitivity and reducing indirect costs in cell culture and sample storage. The method ensures a fast and simple procedure for RNA isolation from eukaryotic cells, with a high yield both in terms of quality and quantity. The technique is amenable to automation and streamlined workflow integration, with possible miniaturization of the sample handling process making it suitable for high-throughput applications.

Chloride channel inhibition by a red wine extract and a synthetic small molecule prevents rotaviral secretory diarrhoea in neonatal mice.

PubMed

Ko, Eun-A; Jin, Byung-Ju; Namkung, Wan; Ma, Tonghui; Thiagarajah, Jay R; Verkman, A S

2014-07-01

Rotavirus is the most common cause of severe secretory diarrhoea in infants and young children globally. The rotaviral enterotoxin, NSP4, has been proposed to stimulate calcium-activated chloride channels (CaCC) on the apical plasma membrane of intestinal epithelial cells. We previously identified red wine and small molecule CaCC inhibitors. To investigate the efficacy of a red wine extract and a synthetic small molecule, CaCCinh-A01, in inhibiting intestinal CaCCs and rotaviral diarrhoea. Inhibition of CaCC-dependent current was measured in T84 cells and mouse ileum. The effectiveness of an orally administered wine extract and CaCCinh-A01 in inhibiting diarrhoea in vivo was determined in a neonatal mouse model of rotaviral infection. Screening of ∼150 red wines revealed a Cabernet Sauvignon that inhibited CaCC current in T84 cells with IC50 at a ∼1:200 dilution, and higher concentrations producing 100% inhibition. A >1 kdalton wine extract prepared by dialysis, which retained full inhibition activity, blocked CaCC current in T84 cells and mouse intestine. In rotavirus-inoculated mice, oral administration of the wine extract prevented diarrhoea by inhibition of intestinal fluid secretion without affecting rotaviral infection. The wine extract did not inhibit the cystic fibrosis chloride channel (CFTR) in cell cultures, nor did it prevent watery stools in neonatal mice administered cholera toxin, which activates CFTR-dependent fluid secretion. CaCCinh-A01 also inhibited rotaviral diarrhoea. Our results support a pathogenic role for enterocyte CaCCs in rotaviral diarrhoea and demonstrate the antidiarrhoeal action of CaCC inhibition by an alcohol-free, red wine extract and by a synthetic small molecule. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

New strategy for protein interactions and application to structure-based drug design

NASA Astrophysics Data System (ADS)

Zou, Xiaoqin

One of the greatest challenges in computational biophysics is to predict interactions between biological molecules, which play critical roles in biological processes and rational design of therapeutic drugs. Biomolecular interactions involve delicate interplay between multiple interactions, including electrostatic interactions, van der Waals interactions, solvent effect, and conformational entropic effect. Accurate determination of these complex and subtle interactions is challenging. Moreover, a biological molecule such as a protein usually consists of thousands of atoms, and thus occupies a huge conformational space. The large degrees of freedom pose further challenges for accurate prediction of biomolecular interactions. Here, I will present our development of physics-based theory and computational modeling on protein interactions with other molecules. The major strategy is to extract microscopic energetics from the information embedded in the experimentally-determined structures of protein complexes. I will also present applications of the methods to structure-based therapeutic design. Supported by NSF CAREER Award DBI-0953839, NIH R01GM109980, and the American Heart Association (Midwest Affiliate) [13GRNT16990076].

mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets.

PubMed

Choi, Cheolwon; Yoon, Seulgi; Moon, Hyesu; Bae, Yun-Ui; Kim, Chae-Bin; Diskul-Na-Ayudthaya, Penchatr; Ngu, Trinh Van; Munir, Javaria; Han, JaeWook; Park, Se Bin; Moon, Jong-Seok; Song, Sujung; Ryu, Seongho

2018-04-11

Techniques to isolate the small RNA fraction (<200nt) by column-based methods are commercially available. However, their use is limited because of the relatively high cost. We found that large RNA molecules, including mRNAs and rRNAs, are aggregated together in the presence of salts when RNA pellets are over-dried. Moreover, once RNA pellets are over-dried, large RNA molecules are barely soluble again during the elution process, whereas small RNA molecules (<100nt) can be eluted. We therefore modified the acid guanidinium thiocyanate-phenol-chloroform (AGPC)-based RNA extraction protocol by skipping the 70% ethanol washing step and over-drying the RNA pellet for 1 hour at room temperature. We named this novel small RNA isolation method "mirRICH." The quality of the small RNA sequences was validated by electrophoresis, next-generation sequencing, and quantitative PCR, and the findings support that our newly developed column-free method can successfully and efficiently isolate small RNAs from over-dried RNA pellets.

Susceptibility of Phytomonas serpens to calpain inhibitors in vitro: interference on the proliferation, ultrastructure, cysteine peptidase expression and interaction with the invertebrate host.

PubMed

Oliveira, Simone Santiago Carvalho de; Gonçalves, Diego de Souza; Garcia-Gomes, Aline Dos Santos; Gonçalves, Inês Correa; Seabra, Sergio Henrique; Menna-Barreto, Rubem Figueiredo; Lopes, Angela Hampshire de Carvalho Santos; D'Avila-Levy, Claudia Masini; Santos, André Luis Souza Dos; Branquinha, Marta Helena

2017-01-01

A pleiotropic response to the calpain inhibitor MDL28170 was detected in the tomato parasite Phytomonas serpens. Ultrastructural studies revealed that MDL28170 caused mitochondrial swelling, shortening of flagellum and disruption of trans Golgi network. This effect was correlated to the inhibition in processing of cruzipain-like molecules, which presented an increase in expression paralleled by decreased proteolytic activity. Concomitantly, a calcium-dependent cysteine peptidase was detected in the parasite extract, the activity of which was repressed by pre-incubation of parasites with MDL28170. Flow cytometry and Western blotting analyses revealed the differential expression of calpain-like proteins (CALPs) in response to the pre-incubation of parasites with the MDL28170, and confocal fluorescence microscopy confirmed their surface location. The interaction of promastigotes with explanted salivary glands of the insect Oncopeltus fasciatus was reduced when parasites were pre-treated with MDL28170, which was correlated to reduced levels of surface cruzipain-like and gp63-like molecules. Treatment of parasites with anti-Drosophila melanogaster (Dm) calpain antibody also decreased the adhesion process. Additionally, parasites recovered from the interaction process presented higher levels of surface cruzipain-like and gp63-like molecules, with similar levels of CALPs cross-reactive to anti-Dm-calpain antibody. The results confirm the importance of exploring the use of calpain inhibitors in studying parasites' physiology.

Susceptibility of Phytomonas serpens to calpain inhibitors in vitro: interference on the proliferation, ultrastructure, cysteine peptidase expression and interaction with the invertebrate host

PubMed Central

de Oliveira, Simone Santiago Carvalho; Gonçalves, Diego de Souza; Garcia-Gomes, Aline dos Santos; Gonçalves, Inês Correa; Seabra, Sergio Henrique; Menna-Barreto, Rubem Figueiredo; Lopes, Angela Hampshire de Carvalho Santos; D’Avila-Levy, Claudia Masini; dos Santos, André Luis Souza; Branquinha, Marta Helena

2016-01-01

A pleiotropic response to the calpain inhibitor MDL28170 was detected in the tomato parasite Phytomonas serpens. Ultrastructural studies revealed that MDL28170 caused mitochondrial swelling, shortening of flagellum and disruption of trans Golgi network. This effect was correlated to the inhibition in processing of cruzipain-like molecules, which presented an increase in expression paralleled by decreased proteolytic activity. Concomitantly, a calcium-dependent cysteine peptidase was detected in the parasite extract, the activity of which was repressed by pre-incubation of parasites with MDL28170. Flow cytometry and Western blotting analyses revealed the differential expression of calpain-like proteins (CALPs) in response to the pre-incubation of parasites with the MDL28170, and confocal fluorescence microscopy confirmed their surface location. The interaction of promastigotes with explanted salivary glands of the insect Oncopeltus fasciatus was reduced when parasites were pre-treated with MDL28170, which was correlated to reduced levels of surface cruzipain-like and gp63-like molecules. Treatment of parasites with anti-Drosophila melanogaster (Dm) calpain antibody also decreased the adhesion process. Additionally, parasites recovered from the interaction process presented higher levels of surface cruzipain-like and gp63-like molecules, with similar levels of CALPs cross-reactive to anti-Dm-calpain antibody. The results confirm the importance of exploring the use of calpain inhibitors in studying parasites’ physiology. PMID:27925020

Extracting conformational structure information of benzene molecules via laser-induced electron diffraction

DOE PAGES

Ito, Yuta; Wang, Chuncheng; Le, Anh-Thu; ...

2016-05-01

Here, we have measured the angular distributions of high energy photoelectrons of benzene molecules generated by intense infrared femtosecond laser pulses. These electrons arise from the elastic collisions between the benzene ions with the previously tunnel-ionized electrons that have been driven back by the laser field. Theory shows that laser-free elastic differential cross sections (DCSs) can be extracted from these photoelectrons, and the DCS can be used to retrieve the bond lengths of gas-phase molecules similar to the conventional electron diffraction method. From our experimental results, we have obtained the C-C and C-H bond lengths of benzene with a spatialmore » resolution of about 10 pm. Our results demonstrate that laser induced electron diffraction (LIED) experiments can be carried out with the present-day ultrafast intense lasers already. Looking ahead, with aligned or oriented molecules, more complete spatial information of the molecule can be obtained from LIED, and applying LIED to probe photo-excited molecules, a “molecular movie” of the dynamic system may be created with sub-A°ngstrom spatial and few-ten femtosecond temporal resolutions.« less

Physicochemical basis for water-actuated movement and stress generation in nonliving plant tissues.

PubMed

Bertinetti, L; Fischer, F D; Fratzl, P

2013-12-06

Generating stresses and strains through water uptake from atmospheric humidity is a common process in nature, e.g., in seed dispersal. Actuation depends on a balance between chemical interactions and the elastic energy required to accomplish the volume change. In order to study the poorly understood chemical interactions, we combine mechanosorption experiments with theoretical calculations of the swelling behavior to estimate the mechanical energy and extract the contribution of the chemical energy per absorbed water molecule. The latter is highest in the completely dry state and stays almost constant at about 1.2 kT for higher hydrations. This suggests that water bound to the macromolecular components of the wood tissues acquires one additional hydrogen bond per eight water molecules, thus providing energy for actuation.

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

DOE PAGES

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S.; ...

2017-02-23

Here, a newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides,more » important for metal extraction chemistry, are parametrized using ParFit.« less

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

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

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S.

Here, a newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides,more » important for metal extraction chemistry, are parametrized using ParFit.« less

Extraction of nucleic acids from yeast cells and plant tissues using ethanol as medium for sample preservation and cell disruption.

PubMed

Linke, Bettina; Schröder, Kersten; Arter, Juliane; Gasperazzo, Tatiana; Woehlecke, Holger; Ehwald, Rudolf

2010-09-01

Here we report that dehydrated ethanol is an excellent medium for both in situ preservation of nucleic acids and cell disruption of plant and yeast cells. Cell disruption was strongly facilitated by prior dehydration of the ethanol using dehydrated zeolite. Following removal of ethanol, nucleic acids were extracted from the homogenate pellet using denaturing buffers. The method provided DNA and RNA of high yield and integrity. Whereas cell wall disruption was essential for extraction of DNA and large RNA molecules, smaller molecules such as tRNAs could be selectively extracted from undisrupted, ethanol-treated yeast cells. Our results demonstrate the utility of absolute ethanol for sample fixation, cell membrane and cell wall disruption, as well as preservation of nucleic acids during sample storage.

A bioassay-guided fractionation system to identify endogenous small molecules that activate plasma membrane H+-ATPase activity in Arabidopsis.

PubMed

Han, Xiuli; Yang, Yongqing; Wu, Yujiao; Liu, Xiaohui; Lei, Xiaoguang; Guo, Yan

2017-05-17

Plasma membrane (PM) H+-ATPase is essential for plant growth and development. Various environmental stimuli regulate its activity, a process that involves many protein cofactors. However, whether endogenous small molecules play a role in this regulation remains unknown. Here, we describe a bio-guided isolation method to identify endogenous small molecules that regulate PM H+-ATPase activity. We obtained crude extracts from Arabidopsis seedlings with or without salt treatment and then purified them into fractions based on polarity and molecular mass by repeated column chromatography. By evaluating the effect of each fraction on PM H+-ATPase activity, we found that fractions containing the endogenous, free unsaturated fatty acids oleic acid (C18:1), linoleic acid (C18:2), and linolenic acid (C18:3) extracted from salt-treated seedlings stimulate PM H+-ATPase activity. These results were further confirmed by the addition of exogenous C18:1, C18:2, or C18:3 in the activity assay. The ssi2 mutant, with reduced levels of C18:1, C18:2, and C18:3, displayed reduced PM H+-ATPase activity. Furthermore, C18:1, C18:2, and C18:3 directly bound to the C-terminus of the PM H+-ATPase AHA2. Collectively, our results demonstrate that the binding of free unsaturated fatty acids to the C-terminus of PM H+-ATPase is required for its activation under salt stress. The bio-guided isolation model described in this study could enable the identification of new endogenous small molecules that modulate essential protein functions, as well as signal transduction, in plants. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Simultaneous cell disruption and lipid extraction of wet aurantiochytrium sp. KRS101 using a high shear mixer.

PubMed

Kwak, Minsoo; Kang, Seul Gi; Hong, Won-Kyung; Han, Jong-In; Chang, Yong Keun

2018-05-01

Microalgae are regarded as a promising source of biofuels, and the concept of a microalgae-based biorefinery has attracted increasing attention in recent years. From an economic perspective, however, the process remains far from competitive with fossil fuels. This is particularly true of lipid extraction, due in part to the energy-intensive drying step. As a result, wet extraction methods have been studied as an economic alternative. In the present study, a novel extraction approach which utilizes high shear stress mixing was adopted and demonstrated for simultaneous lipid extraction and cell disruption to enable the retrieval of lipids directly from concentrated wet biomass. When a high shear mixer (HSM) was used to extract lipid from a dense biomass (> 350 g/L) of the oleaginous algae Aurantiochytrium sp., it exhibited a yield of esterifiable lipids which exceeded 80% in 10 min at 15,000 rpm with various solvent types. The HSM was found to improve the lipid yields substantially with solvents less miscible with either lipids or water, such that the range of Hansen solubility parameters for the usable solvents became 3.3 times wider (14.9-26.5 MPa 1/2 ). The HSM, which appeared effectively to loosen the water barrier that prevents solvent molecules from penetrating through the cell envelope, was found to be more efficient with hexane, hexane/isopropanol, and ethanol, all of which showed nearly identical lipid yields compared to the dry extraction process. The HSM can, indeed, offer a powerful mechanical means of lipid extraction with non-polar and less toxic solvents from wet biomass.

Cytotoxic agents for KB and SiHa cells from n-hexane fraction of Cissampelos pareira and its chemical composition.

PubMed

Bala, Manju; Pratap, Kunal; Verma, Praveen Kumar; Padwad, Yogendra; Singh, Bikram

2015-01-01

Eleven constituents were characterised by gas chromatography-mass spectrometry analysis, and five molecules were isolated using column chromatography. The in vitro study of the extract and isolated molecules against KB and SiHa cell lines revealed oleanolic acid (1) and oleic acid (2) as potent cytotoxic molecules with potential anticancer activity. The IC50 values of n-hexane extract (CPHF), oleanolic acid (1) and oleic acid (2) were >300, 56.08 and 70.7 μg/mL (μM), respectively, against KB cell lines and >300, 47.24 and 80.2 μg/mL (μM), respectively, against SiHa cell lines.

A rapid and sensitive method for the simultaneous analysis of aliphatic and polar molecules containing free carboxyl groups in plant extracts by LC-MS/MS

PubMed Central

2009-01-01

Background Aliphatic molecules containing free carboxyl groups are important intermediates in many metabolic and signalling reactions, however, they accumulate to low levels in tissues and are not efficiently ionized by electrospray ionization (ESI) compared to more polar substances. Quantification of aliphatic molecules becomes therefore difficult when small amounts of tissue are available for analysis. Traditional methods for analysis of these molecules require purification or enrichment steps, which are onerous when multiple samples need to be analyzed. In contrast to aliphatic molecules, more polar substances containing free carboxyl groups such as some phytohormones are efficiently ionized by ESI and suitable for analysis by LC-MS/MS. Thus, the development of a method with which aliphatic and polar molecules -which their unmodified forms differ dramatically in their efficiencies of ionization by ESI- can be simultaneously detected with similar sensitivities would substantially simplify the analysis of complex biological matrices. Results A simple, rapid, specific and sensitive method for the simultaneous detection and quantification of free aliphatic molecules (e.g., free fatty acids (FFA)) and small polar molecules (e.g., jasmonic acid (JA), salicylic acid (SA)) containing free carboxyl groups by direct derivatization of leaf extracts with Picolinyl reagent followed by LC-MS/MS analysis is presented. The presence of the N atom in the esterified pyridine moiety allowed the efficient ionization of 25 compounds tested irrespective of their chemical structure. The method was validated by comparing the results obtained after analysis of Nicotiana attenuata leaf material with previously described analytical methods. Conclusion The method presented was used to detect 16 compounds in leaf extracts of N. attenuata plants. Importantly, the method can be adapted based on the specific analytes of interest with the only consideration that the molecules must contain at least one free carboxyl group. PMID:19939243

Single-molecule strong coupling at room temperature in plasmonic nanocavities

NASA Astrophysics Data System (ADS)

Chikkaraddy, Rohit; de Nijs, Bart; Benz, Felix; Barrow, Steven J.; Scherman, Oren A.; Rosta, Edina; Demetriadou, Angela; Fox, Peter; Hess, Ortwin; Baumberg, Jeremy J.

2016-07-01

Photon emitters placed in an optical cavity experience an environment that changes how they are coupled to the surrounding light field. In the weak-coupling regime, the extraction of light from the emitter is enhanced. But more profound effects emerge when single-emitter strong coupling occurs: mixed states are produced that are part light, part matter, forming building blocks for quantum information systems and for ultralow-power switches and lasers. Such cavity quantum electrodynamics has until now been the preserve of low temperatures and complicated fabrication methods, compromising its use. Here, by scaling the cavity volume to less than 40 cubic nanometres and using host-guest chemistry to align one to ten protectively isolated methylene-blue molecules, we reach the strong-coupling regime at room temperature and in ambient conditions. Dispersion curves from more than 50 such plasmonic nanocavities display characteristic light-matter mixing, with Rabi frequencies of 300 millielectronvolts for ten methylene-blue molecules, decreasing to 90 millielectronvolts for single molecules—matching quantitative models. Statistical analysis of vibrational spectroscopy time series and dark-field scattering spectra provides evidence of single-molecule strong coupling. This dressing of molecules with light can modify photochemistry, opening up the exploration of complex natural processes such as photosynthesis and the possibility of manipulating chemical bonds.

Aqueous biphasic systems in the separation of food colorants.

PubMed

Santos, João H P M; Capela, Emanuel V; Boal-Palheiros, Isabel; Coutinho, João A P; Freire, Mara G; Ventura, Sónia P M

2018-04-25

Aqueous biphasic systems (ABS) composed of polypropylene glycol and carbohydrates, two benign substances are proposed to separate two food colorants (E122 and E133). ABS are promising extractive platforms, particularly for biomolecules, due to their aqueous and mild nature (pH and temperature), reduced environmental impact and processing costs. Another major aspect considered, particularly useful in downstream processing, is the "tuning" ability for the extraction and purification of these systems by a proper choice of the ABS components. In this work, our intention is to show the concept of ABS as an alternative and volatile organic solvent-free tool to separate two different biomolecules in a simple way, so simple that teachers can effectively adopt it in their classes to explain the concept of bioseparation processes. Informative documents and general information about the preparation of binodal curves and their use in the partition of biomolecules is available in this work to be used by teachers in their classes. In this sense, the students use different carbohydrates to build ABS, then study the partition of two food color dyes (synthetic origin), thus evaluating their ability on the separation of both food colorants. Through these experiments, the students get acquainted with ABS, learn how to determine solubility curves and perform extraction procedures using colorant food additives, that can also be applied in the extraction of various (bio)molecules. © 2018 by The International Union of Biochemistry and Molecular Biology, 2018. © 2018 The International Union of Biochemistry and Molecular Biology.

Simultaneous ultrasound-assisted water extraction and β-cyclodextrin encapsulation of polyphenols from Mangifera indica stem bark in counteracting TNFα-induced endothelial dysfunction.

PubMed

Mura, Marzia; Palmieri, Daniela; Garella, Davide; Di Stilo, Antonella; Perego, Patrizia; Cravotto, Giancarlo; Palombo, Domenico

2015-01-01

This study proposes an alternative technique to prevent heat degradation induced by classic procedures of bioactive compound extraction, comparing classical maceration/decoction in hot water of polyphenols from Mango (Mangifera indica L.) (MI) with ultrasound-assisted extraction (UAE) in a water solution of β-cyclodextrin (β-CD) at room temperature and testing their biological activity on TNFα-induced endothelial dysfunction. Both extracts counteracted TNFα effects on EAhy926 cells, down-modulating interleukin-6, interleukin-8, cyclooxygenase-2 and intracellular adhesion molecule-1, while increasing endothelial nitric oxide synthase levels. β-CD extract showed higher efficacy in improving endothelial function. These effects were abolished after pre-treatment with the oestrogen receptor inhibitor ICI1182,780. Moreover, the β-CD extract induced Akt activation and completely abolished the TNFα-induced p38MAPK phosphorylation. UAE and β-CD encapsulation provide an efficient extraction protocol that increases polyphenol bioavailability. Polyphenols from MI play a protective role on endothelial cells and may be further considered as oestrogen-like molecules with vascular protective properties.

A review on plants extract mediated synthesis of silver nanoparticles for antimicrobial applications: A green expertise

PubMed Central

Ahmed, Shakeel; Ahmad, Mudasir; Swami, Babu Lal; Ikram, Saiqa

2015-01-01

Metallic nanoparticles are being utilized in every phase of science along with engineering including medical fields and are still charming the scientists to explore new dimensions for their respective worth which is generally attributed to their corresponding small sizes. The up-and-coming researches have proven their antimicrobial significance. Among several noble metal nanoparticles, silver nanoparticles have attained a special focus. Conventionally silver nanoparticles are synthesized by chemical method using chemicals as reducing agents which later on become accountable for various biological risks due to their general toxicity; engendering the serious concern to develop environment friendly processes. Thus, to solve the objective; biological approaches are coming up to fill the void; for instance green syntheses using biological molecules derived from plant sources in the form of extracts exhibiting superiority over chemical and/or biological methods. These plant based biological molecules undergo highly controlled assembly for making them suitable for the metal nanoparticle syntheses. The present review explores the huge plant diversity to be utilized towards rapid and single step protocol preparatory method with green principles over the conventional ones and describes the antimicrobial activities of silver nanoparticles. PMID:26843966

Human dermatosparaxis: a form of Ehlers-Danlos syndrome that results from failure to remove the amino-terminal propeptide of type I procollagen.

PubMed

Smith, L T; Wertelecki, W; Milstone, L M; Petty, E M; Seashore, M R; Braverman, I M; Jenkins, T G; Byers, P H

1992-08-01

Dermatosparaxis is a recessively inherited connective-tissue disorder that results from lack of the activity of type I procollagen N-proteinase, the enzyme that removes the amino-terminal propeptides from type I procollagen. Initially identified in cattle more than 20 years ago, the disorder was subsequently characterized in sheep, cats, and dogs. Affected animals have fragile skin, lax joints, and often die prematurely because of sepsis following avulsion of portions of skin. We recently identified two children with soft, lax, and fragile skin, which, when examined by transmission electron microscopy, contained the twisted, ribbon-like collagen fibrils characteristic of dermatosparaxis. Skin extracts from one child contained collagen precursors with amino-terminal extensions. Cultured fibroblasts from both children failed to cleave the amino-terminal propeptides from the pro alpha 1(I) and pro alpha 2(I) chains in type I procollagen molecules. Extracts of normal cells cleaved to collagen, the type I procollagen synthesized by cells from both children, demonstrating that the enzyme, not the substrate, was defective. These findings distinguish dermatosparaxis from Ehlers-Danlos syndrome type VII, which results from substrate mutations that prevent proteolytic processing of type I procollagen molecules.

Role of Crystallization in the Morphology of Polymer: Non-fullerene Acceptor Bulk Heterojunctions

DOE PAGES

O’Hara, Kathryn A.; Ostrowski, David P.; Koldemir, Unsal; ...

2017-05-22

Many high efficiency organic photovoltaics use fullerene-based acceptors despite their high production cost, weak optical absorption in the visible range, and limited synthetic variability of electronic and optical properties. To circumvent this deficiency, non-fullerene small-molecule acceptors have been developed that have good synthetic flexibility, allowing for precise tuning of optoelectronic properties, leading to enhanced absorption of the solar spectrum and increased open-circuit voltages ( V OC). We examined the detailed morphology of bulk heterojunctions of poly(3-hexylthiophene) and the small-molecule acceptor HPI-BT to reveal structural changes that lead to improvements in the fill factor of solar cells upon thermal annealing. Themore » kinetics of the phase transformation process of HPI-BT during thermal annealing were investigated through in situ grazing incidence wide-angle X-ray scattering studies, atomic force microscopy, and transmission electron microscopy. The HPI-BT acceptor crystallizes during film formation to form micron-sized domains embedded within the film center and a donor rich capping layer at the cathode interface reducing efficient charge extraction. Thermal annealing changes the surface composition and improves charge extraction. In conclusion, this study reveals the need for complementary methods to investigate the morphology of BHJs.« less

Role of Crystallization in the Morphology of Polymer: Non-fullerene Acceptor Bulk Heterojunctions

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

O’Hara, Kathryn A.; Ostrowski, David P.; Koldemir, Unsal

Many high efficiency organic photovoltaics use fullerene-based acceptors despite their high production cost, weak optical absorption in the visible range, and limited synthetic variability of electronic and optical properties. To circumvent this deficiency, non-fullerene small-molecule acceptors have been developed that have good synthetic flexibility, allowing for precise tuning of optoelectronic properties, leading to enhanced absorption of the solar spectrum and increased open-circuit voltages ( V OC). We examined the detailed morphology of bulk heterojunctions of poly(3-hexylthiophene) and the small-molecule acceptor HPI-BT to reveal structural changes that lead to improvements in the fill factor of solar cells upon thermal annealing. Themore » kinetics of the phase transformation process of HPI-BT during thermal annealing were investigated through in situ grazing incidence wide-angle X-ray scattering studies, atomic force microscopy, and transmission electron microscopy. The HPI-BT acceptor crystallizes during film formation to form micron-sized domains embedded within the film center and a donor rich capping layer at the cathode interface reducing efficient charge extraction. Thermal annealing changes the surface composition and improves charge extraction. In conclusion, this study reveals the need for complementary methods to investigate the morphology of BHJs.« less

Sensitization to cat and dog allergen molecules in childhood and prediction of symptoms of cat and dog allergy in adolescence: A BAMSE/MeDALL study.

PubMed

Asarnoj, Anna; Hamsten, Carl; Wadén, Konrad; Lupinek, Christian; Andersson, Niklas; Kull, Inger; Curin, Mirela; Anto, Josep; Bousquet, Jean; Valenta, Rudolf; Wickman, Magnus; van Hage, Marianne

2016-03-01

Sensitization to individual cat and dog allergen molecules can contribute differently to development of allergy to these animals. We sought to investigate the association between sensitization patterns to cat and dog allergen molecules during childhood and symptoms to these furry animals up to age 16 years. Data from 779 randomly collected children from the Barn/Children Allergy/Asthma Milieu Stockholm Epidemiologic birth cohort at 4, 8, and 16 years were used. IgE levels to cat and dog were determined by using ImmunoCAP, and levels to allergen molecules were determined by using an allergen chip based on ISAC technology (Mechanisms for the Development of Allergy chip). Allergy was defined as reported rhinitis, conjunctivitis, or asthma at exposure to cat or dog. Cross-sectionally, IgE to Fel d 1 and cat extract had similar positive predictive values for cat allergy. IgE to Can f 1 showed a higher positive predictive value for dog allergy than dog extract IgE. Sensitizations to Fel d 1 and Can f 1 in childhood were significantly associated with symptoms to cat or dog at age 16 years. Polysensitization to 3 or more allergen molecules from cat or dog was a better longitudinal predictor of cat or dog symptoms than results of IgE tests with cat or dog allergen extract, respectively. Cross-sectionally, cat/dog-polysensitized children had higher IgE levels and more frequent symptoms to cat and dog than monosensitized children. Sensitization to Fel d 1 and Can f 1 in childhood and polysensitization to either cat or dog allergen molecules predict cat and dog allergy cross-sectionally and longitudinally significantly better than IgE to cat or dog extract. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Dynamics of aqueous binary glass-formers confined in MCM-41.

PubMed

Elamin, Khalid; Jansson, Helén; Swenson, Jan

2015-05-21

Dielectric permittivity measurements were performed on water solutions of propylene glycol (PG) and propylene glycol monomethyl ether (PGME) confined in 21 Å pores of the silica matrix MCM-41 C10 in wide frequency (10(-2)-10(6) Hz) and temperature (130-250 K) ranges. The aim was to elucidate how the formation of large hydrogen bonded structural entities, found in bulk solutions of PGME, was affected by the confined geometry, and to make comparisons with the dynamic behavior of the PG-water system. For all solutions the measurements revealed four almost concentration independent relaxation processes. The intensity of the fastest process is low compared to the other relaxation processes and might be caused by both hydroxyl groups of the pore surfaces and by local motions of water and solute molecules. The second fastest process contains contributions from both the main water relaxation as well as the intrinsic β-relaxation of the solute molecules. The third fastest process is the viscosity related α-relaxation. Its concentration independency is very different compared to the findings for the corresponding bulk systems, particularly for the PGME-water system. The experimental data suggests that the surface interactions induce a micro-phase separation of the two liquids, resulting in a full molecular layer of water molecules coordinating to the hydrophilic hydroxyl groups on the surfaces of the silica pores. This, in turn, increases the geometrical confinement effect for the remaining solution even more and prevents the building up of the same type of larger structural entities in the PGME-water system as in the corresponding bulk solutions. The slowest process is mainly hidden in the high conductivity contribution at low frequencies, but its temperature dependence can be extracted for the PGME-water system. However, its origin is not fully clear, as will be discussed.

Method of detecting luminescent target ions with modified magnetic microspheres

DOEpatents

Shkrob, Ilya A; Kaminski, Michael D

2014-05-13

This invention provides methods of using modified magnetic microspheres to extract target ions from a sample in order to detect their presence in a microfluidic environment. In one or more embodiments, the microspheres are modified with molecules on the surface that allow the target ions in the sample to form complexes with specific ligand molecules on the microsphere surface. In one or more embodiments, the microspheres are modified with molecules that sequester the target ions from the sample, but specific ligand molecules in solution subsequently re-extract the target ions from the microspheres into the solution, where the complexes form independent of the microsphere surface. Once the complexes form, they are exposed to an excitation wavelength light source suitable for exciting the target ion to emit a luminescent signal pattern. Detection of the luminescent signal pattern allows for determination of the presence of the target ions in the sample.

Continuous Flow Liquid Microjunction Surface Sampling Probe Connected On-line with HPLC/MS for Spatially Resolved Analysis of Small Molecules and Proteins

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

Van Berkel, Gary J; Kertesz, Vilmos

RATIONALE: A continuous flow liquid microjunction surface sampling probe extracts soluble material from surfaces for direct ionization and detection by MS. Demonstrated here is the on-line coupling of such a probe with HPLC/MS enabling extraction, separation and detection of small molecules and proteins from surfaces in a spatially resolved (~0.5 mm diameter spots) manner. Methods: A continuous flow liquid microjunction surface sampling probe was connected to a 6-port, 2-position valve for extract collection and injection to an HPLC column. A QTRAP 5500 hybrid triple quadrupole linear ion trap equipped with a Turbo V ion source operated in positive ESI modemore » was used for all experiments. System operation was tested with extraction, separation and detection of propranolol and associated metabolites from drug dosed tissues and proteins from dried sheep blood spots on paper. Results: Confirmed in the tissue were the parent drug and two different hydroxypropranolol glucuronides. The mass spectrometric response for these compounds from different locations in the liver showed an increase with increasing extraction time (5, 20 and 40 s extractions). For on-line separation and detection/identification of extracted proteins from dried sheep blood spots, two major protein peaks dominated the chromatogram and could be correlated with the expected masses for the hemoglobin and chains. Conclusions: Spatially resolved sampling, separation, and detection of small molecules and proteins from surfaces can be accomplished using a continuous flow liquid microjunction surface sampling probe coupled on-line with HPLC/MS detection.« less

Two states or not two states: Single-molecule folding studies of protein L

NASA Astrophysics Data System (ADS)

Aviram, Haim Yuval; Pirchi, Menahem; Barak, Yoav; Riven, Inbal; Haran, Gilad

2018-03-01

Experimental tools of increasing sophistication have been employed in recent years to study protein folding and misfolding. Folding is considered a complex process, and one way to address it is by studying small proteins, which seemingly possess a simple energy landscape with essentially only two stable states, either folded or unfolded. The B1-IgG binding domain of protein L (PL) is considered a model two-state folder, based on measurements using a wide range of experimental techniques. We applied single-molecule fluorescence resonance energy transfer (FRET) spectroscopy in conjunction with a hidden Markov model analysis to fully characterize the energy landscape of PL and to extract the kinetic properties of individual molecules of the protein. Surprisingly, our studies revealed the existence of a third state, hidden under the two-state behavior of PL due to its small population, ˜7%. We propose that this minority intermediate involves partial unfolding of the two C-terminal β strands of PL. Our work demonstrates that single-molecule FRET spectroscopy can be a powerful tool for a comprehensive description of the folding dynamics of proteins, capable of detecting and characterizing relatively rare metastable states that are difficult to observe in ensemble studies.

Production of acyl-homoserine lactone quorum-sensing signals is widespread in gram-negative Methylobacterium.

PubMed

Poonguzhali, Selvaraj; Madhaiyan, Munusamy; Sa, Tongmin

2007-02-01

Members of Methylobacterium, referred as pink-pigmented facultative methylotrophic bacteria, are frequently associated with terrestrial and aquatic plants, tending to form aggregates on the phyllosphere. We report here that the production of autoinducer molecules involved in the cell-to-cell signaling process, which is known as quorum sensing, is common among Methylobacterium species. Several strains of Methylobacterium were tested for their ability to produce N-acyl-homoserine lactone (AHL) signal molecules using different indicators. Most strains of Methylobacterium tested could elicit a positive response in Agrobacterium tumefaciens harboring lacZ fused to a gene that is regulated by autoinduction. The synthesis of these compounds was cell-density dependent, and the maximal activity was reached during the late exponential to stationary phases. The bacterial extracts were separated by thin-layer chromatography and bioassayed with A. tumefaciens NT1 (traR, tra::lacZ749). They revealed the production of various patterns of the signal molecules, which are strain dependent. At least two signal molecules could be detected in most of the strains tested, and comparison of their relative mobilities suggested that they are homologs of N-octanoyl-DL-homoserine lactone (C8-HSL) and N-decanoyl-DL-homoserine lactone (C10-HSL).

Two Photon Spectroscopy Can Serve as a Marker of Protein Denaturation Pathway.

PubMed

Das, Dipak Kumar; Islam, Sk Imadul; Samanta, Nirnay; Yadav, Yogendra; Goswami, Debabrata; Mitra, Rajib Kumar

2018-06-25

Rhodamine group of molecules are widely used dyes for imaging of biological molecules. Application of these dyes however includes a limitation that these molecules absorb in the visible range of the spectrum, which does not fall in the 'biologically transparent window' (BTW). Two photon absorption (TPA) process could come up with an alternate solution to this as these dyes could be excited in the near infrared (NIR) window to extract similar information. To validate this we have investigated TPA cross section (TPACS, σ 2 ) of two rhodamine dyes, namely Rhodamine 6G (R6G), Rhodamine B (RhB), site selectively bound with a model protein, bovine serum albumin (BSA), by exciting at 800 nm. Two photon spectroscopy and imaging confirms the binding of the dye to the protein. The decreases in TPACS with increasing temperature at a fixed BSA concentration excellently follows the temperature induced structural transition of BSA as the protein transforms from a molten globule to unfolded conformation beyond 60 °C, which has previously been established through circular dichroism (CD) measurements. The thus established resemblance in TPACS and CD measurement trends thus strongly affirms the suitability of TPA process in protein imaging and as an alternative marker to tracking its conformational transformations using NIR radiation.

Changes in type I collagen following laser welding.

PubMed

Bass, L S; Moazami, N; Pocsidio, J; Oz, M C; LoGerfo, P; Treat, M R

1992-01-01

Selection of ideal laser parameters for tissue welding is inhibited by poor understanding of the mechanism. We investigated structural changes in collagen molecules extracted from rat tail tendon (> 90% type I collagen) after tissue welding using an 808 nm diode laser and indocyanine green dye applied to the weld site. Mobility patterns on SDS-PAGE were identical in the lasered and untreated tendon extracts with urea or acetic acid. Pepsin incubation after acetic acid extraction revealed a reduction of collagen alpha and beta bands in lasered compared with untreated specimens. Circular dichroism studies of rat tail tendon showed absence of helical structure in collagen from lasered tendon. No evidence for covalent bonding was present in laser-treated tissues. Collagen molecules are denatured by the laser wavelength and parameters used in this study. No significant amount of helical structure is regenerated on cooling. We conclude that non-covalent interactions between denatured collagen molecules may be responsible for the creation of tissue welding.

In situ analysis of dynamic laminar flow extraction using surface-enhanced Raman spectroscopy

PubMed Central

Wang, Fei; Wang, Hua-Lin; Qiu, Yang; Chang, Yu-Long; Long, Yi-Tao

2015-01-01

In this study, we performed micro-scale dynamic laminar flow extraction and site-specific in situ chloride concentration measurements. Surface-enhanced Raman spectroscopy was utilized to investigate the diffusion process of chloride ions from an oil phase to a water phase under laminar flow. In contrast to common logic, we used SERS intensity gradients of Rhodamine 6G to quantitatively calculate the concentration of chloride ions at specific positions on a microfluidic chip. By varying the fluid flow rates, we achieved different extraction times and therefore different chloride concentrations at specific positions along the microchannel. SERS spectra from the water phase were recorded at these different positions, and the spatial distribution of the SERS signals was used to map the degree of nanoparticle aggregation. The concentration of chloride ions in the channel could therefore be obtained. We conclude that this method can be used to explore the extraction behaviour and efficiency of some ions or molecules that enhance the SERS intensity in water or oil by inducing nanoparticle aggregation. PMID:26687436

Tapping the biotechnological potential of insect microbial symbionts: new insecticidal porphyrins.

PubMed

Martinez, Ana Flávia Canovas; de Almeida, Luís Gustavo; Moraes, Luiz Alberto Beraldo; Cônsoli, Fernando Luís

2017-06-27

The demand for sustainable agricultural practices and the limited progress toward newer and safer chemicals for use in pest control maintain the impetus for research and identification of new natural molecules. Natural molecules are preferable to synthetic organic molecules because they are biodegradable, have low toxicity, are often selective and can be applied at low concentrations. Microbes are one source of natural insecticides, and microbial insect symbionts have attracted attention as a source of new bioactive molecules because these microbes are exposed to various selection pressures in their association with insects. Analytical techniques must be used to isolate and characterize new compounds, and sensitive analytical tools such as mass spectrometry and high-resolution chromatography are required to identify the least-abundant molecules. We used classical fermentation techniques combined with tandem mass spectrometry to prospect for insecticidal substances produced by the ant symbiont Streptomyces caniferus. Crude extracts from this bacterium showed low biological activity (less than 10% mortality) against the larval stage of the fall armyworm Spodoptera frugiperda. Because of the complexity of the crude extract, we used fractionation-guided bioassays to investigate if the low toxicity was related to the relative abundance of the active molecule, leading to the isolation of porphyrins as active molecules. Porphyrins are a class of photoactive molecules with a broad range of bioactivity, including insecticidal. The active fraction, containing a mixture of porphyrins, induced up to 100% larval mortality (LD 50  = 37.7 μg.cm -2 ). Tandem mass-spectrometry analyses provided structural information for two new porphyrin structures. Data on the availability of porphyrins in 67 other crude extracts of ant ectosymbionts were also obtained with ion-monitoring experiments. Insect-associated bacterial symbionts are a rich source of bioactive compounds. Exploring microbial diversity through mass-spectrometry analyses is a useful approach for isolating and identifying new compounds. Our results showed high insecticidal activity of porphyrin compounds. Applications of different experiments in mass spectrometry allowed the characterization of two new porphyrins.

Purification and identification of 4-allylbenzene-1,2-diol: an antilisterial and biofilm preventing compound from the leaves of Piper betle L. var Pachaikodi.

PubMed

Kavitha, Sekar; HariKrishnan, Adhikesavan; Jeevaratnam, Kadirvelu

2017-12-22

Antibiotic-resistant food-borne Listeriosis has been rising with up to 30% mortality threat in humans since several decades. Hence, discovering antilisterial from the extracts of ethnomedicinal plants may be of value as a novel antidote. In our preceding study, we reported that ethanolic extract of Piper betle L. var Pachaikodi leaves exhibited antibacterial activity towards Listeria monocytogenes MTCC 657. Consequently in the present study, the bioactive molecule responsible for anti-Listeria activity was purified and identified as 4-allylbenzene-1,2-diol. This identified bioactive compound may have significance while used as antimicrobials and/or food additives in food processing sector as evidenced by dual action: biofilm inhibition and pore formation on cell membrane.

Interaction of bisphenol A with dissolved organic matter in extractive and adsorptive removal processes.

PubMed

Zhu, Fei-Die; Choo, Kwang-Ho; Chang, Hyun-Shik; Lee, Byunghwan

2012-05-01

The fate of endocrine disrupting chemicals (EDCs) in natural and engineered systems is complicated due to their interactions with various water constituents. This study investigated the interaction of bisphenol A (BPA) with dissolved organic matter (DOM) and colloids present in surface water and secondary effluent as well as its adsorptive removal by powdered activated carbons. The solid phase micro-extraction (SPME) method followed by thermal desorption and gas chromatography-mass spectrometry (GC-MS) was utilized for determining the distribution of BPA molecules in water. The BPA removal by SPME decreased with the increased DOM content, where the formation of BPA-DOM complexes in an aqueous matrix was responsible for the reduced extraction of BPA. Colloidal particles in water samples sorbed BPA leading to the marked reduction of liquid phase BPA. BPA-DOM complexes had a negative impact on the adsorptive removal of BPA by powered activated carbons. The complex formation was characterized based on Fourier transform infrared (FTIR) and ultraviolet-visible (UV-Vis) spectroscopy, along with the calculation of molecular interactions between BPA and functional groups in DOM. It was found that the hydrogen bonding between DOM and BPA would be preferred over aromatic interactions. A pseudo-equilibrium molecular coordination model for the complexation between a BPA molecule and a hydroxyl group of the DOM was developed, which enabled estimation of the maximum sorption site and complex formation constant as well as prediction of organic complexes at various DOM levels. Copyright © 2012 Elsevier Ltd. All rights reserved.

Thermally and vibrationally induced conformational isomerizations, infrared spectra, and photochemistry of gallic acid in low-temperature matrices

NASA Astrophysics Data System (ADS)

Justino, Licínia L. G.; Reva, Igor; Fausto, Rui

2016-07-01

Near-infrared (near-IR) narrowband selective vibrational excitation and annealing of gallic acid (3,4,5-trihydroxybenzoic acid) isolated in cryogenic matrices were used to induce interconversions between its most stable conformers. The isomerizations were probed by infrared spectroscopy. An extensive set of quantum chemical calculations, carried out at the DFT(B3LYP)/6-311++G(d,p) level of approximation, was used to undertake a detailed analysis of the ground state potential energy surface of the molecule. This investigation of the molecule conformational space allowed extracting mechanistic insights into the observed annealing- or near-IR-induced isomerization processes. The infrared spectra of the two most stable conformers of gallic acid in N2, Xe, and Ar matrices were fully assigned. Finally, the UV-induced photochemistry of the matrix isolated compound was investigated.

Electrospray Ionization/Ion Mobility Spectrometer/Cylindrical Ion Trap Mass Spectrometer System for In-Situ Detection of Organic Compounds

NASA Technical Reports Server (NTRS)

Kanik, I.; Johnson, P. V.; Beegle, L. W.; Cooks, R. G.; Laughlin, B. C.; Hill, H. H.

2003-01-01

The potential of an Electrospray Ionization/Ion Mobility Spectrometer/Cylindrical Ion Trap Mass Spectrometer (ESI/IMS/CIT-MS) as an analytical instrument for analyzing material extracted from rock and soil samples as part of a suite of instruments on the proposed 2009 Mars Science Lander (MSL) will be demonstrated. This instrument will be able to identify volatile compounds as well as resident organic molecules on the parts-per-billion (ppb) level. Also, it will be able to obtain an inventory of chemical species on the surface of Mars which will result in a better understanding of ongoing surface chemistry. Finally, questions relevant to biological processes will be answered with the complete inventory of surface and near surface organic molecules that the ESI/IMS/CIT is capable of performing.

Exact solutions for kinetic models of macromolecular dynamics.

PubMed

Chemla, Yann R; Moffitt, Jeffrey R; Bustamante, Carlos

2008-05-15

Dynamic biological processes such as enzyme catalysis, molecular motor translocation, and protein and nucleic acid conformational dynamics are inherently stochastic processes. However, when such processes are studied on a nonsynchronized ensemble, the inherent fluctuations are lost, and only the average rate of the process can be measured. With the recent development of methods of single-molecule manipulation and detection, it is now possible to follow the progress of an individual molecule, measuring not just the average rate but the fluctuations in this rate as well. These fluctuations can provide a great deal of detail about the underlying kinetic cycle that governs the dynamical behavior of the system. However, extracting this information from experiments requires the ability to calculate the general properties of arbitrarily complex theoretical kinetic schemes. We present here a general technique that determines the exact analytical solution for the mean velocity and for measures of the fluctuations. We adopt a formalism based on the master equation and show how the probability density for the position of a molecular motor at a given time can be solved exactly in Fourier-Laplace space. With this analytic solution, we can then calculate the mean velocity and fluctuation-related parameters, such as the randomness parameter (a dimensionless ratio of the diffusion constant and the velocity) and the dwell time distributions, which fully characterize the fluctuations of the system, both commonly used kinetic parameters in single-molecule measurements. Furthermore, we show that this formalism allows calculation of these parameters for a much wider class of general kinetic models than demonstrated with previous methods.

[CONTENT OF OXIDATIVE STRESS MARKERS IN BLOOD PLASMA UNDER THE ACTION OF EXTRACTS OF GRATIOLA OFFICINALIS L., HELICHRYSUM ARENARIUM (L.) MOENCH, AND ANTHOCYANIN FORMS OF ZEA MAYS L].

PubMed

Durnova, N A; Afanas'eva, G A; Kurchatova, M N; Zaraeva, N V; Golikov, A G; Bucharskaya, A B; Golikov, A G; Bucharskaya, A B; Plastun, V O; Andreeva, N V

2015-01-01

The effect of aqueous solutions of dry ethanol extracts of Gratiola officinalis L., Helichrysum arenarium (L.) Moench, and anthocyanin forms of Zea mays L. on the dioxidin-induced lipid peroxidation in blood has been studied on rats. It is established that all these extracts are capable of reducing the amount of avera- ge-mass (AM) molecules and malonic dialdehyde (MDA) in rat blood plasma. The extract of Gratiola officinalis L. reduces the concentration of AM and MDA moleules by 43%. The extract of Helichrysum arenarium (L.) Moench reduces the concentration of AM molecules on the average by 18.66% (within 9.22 -34.81%) and MDA by 49.36% (within 34.12-79.75%). The Extract of anthocyanin forms of Zea mays L. does not reduce the concentration of AM mo- lecules, but reduces the amount of MDA in the blood of rats on average by 27.88% (within 21.58-37.82%) (p < 0.01).

Photon-induced Processing of Interstellar Ices in the Laboratory. Focus on Their Non-thermal Desorption.

NASA Astrophysics Data System (ADS)

Martin-Domenech, Rafael; Munoz Caro, Guillermo; Cruz-Diaz, Gustavo A.; Oberg, Karin I.

2018-06-01

Some of the processes that take place in the interstellar medium (ISM)can be simulated in laboratories on Earth under astrophysically relevant conditions. For example, the energetic processing of the ice mantles that accrete on top of dust grains in the coldest regions of the ISM, leading to the production of new species and their desorption to the gas phase. In particular, observation of complex organic molecules (COMs) in cold interstellar environments stress the need for not only a solid state formation but also for non-thermal desorption mechanisms that can account for the observed abundances in regions where thermal desorption is inhibited. Laboratory Astrophysics can be used to test different non-thermal desorption processes and extract yields than can be extrapolated to the astrophysical scenario with theoretical models. 0th generation COMs like CH3OH and H2CO can be formed at very low temperatures. In this talk, we present laboratory simulations of the UV photoprocessing of a binary ice mixture composed by water (the main component of astrophysical ices) and methane. Formation of CO, CO2, CH3OH and H2CO was confirmed by IR spectroscopy and subsequent TPD. At the same time, photodesorption of CO and H2CO was detected by means of a Quadrupole Mass Spectrometer, with yields on the order of 10-4 and 10-5 molecules per incident photon, respectively. In general, photodesorption can take place through a direct mechanism, where the absorbing molecule (or its photofragments) are desorbed; or through an indirect mechanism where the absorbed energy is transferred to a surface molecule which is the one finally desorbing. In the case of photoproducts, the evolution of the photodesorption yield gives information on the photodesorption mechanism: a constant photodesorption yield is observed when the photoproducts are desorbed right after their formation; while an increasing yield is measured when the photoproducts are desorbed later after energy transfer from another absorbing molecule, allowing to roughly distinguish between different mechanisms.

A Phenotypic Screen in Zebrafish Identifies a Novel Small-Molecule Inducer of Ectopic Tail Formation Suggestive of Alterations in Non-Canonical Wnt/PCP Signaling

PubMed Central

Gebruers, Evelien; Cordero-Maldonado, María Lorena; Gray, Alexander I.; Clements, Carol; Harvey, Alan L.; Edrada-Ebel, Ruangelie; de Witte, Peter A. M.; Crawford, Alexander D.; Esguerra, Camila V.

2013-01-01

Zebrafish have recently emerged as an attractive model for the in vivo bioassay-guided isolation and characterization of pharmacologically active small molecules of natural origin. We carried out a zebrafish-based phenotypic screen of over 3000 plant-derived secondary metabolite extracts with the goal of identifying novel small-molecule modulators of the BMP and Wnt signaling pathways. One of the bioactive plant extracts identified in this screen – Jasminum gilgianum, an Oleaceae species native to Papua New Guinea – induced ectopic tails during zebrafish embryonic development. As ectopic tail formation occurs when BMP or non-canonical Wnt signaling is inhibited during the tail protrusion process, we suspected a constituent of this extract to act as a modulator of these pathways. A bioassay-guided isolation was carried out on the basis of this zebrafish phenotype, identifying para-coumaric acid methyl ester (pCAME) as the active compound. We then performed an in-depth phenotypic analysis of pCAME-treated zebrafish embryos, including a tissue-specific marker analysis of the secondary tails. We found pCAME to synergize with the BMP-inhibitors dorsomorphin and LDN-193189 in inducing ectopic tails, and causing convergence-extension defects in compound-treated embryos. These results indicate that pCAME may interfere with non-canonical Wnt signaling. Inhibition of Jnk, a downstream target of Wnt/PCP signaling (via morpholino antisense knockdown and pharmacological inhibition with the kinase inhibitor SP600125) phenocopied pCAME-treated embryos. However, immunoblotting experiments revealed pCAME to not directly inhibit Jnk-mediated phosphorylation of c-Jun, suggesting additional targets of SP600125, and/or other pathways, as possibly being involved in the ectopic tail formation activity of pCAME. Further investigation of pCAME’s mechanism of action will help determine this compound’s pharmacological utility. PMID:24349481

Tunable Single-Cell Extraction for Molecular Analyses.

PubMed

Guillaume-Gentil, Orane; Grindberg, Rashel V; Kooger, Romain; Dorwling-Carter, Livie; Martinez, Vincent; Ossola, Dario; Pilhofer, Martin; Zambelli, Tomaso; Vorholt, Julia A

2016-07-14

Because of cellular heterogeneity, the analysis of endogenous molecules from single cells is of significant interest and has major implications. While micromanipulation or cell sorting followed by cell lysis is already used for subsequent molecular examinations, approaches to directly extract the content of living cells remain a challenging but promising alternative to achieving non-destructive sampling and cell-context preservation. Here, we demonstrate the quantitative extraction from single cells with spatiotemporal control using fluidic force microscopy. We further present a comprehensive analysis of the soluble molecules withdrawn from the cytoplasm or the nucleus, including the detection of enzyme activities and transcript abundances. This approach has uncovered the ability of cells to withstand extraction of up to several picoliters and opens opportunities to study cellular dynamics and cell-cell communication under physiological conditions at the single-cell level. Copyright © 2016 Elsevier Inc. All rights reserved.

Fused Deposition Modeling Enables the Low-Cost Fabrication of Porous, Customized-Shape Sorbents for Small-Molecule Extraction.

PubMed

Belka, Mariusz; Ulenberg, Szymon; Bączek, Tomasz

2017-04-18

Fused deposition modeling, one of the most common techniques in three-dimensional printing and additive manufacturing, has many practical applications in the fields of chemistry and pharmacy. We demonstrate that a thermoplastic elastomer-poly(vinyl alcohol) (PVA) composite material (LAY-FOMM 60), which presents porous properties after PVA removal, is useful for the extraction of small-molecule drug-like compounds from water samples. The usefulness of the proposed approach is demonstrated by the extraction of glimepiride from a water sample, followed by LC-MS analysis. The recovery was 82.24%, with a relative standard deviation of less than 5%. The proposed approach can change the way of thinking about extraction and sample preparation due to a shift to the use of sorbents with customizable size, shape, and chemical properties that do not rely on commercial suppliers.

Activation of bean (Phaseolus vulgaris) [alpha]-amylase inhibitor requires proteolytic processing of the proprotein

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

Pueyo, J.J.; Hunt, D.C.; Chrispeels, M.J.

Seeds of the common bean (Phaseolus vulgaris) contain a plant defense protein that inhibits the [alpha]-amylases of mammals and insects. This [alpha]-amylase inhibitor ([alpha]Al) is synthesized as a proprotein on the endoplasmic reticulum and is proteolytically processed after arrival in the protein storage vacuoles to polypeptides of relative molecular weight (M[sub r]) 15,000 to 18,000. The authors report two types of evidence that proteolytic processing is linked to activation of the inhibitory activity. First, by surveying seed extracts of wild accessions of P. vulgaris and other species in the genus Phaseolus, they found that antibodies to [alpha]Al recognize large (M[submore » r] 30,000-35,000) polypeptides as well as typical [alpha]Al processing products (M[sub r] 15,000-18,000). [alpha]Al activity was found in all extracts that had the typical [alpha]Al processed polypeptides, but was absent from seed extracts that lacked such polypeptides. Second, they made a mutant [alpha]Al in which asparagine-77 is changed to aspartic acid-77. This mutation slows down the proteolytic processing of pro-[alpha]Al when the gene is expressed in tobacco. When pro-[alpha]Al was separated from mature [alpha]Al by gel filtration, pro-[alpha]Al was found not to have [alpha]-amylase inhibitory activity. The authors interpret these results to mean that formation of the active inhibitor is causally related to proteolytic processing of the proprotein. They suggest that the polypeptide cleavage removes a conformation constraint on the precursor to produce the biochemically active molecule. 43 refs., 5 figs., 1 tab.« less

Encapsulation of fluorescence vegetable extracts within a templated sol-gel matrix

NASA Astrophysics Data System (ADS)

Lacatusu, Ioana; Badea, Nicoleta; Nita, Rodica; Murariu, Alina; Miculescu, Florin; Iosub, Ion; Meghea, Aurelia

2010-04-01

The sol-gel encapsulation of labile substances with specific properties and recognition functions within robust polymer matrices remains a challenging task, despite the considerable research that has been focused on this field. Numerous studies have been reported in the field of sol-gel processes regarding different physical and chemical packing of sensitive biomolecules encapsulated in silica matrix. In this paper the classical sol-gel synthesis has been used under mild conditions in order to minimize denaturizing effects on encapsulated active vegetable extracts from flavones class. The silica templated matrix was obtained by using two types of surfactants with different alkyl chain (didodecyldimethyl-ammonium bromide and trioctadecylmetilammonium bromide) as structure-directing agents for the silicon oxide framework. An organic precursor of silicic acid (triethoxymethylsilane) has been used and it was processed by competitive hydrolysis and polycondensation reactions under controlled directions assured by the presence of oriented template. Silica materials thus obtained are used for encapsulation of two flavonoid samples containing as active principles two sources: rutin and a vegetable extract from Begonia plant. The synthesis of encapsulated nanocompounds has been achieved taking into consideration the specific interaction between the colloidal gel precursors and molecular structures of selected biomolecules. The main objective was to improve the encapsulation conditions for specific biomolecules, searching for the highest stability and functionality without loosing the quality of the flavonoid properties, particularly optical properties like fluorescence. The structural properties of the encapsulated samples have been studied by FT-IR and UV-VIS spectroscopy, thermal analysis and SEM/EDX analysis. The fluorescence experiments showed that, in the case of all four encapsulated samples, the fluorescence spectra manifest a significant increase in intensity signals, with more than 10 times for individual flavonoid and 50 times for Begonia extract. This behaviour are mainly assigned to the physical interaction of flavonoid molecules with the residual hydroxyl groups of silica, excellent synergistic properties of silica and the favourable conformation arrangement of organic molecules inside the silica network. The size distribution of synthesised polymeric silica materials have been investigated by dynamic light scattering (DLS) and optical microscopy.

DG-AMMOS: a new tool to generate 3d conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening.

PubMed

Lagorce, David; Pencheva, Tania; Villoutreix, Bruno O; Miteva, Maria A

2009-11-13

Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods.

Photoionization of NaK molecule with a double-well potential in femtosecond pump probe pulse laser fields

NASA Astrophysics Data System (ADS)

Yu, Jie; Wang, Sen-Ming; Yuan, Kai-Jun; Cong, Shu-Lin

2006-09-01

The method of time-dependent quantum wave packet dynamics is used to calculate the femtosecond pump-probe photoelectron spectra and study the wave packet dynamic processes of the double-minimum potential state 61Σ+ of NaK in intense laser fields. The evolutions of the wave packet and the photoelectron energy spectra with time and internuclear distance are described in detail. The wave packet dynamic information of the 61Σ+ state can be extracted from the photoelectron energy spectra.

Seeking organic compounds on Mars : in situ analysis of organic compounds by Gas Chromatography-Mass Spectrometry on MOMA experiment

NASA Astrophysics Data System (ADS)

Buch, A.; Freissinet, C.; Sternberg, R.; Pinnick, V.; Szopa, C.; Coll, P. J.; Rodier, C.; Garnier, C.; Steininger, H.; Moma Team

2010-12-01

The search for signs of past or present life is one of the primary goals of future Mars exploratory missions. The Mars Organic Molecule Analyzer (MOMA) experiment of the ExoMars mission (set to launch 2016-2018) is a joint venture by the European Space Agency and NASA to develop a sensitive detector for organics on Mars. MOMA will be one of the main analytical instruments aboard the ExoMars Rover aimed at characterizing possible “signs-of-life molecules” in the Martian environment such as amino acids, carboxylic acids, nucleobases or polycyclic aromatic hydrocarbons (PAHs). With the aim to separate and detect organic compounds from Martian soil, the French MOMA team has built a gas chromatograph able to work in standalone mode by using a TCD detector. The gas chromatograph can also be coupled with an ion trap mass spectrometer developed by the US MOMA team. Moreover, a GC-MS compatible sample processing system (SPS) allowing the extraction and the chemical transformation of the organic compounds from the soil, that fits within space flight conditions, has also been developed. The sample processing is performed in an oven, dedicated to the MOMA experiment containing the solid sample (50-100mg). The internal temperature of oven can be ranged from 20 to 1000 °C which allows for pyrolysis, thermochemolysis or derivatization. The organic extraction step is achieved by using thermodesorption in the range of 100 to 300°C for 0.5 to 5 min. Then, the chemical derivatization and/or thermochemolysis of the extracted compounds is performed directly on the soil with a mixture of MTBSTFA-DMF, TMAH or DMF-DMA solution when enantiomeric separation is required. By decreasing the polarity of the target molecules, this step allows for their volatilization at a temperature below 250°C without any chemical degradation. Once derivatized, the volatile target molecules are trapped in a cold chemical trap and promptly desorbed into the gas chromatograph coupled to the mass spectrometer. Preliminary tests, performed on several analogue soils such as Atacama soil, with the MOMA SPS-GC/MS experiment demonstrated the capability to detect organic compounds such as amino and carboxylic acids with sensitivities below the ppm level.

Selective Capture of Glycoproteins Using Lectin-modified Nanoporous Gold Monolith

PubMed Central

Alla, Allan J.; d’Andrea, Felipe B.; Bhattarai, Jay K.; Cooper, Jared A.; Tan, Yih Horng; Demchenko, Alexei V.; Stine, Keith J.

2015-01-01

The surface of nanoporous gold (np-Au) monoliths was modified via a flow method with the lectin Concanavalin A (Con A) to develop a substrate for separation and extraction of glycoproteins. Self-assembled monolayers (SAMs) of lipoic acid (LA) on the np-Au monoliths were prepared followed by activation of the terminal carboxyl groups to create amine reactive esters that were utilized in the immobilization of Con A. Thermogravimetric analysis (TGA) was used to determine the surface coverages of LA and Con A on np-Au monoliths which were found to be 1.31 × 1018 molecules m−2 and 1.85 × 1015 molecules m−2, respectively. An in situ solution depletion method was developed that enabled surface coverage characterization without damaging the substrate and suggesting the possibility of regeneration. Using this method, the surface coverages of LA and Con A were found to be 0.989 ×1018 molecules m−2 and 1.32 × 1015 molecules m−2, respectively. The selectivity of the Con A-modified np-Au monolith for the high mannose-containing glycoprotein ovalbumin (OVA) versus negative control non-glycosylated bovine serum albumin (BSA) was demonstrated by the difference in the ratio of the captured molecules to the immobilized Con A molecules, with OVA:Con A = 2.3 and BSA:Con A = 0.33. Extraction of OVA from a 1:3 mole ratio mixture with BSA was demonstrated by the greater amount of depletion of OVA concentration during the circulation with the developed substrate. A significant amount of captured OVA was eluted using α-methyl mannopyranoside as a competitive ligand. This work is motivated by the need to develop new materials for chromatographic separation and extraction substrates for use in preparative and analytical procedures in glycomics. PMID:26554297

Downstream Processing of Synechocystis for Biofuel Production

NASA Astrophysics Data System (ADS)

Sheng, Jie

Lipids and free fatty acids (FFA) from cyanobacterium Synechocystis can be used for biofuel (e.g. biodiesel or renewable diesel) production. In order to utilize and scale up this technique, downstream processes including culturing and harvest, cell disruption, and extraction were studied. Several solvents/solvent systems were screened for lipid extraction from Synechocystis. Chloroform + methanol-based Folch and Bligh & Dyer methods were proved to be "gold standard" for small-scale analysis due to their highest lipid recoveries that were confirmed by their penetration of the cell membranes, higher polarity, and stronger interaction with hydrogen bonds. Less toxic solvents, such as methanol and MTBE, or direct transesterification of biomass (without preextraction step) gave only slightly lower lipid-extraction yields and can be considered for large-scale application. Sustained exposure to high and low temperature extremes severely lowered the biomass and lipid productivity. Temperature stress also triggered changes of lipid quality such as the degree of unsaturation; thus, it affected the productivities and quality of Synechocystis-derived biofuel. Pulsed electric field (PEF) was evaluated for cell disruption prior to lipid extraction. A treatment intensity > 35 kWh/m3 caused significant damage to the plasma membrane, cell wall, and thylakoid membrane, and it even led to complete disruption of some cells into fragments. Treatment by PEF enhanced the potential for the low-toxicity solvent isopropanol to access lipid molecules during subsequent solvent extraction, leading to lower usage of isopropanol for the same extraction efficiency. Other cell-disruption methods also were tested. Distinct disruption effects to the cell envelope, plasma membrane, and thylakoid membranes were observed that were related to extraction efficiency. Microwave and ultrasound had significant enhancement of lipid extraction. Autoclaving, ultrasound, and French press caused significant release of lipid into the medium, which may increase solvent usage and make medium recycling difficult. Production of excreted FFA by mutant Synechocystis has the potential of reducing the complexity of downstream processing. Major problems, such as FFA precipitation and biodegradation by scavengers, account for FFA loss in operation. Even a low concentration of FFA scavengers could consume FFA at a high rate that outpaced FFA production rate. Potential strategies to overcome FFA loss include high pH, adsorptive resin, and sterilization techniques.

Proteomic and Metabolomic Analyses Reveal Contrasting Anti-Inflammatory Effects of an Extract of Mucor Racemosus Secondary Metabolites Compared to Dexamethasone.

PubMed

Meier, Samuel M; Muqaku, Besnik; Ullmann, Ronald; Bileck, Andrea; Kreutz, Dominique; Mader, Johanna C; Knasmüller, Siegfried; Gerner, Christopher

2015-01-01

Classical drug assays are often confined to single molecules and targeting single pathways. However, it is also desirable to investigate the effects of complex mixtures on complex systems such as living cells including the natural multitude of signalling pathways. Evidence based on herbal medicine has motivated us to investigate potential beneficial health effects of Mucor racemosus (M rac) extracts. Secondary metabolites of M rac were collected using a good-manufacturing process (GMP) approved production line and a validated manufacturing process, in order to obtain a stable product termed SyCircue (National Drug Code USA: 10424-102). Toxicological studies confirmed that this product does not contain mycotoxins and is non-genotoxic. Potential effects on inflammatory processes were investigated by treating stimulated cells with M rac extracts and the effects were compared to the standard anti-inflammatory drug dexamethasone on the levels of the proteome and metabolome. Using 2D-PAGE, slight anti-inflammatory effects were observed in primary white blood mononuclear cells, which were more pronounced in primary human umbilical vein endothelial cells (HUVECs). Proteome profiling based on nLC-MS/MS analysis of tryptic digests revealed inhibitory effects of M rac extracts on pro-inflammatory cytoplasmic mediators and secreted cytokines and chemokines in these endothelial cells. This finding was confirmed using targeted proteomics, here treatment of stimulated cells with M rac extracts down-regulated the secretion of IL-6, IL-8, CXCL5 and GROA significantly. Finally, the modulating effects of M rac on HUVECs were also confirmed on the level of the metabolome. Several metabolites displayed significant concentration changes upon treatment of inflammatory activated HUVECs with the M rac extract, including spermine and lysophosphatidylcholine acyl C18:0 and sphingomyelin C26:1, while the bulk of measured metabolites remained unaffected. Interestingly, the effects of M rac treatment on lipids were orthogonal to the effect of dexamethasone underlining differences in the overall mode of action.

The initial stages of NaCl dissolution: Ion or ion pair solvation?

NASA Astrophysics Data System (ADS)

Klimes, Jiri; Michaelides, Angelos

2009-03-01

The interaction of water with rock salt (NaCl) is important in a wide variety of natural processes and human activities. A lot is known about NaCl dissolution at the macroscopic level but we do not yet have a detailed atomic scale picture of how salt crystals dissolve. Here we report an extensive series of density functional theory, forcefield and molecular dynamics studies of water clusters at flat and defective NaCl surfaces and NaCl clusters. The focus is on answering seemingly elementary questions such as how many water molecules are needed before it becomes favorable to extract an ion or a pair of ions from the crystal or the cluster. It turns out, however, that the answers to these questions are not so straightforward: below a certain number of water molecules (˜ 12) solvation of individual ions is less costly and above this number solvation of ion pairs is favored. These results reveal a hitherto unknown complexity in the NaCl dissolution process born out of a subtle interplay between water-water and water-ion interactions.

A hot water extract of Curcuma longa inhibits adhesion molecule protein expression and monocyte adhesion to TNF-α-stimulated human endothelial cells.

PubMed

Kawasaki, Kengo; Muroyama, Koutarou; Yamamoto, Norio; Murosaki, Shinji

2015-01-01

The recruitment of arterial leukocytes to endothelial cells is an important step in the progression of various inflammatory diseases. Therefore, its modulation is thought to be a prospective target for the prevention or treatment of such diseases. Adhesion molecules on endothelial cells are induced by proinflammatory cytokines, including tumor necrosis factor-α (TNF-α), and contribute to the recruitment of leukocytes. In the present study, we investigated the effect of hot water extract of Curcuma longa (WEC) on the protein expression of adhesion molecules, monocyte adhesion induced by TNF-α in human umbilical vascular endothelial cells (HUVECs). Treatment of HUVECs with WEC significantly suppressed both TNF-α-induced protein expression of adhesion molecules and monocyte adhesion. WEC also suppressed phosphorylation and degradation of nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IκBα) induced by TNF-α in HUVECs, suggesting that WEC inhibits the NF-κB signaling pathway.

Altered expression of junctional adhesion molecule 4 in injured podocytes.

PubMed

Harita, Yutaka; Miyauchi, Naoko; Karasawa, Tamaki; Suzuki, Koichi; Han, Gi Dong; Koike, Hiroko; Igarashi, Takashi; Shimizu, Fujio; Kawachi, Hiroshi

2006-02-01

Recent investigations have revealed the importance of glomerular podocytes with its diaphragm as the major filtration barrier. Junctional adhesion molecule 4 (JAM4) has been identified as a protein that interacts with membrane-associated guanyl kinase inverted (MAGI)-1 and is reported to be expressed on podocytes. To elucidate the role of JAM4 on podocytes, we examined the expression of JAM4 and MAGI-1 in normal and two different proteinuric rat models: puromycin aminonucleoside (PAN) nephropathy and anti-nephrin antibody-induced (ANA) nephropathy, one model with and one without effacement of podocyte foot processes. JAM4 was detected by immunomicroscopy at the apical membrane of normal podocytes. JAM4 immunostaining was focally increased in the podocytes in PAN nephropathy but not in ANA nephropathy. In proteinuric podocytes, the expression of JAM4 was distinct from that of MAGI-1 or other slit diaphragm molecules such as nephrin and ZO-1. Close colocalization of JAM4 and ezrin was maintained in PAN nephropathy. By immunoelectron microscopy, the signals for JAM4 were detected at the free apical membrane of the podocytes with effaced foot processes. Studies with selective detergent extract revealed that the subcellular localization of JAM4 was altered in PAN nephropathy. Thus the altered expression of JAM4 appears to be associated with morphological changes in podocytes and can be a useful marker of injured podocytes. JAM4 may have a different role at the apical membrane besides the role as a junctional molecule and is likely associated with the unique structure of this epithelium.

Carbon molecules in space: from astrochemistry to astrobiology.

PubMed

Ehrenfreund, Pascale; Sephton, Mark A

2006-01-01

How complex carbonaceous molecules in space are, what their abundance is and on what timescales they form are crucial questions within cosmochemistry. Despite the large heterogeneity of galactic and interstellar regions the organic chemistry in the universe seems to follow common pathways. The largest fraction of carbon in the universe is incorporated into aromatic molecules (gaseous polycyclic aromatic hydrocarbon as well as solid macromolecular aromatic structures). Macromolecular carbon constitutes more than half of the interstellar carbon, approximately 80% of the carbon in meteorites, and is likely to be present in comets. Molecules of high astrobiological relevance such as N-heterocycles, amino acids and pre-sugars have all been identified in trace quantities (ppb) in extracts of carbonaceous meteorites. Their presence in inter- and circumstellar regions is either unknown or contentious. In any event such fragile species are easily destroyed by UV radiation, shocks and thermal processing and are unlikely to survive incorporation into Solar System material without some degradation. The more refractory material, in particular macromolecular carbon may retain an interstellar heritage more faithfully. We present laboratory measurements on the photostability of organic compounds and discuss their survival in regions with elevated UV radiation. We also show recent observations of diffuse interstellar bands indicating the presence of fullerenes. We investigate the link between the carbon chemistry in interstellar space and in the Solar System by analyzing the carbonaceous fraction of meteorites and by reviewing stable isotopic data. It also seems evident that both volatile and refractory material from carbonaceous meteoritic has been substantially altered owing to thermal and aqueous processing within the Solar System.

Greater Real-Life Diagnostic Efficacy of Allergen Molecule-Based Diagnosis for Prescription of Immunotherapy in an Area with Multiple Pollen Exposure

PubMed Central

Saltabayeva, Ulbosin; Garib, Victoria; Morenko, Marina; Rosenson, Rafail; Ispayeva, Zhanat; Gatauova, Madina; Zulus, Loreta; Karaulov, Alexander; Gastager, Felix; Valenta, Rudolf

2017-01-01

Background Allergen molecule-based diagnosis has been suggested to facilitate the identification of disease-causing allergen sources and the prescription of allergen-specific immunotherapy (AIT). The aim of the current study was to compare allergen molecule-based IgE serology with allergen extract-based skin testing for the identification of the disease-causing allergen sources. The study was conducted in an area where patients are exposed to pollen from multiple sources (trees, grasses, and weeds) at the same time to compare the diagnostic efficiency of the 2 forms of diagnosis. Methods Patients from Astana, Kazakhstan, who suffered from pollen-induced allergy (n = 95) were subjected to skin prick testing (SPT) with a local panel of tree pollen, grass pollen, and weed pollen allergen extracts and IgE antibodies specific for marker allergen molecules (nArt v 1, nArt v 3, rAmb a 1, rPhl p 1, rPhl p 5, rBet v 1) were measured by ImmunoCAP. Direct and indirect costs for diagnosis based on SPT and marker allergen-based IgE serology as well as direct costs for immunotherapy depending on SPT and serological test results were calculated. Results The costs for SPT-based diagnosis per patient were lower than the costs for allergen molecule-based IgE serology. However, allergen molecule-based serology was more precise in detecting the disease-causing allergen sources. A lower number of immunotherapy treatments (n = 119) was needed according to molecular diagnosis as compared to extract-based diagnosis (n = 275), which considerably reduced the total costs for diagnosis and for a 3-year treatment from EUR 1,112.30 to 521.77 per patient. Conclusions The results from this real-life study show that SPT is less expensive than allergen molecule-based diagnostic testing, but molecular diagnosis allowed more precise prescription of immunotherapy which substantially reduced treatment costs and combined costs for diagnosis and treatment. PMID:28654920

Validation of ethnomedicinal potential of Tinospora cordifolia for anticancer and immunomodulatory activities and quantification of bioactive molecules by HPTLC.

PubMed

Bala, Manju; Pratap, Kunal; Verma, Praveen Kumar; Singh, Bikram; Padwad, Yogendra

2015-12-04

Tinospora cordifolia (Willd.) Miers ex Hook. f. & Thomas. (Menispermaceae) is one of the most widely used plants in various traditional medicinal systems including "Ayurveda". The plant is used for the treatment of jaundice, rheumatism, urinary disorder, skin diseases, diabetes and anemia. The phytoconstituents present in the plant belongs to different class of compounds such as alkaloids, diterpenoids lactones, glycosides, steroids, phenol, aliphatic compounds and polysaccharides. The aim of present study was the isolation, structure elucidation, quantification and pharmacological evaluation of secondary metabolites from T. cordifolia for anticancer and immunomodulatory activities. Different extracts and fractions were prepared from the stem of T. cordifolia. Pure molecules were isolated using normal phase chromatography and characterized on the basis of NMR and mass spectroscopic techniques. The anti-cancer and immunomodulatory activities of different extracts, fractions and isolated compounds were evaluated against four different human cancer cell lines, KB (human oral squamous carcinoma), CHOK-1 (hamster ovary), HT-29 (human colon cancer) and SiHa (human cervical cancer) and murine primary cells respectively. A simple, normal phase HPTLC method was also developed for the quantification of three bioactive compounds i.e N-formylannonain (1), 11-hydroxymustakone (5) and yangambin (8) in the stem of T. cordifolia hosted on fifteen different plants. Chromatographic purification of different fractions led to the isolation of eight pure molecules i.e N-formylannonain (1), magnoflorine (2), jatrorrhizine (3) palmatine (4), 11-hydroxymustakone (5), cordifolioside A (6), tinocordiside (7) and yangambin (8). All extracts and fractions were active against KB and CHOK-1 cells whereas among the pure molecules palmatine (4) was found to be active against KB and HT-29; tinocordiside (7) against KB and CHOK-1; yangambin (8) against KB cells however N-formylannonain (1) and 11-hydroxymustakone (5), was found active for immunomodulatory activity. HPTLC quantification of three active molecules i.e N-formylannonain (1), 11-hydroxymustakone (5), and yangambin (8) were found in highest quantity in the stem of T. cordifolia hosted on Mangifera indica, however, other two active molecules were not quantified due to their insufficient quantity. Eight compounds have been isolated and characterized belonging to different classes. The pharmacological evaluation of extract, fractions and pure molecules revealed the ethnomedicinal value of T. cordifolia for anticancer and immunomodulatory activities. Copyright © 2015. Published by Elsevier Ireland Ltd.

Dye sensitized solar cell (DSSC) with natural dyes extracted from Jatropha leaves and purple Chrysanthemum flowers as sensitizer

NASA Astrophysics Data System (ADS)

Tahir, Dahlang; Satriani, Wilda; Gareso, P. L.; Abdullah, B.

2018-03-01

DSSC (Dye-Sensitized Solar Cell) prototype has been investigated using Jatropha leaves and purple Chrysanthemum flowers as natural dyes. DSSC consists of working electrode and counter electrode. A working electrode composed of semiconductor nanoparticles TiO2 that has been coated with dye molecules. Dye molecules serve as light photon catchers, while semiconductor nanoparticles TiO2 function to absorb and forward photons into electrons. In the electrode counter given catalyst carbon, serves to accelerate the reaction kinetics of triiodide reduction process on transparent conductive oxide (TCO). DSSC using TiO2 as a semiconductor material and natural dyes as sensitizer from Jatropha leaves and purple Chrysanthemum flowers are successful produced. The physical properties of the working electrode have been determined by using XRD and the chemical properties of the TiO2 powder and dye powder using FTIR and dye solution using UV-Vis. The resulted fabrications are also examined its I-V characteristics. The best performance is generated by mixed dye 1.91 x 10-3 % compared than those DSSC for dye extracted from Jatropha leaves or purple Chrysanthemum. The characterization results show that the higher of the absorption wavelength of the DSSC efficiency is high.

Dynamic Mass Transfer of Hemoglobin at the Aqueous/Ionic-Liquid Interface Monitored with Liquid Core Optical Waveguide.

PubMed

Chen, Xuwei; Yang, Xu; Zeng, Wanying; Wang, Jianhua

2015-08-04

Protein transfer from aqueous medium into ionic liquid is an important approach for the isolation of proteins of interest from complex biological samples. We hereby report a solid-cladding/liquid-core/liquid-cladding sandwich optical waveguide system for the purpose of monitoring the dynamic mass-transfer behaviors of hemoglobin (Hb) at the aqueous/ionic liquid interface. The optical waveguide system is fabricated by using a hydrophobic IL (1,3-dibutylimidazolium hexafluorophosphate, BBimPF6) as the core, and protein solution as one of the cladding layer. UV-vis spectra are recorded with a CCD spectrophotometer via optical fibers. The recorded spectra suggest that the mass transfer of Hb molecules between the aqueous and ionic liquid media involve accumulation of Hb on the aqueous/IL interface followed by dynamic extraction/transfer of Hb into the ionic liquid phase. A part of Hb molecules remain at the interface even after the accomplishment of the extraction/transfer process. Further investigations indicate that the mass transfer of Hb from aqueous medium into the ionic liquid phase is mainly driven by the coordination interaction between heme group of Hb and the cationic moiety of ionic liquid, for example, imidazolium cation in this particular case. In addition, hydrophobic interactions also contribute to the transfer of Hb.

Human dermatosparaxis: a form of Ehlers-Danlos syndrome that results from failure to remove the amino-terminal propeptide of type I procollagen.

PubMed Central

Smith, L T; Wertelecki, W; Milstone, L M; Petty, E M; Seashore, M R; Braverman, I M; Jenkins, T G; Byers, P H

1992-01-01

Dermatosparaxis is a recessively inherited connective-tissue disorder that results from lack of the activity of type I procollagen N-proteinase, the enzyme that removes the amino-terminal propeptides from type I procollagen. Initially identified in cattle more than 20 years ago, the disorder was subsequently characterized in sheep, cats, and dogs. Affected animals have fragile skin, lax joints, and often die prematurely because of sepsis following avulsion of portions of skin. We recently identified two children with soft, lax, and fragile skin, which, when examined by transmission electron microscopy, contained the twisted, ribbon-like collagen fibrils characteristic of dermatosparaxis. Skin extracts from one child contained collagen precursors with amino-terminal extensions. Cultured fibroblasts from both children failed to cleave the amino-terminal propeptides from the pro alpha 1(I) and pro alpha 2(I) chains in type I procollagen molecules. Extracts of normal cells cleaved to collagen, the type I procollagen synthesized by cells from both children, demonstrating that the enzyme, not the substrate, was defective. These findings distinguish dermatosparaxis from Ehlers-Danlos syndrome type VII, which results from substrate mutations that prevent proteolytic processing of type I procollagen molecules. Images Figure 5 Figure 2 Figure 3 Figure 1 Figure 4 Figure 6 PMID:1642226

Application of molecular imprinted polymer nanoparticles as a selective solid phase extraction for preconcentration and trace determination of 2,4-dichlorophenoxyacetic acid in the human urine and different water samples.

PubMed

Omidi, Fariborz; Behbahani, Mohammad; Sadeghi Abandansari, Hamid; Sedighi, Alireza; Shahtaheri, Seyed Jamaleddin

2014-01-01

A molecular-imprinted polymer nanoparticles (MIP-NP) for the selective preconcentration of 2,4-dichlorophenoxyacetic acid (2,4-D) is described. It was obtained by precipitation polymerization from methacrylic acid (the functional monomer), ethylene glycol dimethacrylate (the cross-linker), 2,2'-azobisisobutyronitrile (the initiator) and 2,4-D (the template molecule) in acetonitrile solution. The MIP-NPs were characterized by thermogravimetric analysis, and by scanning electron microscopy. Imprinted 2,4-D molecules were removed from the polymeric structure using acetic acid in methanol (15:85 v/v %) as the eluting solvent. The sorption and desorption process occur within 10 min and 15 min, respectively. The maximum sorbent capacity of the molecular imprinted polymer is 89.2 mg g(-1). The relative standard deviation and limit of detection for water samples by introduced selective solid phase extraction were 4.2% and 1.25 μg L(-1), and these data for urine samples were 4.7% and 1.80 μg L(-1), respectively. The method was applied to the determination of 2,4-D in the urine and different water samples.

Method and source for producing a high concentration of positively charged molecular hydrogen or deuterium ions

DOEpatents

Ehlers, Kenneth W.; Leung, Ka-Ngo

1988-01-01

A high concentration of positive molecular ions of hydrogen or deuterium gas is extracted from a positive ion source having a short path length of extracted ions, relative to the mean free path of the gas molecules, to minimize the production of other ion species by collision between the positive ions and gas molecules. The ion source has arrays of permanent magnets to produce a multi-cusp magnetic field in regions remote from the plasma grid and the electron emitters, for largely confining the plasma to the space therebetween. The ion source has a chamber which is short in length, relative to its transverse dimensions, and the electron emitters are at an even shorter distance from the plasma grid, which contains one or more extraction apertures.

A novel chlorophyll solar cell

NASA Astrophysics Data System (ADS)

Ludlow, J. C.

The photosynthetic process is reviewed in order to produce a design for a chlorophyll solar cell. In a leaf, antenna chlorophyll absorbs light energy and conducts it to an energy trap composed of a protein and two chlorophyll molecules, which perform the oxidation-reduction chemistry. The redox potential of the trap changes from 0.4 to -0.6 V, which is sufficient to reduce nearby molecules with redox potentials in that range. The reduction occurs by transfer of an electron, and a chlorophyll solar cell would direct the transferred electron to a current carrier. Chlorophyll antenna and traps are placed on a metallic support immersed in an electron acceptor solution, and resulting electrons from exposure to light are gathered by a metallic current collector. Spinach chlorophyll extracted, purified, and applied in a cell featuring a Pt collector and an octane water emulsion resulted in intensity independent voltages.

Structural and energetic properties of La3+ in water/DMSO mixtures

NASA Astrophysics Data System (ADS)

Montagna, Maria; Spezia, Riccardo; Bodo, Enrico

2017-11-01

By using molecular dynamics based on a custom polarizable force field, we have studied the solvation of La3+ in an equimolar mixture of dimethylsulfoxide (DMSO) with water. An extended structural analysis has been performed to provide a complete picture of the physical properties at the basis of the interaction of La3+ with both solvents. Through our simulations we found that, very likely, the first solvation shell in the mixture is not unlike the one found in pure water or pure DMSO and contains 9 solvent molecules. We have also found that the solvation is preferentially due to DMSO molecules with the water initially present in first shell quickly leaving to the bulk. The dehydration process of the first shell has been analyzed by both plain MD simulations and a constrained dynamics approach; the free energy profiles for the extraction of water from first shell have also been computed.

Spectrophotometric and electrical properties of imperatorin: an organic molecule

NASA Astrophysics Data System (ADS)

Mir, Feroz A.

2015-09-01

Imperatorin (molecular formula = C16H14O4, molecular mass = 270) an organic molecule was isolated from ethyl acetate extract of the root parts of the plant Prangos pabularia. The optical study was carried out by ultraviolet-visible spectroscopy, and this compound showed an indirect allowed transition. The optical band gap ( E g ) was found around 3.75 eV. Photoluminescence shows various good emission bands. The frequency-dependent real part of the complex ac conductivity was found to follow the universal dielectric response: σ ac ( ω) α ω s [where σ ac ( ω) is the frequency-dependent total conductivity, ω is the frequency, and s is the frequency exponent]. From ac conductivity data analysis, correlated barrier hopping charge-transport mechanism is the dominant electrical transport process shown by this compound. The good emission, less absorption, wide band gap and good electrical properties shown by this compound project them as a bright choice for organic electronic devices.

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data.

PubMed

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S; Windus, Theresa L; Dick-Perez, Marilu

2017-03-27

A newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides, important for metal extraction chemistry, are parametrized using ParFit. ParFit is in an open source program available for free on GitHub ( https://github.com/fzahari/ParFit ).

Multiple exciton dissociation in CdSe quantum dots by ultrafast electron transfer to adsorbed methylene blue.

PubMed

Huang, Jier; Huang, Zhuangqun; Yang, Ye; Zhu, Haiming; Lian, Tianquan

2010-04-07

Multiexciton generation in quantum dots (QDs) may provide a new approach for improving the solar-to-electric power conversion efficiency in QD-based solar cells. However, it remains unclear how to extract these excitons before the ultrafast exciton-exciton annihilation process. In this study we investigate multiexciton dissociation dynamics in CdSe QDs adsorbed with methylene blue (MB(+)) molecules by transient absorption spectroscopy. We show that excitons in QDs dissociate by ultrafast electron transfer to MB(+) with an average time constant of approximately 2 ps. The charge separated state is long-lived (>1 ns), and the charge recombination rate increases with the number of dissociated excitons. Up to three MB(+) molecules per QD can be reduced by exciton dissociation. Our result demonstrates that ultrafast interfacial charge separation can effectively compete with exciton-exciton annihilation, providing a viable approach for utilizing short-lived multiple excitons in QDs.

Droplet Microfluidics for Compartmentalized Cell Lysis and Extension of DNA from Single-Cells

NASA Astrophysics Data System (ADS)

Zimny, Philip; Juncker, David; Reisner, Walter

Current single cell DNA analysis methods suffer from (i) bias introduced by the need for molecular amplification and (ii) limited ability to sequence repetitive elements, resulting in (iii) an inability to obtain information regarding long range genomic features. Recent efforts to circumvent these limitations rely on techniques for sensing single molecules of DNA extracted from single-cells. Here we demonstrate a droplet microfluidic approach for encapsulation and biochemical processing of single-cells inside alginate microparticles. In our approach, single-cells are first packaged inside the alginate microparticles followed by cell lysis, DNA purification, and labeling steps performed off-chip inside this microparticle system. The alginate microparticles are then introduced inside a micro/nanofluidic system where the alginate is broken down via a chelating buffer, releasing long DNA molecules which are then extended inside nanofluidic channels for analysis via standard mapping protocols.

Localization-based super-resolution imaging meets high-content screening.

PubMed

Beghin, Anne; Kechkar, Adel; Butler, Corey; Levet, Florian; Cabillic, Marine; Rossier, Olivier; Giannone, Gregory; Galland, Rémi; Choquet, Daniel; Sibarita, Jean-Baptiste

2017-12-01

Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcoming is primarily due to the huge amount of data generated during imaging and the lack of software for automation and dedicated data mining. We describe an automated quantitative single-molecule-based super-resolution methodology that operates in standard multiwell plates and uses analysis based on high-content screening and data-mining software. The workflow is compatible with fixed- and live-cell imaging and allows extraction of quantitative data like fluorophore photophysics, protein clustering or dynamic behavior of biomolecules. We demonstrate that the method is compatible with high-content screening using 3D dSTORM and DNA-PAINT based super-resolution microscopy as well as single-particle tracking.

Thermally and vibrationally induced conformational isomerizations, infrared spectra, and photochemistry of gallic acid in low-temperature matrices

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

Justino, Licínia L. G., E-mail: liciniaj@ci.uc.pt; Reva, Igor; Fausto, Rui

2016-07-07

Near-infrared (near-IR) narrowband selective vibrational excitation and annealing of gallic acid (3,4,5-trihydroxybenzoic acid) isolated in cryogenic matrices were used to induce interconversions between its most stable conformers. The isomerizations were probed by infrared spectroscopy. An extensive set of quantum chemical calculations, carried out at the DFT(B3LYP)/6-311++G(d,p) level of approximation, was used to undertake a detailed analysis of the ground state potential energy surface of the molecule. This investigation of the molecule conformational space allowed extracting mechanistic insights into the observed annealing- or near-IR-induced isomerization processes. The infrared spectra of the two most stable conformers of gallic acid in N{sub 2},more » Xe, and Ar matrices were fully assigned. Finally, the UV-induced photochemistry of the matrix isolated compound was investigated.« less

Dynamic fluctuations in single-molecule biophysics experiments. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

NASA Astrophysics Data System (ADS)

Krapf, Diego

2015-06-01

Single-molecule biophysics includes the study of isolated molecules and that of individual molecules within living cells. In both cases, dynamic fluctuations at the nanoscale play a critical role. Colomb and Sarkar emphasize how different noise sources affect the analysis of single molecule data [1]. Fluctuations in biomolecular systems arise from two very different mechanisms. On one hand thermal fluctuations are a predominant feature in the behavior of individual molecules. On the other hand, non-Gaussian fluctuations can arise from inter- and intramolecular interactions [2], spatial heterogeneities [3], non-Poisson external perturbations [4] and complex non-linear dynamics in general [5,6].

Atomic-scale imaging of the dissolution of NaCl islands by water at low temperature

NASA Astrophysics Data System (ADS)

Peng, Jinbo; Guo, Jing; Ma, Runze; Meng, Xiangzhi; Jiang, Ying

2017-03-01

The dissolution of sodium chloride (NaCl) in water is a frequently encountered process in our daily lives. While the NaCl dissolution process in liquid water has been extensively studied, whether and how the dissolution occurs below the freezing point is still not clear. Using a low-temperature scanning tunneling microscope (STM), here we were able to directly visualize the dissolution of Au-supported NaCl (0 0 1) bilayer islands by water at atomic level. We found that the single water molecule on the STM tip can assist the extraction of single Na+ from the NaCl surface even at 5 K, while leaving the Cl- intact. When covered with a full water monolayer, the NaCl islands started to dissolve from the step edges and also showed evidence of dissolution inside the terraces as the temperature was raised up to 145 K. At 155 K, the water molecules completely desorbed from the surface, which was accompanied with the decomposition and restructuring of the bilayer NaCl islands. Those results suggest that the dissolution of NaCl may occur well below the freezing point at the ice/NaCl interfaces and is mainly driven by the interaction between the water molecules and the Na+, which is in clear contrast with the NaCl dissolution in liquid water.

Extracting microtubule networks from superresolution single-molecule localization microscopy data

PubMed Central

Zhang, Zhen; Nishimura, Yukako; Kanchanawong, Pakorn

2017-01-01

Microtubule filaments form ubiquitous networks that specify spatial organization in cells. However, quantitative analysis of microtubule networks is hampered by their complex architecture, limiting insights into the interplay between their organization and cellular functions. Although superresolution microscopy has greatly facilitated high-resolution imaging of microtubule filaments, extraction of complete filament networks from such data sets is challenging. Here we describe a computational tool for automated retrieval of microtubule filaments from single-molecule-localization–based superresolution microscopy images. We present a user-friendly, graphically interfaced implementation and a quantitative analysis of microtubule network architecture phenotypes in fibroblasts. PMID:27852898

Extraction and preliminary chemical characterization of the venom of the spider wasp Pepsis decorata (Hymenoptera: Pompilidae).

PubMed

Nolasco, Matheus; Biondi, Ilka; Pimenta, Daniel C; Branco, Alexsandro

2018-04-26

Arthropod venoms may be considered important sources of bioactive molecules; however, technical difficulties, such as venom extraction and homogeneity may impair the biochemical identification of new molecules. In this context, we have developed a method to maintain wasps in captivity that allows the collection of the venom, without use of chemical, mechanical or electrical stimuli. The crude venom was analyzed by RP-HPLC-ESIQ-ToF and 20 peptides were identified by de novo peptide sequencing, among them Eumenine-Mastoparan and a Ponericin-G2-simile peptide. Copyright © 2018. Published by Elsevier Ltd.

Radiation Stability of Benzyl Tributyl Ammonium Chloride towards Technetium-99 Extraction - 13016

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

Paviet-Hartmann, Patricia; Horkley, Jared; Campbell, Keri

2013-07-01

A closed nuclear fuel cycle combining new separation technologies along with generation III and generation IV reactors is a promising way to achieve a sustainable energy supply. But it is important to keep in mind that future recycling processes of used nuclear fuel (UNF) must minimize wastes, improve partitioning processes, and integrate waste considerations into processes. New separation processes are being developed worldwide to complement the actual industrialized PUREX process which selectively separates U(VI) and Pu(IV) from the raffinate. As an example, the UREX process has been developed in the United States to co-extract hexavalent uranium (U) and hepta-valent technetiummore » (Tc) by tri-n-butyl phosphate (TBP). Tc-99 is recognized to be one of the most abundant, long-lived radio-toxic isotopes in UNF (half-life, t{sub 1/2} = 2.13 x 10{sup 5} years), and as such, is targeted in UNF separation strategies for isolation and encapsulation in solid waste-forms for final disposal in a nuclear waste repository. Immobilization of Tc-99 by a durable solid waste-form is a challenge, and its fate in new advanced technology processes is of importance. It is essential to be able to quantify and locate 1) its occurrence in any new developed flowsheets, 2) its chemical form in the individual phases of a process, 3) its potential quantitative transfer in any waste streams, and consequently, 4) its quantitative separation for either potential transmutation to Ru-100 or isolation and encapsulation in solid waste-forms for ultimate disposal. In addition, as a result of an U(VI)-Tc(VII) co-extraction in a UREX-based process, Tc(VII) could be found in low level waste (LLW) streams. There is a need for the development of new extraction systems that would selectively extract Tc-99 from LLW streams and concentrate it for feed into high level waste (HLW) for either Tc-99 immobilization in metallic waste-forms (Tc-Zr alloys), and/or borosilicate-based waste glass. Studies have been launched to investigate the suitability of new macro-compounds such as crown-ethers, aza-crown ethers, quaternary ammonium salts, and resorcin-arenes for the selective extraction of Tc-99 from nitric acid solutions. The selectivity of the ligand is important in evaluating potential separation processes and also the radiation stability of the molecule is essential for minimization of waste and radiolysis products. In this paper, we are reporting the extraction of TcO{sub 4}{sup -} by benzyl tributyl ammonium chloride (BTBA). Experimental efforts were focused on determining the best extraction conditions by varying the ligand's matrix conditions and concentration, as well as varying the organic phase composition (i.e. diluent variation). Furthermore, the ligand has been investigated for radiation stability. The ?-irradiation was performed on the neat organic phases containing the ligand at different absorbed doses to a maximum of 200 kGy using an external Co-60 source. Post-irradiation solvent extraction measurements will be discussed. (authors)« less

A theoretical study in extracting the essential features and dynamics of molecular motions: Intrinsic geometry methods for PF(5) pseudorotations and statistical methods for argon clusters

NASA Astrophysics Data System (ADS)

Panahi, Nima S.

We studied the problem of understanding and computing the essential features and dynamics of molecular motions through the development of two theories for two different systems. First, we studied the process of the Berry Pseudorotation of PF5 and the rotations it induces in the molecule through its natural and intrinsic geometric nature by setting it in the language of fiber bundles and graph theory. With these tools, we successfully extracted the essentials of the process' loops and induced rotations. The infinite number of pseudorotation loops were broken down into a small set of essential loops called "super loops", with their intrinsic properties and link to the physical movements of the molecule extensively studied. In addition, only the three "self-edge loops" generated any induced rotations, and then only a finite number of classes of them. Second, we studied applying the statistical methods of Principal Components Analysis (PCA) and Principal Coordinate Analysis (PCO) to capture only the most important changes in Argon clusters so as to reduce computational costs and graph the potential energy surface (PES) in three dimensions respectively. Both methods proved successful, but PCA was only partially successful since one will only see advantages for PES database systems much larger than those both currently being studied and those that can be computationally studied in the next few decades to come. In addition, PCA is only needed for the very rare case of a PES database that does not already include Hessian eigenvalues.

Denitration of 2,4,6-trinitrotoluene in aqueous solutions using small-molecular-weight catalyst(s) secreted by Pseudomonas aeruginosa ESA-5.

PubMed

Stenuit, Ben; Eyers, Laurent; Rozenberg, Raoul; Habib-Jiwan, Jean-Louis; Matthijs, Sandra; Cornelis, Pierre; Agathos, Spiros N

2009-03-15

The denitration of 2,4,6-trinitrotoluene (TNT) can produce mono- or dinitro aromatic compounds susceptible to microbial mineralization. In the present study, denitration of TNT and other nitro aromatic compounds was investigated with a solid-phase extract obtained from the culture supernatant of Pseudomonas aeruginosa ESA-5 grown on a chemically defined aerobic medium. When the C18 solid-phase extract containing extracellular catalysts (EC) was incubated with TNT and NAD(P)H, we observed a significant release of nitrite. The concentration of nitrite released in the reaction medium was strongly dependent on the concentration of NAD(P)H and EC. Denitration also occurred with two TNT-related molecules, 2,4,6-trinitrobenzaldehyde, and 2,4,6-trinitrobenzyl alcohol. The release of nitrite was coupled with the formation of two polar metabolites, and mass spectrometry analyses indicated that each of these compounds had lost two nitro groups from the trinitro aromatic parent molecule. During this process, the production of toxic reduced TNT metabolites was minimal. The incubation of EC with TNT, NAD(P)H, and specific scavengers of reactive oxygen species suggested the involvement of superoxide radicals (O2*-) and hydrogen peroxide in the denitration process. Results obtained in this study reveal for the first time that extracellular small-molecular-weight substance(s) of bacterial origin can serve as green catalyst(s) to initiate TNT denitration. In addition, this study gives clear evidence for the production of a TNT metabolite bearing a single nitro groupfollowing a denitration reaction with catalyst(s) of biotic origin.

Above-threshold ionization in multicenter molecules: The role of the initial state

NASA Astrophysics Data System (ADS)

Suárez, Noslen; Chacón, Alexis; Pisanty, Emilio; Ortmann, Lisa; Landsman, Alexandra S.; Picón, Antonio; Biegert, Jens; Lewenstein, Maciej; Ciappina, Marcelo F.

2018-03-01

A possible route to extract electronic and nuclear dynamics from molecular targets with attosecond temporal and nanometer spatial resolution is to employ recolliding electrons as "probes." The recollision process in molecules is, however, very challenging to treat using ab initio approaches. Even for the simplest diatomic systems, such as H2, today's computational capabilities are not enough to give a complete description of the electron and nuclear dynamics initiated by a strong laser field. As a consequence, approximate qualitative descriptions are called to play an important role. In this paper we extend the work presented in Suárez et al. [N. Suárez, A. Chacón, J. A. Pérez-Hernández, J. Biegert, M. Lewenstein, and M. F. Ciappina, High-order-harmonic generation in atomic and molecular systems, Phys. Rev. A 95, 033415 (2017), 10.1103/PhysRevA.95.033415] to three-center molecular targets. Additionally, we incorporate a more accurate description of the molecular ground state, employing information extracted from quantum chemistry software packages. This step forward allows us to include, in a detailed way, both the molecular symmetries and nodes present in the high-occupied molecular orbital. We are able, on the one hand, to keep our formulation as analytical as in the case of diatomics and, on the other hand, to still give a complete description of the underlying physics behind the above-threshold ionization process. The application of our approach to complex multicenter—with more than three centers—targets appears to be straightforward.

DEMONSTRATION BULLETIN: ENVIROGARD™ PCB TEST KIT - MILLIPORE, INC.

EPA Science Inventory

The EnviroGard™ polychlorinated biphenyl (PCB) immunoassay test kit rapidly analyzes for PCB concentrations in soils. Soil sample extracts are added to test tubes coated with antibodies that bind PCB molecules. The excess soil extracts are washed out of the tubes after incubat...

Phytochemical Screening and Acute Toxicity of Aqueous Extract of Leaves of Conocarpus erectus Linnaeus in Swiss Albino Mice.

PubMed

Nascimento, Dayane K D; Souza, Ivone A DE; Oliveira, Antônio F M DE; Barbosa, Mariana O; Santana, Marllon A N; Pereira, Daniel F; Lira, Eduardo C; Vieira, Jeymesson R C

2016-09-01

Mangroves represent areas of high biological productivity and it is a region rich in bioactive substances used in medicine production. Conocarpus erectus (Combretaceae) known as button mangrove is one of the species found in mangroves and it is used in folk medicine in the treatment of anemia, catarrh, conjunctivitis, diabetes, diarrhea, fever, gonorrhea, headache, hemorrhage, orchitis, rash, bumps and syphilis. The present study aimed to investigate the acute toxicity of aqueous extract of leaves of C. erectus in Swiss albino mice. The plant material was collected in Vila Velha mangroves, located in Itamaracá (PE). The material was subjected to a phytochemical screening where extractive protocols to identify majority molecules present in leaves were used. The evaluation of acute toxicity of aqueous extract of C. erectus followed the model of Acute Toxicity Class based on OECD 423 Guideline, 2001. The majority molecules were identified: flavonoids, tannins and saponins. The LD50 was estimated at 2,000 mg/kg bw. Therefore, the aqueous extract showed low acute toxicity classified in category 5.

Fourier transform infrared and Raman spectroscopic study of the effect of the thermal treatment and extraction methods on the characteristics of ayocote bean starches.

PubMed

Bernardino-Nicanor, Aurea; Acosta-García, Gerardo; Güemes-Vera, Norma; Montañez-Soto, José Luis; de Los Ángeles Vivar-Vera, María; González-Cruz, Leopoldo

2017-03-01

Starches isolated from four ayocote bean varieties were modified by thermal treatment to determinate the effect of the treatment on the structural changes of ayocote bean starch. Scanning electron microscopy indicates that the starch granules have oval and round shapes, with heterogeneous sizes and fractures when the extraction method is used. The presence of new bands at 2850 and 1560 cm -1 in the FT-IR spectra showed that the thermal treatment of ayocote beans induced an interaction between the protein or lipid and the amylose or amylopectin, while the sharpest band at 3400 cm -1 indicated a dehydration process in the starch granule in addition to the presence of the band at 1260 cm -1 , indicating the product of the retrogradation process. The thermal treatment reduced the crystallinity as well as short-range order. Raman spectroscopy revealed that acute changes occurred in the polysaccharide bonds after thermal treatment. This study showed that the thermal treatment affected the structural properties of ayocote bean starches, the interactions of the lipids and proteins with starch molecules and the retrogradation process of starch.

Propolis Modulates Fibronectin Expression in the Matrix of Thermal Injury

PubMed Central

Komosinska-Vassev, Katarzyna; Wisowski, Grzegorz; Mencner, Lukasz; Stojko, Jerzy; Kozma, Ewa M.

2014-01-01

The aim of the study was to assess the propolis effect on fibronectin metabolism in the course of burn wounds healing process. A model of burn wound healing of pig skin was applied. The amount of the released glycoprotein was assessed by a surface plasmon resonance. The profile of extracted fibronectin components was also assessed by an electrophoresis in polyacrylamide gel, with a subsequent immunodetection by Western Blotting. Propolis burn treatment decreased the release of fibronectin components from healing wounds in relation to damages treated with silver sulfadiazine. The main reason of decreased extraction of fibronectin components from wounds treated with propolis was a substantial decrease of degradation product release of the mentioned glycoprotein, which was observed particularly from the 3rd to 5th day of the repair. Wounds treatment with propolis demonstrated, especially in relation to damages treated with silver sulfadiazine, the decreased release of synthesized fibronectin molecules. The obtained results suggest that propolis modifies fibronectin metabolism in the course of wound healing process. The influence of propolis is reflected in prevention of fibronectin biosynthesis as well as its degradation in the wound area. The above-mentioned metabolic changes may decrease the risk of complications in the repair wounds process. PMID:24738072

Periplasmic expression of human interferon-alpha 2c in Escherichia coli results in a correctly folded molecule.

PubMed Central

Voss, T; Falkner, E; Ahorn, H; Krystek, E; Maurer-Fogy, I; Bodo, G; Hauptmann, R

1994-01-01

Human interferon-alpha 2c (IFN-alpha 2c) was produced in Escherichia coli under the control of the alkaline phosphatase promoter using a periplasmic expression system. Compared with other leader sequences, the heat-stable enterotoxin II leader of E. coli (STII) resulted in the highest rate of correct processing as judged by Western-blot analysis. The fermentation was designed as a batch-fed process in order to obtain a high yield of biomass. The processing rate of IFN-alpha 2c could be increased from 25% to more than 50% by shifting the fermentation pH from 7.0 to 6.7. IFN-alpha 2c extracted from the periplasm was purified by a new four-step chromatographic procedure. Whereas cytoplasmically produced IFN-alpha 2c does not have its full native structure, IFN-alpha 2c extracted from the periplasm was found to be correctly folded, as shown by c.d. spectroscopy. Peptide-map analysis in combination with m.s. revealed the correct formation of disulphide bridges. N-terminal sequence analysis showed complete removal of the leader sequence, creating the authentic N-terminus starting with cysteine. Images Figure 3 Figure 4 Figure 6 PMID:8141788

Extraction of anionic dye from aqueous solutions by emulsion liquid membrane.

PubMed

Dâas, Attef; Hamdaoui, Oualid

2010-06-15

In this work, the extraction of Congo red (CR), an anionic disazo direct dye, from aqueous solutions by emulsion liquid membrane (ELM) was investigated. The important operational parameters governing emulsion stability and extraction behavior of dye were studied. The extraction of CR was influenced by a number of variables such as surfactant concentration, stirring speed, acid concentration in the feed solution and volume ratios of internal phase to organic phase and of emulsion to feed solution. Under most favorable conditions, practically all the CR molecules present in the feed phase were extracted even in the presence of salt (NaCl). At the optimum experimental conditions, total removal of antharaquinonic dye Acid Blue 25 was attained after only 10 min. Influence of sodium carbonate concentration as internal receiving phase on the stripping efficiency of CR was examined. The best sodium carbonate concentration in the internal phase that conducted to excellent stripping efficiency (>99%) and emulsion stability was 0.1N. The membrane recovery was total and the permeation of CR was not decreased up to seven runs. ELM process is a promising alternative to conventional methods and should increase awareness of the potential for recovery of anionic dyes. Copyright 2010 Elsevier B.V. All rights reserved.

Single Fluorescent Molecules as Nano-Illuminators for Biological Structure and Function

NASA Astrophysics Data System (ADS)

Moerner, W. E.

2011-03-01

Since the first optical detection and spectroscopy of a single molecule in a solid (Phys. Rev. Lett. {62}, 2535 (1989)), much has been learned about the ability of single molecules to probe local nanoenvironments and individual behavior in biological and nonbiological materials in the absence of ensemble averaging that can obscure heterogeneity. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic imaging of individual fluorophores leads naturally to superlocalization, or determination of the position of the molecule with precision beyond the optical diffraction limit, simply by digitization of the point-spread function from the single emitter. For example, the shape of single filaments in a living cell can be extracted simply by allowing a single molecule to move through the filament (PNAS {103}, 10929 (2006)). The addition of photoinduced control of single-molecule emission allows imaging beyond the diffraction limit (super-resolution) and a new array of acronyms (PALM, STORM, F-PALM etc.) and advances have appeared. We have used the native blinking and switching of a common yellow-emitting variant of green fluorescent protein (EYFP) reported more than a decade ago (Nature {388}, 355 (1997)) to achieve sub-40 nm super-resolution imaging of several protein structures in the bacterium Caulobacter crescentus: the quasi-helix of the actin-like protein MreB (Nat. Meth. {5}, 947 (2008)), the cellular distribution of the DNA binding protein HU (submitted), and the recently discovered division spindle composed of ParA filaments (Nat. Cell Biol. {12}, 791 (2010)). Even with these advances, better emitters would provide more photons and improved resolution, and a new photoactivatable small-molecule emitter has recently been synthesized and targeted to specific structures in living cells to provide super-resolution images (JACS {132}, 15099 (2010)). Finally, a new optical method for extracting three-dimensional position information based on a double-helix point spread function enables quantitative tracking of single mRNA particles in living yeast cells with 15 ms time resolution and 25-50 nm spatial precision (PNAS {107}, 17864 (2010)). These examples illustrate the power of single-molecule optical imaging in extracting new structural and functional information in living cells.

Continuous-flow liquid microjunction surface sampling probe connected on-line with high-performance liquid chromatography/mass spectrometry for spatially resolved analysis of small molecules and proteins.

PubMed

Van Berkel, Gary J; Kertesz, Vilmos

2013-06-30

A continuous-flow liquid microjunction surface sampling probe extracts soluble material from surfaces for direct ionization and detection by mass spectrometry. Demonstrated here is the on-line coupling of such a probe with high-performance liquid chromatography/mass spectrometry (HPLC/MS) enabling extraction, separation and detection of small molecules and proteins from surfaces in a spatially resolved (~0.5 mm diameter spots) manner. A continuous-flow liquid microjunction surface sampling probe was connected to a six-port, two-position valve for extract collection and injection to an HPLC column. A QTRAP® 5500 hybrid triple quadrupole linear ion trap equipped with a Turbo V™ ion source operated in positive electrospray ionization (ESI) mode was used for all experiments. The system operation was tested with the extraction, separation and detection of propranolol and associated metabolites from drug dosed tissues, caffeine from a coffee bean, cocaine from paper currency, and proteins from dried sheep blood spots on paper. Confirmed in the tissue were the parent drug and two different hydroxypropranolol glucuronides. The mass spectrometric response for these compounds from different locations in the liver showed an increase with increasing extraction time (5, 20 and 40 s). For on-line separation and detection/identification of extracted proteins from dried sheep blood spots, two major protein peaks dominated the chromatogram and could be correlated with the expected masses for the hemoglobin α and β chains. Spatially resolved sampling, separation, and detection of small molecules and proteins from surfaces can be accomplished using a continuous-flow liquid microjunction surface sampling probe coupled on-line with HPLC/MS detection. Published in 2013. This article is a U.S. Government work and is in the public domain in the USA.

Further Highlighting on the Prevention of Oxidative Damage by Polyphenol-Rich Wine Extracts.

PubMed

Salucci, Sara; Burattini, Sabrina; Giordano, Francesco Maria; Lucarini, Simone; Diamantini, Giuseppe; Falcieri, Elisabetta

2017-04-01

Wine contains various polyphenols such as flavonoids, anthocyanins, and tannins. These molecules are responsible for the quality of wines, influencing their astringency, bitterness, and color and they are considered to have antioxidant activity. Polyphenols, extracted from grapes during the processes of vinification, could protect the body cells against reactive oxygen species level increase and could be useful to rescue several pathologies where oxidative stress represents the main cause. For that, in this study, red and white wine, provided by an Italian vinery (Marche region), have been analyzed. Chromatographic and morphofunctional analyses have been carried out for polyphenol extraction and to evaluate their protective effect on human myeloid U937 cells exposed to hydrogen peroxide. Both types of wines contained a mix of phenolic compounds with antioxidant properties and their content decreased, as expected, in white wine. Ultrastructural observations evidenced that wines, in particular red wine, strongly prevent mitochondrial damage and apoptotic cell death. In conclusion, the considered extracts show a relevant polyphenol content with strong antioxidant properties and abilities to prevent apoptosis. These findings suggest, for these compounds, a potential role in all pathological conditions where the body antioxidant system is overwhelmed.

Acrylamide analysis in food by liquid chromatographic and gas chromatographic methods.

PubMed

Elbashir, Abdalla A; Omar, Mei M Ali; Ibrahim, Wan Aini Wan; Schmitz, Oliver J; Aboul-Enein, Hassan Y

2014-01-01

Acrylamide (AA) is a compound classified as carcinogenic to humans by the International Agency for Research on Cancer. It was first discovered to be present in certain heated processed food by the Swedish National Food Administration (SNFA) and University of Stockholm in early 2002. The major pathway for AA formation in food is the Maillard reaction between reducing sugar and the amino acid asparagine at high temperature. Since the discovery of AA's presence in food, many analytical methods have been developed for determination of AA contents in different food matrices. Also, several studies have been conducted to develop extraction procedures for AA from difficult food matrices. AA is a small, highly polar molecule, which makes its extraction and analysis challenging. Many articles and reviews have been published dealing with AA in food. The aim of the review is to discuss AA formation in food, the factors affecting AA formation and removal, AA exposure assessment, AA extraction and cleanup from food samples, and analytical methods used in AA determination, such as high-performance liquid chromatography (HPLC) and gas chromatography (GC). Special attention is given to sample extraction and cleanup procedures and analytical techniques used for AA determination.

Identification of chemogenomic features from drug–target interaction networks using interpretable classifiers

PubMed Central

Tabei, Yasuo; Pauwels, Edouard; Stoven, Véronique; Takemoto, Kazuhiro; Yamanishi, Yoshihiro

2012-01-01

Motivation: Drug effects are mainly caused by the interactions between drug molecules and their target proteins including primary targets and off-targets. Identification of the molecular mechanisms behind overall drug–target interactions is crucial in the drug design process. Results: We develop a classifier-based approach to identify chemogenomic features (the underlying associations between drug chemical substructures and protein domains) that are involved in drug–target interaction networks. We propose a novel algorithm for extracting informative chemogenomic features by using L1 regularized classifiers over the tensor product space of possible drug–target pairs. It is shown that the proposed method can extract a very limited number of chemogenomic features without loosing the performance of predicting drug–target interactions and the extracted features are biologically meaningful. The extracted substructure–domain association network enables us to suggest ligand chemical fragments specific for each protein domain and ligand core substructures important for a wide range of protein families. Availability: Softwares are available at the supplemental website. Contact: yamanishi@bioreg.kyushu-u.ac.jp Supplementary Information: Datasets and all results are available at http://cbio.ensmp.fr/~yyamanishi/l1binary/ . PMID:22962471

Magnetic cooling at a single molecule level: a spectroscopic investigation of isolated molecules on a surface.

PubMed

Corradini, Valdis; Ghirri, Alberto; Candini, Andrea; Biagi, Roberto; del Pennino, Umberto; Dotti, Gianluca; Otero, Edwige; Choueikani, Fadi; Blagg, Robin J; McInnes, Eric J L; Affronte, Marco

2013-05-28

A sub-monolayer distribution of isolated molecular Fe14 (bta)6 nanomagnets is deposited intact on a Au(111) surface and investigated by X-ray magnetic circular dichroism spectroscopy. The entropy variation with respect to the applied magnetic field is extracted from the magnetization curves and evidences high magnetocaloric values at the single molecule level. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A scanning tunneling microscope break junction method with continuous bias modulation.

PubMed

Beall, Edward; Yin, Xing; Waldeck, David H; Wierzbinski, Emil

2015-09-28

Single molecule conductance measurements on 1,8-octanedithiol were performed using the scanning tunneling microscope break junction method with an externally controlled modulation of the bias voltage. Application of an AC voltage is shown to improve the signal to noise ratio of low current (low conductance) measurements as compared to the DC bias method. The experimental results show that the current response of the molecule(s) trapped in the junction and the solvent media to the bias modulation can be qualitatively different. A model RC circuit which accommodates both the molecule and the solvent is proposed to analyze the data and extract a conductance for the molecule.

Beyond experimental noise: Analyzing single-molecule data of heterogeneous systems. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

NASA Astrophysics Data System (ADS)

Meroz, Yasmine

2015-06-01

In the 1980s the world witnessed the advent of single-molecule experiments. The first atomic resolution characterization of a surface was reported by scanning tunneling microscope (STM) in 1982 [1], followed by atomic force microscope (AFM) in 1986 [2]. The first optical detection and spectroscopy of a single molecule in a solid took place in 1989 [3,4], in a time where essentially all chemical experiments were made on bulk, i.e. averaging over millions of copies of the same molecule.

In Vitro Evaluation of the Antioxidant Activity and Wound Healing Properties of Jaboticaba (Plinia peruviana) Fruit Peel Hydroalcoholic Extract.

PubMed

Pitz, Heloisa da S; Pereira, Aline; Blasius, Mayara B; Voytena, Ana Paula L; Affonso, Regina C L; Fanan, Simone; Trevisan, Adriana C D; Ribeiro-do-Valle, Rosa M; Maraschin, Marcelo

2016-01-01

Jaboticaba is a fruit from a native tree to Brazil, Plinia peruviana. Jaboticaba peels are an important source of antioxidant molecules such as phenolic compounds. This study aimed to evaluate in vitro the activity of a hydroalcoholic extract of jaboticaba fruit peels (HEJFP) in wound healing processes and antioxidant activity in murine fibroblasts (L929 cell line). HEJFP concentrations (0.5, 1, 5, 10, 25, 50, 100, and 200 µg/mL) were tested in MTT assay and cell proliferation was verified at 100 µg/mL after 24 h and at 25, 50, and 100 µg/mL after 48 h of extract exposure. Evaluation of antioxidant activity was performed at 0.5, 5, 25, 50, and 100 µg/mL HEJFP concentrations. Cell treatment with HEJFP at 25, 50, and 100 µg/mL for 24 h followed by H2O2 exposure for 3 h showed a strong cytoprotective effect. In vitro scratch wound healing assay indicated that none of tested HEJFP concentrations (0.5, 5, 25, 50, and 100 µg/mL) were capable of increasing migration rate after 12 h of incubation. These results demonstrate a positive effect of HEJFP on the wound healing process on L929 fibroblasts cell line, probably due to the antioxidant activity exhibited by phytochemicals in the extract.

Beneficial Effect of Jojoba Seed Extracts on Hyperglycemia-Induced Oxidative Stress in RINm5f Beta Cells.

PubMed

Belhadj, Sahla; Hentati, Olfa; Hamdaoui, Ghaith; Fakhreddine, Khaskhoussi; Maillard, Elisa; Dal, Stéphanie; Sigrist, Séverine

2018-03-20

Hyperglycemia occurs during diabetes and insulin resistance. It causes oxidative stress by increasing reactive oxygen species (ROS) levels, leading to cellular damage. Polyphenols play a central role in defense against oxidative stress. In our study, we investigated the antioxidant properties of simmondsin, a pure molecule present in jojoba seeds, and of the aqueous extract of jojoba seeds on fructose-induced oxidative stress in RINm5f beta cells. The exposure of RINm5f beta cells to fructose triggered the loss of cell viability (-48%, p < 0.001) and disruption of insulin secretion ( p < 0.001) associated with of reactive oxygen species (ROS) production and a modulation of pro-oxidant and antioxidant signaling pathway. Cell pre-treatments with extracts considerably increased cell viability (+86% p < 0.001) for simmondsin and +74% ( p < 0.001) for aqueous extract and insulin secretion. The extracts also markedly decreased ROS (-69% ( p < 0.001) for simmondsin and -59% ( p < 0.001) for aqueous extract) and caspase-3 activation and improved antioxidant defense, inhibiting p22phox and increasing nuclear factor (erythroid-derived 2)-like 2 (Nrf2) levels (+70%, p < 0.001) for aqueous extract. Simmondsin had no impact on Nrf2 levels. The richness and diversity of molecules present in jojoba seed extract makes jojoba a powerful agent to prevent the destruction of RINm5f beta cells induced by hyperglycemia.

RECOVERY OF METAL VALUES FROM AQUEOUS SOLUTIONS BY SOLVENT EXTRACTION

DOEpatents

Moore, R.L.

1959-09-01

An organic solvent mixure is described for extracting actinides from aqueous solutions; the solvent mixture consists of from 10 to 25% by volume of tributyl phosphate and the remainder a chlorine-fluorine-substituted saturated hydrocarbon having two carbon atoms in the molecule.

Solid-phase extraction sorbent consisting of alkyltrimethylammonium surfactants immobilized onto strong cation-exchange polystyrene resin.

PubMed

Reid, Kendra R; Kennedy, Lonnie J; Crick, Eric W; Conte, Eric D

2002-10-25

Presented is a solid-phase extraction sorbent material composed of cationic alkyltrimethylammonium surfactants attached to a strong cation-exchange resin via ion-exchange. The original hydrophilic cation-exchange resin is made hydrophobic by covering the surface with alkyl chains from the hydrophobic portion of the surfactant. The sorbent material now has a better ability to extract hydrophobic molecules from aqueous samples. The entire stationary phase (alkyltrimethylammonium surfactant) is removed along with the analyte during the elution step. The elution step requires a mild elution solvent consisting of 0.25 M Mg2+ in a 50% 2-propanol solution. The main advantage of using a removable stationary phase is that traditionally utilized toxic elution solvents such as methylene chloride, which are necessary to efficiently release strongly hydrophobic species from SPE stationary phases, may now be avoided. Also, the final extract is directly compatible with reversed-phase liquid chromatography. The performance of this procedure is presented using pyrene as a test molecule.

Inhibitory effect of indigo naturalis on tumor necrosis factor-α-induced vascular cell adhesion molecule-1 expression in human umbilical vein endothelial cells.

PubMed

Chang, Hsin-Ning; Pang, Jong-Hwei Su; Yang, Sien-Hung; Hung, Chi-Feng; Chiang, Chi-Hsin; Lin, Tung-Yi; Lin, Yin-Ku

2010-09-14

The use of indigo naturalis to treat psoriasis has proved effective in our previous clinical studies. The present study was designed to examine the anti-inflammatory effect of indigo naturalis in primary cultured human umbilical vein endothelial cells (HUVECs). Pretreatment of cells with indigo naturalis extract attenuated TNF-α-induced increase in Jurkat T cell adhesion to HUVECs as well as decreased the protein and messenger (m)RNA expression levels of vascular cell adhesion molecule-1 (VCAM-1) on HUVECs. Indigo naturalis extract also inhibited the protein expression of activator protein-1 (AP-1)/c-Jun, a critical transcription factor for the activation of VCAM-1 gene expression. Since the reduction of lymphocyte adhesion to vascular cells by indigo naturalis extract could subsequently reduce the inflammatory reactions caused by lymphocyte infiltration in the epidermal layer and help to improve psoriasis, this study provides a potential mechanism for the anti-inflammatory therapeutic effect of indigo naturalis extract in psoriasis.

In vitro anti-breast cancer activity of ethanolic extract of Wrightia tomentosa: role of pro-apoptotic effects of oleanolic acid and urosolic acid.

PubMed

Chakravarti, Bandana; Maurya, Ranjani; Siddiqui, Jawed Akhtar; Bid, Hemant Kumar; Rajendran, S M; Yadav, Prem P; Konwar, Rituraj

2012-06-26

Wrightia tomentosa Roem. & Schult. (Apocynaceae) is known in the traditional medicine for anti-cancer activity along with other broad indications like snake and scorpion bites, renal complications, menstrual disorders etc. However, the anti-cancer activity of this plant or its constituents has never been studied systematically in any cancer types so far. To evaluate the anti-cancer activities of the ethanolic extract of W. tomentosa and identified constituent active molecule(s) against breast cancer. Powdered leaves of W. tomentosa were extracted with ethanol. The ethanolic extract, subsequent hexane fractions and fraction F-4 of W. tomentosa were tested for its anti-proliferative and pro-apoptotic effects in breast cancer cells MCF-7 and MDA-MB-231. The ethanolic extract, subsequent hexane fractions and fraction F-4 of W. tomentosa inhibited the proliferation of human breast cancer cell lines, MCF-7 and MDA-MB-231. The fraction F-4 obtained from hexane fraction inhibited proliferation of MCF-7 and MDA-MB-231 cells in concentration and time dependent manner with IC₅₀ of 50 μg/ml and 30 μg/ml for 24 h, 28 μg/ml and 22 μg/ml for 48 h and 25 μg/ml and 20 μg/ml for 72 h respectively. The fraction F-4 induced G1 cell cycle arrest, reactive oxygen species (ROS) generation, loss of mitochondrial membrane potential and subsequent apoptosis. Apoptosis is indicated in terms of increased Bax/Bcl-2 ratio, enhanced Annexin-V positivity, caspase 8 activation and DNA fragmentation. The active molecule isolated from fraction F-4, oleanolic acid and urosolic acid inhibited cell proliferation of MCF-7 and MDA-MB-231 cells at IC₅₀ value of 7.5 μM and 7.0 μM respectively, whereas there is devoid of significant cell inhibiting activity in non-cancer originated cells, HEK-293. In both MCF-7 and MDA-MB-231, oleanolic acid and urosolic acid induced cell cycle arrest and apoptosis as indicated by significant increase in Annexin-V positive apoptotic cell counts. Our results suggest that W. tomentosa extracts has significant anti-cancer activity against breast cancer cells due to induction of apoptosis pathway. Olenolic and urosolic acid are important constituent molecules in the extract responsible for anti-cancer activity of W. tomentosa.

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar

PubMed Central

Leite, D.C.A.; Balieiro, F.C.; Pires, C.A.; Madari, B.E.; Rosado, A.S.; Coutinho, H.L.C.; Peixoto, R.S.

2014-01-01

Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit Miniprep™ (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples. PMID:24948928

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar.

PubMed

Leite, D C A; Balieiro, F C; Pires, C A; Madari, B E; Rosado, A S; Coutinho, H L C; Peixoto, R S

2014-01-01

Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit Miniprep™ (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples.

Optimization of thermochemolysis analysis conditions for the in situ detection of organic compounds in Martian soil with the Mars Organic Molecule Analyzer (MOMA) experiment

NASA Astrophysics Data System (ADS)

Morisson, Marietta; Buch, Arnaud; Szopa, Cyril; Raulin, François; Stambouli, Moncef

2017-04-01

Martian surface is exposed to harsh radiative and oxidative conditions which are destructive for organic molecules. That is why the future ExoMars rover will examine the molecular composition of samples acquired from depths down to two meters below the Martian surface, where organics may have been protected from radiative and oxidative degradation. The samples will then be analyzed by the Pyrolysis-Gas Chromatography-Mass Spectrometry (Pyr-GC-MS) operational mode of the Mars Organic Molecule Analyzer (MOMA) instrument. To prevent thermal alteration of organic molecules during pyrolysis, thermochemolysis with tetramethylammonium hydroxide (TMAH) will extract the organics from the mineral matrix and methylate the polar functional groups, allowing the volatilization of molecules at lower temperatures and protecting the most labile chemical groups from thermal degradation. This study has been carried out on a Martian regolith analogue (JSC-Mars-1) with a high organic content with the aim of optimizing the thermochemolysis temperature within operating conditions similar to the MOMA experiment ones. We also performed Pyrolysis-GC-MS analysis as a comparison. The results show that, unlike pyrolysis alone - which mainly produces aromatics, namely thermally altered molecules - thermochemolysis allows the extraction and identification of numerous organic molecules of astrobiological interest. They also show that the main compounds start to be detectable at low thermochemolysis temperatures ranging from 400°C to 600°C. However, we noticed that the more the temperature increases, the more the chromatograms are saturated with thermally evolved molecules leading to many coelutions and making identification difficult.

A High-Throughput Screening Platform of Microbial Natural Products for the Discovery of Molecules with Antibiofilm Properties against Salmonella

PubMed Central

Paytubi, Sonia; de La Cruz, Mercedes; Tormo, Jose R.; Martín, Jesús; González, Ignacio; González-Menendez, Victor; Genilloud, Olga; Reyes, Fernando; Vicente, Francisca; Madrid, Cristina; Balsalobre, Carlos

2017-01-01

In this report, we describe a High-Throughput Screening (HTS) to identify compounds that inhibit biofilm formation or cause the disintegration of an already formed biofilm using the Salmonella Enteritidis 3934 strain. Initially, we developed a new methodology for growing Salmonella biofilms suitable for HTS platforms. The biomass associated with biofilm at the solid-liquid interface was quantified by staining both with resazurin and crystal violet, to detect living cells and total biofilm mass, respectively. For a pilot project, a subset of 1120 extracts from the Fundación MEDINA's collection was examined to identify molecules with antibiofilm activity. This is the first validated HTS assay of microbial natural product extracts which allows for the detection of four types of activities which are not mutually exclusive: inhibition of biofilm formation, detachment of the preformed biofilm and antimicrobial activity against planktonic cells or biofilm embedded cells. Currently, several extracts have been selected for further fractionation and purification of the active compounds. In one of the natural extracts patulin has been identified as a potent molecule with antimicrobial activity against both, planktonic cells and cells within the biofilm. These findings provide a proof of concept that the developed HTS can lead to the discovery of new natural compounds with antibiofilm activity against Salmonella and its possible use as an alternative to antimicrobial therapies and traditional disinfectants. PMID:28303128

Enzymatic repair of selected cross-linked homoduplex molecules enhances nuclear gene rescue from Pompeii and Herculaneum remains.

PubMed

Di Bernardo, Giovanni; Del Gaudio, Stefania; Cammarota, Marcella; Galderisi, Umberto; Cascino, Antonino; Cipollaro, Marilena

2002-02-15

Ancient DNA (aDNA) samples extracted from the bone remains of six equids buried by the Vesuvius eruption in 79 AD were investigated to test pre-amplification and enzymatic repair procedures designed to enhance the rescue of nuclear genes. The extracts, which proved all positive for Equidae mtDNA amplification, proved positive only four times out of 18 when tested for single-copy Equidae nuclear genes (epsilon globin, p53 and gamma interferon). Pre-amplification did not change the number of retrieved aDNA sequences but 10 times out of 14 enzymatic repair restored the amplifiability of the genes analysed, proving that repair increases the rate of successful rescue from 22 to alpha(lambda)mu(omicron)sigma(tau) 80%. These findings support the hypothesis that some of these cross-linked aDNA molecules, which are not completely separated when DNA is extracted under denaturing conditions, become homoduplex substrates for Pol I and/or T4 ligase action upon renaturation. aDNA authenticity is proved by the homology of the nucleotide sequences of loci tested to the corresponding modern Equidae sequences. Data also indicate that cross-linked homoduplex molecules selected by denaturation of the extract are repaired without any chimera formation. The general features of aDNA amplification with and without denaturation and enzymatic repair are discussed.

Enzymatic repair of selected cross-linked homoduplex molecules enhances nuclear gene rescue from Pompeii and Herculaneum remains

PubMed Central

Di Bernardo, Giovanni; Del Gaudio, Stefania; Cammarota, Marcella; Galderisi, Umberto; Cascino, Antonino; Cipollaro, Marilena

2002-01-01

Ancient DNA (aDNA) samples extracted from the bone remains of six equids buried by the Vesuvius eruption in 79 AD were investigated to test pre-amplification and enzymatic repair procedures designed to enhance the rescue of nuclear genes. The extracts, which proved all positive for Equidae mtDNA amplification, proved positive only four times out of 18 when tested for single-copy Equidae nuclear genes (ɛ globin, p53 and γ interferon). Pre-amplification did not change the number of retrieved aDNA sequences but 10 times out of 14 enzymatic repair restored the amplifiability of the genes analysed, proving that repair increases the rate of successful rescue from 22 to αλµοστ 80%. These findings support the hypothesis that some of these cross-linked aDNA molecules, which are not completely separated when DNA is extracted under denaturing conditions, become homoduplex substrates for Pol I and/or T4 ligase action upon renaturation. aDNA authenticity is proved by the homology of the nucleotide sequences of loci tested to the corresponding modern Equidae sequences. Data also indicate that cross-linked homoduplex molecules selected by denaturation of the extract are repaired without any chimera formation. The general features of aDNA amplification with and without denaturation and enzymatic repair are discussed. PMID:11842122

Lipid-protein stoichiometries in a crystalline biological membrane: NMR quantitative analysis of the lipid extract of the purple membrane.

PubMed

Corcelli, Angela; Lattanzio, Veronica M T; Mascolo, Giuseppe; Papadia, Paride; Fanizzi, Francesco

2002-01-01

The lipid/protein stoichiometries of a naturally crystalline biological membrane, the purple membrane (PM) of Halobacterium salinarum, have been obtained by a combination of (31)P- and (1)H-NMR analyses of the lipid extract. In total, 10 lipid molecules per retinal were found to be present in the PM lipid extract: 2-3 molecules of phosphatidylglycerophosphate methyl ester (PGP-Me), 3 of glycolipid sulfate, 1 of phosphatidylglycerol, 1 of archaeal glycocardiolipin (GlyC), 2 of squalene plus minor amounts of phosphatidylglycerosulfate (PGS) and bisphosphatidylglycerol (archaeal cardiolipin) (BPG) and a negligible amount of vitamin MK8. The novel data of the present study are necessary to identify the lipids in the electron density map, and to shed light on the structural relationships of the lipid and protein components of the PM.

Compounds of parasitic roundworm absorbing in the visible region: target molecules for detection of roundworm in Atlantic cod.

PubMed

Stormo, Svein K; Ernstsen, Arild; Nilsen, Heidi; Heia, Karsten; Sivertsen, Agnar H; Elvevoll, Edel

2004-07-01

The objective of this study was to contribute to the development of technology that will be able to replace manual operations in processing of fish fillets. Removal of parasites, black lining, remnants of skin, and bloodstains are costly and time-consuming operations to the fish processing industry. The presence of parasites in fish products tends to spoil consumers' appetites. Recent reports questioning the safety of eating cod infected with parasites might lower consumer acceptance of seafood. Presently, parasites are detected and removed manually. An average efficiency of about 75% under commercial conditions has been reported. In this study, we focused on biochemical differences between cod muscle and the prevalent anisakine nematode species (Anisakis simplex and Pseudoterranova decipiens) infecting Atlantic cod (Gadus morhua). Using reversed phase high-performance liquid chromatography equipped with a photodiode array detector, substances absorbing in the range 300 to 600 nm were identified in extracts from parasite material. These substances were not detected in extracts from cod tissue. Significant biochemical differences between cod muscle and parasite material have thus been demonstrated.

DNA of a Human Hepatitis B Virus Candidate

PubMed Central

Robinson, William S.; Clayton, David A.; Greenman, Richard L.

1974-01-01

Particles containing DNA polymerase (Dane particles) were purified from the plasma of chronic carriers of hepatitis B antigen. After a DNA polymerase reaction with purified Dane particle preparations treated with Nonidet P-40 detergent, Dane particle core structures containing radioactive DNA product were isolated by sedimentation in a sucrose density gradient. The radioactive DNA was extracted with sodium dodecyl sulfate and isolated by band sedimentation in a preformed CsCl gradient. Examination of the radioactive DNA band by electron microscopy revealed exclusively circular double-stranded DNA molecules approximately 0.78 μm in length. Identical circular molecules were observed when DNA was isolated by a similar procedure from particles that had not undergone a DNA polymerase reaction. The molecules were completely degraded by DNase 1. When Dane particle core structures were treated with DNase 1 before DNA extraction, only 0.78-μm circular DNA molecules were detected. Without DNase treatment of core structures, linear molecules with lengths between 0.5 and 12 μm, in addition to the 0.78-μm circles were found. These results suggest that the 0.78-μm circular molecules were in a protected position within Dane particle cores and the linear molecules were not within core structures. Length measurements on 225 circular molecules revealed a mean length of 0.78 ± 0.09 μm which would correspond to a molecular weight of around 1.6 × 106. The circular molecules probably serve as primer-template for the DNA polymerase reaction carried out by Dane particle cores. Thermal denaturation and buoyant density measurements on the Dane particle DNA polymerase reaction product revealed a guanosine plus cytosine content of 48 to 49%. Images PMID:4847328

Induction of apoptosis in cancer cell lines by the Red Sea brine pool bacterial extracts.

PubMed

Sagar, Sunil; Esau, Luke; Holtermann, Karie; Hikmawan, Tyas; Zhang, Guishan; Stingl, Ulrich; Bajic, Vladimir B; Kaur, Mandeep

2013-12-05

Marine microorganisms are considered to be an important source of bioactive molecules against various diseases and have great potential to increase the number of lead molecules in clinical trials. Progress in novel microbial culturing techniques as well as greater accessibility to unique oceanic habitats has placed the marine environment as a new frontier in the field of natural product drug discovery. A total of 24 microbial extracts from deep-sea brine pools in the Red Sea have been evaluated for their anticancer potential against three human cancer cell lines. Downstream analysis of these six most potent extracts was done using various biological assays, such as Caspase-3/7 activity, mitochondrial membrane potential (MMP), PARP-1 cleavage and expression of γH2Ax, Caspase-8 and -9 using western blotting. In general, most of the microbial extracts were found to be cytotoxic against one or more cancer cell lines with cell line specific activities. Out of the 13 most active microbial extracts, six extracts were able to induce significantly higher apoptosis (>70%) in cancer cells. Mechanism level studies revealed that extracts from Chromohalobacter salexigens (P3-86A and P3-86B(2)) followed the sequence of events of apoptotic pathway involving MMP disruption, caspase-3/7 activity, caspase-8 cleavage, PARP-1 cleavage and Phosphatidylserine (PS) exposure, whereas another Chromohalobacter salexigens extract (K30) induced caspase-9 mediated apoptosis. The extracts from Halomonas meridiana (P3-37B), Chromohalobacter israelensis (K18) and Idiomarina loihiensis (P3-37C) were unable to induce any change in MMP in HeLa cancer cells, and thus suggested mitochondria-independent apoptosis induction. However, further detection of a PARP-1 cleavage product, and the observed changes in caspase-8 and -9 suggested the involvement of caspase-mediated apoptotic pathways. Altogether, the study offers novel findings regarding the anticancer potential of several halophilic bacterial species inhabiting the Red Sea (at the depth of 1500-2500 m), which constitute valuable candidates for further isolation and characterization of bioactive molecules.

Thermal Reactivity Of Organic Molecules With Perchlorates And The Detection Of Organics In Mars Samples With SAM Onboard Curiosity Rover

NASA Astrophysics Data System (ADS)

Szopa, C.; Millan, M.; Buch, A.; Freissinet, C.; Guzman, M.; Glavin, D. P.; Mahaffy, P. R.; Navarro-Gonzalez, R.

2017-12-01

The search for organic molecules at the Mars surface is a key objective to assess the potential for habitability of the planet and to find biomarkers. Both the past Viking landers and the Curiosity rover of today carry onboard instruments based on gas chromatography coupled to mass spectrometry with the aim to analyze the content of organics present in soil or rock samples. These instruments analyze the volatile compounds released from the samples submitted to thermal or chemical treatments. Even though these sample preparation processes are commonly used on Earth for their efficient extraction of organic materials from mineral matrixes, the presence of oxychlorines recently discovered in the Mars soil [1, 2] makes the process for space applications more complex and the results more difficult to interpret. Indeed, the release of volatile inorganic reactive molecules from oxychlorines during the sample heating process induces reactions of chlorination and oxidation of the organic molecules. For this reason, in an effort to contribute to the interpretation of the results obtained with the Viking/GCMS, and the MSL/SAM experiment our team currently operates on Mars, we started to study systematically the thermal reactivity of a series of organic molecules, of interest for Mars and life purposes, mixed with oxychlorines either detected or potentially present in the soil of Mars [3]. In this presentation, we will mainly focus on two sets of results that were obtained while studying the reactivity of calcium perchlorates with polyaromatic hydrocarbons, amino acids and carboxylic acids under pyrolytic conditions similar to those used in the SAM experiment. First of all, we will show the dependence of reactivity on the temperature of sublimation and decomposition of the individual components in the mixture and, secondly, we will discuss the detection of aromatic chlorinated species by SAM in samples collected at the Cumberland site from the results obtained in this study. [1] Kounaves et al. (2010), JGR 115; [2] Glavin et al. (2013), JGR 181; [3] Sutter et al., JGR (in press);

The effects of Nigella sativa (Ns), Anthemis hyalina (Ah) and Citrus sinensis (Cs) extracts on the replication of coronavirus and the expression of TRP genes family.

PubMed

Ulasli, Mustafa; Gurses, Serdar A; Bayraktar, Recep; Yumrutas, Onder; Oztuzcu, Serdar; Igci, Mehri; Igci, Yusuf Ziya; Cakmak, Ecir Ali; Arslan, Ahmet

2014-03-01

Extracts of Anthemis hyalina (Ah), Nigella sativa (Ns) and peels of Citrus sinensis (Cs) have been used as folk medicine to fight antimicrobial diseases. To evaluate the effect of extracts of Ah, Ns and Cs on the replication of coronavirus (CoV) and on the expression of TRP genes during coronavirus infection, HeLa-CEACAM1a (HeLa-epithelial carcinoembryonic antigen-related cell adhesion molecule 1a) cells were inoculated with MHV-A59 (mouse hepatitis virus-A59) at moi of 30. 1/50 dilution of the extracts was found to be the safe active dose. ELISA kits were used to detect the human IL-8 levels. Total RNA was isolated from the infected cells and cDNA was synthesized. Fluidigm Dynamic Array nanofluidic chip 96.96 was used to analyze the mRNA expression of 21 TRP genes and two control genes. Data was analyzed using the BioMark digital array software. Determinations of relative gene expression values were carried out by using the 2(-∆∆Ct) method (normalized threshold cycle (Ct) value of sample minus normalized Ct value of control). TCID50/ml (tissue culture infectious dose that will produce cytopathic effect in 50% of the inoculated tissue culture cells) was found for treatments to determine the viral loads. The inflammatory cytokine IL-8 level was found to increase for both 24 and 48 h time points following Ns extract treatment. TRPA1, TRPC4, TRPM6, TRPM7, TRPM8 and TRPV4 were the genes which expression levels changed significantly after Ah, Ns or Cs extract treatments. The virus load decreased when any of the Ah, Ns or Cs extracts was added to the CoV infected cells with Ah extract treatment leading to undetectable virus load for both 6 and 8 hpi. Although all the extract treatments had an effect on IL-8 secretion, TRP gene expression and virus load after CoV infection, it was the Ah extract treatment that showed the biggest difference in virus load. Therefore Ah extract is the best candidate in our hands that contains potential treatment molecule(s).

Contribution of Massive Stars to the Production of Neutron Capture Elements

NASA Astrophysics Data System (ADS)

Federman, Steven

2010-09-01

Elements beyond the Fe-peak must be synthesized through neutron-capture processes. With the aim of understanding the contribution of massive stars to the synthesis of neutron-capture elements during the current epoch, we propose an archival survey of interstellar arsenic, cadmium, tin, and lead. Nucleosynthesis via the weak slow process and the rapid process are the routes involving massive stars, while the main slow process arises from the evolution of low-mass stars. Ultraviolet lines for the dominant ions for each element will be used to extract interstellar abundances. The survey involves about forty sight lines, many of which are associated with regions of massive star formation shaped by core-collapse supernovae {SNe II}. The sample will increase the number of published determinations by factors of 2 to 5. HST spectra are the only means for determining the elemental abundances for this set of species in diffuse interstellar clouds. The survey contains directions that are both molecule poor and molecule rich, thereby enabling us to examine the overall level of depletion onto grains as a function of gas density. Complementary laboratory determinations of oscillator strengths will place the interstellar measurements on an absolute scale. The results from the proposed study will be combined with published interstellar abundances for other neutron capture elements and the suite of measurements will be compared to results from stars throughout the history of the Galaxy.

Study of the In2O3 molecule in the free state and in the crystal

NASA Astrophysics Data System (ADS)

Kaplan, Ilya G.; Miranda, Ulises; Trakhtenberg, Leonid I.

2018-03-01

The nanomaterials based on the In2O3 molecule are widely used as catalysts and sensors among other applications. In the present study, we discuss the possibility of using nanoclusters of In2O3 as molecular photomotors. A comparative analysis of the electronic structure of the In2O3 molecule in the free state and in the crystal is performed. For the free In2O3 molecule the geometry of its lowest structures, V-shape and linear, was optimised at the CCSD(T) level, which is the most precise computational method applied up to date to study In2O3. Using experimental crystallographic data, we determined the geometry of In2O3 in the crystal. It has a zigzag, not symmetric structure and possesses a dipole moment with magnitude slightly smaller than that of the V-structure of the free molecule (the linear structure due to its symmetry has no dipole moment). According to the Natural Atomic population analysis, the chemical structure of the linear In2O3 can be represented as O = In-O-In = O; the V-shaped molecule has the similar double- and single-bond structure. The construction of nanoclusters from ´bricksʼ of In2O3 with geometry extracted from crystal (or nanoclusters extracted directly from crystal) and their use as photo-driven molecular motors are discussed.

Salting-in effect on muscle protein extracted from giant squid (Dosidicus gigas).

PubMed

Zhang, Rui; Zhou, Ru; Pan, Weichun; Lin, Weiwei; Zhang, Xiuzhen; Li, Mengya; Li, Jianrong; Niu, Fuge; Li, Ang

2017-01-15

The salting-in effect on muscle protein is well-known in food science but hard to explain using conventional theories. Myofibrillar protein extracted from the giant squid (Dosidicus gigas) was selected as a model muscle protein to study this mechanism in KCl solutions. Changes in the secondary structures of myofibrillar protein molecules caused by concentrated salts, particularly in the paramyosin molecule conformation, have been reported. Zeta-potential determinations showed that these secondary structures have modified protein molecule surfaces. The zeta-potential of the myofibrillar protein molecules fell from -7.24±0.82 to -9.99±1.65mV with increasing salt concentration from 0.1 to 0.5M. The corresponding second virial coefficient increased from -85.43±3.8×10(-7) to -3.45±1.3×10(-7) molmLg(-2). The extended law of corresponding states suggests that reduced attractive interactions increase the protein solubility. Solubility measurements in alternating KCl concentrations showed that the conformational change was reversible. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ethanol extracts of black pepper or turmeric down-regulated SIRT1 protein expression in Daudi culture cells.

PubMed

Nishimura, Yuri; Kitagishi, Yasuko; Yoshida, Hitomi; Okumura, Naoko; Matsuda, Satoru

2011-01-01

SIRT1 is a mammalian candidate molecule involved in longevity and diverse metabolic processes. The present study aimed to determine the effects of certain herbs and spices on SIRT1 expression. Human cell lines Daudi, Jurkat, U937 and K562 were cultured in RPMI-1640. Herb and spice powders were prepared and the supernatants were collected. RT-PCR was used to quantify the expression level of the gene. Protein samples were then analyzed by Western blotting. Western blotting revealed the down-regulation of SIRT1 protein expression in Daudi cells treated with extracts of black pepper or turmeric. On the other hand, the effect on the SIRT1 gene expression examined by reverse transcription polymerase chain reaction was unaltered. In conclusion, component(s) of certain herbs and spices may induce the down-regulation of SIRT1 protein.

Ion Exchange and Solvent Extraction: Supramolecular Aspects of Solvent Exchange Volume 21

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

Gloe, Karsten; Tasker, Peter A; Oshima, Tatsuya

Preface The theme of supramolecular chemistry (SC), entailing the organization of multiple species through noncovalent interactions, has permeated virtually all aspects of chemical endeavor over the past several decades. Given that the observed behavior of discrete molecular species depends upon their weak interactions with one another and with matrix components, one would have to conclude that SC must indeed form part of the fabric of chemistry itself. A vast literature now serves to categorize SC phenomena within a body of consistent terminology. The word supramolecular itself appears in the titles of dozens of books, several journals, and a dedicated encyclopedia.more » Not surprisingly, the theme of SC also permeates the field of solvent extraction (SX), inspiring the framework for this volume of Ion Exchange and Solvent Extraction. It is attempted in the six chapters of this volume to identify both how supramolecular behavior occurs and is studied in the context of SX and how SC is influencing the current direction of SX. Researchers and practitioners have long dealt with supramolecular interactions in SX. Indeed, the use of polar extractant molecules in nonpolar media virtually assures that aggregative interactions will dominate the solution behavior of SX. Analytical chemists working in the 1930s to the 1950s with simple mono- and bidentate chelating ligands as extractants noted that extraction of metal ions obeyed complicated mass-action equilibria involving complex stoichiometries. As chemists and engineers developed processes for nuclear and hydrometallurgical applications in the 1950s and 1960s, the preference for aliphatic diluents only enhanced the complexity and supramolecular nature of extraction chemistry. Use of physical techniques such as light scattering and vapor-pressure measurements together with various spectroscopic methods revealed organic-phase aggregates from well-defined dimers to small aggregates containing a few extractant molecules to large inverse micelles swollen with water molecules. Extraction systems involving long-chain cations such as alkylammonium species or long-chain anions such as sulfonates or carboxylates proved especially prone to extensive aggregate formation. The related phenomenon of third-phase formation in SX systems, long misunderstood, is now yielding to spectroscopic and scattering techniques showing extensive long-range organization. Over the last 50 years, tools for studying the structure and thermodynamics of aggregation have grown increasingly sophisticated, leading to a rich and detailed understanding of what we can now recognize as SC phenomena in SX. In the 1970s and 1980s, the rapid growth of SC elicited a paradigm shift in SX. The influence of SC principles had two major effects on the course of SX research. First, it provided a framework for understanding the supramolecular behavior that was already well appreciated in the field of SX, though earlier without the SC terminology. Second, it provided the conceptual tools to control supramolecular behavior in SX, direct it for intended functionality, and to simplify it. Extraction by designed reagents has been steadily progressing ever since, with commercial applications emerging to successfully validate this approach. With the discovery of crown ethers in the late 1960s, the advancement of extractant design has fruitfully employed the concept of inclusion. While considerable initial progress occurred with such molecules, especially because of their affinity and selectivity for alkali and alkaline earth metals, other molecular platforms such as calixarenes have proven more versatile. Multidentate receptors for partial to full inclusion of cations, anions, ion pairs, as well as neutral species, have now become commonplace for selective extraction. This volume of Ion Exchange and Solvent Extraction examines how the principles of SC are being employed both in advancing the design of new highly selective SX systems and in understanding aggregation phenomena in SX systems. Chapter 1 discusses the nature and definition of SC and how it is used generally in design of novel SX reagents. Major approaches using SC principles are outlined and illustrated. Chapter 2 expands upon the theme of ion-pair recognition and introduces outer-sphere recognition of metal complexes, a novel idea with the potential for structural control of solvation, casting a new light on solvent modifiers. Chapter 3 reviews the large literature of calixarenes as extraction reagents for metal ions, where the synthetic versatility of this family of compounds has produced vast possibilities for inclusion and selective separations. Chapter 4 extends such chemistry to extraction of biomolecules, where the potential for selective separations is only beginning to be explored through site recognition in macromolecules. In Chapter 5, a detailed examination of the liquid-liquid interface as an expression of supramolecular phenomena i...« less

Attractive design: an elution solvent optimization platform for magnetic-bead-based fractionation using digital microfluidics and design of experiments.

PubMed

Lafrenière, Nelson M; Mudrik, Jared M; Ng, Alphonsus H C; Seale, Brendon; Spooner, Neil; Wheeler, Aaron R

2015-04-07

There is great interest in the development of integrated tools allowing for miniaturized sample processing, including solid phase extraction (SPE). We introduce a new format for microfluidic SPE relying on C18-functionalized magnetic beads that can be manipulated in droplets in a digital microfluidic platform. This format provides the opportunity to tune the amount (and potentially the type) of stationary phase on-the-fly, and allows the removal of beads after the extraction (to enable other operations in same device-space), maintaining device reconfigurability. Using the new method, we employed a design of experiments (DOE) operation to enable automated on-chip optimization of elution solvent composition for reversed phase SPE of a model system. Further, conditions were selected to enable on-chip fractionation of multiple analytes. Finally, the method was demonstrated to be useful for online cleanup of extracts from dried blood spot (DBS) samples. We anticipate this combination of features will prove useful for separating a wide range of analytes, from small molecules to peptides, from complex matrices.

Evaluation of seed extracts from plants found in the Caatinga biome for the control of Aedes aegypti.

PubMed

Barbosa, Patrícia Batista Barra Medeiros; de Oliveira, Julliete Medeiros; Chagas, Juliana Macêdo; Rabelo, Luciana Maria Araujo; de Medeiros, Guilherme Fulgêncio; Giodani, Raquel Brant; da Silva, Elizeu Antunes; Uchôa, Adriana Ferreira; de Fátima de Freire Melo Ximenes, Maria

2014-10-01

Dengue fever, currently the most important arbovirus, is transmitted by the bite of the Aedes aegypti mosquito. Given the absence of a prophylactic vaccine, the disease can only be controlled by combating the vector insect. However, increasing reports of resistance and environmental damage caused by insecticides have led to the urgent search for new safer alternatives. In this regard, plants stand out as a source of easy-to-obtain biodegradable insecticide molecules. Twenty (20) plant seed extracts from the Caatinga, an exclusively Brazilian biome, were prepared. Sodium phosphate (50 mM, pH 8.0) was used as extractor. The extracts were used in bioassays and submitted to partial characterisation. A Probit analysis of insecticides was carried out, and intergroup differences were verified by the Student's t test and ANOVA. All the extracts exhibited larvicidal and ovipositional deterrence activity. The extracts of Amburana cearenses, Piptadenia viridiflora, Erythrina velutina, Myracrodruon urundeuva and Schinopsis brasiliensis were also pupicides, while the extracts of P. viridiflora, E. velutina, A. cearenses, Anadenanthera colubrina, Diocleia grandiflora, Bauhinia cheilantha, Senna spectabilis, Caesalpinia pyramidalis, Mimosa regnelli and Genipa americana displayed adulticidal activity. Egg laying was compromised when females were fed extracts of Ricinus communis, Croton sonderianus and S. brasiliensis. At least two proteins with insecticidal activity were found in all the extracts. Phenol compounds were identified in all the extracts and flavonoids, triterpenes or alkaloids in 14 of them. The results show the potential of plant seed extracts from the Caatinga as a source of active molecules against A. aegypti mosquitos.

High Efficiency DNA Extraction by Graphite Oxide/Cellulose/Magnetite Composites Under Na+ Free System

NASA Astrophysics Data System (ADS)

Akceoglu, Garbis Atam; Li, Oi Lun; Saito, Nagahiro

2016-04-01

DNA extraction is the key step at various research areas like biotechnology, diagnostic development, paternity determination, and forensic science . Solid support extraction is the most common method for DNA purification. In this method, Na+ ions have often been applied as binding buffers in order to obtain high extraction efficiency and high quality of DNA; however, the presence of Na+ ions might be interfering with the downstream DNA applications. In this study, we proposed graphite oxide (GO)/magnetite composite/cellulose as an innovative material for Na+-free DNA extraction. The total wt.% of GO was fixed at 4.15% in the GO/cellulose/magnetite composite . The concentration of magnetite within the composites were controlled at 0-3.98 wt.%. The extraction yield of DNA increased with increasing weight percentage of magnetite. The highest yield was achieved at 3.98 wt.% magnetite, where the extraction efficiency was reported to be 338.5 ng/µl. The absorbance ratios between 260 nm and 280 nm (A260/A280) of the DNA elution volume was demonstrated as 1.81, indicating the extracted DNA consisted of high purity. The mechanism of adsorption of DNA was provided by (1) π-π interaction between the aromatic ring in GO and nucleobases of DNA molecule, and (2) surface charge interaction between the positive charge magnetite and anions such as phosphates within the DNA molecules. The results proved that the GO/cellulose/magnetite composite provides a Na+-free method for selective DNA extraction with high extraction efficiency of pure DNA.

A Guided Inquiry Liquid/Liquid Extractions Laboratory for Introductory Organic Chemistry

ERIC Educational Resources Information Center

Raydo, Margaret L.; Church, Megan S.; Taylor, Zane W.; Taylor, Christopher E.; Danowitz, Amy M.

2015-01-01

A guided inquiry laboratory experiment for teaching liquid/liquid extractions to first semester undergraduate organic chemistry students is described. This laboratory is particularly useful for introductory students as the analytes that are separated are highly colored dye molecules. This allows students to track into which phase each analyte…

Comparison of distillation and ultrasound-assisted extraction methods for the isolation of sensitive aroma compounds from garlic (Allium sativum).

PubMed

Kimbaris, Athanasios C; Siatis, Nikolaos G; Daferera, Dimitra J; Tarantilis, Petros A; Pappas, Christos S; Polissiou, Moschos G

2006-01-01

A comparative study of traditional simultaneous distillation extraction (SDE), microwave assisted hydrodistillation extraction (MWHD) and ultrasound-assisted extraction (USE) is presented, for the extraction of essential oils from fresh garlic (Allium sativum) cloves. Each method is evaluated in terms of qualitative and quantitative composition of the isolated essential oil. The highly reactive sulfur molecules of the garlic volatile fraction show variable response to the different isolation methods. The application of ultrasound for the extraction of the essential oil is considered to cause a lesser damage of thermal-sensitive molecules, thus, providing a better approach of the compounds primarily responsible for the characteristic odor and taste of freshly chopped garlic. All heat-involving isolation procedures have been shown to differentiate the volatile-fraction profile as analyzed by GC-MS. Especially when grouping the compounds into cyclic and acyclic, the percentage concentrations drop from 77.4% to 8.7% for the acyclic while that of the cyclic compounds increase from 4.7% to 70.8%. The observed fact may be attributed to the effect of the heat applied, which changes from harsh thermal treatment (SDE) to short time thermal (MWHD) and room-temperature isolation (USE). The use of USE proves to be crucial in order to provide reliable insight into garlic's chemistry.

Collagen extraction from mussel byssus: a new marine collagen source with physicochemical properties of industrial interest.

PubMed

Rodríguez, F; Morán, L; González, G; Troncoso, E; Zúñiga, R N

2017-04-01

Mussel byssus is a by-product of mussel production and is a potential source of collagen. The goal of this study was to extract collagen from the byssus of Chilean mussel using an enzymatic method and characterize it. A pepsin-aided extraction method was employed where first an enzymatic hydrolysis at two pepsin/substrate ratios (1:50 or 4:50) and times (4 or 24 h) was done. Extraction was conducted at 80 °C for 24 h, in a 0.5 N acetic acid solution. All samples were analyzed for collagen content, amino acid profile, turbidity, viscosity, solubility, denaturation temperature and surface tension. Hydrolysis time had significant effect on collagen content, hydroxyproline content and extraction yield. Hydrolysis with a pepsin/byssus ratio of 4:50 for 24 h gave the better extraction performance with values of 69 mg/g protein, 1.8 mg/g protein and 30%, for collagen content, hydroxyproline content and extraction yield, respectively. No differences were found for the viscosity and surface tension of collagen dispersions, suggesting that the enzymatic hydrolysis did not affect the integrity of the collagen molecule. Denaturation temperature of freeze-dried byssus collagen presented a high value (83-91 °C), making this kind of collagen a very interesting material for encapsulation of bioactive molecules and for biomedical applications.

Anti-inflammatory and anti-angiogenic effects of flavonoids isolated from Lycium barbarum Linnaeus on human umbilical vein endothelial cells.

PubMed

Wu, Wen-Bin; Hung, Dian-Kun; Chang, Fung-Wei; Ong, Eng-Thaim; Chen, Bing-Huei

2012-10-01

Anti-inflammatory and anti-angiogenic effects of flavonoids isolated from Lycium barbarum fruits, a traditional Chinese medicine, on human umbilical vein endothelial cells (HUVECs) were investigated. Initially, flavonoids were extracted with 80% ethanol and separated using a Cosmosil 140 C18-OPN column, with the acidic fraction eluted with deionized water being composed of chlorogenic acid, caffeoyl quinic acid, caffeic acid and p-coumaric acid and the neutral fraction eluted with methanol composed of quercetin-diglycoside, rutin and kaempferol-O-rutinoside. Flavonoid extract was effective in inhibiting expression of intercellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule (VCAM-1) induced by TNF-α in HUVECs. The RT-PCR analysis indicated that ICAM-1 mRNA induced by TNF-α was inhibited by flavonoid extract. The flavonoid extract attenuated TNF-α-induced IκB phosphorylation as well as NF-κB, p65 and p50 translocation from cytosol to nucleus, through inhibition on TNF-α- and H(2)O(2)-induced intracellular reactive oxygen species (ROS) production. For the anti-angiogenic study, the flavonoid extract inhibited vascular endothelial growth factor (VEGF)-induced cell proliferation and migration in HUVECs, as well as angiogenesis. However, the flavonoid extract did not inhibit VEGF signaling. Surprisingly, HUVECs adhesion to the extracellular matrix was compromised and adhesion-induced signaling was retarded by the flavonoid extract.

Identification of (Z)-2,3-Diphenylacrylonitrile as Anti-Cancer Molecule in Persian Gulf Sea Cucumber Holothuria parva

PubMed Central

Amidi, Salimeh; Hashemi, Zahra; Motallebi, Abbasali; Nazemi, Melika; Farrokhpayam, Hoda; Seydi, Enayatollah

2017-01-01

Hepatocellular carcinoma (HCC), also named cancerous hepatoma, is the most common type of malignant neoplasia of the liver. In this research, we screened the Persian Gulf sea cucumber Holothuria parva (H. parva) methanolic sub-fractions for the possible existence of selective toxicity on liver mitochondria isolated from an animal model of HCC. Next, we purified the most active fraction. Thus the structure of the active molecule was identified. HCC was induced by diethylnitrosamine (DEN) and 2-acetylaminofluorene (2-AAF) protocol. Rat liver mitochondria for evaluation of the selective cytotoxic effects of sub-fractions of H. parva were isolated and then mitochondrial parameters were determined. Our results showed that C1 sub-fraction of methanolic extract of H. parva considerably increased reactive oxygen species (ROS) generation, collapse of mitochondrial membrane potential (MMP), swelling in mitochondria and cytochrome c release only on HCC liver mitochondria. Furthermore, the methanolic extract of H. parva was investigated furthermore and the active fraction was extracted. In this fraction, (Z)-2,3-diphenylacrylonitrile molecule, which is also known as α-cyanostilbene, was identified by mass analysis. This molecule increased ROS generation, collapse of MMP, swelling in mitochondria and finally cytochrome c release only on HCC liver mitochondria. The derivatives of (Z)-2,3-diphenylacrylonitrile in other natural products were also reported as an anti-cancer agent. These results suggest the eligibility of the (Z)-2,3-diphenylacrylonitrile as a complementary therapeutic agent for patients with HCC. PMID:29035293

Greater Real-Life Diagnostic Efficacy of Allergen Molecule-Based Diagnosis for Prescription of Immunotherapy in an Area with Multiple Pollen Exposure.

PubMed

Saltabayeva, Ulbosin; Garib, Victoria; Morenko, Marina; Rosenson, Rafail; Ispayeva, Zhanat; Gatauova, Madina; Zulus, Loreta; Karaulov, Alexander; Gastager, Felix; Valenta, Rudolf

2017-01-01

Allergen molecule-based diagnosis has been suggested to facilitate the identification of disease-causing allergen sources and the prescription of allergen-specific immunotherapy (AIT). The aim of the current study was to compare allergen molecule-based IgE serology with allergen extract-based skin testing for the identification of the disease-causing allergen sources. The study was conducted in an area where patients are exposed to pollen from multiple sources (trees, grasses, and weeds) at the same time to compare the diagnostic efficiency of the 2 forms of diagnosis. Patients from Astana, Kazakhstan, who suffered from pollen-induced allergy (n = 95) were subjected to skin prick testing (SPT) with a local panel of tree pollen, grass pollen, and weed pollen allergen extracts and IgE antibodies specific for marker allergen molecules (nArt v 1, nArt v 3, rAmb a 1, rPhl p 1, rPhl p 5, rBet v 1) were measured by ImmunoCAP. Direct and indirect costs for diagnosis based on SPT and marker allergen-based IgE serology as well as direct costs for immunotherapy depending on SPT and serological test results were calculated. The costs for SPT-based diagnosis per patient were lower than the costs for allergen molecule-based IgE serology. However, allergen molecule-based serology was more precise in detecting the disease-causing allergen sources. A lower number of immunotherapy treatments (n = 119) was needed according to molecular diagnosis as compared to extract-based diagnosis (n = 275), which considerably reduced the total costs for diagnosis and for a 3-year treatment from EUR 1,112.30 to 521.77 per patient. The results from this real-life study show that SPT is less expensive than allergen molecule-based diagnostic testing, but molecular diagnosis allowed more precise prescription of immunotherapy which substantially reduced treatment costs and combined costs for diagnosis and treatment. © 2017 The Author(s) Published by S. Karger AG, Basel.

Extract of corn silk (stigma of Zea mays) inhibits the tumour necrosis factor-alpha- and bacterial lipopolysaccharide-induced cell adhesion and ICAM-1 expression.

PubMed

Habtemariam, S

1998-05-01

Treatment of human endothelial cells with cytokines such as tumour necrosis factor-alpha (TNF) or E. coli lipopolysaccharide (LPS) induces the expression of several adhesion molecules and enhances leukocyte adhesion to endothelial cell surface. Interfering with this leukocyte adhesion or adhesion molecules upregulation is an important therapeutic target for the treatment of bacterial sepsis and various inflammatory diseases. In the course of screening marketed European anti-inflammatory herbal drugs for TNF antagonistic activity, a crude ethanolic extract of corn silk (stigma of Zea mays) exhibited significant activity. The extract at concentrations of 9-250 micrograms/ml effectively inhibited the TNF- and LPS-induced adhesiveness of EAhy 926 endothelial cells to monocytic U937 cells. Similar concentration ranges of corn silk extract did also block the TNF and LPS but not the phorbol 12-myristate 13-acetate-induced ICAM-1 expression on EAhy 926 endothelial cell surface. The extract did not alter the production of TNF by LPS-activated macrophages and failed to inhibit the cytotoxic activity of TNF. It is concluded that corn silk possesses important therapeutic potential for TNF- and LPS-mediated leukocyte adhesion and trafficking.

Extending the spectrum of DNA sequences retrieved from ancient bones and teeth

PubMed Central

Glocke, Isabelle; Meyer, Matthias

2017-01-01

The number of DNA fragments surviving in ancient bones and teeth is known to decrease with fragment length. Recent genetic analyses of Middle Pleistocene remains have shown that the recovery of extremely short fragments can prove critical for successful retrieval of sequence information from particularly degraded ancient biological material. Current sample preparation techniques, however, are not optimized to recover DNA sequences from fragments shorter than ∼35 base pairs (bp). Here, we show that much shorter DNA fragments are present in ancient skeletal remains but lost during DNA extraction. We present a refined silica-based DNA extraction method that not only enables efficient recovery of molecules as short as 25 bp but also doubles the yield of sequences from longer fragments due to improved recovery of molecules with single-strand breaks. Furthermore, we present strategies for monitoring inefficiencies in library preparation that may result from co-extraction of inhibitory substances during DNA extraction. The combination of DNA extraction and library preparation techniques described here substantially increases the yield of DNA sequences from ancient remains and provides access to a yet unexploited source of highly degraded DNA fragments. Our work may thus open the door for genetic analyses on even older material. PMID:28408382

Shell extracts of the edible mussel and oyster induce an enhancement of the catabolic pathway of human skin fibroblasts, in vitro.

PubMed

Latire, Thomas; Legendre, Florence; Bouyoucef, Mouloud; Marin, Frédéric; Carreiras, Franck; Rigot-Jolivet, Muriel; Lebel, Jean-Marc; Galéra, Philippe; Serpentini, Antoine

2017-10-01

Mollusc shells are composed of more than 95% calcium carbonate and less than 5% organic matrix consisting mostly of proteins, glycoproteins and polysaccharides. In this study, we investigated the effects of matrix macromolecular components extracted from the shells of two edible molluscs of economic interest, i.e., the blue mussel Mytilus edulis and the Pacific oyster Crassostrea gigas. The potential biological activities of these organic molecules were analysed on human dermal fibroblasts in primary culture. Our results demonstrate that shell extracts of the two studied molluscs modulate the metabolic activities of the cells. In addition, the extracts caused a decrease of type I collagen and a concomitant increase of active MMP-1, both at the mRNA and the protein levels. Therefore, our results suggest that shell extracts from M. edulis and C. gigas contain molecules that promote the catabolic pathway of human dermal fibroblasts. This work emphasises the potential use of these shell matrices in the context of anti-fibrotic strategies, particularly against scleroderma. More generally, it stresses the usefulness to valorise bivalve shells that are coproducts of shellfish farming activity.

Unraveling Hydrophobic Interactions at the Molecular Scale Using Force Spectroscopy and Molecular Dynamics Simulations.

PubMed

Stock, Philipp; Monroe, Jacob I; Utzig, Thomas; Smith, David J; Shell, M Scott; Valtiner, Markus

2017-03-28

Interactions between hydrophobic moieties steer ubiquitous processes in aqueous media, including the self-organization of biologic matter. Recent decades have seen tremendous progress in understanding these for macroscopic hydrophobic interfaces. Yet, it is still a challenge to experimentally measure hydrophobic interactions (HIs) at the single-molecule scale and thus to compare with theory. Here, we present a combined experimental-simulation approach to directly measure and quantify the sequence dependence and additivity of HIs in peptide systems at the single-molecule scale. We combine dynamic single-molecule force spectroscopy on model peptides with fully atomistic, both equilibrium and nonequilibrium, molecular dynamics (MD) simulations of the same systems. Specifically, we mutate a flexible (GS) 5 peptide scaffold with increasing numbers of hydrophobic leucine monomers and measure the peptides' desorption from hydrophobic self-assembled monolayer surfaces. Based on the analysis of nonequilibrium work-trajectories, we measure an interaction free energy that scales linearly with 3.0-3.4 k B T per leucine. In good agreement, simulations indicate a similar trend with 2.1 k B T per leucine, while also providing a detailed molecular view into HIs. This approach potentially provides a roadmap for directly extracting qualitative and quantitative single-molecule interactions at solid/liquid interfaces in a wide range of fields, including interactions at biointerfaces and adhesive interactions in industrial applications.

The GSTome Reflects the Chemical Environment of White-Rot Fungi

PubMed Central

Deroy, Aurélie; Saiag, Fanny; Kebbi-Benkeder, Zineb; Touahri, Nassim; Hecker, Arnaud; Morel-Rouhier, Mélanie; Colin, Francis; Dumarcay, Stephane; Gérardin, Philippe; Gelhaye, Eric

2015-01-01

White-rot fungi possess the unique ability to degrade and mineralize all the different components of wood. In other respects, wood durability, among other factors, is due to the presence of extractives that are potential antimicrobial molecules. To cope with these molecules, wood decay fungi have developed a complex detoxification network including glutathione transferases (GST). The interactions between GSTs from two white-rot fungi, Trametes versicolor and Phanerochaete chrysosporium, and an environmental library of wood extracts have been studied. The results demonstrate that the specificity of these interactions is closely related to the chemical composition of the extracts in accordance with the tree species and their localization inside the wood (sapwood vs heartwood vs knotwood). These data suggest that the fungal GSTome could reflect the chemical environment encountered by these fungi during wood degradation and could be a way to study their adaptation to their way of life. PMID:26426695

Extracting Social Information from Chemosensory Cues: Consideration of Several Scenarios and Their Functional Implications

PubMed Central

Ben-Shaul, Yoram

2015-01-01

Across all sensory modalities, stimuli can vary along multiple dimensions. Efficient extraction of information requires sensitivity to those stimulus dimensions that provide behaviorally relevant information. To derive social information from chemosensory cues, sensory systems must embed information about the relationships between behaviorally relevant traits of individuals and the distributions of the chemical cues that are informative about these traits. In simple cases, the mere presence of one particular compound is sufficient to guide appropriate behavior. However, more generally, chemosensory information is conveyed via relative levels of multiple chemical cues, in non-trivial ways. The computations and networks needed to derive information from multi-molecule stimuli are distinct from those required by single molecule cues. Our current knowledge about how socially relevant information is encoded by chemical blends, and how it is extracted by chemosensory systems is very limited. This manuscript explores several scenarios and the neuronal computations required to identify them. PMID:26635515

Error-based Extraction of States and Energy Landscapes from Experimental Single-Molecule Time-Series

NASA Astrophysics Data System (ADS)

Taylor, J. Nicholas; Li, Chun-Biu; Cooper, David R.; Landes, Christy F.; Komatsuzaki, Tamiki

2015-03-01

Characterization of states, the essential components of the underlying energy landscapes, is one of the most intriguing subjects in single-molecule (SM) experiments due to the existence of noise inherent to the measurements. Here we present a method to extract the underlying state sequences from experimental SM time-series. Taking into account empirical error and the finite sampling of the time-series, the method extracts a steady-state network which provides an approximation of the underlying effective free energy landscape. The core of the method is the application of rate-distortion theory from information theory, allowing the individual data points to be assigned to multiple states simultaneously. We demonstrate the method's proficiency in its application to simulated trajectories as well as to experimental SM fluorescence resonance energy transfer (FRET) trajectories obtained from isolated agonist binding domains of the AMPA receptor, an ionotropic glutamate receptor that is prevalent in the central nervous system.

Beneficial Effect of Jojoba Seed Extracts on Hyperglycemia-Induced Oxidative Stress in RINm5f Beta Cells

PubMed Central

Belhadj, Sahla; Hentati, Olfa; Hamdaoui, Ghaith; Fakhreddine, Khaskhoussi; Maillard, Elisa; Dal, Stéphanie; Sigrist, Séverine

2018-01-01

Hyperglycemia occurs during diabetes and insulin resistance. It causes oxidative stress by increasing reactive oxygen species (ROS) levels, leading to cellular damage. Polyphenols play a central role in defense against oxidative stress. In our study, we investigated the antioxidant properties of simmondsin, a pure molecule present in jojoba seeds, and of the aqueous extract of jojoba seeds on fructose-induced oxidative stress in RINm5f beta cells. The exposure of RINm5f beta cells to fructose triggered the loss of cell viability (−48%, p < 0.001) and disruption of insulin secretion (p < 0.001) associated with of reactive oxygen species (ROS) production and a modulation of pro-oxidant and antioxidant signaling pathway. Cell pre-treatments with extracts considerably increased cell viability (+86% p < 0.001) for simmondsin and +74% (p < 0.001) for aqueous extract and insulin secretion. The extracts also markedly decreased ROS (−69% (p < 0.001) for simmondsin and −59% (p < 0.001) for aqueous extract) and caspase-3 activation and improved antioxidant defense, inhibiting p22phox and increasing nuclear factor (erythroid-derived 2)-like 2 (Nrf2) levels (+70%, p < 0.001) for aqueous extract. Simmondsin had no impact on Nrf2 levels. The richness and diversity of molecules present in jojoba seed extract makes jojoba a powerful agent to prevent the destruction of RINm5f beta cells induced by hyperglycemia. PMID:29558444

Cytoprotective action against oxidative stress in astrocytes and neurons by Bactris guineensis (L.) H.E. Moore (corozo) fruit extracts.

PubMed

López, Sergio; Martá, Mitchell; Sequeda, Luis Gonzalo; Celis, Crispin; Sutachan, Jhon Jairo; Albarracín, Sonia Luz

2017-11-01

Neurodegenerative conditions such as Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis are characterized by having a significant increase in oxidative stress that can lead to the cellular damage of both neurons and astrocytes. Therefore, the search for molecules that can modulate oxidative stress in these diseases has recently gain interest, especially for those non-traditional antioxidants that can be gained from diet. In the present work, pulp and seed extracts from the fruit of the palm, Bactris guineensis were obtained by hydro-alcoholic solution and by a solid-liquid phase using solvents with different polarities and evaluated for their capacity to protect both neurons and astrocytes against rotenone-induced oxidative stress. Analysis of the chemical antioxidant activity showed that Bactris guineensis pulp crude extract and seed ethyl acetate and ethanol extracts had a high scavenging capacity when compared with extracts obtained in Hexane and dichloromethane. Toxicity assays also showed that the pulp crude extract and seed ethyl acetate and ethanol extracts at low doses did not affect the cell viability of primary astrocyte and SH-SY5Y neuroblastoma cells. In addition, ethyl acetate and ethanol extracts, not only decreased O 2 - radicals production but also protected both SHSY5Y and astrocytes oxidative stress induced by rotenone. Together our results suggest that Bactris guineensis fruit contain antioxidant molecules that can have therapeutic potential. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Radiolysis and Ageing of C2-BTP in Cinnamaldehyde/Hexanol Mixtures

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

Fermvik, Anna; Ekberg, Christian; Retegan, Teodora

2007-07-01

The separation of actinides from lanthanides is an important step in the alternative methods for nuclear waste treatment currently under development. Polycyclic molecules containing nitrogen are synthesised and used for solvent extraction. A potential problem in the separation process is the degradation of the molecule due to irradiation or ageing. An addition of nitrobenzene has proved to have an inhibitory effect on degradation when added to a system containing C2-BTP in hexanol before irradiation. In this study, 2,6-di(5,6-diethyl-1,2,4-triazine-3-yl)pyridine (C2-BTP) was dissolved in different mixtures of cinnamaldehyde and hexanol and the effects on extraction after ageing and irradiation were investigated. Similarmore » to nitrobenzene, cinnamaldehyde contains an aromatic ring which generally has a relatively high resistance towards radiolysis. Both C2-BTP in cinnamaldehyde and C2-BTP in hexanol seem to degrade with time. The system with C2-BTP in pure hexanol is relatively stable up to 17 days but then starts slowly to degrade. The solution with pure cinnamaldehyde as diluent started to degrade after only {approx}20 hours. The opposite is true for degradation caused by radiolysis; hexanol systems are more sensitive to radiolysis than cinnamaldehyde systems. Most of the radiolytic degradation took place during the first days of irradiation, up to a dose of 4 kGy. (authors)« less

Analysis of the cyanolichen Lichina pygmaea metabolites using in situ DART-MS: from detection to thermochemistry of mycosporine serinol.

PubMed

Le Pogam, Pierre; Legouin, Béatrice; Le Lamer, Anne-Cécile; Boustie, Joël; Rondeau, David

2015-03-01

Direct Analysis in Real Time DART-HRMS is here first applied to the detection of molecules from a lichen, Lichina pygmaea. The aim was to propose an innovative method of in situ detection of lichen secondary metabolites using the possibilities of elemental composition determination available when a DART source is interfaced with a TOF analyzer. Three kinds of samples have been submitted to DART ionization, i.e. an intact thallus, a powder obtained from the crushed lichen and an aqueous extract. In situ analysis of crushed lichen, yields an extensive chemical profile, comparable to what is obtained from the aqueous extract, comprising both major polar metabolites described in literature along with some other signals that could correspond to potentially unknown metabolites. One of the detected secondary metabolites, mycosporine serinol, underwent a dehydration reaction prior to its transfer in the gas-phase by DART ionization. The consideration of the thermal transfers involved in the DART ionization process and the possibility to record time-dependent mass spectra through the use of the TOF analyzer allowed establishing Arrhenius plots of this water molecule loss to obtain associated thermodynamic quantities. The low values of corresponding activation enthalpy (Δr‡Hm° of the order of 25 kJ mol(-1)) enabled formulating some assumption regarding a possible role of such metabolites in the lichen. Copyright © 2015 John Wiley & Sons, Ltd.

Bio-effectors from waste materials as growth promoters, an agronomic and metabolomic study

NASA Astrophysics Data System (ADS)

Alwanney, Deaa; Chami, Ziad Al; Angelica De Pascali, Sandra; Cavoski, Ivana; Fanizzi, Francesco Paolo

2014-05-01

Nowadays, improving plant performance by providing growth promoters is a main concern of the organic agriculture. As a consequence of increased food demands, more efficient and alternatives of the current plant nutrition strategies are becoming urgent. Recently, a novel concept "bio-effectors" raised on to describe a group of products that are able to improve plant performance and do not belong to fertilizers or pesticides. Agro-Food processing residues are promising materials as bio-effector. Three plant-derived materials: brewers' spent grain (BSG), fennel processing residues (FPR) and lemon processing residues (LPR) were chosen as bio-effector candidates. Plant-derived materials were characterized in term of total macro and micronutrients content. Green extraction methodology and solvent choice (aqueous; ethanol; and aqueous: ethanol mixture 1:1) was based on the extraction yield as main factor. Optimum extracts, to be used on the tomato test plant, were determined using phytotoxicity test (seed germination test) as main constraint. Thereafter, selected extracts were characterized and secondary metabolites profiling were detected by NMR technique. Selected extracts were applied on tomato in a growth chamber at different doses in comparison to humic-like substances as positive control (Ctrl+) and to a Hoagland solution as negative control (Ctrl-). At the end of the experiment, agronomical parameters were determined and NMR-metabolomic profiling were conducted on tomato seedlings. Results are summarized as follow: (i) raw showed an interesting content, either at nutritional or biological level; (ii) aqueous extraction resulted higher yield than other used solvent; (iii) at high extraction ratio (1:25 for BSG; 1:100 for FPR; and 1:200 for LPR) aqueous extracts were not phytotoxic on the tomato test plant; (iv) all aqueous extract are differently rich in nutrients, aminoacids, sugars and low molecular weight molecules; (v) all extract exhibited a growth promotion at low application doses; (vi) regarding plant metabolomics study, all treatments showed a different metabolites in respect to Ctrl- treatment. BSG, LPR and Ctrl+ treatments had similar metabolic profile. Finally, Metabolomic study provided an efficient tool and a key reporter about bio-effectors impact on plants. The visible effect and measured agronomical parameters was emphasized and demonstrated by metabolic profiling which offer insights into the affected plant metabolic pathways. As conclusion, our results supported the prediction that plant derived materials may interfere again in plant production regardless their nutritional content. Keywords: Bio-effectors; Metabolomics; Nuclear Magnetic Resonance (NMR); Barley; Fennel; Lemon; Tomato.

An in vitro evaluation of graphene oxide reduced by Ganoderma spp. in human breast cancer cells (MDA-MB-231).

PubMed

Gurunathan, Sangiliyandi; Han, Jaewoong; Park, Jung Hyun; Kim, Jin Hoi

2014-01-01

Recently, graphene and graphene-related materials have attracted much attention due their unique properties, such as their physical, chemical, and biocompatibility properties. This study aimed to determine the cytotoxic effects of graphene oxide (GO) that is reduced biologically using Ganoderma spp. mushroom extracts in MDA-MB-231 human breast cancer cells. Herein, we describe a facile and green method for the reduction of GO using extracts of Ganoderma spp. as a reducing agent. GO was reduced without any hazardous chemicals in an aqueous solution, and the reduced GO was characterized using a range of analytical procedures. The Ganoderma extract (GE)-reduced GO (GE-rGO) was characterized by ultraviolet-visible absorption spectroscopy, X-ray diffraction, Fourier-transform infrared spectroscopy, X-ray photoelectron spectroscopy, dynamic light scattering, scanning electron microscopy, Raman spectroscopy, and atomic force microscopy. Furthermore, the toxicity of GE-rGO was evaluated using a sequence of assays such as cell viability, lactate dehydrogenase leakage, and reactive oxygen species generation in human breast cancer cells (MDA-MB-231). The preliminary characterization of reduction of GO was confirmed by the red-shifting of the absorption peak for GE-rGO to 265 nm from 230 nm. The size of GO and GE-rGO was found to be 1,880 and 3,200 nm, respectively. X-ray diffraction results confirmed that reduction processes of GO and the processes of removing intercalated water molecules and the oxide groups. The surface functionalities and chemical natures of GO and GE-rGO were confirmed using Fourier-transform infrared spectroscopy and X-ray photoelectron spectroscopy. The surface morphologies of the synthesized graphene were analyzed using high-resolution scanning electron microscopy. Raman spectroscopy revealed single- and multilayer properties of GE-rGO. Atomic force microscopy images provided evidence for the formation of graphene. Furthermore, the effect of GO and GE-rGO was examined using a series of assays, such as cell viability, membrane integrity, and reactive oxygen species generation, which are key molecules involved in apoptosis. The results obtained from cell viability and lactate dehydrogenase assay suggest that GO and GE-rGO cause dose-dependent toxicity in the cells. Interestingly, it was found that biologically derived GE-rGO is more toxic to cancer cells than GO. We describe a simple, green, nontoxic, and cost-effective approach to producing graphene using mushroom extract as a reducing and stabilizing agent. The proposed method could enable synthesis of graphene with potential biological and biomedical applications such as in cancer and angiogenic disorders. To our knowledge, this is the first report using mushroom extract as a reducing agent for the synthesis of graphene. Mushroom extract can be used as a biocatalyst for the production of graphene.

Organic Analysis in the Miller Range 090657 CR2 Chondrite: Part 2 Amino Acid Analyses

NASA Technical Reports Server (NTRS)

Burton, A. S.; Cao, T.; Nakamura-Messenger, K.; Berger, E. L.; Messenger, S.; Clemett, S. J.; Aponte, J. C.; Elsila, J. E.

2016-01-01

Primitive carbonaceous chondrites contain a wide variety of organic material, ranging from soluble discrete molecules to insoluble, unstructured kerogen-like components, as well as structured nano-globules of macromolecular carbon. The relationship between the soluble organic molecules, macromolecular organic material, and host minerals are poorly understood. Due to the differences in extractability of soluble and insoluble organic materials, the analysis methods for each differ and are often performed independently. The combination of soluble and insoluble analyses, when performed concurrently, can provide a wider understanding of spatial distribution, and elemental, structural and isotopic composition of organic material in primitive meteorites. Using macroscale extraction and analysis techniques in combination with in situ microscale observation, we have been studying both insoluble and soluble organic material in the primitive CR2 chondrite Miller Range (MIL) 090657. In accompanying abstracts (Cao et al. and Messenger et al.) we discuss insoluble organic material in the samples. By performing the consortium studies, we aim to improve our understanding of the relationship between the meteorite minerals and the soluble and insoluble organic phases and to delineate which species formed within the meteorite and those that formed in nebular or presolar environments. In this abstract, we present the results of amino acid analyses of MIL 090657 by ultra performance liquid chromatography with fluorescence detection and quadrupole-time of flight mass spectrometry. Amino acids are of interest because they are essential to life on Earth, and because they are present in sufficient structural, enantiomeric and isotopic diversity to allow insights into early solar system chemical processes. Furthermore, these are among the most isotopically anomalous species, yet at least some fraction are thought to have formed by aqueously-mediated processes during parent body alteration.

Porous Aromatic Framework 48/Gel Hybrid Material Coated Solid-Phase Microextraction Fiber for the Determination of the Migration of Styrene from Polystyrene Food Contact Materials.

PubMed

Jin, Yuanyuan; Li, Zhongyue; Yang, Lei; Xu, Jun; Zhao, Le; Li, Zhonghao; Niu, Jiajia

2017-01-17

A novel solid-phase microextraction (SPME) fiber was fabricated by a porous aromatic framework 48 (PAF-48)/gel hybrid material through a sol-gel process. PAF-48 is a porous organic framework (POF) material that was polymerized from 1,3,5-triphenylbenzene. The uniform pore structure, high surface area, continuous conjugate network, and hydrophobicity make PAF-48 expected to have special abilities to absorb and extract styrene as well as some other harmful volatile aromatic compounds (VACs). The PAF-48/gel-coated fiber was explored for the extraction of styrene and six VACs (benzene, toluene, ethylbenzene, and xylenes) from aqueous food simulants followed by gas chromatography (GC) separation. The fiber was found to be very sensitive for the determination of the target molecules with wide linear ranges (0.1-200 or 500 μg·kg -1 ), low limits of detection (LODs, 0.003-0.060 μg·kg -1 ), acceptable precisions (intraday relative standard deviation, RSD < 5.9%, interday RSD < 7.3%), and long lifetime (>200 times). Particularly for styrene, the PAF-48/gel-coated fiber exhibited a much lower LOD (0.006 μg·kg -1 ) compared with most of the reported fibers. Moreover, the PAF-48/gel-coated fiber had a high extraction selectivity for styrene and VACs over alcohols, phenols, aromatic amines, and alkanes and show a molecular sieving effect for the different molecule sizes. Finally, the PAF-48/gel-coated SPME fiber was successfully applied in GC for the determination of the specific migrations of styrene and VACs from polystyrene (PS) plastic food contact materials (FCMs).

Cleavage of poly(cis-1,4-isoprene) rubber as solid substrate by cultures of Gordonia polyisoprenivorans.

PubMed

Andler, R; Hiessl, S; Yücel, O; Tesch, M; Steinbüchel, A

2018-03-09

Potential biotechnological recycling processes for rubber products include the bacterial degradation of poly(cis-1,4-isoprene) (IR) in order to achieve its total biodegradation or its biotransformation into useful products. The actinomycete Gordonia polyisoprenivorans strain VH2 catalyzes the degradation of IR and enables its use as a sole carbon source via β-oxidation. The initial cleavage reaction is catalyzed by the extracellular latex clearing protein (Lcp). This dioxygenase is the key enzyme for the formation of oligo(cis-1,4-isoprene) molecules with different lengths, i.e., numbers of isoprene units. For the first time, IR was used as a solid substrate in 2-l fermenters. Two different particle size fractions (63-500 and 500-1000 μm) and three stirring rates (300, 400 and 500 rpm) were evaluated in the process. An increase of the cell concentration was achieved by using smaller particles and by using lower stirring rates, reaching a final biomass concentration of 0.52 g l -1 at 300 rpm after 12 days of cultivation. In order to enhance the formation of oligo(cis-1,4-isoprene) molecules, a transposon insertion mutant (TH5) of G. polyisoprenivorans strain VH2 that has lost the ability to transport the partial degradation products into the cells was used, thereby allowing the accumulation of the degradation products in the culture supernatants. Propionate, glucose and glycerol were evaluated as additional carbon sources besides IR, and the highest yields were observed on propionate. In 2-l bioreactors with pH control, different feeding regimes were performed during cultivation by the addition of propionate every 24 or 48 h for 16 days. After liquid-liquid extraction and a derivatization with Girard's T reagent, the oligo(cis-1,4-isoprene) molecules were detected by ESI-MS. The mass distribution of the degradation products was affected by the selection of the extraction solvent, but no influence of longer cultivation periods was detected. Copyright © 2018. Published by Elsevier B.V.

A microfluidic cigarette smoke collecting platform for simultaneous sample extraction and multiplex analysis.

PubMed

Hu, Shan-Wen; Xu, Bi-Yi; Qiao, Shu; Zhao, Ge; Xu, Jing-Juan; Chen, Hong-Yuan; Xie, Fu-Wei

2016-04-01

In this work, we report a novel microfluidic gas collecting platform aiming at simultaneous sample extraction and multiplex mass spectrometry (MS) analysis. An alveolar-mimicking elastic polydimethylsiloxane (PDMS) structures was designed to move dynamically driven by external pressure. The movement was well tuned both by its amplitude and rhythm following the natural process of human respiration. By integrating the alveolar units into arrays and assembling them to gas channels, a cyclic contraction/expansion system for gas inhale and exhale was successfully constructed. Upon equipping this system with a droplet array on the alveolar array surface, we were able to get information of inhaled smoke in a new strategy. Here, with cigarette smoke as an example, analysis of accumulation for target molecules during passive smoking is taken. Relationships between the breathing times, distances away from smokers and inhaled content of nicotine are clarified. Further, by applying different types of extraction solvent droplets on different locations of the droplet array, simultaneous extraction of nicotine, formaldehyde and caproic acid in sidestream smoke (SS) are realized. Since the extract droplets are spatially separated, they can be directly analyzed by MS which is fast and can rid us of all complex sample separation and purification steps. Combining all these merits, this small, cheap and portable platform might find wide application in inhaled air pollutant analysis both in and outdoors. Copyright © 2015 Elsevier B.V. All rights reserved.

The Cytolethal Distending Toxin Induces Receptor Activator of NF-κB Ligand Expression in Human Gingival Fibroblasts and Periodontal Ligament Cells

PubMed Central

Belibasakis, G. N.; Johansson, A.; Wang, Y.; Chen, C.; Kalfas, S.; Lerner, U. H.

2005-01-01

Actinobacillus actinomycetemcomitans is associated with localized aggressive periodontitis, a disease characterized by rapid loss of the alveolar bone surrounding the teeth. Receptor activator of NF-κB Ligand (RANKL) and osteoprotegerin (OPG) are two molecules that regulate osteoclast formation and bone resorption. RANKL induces osteoclast differentiation and activation, whereas OPG blocks this process by acting as a decoy receptor for RANKL. The purpose of this study was to investigate the effect of A. actinomycetemcomitans on the expression of RANKL and OPG in human gingival fibroblasts and periodontal ligament cells. RANKL mRNA expression was induced in both cell types challenged by A. actinomycetemcomitans extract, whereas OPG mRNA expression remained unaffected. Cell surface RANKL protein was also induced by A. actinomycetemcomitans, whereas there was no change in OPG protein secretion. A cytolethal distending toxin (Cdt) gene-knockout strain of A. actinomycetemcomitans did not induce RANKL expression, in contrast to its wild-type strain. Purified Cdt from Haemophilus ducreyi alone, or in combination with extract from the A. actinomycetemcomitans cdt mutant strain, induced RANKL expression. Pretreatment of A. actinomycetemcomitans wild-type extract with Cdt antiserum abolished RANKL expression. In conclusion, A. actinomycetemcomitans induces RANKL expression in periodontal connective tissue cells. Cdt is crucial for this induction and may therefore be involved in the pathological bone resorption during the process of localized aggressive periodontitis. PMID:15618171

Green Synthesis of Silver Nanoparticles by using Eucalyptus Globulus Leaf Extract

NASA Astrophysics Data System (ADS)

Balamurugan, Madheswaran; Saravanan, Shanmugam

2017-12-01

A single step eco-friendly, energy efficient and economically scalable green method was employed to synthesize silver nanoparticles. In this work, the synthesis of silver nanoparticles using Eucalyptus globulus leaf extract as reducing and capping agent along with water as solvent at normal room temperature is described. Silver nanoparticles were prepared from aqueous silver nitrate solution by adding the leaf extract. The prepared nanoparticles were characterized by using UV-visible Spectrophotometer, X-ray diffractometer, High Resolution Transmission Electron Microscope (HR-TEM) and Fourier Transform Infrared Spectroscope (FTIS). X-ray diffraction studies brought to light the crystalline nature and the face centered cubic structure of the silver nanoparticles. Using HR-TEM. the nano sizes and morphology of the particles were studied. The mean sizes of the prepared silver nanoparticles ranged from 30 to 36 nm. The density of the particles was tuned by varying the molar ratio of silver nitrate. FTIS studies showed the functional group of organic molecules which were located on the surface of the silver nanoparticles. Originating from the leaf extracts, these organic molecules reduced and capped the particles.

Green fabricated CuO nanobullets via Olea europaea leaf extract shows auspicious antimicrobial potential.

PubMed

Maqbool, Qaisar; Iftikhar, Sidra; Nazar, Mudassar; Abbas, Fazal; Saleem, Asif; Hussain, Talib; Kausar, Rizwan; Anwaar, Sadaf; Jabeen, Nyla

2017-06-01

In present investigation, copper oxide (CuO) nanostructures have been prepared via green chemistry. Olea europaea leaf extract act as strong chelating agent for tailoring physical as well as bio-medical characteristics of CuO at the nano-size. Physical characterisation such as scanning electron microscope analysis depicts the formation of homogenised spherical shape nanoparticles (NPs) with average size of 42 nm. X-ray diffraction and Fourier transform infrared spectroscopy further confirmed the crystalline pure phase and monoclinic structure. High performance liquid chromatography (HPLC) testing is performed to evaluate the relative concentration of bioactive molecules in the O. europaea leaf extract. From HPLC results capping action of organic molecules around CuO-NPs is hypothesised. The antimicrobial potency of biosynthesised CuO-NPs have been evaluated using colony forming unit (CFU) counting assay and disc diffusion method which shows a significant zone of inhibition against bacterial and fungal strains may be highly potential for future antimicrobial pharmaceutics. Furthermore, reduction of various precursors by plant extract will reduce environmental impact over chemical synthesis.

Comprehensive analysis of oil sands processed water by direct-infusion Fourier-transform ion cyclotron resonance mass spectrometry with and without offline UHPLC sample prefractionation.

PubMed

Nyakas, Adrien; Han, Jun; Peru, Kerry M; Headley, John V; Borchers, Christoph H

2013-05-07

Oil sands processed water (OSPW) is the main byproduct of the large-scale bitumen extraction activity in the Athabasca oil sands region (Alberta, Canada). We have investigated the acid-extractable fraction (AEF) of OSPW by extraction-only (EO) direct infusion (DI) negative-ion mode electrospray ionization (ESI) on a 12T-Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS), as well as by offline ultrahigh performance liquid chromatography (UHPLC) followed by DI-FTICR-MS. A preliminary offline UHPLC separation into 8 fractions using a reversed-phase C4 column led to approximately twice as many detected peaks and identified compounds (973 peaks versus 2231 peaks, of which 856 and 1734 peaks, respectively, could be assigned to chemical formulas based on accurate mass measurements). Conversion of these masses to the Kendrick mass scale allowed the straightforward recognition of homologues. Naphthenic (CnH2n+zO2) and oxy-naphthenic (CnH2n+zOx) acids represented the largest group of molecules with assigned formulas (64%), followed by sulfur-containing compounds (23%) and nitrogen-containing compounds (8%). Pooling of corresponding fractions from two consecutive offline UHPLC runs prior to MS analysis resulted in ~50% more assignments than a single injection, resulting in 3-fold increase of identifications compared to EO-DI-FTICR-MS using the same volume of starting material. Liquid-liquid extraction followed by offline UHPLC fractionation thus holds enormous potential for a more comprehensive profiling of OSPW, which may provide a deeper understanding of its chemical nature and environmental impact.

Optical Analysis of Power Distribution in Top-Emitting Organic Light Emitting Diodes Integrated with Nanolens Array Using Finite Difference Time Domain.

PubMed

Han, Kyung-Hoon; Park, Young-Sam; Cho, Doo-Hee; Han, Yoonjay; Lee, Jonghee; Yu, Byounggon; Cho, Nam Sung; Lee, Jeong-Ik; Kim, Jang-Joo

2018-06-06

Recently, we have addressed that a formation mechanism of a nanolens array (NLA) fabricated by using a maskless vacuum deposition is explained as the increase in surface tension of organic molecules induced by their crystallization. Here, as another research using finite difference time domain simulations, not electric field intensities but transmitted energies of electromagnetic waves inside and outside top-emitting blue organic light-emitting diodes (TOLEDs), without and with NLAs, are obtained, to easily grasp the effect of NLA formation on the light extraction of TOLEDs. Interestingly, the calculations show that NLA acts as an efficient light extraction structure. With NLA, larger transmitted energies in the direction from emitting layer to air are observed, indicating that NLAs send more light to air otherwise trapped in the devices by reducing the losses by waveguide and absorption. This is more significant for higher refractive index of NLA. Simulation and measurement results are consistent. A successful increase in both light extraction efficiency and color stability of blue TOLEDs, rarely reported before, is accomplished by introducing the highly process-compatible NLA technology using the one-step dry process. Blue TOLEDs integrated with a N, N'-di(1-naphthyl)- N, N'-diphenyl-(1,1'-biphenyl)-4,4'-diamine NLA with a refractive index of 1.8 show a 1.55-times-higher light extraction efficiency, compared to those without it. In addition, viewing angle characteristics are enhanced and image blurring is reduced, indicating that the manufacturer-adaptable technology satisfies the requirements of highly efficient and color-stable top-emission displays.

Easy and fast method for expression and native extraction of Plasmodium vivax Duffy binding protein fragments.

PubMed

Moreno-Pérez, Darwin Andrés; Baquero, Luis Alfredo; Bermúdez, Maritza; Gómez-Muñoz, Laura Alejandra; Varela, Yahson; Patarroyo, Manuel Alfonso

2018-02-08

The Plasmodium vivax Duffy binding protein (PvDBP) has been the most studied ligand binding human reticulocytes to date. This molecule has a cysteine-rich domain in region II (RII) which has been used as control for evaluating the target cell binding activity of several parasite molecules. However, obtaining rPvDBP-RII in a soluble form using the Escherichia coli expression system usually requires laborious and time-consuming steps for recovering the molecule's structure and function, considering it is extracted from inclusion bodies. The present study describes an easy and fast method for expressing and obtaining several PvDBP fragments which should prove ideal for use in protein-cell interaction assays. Two PvDBP encoding regions (rii and riii/v) were cloned in pEXP5-CT vector and expressed in E. coli and extracted from the soluble fraction (rPvDBP-RII S and rPvDBP-RIII/V S ) using a simple freezing/thawing protocol. After the purification, dichroism analysis enabled verifying high rPvDBP-RII S and rPvDBP-RIII/V S secondary structure α-helix content, which was lowered when molecules were extracted from inclusion bodies (rPvDBP-RII IB and rPvDBP-RIII/V IB ) using a denaturing step. Interestingly, rPvDBP-RII S , but not rPvDBP-RII IB , bound to human reticulocytes, while rPvDBP-RIII/V S and rPvDBP-RIII/V IB bound to such cells in a similar way to negative control (cells incubated without recombinant proteins). This research has shown for the first time how rPvDBP-RII can be expressed and obtained in soluble form using the E. coli system and avoiding the denaturation and refolding steps commonly used. The results highlight the usefulness of the rPvDBP-RIII/V S fragment as a non-binding control for protein-cell target interaction assays. The soluble extraction protocol described is a good alternative to obtain fully functional P. vivax proteins in a fast and easy way, which will surely prove useful to laboratories working in studying this parasite's biology.

γ-Heptalactone is an endogenously produced quorum-sensing molecule regulating growth and secondary metabolite production by Aspergillus nidulans.

PubMed

Williams, Headley E; Steele, Jonathan C P; Clements, Mark O; Keshavarz, Tajalli

2012-11-01

Microbes monitor their population density through a mechanism termed quorum sensing. It is believed that quorum-sensing molecules diffuse from the microbial cells and circulate in the surrounding environment as a function of cell density. When these molecules reach a threshold concentration, the gene expression of the entire population is altered in a coordinated manner. This work provides evidence that Aspergillus nidulans produces at least one small diffusible molecule during its growth cycle which accumulates at high cell density and alters the organism's behaviour. When added to low-density cell cultures, ethyl acetate extracts from stationary phase culture supernatants of A. nidulans resulted in the abolition of the lag phase, induced an earlier deceleration phase with 16.3 % decrease in the final cell dry weight and resulted in a 37.8 % increase in the expression of ipnA::lacZ reporter gene construct, which was used as a marker for penicillin production compared to non-treated controls. The bioactive molecule present in the stationary phase extract was purified to homogeneity and was identified by liquid chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy to be γ-heptalactone. This study provides the first evidence that A. nidulans produces γ-heptalactone at a high cell density and it can alter the organism's behaviour at a low cell density. γ-Heptalactone hence acts as a quorum-sensing molecule in the producing strain.

Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis.

PubMed

Cao, Chan; Long, Yi-Tao

2018-02-20

Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis, we develop an integrated current measurement system and an accurate data processing method for nanopore sensing. The unique geometric structure of a biological nanopore offers a distinct advantage as a nanosensor for single-molecule sensing. The construction of the pore entrance is responsible for capturing the target molecule, while the lumen region determines the translocation process of the single molecule. Since the capture of the target molecule is predominantly diffusion-limited, it is expected that the capture ability of the nanopore toward the target analyte could be effectively enhanced by site-directed mutations of key amino acids with desirable groups. Additionally, changing the side chains inside the wall of the biological nanopore could optimize the geometry of the pore and realize an optimal interaction between the single-molecule interface and the analyte. These improvements would allow for high spatial and current resolution of nanopore sensors, which would ensure the possibility of dynamic study of single biomolecules, including their metastable conformations, charge distributions, and interactions. In the future, data analysis with powerful algorithms will make it possible to automatically and statistically extract detailed information while an analyte translocates through the pore. We conclude that these improvements could have tremendous potential applications for nanopore sensing in the near future.

X-ray coherent diffraction imaging of cellulose fibrils in situ.

PubMed

Lal, Jyotsana; Harder, Ross; Makowski, Lee

2011-01-01

Cellulose is the most abundant renewable source of organic molecules on earth[1]. As fossil fuel reserves become depleted, the use of cellulose as a feed stock for fuels and chemicals is being aggressively explored. Cellulose is a linear polymer of glucose that packs tightly into crystalline fibrils that make up a substantial proportion of plant cell walls. Extraction of the cellulose chains from these fibrils in a chemically benign process has proven to be a substantial challenge [2]. Monitoring the deconstruction of the fibrils in response to physical and chemical treatments would expedite the development of efficient processing methods. As a step towards achieving that goal, we here describe Bragg-coherent diffraction imaging (CDI) as an approach to producing images of cellulose fibrils in situ within vascular bundles from maize.

Quantum monodromy and quantum phase transitions in floppy molecules

NASA Astrophysics Data System (ADS)

Larese, Danielle

2012-10-01

A simple algebraic Hamiltonian has been used to explore the vibrational and rotational spectra of the skeletal bending modes of HCNO, BrCNO, NCNCS, and other "floppy" (quasi-linear or quasi-bent) molecules. These molecules have large-amplitude, low-energy bending modes and champagne-bottle potential surfaces, making them good candidates for observing quantum phase transitions (QPT). We describe the geometric phase transitions from bent to linear in these and other non-rigid molecules, quantitatively analyzing the spectroscopic signatures of ground state QPT, excited state QPT, and quantum monodromy. The algebraic framework is ideal for this work because of its small calculational effort yet robust results. Although these methods have historically found success with tri-and four-atomic molecules, we now address five-atomic and simple branched molecules such as CH3NCO and GeH3NCO. Extraction of potential functions are completed for several molecules, resulting in predictions of barriers to linearity and equilibrium bond angles.

Interspecies scaling and prediction of human clearance: comparison of small- and macro-molecule drugs

PubMed Central

Huh, Yeamin; Smith, David E.; Feng, Meihau Rose

2014-01-01

Human clearance prediction for small- and macro-molecule drugs was evaluated and compared using various scaling methods and statistical analysis.Human clearance is generally well predicted using single or multiple species simple allometry for macro- and small-molecule drugs excreted renally.The prediction error is higher for hepatically eliminated small-molecules using single or multiple species simple allometry scaling, and it appears that the prediction error is mainly associated with drugs with low hepatic extraction ratio (Eh). The error in human clearance prediction for hepatically eliminated small-molecules was reduced using scaling methods with a correction of maximum life span (MLP) or brain weight (BRW).Human clearance of both small- and macro-molecule drugs is well predicted using the monkey liver blood flow method. Predictions using liver blood flow from other species did not work as well, especially for the small-molecule drugs. PMID:21892879

Circular dichroism in photoelectron images from aligned nitric oxide molecules

DOE PAGES

Sen, Ananya; Pratt, S. T.; Reid, K. L.

2017-05-03

We have used velocity map photoelectron imaging to study circular dichroism of the photoelectron angular distributions (PADs) of nitric oxide following two-color resonanceenhanced two-photon ionization via selected rotational levels of the A 2Σ +, v' = 0 state. By using a circularly polarized pump beam and a counter-propagating, circularly polarized probe beam, cylindrical symmetry is preserved in the ionization process, and the images can be reconstructed using standard algorithms. The VMI set up enables individual ion rotational states to be resolved with excellent collection efficiency, rendering the measurements considerably simpler to perform than previous measurements conducted with a conventional photoelectronmore » spectrometer. The results demonstrate that circular dichroism is observed even when cylindrical symmetry is maintained, and serve as a reminder that dichroism is a general feature of the multiphoton ionization of atoms and molecules. Furthermore, the observed PADs are in good agreement with calculations based on parameters extracted from previous experimental results obtained by using a time-offlight electron spectrometer.« less

Advanced nanoelectronic architectures for THz-based biological agent detection

NASA Astrophysics Data System (ADS)

Woolard, Dwight L.; Jensen, James O.

2009-02-01

The U.S. Army Research Office (ARO) and the U.S. Army Edgewood Chemical Biological Center (ECBC) jointly lead and support novel research programs that are advancing the state-of-the-art in nanoelectronic engineering in application areas that have relevance to national defense and security. One fundamental research area that is presently being emphasized by ARO and ECBC is the exploratory investigation of new bio-molecular architectural concepts that can be used to achieve rapid, reagent-less detection and discrimination of biological warfare (BW) agents, through the control of multi-photon and multi-wavelength processes at the nanoscale. This paper will overview an ARO/ECBC led multidisciplinary research program presently under the support of the U.S. Defense Threat Reduction Agency (DTRA) that seeks to develop new devices and nanoelectronic architectures that are effective for extracting THz signatures from target bio-molecules. Here, emphasis will be placed on the new nanosensor concepts and THz/Optical measurement methodologies for spectral-based sequencing/identification of genetic molecules.

FANTOM5 CAGE profiles of human and mouse samples.

PubMed

Noguchi, Shuhei; Arakawa, Takahiro; Fukuda, Shiro; Furuno, Masaaki; Hasegawa, Akira; Hori, Fumi; Ishikawa-Kato, Sachi; Kaida, Kaoru; Kaiho, Ai; Kanamori-Katayama, Mutsumi; Kawashima, Tsugumi; Kojima, Miki; Kubosaki, Atsutaka; Manabe, Ri-Ichiroh; Murata, Mitsuyoshi; Nagao-Sato, Sayaka; Nakazato, Kenichi; Ninomiya, Noriko; Nishiyori-Sueki, Hiromi; Noma, Shohei; Saijyo, Eri; Saka, Akiko; Sakai, Mizuho; Simon, Christophe; Suzuki, Naoko; Tagami, Michihira; Watanabe, Shoko; Yoshida, Shigehiro; Arner, Peter; Axton, Richard A; Babina, Magda; Baillie, J Kenneth; Barnett, Timothy C; Beckhouse, Anthony G; Blumenthal, Antje; Bodega, Beatrice; Bonetti, Alessandro; Briggs, James; Brombacher, Frank; Carlisle, Ailsa J; Clevers, Hans C; Davis, Carrie A; Detmar, Michael; Dohi, Taeko; Edge, Albert S B; Edinger, Matthias; Ehrlund, Anna; Ekwall, Karl; Endoh, Mitsuhiro; Enomoto, Hideki; Eslami, Afsaneh; Fagiolini, Michela; Fairbairn, Lynsey; Farach-Carson, Mary C; Faulkner, Geoffrey J; Ferrai, Carmelo; Fisher, Malcolm E; Forrester, Lesley M; Fujita, Rie; Furusawa, Jun-Ichi; Geijtenbeek, Teunis B; Gingeras, Thomas; Goldowitz, Daniel; Guhl, Sven; Guler, Reto; Gustincich, Stefano; Ha, Thomas J; Hamaguchi, Masahide; Hara, Mitsuko; Hasegawa, Yuki; Herlyn, Meenhard; Heutink, Peter; Hitchens, Kelly J; Hume, David A; Ikawa, Tomokatsu; Ishizu, Yuri; Kai, Chieko; Kawamoto, Hiroshi; Kawamura, Yuki I; Kempfle, Judith S; Kenna, Tony J; Kere, Juha; Khachigian, Levon M; Kitamura, Toshio; Klein, Sarah; Klinken, S Peter; Knox, Alan J; Kojima, Soichi; Koseki, Haruhiko; Koyasu, Shigeo; Lee, Weonju; Lennartsson, Andreas; Mackay-Sim, Alan; Mejhert, Niklas; Mizuno, Yosuke; Morikawa, Hiromasa; Morimoto, Mitsuru; Moro, Kazuyo; Morris, Kelly J; Motohashi, Hozumi; Mummery, Christine L; Nakachi, Yutaka; Nakahara, Fumio; Nakamura, Toshiyuki; Nakamura, Yukio; Nozaki, Tadasuke; Ogishima, Soichi; Ohkura, Naganari; Ohno, Hiroshi; Ohshima, Mitsuhiro; Okada-Hatakeyama, Mariko; Okazaki, Yasushi; Orlando, Valerio; Ovchinnikov, Dmitry A; Passier, Robert; Patrikakis, Margaret; Pombo, Ana; Pradhan-Bhatt, Swati; Qin, Xian-Yang; Rehli, Michael; Rizzu, Patrizia; Roy, Sugata; Sajantila, Antti; Sakaguchi, Shimon; Sato, Hiroki; Satoh, Hironori; Savvi, Suzana; Saxena, Alka; Schmidl, Christian; Schneider, Claudio; Schulze-Tanzil, Gundula G; Schwegmann, Anita; Sheng, Guojun; Shin, Jay W; Sugiyama, Daisuke; Sugiyama, Takaaki; Summers, Kim M; Takahashi, Naoko; Takai, Jun; Tanaka, Hiroshi; Tatsukawa, Hideki; Tomoiu, Andru; Toyoda, Hiroo; van de Wetering, Marc; van den Berg, Linda M; Verardo, Roberto; Vijayan, Dipti; Wells, Christine A; Winteringham, Louise N; Wolvetang, Ernst; Yamaguchi, Yoko; Yamamoto, Masayuki; Yanagi-Mizuochi, Chiyo; Yoneda, Misako; Yonekura, Yohei; Zhang, Peter G; Zucchelli, Silvia; Abugessaisa, Imad; Arner, Erik; Harshbarger, Jayson; Kondo, Atsushi; Lassmann, Timo; Lizio, Marina; Sahin, Serkan; Sengstag, Thierry; Severin, Jessica; Shimoji, Hisashi; Suzuki, Masanori; Suzuki, Harukazu; Kawai, Jun; Kondo, Naoto; Itoh, Masayoshi; Daub, Carsten O; Kasukawa, Takeya; Kawaji, Hideya; Carninci, Piero; Forrest, Alistair R R; Hayashizaki, Yoshihide

2017-08-29

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.

FANTOM5 CAGE profiles of human and mouse samples

PubMed Central

Noguchi, Shuhei; Arakawa, Takahiro; Fukuda, Shiro; Furuno, Masaaki; Hasegawa, Akira; Hori, Fumi; Ishikawa-Kato, Sachi; Kaida, Kaoru; Kaiho, Ai; Kanamori-Katayama, Mutsumi; Kawashima, Tsugumi; Kojima, Miki; Kubosaki, Atsutaka; Manabe, Ri-ichiroh; Murata, Mitsuyoshi; Nagao-Sato, Sayaka; Nakazato, Kenichi; Ninomiya, Noriko; Nishiyori-Sueki, Hiromi; Noma, Shohei; Saijyo, Eri; Saka, Akiko; Sakai, Mizuho; Simon, Christophe; Suzuki, Naoko; Tagami, Michihira; Watanabe, Shoko; Yoshida, Shigehiro; Arner, Peter; Axton, Richard A.; Babina, Magda; Baillie, J. Kenneth; Barnett, Timothy C.; Beckhouse, Anthony G.; Blumenthal, Antje; Bodega, Beatrice; Bonetti, Alessandro; Briggs, James; Brombacher, Frank; Carlisle, Ailsa J.; Clevers, Hans C.; Davis, Carrie A.; Detmar, Michael; Dohi, Taeko; Edge, Albert S.B.; Edinger, Matthias; Ehrlund, Anna; Ekwall, Karl; Endoh, Mitsuhiro; Enomoto, Hideki; Eslami, Afsaneh; Fagiolini, Michela; Fairbairn, Lynsey; Farach-Carson, Mary C.; Faulkner, Geoffrey J.; Ferrai, Carmelo; Fisher, Malcolm E.; Forrester, Lesley M.; Fujita, Rie; Furusawa, Jun-ichi; Geijtenbeek, Teunis B.; Gingeras, Thomas; Goldowitz, Daniel; Guhl, Sven; Guler, Reto; Gustincich, Stefano; Ha, Thomas J.; Hamaguchi, Masahide; Hara, Mitsuko; Hasegawa, Yuki; Herlyn, Meenhard; Heutink, Peter; Hitchens, Kelly J.; Hume, David A.; Ikawa, Tomokatsu; Ishizu, Yuri; Kai, Chieko; Kawamoto, Hiroshi; Kawamura, Yuki I.; Kempfle, Judith S.; Kenna, Tony J.; Kere, Juha; Khachigian, Levon M.; Kitamura, Toshio; Klein, Sarah; Klinken, S. Peter; Knox, Alan J.; Kojima, Soichi; Koseki, Haruhiko; Koyasu, Shigeo; Lee, Weonju; Lennartsson, Andreas; Mackay-sim, Alan; Mejhert, Niklas; Mizuno, Yosuke; Morikawa, Hiromasa; Morimoto, Mitsuru; Moro, Kazuyo; Morris, Kelly J.; Motohashi, Hozumi; Mummery, Christine L.; Nakachi, Yutaka; Nakahara, Fumio; Nakamura, Toshiyuki; Nakamura, Yukio; Nozaki, Tadasuke; Ogishima, Soichi; Ohkura, Naganari; Ohno, Hiroshi; Ohshima, Mitsuhiro; Okada-Hatakeyama, Mariko; Okazaki, Yasushi; Orlando, Valerio; Ovchinnikov, Dmitry A.; Passier, Robert; Patrikakis, Margaret; Pombo, Ana; Pradhan-Bhatt, Swati; Qin, Xian-Yang; Rehli, Michael; Rizzu, Patrizia; Roy, Sugata; Sajantila, Antti; Sakaguchi, Shimon; Sato, Hiroki; Satoh, Hironori; Savvi, Suzana; Saxena, Alka; Schmidl, Christian; Schneider, Claudio; Schulze-Tanzil, Gundula G.; Schwegmann, Anita; Sheng, Guojun; Shin, Jay W.; Sugiyama, Daisuke; Sugiyama, Takaaki; Summers, Kim M.; Takahashi, Naoko; Takai, Jun; Tanaka, Hiroshi; Tatsukawa, Hideki; Tomoiu, Andru; Toyoda, Hiroo; van de Wetering, Marc; van den Berg, Linda M.; Verardo, Roberto; Vijayan, Dipti; Wells, Christine A.; Winteringham, Louise N.; Wolvetang, Ernst; Yamaguchi, Yoko; Yamamoto, Masayuki; Yanagi-Mizuochi, Chiyo; Yoneda, Misako; Yonekura, Yohei; Zhang, Peter G.; Zucchelli, Silvia; Abugessaisa, Imad; Arner, Erik; Harshbarger, Jayson; Kondo, Atsushi; Lassmann, Timo; Lizio, Marina; Sahin, Serkan; Sengstag, Thierry; Severin, Jessica; Shimoji, Hisashi; Suzuki, Masanori; Suzuki, Harukazu; Kawai, Jun; Kondo, Naoto; Itoh, Masayoshi; Daub, Carsten O.; Kasukawa, Takeya; Kawaji, Hideya; Carninci, Piero; Forrest, Alistair R.R.; Hayashizaki, Yoshihide

2017-01-01

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities. PMID:28850106

One-pot synthesis of amino acid precursors with insoluble organic matter in planetesimals with aqueous activity.

PubMed

Kebukawa, Yoko; Chan, Queenie H S; Tachibana, Shogo; Kobayashi, Kensei; Zolensky, Michael E

2017-03-01

The exogenous delivery of organic molecules could have played an important role in the emergence of life on the early Earth. Carbonaceous chondrites are known to contain indigenous amino acids as well as various organic compounds and complex macromolecular materials, such as the so-called insoluble organic matter (IOM), but the origins of the organic matter are still subject to debate. We report that the water-soluble amino acid precursors are synthesized from formaldehyde, glycolaldehyde, and ammonia with the presence of liquid water, simultaneously with macromolecular organic solids similar to the chondritic IOM. Amino acid products from hydrothermal experiments after acid hydrolysis include α-, β-, and γ-amino acids up to five carbons, for which relative abundances are similar to those extracted from carbonaceous chondrites. One-pot aqueous processing from simple ubiquitous molecules can thus produce a wide variety of meteoritic organic matter from amino acid precursors to macromolecular IOM in chondrite parent bodies.

Exploring the Nature of Cellulose Microfibrils

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

Su, Ying; Burger, Christian; Ma, Hongyang

2015-03-20

Ultrathin cellulose microfibril fractions were extracted from spruce wood powder using combined delignification, TEMPO-catalyzed oxidation, and sonication processes. Small-angle X-ray scattering of these microfibril fractions in a “dilute” aqueous suspension (concentration 0.077 wt %) revealed that their shape was in the form of nanostrip with 4 nm width and only about 0.5 nm thicknesses. We found that these dimensions were further confirmed by TEM and AFM measurements. The 0.5 nm thickness implied that the nanostrip could contain only a single layer of cellulose chains. At a higher concentration (0.15 wt %), SAXS analysis indicated that these nanostrips aggregated into amore » layered structure. The X-ray diffraction of samples collected at different preparation stages suggested that microfibrils were delaminated along the (110) planes from the Iβ cellulose crystals. Moreover, the degree of oxidation and solid-state 13C NMR characterizations indicated that, in addition to the surface molecules, some inner molecules of microfibrils were also oxidized, facilitating the delamination into cellulose nanostrips.« less

Exploring the nature of cellulose microfibrils.

PubMed

Su, Ying; Burger, Christian; Ma, Hongyang; Chu, Benjamin; Hsiao, Benjamin S

2015-04-13

Ultrathin cellulose microfibril fractions were extracted from spruce wood powder using combined delignification, TEMPO-catalyzed oxidation, and sonication processes. Small-angle X-ray scattering of these microfibril fractions in a "dilute" aqueous suspension (concentration 0.077 wt %) revealed that their shape was in the form of nanostrip with 4 nm width and only about 0.5 nm thicknesses. These dimensions were further confirmed by TEM and AFM measurements. The 0.5 nm thickness implied that the nanostrip could contain only a single layer of cellulose chains. At a higher concentration (0.15 wt %), SAXS analysis indicated that these nanostrips aggregated into a layered structure. The X-ray diffraction of samples collected at different preparation stages suggested that microfibrils were delaminated along the (11̅0) planes from the Iβ cellulose crystals. The degree of oxidation and solid-state (13)C NMR characterizations indicated that, in addition to the surface molecules, some inner molecules of microfibrils were also oxidized, facilitating the delamination into cellulose nanostrips.

Circular dichroism in photoelectron images from aligned nitric oxide molecules

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

Sen, Ananya; Pratt, S. T.; Reid, K. L.

We have used velocity map photoelectron imaging to study circular dichroism of the photoelectron angular distributions (PADs) of nitric oxide following two-color resonanceenhanced two-photon ionization via selected rotational levels of the A 2Σ +, v' = 0 state. By using a circularly polarized pump beam and a counter-propagating, circularly polarized probe beam, cylindrical symmetry is preserved in the ionization process, and the images can be reconstructed using standard algorithms. The VMI set up enables individual ion rotational states to be resolved with excellent collection efficiency, rendering the measurements considerably simpler to perform than previous measurements conducted with a conventional photoelectronmore » spectrometer. The results demonstrate that circular dichroism is observed even when cylindrical symmetry is maintained, and serve as a reminder that dichroism is a general feature of the multiphoton ionization of atoms and molecules. Furthermore, the observed PADs are in good agreement with calculations based on parameters extracted from previous experimental results obtained by using a time-offlight electron spectrometer.« less

Tracking of Nuclear Production using Indigenous Species: Final LDRD Report

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

Alam, Todd Michael; Alam, Mary Kathleen; McIntyre, Sarah K.

Our LDRD research project sought to develop an analytical method for detection of chemicals used in nuclear materials processing. Our approach is distinctly different than current research involving hardware-based sensors. By utilizing the response of indigenous species of plants and/or animals surrounding (or within) a nuclear processing facility, we propose tracking 'suspicious molecules' relevant to nuclear materials processing. As proof of concept, we have examined TBP, tributylphosphate, used in uranium enrichment as well as plutonium extraction from spent nuclear fuels. We will compare TBP to the TPP (triphenylphosphate) analog to determine the uniqueness of the metabonomic response. We show thatmore » there is a unique metabonomic response within our animal model to TBP. The TBP signature can further be delineated from that of TPP. We have also developed unique methods of instrumental transfer for metabonomic data sets.« less

Soy-Leaf Extract Exerts Atheroprotective Effects via Modulation of Krüppel-Like Factor 2 and Adhesion Molecules

PubMed Central

Han, Jong-Min; Li, Hua; Cho, Moon-Hee; Baek, Seung-Hwa; Lee, Chul-Ho; Park, Ho-Yong; Jeong, Tae-Sook

2017-01-01

Soy-leaf extracts exert their cardioprotective effects by inducing endothelium-dependent vasodilation in the arteries, and they favorably modulate the serum lipid profile. In this study, we investigated the atheroprotective effects of an ethanol extract of soy leaf (ESL) in human umbilical vein endothelial cells (HUVECs) and high-cholesterol diet (HCD)-fed low-density lipoprotein receptor deficient (LDLR−/−) mice. ESL induced the expression of Krüppel-like factor 2 (KLF2), an endothelial transcription factor, and endothelial nitric oxide synthase (eNOS), and suppressed the expression of vascular cell adhesion molecule-1 (VCAM-1) and intercellular adhesion molecule-1 (ICAM-1) through moderate inflammatory signal activation, not only in tumor necrosis factor-α (TNF-α)-stimulated HUVECs but also in 7-ketocholesterol (7-KC)-stimulated HUVECs. ESL supplementation reduced aortic lesion formation in Western diet-fed LDLR−/− mice by 46% (p < 0.01) compared to the HCD group. ESL also markedly decreased the aortic expression levels of VCAM-1, ICAM-1, monocyte chemotactic protein-1 (MCP-1), TNF-α, IL-6, IL-1β, matrix metallopeptidase 9 (MMP-9), and fractalkine, while the expression of KLF2 was significantly increased. These results suggest that ESL supplementation has potential for preventing HCD-induced atherosclerosis effectively. PMID:28208647

Direct manipulation of insect reproduction by agents of parasite origin

PubMed Central

Webb, T. J.; Hurd, H.

1999-01-01

Reproductive output of female Tenebrio molitor beetles is reduced upon infection with metacestodes of the rat tapeworm, Hymenolepis diminuta. We are using this as a model to investigate the adaptive significance of parasite-induced curtailment of insect reproduction. Production of the yolk protein vitellogenin (Vg) in the insect fat body is significantly reduced both in vitro and in vivo by metacestodes. Synthesis can be measured by using [14C]L-leucine incorporation, followed by immunoprecipitation. In this paper we demonstrate that a significant decrease in [14C]Vg can be produced by an acetic acid extract of the parasite. Conclusive evidence is presented that the active component(s) originate from the metacestodes: an extract of parasites grown entirely axenically has similar deleterious effects. The developmental stage of the metacestode is important: immature (stage I to II) parasites had greater capacity to suppress Vg synthesis than mature ones (stage V to VI). Examination of the chemical nature of the effector molecule(s) revealed that acetic-acid-extractable, boiling-resistant, pronase-sensitive agents in the molecular mass range 10 to 50 kDa reduced Vg synthesis by 47.4%. These data suggest that metacestodes produce a modulator molecule that directly affects insect vitellogenesis and, therefore, that reduction of host fitness may confer a selective advantage upon the parasite.

Quantitative Analysis of Bioactive Compounds from Aromatic Plants by Means of Dynamic Headspace Extraction and Multiple Headspace Extraction-Gas Chromatography-Mass Spectrometry.

PubMed

Omar, Jone; Olivares, Maitane; Alonso, Ibone; Vallejo, Asier; Aizpurua-Olaizola, Oier; Etxebarria, Nestor

2016-04-01

Seven monoterpenes in 4 aromatic plants (sage, cardamom, lavender, and rosemary) were quantified in liquid extracts and directly in solid samples by means of dynamic headspace-gas chromatography-mass spectrometry (DHS-GC-MS) and multiple headspace extraction-gas chromatography-mass spectrometry (MHSE), respectively. The monoterpenes were 1st extracted by means of supercritical fluid extraction (SFE) and analyzed by an optimized DHS-GC-MS. The optimization of the dynamic extraction step and the desorption/cryo-focusing step were tackled independently by experimental design assays. The best working conditions were set at 30 °C for the incubation temperature, 5 min of incubation time, and 40 mL of purge volume for the dynamic extraction step of these bioactive molecules. The conditions of the desorption/cryo-trapping step from the Tenax TA trap were set at follows: the temperature was increased from 30 to 300 °C at 150 °C/min, although the cryo-trapping was maintained at -70 °C. In order to estimate the efficiency of the SFE process, the analysis of monoterpenes in the 4 aromatic plants was directly carried out by means of MHSE because it did not require any sample preparation. Good linearity (r2) > 0.99) and reproducibility (relative standard deviation % <12) was obtained for solid and liquid quantification approaches, in the ranges of 0.5 to 200 ng and 10 to 500 ng/mL, respectively. The developed methods were applied to analyze the concentration of 7 monoterpenes in aromatic plants obtaining concentrations in the range of 2 to 6000 ng/g and 0.25 to 110 μg/mg, respectively. © 2016 Institute of Food Technologists®

HoPaCI-DB: host-Pseudomonas and Coxiella interaction database

PubMed Central

Bleves, Sophie; Dunger, Irmtraud; Walter, Mathias C.; Frangoulidis, Dimitrios; Kastenmüller, Gabi; Voulhoux, Romé; Ruepp, Andreas

2014-01-01

Bacterial infectious diseases are the result of multifactorial processes affected by the interplay between virulence factors and host targets. The host-Pseudomonas and Coxiella interaction database (HoPaCI-DB) is a publicly available manually curated integrative database (http://mips.helmholtz-muenchen.de/HoPaCI/) of host–pathogen interaction data from Pseudomonas aeruginosa and Coxiella burnetii. The resource provides structured information on 3585 experimentally validated interactions between molecules, bioprocesses and cellular structures extracted from the scientific literature. Systematic annotation and interactive graphical representation of disease networks make HoPaCI-DB a versatile knowledge base for biologists and network biology approaches. PMID:24137008

Multielectron, multisubstrate molecular catalysis of electrochemical reactions: Formal kinetic analysis in the total catalysis regime.

PubMed

Costentin, Cyrille; Nocera, Daniel G; Brodsky, Casey N

2017-10-24

Cyclic voltammetry responses are derived for two-electron, two-step homogeneous electrocatalytic reactions in the total catalysis regime. The models developed provide a framework for extracting kinetic information from cyclic voltammograms (CVs) obtained in conditions under which the substrate or cosubstrate is consumed in a multielectron redox process, as is particularly prevalent for very active catalysts that promote energy conversion reactions. Such determination of rate constants in the total catalysis regime is a prerequisite for the rational benchmarking of molecular electrocatalysts that promote multielectron conversions of small-molecule reactants. The present analysis is illustrated with experimental systems encompassing various limiting behaviors.

Single cell and single molecule techniques for the analysis of the epigenome

NASA Astrophysics Data System (ADS)

Wallin, Christopher Benjamin

Epigenetic regulation is a critical biological process for the health and development of a cell. Epigenetic regulation is facilitated by covalent modifications to the underlying DNA and chromatin proteins. A fundamental understanding of these epigenetic modifications and their associated interactions at the molecular scale is necessary to explain phenomena including cellular identity, stem cell plasticity, and neoplastic transformation. It is widely known that abnormal epigenetic profiles have been linked to many diseases, most notably cancer. While the field of epigenetics has progressed rapidly with conventional techniques, significant advances remain to be made with respect to combinatoric analysis of epigenetic marks and single cell epigenetics. Therefore, in this dissertation, I will discuss our development of devices and methodologies to address these pertinent issues. First, we designed a preparatory polydimethylsiloxane (PDMS) microdevice for the extraction, purification, and stretching of human chromosomal DNA and chromatin from small cell populations down to a single cell. The valveless device captures cells by size exclusion within the micropillars, entraps the DNA or chromatin in the micropillars after cell lysis, purifies away the cellular debris, and fluorescently labels the DNA and/or chromatin all within a single reaction chamber. With the device, we achieve nearly 100% extraction efficiency of the DNA. The device is also used for in-channel immunostaining of chromatin followed by downstream single molecule chromatin analysis in nanochannels (SCAN). Second, using multi-color, time-correlated single molecule measurements in nanochannels, simultaneous coincidence detection of 2 epigenetic marks is demonstrated. Coincidence detection of 3 epigenetic marks is also established using a pulsed interleaved excitation scheme. With these two promising results, genome-wide quantification of epigenetic marks was pursued. Unfortunately, quantitative SCAN never materialized. Reasons for this, including poor signal to background, are explained in detail. Third, development of mobility-SCAN, an analytical technique for measuring and analyzing single molecules based on their fluorescent signature and their electrophoretic mobility in nanochannels is described. We use the technique to differentiate biomolecules from complex mixtures and derive parameters such as diffusion coefficients and effective charges. Finally, the device is used to detect binding interactions of various complexes similar to affinity capillary electrophoresis, but on a single molecule level. Fourth, we conclude by briefly discussing SCAN-sort, a technique to sort individual chromatin molecules based on their fluorescent emissions for further downstream analysis such as DNA sequencing. We demonstrate a 2-fold enrichment of chromatin from sorting and discuss possible system modifications for better performance in the future.

Effect of gamma radiation on antioxidant capacity of green tea, yerba mate, and chamomile tea as evaluated by different methods

NASA Astrophysics Data System (ADS)

Gerolis, Luanai Grazieli Luquini; Lameiras, Fernando Soares; Krambrock, Klaus; Neves, Maria Jose.

2017-01-01

Tea is a traditional plant extract with important cultural ties. It is the most widely consumed beverage in the world. Tea consumption has some health benefits including antioxidant stimulus. Gamma radiation is currently used to control of postharvest pathogens on tea herb. However, free radicals can be generated, which consumes antioxidant molecules. A positive relation was found between radiation doses used and free radicals generation in green tea (Camellia sinensis), yerba mate (Ilex paraguariensis), and chamomile tea (Matricaria recutita). Total antioxidant capacity (TAC) of aqueous and methanol extracts of these herbs was determined by various methods to compare the effect of irradiation of herb on antioxidant capacity of the extracts. TAC was evaluated by measuring: total phenols (decreased with irradiation in mate and green teas), total flavonoids (stable in aqueous extracts and decreased with irradiation in methanol extract of mate and chamomile), Trolox equivalent or ABTS (unchanged under irradiation), DPPH* scavenging capacity (stable on aqueous extract but diminished in methanol extract after irradiation), β carotene/acid linoleic ability (stable with the exception of chamomile tea that increased after irradiation) and, capacity to chelate ferrous ions (unchanged with irradiation). In conclusion, gamma irradiation reduced the capacity of some antioxidants but preserved the capacity of others. This study showed that one isolated test does not suffice to perform this evaluation reliably, which is a reflection of the diversity and complexity of the effects of irradiation on antioxidant molecules present in different samples.

Research on the Composition and Distribution of Organic Sulfur in Coal.

PubMed

Zhang, Lanjun; Li, Zenghua; Yang, Yongliang; Zhou, Yinbo; Li, Jinhu; Si, Leilei; Kong, Biao

2016-05-13

The structure and distribution of organic sulfur in coals of different rank and different sulfur content were studied by combining mild organic solvent extraction with XPS technology. The XPS results have shown that the distribution of organic sulfur in coal is related to the degree of metamorphism of coal. Namely, thiophenic sulfur content is reduced with decreasing metamorphic degree; sulfonic acid content rises with decreasing metamorphic degree; the contents of sulfate sulfur, sulfoxide and sulfone are rarely related with metamorphic degree. The solvent extraction and GC/MS test results have also shown that the composition and structure of free and soluble organic sulfur small molecules in coal is closely related to the metamorphic degree of coal. The free organic sulfur small molecules in coal of low metamorphic degree are mainly composed of aliphatic sulfides, while those in coal of medium and high metamorphic degree are mainly composed of thiophenes. Besides, the degree of aromatization of organic sulfur small molecules rises with increasing degree of coalification.

Analytical Protocols for Analysis of Organic Molecules in Mars Analog Materials

NASA Technical Reports Server (NTRS)

Mahaffy, Paul R.; Brinkerhoff, W.; Buch, A.; Demick, J.; Glavin, D. P.

2004-01-01

A range of analytical techniques and protocols that might be applied b in situ investigations of martian fines, ices, and rock samples are evaluated by analysis of organic molecules m Mars analogues. These simulants 6om terrestrial (i.e. tephra from Hawaii) or extraterrestrial (meteoritic) samples are examined by pyrolysis gas chromatograph mass spectrometry (GCMS), organic extraction followed by chemical derivatization GCMS, and laser desorption mass spectrometry (LDMS). The combination of techniques imparts analysis breadth since each technique provides a unique analysis capability for Certain classes of organic molecules.

Characterization of heterotrimeric collagen molecules in a sea-pen (Cnidaria, Octocorallia).

PubMed

Tillet-Barret, E; Franc, J M; Franc, S; Garrone, R

1992-01-15

The collagen of a primitive invertebrate, the sea-pen Veretillum Cnidaria, Octocorallia), was studied with respect to its molecular-chain composition. The soft extracellular tissues (mesoglea) were solubilized by limited pepsin proteolysis and the collagen was isolated by selective precipitation at 0.7 M NaCl under acidic conditions. The pepsinized molecules were 260 nm in length, as demonstrated by electron microscope studies of rotary-shadowed molecules and of the segment-long-spacing crystallites obtained by dialysis against ATP. SDS/PAGE of the extract produced two main bands susceptible to bacterial collagenase, designated as the alpha 1 and alpha 2 chain, which were differentiated clearly by their CNBr cleavage products and the higher glycosylation rate of the alpha 2 chain. The latter finding corresponds with the high hydroxylysine content of the alpha 2 chain. The alpha 1/alpha 2 chain ratio observed in SDS/PAGE and the fact that only one peak was obtained by concanavalin-A affinity chromatography of a non-denatured 0.7 M NaCl extract demonstrate the alpha 1 [alpha 2]2 molecular structure of this collagen. These results contrast with data on the structure of other coelenterates (i.e. [alpha]3 for sea anemone collagen molecules and alpha 1 alpha 2 alpha 3 for jellyfish collagen molecules). They are discussed in relation to the evolution of collagen.

Physical Selectivity of Molecularly Imprinted polymers evaluated through free volume size distributions derived from Positron Lifetime Spectroscopy

NASA Astrophysics Data System (ADS)

Pasang, T.; Ranganathaiah, C.

2015-06-01

The technique of imprinting molecules of various sizes in a stable structure of polymer matrix has derived multitudes of applications. Once the template molecule is extracted from the polymer matrix, it leaves behind a cavity which is physically (size and shape) and chemically (functional binding site) compatible to the particular template molecule. Positron Annihilation Lifetime Spectroscopy (PALS) is a well known technique to measure cavity sizes precisely in the nanoscale and is not being used in the field of MIPs effectively. This method is capable of measuring nanopores and hence suitable to understand the physical selectivity of the MIPs better. With this idea in mind, we have prepared molecular imprinted polymers (MIPs) with methacrylicacid (MAA) as monomer and EGDMA as cross linker in different molar ratio for three different size template molecules, viz. 4-Chlorophenol (4CP)(2.29 Å), 2-Nephthol (2NP) (3.36 Å) and Phenolphthalein (PP) (4.47Å). FTIR and the dye chemical reactions are used to confirm the complete extraction of the template molecules from the polymer matrix. The free volume size and its distribution have been derived from the measured o-Ps lifetime spectra. Based on the free volume distribution analysis, the percentage of functional cavities for the three template molecules are determined. Percentage of functional binding cavities for 4-CP molecules has been found out to be 70.2% and the rest are native cavities. Similarly for 2NP it is 81.5% and nearly 100% for PP. Therefore, PALS method proves to be very precise and accurate for determining the physical selectivity of MIPs.

Intracellular nucleotide and nucleotide sugar contents of cultured CHO cells determined by a fast, sensitive, and high-resolution ion-pair RP-HPLC.

PubMed

Kochanowski, N; Blanchard, F; Cacan, R; Chirat, F; Guedon, E; Marc, A; Goergen, J-L

2006-01-15

Analysis of intracellular nucleotide and nucleotide sugar contents is essential in studying protein glycosylation of mammalian cells. Nucleotides and nucleotide sugars are the donor substrates of glycosyltransferases, and nucleotides are involved in cellular energy metabolism and its regulation. A sensitive and reproducible ion-pair reverse-phase high-performance liquid chromatography (RP-HPLC) method has been developed, allowing the direct and simultaneous detection and quantification of some essential nucleotides and nucleotide sugars. After a perchloric acid extraction, 13 molecules (8 nucleotides and 5 nucleotide sugars) were separated, including activated sugars such as UDP-glucose, UDP-galactose, GDP-mannose, UDP-N-acetylglucosamine, and UDP-N-acetylgalactosamine. To validate the analytical parameters, the reproducibility, linearity of calibration curves, detection limits, and recovery were evaluated for standard mixtures and cell extracts. The developed method is capable of resolving picomolar quantities of nucleotides and nucleotide sugars in a single chromatographic run. The HPLC method was then applied to quantify intracellular levels of nucleotides and nucleotide sugars of Chinese hamster ovary (CHO) cells cultivated in a bioreactor batch process. Evolutions of the titers of nucleotides and nucleotide sugars during the batch process are discussed.

Rare reaction channels in real-time time-dependent density functional theory: the test case of electron attachment

NASA Astrophysics Data System (ADS)

Lacombe, Lionel; Dinh, P. Huong Mai; Reinhard, Paul-Gerhard; Suraud, Eric; Sanche, Leon

2015-08-01

We present an extension of standard time-dependent density functional theory (TDDFT) to include the evaluation of rare reaction channels, taking as an example of application the theoretical modelling of electron attachment to molecules. The latter process is of great importance in radiation-induced damage of biological tissue for which dissociative electron attachment plays a decisive role. As the attachment probability is very low, it cannot be extracted from the TDDFT propagation whose mean field provides an average over various reaction channels. To extract rare events, we augment TDDFT by a perturbative treatment to account for the occasional jumps, namely electron capture in our test case. We apply the modelling to electron attachment to H2O, H3O+, and (H2O)2. Dynamical calculations have been done at low energy (3-16 eV). We explore, in particular, how core-excited states of the targets show up as resonances in the attachment probability. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

Biosurfactants: Promising Molecules for Petroleum Biotechnology Advances.

PubMed

De Almeida, Darne G; Soares Da Silva, Rita de Cássia F; Luna, Juliana M; Rufino, Raquel D; Santos, Valdemir A; Banat, Ibrahim M; Sarubbo, Leonie A

2016-01-01

The growing global demand for sustainable technologies that improves the efficiency of petrochemical processes in the oil industry has driven advances in petroleum biotechnology in recent years. Petroleum industry uses substantial amounts of petrochemical-based synthetic surfactants in its activities as mobilizing agents to increase the availability or recovery of hydrocarbons as well as many other applications related to extraction, treatment, cleaning, and transportation. However, biosurfactants have several potential applications for use across the oil processing chain and in the formulations of petrochemical products such as emulsifying/demulsifying agents, anticorrosive, biocides for sulfate-reducing bacteria, fuel formulation, extraction of bitumen from tar sands, and many other innovative applications. Due to their versatility and proven efficiency, biosurfactants are often presented as valuable versatile tools that can transform and modernize petroleum biotechnology in an attempt to provide a true picture of state of the art and directions or use in the oil industry. We believe that biosurfactants are going to have a significant role in many future applications in the oil industries and in this review therefore, we highlight recent important relevant applications, patents disclosures and potential future applications for biosurfactants in petroleum and related industries.

Biosurfactants: Promising Molecules for Petroleum Biotechnology Advances

PubMed Central

De Almeida, Darne G.; Soares Da Silva, Rita de Cássia F.; Luna, Juliana M.; Rufino, Raquel D.; Santos, Valdemir A.; Banat, Ibrahim M.; Sarubbo, Leonie A.

2016-01-01

The growing global demand for sustainable technologies that improves the efficiency of petrochemical processes in the oil industry has driven advances in petroleum biotechnology in recent years. Petroleum industry uses substantial amounts of petrochemical-based synthetic surfactants in its activities as mobilizing agents to increase the availability or recovery of hydrocarbons as well as many other applications related to extraction, treatment, cleaning, and transportation. However, biosurfactants have several potential applications for use across the oil processing chain and in the formulations of petrochemical products such as emulsifying/demulsifying agents, anticorrosive, biocides for sulfate-reducing bacteria, fuel formulation, extraction of bitumen from tar sands, and many other innovative applications. Due to their versatility and proven efficiency, biosurfactants are often presented as valuable versatile tools that can transform and modernize petroleum biotechnology in an attempt to provide a true picture of state of the art and directions or use in the oil industry. We believe that biosurfactants are going to have a significant role in many future applications in the oil industries and in this review therefore, we highlight recent important relevant applications, patents disclosures and potential future applications for biosurfactants in petroleum and related industries. PMID:27843439

Attractive interactions between reverse aggregates and phase separation in concentrated malonamide extractant solutions

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

Erlinger, C.; Belloni, L.; Zemb, T.

1999-03-30

Using small angle X-ray scattering, conductivity, and phase behavior determination, the authors show that concentrated solutions of malonamide extractants, dimethyldibutyltetradecylmalonamide (DMDBTDMA), are organized in reverse oligomeric aggregates which have many features in common with reverse micelles. The aggregation numbers of these reverse globular aggregates as well as their interaction potential are determined from absolute scattering curves. An attractive interaction is responsible for the demixing of the oil phase when in equilibrium with excess oil. Prediction of conductivity as well as the formation conditions for the third phase is possible using standard liquid theory applied to the extractant aggregates. The interactions,more » modeled with the sticky sphere model proposed by Baster, are shown to be due to steric interactions resulting from the hydrophobic tails of the extractant molecule and van der Waals forces between the highly polarizable water core of the reverse micelles. The attractive interaction in the oil phase, equilibrated with water, is determined as a function of temperature, extractant molecule concentration, and proton and neodynium(III) cation concentration. It is shown that van der Waals interactions, with an effective Hamaker constant of 3kT, quantitatively explain the behavior of DMDBTDMA in n-dodecane in terms of scattering as well as phase stability limits.« less

Mosquitocidal Effect of Glycosmis pentaphylla Leaf Extracts against Three Mosquito Species (Diptera: Culicidae)

PubMed Central

Ramkumar, Govindaraju; Karthi, Sengodan; Muthusamy, Ranganathan; Suganya, Ponnusamy; Natarajan, Devarajan; Kweka, Eliningaya J.; Shivakumar, Muthugounder S.

2016-01-01

Background The resistance status of malaria vectors to different classes of insecticides used for public health has raised concern for vector control programmes. Alternative compounds to supplement the existing tools are important to be searched to overcome the existing resistance and persistence of pesticides in vectors and the environment respectively. The mosquitocidal effects of Glycosmis pentaphylla using different solvents of acetone, methanol, chloroform and ethyl acetate extracts against three medically important mosquito vectors was conducted. Methods Glycosmis pentaphylla plant leaves were collected from Kolli Hills, India. The WHO test procedures for larval and adult bioassays were used to evaluate extracts against mosquito vectors, and the chemical composition of extracts identified using GC-MS analysis. Results The larvicidal and adulticidal activity of G. pentaphylla plant extracts clearly impacted the three species of major mosquitoes vectors. Acetone extracts had the highest larvicidal effect against An. stephensi, Cx. quinquefasciatus and Ae. aegypti with the LC50 and LC90 values of 0.0004, 138.54; 0.2669, 73.7413 and 0.0585, 303.746 mg/ml, respectively. The LC50 and LC90 adulticide values of G. pentaphylla leaf extracts in acetone, methanol, chloroform and ethyl acetate, solvents were as follows for Cx. quinquefasciatus, An. stephensi and Ae. Aegypti: 2.957, 5.458, 2.708, and 4.777, 3.449, 6.676 mg/ml respectively. The chemical composition of G. pentaphylla leaf extract has been found in 20 active compounds. Conclusions The plant leaf extracts of G. pentaphylla bioactive molecules which are effective and can be developed as an eco-friendly approach for larvicides and adulticidal mosquitoes vector control. Detailed identification and characterization of mosquitocidal effect of individual bioactive molecules ingredient may result into biodegradable effective tools for the control of mosquito vectors. PMID:27391146

Mosquitocidal Effect of Glycosmis pentaphylla Leaf Extracts against Three Mosquito Species (Diptera: Culicidae).

PubMed

Ramkumar, Govindaraju; Karthi, Sengodan; Muthusamy, Ranganathan; Suganya, Ponnusamy; Natarajan, Devarajan; Kweka, Eliningaya J; Shivakumar, Muthugounder S

2016-01-01

The resistance status of malaria vectors to different classes of insecticides used for public health has raised concern for vector control programmes. Alternative compounds to supplement the existing tools are important to be searched to overcome the existing resistance and persistence of pesticides in vectors and the environment respectively. The mosquitocidal effects of Glycosmis pentaphylla using different solvents of acetone, methanol, chloroform and ethyl acetate extracts against three medically important mosquito vectors was conducted. Glycosmis pentaphylla plant leaves were collected from Kolli Hills, India. The WHO test procedures for larval and adult bioassays were used to evaluate extracts against mosquito vectors, and the chemical composition of extracts identified using GC-MS analysis. The larvicidal and adulticidal activity of G. pentaphylla plant extracts clearly impacted the three species of major mosquitoes vectors. Acetone extracts had the highest larvicidal effect against An. stephensi, Cx. quinquefasciatus and Ae. aegypti with the LC50 and LC90 values of 0.0004, 138.54; 0.2669, 73.7413 and 0.0585, 303.746 mg/ml, respectively. The LC50 and LC90 adulticide values of G. pentaphylla leaf extracts in acetone, methanol, chloroform and ethyl acetate, solvents were as follows for Cx. quinquefasciatus, An. stephensi and Ae. Aegypti: 2.957, 5.458, 2.708, and 4.777, 3.449, 6.676 mg/ml respectively. The chemical composition of G. pentaphylla leaf extract has been found in 20 active compounds. The plant leaf extracts of G. pentaphylla bioactive molecules which are effective and can be developed as an eco-friendly approach for larvicides and adulticidal mosquitoes vector control. Detailed identification and characterization of mosquitocidal effect of individual bioactive molecules ingredient may result into biodegradable effective tools for the control of mosquito vectors.

Identification of myo-inositol hexakisphosphate (IP6) as a β-secretase 1 (BACE1) inhibitory molecule in rice grain extract and digest

PubMed Central

Abe, Takako K.; Taniguchi, Masayuki

2014-01-01

Alzheimer’s disease (AD) is widely considered to be caused by amyloid-β peptide (Aβ) accumulation in the brain. Aβ is excised from amyloid-β precursor protein through sequential cleavage by β-secretase 1 (BACE1) and γ-secretase. Thus, BACE1 inhibition could prevent Aβ accumulation. Here, we identified myo-inositol hexakisphosphate (IP6) as a BACE1 inhibitory molecule in rice grain extract and digest. The rice digest and IP6 significantly inhibited Aβ production in neuroblastoma cells without cytotoxicity. These results suggested that rice components, including IP6, may be promising starting materials for the development of potent and safe drugs and/or food to prevent AD. PMID:24649396

How to get more from less. Comments on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

NASA Astrophysics Data System (ADS)

Sachs, Frederick; Flomenbom, Ophir

2015-06-01

Measuring individual entities at room temperature has become routine due to improvements in technology. We can study ion channels (since the 70s), quantum dots (since the 80s), and receptors, molecular engines and enzymes (since the 90s). The inherent nature of these small systems is that the standard deviation of the measurement is comparable to the mean - the definition of a small system [1]. Individual probes are detected, measured, and the trajectories are then analyzed to extract the mean properties of the system. The review [2] provides links to many examples of single molecule studies, mostly those using optical probes.

Dynamic Covalent Chemistry of Carbon Dioxide: Opportunities to Address Environmental Issues.

PubMed

Septavaux, Jean; Germain, Geoffroy; Leclaire, Julien

2017-07-18

Extraction and purification of basic chemicals from complex mixtures has been a persistent issue throughout the development of the chemical sciences. The chemical industry and academic research have grown over the centuries by following a deconstruction-reconstruction approach, reminiscent of the metabolism process. Chemists have designed and optimized extraction, purification, and transformation processes of molecules from natural deposits (fossil fuels, biomass, ores), in order to reassemble them into complex adducts. These highly selective and cost-effective techniques arose from developments in physical chemistry but also in supramolecular chemistry, long before the term was even coined. Thanks to the extremely diverse toolbox currently available to the scientific community, artificial molecular systems of increasing complexity can be built and integrated into high-technology products. If humanity has proven through the ages how gifted it can be at this deconstruction-reconstruction game, which has transformed the natural world to a human-shaped one, it has been confronted for more than a century by a new challenge: the deconstruction and reconstruction from a new type of deposit, the waste resulting from the mass production of disposable manufactured goods. In this Account, we will explore the potential contribution of controlled molecular and supramolecular self-assembly phenomena to the challenge of selective and efficient capture of valuable target molecules from mixtures found in postconsumer waste. While it may appear paradoxical to add more molecular ingredients to an already compositionally complex system in order to address a purification issue, we will compare the selectivity, yield, and cost of such an atypical procedure with traditional physical techniques. In the context of carbon dioxide capture or release, we will specifically focus on the coupling between this reversible covalent fixation of the gas by amines and an additional chemical equilibrium. This equilibrium may involve covalent or noncovalent bond formation between a supplementary species and either the unloaded reactant or the CO 2 -loaded product. Thereby, this new reactive species may act as a CO 2 capture agonist or antagonist by either thermodynamically favoring the carbamation or decarbamation direction. Indeed, superagonism, the increase of CO 2 loading per amine site upon carbamation beyond the theoretical limit of 0.5, can be achieved using tightly bound cationic metal counterions. In all cases, upon binding and adduct formation, a mutual selection process occurs between one member of the CO 2 -based dynamic combinatorial library and one agonist or antagonist, which can itself be contained in a complex mixture of analogues. If this adduct is the only species that, upon formation, can self-aggregate into a separate solid phase, selection and binding are accompanied by translocation, rendering the purification procedure operationally straightforward. This general strategy, based on a simple design of coupled molecular systems, may easily be implemented within new, disruptive technologies for selective extraction of target molecules, thereby providing a substantial environmental and economic benefit.

[Study on different extracts of Chrysanthemum indicum by Fourier transform infrared spectroscopy].

PubMed

Zhang, Yan-Ling; Xia, Yuan; Tsogt; Zhou, Qun; Sun, Su-Qin

2012-12-01

According to the macro-fingerprint characteristic of infrared spectroscopy, Fourier transform infrared spectroscopy and second-derivative infrared spectroscopy were used to analyze the extracts of chrysanthemum indicum L. by different solvents. It was speculated preliminarily that the main component of petroleum ether extract was long chain fatty acids (esters) and terpenes of small molecules, ethyl acetate extract contains terpenes and flavonoids mainly, ethanol and 95% ethanol extract was mainly composed of flavonoids and flavonoid glycosides, and deionized water extract contains polysaccharides and tannins mainly. Besides, the content of flavonoids in ethanol extract is the highest by comparison of the infrared spectroscopy of different extracts with that of buddleoside. Thus, the infrared spectroscopy can analyze directly the extracts of traditional Chinese medicines, recognize the main ingredient preliminarily, and then supply directional reference for further planning the extract scheme and detection methods.

International Workshop on Structural and Functional Aspects of the Cholinergic Synapse Held in Jerusalem, Isreal on 30 August-4 September 1987

DTIC Science & Technology

1987-09-01

77) Large scale purification of the acetylcholine receptor protein In its membrane-bound and detergent extracted forms from Torpedo marmorata...maintenance of the postsynaptic apparatus in the adult. Our studies have alac led to the Identification of agrin, a protein that is extracted from the synapse...in extracts of muscle, and monoclonal antibodies directed against &grin recognize molecules highly concentrated in the synaptic basal lamina at the

Spectroscopic Studies on Organic Matter from Triassic Reptile Bones, Upper Silesia, Poland

PubMed Central

Surmik, Dawid; Boczarowski, Andrzej; Balin, Katarzyna; Dulski, Mateusz; Szade, Jacek; Kremer, Barbara; Pawlicki, Roman

2016-01-01

Fossil biomolecules from an endogenous source were previously identified in Cretaceous to Pleistocene fossilized bones, the evidence coming from molecular analyses. These findings, however, were called into question and an alternative hypothesis of the invasion of the bone by bacterial biofilm was proposed. Herewith we report a new finding of morphologically preserved blood-vessel-like structures enclosing organic molecules preserved in iron-oxide-mineralized vessel walls from the cortical region of nothosaurid and tanystropheid (aquatic and terrestrial diapsid reptiles) bones. These findings are from the Early/Middle Triassic boundary (Upper Roetian/Lowermost Muschelkalk) strata of Upper Silesia, Poland. Multiple spectroscopic analyses (FTIR, ToF-SIMS, and XPS) of the extracted "blood vessels" showed the presence of organic compounds, including fragments of various amino acids such as hydroxyproline and hydroxylysine as well as amides, that may suggest the presence of collagen protein residues. Because these amino acids are absent from most proteins other than collagen, we infer that the proteinaceous molecules may originate from endogenous collagen. The preservation of molecular signals of proteins within the "blood vessels" was most likely made possible through the process of early diagenetic iron oxide mineralization. This discovery provides the oldest evidence of in situ preservation of complex organic molecules in vertebrate remains in a marine environment. PMID:26977600

Spectroscopic Studies on Organic Matter from Triassic Reptile Bones, Upper Silesia, Poland.

PubMed

Surmik, Dawid; Boczarowski, Andrzej; Balin, Katarzyna; Dulski, Mateusz; Szade, Jacek; Kremer, Barbara; Pawlicki, Roman

2016-01-01

Fossil biomolecules from an endogenous source were previously identified in Cretaceous to Pleistocene fossilized bones, the evidence coming from molecular analyses. These findings, however, were called into question and an alternative hypothesis of the invasion of the bone by bacterial biofilm was proposed. Herewith we report a new finding of morphologically preserved blood-vessel-like structures enclosing organic molecules preserved in iron-oxide-mineralized vessel walls from the cortical region of nothosaurid and tanystropheid (aquatic and terrestrial diapsid reptiles) bones. These findings are from the Early/Middle Triassic boundary (Upper Roetian/Lowermost Muschelkalk) strata of Upper Silesia, Poland. Multiple spectroscopic analyses (FTIR, ToF-SIMS, and XPS) of the extracted "blood vessels" showed the presence of organic compounds, including fragments of various amino acids such as hydroxyproline and hydroxylysine as well as amides, that may suggest the presence of collagen protein residues. Because these amino acids are absent from most proteins other than collagen, we infer that the proteinaceous molecules may originate from endogenous collagen. The preservation of molecular signals of proteins within the "blood vessels" was most likely made possible through the process of early diagenetic iron oxide mineralization. This discovery provides the oldest evidence of in situ preservation of complex organic molecules in vertebrate remains in a marine environment.

Sachem: a chemical cartridge for high-performance substructure search.

PubMed

Kratochvíl, Miroslav; Vondrášek, Jiří; Galgonek, Jakub

2018-05-23

Structure search is one of the valuable capabilities of small-molecule databases. Fingerprint-based screening methods are usually employed to enhance the search performance by reducing the number of calls to the verification procedure. In substructure search, fingerprints are designed to capture important structural aspects of the molecule to aid the decision about whether the molecule contains a given substructure. Currently available cartridges typically provide acceptable search performance for processing user queries, but do not scale satisfactorily with dataset size. We present Sachem, a new open-source chemical cartridge that implements two substructure search methods: The first is a performance-oriented reimplementation of substructure indexing based on the OrChem fingerprint, and the second is a novel method that employs newly designed fingerprints stored in inverted indices. We assessed the performance of both methods on small, medium, and large datasets containing 1, 10, and 94 million compounds, respectively. Comparison of Sachem with other freely available cartridges revealed improvements in overall performance, scaling potential and screen-out efficiency. The Sachem cartridge allows efficient substructure searches in databases of all sizes. The sublinear performance scaling of the second method and the ability to efficiently query large amounts of pre-extracted information may together open the door to new applications for substructure searches.

Molecular separation method and apparatus

DOEpatents

Villa-Aleman, Eliel

1996-01-01

A method and apparatus for separating a gaseous mixture of chemically identical but physically different molecules based on their polarities. The gaseous mixture of molecules is introduced in discrete quantities into the proximal end of a porous glass molecular. The molecular sieve is exposed to microwaves to excite the molecules to a higher energy state from a lower energy state, those having a higher dipole moment being excited more than those with a lower energy state. The temperature of the sieve kept cold by a flow of liquid nitrogen through a cooling jacket so that the heat generated by the molecules colliding with the material is transferred away from the material. The molecules thus alternate between a higher energy state and a lower one, with the portion of molecules having the higher dipole moment favored over the others. The former portion can then be extracted separately from the distal end of the molecular sieve.

Molecular separation method and apparatus

DOEpatents

Villa-Aleman, E.

1996-04-09

A method and apparatus are disclosed for separating a gaseous mixture of chemically identical but physically different molecules based on their polarities. The gaseous mixture of molecules is introduced in discrete quantities into the proximal end of a porous glass molecular sieve. The molecular sieve is exposed to microwaves to excite the molecules to a higher energy state from a lower energy state, those having a higher dipole moment being excited more than those with a lower energy state. The temperature of the sieve kept cold by a flow of liquid nitrogen through a cooling jacket so that the heat generated by the molecules colliding with the material is transferred away from the material. The molecules thus alternate between a higher energy state and a lower one, with the portion of molecules having the higher dipole moment favored over the others. The former portion can then be extracted separately from the distal end of the molecular sieve. 2 figs.

Partition coefficients of organic compounds between water and imidazolium-, pyridinium-, and phosphonium-based ionic liquids.

PubMed

Padró, Juan M; Pellegrino Vidal, Rocío B; Reta, Mario

2014-12-01

The partition coefficients, P IL/w, of several compounds, some of them of biological and pharmacological interest, between water and room-temperature ionic liquids based on the imidazolium, pyridinium, and phosphonium cations, namely 1-octyl-3-methylimidazolium hexafluorophosphate, N-octylpyridinium tetrafluorophosphate, trihexyl(tetradecyl)phosphonium chloride, trihexyl(tetradecyl)phosphonium bromide, trihexyl(tetradecyl)phosphonium bis(trifluoromethylsulfonyl)imide, and trihexyl(tetradecyl)phosphonium dicyanamide, were accurately measured. In this way, we extended our database of partition coefficients in room-temperature ionic liquids previously reported. We employed the solvation parameter model with different probe molecules (the training set) to elucidate the chemical interactions involved in the partition process and discussed the most relevant differences among the three types of ionic liquids. The multiparametric equations obtained with the aforementioned model were used to predict the partition coefficients for compounds (the test set) not present in the training set, most being of biological and pharmacological interest. An excellent agreement between calculated and experimental log P IL/w values was obtained. Thus, the obtained equations can be used to predict, a priori, the extraction efficiency for any compound using these ionic liquids as extraction solvents in liquid-liquid extractions.

A Solution Processed Flexible Nanocomposite Electrode with Efficient Light Extraction for Organic Light Emitting Diodes

NASA Astrophysics Data System (ADS)

Li, Lu; Liang, Jiajie; Chou, Shu-Yu; Zhu, Xiaodan; Niu, Xiaofan; Zhibinyu; Pei, Qibing

2014-03-01

Highly efficient organic light emitting diodes (OLEDs) based on multiple layers of vapor evaporated small molecules, indium tin oxide transparent electrode, and glass substrate have been extensively investigated and are being commercialized. The light extraction from the exciton radiative decay is limited to less than 30% due to plasmonic quenching on the metallic cathode and the waveguide in the multi-layer sandwich structure. Here we report a flexible nanocomposite electrode comprising single-walled carbon nanotubes and silver nanowires stacked and embedded in the surface of a polymer substrate. Nanoparticles of barium strontium titanate are dispersed within the substrate to enhance light extraction efficiency. Green polymer OLED (PLEDs) fabricated on the nanocomposite electrode exhibit a maximum current efficiency of 118 cd/A at 10,000 cd/m2 with the calculated external quantum efficiency being 38.9%. The efficiencies of white PLEDs are 46.7 cd/A and 30.5%, respectively. The devices can be bent to 3 mm radius repeatedly without significant loss of electroluminescent performance. The nanocomposite electrode could pave the way to high-efficiency flexible OLEDs with simplified device structure and low fabrication cost.

A solution processed flexible nanocomposite electrode with efficient light extraction for organic light emitting diodes.

PubMed

Li, Lu; Liang, Jiajie; Chou, Shu-Yu; Zhu, Xiaodan; Niu, Xiaofan; ZhibinYu; Pei, Qibing

2014-03-17

Highly efficient organic light emitting diodes (OLEDs) based on multiple layers of vapor evaporated small molecules, indium tin oxide transparent electrode, and glass substrate have been extensively investigated and are being commercialized. The light extraction from the exciton radiative decay is limited to less than 30% due to plasmonic quenching on the metallic cathode and the waveguide in the multi-layer sandwich structure. Here we report a flexible nanocomposite electrode comprising single-walled carbon nanotubes and silver nanowires stacked and embedded in the surface of a polymer substrate. Nanoparticles of barium strontium titanate are dispersed within the substrate to enhance light extraction efficiency. Green polymer OLED (PLEDs) fabricated on the nanocomposite electrode exhibit a maximum current efficiency of 118 cd/A at 10,000 cd/m(2) with the calculated external quantum efficiency being 38.9%. The efficiencies of white PLEDs are 46.7 cd/A and 30.5%, respectively. The devices can be bent to 3 mm radius repeatedly without significant loss of electroluminescent performance. The nanocomposite electrode could pave the way to high-efficiency flexible OLEDs with simplified device structure and low fabrication cost.

A Solution Processed Flexible Nanocomposite Electrode with Efficient Light Extraction for Organic Light Emitting Diodes

PubMed Central

Li, Lu; Liang, Jiajie; Chou, Shu-Yu; Zhu, Xiaodan; Niu, Xiaofan; ZhibinYu; Pei, Qibing

2014-01-01

Highly efficient organic light emitting diodes (OLEDs) based on multiple layers of vapor evaporated small molecules, indium tin oxide transparent electrode, and glass substrate have been extensively investigated and are being commercialized. The light extraction from the exciton radiative decay is limited to less than 30% due to plasmonic quenching on the metallic cathode and the waveguide in the multi-layer sandwich structure. Here we report a flexible nanocomposite electrode comprising single-walled carbon nanotubes and silver nanowires stacked and embedded in the surface of a polymer substrate. Nanoparticles of barium strontium titanate are dispersed within the substrate to enhance light extraction efficiency. Green polymer OLED (PLEDs) fabricated on the nanocomposite electrode exhibit a maximum current efficiency of 118 cd/A at 10,000 cd/m2 with the calculated external quantum efficiency being 38.9%. The efficiencies of white PLEDs are 46.7 cd/A and 30.5%, respectively. The devices can be bent to 3 mm radius repeatedly without significant loss of electroluminescent performance. The nanocomposite electrode could pave the way to high-efficiency flexible OLEDs with simplified device structure and low fabrication cost. PMID:24632742

Preparation of ellagic acid molecularly imprinted polymeric microspheres based on distillation-precipitation polymerization for the efficient purification of a crude extract.

PubMed

Zhang, Hua; Zhao, Shangge; Zhang, Lu; Han, Bo; Yao, Xincheng; Chen, Wen; Hu, Yanli

2016-08-01

Molecularly imprinted polymeric microspheres with a high recognition ability toward the template molecule, ellagic acid, were synthesized based on distillation-precipitation polymerization. The as-obtained polymers were characterized by scanning electron microscopy, infrared spectroscopy, and thermogravimetric analysis. Static, dynamic, and selective binding tests were adopted to study the binding properties and the molecular recognition ability of the prepared polymers for ellagic acid. The results indicated that the maximum static adsorption capacity of the prepared polymers toward ellagic acid was 37.07 mg/g and the adsorption equilibrium time was about 100 min when the concentration of ellagic acid was 40 mg/mL. Molecularly imprinted polymeric microspheres were also highly selective toward ellagic acid compared with its analogue quercetin. It was found that the content of ellagic acid in the pomegranate peel extract was enhanced from 23 to 86% after such molecularly imprinted solid-phase extraction process. This work provides an efficient way for effective separation and enrichment of ellagic acid from complex matrix, which is especially valuable in industrial production. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cloning of Sucrose:Sucrose 1-Fructosyltransferase from Onion and Synthesis of Structurally Defined Fructan Molecules from Sucrose1

PubMed Central

Vijn, Irma; van Dijken, Anja; Lüscher, Marcel; Bos, Antoine; Smeets, Edward; Weisbeek, Peter; Wiemken, Andres; Smeekens, Sjef

1998-01-01

Sucrose (Suc):Suc 1-fructosyltransferase (1-SST) is the key enzyme in plant fructan biosynthesis, since it catalyzes de novo fructan synthesis from Suc. We have cloned 1-SST from onion (Allium cepa) by screening a cDNA library using acid invertase from tulip (Tulipa gesneriana) as a probe. Expression assays in tobacco (Nicotiana plumbaginifolia) protoplasts showed the formation of 1-kestose from Suc. In addition, an onion acid invertase clone was isolated from the same cDNA library. Protein extracts of tobacco protoplasts transformed with this clone showed extensive Suc-hydrolyzing activity. Conditions that induced fructan accumulation in onion leaves also induced 1-SST mRNA accumulation, whereas the acid invertase mRNA level decreased. Structurally different fructan molecules could be produced from Suc by a combined incubation of protein extract of protoplasts transformed with 1-SST and protein extract of protoplasts transformed with either the onion fructan:fructan 6G-fructosyltransferase or the barley Suc:fructan 6-fructosyltransferase. PMID:9701606

A novel superparamagnetic surface molecularly imprinted nanoparticle adopting dummy template: an efficient solid-phase extraction adsorbent for bisphenol A.

PubMed

Lin, Zhenkun; Cheng, Wenjing; Li, Yanyan; Liu, Zhiren; Chen, Xiangping; Huang, Changjiang

2012-03-30

Leakage of the residual template molecules is one of the biggest challenges for application of molecularly imprinted polymer (MIP) in solid-phase extraction (SPE). In this study, bisphenol F (BPF) was adopted as a dummy template to prepare MIP of bisphenol A (BPA) with a superparamagnetic core-shell nanoparticle as the supporter, aiming to avoid residual template leakage and to increase the efficiency of SPE. Characterization and test of the obtained products (called mag-DMIP beads) revealed that these novel nanoparticles not only had excellent magnetic property but also displayed high selectivity to the target molecule BPA. As mag-DMIP beads were adopted as the adsorbents of solid-phase extraction for detecting BPA in real water samples, the recoveries of spiked samples ranged from 84.7% to 93.8% with the limit of detection of 2.50 pg mL(-1), revealing that mag-DMIP beads were efficient SPE adsorbents. Copyright © 2012 Elsevier B.V. All rights reserved.

Combination of aspartic acid and glutamic acid inhibits tumor cell proliferation.

PubMed

Yamaguchi, Yoshie; Yamamoto, Katsunori; Sato, Yoshinori; Inoue, Shinjiro; Morinaga, Tetsuo; Hirano, Eiichi

2016-01-01

Placental extract contains several biologically active compounds, and pharmacological induction of placental extract has therapeutic effects, such as improving liver function in patients with hepatitis or cirrhosis. Here, we searched for novel molecules with an anti-tumor activity in placental extracts. Active molecules were separated by chromatographic analysis, and their antiproliferative activities were determined by a colorimetric assay. We identified aspartic acid and glutamic acid to possess the antiproliferative activity against human hepatoma cells. Furthermore, we showed that the combination of aspartic acid and glutamic acid exhibited enhanced antiproliferative activity, and inhibited Akt phosphorylation. We also examined in vivo tumor inhibition activity using the rabbit VX2 liver tumor model. The treatment mixture (emulsion of the amino acids with Lipiodol) administered by hepatic artery injection inhibited tumor cell growth of the rabbit VX2 liver. These results suggest that the combination of aspartic acid and glutamic acid may be useful for induction of tumor cell death, and has the potential for clinical use as a cancer therapeutic agent.

Different effects of water molecules on CO oxidation with different reaction mechanisms.

PubMed

Liu, Shan Ping; Zhao, Ming; Sun, Guo En; Gao, Wang; Jiang, Qing

2018-03-28

The effects of water molecules (promotion/prohibition) on CO oxidation remain debated. Herein, using density functional theory calculations, we demonstrate that water molecules can facilitate the CO + O/O 2 oxidation process, but prohibit the CO + OH oxidation process, which is consistent with the experimental finding that water molecules have two distinct effects on CO oxidation. For the CO + O/O 2 oxidation mechanisms, we find that the reactants were pushed towards each other due to the steric effect of the water molecules, which decreases the reaction barriers and promotes the CO + O/O 2 oxidation process. For the CO + OH oxidation mechanisms, water molecules increase the stability of the COOH* intermeditae by H-bonds and van der Waals forces, which increase the barriers of the COOH* transformation process and the COOH*-tra dissociation process, and prohibit the CO + OH oxidation process. These results clarify the different effects of water molecules on CO oxidation and shed light on catalyst usage in the CO oxidation industry.

Non-Markovian properties and multiscale hidden Markovian network buried in single molecule time series

NASA Astrophysics Data System (ADS)

Sultana, Tahmina; Takagi, Hiroaki; Morimatsu, Miki; Teramoto, Hiroshi; Li, Chun-Biu; Sako, Yasushi; Komatsuzaki, Tamiki

2013-12-01

We present a novel scheme to extract a multiscale state space network (SSN) from single-molecule time series. The multiscale SSN is a type of hidden Markov model that takes into account both multiple states buried in the measurement and memory effects in the process of the observable whenever they exist. Most biological systems function in a nonstationary manner across multiple timescales. Combined with a recently established nonlinear time series analysis based on information theory, a simple scheme is proposed to deal with the properties of multiscale and nonstationarity for a discrete time series. We derived an explicit analytical expression of the autocorrelation function in terms of the SSN. To demonstrate the potential of our scheme, we investigated single-molecule time series of dissociation and association kinetics between epidermal growth factor receptor (EGFR) on the plasma membrane and its adaptor protein Ash/Grb2 (Grb2) in an in vitro reconstituted system. We found that our formula successfully reproduces their autocorrelation function for a wide range of timescales (up to 3 s), and the underlying SSNs change their topographical structure as a function of the timescale; while the corresponding SSN is simple at the short timescale (0.033-0.1 s), the SSN at the longer timescales (0.1 s to ˜3 s) becomes rather complex in order to capture multiscale nonstationary kinetics emerging at longer timescales. It is also found that visiting the unbound form of the EGFR-Grb2 system approximately resets all information of history or memory of the process.

Kinetic Energy Release of the Singly and Doubly Charged Methylene Chloride Molecule: The Role of Fast Dissociation.

PubMed

Alcantara, K F; Rocha, A B; Gomes, A H A; Wolff, W; Sigaud, L; Santos, A C F

2016-09-01

The center of mass kinetic energy release distribution (KERD) spectra of selected ionic fragments, formed through dissociative single and double photoionization of CH2Cl2 at photon energies around the Cl 2p edge, were extracted from the shape and width of the experimentally obtained time-of-flight (TOF) distributions. The KERD spectra exhibit either smooth profiles or structures, depending on the moiety and photon energy. In general, the heavier the ionic fragments, the lower their average KERDs are. In contrast, the light H(+) fragments are observed with kinetic energies centered around 4.5-5.5 eV, depending on the photon energy. It was observed that the change in the photon energy involves a change in the KERDs, indicating different processes or transitions taking place in the breakup process. In the particular case of double ionization with the ejection of two charged fragments, the KERDs present have characteristics compatible with the Coulombic fragmentation model. Intending to interpret the experimental data, singlet and triplet states at Cl 2p edge of the CH2Cl2 molecule, corresponding to the Cl (2p → 10a1*) and Cl (2p → 4b1*) transitions, were calculated at multiconfigurational self-consistent field (MCSCF) level and multireference configuration interaction (MRCI). These states were selected to form the spin-orbit coupling matrix elements, which after diagonalization result in a spin-orbit manifold. Minimum energy pathways for dissociation of the molecule were additionally calculated aiming to give support to the presence of the ultrafast dissociation mechanism in the molecular breakup.

CORSEN, a new software dedicated to microscope-based 3D distance measurements: mRNA-mitochondria distance, from single-cell to population analyses.

PubMed

Jourdren, Laurent; Delaveau, Thierry; Marquenet, Emelie; Jacq, Claude; Garcia, Mathilde

2010-07-01

Recent improvements in microscopy technology allow detection of single molecules of RNA, but tools for large-scale automatic analyses of particle distributions are lacking. An increasing number of imaging studies emphasize the importance of mRNA localization in the definition of cell territory or the biogenesis of cell compartments. CORSEN is a new tool dedicated to three-dimensional (3D) distance measurements from imaging experiments especially developed to access the minimal distance between RNA molecules and cellular compartment markers. CORSEN includes a 3D segmentation algorithm allowing the extraction and the characterization of the cellular objects to be processed--surface determination, aggregate decomposition--for minimal distance calculations. CORSEN's main contribution lies in exploratory statistical analysis, cell population characterization, and high-throughput assays that are made possible by the implementation of a batch process analysis. We highlighted CORSEN's utility for the study of relative positions of mRNA molecules and mitochondria: CORSEN clearly discriminates mRNA localized to the vicinity of mitochondria from those that are translated on free cytoplasmic polysomes. Moreover, it quantifies the cell-to-cell variations of mRNA localization and emphasizes the necessity for statistical approaches. This method can be extended to assess the evolution of the distance between specific mRNAs and other cellular structures in different cellular contexts. CORSEN was designed for the biologist community with the concern to provide an easy-to-use and highly flexible tool that can be applied for diverse distance quantification issues.

Characterization of gold kiwifruit pectin from fruit of different maturities and extraction methods.

PubMed

Yuliarti, Oni; Matia-Merino, Lara; Goh, Kelvin K T; Mawson, John; Williams, Martin A K; Brennan, Charles

2015-01-01

Studies on gold kiwifruit pectins are limited. In this work, the characterization of pectin isolated from two different stages of maturity of gold kiwifruit, namely early harvested fruit (EHF) and main harvested fruit (MHF) isolated by three methods (acid, water, enzymatic) was carried out. Pectins isolated from MHF were higher in galacturonic acid content (52-59% w/w) and weight-average molecular weights (Mw, 1.7-3.8 × 10(6)g/mol) compared with EHF pectins (29-49% w/w and 0.2-1.7 × 10(6)g/mol respectively). Enzymatic treatment gave the highest yield but lowest in Mw, viscosity and mechanical spectra for both maturities. The pectin of both maturities was classified as high-methoxyl pectin with the degree of esterification ranged from 82% to 90%. Water-extracted MHF pectin molecules had the highest RMS radius (182.7 nm) and Mw (3.75 × 10(6)g/mol). The water extraction method appeared to retain the native state of pectin molecules compared with acid and enzymatic extraction methods based on the Mw and viscosity data. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites.

PubMed

Covington, Brett C; McLean, John A; Bachmann, Brian O

2017-01-04

Covering: 2000 to 2016The labor-intensive process of microbial natural product discovery is contingent upon identifying discrete secondary metabolites of interest within complex biological extracts, which contain inventories of all extractable small molecules produced by an organism or consortium. Historically, compound isolation prioritization has been driven by observed biological activity and/or relative metabolite abundance and followed by dereplication via accurate mass analysis. Decades of discovery using variants of these methods has generated the natural pharmacopeia but also contributes to recent high rediscovery rates. However, genomic sequencing reveals substantial untapped potential in previously mined organisms, and can provide useful prescience of potentially new secondary metabolites that ultimately enables isolation. Recently, advances in comparative metabolomics analyses have been coupled to secondary metabolic predictions to accelerate bioactivity and abundance-independent discovery work flows. In this review we will discuss the various analytical and computational techniques that enable MS-based metabolomic applications to natural product discovery and discuss the future prospects for comparative metabolomics in natural product discovery.

Evaluation of processing effects on anthocyanin content and colour modifications of blueberry (Vaccinium spp.) extracts: Comparison between HPLC-DAD and CIELAB analyses.

PubMed

Cesa, Stefania; Carradori, Simone; Bellagamba, Giuseppe; Locatelli, Marcello; Casadei, Maria Antonietta; Masci, Alessandra; Paolicelli, Patrizia

2017-10-01

Colour is the first organoleptic property that consumers appreciate of a foodstuff. In blueberry (Vaccinium spp.) fruits, the anthocyanins are the principal pigments determining the colour as well as many of the beneficial effects attributed to this functional food. Commercial blueberry-derived products represent important sources of these healthy molecules all year round. In this study, blueberries were produced into purees comparing two homogenization methods and further heated following different thermal treatments. All the supernatants of the homogenates were monitored for pH. Then, the hydroalcoholic extracts of the same samples were characterized by CIELAB and HPLC-DAD analyses. These analytical techniques provide complementary information on fruit pigments content as a whole and on quali-quantitative profile of the single bioactive colorants. These data could be very interesting to know the best manufacturing procedure to prepare blueberry-derived products, well accepted by the consumers, while maintaining their healthy properties unaltered. Copyright © 2017. Published by Elsevier Ltd.

Kinase Pathway Database: An Integrated Protein-Kinase and NLP-Based Protein-Interaction Resource

PubMed Central

Koike, Asako; Kobayashi, Yoshiyuki; Takagi, Toshihisa

2003-01-01

Protein kinases play a crucial role in the regulation of cellular functions. Various kinds of information about these molecules are important for understanding signaling pathways and organism characteristics. We have developed the Kinase Pathway Database, an integrated database involving major completely sequenced eukaryotes. It contains the classification of protein kinases and their functional conservation, ortholog tables among species, protein–protein, protein–gene, and protein–compound interaction data, domain information, and structural information. It also provides an automatic pathway graphic image interface. The protein, gene, and compound interactions are automatically extracted from abstracts for all genes and proteins by natural-language processing (NLP).The method of automatic extraction uses phrase patterns and the GENA protein, gene, and compound name dictionary, which was developed by our group. With this database, pathways are easily compared among species using data with more than 47,000 protein interactions and protein kinase ortholog tables. The database is available for querying and browsing at http://kinasedb.ontology.ims.u-tokyo.ac.jp/. PMID:12799355

Switching Hole and Electron Transports of Molecules on Metal Oxides by Energy Level Alignment Tuning.

PubMed

Bao, Zhong-Min; Xu, Rui-Peng; Li, Chi; Xie, Zhong-Zhi; Zhao, Xin-Dong; Zhang, Yi-Bo; Li, Yan-Qing; Tang, Jian-Xin

2016-08-31

Charge transport at organic/inorganic hybrid contacts significantly affects the performance of organic optoelectronic devices because the unfavorable energy level offsets at these interfaces can hinder charge injection or extraction due to large barrier heights. Herein, we report a technologically relevant method to functionalize a traditional hole-transport layer of solution-processed nickel oxide (NiOx) with various interlayers. The photoemission spectroscopy measurements reveal the continuous tuning of the NiOx substrate work function ranging from 2.5 to 6.6 eV, enabling the alignment transition of energy levels between the Schottky-Mott limit and Fermi level pinning at the organic/composite NiOx interface. As a result, switching hole and electron transport for the active organic material on the composite NiOx layer is achieved due to the controlled carrier injection/extraction barriers. The experimental findings indicate that tuning the work function of metal oxides with optimum energy level offsets can facilitate the charge transport at organic/electrode contacts.

Antimicrobial Activity and Phytochemical Analysis of Organic Extracts from Cleome spinosa Jaqc.

PubMed Central

da Silva, Ana P. Sant'Anna; Nascimento da Silva, Luís C.; Martins da Fonseca, Caíque S.; de Araújo, Janete M.; Correia, Maria T. dos Santos; Cavalcanti, Marilene da Silva; Lima, Vera L. de Menezes

2016-01-01

Due to the use of Cleome spinosa Jacq. (Cleomaceae) in traditional medicine against inflammatory and infectious processes, this study evaluated the in vitro antimicrobial potential and phytochemical composition of extracts from its roots and leaves. From leaves (L) and roots (R) of C. spinosa different extracts were obtained (cyclohexane: ChL and ChR; chloroform: CL and CR; ethyl acetate: EAL and EAR, methanol: ML and MR). The antimicrobial activity was evaluated by the broth microdilution method to obtain the minimum inhibitory (MIC) and microbicidal (MMC) concentrations against 17 species, including bacteria and yeasts. Additionally, antimicrobial and combinatory effects with oxacillin were assessed against eight clinical isolates of Staphylococcus aureus. All C. spinosa extracts showed a broad spectrum of antimicrobial activity, as they have inhibited all tested bacteria and yeasts. This activity seems to be related to the phytochemicals (flavonoid, terpenoids and saponins) detected into the extracts of C. spinosa. ChL and CL extracts were the most actives, with MIC less than 1 mg/mL against S. aureus, Bacillus subtilis, and Micrococcus luteus. It is important to note that these concentrations are much lower than their 50% hemolysis concentration (HC50) values. Strong correlations were found between the average MIC against S. aureus and their phenolic (r = −0.89) and flavonoid content (r = −0.87), reinforcing the possible role of these metabolite classes on the antimicrobial activity of C. spinosa derived extracts. Moreover, CL and CR showed the best inhibitory activity against S. aureus clinical isolates, they also showed synergistic action with oxacillin against all these strains (at least at one combined proportion). These results encourage the identification of active substances which could be used as lead(s) molecules in the development of new antimicrobial drugs. PMID:27446005

An Algebraic Method for Exploring Quantum Monodromy and Quantum Phase Transitions in Non-Rigid Molecules

NASA Astrophysics Data System (ADS)

Larese, D.; Iachello, F.

2011-06-01

A simple algebraic Hamiltonian has been used to explore the vibrational and rotational spectra of the skeletal bending modes of HCNO, BrCNO, NCNCS, and other ``floppy`` (quasi-linear or quasi-bent) molecules. These molecules have large-amplitude, low-energy bending modes and champagne-bottle potential surfaces, making them good candidates for observing quantum phase transitions (QPT). We describe the geometric phase transitions from bent to linear in these and other non-rigid molecules, quantitatively analysing the spectroscopy signatures of ground state QPT, excited state QPT, and quantum monodromy.The algebraic framework is ideal for this work because of its small calculational effort yet robust results. Although these methods have historically found success with tri- and four-atomic molecules, we now address five-atomic and simple branched molecules such as CH_3NCO and GeH_3NCO. Extraction of potential functions is completed for several molecules, resulting in predictions of barriers to linearity and equilibrium bond angles.

Dupuytren's: a systems biology disease

PubMed Central

2011-01-01

Dupuytren's disease (DD) is an ill-defined fibroproliferative disorder of the palm of the hands leading to digital contracture. DD commonly occurs in individuals of northern European extraction. Cellular components and processes associated with DD pathogenesis include altered gene and protein expression of cytokines, growth factors, adhesion molecules, and extracellular matrix components. Histology has shown increased but varying levels of particular types of collagen, myofibroblasts and myoglobin proteins in DD tissue. Free radicals and localised ischaemia have been suggested to trigger the proliferation of DD tissue. Although the existing available biological information on DD may contain potentially valuable (though largely uninterpreted) information, the precise aetiology of DD remains unknown. Systems biology combines mechanistic modelling with quantitative experimentation in studies of networks and better understanding of the interaction of multiple components in disease processes. Adopting systems biology may be the ideal approach for future research in order to improve understanding of complex diseases of multifactorial origin. In this review, we propose that DD is a disease of several networks rather than of a single gene, and show that this accounts for the experimental observations obtained to date from a variety of sources. We outline how DD may be investigated more effectively by employing a systems biology approach that considers the disease network as a whole rather than focusing on any specific single molecule. PMID:21943049

Improved Detection of Norovirus and Hepatitis A Virus in Surface Water by Applying Pre-PCR Processing.

PubMed

Borgmästars, Emmy; Jazi, Mehrdad Mousavi; Persson, Sofia; Jansson, Linda; Rådström, Peter; Simonsson, Magnus; Hedman, Johannes; Eriksson, Ronnie

2017-12-01

Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) detection of waterborne RNA viruses generally requires concentration of large water volumes due to low virus levels. A common approach is to use dead-end ultrafiltration followed by precipitation with polyethylene glycol. However, this procedure often leads to the co-concentration of PCR inhibitors that impairs the limit of detection and causes false-negative results. Here, we applied the concept of pre-PCR processing to optimize RT-qPCR detection of norovirus genogroup I (GI), genogroup II (GII), and hepatitis A virus (HAV) in challenging water matrices. The RT-qPCR assay was improved by screening for an inhibitor-tolerant master mix and modifying the primers with twisted intercalating nucleic acid molecules. Additionally, a modified protocol based on chaotropic lysis buffer and magnetic silica bead nucleic acid extraction was developed for complex water matrices. A validation of the modified extraction protocol on surface and drinking waters was performed. At least a 26-fold improvement was seen in the most complex surface water studied. The modified protocol resulted in average recoveries of 33, 13, 8, and 4% for mengovirus, norovirus GI, GII, and HAV, respectively. The modified protocol also improved the limit of detection for norovirus GI and HAV. RT-qPCR inhibition with C q shifts of 1.6, 2.8, and 3.5 for norovirus GI, GII, and HAV, respectively, obtained for the standard nucleic acid extraction were completely eliminated by the modified protocol. The standard nucleic acid extraction method worked well on drinking water with no RT-qPCR inhibition observed and average recoveries of 80, 124, 89, and 32% for mengovirus, norovirus GI, GII, and HAV, respectively.

Depth Filters Containing Diatomite Achieve More Efficient Particle Retention than Filters Solely Containing Cellulose Fibers

PubMed Central

Buyel, Johannes F.; Gruchow, Hannah M.; Fischer, Rainer

2015-01-01

The clarification of biological feed stocks during the production of biopharmaceutical proteins is challenging when large quantities of particles must be removed, e.g., when processing crude plant extracts. Single-use depth filters are often preferred for clarification because they are simple to integrate and have a good safety profile. However, the combination of filter layers must be optimized in terms of nominal retention ratings to account for the unique particle size distribution in each feed stock. We have recently shown that predictive models can facilitate filter screening and the selection of appropriate filter layers. Here we expand our previous study by testing several filters with different retention ratings. The filters typically contain diatomite to facilitate the removal of fine particles. However, diatomite can interfere with the recovery of large biopharmaceutical molecules such as virus-like particles and aggregated proteins. Therefore, we also tested filtration devices composed solely of cellulose fibers and cohesive resin. The capacities of both filter types varied from 10 to 50 L m−2 when challenged with tobacco leaf extracts, but the filtrate turbidity was ~500-fold lower (~3.5 NTU) when diatomite filters were used. We also tested pre–coat filtration with dispersed diatomite, which achieved capacities of up to 120 L m−2 with turbidities of ~100 NTU using bulk plant extracts, and in contrast to the other depth filters did not require an upstream bag filter. Single pre-coat filtration devices can thus replace combinations of bag and depth filters to simplify the processing of plant extracts, potentially saving on time, labor and consumables. The protein concentrations of TSP, DsRed and antibody 2G12 were not affected by pre-coat filtration, indicating its general applicability during the manufacture of plant-derived biopharmaceutical proteins. PMID:26734037

Depth Filters Containing Diatomite Achieve More Efficient Particle Retention than Filters Solely Containing Cellulose Fibers.

PubMed

Buyel, Johannes F; Gruchow, Hannah M; Fischer, Rainer

2015-01-01

The clarification of biological feed stocks during the production of biopharmaceutical proteins is challenging when large quantities of particles must be removed, e.g., when processing crude plant extracts. Single-use depth filters are often preferred for clarification because they are simple to integrate and have a good safety profile. However, the combination of filter layers must be optimized in terms of nominal retention ratings to account for the unique particle size distribution in each feed stock. We have recently shown that predictive models can facilitate filter screening and the selection of appropriate filter layers. Here we expand our previous study by testing several filters with different retention ratings. The filters typically contain diatomite to facilitate the removal of fine particles. However, diatomite can interfere with the recovery of large biopharmaceutical molecules such as virus-like particles and aggregated proteins. Therefore, we also tested filtration devices composed solely of cellulose fibers and cohesive resin. The capacities of both filter types varied from 10 to 50 L m(-2) when challenged with tobacco leaf extracts, but the filtrate turbidity was ~500-fold lower (~3.5 NTU) when diatomite filters were used. We also tested pre-coat filtration with dispersed diatomite, which achieved capacities of up to 120 L m(-2) with turbidities of ~100 NTU using bulk plant extracts, and in contrast to the other depth filters did not require an upstream bag filter. Single pre-coat filtration devices can thus replace combinations of bag and depth filters to simplify the processing of plant extracts, potentially saving on time, labor and consumables. The protein concentrations of TSP, DsRed and antibody 2G12 were not affected by pre-coat filtration, indicating its general applicability during the manufacture of plant-derived biopharmaceutical proteins.

Behavior of Multiclass Pesticide Residue Concentrations during the Transformation from Rose Petals to Rose Absolute.

PubMed

Tascone, Oriane; Fillâtre, Yoann; Roy, Céline; Meierhenrich, Uwe J

2015-05-27

This study investigates the concentrations of 54 multiclass pesticides during the transformation processes from rose petal to concrete and absolute using roses spiked with pesticides as a model. The concentrations of the pesticides were followed during the process of transforming the spiked rose flowers from an organic field into concrete and then into absolute. The rose flowers, the concrete, and the absolute, as well as their transformation intermediates, were analyzed for pesticide content using gas chromatography/tandem mass spectrometry. We observed that all the pesticides were extracted and concentrated in the absolute, with the exception of three molecules: fenthion, fenamiphos, and phorate. Typical pesticides were found to be concentrated by a factor of 100-300 from the rose flowers to the rose absolute. The observed effect of pesticide enrichment was also studied in roses and their extracts from four classically phytosanitary treated fields. Seventeen pesticides were detected in at least one of the extracts. Like the case for the spiked samples in our model, the pesticides present in the rose flowers from Turkey were concentrated in the absolute. Two pesticides, methidathion and chlorpyrifos, were quantified in the rose flowers at approximately 0.01 and 0.01-0.05 mg kg(-1), respectively, depending on the treated field. The concentrations determined for the corresponding rose absolutes were 4.7 mg kg(-1) for methidathion and 0.65-27.25 mg kg(-1) for chlorpyrifos.

Present and potential applications of cellulases in agriculture, biotechnology, and bioenergy.

PubMed

Phitsuwan, Paripok; Laohakunjit, Natta; Kerdchoechuen, Orapin; Kyu, Khin Lay; Ratanakhanokchai, Khanok

2013-03-01

Cellulase (CEL) presently constitutes a major group of industrial enzyme based on its diverse ranges of utilization. Apart from such current and well-established applications-as in cotton processing, paper recycling, detergent formulation, juice extraction, and animal feed additives-their uses in agricultural biotechnology and bioenergy have been exploited. Supplementation of CELs to accelerate decomposition of plant residues in soil results in improved soil fertility. So far, applying CELs/antagonistic cellulolytic fungi to crops has shown to promote plant growth performance, including enhanced seed germination and protective effects. Their actions are believed mainly to trigger plant defense mechanisms and/or to act as biocontrol agents that mediate disease suppression. However, the exact interaction between the enzymes/fungi and plants has not been clearly elucidated. Under mild conditions, removal of plant cell wall polysaccharides by CELs for protoplast preparation results in reduced protoplast damage and increased viability and yields. CELs have recently shown great potential in enzyme aid extraction of bioactive compounds from plant materials before selective extraction through enhancing release of target molecules, especially those associated with the wall matrix. To date, attempts have been made to formulate CEL preparation for cellulosic-based bioethanol production. The high cost of CELs has created a bottleneck, resulting in an uneconomic production process. The utilization of low-cost carbohydrates, strain improvement, and gene manipulations has been alternatively aimed at reducing the cost of CEL production. In this review, we focus on and discuss current knowledge of CELs and their applications in agriculture, biotechnology, and bioenergy.

Fire resistant behaviour of cellulosic textile functionalized with wastage plant bio-molecules: A comparative scientific report.

PubMed

Basak, Santanu; Wazed Ali, S

2018-07-15

Three different wastage plant based bio-molecules named banana peel powder (Musa acuminata) (BPP), coconut shell (Cocos nucifera) extract (CSE) and pomegranate rind (Punica granatum) extract (PRE) have been explored as fire resistant material on the cellulosic polymer (cotton fabric). To this end, extracts have been applied to the cotton fabric in different concentration at elevated temperature for specific time period. Treated cotton fabric showed 6 (BPP), 8.5 (CSE) and 12 (PRE) times lower vertical burning rate compared to the control cotton fabric. Thermo-gravimetry (TG) curves and the limiting oxygen index (LOI) value revealed that the PRE extract (LOI: 32) treated fabric encompassed more thermal stability compared to the BPP (LOI:26) and the CSE (LOI: 27) treated fabric as it showed higher oxygen index and more weight retention (40%) at higher temperature 450°C. Moreover, the carbonaceous samples remained after the burning of the extracts and the treated fabrics showed structural integration and more carbon content [65.6 (PRE extract) and 76.3% (PRE treated cotton)] compared to the fragile, net like char of the control cotton fabric, having less carbon content (49.8%). Gas Chromatography Mass spectroscopy (GC-MS) of the different extracts (CSE, PRE, BPP) used for the study showed the presence of high molecular weight aromatic phenolic compounds, tannin based compound and the nitrogen containing alkaloids, responsible for fire resistant effect of the different extract treated fabric. Besides fire retardancy, all the treated fabric showed attractive natural colour (measured by colour strength values) and there has been no adverse effect on the tensile strength property of the fabric after the treatment. Copyright © 2018 Elsevier B.V. All rights reserved.

An in vitro evaluation of graphene oxide reduced by Ganoderma spp. in human breast cancer cells (MDA-MB-231)

PubMed Central

Gurunathan, Sangiliyandi; Han, JaeWoong; Park, Jung Hyun; Kim, Jin Hoi

2014-01-01

Background Recently, graphene and graphene-related materials have attracted much attention due their unique properties, such as their physical, chemical, and biocompatibility properties. This study aimed to determine the cytotoxic effects of graphene oxide (GO) that is reduced biologically using Ganoderma spp. mushroom extracts in MDA-MB-231 human breast cancer cells. Methods Herein, we describe a facile and green method for the reduction of GO using extracts of Ganoderma spp. as a reducing agent. GO was reduced without any hazardous chemicals in an aqueous solution, and the reduced GO was characterized using a range of analytical procedures. The Ganoderma extract (GE)-reduced GO (GE-rGO) was characterized by ultraviolet-visible absorption spectroscopy, X-ray diffraction, Fourier-transform infrared spectroscopy, X-ray photoelectron spectroscopy, dynamic light scattering, scanning electron microscopy, Raman spectroscopy, and atomic force microscopy. Furthermore, the toxicity of GE-rGO was evaluated using a sequence of assays such as cell viability, lactate dehydrogenase leakage, and reactive oxygen species generation in human breast cancer cells (MDA-MB-231). Results The preliminary characterization of reduction of GO was confirmed by the red-shifting of the absorption peak for GE-rGO to 265 nm from 230 nm. The size of GO and GE-rGO was found to be 1,880 and 3,200 nm, respectively. X-ray diffraction results confirmed that reduction processes of GO and the processes of removing intercalated water molecules and the oxide groups. The surface functionalities and chemical natures of GO and GE-rGO were confirmed using Fourier-transform infrared spectroscopy and X-ray photoelectron spectroscopy. The surface morphologies of the synthesized graphene were analyzed using high-resolution scanning electron microscopy. Raman spectroscopy revealed single- and multilayer properties of GE-rGO. Atomic force microscopy images provided evidence for the formation of graphene. Furthermore, the effect of GO and GE-rGO was examined using a series of assays, such as cell viability, membrane integrity, and reactive oxygen species generation, which are key molecules involved in apoptosis. The results obtained from cell viability and lactate dehydrogenase assay suggest that GO and GE-rGO cause dose-dependent toxicity in the cells. Interestingly, it was found that biologically derived GE-rGO is more toxic to cancer cells than GO. Conclusion We describe a simple, green, nontoxic, and cost-effective approach to producing graphene using mushroom extract as a reducing and stabilizing agent. The proposed method could enable synthesis of graphene with potential biological and biomedical applications such as in cancer and angiogenic disorders. To our knowledge, this is the first report using mushroom extract as a reducing agent for the synthesis of graphene. Mushroom extract can be used as a biocatalyst for the production of graphene. PMID:24741313

Secondary metabolites extracted from marine sponge associated Comamonas testosteroni and Citrobacter freundii as potential antimicrobials against MDR pathogens and hypothetical leads for VP40 matrix protein of Ebola virus: an in vitro and in silico investigation.

PubMed

Skariyachan, Sinosh; Acharya, Archana B; Subramaniyan, Saumya; Babu, Sumangala; Kulkarni, Shruthi; Narayanappa, Rajeswari

2016-09-01

The current study explores therapeutic potential of metabolites extracted from marine sponge (Cliona sp.)-associated bacteria against MDR pathogens and predicts the binding prospective of probable lead molecules against VP40 target of Ebola virus. The metabolite-producing bacteria were characterized by agar overlay assay and as per the protocols in Bergey's manual of determinative bacteriology. The antibacterial activities of extracted metabolites were tested against clinical pathogens by well-diffusion assay. The selected metabolite producers were characterized by 16S rDNA sequencing. Chemical screening and Fourier Transform Infrared (FTIR) analysis for selected compounds were performed. The probable lead molecules present in the metabolites were hypothesized based on proximate analysis, FTIR data, and literature survey. The drug-like properties and binding potential of lead molecules against VP40 target of Ebola virus were hypothesized by computational virtual screening and molecular docking. The current study demonstrated that clear zones around bacterial colonies in agar overlay assay. Antibiotic sensitivity profiling demonstrated that the clinical isolates were multi-drug resistant, however; most of them showed sensitivity to secondary metabolites (MIC-15 μl/well). The proximate and FTIR analysis suggested that probable metabolites belonged to alkaloids with O-H, C-H, C=O, and N-H groups. 16S rDNA characterization of selected metabolite producers demonstrated that 96% and 99% sequence identity to Comamonas testosteroni and Citrobacter freundii, respectively. The docking studies suggested that molecules such as Gymnastatin, Sorbicillactone, Marizomib, and Daryamide can designed as probable lead candidates against VP40 target of Ebola virus.

Separating spectral mixtures in hyperspectral image data using independent component analysis: validation with oral cancer tissue sections

NASA Astrophysics Data System (ADS)

Duann, Jeng-Ren; Jan, Chia-Ing; Ou-Yang, Mang; Lin, Chia-Yi; Mo, Jen-Feng; Lin, Yung-Jiun; Tsai, Ming-Hsui; Chiou, Jin-Chern

2013-12-01

Recently, hyperspectral imaging (HSI) systems, which can provide 100 or more wavelengths of emission autofluorescence measures, have been used to delineate more complete spectral patterns associated with certain molecules relevant to cancerization. Such a spectral fingerprint may reliably correspond to a certain type of molecule and thus can be treated as a biomarker for the presence of that molecule. However, the outcomes of HSI systems can be a complex mixture of characteristic spectra of a variety of molecules as well as optical interferences due to reflection, scattering, and refraction. As a result, the mixed nature of raw HSI data might obscure the extraction of consistent spectral fingerprints. Here we present the extraction of the characteristic spectra associated with keratinized tissues from the HSI data of tissue sections from 30 oral cancer patients (31 tissue samples in total), excited at two different wavelength ranges (330 to 385 and 470 to 490 nm), using independent and principal component analysis (ICA and PCA) methods. The results showed that for both excitation wavelength ranges, ICA was able to resolve much more reliable spectral fingerprints associated with the keratinized tissues for all the oral cancer tissue sections with significantly higher mean correlation coefficients as compared to PCA (p<0.001).

Method of monitoring photoactive organic molecules in-situ during gas-phase deposition of the photoactive organic molecules

DOEpatents

Forrest, Stephen R.; Vartanian, Garen; Rolin, Cedric

2015-06-23

A method for in-situ monitoring of gas-phase photoactive organic molecules in real time while depositing a film of the photoactive organic molecules on a substrate in a processing chamber for depositing the film includes irradiating the gas-phase photoactive organic molecules in the processing chamber with a radiation from a radiation source in-situ while depositing the film of the one or more organic materials and measuring the intensity of the resulting photoluminescence emission from the organic material. One or more processing parameters associated with the deposition process can be determined from the photoluminescence intensity data in real time providing useful feedback on the deposition process.

Effect of processing conditions on the organosulfides of shallot (Allium cepa L. Aggregatum group).

PubMed

Tocmo, Restituto; Lin, Yi; Huang, Dejian

2014-06-11

There is a growing account of the health benefits of H2S as an endogenous cell-signaling molecule. H2S from organic polysulfides, in particular, is increasingly gaining attention for their beneficial effects to cardiovascular health. Here, we studied shallot as a potential dietary source of organic polysulfides and examined the effects of processing conditions on its polysulfide profiles. Boiling, autoclaving, and freeze-drying were tested on whole and crushed shallot bulbs, analyzing their effect on the yield of organosulfides. Seventeen organosulfides, including disulfides, trisulfides, and cyclic polysulfides, were identified. Significant differences in the quantitative and qualitative profiles of organosulfides in the hydrodistilled and solvent extracted oils were observed. Freeze-drying retained the majority of the organosulfides, but the whole-autoclaved and whole-boiled shallots lost more than 95% of their organic polysulfides. Crushed-boiled and crushed-autoclaved shallot lost 76-80% of their organosulfides, likely due to the thermal sensitivity of these compounds. The organosulfide profiles are sensitive to the pH values of the processing media. In general, disulfides increased at basic pH (pH 9.0) while trisulfides and cyclic organosulfides are much higher at the acidic to neutral pH values (pH 3.0-5.0). Our results provide important information on the effects of processing conditions that are relevant for optimizing extraction of organosulfides from shallot for further studies evaluating their H2S-releasing activity.

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

PubMed Central

Ma, Jian; Casey, Cameron P.; Zheng, Xueyun; Ibrahim, Yehia M.; Wilkins, Christopher S.; Renslow, Ryan S.; Thomas, Dennis G.; Payne, Samuel H.; Monroe, Matthew E.; Smith, Richard D.; Teeguarden, Justin G.; Baker, Erin S.; Metz, Thomas O.

2017-01-01

Abstract Motivation: Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses. Results: We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software. Availability and implementation: PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library. Contact: erin.baker@pnnl.gov or thomas.metz@pnnl.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28505286

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association.

PubMed

Ma, Jian; Casey, Cameron P; Zheng, Xueyun; Ibrahim, Yehia M; Wilkins, Christopher S; Renslow, Ryan S; Thomas, Dennis G; Payne, Samuel H; Monroe, Matthew E; Smith, Richard D; Teeguarden, Justin G; Baker, Erin S; Metz, Thomas O

2017-09-01

Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses. We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software. PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library . erin.baker@pnnl.gov or thomas.metz@pnnl.gov. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Wound healing potential of adipose tissue stem cell extract.

PubMed

Na, You Kyung; Ban, Jae-Jun; Lee, Mijung; Im, Wooseok; Kim, Manho

2017-03-25

Adipose tissue stem cells (ATSCs) are considered as a promising source in the field of cell therapy and regenerative medicine. In addition to direct cell replacement using stem cells, intercellular molecule exchange by stem cell secretory factors showed beneficial effects by reducing tissue damage and augmentation of endogenous repair. Delayed cutaneous wound healing is implicated in many conditions such as diabetes, aging, stress and alcohol consumption. However, the effects of cell-free extract of ATSCs (ATSC-Ex) containing secretome on wound healing process have not been investigated. In this study, ATSC-Ex was topically applied on the cutaneous wound and healing speed was examined. As a result, wound closure was much faster in the cell-free extract treated wound than control wound at 4, 6, 8 days after application of ATSC-Ex. Dermal fibroblast proliferation, migration and extracellular matrix (ECM) production are critical aspects of wound healing, and the effects of ATSC-Ex on human dermal fibroblast (HDF) was examined. ATSC-Ex augmented HDF proliferation in a dose-dependent manner and migration ability was enhanced by extract treatment. Representative ECM proteins, collagen type I and matrix metalloproteinase-1, are significantly up-regulated by treatment of ATSC-Ex. Our results suggest that the ATSC-Ex have improving effect of wound healing and can be the potential therapeutic candidate for cutaneous wound healing. Copyright © 2017 Elsevier Inc. All rights reserved.

Development of suspect and non-target screening methods for detection of organic contaminants in highway runoff and fish tissue with high-resolution time-of-flight mass spectrometry.

PubMed

Du, Bowen; Lofton, Jonathan M; Peter, Katherine T; Gipe, Alexander D; James, C Andrew; McIntyre, Jenifer K; Scholz, Nathaniel L; Baker, Joel E; Kolodziej, Edward P

2017-09-20

Untreated urban stormwater runoff contributes to poor water quality in receiving waters. The ability to identify toxicants and other bioactive molecules responsible for observed adverse effects in a complex mixture of contaminants is critical to effective protection of ecosystem and human health, yet this is a challenging analytical task. The objective of this study was to develop analytical methods using liquid chromatography coupled to high-resolution quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) to detect organic contaminants in highway runoff and in runoff-exposed fish (adult coho salmon, Oncorhynchus kisutch). Processing of paired water and tissue samples facilitated contaminant prioritization and aided investigation of chemical bioavailability and uptake processes. Simple, minimal processing effort solid phase extraction (SPE) and elution procedures were optimized for water samples, and selective pressurized liquid extraction (SPLE) procedures were optimized for fish tissues. Extraction methods were compared by detection of non-target features and target compounds (e.g., quantity and peak area), while minimizing matrix interferences. Suspect screening techniques utilized in-house and commercial databases to prioritize high-risk detections for subsequent MS/MS characterization and identification efforts. Presumptive annotations were also screened with an in-house linear regression (log K ow vs. retention time) to exclude isobaric compounds. Examples of confirmed identifications (via reference standard comparison) in highway runoff include ethoprophos, prometon, DEET, caffeine, cotinine, 4(or 5)-methyl-1H-methylbenzotriazole, and acetanilide. Acetanilide was also detected in runoff-exposed fish gill and liver samples. Further characterization of highway runoff and fish tissues (14 and 19 compounds, respectively with tentative identification by MS/MS data) suggests that many novel or poorly characterized organic contaminants exist in urban stormwater runoff and exposed biota.

Development of a methodology to compute solvation free energies on the basis of the theory of energy representation for solutions represented with a polarizable force field.

PubMed

Suzuoka, Daiki; Takahashi, Hideaki; Ishiyama, Tatsuya; Morita, Akihiro

2012-12-07

We have developed a method of molecular simulations utilizing a polarizable force field in combination with the theory of energy representation (ER) for the purpose of establishing an efficient and accurate methodology to compute solvation free energies. The standard version of the ER method is, however, based on the assumption that the solute-solvent interaction is pairwise additive for its construction. A crucial step in the present method is to introduce an intermediate state in the solvation process to treat separately the many-body interaction associated with the polarizable model. The intermediate state is chosen so that the solute-solvent interaction can be formally written in the pairwise form, though the solvent molecules are interacting with each other with polarizable charges dependent on the solvent configuration. It is, then, possible to extract the free energy contribution δμ due to the many-body interaction between solute and solvent from the total solvation free energy Δμ. It is shown that the free energy δμ can be computed by an extension of the recent development implemented in quantum mechanical∕molecular mechanical simulations. To assess the numerical robustness of the approach, we computed the solvation free energies of a water and a methanol molecule in water solvent, where two paths for the solvation processes were examined by introducing different intermediate states. The solvation free energies of a water molecule associated with the two paths were obtained as -5.3 and -5.8 kcal∕mol. Those of a methanol molecule were determined as -3.5 and -3.7 kcal∕mol. These results of the ER simulations were also compared with those computed by a numerically exact approach. It was demonstrated that the present approach produces the solvation free energies in comparable accuracies to simulations of thermodynamic integration (TI) method within a tenth of computational time used for the TI simulations.

Calixarene-Mediated Liquid-Membrane Transport of Choline Conjugates.

PubMed

Adhikari, Birendra Babu; Fujii, Ayu; Schramm, Michael P

2014-05-01

A series of supramolecular calixarenes efficiently transport distinct molecular species through a liquid membrane when attached to a receptor-complementary choline handle. Calix-[6]arene hexacarboxylic acid was highly effective at transporting different target molecules against a pH gradient. Both carboxylic- and phosphonic-acid-functionalized calix[4]arenes effect transport without requiring a pH or ion gradient. NMR binding studies, two-phase solvent extraction, and three-phase transport experiments reveal the necessary and subtle parameters to effect the transport of molecules attached to a choline "handle". On the other hand, rescorin[4]arene cavitands, which have similar guest recognition profiles, did not transport guest molecules. These developments reveal new approaches towards attempting synthetic-receptor-mediated selective small-molecule transport in vesicular and cellular systems.

Selective Separation of Trivalent Actinides from Lanthanides by Aqueous Processing with Introduction of Soft Donor Atoms

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

Kenneth L. Nash

2009-09-22

Implementation of a closed loop nuclear fuel cycle requires the utilization of Pu-containing MOX fuels with the important side effect of increased production of the transplutonium actinides, most importantly isotopes of Am and Cm. Because the presence of these isotopes significantly impacts the long-term radiotoxicity of high level waste, it is important that effective methods for their isolation and/or transmutation be developed. Furthermore, since transmutation is most efficiently done in the absence of lanthanide fission products (high yield species with large thermal neutron absorption cross sections) it is important to have efficient procedures for the mutual separation of Am andmore » Cm from the lanthanides. The chemistries of these elements are nearly identical, differing only in the slightly stronger strength of interaction of trivalent actinides with ligand donor atoms softer than O (N, Cl-, S). Research being conducted around the world has led to the development of new reagents and processes with considerable potential for this task. However, pilot scale testing of these reagents and processes has demonstrated the susceptibility of the new classes of reagents to radiolytic and hydrolytic degradation. In this project, separations of trivalent actinides from fission product lanthanides have been investigated in studies of 1) the extraction and chemical stability properties of a class of soft-donor extractants that are adapted from water-soluble analogs, 2) the application of water soluble soft-donor complexing agents in tandem with conventional extractant molecules emphasizing fundamental studies of the TALSPEAK Process. This research was conducted principally in radiochemistry laboratories at Washington State University. Collaborators at the Radiological Processing Laboratory (RPL) at the Pacific Northwest National Laboratory (PNNL) have contributed their unique facilities and capabilities, and have supported student internships at PNNL to broaden their academic experience. New information has been developed to qualify the extraction potential of a class of pyridine-functionalized tetraaza complexants indicating potential single contact Am-Nd separation factors of about 40. The methodology developed for characterization will find further application in our continuing efforts to synthesize and characterize new reagents for this separation. Significant new insights into the performance envelope and supporting information on the TALSPEAK process has also been developed.« less

Synthesis of silver nanoparticles using reducing agents obtained from natural sources (Rumex hymenosepalus extracts)

PubMed Central

2013-01-01

We have synthesized silver nanoparticles from silver nitrate solutions using extracts of Rumex hymenosepalus, a plant widely found in a large region in North America, as reducing agent. This plant is known to be rich in antioxidant molecules which we use as reducing agents. Silver nanoparticles grow in a single-step method, at room temperature, and with no addition of external energy. The nanoparticles have been characterized by ultraviolet-visible spectroscopy and transmission electron microscopy, as a function of the ratio of silver ions to reducing agent molecules. The nanoparticle diameters are in the range of 2 to 40 nm. High-resolution transmission electron microscopy and fast Fourier transform analysis show that two kinds of crystal structures are obtained: face-centered cubic and hexagonal. PMID:23841946

Stability of integral membrane proteins under high hydrostatic pressure: the LH2 and LH3 antenna pigment-protein complexes from photosynthetic bacteria.

PubMed

Kangur, Liina; Timpmann, Kõu; Freiberg, Arvi

2008-07-03

The bacteriochlorophyll a-containing LH2 and LH3 antenna complexes are the integral membrane proteins that catalyze the photosynthetic process in purple photosynthetic bacteria. The LH2 complex from Rhodobacter sphaeroides shows characteristic strong absorbance at 800 and 850 nm due to the pigment molecules confined in two separate areas of the protein. In the LH3 complex from Rhodopesudomonas acidophila the corresponding bands peak at 800 and 820 nm. Using the bacteriochlorophyll a cofactors as intrinsic probes to monitor local changes in the protein structure, we investigate spectral responses of the antenna complexes to very high hydrostatic pressures up to 2.5 GPa when embedded into natural membrane environment or extracted with detergent. We first demonstrate that high pressure does induce significant alterations to the tertiary structure of the proteins not only in proximity of the 800 nm-absorbing bacteriochlorophyll a molecules known previously (Gall, A.; et al. Biochemistry 2003, 42, 13019) but also of the 850 nm- and 820 nm-absorbing molecules, including breakage of the hydrogen bond they are involved in. The membrane-protected complexes appear more resilient to damaging effects of the compression compared with the complexes extracted into mixed detergent-buffer environment. Increased resistance of the isolated complexes is observed at high protein concentration resulting aggregation as well as when cosolvent (glycerol) is added into the solution. These stability variations correlate with ability of penetration of the surrounding polar solvent (water) into the hydrophobic protein interiors, being thus the principal reason of the pressure-induced denaturation of the proteins. Considerable variability of elastic properties of the isolated complexes was also observed, tentatively assigned to heterogeneous protein packing in detergent micelles. While a number of the isolated complexes release most of their bacteriochlorophyll a content under high pressure, quite some of them remain apparently intact. The pigmented photosynthetic antenna complexes thus constitute a suitable model system for studying in detail the stability of integral membrane proteins.

On-line miniaturized asymmetrical flow field-flow fractionation-electrospray ionization-tandem mass spectrometry with selected reaction monitoring for quantitative analysis of phospholipids in plasma lipoproteins.

PubMed

Yang, Iseul; Kim, Ki Hun; Lee, Ju Yong; Moon, Myeong Hee

2014-01-10

A direct analytical method for high speed quantitative analysis of lipids in human blood plasma using on-line chip-type asymmetrical flow field-flow fractionation-electrospray ionization-tandem mass spectrometry (cAF4-ESI-MS/MS) with selected reaction monitoring (SRM) is described in this study. Utilizing a miniaturized cAF4 channel, high speed size separation of high density lipoproteins (HDL) and low density lipoproteins (LDL) from plasma samples can be accomplished at a microflow rate along with simultaneous desalting of lipoproteins, both of which are conducive to direct ESI of lipids in lipoproteins. This study demonstrates that the SRM method to monitor phospholipids during cAF4-ESI-MS/MS can be successfully applied to the quantitation of lipid molecules in plasma lipoproteins without the need of a separate lipid extraction process. For quantitation of lipids in HDL and LDL during cAF4-ESI-MS/MS runs, a protein standard (carbonic anhydrase, 29 kDa) was added to each plasma sample as an internal standard such that a peak intensity of y67(+5) ions, which are high abundant SRM product ions of CA, could be utilized to calculate the relative intensity of each lipid molecule. The developed method was applied to plasma samples from 10 patients with coronary artery disease (CAD) and 10 healthy control samples, and quantitative analysis of 39 lipid molecules including phosphatidylcholines, phosphatidylethanolamines, sphingomyelins, phosphatidylglycerols, and phosphatidylinositols, resulted in the selection of 13 PL species showing more than 2.5 fold difference in relative abundance (p<0.01) between the groups. The present study demonstrates a high speed analytical method for determining plasma lipid content and distribution without an organic solvent extraction of lipids from plasma. Copyright © 2013 Elsevier B.V. All rights reserved.

New drugs from ancient natural foods. Oleocanthal, the natural occurring spicy compound of olive oil: a brief history.

PubMed

Scotece, Morena; Conde, Javier; Abella, Vanessa; Lopez, Veronica; Pino, Jesús; Lago, Francisca; Smith, Amos B; Gómez-Reino, Juan J; Gualillo, Oreste

2015-04-01

Extra-virgin olive oil (EVOO), a principal component of the Mediterranean diet (Med diet), is one of the most ancient known foods and has long been associated with health benefits. Many phenolic compounds extracted from Olea europea L. have attracted attention since their discovery. Among these phenolic constituents, oleocanthal has recently emerged as a potential therapeutic molecule for different diseases, showing relevant pharmacological properties in various pathogenic processes, including inflammation, cancers and neurodegenerative diseases. Here, we discuss and summarize the most recent pharmacological evidence for the medical relevance of oleocanthal, focusing our attention on its anti-inflammatory and chemotherapeutic roles. Copyright © 2014 Elsevier Ltd. All rights reserved.

Plant Nutrition 2: Macronutrients (N, P, K, S, Mg, and Ca)

PubMed Central

2014-01-01

Summary In the second of three lessons spanning the topic of Plant Nutrition, we examine how macronutrients affect plant growth. Specifically, we look at (1) the availability of nutrients in the soil along with the effects of soil microbes and physical properties on their availability; (2) nutrient uptake from the external environment, across plasma membranes and into plant cells; (3) in some cases, the assimilation of the nutrient into organic molecules; (4) the distribution and redistribution of nutrients throughout the plant; and (5) regulation of these processes. In parallel, we examine the genetic basis of a plant's nutrient use efficiency (NUE) and evaluate strategies by which to replenish nutrients that growing plants extract from soil.

Aronia melanocarpa fruit extract exhibits anti-inflammatory activity in human aortic endothelial cells.

PubMed

Zapolska-Downar, D; Bryk, D; Małecki, M; Hajdukiewicz, K; Sitkiewicz, D

2012-08-01

Altered expression of cell adhesion molecules (CAMs) has been implicated in a variety of chronic inflammatory conditions, including atherosclerosis. Regulation of adhesion molecule expression by specific redox-sensitive mechanisms has been reported. Additionally, it has been observed that the extract of Aronia melanocarpa (A. Melanocarpa) fruits, rich in polyphenols, exhibits potent anti-oxidant properties and displays cardioprotective activity. Human aortic endothelial cells (HAECs) were pretreated with various concentrations (primarily 50 μg/mL) of Aronia Melanocarpa fruit extract prior to treatment with TNFα (10 ng/mL) for various periods of time. The surface protein and mRNA expression of ICAM-1 and VCAM-1 were determined using flow cytometry and real-time RT-PCR, respectively. Adhesion of peripheral blood mononuclear leucocytes (PBMLs) to TNFα-treated HAECs was evaluated by an adhesion assay. Activation of NF-κB was evaluated by measuring NF-κB p65 phosphorylation using flow cytometry. ROS production was determined by reduction in fluorescent 2',7'-dichlorofluorescein diacetate (DCFH-DA). Tested A. Melanocarpa extract significantly inhibited the expression of ICAM-1 and VCAM-1, attenuated the phosphorylation of NF-κB p65 and decreased intracellular ROS production in TNFα-treated HAECs. We conclude that A. Melanocarpa fruit extract exhibits anti-inflammatory effects in HAECs by inhibiting the expression of endothelial CAMs, activation of NF-κB and production of ROS.

N-butanol extracts of Morinda citrifolia suppress advanced glycation end products (AGE)-induced inflammatory reactions in endothelial cells through its anti-oxidative properties.

PubMed

Ishibashi, Yuji; Matsui, Takanori; Isami, Fumiyuki; Abe, Yumi; Sakaguchi, Tatsuya; Higashimoto, Yuichiro; Yamagishi, Sho-Ichi

2017-03-04

Advanced glycation end products (AGEs), senescent macroprotein derivatives formed during a normal aging process and acceleratedly under diabetic conditions, play a role in atherosclerotic cardiovascular disease. AGEs cause endothelial cell (EC) damage, an initial trigger for atherosclerosis through the interaction with a receptor for AGEs (RAGE). We have previously shown that n-butanol extracts of Morinda citrifolia (noni), a plant belonging to the family Rubiaceae, block the binding of AGEs to RAGE in vitro. In this study, we examined the effects of n-butanol extracts of noni on reactive oxygen species (ROS) generation and inflammatory reactions on AGE-exposed human umbilical vein ECs (HUVECs). HUVECs were treated with 100 μg/ml AGE-bovine serum albumin (AGE-BSA) or non-glycated BSA in the presence or absence of 670 ng/ml n-butanol extracts of noni for 4 h. Then ROS generation and inflammatory and gene expression in HUVECs were evaluated by dihydroethidium staining and real-time reverse transcription-polymerase chain reaction analyses, respectively. THP-1 cell adhesion to HUVECs was measured after 2-day incubation of AGE-BSA or BSA in the presence or absence of 670 ng/ml n-butanol extracts of noni. N-butanol extracts of noni at 670 ng/ml significantly inhibited the AGE-induced ROS generation and RAGE, intercellular adhesion molecule-1 and plasminogen activator inhibitor-1 gene expressions in HUVECs. AGEs significantly increased monocytic THP-1 cell adhesion to HUVECs, which was also prevented by 670 ng/ml n-butanol extracts of noni. The present study demonstrated for the first time that N-butanol extracts of noni could suppress the AGE-induced inflammatory reactions in HUVECs through its anti-oxidative properties via blocking of the interaction of AGEs with RAGE. Inhibition of the AGE-RAGE axis by n-butanol extracts of noni may be a novel nutraceutical strategy for the treatment of cardiovascular disease.

Solid Phase Micro Extraction (SPME)

NASA Technical Reports Server (NTRS)

1998-01-01

Internation Flavors and Fragrances Inc. proprietary research technology, Solid Phase Micro Extraction (SPME) utilizes a special fiber needle placed directly next to the bloom of the living flower to collect the fragrance molecules. SPME was used in the Space Flower experiment aboard STS-95 space shuttle mission, after which Dr. Braja Mookherjee (left) and Subha Patel of IFF will analyze the effects of gravity on the Overnight Scentsation rose plant.

Cinnamon extract suppresses experimental colitis through modulation of antigen-presenting cells.

PubMed

Kwon, Ho-Keun; Hwang, Ji-Sun; Lee, Choong-Gu; So, Jae-Seon; Sahoo, Anupama; Im, Chang-Rok; Jeon, Won Kyung; Ko, Byoung Seob; Lee, Sung Haeng; Park, Zee Yong; Im, Sin-Hyeog

2011-02-28

To investigate the anti-inflammatory effects of cinnamon extract and elucidate its mechanisms for targeting the function of antigen presenting cells. Cinnamon extract was used to treat murine macrophage cell line (Raw 264.7), mouse primary antigen-presenting cells (APCs, MHCII(+)) and CD11c(+) dendritic cells to analyze the effects of cinnamon extract on APC function. The mechanisms of action of cinnamon extract on APCs were investigated by analyzing cytokine production, and expression of MHC antigens and co-stimulatory molecules by quantitative real-time PCR and flow cytometry. In addition, the effect of cinnamon extract on antigen presentation capacity and APC-dependent T-cell differentiation were analyzed by [H(3)]-thymidine incorporation and cytokine analysis, respectively. To confirm the anti-inflammatory effects of cinnamon extract in vivo, cinnamon or PBS was orally administered to mice for 20 d followed by induction of experimental colitis with 2,4,6 trinitrobenzenesulfonic acid. The protective effects of cinnamon extract against experimental colitis were measured by checking clinical symptoms, histological analysis and cytokine expression profiles in inflamed tissue. Treatment with cinnamon extract inhibited maturation of MHCII(+) APCs or CD11c(+) dendritic cells (DCs) by suppressing expression of co-stimulatory molecules (B7.1, B7.2, ICOS-L), MHCII and cyclooxygenase (COX)-2. Cinnamon extract induced regulatory DCs (rDCs) that produce low levels of pro-inflammatory cytokines [interleukin (IL)-1β, IL-6, IL-12, interferon (IFN)-γ and tumor necrosis factor (TNF)-α] while expressing high levels of immunoregulatory cytokines (IL-10 and transforming growth factor-β). In addition, rDCs generated by cinnamon extract inhibited APC-dependent T-cell proliferation, and converted CD4(+) T cells into IL-10(high) CD4(+) T cells. Furthermore, oral administration of cinnamon extract inhibited development and progression of intestinal colitis by inhibiting expression of COX-2 and pro-inflammatory cytokines (IL-1β, IFN-γ and TNF-α), while enhancing IL-10 levels. Our study suggests the potential of cinnamon extract as an anti-inflammatory agent by targeting the generation of regulatory APCs and IL-10(+) regulatory T cells.

Antiatherosclerotic effects of Artemisia princeps Pampanini cv. Sajabal in LDL receptor deficient mice.

PubMed

Han, Jong-Min; Kim, Min-Jung; Baek, Seung-Hwa; An, Sojin; Jin, Yue-Yan; Chung, Hae-Gon; Baek, Nam-In; Choi, Myung-Sook; Lee, Kyung-Tae; Jeong, Tae-Sook

2009-02-25

Antiatherosclerotic effects of ethanolic extracts of Artemisia princeps Pampanini cv. Sajabal (ESJ) were investigated in low-density lipoprotein receptor deficient (LDLR(-/-)) mice. The Western diet-induced high levels of total cholesterol and triglyceride were similar in the ESJ and control groups. However, circulating oxidized LDL was significantly decreased in the ESJ group (p < 0.05). ESJ also markedly decreased aortic expression levels of intercellular adhesion molecule-1 (ICAM-1), vascular cell adhesion molecule-1 (VCAM-1), tumor necrosis factor-alpha (TNF-alpha), and interleukin-1 beta (IL-1 beta), and reduced the aortic lesion formation and macrophage accumulation by 36.7% (p < 0.05) and 43% (p < 0.01) in the control group, respectively. Additionally, ESJ inhibited atherogenic properties with cytokine-induced surface expression of cell adhesion molecules, chemokines, and monocyte adhesion to the human umbilical vein endothelial cells (HUVECs), and simultaneously suppressed nuclear factor-kappaB (NF-kappaB) activation. These results suggest that ethanolic extracts of Artemisia princeps Pampanini cv. Sajabal contributes to the antiatherosclerotic and anti-inflammatory activities in LDLR(-/-) mice.

Preparation of mixed molecularly imprinted polymer magnetic nanoparticles and its application in separation of Chinese traditional medicine

NASA Astrophysics Data System (ADS)

Xie, Yihui; Ma, Yajuan; Bai, Wenting; Zhu, Xiaofang; Liu, Min; Huang, Liping

2017-08-01

A mixed imprinted polymer which can rapidly adsorb all flavonoids from raspberry extract was prepared and recycled. The hybrid molecular surface imprinted polymers were prepared by using quercetin as the template molecule and Fe3O4 magnetic nanospheres as the carrier. The molecular imprinting polymer was prepared by using the "initial template molecule, molecularly imprinted polymer, mixed template molecule, molecularly imprint ted polymers (MIPS)". The adsorption performance and durability of the hybrid molecularly imprinted polymers were investigated by using the fingerprints of the ethyl acetate fraction of raspberry as an index. The adsorption of flavonoids from raspberry extract, lindenoside, cis-lindenin, quercetin, kaempferol and other flavonoids was completely adsorbed by mixed molecular-imprinted polymer, and the other components were basically adsorbed. When Mix-IMPs were repeatedly used 10 times, the fingerprints showed that the content and content of flavonoids were basically the same. The experimental results show that Mix-IMPs has good adsorption performance, can be recycled and used for rapid enrichment of flavonoids in raspberry.

Synthesis and radiometric evaluation of diglycolamide functionalized mesoporous silica for the chromatographic separation of actinides Th, Pa and U.

PubMed

Hopkins, Philip D; Mastren, Tara; Florek, Justyna; Copping, Roy; Brugh, Mark; John, Kevin D; Nortier, Meiring F; Birnbaum, Eva R; Kleitz, Freddy; Fassbender, Michael E

2018-04-17

The separation of Th, Pa, and U is of high importance in many applications including nuclear power, nuclear waste, environmental and geochemistry, nuclear forensics and nuclear medicine. Diglycolamide (DGA)-based resins have shown the ability to separate many elements, however, these resins consist of non-covalent impregnation of the DGA molecules on the resin backbone resulting in co-elution of the extraction molecule during separation cycles, therefore limiting their long-term and repeated use. Covalently binding the DGA molecules onto silica is one way to overcome this issue. Herein, measured equilibrium distribution coefficients of normal extraction chromatographic DGA resin and a covalently bound form (KIT-6-N-DGA sorbent) are reported. Several differences are observed between the two systems, the most significant being observed for uranium, which demonstrated significantly lower sorption behavior on KIT-6-N-DGA. These results indicate that U can effectively be separated from Th and Pa using KIT-6-N-DGA, a task that could not be completed with the use of normal DGA alone.

The surface reactivity of chalk (biogenic calcite) with hydrophilic and hydrophobic functional groups

NASA Astrophysics Data System (ADS)

Okhrimenko, D. V.; Dalby, K. N.; Skovbjerg, L. L.; Bovet, N.; Christensen, J. H.; Stipp, S. L. S.

2014-03-01

The surface properties of calcium carbonate minerals play an important role in a number of industrial and biological processes. Properties such as wettability and adsorption control liquid-solid interface behaviour and thus have a strong influence on processes such as biomineralisation, remediation of aquifers and oil recovery. We investigated how two model molecules of different polarity, namely water and ethanol, interact with reservoir and outcrop chalk samples and we compared their behaviour with that of pure, inorganically precipitated calcite. Thermodynamic quantities, such as the work of wetting, surface energy and isosteric adsorption enthalpy, were determined from vapour adsorption isotherms. The chalks were studied fresh and after extraction of organic residues that were originally present in these samples. The work of wetting correlates with the amount of organic matter present in the chalk samples but we observed a fundamental difference between the adsorption properties of chalk and pure, inorganically precipitated calcite toward the less polar, ethanol molecule. Further analysis of the chemical composition of the organic matter extracted from the chalk samples was made by gas chromatography (GC-MS). Monitoring surface composition by X-ray photoelectron spectroscopy (XPS) before and after extraction of the organic material, and with atomic force microscopy (AFM), showed that nanometer sized clay crystals observed on the chalk particle surfaces could be an important part of the reason for the differences. Removal of the extractable portion of the hydrocarbons liberates adsorption sites that have different wetting properties than the rest of the chalk and these have an energy distribution that is similar to clays. Thus, the results exemplify the complexity of biogenic calcite adsorption behaviour and demonstrate that chalk wetting in drinking water aquifers as well as oil reservoirs is controlled partly by the nanoparticles of clay that have grown on the chalk surfaces and partly by adsorbed organic material. GS < GS after extraction < WS < WS after extraction < Ålborg after extraction ⩽ Ålborg. The increase of spreading work for WS chalk for ethanol is 21 mN/m and for water is 26 mN/m, a ratio of 21/26 = 0.81. The increase of spreading work for GS chalk for ethanol and water are 36 and 42 mN/m, a ratio of 36/42 = 0.86. The similarity between these ratios leads us to conclude, that the surface that was produced by extraction of the organic material is quite similar for these two samples.The total surface energy increase, after the extraction of organics, for GS and WS was 67 and 49 mJ/m2. Further separation of surface energy into polar and dispersive parts showed that, for both samples, removing organic matter by extraction preferably increases the dispersive component of the surface energy. The contribution from dispersive surface energy to the increase in total surface energy was 87% for GS and 73% for WS chalk. A high relative proportion of dispersive component in the total surface energy is also typical for clay minerals (Chassin et al., 1986; Jouany and Chassin, 1987; Kádár et al., 2006).This demonstrates that the additional adsorption sites that are exposed by the extraction procedure are less polar than the sites originally exposed. Based on these results, we can conclude that chalk particles have surface sites of different polarity and that organic compounds preferentially adsorb at the less polar sites. These additional sites have quite similar surface properties for both North Sea chalk samples with an energy distribution that is similar to clays, that are described in the literature (Chassin et al., 1986; Jouany and Chassin, 1987; Kádár et al., 2006).The Ålborg chalk initially has minimal adsorbed organic material and the work of wetting changes very little after the treatment for extracting organic material. Considering the lower reproducibility of the results on Ålborg chalk, the differences in surface energies before and after extraction are considered insignificant and we conclude that the sample is not affected by the extraction procedure.The absolute values for the dispersive component of surface energy for North Sea chalks determined here are consistent with data obtained earlier by inverse gas chromatography (IGC) (Skovbjerg et al., 2013). Skovbjerg and colleagues reported values of γd for GS and WS chalk equal to 36.3 and 47.0 mJ/m2. The values reported for the polar components of the surface energy are, however, much lower. This difference is probably associated with the differences in the theoretical background for the two techniques. IGC measures surface interaction with vapours at close to zero coverage, using the Good-van Oss approach (van Oss et al., 1988), whereas the results obtained here are for surfaces fully covered by several layers of adsorbate and use the Owens-Wendt approach (Owens and Wendt, 1969). Our probe molecules (water and ethanol) are also more polar than the probe molecules used for the IGC experiments (dichloromethane and ethyl acetate), which probably leads to overestimation of values for the polar component of the surface energy.The total surface energy of the calcite samples that we obtained is close to reports for marble (Janczuk et al., 1983) and calcite (Goujon and Mutaftschiev, 1976; Okayama et al., 1997). There are, however, considerable differences in the values reported by different groups and in one case (Douillard et al., 1995), values reported are three times higher than our observations. We propose that the history of the samples, thus what is adsorbed on the surfaces, has a great deal to do with the surface tension measured.

Spectroscopy for Industrial Applications: High-Temperature Processes

NASA Astrophysics Data System (ADS)

Fateev, Alexander; Grosch, Helge; Clausen, Sonnik; Barton, Emma J.; Yurchenko, Sergei N.; Tennyson, Jonathan

2014-06-01

The continuous development of the spectroscopic databases brings new perspectives in the environmental and industrial on-line process control, monitoring and stimulates further optical sensor developments. This is because no calibration gases are needed and, in general, temperature-dependent spectral absorption features gases of interest for a specific instrument can in principle be calculated by knowing only the gas temperature and pressure in the process under investigation/monitoring. The latest HITRAN-2012 database contains IR/UV spectral data for 47 molecules and it is still growing. However use of HITRAN is limited to low-temperature processes (< 400 K) and therefor can be used for absorption spectra calculations at limited temperature/pressure ranges. For higher temperatures, the HITEMP-2010 database is available. Only a few molecules CO2, H2O, CO and NO are those of interest for e.g. various combustion and astronomical applications are included. In the recent few years, several efforts towards a development of hot line lists have been made; those have been implemented in the latest HITRAN2012 database1. High-resolution absorption measurements of NH3 (IR, 0.1 cm-1) and phenol (UV, 0.019 nm) on a flow gas cell2 up to 800 K are presented. Molecules are of great interest in various high-temperature environments including exoplanets, combustion and gasification. Measured NH3 hot lines have been assigned and spectra have been compared with that obtained by calculations based on the BYTe hot line list1. High-temperature NH3 absorption spectra have been used in the analysis of in situ high-resolution IR absorption measurements on the producer gas in low-temperature gasification process on a large scale. High-resolution UV temperature-dependent absorption cross-sections of phenol are reported for the first time. All UV data have been calibrated by relevant GC/MS measurements. Use of the data is demonstrated by the analysis of in situ UV absorption measurements on a small-scale low-temperature gasifier. A comparison between in situ, gas extraction and conventional gas sampling measurements is presented. Overall the presentation shows an example of successful industrial and academic partnerships within the framework of national and international ongoing projects.

A critical overview on the biological and molecular features of red and processed meat in colorectal carcinogenesis.

PubMed

Jeyakumar, Arunan; Dissabandara, Lakal; Gopalan, Vinod

2017-04-01

A recent investigation by the World Health Organisation (WHO) has found that the consumption of processed meat and potentially red meat promotes carcinogenesis and can increase the risk of colorectal cancer. This literature review aims to summarise both the red and processed meat molecules associated with colorectal carcinogenesis and investigate their relationship with the pathogenic process of colorectal cancer. Literature relating to the carcinogenic effect of red and processed meat molecules was critically reviewed. There are multiple molecules present in red and processed meat with a potential carcinogenic effect on colorectal tissues. Processed meat is more carcinogenic compared to red meat because of the abundance of potent nitrosyl-heme molecules that form N-nitroso compounds. Studies have also noted that other molecules such as polycyclic aromatic hydrocarbons and heterocyclic amines have potential mechanisms for the initiation of colorectal cancer pathogenesis. The non-human sugar molecule N-glycolylneuraminic acid may account for the carcinogenic effects of pork despite its heme content being comparable to that of chicken. Red meat products, especially those that have been processed, have a wide variety of carcinogenic molecules known to increase the risk of colorectal cancer. Thus, the outcome of this review is consistent with the recent findings of WHO.

Improved HCP Reduction Using a New, All-Synthetic Depth Filtration Media Within an Antibody Purification Process.

PubMed

Nguyen, Hoang C; Langland, Amie L; Amara, John P; Dullen, Michael; Kahn, David S; Costanzo, Joseph A

2018-04-30

Biologic manufacturing processes typically employ clarification technologies like depth filtration to remove insoluble and soluble impurities. Conventional depth filtration media used in these processes contain naturally-derived components like diatomaceous earth and cellulose. These components may introduce performance variability and contribute extractable/leachable components like beta-glucans that could interfere with limulus amebocyte lysate endotoxin assays. Recently a novel, all-synthetic depth filtration media is developed (Millistak+ ® HC Pro X0SP) that may improve process consistency, efficiency, and drug substance product quality by reducing soluble process impurities. This new media is evaluated against commercially available benchmark filters containing naturally-derived components (Millistak+ ® HC X0HC and B1HC). Using model proteins, the synthetic media demonstrates increased binding capacity of positively charged proteins (72-126 mg g -1 media) compared to conventional media (0.3-8.6 mg g -1 media); and similar values for negatively charged species (1.3-5.6 mg g -1 media). Several CHO-derived monoclonal antibodies (mAbs) or mAb-like molecules are also evaluated. The X0SP filtration performance behaves similarly to benchmarks, and exhibits improved HCP reduction (at least 50% in 55% of cases tested). X0SP filtrates contained increased silicon extractables relative to benchmarks, but these were readily removed downstream. Finally, the X0SP devices demonstrates suitable lot-to-lot robustness when specific media components are altered intentionally to manufacturing specification limits. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conformation-based signal transfer and processing at the single-molecule level

NASA Astrophysics Data System (ADS)

Li, Chao; Wang, Zhongping; Lu, Yan; Liu, Xiaoqing; Wang, Li

2017-11-01

Building electronic components made of individual molecules is a promising strategy for the miniaturization and integration of electronic devices. However, the practical realization of molecular devices and circuits for signal transmission and processing at room temperature has proven challenging. Here, we present room-temperature intermolecular signal transfer and processing using SnCl2Pc molecules on a Cu(100) surface. The in-plane orientations of the molecules are effectively coupled via intermolecular interaction and serve as the information carrier. In the coupled molecular arrays, the signal can be transferred from one molecule to another in the in-plane direction along predesigned routes and processed to realize logical operations. These phenomena enable the use of molecules displaying intrinsic bistable states as complex molecular devices and circuits with novel functions.

Studying DNA looping by single-molecule FRET.

PubMed

Le, Tung T; Kim, Harold D

2014-06-28

Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can also affect the apparent looping rate through mechanisms such as nonspecific binding. Here, we show how to measure dsDNA looping kinetics without ligase by detecting transient DNA loop formation by FRET (Fluorescence Resonance Energy Transfer). dsDNA molecules are constructed using a simple PCR-based protocol with a FRET pair and a biotin linker. The looping probability density known as the J factor is extracted from the looping rate and the annealing rate between two disconnected sticky ends. By testing two dsDNAs with different intrinsic curvatures, we show that the J factor is sensitive to the intrinsic shape of the dsDNA.

Deducing receptor signaling parameters from in vivo analysis: LuxN/AI-1 quorum sensing in Vibrio harveyi

PubMed Central

Swem, Lee R.; Swem, Danielle L.; Wingreen, Ned S.; Bassler, Bonnie L.

2008-01-01

Summary Quorum sensing, a process of bacterial cell-cell communication, relies on production, detection, and response to autoinducer signaling molecules. Here we focus on LuxN, a nine transmembrane domain protein from Vibrio harveyi, and the founding example of membrane-bound receptors for acyl-homoserine lactone (AHL) autoinducers. Previously, nothing was known about signal recognition by membrane-bound AHL receptors. We used mutagenesis and suppressor analyses to identify the AHL-binding domain of LuxN, and discovered LuxN mutants that confer decreased and increased AHL sensitivity. Our analysis of dose-response curves of multiple LuxN mutants pins these inverse phenotypes on quantifiable opposing shifts in the free-energy bias of LuxN for its kinase and phosphatase states. To extract signaling parameters, we exploited a strong LuxN antagonist, one of fifteen small-molecule antagonists we identified. We find that quorum-sensing-mediated communication can be manipulated positively and negatively to control bacterial behavior, and that signaling parameters can be deduced from in vivo data. PMID:18692469

Studying DNA Looping by Single-Molecule FRET

PubMed Central

Le, Tung T.; Kim, Harold D.

2014-01-01

Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can also affect the apparent looping rate through mechanisms such as nonspecific binding. Here, we show how to measure dsDNA looping kinetics without ligase by detecting transient DNA loop formation by FRET (Fluorescence Resonance Energy Transfer). dsDNA molecules are constructed using a simple PCR-based protocol with a FRET pair and a biotin linker. The looping probability density known as the J factor is extracted from the looping rate and the annealing rate between two disconnected sticky ends. By testing two dsDNAs with different intrinsic curvatures, we show that the J factor is sensitive to the intrinsic shape of the dsDNA. PMID:24998459

THE NITROGEN ISOTOPIC COMPOSITION OF METEORITIC HCN

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

Pizzarello, Sandra, E-mail: pizzar@asu.edu

2014-12-01

HCN is ubiquitous in extraterrestrial environments and is central to current theories on the origin of early solar system organic compounds such as amino acids. These compounds, observed in carbonaceous meteorites, were likely important in the origin and/or evolution of early life. As part of our attempts to understand the origin(s) of meteoritic CN{sup –}, we have analyzed the {sup 15}N/{sup 14}N isotopic composition of HCN gas released from water extracts of the Murchison meteorite and found its value to be near those of the terrestrial atmosphere. The findings, when evaluated viz-a-viz molecular abundances and isotopic data of meteoritic organicmore » compounds, suggest that HCN formation could have occurred during the protracted water alteration processes known to have affected the mineralogy of many asteroidal bodies during their solar residence. This was an active synthetic stage, which likely involved simple gasses, organic molecules, their presolar precursors, as well as mineral catalysts and would have lead to the formation of molecules of differing isotopic composition, including some with solar values.« less

Comparison of Artemisia annua Bioactivities between Traditional Medicine and Chemical Extracts

PubMed Central

Nageeb, Ahmed; Al-Tawashi, Azza; Mohammad Emwas, Abdul-Hamid; Abdel-Halim Al-Talla, Zeyad; Al-Rifai, Nahla

2013-01-01

The present work investigates the efficacy of using Artemisia annua in traditional medicine in comparison with chemical extracts of its bioactive molecules. In addition, the effects of location (Egypt and Jericho) on the bioactivities of the plant were investigated. The results showed that water extracts of Artemisia annua from Jericho have stronger antibacterial activities than organic solvent extracts. In contrast, water and organic solvent extracts of the Artemisia annua from Egypt do not have anti-bacterial activity. Furthermore, while the methanol extract of EA displayed high anticancer affects, the water extract of Egypt and the extracts of Jericho did not show significant anticancer activity. Finally, the results showed that the methanol and water extracts of Jericho had the highest antioxidant activity, while the extracts of Egypt had none. The current results validate the scientific bases for the use of Artemisia annua in traditional medicine. In addition, our results suggest that the collection location of the Artemisia annua has an effect on its chemical composition and bioactivities. PMID:24761137

Cryogenic buffer-gas loading and magnetic trapping of CrH and MnH molecules

NASA Astrophysics Data System (ADS)

Stoll, Michael; Bakker, Joost M.; Steimle, Timothy C.; Meijer, Gerard; Peters, Achim

2008-09-01

We report on the buffer-gas cooling and trapping of CrH and MnH molecules in a magnetic quadrupole trap with densities on the order of 106cm-3 at a temperature of 650mK . Storage times of up to 180ms have been observed, corresponding to a 20-fold lifetime enhancement with respect to the field-free diffusion through the He3 buffer-gas. Using Monte Carlo trajectory simulations, inelastic molecule- He3 collision cross sections of 1.6×10-18 and 3.1×10-17cm2 are extracted for CrH and MnH, respectively. Furthermore, elastic molecule- He3 collision cross sections of 1.4(±0.5)×10-14cm2 are determined for both species. We conclude that the confinement time of these molecules in a magnetic trapping field is limited by inelastic collisions with the helium atoms leading to Zeeman relaxation.

Electron Spin Relaxation: The Role of Spin-Orbit Coupling in Organic Semiconductors

NASA Astrophysics Data System (ADS)

Willis, M.; Nuccio, L.; Schulz, L.; Gillin, W.; Kreouzis, T.; Pratt, F.; Lord, J.; Heeney, M.; Fratini, S.; Bernhard, C.; Drew, A.

2012-02-01

Rapid development of organic materials has lead to their availability in commercial products. Until now, the spin degree of freedom has not generally been used in organic materials. As well as engineering difficulties, there are fundamental questions with respect to the electron spin relaxation (eSR) mechanisms in organic molecules. Muons used as a microscopic spin probe, localized to a single molecule, can access information needed to identify the relevant model for eSR. In this presentation I will introduce the ALC-MuSR technique describing how eSR can be extracted and the expected effects. I will show how the technique has been applied to small organic molecules such as the group III Quinolate series and functionalized molecules with a pentacene-like backbone. Lastly I will present the Z-number and temperature dependence in these organic molecules and show strong evidence for a spin-orbit based eSR mechanism.

A Computational Scheme To Evaluate Hamaker Constants of Molecules with Practical Size and Anisotropy.

PubMed

Hongo, Kenta; Maezono, Ryo

2017-11-14

We propose a computational scheme to evaluate Hamaker constants, A, of molecules with practical sizes and anisotropies. Upon the increasing feasibility of diffusion Monte Carlo (DMC) methods to evaluate binding curves for such molecules to extract the constants, we discussed how to treat the averaging over anisotropy and how to correct the bias due to the nonadditivity. We have developed a computational procedure for dealing with the anisotropy and reducing statistical errors and biases in DMC evaluations, based on possible validations on predicted A. We applied the scheme to cyclohexasilane molecule, Si 6 H 12 , used in "printed electronics" fabrications, getting A ≈ 105 ± 2 zJ, being in plausible range supported even by other possible extrapolations. The scheme provided here would open a way to use handy ab initio evaluations to predict wettabilities as in the form of materials informatics over broader molecules.

Electrochemical Probing through a Redox Capacitor To Acquire Chemical Information on Biothiols

PubMed Central

2016-01-01

The acquisition of chemical information is a critical need for medical diagnostics, food/environmental monitoring, and national security. Here, we report an electrochemical information processing approach that integrates (i) complex electrical inputs/outputs, (ii) mediators to transduce the electrical I/O into redox signals that can actively probe the chemical environment, and (iii) a redox capacitor that manipulates signals for information extraction. We demonstrate the capabilities of this chemical information processing strategy using biothiols because of the emerging importance of these molecules in medicine and because their distinct chemical properties allow evaluation of hypothesis-driven information probing. We show that input sequences can be tailored to probe for chemical information both qualitatively (step inputs probe for thiol-specific signatures) and quantitatively. Specifically, we observed picomolar limits of detection and linear responses to concentrations over 5 orders of magnitude (1 pM–0.1 μM). This approach allows the capabilities of signal processing to be extended for rapid, robust, and on-site analysis of chemical information. PMID:27385047

Electrochemical Probing through a Redox Capacitor To Acquire Chemical Information on Biothiols.

PubMed

Liu, Zhengchun; Liu, Yi; Kim, Eunkyoung; Bentley, William E; Payne, Gregory F

2016-07-19

The acquisition of chemical information is a critical need for medical diagnostics, food/environmental monitoring, and national security. Here, we report an electrochemical information processing approach that integrates (i) complex electrical inputs/outputs, (ii) mediators to transduce the electrical I/O into redox signals that can actively probe the chemical environment, and (iii) a redox capacitor that manipulates signals for information extraction. We demonstrate the capabilities of this chemical information processing strategy using biothiols because of the emerging importance of these molecules in medicine and because their distinct chemical properties allow evaluation of hypothesis-driven information probing. We show that input sequences can be tailored to probe for chemical information both qualitatively (step inputs probe for thiol-specific signatures) and quantitatively. Specifically, we observed picomolar limits of detection and linear responses to concentrations over 5 orders of magnitude (1 pM-0.1 μM). This approach allows the capabilities of signal processing to be extended for rapid, robust, and on-site analysis of chemical information.

In vitro antioxidant properties, free radicals scavenging activities of extracts and polyphenol composition of a non-timber forest product used as spice: Monodora myristica.

PubMed

Moukette, Bruno Moukette; Pieme, Constant Anatole; Njimou, Jacques Romain; Biapa, Cabral Prosper Nya; Marco, Bravi; Ngogang, Jeanne Yonkeu

2015-03-14

Excessive production of free radicals causes direct damage to biological molecules such as DNA, proteins, lipids, carbohydrates leading to tumor development and progression. Natural antioxidant molecules from phytochemicals of plant origin may directly inhibit either their production or limit their propagation or destroy them to protect the system. In the present study, Monodora myristica a non-timber forest product consumed in Cameroon as spice was screened for its free radical scavenging properties, antioxidant and enzymes protective activities. Its phenolic compound profile was also realized by HPLC. This study demonstrated that M. myristica has scavenging properties against DPPH(•), OH(•), NO(•), and ABTS(•) radicals which vary in a dose depending manner. It also showed an antioxidant potential that was comparable with that of Butylated Hydroxytoluene (BHT) and vitamin C used as standard. The aqueous ethanol extract of M. myristica barks (AEH); showed a significantly higher content in polyphenolic compounds (21.44 ± 0.24 mg caffeic acid/g dried extract) and flavonoid (5.69 ± 0.07 quercetin equivalent mg/g of dried weight) as compared to the other studied extracts. The HPLC analysis of the barks and leaves revealed the presence of several polyphenols. The acids (3,4-OH-benzoic, caffeic, gallic, O- and P- coumaric, syringic, vanillic), alcohols (tyrosol and OH-tyrosol), theobromine, quercetin, rutin, catechine and apigenin were the identified and quantified polyphenols. All the tested extracts demonstrated a high protective potential on the superoxide dismutase (SOD), catalase and peroxidase activities. Finally, the different extracts from M. myristica and specifically the aqueous ethanol extract reveal several properties such as higher free radical scavenging properties, significant antioxidant capacities and protective potential effects on liver enzymes.

Investigation of the Lignan Content in Extracts from Linum, Callitris and Juniperus Species in Relation to Their In Vitro Antiproliferative Activities.

PubMed

Doussot, Joël; Mathieu, Véronique; Colas, Cyril; Molinié, Roland; Corbin, Cyrielle; Montguillon, Josiane; Moreno Y Banuls, Laeticia; Renouard, Sullivan; Lamblin, Frédéric; Dupré, Patricia; Maunit, Benoit; Kiss, Robert; Hano, Christophe; Lainé, Eric

2017-04-01

Podophyllotoxin, a lignan still extracted from the rhizomes of Podophyllum hexandrum (Berberidaceae), is the starting molecule for the semisynthesis of widely used anticancer drugs such as etoposide. However, this source is threatened by the over-collection of P. hexandrum . Plants belonging to the Linaceae and Cupressaceae families could be attractive alternative sources with species that contain the lignan podophyllotoxin or its precursors and derivatives. Wild flax species, such as Linum flavum , as well as some Juniperus and Callitris species were investigated for their lignan content, and the in vitro antiproliferative capacity of their extracts was assayed on four tumor cell lines. Some of the lignans were detected by LC-HRMS for the first time in these extracts.In addition, lignans purified from these plants and compounds semisynthesized from commercially available podophyllotoxin were tested in terms of their in vitro antiproliferative activity. The genus Juniperus was the most promising given its in vitro antiproliferative effects, which were also observed with extracts from L. flavum and Callitris species.The in vitro antiproliferative effect of the plant extracts studied here appears to correlate well with the contents of the aryltetralin lignan podophyllotoxin and its glycoside as well as with deoxypodophyllotoxin and 6-methoxypodophyllotoxin. The strongest correlation between the lignan content of the extracts and the antiproliferative activity was observed for 6-methoxypodophyllotoxin. Regarding the possibility of producing large renewable amounts of 6-methoxypodophyllotoxin, this molecule could be of interest to produce new anticancer drugs and to bypass the resistance mechanisms against podophyllotoxin-derived drugs. Georg Thieme Verlag KG Stuttgart · New York.

Dietary Selenium Supplementation Modulates Growth of Brain Metastatic Tumors and Changes the Expression of Adhesion Molecules in Brain Microvessels.

PubMed

Wrobel, Jagoda K; Wolff, Gretchen; Xiao, Rijin; Power, Ronan F; Toborek, Michal

2016-08-01

Various dietary agents can modulate tumor invasiveness. The current study explored whether selenoglycoproteins (SeGPs) extracted from selenium-enriched yeast affect tumor cell homing and growth in the brain. Mice were fed diets enriched with specific SeGPs (SeGP40 or SeGP65, 1 mg/kg Se each), glycoproteins (GP40 or GP65, 0.2-0.3 mg/kg Se each) or a control diet (0.2-0.3 mg/kg Se) for 12 weeks. Then, murine Lewis lung carcinoma cells were infused into the brain circulation. Analyses were performed at early (48 h) and late stages (3 weeks) post tumor cell infusion. Imaging of tumor progression in the brain revealed that mice fed SeGP65-enriched diet displayed diminished metastatic tumor growth, fewer extravasating tumor cells and smaller metastatic lesions. While administration of tumor cells resulted in a significant upregulation of adhesion molecules in the early stage of tumor progression, overexpression of VCAM-1 (vascular call adhesion molecule-1) and ALCAM (activated leukocyte cell adhesion molecule) messenger RNA (mRNA) was diminished in SeGP65 supplemented mice. Additionally, mice fed SeGP65 showed decreased expression of acetylated NF-κB p65, 48 h post tumor cell infusion. The results indicate that tumor progression in the brain can be modulated by specific SeGPs. Selenium-containing compounds were more effective than their glycoprotein controls, implicating selenium as a potential negative regulator of metastatic process.

Directional ratio based on parabolic molecules and its application to the analysis of tubular structures

NASA Astrophysics Data System (ADS)

Labate, Demetrio; Negi, Pooran; Ozcan, Burcin; Papadakis, Manos

2015-09-01

As advances in imaging technologies make more and more data available for biomedical applications, there is an increasing need to develop efficient quantitative algorithms for the analysis and processing of imaging data. In this paper, we introduce an innovative multiscale approach called Directional Ratio which is especially effective to distingush isotropic from anisotropic structures. This task is especially useful in the analysis of images of neurons, the main units of the nervous systems which consist of a main cell body called the soma and many elongated processes called neurites. We analyze the theoretical properties of our method on idealized models of neurons and develop a numerical implementation of this approach for analysis of fluorescent images of cultured neurons. We show that this algorithm is very effective for the detection of somas and the extraction of neurites in images of small circuits of neurons.

Extracting biomarkers of commitment to cancer development: potential role of vibrational spectroscopy in systems biology.

PubMed

Theophilou, Georgios; Paraskevaidi, Maria; Lima, Kássio M G; Kyrgiou, Maria; Martin-Hirsch, Pierre L; Martin, Francis L

2015-05-01

The complex processes driving cancer have so far impeded the discovery of dichotomous biomarkers associated with its initiation and progression. Reductionist approaches utilizing 'omics' technologies have met some success in identifying molecular alterations associated with carcinogenesis. Systems biology is an emerging science that combines high-throughput investigation techniques to define the dynamic interplay between regulatory biological systems in response to internal and external cues. Vibrational spectroscopy has the potential to play an integral role within systems biology research approaches. It is capable of examining global models of carcinogenesis by scrutinizing chemical bond alterations within molecules. The application of infrared or Raman spectroscopic approaches coupled with computational analysis under the systems biology umbrella can assist the transition of biomarker research from the molecular level to the system level. The comprehensive representation of carcinogenesis as a multilevel biological process will inevitably revolutionize cancer-related healthcare by personalizing risk prediction and prevention.

Driving Forces Controlling Host-Guest Recognition in Supercritical Carbon Dioxide Solvent.

PubMed

Ingrosso, Francesca; Altarsha, Muhannad; Dumarçay, Florence; Kevern, Gwendal; Barth, Danielle; Marsura, Alain; Ruiz-López, Manuel F

2016-02-24

The formation of supramolecular host-guest complexes is a very useful and widely employed tool in chemistry. However, supramolecular chemistry in non-conventional solvents such as supercritical carbon dioxide (scCO2 ), one of the most promising sustainable solvents, is still in its infancy. In this work, we explored a successful route to the development of green processes in supercritical CO2 by combining a theoretical approach with experiments. We were able to synthesize and characterize an inclusion complex between a polar aromatic molecule (benzoic acid) and peracetylated-β-cyclodextrin, which is soluble in the supercritical medium. This finding opens the way to wide, environmental friendly, applications of scCO2 in many areas of chemistry, including supramolecular synthesis, reactivity and catalysis, micro and nano-particle formation, molecular recognition, as well as enhanced extraction processes with increased selectivity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quo vadis plant hormone analysis?

PubMed

Tarkowská, Danuše; Novák, Ondřej; Floková, Kristýna; Tarkowski, Petr; Turečková, Veronika; Grúz, Jiří; Rolčík, Jakub; Strnad, Miroslav

2014-07-01

Plant hormones act as chemical messengers in the regulation of myriads of physiological processes that occur in plants. To date, nine groups of plant hormones have been identified and more will probably be discovered. Furthermore, members of each group may participate in the regulation of physiological responses in planta both alone and in concert with members of either the same group or other groups. The ideal way to study biochemical processes involving these signalling molecules is 'hormone profiling', i.e. quantification of not only the hormones themselves, but also their biosynthetic precursors and metabolites in plant tissues. However, this is highly challenging since trace amounts of all of these substances are present in highly complex plant matrices. Here, we review advances, current trends and future perspectives in the analysis of all currently known plant hormones and the associated problems of extracting them from plant tissues and separating them from the numerous potentially interfering compounds.

Detecting Nonvolatile Life- and Nonlife-Derived Organics in a Carbonaceous Chondrite Analogue with a New Multiplex Immunoassay and Its Relevance for Planetary Exploration.

PubMed

Moreno-Paz, Mercedes; Gómez-Cifuentes, Ana; Ruiz-Bermejo, Marta; Hofstetter, Oliver; Maquieira, Ángel; Manchado, Juan M; Morais, Sergi; Sephton, Mark A; Niessner, Reinhard; Knopp, Dietmar; Parro, Victor

2018-04-11

Potential martian molecular targets include those supplied by meteoritic carbonaceous chondrites such as amino acids and polycyclic aromatic hydrocarbons and true biomarkers stemming from any hypothetical martian biota (organic architectures that can be directly related to once living organisms). Heat extraction and pyrolysis-based methods currently used in planetary exploration are highly aggressive and very often modify the target molecules making their identification a cumbersome task. We have developed and validated a mild, nondestructive, multiplex inhibitory microarray immunoassay and demonstrated its implementation in the SOLID (Signs of Life Detector) instrument for simultaneous detection of several nonvolatile life- and nonlife-derived organic molecules relevant in planetary exploration and environmental monitoring. By utilizing a set of highly specific antibodies that recognize D- or L- aromatic amino acids (Phe, Tyr, Trp), benzo[a]pyrene (B[a]P), pentachlorophenol, and sulfone-containing aromatic compounds, respectively, the assay was validated in the SOLID instrument for the analysis of carbon-rich samples used as analogues of the organic material in carbonaceous chondrites or even Mars samples. Most of the antibodies enabled sensitivities at the 1-10 ppb level and some even at the ppt level. The multiplex immunoassay allowed the detection of B[a]P as well as aromatic sulfones in a water/methanol extract of an Early Cretaceous lignite sample (c.a., 140 Ma) representing type IV kerogen. No L- or D-aromatic amino acids were detected, reflecting the advanced diagenetic stage and the fossil nature of the sample. The results demonstrate the ability of the liquid extraction by ultrasonication and the versatility of the multiplex inhibitory immunoassays in the SOLID instrument to discriminate between organic matter derived from life and nonlife processes, an essential step toward life detection outside Earth. Key Words: Planetary exploration-Molecular biomarkers-D- and L- aromatic amino acids-Life detection-Multiplex inhibitory/competitive immunoassay-Kerogen type IV. Astrobiology 18, xxx-xxx.

VizieR Online Data Catalog: Partition functions for molecules and atoms (Barklem+, 2016)

NASA Astrophysics Data System (ADS)

Barklem, P. S.; Collet, R.

2016-02-01

The results and input data are presented in the following files. Table 1 contains dissociation energies from the literature, and final adopted values, for 291 molecules. The literature values are from the compilations of Huber & Herzberg (1979, Constants of Diatomic Molecules (Van Nostrand Reinhold), Luo (2007, Comprehensive Handbook of Chemical Bond Energies (CRC Press)) and G2 theory calculations of Curtiss et al. (1991, J. Chem. Phys., 94, 7221). Table 2 contains the input data for the molecular calculations including adopted dissociation energy, nuclear spins, molecular spectroscopic constants and their sources. There are 291 files, one for each molecule, labelled by the molecule name. The various molecular spectroscopic constants are as defined in the paper. Table 4 contains the first, second and third ionisation energies for all chemical elements from H to U. The data comes from the CRC Handbook of Chemistry and Physics (Haynes, W.M. 2010, CRC Handbook of Chemistry and Physics, 91st edn. (CRC Press, Taylor and Francis Group)). Table 5a contains a list of keys to bibliographic references for the atomic energy level data that was extracted from NIST Atomic Spectra Database and used in the present work to compute atomic partition functions. The citation keys are abbreviations of the full bibliographic references which are made available in Table 5b in BibTeX format. Table 5b contains the full bibliographic references for the atomic energy level data that was extracted from the NIST Atomic Spectra Database. Table 6 contains tabulated partition function data as a function of temperature for 291 molecules. Table 7 contains tabulated equilibrium constant data as a function of temperature for 291 molecules. Table 8 contains tabulated partition function data as a function of temperature for 284 atoms and ions. The paper should be consulted for further details. (10 data files).

Single molecule optical measurements of orientation and rotations of biological macromolecules.

PubMed

Shroder, Deborah Y; Lippert, Lisa G; Goldman, Yale E

2016-11-22

Subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measurement of their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, review the relevant types of probes and labeling techniques, and highlight the advantages and disadvantages of these technologies for addressing specific inquiries.

Aptamer entrapment in microfluidic channel using one-step sol-gel process, in view of the integration of a new selective extraction phase for lab-on-a-chip.

PubMed

Perréard, Camille; d'Orlyé, Fanny; Griveau, Sophie; Liu, Baohong; Bedioui, Fethi; Varenne, Anne

2017-10-01

There is a great demand for integrating sample treatment into μTASs. In this context, we developed a new sol-gel phase for extraction of trace compounds in complex matrices. For this purpose, the incorporation of aptamers in silica-based gel within PDMS/glass microfluidic channels was performed for the first time by a one-step sol-gel process. The effective gel attachment onto microchannel walls and aptamer incorporation in the polymerized gel were evaluated using fluorescence microscopy. A good gel stability and aptamer incorporation inside the microchannel was demonstrated upon rinsing and over storage time. The ability of gel-encapsulated aptamers to interact with its specific target (either sulforhodamine B as model fluorescent target, or diclofenac, a pain killer drug) was assessed too. The binding capacity of entrapped aptamers was quantified (in the micromolar range) and the selectivity of the interaction was evidenced. Preservation of aptamers binding affinity to target molecules was therefore demonstrated. Dissociation constant of the aptamer-target complex and interaction selectivity were evaluated similar to those in bulk solution. This opens the way to new selective on-chip SPE techniques for sample pretreatment. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid Analysis of Microalgal Triacylglycerols with Direct-Infusion Mass Spectrometry

DOE PAGES

Christensen, Earl; Sudasinghe, Nilusha; Dandamudi, Kodanda Phani Raj; ...

2015-09-01

Cultivation of microalgae has the potential to provide lipid-derived feedstocks for conversion to liquid transportation fuels. Lipid extracts from microalgae are significantly more complex than those of traditional seed oils, and their composition changes significantly throughout the microalgal growth period. With three acyl side chains per molecule, triglycerides (TAGs) are an important fuel precursor, and the distribution of acyl chain composition for TAGs has a significant impact on fuel properties and processing. Therefore, determination of the distribution of microalgal TAG production is needed to assess the value of algal extracts designed for fuel production and to optimize strain, cultivation, andmore » harvesting practices. Methods utilized for TAG speciation commonly involve complicated and time-consuming chromatographic techniques. Here we present a method for TAG speciation and quantification based on direct-infusion mass spectrometry, which provides rapid characterization of TAG profiles without chromatographic separation. Specifically, we utilize Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to provide a reference library of TAGs for the microalgae Nannochloropsis sp. that provides the basis for high-throughput TAG quantitation by time-of-flight mass spectrometry (TOF MS). In conclusion, we demonstrate the application of this novel approach for lipid characterization with respect to TAG compound distribution, which informs both immediate and future strain and process optimization strategies.« less

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

Christensen, Earl; Sudasinghe, Nilusha; Dandamudi, Kodanda Phani Raj

Cultivation of microalgae has the potential to provide lipid-derived feedstocks for conversion to liquid transportation fuels. Lipid extracts from microalgae are significantly more complex than those of traditional seed oils, and their composition changes significantly throughout the microalgal growth period. With three acyl side chains per molecule, triglycerides (TAGs) are an important fuel precursor, and the distribution of acyl chain composition for TAGs has a significant impact on fuel properties and processing. Therefore, determination of the distribution of microalgal TAG production is needed to assess the value of algal extracts designed for fuel production and to optimize strain, cultivation, andmore » harvesting practices. Methods utilized for TAG speciation commonly involve complicated and time-consuming chromatographic techniques. Here we present a method for TAG speciation and quantification based on direct-infusion mass spectrometry, which provides rapid characterization of TAG profiles without chromatographic separation. Specifically, we utilize Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to provide a reference library of TAGs for the microalgae Nannochloropsis sp. that provides the basis for high-throughput TAG quantitation by time-of-flight mass spectrometry (TOF MS). In conclusion, we demonstrate the application of this novel approach for lipid characterization with respect to TAG compound distribution, which informs both immediate and future strain and process optimization strategies.« less

Green synthesis of gold nanoparticles by Allium sativum extract and their assessment as SERS substrate

NASA Astrophysics Data System (ADS)

Coman, Cristina; Leopold, Loredana Florina; Rugină, Olivia Dumitriţa; Barbu-Tudoran, Lucian; Leopold, Nicolae; Tofană, Maria; Socaciu, Carmen

2014-01-01

A green synthesis was used for preparing stable colloidal gold nanoparticles by using Allium sativum aqueous extract both as reducing and capping agent. The obtained nanoparticles were characterized by UV-Vis spectroscopy, Fourier-transform infrared spectroscopy (FTIR), and transmission electron microscopy. Moreover, their potential to be used as surface-enhanced Raman scattering (SERS) substrate was investigated. The obtained gold nanoparticles have spherical shape with mean diameters of 9-15 nm (depending on the amount of reducing agent used under boiling conditions) and are stable up to several months. FTIR spectroscopy shows that the nanoparticles are capped by protein molecules from the extract. The protein shell offers a protective coating, relatively impervious to external molecules, thus, rendering the nanoparticles stable and quite inert. These nanoparticles have the potential to be used as SERS substrates, both in solution and inside human fetal lung fibroblast HFL-1 living cells. We were able to demonstrate both the internalization of the nanoparticles inside HFL-1 cells and their ability to preserve the SERS signal after cellular internalization.

French Brittany macroalgae screening: composition and methane potential for potential alternative sources of energy and products.

PubMed

Jard, G; Marfaing, H; Carrère, H; Delgenes, J P; Steyer, J P; Dumas, C

2013-09-01

Macroalgae are biomass resources that represent a valuable feedstock to be used entirely for human consumption or for food additives after some extractions (mainly colloids) and/or for energy production. In order to better develop the algal sector, it is important to determine the capacity of macroalgae to produce these added-values molecules for food and/or for energy industries on the basis of their biochemical characteristics. In this study, ten macroalgae obtained from French Brittany coasts (France) were selected. The global biochemical composition (proteins, lipids, carbohydrates, fibers), the presence and characteristics of added-values molecules (alginates, polyphenols) and the biochemical methane potential of these algae were determined. Regarding its biochemical composition, Palmaria palmata is interesting for food (rich in nutrients) and for anaerobic digestion (0.279 LCH4/gVS). Saccharina latissima could be used for alginate extraction (242 g/kgTS, ratio between mannuronic and guluronic acid M/G=1.4) and Sargassum muticum for polyphenol extraction (19.8 g/kgTS). Copyright © 2013 Elsevier Ltd. All rights reserved.

Carbon dioxide induced bubble formation in a CH4-CO2-H2O ternary system: a molecular dynamics simulation study.

PubMed

Sujith, K S; Ramachandran, C N

2016-02-07

The extraction of methane from its hydrates using carbon dioxide involves the decomposition of the hydrate resulting in a CH4-CO2-H2O ternary solution. Using classical molecular dynamics simulations, we investigate the evolution of dissolved gas molecules in the ternary system at different concentrations of CO2. Various compositions considered in the present study resemble the solution formed during the decomposition of methane hydrates at the initial stages of the extraction process. We find that the presence of CO2 aids the formation of CH4 bubbles by causing its early nucleation. Elucidation of the composition of the bubble revealed that in ternary solutions with high concentration of CO2, mixed gas bubbles composed of CO2 and CH4 are formed. To understand the role of CO2 in the nucleation of CH4 bubbles, the structure of the bubble formed was analyzed, which revealed that there is an accumulation of CO2 at the interface of the bubble and the surrounding water. The aggregation of CO2 at the bubble-water interface occurs predominantly when the concentration of CO2 is high. Radial distribution function for the CH4-CO2 pair indicates that there is an increasingly favorable direct contact between dissolved CH4 and CO2 molecules in the bubble-water interface. It is also observed that the presence of CO2 at the interface results in the decrease in surface tension. Thus, CO2 leads to greater stability of the bubble-water interface thereby bringing down the critical size of the bubble nuclei. The results suggest that a rise in concentration of CO2 helps in the removal of dissolved CH4 thereby preventing the accumulation of methane in the liquid phase. Thus, the presence of CO2 is predicted to assist the decomposition of methane hydrates in the initial stages of the replacement process.

Isolation and in silico evaluation of antidiabetic molecules of Cynodon dactylon (L.).

PubMed

Annapurna, Hasthi V; Apoorva, Babu; Ravichandran, Natesan; Arun, Kallur Purushothaman; Brindha, Pemaiah; Swaminathan, Sethuraman; Vijayalakshmi, Mahadevan; Nagarajan, Arumugam

2013-02-01

Cynodon dactylon is a potential source of metabolites such as flavanoids, alkaloids, glycosides and β-sitosterol and has been traditionally employed to treat urinary tract and other microbial infections and dysentery. The present work attempts to evaluate the activity of C. dactylon extracts for glycemic control. Aqueous extracts of C. dactylon analyzed by HPLC-ESI MS have identified the presence of apigenin, luteolin, 6-C-pentosyl-8-C-hexosyl apigenin and 6-C-hexosyl-8-C-pentosyl luteolin. Evaluation of hypoglycemic activity through an extensive in silico docking approach with PPARγ (Peroxisome Proliferator-Activated Receptor), GLUT-4 (glucose transporter-4) and SGLT2 (sodium glucose co-transporter-2) revealed that luteolin, apigenin, 6-C-pentosyl-8-C-hexosyl apigenin, 6-C-hexosyl-8-C-pentosyl luteolin interact with SGLT2. Interactions of these molecules with Gln 295 and Asp 294 residues of SGLT2 have been shown to compare well with that of the phase III drug, dapagliflozin. These residues have been proven to be responsible for sugar sensing and transport. This work establishes C. dactylon extract as a potential SGLT2 inhibitor for diabetic neuropathy thus enabling a possibility of this plant extract as a new alternative to existing diabetic approaches. Copyright © 2012 Elsevier Inc. All rights reserved.

Pro-apoptotic activities of polyphenolics from açai (Euterpe oleracea Martius) in human SW-480 colon cancer cells.

PubMed

Dias, Manoela Maciel dos Santos; Noratto, Giuliana; Martino, Hercia Stampini Duarte; Arbizu, Shirley; Peluzio, Maria do Carmo Gouveia; Talcott, Stephen; Ramos, Afonso Mota; Mertens-Talcott, Susanne U

2014-01-01

This study aimed to evaluate the cell growth inhibition activity of açai (Euterpe oleracea Mart.) polyphenolic extract against colon cancer HT-29 and SW-480 cells and the nonmalignant CCD-18Co colon fibroblast cells. Results showed that açai polyphenolic extract (5-20 mg/L) inhibited preferentially the growth of SW-480 cells with no toxicity in CCD-18Co cells, and this was accompanied by reduction of H2O2-induced reactive oxygen species (ROS) generation. The mechanisms involved in SW-480 cell growth-inhibition by açai polyphenolic extract included the downregulation of NF-κB proinflammatory transcription factor and the nuclear factor-kappa B targets intracellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1). Furthermore, prooncogenic specificity proteins (Sp) were downregulated as well as Sp-targets Bcl-2, vascular endothelial growth factor, and survivin. This was accompanied by activation of mitochondrial proapoptotic pathway involving increase of cytochrome c, cleavage of caspase-3, and decrease of PARP-1. Results strongly suggest that açai polyphenolic extract has antiinflammatory and cytotoxic activities in colon cancer cells and can be effective as natural colon cancer chemopreventive agents.

Computational investigations of organic materials for hybrid nanodevice and optoelectronic applications

NASA Astrophysics Data System (ADS)

Crenshaw, Jasmine Davenport

2011-12-01

This dissertation examines two organic material systems, biotinylated microtubule filaments and thiophene. Biotinylated microtubule filaments partially coated with streptavidin and gliding on surface-adhered kinesin motor proteins converge to form linear "nanowire" and circular "nanospool" structures. We present a cellular automaton simulation tool that models the dynamics of microtubule gliding and interactions. In this method, each microtubule is composed of a head, body, and tail segments. The microtubule surface density, lengths, persistence length, and modes of interaction are dictated by the user. The microtubules are randomly arranged and move across a hexagonal lattice surface with the direction of motion of the head segment being determined probabilistically: the body and tail segments follow the path of the head. The analysis of the motion and interactions allow statistically meaningful data to be obtained regarding the number of generated spools, radial distribution in the distance between spools, and the average spool circumference lengths which can be compared to experimental results. This technique will aid in predictions of the formation process of nanowires and nanospools. Information regarding the kinetics and microstructure of any system can be extracted through this tool by the manipulation in the time and space dimensions. Chemical reactions of thiophene with organic molecules are of interest to chemically modify thermally deposited coatings or thin films of conductive polymers. Energy barriers are identified for reactive systems involving thiophene and small hydrocarbon radicals. The transition states for these reactive systems occurred through hydrogen abstraction. The results provide quantum mechanical level insights into the chemical processes that occur in the chemical modification processes described above, such as Surface Polymerization by Ion-Assisted Deposition (SPIAD), electropolymerization, and ion beam deposition. Enthalpies of formation are calculated for organic molecules using B3LYP, BMK, and B98 hybrid functionals. G3 and CBS-QB3 are used as standards in conjunction, due to their accurate thermochemistry parameters, with experimental values. The BMK functional proves to perform best with the selected organic molecules.

Distance measurements across randomly distributed nitroxide probes from the temperature dependence of the electron spin phase memory time at 240 GHz

NASA Astrophysics Data System (ADS)

Edwards, Devin T.; Takahashi, Susumu; Sherwin, Mark S.; Han, Songi

2012-10-01

At 8.5 T, the polarization of an ensemble of electron spins is essentially 100% at 2 K, and decreases to 30% at 20 K. The strong temperature dependence of the electron spin polarization between 2 and 20 K leads to the phenomenon of spin bath quenching: temporal fluctuations of the dipolar magnetic fields associated with the energy-conserving spin "flip-flop" process are quenched as the temperature of the spin bath is lowered to the point of nearly complete spin polarization. This work uses pulsed electron paramagnetic resonance (EPR) at 240 GHz to investigate the effects of spin bath quenching on the phase memory times (TM) of randomly-distributed ensembles of nitroxide molecules below 20 K at 8.5 T. For a given electron spin concentration, a characteristic, dipolar flip-flop rate (W) is extracted by fitting the temperature dependence of TM to a simple model of decoherence driven by the spin flip-flop process. In frozen solutions of 4-Amino-TEMPO, a stable nitroxide radical in a deuterated water-glass, a calibration is used to quantify average spin-spin distances as large as r¯=6.6 nm from the dipolar flip-flop rate. For longer distances, nuclear spin fluctuations, which are not frozen out, begin to dominate over the electron spin flip-flop processes, placing an effective ceiling on this method for nitroxide molecules. For a bulk solution with a three-dimensional distribution of nitroxide molecules at concentration n, we find W∝n∝1/r, which is consistent with magnetic dipolar spin interactions. Alternatively, we observe W∝n for nitroxides tethered to a quasi two-dimensional surface of large (Ø ˜ 200 nm), unilamellar, lipid vesicles, demonstrating that the quantification of spin bath quenching can also be used to discern the geometry of molecular assembly or organization.

Evaluation and prevention of the negative matrix effect of terpenoids on pesticides in apples quantification by gas chromatography-tandem mass spectrometry.

PubMed

Giacinti, Géraldine; Raynaud, Christine; Capblancq, Sophie; Simon, Valérie

2016-12-21

The sample matrix can enhance the gas chromatography signal of pesticide residues relative to that obtained with the same concentration of pesticide in solvent. This paper is related to negative matrix effects observed in coupled gas chromatography-mass spectrometry ion trap (GC/MS 2 ) quantification of pesticides in concentrated extracts of apple peel prepared by the Quick Easy Cheap Effective Rugged and Safe (QuEChERS) method. It is focused on the pesticides most frequently used on the apple varieties studied, throughout the crop cycle, right up to harvest, to combat pests and diseases and to improve fruit storage properties. Extracts from the fleshy receptacle (flesh), the epiderm (peel) and fruit of three apple varieties were studied by high-performance thin-layer chromatography hyphenated with UV-vis light detection (HPTLC/UV visible). The peel extracts had high concentrations of triterpenic acids (oleanolic and ursolic acids), reaching 25mgkg -1 , whereas these compounds were not detected in the flesh extracts (<0.05mgkg -1 ). A significant relationship has been found between the levels of these molecules and negative matrix effects in GC/MS 2 . The differences in the behavior of pesticides with respect to matrix effects can be accounted for by the physicochemical characteristics of the molecules (lone pairs, labile hydrogen, conjugation). The HPTLC/UV visible method developed here for the characterization of QuEChERS extracts acts as a complementary clean-up method, aimed to decrease the negative matrix effects of such extracts. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation and prevention of the negative matrix effect of terpenoids on pesticides in apples quantification by gas chromatography-tandem mass spectrometry.

PubMed

Giacinti, Géraldine; Raynaud, Christine; Capblancq, Sophie; Simon, Valérie

2017-02-03

The sample matrix can enhance the gas chromatography signal of pesticide residues relative to that obtained with the same concentration of pesticide in solvent. This paper is related to negative matrix effects observed in coupled gas chromatography-mass spectrometry ion trap (GC/MS 2 ) quantification of pesticides in concentrated extracts of apple peel prepared by the Quick Easy Cheap Effective Rugged and Safe (QuEChERS) method. It is focused on the pesticides most frequently used on the apple varieties studied, throughout the crop cycle, right up to harvest, to combat pests and diseases and to improve fruit storage properties. Extracts from the fleshy receptacle (flesh), the epiderm (peel) and fruit of three apple varieties were studied by high-performance thin-layer chromatography hyphenated with UV-vis light detection (HPTLC/UV visible). The peel extracts had high concentrations of triterpenic acids (oleanolic and ursolic acids), reaching 25mgkg -1 , whereas these compounds were not detected in the flesh extracts (<0.05mgkg -1 ). A significant relationship has been found between the levels of these molecules and negative matrix effects in GC/MS 2 . The differences in the behavior of pesticides with respect to matrix effects can be accounted for by the physicochemical characteristics of the molecules (lone pairs, labile hydrogen, conjugation). The HPTLC/UV visible method developed here for the characterization of QuEChERS extracts acts as a complementary clean-up method, aimed to decrease the negative matrix effects of such extracts. Copyright © 2016 Elsevier B.V. All rights reserved.

Calixarene-Mediated Liquid-Membrane Transport of Choline Conjugates

PubMed Central

Adhikari, Birendra Babu; Fujii, Ayu

2015-01-01

A series of supramolecular calixarenes efficiently transport distinct molecular species through a liquid membrane when attached to a receptor-complementary choline handle. Calix-[6]arene hexacarboxylic acid was highly effective at transporting different target molecules against a pH gradient. Both carboxylic- and phosphonic-acid-functionalized calix[4]arenes effect transport without requiring a pH or ion gradient. NMR binding studies, two-phase solvent extraction, and three-phase transport experiments reveal the necessary and subtle parameters to effect the transport of molecules attached to a choline “handle”. On the other hand, rescorin[4]arene cavitands, which have similar guest recognition profiles, did not transport guest molecules. These developments reveal new approaches towards attempting synthetic-receptor-mediated selective small-molecule transport in vesicular and cellular systems. PMID:26161034

Optimization of Polycyclic Aromatic Hydrocarbon (PAH) Extraction Efficiency Parameters for Sub- and Supercritical Water Extraction (SCWE) Instrument

NASA Technical Reports Server (NTRS)

Okada, Asahi A.

2005-01-01

Polycyclic aromatic hydrocarbons are a class of molecules composed of multiple, bonded benzene rings. As PAHS are believed to be present on Mars, positive confirmation of their presence on Mars is highly desirable. To extract PAHS, which have low volatility, a fluid extraction method is ideal, and one that does not utilize organic solvents is especially ideal for in situ instrumental analysis. The use of water as a solvent, which at subcritical pressures and temperatures is relatively non-Polar, has significant potential. As SCWE instruments have not yet been commercialized, all instruments are individually-built research prototypes: thus, initial efforts were intended to determine if extraction efficiencies on the JPL-built laboratory-scale SCWE instrument are comparable to differing designs built elsewhere. Samples of soil with certified reference concentrations of PAHs were extracted using SCWE as well as conventional Soxhlet extraction. Continuation of the work would involve extractions on JPL'S newer, portable SCWE instrument prototype to determine its efficiency in extracting PAHs.

An integrated one-step system to extract, analyze and annotate all relevant information from image-based cell screening of chemical libraries.

PubMed

Rabal, Obdulia; Link, Wolfgang; Serelde, Beatriz G; Bischoff, James R; Oyarzabal, Julen

2010-04-01

Here we report the development and validation of a complete solution to manage and analyze the data produced by image-based phenotypic screening campaigns of small-molecule libraries. In one step initial crude images are analyzed for multiple cytological features, statistical analysis is performed and molecules that produce the desired phenotypic profile are identified. A naïve Bayes classifier, integrating chemical and phenotypic spaces, is built and utilized during the process to assess those images initially classified as "fuzzy"-an automated iterative feedback tuning. Simultaneously, all this information is directly annotated in a relational database containing the chemical data. This novel fully automated method was validated by conducting a re-analysis of results from a high-content screening campaign involving 33 992 molecules used to identify inhibitors of the PI3K/Akt signaling pathway. Ninety-two percent of confirmed hits identified by the conventional multistep analysis method were identified using this integrated one-step system as well as 40 new hits, 14.9% of the total, originally false negatives. Ninety-six percent of true negatives were properly recognized too. A web-based access to the database, with customizable data retrieval and visualization tools, facilitates the posterior analysis of annotated cytological features which allows identification of additional phenotypic profiles; thus, further analysis of original crude images is not required.

Extractables analysis of single-use flexible plastic biocontainers.

PubMed

Marghitoiu, Liliana; Liu, Jian; Lee, Hans; Perez, Lourdes; Fujimori, Kiyoshi; Ronk, Michael; Hammond, Matthew R; Nunn, Heather; Lower, Asher; Rogers, Gary; Nashed-Samuel, Yasser

2015-01-01

Studies of the extractable profiles of bioprocessing components have become an integral part of drug development efforts to minimize possible compromise in process performance, decrease in drug product quality, and potential safety risk to patients due to the possibility of small molecules leaching out from the components. In this study, an effective extraction solvent system was developed to evaluate the organic extractable profiles of single-use bioprocess equipment, which has been gaining increasing popularity in the biopharmaceutical industry because of the many advantages over the traditional stainless steel-based bioreactors and other fluid mixing and storage vessels. The chosen extraction conditions were intended to represent aggressive conditions relative to the application of single-use bags in biopharmaceutical manufacture, in which aqueous based systems are largely utilized. Those extraction conditions, along with a non-targeted analytical strategy, allowed for the generation and identification of an array of extractable compounds; a total of 53 organic compounds were identified from four types of commercially available single-use bags, the majority of which are degradation products of polymer additives. The success of this overall extractables analysis strategy was reflected partially by the effectiveness in the extraction and identification of a compound that was later found to be highly detrimental to mammalian cell growth. The usage of single-use bioreactors has been increasing in biopharmaceutical industry because of the appealing advantages that it promises regarding to the cleaning, sterilization, operational flexibility, and so on, during manufacturing of biologics. However, compared to its conventional counterparts based mainly on stainless steel, single-use bioreactors are more susceptible to potential problems associated with compound leaching into the bioprocessing fluid. As a result, extractable profiling of the single-use system has become essential in the qualification of such systems for its use in drug manufacturing. The aim of this study is to evaluate the effectiveness of an extraction solvent system developed to study the extraction profile of single-use bioreactors in which aqueous-based systems are largely used. The results showed that with a non-targeted analytical approach, the extraction solvent allowed the generation and identification of an array of extractable compounds from four commercially available single-use bioreactors. Most of extractables are degradation products of polymer additives, among which was a compound that was later found to be highly detrimental to mammalian cell growth. © PDA, Inc. 2015.

A new class of sulfoxide surfactants derived from Tris. Synthesis and preliminary assessments of their properties.

PubMed

Barthélémy, P; Maurizis, J C; Lacombe, J M; Pucci, B

1998-06-16

A new class of non-ionic amphiphilic molecules suitable for biological purposes, especially extraction of membrane proteins, is reported. Such surfactants were prepared in two steps: addition of alkyl or fluoroalkyl mercaptan on Tris(hydroxymethyl)acrylamidomethane (THAM) derivatives, followed by the oxydation of sulfide group in sulfoxide moiety in order to provide water solubility to the molecule. The detergent efficiency of these new surfactants were assayed on rat liver cells.

Contamination Analysis Tools

NASA Technical Reports Server (NTRS)

Brieda, Lubos

2015-01-01

This talk presents 3 different tools developed recently for contamination analysis:HTML QCM analyzer: runs in a web browser, and allows for data analysis of QCM log filesJava RGA extractor: can load in multiple SRS.ana files and extract pressure vs. time dataC++ Contamination Simulation code: 3D particle tracing code for modeling transport of dust particulates and molecules. Uses residence time to determine if molecules stick. Particulates can be sampled from IEST-STD-1246 and be accelerated by aerodynamic forces.

Acridine orange--its use in the specific staining of DNA in mammalian tissue sections.

PubMed

Dutt, M K

1981-01-01

This paper reports on a new method for the use of acridine orange (AO) in an aqueous solution at pH 4.5 for staining DNA of rat tissue sections from which RNA has been extracted selectively with cold phosphoric acid. Not only this, AO can also be used as dye-SO2 reagent, prepared with NHCl and potassium metabisulphite, for staining DNA-aldehyde molecules of acid-hydrolysed tissue sections. AO samples, manufactured by the National Aniline Division as well as by G. T. Gurr have been used with equal success. Studies of stained sections under light microscope reveal the presence of specifically stained yellowish-orange nuclei. Those sections under fluorescent microscope with proper exciter and barrier filters reveal nuclei of maroon colour. The in situ absorption spectra of nuclei stained with AO-SO2 following acid-hydrolysis of tissue sections as well as those of nuclei stained with an aqueous solution of the dye following extraction of RNA have been presented herein. The mode of binding in the former case has been considered to be due to binding of the teritary amino group of the dye molecules with the DNA-aldehyde molecules and in the latter case to be due to electrostatic binding between the positively charged dye molecules with negatively charged phosphate groups of DNA. Implications of all these findings have been discussed.

ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons.

PubMed

Scala, Giovanni; Affinito, Ornella; Palumbo, Domenico; Florio, Ermanno; Monticelli, Antonella; Miele, Gennaro; Chiariotti, Lorenzo; Cocozza, Sergio

2016-11-25

CpG sites in an individual molecule may exist in a binary state (methylated or unmethylated) and each individual DNA molecule, containing a certain number of CpGs, is a combination of these states defining an epihaplotype. Classic quantification based approaches to study DNA methylation are intrinsically unable to fully represent the complexity of the underlying methylation substrate. Epihaplotype based approaches, on the other hand, allow methylation profiles of cell populations to be studied at the single molecule level. For such investigations, next-generation sequencing techniques can be used, both for quantitative and for epihaplotype analysis. Currently available tools for methylation analysis lack output formats that explicitly report CpG methylation profiles at the single molecule level and that have suited statistical tools for their interpretation. Here we present ampliMethProfiler, a python-based pipeline for the extraction and statistical epihaplotype analysis of amplicons from targeted deep bisulfite sequencing of multiple DNA regions. ampliMethProfiler tool provides an easy and user friendly way to extract and analyze the epihaplotype composition of reads from targeted bisulfite sequencing experiments. ampliMethProfiler is written in python language and requires a local installation of BLAST and (optionally) QIIME tools. It can be run on Linux and OS X platforms. The software is open source and freely available at http://amplimethprofiler.sourceforge.net .

Classification of SD-OCT volumes for DME detection: an anomaly detection approach

NASA Astrophysics Data System (ADS)

Sankar, S.; Sidibé, D.; Cheung, Y.; Wong, T. Y.; Lamoureux, E.; Milea, D.; Meriaudeau, F.

2016-03-01

Diabetic Macular Edema (DME) is the leading cause of blindness amongst diabetic patients worldwide. It is characterized by accumulation of water molecules in the macula leading to swelling. Early detection of the disease helps prevent further loss of vision. Naturally, automated detection of DME from Optical Coherence Tomography (OCT) volumes plays a key role. To this end, a pipeline for detecting DME diseases in OCT volumes is proposed in this paper. The method is based on anomaly detection using Gaussian Mixture Model (GMM). It starts with pre-processing the B-scans by resizing, flattening, filtering and extracting features from them. Both intensity and Local Binary Pattern (LBP) features are considered. The dimensionality of the extracted features is reduced using PCA. As the last stage, a GMM is fitted with features from normal volumes. During testing, features extracted from the test volume are evaluated with the fitted model for anomaly and classification is made based on the number of B-scans detected as outliers. The proposed method is tested on two OCT datasets achieving a sensitivity and a specificity of 80% and 93% on the first dataset, and 100% and 80% on the second one. Moreover, experiments show that the proposed method achieves better classification performances than other recently published works.

Inflammation-Related Effects of Diesel Engine Exhaust Particles: Studies on Lung Cells In Vitro

PubMed Central

Schwarze, P. E.; Totlandsdal, A. I.; Låg, M.; Refsnes, M.; Holme, J. A.; Øvrevik, J.

2013-01-01

Diesel exhaust and its particles (DEP) have been under scrutiny for health effects in humans. In the development of these effects inflammation is regarded as a key process. Overall, in vitro studies report similar DEP-induced changes in markers of inflammation, including cytokines and chemokines, as studies in vivo. In vitro studies suggest that soluble extracts of DEP have the greatest impact on the expression and release of proinflammatory markers. Main DEP mediators of effects have still not been identified and are difficult to find, as fuel and engine technology developments lead to continuously altered characteristics of emissions. Involved mechanisms remain somewhat unclear. DEP extracts appear to comprise components that are able to activate various membrane and cytosolic receptors. Through interactions with receptors, ion channels, and phosphorylation enzymes, molecules in the particle extract will trigger various cell signaling pathways that may lead to the release of inflammatory markers directly or indirectly by causing cell death. In vitro studies represent a fast and convenient system which may have implications for technology development. Furthermore, knowledge regarding how particles elicit their effects may contribute to understanding of DEP-induced health effects in vivo, with possible implications for identifying susceptible groups of people and effect biomarkers. PMID:23509760

Chemical Characterization and Cytotoxic Activity of Blueberry Extracts (cv. Misty) Cultivated in Brazil.

PubMed

Massarotto, Giovana; Barcellos, Thiago; Garcia, Charlene Silvestrin Celi; Brandalize, Ana Paula Carneiro; Moura, Sidnei; Schwambach, Joséli; Henriques, João Antonio Pêgas; Roesch-Ely, Mariana

2016-08-01

Vaccinium corymbosum (L.) varieties cultivation is relatively recent in Brazil, but its production has been intensified given its good adaptability to the Southern Brazil climate. Blueberries are a rich source of phenolic compounds and contain significant levels of anthocyanins, flavonols, chlorogenic acids, and procyanidins, which lead to different biological activities. Chemical identification of skin and whole hydroalcoholic blueberry extracts (ExtSB and ExtWB) revealed the presence of anthocyanins concentrated in the skin and others chemicals compounds as quercetin glycosides, proanthocyanins dimers, citric, and chlorogenic acid in the pulp. Selectivity for tumor cell lines (Hep-2, HeLa, HT-29) using ExtSB and ExtWB extracts was observed through MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay after 24 h of treatment when compared to nontumor cells (MRC-5). Morphological changes and late stages of apoptotic and necrosis process were seen in HT-29 cell line after ExtWB treatment, compared to nontumor cell line MRC-5. These results are in agreement with other studies that indicate the activity of compounds such as anthocyanins and other molecules found in Southern Highbush blueberry variety, attributed to promote beneficial effects on health that may respond as cytotoxic natural agent and contribute to cancer treatment. © 2016 Institute of Food Technologists®

Biological implications of polydimethylsiloxane-based microfluidic cell culture†

PubMed Central

Regehr, Keil J.; Domenech, Maribella; Koepsel, Justin T.; Carver, Kristopher C.; Ellison-Zelski, Stephanie J.; Murphy, William L.; Schuler, Linda A.; Alarid, Elaine T.; Beebe, David J.

2009-01-01

Polydimethylsiloxane (PDMS) has become a staple of the microfluidics community by virtue of its simple fabrication process and material attributes, such as gas permeability, optical transparency, and flexibility. As microfluidic systems are put toward biological problems and increasingly utilized as cell culture platforms, the material properties of PDMS must be considered in a biological context. Two properties of PDMS were addressed in this study: the leaching of uncured oligomers from the polymer network into microchannel media, and the absorption of small, hydrophobic molecules (i.e. estrogen) from serum-containing media into the polymer bulk. Uncured PDMS oligomers were detectable via MALDI-MS in microchannel media both before and after Soxhlet extraction of PDMS devices in ethanol. Additionally, PDMS oligomers were identified in the plasma membranes of NMuMG cells cultured in PDMS microchannels for 24 hours. Cells cultured in extracted microchannels also contained a detectable amount of uncured PDMS. It was shown that MCF-7 cells seeded directly on PDMS inserts were responsive to hydrophilic prolactin but not hydrophobic estrogen, reflecting its specificity for absorbing small, hydrophobic molecules; and the presence of PDMS floating in wells significantly reduced cellular response to estrogen in a serum-dependent manner. Quantification of estrogen via ELISA revealed that microchannel estrogen partitioned rapidly into the surrounding PDMS to a ratio of approximately 9:1. Pretreatments such as blocking with serum or pre-absorbing estrogen for 24 hours did not affect estrogen loss from PDMS-based microchannels. These findings highlight the importance of careful consideration of culture system properties when determining an appropriate environment for biological experiments. PMID:19606288

Factors Affecting the Extraction of Intact Ribonucleic Acid from Plant Tissues Containing Interfering Phenolic Compounds

PubMed Central

Newbury, H. John; Possingham, John V.

1977-01-01

Using conventional methods it is impossible to extract RNA as uncomplexed intact molecules from the leaves of grapevines (Vitis vinifera L.) and from a number of woody perennial species that contain high levels of reactive phenolic compounds. A procedure involving the use of high concentrations of the chaotropic agent sodium perchlorate prevents the binding of phenolic compounds to RNA during extraction. Analyses of the phenolics present in plant tissues used in these experiments indicate that there is a poor correlation between the total phenolic content and the complexing of RNA. However, qualitative analyses suggest that proanthocyanidins are involved in the tanning of RNA during conventional extractions. PMID:16660134

The use of carrier RNA to enhance DNA extraction from microfluidic-based silica monoliths.

PubMed

Shaw, Kirsty J; Thain, Lauren; Docker, Peter T; Dyer, Charlotte E; Greenman, John; Greenway, Gillian M; Haswell, Stephen J

2009-10-12

DNA extraction was carried out on silica-based monoliths within a microfluidic device. Solid-phase DNA extraction methodology was applied in which the DNA binds to silica in the presence of a chaotropic salt, such as guanidine hydrochloride, and is eluted in a low ionic strength solution, such as water. The addition of poly-A carrier RNA to the chaotropic salt solution resulted in a marked increase in the effective amount of DNA that could be recovered (25ng) compared to the absence of RNA (5ng) using the silica-based monolith. These findings confirm that techniques utilising nucleic acid carrier molecules can enhance DNA extraction methodologies in microfluidic applications.

High-throughput simultaneous analysis of RNA, protein, and lipid biomarkers in heterogeneous tissue samples.

PubMed

Reiser, Vladimír; Smith, Ryan C; Xue, Jiyan; Kurtz, Marc M; Liu, Rong; Legrand, Cheryl; He, Xuanmin; Yu, Xiang; Wong, Peggy; Hinchcliffe, John S; Tanen, Michael R; Lazar, Gloria; Zieba, Renata; Ichetovkin, Marina; Chen, Zhu; O'Neill, Edward A; Tanaka, Wesley K; Marton, Matthew J; Liao, Jason; Morris, Mark; Hailman, Eric; Tokiwa, George Y; Plump, Andrew S

2011-11-01

With expanding biomarker discovery efforts and increasing costs of drug development, it is critical to maximize the value of mass-limited clinical samples. The main limitation of available methods is the inability to isolate and analyze, from a single sample, molecules requiring incompatible extraction methods. Thus, we developed a novel semiautomated method for tissue processing and tissue milling and division (TMAD). We used a SilverHawk atherectomy catheter to collect atherosclerotic plaques from patients requiring peripheral atherectomy. Tissue preservation by flash freezing was compared with immersion in RNAlater®, and tissue grinding by traditional mortar and pestle was compared with TMAD. Comparators were protein, RNA, and lipid yield and quality. Reproducibility of analyte yield from aliquots of the same tissue sample processed by TMAD was also measured. The quantity and quality of biomarkers extracted from tissue prepared by TMAD was at least as good as that extracted from tissue stored and prepared by traditional means. TMAD enabled parallel analysis of gene expression (quantitative reverse-transcription PCR, microarray), protein composition (ELISA), and lipid content (biochemical assay) from as little as 20 mg of tissue. The mean correlation was r = 0.97 in molecular composition (RNA, protein, or lipid) between aliquots of individual samples generated by TMAD. We also demonstrated that it is feasible to use TMAD in a large-scale clinical study setting. The TMAD methodology described here enables semiautomated, high-throughput sampling of small amounts of heterogeneous tissue specimens by multiple analytical techniques with generally improved quality of recovered biomolecules.

In Situ Analysis of Organics with a Portable Mass Spectrometer

NASA Technical Reports Server (NTRS)

Soparawalla, Santosh

2011-01-01

The search for extra-terrestrial life starts at home. In order to find life on other planets, we start by examining life processes we understand on the earth. Though it may not be possible to see the life in the form of macroscopic organisms, telltale signs of life can exist in the form of small organic molecules such as peptides and amino acids. Our overall goal is to test a portable mass spectrometer (MS) system, the Mini 10.5, for astrobiological applications including in situ hydrocarbon analysis and sediments analysis using an additional automated sample processing system (ASPS). The collaborative research focuses on two current projects in the field of astrobiology. Both projects are geared towards examining organics distributed in extreme environments. One portion of study attempts to qualitatively analyze the effect of volatile organic compounds (VOC) produced by diesel exhaust on lichens growing in the desert. This requires measurements to be taken by bringing the instrument to the Mojave Desert and monitoring atmospheric composition of VOCs in situ. The second project is to evaluate the miniature MS system as a detector for the ASPS extraction system. A major obstacle of any chemometric in situ analysis is the suppression of analyte signal by concomitant signal from the surrounding environment. The ASPS extraction device has been developed at JPL to extract amino acids from sediment samples and elute them in solution. The solution is eluted at a high pH and needs to be conditioned to a more neutral pH so that dissolved amino acids can be readily protonated and subsequently analyzed by electrospray MS.

A Review of PAT Strategies in Secondary Solid Oral Dosage Manufacturing of Small Molecules.

PubMed

Laske, Stephan; Paudel, Amrit; Scheibelhofer, Otto

2017-03-01

Pharmaceutical solid oral dosage product manufacturing is a well-established, yet revolutionizing area. To this end, process analytical technology (PAT) involves interdisciplinary and multivariate (chemical, physical, microbiological, and mathematical) methods for material (e.g., materials, intermediates, products) and process (e.g., temperature, pressure, throughput, etc.) analysis. This supports rational process modeling and enhanced control strategies for improved product quality and process efficiency. Therefore, it is often difficult to orient and find the relevant, integrated aspects of the current state-of-the-art. Especially, the link between fundamental research, in terms of sensor and control system development, to the application both in laboratory and manufacturing scale, is difficult to comprehend. This review compiles a nonexhaustive overview on current approaches from the recognized academia and industrial practices of PAT, including screening, selection, and final implementations in solid oral dosage manufacturing, through a wide diversity of use cases. Finally, the authors attempt to extract a common consensus toward developing PAT application guidance for different unit operations of drug product manufacturing. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Ultrafast Electron Dynamics in Solar Energy Conversion.

PubMed

Ponseca, Carlito S; Chábera, Pavel; Uhlig, Jens; Persson, Petter; Sundström, Villy

2017-08-23

Electrons are the workhorses of solar energy conversion. Conversion of the energy of light to electricity in photovoltaics, or to energy-rich molecules (solar fuel) through photocatalytic processes, invariably starts with photoinduced generation of energy-rich electrons. The harvesting of these electrons in practical devices rests on a series of electron transfer processes whose dynamics and efficiencies determine the function of materials and devices. To capture the energy of a photogenerated electron-hole pair in a solar cell material, charges of opposite sign have to be separated against electrostatic attractions, prevented from recombining and being transported through the active material to electrodes where they can be extracted. In photocatalytic solar fuel production, these electron processes are coupled to chemical reactions leading to storage of the energy of light in chemical bonds. With the focus on the ultrafast time scale, we here discuss the light-induced electron processes underlying the function of several molecular and hybrid materials currently under development for solar energy applications in dye or quantum dot-sensitized solar cells, polymer-fullerene polymer solar cells, organometal halide perovskite solar cells, and finally some photocatalytic systems.

Sida rhomboidea.Roxb aqueous extract down-regulates in vivo expression of vascular cell adhesion molecules in atherogenic rats and inhibits in vitro macrophage differentiation and foam cell formation.

PubMed

Thounaojam, Menaka C; Jadeja, Ravirajsinh N; Salunke, Sunita P; Devkar, Ranjitsinh V; Ramachandran, A V

2012-10-01

The present study evaluates efficacy of Sida rhomboidea.Roxb (SR) leaves extract in ameliorating experimental atherosclerosis using in vitro and in vivo experimental models. Atherogenic (ATH) diet fed rats recorded significant increment in the serum total cholesterol (TC), triglycerides (TG), low-density lipoprotein (LDL), very LDL (VLDL), autoantibody against oxidized LDL (Ox-LDL), markers of LDL oxidation and decrement in high-density lipoprotein (HDL) along with increment in aortic TC and TG. The ex vivo LDL oxidation assay revealed an increased susceptibility of LDL isolated from ATH rats to undergo copper mediated oxidation. These set of changes were minimized by simultaneous co-supplementation of SR extract to ATH diet fed rats. Histopathology of aorta and immunolocalization studies recorded pronounced atheromatous plaque formation, vascular calcification, significant elastin derangements and higher expression of macrophage surface marker (F4/80), vascular cell adhesion molecule-1 (VCAM-1) and p-selectin in ATH rats. Whereas, ATH+SR rats depicted minimal evidence of atheromatous plaque formation, calcium deposition, distortion/defragmentation of elastin and accumulation of macrophages along with lowered expression of VCAM-1 and P-selectin compared to ATH rats. Further, monocyte to macrophage differentiation and in vitro foam cell formation were significantly attenuated in presence of SR extract. In conclusion, SR extract has the potency of controlling experimental atherosclerosis and can be used as promising herbal supplement in combating atherosclerosis.

Malvidin and cyanidin derivatives from açai fruit (Euterpe oleracea Mart.) counteract UV-A-induced oxidative stress in immortalized fibroblasts.

PubMed

Petruk, Ganna; Illiano, Anna; Del Giudice, Rita; Raiola, Assunta; Amoresano, Angela; Rigano, Maria Manuela; Piccoli, Renata; Monti, Daria Maria

2017-07-01

UV-A radiations are known to induce cellular oxidative stress, leading to premature skin aging. Consumption of açai fruit (Euterpe oleracea Martius) is known to have many health benefits due to its high level of antioxidants. Herein, we analyzed the ability of phenolic compounds extracted from this fruit to attenuate UV-A-induced oxidative stress in immortalized fibroblast. A methanol/water açai extract was fractionated by HPLC and each fraction tested for anti-oxidant stress activity. Immortalized fibroblasts were pre-incubated with açai fractions and then exposed to UV-A radiations. Açai extract was found to be able to strongly protect cells from oxidative stress. In particular, reactive oxygen species (ROS) production, GSH depletion, lipid peroxidation and no increase in the phosphorylation levels of proteins involved in the oxidative stress pathway was observed in cells pre-incubated with the extract and then irradiated by UV-A. Mass spectrometry analyses of HPLC fractionated extract led us to the identification of malvidin and cyanidin derivatives as the most active molecules able to counteract the negative effects induced by UV-A irradiation. Our results indicate, for the first time, that açai fruit is a valuable natural source for malvidin and cyanidin to be used as anti-stress molecules and represent good candidates for dietary intervention in the prevention of age related skin damage. Copyright © 2017 Elsevier B.V. All rights reserved.

In vitro anti-plasmodial activity of some traditionally used medicinal plants against Plasmodium falciparum.

PubMed

Venkatesalu, V; Gopalan, N; Pillai, C R; Singh, Vineeta; Chandrasekaran, M; Senthilkumar, A; Chandramouli, N

2012-07-01

The anti-plasmodial activity of different solvent extracts of Adhatoda vasica (root), Caesalpinia pulcherrima (leaf), Carica papaya (pulp), Erythroxylum monogynum (leaf), Lantana camara (whole plant), Ocimum sanctum (root) and Phyllanthus niruri (whole plant) were studied against Plasmodium falciparum. Of the 35 extracts tested, seven extracts showed good anti-plasmodial activity. Methanol extract of C. pulcherrima showed the lowest IC50 value (10.96 μg/mL) followed by methanol extract of A. vasica (IC(50)=11.1 μg/mL), chloroform extract of O. sanctum (IC(50)=11.47 μg/mL), methanol extract of E. monogynum (IC(50)=12.23 μg/mL), acetone extract of C. pulcherrima (IC(50)=12.49 μg/mL), methanol extract of O. sanctum and acetone extract of A. vasica (IC(50)=14.04 μg/mL). The results of the present study justify the use of these medicinal plants in traditional practice, and also, a further study on the isolation of anti-plasmodial molecules from their active crude extracts is in progress.

Investigations of nanoscale variations in spin and charge transport in manganites and organic semiconductors using spin polarized scanning tunneling spectroscopy

NASA Astrophysics Data System (ADS)

Hughes, Cameron Richard

Analysis of DNA structure and behavior, up to and including full sequencing of a genome's bases, and of biological processes such as replication, transcription and translation, is essential for an understanding of genetic variation, heritable diseases and the effects of environmental factors. Recently, single-molecule techniques have been developed to study DNA properties in unprecedented detail. For a number of these techniques, controlled adsorption of linearly stretched DNA molecules on surfaces is necessary. In experiments where hybridization of adsorbed molecules to labeled probes is used to determine DNA structure, single-stranded DNA is needed. Conventionally, for long DNA's (up to Mbp), double-stranded DNA is deposited on a surface and denatured in-situ. While successful, this method has several disadvantages. This thesis reports efforts to directly adsorb long single-stranded DNA's out of solution as an alternative strategy. It consists of three parts: (1) Establishment of a simple method using Acridine Orange (AO) staining dye to determine whether DNA's are ss or ds on the surface. The method allows for the assessment of the degree of renaturation during deposition. Incubation of surface-adsorbed DNA in solutions of AO dye in the concentration range of 10--15uM were found to be effective for discriminating between ss DNA and ds DNA based on differences in the fluorescence emission spectra. (2) Deposition of ss DNA produced by heat denaturation on polymer-coated surfaces. Lambda DNA (48502bp) was adsorbed by drop evaporation or dipping/extraction of surface out of a buffered solution. The efficiency of deposition was optimized with respect to DNA concentration, buffer type and pH. (3) Separation of complementary single strands of Lambda, mono-cut digest and HindIII digest by gel electrophoresis. Using agarose gels in concentrations ranging from 0.4% to 1.4% (weight/volume), electric fields in the range 1--4V/cm in 1x Tris-Acetate-EDTA (TAE) buffer, good strand separation could be obtained. Both DC and pulsed electric fields were used and compared. Following separation, sense and anti-sense strands of lambda DNA were extracted from gels and deposited separately onto surfaces, and length distributions of the isolated molecules were measured by fluorescence microscopy.

Comparison between several techniques of olive tree bark extraction (Tunisian Chemlali variety).

PubMed

Issaoui, Aimen; Ksibi, Hatem; Ksibi, Mohamed

2017-01-01

In order to better understand the chemical composition of the olive tree bark of Tunisian chemlali variety (Olea europaea cv. 'Chemlali'), this material was extracted by different ways. Compositions of extracts were used at best-selected conditions for each technique, and characterised using HPLC, LC/MS and GC-MS techniques. Analyses are conducted to an important variety of high carbon number compounds such as aliphatic compounds as nanocosane and heptacosane, and molecules with high value added tax (VAT) which can be classified as follows: diterpenes as phytol, triterpenes as squalene and also esters as Benzyl cinnamate. Hydrodistillation at high pressure seems to be a very common method to get a wide variety of compounds, the results are better than the ones obtained using supercritical fluid extraction and solvent extraction.

High impact technologies for natural products screening.

PubMed

Koehn, Frank E

2008-01-01

Natural products have historically been a rich source of lead molecules in drug discovery. However, natural products have been de-emphasized as high throughput screening resources in the recent past, in part because of difficulties in obtaining high quality natural products screening libraries, or in applying modern screening assays to these libraries. In addition, natural products programs based on screening of extract libraries, bioassay-guided isolation, structure elucidation and subsequent production scale-up are challenged to meet the rapid cycle times that are characteristic of the modern HTS approach. Fortunately, new technologies in mass spectrometry, NMR and other spectroscopic techniques can greatly facilitate the first components of the process - namely the efficient creation of high-quality natural products libraries, bimolecular target or cell-based screening, and early hit characterization. The success of any high throughput screening campaign is dependent on the quality of the chemical library. The construction and maintenance of a high quality natural products library, whether based on microbial, plant, marine or other sources is a costly endeavor. The library itself may be composed of samples that are themselves mixtures - such as crude extracts, semi-pure mixtures or single purified natural products. Each of these library designs carries with it distinctive advantages and disadvantages. Crude extract libraries have lower resource requirements for sample preparation, but high requirements for identification of the bioactive constituents. Pre-fractionated libraries can be an effective strategy to alleviate interferences encountered with crude libraries, and may shorten the time needed to identify the active principle. Purified natural product libraries require substantial resources for preparation, but offer the advantage that the hit detection process is reduced to that of synthetic single component libraries. Whether the natural products library consists of crude or partially fractionated mixtures, the library contents should be profiled to identify the known components present - a process known as dereplication. The use of mass spectrometry and HPLC-mass spectrometry together with spectral databases is a powerful tool in the chemometric profiling of bio-sources for natural product production. High throughput, high sensitivity flow NMR is an emerging tool in this area as well. Whether by cell based or biomolecular target based assays, screening of natural product extract libraries continues to furnish novel lead molecules for further drug development, despite challenges in the analysis and prioritization of natural products hits. Spectroscopic techniques are now being used to directly screen natural product and synthetic libraries. Mass spectrometry in the form of methods such as ESI-ICRFTMS, and FACS-MS as well as NMR methods such as SAR by NMR and STD-NMR have been utilized to effectively screen molecular libraries. Overall, emerging advances in mass spectrometry, NMR and other technologies are making it possible to overcome the challenges encountered in screening natural products libraries in today's drug discovery environment. As we apply these technologies and develop them even further, we can look forward to increased impact of natural products in the HTS based drug discovery.

Evolution in the design of a low sheath-flow interface for CE-MS and application to biological samples.

PubMed

González-Ruiz, Víctor; Codesido, Santiago; Rudaz, Serge; Schappler, Julie

2018-03-01

Although several interfaces for CE-MS hyphenation are commercially available, the development of new versatile, simple and yet efficient and sensitive alternatives remains an important field of research. In a previous work, a simple low sheath-flow interface was developed from inexpensive parts. This interface features a design easy to build, maintain, and adapt to particular needs. The present work introduces an improved design of the previous interface. By reducing the diameter of the separation capillary and the emitter, a smaller Taylor cone is spontaneously formed, minimizing the zone dispersion while the analytes go through the interface and leading to less peak broadening associated to the ESI process. Numerical modeling allowed studying the mixing and diffusion processes taking place in the Taylor cone. The analytical performance of this new interface was tested with pharmaceutically relevant molecules and endogenous metabolites. The interface was eventually applied to the analysis of neural cell culture samples, allowing the identification of a panel of neurotransmission-related molecules. An excellent migration time repeatability was obtained (intra-day RSD <0.5% for most compounds, and <3.0% for inter-day precision). Most metabolites showed S/N ratios >10 with an injected volume of 6.7 nL of biological extract. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Covalent Bonding of Chlorogenic Acid Induces Structural Modifications on Sunflower Proteins.

PubMed

Karefyllakis, Dimitris; Salakou, Stavroula; Bitter, J Harry; van der Goot, Atze J; Nikiforidis, Constantinos V

2018-02-19

Proteins and phenols coexist in the confined space of plant cells leading to reactions between them, which result in new covalently bonded complex molecules. This kind of reactions has been widely observed during storage and processing of plant materials. However, the nature of the new complex molecules and their physicochemical properties are largely unknown. Therefore, we investigated the structural characteristics of covalently bonded complexes between sunflower protein isolate (SFPI, protein content 85 wt %) and the dominant phenol in the confined space of a sunflower seed cell (chlorogenic acid, CGA). It was shown that the efficiency of bond formation goes through a maximum as a function of the SFPI:CGA ratio. Moreover, the bonding of CGA with proteins resulted in changes in the secondary and tertiary structure of the protein. It was also shown that the phenol bound strongly to the protein, which resulted in new crosslinks between the polypeptide chains. As a result, secondary structures like α-helices and β-sheets diminished, which in turn resulted in more disordered domains and a subsequent modification of the tertiary structure of the proteins. These findings are relevant for establishing future protocols for extraction of high-quality proteins and phenols when utilizing plant material and offer insight into the impact of processing that these ingredients endure. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

TROSY-based z-exchange spectroscopy: application to the determination of the activation energy for intermolecular protein translocation between specific sites on different DNA molecules.

PubMed

Sahu, Debashish; Clore, G Marius; Iwahara, Junji

2007-10-31

A two-dimensional TROSY-based z-exchange 1H-15N correlation experiment for the quantitative analysis of kinetic processes in the slow exchange regime is presented. The pulse scheme converts the product operator terms Nz into 2NzHz and 2NzHz into -Nz in the middle of the z-mixing period, thereby suppressing the buildup of spurious semi-TROSY peaks arising from the different relaxation rates for the Nz and 2NzHz terms and simplifying the behavior of longitudinal magnetization for an exchanging system during the mixing period. Theoretical considerations and experimental data demonstrate that the TROSY-based z-exchange experiment permits quantitative determination of rate constants using the same procedure as that for the conventional non-TROSY 15Nz-exchange experiment. Line narrowing as a consequence of the use of the TROSY principle makes the method particularly suitable for kinetic studies at low temperature, thereby permitting activation energies to be extracted from data acquired over a wider temperature range. We applied this method to the investigation of the process whereby the HoxD9 homeodomain translocates between specific target sites on different DNA molecules via a direct transfer mechanism without going through the intermediary of free protein. The activation enthalpy for intermolecular translocation was determined to be 17 kcal/mol.

Coefficients of caffeine distribution in aliphatic alcohol-ammonium sulfate-water systems

NASA Astrophysics Data System (ADS)

Korenman, Ya. I.; Krivosheeva, O. A.; Mokshina, N. Ya.

2012-11-01

The extraction of caffeine with aliphatic alcohols C3-C9 from aqueous solutions in the presence of a salting-out agent (ammonium sulfate) is studied. Quantitative characteristics of extraction are calculated: the distribution coefficients ( D) and the degree of recovery ( R, %). Relations are found between log D of caffeine and the length of the hydrocarbon radical in the alcohol molecule, along with certain physicochemical properties of the extragents.

Macromolecules of extracellular matrix: determination of selective structures and their functional significance.

PubMed

Butler, William T

2008-01-01

In this brief review, I recount events and scientific endeavors in which I have been privileged to participate. The descriptive information includes discovery and characterization of hydroxylysine glycosides from collagen, isolation of dentin sialoprotein (DSP), investigations on dentin phosphoprotein (DPP), and the discovery of a single gene for both DSP and DPP that requires posttranslational proteolytic cleavage of the parent DSPP molecule to generate the two fragments. Finally, I address our unexpected finding of fragments of DMP1 in bone extracts. These fragments are from the NH2-terminal (37 kDa) and COOH-terminal (57 kDa) regions of DMP1. Our studies showed that, similar to DSPP, DMP1 is proteolytically processed by cleavages at X-Asp bonds.

Efimov effect for heteronuclear three-body systems at positive scattering length and finite temperature

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

Emmons, Samuel B.; Kang, Daekyoung; Acharya, Bijaya

2017-09-08

Here, we study the recombination process of three atoms scattering into an atom and diatomic molecule in heteronuclear mixtures of ultracold atomic gases with large and positive interspecies scattering length at finite temperature. We calculate the temperature dependence of the three-body recombination rates by extracting universal scaling functions that parametrize the energy dependence of the scattering matrix. We compare our results to experimental data for the 40K– 87Rb mixture and make a prediction for 6Li– 87Rb. We find that contributions from higher partial wave channels significantly impact the total rate and, in systems with particularly large mass imbalance, can evenmore » obliterate the recombination minima associated with the Efimov effect.« less

Force spectroscopy of biomolecular folding and binding: theory meets experiment

NASA Astrophysics Data System (ADS)

Dudko, Olga

2015-03-01

Conformational transitions in biological macromolecules usually serve as the mechanism that brings biomolecules into their working shape and enables their biological function. Single-molecule force spectroscopy probes conformational transitions by applying force to individual macromolecules and recording their response, or ``mechanical fingerprints,'' in the form of force-extension curves. However, how can we decode these fingerprints so that they reveal the kinetic barriers and the associated timescales of a biological process? I will present an analytical theory of the mechanical fingerprints of macromolecules. The theory is suitable for decoding such fingerprints to extract the barriers and timescales. The application of the theory will be illustrated through recent studies on protein-DNA interactions and the receptor-ligand complexes involved in blood clot formation.

Lasing properties of polymerized chiral nematic Bragg onion microlasers.

PubMed

Humar, Matjaž; Araoka, Fumito; Takezoe, Hideo; Muševič, Igor

2016-08-22

Dye doped photocurable cholesteric liquid crystal was used to produce solid Bragg onion omnidirectional lasers. The lasers were produced by dispersing and polymerizing chiral nematic LC with parallel surface anchoring of LC molecules at the interface, extracted and transferred into another medium. Lasing characteristics were studied in carrier medium with different refractive index. The lasing in spherical cholesteric liquid crystal was attributed to two mechanisms, photonic bandedge lasing and lasing of whispering-gallery modes. The latter can be suppressed by using a higher index carrier fluid to prevent total internal reflection on the interface of the spheres. Pulse-to-pulse stability and threshold characteristics were also studied and compared to non-polymerized lasers. The polymerization process greatly increases the lasing stability.

Bioflavoring and beer refermentation.

PubMed

Vanderhaegen, B; Neven, H; Coghe, S; Verstrepen, K J; Derdelinckx, G; Verachtert, H

2003-08-01

Various techniques are used to adjust the flavors of foods and beverages to new market demands. Although synthetic flavoring chemicals are still widely used, flavors produced by biological methods (bioflavors) are now more and more requested by consumers, increasingly concerned with health and environmental problems caused by synthetic chemicals. Bioflavors can be extracted from plants or produced with plant cell cultures, microorganisms or isolated enzymes. This Mini-Review paper gives an overview of different systems for the microbial production of natural flavors, either de novo, or starting with selected flavor precursor molecules. Emphasis is put on the bioflavoring of beer and the possibilities offered by beer refermentation processes. The use of flavor precursors in combination with non-conventional or genetically modified yeasts for the production of new products is discussed.

Single hair analysis of small molecules using MALDI-triple quadrupole MS imaging and LC-MS/MS: investigations on opportunities and pitfalls.

PubMed

Poetzsch, Michael; Steuer, Andrea E; Roemmelt, Andreas T; Baumgartner, Markus R; Kraemer, Thomas

2014-12-02

Single hair analysis normally requires extensive sample preparation microscale protocols including time-consuming steps like segmentation and extraction. Matrix assisted laser desorption and ionization mass spectrometric imaging (MALDI-MSI) was shown to be an alternative tool in single hair analysis, but still, questions remain. Therefore, an investigation of MALDI-MSI in single hair analysis concerning the extraction process, usage of internal standard (IS), and influences on the ionization processes were systematically investigated to enable the reliable application to hair analysis. Furthermore, single dose detection, quantitative correlation to a single hair, and hair strand LC-MS/MS results were performed, and the performance was compared to LC-MS/MS single hair monitoring. The MALDI process was shown to be independent from natural hair color and not influenced by the presence of melanin. Ionization was shown to be reproducible along and in between different hair samples. MALDI image intensities in single hair and hair snippets showed good semiquantitative correlation to zolpidem hair concentrations obtained from validated routine LC-MS/MS methods. MALDI-MSI is superior to LC-MS/MS analysis when a fast, easy, and cheap sample preparation is necessary, whereas LC-MS/MS showed higher sensitivity with the ability of single dose detection for zolpidem. MALDI-MSI and LC-MS/MS segmental single hair analysis showed good correlation, and both are suitable for consumption monitoring of drugs of abuse with a high time resolution.

Crystallization-assisted nano-lens array fabrication for highly efficient and color stable organic light emitting diodes.

PubMed

Park, Young-Sam; Han, Kyung-Hoon; Kim, Jehan; Cho, Doo-Hee; Lee, Jonghee; Han, Yoonjay; Lim, Jong Tae; Cho, Nam Sung; Yu, Byounggon; Lee, Jeong-Ik; Kim, Jang-Joo

2017-01-07

To date, all deposition equipment has been developed to produce planar films. Thus lens arrays with a lens diameter of <1 mm have been manufactured by combining deposition with other technologies, such as masks, surface treatment, molding etc. Furthermore, a nano-lens array (NLA) with a sufficiently small lens diameter (<1 μm) is necessary to avoid image quality degradation in high resolution displays. In this study, an organic NLA made using a conventional deposition technique - without combining with other techniques - is reported. Very interestingly, grazing-incidence small-angle X-ray scattering (GI-SAXS) experiments indicate that the NLA is formed by the crystallization of organic molecules and the resulting increase in surface tension. The lens diameter can be tuned for use with any kind of light by controlling the process parameters. As an example of their potential applications, we use NLAs as a light extraction film for organic light emitting diodes (OLEDs). The NLA is integrated by directly depositing it on the top electrode of a collection of OLEDs. This is a dry process, meaning that it is fully compatible with the current OLED production process. Devices with NLAs exhibited a light extraction efficiency 1.5 times higher than devices without, which corresponds well with simulation results. The simulations show that this high efficiency is due to the reduction of the guided modes by scattering at the NLA. The NLAs also reduce image blurring, indicating that they increase color stability.

Role of the DIP Molecules in DCC Signaling

DTIC Science & Technology

1999-09-01

to policies of applicable Federal Law 45 CFR 46. N/A In conducting research utilizing recombinant DNA technology , the investigator(s) adhered to...for 1 h, then with 0.1 mg/ml of proteinase K, 0.1% SDS at 50’C Ihle, 1995; Fraser and Evan, 1996). These molecules overnight. Samples were extracted ...incubated with 20 yg/ml of anti-DCC antibody diluted in PBS-0.1% saponin for 1 h, washed with PBS, blocked Western blotting with 5% normal donkey serum for 1

Investigation of interaction between magnetic silica particles and lambda phage DNA fragment.

PubMed

Smerkova, Kristyna; Dostalova, Simona; Vaculovicova, Marketa; Kynicky, Jindrich; Trnkova, Libuse; Kralik, Miroslav; Adam, Vojtech; Hubalek, Jaromir; Provaznik, Ivo; Kizek, Rene

2013-12-01

Nucleic acids belong to the most important molecules and therefore the understanding of their properties, function and behavior is crucial. Even though a range of analytical and biochemical methods have been developed for this purpose, one common step is essential for all of them - isolation of the nucleic acid from the from complex sample matrix. The use of magnetic particles for the separation of nucleic acids has many advantages over other isolation methods. In this study, an isolation procedure for extraction of DNA was optimized. Each step of the isolation process including washing, immobilization and elution was optimized and therefore the efficiency was increased from 1.7% to 28.7% and the total time was shortened from 75 to 30min comparing to the previously described method. Quantification of the particular parameter influence was performed by square-wave voltammetry using hanging drop mercury electrode. Further, we compared the optimized method with standard chloroform extraction and applied on isolation of DNA from Staphylococcus aureus and Escherichia coli. Copyright © 2013 Elsevier B.V. All rights reserved.

Revalorization of sunflower stalks as novel sources of cellulose nanofibrils and nanocrystals and their effect on wheat gluten bionanocomposite properties.

PubMed

Fortunati, E; Luzi, F; Jiménez, A; Gopakumar, D A; Puglia, D; Thomas, S; Kenny, J M; Chiralt, A; Torre, L

2016-09-20

Novel gluten based bionanocomposites reinforced with cellulose nanofibrils (CNF) and cellulose nanocrystals (CNC) extracted from sunflower stalks by respectively a steam explosion treatment and a hydrolysis procedure, were prepared by casting/evaporation. The extracted cellulose nanomaterials, both CNC and CNF, were embedded in gluten matrix and their effect was investigated. Morphological investigations highlighted that gluten based bionanocomposites showed a homogenous morphology, the absence of visible cellulose nanoreinforcements, and the presence of holes for Gluten_CNF nanocomposites. Gluten_CNF showed a reduction of water vapour permeability coefficients but the values are higher respect to gluten reinforced with CNC. This behaviour could be related to the ability of CNC to increase the tortuous path of gas molecules. Moreover, the results from thermal, mechanical and barrier properties confirmed the strong interactions obtained between CNC and gluten matrix during the process. The study suggested the possibility to re-valorise agricultural wastes with potential applications as reinforcement in polymer matrix bionanocomposites. Copyright © 2016 Elsevier Ltd. All rights reserved.

Lyophilization, a practical way to store and transport tissues prior to protein extraction for 2DE analysis?

PubMed

Carpentier, Sebastien C; Dens, Koen; Van den houwe, Ines; Swennen, Rony; Panis, Bart

2007-09-01

To date, lyophilized samples are rarely utilized in proteomics experiments. This is most likely because researchers are concerned about inducing cross-linking of proteins via amide bonds, leading to artefactual charge modification and thus resulting in irreproducible results and bad gels. Indeed, it is known that lyophilization can cause crosslinking. The potential reaction is a reaction of free amino groups of a protein (N-terminal alpha-amino groups and epsilon-amino groups from lysine) with the reducing group of sugar molecules. The rate and extent of this reaction depends on the sugar content of the sample, the efficiency of lyophilization process, the residual water content of the material and the storage temperature. Lyophilization is a cheap, practical and safe alternative for the storage and transportation of samples prior to protein extraction, separation and quantification via 2DE, when care is taken (i) to dry the samples to the lowest practicable moisture content, (ii) to transport and store them under water- and airtight conditions and (iii) to avoid heating of the sample.

Physicochemical regeneration of high silica zeolite Y used to clean-up water polluted with sulfonamide antibiotics.

PubMed

Braschi, I; Blasioli, S; Buscaroli, E; Montecchio, D; Martucci, A

2016-05-01

High silica zeolite Y has been positively evaluated to clean-up water polluted with sulfonamides, an antibiotic family which is known to be involved in the antibiotic resistance evolution. To define possible strategies for the exhausted zeolite regeneration, the efficacy of some chemico-physical treatments on the zeolite loaded with four different sulfonamides was evaluated. The evolution of photolysis, Fenton-like reaction, thermal treatments, and solvent extractions and the occurrence in the zeolite pores of organic residues eventually entrapped was elucidated by a combined thermogravimetric (TGA-DTA), diffractometric (XRPD), and spectroscopic (FT-IR) approach. The chemical processes were not able to remove the organic guest from zeolite pores and a limited transformation on embedded molecules was observed. On the contrary, both thermal treatment and solvent extraction succeeded in the regeneration of the zeolite loaded from deionized and natural fresh water. The recyclability of regenerated zeolite was evaluated over several adsorption/regeneration cycles, due to the treatment efficacy and its stability as well as the ability to regain the structural features of the unloaded material. Copyright © 2015. Published by Elsevier B.V.

Organ-Protective Effects of Red Wine Extract, Resveratrol, in Oxidative Stress-Mediated Reperfusion Injury

PubMed Central

Liu, Fu-Chao; Tsai, Hsin-I; Yu, Huang-Ping

2015-01-01

Resveratrol, a polyphenol extracted from red wine, possesses potential antioxidative and anti-inflammatory effects, including the reduction of free radicals and proinflammatory mediators overproduction, the alteration of the expression of adhesion molecules, and the inhibition of neutrophil function. A growing body of evidence indicates that resveratrol plays an important role in reducing organ damage following ischemia- and hemorrhage-induced reperfusion injury. Such protective phenomenon is reported to be implicated in decreasing the formation and reaction of reactive oxygen species and pro-nflammatory cytokines, as well as the mediation of a variety of intracellular signaling pathways, including the nitric oxide synthase, nicotinamide adenine dinucleotide phosphate oxidase, deacetylase sirtuin 1, mitogen-activated protein kinase, peroxisome proliferator-activated receptor-gamma coactivator 1 alpha, hemeoxygenase-1, and estrogen receptor-related pathways. Reperfusion injury is a complex pathophysiological process that involves multiple factors and pathways. The resveratrol is an effective reactive oxygen species scavenger that exhibits an antioxidative property. In this review, the organ-protective effects of resveratrol in oxidative stress-related reperfusion injury will be discussed. PMID:26161238

A new biological recovery approach for PHA using mealworm, Tenebrio molitor.

PubMed

Murugan, Paramasivam; Han, Lizhu; Gan, Chee-Yuen; Maurer, Frans H J; Sudesh, Kumar

2016-12-10

Bacterial polyhydroxyalkanoates (PHA) are expensive partly due to the recovery and purification processes. Thus, many studies have been carried out in order to minimize the cost. Here we report on the use of mealworm, which is the larva of mealworm beetle (Tenebrio molitor) to recover PHA granules from Cupriavidus necator. Mealworms were shown to readily consume the freeze-dried C. necator cells and excrete the PHA granules in the form of whitish feces. Further purification using water, detergent and heat resulted in almost 100% pure PHA granules. Comparison with chloroform extraction showed no signs of reduction in the molecular weight and dispersion of the PHA molecules. Scanning electron microscopy and dynamic light scattering measurements revealed that the biologically recovered PHA granules retained their native spherical morphology. The PHA granules were subjected to a battery of tests to determine their purity and properties in comparison to the chloroform extracted PHA. This study has demonstrated the possibility of using mealworms as a biological agent to partially purify the PHA granules. Copyright © 2016 Elsevier B.V. All rights reserved.

Antimicrobial flavonoids isolated from Indian medicinal plant Scutellaria oblonga inhibit biofilms formed by common food pathogens.

PubMed

Rajendran, Narendran; Subramaniam, Shankar; Christena, Lowrence Rene; Muthuraman, Meenakshi Sundaram; Subramanian, Nagarajan Sai; Pemiah, Brindha; Sivasubramanian, Aravind

2016-09-01

Scutellaria oblonga Benth., a hitherto phytochemically unexplored Indian medicinal folklore plant was extracted with acetone and subjected to chromatography to yield nine flavonoids, for the first time from this plant. Antimicrobial assays were performed against 11 foodborne pathogens, and three molecules (Techtochrysin, Negletein and Quercitin-3-glucoside) depicted significant activity. These molecules were assessed for their rate of antibacterial action using time-kill curves which depicted complete inhibition of most of the bacteria within 12-16 h. The significant biofilm-reducing capability exhibited by these three molecules formed a significant finding of the current study. In most of the experiments, a 90-95% reduction in biofilms was observed. Thus, flavonoids as natural molecules from S. oblonga could be further researched to be used as potent antimicrobial and antibiofilm agents.

Single molecule optical measurements of orientation and rotations of biological macromolecules

PubMed Central

Shroder, Deborah Y; Lippert, Lisa G; Goldman, Yale E

2016-01-01

The subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measuring their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, we review the relevant types of probes and labeling techniques, and we highlight the advantages and disadvantages of these technologies for addressing specific inquiries. PMID:28192292

Reverse Transcriptase Activity in Mature Spermatozoa of Mouse

PubMed Central

Giordano, Roberto; Magnano, Anna Rosa; Zaccagnini, Germana; Pittoggi, Carmine; Moscufo, Nicola; Lorenzini, Rodolfo; Spadafora, Corrado

2000-01-01

We show here that a reverse transcriptase (RT) activity is present in murine epididymal spermatozoa. Sperm cells incubated with human poliovirus RNA can take up exogenous RNA molecules and internalize them in nuclei. Direct PCR amplification of DNA extracted from RNA-incubated spermatozoa indicate that poliovirus RNA is reverse-transcribed in cDNA fragments. PCR analysis of two-cell embryos shows that poliovirus RNA-challenged spermatozoa transfer retrotranscribed cDNA molecules into eggs during in vitro fertilization. Finally, RT molecules can be visualized on sperm nuclear scaffolds by immunogold electron microscopy. These results, therefore, reveal a novel metabolic function in spermatozoa, which may play a role during early embryonic development. PMID:10725323

Relativistic and QED Effects in the Fundamental Vibration of T2

NASA Astrophysics Data System (ADS)

Trivikram, T. Madhu; Schlösser, M.; Ubachs, W.; Salumbides, E. J.

2018-04-01

The hydrogen molecule has become a test ground for quantum electrodynamical calculations in molecules. Expanding beyond studies on stable hydrogenic species to the heavier radioactive tritium-bearing molecules, we report on a measurement of the fundamental T2 vibrational splitting (v =0 →1 ) for J =0 - 5 rotational levels. Precision frequency metrology is performed with high-resolution coherent anti-Stokes Raman spectroscopy at an experimental uncertainty of 10-12 MHz, where sub-Doppler saturation features are exploited for the strongest transition. The achieved accuracy corresponds to a 50-fold improvement over a previous measurement, and it allows for the extraction of relativistic and QED contributions to T2 transition energies.

Study on Anticancer Activity of Extracts of Sponges Collected from Biak Water, Indonesia

NASA Astrophysics Data System (ADS)

Trianto, A.; Ridhlo, A.; Triningsih, D. W.; Tanaka, J.

2017-02-01

Indonesia is center of biodiversity where marine sponges are abundant. a source of bioactive compounds with various pharmaceutical properties such as anticancer, antifungal, antibacterial, antioxidants, anti-inflammatory, and anti-malarial. In a continuation of a search for biologically active molecules from marine organisms we investigated the potency of marine sponges as anticancer. A total of 106 sponge specimens were collected between 3-40 m depths by SCUBA diving in Biak waters during August 2005. The specimens were extracted with methanol to provided crude extracts. The methanolic extracts were tested against NBT-T2 cell line. The assay result showed that 8.5 %, 29.2 % and 46.2 % of the extract have activity against the cell line at 0.1, 1.0 and 10.0 μg/mL. While, a 16.0 % of the extract did not showed activity against the cell line.

Streamlining plant sample preparation: the use of high-throughput robotics to process echinacea samples for biomarker profiling by MALDI-TOF mass spectrometry.

PubMed

Greene, Leasa A; Isaac, Issa; Gray, Dean E; Schwartz, Sarah A

2007-09-01

Several species in the genus Echinacea are beneficial herbs popularly used for many ailments. The most popular Echinacea species for cultivation, wild collection, and herbal products include E. purpurea (L.) Moench, E. pallida (Nutt.) Nutt., and E. angustifolia (DC). Product adulteration is a key concern for the natural products industry, where botanical misidentification and introduction of other botanical and nonbotanical contaminants exist throughout the formulation and production process. Therefore, rapid and cost-effective methods that can be used to monitor these materials for complex product purity and consistency are of benefit to consumers and producers. The objective of this continuing research was to develop automated, high-throughput processing methods that, teamed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis, differentiate Echinacea species by their mass profiles. Small molecules, peptide, and proteins from aerial parts (leaf/stem/flowers), seeds, and roots from E. purpurea and E. angustifolia; seeds and roots from E. pallida; and off-the-shelf Echinacea supplements were extracted and analyzed by MS using methods developed on the ProPrep liquid handling system (Genomic Solutions). Analysis of these samples highlighted key MS signal patterns from both small molecules and proteins that characterized the individual Echinacea materials analyzed. Based on analysis of pure Echinacea samples, off-the-shelf products containing Echinacea could then be evaluated in a streamlined process. Corresponding analysis of dietary supplements was used to monitor for product composition, including Echinacea species and plant materials used. These results highlight the potential for streamlined, automated approaches for agricultural species differentiation and botanical product evaluation.

Studying DNA in the Classroom.

ERIC Educational Resources Information Center

Zarins, Silja

1993-01-01

Outlines a workshop for teachers that illustrates a method of extracting DNA and provides instructions on how to do some simple work with DNA without sophisticated and expensive equipment. Provides details on viscosity studies and breaking DNA molecules. (DDR)