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Sample records for biodegradable macromolecular contrast

  1. Liver-targeting macromolecular MRI contrast agents

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Macromolecular ligands with liver-targeting group (pyridoxamine, PM) PHEA-DTPA-PM and PAEA-DTPA-PM were prepared by the incorporation of different amount of diethylenetriaminepentaacetic acid monopyridoxamine group (DTPA-PM) into poly-a, b-[N-(2-hydroxyethyl)-L- aspartamide] (PHEA) and poly-a, b-[N-(2-aminoethyl)-L-aspartamide] (PAEA). The macromolecular ligands thus obtained were further complexed with gadolinium chloride to give macromolecular MRI contrast agents with different Gd(Ⅲ) contents. These macromolecular ligands and their gadolinium complexes were characterized by 1H NMR, IR, UV and elementary analysis. Relaxivity studies showed that these polyaspartamide gadolinium complexes possess higher relaxation effectiveness than that of the clinically used Gd-DTPA. Magnetic resonance imaging of the liver in rats and experimental data of biodistribution in mice indicate that these macromolecular MRI contrast agents containing pyridoxamine exhibit liver-targeting property.

  2. The contrasting effect of macromolecular crowding on amyloid fibril formation.

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    Qian Ma

    Full Text Available BACKGROUND: Amyloid fibrils associated with neurodegenerative diseases can be considered biologically relevant failures of cellular quality control mechanisms. It is known that in vivo human Tau protein, human prion protein, and human copper, zinc superoxide dismutase (SOD1 have the tendency to form fibril deposits in a variety of tissues and they are associated with different neurodegenerative diseases, while rabbit prion protein and hen egg white lysozyme do not readily form fibrils and are unlikely to cause neurodegenerative diseases. In this study, we have investigated the contrasting effect of macromolecular crowding on fibril formation of different proteins. METHODOLOGY/PRINCIPAL FINDINGS: As revealed by assays based on thioflavin T binding and turbidity, human Tau fragments, when phosphorylated by glycogen synthase kinase-3β, do not form filaments in the absence of a crowding agent but do form fibrils in the presence of a crowding agent, and the presence of a strong crowding agent dramatically promotes amyloid fibril formation of human prion protein and its two pathogenic mutants E196K and D178N. Such an enhancing effect of macromolecular crowding on fibril formation is also observed for a pathological human SOD1 mutant A4V. On the other hand, rabbit prion protein and hen lysozyme do not form amyloid fibrils when a crowding agent at 300 g/l is used but do form fibrils in the absence of a crowding agent. Furthermore, aggregation of these two proteins is remarkably inhibited by Ficoll 70 and dextran 70 at 200 g/l. CONCLUSIONS/SIGNIFICANCE: We suggest that proteins associated with neurodegenerative diseases are more likely to form amyloid fibrils under crowded conditions than in dilute solutions. By contrast, some of the proteins that are not neurodegenerative disease-associated are unlikely to misfold in crowded physiological environments. A possible explanation for the contrasting effect of macromolecular crowding on these two sets of

  3. Macromolecular and dendrimer-based magnetic resonance contrast agents

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    Bumb, Ambika; Brechbiel, Martin W. (Radiation Oncology Branch, National Cancer Inst., National Inst. of Health, Bethesda, MD (United States)), e-mail: pchoyke@mail.nih.gov; Choyke, Peter (Molecular Imaging Program, National Cancer Inst., National Inst. of Health, Bethesda, MD (United States))

    2010-09-15

    Magnetic resonance imaging (MRI) is a powerful imaging modality that can provide an assessment of function or molecular expression in tandem with anatomic detail. Over the last 20-25 years, a number of gadolinium-based MR contrast agents have been developed to enhance signal by altering proton relaxation properties. This review explores a range of these agents from small molecule chelates, such as Gd-DTPA and Gd-DOTA, to macromolecular structures composed of albumin, polylysine, polysaccharides (dextran, inulin, starch), poly(ethylene glycol), copolymers of cystamine and cystine with GD-DTPA, and various dendritic structures based on polyamidoamine and polylysine (Gadomers). The synthesis, structure, biodistribution, and targeting of dendrimer-based MR contrast agents are also discussed

  4. Effect of the macromolecular architecture of biodegradable polyurethanes on the controlled delivery of ocular drugs.

    Science.gov (United States)

    da Silva, Gisele Rodrigues; da Silva Cunha, Armando; Ayres, Eliane; Oréfice, Rodrigo L

    2009-02-01

    Controlled delivery of drugs is a major issue in the treatment of ocular diseases, such as in the treatment of uveitis. In this study, dexamethasone acetate, an important type of corticoid used in the treatment of some uveitis, was incorporated into biodegradable polyurethanes (PU) having different macromolecular architectures. The biodegradable polyurethanes were obtained by preparing PU aqueous dispersions having poly(caprolactone) and/or poly(ethylene glycol) as soft segments. The drug was incorporated into the polymer by dissolving it in the PU aqueous dispersion. FTIR results showed the presence of the drug in the polymer with its original chemical structure. Small angle X-ray scattering (SAXS) results were explored to show that the incorporation of dexamethasone acetate led to the modification of the nanostructure of the polyurethane having only poly(caprolactone) as the soft segment, while the drug did not change significantly the microphase separated structure of PU having both poly(caprolactone) and poly(ethylene glycol) as soft segments. The evaluation of the release of the drug in vitro demonstrated that the obtained biodegradable polyurethanes were well succeeded in delivering dexamethasone acetate at an almost constant rate for 53 weeks. The presence of poly(ethylene glycol) together with poly(caprolactone) as soft segment in biodegradable PU was able to increase the rate of dexamethasone acetate release when compared to the rate of drug release from PU having only poly(caprolactone).

  5. β-Cyclodextrin-Based Inclusion Complexation Bridged Biodegradable Self-Assembly Macromolecular Micelle for the Delivery of Paclitaxel.

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    Yanzuo Chen

    Full Text Available In this study, a novel adamantanamine-paclitaxel (AD-PTX incorporated oligochitosan- carboxymethyl-β-cyclodextrin (CSO-g-CM-β-CD self-assembly macromolecular (CSO-g-CM-β-CD@AD-PTX micelle was successfully prepared in water through sonication. The formed molecules were characterized by Fourier transform infrared spectroscopy, proton nuclear magnetic resonance (NMR spectroscopy, two-dimensional NMR, elemental analysis, and liquid chromatography-mass spectrometry, while the correspondent micelles were characterized by dynamic light scattering and transmission electron microscopy. We showed that the macromolecular micelle contained a spherical core-shell structure with a diameter of 197.1 ± 3.3 nm and zeta potential of -19.1 ± 4.3 mV. The CSO-g-CM-β-CD@AD-PTX micelle exhibited a high drug-loading efficacy up to 31.3%, as well as a critical micelle concentration of 3.4 × 10-7 M, which indicated good stability. Additionally, the in vitro release profile of the CSO-g-CM-β-CD@AD-PTX micelle demonstrated a long-term release pattern, 63.1% of AD-PTX was released from the micelle during a 30-day period. Moreover, the CSO-g-CM-β-CD@AD-PTX micelle displayed cytotoxicity at a sub-μM scale similar to PTX in U87 MG cells, and CSO-g-CM-β-CD exhibited a good safety profile by not manifesting significant toxicity at concentrations up to 100 μM. These results indicated that β-CD-based inclusion complexation resulting in biodegradable self-assembled macromolecular micelles can be utilized as nanocarrier, and may provide a promising platform for drug delivery in the future medical applications.

  6. Enhanced conjugation stability and blood circulation time of macromolecular gadolinium-DTPA contrast agent

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    Jenjob, Ratchapol [Department of New Drug Development, School of Medicine, Inha University, 2F A-dong, Jeongseok Bldg., Sinheung-dong 3-ga, Jung-gu, Incheon 400-712 (Korea, Republic of); Kun, Na [Department of Biotechnology, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do 420-743 (Korea, Republic of); Ghee, Jung Yeon [Utah-Inha DDS and Advanced Therapeutics, B-403 Meet-You-All Tower, SongdoTechnopark, 7–50, Songdo-dong, Yeonsu-gu, Incheon 406-840 (Korea, Republic of); Shen, Zheyu; Wu, Xiaoxia [Division of Functional Materials and Nano-Devices, Ningbo Institute of Materials Technology & Engineering (NIMTE), Chinese Academy of Sciences, 519 Zhuangshi Street, Zhenhai District, Ningbo, Zhejiang 315201 (China); Cho, Steve K., E-mail: scho@gist.ac.kr [Division of Liberal Arts and Science, GIST College, Gwangju Institute of Science and Technology, Gwangju 500-712 (Korea, Republic of); Lee, Don Haeng [Utah-Inha DDS and Advanced Therapeutics, B-403 Meet-You-All Tower, SongdoTechnopark, 7–50, Songdo-dong, Yeonsu-gu, Incheon 406-840 (Korea, Republic of); Department of Internal Medicine, School of Medicine, Inha University Hospital, Incheon 420-751 (Korea, Republic of); Yang, Su-Geun, E-mail: Sugeun.Yang@Inha.ac.kr [Department of New Drug Development, School of Medicine, Inha University, 2F A-dong, Jeongseok Bldg., Sinheung-dong 3-ga, Jung-gu, Incheon 400-712 (Korea, Republic of)

    2016-04-01

    In this study, we prepared macromolecular MR T1 contrast agent: pullulan-conjugated Gd diethylene triamine pentaacetate (Gd-DTPA-Pullulan) and estimated residual free Gd{sup 3+}, chelation stability in competition with metal ions, plasma and tissue pharmacokinetics, and abdominal MR contrast on rats. Residual free Gd{sup 3+} in Gd-DTPA-Pullulan was measured using colorimetric spectroscopy. The transmetalation of Gd{sup 3+} incubated with Ca{sup 2+} was performed by using a dialysis membrane (MWCO 100–500 Da) and investigated by ICP-OES. The plasma concentration profiles of Gd-DTPA-Pullulan were estimated after intravenous injection at a dose 0.1 mmol/kg of Gd. The coronal-plane abdominal images of normal rats were observed by MR imaging. The content of free Gd{sup 3+}, the toxic residual form, was less than 0.01%. Chelation stability of Gd-DTPA-Pullulan was estimated, and only 0.2% and 0.00045% of Gd{sup 3+} were released from Gd-DTPA-Pullulan after 2 h incubation with Ca{sup 2+} and Fe{sup 2+}, respectively. Gd-DTPA-Pullulan displayed the extended plasma half-life (t{sub 1/2,α} = 0.43 h, t{sub 1/2,β} = 2.32 h), much longer than 0.11 h and 0.79 h of Gd-EOB-DTPA. Abdominal MR imaging showed Gd-DTPA-Pullulan maintained initial MR contrast for 30 min. The extended plasma half-life of Gd-DTPA-Pullulan probably allows the prolonged MR acquisition time in clinic with enhanced MR contrast. - Highlights: • Macromolecule (pullulan) conjugated Gd contrast agent (Gd-DTPA-Pullulan) showed the extended plasma half-life (t{sub 1/2,α} = 0.43 h, t{sub 1/2,β} = 2.32 h) in comparison with Gd-EOB-DTPA • Gd-DTPA-pullulan T1 contrast agent exhibited strong chelation stability against Gd. • The extended blood circulation attributed the enhanced and prolonged MR contrast on abdominal region of rats. • The extended blood circulation may provide prolonged MR acquisition time window in clinics.

  7. Cellulose nanoparticles: photoacoustic contrast agents that biodegrade to simple sugars

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    Jokerst, Jesse V.; Bohndiek, Sarah E.; Gambhir, Sanjiv S.

    2014-03-01

    In photoacoustic imaging, nanoparticle contrast agents offer strong signal intensity and long-term stability, but are limited by poor biodistribution and clearance profiles. Conversely, small molecules offer renal clearance, but relatively low photoacoustic signal. Here we describe a cellulose-based nanoparticle with photoacoustic signal superior to gold nanorods, but that undergoes enzymatic cleavage into constituent glucose molecules for renal clearance. Cellulose nanoparticles (CNPs) were synthesized through acidic cleavage of cellulose linters and purified with centrifugation. TEM indicated that the nanoparticles were 132 +/- 46 nm; the polydispersity index was 0.138. Ex vivo characterization showed a photoacoustic limit of detection of 0.02 mg/mL CNPs, and the photoacoustic signal of CNPs was 1.5- to 3.0-fold higher than gold nanorods (also at 700 nm resonance) on a particle-to-particle basis. Cell toxicity assays suggested that overnight doses below 0.31 mg/mL CNPs produced no significant (p>0.05) impact on cell metabolism. Intravenous doses up to 0.24 mg were tolerated well in nude mice. Subcutaneous and orthotopic tumor xenografts of the OV2008 ovarian cancer cell line were then created in nude mice. Data was collected with a Nexus128 scanner from Endra LifeSciences. Spectral data used a LAZR system from Visualsonics both at 700 nm excitation. We injected CNPs (0.024 mg, 0.048 mg, and 0.80 mg) via tail vein and showed that the tumor photoacoustic signal reached maximum increase between 10 and 20 minutes. All injected concentrations were statistically (p0.96 suggesting quantitative signal. CNP biodegradation was demonstrated ex vivo with a glucose assay. CNPs in the presence of cellulase were reduced to free glucose in under than four hours. The glucose concentration before addition of cellulase was not detectable, but increased to 92.1 μg/mL in four hours. CNPs in the absence of cellulase did not produce glucose. Small fragments of nanoparticle in the

  8. Synthesis and evaluation of nanoglobule-cystamine-(Gd-DO3A, a biodegradable nanosized magnetic resonance contrast agent for dynamic contrast-enhanced magnetic resonance urography

    Directory of Open Access Journals (Sweden)

    Rongzuo Xu

    2010-09-01

    Full Text Available Rongzuo Xu1, Todd Lyle Kaneshiro1, Eun-Kee Jeong2, Dennis L Parker2, Zheng-Rong Lu31Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT, USA; 2Department of Radiology, University of Utah, Salt Lake City, UT, USA; 3Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USAAbstract: Dynamic contrast-enhanced magnetic resonance imaging has been recently shown to be effective for diagnostic urography. High-resolution urographic images can be acquired with T1 contrast agents for the kidney and urinary tract with minimal noise in the abdomen. Currently, clinical contrast agents are low molecular weight agents and can rapidly extravasate from blood circulation, leading to slow contrast agent elimination through kidney and consequently providing limited contrast enhancement in urinary tract. In this study, a new biodegradable macromolecular contrast agent, nanoglobule-G4-cystamine-(Gd-DO3A, was prepared by conjugating Gd-DO3A chelates on the surface of a generation 4 nanoglobule, poly-l-lysine octa(3-aminopropylsilsesquioxane dendrimer, via a disulfide spacer, where the carrier had a precisely defined nanosize that is far smaller than the renal filtration threshold. The in vivo contrast enhancement and dynamic imaging of the urinary tract of the agent was evaluated in nude mice using a low molecular weight agent Gd(DTPA-BMA as a control. The agent eliminated rapidly from blood circulation and accumulated more abundantly in urinary tract than Gd(DTPA-BMA. The fast elimination kinetics is ideal for functional evaluation of the kidneys. The morphology of the kidneys and urinary tract was better visualized by the biodegradable nanoglobular contrast agent than Gd(DTPA-BMA. The agent also resulted in low liver contrast enhancement, indicating low nonspecific tissue deposition. These features render the G4 nanoglobule-cystamine-(Gd-DO3A conjugate a promising contrast agent for magnetic

  9. Dynamic contrast-enhanced MRI using a macromolecular MR contrast agent (P792): Evaluation of antivascular drug effect in a rabbit VX2 liver tumor model

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    Park, Hee Sun [Dept. of Radiology, Konkuk University School of Medicine, Seoul (Korea, Republic of); Han, Joon Koo; Lee, Jeong Min; Woo, Sung Min; Choi, Byung Ihn [Seoul National University Hospital, Seoul (Korea, Republic of); Kim, Young Il [Dept. of Radiology, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah (United Arab Emirates); Choi, Jin Young [Dept. of Radiology, Yonsei University College of Medicine, Seoul (Korea, Republic of)

    2015-10-15

    To evaluate the utility of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) using macromolecular contrast agent (P792) for assessment of vascular disrupting drug effect in rabbit VX2 liver tumor models. This study was approved by our Institutional Animal Care and Use Committee. DCE-MRI was performed with 3-T scanner in 13 VX2 liver tumor-bearing rabbits, before, 4 hours after, and 24 hours after administration of vascular disrupting agent (VDA), using gadomelitol (P792, n = 7) or low molecular weight contrast agent (gadoterate meglumine [Gd-DOTA], n = 6). P792 was injected at a of dose 0.05 mmol/kg, while that of Gd-DOTA was 0.2 mmol/kg. DCE-MRI parameters including volume transfer coefficient (Ktrans) and initial area under the gadolinium concentration-time curve until 60 seconds (iAUC) of tumors were compared between the 2 groups at each time point. DCE-MRI parameters were correlated with tumor histopathology. Reproducibility in measurement of DCE-MRI parameters and image quality of source MR were compared between groups. P792 group showed a more prominent decrease in Ktrans and iAUC at 4 hours and 24 hours, as compared to the Gd-DOTA group. Changes in DCE-MRI parameters showed a weak correlation with histologic parameters (necrotic fraction and microvessel density) in both groups. Reproducibility of DCE-MRI parameters and overall image quality was not significantly better in the P792 group, as compared to the Gd-DOTA group. Dynamic contrast-enhanced magnetic resonance imaging using a macromolecular contrast agent shows changes of hepatic perfusion more clearly after administration of the VDA. Gadolinium was required at smaller doses than a low molecular contrast agent.

  10. Investigation of a potential macromolecular MRI contrast agent prepared from PPI (G = 2, polypropyleneimine, generation 2) dendrimer bifunctional chelates

    Science.gov (United States)

    Wang, Jianxin Steven

    The long-term objective is to develop magnetic resonance (MR) contrast agents that actively and passively target tumors for diagnosis and therapy. Many diagnostic imaging techniques for cancer lack specificity. A dendrimer based magnetic resonance imaging contrast agent has been developed with large proton relaxation enhancements and high molecular relaxivities. A new type of linear dendrimer based MRI contrast agent that is built from the polypropyleneimine and polyamidoamine dendrimers in which free amines have been conjugated to the chelate DTPA, which further formed the complex with Gadolinium (Gd) was studied. The specific research goals were to test the hypothesis that a linear chelate with macromolecular agents can be used in vitro and in vivo. This work successfully examined the adequacy and viability of the application for this agent in vitro and in vivo. A small animal whole body counter was designed and constructed to allow us to monitor biodistribution and kinetic mechanisms using a radioisotope labeled complex. The procedures of metal labeling, separation and purification have been established from this work. A biodistribution study has been performed using radioisotope induced organ/tissue counting and gamma camera imaging. The ratio of percentage of injected dose per gram organ/tissue for kidney and liver is 3.71 from whole body counter and 3.77 from the gamma camera. The results suggested that retention of Gd (III) is too high and a more kinetically stable chelate should be developed. The pharmacokinetic was evaluated in the whole animal model with the whole body clearance, and a kinetics model was developed. The pharmacokinetic results showed a bi-exponential decay in the animal model with two component excretion constants 1.43e(-5) and 0.0038511, which give half-lives of 3 hours and 33.6 days, respectively. Magnetic resonance imaging of this complex resulted in a 52% contrast enhancement in the rat kidney following the agents' administration in

  11. A new biodegradable and biocompatible gadolinium (III) -polymer for liver magnetic resonance imaging contrast agent.

    Science.gov (United States)

    Xiao, Yan; Xue, Rong; You, Tianyan; Li, Xiaojing; Pei, Fengkui

    2015-07-01

    A new biodegradable and biocompatible gadolinium (III) -copolymer (ACL-A2-DOTA-Gd) has been developed as a potential liver magnetic resonance imaging (MRI) contrast agent. ACL-A2-DOTA-Gd consisted of a poly (aspartic acid-co-leucine) unit bound with 1,4,7,10-tetraazacyclododecan-1,4,7,10-tetraacetic acid-gadolinium (Gd-DOTA) via the linkage of ethylenediamine. In vitro, the biodegradable experiment and cytotoxicity assay showed the biodegradability and biocompatibility of this gadolinium-polymer. ACL-A2-DOTA-Gd presented an increase in relaxivity of 2.4 times than the clinical Gd-DOTA. In vivo, gadolinium (III)-copolymer was mainly accumulated in the liver, and it could be excreted via the renal and hepatobiliary mechanism. The average enhancement of ACL-A2-DOTA-Gd (60.71±5.93%, 50-80 min) in liver was 2.62-fold greater than that of Gd-DOTA (23.16±3.55%, 10-30 min). ACL-A2-DOTA-Gd could be as a potential liver MRI contrast agent with a long time-window.

  12. Stimuli-Responsive Biodegradable Hyperbranched Polymer-Gadolinium Conjugates as Efficient and Biocompatible Nanoscale Magnetic Resonance Imaging Contrast Agents.

    Science.gov (United States)

    Sun, Ling; Li, Xue; Wei, Xiaoli; Luo, Qiang; Guan, Pujun; Wu, Min; Zhu, Hongyan; Luo, Kui; Gong, Qiyong

    2016-04-27

    The efficacy and biocompatibility of nanoscale magnetic resonance imaging (MRI) contrast agents depend on optimal molecular structures and compositions. Gadolinium [Gd(III)] based dendritic macromolecules with well-defined and tunable nanoscale sizes are excellent candidates as multivalent MRI contrast agents. Here, we propose a novel alternate preparation of biodegradable hyperbranched polymer-gadolinium conjugates via a simple strategy and report potentially efficient and biocompatible nanoscale MRI contrast agents for cancer diagnosis. The enzyme-responsive hyperbranched poly(oligo-(ethylene glycol) methacrylate)-gadolinium conjugate (HB-POEGMA-Gd) was prepared via one-step reversible addition-fragmentation chain transfer (RAFT) polymerization and Gd(III) chelating, and the cRGDyK functionalized polymer (HB-POEGMA-cRGD-Gd) was obtained via click chemistry. By using an enzyme similar to lysosomal cathepsin B, hyperbranched conjugates of high molecular weights (MW) (180 and 210 kDa) and nanoscale sizes (38 and 42 nm) were degraded into low MW (25 and 30 kDa) and smaller products (4.8 and 5.2 nm) below the renal threshold. Conjugate-based nanoscale systems had three-fold more T1 relaxivity compared to clinical agent diethylenediaminepentaacetic acid (DTPA)-Gd. Animal studies with the nanoscale system offered greater tumor accumulation and enhanced signal intensity (SI) in mouse U87 tumors of which the greatest activity was conferred by the cRGDyK moiety functionalized hyperbranched conjugate. In vitro cytotoxicity, hemocompatibility and in vivo toxicity studies confirmed no adverse events. This design strategy for multifunctional Gd(III)-labeled biodegradable dendritic macromolecules may have significant potential as future efficient, biocompatible polymeric nanoscale MRI diagnostic contrast agents for cancer.

  13. Novel ultrasound contrast agents--Biodegradable poly(lactic acid) microcapsules

    Institute of Scientific and Technical Information of China (English)

    王身国; 崔文瑾; 李光明; 蔡晴; 智光; 赵玉英; 杨波; 徐勇

    2003-01-01

    As a novel ultrasound diagnostic contrast agent, the preparation, characterization and ultrasound imaging in the body of dog about poly(lactic acid) (PLLA) microcapsules have been studied. The behavior of this kind of contrast agent in the microcirculation was also investigated. Prepared by (water/oil/water) emulsion-solvent evaporation protocol, the PLLA microcapsules with hollow structure can enhance the ultrasound image both in vitro and in vivo, and the enduring time can last as long as 3 h. The microcirculation examination shows that the PLLA microcapsules with a diameter ranging from 2 to 8 μm could pass through the pulmonary capillaries without retention. All the results prove the PLLA microcapsules for potential use for the clinical application.

  14. Preparation and initial characterization of biodegradable particles containing gadolinium-DTPA contrast agent for enhanced MRI

    Science.gov (United States)

    Doiron, Amber L.; Chu, Kevin; Ali, Adeel; Brannon-Peppas, Lisa

    2008-01-01

    Accurate imaging of atherosclerosis is a growing necessity for timely treatment of the disease. Magnetic resonance imaging (MRI) is a promising technique for plaque imaging. The goal of this study was to create polymeric particles of a small size with high loading of diethylenetriaminepentaacetic acid gadolinium (III) (Gd-DTPA) and demonstrate their usefulness for MRI. A water-in-oil-in-oil double emulsion solvent evaporation technique was used to encapsulate the MRI agent in a poly(lactide-co-glycolide) (PLGA) or polylactide-poly(ethylene glycol) (PLA-PEG) particle for the purpose of concentrating the agent at an imaging site. PLGA particles with two separate average sizes of 1.83 μm and 920 nm, and PLA-PEG particles with a mean diameter of 952 nm were created. Loading of up to 30 wt % Gd-DTPA was achieved, and in vitro release occurred over 5 h. PLGA particles had highly negative zeta potentials, whereas the particles incorporating PEG had zeta potentials closer to neutral. Cytotoxicity of the particles on human umbilical vein endothelial cells (HUVEC) was shown to be minimal. The ability of the polymeric contrast agent formulation to create contrast was similar to that of Gd-DTPA alone. These results demonstrate the possible utility of the contrast agent-loaded polymeric particles for plaque detection with MRI. PMID:18796605

  15. Separation and characterization of the two diastereomers for [Gd(DTPA-bz-NH2)(H2O)]2-, a common synthon in macromolecular MRI contrast agents: their water exchange and isomerization kinetics.

    Science.gov (United States)

    Burai, László; Tóth, Eva; Sour, Angélique; Merbach, André E

    2005-05-16

    Chiral, bifunctional poly(amino carboxylate) ligands are commonly used for the synthesis of macromolecular, Gd(III)-based MRI contrast agents, prepared in the objective of increasing relaxivity or delivering the paramagnetic Gd(III) to a specific site (targeting). Complex formation with such ligands results in two diastereomeric forms for the complex which can be separated by HPLC. We demonstrated that the diastereomer ratio for Ln(III) DTPA derivatives (approximately 60:40) remains constant throughout the lanthanide series, in contrast to Ln(III) EPTPA derivatives, where it varies as a function of the cation size with a maximum for the middle lanthanides (DTPA(5-) = diethylenetriaminepentaacetate; EPTPA(5-) = ethylenepropylenetriaminepentaacetate). The interconversion of the two diastereomers, studied by HPLC, is a proton-catalyzed process (k(obs) = k(1)[H(+)]). It is relatively fast for [Gd(EPTPA-bz-NH(2))(H(2)O)](2-) but slow enough for [Gd(DTPA-bz-NH(2))(H(2)O)](2-) to allow investigation of pure individual isomers (isomerization rate constants are k(1) = (3.03 +/- 0.07) x 10(4) and 11.6 +/- 0.5 s(-1) M(-1) for [Gd(EPTPA-bz-NH(2))(H(2)O)](2)(-) and [Gd(DTPA-bz-NH(2))(H(2)O)](2-), respectively). Individual water exchange rates have been determined for both diastereomers of [Gd(DTPA-bz-NH(2))(H(2)O)](2-) by a variable-temperature (17)O NMR study. Similarly to Ln(III) EPTPA derivatives, k(ex) values differ by a factor of 2 (k(ex)(298) = (5.7 +/- 0.2) x 10(6) and (3.1 +/- 0.1) x 10(6) s(-1)). This variance in the exchange rate has no consequence on the proton relaxivity of the two diastereomers, since it is solely limited by fast rotation. However, such difference in k(ex) will affect proton relaxivity when these diastereomers are linked to a slowly rotating macromolecule. Once the rotation is optimized, slow water exchange will limit relaxivity; thus, a factor of 2 in the exchange rate can lead to a remarkably different relaxivity for the diastereomer complexes

  16. CONTRAST

    DEFF Research Database (Denmark)

    Kristensen, Thomas Krogsgaard

    2007-01-01

    Dette er en afrapportering fra den årlige CONTRAST workshop, der i 2007 blev afholdt i Yaoundé, Cameroon.......Dette er en afrapportering fra den årlige CONTRAST workshop, der i 2007 blev afholdt i Yaoundé, Cameroon....

  17. X-ray phase-contrast computed tomography visualizes the microstructure and degradation profile of implanted biodegradable scaffolds after spinal cord injury

    Energy Technology Data Exchange (ETDEWEB)

    Takashima, Kenta, E-mail: takashima-k@med.tohoku.ac.jp [Tohoku University Graduate School of Medicine, Sendai (Japan); University of Tokyo, Tokyo (Japan); Hoshino, Masato; Uesugi, Kentaro; Yagi, Naoto [SPring-8, Hyogo (Japan); Matsuda, Shojiro [Gunze Limited, Shiga (Japan); Nakahira, Atsushi [Osaka Prefecture University, Osaka (Japan); Osumi, Noriko; Kohzuki, Masahiro [Tohoku University Graduate School of Medicine, Sendai (Japan); Onodera, Hiroshi [University of Tokyo, Tokyo (Japan)

    2015-01-01

    X-ray phase-contrast computed tomography imaging based on the Talbot grating interferometer is described, and the way it can visualize the polyglycolic acid scaffold, including its microfibres, after implantation into the injured spinal cord is shown. Tissue engineering strategies for spinal cord repair are a primary focus of translational medicine after spinal cord injury (SCI). Many tissue engineering strategies employ three-dimensional scaffolds, which are made of biodegradable materials and have microstructure incorporated with viable cells and bioactive molecules to promote new tissue generation and functional recovery after SCI. It is therefore important to develop an imaging system that visualizes both the microstructure of three-dimensional scaffolds and their degradation process after SCI. Here, X-ray phase-contrast computed tomography imaging based on the Talbot grating interferometer is described and it is shown how it can visualize the polyglycolic acid scaffold, including its microfibres, after implantation into the injured spinal cord. Furthermore, X-ray phase-contrast computed tomography images revealed that degradation occurred from the end to the centre of the braided scaffold in the 28 days after implantation into the injured spinal cord. The present report provides the first demonstration of an imaging technique that visualizes both the microstructure and degradation of biodegradable scaffolds in SCI research. X-ray phase-contrast imaging based on the Talbot grating interferometer is a versatile technique that can be used for a broad range of preclinical applications in tissue engineering strategies.

  18. Macromolecular Prodrugs of Ribavirin

    DEFF Research Database (Denmark)

    Riber, Camilla Frich; Hinton, Tracey M; Gajda, Paulina

    2017-01-01

    The requirement for new antiviral therapeutics is an ever present need. Particularly lacking are broad spectrum antivirals that have low toxicity. We develop such agents based on macromolecular prodrugs whereby both the polymer chain and the drug released from the polymer upon cell entry have ant...

  19. Liver-targeting macromolecular MRI contrast agents

    Institute of Scientific and Technical Information of China (English)

    XU; Mianyi

    2001-01-01

    Chitosans with various degrees of deacetylation (D.D.), which were used as standard sample for FTIR determination, were prepared from completely deacetylated chitosan by homogeneous N-acetylation reaction. By combining four probable probe bands, i.e. 1655, 1560, 1380 and 1320 cm-1, eight probable reference bands, i.e. 3430, 2920, 2880, 1425, 1155, 1070, 1030 and 895 cm-1 and two baseline methods, the most suitable ratios Aprobe band/Areference band from IR spectra to determine the degree of acetylation of chitosan were evaluated from 48 combinations to be A1560/A2880, A1560/A2920 and A1655/A3430(A1560/A2880 is mostly recommended). The second baseline method, i.e. linking between adjacent two valleys, was better for measuring the absorbances of 1560 and 1655 cm-1 bands. The determination range of the D.D. (1%-100%) covered almost the whole range. The standard curves with A1560/A2880 and A1655/A3430 were also suitable for the determination of degree of substitution of other N-acylated chitosan, such as N-propionyl chitosan, N-butyryl chitosan and N-hexanoyl chitosan.

  20. Macromolecular Crystallization in Microgravity

    Science.gov (United States)

    Snell, Edward H.; Helliwell, John R.

    2004-01-01

    The key concepts that attracted crystal growers, macromolecular or solid state, to microgravity research is that density difference fluid flows and sedimentation of the growing crystals are greatly reduced. Thus, defects and flaws in the crystals can be reduced, even eliminated, and crystal volume can be increased. Macromolecular crystallography differs from the field of crystalline semiconductors. For the latter, crystals are harnessed for their electrical behaviors. A crystal of a biological macromolecule is used instead for diffraction experiments (X-ray or neutron) to determine the three-dimensional structure of the macromolecule. The better the internal order of the crystal of a biological macromolecule then the more molecular structure detail that can be extracted. This structural information that enables an understanding of how the molecule functions. This knowledge is changing the biological and chemical sciences with major potential in understanding disease pathologies. Macromolecular structural crystallography in general is a remarkable field where physics, biology, chemistry, and mathematics meet to enable insight to the basic fundamentals of life. In this review, we examine the use of microgravity as an environment to grow macromolecular crystals. We describe the crystallization procedures used on the ground, how the resulting crystals are studied and the knowledge obtained from those crystals. We address the features desired in an ordered crystal and the techniques used to evaluate those features in detail. We then introduce the microgravity environment, the techniques to access that environment, and the theory and evidence behind the use of microgravity for crystallization experiments. We describe how ground-based laboratory techniques have been adapted to microgravity flights and look at some of the methods used to analyze the resulting data. Several case studies illustrate the physical crystal quality improvements and the macromolecular structural

  1. Macromolecular crystallization in microgravity

    Energy Technology Data Exchange (ETDEWEB)

    Snell, Edward H [Biophysics Group, NASA Marshall Space Flight Center, Code XD42, Huntsville, AL 35812 (United States); Helliwell, John R [Department of Chemistry, The University of Manchester, Manchester, M13 9PL (United Kingdom)

    2005-04-01

    Density difference fluid flows and sedimentation of growing crystals are greatly reduced when crystallization takes place in a reduced gravity environment. In the case of macromolecular crystallography a crystal of a biological macromolecule is used for diffraction experiments (x-ray or neutron) so as to determine the three-dimensional structure of the macromolecule. The better the internal order of the crystal then the greater the molecular structure detail that can be extracted. It is this structural information that enables an understanding of how the molecule functions. This knowledge is changing the biological and chemical sciences, with major potential in understanding disease pathologies. In this review, we examine the use of microgravity as an environment to grow macromolecular crystals. We describe the crystallization procedures used on the ground, how the resulting crystals are studied and the knowledge obtained from those crystals. We address the features desired in an ordered crystal and the techniques used to evaluate those features in detail. We then introduce the microgravity environment, the techniques to access that environment and the theory and evidence behind the use of microgravity for crystallization experiments. We describe how ground-based laboratory techniques have been adapted to microgravity flights and look at some of the methods used to analyse the resulting data. Several case studies illustrate the physical crystal quality improvements and the macromolecular structural advances. Finally, limitations and alternatives to microgravity and future directions for this research are covered. Macromolecular structural crystallography in general is a remarkable field where physics, biology, chemistry and mathematics meet to enable insight to the fundamentals of life. As the reader will see, there is a great deal of physics involved when the microgravity environment is applied to crystallization, some of it known, and undoubtedly much yet to

  2. Microgravity and Macromolecular Crystallography

    Science.gov (United States)

    Kundrot, Craig E.; Judge, Russell A.; Pusey, Marc L.; Snell, Edward H.; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    Macromolecular crystal growth has been seen as an ideal experiment to make use of the reduced acceleration environment provided by an orbiting spacecraft. The experiments are small, simply operated and have a high potential scientific and economic impact. In this review we examine the theoretical reasons why microgravity should be a beneficial environment for crystal growth and survey the history of experiments on the Space Shuttle Orbiter, on unmanned spacecraft, and on the Mir space station. Finally we outline the direction for optimizing the future use of orbiting platforms.

  3. Biodegradable human serum albumin nanoparticles as contrast agents for the detection of hepatocellular carcinoma by magnetic resonance imaging.

    Science.gov (United States)

    Watcharin, Waralee; Schmithals, Christian; Pleli, Thomas; Köberle, Verena; Korkusuz, Hüdayi; Huebner, Frank; Zeuzem, Stefan; Korf, Hans W; Vogl, Thomas J; Rittmeyer, Claudia; Terfort, Andreas; Piiper, Albrecht; Gelperina, Svetlana; Kreuter, Jörg

    2014-05-01

    Tumor visualization by magnetic resonance imaging (MRI) and nanoparticle-based contrast agents may improve the imaging of solid tumors such as hepatocellular carcinoma (HCC). In particular, human serum albumin (HSA) nanoparticles appear to be a suitable carrier due to their safety and feasibility of functionalization. In the present study HSA nanoparticles were conjugated with gadolinium diethylenetriaminepentaacetic acid (Gd-DTPA) using carbodiimide chemistry. The nanoparticles had a uniform spherical shape and a diameter of 235±19nm. For better optical visualization in vitro and in vivo, the HSA-Gd nanoparticles were additionally labeled with rhodamine 123. As shown by confocal microscopy and flow cytometry analysis, the fluorescent nanoparticles were readily taken up by Huh-7 hepatocellular carcinoma cells. After 24h incubation in blood serum, less than 5% of the Gd(III) was released from the particles, which suggests that this nanoparticulate system may be stable in vivo and, therefore, may serve as potentially safe T1 MRI contrast agent for MRI of hepatocellular carcinoma.

  4. Macromolecular diffusion in self-assembling biodegradable thermosensitive hydrogels

    NARCIS (Netherlands)

    Vermonden, T.; Jena, S.S.; Barriet, D.; Censi, R.; Gucht, van der J.; Hennink, W.E.; Siegel, R.A.

    2010-01-01

    Hydrogel formation triggered by a change in temperature is an attractive mechanism for in situ gelling biomaterials for pharmaceutical applications such as the delivery of therapeutic proteins. In this study, hydrogels were prepared from ABA triblock polymers having thermosensitive poly(N-(2-hydroxy

  5. Generating triangulated macromolecular surfaces by Euclidean Distance Transform.

    Directory of Open Access Journals (Sweden)

    Dong Xu

    Full Text Available Macromolecular surfaces are fundamental representations of their three-dimensional geometric shape. Accurate calculation of protein surfaces is of critical importance in the protein structural and functional studies including ligand-protein docking and virtual screening. In contrast to analytical or parametric representation of macromolecular surfaces, triangulated mesh surfaces have been proved to be easy to describe, visualize and manipulate by computer programs. Here, we develop a new algorithm of EDTSurf for generating three major macromolecular surfaces of van der Waals surface, solvent-accessible surface and molecular surface, using the technique of fast Euclidean Distance Transform (EDT. The triangulated surfaces are constructed directly from volumetric solids by a Vertex-Connected Marching Cube algorithm that forms triangles from grid points. Compared to the analytical result, the relative error of the surface calculations by EDTSurf is <2-4% depending on the grid resolution, which is 1.5-4 times lower than the methods in the literature; and yet, the algorithm is faster and costs less computer memory than the comparative methods. The improvements in both accuracy and speed of the macromolecular surface determination should make EDTSurf a useful tool for the detailed study of protein docking and structure predictions. Both source code and the executable program of EDTSurf are freely available at http://zhang.bioinformatics.ku.edu/EDTSurf.

  6. Macromolecular architectures for organic photovoltaics.

    Science.gov (United States)

    Popere, Bhooshan C; Della Pelle, Andrea M; Poe, Ambata; Thayumanavan, S

    2012-03-28

    Research in the field of organic photovoltaics has gained considerable momentum in the last two decades owing to the need for developing low-cost and efficient energy harvesting systems. Elegant molecular architectures have been designed, synthesized and employed as active materials for photovoltaic devices thereby leading to a better molecular structure-device property relationship understanding. In this perspective, we outline new macromolecular scaffolds that have been designed within the purview of each of the three fundamental processes involving light harvesting, charge separation and charge transport.

  7. Biodegradable Polymers

    Directory of Open Access Journals (Sweden)

    Isabelle Vroman

    2009-04-01

    Full Text Available Biodegradable materials are used in packaging, agriculture, medicine and other areas. In recent years there has been an increase in interest in biodegradable polymers. Two classes of biodegradable polymers can be distinguished: synthetic or natural polymers. There are polymers produced from feedstocks derived either from petroleum resources (non renewable resources or from biological resources (renewable resources. In general natural polymers offer fewer advantages than synthetic polymers. The following review presents an overview of the different biodegradable polymers that are currently being used and their properties, as well as new developments in their synthesis and applications.

  8. Data Mining of Macromolecular Structures.

    Science.gov (United States)

    van Beusekom, Bart; Perrakis, Anastassis; Joosten, Robbie P

    2016-01-01

    The use of macromolecular structures is widespread for a variety of applications, from teaching protein structure principles all the way to ligand optimization in drug development. Applying data mining techniques on these experimentally determined structures requires a highly uniform, standardized structural data source. The Protein Data Bank (PDB) has evolved over the years toward becoming the standard resource for macromolecular structures. However, the process selecting the data most suitable for specific applications is still very much based on personal preferences and understanding of the experimental techniques used to obtain these models. In this chapter, we will first explain the challenges with data standardization, annotation, and uniformity in the PDB entries determined by X-ray crystallography. We then discuss the specific effect that crystallographic data quality and model optimization methods have on structural models and how validation tools can be used to make informed choices. We also discuss specific advantages of using the PDB_REDO databank as a resource for structural data. Finally, we will provide guidelines on how to select the most suitable protein structure models for detailed analysis and how to select a set of structure models suitable for data mining.

  9. Emergent Property in Macromolecular Motion

    Institute of Scientific and Technical Information of China (English)

    吴嘉麟

    2003-01-01

    In this paper, the model of inverse cascade fractal super-blocks along one direction (in the positive or negative) in the 3-dimensional space is developed to describe the self-similar motion in macromolecular system. Microscopically the cohesive and dispersed states of the motion blocks are co-existent states with vastly different probability of occurrence.Experimental results and theoretical analysis show that the microscopic cohesive state energy and dispersed state energy of each motion block are respectively equal to the macroscopic glassy state energy kT8 and molten state energy kTm of the system. This singularity unveils topologically the nonintegrability, mathematically the anholonomy, and macroscopically the emergent property. This singularity also reveals that the glass, viscoelastic and melt states are three distinct emergent properties of macromolecular motion from a macroscopic viewpoint. The fractal concept of excluded volume is introduced to depict the random motion at various scales in the system. The Hausdorff dimensions of the excluded volune and the motion blocks are both found equal to 3/2.

  10. Phase Sensitive X-Ray Diffraction Imaging of Defects in Biological Macromolecular Crystals

    Science.gov (United States)

    Hu, Z. W.; Lai, B.; Chu, Y. S.; Cai, Z.; Mancini, D. C.; Thomas, B. R.; Chernov, A. A.; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    Characterization of defects and/or disorder in biological macromolecular crystals presents much greater challenges than in conventional small-molecule crystals. The lack of sufficient contrast of defects is often a limiting factor in x-ray diffraction topography of protein crystals. This has seriously hampered efforts to understand mechanisms and origins of formation of imperfections, and the role of defects as essential entities in the bulk of macromolecular crystals. In this report, we employ a phase sensitive x-ray diffraction imaging approach for augmenting the contrast of defects in protein crystals.

  11. Automated data collection for macromolecular crystallography.

    Science.gov (United States)

    Winter, Graeme; McAuley, Katherine E

    2011-09-01

    An overview, together with some practical advice, is presented of the current status of the automation of macromolecular crystallography (MX) data collection, with a focus on MX beamlines at Diamond Light Source, UK.

  12. Energy transfer in macromolecular arrays

    Science.gov (United States)

    Andrews, David L.; Jenkins, Robert D.

    2003-11-01

    Macromolecular systems comprised of many light-sensitive centres (the photosynthetic unit, dendrimers, and other highly symmetric multichromophore arrays) are important structures offering challenges to theoreticians and synthetic chemists alike. Here we outline novel photophysical interactions predicted and observed in such arrays. Using the tools of molecular quantum electrodynamics (QED) we present quantum amplitudes for a variety of higher-order resonance energy transfer (RET) schemes associated with well-known nonlinear optical effects such as two- and three-photon absorption. The initial analysis is extended to account for situations where the participant donor species are identical and exist in a highly symmetric environment, leading to the possible formation of excitons. It emerges from the QED theory that such excitons are closely associated with the higher-order RET processes. General results are interpreted by analyzing particular molecular architectures which offer interesting features such as rate enhancement or limitation and exciton pathway quenching. Applications in the areas of photosynthesis, molecular logic gates and low-intensity fluorescence energy transfer are predicted.

  13. Effects of macromolecular crowding on genetic networks.

    Science.gov (United States)

    Morelli, Marco J; Allen, Rosalind J; Wolde, Pieter Rein ten

    2011-12-21

    The intracellular environment is crowded with proteins, DNA, and other macromolecules. Under physiological conditions, macromolecular crowding can alter both molecular diffusion and the equilibria of bimolecular reactions and therefore is likely to have a significant effect on the function of biochemical networks. We propose a simple way to model the effects of macromolecular crowding on biochemical networks via an appropriate scaling of bimolecular association and dissociation rates. We use this approach, in combination with kinetic Monte Carlo simulations, to analyze the effects of crowding on a constitutively expressed gene, a repressed gene, and a model for the bacteriophage λ genetic switch, in the presence and absence of nonspecific binding of transcription factors to genomic DNA. Our results show that the effects of crowding are mainly caused by the shift of association-dissociation equilibria rather than the slowing down of protein diffusion, and that macromolecular crowding can have relevant and counterintuitive effects on biochemical network performance.

  14. Macromolecular mimicry of nucleic acid and protein

    DEFF Research Database (Denmark)

    Nautrup Pedersen, Gitte; Nyborg, Jens; Clark, Brian F

    1999-01-01

    of the concept of macromolecular mimicry. Macromolecular mimicry has further been proposed among initiation and release factors, thereby adding a new element to the description of protein synthesis in bacteria. Such mimicry has also been observed in other biological processes such as autoimmunity, DNA repair......Although proteins and nucleic acids consist of different chemical components, proteins can mimic structures and possibly also functions of nucleic acids. Recently, structural mimicry was observed between two elongation factors in bacterial protein biosynthesis leading to the introduction...

  15. New concepts and applications in the macromolecular chemistry of fullerenes.

    Science.gov (United States)

    Giacalone, Francesco; Martín, Nazario

    2010-10-08

    A new classification on the different types of fullerene-containing polymers is presented according to their different properties and applications they exhibit in a variety of fields. Because of their interest and novelty, water-soluble and biodegradable C(60)-polymers are discussed first, followed by polyfullerene-based membranes where unprecedented supramolecular structures are presented. Next are compounds that involve hybrid materials formed from fullerenes and other components such as silica, DNA, and carbon nanotubes (CNTs) where the most recent advances have been achieved. A most relevant topic is still that of C(60)-based donor-acceptor (D-A) polymers. Since their application in photovoltaics D-A polymers are among the most realistic applications of fullerenes in the so-called molecular electronics. The most relevant aspects in these covalently connected fullerene/polymer hybrids as well as new concepts to improve energy conversion efficiencies are presented.The last topics disccused relate to supramolecular aspects that are in involved in C(60)-polymer systems and in the self-assembly of C(60)-macromolecular structures, which open a new scenario for organizing, by means of non-covalent interactions, new supramolecular structures at the nano- and micrometric scale, in which the combination of the hydrofobicity of fullerenes with the versatility of the noncovalent chemistry afford new and spectacular superstructures.

  16. Anaerobic biodegradability of macropollutants

    DEFF Research Database (Denmark)

    Angelidaki, Irini

    2002-01-01

    A variety of test procedures for determination of anaerobic biodegradability has been reported. This paper reviews the methods developed for determination of anaerobic biodegradability of macro-pollutants. Anaerobic biodegradability of micro-pollutants is not included. Furthermore, factors import...

  17. Biodegradation and bioremediation

    DEFF Research Database (Denmark)

    Albrechtsen, H.-J.

    1996-01-01

    Anmeldelse af Alexander,M.: Biodegradation and bioremediation. Academic Press, Sandiego, USA, 1994......Anmeldelse af Alexander,M.: Biodegradation and bioremediation. Academic Press, Sandiego, USA, 1994...

  18. In situ macromolecular crystallography using microbeams.

    Science.gov (United States)

    Axford, Danny; Owen, Robin L; Aishima, Jun; Foadi, James; Morgan, Ann W; Robinson, James I; Nettleship, Joanne E; Owens, Raymond J; Moraes, Isabel; Fry, Elizabeth E; Grimes, Jonathan M; Harlos, Karl; Kotecha, Abhay; Ren, Jingshan; Sutton, Geoff; Walter, Thomas S; Stuart, David I; Evans, Gwyndaf

    2012-05-01

    Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side-stepped. Using a dedicated goniometer installed on the microfocus macromolecular crystallography beamline I24 at Diamond Light Source, crystals have been studied in situ with an intense and flexible microfocus beam, allowing weakly diffracting samples to be assessed without a manual crystal-handling step but with good signal to noise, despite the background scatter from the plate. A number of case studies are reported: the structure solution of bovine enterovirus 2, crystallization screening of membrane proteins and complexes, and structure solution from crystallization hits produced via a high-throughput pipeline. These demonstrate the potential for in situ data collection and structure solution with microbeams.

  19. Growth and dissolution of macromolecular Markov chains

    CERN Document Server

    Gaspard, Pierre

    2016-01-01

    The kinetics and thermodynamics of free living copolymerization are studied for processes with rates depending on k monomeric units of the macromolecular chain behind the unit that is attached or detached. In this case, the sequence of monomeric units in the growing copolymer is a kth-order Markov chain. In the regime of steady growth, the statistical properties of the sequence are determined analytically in terms of the attachment and detachment rates. In this way, the mean growth velocity as well as the thermodynamic entropy production and the sequence disorder can be calculated systematically. These different properties are also investigated in the regime of depolymerization where the macromolecular chain is dissolved by the surrounding solution. In this regime, the entropy production is shown to satisfy Landauer's principle.

  20. Growth and Dissolution of Macromolecular Markov Chains

    Science.gov (United States)

    Gaspard, Pierre

    2016-07-01

    The kinetics and thermodynamics of free living copolymerization are studied for processes with rates depending on k monomeric units of the macromolecular chain behind the unit that is attached or detached. In this case, the sequence of monomeric units in the growing copolymer is a kth-order Markov chain. In the regime of steady growth, the statistical properties of the sequence are determined analytically in terms of the attachment and detachment rates. In this way, the mean growth velocity as well as the thermodynamic entropy production and the sequence disorder can be calculated systematically. These different properties are also investigated in the regime of depolymerization where the macromolecular chain is dissolved by the surrounding solution. In this regime, the entropy production is shown to satisfy Landauer's principle.

  1. Dextran: A promising macromolecular drug carrier

    Directory of Open Access Journals (Sweden)

    Dhaneshwar Suneela

    2006-01-01

    Full Text Available Over the past three decades intensive efforts have been made to design novel systems able to deliver the drug more effectively to the target site. The ongoing intense search for novel and innovative drug delivery systems is predominantly a consequence of the well-established fact that the conventional dosage forms are not sufficiently effective in conveying the drug compound to its site of action and once in the target area, in releasing the active agent over a desired period of time. The potential use of macromolecular prodrugs as a means of achieving targeted drug delivery has attracted considerable interest in recent years. Macromolecules such as antibodies, lipoproteins, lectins, proteins, polypeptides, polysaccharides, natural as well as synthetic polymers offer potential applicabilities as high molecular weight carriers for various therapeutically active compounds. Dextrans serve as one of the most promising macromolecular carrier candidates for a wide variety of therapeutic agents due to their excellent physico-chemical properties and physiological acceptance. The present contribution attempts to review various features of the dextran carrier like its source, structural and physico-chemical characteristics, pharmacokinetic fate and its applications as macromolecular carrier with special emphasis on dextran prodrugs.

  2. Biodegradable thermogels.

    Science.gov (United States)

    Park, Min Hee; Joo, Min Kyung; Choi, Bo Gyu; Jeong, Byeongmoon

    2012-03-20

    All living creatures respond to external stimuli. Similarly, some polymers undergo conformational changes in response to changes in temperature, pH, magnetic field, electrical field, or the wavelength of light. In one type of stimuli-responsive polymer, thermogel polymers, the polymer aqueous solution undergoes sol-to-gel transition as the temperature increases. Drugs or cells can be mixed into the polymer aqueous solution when it is in its lower viscosity solution state. After injection of the solution into a target site, heating prompts the formation of a hydrogel depot in situ, which can then act as a drug releasing system or a cell growing matrix. In this Account, we describe key materials developed in our laboratory for the construction of biodegradable thermogels. We particularly emphasize recently developed polypeptide-based materials where the secondary structure and nanoassembly play an important role in the determining the material properties. This Account will provide insights for controlling parameters, such as the sol-gel transition temperature, gel modulus, critical gel concentration, and degradability of the polymer, when designing a new thermogel system for a specific biomedical application. By varying the stereochemistry of amino acids in polypeptides, the molecular weight of hydrophobic/hydrophilic blocks, the composition of the polypeptides, the hydrophobic end-capping of the polypeptides, and the microsequences of a block copolymer, we have controlled the thermosensitivity and nanoassembly patterns of the polymers. We have investigated a series of thermogel biodegradable polymers. Polymers such as poly(lactic acid-co-glycolic acid), polycaprolactone, poly(trimethylene carbonate), polycyanoacrylate, sebacic ester, polypeptide were used as hydrophobic blocks, and poly(ethylene glycol) and poly(vinyl pyrrolidone) were used as hydrophilic blocks. To prepare a polymer sensitive to pH and temperature, carboxylic acid or amine groups were introduced

  3. Smoothing techniques for macromolecular global optimization

    Energy Technology Data Exchange (ETDEWEB)

    More, J.J.; Wu, Zhijun

    1995-09-01

    We study global optimization problems that arise in macromolecular modeling, and the solution of these problems via continuation and smoothing. Our results unify and extend the theory associated with the use of the Gaussian transform for smoothing. We show that the, Gaussian transform can be viewed as a special case of a generalized transform and that these generalized transforms share many of the properties of the Gaussian transform. We also show that the smoothing behavior of the generalized transform can be studied in terms of the Fourier transform and that these results indicate that the Gaussian transform has superior smoothing properties.

  4. Celebrating macromolecular crystallography: A personal perspective

    Directory of Open Access Journals (Sweden)

    Abad-Zapatero, Celerino

    2015-04-01

    Full Text Available The twentieth century has seen an enormous advance in the knowledge of the atomic structures that surround us. The discovery of the first crystal structures of simple inorganic salts by the Braggs in 1914, using the diffraction of X-rays by crystals, provided the critical elements to unveil the atomic structure of matter. Subsequent developments in the field leading to macromolecular crystallography are presented with a personal perspective, related to the cultural milieu of Spain in the late 1950’s. The journey of discovery of the author, as he developed professionally, is interwoven with the expansion of macromolecular crystallography from the first proteins (myoglobin, hemoglobin to the ‘coming of age’ of the field in 1971 and the discoveries that followed, culminating in the determination of the structure of the ribosomes at the turn of the century. A perspective is presented exploring the future of the field and also a reflection about the future generations of Spanish scientists.El siglo XX ha sido testigo del increíble avance que ha experimentado el conocimiento de la estructura atómica de la materia que nos rodea. El descubrimiento de las primeras estructuras atómicas de sales inorgánicas por los Bragg en 1914, empleando difracción de rayos X con cristales, proporcionó los elementos clave para alcanzar tal conocimiento. Posteriores desarrollos en este campo, que condujeron a la cristalografía macromolecular, se presentan aquí desde una perspectiva personal, relacionada con el contexto cultural de la España de la década de los 50. La experiencia del descubrimiento científico, durante mi desarrollo profesional, se integra en el desarrollo de la cristalografía macromolecular, desde las primeras proteínas (míoglobina y hemoglobina, hasta su madurez en 1971 que, con los posteriores descubrimientos, culmina con la determinación del la estructura del ribosoma. Asimismo, se explora el futuro de esta disciplina y se

  5. Macromolecular recognition in the Protein Data Bank

    Energy Technology Data Exchange (ETDEWEB)

    Janin, Joël, E-mail: joel.janin@ibbmc.u-psud.fr [Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France); Institut de Biochimie et Biologie Moléculaire et Cellulaire, UMR8619, Bâtiment 430, Université Paris-Sud, 91405 Orsay (France); Rodier, Francis [Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France); Chakrabarti, Pinak [Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054 (India); Bahadur, Ranjit P. [Institut de Biochimie et Biologie Moléculaire et Cellulaire, UMR8619, Bâtiment 430, Université Paris-Sud, 91405 Orsay (France); Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054 (India); Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France)

    2007-01-01

    X-ray structures in the PDB illustrate both the specific recognition of two polypeptide chains in protein–protein complexes and dimeric proteins and their nonspecific interaction at crystal contacts. Crystal structures deposited in the Protein Data Bank illustrate the diversity of biological macromolecular recognition: transient interactions in protein–protein and protein–DNA complexes and permanent assemblies in homodimeric proteins. The geometric and physical chemical properties of the macromolecular interfaces that may govern the stability and specificity of recognition are explored in complexes and homodimers compared with crystal-packing interactions. It is found that crystal-packing interfaces are usually much smaller; they bury fewer atoms and are less tightly packed than in specific assemblies. Standard-size interfaces burying 1200–2000 Å{sup 2} of protein surface occur in protease–inhibitor and antigen–antibody complexes that assemble with little or no conformation changes. Short-lived electron-transfer complexes have small interfaces; the larger size of the interfaces observed in complexes involved in signal transduction and homodimers correlates with the presence of conformation changes, often implicated in biological function. Results of the CAPRI (critical assessment of predicted interactions) blind prediction experiment show that docking algorithms efficiently and accurately predict the mode of assembly of proteins that do not change conformation when they associate. They perform less well in the presence of large conformation changes and the experiment stimulates the development of novel procedures that can handle such changes.

  6. Multiscale macromolecular simulation: role of evolving ensembles.

    Science.gov (United States)

    Singharoy, A; Joshi, H; Ortoleva, P J

    2012-10-22

    Multiscale analysis provides an algorithm for the efficient simulation of macromolecular assemblies. This algorithm involves the coevolution of a quasiequilibrium probability density of atomic configurations and the Langevin dynamics of spatial coarse-grained variables denoted order parameters (OPs) characterizing nanoscale system features. In practice, implementation of the probability density involves the generation of constant OP ensembles of atomic configurations. Such ensembles are used to construct thermal forces and diffusion factors that mediate the stochastic OP dynamics. Generation of all-atom ensembles at every Langevin time step is computationally expensive. Here, multiscale computation for macromolecular systems is made more efficient by a method that self-consistently folds in ensembles of all-atom configurations constructed in an earlier step, history, of the Langevin evolution. This procedure accounts for the temporal evolution of these ensembles, accurately providing thermal forces and diffusions. It is shown that efficiency and accuracy of the OP-based simulations is increased via the integration of this historical information. Accuracy improves with the square root of the number of historical timesteps included in the calculation. As a result, CPU usage can be decreased by a factor of 3-8 without loss of accuracy. The algorithm is implemented into our existing force-field based multiscale simulation platform and demonstrated via the structural dynamics of viral capsomers.

  7. The role of macromolecular stability in desiccation tolerance.

    NARCIS (Netherlands)

    Wolkers, W.

    1998-01-01

    The work presented in this thesis concerns a study on the molecular interactions that play a role in the macromolecular stability of desiccation-tolerant higher plant organs. Fourier transform infrared microspectroscopy was used as the main experimental technique to assess macromolecular structures

  8. Biodegradable synthetic bone composites

    Science.gov (United States)

    Liu, Gao; Zhao, Dacheng; Saiz, Eduardo; Tomsia, Antoni P.

    2013-01-01

    The invention provides for a biodegradable synthetic bone composition comprising a biodegradable hydrogel polymer scaffold comprising a plurality of hydrolytically unstable linkages, and an inorganic component; such as a biodegradable poly(hydroxyethylmethacrylate)/hydroxyapatite (pHEMA/HA) hydrogel composite possessing mineral content approximately that of human bone.

  9. [Biodegradation of polyethylene].

    Science.gov (United States)

    Yang, Jun; Song, Yi-ling; Qin, Xiao-yan

    2007-05-01

    Plastic material is one of the most serious solid wastes pollution. More than 40 million tons of plastics produced each year are discarded into environment. Plastics accumulated in the environment is highly resistant to biodegradation and not be able to take part in substance recycle. To increase the biodegradation efficiency of plastics by different means is the main research direction. This article reviewed the recent research works of polyethylene biodegradation that included the modification and pretreatment of polyethylene, biodegradation pathway, the relevant microbes and enzymes and the changes of physical, chemical and biological properties after biodegradation. The study directions of exploiting the kinds of life-forms of biodegradation polyethylene except the microorganisms, isolating and cloning the key enzymes and gene that could produce active groups, and enhancing the study on polyethylene biodegradation without additive were proposed.

  10. Functional Sub-states by High-pressure Macromolecular Crystallography.

    Science.gov (United States)

    Dhaussy, Anne-Claire; Girard, Eric

    2015-01-01

    At the molecular level, high-pressure perturbation is of particular interest for biological studies as it allows trapping conformational substates. Moreover, within the context of high-pressure adaptation of deep-sea organisms, it allows to decipher the molecular determinants of piezophily. To provide an accurate description of structural changes produced by pressure in a macromolecular system, developments have been made to adapt macromolecular crystallography to high-pressure studies. The present chapter is an overview of results obtained so far using high-pressure macromolecular techniques, from nucleic acids to virus capsid through monomeric as well as multimeric proteins.

  11. Synthesis and characterization of new biodegradable thermosensitive polyphosphazenes with lactic acid ester and methoxyethoxyethoxy side groups

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Two novel biodegradable thermosensitive polyphosphazenes with lactic acid ester and methoxyethoxyethoxy side groups were synthesized via the macromolecular substitution reactions of poly(dichlorophosphazene) with the sodium salt of lactic acid ester and sodium methoxyethoxyethoxide.Their structures were confirmed by ~(31)p NMR,~1H NMR,~(13)C NMR,IR,DSC,and elemental analysis.The lower critical solution temperature(LCST) behavior in water and in vitro degradation property of the polymers was investigated....

  12. Research progress of magnetic resonance imaging contrast agents

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Magnetic resonance imaging (MRI) is a clinical diagnostic modality, which has become popular in hospitals around the world. Approximately 30% of MRI exams include the use of contrast agents. The research progress of the paramagnetic resonance imaging contrast agents was described briefly. Three important approaches in the soluble paramagnetic resonance imaging contrast agents design including nonionic, tissue-specific and macromolecular contrast agents were investigated. In addition, the problems in the research and development in future were discussed.

  13. Sequential recovery of macromolecular components of the nucleolus.

    Science.gov (United States)

    Bai, Baoyan; Laiho, Marikki

    2015-01-01

    The nucleolus is involved in a number of cellular processes of importance to cell physiology and pathology, including cell stress responses and malignancies. Studies of macromolecular composition of the nucleolus depend critically on the efficient extraction and accurate quantification of all macromolecular components (e.g., DNA, RNA, and protein). We have developed a TRIzol-based method that efficiently and simultaneously isolates these three macromolecular constituents from the same sample of purified nucleoli. The recovered and solubilized protein can be accurately quantified by the bicinchoninic acid assay and assessed by polyacrylamide gel electrophoresis or by mass spectrometry. We have successfully applied this approach to extract and quantify the responses of all three macromolecular components in nucleoli after drug treatments of HeLa cells, and conducted RNA-Seq analysis of the nucleolar RNA.

  14. Biodegradability of plastics.

    Science.gov (United States)

    Tokiwa, Yutaka; Calabia, Buenaventurada P; Ugwu, Charles U; Aiba, Seiichi

    2009-08-26

    Plastic is a broad name given to different polymers with high molecular weight, which can be degraded by various processes. However, considering their abundance in the environment and their specificity in attacking plastics, biodegradation of plastics by microorganisms and enzymes seems to be the most effective process. When plastics are used as substrates for microorganisms, evaluation of their biodegradability should not only be based on their chemical structure, but also on their physical properties (melting point, glass transition temperature, crystallinity, storage modulus etc.). In this review, microbial and enzymatic biodegradation of plastics and some factors that affect their biodegradability are discussed.

  15. The solvent component of macromolecular crystals

    Energy Technology Data Exchange (ETDEWEB)

    Weichenberger, Christian X. [European Academy of Bozen/Bolzano (EURAC), Viale Druso 1, Bozen/Bolzano, I-39100 Südtirol/Alto Adige (Italy); Afonine, Pavel V. [Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Mail Stop 64R0121, Berkeley, CA 94720 (United States); Kantardjieff, Katherine [California State University, San Marcos, CA 92078 (United States); Rupp, Bernhard, E-mail: br@hofkristallamt.org [k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084 (United States); Medical University of Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck (Austria)

    2015-04-30

    On average, the mother liquor or solvent and its constituents occupy about 50% of a macromolecular crystal. Ordered as well as disordered solvent components need to be accurately accounted for in modelling and refinement, often with considerable complexity. The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initial phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.

  16. Macromolecular components of tomato fruit pectin.

    Science.gov (United States)

    Fishman, M L; Gross, K C; Gillespie, D T; Sondey, S M

    1989-10-01

    Chelate and alkaline-soluble pectin extracted from cell walls of pericarp tissue from mature green, turning, and red ripe (Lycopersicon esculentum Mill.) fruit (cv. Rutgers), were studied by high-performance size-exclusion chromatography. Computer-aided curve fitting of the chromatograms to a series of Gaussian-shaped components revealed that pectin from all fractions was composed of a linear combination of five macromolecular-sized species. The relative sizes of these macromolecules as obtained from their radii of gyration were 1:2:4:8:16. Dialysis against 0.05 M NaCl induced partial dissociation of the biopolymers. Apparently, the weight fraction of smaller sized species increased at the expense of larger ones. Also, the dissociation produced low-molecular-weight fragments. Behavior in the presence of 0.05 M NaCl led to the conclusion that cell wall pectin acted as if it were an aggregated mosaic, held together at least partially through noncovalent interactions.

  17. An upper limit for macromolecular crowding effects

    Directory of Open Access Journals (Sweden)

    Miklos Andrew C

    2011-05-01

    Full Text Available Abstract Background Solutions containing high macromolecule concentrations are predicted to affect a number of protein properties compared to those properties in dilute solution. In cells, these macromolecular crowders have a large range of sizes and can occupy 30% or more of the available volume. We chose to study the stability and ps-ns internal dynamics of a globular protein whose radius is ~2 nm when crowded by a synthetic microgel composed of poly(N-isopropylacrylamide-co-acrylic acid with particle radii of ~300 nm. Results Our studies revealed no change in protein rotational or ps-ns backbone dynamics and only mild (~0.5 kcal/mol at 37°C, pH 5.4 stabilization at a volume occupancy of 70%, which approaches the occupancy of closely packing spheres. The lack of change in rotational dynamics indicates the absence of strong crowder-protein interactions. Conclusions Our observations are explained by the large size discrepancy between the protein and crowders and by the internal structure of the microgels, which provide interstitial spaces and internal pores where the protein can exist in a dilute solution-like environment. In summary, microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects.

  18. Biodegradable fiksasyon malzemeleri

    OpenAIRE

    Seber, Sinan

    2004-01-01

    Problems related to metallic implant had increased the interest to biodegradables. In this paper, the physical and chemical properties, degradation modalities, implant design, clinical studies with techniques, and complications of biodegradable implants, especially polylactic and polyglycolic acid, were reviewed. Also our studies, on the antibiotic delivery capacities of these implants; and the prediction of immunological reactions with our clinical experiences were presented.

  19. Macromolecular networks and intelligence in microorganisms

    Science.gov (United States)

    Westerhoff, Hans V.; Brooks, Aaron N.; Simeonidis, Evangelos; García-Contreras, Rodolfo; He, Fei; Boogerd, Fred C.; Jackson, Victoria J.; Goncharuk, Valeri; Kolodkin, Alexey

    2014-01-01

    Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological networks constitute a type of information and communication technology (ICT): they receive information from the outside and inside of cells, integrate and interpret this information, and then activate a response. Biological networks enable molecules within cells, and even cells themselves, to communicate with each other and their environment. We have become accustomed to associating brain activity – particularly activity of the human brain – with a phenomenon we call “intelligence.” Yet, four billion years of evolution could have selected networks with topologies and dynamics that confer traits analogous to this intelligence, even though they were outside the intercellular networks of the brain. Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected. We propose that, if we were to leave terms such as “human” and “brain” out of the defining features of “intelligence,” all forms of life – from microbes to humans – exhibit some or all characteristics consistent with “intelligence.” We then review advances in genome-wide data production and analysis, especially in microbes, that provide a lens into microbial intelligence and propose how the insights derived from quantitatively characterizing biomolecular networks may enable synthetic biologists to create intelligent molecular networks for biotechnology, possibly generating new forms of intelligence, first in silico and then in vivo. PMID:25101076

  20. Macromolecular Topography Leaps into the Digital Age

    Science.gov (United States)

    Lovelace, J.; Bellamy, H.; Snell, E. H.; Borgstahl, G.

    2003-01-01

    A low-cost, real-time digital topography system is under development which will replace x-ray film and nuclear emulsion plates. The imaging system is based on an inexpensive surveillance camera that offers a 1000x1000 array of 8 im square pixels, anti-blooming circuitry, and very quick read out. Currently, the system directly converts x-rays to an image with no phosphor. The system is small and light and can be easily adapted to work with other crystallographic equipment. Preliminary images have been acquired of cubic insulin at the NSLS x26c beam line. NSLS x26c was configured for unfocused monochromatic radiation. Six reflections were collected with stills spaced from 0.002 to 0.001 degrees apart across the entire oscillation range that the reflections were in diffracting condition. All of the reflections were rotated to the vertical to reduce Lorentz and beam related effects. This particular CCD is designed for short exposure applications (much less than 1 sec) and so has a relatively high dark current leading to noisy raw images. The images are processed to remove background and other system noise with a multi-step approach including the use of wavelets, histogram, and mean window filtering. After processing, animations were constructed with the corresponding reflection profile to show the diffraction of the crystal volume vs. the oscillation angle as well as composite images showing the parts of the crystal with the strongest diffraction for each reflection. The final goal is to correlate features seen in reflection profiles captured with fine phi slicing to those seen in the topography images. With this development macromolecular topography finally comes into the digital age.

  1. Macromolecular networks and intelligence in microorganisms

    Directory of Open Access Journals (Sweden)

    Hans V Westerhoff

    2014-07-01

    Full Text Available Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological networks constitute a type of Information and Communication Technology (ICT: they receive information from the outside and inside of cells, integrate and interpret this information, and then activate a response. Biological networks enable molecules within cells, and even cells themselves, to communicate with each other and their environment. We have become accustomed to associating brain activity – particularly activity of the human brain – with a phenomenon we call intelligence. Yet, four billion years of evolution could have selected networks with topologies and dynamics that confer traits analogous to this intelligence, even though they were outside the intercellular networks of the brain. Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected. We propose that, if we were to leave terms such as human and brain out of the defining features of intelligence, all forms of life – from microbes to humans – exhibit some or all characteristics consistent with intelligence. We then review advances in genome-wide data production and analysis, especially in microbes, that provide a lens into microbial intelligence and propose how the insights derived from quantitatively characterizing biomolecular networks may enable synthetic biologists to create intelligent molecular networks for biotechnology, possibly generating new forms of intelligence, first in silico and then in vivo.

  2. Macromolecular Antioxidants and Dietary Fiber in Edible Seaweeds.

    Science.gov (United States)

    Sanz-Pintos, Nerea; Pérez-Jiménez, Jara; Buschmann, Alejandro H; Vergara-Salinas, José Rodrigo; Pérez-Correa, José Ricardo; Saura-Calixto, Fulgencio

    2017-02-01

    Seaweeds are rich in different bioactive compounds with potential uses in drugs, cosmetics and the food industry. The objective of this study was to analyze macromolecular antioxidants or nonextractable polyphenols, in several edible seaweed species collected in Chile (Gracilaria chilensis, Callophyllis concepcionensis, Macrocystis pyrifera, Scytosyphon lomentaria, Ulva sp. and Enteromorpha compressa), including their 1st HPLC characterization. Macromolecular antioxidants are commonly ignored in studies of bioactive compounds. They are associated with insoluble dietary fiber and exhibit significant biological activity, with specific features that are different from those of both dietary fiber and extractable polyphenols. We also evaluated extractable polyphenols and dietary fiber, given their relationship with macromolecular antioxidants. Our results show that macromolecular antioxidants are a major polyphenol fraction (averaging 42% to total polyphenol content), with hydroxycinnamic acids, hydroxybenzoic acids and flavonols being the main constituents. This fraction also showed remarkable antioxidant capacity, as determined by 2 complementary assays. The dietary fiber content was over 50% of dry weight, with some samples exhibiting the target proportionality between soluble and insoluble dietary fiber for adequate nutrition. Overall, our data show that seaweed could be an important source of commonly ignored macromolecular antioxidants.

  3. Complex Macromolecular Architectures by Living Cationic Polymerization

    KAUST Repository

    Alghamdi, Reem D.

    2015-05-01

    Poly (vinyl ether)-based graft polymers have been synthesized by the combination of living cationic polymerization of vinyl ethers with other living or controlled/ living polymerization techniques (anionic and ATRP). The process involves the synthesis of well-defined homopolymers (PnBVE) and co/terpolymers [PnBVE-b-PCEVE-b-PSiDEGVE (ABC type) and PSiDEGVE-b-PnBVE-b-PSiDEGVE (CAC type)] by sequential living cationic polymerization of n-butyl vinyl ether (nBVE), 2-chloroethyl vinyl ether (CEVE) and tert-butyldimethylsilyl ethylene glycol vinyl ether (SiDEGVE), using mono-functional {[n-butoxyethyl acetate (nBEA)], [1-(2-chloroethoxy) ethyl acetate (CEEA)], [1-(2-(2-(t-butyldimethylsilyloxy)ethoxy) ethoxy) ethyl acetate (SiDEGEA)]} or di-functional [1,4-cyclohexanedimethanol di(1-ethyl acetate) (cHMDEA), (VEMOA)] initiators. The living cationic polymerizations of those monomers were conducted in hexane at -20 0C using Et3Al2Cl3 (catalyst) in the presence of 1 M AcOEt base.[1] The PCEVE segments of the synthesized block terpolymers were then used to react with living macroanions (PS-DPE-Li; poly styrene diphenyl ethylene lithium) to afford graft polymers. The quantitative desilylation of PSiDEGVE segments by n-Bu4N+F- in THF at 0 °C led to graft co- and terpolymers in which the polyalcohol is the outer block. These co-/terpolymers were subsequently subjected to “grafting-from” reactions by atom transfer radical polymerization (ATRP) of styrene to afford more complex macromolecular architectures. The base assisted living cationic polymerization of vinyl ethers were also used to synthesize well-defined α-hydroxyl polyvinylether (PnBVE-OH). The resulting polymers were then modified into an ATRP macro-initiator for the synthesis of well-defined block copolymers (PnBVE-b-PS). Bifunctional PnBVE with terminal malonate groups was also synthesized and used as a precursor for more complex architectures such as H-shaped block copolymer by “grafting-from” or

  4. Distribution and enzymatic activity of heterotrophic bacteria decomposing selected macromolecular compounds in a Baltic Sea sandy beach

    Science.gov (United States)

    Podgórska, B.; Mudryk, Z. J.

    2003-03-01

    The potential capability to decompose macromolecular compounds, and the level of extracellular enzyme activities were determined in heterotrophic bacteria isolated from a sandy beach in Sopot on the Southern Baltic Sea coast. Individual isolates were capable of hydrolysing a wide spectrum of organic macromolecular compounds. Lipids, gelatine, and DNA were hydrolyzed most efficiently. Only a very small percentage of strains were able to decompose cellulose, and no pectinolytic bacteria were found. Except for starch-hydrolysis, no significant differences in the intensity of organic compound decomposition were recorded between horizontal and vertical profiles of the studied beach. Of all the studied extracellular enzymes, alkaline phosphatase, esterase lipase, and leucine acrylaminidase were most active; in contrast, the activity α-fucosidase, α-galactosidase and β-glucouronidase was the weakest. The level of extracellular enzyme activity was similar in both sand layers.

  5. Macromolecular crystallography beamline X25 at the NSLS.

    Science.gov (United States)

    Héroux, Annie; Allaire, Marc; Buono, Richard; Cowan, Matthew L; Dvorak, Joseph; Flaks, Leon; Lamarra, Steven; Myers, Stuart F; Orville, Allen M; Robinson, Howard H; Roessler, Christian G; Schneider, Dieter K; Shea-McCarthy, Grace; Skinner, John M; Skinner, Michael; Soares, Alexei S; Sweet, Robert M; Berman, Lonny E

    2014-05-01

    Beamline X25 at the NSLS is one of the five beamlines dedicated to macromolecular crystallography operated by the Brookhaven National Laboratory Macromolecular Crystallography Research Resource group. This mini-gap insertion-device beamline has seen constant upgrades for the last seven years in order to achieve mini-beam capability down to 20 µm × 20 µm. All major components beginning with the radiation source, and continuing along the beamline and its experimental hutch, have changed to produce a state-of-the-art facility for the scientific community.

  6. BIODEGRADABLE MICROSPHERES: A REVIEW

    Directory of Open Access Journals (Sweden)

    Kaur Dupinder

    2012-12-01

    Full Text Available Microspheres are characteristically free flowing powders consisting of proteins or synthetic polymers having a particle size ranging from 1-1000 μm. The range of techniques for the preparation of microspheres offers a variety of opportunities to control aspects of drug administration and enhance the therapeutic efficacy of a given drug. Of the many polymeric drug delivery systems, biodegradable polymers have been used widely as drug delivery systems because of their biocompatibility and biodegradability. The majority of biodegradable polymers have been used in the form of microparticles, from which the incorporated drug is released to the environment in a controlled manner. They can be employed to deliver medication in a rate-controlled and sometimes targeted manner. Medication is released from a microsphere by drug leaching from the polymer or by degradation of the polymer matrix. This review discusses characteristics and degradation behaviors of biodegradable polymers which are currently used in drug delivery.

  7. Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION.

    Science.gov (United States)

    Bharat, Tanmay A M; Scheres, Sjors H W

    2016-11-01

    Electron cryo-tomography (cryo-ET) is a technique that is used to produce 3D pictures (tomograms) of complex objects such as asymmetric viruses, cellular organelles or whole cells from a series of tilted electron cryo-microscopy (cryo-EM) images. Averaging of macromolecular complexes found within tomograms is known as subtomogram averaging, and this technique allows structure determination of macromolecular complexes in situ. Subtomogram averaging is also gaining in popularity for the calculation of initial models for single-particle analysis. We describe herein a protocol for subtomogram averaging from cryo-ET data using the RELION software (http://www2.mrc-lmb.cam.ac.uk/relion). RELION was originally developed for cryo-EM single-particle analysis, and the subtomogram averaging approach presented in this protocol has been implemented in the existing workflow for single-particle analysis so that users may conveniently tap into existing capabilities of the RELION software. We describe how to calculate 3D models for the contrast transfer function (CTF) that describe the transfer of information in the imaging process, and we illustrate the results of classification and subtomogram averaging refinement for cryo-ET data of purified hepatitis B capsid particles and Saccharomyces cerevisiae 80S ribosomes. Using the steps described in this protocol, along with the troubleshooting and optimization guidelines, high-resolution maps can be obtained in which secondary structure elements are resolved subtomogram.

  8. Two-center-multipole expansion method: application to macromolecular systems

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.;

    2007-01-01

    We propose a theoretical method for the calculation of the interaction energy between macromolecular systems at large distances. The method provides a linear scaling of the computing time with the system size and is considered as an alternative to the well-known fast multipole method. Its...

  9. Molecularly Imprinted Biodegradable Nanoparticles

    Science.gov (United States)

    Gagliardi, Mariacristina; Bertero, Alice; Bifone, Angelo

    2017-01-01

    Biodegradable polymer nanoparticles are promising carriers for targeted drug delivery in nanomedicine applications. Molecu- lar imprinting is a potential strategy to target polymer nanoparticles through binding of endogenous ligands that may promote recognition and active transport into specific cells and tissues. However, the lock-and-key mechanism of molecular imprinting requires relatively rigid cross-linked structures, unlike those of many biodegradable polymers. To date, no fully biodegradable molecularly imprinted particles have been reported in the literature. This paper reports the synthesis of a novel molecularly- imprinted nanocarrier, based on poly(lactide-co-glycolide) (PLGA) and acrylic acid, that combines biodegradability and molec- ular recognition properties. A novel three-arm biodegradable cross-linker was synthesized by ring-opening polymerization of glycolide and lactide initiated by glycerol. The resulting macromer was functionalized by introduction of end-functions through reaction with acryloyl chloride. Macromer and acrylic acid were used for the synthesis of narrowly-dispersed nanoparticles by radical polymerization in diluted conditions in the presence of biotin as template molecule. The binding capacity of the imprinted nanoparticles towards biotin and biotinylated bovine serum albumin was twentyfold that of non-imprinted nanoparti- cles. Degradation rates and functional performances were assessed in in vitro tests and cell cultures, demonstrating effective biotin-mediated cell internalization. PMID:28071745

  10. Molecularly Imprinted Biodegradable Nanoparticles

    Science.gov (United States)

    Gagliardi, Mariacristina; Bertero, Alice; Bifone, Angelo

    2017-01-01

    Biodegradable polymer nanoparticles are promising carriers for targeted drug delivery in nanomedicine applications. Molecu- lar imprinting is a potential strategy to target polymer nanoparticles through binding of endogenous ligands that may promote recognition and active transport into specific cells and tissues. However, the lock-and-key mechanism of molecular imprinting requires relatively rigid cross-linked structures, unlike those of many biodegradable polymers. To date, no fully biodegradable molecularly imprinted particles have been reported in the literature. This paper reports the synthesis of a novel molecularly- imprinted nanocarrier, based on poly(lactide-co-glycolide) (PLGA) and acrylic acid, that combines biodegradability and molec- ular recognition properties. A novel three-arm biodegradable cross-linker was synthesized by ring-opening polymerization of glycolide and lactide initiated by glycerol. The resulting macromer was functionalized by introduction of end-functions through reaction with acryloyl chloride. Macromer and acrylic acid were used for the synthesis of narrowly-dispersed nanoparticles by radical polymerization in diluted conditions in the presence of biotin as template molecule. The binding capacity of the imprinted nanoparticles towards biotin and biotinylated bovine serum albumin was twentyfold that of non-imprinted nanoparti- cles. Degradation rates and functional performances were assessed in in vitro tests and cell cultures, demonstrating effective biotin-mediated cell internalization.

  11. Green and biodegradable electronics

    Directory of Open Access Journals (Sweden)

    Mihai Irimia-Vladu

    2012-07-01

    Full Text Available We live in a world where the lifetime of electronics is becoming shorter, now approaching an average of several months. This poses a growing ecological problem. This brief review will present some of the initial steps taken to address the issue of electronic waste with biodegradable organic electronic materials. Many organic materials have been shown to be biodegradable, safe, and nontoxic, including compounds of natural origin. Additionally, the unique features of such organic materials suggest they will be useful in biofunctional electronics; demonstrating functions that would be inaccessible for traditional inorganic compounds. Such materials may lead to fully biodegradable and even biocompatible/biometabolizable electronics for many low-cost applications. This review highlights recent progress in these classes of material, covering substrates and insulators, semiconductors, and finally conductors.

  12. Editorial: Biodegradable Materials

    Directory of Open Access Journals (Sweden)

    Carl Schaschke

    2014-11-01

    Full Text Available This Special Issue “Biodegradable Materials” features research and review papers concerning recent advances on the development, synthesis, testing and characterisation of biomaterials. These biomaterials, derived from natural and renewable sources, offer a potential alternative to existing non-biodegradable materials with application to the food and biomedical industries amongst many others. In this Special Issue, the work is expanded to include the combined use of fillers that can enhance the properties of biomaterials prepared as films. The future application of these biomaterials could have an impact not only at the economic level, but also for the improvement of the environment.

  13. Contrast-enhanced peripheral MRA. Technique and contrast agents

    Energy Technology Data Exchange (ETDEWEB)

    Nielsen, Yousef W. [Dept. of Radiology, Copenhagen Univ. Hospital Bispebjerg, Bispebjerg (Denmark)], e-mail: ywnielsen@gmail.com; Thomsen, Henrik S. [Dept. of Diagnostic Radiology, Copenhagen Univ. Hospital Herlev, Herlev (Denmark)

    2012-09-15

    In the last decade contrast-enhanced magnetic resonance angiography (CE-MRA) has gained wide acceptance as a valuable tool in the diagnostic work-up of patients with peripheral arterial disease. This review presents current concepts in peripheral CE-MRA with emphasis on MRI technique and contrast agents. Peripheral CE-MRA is defined as an MR angiogram of the arteries from the aortic bifurcation to the feet. Advantages of CE-MRA include minimal invasiveness and lack of ionizing radiation. The basic technique employed for peripheral CE-MRA is the bolus-chase method. With this method a paramagnetic MRI contrast agent is injected intravenously and T1-weighted images are acquired in the subsequent arterial first-pass phase. In order to achieve high quality MR angiograms without interfering venous contamination or artifacts, a number of factors need to be taken into account. This includes magnetic field strength of the MRI system, receiver coil configuration, use of parallel imaging, contrast bolus timing technique, and k-space filling strategies. Furthermore, it is possible to optimize peripheral CE-MRA using venous compression techniques, hybrid scan protocols, time-resolved imaging, and steady-state MRA. Gadolinium(Gd)-based contrast agents are used for CE-MRA of the peripheral arteries. Extracellular Gd agents have a pharmacokinetic profile similar to iodinated contrast media. Accordingly, these agents are employed for first-pass MRA. Blood-pool Gd-based agents are characterized by prolonged intravascular stay, due to macromolecular structure or protein binding. These agents can be used for first-pass, as well as steady-state MRA. Some Gd-based contrast agents with low thermodynamic stability have been linked to development of nephrogenic systemic fibrosis in patients with severe renal insufficiency. Using optimized technique and a stable MRI contrast agent, peripheral CE-MRA is a safe procedure with diagnostic accuracy close to that of conventional catheter X

  14. Repetitive subcutaneous implantation of different types of (biodegradable) biomaterials alters the foreign body reaction

    NARCIS (Netherlands)

    van Luyn, MJA; Plantinga, JA; Brouwer, LA; Khouw, IMSL; de Leij, LFMH; van Wachem, PB

    2001-01-01

    In the present study two biodegradable materials (cross-linked collagens) and two non-biodegradable materials (polyurethane and silicone) were applied in a repetitive subcutaneous implantation model in rats. In contrast to the first challenge, the second challenge with the same type of material, but

  15. Contrastive Lexicology.

    Science.gov (United States)

    Hartmann, R. R. K.

    This paper deals with the relation between etymologically related words in different languages. A survey is made of seven stages in the development of contrastive lexicology. These are: prelinguistic word studies, semantics, lexicography, translation, foreign language learning, bilingualism, and finally contrastive analysis. Concerning contrastive…

  16. Controlled architecture for improved macromolecular memory within polymer networks.

    Science.gov (United States)

    DiPasquale, Stephen A; Byrne, Mark E

    2016-08-01

    This brief review analyzes recent developments in the field of living/controlled polymerization and the potential of this technique for creating imprinted polymers with highly structured architecture with macromolecular memory. As a result, it is possible to engineer polymers at the molecular level with increased homogeneity relating to enhanced template binding and transport. Only recently has living/controlled polymerization been exploited to decrease heterogeneity and substantially improve the efficiency of the imprinting process for both highly and weakly crosslinked imprinted polymers. Living polymerization can be utilized to create imprinted networks that are vastly more efficient than similar polymers produced using conventional free radical polymerization, and these improvements increase the role that macromolecular memory can play in the design and engineering of new drug delivery and sensing platforms.

  17. Refinement of macromolecular structures against neutron data with SHELXL2013.

    Science.gov (United States)

    Gruene, Tim; Hahn, Hinrich W; Luebben, Anna V; Meilleur, Flora; Sheldrick, George M

    2014-02-01

    Some of the improvements in SHELX2013 make SHELXL convenient to use for refinement of macromolecular structures against neutron data without the support of X-ray data. The new NEUT instruction adjusts the behaviour of the SFAC instruction as well as the default bond lengths of the AFIX instructions. This work presents a protocol on how to use SHELXL for refinement of protein structures against neutron data. It includes restraints extending the Engh & Huber [Acta Cryst. (1991), A47, 392-400] restraints to H atoms and discusses several of the features of SHELXL that make the program particularly useful for the investigation of H atoms with neutron diffraction. SHELXL2013 is already adequate for the refinement of small molecules against neutron data, but there is still room for improvement, like the introduction of chain IDs for the refinement of macromolecular structures.

  18. Stochastic reaction–diffusion algorithms for macromolecular crowding

    Science.gov (United States)

    Sturrock, Marc

    2016-06-01

    Compartment-based (lattice-based) reaction–diffusion algorithms are often used for studying complex stochastic spatio-temporal processes inside cells. In this paper the influence of macromolecular crowding on stochastic reaction–diffusion simulations is investigated. Reaction–diffusion processes are considered on two different kinds of compartmental lattice, a cubic lattice and a hexagonal close packed lattice, and solved using two different algorithms, the stochastic simulation algorithm and the spatiocyte algorithm (Arjunan and Tomita 2010 Syst. Synth. Biol. 4, 35–53). Obstacles (modelling macromolecular crowding) are shown to have substantial effects on the mean squared displacement and average number of molecules in the domain but the nature of these effects is dependent on the choice of lattice, with the cubic lattice being more susceptible to the effects of the obstacles. Finally, improvements for both algorithms are presented.

  19. The vibron dressing in α-helicoidal macromolecular chains

    Institute of Scientific and Technical Information of China (English)

    D.(C)evizovi(c); S.Galovi(c); A.Reshetnyak; Z.Ivi(c)

    2013-01-01

    We present a study of the physical properties of the vibrational excitation in α-helicoidal macromolecular chains,caused by the interaction with acoustical and optical phonon modes.The influence of the temperature and the basic system parameters on the vibron dressing have been analyzed by employing the simple mean-field approach based on the variational extension of the Lang-Firsov unitary transformation.The applied approach predicts a region in system parameter space where one has an abrupt transition from a partially dressed (light and mobile) to a fully dressed (immobile) vibron state.We found that the boundary of this region depends on system temperature and the type of bond among structural elements in the macromolecular chain.

  20. Isotope labeling for NMR studies of macromolecular structure and interactions

    Energy Technology Data Exchange (ETDEWEB)

    Wright, P.E. [Scripps Research Institute, La Jolla, CA (United States)

    1994-12-01

    Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform {sup 13}C, {sup 15}N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific {sup 13}C and {sup 15}N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions.

  1. A macromolecular model for the endothelial surface layer

    Science.gov (United States)

    Harden, James; Danova-Okpetu, Darina; Grest, Gary

    2006-03-01

    The endothelial surface layer (ESL) is a micron-scale macromolecular lining of the luminal side of blood vessels composed of proteoglycans, glycoproteins, polysaccharides and associated plasma proteins all in dynamic equilibrium. It has numerous physiological roles including the regulation of blood flow and microvascular permeability, and active participation in mechanotransduction and stress regulation, coagulation, cell adhesion, and inflammatory response. The dynamic structure and the mechanical properties of the ESL are crucial for many of its physiological properties. We present a topological model for the ESL composed of three basic macromolecular elements: branched proteoglycans, linear polysaccharide chains, and small plasma proteins. The model was studied using non-equilibrium molecular dynamics simulations and compared with scaling theories for associating tethered polymers. We discuss the observed dynamical and mechanical properties of the ESL captured by this model, and the possible physical insight it provides into the physiological behavior of the ESL.

  2. Temperature-dependent macromolecular X-ray crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Weik, Martin, E-mail: martin.weik@ibs.fr; Colletier, Jacques-Philippe [CEA, IBS, Laboratoire de Biophysique Moléculaire, F-38054 Grenoble (France); CNRS, UMR5075, F-38027 Grenoble (France); Université Joseph Fourier, F-38000 Grenoble (France)

    2010-04-01

    The dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. X-ray crystallography provides structural details of biological macromolecules. Whereas routine data are collected close to 100 K in order to mitigate radiation damage, more exotic temperature-controlled experiments in a broader temperature range from 15 K to room temperature can provide both dynamical and structural insights. Here, the dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. Experimental strategies of kinetic crystallography are discussed that have allowed the generation and trapping of macromolecular intermediate states by combining reaction initiation in the crystalline state with appropriate temperature profiles. A particular focus is on recruiting X-ray-induced changes for reaction initiation, thus unveiling useful aspects of radiation damage, which otherwise has to be minimized in macromolecular crystallography.

  3. Mechanism on impact of internal-electrolysis pre-treatment on biodegradability of yeast wastewater

    Institute of Scientific and Technical Information of China (English)

    SHI Yu; LIU Hui; ZHOU Xuan; XIE An; HU ChaoYong

    2009-01-01

    The internal-electrolysis (IE) process can be used as pretreatment to improve the biodegradability of yeast wastewater. The water before and after IE pretreatment was analyzed by UV, GPC, GC-MS to determine the changes in its chemical composition. The mechanism on the improvement of biodegrad-ability by the IE process was discussed in two aspects according to the changes of chemical composition, (i) Some reactions occurred during the IE process, such as hydrolytic reaction, cracking, and re-dox reaction. Thus, the cyclic structure opened and changed into chains, and the macromolecular compounds were spilt to small molecule substances. All these reactions tended to simplify the structure of molecules and increase the donating electron groups so as to improve the biodegradability. (ii)The small molecule acids and alcohols in raw water or produced by the internal electrolysis process could be removed through volatilization and electrochemical adhesion, which was conducive to the removal of COD and the improvement of biodegradability of yeast wastewater.

  4. Biodegradable Materials for Nonwovens

    Science.gov (United States)

    Demand for nonwovens is increasing globally, particularly in the disposable products area. As the consumption of nonwoven products with short life increases, the burden on waste disposal also rises. In this context, biodegradable nonwovens become more important today and for the future. Several new ...

  5. Grey water biodegradability

    NARCIS (Netherlands)

    Abu Ghunmi, L.; Zeeman, G.; Fayyad, M.; Van Lier, J.B.

    2010-01-01

    Knowing the biodegradability characteristics of grey water constituents is imperative for a proper design and operation of a biological treatment system of grey water. This study characterizes the different COD fractions of dormitory grey water and investigates the effect of applying different condi

  6. Grey water biodegradability

    NARCIS (Netherlands)

    Abu Ghunmi, L.; Zeeman, G.; Fayyad, M.; Lier, van J.B.

    2011-01-01

    Knowing the biodegradability characteristics of grey water constituents is imperative for a proper design and operation of a biological treatment system of grey water. This study characterizes the different COD fractions of dormitory grey water and investigates the effect of applying different condi

  7. Single-particle cryo-electron microscopy of macromolecular assemblies

    OpenAIRE

    Cheng, Kimberley

    2009-01-01

    In this thesis, single-particle cryo-electron microscopy (cryo-EM) was used to study the structure of three macromolecular assemblies: the two hemocyanin isoforms from Rapana thomasiana, the Pyrococcus furiosus chaperonin, and the ribosome from Escherichia coli. Hemocyanins are large respiratory proteins in arthropods and molluscs. Most molluscan hemocyanins exist as two distinct isoforms composed of related polypeptides. In most species the two isoforms differ in terms of their oligomeric st...

  8. Facilitating structure determination: workshop on robotics andautomation in macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Ralston, Corie; Cork, C.W.; McDermott, G.; Earnest, T.N.

    2006-03-28

    As part of the annual Advanced Light Source (ALS) andStanford Synchrotron Radiation Laboratory (SSRL) Users' Meeting inOctober of this year, the macromolecular crystallography staff at bothsynchrotrons held a joint hands-on workshop to address automation issuesin crystal mounting and data collection at the beamline. This paperdescribes the ALS portion of the workshop, while the accompanying paperreviews the SSRL workshop.

  9. Macromolecular Assemblage in the Design of a Synthetic AIDS Vaccine

    Science.gov (United States)

    Defoort, Jean-Philippe; Nardelli, Bernardetta; Huang, Wolin; Ho, David D.; Tam, James P.

    1992-05-01

    We describe a peptide vaccine model based on the mimicry of surface coat protein of a pathogen. This model used a macromolecular assemblage approach to amplify peptide antigens in liposomes or micelles. The key components of the model consisted of an oligomeric lysine scaffolding to amplify peptide antigens covalently 4-fold and a lipophilic membrane-anchoring group to further amplify noncovalently the antigens many-fold in liposomal or micellar form. A peptide antigen derived from the third variable domain of glycoprotein gp120 of human immunodeficiency virus type 1 (HIV-1), consisting of neutralizing, T-helper, and T-cytotoxic epitopes, was used in a macromolecular assemblage model (HIV-1 linear peptide amino acid sequence 308-331 in a tetravalent multiple antigen peptide system linked to tripalmitoyl-S-glycerylcysteine). The latter complex, in liposome or micelle, was used to immunize mice and guinea pigs without any adjuvant and found to induce gp120-specific antibodies that neutralize virus infectivity in vitro, elicit cytokine production, and prime CD8^+ cytotoxic T lymphocytes in vivo. Our results show that the macromolecular assemblage approach bears immunological mimicry of the gp120 of HIV virus and may lead to useful vaccines against HIV infection.

  10. REFMAC5 for the refinement of macromolecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Murshudov, Garib N., E-mail: garib@ysbl.york.ac.uk [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom); Skubák, Pavol [Biophysical Structural Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden (Netherlands); Lebedev, Andrey A. [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom); Pannu, Navraj S. [Biophysical Structural Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden (Netherlands); Steiner, Roberto A. [Randall Division of Cell and Molecular Biophysics, New Hunt’s House, King’s College London, London (United Kingdom); Nicholls, Robert A. [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom); Winn, Martyn D. [STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Long, Fei; Vagin, Alexei A. [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom)

    2011-04-01

    The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described. This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement tools such as secondary-structure restraints, restraints to known homologous structures, automatic global and local NCS restraints, ‘jelly-body’ restraints and the use of novel long-range restraints on atomic displacement parameters (ADPs) based on the Kullback–Leibler divergence. REFMAC5 additionally offers TLS parameterization and, when high-resolution data are available, fast refinement of anisotropic ADPs. Refinement in the presence of twinning is performed in a fully automated fashion. REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography.

  11. Macromolecular amplification of binding response in superaptamer hydrogels.

    Science.gov (United States)

    Bai, Wei; Gariano, Nicholas A; Spivak, David A

    2013-05-08

    It is becoming more important to detect ultralow concentrations of analytes for biomedical, environmental, and national security applications. Equally important is that new methods should be easy to use, inexpensive, portable, and if possible allow detection by the naked eye. By and large, detection of low concentrations of analytes cannot be achieved directly but requires signal amplification by catalysts, macromolecules, metal surfaces, or supramolecular aggregates. The rapidly progressing field of macromolecular signal amplification has been advanced using conjugated polymers, chirality in polymers, solvating polymers, and polymerization/depolymerization strategies. A new type of aptamer-based hydrogel with specific response to target proteins presented in this report demonstrates an additional category of macromolecular signal amplification. This superaptamer assembly provides the first example of using protein-specific aptamers to create volume-changing hydrogels with amplified response to the target protein. A remarkable aspect of these superaptamer hydrogels is that volume shrinking is visible to the naked eye down to femtomolar concentrations of protein. This extraordinary macromolecular amplification is attributed to a complex interplay between protein-aptamer supramolecular cross-links and the consequential reduction of excluded volume in the hydrogel. Specific recognition is even maintained in biological matrices such as urine and tears. Furthermore, the gels can be dried for long-term storage and regenerated for use without loss of activity. In practice, the ease of this biomarker detection method offers an alternative to traditional analytical techniques that require sophisticated instrumentation and highly trained personnel.

  12. Absorbable and biodegradable polymers

    CERN Document Server

    Shalaby, Shalaby W

    2003-01-01

    INTRODUCTION NOTES: Absorbable/Biodegradable Polymers: Technology Evolution. DEVELOPMENT AND APPLICATIONOF NEW SYSTEMS: Segmented Copolyesters with Prolonged Strength Retention Profiles. Polyaxial Crystalline Fiber-Forming Copolyester. Polyethylene Glycol-Based Copolyesters. Cyanoacrylate-Based Systems as Tissue Adhesives. Chitosan-Based Systems. Hyaluronic Acid-Based Systems. DEVELOPMENTS IN PREPARATIVE, PROCESSING, AND EVALUATION METHODS: New Approaches to the Synthesis of Crystalline. Fiber-Forming Aliphatic Copolyesters. Advances in Morphological Development to Tailor the Performance of Me

  13. Safe biodegradable fluorescent particles

    Science.gov (United States)

    Martin, Sue I.; Fergenson, David P.; Srivastava, Abneesh; Bogan, Michael J.; Riot, Vincent J.; Frank, Matthias

    2010-08-24

    A human-safe fluorescence particle that can be used for fluorescence detection instruments or act as a safe simulant for mimicking the fluorescence properties of microorganisms. The particle comprises a non-biological carrier and natural fluorophores encapsulated in the non-biological carrier. By doping biodegradable-polymer drug delivery microspheres with natural or synthetic fluorophores, the desired fluorescence can be attained or biological organisms can be simulated without the associated risks and logistical difficulties of live microorganisms.

  14. Biodegradation of Silk Biomaterials

    OpenAIRE

    Bochu Wang; Yang Cao

    2009-01-01

    Silk fibroin from the silkworm, Bombyx mori, has excellent properties such as biocompatibility, biodegradation, non-toxicity, adsorption properties, etc. As a kind of ideal biomaterial, silk fibroin has been widely used since it was first utilized for sutures a long time ago. The degradation behavior of silk biomaterials is obviously important for medical applications. This article will focus on silk-based biomaterials and review the degradation behaviors of silk materials.

  15. Workshop on algorithms for macromolecular modeling. Final project report, June 1, 1994--May 31, 1995

    Energy Technology Data Exchange (ETDEWEB)

    Leimkuhler, B.; Hermans, J.; Skeel, R.D.

    1995-07-01

    A workshop was held on algorithms and parallel implementations for macromolecular dynamics, protein folding, and structural refinement. This document contains abstracts and brief reports from that workshop.

  16. Anaerobic Biodegradation of Detergent Surfactants

    Directory of Open Access Journals (Sweden)

    Erich Jelen

    2009-03-01

    Full Text Available Detergent surfactantscan be found in wastewater in relevant concentrations. Most of them are known as ready degradable under aerobic conditions, as required by European legislation. Far fewer surfactants have been tested so far for biodegradability under anaerobic conditions. The natural environment is predominantly aerobic, but there are some environmental compartments such as river sediments, sub-surface soil layer and anaerobic sludge digesters of wastewater treatment plants which have strictly anaerobic conditions. This review gives an overview on anaerobic biodegradation processes, the methods for testing anaerobic biodegradability, and the anaerobic biodegradability of different detergent surfactant types (anionic, nonionic, cationic, amphoteric surfactants.

  17. BLOOD FLOW AND MACROMOLECULAR TRANSPORT IN CURVED BLOOD VESSELS

    Institute of Scientific and Technical Information of China (English)

    WEI Lan; WEN Gong-bi; TAN Wen-chang

    2006-01-01

    A numerical analysis of the steady/pulsatile flow and macromolecular (such as LDL and Albumin) transport in curved blood vessels was carried out. The computational results predict that the vortex of the secondary flow is time-dependent in the aortic arch.The concentration of macromolecule concentrates at the region of sharp curve, and the wall concentration at the outer part is higher than that at the inner part. Atherosclerosis and thrombosis are prone to develop in such regions with sharp flow.

  18. Bringing macromolecular machinery to life using 3D animation.

    Science.gov (United States)

    Iwasa, Janet H

    2015-04-01

    Over the past decade, there has been a rapid rise in the use of three-dimensional (3D) animation to depict molecular and cellular processes. Much of the growth in molecular animation has been in the educational arena, but increasingly, 3D animation software is finding its way into research laboratories. In this review, I will discuss a number of ways in which 3d animation software can play a valuable role in visualizing and communicating macromolecular structures and dynamics. I will also consider the challenges of using animation tools within the research sphere.

  19. Compared in vivo toxicity in mice of lung delivered biodegradable and non-biodegradable nanoparticles.

    Science.gov (United States)

    Aragao-Santiago, Letícia; Hillaireau, Hervé; Grabowski, Nadège; Mura, Simona; Nascimento, Thais L; Dufort, Sandrine; Coll, Jean-Luc; Tsapis, Nicolas; Fattal, Elias

    2016-01-01

    To design nanoparticle (NP)-based drug delivery systems for pulmonary administration, biodegradable materials are considered safe, but their potential toxicity is poorly explored. We here explore the lung toxicity in mice of biodegradable nanoparticles (NPs) and compare it to the toxicity of non-biodegradable ones. NP formulations of poly(d,l-lactide-co-glycolide) (PLGA) coated with chitosan (CS), poloxamer 188 (PF68) or poly(vinyl alcohol) (PVA), which renders 200 nm NPs of positive, negative or neutral surface charge respectively, were analyzed for their biodistribution by in vivo fluorescence imaging and their inflammatory potential after single lung nebulization in mice. After exposure, analysis of bronchoalveolar lavage (BAL) cell population, protein secretion and cytokine release as well as lung histology were carried out. The inflammatory response was compared to the one induced by non-biodegradable counterparts, namely, TiO2 of rutile and anatase crystal form and polystyrene (PS). PLGA NPs were mostly present in mice lungs, with little passage to other organs. An increase in neutrophil recruitment was observed in mice exposed to PS NPs 24 h after nebulization, which declined at 48 h. This result was supported by an increase in interleukin (IL)-6 and tumor necrosis factor α (TNFα) in BAL supernatant at 24 h. TiO2 anatase NPs were still present in lung cells 48 h after nebulization and induced the expression of pro-inflammatory cytokines and the recruitment of polymorphonuclear cells to BAL. In contrast, regardless of their surface charge, PLGA NPs did not induce significant changes in the inflammation markers analyzed. In conclusion, these results point out to a safe use of PLGA NPs regardless of their surface coating compared to non-biodegradable ones.

  20. Macromolecular Crowding Enhances Thermal Stability of Rabbit Muscle Creatine Kinase

    Institute of Scientific and Technical Information of China (English)

    ZHU Jiang; HE Huawei; LI Sen

    2008-01-01

    The effect of dextran on the conformation (or secondary structure) and thermal stability of creatine kinase (CK) was studied using the far-ultraviolet (UV) circular dichroism (CD) spectra.The results showed that lower concentrations of dextran (less than 60 g/L) induced formation of the secondary CK structures.However,the secondary structure content of CK decreased when the dextran concentrations exceeded 60 g/L.Thermally induced transition curves were measured for CK in the presence of different concentrations of dextran by far-UV CD.The thermal transition curves were fitted to a two-state model by a nonlinear,least-squares method to obtain the transition temperature of the unfolding transition.An increase in the tran- sition temperature was observed with the increase of the dextran concentration.These observations qualita-tively accord with predictions of a previously proposed model for the effect of intermolecular excluded volume (macromolecular crowding) on protein stability and conformation.These findings imply that the effects of macromolecular crowding can have an important influence on our understanding of how protein folding oc-curs in vivo.

  1. Identifying and visualizing macromolecular flexibility in structural biology

    Directory of Open Access Journals (Sweden)

    Martina Palamini

    2016-09-01

    Full Text Available Structural biology comprises a variety of tools to obtain atomic resolution data for the investigation of macromolecules. Conventional structural methodologies including crystallography, NMR and electron microscopy often do not provide sufficient details concerning flexibility and dynamics, even though these aspects are critical for the physiological functions of the systems under investigation. However, the increasing complexity of the molecules studied by structural biology (including large macromolecular assemblies, integral membrane proteins, intrinsically disordered systems, and folding intermediates continuously demands in-depth analyses of the roles of flexibility and conformational specificity involved in interactions with ligands and inhibitors. The intrinsic difficulties in capturing often subtle but critical molecular motions in biological systems have restrained the investigation of flexible molecules into a small niche of structural biology. Introduction of massive technological developments over the recent years, which include time-resolved studies, solution X-ray scattering, and new detectors for cryo-electron microscopy, have pushed the limits of structural investigation of flexible systems far beyond traditional approaches of NMR analysis. By integrating these modern methods with powerful biophysical and computational approaches such as generation of ensembles of molecular models and selective particle picking in electron microscopy, more feasible investigations of dynamic systems are now possible. Using some prominent examples from recent literature, we review how current structural biology methods can contribute useful data to accurately visualize flexibility in macromolecular structures and understand its important roles in regulation of biological processes.

  2. MMDB and VAST+: tracking structural similarities between macromolecular complexes.

    Science.gov (United States)

    Madej, Thomas; Lanczycki, Christopher J; Zhang, Dachuan; Thiessen, Paul A; Geer, Renata C; Marchler-Bauer, Aron; Bryant, Stephen H

    2014-01-01

    The computational detection of similarities between protein 3D structures has become an indispensable tool for the detection of homologous relationships, the classification of protein families and functional inference. Consequently, numerous algorithms have been developed that facilitate structure comparison, including rapid searches against a steadily growing collection of protein structures. To this end, NCBI's Molecular Modeling Database (MMDB), which is based on the Protein Data Bank (PDB), maintains a comprehensive and up-to-date archive of protein structure similarities computed with the Vector Alignment Search Tool (VAST). These similarities have been recorded on the level of single proteins and protein domains, comprising in excess of 1.5 billion pairwise alignments. Here we present VAST+, an extension to the existing VAST service, which summarizes and presents structural similarity on the level of biological assemblies or macromolecular complexes. VAST+ simplifies structure neighboring results and shows, for macromolecular complexes tracked in MMDB, lists of similar complexes ranked by the extent of similarity. VAST+ replaces the previous VAST service as the default presentation of structure neighboring data in NCBI's Entrez query and retrieval system. MMDB and VAST+ can be accessed via http://www.ncbi.nlm.nih.gov/Structure.

  3. Enzymes as Green Catalysts for Precision Macromolecular Synthesis.

    Science.gov (United States)

    Shoda, Shin-ichiro; Uyama, Hiroshi; Kadokawa, Jun-ichi; Kimura, Shunsaku; Kobayashi, Shiro

    2016-02-24

    The present article comprehensively reviews the macromolecular synthesis using enzymes as catalysts. Among the six main classes of enzymes, the three classes, oxidoreductases, transferases, and hydrolases, have been employed as catalysts for the in vitro macromolecular synthesis and modification reactions. Appropriate design of reaction including monomer and enzyme catalyst produces macromolecules with precisely controlled structure, similarly as in vivo enzymatic reactions. The reaction controls the product structure with respect to substrate selectivity, chemo-selectivity, regio-selectivity, stereoselectivity, and choro-selectivity. Oxidoreductases catalyze various oxidation polymerizations of aromatic compounds as well as vinyl polymerizations. Transferases are effective catalysts for producing polysaccharide having a variety of structure and polyesters. Hydrolases catalyzing the bond-cleaving of macromolecules in vivo, catalyze the reverse reaction for bond forming in vitro to give various polysaccharides and functionalized polyesters. The enzymatic polymerizations allowed the first in vitro synthesis of natural polysaccharides having complicated structures like cellulose, amylose, xylan, chitin, hyaluronan, and chondroitin. These polymerizations are "green" with several respects; nontoxicity of enzyme, high catalyst efficiency, selective reactions under mild conditions using green solvents and renewable starting materials, and producing minimal byproducts. Thus, the enzymatic polymerization is desirable for the environment and contributes to "green polymer chemistry" for maintaining sustainable society.

  4. PRIGo: a new multi-axis goniometer for macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Waltersperger, Sandro; Olieric, Vincent, E-mail: vincent.olieric@psi.ch; Pradervand, Claude [Paul Scherrer Institute, Villigen PSI (Switzerland); Glettig, Wayne [Centre Suisse d’Electronique et Microtechnique SA, Neuchâtel 2002 (Switzerland); Salathe, Marco; Fuchs, Martin R.; Curtin, Adrian; Wang, Xiaoqiang; Ebner, Simon; Panepucci, Ezequiel; Weinert, Tobias [Paul Scherrer Institute, Villigen PSI (Switzerland); Schulze-Briese, Clemens [Dectris Ltd, Baden 5400 (Switzerland); Wang, Meitian, E-mail: vincent.olieric@psi.ch [Paul Scherrer Institute, Villigen PSI (Switzerland)

    2015-05-09

    The design and performance of the new multi-axis goniometer PRIGo developed at the Swiss Light Source at Paul Scherrer Institute is described. The Parallel Robotics Inspired Goniometer (PRIGo) is a novel compact and high-precision goniometer providing an alternative to (mini-)kappa, traditional three-circle goniometers and Eulerian cradles used for sample reorientation in macromolecular crystallography. Based on a combination of serial and parallel kinematics, PRIGo emulates an arc. It is mounted on an air-bearing stage for rotation around ω and consists of four linear positioners working synchronously to achieve x, y, z translations and χ rotation (0–90°), followed by a ϕ stage (0–360°) for rotation around the sample holder axis. Owing to the use of piezo linear positioners and active correction, PRIGo features spheres of confusion of <1 µm, <7 µm and <10 µm for ω, χ and ϕ, respectively, and is therefore very well suited for micro-crystallography. PRIGo enables optimal strategies for both native and experimental phasing crystallographic data collection. Herein, PRIGo hardware and software, its calibration, as well as applications in macromolecular crystallography are described.

  5. Critical review and perspective of macromolecularly imprinted polymers.

    Science.gov (United States)

    Kryscio, David R; Peppas, Nicholas A

    2012-02-01

    Molecular recognition is a fundamental and ubiquitous process that is the driving force behind life. Natural recognition elements - including antibodies, enzymes, nucleic acids, and cells - exploit non-covalent interactions to bind to their targets with exceptionally strong affinities. Due to this unparalleled proficiency, scientists have long sought to mimic natural recognition pathways. One promising approach is molecularly imprinted polymers (MIPs), which are fully synthetic systems formed via the crosslinking of organic polymers in the presence of a template molecule, which results in stereo-specific binding sites for this analyte of interest. Macromolecularly imprinted polymers, those synthesized in the presence of macromolecule templates (>1500 Da), are of particular importance because they open up the field for a whole new set of robust diagnostic tools. Although the specific recognition of small-molecular-weight analytes is now considered routine, extension of these efficacious procedures to the protein regime has, thus far, proved challenging. This paper reviews the main approaches employed, highlights studies of interest with an emphasis on recent work, and offers suggestions for future success in the field of macromolecularly imprinted polymers.

  6. Enhancing Endosomal Escape for Intracellular Delivery of Macromolecular Biologic Therapeutics.

    Science.gov (United States)

    Lönn, Peter; Kacsinta, Apollo D; Cui, Xian-Shu; Hamil, Alexander S; Kaulich, Manuel; Gogoi, Khirud; Dowdy, Steven F

    2016-09-08

    Bioactive macromolecular peptides and oligonucleotides have significant therapeutic potential. However, due to their size, they have no ability to enter the cytoplasm of cells. Peptide/Protein transduction domains (PTDs), also called cell-penetrating peptides (CPPs), can promote uptake of macromolecules via endocytosis. However, overcoming the rate-limiting step of endosomal escape into the cytoplasm remains a major challenge. Hydrophobic amino acid R groups are known to play a vital role in viral escape from endosomes. Here we utilize a real-time, quantitative live cell split-GFP fluorescence complementation phenotypic assay to systematically analyze and optimize a series of synthetic endosomal escape domains (EEDs). By conjugating EEDs to a TAT-PTD/CPP spilt-GFP peptide complementation assay, we were able to quantitatively measure endosomal escape into the cytoplasm of live cells via restoration of GFP fluorescence by intracellular molecular complementation. We found that EEDs containing two aromatic indole rings or one indole ring and two aromatic phenyl groups at a fixed distance of six polyethylene glycol (PEG) units from the TAT-PTD-cargo significantly enhanced cytoplasmic delivery in the absence of cytotoxicity. EEDs address the critical rate-limiting step of endosomal escape in delivery of macromolecular biologic peptide, protein and siRNA therapeutics into cells.

  7. Microbial biosurfactants and biodegradation.

    Science.gov (United States)

    Ward, Owen P

    2010-01-01

    Microbial biosurfactants are amphipathic molecules having typical molecular weights of 500-1500 Da, made up of peptides, saccharides or lipids or their combinations. In biodegradation processes they mediate solubilisation, mobilization and/or accession of hydrophobic substrates to microbes. They may be located on the cell surface or be secreted into the extracellular medium and they facilitate uptake of hydrophobic molecules through direct cellular contact with hydrophobic solids or droplets or through micellarisation. They are also involved in cell physiological processes such as biofilm formation and detachment, and in diverse biofilm associated processes such as wastewater treatment and microbial pathogenesis. The protection of contaminants in biosurfactants micelles may also inhibit uptake of contaminants by microbes. In bioremediation processes biosurfactants may facilitate release of contaminants from soil, but soils also tend to bind surfactants strongly which makes their role in contaminant desorption more complex. A greater understanding of the underlying roles played by biosurfactants in microbial physiology and in biodegradative processes is developing through advances in cell and molecular biology.

  8. High-resolution three-dimensional quantitative map of the macromolecular proton fraction distribution in the normal rat brain

    Directory of Open Access Journals (Sweden)

    Anna V. Naumova

    2017-02-01

    Full Text Available The presented dataset provides a normative high-resolution three-dimensional (3D macromolecular proton fraction (MPF map of the healthy rat brain in vivo and source images used for its reconstruction. The images were acquired using the protocol described elsewhere (Naumova, et al. High-resolution three-dimensional macromolecular proton fraction mapping for quantitative neuroanatomical imaging of the rodent brain in ultra-high magnetic fields. Neuroimage (2016 doi: 10.1016/j.neuroimage.2016.09.036. The map was reconstructed from three source images with different contrast weightings (proton density, T1, and magnetization transfer using the single-point algorithm with a synthetic reference image. Source images were acquired from a living animal on an 11.7 T small animal MRI scanner with isotropic spatial resolution of 170 µm3 and total acquisition time about 1.5 h. The 3D dataset can be used for multiple purposes including interactive viewing of rat brain anatomy, measurements of reference MPF values in various brain structures, and development of image processing techniques for the rodent brain segmentation. It also can serve as a gold standard image for implementation and optimization of rodent brain MRI protocols.

  9. Biodegradation of Polypropylene Nonwovens

    Science.gov (United States)

    Keene, Brandi Nechelle

    The primary aim of the current research is to document the biodegradation of polypropylene nonwovens and filament under composting environments. To accelerate the biodegradat ion, pre-treatments and additives were incorporated into polypropylene filaments and nonwovens. The initial phase (Chapter 2) of the project studied the biodegradation of untreated polypropylene with/without pro-oxidants in two types of composting systems. Normal composting, which involved incubation of samples in food waste, had little effect on the mechanical properties of additive-free spunbond nonwovens in to comparison prooxidant containing spunbond nonwovens which were affected significantly. Modified composting which includes the burial of samples with food and compressed air, the polypropylene spunbond nonwovens with/without pro-oxidants displayed an extreme loss in mechanical properties and cracking on the surface cracking. Because the untreated spunbond nonwovens did not completely decompose, the next phase of the project examined the pre-treatment of gamma-irradiation or thermal aging prior to composting. After exposure to gamma-irradiation and thermal aging, polypropylene is subjected to oxidative degradation in the presence of air and during storage after irradiat ion. Similar to photo-oxidation, the mechanism of gamma radiation and thermal oxidative degradation is fundamentally free radical in nature. In Chapter 3, the compostability of thermal aged spunbond polypropylene nonwovens with/without pro-oxidant additives. The FTIR spectrum confirmed oxidat ion of the polypropylene nonwovens with/without additives. Cracking on both the pro-oxidant and control spunbond nonwovens was showed by SEM imaging. Spunbond polypropylene nonwovens with/without pro-oxidants were also preirradiated by gamma rays followed by composting. Nonwovens with/without pro-oxidants were severely degraded by gamma-irradiation after up to 20 kGy exposure as explained in Chapter 4. Furthermore (Chapter 5), gamma

  10. Extracting trends from two decades of microgravity macromolecular crystallization history

    Science.gov (United States)

    Judge, Russell A.; Snell, Edward H.; van der Woerd, Mark J.

    2005-01-01

    Since the 1980s hundreds of macromolecular crystal growth experiments have been performed in the reduced acceleration environment of an orbiting spacecraft. Significant enhancements in structural knowledge have resulted from X-ray diffraction of the crystals grown. Similarly, many samples have shown no improvement or degradation in comparison to those grown on the ground. A complex series of interrelated factors affect these experiments and by building a comprehensive archive of the results it was aimed to identify factors that result in success and those that result in failure. Specifically, it was found that dedicated microgravity missions increase the chance of success when compared with those where crystallization took place as a parasitic aspect of the mission. It was also found that the chance of success could not be predicted based on any discernible property of the macromolecule available to us.

  11. An analysis of fractal geometry of macromolecular gelation

    Institute of Scientific and Technical Information of China (English)

    左榘; 陈天红; 冉少峰; 何炳林; 董宝中; 生文君; 杨恒林

    1996-01-01

    With fractal geometry theory and based on experiments, an analysis of fractal geometry behavior of gelation of macromolecules was carried out. Using the cross-linking copolymerization of styrene-divinylbenzene (DVB) as an example, through the determinations of the evolution of the molecular weight, size and the dependence of scattering intensity on the angle of macromolecules by employing laser and synchrotron small angle X-ray scattering, respectively, this chemical reaction was described quantitatively, its fractal behavior was analyzed and the fractal dimension was also measured. By avoiding the complex theories on gelation, this approach is based on modern physical techniques and theories to perform the analysis of the behavior of fractal geometry of macromolecular gelation and thus is able to reveal the rules of this kind of complicated gelation more essentially and profoundly.

  12. Macromolecular Crystallization with Microfluidic Free-Interface Diffusion

    Energy Technology Data Exchange (ETDEWEB)

    Segelke, B

    2005-02-24

    Fluidigm released the Topaz 1.96 and 4.96 crystallization chips in the fall of 2004. Topaz 1.96 and 4.96 are the latest evolution of Fluidigm's microfluidics crystallization technologies that enable ultra low volume rapid screening for macromolecular crystallization. Topaz 1.96 and 4.96 are similar to each other but represent a major redesign of the Topaz system and have of substantially improved ease of automation and ease of use, improved efficiency and even further reduced amount of material needed. With the release of the new Topaz system, Fluidigm continues to set the standard in low volume crystallization screening which is having an increasing impact in the field of structural genomics, and structural biology more generally. In to the future we are likely to see further optimization and increased utility of the Topaz crystallization system, but we are also likely to see further innovation and the emergence of competing technologies.

  13. Macromolecularly "Caged" Carbon Nanoparticles for Intracellular Trafficking via Switchable Photoluminescence.

    Science.gov (United States)

    Misra, Santosh K; Srivastava, Indrajit; Tripathi, Indu; Daza, Enrique; Ostadhossein, Fatemeh; Pan, Dipanjan

    2017-02-08

    Reversible switching of photoluminescence (PL) of carbon nanoparticles (CNP) can be achieved with counterionic macromolecular caging and decaging at the nanoscale. A negatively charged uncoated, "bare" CNP with high luminescence loses its PL when positively charged macromolecules are wrapped around its surface. Prepared caged carbons could regain their emission only through interaction with anionic surfactant molecules, representing anionic amphiphiles of endocytic membranes. This process could be verified by gel electrophoresis, spectroscopically and in vitro confocal imaging studies. Results indicated for the first time that luminescence switchable CNPs can be synthesized for efficient intracellular tracking. This study further supports the origin of photoluminescence in CNP as a surface phenomenon correlated a function of characteristic charged macromolecules.

  14. Large-volume protein crystal growth for neutron macromolecular crystallography.

    Science.gov (United States)

    Ng, Joseph D; Baird, James K; Coates, Leighton; Garcia-Ruiz, Juan M; Hodge, Teresa A; Huang, Sijay

    2015-04-01

    Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for the growth of crystals to significant dimensions that are now relevant to NMC are revisited. These include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.

  15. In-vacuum long-wavelength macromolecular crystallography.

    Science.gov (United States)

    Wagner, Armin; Duman, Ramona; Henderson, Keith; Mykhaylyk, Vitaliy

    2016-03-01

    Structure solution based on the weak anomalous signal from native (protein and DNA) crystals is increasingly being attempted as part of synchrotron experiments. Maximizing the measurable anomalous signal by collecting diffraction data at longer wavelengths presents a series of technical challenges caused by the increased absorption of X-rays and larger diffraction angles. A new beamline at Diamond Light Source has been built specifically for collecting data at wavelengths beyond the capability of other synchrotron macromolecular crystallography beamlines. Here, the theoretical considerations in support of the long-wavelength beamline are outlined and the in-vacuum design of the endstation is discussed, as well as other hardware features aimed at enhancing the accuracy of the diffraction data. The first commissioning results, representing the first in-vacuum protein structure solution, demonstrate the promising potential of the beamline.

  16. On macromolecular refinement at subatomic resolution withinteratomic scatterers

    Energy Technology Data Exchange (ETDEWEB)

    Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.; Lunin, Vladimir Y.; Urzhumtsev, Alexandre

    2007-11-09

    A study of the accurate electron density distribution in molecular crystals at subatomic resolution, better than {approx} 1.0 {angstrom}, requires more detailed models than those based on independent spherical atoms. A tool conventionally used in small-molecule crystallography is the multipolar model. Even at upper resolution limits of 0.8-1.0 {angstrom}, the number of experimental data is insufficient for the full multipolar model refinement. As an alternative, a simpler model composed of conventional independent spherical atoms augmented by additional scatterers to model bonding effects has been proposed. Refinement of these mixed models for several benchmark datasets gave results comparable in quality with results of multipolar refinement and superior of those for conventional models. Applications to several datasets of both small- and macro-molecules are shown. These refinements were performed using the general-purpose macromolecular refinement module phenix.refine of the PHENIX package.

  17. Revealing the macromolecular targets of complex natural products

    Science.gov (United States)

    Reker, Daniel; Perna, Anna M.; Rodrigues, Tiago; Schneider, Petra; Reutlinger, Michael; Mönch, Bettina; Koeberle, Andreas; Lamers, Christina; Gabler, Matthias; Steinmetz, Heinrich; Müller, Rolf; Schubert-Zsilavecz, Manfred; Werz, Oliver; Schneider, Gisbert

    2014-12-01

    Natural products have long been a source of useful biological activity for the development of new drugs. Their macromolecular targets are, however, largely unknown, which hampers rational drug design and optimization. Here we present the development and experimental validation of a computational method for the discovery of such targets. The technique does not require three-dimensional target models and may be applied to structurally complex natural products. The algorithm dissects the natural products into fragments and infers potential pharmacological targets by comparing the fragments to synthetic reference drugs with known targets. We demonstrate that this approach results in confident predictions. In a prospective validation, we show that fragments of the potent antitumour agent archazolid A, a macrolide from the myxobacterium Archangium gephyra, contain relevant information regarding its polypharmacology. Biochemical and biophysical evaluation confirmed the predictions. The results obtained corroborate the practical applicability of the computational approach to natural product ‘de-orphaning’.

  18. Identification of macromolecular complexes in cryoelectron tomograms of phantom cells

    Science.gov (United States)

    Frangakis, Achilleas S.; Böhm, Jochen; Förster, Friedrich; Nickell, Stephan; Nicastro, Daniela; Typke, Dieter; Hegerl, Reiner; Baumeister, Wolfgang

    2002-01-01

    Electron tomograms of intact frozen-hydrated cells are essentially three-dimensional images of the entire proteome of the cell, and they depict the whole network of macromolecular interactions. However, this information is not easily accessible because of the poor signal-to-noise ratio of the tomograms and the crowded nature of the cytoplasm. Here, we describe a template matching algorithm that is capable of detecting and identifying macromolecules in tomographic volumes in a fully automated manner. The algorithm is based on nonlinear cross correlation and incorporates elements of multivariate statistical analysis. Phantom cells, i.e., lipid vesicles filled with macromolecules, provide a realistic experimental scenario for an assessment of the fidelity of this approach. At the current resolution of ≈4 nm, macromolecules in the size range of 0.5–1 MDa can be identified with good fidelity. PMID:12391313

  19. Biodegradable plastics from renewable sources.

    Science.gov (United States)

    Flieger, M; Kantorová, M; Prell, A; Rezanka, T; Votruba, J

    2003-01-01

    Plastic waste disposal is a huge ecotechnological problem and one of the approaches to solving this problem is the development of biodegradable plastics. This review summarizes data on their use, biodegradability, commercial reliability and production from renewable resources. Some commercially successful biodegradable plastics are based on chemical synthesis (i.e. polyglycolic acid, polylactic acid, polycaprolactone, and polyvinyl alcohol). Others are products of microbial fermentations (i.e. polyesters and neutral polysaccharides) or are prepared from chemically modified natural products (e.g., starch, cellulose, chitin or soy protein).

  20. Lung toxicity of biodegradable nanoparticles.

    Science.gov (United States)

    Fattal, Elias; Grabowski, Nadége; Mura, Simona; Vergnaud, Juliette; Tsapis, Nicolas; Hillaireau, Hervé

    2014-10-01

    Biodegradable nanoparticles exhibit high potentialities for local or systemic drug delivery through lung administration making them attractive as nanomedicine carriers. However, since particulate matter or some inorganic manufactured nanoparticles exposed to lung cells have provoked cytotoxic effects, inflammatory and oxidative stress responses, it becomes important to investigate nanomedicine toxicity towards the lungs. This is the reason why, in the present review, the behavior of biodegradable nanoparticles towards the different parts of the respiratory tract as well as the toxicological consequences, measured on several models in vitro, ex vivo or in vivo, are described. Taken all together, the different studies carried out so far conclude on no or slight toxicity of biodegradable nanoparticles.

  1. Biodegradable micromechanical sensors

    DEFF Research Database (Denmark)

    Keller, Stephan Sylvest; Greve, Anders; Schmid, Silvan

    The development of biopolymers for food packaging, medical engineering or drug delivery is a growing field of research [1]. At the same time, the interest in methods for detailed analysis of biopolymers is increasing. Micromechanical sensors are versatile tools for the characterization of mechani......The development of biopolymers for food packaging, medical engineering or drug delivery is a growing field of research [1]. At the same time, the interest in methods for detailed analysis of biopolymers is increasing. Micromechanical sensors are versatile tools for the characterization...... of biopolymers to microfabrication is challenging, as these polymers are affected by common processes such as photolithography or wet etching. Here, we present two methods for fabrication of biodegradable micromechanical sensors. First, we fabricated bulk biopolymer microcantilevers using nanoimprint lithography...

  2. Biodegradation of propellant ingredients

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Y.Z.; Sundaram, S.T.; Sharma, A. [Geo-centers, Inc., Lake Hopatcong, NJ (United States)] [and others

    1995-12-31

    This paper summarizes efforts to degrade nitrocellulose (NC) and nitroglycerin (NG) with fungi. Screening experiments were performed to determine the ability of mycelial fungi to biodegrade NC. The greatest amount of NC degradation was obtained with Sclerotium rolfsii ATCC 24459 and Fusarium solani IFO 31093. These fungi were then tested for NG degradation. It was found that the combined culture aerobically degraded 100% of the NG to form a mixture of 55% dinitroglycerin (DNG) and 5% of mononitroglycerin (MNG) in two days, with no further change observed afterward. In the presence of 1.2% glucose and 0.05% ammonium nitrate, NG was completely degraded in two days and a mixture of 20% DNG and 16% MNG was formed after 11 days. Based on these results, it appears that the combination of the fungi in a one to one ratio can be used to degrade both of these energetic compounds.

  3. Biofilm formation and partial biodegradation of polystyrene by the actinomycete Rhodococcus ruber: biodegradation of polystyrene.

    Science.gov (United States)

    Mor, Roi; Sivan, Alex

    2008-11-01

    Polystyrene, which is one of the most utilized thermoplastics, is highly durable and is considered to be non-biodegradable. Hence, polystyrene waste accumulates in the environment posing an increasing ecological threat. In a previous study we have isolated a biofilm-producing strain (C208) of the actinomycete Rhodococcus ruber that degraded polyethylene films. Formation of biofilm, by C208, improved the biodegradation of polyethylene. Consequently, the present study aimed at monitoring the kinetics of biofilm formation by C208 on polystyrene, determining the physiological activity of the biofilm and analyzing its capacity to degrade polystyrene. Quantification of the biofilm biomass was performed using a modified crystal violet (CV) staining or by monitoring the protein content in the biofilm. When cultured on polystyrene flakes, most of the bacterial cells adhered to the polystyrene surface within few hours, forming a biofilm. The growth of the on polystyrene showed a pattern similar to that of a planktonic culture. Furthermore, the respiration rate, of the biofilm, exhibited a pattern similar to that of the biofilm growth. In contrast, the respiration activity of the planktonic population showed a constant decline with time. Addition of mineral oil (0.005% w/v), but not non-ionic surfactants, increased the biofilm biomass. Extended incubation of the biofilm for up to 8 weeks resulted in a small reduction in the polystyrene weight (0.8% of gravimetric weight loss). This study demonstrates the high affinity of C208 to polystyrene which lead to biofilm formation and, presumably, induced partial biodegradation.

  4. Biomedical Applications of Biodegradable Polyesters

    OpenAIRE

    Iman Manavitehrani; Ali Fathi; Hesham Badr; Sean Daly; Ali Negahi Shirazi; Fariba Dehghani

    2016-01-01

    The focus in the field of biomedical engineering has shifted in recent years to biodegradable polymers and, in particular, polyesters. Dozens of polyester-based medical devices are commercially available, and every year more are introduced to the market. The mechanical performance and wide range of biodegradation properties of this class of polymers allow for high degrees of selectivity for targeted clinical applications. Recent research endeavors to expand the application of polymers have be...

  5. Macromolecular composition of terrestrial and marine organic matter in sediments across the East Siberian Arctic Shelf

    Science.gov (United States)

    Sparkes, Robert B.; Doğrul Selver, Ayça; Gustafsson, Örjan; Semiletov, Igor P.; Haghipour, Negar; Wacker, Lukas; Eglinton, Timothy I.; Talbot, Helen M.; van Dongen, Bart E.

    2016-10-01

    Mobilisation of terrestrial organic carbon (terrOC) from permafrost environments in eastern Siberia has the potential to deliver significant amounts of carbon to the Arctic Ocean, via both fluvial and coastal erosion. Eroded terrOC can be degraded during offshore transport or deposited across the wide East Siberian Arctic Shelf (ESAS). Most studies of terrOC on the ESAS have concentrated on solvent-extractable organic matter, but this represents only a small proportion of the total terrOC load. In this study we have used pyrolysis-gas chromatography-mass spectrometry (py-GCMS) to study all major groups of macromolecular components of the terrOC; this is the first time that this technique has been applied to the ESAS. This has shown that there is a strong offshore trend from terrestrial phenols, aromatics and cyclopentenones to marine pyridines. There is good agreement between proportion phenols measured using py-GCMS and independent quantification of lignin phenol concentrations (r2 = 0.67, p < 0.01, n = 24). Furfurals, thought to represent carbohydrates, show no offshore trend and are likely found in both marine and terrestrial organic matter. We have also collected new radiocarbon data for bulk OC (14COC) which, when coupled with previous measurements, allows us to produce the most comprehensive 14COC map of the ESAS to date. Combining the 14COC and py-GCMS data suggests that the aromatics group of compounds is likely sourced from old, aged terrOC, in contrast to the phenols group, which is likely sourced from modern woody material. We propose that an index of the relative proportions of phenols and pyridines can be used as a novel terrestrial vs. marine proxy measurement for macromolecular organic matter. Principal component analysis found that various terrestrial vs. marine proxies show different patterns across the ESAS, and it shows that multiple river-ocean transects of surface sediments transition from river-dominated to coastal-erosion-dominated to marine

  6. Solid-state NMR in macromolecular systems: insights on how molecular entities move.

    Science.gov (United States)

    Hansen, Michael Ryan; Graf, Robert; Spiess, Hans Wolfgang

    2013-09-17

    sciences have emphasized structure. By contrast, following X-ray crystallographers, researchers studying proteins using solution NMR introduced the combination of NMR with computer simulation before that became common practice in solid-state NMR. Today's simulation methods can handle partially ordered or even disordered systems common in synthetic polymers. Thus, the multitechnique approaches employed in NMR of synthetic and biological macromolecules have converged. Therefore, this Account will be relevant to both researchers studying synthetic macromolecular and supramolecular systems and those studying biological complexes.

  7. Biodegradable intestinal stents:A review

    Institute of Scientific and Technical Information of China (English)

    Zhanhui Wang; Nan Li; Rui Li; Yawei Li; Liqun Ruan

    2014-01-01

    Biodegradable stents are an attractive alternative to self-expanding metal stents in the treatment of intestinal strictures. Biodegradable stent can be made of biodegradable polymers and biodegradable metals (magnesium alloys). An overview on current biodegradable intestinal stents is presented. The future trends and perspectives in the development of biodegradable intestinal stents are proposed. For the biodegradable polymer intestinal stents, the clinical trials have shown promising results, although improved design of stents and reduced migration rate are expected. For the biodegradable magnesium intestinal stents, results of preliminary studies indicate magnesium alloys to have good biocompatibility. With many of the key fundamental and practical issues resolved and better methods for adjusting corrosion resistance and progressing biocompatibilities of magnesium alloys, it is possible to use biodegradable intestinal stents made of magnesium alloys in hospital in the not too distant future.

  8. Progress of biodegradable metals

    Institute of Scientific and Technical Information of China (English)

    Huafang Li; Yufeng Zheng; Ling Qin

    2014-01-01

    Biodegradable metals (BMs) are metals and alloys expected to corrode gradually in vivo, with an appropriate host response elicited by released corrosion products, then dissolve completely upon fulfilling the mission to assist with tissue healing with no implant residues. In the present review article, three classes of BMs have been systematically reviewed, including Mg-based, Fe-based and Zn-based BMs. Among the three BM systems, Mg-based BMs, which now have several systems reported the successful of clinical trial results, are considered the vanguards and main force. Fe-based BMs, with pure iron and Fe–Mn based alloys as the most promising, are still on the animal test stage. Zn-based BMs, supposed to have the degradation rate between the fast Mg-based BMs and the slow Fe-based BMs, are a rising star with only several reports and need much further research. The future research and development direction for the BMs are proposed, based on the clinical requirements on controllable degradation rate, prolonged mechanical stability and excellent biocompat-ibility, by optimization of alloy composition design, regulation on microstructure and mechanical properties, and following surface modification.

  9. Progress of biodegradable metals

    Directory of Open Access Journals (Sweden)

    Huafang Li

    2014-10-01

    Full Text Available Biodegradable metals (BMs are metals and alloys expected to corrode gradually in vivo, with an appropriate host response elicited by released corrosion products, then dissolve completely upon fulfilling the mission to assist with tissue healing with no implant residues. In the present review article, three classes of BMs have been systematically reviewed, including Mg-based, Fe-based and Zn-based BMs. Among the three BM systems, Mg-based BMs, which now have several systems reported the successful of clinical trial results, are considered the vanguards and main force. Fe-based BMs, with pure iron and Fe–Mn based alloys as the most promising, are still on the animal test stage. Zn-based BMs, supposed to have the degradation rate between the fast Mg-based BMs and the slow Fe-based BMs, are a rising star with only several reports and need much further research. The future research and development direction for the BMs are proposed, based on the clinical requirements on controllable degradation rate, prolonged mechanical stability and excellent biocompatibility, by optimization of alloy composition design, regulation on microstructure and mechanical properties, and following surface modification.

  10. Biodegradation of polyethoxylated nonylphenols.

    Science.gov (United States)

    Ruiz, Yassellis; Medina, Luis; Borusiak, Margarita; Ramos, Nairalith; Pinto, Gilberto; Valbuena, Oscar

    2013-01-01

    Polyethoxylated nonylphenols, with different ethoxylation degrees (NPEO x ), are incorporated into many commercial and industrial products such as detergents, domestic disinfectants, emulsifiers, cosmetics, and pesticides. However, the toxic effects exerted by their degradation products, which are persistent in natural environments, have been demonstrated in several animal and invertebrate aquatic species. Therefore, it seems appropriate to look for indigenous bacteria capable of degrading native NPEO x and its derivatives. In this paper, the isolation of five bacterial strains, capable of using NPEO 15 , as unique carbon source, is described. The most efficient NPEO 15 degrader bacterial strains were identified as Pseudomonas fluorescens (strain Yas2) and Klebsiella pneumoniae (strain Yas1). Maximal growth rates were reached at pH 8, 27°C in a 5% NPEO 15 medium. The NPEO 15 degradation extension, followed by viscometry assays, reached 65% after 54.5 h and 134 h incubation times, while the COD values decreased by 95% and 85% after 24 h for the Yas1 and Yas2 systems, respectively. The BOD was reduced by 99% and 99.9% levels in 24 h and 48 h incubations. The viscosity data indicated that the NPEO 15 biodegradation by Yas2 follows first-order kinetics. Kinetic rate constant (k) and half life time (τ) for this biotransformation were estimated to be 0.0072 h(-1) and 96.3 h, respectively.

  11. NMR RELAXIVITY AND IMAGING OF NEUTRAL MACROMOLECULAR POLYESTER GADOLINIUM (Ⅲ) COMPLEXES

    Institute of Scientific and Technical Information of China (English)

    Kai-chao Yu; Hong-bing Hu; Mai-li Liu; Han-zhen Yuan; Chao-hui Ye; Ren-xi Zhuo

    1999-01-01

    Five neutral macromolecular polyester gadolinium (Ⅲ) complexes with pendant hydrophobic alkyl and aromatic functional groups were prepared. The longitudinal relaxation rates of these complexes were measured. One of these Gd (Ⅲ) complexes was chosen for the acute toxicity test and T1-weighted imaging measurement. Preliminary results showed that. compared with Gd-DTPA, the neutral macromolecular gadolinium (Ⅲ) complexes provide higher T1 relaxivity enhancement and longer function duration.

  12. A versatile microparticle-based immunoaggregation assay for macromolecular biomarker detection and quantification.

    Directory of Open Access Journals (Sweden)

    Haiyan Wu

    Full Text Available The rapid, sensitive and low-cost detection of macromolecular biomarkers is critical in clinical diagnostics, environmental monitoring, research, etc. Conventional assay methods usually require bulky, expensive and designated instruments and relative long assay time. For hospitals and laboratories that lack immediate access to analytical instruments, fast and low-cost assay methods for the detection of macromolecular biomarkers are urgently needed. In this work, we developed a versatile microparticle (MP-based immunoaggregation method for the detection and quantification of macromolecular biomarkers. Antibodies (Abs were firstly conjugated to MP through streptavidin-biotin interaction; the addition of macromolecular biomarkers caused the aggregation of Ab-MPs, which were subsequently detected by an optical microscope or optical particle sizer. The invisible nanometer-scale macromolecular biomarkers caused detectable change of micrometer-scale particle size distributions. Goat anti-rabbit immunoglobulin and human ferritin were used as model biomarkers to demonstrate MP-based immunoaggregation assay in PBS and 10% FBS to mimic real biomarker assay in the complex medium. It was found that both the number ratio and the volume ratio of Ab-MP aggregates caused by biomarker to all particles were directly correlated to the biomarker concentration. In addition, we found that the detection range could be tuned by adjusting the Ab-MP concentration. We envision that this novel MP-based immunoaggregation assay can be combined with multiple detection methods to detect and quantify macromolecular biomarkers at the nanogram per milliliter level.

  13. Macromolecular Engineering: New Routes Towards the Synthesis of Well-??Defined Polyethers/Polyesters Co/Terpolymers with Different Architectures

    KAUST Repository

    Alamri, Haleema

    2016-05-18

    The primary objective of this research was to develop a new and efficient pathway for well-defined multicomponent homo/co/terpolymers of cyclic esters/ethers using an organocatalytic approach with an emphasis on the macromolecular engineering aspects of the overall synthesis. Macromolecular engineering (as discussed in the first chapter) of homo/copolymers refers to the specific tailoring of these materials for achieving an easy and reproducible synthesis that results in precise molecular characteristics, i.e. molecular weight and polydispersity, as well as specific structure and end?group choices. Precise control of these molecular characteristics will provide access to new materials that can be used for pre-targeted purposes such as biomedical applications. Among the most commonly used engineering materials are polyesters (biocompatible and biodegradable) and polyethers (biocompatible), either as homopolymers or when or copolymers with linear structures. The ability to create non-linear structures, for example stars, will open new horizons in the applications of these important polymeric materials. The second part of this thesis describes the synthesis of aliphatic polyesters, particularly polycaprolactone and polylactide, using a metal-free initiator/catalyst system. A phosphazene base (t?BuP2) was used as the catalyst for the ring-opening copolymerization of ?-aprolactone (??CL) and L,Lactide (LLA) at room temperature with a variety of protic initiators in different solvents. These studies provided important information for the design of a metal-free route toward the synthesis of polyester?based (bio) materials. The third part of the thesis describes a novel route for the one?pot synthesis of polyether-b polyester block copolymers with either a linear or a specific macromolecular architecture. Poly (styrene oxide)?b?poly(caprolactone)?b?poly(L,lactide) was prepared using this method with the goal of synthesizing poly(styrene oxide)-based materials since this

  14. Macromolecular metallurgy of binary mesocrystals via designed multiblock terpolymers.

    Science.gov (United States)

    Xie, Nan; Liu, Meijiao; Deng, Hanlin; Li, Weihua; Qiu, Feng; Shi, An-Chang

    2014-02-26

    Self-assembling block copolymers provide access to the fabrication of various ordered phases. In particular, the ordered spherical phases can be used to engineer soft mesocrystals with domain size at the 5-100 nm scales. Simple block copolymers, such as diblock copolymers, form a limited number of mesocrystals. However multiblock copolymers are capable to form more complex mesocrystals. We demonstrate that designed B1AB2CB3 multiblock terpolymers, in which the A- and C-blocks form spherical domains and the packing of these spheres can be controlled by changing the lengths of the middle and terminal B-blocks, self-assemble into various binary mesocrystals with space group symmetries of a large number of binary ionic crystals, including NaCl, CsCl, ZnS, α-BN, AlB2, CaF2, TiO2, ReO3, Li3Bi, Nb3Sn(A15), and α-Al2O3. This approach can be generalized to other terpolymers as well as to tetrapolymers to obtain ternary mesocrystals. Our study provides a new concept of macromolecular metallurgy for producing crystal phases in a mesoscale and thus makes multiblock copolymers a robust platform for the engineering of functional materials.

  15. Macromolecular Powder Diffraction: Ready for genuine biological problems.

    Science.gov (United States)

    Karavassili, Fotini; Margiolaki, Irene

    2016-01-01

    Knowledge of 3D structures of biological molecules plays a major role in both understanding important processes of life and developing pharmaceuticals. Among several methods available for structure determination, macromolecular X-ray powder diffraction (XRPD) has transformed over the past decade from an impossible dream to a respectable method. XRPD can be employed in biosciences for various purposes such as observing phase transitions, characterizing bulk pharmaceuticals, determining structures via the molecular replacement method, detecting ligands in protein-ligand complexes, as well as combining micro-sized single crystal crystallographic data and powder diffraction data. Studies using synchrotron and laboratory sources in some standard configuration setups are reported in this review, including their respective advantages and disadvantages. Methods presented here provide an alternative, complementary set of tools to resolve structural problems. A variety of already existing software packages for powder diffraction data processing and analysis, some of which have been adapted to large unit cell studies, are briefly described. This review aims to provide necessary elements of theory and current methods, along with practical explanations, available software packages and highlighted case studies.

  16. Canadian macromolecular crystallography facility: a suite of fully automated beamlines.

    Science.gov (United States)

    Grochulski, Pawel; Fodje, Michel; Labiuk, Shaunivan; Gorin, James; Janzen, Kathryn; Berg, Russ

    2012-06-01

    The Canadian light source is a 2.9 GeV national synchrotron radiation facility located on the University of Saskatchewan campus in Saskatoon. The small-gap in-vacuum undulator illuminated beamline, 08ID-1, together with the bending magnet beamline, 08B1-1, constitute the Canadian Macromolecular Crystallography Facility (CMCF). The CMCF provides service to more than 50 Principal Investigators in Canada and the United States. Up to 25% of the beam time is devoted to commercial users and the general user program is guaranteed up to 55% of the useful beam time through a peer-review process. CMCF staff provides "Mail-In" crystallography service to users with the highest scored proposals. Both beamlines are equipped with very robust end-stations including on-axis visualization systems, Rayonix 300 CCD series detectors and Stanford-type robotic sample auto-mounters. MxDC, an in-house developed beamline control system, is integrated with a data processing module, AutoProcess, allowing full automation of data collection and data processing with minimal human intervention. Sample management and remote monitoring of experiments is enabled through interaction with a Laboratory Information Management System developed at the facility.

  17. Patch-clamp detection of macromolecular translocation along nuclear pores

    Directory of Open Access Journals (Sweden)

    Bustamante J.O.

    1998-01-01

    Full Text Available The present paper reviews the application of patch-clamp principles to the detection and measurement of macromolecular translocation along the nuclear pores. We demonstrate that the tight-seal 'gigaseal' between the pipette tip and the nuclear membrane is possible in the presence of fully operational nuclear pores. We show that the ability to form a gigaseal in nucleus-attached configurations does not mean that only the activity of channels from the outer membrane of the nuclear envelope can be detected. Instead, we show that, in the presence of fully operational nuclear pores, it is likely that the large-conductance ion channel activity recorded derives from the nuclear pores. We conclude the technical section with the suggestion that the best way to demonstrate that the nuclear pores are responsible for ion channel activity is by showing with fluorescence microscopy the nuclear translocation of ions and small molecules and the exclusion of the same from the cisterna enclosed by the two membranes of the envelope. Since transcription factors and mRNAs, two major groups of nuclear macromolecules, use nuclear pores to enter and exit the nucleus and play essential roles in the control of gene activity and expression, this review should be useful to cell and molecular biologists interested in understanding how patch-clamp can be used to quantitate the translocation of such macromolecules into and out of the nucleus

  18. Timely deposition of macromolecular structures is necessary for peer review

    Energy Technology Data Exchange (ETDEWEB)

    Joosten, Robbie P. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Soueidan, Hayssam; Wessels, Lodewyk F. A. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam (Netherlands); Perrakis, Anastassis, E-mail: a.perrakis@nki.nl [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands)

    2013-12-01

    Deposition of crystallographic structures should be concurrent with or prior to manuscript submission for peer review, enabling validation and increasing reliability of the PDB. Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found that a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature.

  19. Synchrotron radiation macromolecular crystallography: science and spin-offs

    Directory of Open Access Journals (Sweden)

    John R. Helliwell

    2015-03-01

    Full Text Available A current overview of synchrotron radiation (SR in macromolecular crystallography (MX instrumentation, methods and applications is presented. Automation has been and remains a central development in the last decade, as have the rise of remote access and of industrial service provision. Results include a high number of Protein Data Bank depositions, with an increasing emphasis on the successful use of microcrystals. One future emphasis involves pushing the frontiers of using higher and lower photon energies. With the advent of X-ray free-electron lasers, closely linked to SR developments, the use of ever smaller samples such as nanocrystals, nanoclusters and single molecules is anticipated, as well as the opening up of femtosecond time-resolved diffraction structural studies. At SR sources, a very high-throughput assessment for the best crystal samples and the ability to tackle just a few micron and sub-micron crystals will become widespread. With higher speeds and larger detectors, diffraction data volumes are becoming long-term storage and archiving issues; the implications for today and the future are discussed. Together with the rise of the storage ring to its current pre-eminence in MX data provision, the growing tendency of central facility sites to offer other centralized facilities complementary to crystallography, such as cryo-electron microscopy and NMR, is a welcome development.

  20. JBluIce-EPICS control system for macromolecular crystallography.

    Energy Technology Data Exchange (ETDEWEB)

    Stepanov, S.; Makarov, O.; Hilgart, M.; Pothineni, S.; Urakhchin, A.; Devarapalli, S.; Yoder, D.; Becker, M.; Ogata, C.; Sanishvili, R.; Nagarajan, V.; Smith, J. L.; Fischetti, R. F. (Biosciences Division); (Univ. of Michigan)

    2011-01-01

    The trio of macromolecular crystallography beamlines constructed by the General Medicine and Cancer Institutes Collaborative Access Team (GM/CA-CAT) in Sector 23 of the Advanced Photon Source (APS) have been in growing demand owing to their outstanding beam quality and capacity to measure data from crystals of only a few micrometres in size. To take full advantage of the state-of-the-art mechanical and optical design of these beamlines, a significant effort has been devoted to designing fast, convenient, intuitive and robust beamline controls that could easily accommodate new beamline developments. The GM/CA-CAT beamline controls are based on the power of EPICS for distributed hardware control, the rich Java graphical user interface of Eclipse RCP and the task-oriented philosophy as well as the look and feel of the successful SSRL BluIce graphical user interface for crystallography. These beamline controls feature a minimum number of software layers, the wide use of plug-ins that can be written in any language and unified motion controls that allow on-the-fly scanning and optimization of any beamline component. This paper describes the ways in which BluIce was combined with EPICS and converted into the Java-based JBluIce, discusses the solutions aimed at streamlining and speeding up operations and gives an overview of the tools that are provided by this new open-source control system for facilitating crystallographic experiments, especially in the field of microcrystallography.

  1. Adhesion of biocompatible and biodegradable micropatterned surfaces

    NARCIS (Netherlands)

    Kaiser, J.S.; Kamperman, M.M.G.; Souza, E.J.; Schick, B.; Arzt, E.

    2011-01-01

    We studied the effects of pillar dimensions and stiffness of biocompatible and biodegradable micropatterned surfaces on adhesion on different compliant substrates. The micropatterned adhesives were based on biocompatible polydimethylsiloxane (PDMS) and biodegradable poly(lactic-co-glycolic) acid (PL

  2. Classification and basic properties of contrast agents for magnetic resonance imaging.

    Science.gov (United States)

    Geraldes, Carlos F G C; Laurent, Sophie

    2009-01-01

    A comprehensive classification of contrast agents currently used or under development for magnetic resonance imaging (MRI) is presented. Agents based on small chelates, macromolecular systems, iron oxides and other nanosystems, as well as responsive, chemical exchange saturation transfer (CEST) and hyperpolarization agents are covered in order to discuss the various possibilities of using MRI as a molecular imaging technique. The classification includes composition, magnetic properties, biodistribution and imaging applications. Chemical compositions of various classes of MRI contrast agents are tabulated, and their magnetic status including diamagnetic, paramagnetic and superparamagnetic are outlined. Classification according to biodistribution covers all types of MRI contrast agents including, among others, extracellular, blood pool, polymeric, particulate, responsive, oral, and organ specific (hepatobiliary, RES, lymph nodes, bone marrow and brain). Various targeting strategies of molecular, macromolecular and particulate carriers are also illustrated.

  3. CaMKII binding to GluN2B is differentially affected by macromolecular crowding reagents.

    Directory of Open Access Journals (Sweden)

    Dayton J Goodell

    Full Text Available Binding of the Ca2+/calmodulin(CaM-dependent protein kinase II (CaMKII to the NMDA-type glutamate receptor (NMDAR subunit GluN2B controls long-term potentiation (LTP, a form of synaptic plasticity thought to underlie learning and memory. Regulation of this interaction is well-studied biochemically, but not under conditions that mimic the macromolecular crowding found within cells. Notably, previous molecular crowding experiments with lysozyme indicated an effect on the CaMKII holoenzyme conformation. Here, we found that the effect of molecular crowding on Ca2+/CaM-induced CaMKII binding to immobilized GluN2B in vitro depended on the specific crowding reagent. While binding was reduced by lysozyme, it was enhanced by BSA. The ATP content in the BSA preparation caused CaMKII autophosphorylation at T286 during the binding reaction; however, enhanced binding was also observed when autophosphorylation was blocked. Importantly, the positive regulation by nucleotide and BSA (as well as other macromolecular crowding reagents did not alleviate the requirement for CaMKII stimulation to induce GluN2B binding. The differential effect of lysozyme (14 kDa and BSA (66 kDa was not due to size difference, as both dextran-10 and dextran-70 enhanced binding. By contrast, crowding with immunoglobulin G (IgG reduced binding. Notably, lysozyme and IgG but not BSA directly bound to Ca2+/CaM in an overlay assay, suggesting a competition of lysozyme and IgG with the Ca2+/CaM-stimulus that induces CaMKII/GluN2B binding. However, lysozyme negatively regulated binding even when it was instead induced by CaMKII T286 phosphorylation. Alternative modes of competition would be with CaMKII or GluN2B, and the negative effects of lysozyme and IgG indeed also correlated with specific or non-specific binding to the immobilized GluN2B. Thus, the effect of any specific crowding reagent can differ, depending on its additional direct effects on CaMKII/GluN2B binding. However, the

  4. DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions.

    Science.gov (United States)

    Kuang, Xingyan; Dhroso, Andi; Han, Jing Ginger; Shyu, Chi-Ren; Korkin, Dmitry

    2016-01-01

    Macromolecular interactions are formed between proteins, DNA and RNA molecules. Being a principle building block in macromolecular assemblies and pathways, the interactions underlie most of cellular functions. Malfunctioning of macromolecular interactions is also linked to a number of diseases. Structural knowledge of the macromolecular interaction allows one to understand the interaction's mechanism, determine its functional implications and characterize the effects of genetic variations, such as single nucleotide polymorphisms, on the interaction. Unfortunately, until now the interactions mediated by different types of macromolecules, e.g. protein-protein interactions or protein-DNA interactions, are collected into individual and unrelated structural databases. This presents a significant obstacle in the analysis of macromolecular interactions. For instance, the homogeneous structural interaction databases prevent scientists from studying structural interactions of different types but occurring in the same macromolecular complex. Here, we introduce DOMMINO 2.0, a structural Database Of Macro-Molecular INteractiOns. Compared to DOMMINO 1.0, a comprehensive database on protein-protein interactions, DOMMINO 2.0 includes the interactions between all three basic types of macromolecules extracted from PDB files. DOMMINO 2.0 is automatically updated on a weekly basis. It currently includes ∼1,040,000 interactions between two polypeptide subunits (e.g. domains, peptides, termini and interdomain linkers), ∼43,000 RNA-mediated interactions, and ∼12,000 DNA-mediated interactions. All protein structures in the database are annotated using SCOP and SUPERFAMILY family annotation. As a result, protein-mediated interactions involving protein domains, interdomain linkers, C- and N- termini, and peptides are identified. Our database provides an intuitive web interface, allowing one to investigate interactions at three different resolution levels: whole subunit network

  5. A Compact X-Ray System for Macromolecular Crystallography. 5

    Science.gov (United States)

    Gubarev, Mikhail; Ciszak, Ewa; Ponomarev, Igor; Joy, Marshall

    2000-01-01

    We describe the design and performance of a high flux x-ray system for macromolecular crystallography that combines a microfocus x-ray generator (40 gm FWHM spot size at a power level of 46.5Watts) and a 5.5 mm focal distance polycapillary optic. The Cu K(sub alpha) X-ray flux produced by this optimized system is 7.0 times above the X-ray flux previously reported. The X-ray flux from the microfocus system is also 3.2 times higher than that produced by the rotating anode generator equipped with a long focal distance graded multilayer monochromator (Green optic; CMF24-48-Cu6) and 30% less than that produced by the rotating anode generator with the newest design of graded multilayer monochromator (Blue optic; CMF12-38-Cu6). Both rotating anode generators operate at a power level of 5000 Watts, dissipating more than 100 times the power of our microfocus x-ray system. Diffraction data collected from small test crystals are of high quality. For example, 42,540 reflections collected at ambient temperature from a lysozyme crystal yielded R(sub sym) 5.0% for the data extending to 1.7A, and 4.8% for the complete set of data to 1.85A. The amplitudes of the reflections were used to calculate difference electron density maps that revealed positions of structurally important ions and water molecules in the crystal of lysozyme using the phases calculated from the protein model.

  6. A Compact X-Ray System for Macromolecular Crystallography

    Science.gov (United States)

    Gubarev, Mikhail; Ciszak, Ewa; Ponomarev, Igor; Gibson, Walter; Joy, Marshall

    2000-01-01

    We describe the design and performance of a high flux x-ray system for a macromolecular crystallography that combines a microfocus x-ray generator (40 micrometer full width at half maximum spot size at a power level of 46.5 W) and a collimating polycapillary optic. The Cu Ka lpha x-ray flux produced by this optimized system through a 500,um diam orifice is 7.0 times greater than the x-ray flux previously reported by Gubarev et al. [M. Gubarev et al., J. Appl. Crystallogr. 33, 882 (2000)]. The x-ray flux from the microfocus system is also 2.6 times higher than that produced by a rotating anode generator equipped with a graded multilayer monochromator (green optic, Osmic Inc. CMF24-48-Cu6) and 40% less than that produced by a rotating anode generator with the newest design of graded multilayer monochromator (blue optic, Osmic, Inc. CMF12-38-Cu6). Both rotating anode generators operate at a power level of 5000 W, dissipating more than 100 times the power of our microfocus x-ray system. Diffraction data collected from small test crystals are of high quality. For example, 42 540 reflections collected at ambient temperature from a lysozyme crystal yielded R(sub sym)=5.0% for data extending to 1.70 A, and 4.8% for the complete set of data to 1.85 A. The amplitudes of the observed reflections were used to calculate difference electron density maps that revealed positions of structurally important ions and water molecules in the crystal of lysozyme using the phases calculated from the protein model.

  7. Biodegradable congress 2012; Bioschmierstoff-Kongress 2012

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-11-01

    Within the Guelzower expert discussions at 5th and 6th June, 2012 in Oberhausen (Federal Republic of Germany) the following lectures were held: (1) Promotion of biodegradable lubricants by means of research and development as well as public relations (Steffen Daebeler); (2) Biodegradable lubricants - An overview of the advantages and disadvantages of the engaged product groups (Hubertus Murrenhoff); (3) Standardization of biodegradable lubricants - CEN/DIN standard committees - state of the art (Rolf Luther); (4) Market research for the utilization of biodegradable lubricants and means of proof of sustainability (Norbert Schmitz); (5) Fields of application for high performance lubricants and requirements upon the products (Gunther Kraft); (6) Investigations of biodegradable lubricants in rolling bearings and gears (Christoph Hentschke); (7) Biodegradable lubricants in central lubrication systems Development of gears and bearings of offshore wind power installations (Reiner Wagner); (8) Investigations towards environmental compatibility of biodegradable lubricants used in offshore wind power installations (Tolf Schneider); (9) Development of glycerine based lubricants for the industrial metalworking (Harald Draeger); (10) Investigations and utilization of biodegradable oils as electroinsulation oils in transformers (Stefan Tenbohlen); (11) Operational behaviour of lubricant oils in vegetable oil operation and Biodiesel operation (Horst Hamdorf); (12) Lubrication effect of lubricating oil of the third generation (Stefan Heitzig); (13) Actual market development from the view of a producer of biodegradable lubricants (Frank Lewen); (14) Utilization of biodegradable lubricants in forestry harvesters (Guenther Weise); (15) New biodegradable lubricants based on high oleic sunflower oil (Otto Botz); (16) Integrated fluid concept - optimized technology and service package for users of biodegradable lubricants (Juergen Baer); (17) Utilization of a bio oil sensor to control

  8. A simple quantitative model of macromolecular crowding effects on protein folding: Application to the murine prion protein(121-231)

    Science.gov (United States)

    Bergasa-Caceres, Fernando; Rabitz, Herschel A.

    2013-06-01

    A model of protein folding kinetics is applied to study the effects of macromolecular crowding on protein folding rate and stability. Macromolecular crowding is found to promote a decrease of the entropic cost of folding of proteins that produces an increase of both the stability and the folding rate. The acceleration of the folding rate due to macromolecular crowding is shown to be a topology-dependent effect. The model is applied to the folding dynamics of the murine prion protein (121-231). The differential effect of macromolecular crowding as a function of protein topology suffices to make non-native configurations relatively more accessible.

  9. Connexin26 regulates assembly and maintenance of cochlear gap junction macromolecular complex for normal hearing

    Science.gov (United States)

    Kamiya, Kazusaku; Fukunaga, Ichiro; Hatakeyama, Kaori; Ikeda, Katsuhisa

    2015-12-01

    Hereditary deafness affects about 1 in 2000 children and GJB2 gene mutation is most frequent cause for this disease in the world. GJB2 encodes connexin26 (Cx26), a component in cochlear gap junction. Recently, we found macromolecular change of gap junction plaques with two different types of Cx26 mutation as major classification of clinical case, one is a model of dominant negative type, Cx26R75W+ and the other is conditional gene deficient mouse, Cx26f/fP0Cre as a model for insufficiency of gap junction protein [6]. Gap junction composed mainly of Cx26 and Cx30 in wild type mice formed large planar gap junction plaques (GJP). In contrast, Cx26R75W+ and Cx26f/fP0Cre showed fragmented small round GJPs around the cell border. In Cx26f/fP0Cre, some of the cells with Cx26 expression due to their cellular mosaicism showed normal large GJP with Cx26 and Cx30 only at the cell junction site between two Cx26 positive cells. These indicate that bilateral Cx26 expressions from both adjacent cells are essential for the formation of the cochlear linear GJP, and it is not compensated by other cochlear Connexins such as Connexin30. In the present study, we demonstrated a new molecular pathology in most common hereditary deafness with different types of Connexin26 mutations, and this machinery can be a new target for drag design of hereditary deafness.

  10. The second green revolution? Production of plant-based biodegradable plastics.

    Science.gov (United States)

    Mooney, Brian P

    2009-03-01

    Biodegradable plastics are those that can be completely degraded in landfills, composters or sewage treatment plants by the action of naturally occurring micro-organisms. Truly biodegradable plastics leave no toxic, visible or distinguishable residues following degradation. Their biodegradability contrasts sharply with most petroleum-based plastics, which are essentially indestructible in a biological context. Because of the ubiquitous use of petroleum-based plastics, their persistence in the environment and their fossil-fuel derivation, alternatives to these traditional plastics are being explored. Issues surrounding waste management of traditional and biodegradable polymers are discussed in the context of reducing environmental pressures and carbon footprints. The main thrust of the present review addresses the development of plant-based biodegradable polymers. Plants naturally produce numerous polymers, including rubber, starch, cellulose and storage proteins, all of which have been exploited for biodegradable plastic production. Bacterial bioreactors fed with renewable resources from plants--so-called 'white biotechnology'--have also been successful in producing biodegradable polymers. In addition to these methods of exploiting plant materials for biodegradable polymer production, the present review also addresses the advances in synthesizing novel polymers within transgenic plants, especially those in the polyhydroxyalkanoate class. Although there is a stigma associated with transgenic plants, especially food crops, plant-based biodegradable polymers, produced as value-added co-products, or, from marginal land (non-food), crops such as switchgrass (Panicum virgatum L.), have the potential to become viable alternatives to petroleum-based plastics and an environmentally benign and carbon-neutral source of polymers.

  11. Poly (3-Hydroxyalkanoates): Biodegradable Plastics

    OpenAIRE

    2013-01-01

    During the 1920’s, a polyester called poly (3-hydroxybutyrate) was discovered in bacterial cells. This compound, otherwise known as PHB, is part of a polyester family called polyhydroxyalkanoates (PHAs). Polyhydroxyalkanoates are used as an energy and carbon sto rage compound within certain bacterial cells. Polyhydroxyalkanoates (PHAs) are thermoplastic, biodegradable polyesters synthesized by some bacteria from rene...

  12. Biodegradable polymeric prodrugs of naltrexone

    NARCIS (Netherlands)

    Bennet, D.B.; Li, X.; Adams, N.W.; Kim, S.W.; Hoes, C.J.T.; Feijen, J.

    1991-01-01

    The development of a biodegradable polymeric drug delivery system for the narcotic antagonist naltrexone may improve patient compliance in the treatment of opiate addiction. Random copolymers consisting of the ¿-amino acids N5-(3-hydroxypropyl--glutamine and -leucine were synthesized with equimolar

  13. Biodegradation kinetics at low concentrations (

    DEFF Research Database (Denmark)

    Toräng, Lars; Albrechtsen, Hans-Jørgen; Nyholm, Niels

    2000-01-01

    Aerobic biodegradation of 2,4-dichlorophenoxyacetic acid (2,4-D) was studied in groundwater added sediment fines. At concentrations at or below 1 mu g/L of 2,4-D degradation kinetic was of true first order without significant growth of specific degraders and with half-life for mineralization...

  14. Biodegradable Pectin/clay Aerogels

    Science.gov (United States)

    Biodegradable, foamlike materials based on renewable pectin and sodium montmorillonite clay were fabricated through a simple, environmentally friendly freeze-drying process. Addition of multivalent cations (Ca2+ and Al3+) resulted in apparent crosslinking of the polymer, and enhancement of aerogel p...

  15. A kinetic model for predicting biodegradation.

    Science.gov (United States)

    Dimitrov, S; Pavlov, T; Nedelcheva, D; Reuschenbach, P; Silvani, M; Bias, R; Comber, M; Low, L; Lee, C; Parkerton, T; Mekenyan, O

    2007-01-01

    Biodegradation plays a key role in the environmental risk assessment of organic chemicals. The need to assess biodegradability of a chemical for regulatory purposes supports the development of a model for predicting the extent of biodegradation at different time frames, in particular the extent of ultimate biodegradation within a '10 day window' criterion as well as estimating biodegradation half-lives. Conceptually this implies expressing the rate of catabolic transformations as a function of time. An attempt to correlate the kinetics of biodegradation with molecular structure of chemicals is presented. A simplified biodegradation kinetic model was formulated by combining the probabilistic approach of the original formulation of the CATABOL model with the assumption of first order kinetics of catabolic transformations. Nonlinear regression analysis was used to fit the model parameters to OECD 301F biodegradation kinetic data for a set of 208 chemicals. The new model allows the prediction of biodegradation multi-pathways, primary and ultimate half-lives and simulation of related kinetic biodegradation parameters such as biological oxygen demand (BOD), carbon dioxide production, and the nature and amount of metabolites as a function of time. The model may also be used for evaluating the OECD ready biodegradability potential of a chemical within the '10-day window' criterion.

  16. Detection of Macromolecular Fractions in HCN Polymers Using Electrophoretic and Ultrafiltration Techniques.

    Science.gov (United States)

    Marín-Yaseli, Margarita R; Cid, Cristina; Yagüe, Ana I; Ruiz-Bermejo, Marta

    2017-02-01

    Elucidating the origin of life involves synthetic as well as analytical challenges. Herein, for the first time, we describe the use of gel electrophoresis and ultrafiltration to fractionate HCN polymers. Since the first prebiotic synthesis of adenine by Oró, HCN polymers have gained much interest in studies on the origins of life due to the identification of biomonomers and related compounds within them. Here, we demonstrate that macromolecular fractions with electrophoretic mobility can also be detected within HCN polymers. The migration of polymers under the influence of an electric field depends not only on their sizes (one-dimensional electrophoresis) but also their different isoelectric points (two-dimensional electrophoresis, 2-DE). The same behaviour was observed for several macromolecular fractions detected in HCN polymers. Macromolecular fractions with apparent molecular weights as high as 250 kDa were detected by tricine-SDS gel electrophoresis. Cationic macromolecular fractions with apparent molecular weights as high as 140 kDa were also detected by 2-DE. The HCN polymers synthesized were fractionated by ultrafiltration. As a result, the molecular weight distributions of the macromolecular fractions detected in the HCN polymers directly depended on the synthetic conditions used to produce these polymers. The implications of these results for prebiotic chemistry will be discussed.

  17. Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography

    Directory of Open Access Journals (Sweden)

    Julian C.-H. Chen

    2017-01-01

    Full Text Available The Protein Crystallography Station (PCS, located at the Los Alamos Neutron Scattering Center (LANSCE, was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER for 13 years (2002–2014. The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallography in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.

  18. Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography.

    Science.gov (United States)

    Chen, Julian C-H; Unkefer, Clifford J

    2017-01-01

    The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002-2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallo-graphy in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.

  19. Synthesis and characterization of miktoarm star copolymer of styrene and butadiene using multifunctional macromolecular initiator

    Institute of Scientific and Technical Information of China (English)

    Hai Yan Zhang; Xing Ying Zhang

    2009-01-01

    A new kind of multifunctional macromolecular initiator with Sn-C bonds and polydiene arms was synthesized by living anionic polymerization.At first,polydiene-stannum chloride(PD-SnCl3)was prepared by the reaction of n-butyl-Li(n-BuLi),stannic chloride(SnCl4)and diene.Then PD-SnCl3 was used to react with the dilithium initiator to prepare the multifunctional organic macromolecular initiators.The result suggested that the initiators had a remarkable yield by GPC,nearly 90%.By using these multifunctional macromolecular initiators,styrene and butadiene were effectively polymerized via anionic polymerization,which gave birth to novel miktoarm star copolymers.The relative molecular weight and polydispersity index,microstructure contents,copolymerization components,glass transition temperature(Tg)and morphology of the miktoarm star copolymers were investigated by GPC-UV,1H NMR,DSC and TEM,respectively.

  20. Use of Site-Specifically Tethered Chemical Nucleases to Study Macromolecular Reactions

    Directory of Open Access Journals (Sweden)

    Mukherjee Srabani

    2003-01-01

    Full Text Available During a complex macromolecular reaction multiple changes in molecular conformation and interactions with ligands may occur. X-ray crystallography may provide only a limited set of snapshots of these changes. Solution methods can augment such structural information to provide a more complete picture of a macromolecular reaction. We analyzed the changes in protein conformation and protein:nucleic acid interactions which occur during transcription initiation by using a chemical nuclease tethered to cysteines introduced site-specifically into the RNA polymerase of bacteriophage T7 (T7 RNAP. Changes in cleavage patterns as the polymerase steps through transcription reveal a series of structural transitions which mediate transcription initiation. Cleavage by tethered chemical nucleases is seen to be a powerful method for revealing the conformational dynamics of macromolecular reactions, and has certain advantages over cross-linking or energy transfer approaches.

  1. Macromolecular Hydrogen Sulfide Donors Trigger Spatiotemporally Confined Changes in Cell Signaling.

    Science.gov (United States)

    Ercole, Francesca; Mansfeld, Friederike M; Kavallaris, Maria; Whittaker, Michael R; Quinn, John F; Halls, Michelle L; Davis, Thomas P

    2016-01-11

    Hydrogen sulfide (H2S) is involved in a myriad of cell signaling processes that trigger physiological events ranging from vasodilation to cell proliferation. Moreover, disturbances to H2S signaling have been associated with numerous pathologies. As such, the ability to release H2S in a cellular environment and stimulate signaling events is of considerable interest. Herein we report the synthesis of macromolecular H2S donors capable of stimulating cell signaling pathways in both the cytosol and at the cell membrane. Specifically, copolymers having pendent oligo(ethylene glycol) and benzonitrile groups were synthesized, and the benzonitrile groups were subsequently transformed into primary aryl thioamide groups via thionation using sodium hydrosulfide. These thioamide moieties could be incorporated into a hydrophilic copolymer or a block copolymer (i.e., into either the hydrophilic or hydrophobic domain). An electrochemical sensor was used to demonstrate release of H2S under simulated physiological conditions. Subsequent treatment of HEK293 cells with a macromolecular H2S donor elicited a slow and sustained increase in cytosolic ERK signaling, as monitored using a FRET-based biosensor. The macromolecular donor was also shown to induce a small, fast and sustained increase in plasma membrane-localized PKC activity immediately following addition to cells. Studies using an H2S-selective fluorescent probe in live cells confirmed release of H2S from the macromolecular donor over physiologically relevant time scales consistent with the signaling observations. Taken together, these results demonstrate that by using macromolecular H2S donors it is possible to trigger spatiotemporally confined cell signaling events. Moreover, the localized nature of the observed signaling suggests that macromolecular donor design may provide an approach for selectively stimulating certain cellular biochemical pathways.

  2. UV photolysis for accelerating pyridine biodegradation.

    Science.gov (United States)

    Zhang, Yongming; Chang, Ling; Yan, Ning; Tang, Yingxia; Liu, Rui; Rittmann, Bruce E

    2014-01-01

    Pyridine, a nitrogen-containing heterocyclic compound, is slowly biodegradable, and coupling biodegradation with UV photolysis is a potential means to accelerate its biotransformation and mineralization. The initial steps of pyridine biodegradation involve mono-oxygenation reactions that have molecular oxygen and an intracellular electron carrier as cosubstrates. We employed an internal circulation baffled biofilm reactor for pyridine biodegradation following three protocols: direct biodegradation (B), biodegradation after photolysis (P+B), and biodegradation with succinic acid added (B+S). Succinic acid was the main UV-photolysis product from pyridine, and its catabolic oxidation generates internal electron carriers that may accelerate the initial steps of pyridine biodegradation. Compared with direct biodegradation of pyridine (B), the removal rate for the same concentration of photolyzed pyridine (P+B) was higher by 15 to 43%, depending on the initial pyridine concentrations (increasing through the range of 130 to 310 mg/L). Adding succinic acid alone (B+S) gave results similar to P+B, which supports that succinic acid was the main agent for accelerating the pyridine biodegradation rate. In addition, protocols P+B and B+S were similar in terms of increasing pyridine mineralization over 10 h: 84% and 87%, respectively, which were higher than with protocol B (72%). The positive impact of succinic acid-whether added directly or produced via UV photolysis-confirms that its catabolism, which produced intracellular electron carriers, accelerated the initial steps of pyridine biotransformation.

  3. Aerobic biodegradation of a nonylphenol polyethoxylate and toxicity of the biodegradation metabolites.

    Science.gov (United States)

    Jurado, Encarnación; Fernández-Serrano, Mercedes; Núñez-Olea, Josefa; Lechuga, Manuela

    2009-09-01

    In this paper a study was made of the biodegradation of a non-ionic surfactant, a nonylphenol polyethoxylate, in biodegradability tests by monitoring the residual surfactant matter. The influence of the concentration on the extent of primary biodegradation, the toxicity of biodegradation metabolites, and the kinetics of degradation were also determined. The primary biodegradation was studied at different initial concentrations: 5, 25 and 50 mg/L, (at sub-and supra-critical micelle concentration). The NPEO used in this study can be considered biodegradable since the primary biodegradation had already taken place (a biodegradation greater than 80% was found for the different initial concentration tested). The initial concentration affected the shape of the resulting curve, the mean biodegradation rate and the percentage of biodegradation reached (99% in less than 8 days at 5 mg/L, 98% in less than 13 days at 25 mg/L and 95% in 14 days at 50 mg/L). The kinetic model of Quiroga and Sales (1991) was applied to predict the biodegradation of the NPEO. The toxicity value was measured as EC(20) and EC(50). In addition, during the biodegradation process of the surfactant a toxicity analysis was made of the evolution of metabolites generated, confirming that the subproducts of the biodegradation process were more toxic than the original.

  4. The Joint Structural Biology Group beam lines at the ESRF: Modern macromolecular crystallography

    CERN Document Server

    Mitchell, E P

    2001-01-01

    Macromolecular crystallography has evolved considerably over the last decade. Data sets in under an hour are now possible on high throughput beam lines leading to electron density and, possibly, initial models calculated on-site. There are five beam lines currently dedicated to macromolecular crystallography: the ID14 complex and BM-14 (soon to be superseded by ID-29). These lines handle over five hundred projects every six months and demand is increasing. Automated sample handling, alignment and data management protocols will be required to work efficiently with this demanding load. Projects developing these themes are underway within the JSBG.

  5. Poly(isophthalic acid)(ethylene oxide) as a Macromolecular Modulator for Metal-Organic Polyhedra.

    Science.gov (United States)

    Chen, Teng-Hao; Wang, Le; Trueblood, Jonathan V; Grassian, Vicki H; Cohen, Seth M

    2016-08-03

    A new strategy was developed by using a polymer ligand, poly(isophthalic acid)(ethylene oxide), to modulate the growth of metal-organic polyhedra (MOP) crystals. This macromolecular modulator can effectively control the crystal habit of several different Cu24L24 (L = isophthalic acid derivatives) MOPs. The polymer also directed the formation of MOP structures under reaction conditions that only produce metal-organic frameworks in the absence of modulator. Moreover, the polymer also enabled the deposition of MOP crystals on glass surfaces. This macromolecular modulator strategy provides an innovative approach to control the morphology and assembly of MOP particles.

  6. Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding

    Science.gov (United States)

    Wang, Po-hung; Yu, Isseki; Feig, Michael; Sugita, Yuji

    2017-03-01

    We investigate the effects of protein crowder sizes on hydration structure and dynamics in macromolecular crowded systems by all-atom MD simulations. The crowded systems consisting of only small proteins showed larger total surface areas than those of large proteins at the same volume fractions. As a result, more water molecules were trapped within the hydration shells, slowing down water diffusion. The simulation results suggest that the protein crowder size is another factor to determine the effect of macromolecular crowding and to explain the experimental kinetic data of proteins and DNAs in the presence of crowding agents.

  7. THE STEADY/PULSATILE FLOW AND MACROMOLECULAR TRANSPORT IN T-BIFURCATION BLOOD VESSELS

    Institute of Scientific and Technical Information of China (English)

    李丁; 温功碧

    2003-01-01

    A numerical analysis of the steady and pulsatile, macromolecular( such as lowdensity lipopotein ( LDL ), Albumin ) transport in T-bifurcation was proposed. Theinfluence of Reynolds number and mass flow ratio etc. parameters on the velocity field andmass transport were calculated. The computational results predict that the blood flow factorsaffect the macromolecular distribution and the transport across the wall, it shows thathemodynamic play an important role in the process of atherosclerosis . The LDL and Albuminconcentration on the wall varies most greatly in flow bifurcation area where the wall shearstress varies greatly at the branching vessel and the atherosclerosis often appears there.

  8. Accounting for large amplitude protein deformation during in silico macromolecular docking.

    Science.gov (United States)

    Bastard, Karine; Saladin, Adrien; Prévost, Chantal

    2011-02-22

    Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA. We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success.

  9. Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking

    Directory of Open Access Journals (Sweden)

    Chantal Prévost

    2011-02-01

    Full Text Available Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA.We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success.

  10. Effect of macromolecular crowding on the rate of diffusion-limited enzymatic reaction

    Indian Academy of Sciences (India)

    Manish Agrawal; S B Santra; Rajat Anand; Rajaram Swaminathan

    2008-08-01

    The cytoplasm of a living cell is crowded with several macromolecules of different shapes and sizes. Molecular diffusion in such a medium becomes anomalous due to the presence of macromolecules and diffusivity is expected to decrease with increase in macromolecular crowding. Moreover, many cellular processes are dependent on molecular diffusion in the cell cytosol. The enzymatic reaction rate has been shown to be affected by the presence of such macromolecules. A simple numerical model is proposed here based on percolation and diffusion in disordered systems to study the effect of macromolecular crowding on the enzymatic reaction rates. The model qualitatively explains some of the experimental observations.

  11. Biodegradation of the low concentration of polycyclic aromatic hydrocarbons in soil by microbial consortium during incubation.

    Science.gov (United States)

    Li, Xiaojun; Lin, Xin; Li, Peijun; Liu, Wan; Wang, Li; Ma, Fang; Chukwuka, K S

    2009-12-30

    The biodegradation of polycyclic aromatic hydrocarbons (PAHs) (8.15 mg PAHs kg(-1) soil) in aged contaminated soil by isolated microbial consortium (five fungi and three bacteria) during the incubation of 64d is reported. The applied treatments were: (1) biodegradation by adding microbial consortium in sterile soils (BM); (2) biodegradation by adding microbial consortium in non-sterile soils (BMN); and (3) biodegradation by in situ "natural" microbes in non-sterile soils (BNN). The fungi in BM and BMN soils grew rapidly 0-4d during the incubation and then reached a relative equilibrium. In contrast the fungi in BNN soil remained at a constant level for the entire time. Comparison with the fungi, the bacteria in BNN soils grew rapidly during the incubation 0-2d and then reached a relative equilibrium, and those in BM and BMN soils grew slowly during the incubation of 64 d. After 64 d of incubation, the PAH biodegradations were 35%, 40.7% and 41.3% in BNN, BMN and BM, respectively. The significant release of sequestrated PAHs in aged contaminated soil was observed in this experiment, especially in the BM soil. Therefore, although bioaugmentation of introduced microbial consortium increased significantly the biodegradation of PAHs in aged contaminated soil with low PAH concentration, the creation of optimum of the environmental situation might be the best way to use bioremediation successfully in the field.

  12. BIODEGRADABLE COATING FROM AGATHIS ALBA

    Directory of Open Access Journals (Sweden)

    NORYAWATI MULYONO

    2012-11-01

    Full Text Available The adhesive property of copal makes it as a potential coating onto aluminum foil to replace polyethylene. This research aimed to develop copal-based coating. The coating was prepared by extracting the copal in ethyl acetate and dipping the aluminium foil in ethyl acetate soluble extract of copal. The characterization of coating included its thickness, weight, thermal and chemical resistance, and biodegradation. The results showed that the coating thickness and weight increased as the copal concentration and dipping frequency increased. Thermal resistance test showed that the coating melted after being heated at 110°C for 30 min. Copal-based coating wasresistant to acidic solution (pH 4.0, water, and coconut oil, but was deteriorated in detergent 1% (w/v and basic solution (pH 10.0. Biodegradability test using Pseudomonas aeruginosa showed weight reduction of 76.82% in 30 days.

  13. Biomedical Applications of Biodegradable Polyesters

    Directory of Open Access Journals (Sweden)

    Iman Manavitehrani

    2016-01-01

    Full Text Available The focus in the field of biomedical engineering has shifted in recent years to biodegradable polymers and, in particular, polyesters. Dozens of polyester-based medical devices are commercially available, and every year more are introduced to the market. The mechanical performance and wide range of biodegradation properties of this class of polymers allow for high degrees of selectivity for targeted clinical applications. Recent research endeavors to expand the application of polymers have been driven by a need to target the general hydrophobic nature of polyesters and their limited cell motif sites. This review provides a comprehensive investigation into advanced strategies to modify polyesters and their clinical potential for future biomedical applications.

  14. Anaerobic Biodegradation of Detergent Surfactants

    OpenAIRE

    Erich Jelen; Ute Merrettig-Bruns

    2009-01-01

    Detergent surfactantscan be found in wastewater in relevant concentrations. Most of them are known as ready degradable under aerobic conditions, as required by European legislation. Far fewer surfactants have been tested so far for biodegradability under anaerobic conditions. The natural environment is predominantly aerobic, but there are some environmental compartments such as river sediments, sub-surface soil layer and anaerobic sludge digesters of wastewater treatment plants which have str...

  15. Effects of plant species identity, diversity and soil fertility on biodegradation of phenanthrene in soil

    NARCIS (Netherlands)

    Oyelami, A.O.; Okere, U.V.; Orwin, K.; Deyn, de G.B.; Jones, K.C.; Semple, K.T.

    2013-01-01

    The work presented in this paper investigated the effects of plant species composition, species diversity and soil fertility on biodegradation of 14C-phenanthrene in soil. The two soils used were of contrasting fertility, taken from long term unfertilised and fertilised grassland, showing difference

  16. Engineering Flame Retardant Biodegradable Nanocomposites

    Science.gov (United States)

    He, Shan; Yang, Kai; Guo, Yichen; Zhang, Linxi; Pack, Seongchan; Davis, Rachel; Lewin, Menahem; Ade, Harald; Korach, Chad; Kashiwagi, Takashi; Rafailovich, Miriam

    2013-03-01

    Cellulose-based PLA/PBAT polymer blends can potentially be a promising class of biodegradable nanocomposites. Adding cellulose fiber reinforcement can improve mechanical properties of biodegradable plastics, but homogeneously dispersing hydrophilic cellulose in the hydrophobic polymer matrix poses a significant challenge. We here show that resorcinol diphenyl phosphates (RDP) can be used to modify the surface energy, not only reducing phase separation between two polymer kinds but also allowing the cellulose particles and the Halloysite clay to be easily dispersed within polymer matrices to achieve synergy effect using melt blending. Here in this study we describe the use of cellulose fiber and Halloysite clay, coated with RDP surfactant, in producing the flame retardant polymer blends of PBAT(Ecoflex) and PLA which can pass the stringent UL-94 V0 test. We also utilized FTIR, SEM and AFM nanoindentation to elucidate the role RDP plays in improving the compatibility of biodegradable polymers, and to determine structure property of chars that resulted in composites that could have optimized mechanical and thermal properties. Supported by Garcia Polymer Center and NSF Foundation.

  17. Biodegradation of MC252 oil in oil:sand aggregates in a coastal headland beach environment

    Directory of Open Access Journals (Sweden)

    Vijaikrishnah eElango

    2014-04-01

    Full Text Available Biodegradation potential of MC252 in oil:sand aggregates, termed surface residue balls (SRBs, was examined using multiple lines of evidence on a heavily-impacted coastal headland beach in Louisiana, USA. SRBs were sampled over a 16-month period on the supratidal beach environment where reasonable control existed on the residence time of the aggregates on the beach surface. PAH and alkane concentration ratios were measured including PAH/C30-hopane, C2/C3 phenanthrenes, C2/C3 dibenzothiophenes and alkane/C30-hopane and demonstrated unequivocally that biodegradation was occurring in SRBs in the supratidal. These biodegradation reactions occurred over time frames relevant to the coastal processes moving SRBs off the beach. In contrast, submerged oil mat (SOM samples did not demonstrate chemical changes consistent with biodegradation. Review and analysis of additional biogeochemical parameters suggested the existence of a moisture and N-limited biodegradation regime on the supratidal beach environment. At this location, SRBs possess moisture contents < 2% and molar C:N ratios from 131-323, well outside of optimal values for biodegradation in the literature. Despite these limitations, biodegradation of PAHs and alkanes proceeded at relevant rates (2-8 year-1 due in part to the presence of degrading populations, i.e., Mycobacterium sp., adapted to these conditions. For SOM samples in the intertidal, an oxygen and salinity-impacted regime is proposed that severely limits biodegradation of alkanes and PAHs in this environment. These results support the hypothesis that SRBs deposited at different locations on the beach have different biogeochemical characteristics (e.g., moisture; salinity; terminal electron acceptors; nutrient; and oil composition due, in part, to their location on the landscape.

  18. Biodegradation of MC252 oil in oil:sand aggregates in a coastal headland beach environment.

    Science.gov (United States)

    Elango, Vijaikrishnah; Urbano, Marilany; Lemelle, Kendall R; Pardue, John H

    2014-01-01

    Unique oil:sand aggregates, termed surface residue balls (SRBs), were formed on coastal headland beaches along the northern Gulf of Mexico as emulsified MC252 crude oil mixed with sand following the Deepwater Horizon spill event. The objective of this study is to assess the biodegradation potential of crude oil components in these aggregates using multiple lines of evidence on a heavily-impacted coastal headland beach in Louisiana, USA. SRBs were sampled over a 19-month period on the supratidal beach environment with reasonable control over and knowledge of the residence time of the aggregates on the beach surface. Polycyclic aromatic hydrocarbons (PAHs) and alkane concentration ratios were measured including PAH/C30-hopane, C2/C3 phenanthrenes, C2/C3 dibenzothiophenes and alkane/C30-hopane and demonstrated that biodegradation was occurring in SRBs in the supratidal. These biodegradation reactions occurred over time frames relevant to the coastal processes moving SRBs off the beach. In contrast, submerged oil mat samples from the intertidal did not demonstrate chemical changes consistent with biodegradation. Review and analysis of additional biogeochemical parameters suggested the existence of a moisture and nutrient-limited biodegradation regime on the supratidal beach environment. At this location, SRBs possess moisture contents biodegradation in the literature. Despite these limitations, biodegradation of PAHs and alkanes proceeded at relevant rates (2-8 year(-1)) due in part to the presence of degrading populations, i.e., Mycobacterium sp., adapted to these conditions. For submerged oil mat samples in the intertidal, an oxygen and salinity-impacted regime is proposed that severely limits biodegradation of alkanes and PAHs in this environment. These results support the hypothesis that SRBs deposited at different locations on the beach have different biogeochemical characteristics (e.g., moisture, salinity, terminal electron acceptors, nutrient, and oil

  19. Chloroethene Biodegradation Potential, ADOT/PF Peger Road Maintenance Facility, Fairbanks, Alaska

    Science.gov (United States)

    Bradley, Paul M.; Chapelle, Frances H.

    2004-01-01

    A series of 14C-radiotracer-based microcosm experiments were conducted to assess: 1) the extent, rate and products of microbial dechlorination of trichloroethene (TCE), cis-dichloroethene (cis-DCE) and vinyl chloride (VC) in sediments at the Peger Road site; 2) the effect of three electron donor amendments (molasses, shrimp and crab chitin, and 'Hydrogen Release Compound' (HRC)) on microbial degradation of TCE in three Peger Road sediments; and 3) the potential significance at the site of chloroethene biodegradation processes other than reductive dechlorination. In these experiments, TCE biodegradation yielded the reduced products, DCE and VC, and the oxidation product CO 2. Biodegradation of DCE and VC involved stoichiometric oxidation to CO 2. Both laboratory microcosm study and field redox assessment results indicated that the predominant terminal electron accepting process in Peger Road plume sediments under anoxic conditions was Mn/Fe-reduction. The rates of chloroethene biodegradation observed in Peger Road sediment microcosms under low temperature conditions (4?C) were within the range of those observed in sediments from temperate (20?C) aquifer systems. This result confirmed that biodegradation can be a significant mechanism for in situ contaminant remediation even in cold temperature aquifers. The fact that CO2 was the sole product of cis-DCE and VC biodegradation detected in Peger Road sediments indicated that a natural attenuation assessment based on reduced daughter product accumulation may significantly underestimate the potential for DCE and VC biodegradation at the Peger Road. Neither HRC nor molasses addition stimulated TCE reductive dechlorination. The fact that molasses and HRC amendment did stimulate Mn/Fe-reduction suggests that addition of these electron donors favored microbial Mn/Fe-reduction to the detriment of microbial TCE dechlorinating activity. In contrast, amendment of sediment microcosms with shrimp and crab chitin resulted in the

  20. A review of plastic waste biodegradation.

    Science.gov (United States)

    Zheng, Ying; Yanful, Ernest K; Bassi, Amarjeet S

    2005-01-01

    With more and more plastics being employed in human lives and increasing pressure being placed on capacities available for plastic waste disposal, the need for biodegradable plastics and biodegradation of plastic wastes has assumed increasing importance in the last few years. This review looks at the technological advancement made in the development of more easily biodegradable plastics and the biodegradation of conventional plastics by microorganisms. Additives, such as pro-oxidants and starch, are applied in synthetic materials to modify and make plastics biodegradable. Recent research has shown that thermoplastics derived from polyolefins, traditionally considered resistant to biodegradation in ambient environment, are biodegraded following photo-degradation and chemical degradation. Thermoset plastics, such as aliphatic polyester and polyester polyurethane, are easily attacked by microorganisms directly because of the potential hydrolytic cleavage of ester or urethane bonds in their structures. Some microorganisms have been isolated to utilize polyurethane as a sole source of carbon and nitrogen source. Aliphatic-aromatic copolyesters have active commercial applications because of their good mechanical properties and biodegradability. Reviewing published and ongoing studies on plastic biodegradation, this paper attempts to make conclusions on potentially viable methods to reduce impacts of plastic waste on the environment.

  1. Biodegradation of high molecular weight polylactic acid

    Science.gov (United States)

    Stloukal, Petr; Koutny, Marek; Sedlarik, Vladimir; Kucharczyk, Pavel

    2012-07-01

    Polylactid acid seems to be an appropriate replacement of conventional non-biodegradable synthetic polymer primarily due to comparable mechanical, thermal and processing properties in its high molecular weight form. Biodegradation of high molecular PLA was studied in compost for various forms differing in their specific surface area. The material proved its good biodegradability under composting conditions and all investigated forms showed to be acceptable for industrial composting. Despite expectations, no significant differences in resulting mineralizations were observed for fiber, film and powder sample forms with different specific surface areas. The clearly faster biodegradation was detected only for the thin coating on porous material with high specific surface area.

  2. Study on biodegradable aromatic/aliphatic copolyesters

    Energy Technology Data Exchange (ETDEWEB)

    Yiwang Chen; Licheng Tan; Lie Chen; Yan, Yang; Xiaofeng Wang [Nanchang University, Nanchang (China). School of Materials Science and Engineering. Inst. of Polymer Materials]. E-mail: ywchen@ncu.edu.cn

    2008-04-15

    Progress on biodegradable aromatic/aliphatic copolyesters based on aliphatic and aromatic diacids, diols and ester monomers was reviewed. The aromatic/aliphatic copolyesters combined excellent mechanical properties with biodegradability. Physical properties and biodegradability of copolyesters varied with chain length of the aliphatic polyester segment and atacticity of copolyesters. The process ability of copolyesters could be improved significantly after incorporating a stiff chain segment through copolymerization of aliphatic polyesters with an aromatic liquid crystal element. The aromatic/aliphatic copolyesters as a new type of biodegradable materials could replace some general plastics in certain applications, namely biomedical and environmental friendly fields. (author)

  3. Biodegradable materials as foundry moulding sands binders

    Directory of Open Access Journals (Sweden)

    K. Major - Gabryś

    2015-07-01

    Full Text Available The aim of this article is to show the possibility of using biodegradable materials as part of the composition of foundry moulding and core sand binders. Research shows that moulding sands with biodegradable materials selected as binders are not only less toxic but are also better suited to mechanical reclamation than moulding sands with phenol-furfuryl resin. The use of biodegradable materials as additives to typical synthetic resins can result in their decreased toxicity and improved ability to reclamation as well as in accelerated biodegradation of binding material leftovers of mechanical reclamation.

  4. Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

    DEFF Research Database (Denmark)

    Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.

    2017-01-01

    Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many...

  5. Isolation and chemical characterization of resistant macromolecular constituents in microalgae and marine sediments

    NARCIS (Netherlands)

    Gelin, F.

    1996-01-01

    The recognition of novel, insoluble and non-hydrolysable macromolecular constituents in protective tissues of fresh-water algae and higher plants has had a major impact on our understanding of the origin and fate of sedimentary organic matter (OM) in terrestrial and lacustrine deposits. The investig

  6. Interplay between the bacterial nucleoid protein H-NS and macromolecular crowding in compacting DNA

    NARCIS (Netherlands)

    Wintraecken, C.H.J.M.

    2012-01-01

      In this dissertation we discuss H-NS and its connection to nucleoid compaction and organization. Nucleoid formation involves a dramatic reduction in coil volume of the genomic DNA. Four factors are thought to influence coil volume: supercoiling, DNA charge neutralization, macromolecular crow

  7. A kinetic type extended model for dense gases and macromolecular fluids

    Directory of Open Access Journals (Sweden)

    M. Cristina Carrisi

    2005-05-01

    Full Text Available Extended thermodynamics is an important theory which is appreciated from mathematicians and physicists. Following its ideas and considering the macroscopic approach with suggestions from the kinetic one, we find in this paper, the solution of an interesting model: the model for dense gases and macromolecular fluids.

  8. Macromolecular Crowding Modulates Folding Mechanism of α/β Protein Apoflavodoxin

    Science.gov (United States)

    Homouz, D.; Stagg, L.; Wittungstafshede, P.; Cheung, M.

    2009-01-01

    Protein dynamics in cells may be different from that in dilute solutions in vitro since the environment in cells is highly concentrated with other macromolecules. This volume exclusion due to macromolecular crowding is predicted to affect both equilibrium and kinetic processes involving protein conformational changes. To quantify macromolecular crowding effects on protein folding mechanisms, here we have investigated the folding energy landscape of an alpha/beta protein, apoflavodoxin, in the presence of inert macromolecular crowding agents using in silico and in vitro approaches. By coarse-grained molecular simulations and topology-based potential interactions, we probed the effects of increased volume fraction of crowding agents (phi_c) as well as of crowding agent geometry (sphere or spherocylinder) at high phi_c. Parallel kinetic folding experiments with purified Desulfovibro desulfuricans apoflavodoxin in vitro were performed in the presence of Ficoll (sphere) and Dextran (spherocylinder) synthetic crowding agents. In conclusion, we have identified in silico crowding conditions that best enhance protein stability and discovered that upon manipulation of the crowding conditions, folding routes experiencing topological frustrations can be either enhanced or relieved. The test-tube experiments confirmed that apoflavodoxin's time-resolved folding path is modulated by crowding agent geometry. We propose that macromolecular crowding effects may be a tool for manipulation of protein folding and function in living cells.

  9. Hydropyrolysis: A new technique for the analysis of macromolecular material in meteorites

    Science.gov (United States)

    Sephton, Mark A.; Love, Gordon D.; Meredith, Will; Snape, Colin E.; Sun, Cheng-Gong; Watson, Jonathan S.

    2005-10-01

    The carbonaceous chondrite meteorites are fragments of asteroids that have remained relatively unprocessed since the formation of the Solar System 4.56 billion years ago. The major organic component in these meteorites is a macromolecular phase that is resistant to solvent extraction. The information contained within macromolecular material can be accessed by degradative techniques such as pyrolysis. Hydropyrolysis refers to pyrolysis assisted by high hydrogen gas pressures and a dispersed sulphided molybdenum catalyst. Hydropyrolysis of the Murchison macromolecular material successfully releases much greater quantities of hydrocarbons than traditional pyrolysis techniques (twofold greater than hydrous pyrolysis) including significant amounts of high molecular weight polyaromatic hydrocarbons (PAH) such as phenanthrene, carbazole, fluoranthene, pyrene, chrysene, perylene, benzoperylene and coronene units with varying degrees of alkylation. When hydropyrolysis products are collected using a silica trap immersed in liquid nitrogen, the technique enables the solubilisation and retention of compounds with a wide range of volatilities (i.e. benzene to coronene). This report describes the hydropyrolysis method and the information it can provide about meteorite macromolecular material constitution.

  10. Prazosin-Conjugated Matrices Based on Biodegradable Polymers and α-Amino Acids—Synthesis, Characterization, and in Vitro Release Study

    Directory of Open Access Journals (Sweden)

    Ewa Oledzka

    2015-08-01

    Full Text Available Novel and promising macromolecular conjugates of the α1-adrenergic blocker prazosin were directly synthesized by covalent incorporation of the drug to matrices composed of biodegradable polymers and α-amino acids for the development of a polymeric implantable drug delivery carrier. The cyto- and genotoxicity of the synthesized matrices were evaluated using a bacterial luminescence test, protozoan assay, and Salmonella typhimurium TA1535. A new urethane bond was formed between the hydroxyl end-groups of the synthesized polymer matrices and an amine group of prazosin, using 1,1′-carbonyldiimidazole (CDI as a coupling agent. The structure of the polymeric conjugates was characterized by various spectroscopy techniques. A study of hydrogen nuclear magnetic resonance (1H-NMR and differential scanning calorimetry (DSC thermodiagrams indicated that the presence of prazosin pendant groups in the macromolecule structures increased the polymer’s rigidity alongside increasing glass transition temperature. It has been found that the kinetic release of prazosin from the obtained macromolecular conjugates, tested in vitro under different conditions, is strongly dependent on the physicochemical properties of polymeric matrices. Furthermore, the presence of a urethane bond in the macromolecular conjugates allowed for obtaining a relatively controlled release profile of the drug. The obtained results confirm that the pharmacokinetics of prazosin might be improved through the synthesis of polymeric conjugates containing biomedical polymers and α-amino acids in the macromolecule.

  11. Here today, gone tomorrow: biodegradable soft robots

    Science.gov (United States)

    Rossiter, Jonathan; Winfield, Jonathan; Ieropoulos, Ioannis

    2016-04-01

    One of the greatest challenges to modern technologies is what to do with them when they go irreparably wrong or come to the end of their productive lives. The convention, since the development of modern civilisation, is to discard a broken item and then procure a new one. In the 20th century enlightened environmentalists campaigned for recycling and reuse (R and R). R and R has continued to be an important part of new technology development, but there is still a huge problem of non-recyclable materials being dumped into landfill and being discarded in the environment. The challenge is even greater for robotics, a field which will impact on all aspects of our lives, where discards include motors, rigid elements and toxic power supplies and batteries. One novel solution is the biodegradable robot, an active physical machine that is composed of biodegradable materials and which degrades to nothing when released into the environment. In this paper we examine the potential and realities of biodegradable robotics, consider novel solutions to core components such as sensors, actuators and energy scavenging, and give examples of biodegradable robotics fabricated from everyday, and not so common, biodegradable electroactive materials. The realisation of truly biodegradable robots also brings entirely new deployment, exploration and bio-remediation capabilities: why track and recover a few large non-biodegradable robots when you could speculatively release millions of biodegradable robots instead? We will consider some of these exciting developments and explore the future of this new field.

  12. Primary biodegradation of petroleum hydrocarbons in seawater

    Energy Technology Data Exchange (ETDEWEB)

    Comber, M.I.H.; Den Haan, K.H.; Djemel, N.; Eadsforth, C.V.; King, D.; Paumen, M.L.; Parkerton, T.; Dmytrasz, B.

    2012-12-15

    This report describes primary biodegradation experiments performed to determine the persistence of higher molecular weight petroleum hydrocarbons in seawater. Results from the biodegradation experiments show that the majority of tested petroleum hydrocarbons have half-lives in seawater less than 60 days.

  13. Biodegradation of aliphatic and aromatic polycarbonates.

    Science.gov (United States)

    Artham, Trishul; Doble, Mukesh

    2008-01-01

    Polycarbonate is one of the most widely used engineering plastics because of its superior physical, chemical, and mechanical properties. Understanding the biodegradation of this polymer is of great importance to answer the increasing problems in waste management of this polymer. Aliphatic polycarbonates are known to biodegrade either through the action of pure enzymes or by bacterial whole cells. Very little information is available that deals with the biodegradation of aromatic polycarbonates. Biodegradation is governed by different factors that include polymer characteristics, type of organism, and nature of pretreatment. The polymer characteristics such as its mobility, tacticity, crystallinity, molecular weight, the type of functional groups and substituents present in its structure, and plasticizers or additives added to the polymer all play an important role in its degradation. The carbonate bond in aliphatic polycarbonates is facile and hence this polymer is easily biodegradable. On the other hand, bisphenol A polycarbonate contains benzene rings and quaternary carbon atoms which form bulky and stiff chains that enhance rigidity. Even though this polycarbonate is amorphous in nature because of considerable free volume, it is non-biodegradable since the carbonate bond is inaccessible to enzymes because of the presence of bulky phenyl groups on either side. In order to facilitate the biodegradation of polymers few pretreatment techniques which include photo-oxidation, gamma-irradiation, or use of chemicals have been tested. Addition of biosurfactants to improve the interaction between the polymer and the microorganisms, and blending with natural or synthetic polymers that degrade easily, can also enhance the biodegradation.

  14. Nylon biodegradation by lignin-degrading fungi.

    OpenAIRE

    Deguchi, T; Kakezawa, M; Nishida, T

    1997-01-01

    The biodegradation of nylon by lignin-degrading fungi was investigated. The fungus IZU-154 significantly degraded nylon-66 membrane under ligninolytic conditions. Nuclear magnetic resonance analysis showed that four end groups, CHO, NHCHO, CH3, and CONH2, were formed in the biodegraded nylon-66 membranes, suggesting that nylon-66 was degraded oxidatively.

  15. Biodegradation of Crystal Violet by Agrobacterium radiobacter

    DEFF Research Database (Denmark)

    Parshetti, G.K.; Parshetti, S.G.; Telke, A.A.

    2011-01-01

    and phenol. We proposed the hypothetical metabolic pathway of Crystal Violet biodegradation by A. radiobacter. Phytotoxicity and microbial toxicity study showed that Crystal Violet biodegradation metabolites were less toxic to bacteria (A. radiobacter, P. aurugenosa and A. vinelandii) contributing to soil...

  16. Current trends in biodegradable polyhydroxyalkanoates.

    Science.gov (United States)

    Chanprateep, Suchada

    2010-12-01

    The microbial polyesters known as polyhydroxyalkanoates (PHAs) positively impact global climate change scenarios by reducing the amount of non-degradable plastic used. A wide variety of different monomer compositions of PHAs has been described, as well as their future prospects for applications where high biodegradability or biocompatibility is required. PHAs can be produced from renewable raw materials and are degraded naturally by microorganisms that enable carbon dioxide and organic compound recycling in the ecosystem, providing a buffer to climate change. This review summarizes recent research on PHAs and addresses the opportunities as well as challenges for their place in the global market.

  17. Flexibility damps macromolecular crowding effects on protein folding dynamics: Application to the murine prion protein (121-231)

    Science.gov (United States)

    Bergasa-Caceres, Fernando; Rabitz, Herschel A.

    2014-01-01

    A model of protein folding kinetics is applied to study the combined effects of protein flexibility and macromolecular crowding on protein folding rate and stability. It is found that the increase in stability and folding rate promoted by macromolecular crowding is damped for proteins with highly flexible native structures. The model is applied to the folding dynamics of the murine prion protein (121-231). It is found that the high flexibility of the native isoform of the murine prion protein (121-231) reduces the effects of macromolecular crowding on its folding dynamics. The relevance of these findings for the pathogenic mechanism are discussed.

  18. Biodegradable polymers for electrospinning: towards biomedical applications.

    Science.gov (United States)

    Kai, Dan; Liow, Sing Shy; Loh, Xian Jun

    2014-12-01

    Electrospinning has received much attention recently due to the growing interest in nano-technologies and the unique material properties. This review focuses on recent progress in applying electrospinning technique in production of biodegradable nanofibers to the emerging field of biomedical. It first introduces the basic theory and parameters of nanofibers fabrication, with focus on factors affecting the morphology and fiber diameter of biodegradable nanofibers. Next, commonly electrospun biodegradable nanofibers are discussed, and the comparison of the degradation rate of nanoscale materials with macroscale materials are highlighted. The article also assesses the recent advancement of biodegradable nanofibers in different biomedical applications, including tissue engineering, drug delivery, biosensor and immunoassay. Future perspectives of biodegradable nanofibers are discussed in the last section, which emphasizes on the innovation and development in electrospinning of hydrogels nanofibers, pore size control and scale-up productions.

  19. Biodegradation and toxicological evaluation of lubricant oils

    Directory of Open Access Journals (Sweden)

    Ivo Shodji Tamada

    2012-12-01

    Full Text Available The aim of this work was to compare different toxicity levels of lubricant oils. The tests were performed using the earthworm (Eisenia andrei, arugula seeds (Eruca sativa and lettuce seeds (Lactuca sativa, with three types of contaminants (mineral lubricant oil, synthetic lubricant oil and used lubricant oil for various biodegradation periods in the soil. The toxicity tests indirectly measured the biodegradation of the contaminants. The samples were analyzed at t0, t60, t120 and t180 days of biodegradation. The used lubricant oil was proved very toxic in all the tests and even after biodegradation its toxicity was high. The mineral and synthetic oils were biodegraded efficiently in the soil although their toxicity did not disappear completely after 180 days.

  20. Biodegradation of disinfection byproducts as a potential removal process during aquifer storage recovery

    Science.gov (United States)

    Landmeyer, J.E.; Bradley, P.M.; Thomas, J.M.

    2000-01-01

    The biodegradation potential of two drinking water disinfection byproducts was investigated using aquifer materials obtained from approximately 100 and 200 meters below land surface in an aerobic aquifer system undergoing aquifer storage recovery of treated surface water. No significant biodegradation of a model trihalomethane compound, chloroform, was observed in aquifer microcosms under aerobic or anaerobic conditions. In contrast, between 16 and 27 percent mineralization of a radiolabeled model haloacetic acid compound, chloroacetic acid, was observed. These results indicate that although the potential for biodegradation of chloroacetic acid exists in deep aquifer systems, chloroform entrained within these aquifers or formed in situ will tend to persist. These results have important implications for water managers planning to meet anticipated lowered permissible levels of tri-halomethanes in drinking water.The biodegradation potential of two drinking water disinfection byproducts was investigated using aquifer materials obtained from approximately 100 and 200 meters below land surface in an aerobic aquifer system undergoing aquifer storage recovery of treated surface water. No significant biodegradation of a model trihalomethane compound, chloroform, was observed in aquifer microcosms under aerobic or anaerobic conditions. In contrast, between 16 and 27 percent mineralization of a radiolabeled model haloacetic acid compound, chloroacetic acid, was observed. These results indicate that although the potential for biodegradation of chloroacetic acid exists in deep aquifer systems, chloroform entrained within these aquifers or formed in situ will tend to persist. These results have important implications for water managers planning to meet anticipated lowered permissible levels of trihalomethanes in drinking water.Aquifer-storage-recovery injection water often contains disinfection byproducts. Results are presented from a study in which two model disinfection

  1. Biodegradability of iopromide products after UV/H₂O₂ advanced oxidation.

    Science.gov (United States)

    Keen, Olya S; Love, Nancy G; Aga, Diana S; Linden, Karl G

    2016-02-01

    Iopromide is an X-ray and MRI contrast agent that is virtually non-biodegradable and persistent through typical wastewater treatment processes. This study determined whether molecular transformation of iopromide in a UV/H2O2 advanced oxidation process (AOP) can result in biodegradable products. The experiments used iopromide labeled with carbon-14 on the aromatic ring to trace degradation of iopromide through UV/H2O2 advanced oxidation and subsequent biodegradation. The biotransformation assay tracked the formation of radiolabeled (14)CO2 which indicated full mineralization of the molecule. The results indicated that AOP formed biodegradable iopromide products. There was no (14)C released from the pre-AOP samples, but up to 20% of all radiolabeled carbon transformed into (14)CO2 over the course of 42 days of biodegradation after iopromide was exposed to advanced oxidation (compared to 10% transformation in inactivated post-AOP controls). In addition, the quantum yield of photolysis of iopromide was determined using low pressure (LP) and medium pressure (MP) mercury lamps as 0.069 ± 0.005 and 0.080 ± 0.007 respectively. The difference in the quantum yields for the two UV sources was not statistically significant at the 95% confidence interval (p = 0.08), which indicates the equivalency of using LP or MP UV sources for iopromide treatment. The reaction rate between iopromide and hydroxyl radicals was measured to be (2.5 ± 0.2) × 10(9) M(-1) s(-1). These results indicate that direct photolysis is a dominant degradation pathway in UV/H2O2 AOP treatment of iopromide. Other iodinated contrast media may also become biodegradable after exposure to UV or UV/H2O2.

  2. Intimately coupling of photolysis accelerates nitrobenzene biodegradation, but sequential coupling slows biodegradation

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Lihui [Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University, Shanghai 200234 (China); Zhang, Yongming, E-mail: zhym@shnu.edu.cn [Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University, Shanghai 200234 (China); Bai, Qi; Yan, Ning; Xu, Hua [Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University, Shanghai 200234 (China); Rittmann, Bruce E. [Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5701 (United States)

    2015-04-28

    Highlights: • Intimately coupled UV photolysis accelerated nitrobenzene biodegradation. • NB biodegradation was slowed by accumulation of nitrophenol. • Oxalic acid was a key product of UV photolysis. • Oxalic acid accelerated biodegradation of nitrobenzene and nitrophenol by a co-substrate effect. • Intimate coupling of UV and biodegradation accentuated the benefits of oxalic acid. - Abstract: Photo(cata)lysis coupled with biodegradation is superior to photo(cata)lysis or biodegradation alone for removal of recalcitrant organic compounds. The two steps can be carried out sequentially or simultaneously via intimate coupling. We studied nitrobenzene (NB) removal and mineralization to evaluate why intimate coupling of photolysis with biodegradation was superior to sequential coupling. Employing an internal circulation baffled biofilm reactor, we compared direct biodegradation (B), biodegradation after photolysis (P + B), simultaneous photolysis and biodegradation (P&B), and biodegradation with nitrophenol (NP) and oxalic acid (OA) added individually and simultaneously (B + NP, B + OA, and B + NP + OA); NP and OA were NB’s main UV-photolysis products. Compared with B, the biodegradation rate P + B was lower by 13–29%, but intimately coupling (P&B) had a removal rate that was 10–13% higher; mineralization showed similar trends. B + OA gave results similar to P&B, B + NP gave results similar to P + B, and B + OA + NP gave results between P + B and P&B, depending on the amount of OA and NP added. The photolysis product OA accelerated NB biodegradation through a co-substrate effect, but NP was inhibitory. Although decreasing the UV photolysis time could minimize the inhibition impact of NP in P + B, P&B gave the fastest removal of NB by accentuating the co-substrate effect of OA.

  3. Contrast-induced nephropathy

    Directory of Open Access Journals (Sweden)

    Ricardo A. García Hernández

    2016-06-01

    Full Text Available Contrast-induced nephropathy is an important complication associated with the use of contrast media. Favoring factors for the development of contrast-induced nephronpathy have been widely described, being diabetes mellitus and previous renal disease the greatest risk. The pathophysiology is a complex process where the medullary hypoxia represents the trigger element. Previous hydration and the use of low osmolality contrast are the most recommended measures to prevent its development.

  4. Using chemical desorption of PAHs from sediment to model biodegradation during bioavailability assessment.

    Science.gov (United States)

    Spasojević, Jelena M; Maletić, Snežana P; Rončević, Srđan D; Radnović, Dragan V; Cučak, Dragana I; Tričković, Jelena S; Dalmacija, Božo D

    2015-01-01

    This work compares the biodegradation potential of four polycyclic aromatic hydrocarbons (PAH) (phenanthrene, pyrene, chrysene and benzo(a)pyrene, chosen as representatives of the 3, 4 and 5 ring PAHs) with their desorption from sediment by XAD4 resin and methyl-β-cyclodextrin (MCD). The biodegradation study was conducted under various conditions (biostimulation, bioaugmentation and their combination). The results show that total PAH removal in all treatments except biostimulation gave similar results, whereby the total amount of PAHs was decreased by about 30-35%. The desorption experiment showed that XAD4 desorbed a greater fraction of phenanthrene (77% versus 52%), and benzo(a)pyrene (44% versus 25%) than MCD. The results for four ring PAHs were similar for both desorption agents (about 30%). Comparing the maximum biodegraded amount of each PAH with the rapidly desorbed XAD4 and MCD fraction, XAD4 was found to correlate better with biodegradation for the high molecular PAHs (pyrene, chrysene, benzo(a)pyrene), although it overestimated the availability of phenanthrene. In contrast, MCD showed better correlation with the biodegradation of low molecular weight PAHs.

  5. Environmentally Relevant Inoculum Concentrations Improve the Reliability of Persistent Assessments in Biodegradation Screening Tests.

    Science.gov (United States)

    Martin, Timothy J; Snape, Jason R; Bartram, Abigail; Robson, Aidan; Acharya, Kishor; Davenport, Russell J

    2017-02-23

    Standard OECD biodegradation screening tests (BSTs) have not evolved at the same rate as regulatory concerns, which now place an increased emphasis on environmental persistence. Consequently, many chemicals are falsely assigned as being potentially persistent based on results from BSTs. The present study increased test duration and increased inoculum concentrations to more environmentally relevant levels to assess their impact on biodegradation outcome and intratest replicate variability for chemicals with known environmental persistence. Chemicals were assigned to potential persistence categories based on existing degradation data. These more environmentally relevant BSTs (erBSTs) improved the reliability of persistence assignment by reducing the high variability associated with these tests and the occurrence of failures at low inoculum concentrations due to the exclusion of specific degraders. Environmental fate was determined using a reference set of (14)C-labeled compounds with a range of potential environmental persistences, and full mass balance data were collated. The erBST correctly assigned five reference chemicals of known biodegradabilities to their appropriate persistence category in contrast to a standard OECD Ready Biodegradation Test (RBTs, P < 0.05). The erBST was significantly more reproducible than an OECD RBT (ANOVA, P < 0.05), with more consistent rates and extent of biodegradation observed in the erBST.

  6. 生物可降解微针的研究进展%Research and development of biodegradable microneedles

    Institute of Scientific and Technical Information of China (English)

    周友军; 杨云珂; 桂双英

    2013-01-01

    Microneedles are a new type of transdermal drug delivery. It can create a micron-level drug delivery channel on the skin and enhance the permeability of skin for drugs, especially macromolecular drugs, and it does not reach to the nerves in deep skin tissue. Because of using biodegradable materials as a substrate, biodegradable microneedle has the characteristics of biodegradable, self-degradation in the skin, which can solve the difficulty of microneedles broken into skin. As a new transdermal drug delivery technology, it might be an ideal vehicle for biological macromolecules, peptides, vaccines and other drugs. This article provided an overview of the characteristics of biodegradable microneedles, manufacture method, the matrix of choice, application, existing problems and so on.%微针给药是一种新型的经皮给药方式,可在皮肤上创造微米级的药物运输通道,增强皮肤对药物尤其是大分子药物的渗透性,且不会到达神经分布丰富的皮肤深层组织.生物可降解微针是以生物可降解材料为基质制作出的微针,除具有一般微针的优点,其具有的生物可降解特性解决了微针一旦断裂于皮肤内难以处理这一难题.因此生物可降解微针有望成为经皮给药的理想载体.本文对生物可降解微针的特点、制作方法、基质的选择、在经皮给药系统中的应用以及存在的问题等进行了概述.

  7. Advances in electron microscopy: A qualitative view of instrumentation development for macromolecular imaging and tomography.

    Science.gov (United States)

    Schröder, Rasmus R

    2015-09-01

    Macromolecular imaging and tomography of ice embedded samples has developed into a mature imaging technology, in structural biology today widely referred to simply as cryo electron microscopy.(1) While the pioneers of the technique struggled with ill-suited instruments, state-of-the-art cryo microscopes are now readily available and an increasing number of groups are producing excellent high-resolution structural data of macromolecular complexes, of cellular organelles, or the morphology of whole cells. Instrumentation developers, however, are offering yet more novel electron optical devices, such as energy filters and monochromators, aberration correctors or physical phase plates. Here we discuss how current instrumentation has already changed cryo EM, and how newly available instrumentation - often developed in other fields of electron microscopy - may further develop the use and applicability of cryo EM to the imaging of single isolated macromolecules of smaller size or molecules embedded in a crowded cellular environment.

  8. Macromolecular crowding increases binding of DNA polymerase to DNA: an adaptive effect

    Energy Technology Data Exchange (ETDEWEB)

    Zimmerman, S.B.; Harrison, B.

    1987-05-01

    Macromolecular crowding extends the range of ionic conditions supporting high DNA polymerase reaction rates. Reactions tested were nick translation and gap-filling by DNA polymerase I of E. coli, nuclease and polymerase activities of the large fragment of that polymerase, and polymerization by the T4 DNA polymerase. For all of these reactions, high concentrations of nonspecific polymers increased enzymatic activity under otherwise inhibitory conditions resulting from relatively high ionic strength. The primary mechanism of the polymer effect seems to be to increase the binding of polymerase to DNA. They suggest that this effect of protein-DNA complexes is only one example of a general metabolic buffering action of crowded solutions on a variety of macromolecular interactions.

  9. 3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy.

    Science.gov (United States)

    Nogales-Cadenas, R; Jonic, S; Tama, F; Arteni, A A; Tabas-Madrid, D; Vázquez, M; Pascual-Montano, A; Sorzano, C O S

    2013-07-01

    Electron microscopy (EM) provides access to structural information of macromolecular complexes in the 3-20 Å resolution range. Normal mode analysis has been extensively used with atomic resolution structures and successfully applied to EM structures. The major application of normal modes is the identification of possible conformational changes in proteins. The analysis can throw light on the mechanism following ligand binding, protein-protein interactions, channel opening and other functional macromolecular movements. In this article, we present a new web server, 3DEM Loupe, which allows normal mode analysis of any uploaded EM volume using a user-friendly interface and an intuitive workflow. Results can be fully explored in 3D through animations and movies generated by the server. The application is freely available at http://3demloupe.cnb.csic.es.

  10. Romp: The Method of Choice for Precise Macromolecular Engineering and Synthesis of Smart Materials

    Science.gov (United States)

    Khosravi, Ezat; Castle, Thomas C.; Kujawa, Margaret; Leejarkpai, Jan; Hutchings, Lian R.; Hine, Peter J.

    The recent advances in olefin metathesis highlight the impact of Ring Opening Metathesis Polymerisation (ROMP) as a powerful technique for macromolecular engineering and synthesis of smart materials with well-defined structures. ROMP has attracted a considerable research attention recently particularly by industry largely due to the development of well-defined metal complexes as initiators and also because of the award of the Noble Prize for Chemistry in 2005 to three scientists (Chauvin, Grubbs, Schrock) for their contributions in this area. This chapter discusses several interesting examples in order to demonstrate that ROMP is a power tool in macromolecular engineering and that it allows the design and synthesis of polymers with novel topologies.

  11. The macromolecular crystallography beamline I911-3 at the MAX IV laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Ursby, Thomas, E-mail: thomas.ursby@maxlab.lu.se; Unge, Johan; Appio, Roberto [Lund University, POB 118, Lund SE-221 00 (Sweden); Logan, Derek T. [Lund University, POB 124, Lund SE-221 00 (Sweden); Fredslund, Folmer; Svensson, Christer; Larsson, Krister; Labrador, Ana [Lund University, POB 118, Lund SE-221 00 (Sweden); Thunnissen, Marjolein M. G. M. [Lund University, POB 124, Lund SE-221 00 (Sweden)

    2013-07-01

    The updated macromolecular crystallography beamline I911-3 at the MAX II storage ring is described. The macromolecular crystallography beamline I911-3, part of the Cassiopeia/I911 suite of beamlines, is based on a superconducting wiggler at the MAX II ring of the MAX IV Laboratory in Lund, Sweden. The beamline is energy-tunable within a range between 6 and 18 keV. I911-3 opened for users in 2005. In 2010–2011 the experimental station was completely rebuilt and refurbished such that it has become a state-of-the-art experimental station with better possibilities for rapid throughput, crystal screening and work with smaller samples. This paper describes the complete I911-3 beamline and how it is embedded in the Cassiopeia suite of beamlines.

  12. Optimal cytoplasmatic density and flux balance model under macromolecular crowding effects.

    Science.gov (United States)

    Vazquez, Alexei

    2010-05-21

    Macromolecules occupy between 34% and 44% of the cell cytoplasm, about half the maximum packing density of spheres in three dimension. Yet, there is no clear understanding of what is special about this value. To address this fundamental question we investigate the effect of macromolecular crowding on cell metabolism. We develop a cell scale flux balance model capturing the main features of cell metabolism at different nutrient uptakes and macromolecular densities. Using this model we show there are two metabolic regimes at low and high nutrient uptakes. The latter regime is characterized by an optimal cytoplasmatic density where the increase of reaction rates by confinement and the decrease by diffusion slow-down balance. More important, the predicted optimal density is in the range of the experimentally determined density of Escherichia coli.

  13. STUDIES ON PAN MACROMOLECULAR SEMICONDUCTING FIBER 1. PREPARATION OF PAN CONDUCTING FIBER TREATED BY STANNIC CHLORIDE AND ITS SEMICONDUCTING BEHAVIOUR

    Institute of Scientific and Technical Information of China (English)

    WANG Dexi; CUI Dayuan; LUO Boliang; WANG Xiugang; WU Renjie

    1984-01-01

    The PAN fiber treated by Lewis acid (e.g. stannic chloride) could be transformed into a macromolecular conducting fiber by further thermal treatment. Depending on thermal treatment condition the resistance of the fiber varied from 103 to 1012 Ω and kept stable after hydrolysis. The fiber has enough strength to be processed by various means. This is a new kind of macromolecular semiconducting fiber having some characteristics similar to those of organic semiconductors.

  14. Contrast-enhanced and targeted ultrasound

    Institute of Scientific and Technical Information of China (English)

    Michiel Postema; Odd Helge Gilja

    2011-01-01

    Ultrasonic imaging is becoming the most popular medical imaging modality,owing to the low price per examination and its safety.However,blood is a poor scatterer of ultrasound waves at clinical diagnostic transmit frequencies.For perfusion imaging,markers have been designed to enhance the contrast in B-mode imaging.These so-called ultrasound contrast agents consist of microscopically small gas bubbles encapsulated in biodegradable shells.In this review,the physical principles of ultrasound contrast agent microbubble behavior and their adjustment for drug delivery including sonoporation are described.Furthermore,an outline of clinical imaging applications of contrast-enhanced ultrasound is given.It is a challenging task to quantify and predict which bubble phenomenon occurs under which acoustic condition,and how these phenomena may be utilized in ultrasonic imaging.Aided by high-speed photography,our improved understanding of encapsulated microbubble behavior will lead to more sophisticated detection and delivery techniques.More sophisticated methods use quantitative approaches to measure the amount and the time course of bolus or reperfusion curves,and have shown great promise in revealing effective tumor responses to anti-angiogenic drugs in humans before tumor shrinkage occurs.These are beginning to be accepted into clinical practice.In the long term,targeted microbubbles for molecular imaging and eventually for directed anti-tumor therapy are expected to be tested.

  15. Contrast-enhanced and targeted ultrasound.

    Science.gov (United States)

    Postema, Michiel; Gilja, Odd Helge

    2011-01-07

    Ultrasonic imaging is becoming the most popular medical imaging modality, owing to the low price per examination and its safety. However, blood is a poor scatterer of ultrasound waves at clinical diagnostic transmit frequencies. For perfusion imaging, markers have been designed to enhance the contrast in B-mode imaging. These so-called ultrasound contrast agents consist of microscopically small gas bubbles encapsulated in biodegradable shells. In this review, the physical principles of ultrasound contrast agent microbubble behavior and their adjustment for drug delivery including sonoporation are described. Furthermore, an outline of clinical imaging applications of contrast-enhanced ultrasound is given. It is a challenging task to quantify and predict which bubble phenomenon occurs under which acoustic condition, and how these phenomena may be utilized in ultrasonic imaging. Aided by high-speed photography, our improved understanding of encapsulated microbubble behavior will lead to more sophisticated detection and delivery techniques. More sophisticated methods use quantitative approaches to measure the amount and the time course of bolus or reperfusion curves, and have shown great promise in revealing effective tumor responses to anti-angiogenic drugs in humans before tumor shrinkage occurs. These are beginning to be accepted into clinical practice. In the long term, targeted microbubbles for molecular imaging and eventually for directed anti-tumor therapy are expected to be tested.

  16. Biodegradable and compostable alternatives to conventional plastics.

    Science.gov (United States)

    Song, J H; Murphy, R J; Narayan, R; Davies, G B H

    2009-07-27

    Packaging waste forms a significant part of municipal solid waste and has caused increasing environmental concerns, resulting in a strengthening of various regulations aimed at reducing the amounts generated. Among other materials, a wide range of oil-based polymers is currently used in packaging applications. These are virtually all non-biodegradable, and some are difficult to recycle or reuse due to being complex composites having varying levels of contamination. Recently, significant progress has been made in the development of biodegradable plastics, largely from renewable natural resources, to produce biodegradable materials with similar functionality to that of oil-based polymers. The expansion in these bio-based materials has several potential benefits for greenhouse gas balances and other environmental impacts over whole life cycles and in the use of renewable, rather than finite resources. It is intended that use of biodegradable materials will contribute to sustainability and reduction in the environmental impact associated with disposal of oil-based polymers. The diversity of biodegradable materials and their varying properties makes it difficult to make simple, generic assessments such as biodegradable products are all 'good' or petrochemical-based products are all 'bad'. This paper discusses the potential impacts of biodegradable packaging materials and their waste management, particularly via composting. It presents the key issues that inform judgements of the benefits these materials have in relation to conventional, petrochemical-based counterparts. Specific examples are given from new research on biodegradability in simulated 'home' composting systems. It is the view of the authors that biodegradable packaging materials are most suitable for single-use disposable applications where the post-consumer waste can be locally composted.

  17. Controlling Macromolecular Topology with Genetically Encoded SpyTag-SpyCatcher Chemistry

    OpenAIRE

    Zhang, Wen-Bin; Sun, Fei; Tirrell, David A.; Arnold, Frances H.

    2013-01-01

    Control of molecular topology constitutes a fundamental challenge in macromolecular chemistry. Here we describe the synthesis and characterization of artificial elastin-like proteins (ELPs) with unconventional nonlinear topologies including circular, tadpole, star, and H-shaped proteins using genetically encoded SpyTag–SpyCatcher chemistry. SpyTag is a short polypeptide that binds its protein partner SpyCatcher and forms isopeptide bonds under physiological conditions. Sequences encoding SpyT...

  18. CplexA: a Mathematica package to study macromolecular-assembly control of gene expression

    OpenAIRE

    Vilar, J. M. G.; Saiz, L

    2010-01-01

    Summary: Macromolecular assembly vertebrates essential cellular processes, such as gene regulation and signal transduction. A major challenge for conventional computational methods to study these processes is tackling the exponential increase of the number of configurational states with the number of components. CplexA is a Mathematica package that uses functional programming to efficiently compute probabilities and average properties over such exponentially large number of states from the en...

  19. Porphyrin-Cored Polymer Nanoparticles: Macromolecular Models for Heme Iron Coordination.

    Science.gov (United States)

    Rodriguez, Kyle J; Hanlon, Ashley M; Lyon, Christopher K; Cole, Justin P; Tuten, Bryan T; Tooley, Christian A; Berda, Erik B; Pazicni, Samuel

    2016-10-03

    Porphyrin-cored polymer nanoparticles (PCPNs) were synthesized and characterized to investigate their utility as heme protein models. Created using collapsible heme-centered star polymers containing photodimerizable anthracene units, these systems afford model heme cofactors buried within hydrophobic, macromolecular environments. Spectroscopic interrogations demonstrate that PCPNs display redox and ligand-binding reactivity similar to that of native systems and thus are potential candidates for modeling biological heme iron coordination.

  20. STUDY ON HYDROLYSIS OF MACROMOLECULAR GELATIN WITH ENZYMES IN COMBINATION MODE

    Institute of Scientific and Technical Information of China (English)

    Ya-qin Huang; Rui Guan; Ming-zhi Huang

    2004-01-01

    The enzymatic hydrolysis of macromolecular gelatin with AS1.398 neutral protease, bromelain and their combinations was studied by estimating the molecular weights of their hydrolytic products. It was discovered that the products hydrolyzed by using combination enzymes had lower molecular weight than those obtained by using single ones,and the kind of enzymes, their combination mode and addition sequence are effective ways to control the molecular weights of gelatin hydrolyzates.

  1. Biodegradable Metals From Concept to Applications

    CERN Document Server

    Hermawan, Hendra

    2012-01-01

    This book in the emerging research field of biomaterials covers biodegradable metals for biomedical applications. The book contains two main parts where each of them consists of three chapters. The first part introduces the readers to the field of metallic biomaterials, exposes the state of the art of biodegradable metals, and reveals its application for cardiovascular implants. It includes some fundamental aspects to give basic understanding on metals for further review on the degradable ones is covered in chapter one. The second chapter introduces the concept of biodegradable metals, it's st

  2. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

    Directory of Open Access Journals (Sweden)

    Tatiana Maximova

    2016-04-01

    Full Text Available Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.

  3. Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination.

    Science.gov (United States)

    Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

    2013-11-01

    The number of macromolecular structures deposited in the Protein Data Bank now approaches 100,000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation.

  4. Macromolecular (pro)drugs with concurrent direct activity against the hepatitis C virus and inflammation.

    Science.gov (United States)

    Wohl, Benjamin M; Smith, Anton A A; Jensen, Bettina E B; Zelikin, Alexander N

    2014-12-28

    Macromolecular prodrugs (MPs) are a powerful tool to alleviate side-effects and improve the efficacy of the broad-spectrum antiviral agent ribavirin. In this work, we sought an understanding of what makes an optimal formulation within the macromolecular parameter space--nature of the polymer carrier, average molar mass, drug loading, or a good combination thereof. A panel of MPs based on biocompatible synthetic vinylic and (meth)acrylic polymers was tested in an anti-inflammatory assay with relevance to alleviating inflammation in the liver during hepatitis C infection. Pristine polymer carriers proved to have a pronounced anti-inflammatory activity, a notion which may prove significant in developing MPs for antiviral and anticancer treatments. With conjugated ribavirin, MPs revealed enhanced activity but also higher toxicity. Therapeutic windows and therapeutic indices were determined and discussed to reveal the most potent formulation and those with optimized safety. Polymers were also tested as inhibitors of replication of the hepatitis C viral RNA using a subgenomic viral replicon system. For the first time, negatively charged polymers are revealed to have an intracellular activity against hepatitis C virus replication. Concerted activity of the polymer and ribavirin afforded MPs which significantly increased the therapeutic index of ribavirin-based treatment. Taken together, the systematic investigation of the macromolecular space identified lead candidates with high efficacy and concurrent direct activity against the hepatitis C virus and inflammation.

  5. Preparation and degradation mechanisms of biodegradable polymer: a review

    Science.gov (United States)

    Zeng, S. H.; Duan, P. P.; Shen, M. X.; Xue, Y. J.; Wang, Z. Y.

    2016-07-01

    Polymers are difficult to degrade completely in Nature, and their catabolites may pollute the environment. In recent years, biodegradable polymers have become the hot topic in people's daily life with increasing interest, and a controllable polymer biodegradation is one of the most important directions for future polymer science. This article presents the main preparation methods for biodegradable polymers and discusses their degradation mechanisms, the biodegradable factors, recent researches and their applications. The future researches of biodegradable polymers are also put forward.

  6. Polypeptoids: A perfect match for molecular definition and macromolecular engineering?

    KAUST Repository

    Luxenhofer, Robert

    2013-04-19

    Precision synthesis of polymers has been a hot topic in recent years. While this is notoriously difficult to address for polymers with a CC backbone, Merrifield has discovered a way many decades ago for polypeptides. Using a similar approach, N-substituted polypeptides, so-called polypeptoids have been synthesized and studied for about 20 years. In contrast, the living ring-opening polymerization (ROP) of N-substituted N-carboxyanhydrides was among the first living polymerizations to be discovered. More recently, a surge in new synthetic approaches led to the efficient synthesis of cyclic or linear multiblock copolypeptoids. Thus, polypeptoids can be synthesized either by solid phase synthesis to yield complex and exactly defined oligo- and small polymers or by ROP of appropriately N-substituted N-carboxyanhydrides (NNCA) to give linear, cyclic, or star-like polymers. Together with an excellent biocompatibility, this polymer family may have a bright future ahead as biomaterials. © 2013 Wiley Periodicals, Inc.

  7. Amylopectin molecular structure reflected in macromolecular organization of granular starch.

    Science.gov (United States)

    Vermeylen, Rudi; Goderis, Bart; Reynaers, Harry; Delcour, Jan A

    2004-01-01

    For lintners with negligible amylose retrogradation, crystallinity related inversely to starch amylose content and, irrespective of starch source, incomplete removal of amorphous material was shown. The latter was more pronounced for B-type than for A-type starches. The two predominant lintner populations, with modal degrees of polymerization (DP) of 13-15 and 23-27, were best resolved for amylose-deficient and A-type starches. Results indicate a more specific hydrolysis of amorphous lamellae in such starches. Small-angle X-ray scattering showed a more intense 9-nm scattering peak for native amylose-deficient A-type starches than for their regular or B-type analogues. The experimental evidence indicates a lower contrasting density within the "crystalline" shells of the latter starches. A higher density in the amorphous lamellae, envisaged by the lamellar helical model, explains the relative acid resistance of linear amylopectin chains with DP > 20, observed in lintners of B-type starches. Because amylopectin chain length distributions were similar for regular and amylose-deficient starches of the same crystal type, we deduce that the more dense (and ordered) packing of double helices into lamellar structures in amylose-deficient starches is due to a different amylopectin branching pattern.

  8. Engineered biosynthesis of biodegradable polymers.

    Science.gov (United States)

    Jambunathan, Pooja; Zhang, Kechun

    2016-08-01

    Advances in science and technology have resulted in the rapid development of biobased plastics and the major drivers for this expansion are rising environmental concerns of plastic pollution and the depletion of fossil-fuels. This paper presents a broad view on the recent developments of three promising biobased plastics, polylactic acid (PLA), polyhydroxyalkanoate (PHA) and polybutylene succinate (PBS), well known for their biodegradability. The article discusses the natural and recombinant host organisms used for fermentative production of monomers, alternative carbon feedstocks that have been used to lower production cost, different metabolic engineering strategies used to improve product titers, various fermentation technologies employed to increase productivities and finally, the different downstream processes used for recovery and purification of the monomers and polymers.

  9. High-resolution three-dimensional macromolecular proton fraction mapping for quantitative neuroanatomical imaging of the rodent brain in ultra-high magnetic fields.

    Science.gov (United States)

    Naumova, Anna V; Akulov, Andrey E; Khodanovich, Marina Yu; Yarnykh, Vasily L

    2017-02-15

    A well-known problem in ultra-high-field MRI is generation of high-resolution three-dimensional images for detailed characterization of white and gray matter anatomical structures. T1-weighted imaging traditionally used for this purpose suffers from the loss of contrast between white and gray matter with an increase of magnetic field strength. Macromolecular proton fraction (MPF) mapping is a new method potentially capable to mitigate this problem due to strong myelin-based contrast and independence of this parameter of field strength. MPF is a key parameter determining the magnetization transfer effect in tissues and defined within the two-pool model as a relative amount of macromolecular protons involved into magnetization exchange with water protons. The objectives of this study were to characterize the two-pool model parameters in brain tissues in ultra-high magnetic fields and introduce fast high-field 3D MPF mapping as both anatomical and quantitative neuroimaging modality for small animal applications. In vivo imaging data were obtained from four adult male rats using an 11.7T animal MRI scanner. Comprehensive comparison of brain tissue contrast was performed for standard R1 and T2 maps and reconstructed from Z-spectroscopic images two-pool model parameter maps including MPF, cross-relaxation rate constant, and T2 of pools. Additionally, high-resolution whole-brain 3D MPF maps were obtained with isotropic 170µm voxel size using the single-point synthetic-reference method. MPF maps showed 3-6-fold increase in contrast between white and gray matter compared to other parameters. MPF measurements by the single-point synthetic reference method were in excellent agreement with the Z-spectroscopic method. MPF values in rat brain structures at 11.7T were similar to those at lower field strengths, thus confirming field independence of MPF. 3D MPF mapping provides a useful tool for neuroimaging in ultra-high magnetic fields enabling both quantitative tissue

  10. KinImmerse: Macromolecular VR for NMR ensembles

    Directory of Open Access Journals (Sweden)

    Vinson E Claire

    2009-02-01

    Full Text Available Abstract Background In molecular applications, virtual reality (VR and immersive virtual environments have generally been used and valued for the visual and interactive experience – to enhance intuition and communicate excitement – rather than as part of the actual research process. In contrast, this work develops a software infrastructure for research use and illustrates such use on a specific case. Methods The Syzygy open-source toolkit for VR software was used to write the KinImmerse program, which translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE. Results In addition to molecular visualizations and navigation, KinImmerse provides a set of research tools for manipulation, identification, co-centering of multiple models, free-form 3D annotation, and output of results. The molecular research test case analyzes the local neighborhood around an individual atom within an ensemble of nuclear magnetic resonance (NMR models, enabling immersive visual comparison of the local conformation with the local NMR experimental data, including target curves for residual dipolar couplings (RDCs. Conclusion The promise of KinImmerse for production-level molecular research in the DiVE is shown by the locally co-centered RDC visualization developed there, which gave new insights now being pursued in wider data analysis.

  11. Lubricant Biodegradation Enhancers:Designed Chemistry and Engineered Technology

    Institute of Scientific and Technical Information of China (English)

    Chen Boshui; Gao Lingyue; Fang Jianhua; Zhang Nan; Wu Jiang; Wang Jiu

    2015-01-01

    In recent decades, a growing worldwide trend of developing the biodegradable lubricants has been prevailing to form a speciifc ifeld of green chemistry and green engineering. Enhancement of biodegradability of unreadily biodegradable petroleum-based lubricants has as such become an urgent must. For over a decade the authors have been focusing on the im-provement of biodegradability of unreadily biodegradable lubricants such as petroleum-based lubricating oils and greases. A new idea of lubricant biodegradation enhancer was put forward by the authors with the aim to stimulate the biodegradation of unreadily biodegradable lubricants by incorporating the enhancer into the lubricants in order to turn the lubricants into greener biodegradable ones and to help in situ bioremediation of lubricant-contaminated environment. This manuscript sum-marizes our recent efforts relating to the chemistry and technology of biodegradation enhancers for lubricants. Firstly, the chemistry of lubricant biodegradation enhancers was designed based on the principles of bioremediation for the treatment of hydrocarbon contaminated environment. Secondly, the ability of the designed biodegradation enhancers for increasing the biodegradability of unreadily biodegradable industrial lubricants was investigated through biodegradability evaluation tests, microbial population analysis, and biodegradation kinetics modeling. Finally, the impact of biodegradation enhancers on some crucial performance characteristics of lubricants such as lubricity and oxidation stability was tested via tribological evaluation and oxidation determinations. Our results have shown that the designed chemistry of nitrogenous and/or phos-phorous compounds such as lauroyl glutamine, oleoyl glycine, oleic diethanolamide phosphate and lauric diethanolamide borate was outstanding in boosting biodegradation of petroleum-based lubricants which was ascribed to increase the micro-bial population and decrease the oil-water interfacial

  12. Phyllosphere yeasts rapidly break down biodegradable plastics.

    Science.gov (United States)

    Kitamoto, Hiroko K; Shinozaki, Yukiko; Cao, Xiao-Hong; Morita, Tomotake; Konishi, Masaaki; Tago, Kanako; Kajiwara, Hideyuki; Koitabashi, Motoo; Yoshida, Shigenobu; Watanabe, Takashi; Sameshima-Yamashita, Yuka; Nakajima-Kambe, Toshiaki; Tsushima, Seiya

    2011-11-29

    The use of biodegradable plastics can reduce the accumulation of environmentally persistent plastic wastes. The rate of degradation of biodegradable plastics depends on environmental conditions and is highly variable. Techniques for achieving more consistent degradation are needed. However, only a few microorganisms involved in the degradation process have been isolated so far from the environment. Here, we show that Pseudozyma spp. yeasts, which are common in the phyllosphere and are easily isolated from plant surfaces, displayed strong degradation activity on films made from poly-butylene succinate or poly-butylene succinate-co-adipate. Strains of P. antarctica isolated from leaves and husks of paddy rice displayed strong degradation activity on these films at 30°C. The type strain, P. antarctica JCM 10317, and Pseudozyma spp. strains from phyllosphere secreted a biodegradable plastic-degrading enzyme with a molecular mass of about 22 kDa. Reliable source of biodegradable plastic-degrading microorganisms are now in our hands.

  13. Phase contrast image synthesis

    DEFF Research Database (Denmark)

    Glückstad, J.

    1996-01-01

    A new method is presented for synthesizing arbitrary intensity patterns based on phase contrast imaging. The concept is grounded on an extension of the Zernike phase contrast method into the domain of full range [0; 2 pi] phase modulation. By controlling the average value of the input phase...... function and by choosing appropriate phase retardation at the phase contrast filter, a pure phase to intensity imaging is accomplished. The method presented is also directly applicable in dark field image synthesis....

  14. The effect of macromolecular crowding on the structure of the protein complex superoxide dismutase

    Science.gov (United States)

    Rajapaksha Mudalige, Ajith Rathnaweera

    Biological environments contain between 7 - 40% macromolecules by volume. This reduces the available volume for macromolecules and elevates the osmotic pressure relative to pure water. Consequently, biological macromolecules in their native environments tend to adopt more compact and dehydrated conformations than those in vitro. This effect is referred to as macromolecular crowding and constitutes an important physical difference between native biological environments and the simple solutions in which biomolecules are usually studied. We used small angle scattering (SAS) to measure the effects of macromolecular crowding on the size of a protein complex, superoxide dismutase (SOD). Crowding was induced using 400 MW polyethylene glycol (PEG), triethylene glycol (TEG), methyl-alpha-glucoside (alpha-MG) and trimethylamine N-oxide (TMAO). Parallel small angle neutron scattering (SANS) and small angle X-ray scattering (SAXS) allowed us to unambiguously attribute apparent changes in radius of gyration to changes in the structure of SOD. For a 40% PEG solution, we find that the volume of SOD was reduced by 9%. SAS coupled with osmotic pressure measurements allowed us to estimate a compressibility modulus for SOD. We believe this to be the first time the osmotic compressibility of a protein complex was measured. Molecular Dynamics (MD) simulations are widely used to obtain insights on biomolecular processes. However, it is not clear whether MD is capable of predicting subtle effects of macromolecular crowding. We used our experimentally observed compressibility of SOD to evaluate the ability of MD to predict macromolecular crowding. Effects of macromolecular crowding due to PEG on SOD were modeled using an all atom MD simulation with the CHARMM forcefield and the crystallographically resolved structures of SOD and PEG. Two parallel MD simulations were performed for SOD in water and SOD in 40% PEG for over 150~ns. Over the period of the simulation the SOD structure in 40

  15. Contrast induced nephropathy

    DEFF Research Database (Denmark)

    Stacul, Fulvio; van der Molen, Aart J; Reimer, Peter

    2011-01-01

    measures used to reduce the incidence of CIN, and the management of patients receiving metformin. Key Points • Definition, risk factors and prevention of contrast medium induced nephropathy are reviewed. • CIN risk is lower with intravenous than intra-arterial iodinated contrast medium. • eGFR of 45 ml....../min/1.73 m (2) is CIN risk threshold for intravenous contrast medium. • Hydration with either saline or sodium bicarbonate reduces CIN incidence. • Patients with eGFR ≥ 60 ml/min/1.73 m (2) receiving contrast medium can continue metformin normally....

  16. Contrast induced nephropathy

    DEFF Research Database (Denmark)

    Stacul, Fulvio; van der Molen, Aart J; Reimer, Peter

    2011-01-01

    measures used to reduce the incidence of CIN, and the management of patients receiving metformin. Key Points • Definition, risk factors and prevention of contrast medium induced nephropathy are reviewed. • CIN risk is lower with intravenous than intra-arterial iodinated contrast medium. • eGFR of 45 ml....../min/1.73 m (2) is CIN risk threshold for intravenous contrast medium. • Hydration with either saline or sodium bicarbonate reduces CIN incidence. • Patients with eGFR = 60 ml/min/1.73 m (2) receiving contrast medium can continue metformin normally....

  17. Transport of nonlinearly biodegradable contaminants in aquifers

    OpenAIRE

    Keijzer, H.

    2001-01-01

    This thesis deals with the transport behavior of nonlinearly biodegradable contaminants in aquifers. Such transport occurs during in situ bioremediation which is based on the injection of an electron acceptor or electron donor. The main interests in this thesis are the mutual influences of underlying processes, i.e. transport, adsorption and biodegradation, and their influence on in situ bioremediation performance. To gain insight in these influences, the processes in a homogeneous aquifer ar...

  18. Ball Powder Production Wastewater Biodegradation Support Studies

    Science.gov (United States)

    1989-02-01

    Any unusual removal criteria (NO3, toxic compound, etc.): * None 9 Type of wastewater treated: Dairy ( whey and grease) 1 Design basis for scale-up... WASTEWATER BIODEGRADATION SUPPORT STUDIES (TASK ORDER NO. 11) February 1989 Contract No. DAAK11-85-D-0008 w MAR 2 9 1983 Prepared by: Arthur D...United States Army Toxic and Hazardous Materials Agency February 1989 I Ball Powder Production Wastewater Pilot-Scale £ Biodegradation Support Studies I

  19. Biodegradability of Chlorinated Anilines in Waters

    Institute of Scientific and Technical Information of China (English)

    CHAO WANG; GUAN-GHUA LU; YAN-JIE ZHOU

    2007-01-01

    Objective To identify the bacteria tolerating chlorinated anilines and to study the biodegradability of o-chloroaniline and its coexistent compounds. Methods Microbial community of complex bacteria was identified by plate culture observation techniques and Gram stain method. Bacterial growth inhibition test was used to determine the tolerance of complex bacteria to toxicant. Biodegradability of chlorinated anilines was determined using domesticated complex bacteria as an inoculum by shaking-flask test. Results The complex bacteria were identified, consisting of Xanthomonas, Bacillus alcaligenes,Acinetobacter, Pseudomonas, and Actinomycetaceae nocardia. The obtained complex bacteria were more tolerant to o-chloroaniline than mixture bacteria in natural river waters. The effects of exposure concentration and inoculum size on the biodegradability of o-chloroaniline were analyzed, and the biodegradation characteristics of single o-chloroaniline and 2,4-dichloroaniline were compared with the coexistent compounds. Conclusion The biodegradation rates can be improved by decreasing concentration of compounds and increasing inoculum size of complex bacteria. When o-chloroaniline coexists with aniline, the latter is biodegraded prior to the former, and as a consequence the metabolic efficiency of o-chloroaniline is improved with the increase of aniline concentration. Meanwhile, when o-chloroaniline coexists with 2,4-dichloroaniline, the metabolic efficiency of 2,4-dichloroaniline is markedly improved.

  20. Extracellular polymeric substances govern the development of biofilm and mass transfer of polycyclic aromatic hydrocarbons for improved biodegradation.

    Science.gov (United States)

    Zhang, Yinping; Wang, Fang; Zhu, Xiaoshu; Zeng, Jun; Zhao, Qiguo; Jiang, Xin

    2015-10-01

    The hypothesis that extracellular polymeric substances (EPS) affect the formation of biofilms for subsequent enhanced biodegradation of polycyclic aromatic hydrocarbons was tested. Controlled formation of biofilms on humin particles and biodegradation of phenanthrene and pyrene were performed with bacteria and EPS-extracted bacteria of Micrococcus sp. PHE9 and Mycobacterium sp. NJS-P. Bacteria without EPS extraction developed biofilms on humin, in contrast the EPS-extracted bacteria could not attach to humin particles. In the subsequent biodegradation of phenanthrene and pyrene, the biodegradation rates by biofilms were significantly higher than those of EPS-extracted bacteria. Although, both the biofilms and EPS-extracted bacteria showed increases in EPS contents, only the EPS contents in biofilms displayed significant correlations with the biodegradation efficiencies of phenanthrene and pyrene. It is proposed that the bacterial-produced EPS was a key factor to mediate bacterial attachment to other surfaces and develop biofilms, thereby increasing the bioavailability of poorly soluble PAH for enhanced biodegradation.

  1. Immersed multilayer biodegradable ureteral stent with reformed biodegradation: An in vitro experiment.

    Science.gov (United States)

    Yang, Ganggang; Xie, Hua; Huang, Yichen; Lv, Yiqing; Zhang, Mingqing; Shang, Yafeng; Zhou, Junmei; Wang, Liping; Wang, Jin-Ye; Chen, Fang

    2017-03-01

    Objective The aim of this study was to develop a novel immersed multilayer biodegradable ureteral stent with reformed biodegradation and evaluate it in vitro. Methods Poly(glycolic-co-lactic acid) (PGLA), microsphere zein and BaSO4 were employed to produce a multilayer biodegradable stent using immersion technology. Tests of the biodegradable stents and conventional control stents were conducted in human urine in vitro to evaluate the biodegradable properties. The biocompatibility was assessed by the morphology and proliferation of urine-derived cells cultured with extracted media from the biodegradable stent and a latex material positive control. Results An immersed multilayer biodegradable stent was successfully produced. It began to degrade in week 2 and was fully degraded by week 4. The mass loss ratio in the first 2 weeks was low (approximately 10.0% at 1 week, 20.0% at 2 weeks) and increased after 3 weeks (approximately 70%) to the end of testing. During the first 2 weeks, the radial compression load performances of the biodegradable stents were better than those of the control stents with statistically significant differences ( p = 0.00, p = 0.01) and the tensile strengths were lower in the biodegradable stents than those in the control stents throughout the experiment. SEM showed that the stents degraded layer by layer from the outer to the inner wall. The influences on the cells of extracted medium from the biodegradable stents were morphologically slight and lower than 10% in relative growth rates. Conclusions This preliminary study demonstrates that the immersed multilayer biodegradable ureteral stent has good radial compression and biocompatible performance and can be degraded in vitro within 4 weeks in a moderate manner.

  2. Quantification of in Situ Biodegradation Rate Constants Using a Novel Combined Isotope Approach

    Science.gov (United States)

    Blum, P.; Sültenfuß, J.; Martus, P.

    2014-12-01

    Numerous studies have shown the enormous potential of the compound-specific isotope analysis (CSIA) for studying the biodegradation of organic compounds such as monoaromatic hydrocarbons (BTEX), polyaromatic hydrocarbons (PAH), chlorinated solvents and other organic contaminants and environmental transformation mechanisms in groundwater. In addition, two-dimensional isotope analysis such as carbon and hydrogen have been successfully studied indicating the potential to also investigate site-specific reaction mechanisms. The main objective of the current study however is to quantify real effective in situ biodegradation rate constants in a coal-tar contaminated aquifer by combining compound-specific isotope analysis (CSIA) and tracer-based (3H-3He) ground-water dating (TGD). Hence, groundwater samples are used to determine groundwater residence times, and carbon and hydrogen stable isotopes are analyzed for selected BTEX and PAH. The results of the hydrogen stable isotopes surprisingly indicate no isotope fractionation and therefore no biodegradation. In contrast, for stable carbon isotopes of selected BTEX such as o-xylene and toluene, isotope shifts are detected indicating active biodegradation under sulfate-reducing conditions. These and previous results of stable carbon isotopes show that only for o-xylene a clear evidence for biodegradation is possible for the studied site. Nevertheless, in combining these results with the groundwater residence times, which range between 1 year for the shallow wells (20 m below surface) and 41 years for the deeper wells (40 m below surface), it is feasible to effectively determine in situ biodegradation rate constants for o-xylene. Conversely, the outcome also evidently demonstrate the major limitations of the novel combined isotope approach for a successful implementation of monitored natural attenuation (MNA) at such field sites.

  3. Dissolved oxygen saturation controls PAH biodegradation in freshwater estuary sediments.

    Science.gov (United States)

    Boyd, T J; Montgomery, M T; Steele, J K; Pohlman, J W; Reatherford, S R; Spargo, B J; Smith, D C

    2005-02-01

    Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in terrestrial and aquatic environments and can represent a significant constituent of the carbon pool in coastal sediments. We report here the results of an 18-month seasonal study of PAH biodegradation and heterotrophic bacterial production and their controlling biogeochemical factors from 186 sediment samples taken in a tidally influenced freshwater estuary. For each sampling event, measurements were averaged from 25-45 stations covering approximately 250 km(2). There was a clear relationship between bacterial production and ambient temperature, but none between production and bottom water dissolved oxygen (DO) % saturation or PAH concentrations. In contrast with other studies, we found no effect of temperature on the biodegradation of naphthalene, phenanthrene, or fluoranthene. PAH mineralization correlated with bottom water DO saturation above 70% (r(2) > 0.99). These results suggest that the proportional utilization of PAH carbon to natural organic carbon is as much as three orders of magnitude higher during cooler months, when water temperatures are lower and DO % saturation is higher. Infusion of cooler, well-oxygenated water to the water column overlying contaminated sediments during the summer months may stimulate PAH metabolism preferentially over non-PAH organic matter.

  4. Methanogenic biodegradation of two-ringed polycyclic aromatic hydrocarbons.

    Science.gov (United States)

    Berdugo-Clavijo, Carolina; Dong, Xiaoli; Soh, Jung; Sensen, Christoph W; Gieg, Lisa M

    2012-07-01

    Polycyclic aromatic hydrocarbons (PAH) are widespread in methane-rich subsurface environments, such as oil reservoirs and fuel-contaminated aquifers; however, little is known about the biodegradation of these compounds under methanogenic conditions. To assess the metabolism of PAH in the absence of electron acceptors, a crude oil-degrading methanogenic enrichment culture was tested for the ability to biodegrade naphthalene, 1-methylnaphthalene (1-MN), 2-methylnaphthalene (2-MN), and 2, 6-dimethylnaphthalene (2, 6-diMN). When methane was measured as an indicator of metabolism, nearly 400 μmol of methane was produced in the 2-MN- and 2, 6-diMN-amended cultures relative to substrate-unamended controls, which is close to the amount of methane stoichiometrically predicted based on the amount of substrate added (51-56 μmol). In contrast, no substantial methane was produced in the naphthalene- and 1-MN-amended enrichments. In time course experiments, metabolite analysis of enrichments containing 2-MN and 2, 6-diMN revealed the formation of 2-naphthoic acid and 6-methyl-2-naphthoic acid, respectively. Microbial community analysis by 454 pyrosequencing revealed that these PAH-utilizing enrichments were dominated by archaeal members most closely affiliated with Methanosaeta and Methanoculleus species and bacterial members most closely related to the Clostridiaceae, suggesting that these organisms play an important role in the methanogenic metabolism of the substituted naphthalenes in these cultures.

  5. Biodegradability of selected highly energetic pollutants under aerobic conditions

    Energy Technology Data Exchange (ETDEWEB)

    Jones, A.M.; Greer, C.W.; Hawari, J. [National Research Council of Canada, Montreal, Quebec (Canada). Biotechnology Research Inst.; Ampleman, G. [Defence Research Establishment Valcartier, Courcelette, Quebec (Canada). Div. des Materiaux Energetiques; Lavigne, J. [Canadian Embassy, Washington, DC (United States)

    1995-12-31

    Laboratory studies were conducted to assess the biodegradation potential of four energetic compounds--1,3,5-trinitro-1,3,5-triazacyclohexane (RDX), 2,4,6-trinitrotoluene (TNT), glycidyl azide polymer (GAP), and nitrocellulose (NC)--under aerobic conditions. Soils contaminated with energetic compounds were screened for microorganisms able to degrade these compounds. Rhodococcus sp. strain A was enriched and purified from RDX-contaminated soil by its ability to use RDX as sole source of nitrogen. Using [{sup 14}C]-labeled RDX, its ability to mineralize RDX to CO{sub 2} in pure culture under aerobic conditions was verified. Bioaugmentation of RDX-contaminated soil with this bacterium enhanced the rate and extent of biodegradation. Although TNT is a more toxic and recalcitrant pollutant, concentration-dependent [{sup 14}C]TNT mineralization activity was detected in TNT-contaminated soil. A Pseudomonas sp., enriched from this soil, was able to extensively transform TNT to partially reduced amine metabolites in axenic liquid culture. In contrast to these isolates, which utilized RDX and TNT as sources of nitrogen, soil consortia developed from soils exhibiting [{sup 14}C]GAP and [{sup 14}C]NC mineralization activities used GAP and NC as sole carbon sources for growth.

  6. Biodegradation of nitroglycerin from propellant residues on military training ranges.

    Science.gov (United States)

    Bordeleau, Geneviève; Martel, Richard; Drouin, Mathieu; Ampleman, Guy; Thiboutot, Sonia

    2014-03-01

    Nitroglycerin (NG) is often present in soils and sometimes in pore water at antitank firing positions due to incomplete combustion of propellants. Various degradation processes can contribute to the natural attenuation of NG in soils and pore water, thus reducing the risks of groundwater contamination. However, until now these processes have been sparsely documented. This study aimed at evaluating the ability of microorganisms from a legacy firing position to degrade dissolved NG, as well as NG trapped within propellant particles. Results from the shake-flask experiments showed that the isolated culture is capable of degrading dissolved NG but not the nitrocellulose matrix of propellant particles, so that the deeply embedded NG molecules cannot be degraded. Furthermore, the results from column experiments showed that in a nutrient-poor sand, degradation of dissolved NG may not be sufficiently rapid to prevent groundwater contamination. Therefore, the results from this study indicate that, under favorable soil conditions, biodegradation can be an important natural attenuation process for NG dissolving out of fresh propellant residues. In contrast, biodegradation does not contribute to the long-term attenuation of NG within old, weathered propellant residues. Although NG in these old residues no longer poses a threat to groundwater quality, if soil clean-up of a legacy site is required, active remediation approaches should be sought.

  7. Biomechanical Challenges to Polymeric Biodegradable Stents.

    Science.gov (United States)

    Soares, Joao S; Moore, James E

    2016-02-01

    Biodegradable implants have demonstrated clinical success in simple applications (e.g., absorbable sutures) and have shown great potential in many other areas of interventional medicine, such as localized drug delivery, engineered tissue scaffolding, and structural implants. For endovascular stenting and musculoskeletal applications, they can serve as temporary mechanical support that provides a smooth stress-transfer from the degradable implant to the healing tissue. However, for more complex device geometries, in vivo environments, and evolving load-bearing functions, such as required for vascular stents, there are considerable challenges associated with the use of biodegradable materials. A biodegradable stent must restore blood flow and provide support for a predictable appropriate period to facilitate artery healing, and subsequently, fail safely and be absorbed in a controllable manner. Biodegradable polymers are typically weaker than metals currently employed to construct stents, so it is difficult to ensure sufficient strength to keep the artery open and alleviate symptoms acutely while keeping other design parameters within clinically acceptable ranges. These design challenges are serious, given the general lack of understanding of biodegradable polymer behavior and evolution in intimal operating conditions. The modus operandi is mainly empirical and relies heavily on trial-and-error methodologies burdened by difficult, resource-expensive, and time-consuming experiments. We are striving for theoretical advancements systematizing the empirical knowledge into rational frameworks that could be cast into in silico tools for simulation and product development optimization. These challenges are evident when one considers that there are no biodegradable stents on the US market despite more than 30 years of development efforts (and currently only a couple with CE mark). This review summarizes previous efforts at implementing biodegradable stents, discusses the

  8. Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect.

    Science.gov (United States)

    Coquel, Anne-Sophie; Jacob, Jean-Pascal; Primet, Mael; Demarez, Alice; Dimiccoli, Mariella; Julou, Thomas; Moisan, Lionel; Lindner, Ariel B; Berry, Hugues

    2013-04-01

    Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli) where protein aggregates accumulate at the old pole region of the aging bacterium. Because of the potential of E. coli as a model organism, elucidating aging and protein aggregation in this bacterium may pave the way to significant advances in our global understanding of aging. A first obstacle along this path is to decipher the mechanisms by which protein aggregates are targeted to specific intercellular locations. Here, using an integrated approach based on individual-based modeling, time-lapse fluorescence microscopy and automated image analysis, we show that the movement of aging-related protein aggregates in E. coli is purely diffusive (Brownian). Using single-particle tracking of protein aggregates in live E. coli cells, we estimated the average size and diffusion constant of the aggregates. Our results provide evidence that the aggregates passively diffuse within the cell, with diffusion constants that depend on their size in agreement with the Stokes-Einstein law. However, the aggregate displacements along the cell long axis are confined to a region that roughly corresponds to the nucleoid-free space in the cell pole, thus confirming the importance of increased macromolecular crowding in the nucleoids. We thus used 3D individual-based modeling to show that these three ingredients (diffusion, aggregation and diffusion hindrance in the nucleoids) are sufficient and necessary to reproduce the available experimental data on aggregate localization in the cells. Taken together, our results strongly support the hypothesis that the localization of aging-related protein aggregates in the poles of E. coli results from the coupling of passive diffusion-aggregation with spatially non-homogeneous macromolecular crowding. They further support the importance of "soft" intracellular structuring (based on macromolecular

  9. D3, the new diffractometer for the macromolecular crystallography beamlines of the Swiss Light Source

    Energy Technology Data Exchange (ETDEWEB)

    Fuchs, Martin R., E-mail: mfuchs@bnl.gov [Paul Scherrer Institute, 5232 Villigen PSI (Switzerland); Brookhaven National Laboratory, Mail Stop 745, Upton, NY 11973 (United States); Pradervand, Claude; Thominet, Vincent; Schneider, Roman; Panepucci, Ezequiel; Grunder, Marcel; Gabadinho, Jose; Dworkowski, Florian S. N.; Tomizaki, Takashi; Schneider, Jörg; Mayer, Aline; Curtin, Adrian; Olieric, Vincent; Frommherz, Uli; Kotrle, Goran; Welte, Jörg; Wang, Xinyu; Maag, Stephan [Paul Scherrer Institute, 5232 Villigen PSI (Switzerland); Schulze-Briese, Clemens [DECTRIS Ltd, Neuenhoferstrasse 107, 5400 Baden (Switzerland); Wang, Meitian [Paul Scherrer Institute, 5232 Villigen PSI (Switzerland)

    2014-02-04

    A new diffractometer for microcrystallography has been developed for the three macromolecular crystallography beamlines of the Swiss Light Source. A new diffractometer for microcrystallography has been developed for the three macromolecular crystallography beamlines of the Swiss Light Source. Building upon and critically extending previous developments realised for the high-resolution endstations of the two undulator beamlines X06SA and X10SA, as well as the super-bend dipole beamline X06DA, the new diffractometer was designed to the following core design goals. (i) Redesign of the goniometer to a sub-micrometer peak-to-peak cylinder of confusion for the horizontal single axis. Crystal sizes down to at least 5 µm and advanced sample-rastering and scanning modes are supported. In addition, it can accommodate the new multi-axis goniometer PRIGo (Parallel Robotics Inspired Goniometer). (ii) A rapid-change beam-shaping element system with aperture sizes down to a minimum of 10 µm for microcrystallography measurements. (iii) Integration of the on-axis microspectrophotometer MS3 for microscopic sample imaging with 1 µm image resolution. Its multi-mode optical spectroscopy module is always online and supports in situ UV/Vis absorption, fluorescence and Raman spectroscopy. (iv) High stability of the sample environment by a mineral cast support construction and by close containment of the cryo-stream. Further features are the support for in situ crystallization plate screening and a minimal achievable detector distance of 120 mm for the Pilatus 6M, 2M and the macromolecular crystallography group’s planned future area detector Eiger 16M.

  10. Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect.

    Directory of Open Access Journals (Sweden)

    Anne-Sophie Coquel

    2013-04-01

    Full Text Available Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli where protein aggregates accumulate at the old pole region of the aging bacterium. Because of the potential of E. coli as a model organism, elucidating aging and protein aggregation in this bacterium may pave the way to significant advances in our global understanding of aging. A first obstacle along this path is to decipher the mechanisms by which protein aggregates are targeted to specific intercellular locations. Here, using an integrated approach based on individual-based modeling, time-lapse fluorescence microscopy and automated image analysis, we show that the movement of aging-related protein aggregates in E. coli is purely diffusive (Brownian. Using single-particle tracking of protein aggregates in live E. coli cells, we estimated the average size and diffusion constant of the aggregates. Our results provide evidence that the aggregates passively diffuse within the cell, with diffusion constants that depend on their size in agreement with the Stokes-Einstein law. However, the aggregate displacements along the cell long axis are confined to a region that roughly corresponds to the nucleoid-free space in the cell pole, thus confirming the importance of increased macromolecular crowding in the nucleoids. We thus used 3D individual-based modeling to show that these three ingredients (diffusion, aggregation and diffusion hindrance in the nucleoids are sufficient and necessary to reproduce the available experimental data on aggregate localization in the cells. Taken together, our results strongly support the hypothesis that the localization of aging-related protein aggregates in the poles of E. coli results from the coupling of passive diffusion-aggregation with spatially non-homogeneous macromolecular crowding. They further support the importance of "soft" intracellular structuring (based on

  11. Optimized beamline design for macromolecular crystallography at the Cornell High Energy Synchrotron Source (CHESS) (abstract)

    Science.gov (United States)

    Schildkamp, Wilfried; Bilderback, Donald; Moffat, Keith

    1989-07-01

    The A1 station on the CHESS wiggler beamline has been the workhorse for most macromolecular crystallographic experiments. This station is equipped with a fixed energy focusing germanium (111) monochromator and a focusing total reflection mirror. Our macromolecular crystallographers made full use of the high flux of more than 1012 photons/s/mm2 and the stable beam conditions, both in position and energy resolution. As a result, the A1 station was heavily oversubscribed. CHESS is presently expanding its capabilities and a new diffraction station for macromolecular crystallography is under construction. This beamline will be powered by a 24-pole hybrid permanent magnet wiggler with a critical energy of 25 keV. A focusing monochromator, which handles a specific heat load of 10 W/mm2, will have a range of tunability which covers all relevant absorption edges from 7 to 15 keV using a Ge(111) crystal. The energy resolution and the focusing properties remain constant within a factor of 2 over the entire tunability range. We expect a brilliance of about 1013 photons/s/mm2/mrad2/0.1% bandpass. The diffraction station will be equipped with an oscillation camera which can be used with x-ray film of 5×5 or 8×10 in. size or alternatively with Kodak storage phosphors. A wide variety of clamp-on accessories, like crystal coolers, fast shutters, helium pathways, polarimeter, etc. are available. The station will contain a beampipe system, which can also be used for small angle scattering experiments with sample-to-detector distances of up to 3000 mm. The entire diffraction station, its control area, a biological preparation area, and a darkroom are to be embedded in a biological safety containment of the level BL3. This will allow diffraction studies of virulent strains of viruses and other biohazards, which could not previously be studied at synchrotron radiation sources before without causing major disruption to the normal laboratory procedure.

  12. Enhanced delivery of the RAPTA-C macromolecular chemotherapeutic by conjugation to degradable polymeric micelles.

    Science.gov (United States)

    Blunden, Bianca M; Lu, Hongxu; Stenzel, Martina H

    2013-12-09

    Macromolecular ruthenium complexes are a promising avenue to better and more selective chemotherapeutics. We have previously shown that RAPTA-C [RuCl2(p-cymene)(PTA)], with the water-soluble 1,3,5-phosphaadamantane (PTA) ligand, could be attached to a polymer moiety via nucleophilic substitution of an available iodide with an amide in the PTA ligand. To increase the cell uptake of this macromolecule, we designed an amphiphilic block copolymer capable of self-assembling into polymeric micelles. The block copolymer was prepared by ring-opening polymerization of d,l-lactide (3,6-dimethyl-1,4-dioxane-2,5-dione) using a RAFT agent with an additional hydroxyl functionality, followed by the RAFT copolymerization of 2-hydroxyethyl acrylate (HEA) and 2-chloroethyl methacrylate (CEMA). The Finkelstein reaction and reaction with PTA led to polymers that can readily react with the dimer of RuCl2(p-cymene) to create a macromolecular RAPTA-C drug. RAPTA-C conjugation, micellization, and subsequent cytotoxicity and cell uptake of these polymeric moieties was tested on ovarian cancer A2780, A2780cis, and Ovcar-3 cell lines. Confocal microscopy images confirmed cell uptake of the micelles into the lysosome of the cells, indicative of an endocytic pathway. On average, a 10-fold increase in toxicity was found for the macromolecular drugs when compared to the RAPTA-C molecule. Furthermore, the cell uptake of ruthenium was analyzed and a significant increase was found for the micelles compared to RAPTA-C. Notably, micelles prepared from the polymer containing fewer HEA units had the highest cytotoxicity, the best cell uptake of ruthenium and were highly effective in suppressing the colony-forming ability of cells.

  13. A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.

    Directory of Open Access Journals (Sweden)

    Shane Ó Conchúir

    Full Text Available The development and validation of computational macromolecular modeling and design methods depend on suitable benchmark datasets and informative metrics for comparing protocols. In addition, if a method is intended to be adopted broadly in diverse biological applications, there needs to be information on appropriate parameters for each protocol, as well as metrics describing the expected accuracy compared to experimental data. In certain disciplines, there exist established benchmarks and public resources where experts in a particular methodology are encouraged to supply their most efficient implementation of each particular benchmark. We aim to provide such a resource for protocols in macromolecular modeling and design. We present a freely accessible web resource (https://kortemmelab.ucsf.edu/benchmarks to guide the development of protocols for protein modeling and design. The site provides benchmark datasets and metrics to compare the performance of a variety of modeling protocols using different computational sampling methods and energy functions, providing a "best practice" set of parameters for each method. Each benchmark has an associated downloadable benchmark capture archive containing the input files, analysis scripts, and tutorials for running the benchmark. The captures may be run with any suitable modeling method; we supply command lines for running the benchmarks using the Rosetta software suite. We have compiled initial benchmarks for the resource spanning three key areas: prediction of energetic effects of mutations, protein design, and protein structure prediction, each with associated state-of-the-art modeling protocols. With the help of the wider macromolecular modeling community, we hope to expand the variety of benchmarks included on the website and continue to evaluate new iterations of current methods as they become available.

  14. A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.

    Science.gov (United States)

    Ó Conchúir, Shane; Barlow, Kyle A; Pache, Roland A; Ollikainen, Noah; Kundert, Kale; O'Meara, Matthew J; Smith, Colin A; Kortemme, Tanja

    2015-01-01

    The development and validation of computational macromolecular modeling and design methods depend on suitable benchmark datasets and informative metrics for comparing protocols. In addition, if a method is intended to be adopted broadly in diverse biological applications, there needs to be information on appropriate parameters for each protocol, as well as metrics describing the expected accuracy compared to experimental data. In certain disciplines, there exist established benchmarks and public resources where experts in a particular methodology are encouraged to supply their most efficient implementation of each particular benchmark. We aim to provide such a resource for protocols in macromolecular modeling and design. We present a freely accessible web resource (https://kortemmelab.ucsf.edu/benchmarks) to guide the development of protocols for protein modeling and design. The site provides benchmark datasets and metrics to compare the performance of a variety of modeling protocols using different computational sampling methods and energy functions, providing a "best practice" set of parameters for each method. Each benchmark has an associated downloadable benchmark capture archive containing the input files, analysis scripts, and tutorials for running the benchmark. The captures may be run with any suitable modeling method; we supply command lines for running the benchmarks using the Rosetta software suite. We have compiled initial benchmarks for the resource spanning three key areas: prediction of energetic effects of mutations, protein design, and protein structure prediction, each with associated state-of-the-art modeling protocols. With the help of the wider macromolecular modeling community, we hope to expand the variety of benchmarks included on the website and continue to evaluate new iterations of current methods as they become available.

  15. Generalized phase contrast:

    DEFF Research Database (Denmark)

    Glückstad, Jesper; Palima, Darwin

    Generalized Phase Contrast elevates the phase contrast technique not only to improve phase imaging but also to cross over and interface with diverse and seemingly disparate fields of contemporary optics and photonics. This book presents a comprehensive introduction to the Generalized Phase Contrast...... (GPC) method including an overview of the range of current and potential applications of GPC in wavefront sensing and phase imaging, structured laser illumination and image projection, optical trapping and manipulation, and optical encryption and decryption. The GPC method goes further than...... efficiency. Optimization can address practical issues, such as finding an optimal spatial filter for the chosen application, and can even enable a Reverse Phase Contrast mode where intensity patterns are converted into a phase modulation....

  16. A vibrating membrane bioreactor (VMBR): Macromolecular transmission-influence of extracellular polymeric substances

    DEFF Research Database (Denmark)

    Beier, Søren; Jonsson, Gunnar Eigil

    2009-01-01

    The vibrating membrane bioreactor (VMBR) system facilitates the possibility of conducting a separation of macromolecules (BSA) from larger biological components (yeast cells) with a relatively high and stable macromolecular transmission at sub-critical flux. This is not possible to achieve...... for a static non-vibrating membrane module. A BSA transmission of 74% has been measured in the separation of 4g/L BSA from 8 g/L dry weight yeast cells in suspension at sub-critical flux (20L/(m(2) h)). However, this transmission is lower than the 85% BSA transmission measured for at pure 4g/L BSA solution...

  17. Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique

    Science.gov (United States)

    Peters, J. H.; Klein, R.; Delle Site, L.

    2016-08-01

    We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle the change of representation of large molecules. The robustness of the approach is shown by calculating several relevant structural properties and comparing them with the results of full atomistic simulations. The extended scheme represents a robust prototype for the simulation of macromolecular systems of interest in several fields, from material science to biophysics.

  18. The "macromolecular tourist": universal temperature dependence of thermal diffusion in aqueous colloidal suspensions.

    Science.gov (United States)

    Iacopini, S; Rusconi, R; Piazza, R

    2006-01-01

    By performing measurements on a large class of macromolecular and colloidal systems, we show that thermophoresis (particle drift induced by thermal gradients) in aqueous solvents displays a distinctive universal dependence on temperature. For systems of particles interacting via temperature-independent forces, this behavior is strictly related to the solvent thermal expansivity, while an additional, T-independent term is needed to account for the behavior of "thermophilic" (migrating to the warmth) particles. The former relation between thermophoresis and thermal expansion may be exploited to envisage other fruitful studies of colloidal diffusion in inhomogeneous fluids.

  19. INFLUENCE OF THE SOLVENT SWELLING ON MACROMOLECULAR CHOLESTERIC LIQUID CRYSTALLINE STRUCTURE

    Institute of Scientific and Technical Information of China (English)

    Jia Zeng; Yong Huang

    1999-01-01

    Ethyl-cyanoethyl cellulose [(E-CE)C]/cross-linked polyacrylic acid [PAA] molecular composites with cholesteric order were prepared. It was found that the macromolecular cholesteric structure was changed with the swelling of PAA in the composites. The selective reflection of the cholesteric phase shifted to the longer wavelength and the X-ray diffraction angle shifted to the high angle direction during swelling, which suggested that the cholesteric pitch and the number of the layers of ordered (E-CE)C chains in the cholesteric phase were increased.

  20. Chirality as a physical aspect of structure formation in biological macromolecular systems

    Science.gov (United States)

    Malyshko, E. V.; Tverdislov, V. A.

    2016-08-01

    A novel regularity of hierarchical structures is found in the formation of chiral biological macromolecular systems. The formation of structures with alternating chirality (helical structures) serves as an instrument of stratification. The ability of a carbon atom to form chiral compounds is an important factor that determined the carbon basis of living systems on the Earth as well as their development through a series of chiral bifurcations. In the course of biological evolution, the helical structures became basic elements of the molecular machines in the cell. The discreteness of structural levels allowed the mechanical degrees of freedom formation in the molecular machines in the cell.

  1. Biodegradable compounds: Rheological, mechanical and thermal properties

    Science.gov (United States)

    Nobile, Maria Rossella; Lucia, G.; Santella, M.; Malinconico, M.; Cerruti, P.; Pantani, R.

    2015-12-01

    Recently great attention from industry has been focused on biodegradable polyesters derived from renewable resources. In particular, PLA has attracted great interest due to its high strength and high modulus and a good biocompatibility, however its brittleness and low heat distortion temperature (HDT) restrict its wide application. On the other hand, Poly(butylene succinate) (PBS) is a biodegradable polymer with a low tensile modulus but characterized by a high flexibility, excellent impact strength, good thermal and chemical resistance. In this work the two aliphatic biodegradable polyesters PBS and PLA were selected with the aim to obtain a biodegradable material for the industry of plastic cups and plates. PBS was also blended with a thermoplastic starch. Talc was also added to the compounds because of its low cost and its effectiveness in increasing the modulus and the HDT of polymers. The compounds were obtained by melt compounding in a single screw extruder and the rheological, mechanical and thermal properties were investigated. The properties of the two compounds were compared and it was found that the values of the tensile modulus and elongation at break measured for the PBS/PLA/Talc compound make it interesting for the production of disposable plates and cups. In terms of thermal resistance the compounds have HDTs high enough to contain hot food or beverages. The PLA/PBS/Talc compound can be, then, considered as biodegradable substitute for polystyrene for the production of disposable plates and cups for hot food and beverages.

  2. Development of mold for biodegradable materials

    Energy Technology Data Exchange (ETDEWEB)

    Japitana, F.H.; Jabrica, A.M. [Metals Industry Research and Develeopment Center, Manila (Philippines). Dept. of Science and Technology; Komatsu, M. [Komatsu Consulting Engineer Office, Iwaki City, Fukushima (Japan); Takeuchi, Y. [Osaka Univ., Osaka (Japan). Dept. of Mechanical Engineering

    2008-07-01

    The improper disposal of non-biodegradable plastics adversely affect global environmental factors, principles of sustainability, industrial ecology and ecoefficiency. Therefore, a new generation of bio-based polymeric products has been developed. These polylactides (PLA), cellulose esters, starch plastics and polyhydroxyalkanoates (PHAs) are made from renewable natural resources and are biodegradable. They meet environmental conditions and can compete with their petrochemical counterparts. Among them, PLA is particularly attractive as a sustainable alternative to synthetic polymers and a potential candidate for the fabrication of biocomposites. Certain blends have proved successful in medical implants, sutures and drug delivery systems because of their capacity to dissolve away with time. However, widespread use of PLA is limited because of cost. Biodegradable plastic products are currently 6 to 10 times more expensive than traditional plastics. Environmentalists argue that the cheaper price of traditional plastics does not reflect their true cost when their impact is considered. This paper presented a solution to reduce the production cost of biodegradable plastics. In particular, it described a newly developed plastic injection mold for biodegradable materials which can produce a scrapless product. The system reduces processing time because it is not necessary to remove any gating or runners after the injection process. Takeout robots ensure that the quality of the product is maintained. 12 figs.

  3. Bio-Degradable Plastics Impact On Environment

    Directory of Open Access Journals (Sweden)

    T.SUBRAMANI

    2014-06-01

    Full Text Available The potential of biodegradable polymers and more particularly that of polymers obtained from renewable resources such as the polysaccharides (e.g., starch have long been recognized. However, these biodegradable polymers have been largely used in some applications (e.g., food industry and have not found extensive applications in the packaging industries to replace conventional plastic materials, although they could be an interesting way to overcome the limitation of the petrochemical resources in the future. The fossil fuel and gas could be partially replaced by greener agricultural sources, which should participate in the reduction of CO2 emissions. Bio-based and biodegradable plastics can form the basis for environmentally preferable, sustainable alternative to current materials based exclusively on petroleum feed stocks. These bio-based materials offer value in the sustainability/life-cycle equation by being a part of the biological carbon cycle, especially as it relates to carbon-based polymeric materials such as plastics, water soluble polymers and other carbon based products like lubricants, biodiesel, and detergents. Identification and quantification of bio based content uses radioactive C-14 signature. Biopolymers are generally capable of being utilized by living matter (biodegraded, and so can be disposed in safe and ecologically sound ways through disposal processes (waste management like composting, soil application, and biological wastewater treatment. Single use, short-life, disposable products can be engineered to be bio-based and biodegradable.

  4. The effects of biodegradation on the compositions of aromatic hydrocarbons and maturity indicators in biodegraded oils from Liaohe Basin

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    By the aid of GC-MS technique,a series of sequentially biodegraded oils from Liaohe Basin have been analyzed. The results show that the concentrations and relative compositions of various aromatic compounds in the biodegraded crude oils will change with increasing biodegradation degree. The concentrations of alkyl naphthalenes,alkyl phenanthrenes,alkyl dibenzothiophene are decreased,and the concentration of triaromatic steroids will increase with increasing biodegradation degree in biodegraded oils. Those phenomena indicate that various aromatic compounds are more easily biodegraded by bacteria like other kinds of hydrocarbons such as alkanes,but different series of aromatic compounds have a varied ability to resistant to biodegradation. The ratios of dibenzothiophene to phenenthrene(DBTH/P) and methyl dibenzothiophene to methyl phenanthrene(MDBTH/MP) are related to the features of depositional environment for source rocks such as redox and ancient salinity. However,in biodegraded oils,the two ratios increase quickly with the increase of the biodegradation degree,indicating that they have lost their geochemical significance. In this case,they could not be used to evaluate the features of depositional environment. Methyl phenanthrene index,methyl phenanthrene ratio and methyl dibenzoyhiophene ratio are useful aromatic maturity indicators for the crude oils and the source rocks without vitrinite. But for biodegraded oils,those aromatic maturity indicators will be affected by biodegradation and decrease with the increase of the biodegradation degree. Therefore,those aromatic molecular maturity indicators could not be used for biodegraded oils.

  5. Biodegradability of degradable plastic waste.

    Science.gov (United States)

    Agamuthu, P; Faizura, Putri Nadzrul

    2005-04-01

    Plastic waste constitutes the third largest waste volume in Malaysian municipal solid waste (MSW), next to putrescible waste and paper. The plastic component in MSW from Kuala Lumpur averages 24% (by weight), whereas the national mean is about 15%. The 144 waste dumps in the country receive about 95% of the MSW, including plastic waste. The useful life of the landfills is fast diminishing as the plastic waste stays un-degraded for more than 50 years. In this study the compostability of polyethylene and pro-oxidant additive-based environmentally degradable plastics (EDP) was investigated. Linear low-density polyethylene (LLDPE) samples exposed hydrolytically or oxidatively at 60 degrees C showed that the abiotic degradation path was oxidative rather than hydrolytic. There was a weight loss of 8% and the plastic has been oxidized as shown by the additional carbonyl group exhibited in the Fourier transform infra red (FTIR) Spectrum. Oxidation rate seemed to be influenced by the amount of pro-oxidant additive, the chemical structure and morphology of the plastic samples, and the surface area. Composting studies during a 45-day experiment showed that the percentage elongation (reduction) was 20% for McD samples [high-density polyethylene, (HDPE) with 3% additive] and LL samples (LLDPE with 7% additive) and 18% reduction for totally degradable plastic (TDP) samples (HDPE with 3% additive). Lastly, microbial experiments using Pseudomonas aeroginosa on carbon-free media with degradable plastic samples as the sole carbon source, showed confirmatory results. A positive bacterial growth and a weight loss of 2.2% for degraded polyethylene samples were evident to show that the degradable plastic is biodegradable.

  6. Introduction of environmentally degradable parameters to evaluate the biodegradability of biodegradable polymers.

    Directory of Open Access Journals (Sweden)

    Wenbin Guo

    Full Text Available Environmentally Degradable Parameter ((EdK is of importance in the describing of biodegradability of environmentally biodegradable polymers (BDPs. In this study, a concept (EdK was introduced. A test procedure of using the ISO 14852 method and detecting the evolved carbon dioxide as an analytical parameter was developed, and the calculated (EdK was used as an indicator for the ultimate biodegradability of materials. Starch and polyethylene used as reference materials were defined as the (EdK values of 100 and 0, respectively. Natural soil samples were inoculated into bioreactors, followed by determining the rates of biodegradation of the reference materials and 15 commercial BDPs over a 2-week test period. Finally, a formula was deduced to calculate the value of (EdK for each material. The (EdK values of the tested materials have a positive correlation to their biodegradation rates in the simulated soil environment, and they indicated the relative biodegradation rate of each material among all the tested materials. Therefore, the (EdK was shown to be a reliable indicator for quantitatively evaluating the potential biodegradability of BDPs in the natural environment.

  7. The catalytic microwave synthesis of biodegradable polyester polyols based on castor oil and l-lactide

    Science.gov (United States)

    Kojić, D.; Erceg, T.; Vukić, N.; Teofilović, V.; Ristić, I.; Budinski-Simendić, J.; Aleksić, V.

    2017-01-01

    Various strategies for achieving a functional poly(lactic acid) (PLA) have been developed such as ring-opening copolymerization with a functional monomer, the use of functional initiator and various post polymerization modifications. It is possible to obtain the star shaped polymer using natural oil with at least three OH groups as an initiator. It was estimated that despite of low-molecular mass of star-shaped PLA, the hydrophobic castor oil central core influenced the slow degradation rate in the case of injectable biomedical application. The star-shaped polymers with low-molecular-mass have a lower melt viscosity correlated with linear counterparts. In soft tissue reparation the polymer viscosity increases with fluid body contact and the solid implant can be formed. To ensure liquid state at injection temperature the low molar mass polymer is favorable. There is a particular size for each macromolecular chains at which chain entanglement occurs. In this work the influence of the l-lactide (LA) and the castor oil (CO) contents on the size of biodegradable branched polyester polyols was studied. The average molecular masses of synthesized polymers were estimated by GPC procedure. In sample formulations the [LA]/[CO] ratios were from to 113 to 533. Mn values for obtained polymers were from 5000 to 20000 Da. The molecular mass distribution for the resulting polymers was between 1.09 and 1.37.

  8. Biodegradable nanoparticles for gene therapy technology

    Energy Technology Data Exchange (ETDEWEB)

    Hosseinkhani, Hossein, E-mail: hosseinkhani@mail.ntust.edu.tw; He, Wen-Jie [National Taiwan University of Science and Technology (Taiwan Tech), Graduate Institute of Biomedical Engineering (China); Chiang, Chiao-Hsi [School of Pharmacy, National Defense Medical Center (China); Hong, Po-Da [National Taiwan University of Science and Technology (Taiwan Tech), Graduate Institute of Biomedical Engineering (China); Yu, Dah-Shyong [Nanomedicine Research Center, National Defense Medical Center (China); Domb, Abraham J. [The Hebrew University of Jerusalem, Institute of Drug Research, School of Pharmacy, Faculty of Medicine, Center for Nanoscience and Nanotechnology and The Alex Grass Center for Drug Design and Synthesis (Israel); Ou, Keng-Liang [College of Oral Medicine, Taipei Medical University, Research Center for Biomedical Devices and Prototyping Production (China)

    2013-07-15

    Rapid propagations in materials technology together with biology have initiated great hopes in the possibility of treating many diseases by gene therapy technology. Viral and non-viral gene carriers are currently applied for gene delivery. Non-viral technology is safe and effective for the delivery of genetic materials to cells and tissues. Non-viral systems are based on plasmid expression containing a gene encoding a therapeutic protein and synthetic biodegradable nanoparticles as a safe carrier of gene. Biodegradable nanoparticles have shown great interest in drug and gene delivery systems as they are easy to be synthesized and have no side effect in cells and tissues. This review provides a critical view of applications of biodegradable nanoparticles on gene therapy technology to enhance the localization of in vitro and in vivo and improve the function of administered genes.

  9. Biodegradable Materials for Bone Repairs: A Review

    Institute of Scientific and Technical Information of China (English)

    Lili Tan; Xiaoming Yu; Peng Wan; Ke Yang

    2013-01-01

    With attractive research and development of biomaterials,more and more opportunities have been brought to the treatments of human tissue repairs.The implant is usually no need to exist in the body accompanied with the recovery or regeneration of the tissue lesions,and the long-term effect of exotic substance to human body should be reduced as lower as possible.For this purpose,biodegradable materials,including polymers,magnesium alloys and ceramics,have attracted much attention for medical applications due to their biodegradable characters in body environment.This paper in turn introduces these three different types of widely studied biodegradable materials as well as their advantages as implants in applications for bone repairs.Relevant history and research progresses are summarized.

  10. Novel biodegradable nanocarriers for enhanced drug delivery.

    Science.gov (United States)

    Gagliardi, Mariacristina

    2016-12-01

    With the refinement of functional properties, the interest around biodegradable materials, in biorelated applications and, in particular, in their use as controlled drug-delivery systems, increased in the last decades. Biodegradable materials are an ideal platform to obtain nanoparticles for spatiotemporal controlled drug delivery for the in vivo administration, thanks to their biocompatibility, functionalizability, the control exerted on delivery rates and the complete degradation. Their application in systems for cancer treatment, brain and cardiovascular diseases is already a consolidated practice in research, while the bench-to-bedside translation is still late. This review aims at summarizing reported applications of biodegradable materials to obtain drug-delivery nanoparticles in the last few years, giving a complete overview of pros and cons related to degradable nanomedicaments.

  11. Biodegradable Hybrid Stomatocyte Nanomotors for Drug Delivery.

    Science.gov (United States)

    Tu, Yingfeng; Peng, Fei; André, Alain A M; Men, Yongjun; Srinivas, Mangala; Wilson, Daniela A

    2017-02-28

    We report the self-assembly of a biodegradable platinum nanoparticle-loaded stomatocyte nanomotor containing both PEG-b-PCL and PEG-b-PS as a potential candidate for anticancer drug delivery. Well-defined stomatocyte structures could be formed even after incorporation of 50% PEG-b-PCL polymer. Demixing of the two polymers was expected at high percentage of semicrystalline poly(ε-caprolactone) (PCL), resulting in PCL domain formation onto the membrane due to different properties of two polymers. The biodegradable motor system was further shown to move directionally with speeds up to 39 μm/s by converting chemical fuel, hydrogen peroxide, into mechanical motion as well as rapidly delivering the drug to the targeted cancer cell. Uptake by cancer cells and fast doxorubicin drug release was demonstrated during the degradation of the motor system. Such biodegradable nanomotors provide a convenient and efficient platform for the delivery and controlled release of therapeutic drugs.

  12. Biodegradation of resorcinol by Pseudomonas sp.

    Directory of Open Access Journals (Sweden)

    Nader Hajizadeh

    2016-11-01

    Full Text Available Objective: To investigate the ability of Pseudomonas sp. isolated from East Azarbaijan, Iran in bioremediation of resorcinol. Methods: Resorcinol biodegradation was evaluated using spectrophotometry and confirmed by gas chromatography-mass spectroscopy. Results: This isolate was able to remove up to 37.12% of resorcinol from contaminated water. Reusability experiments had confirmed the biodegradation process which produced seven intermediate compounds. These intermediates were characterized by gas chromatographymass spectroscopy technique. The products of resorcinol biodegradation were apparently 1, 4-cyclohexadiene, nonadecene, 2-heptadecanone, 1-isopropyl-2-methoxy-4-methylbenzene, hexadecanoic acid, 9-octadecenoic acid, phenol and 5-methyl-2-(1-methylethyl. Conclusions: The findings revealed that Pseudomonas sp. is able to degrade resorcinol. Because of being an indigenous organism, this isolate is more compatible with the climate of the northwest region of Iran and possibly will be used for degradation of other similar aromatic compounds.

  13. Biodegradation of resorcinol byPseudomonas sp.

    Institute of Scientific and Technical Information of China (English)

    Nader Hajizadeh; Najibeh Shirzad; Ali Farzi; Mojtaba Salouti; Azra Momeni

    2016-01-01

    ABSTRACT Objective:To investigate the ability ofPseudomonas sp. isolated from East Azarbaijan, Iran in bioremediation of resorcinol. Methods: Resorcinol biodegradation was evaluated using spectrophotometry and confirmed by gas chromatography-mass spectroscopy. Results:This isolate was able to remove up to 37.12% of resorcinol from contaminated water. Reusability experiments had confirmed the biodegradation process which produced seven intermediate compounds. These intermediates were characterized by gas chromatography-mass spectroscopy technique. The products of resorcinol biodegradation were apparently 1, 4-cyclohexadiene, nonadecene, 2-heptadecanone, 1-isopropyl-2-methoxy-4-methylbenzene, hexadecanoic acid, 9-octadecenoic acid, phenol and 5-methyl-2-(1-methylethyl). Conclusions: The findings revealed thatPseudomonas sp. is able to degrade resorcinol. Because of being an indigenous organism, this isolate is more compatible with the climate of the northwest region of Iran and possibly will be used for degradation of other similar aromatic compounds.

  14. Biodegradation of malachite green by Ochrobactrum sp.

    Science.gov (United States)

    Vijayalakshmidevi, S R; Muthukumar, Karuppan

    2014-02-01

    This study presents the biodegradation of malachite green (MG), a triphenylmethane dye, using a novel microorganism isolated from textile effluent contaminated environment. The organism responsible for degradation was identified as Ochrobactrum sp JN214485 by 16S rRNA analysis. The effect of operating parameters such as temperature, pH, immobilized bead loading, and initial dye concentration on % degradation was studied, and their optimal values were found to be 30 °C, 6, 20 g/L and 100 mg/L, respectively. The analysis showed that the extracellular enzymes were responsible for the degradation. The biodegradation of MG was confirmed by UV-visible spectroscopic and FTIR analysis. The phytotoxicity test concluded that the degradation products were less toxic compared to MG. The kinetics of biodegradation was studied and the activation energy was found to be 10.65 kcal/mol.

  15. Biodegradable Polymers and Stem Cells for Bioprinting.

    Science.gov (United States)

    Lei, Meijuan; Wang, Xiaohong

    2016-04-29

    It is imperative to develop organ manufacturing technologies based on the high organ failure mortality and serious donor shortage problems. As an emerging and promising technology, bioprinting has attracted more and more attention with its super precision, easy reproduction, fast manipulation and advantages in many hot research areas, such as tissue engineering, organ manufacturing, and drug screening. Basically, bioprinting technology consists of inkjet bioprinting, laser-based bioprinting and extrusion-based bioprinting techniques. Biodegradable polymers and stem cells are common printing inks. In the printed constructs, biodegradable polymers are usually used as support scaffolds, while stem cells can be engaged to differentiate into different cell/tissue types. The integration of biodegradable polymers and stem cells with the bioprinting techniques has provided huge opportunities for modern science and technologies, including tissue repair, organ transplantation and energy metabolism.

  16. Biodegradable Polymers and Stem Cells for Bioprinting

    Directory of Open Access Journals (Sweden)

    Meijuan Lei

    2016-04-01

    Full Text Available It is imperative to develop organ manufacturing technologies based on the high organ failure mortality and serious donor shortage problems. As an emerging and promising technology, bioprinting has attracted more and more attention with its super precision, easy reproduction, fast manipulation and advantages in many hot research areas, such as tissue engineering, organ manufacturing, and drug screening. Basically, bioprinting technology consists of inkjet bioprinting, laser-based bioprinting and extrusion-based bioprinting techniques. Biodegradable polymers and stem cells are common printing inks. In the printed constructs, biodegradable polymers are usually used as support scaffolds, while stem cells can be engaged to differentiate into different cell/tissue types. The integration of biodegradable polymers and stem cells with the bioprinting techniques has provided huge opportunities for modern science and technologies, including tissue repair, organ transplantation and energy metabolism.

  17. Macromolecular liquids

    Energy Technology Data Exchange (ETDEWEB)

    Safinya, C.R.; Safran, S.A. (Exxon Research and Engineering Co., Annandale, NJ (US)); Pincus, P.A. (Univ. of California at Santa Barbara, Santa Barbara, CA (US))

    1990-01-01

    Liquids include a broad range of material systems which are of high scientific and technological interest. Generally speaking, these are partially ordered or disordered phases where the individual molecular species have organized themselves on length scales which are larger than simple fluids, typically between 10 Angstroms and several microns. The specific systems reported on in this book include membranes, microemulsions, micelles, liquid crystals, colloidal suspensions, and polymers. They have a major impact on a broad spectrum of technological industries such as displays, plastics, soap and detergents, chemicals and petroleum, and pharmaceuticals.

  18. Histological evaluation of different biodegradable and non-biodegradable membranes implanted subcutaneously in rats

    DEFF Research Database (Denmark)

    Zhao, S; Pinholt, E M; Madsen, J E

    2000-01-01

    Different types of biodegradable membranes have become available for guided tissue regeneration. The purpose of this study was to evaluate histologically three different biodegradable membranes (Bio-Gide, Resolut and Vicryl) and one non-biodegradable membrane (expanded polytetrafluoroethylene/e-PTFE...... that e-PTFE was well tolerated and encapsulated by a fibrous connective tissue capsule. There was capsule formation around Resolut and Vicryl and around Bio-Gide in the early phase there was a wide inflammatory zone already. e-PTFE and Vicryl were stable materials while Resolut and Bio-Gide fragmented...

  19. Biodegradable polyesters based on succinic acid

    Directory of Open Access Journals (Sweden)

    Nikolić Marija S.

    2003-01-01

    Full Text Available Two series of aliphatic polyesters based on succinic acid were synthesized by copolymerization with adipic acid for the first series of saturated polyesters, and with fumaric acid for the second series. Polyesters were prepared starting from the corresponding dimethyl esters and 1,4-butanediol by melt transesterification in the presence of a highly effective catalyst tetra-n-butyl-titanate, Ti(0Bu4. The molecular structure and composition of the copolyesters was determined by 1H NMR spectroscopy. The effect of copolymer composition on the physical and thermal properties of these random polyesters were investigated using differential scanning calorimetry. The degree of crystallinity was determined by DSC and wide angle X-ray. The degrees of crystallinity of the saturated and unsaturated copolyesters were generally reduced with respect to poly(butylene succinate, PBS. The melting temperatures of the saturated polyesters were lower, while the melting temperatures of the unsaturated copolyesters were higher than the melting temperature of PBS. The biodegradability of the polyesters was investigated by enzymatic degradation tests. The enzymatic degradation tests were performed in a buffer solution with Candida cylindracea lipase and for the unsaturated polyesters with Rhizopus arrhizus lipase. The extent of biodegradation was quantified as the weight loss of polyester films. Also the surface of the polyester films after degradation was observed using optical microscopy. It could be concluded that the biodegradability depended strongly on the degree of crystallinity, but also on the flexibility of the chain backbone. The highest biodegradation was observed for copolyesters containing 50 mol.% of adipic acid units, and in the series of unsaturated polyesters for copolyesters containing 5 and 10 mol.% of fumarate units. Although the degree of crystallinity of the unsaturated polyesters decreased slightly with increasing unsaturation, the biodegradation

  20. A NEW UNSTEADY THREE DIMENSIONAL MODEL FOR MACROMOLECULAR TRANSPORT AND WATER FILTRATION ACROSS THE ARTERIAL WALL

    Institute of Scientific and Technical Information of China (English)

    黄浩; 温功碧

    2001-01-01

    A new unsteady three-dimensional convective-diffusive mathematical model for the transportation of macromolecules and water across the arterial wall was proposed . After the formation of leaky junctions due to the mitosis of endothelial cell of the arterial wall, the macromolecular transport happens surrounding the leaky cells. The arterial wall was divided into four layers: the endothelial layer, the subendothelial intima, the internal elastic lamina and the media for the convenience of research. The time-dependent concentration growth,the effect of the shape of endothelial cell and the effect of physiological parameters were analyzed. The analytical solution of velocity field and pressure field of water flow across the arterial wall were obtained; and concentration distribution of three macromolecules ; LDL,HRP and Albumin, were calculated with numerical simulation method. The new theory predicts, the maximum and distribution areas of time dependent concentration with round shape endothelial cell are both larger than that with ellipse-shape endothelial cell. The model also predicts the concentration growth is much alike that of a two-dimensional model and it shows that the concentration reaches its peak at the leaky junction where atherosclerotic formation frequently occurs and falls down rapidly in a limited area beginning from its earlier time growth to the state when macromolecular transfer approaches steadily. These predictions of the new model are in agreement with the experimental observation for the growth and concentration distribution of LDL and Albumin.

  1. X-ray Diffraction of Cotton Treated with Neutralized Vegetable Oil-based Macromolecular Crosslinkers

    Directory of Open Access Journals (Sweden)

    James W. Rawlins, Ph.D.

    2010-03-01

    Full Text Available Maleinized soybean oil (MSO has been investigated as a flexible, macromolecular crosslinker for cotton fabrics. The ability of MSO to penetrate crystalline cellulose and crosslink aligned cellulose chains upon cure has been in question. This study compares the penetration capability of MSO to dimethyloldihydroxyethyleneurea (DMDHEU, which is the commercial standard for durable press finishing and is an efficient cellulose crosslinker. X-ray diffraction was employed to characterize changes in the crystalline morphology upon heating un-mercerized cotton fabrics treated with aqueous DMDHEU and soybean oil derivatives. Displacement of characteristic interplanar spacings and the genesis/elimination of diffraction intensities from quintessential planes were evidence of structural modification. The penetration of ammonia neutralized MSO (acid value 230.00 mg KOH/g into the microstructure of cotton cellulose is similar to that of DMDHEU in terms of expanding the interplanar spacings of characteristic planes. Moreover, polymorphism of cotton and mercerized cotton occurred upon treatment with aqueous solutions of MSO. These findings suggest that macromolecular reagents can diffuse into cellulose fibrils if they are sufficiently hydrated or enshrouded by more favored penetrants.

  2. Influence of macromolecular architecture on necking in polymer extrusion film casting process

    Energy Technology Data Exchange (ETDEWEB)

    Pol, Harshawardhan; Banik, Sourya; Azad, Lal Busher; Doshi, Pankaj; Lele, Ashish [CSIR-National Chemical Laboratory, Pune, Maharashtra (India); Thete, Sumeet [Purdue University, West Lafayette, Indiana (United States)

    2015-05-22

    Extrusion film casting (EFC) is an important polymer processing technique that is used to produce several thousand tons of polymer films/coatings on an industrial scale. In this research, we are interested in understanding quantitatively how macromolecular chain architecture (for example long chain branching (LCB) or molecular weight distribution (MWD or PDI)) influences the necking and thickness distribution of extrusion cast films. We have used different polymer resins of linear and branched molecular architecture to produce extrusion cast films under controlled experimental conditions. The necking profiles of the films were imaged and the velocity profiles during EFC were monitored using particle tracking velocimetry (PTV) technique. Additionally, the temperature profiles were captured using an IR thermography and thickness profiles were calculated. The experimental results are compared with predictions of one-dimensional flow model of Silagy et al{sup 1} wherein the polymer resin rheology is modeled using molecular constitutive equations such as the Rolie-Poly (RP) and extended Pom Pom (XPP). We demonstrate that the 1-D flow model containing the molecular constitutive equations provides new insights into the role of macromolecular chain architecture on film necking.{sup 1}D. Silagy, Y. Demay, and J-F. Agassant, Polym. Eng. Sci., 36, 2614 (1996)

  3. A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits.

    Science.gov (United States)

    Jaskolski, Mariusz; Dauter, Zbigniew; Wlodawer, Alexander

    2014-09-01

    As a contribution to the celebration of the year 2014, declared by the United Nations to be 'The International Year of Crystallography', the FEBS Journal is dedicating this issue to papers showcasing the intimate union between macromolecular crystallography and structural biology, both in historical perspective and in current research. Instead of a formal editorial piece, by way of introduction, this review discusses the most important, often iconic, achievements of crystallographers that led to major advances in our understanding of the structure and function of biological macromolecules. We identified at least 42 scientists who received Nobel Prizes in Physics, Chemistry or Medicine for their contributions that included the use of X-rays or neutrons and crystallography, including 24 who made seminal discoveries in macromolecular sciences. Our spotlight is mostly, but not only, on the recipients of this most prestigious scientific honor, presented in approximately chronological order. As a summary of the review, we attempt to construct a genealogy tree of the principal lineages of protein crystallography, leading from the founding members to the present generation.

  4. MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments.

    Science.gov (United States)

    Gabadinho, José; Beteva, Antonia; Guijarro, Matias; Rey-Bakaikoa, Vicente; Spruce, Darren; Bowler, Matthew W; Brockhauser, Sandor; Flot, David; Gordon, Elspeth J; Hall, David R; Lavault, Bernard; McCarthy, Andrew A; McCarthy, Joanne; Mitchell, Edward; Monaco, Stéphanie; Mueller-Dieckmann, Christoph; Nurizzo, Didier; Ravelli, Raimond B G; Thibault, Xavier; Walsh, Martin A; Leonard, Gordon A; McSweeney, Sean M

    2010-09-01

    The design and features of a beamline control software system for macromolecular crystallography (MX) experiments developed at the European Synchrotron Radiation Facility (ESRF) are described. This system, MxCuBE, allows users to easily and simply interact with beamline hardware components and provides automated routines for common tasks in the operation of a synchrotron beamline dedicated to experiments in MX. Additional functionality is provided through intuitive interfaces that enable the assessment of the diffraction characteristics of samples, experiment planning, automatic data collection and the on-line collection and analysis of X-ray emission spectra. The software can be run in a tandem client-server mode that allows for remote control and relevant experimental parameters and results are automatically logged in a relational database, ISPyB. MxCuBE is modular, flexible and extensible and is currently deployed on eight macromolecular crystallography beamlines at the ESRF. Additionally, the software is installed at MAX-lab beamline I911-3 and at BESSY beamline BL14.1.

  5. Fast Method for Computing Chemical Potentials and Liquid-Liquid Phase Equilibria of Macromolecular Solutions.

    Science.gov (United States)

    Qin, Sanbo; Zhou, Huan-Xiang

    2016-08-25

    Chemical potential is a fundamental property for determining thermodynamic equilibria involving exchange of molecules, such as between two phases of molecular systems. Previously, we developed the fast Fourier transform (FFT)-based method for Modeling Atomistic Protein-crowder interactions (FMAP) to calculate excess chemical potentials according to the Widom insertion. Intermolecular interaction energies were expressed as correlation functions and evaluated via FFT. Here, we extend this method to calculate liquid-liquid phase equilibria of macromolecular solutions. Chemical potentials are calculated by FMAP over a wide range of molecular densities, and the condition for coexistence of low- and high-density phases is determined by the Maxwell equal-area rule. When benchmarked on Lennard-Jones fluids, our method produces an accurate phase diagram at 18% of the computational cost of the current best method. Importantly, the gain in computational speed increases dramatically as the molecules become more complex, leading to many orders of magnitude in speed up for atomistically represented proteins. We demonstrate the power of FMAP by reporting the first results for the liquid-liquid coexistence curve of γII-crystallin represented at the all-atom level. Our method may thus open the door to accurate determination of phase equilibria for macromolecular mixtures such as protein-protein mixtures and protein-RNA mixtures, that are known to undergo liquid-liquid phase separation, both in vitro and in vivo.

  6. Assessing physio-macromolecular effects of lactic acid on Zygosaccharomyces bailii cells during microaerobic fermentation.

    Science.gov (United States)

    Kuanyshev, Nurzhan; Ami, Diletta; Signori, Lorenzo; Porro, Danilo; Morrissey, John P; Branduardi, Paola

    2016-08-01

    The ability of Zygosaccharomyces bailii to grow at low pH and in the presence of considerable amounts of weak organic acids, at lethal condition for Saccharomyces cerevisiae, increased the interest in the biotechnological potential of the yeast. To understand the mechanism of tolerance and growth effect of weak acids on Z. bailii, we evaluated the physiological and macromolecular changes of the yeast exposed to sub lethal concentrations of lactic acid. Lactic acid represents one of the important commodity chemical which can be produced by microbial fermentation. We assessed physiological effect of lactic acid by bioreactor fermentation using synthetic media at low pH in the presence of lactic acid. Samples collected from bioreactors were stained with propidium iodide (PI) which revealed that, despite lactic acid negatively influence the growth rate, the number of PI positive cells is similar to that of the control. Moreover, we have performed Fourier Transform Infra-Red (FTIR) microspectroscopy analysis on intact cells of the same samples. This technique has been never applied before to study Z. bailii under this condition. The analyses revealed lactic acid induced macromolecular changes in the overall cellular protein secondary structures, and alterations of cell wall and membrane physico-chemical properties.

  7. Force interacts with macromolecular structure in activation of TGF-β.

    Science.gov (United States)

    Dong, Xianchi; Zhao, Bo; Iacob, Roxana E; Zhu, Jianghai; Koksal, Adem C; Lu, Chafen; Engen, John R; Springer, Timothy A

    2017-02-02

    Integrins are adhesion receptors that transmit force across the plasma membrane between extracellular ligands and the actin cytoskeleton. In activation of the transforming growth factor-β1 precursor (pro-TGF-β1), integrins bind to the prodomain, apply force, and release the TGF-β growth factor. However, we know little about how integrins bind macromolecular ligands in the extracellular matrix or transmit force to them. Here we show how integrin αVβ6 binds pro-TGF-β1 in an orientation biologically relevant for force-dependent release of TGF-β from latency. The conformation of the prodomain integrin-binding motif differs in the presence and absence of integrin binding; differences extend well outside the interface and illustrate how integrins can remodel extracellular matrix. Remodelled residues outside the interface stabilize the integrin-bound conformation, adopt a conformation similar to earlier-evolving family members, and show how macromolecular components outside the binding motif contribute to integrin recognition. Regions in and outside the highly interdigitated interface stabilize a specific integrin/pro-TGF-β orientation that defines the pathway through these macromolecules which actin-cytoskeleton-generated tensile force takes when applied through the integrin β-subunit. Simulations of force-dependent activation of TGF-β demonstrate evolutionary specializations for force application through the TGF-β prodomain and through the β- and not α-subunit of the integrin.

  8. Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Amninder S Virk

    2015-02-01

    Full Text Available Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction. Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.

  9. Soluble Eggshell Mebrane Protein:Antibacterial Property and Biodegradability

    Institute of Scientific and Technical Information of China (English)

    YI Feng; YU Jian; LI Qiang; GUO Zhaoxia

    2007-01-01

    The antibacterial property and biodegradability of soluble eggshell membrane protein (SEP)are reported. Unlike the natural eggshell membrane (ESM), SEP does not possess antibacterial property against E.coli. The biodegradation tests with trypsin show that both ESM and SEP are biodegradable.

  10. MX1: a bending-magnet crystallography beamline serving both chemical and macromolecular crystallography communities at the Australian Synchrotron

    Energy Technology Data Exchange (ETDEWEB)

    Cowieson, Nathan Philip; Aragao, David; Clift, Mark; Ericsson, Daniel J.; Gee, Christine; Harrop, Stephen J.; Mudie, Nathan; Panjikar, Santosh; Price, Jason R.; Riboldi-Tunnicliffe, Alan; Williamson, Rachel; Caradoc-Davies, Tom, E-mail: tom.caradoc-davies@synchrotron.org.au [Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168 (Australia)

    2015-01-01

    The macromolecular crystallography beamline MX1 at the Australian Synchrotron is described. MX1 is a bending-magnet crystallography beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the energy range from 8 to 18 keV to a focal spot at the sample position of 120 µm FWHM. The beamline endstation and ancillary equipment facilitate local and remote access for both chemical and biological macromolecular crystallography. Here, the design of the beamline and endstation are discussed. The beamline has enjoyed a full user program for the last seven years and scientific highlights from the user program are also presented.

  11. Anisotropic Contrast Optical Microscope

    CERN Document Server

    Peev, D; Kananizadeh, N; Wimer, S; Rodenhausen, K B; Herzinger, C M; Kasputis, T; Pfaunmiller, E; Nguyen, A; Korlacki, R; Pannier, A; Li, Y; Schubert, E; Hage, D; Schubert, M

    2016-01-01

    An optical microscope is described that reveals contrast in the Mueller matrix images of a thin, transparent or semi-transparent specimen located within an anisotropic object plane (anisotropic filter). The specimen changes the anisotropy of the filter and thereby produces contrast within the Mueller matrix images. Here we use an anisotropic filter composed of a semi-transparent, nanostructured thin film with sub-wavelength thickness placed within the object plane. The sample is illuminated as in common optical microscopy but the light is modulated in its polarization using combinations of linear polarizers and phase plate (compensator) to control and analyze the state of polarization. Direct generalized ellipsometry data analysis approaches permit extraction of fundamental Mueller matrix object plane images dispensing with the need of Fourier expansion methods. Generalized ellipsometry model approaches are used for quantitative image analyses. We demonstrate the anisotropic contrast optical microscope by mea...

  12. Radiation crosslinking of Bionolle and its biodegradation

    Energy Technology Data Exchange (ETDEWEB)

    Suhartini, Meri; Mitomo, H. [Gunma Univ., Faculty of Engineering, Dept. of Biological and Chemical Engineering, Kiryu, Gunma (Japan); Nagasawa, Naotsugu; Yoshii, Fumio; Kume, Tamikazu [Japan Atomic Energy Research Inst., Takasaki, Gunma (Japan). Takasaki Radiation Chemistry Research Establishment

    2002-03-01

    Biodegradable aliphatic polymer such as poly(butylene succinate) (Bionolle no.1001), poly(butylene succinate adipate copolymer) (Bionolle no.3001 and no.3020) were irradiated to give crosslinking structure in the presence of inorganic materials. Pure Bionolle no.1001, Bionolle no.3001 and no. 3020 have low gel fraction in radiation. These samples have high gel fraction by irradiation in the presence of silicon dioxide and carbon black, especially for Bionolle no.3001. Biodegradability of crosslinked Bionolle no.3001 evaluated by enzymatic and soil burial tests were accelerated by addition of inorganic materials. (author)

  13. Biodegradable containers from green waste materials

    Science.gov (United States)

    Sartore, Luciana; Schettini, Evelia; Pandini, Stefano; Bignotti, Fabio; Vox, Giuliano; D'Amore, Alberto

    2016-05-01

    Novel biodegradable polymeric materials based on protein hydrolysate (PH), derived from waste products of the leather industry, and poly(ethylene glycol) diglycidyl ether (PEG) or epoxidized soybean oil (ESO) were obtained and their physico-chemical properties and mechanical behaviour were evaluated. Different processing conditions and the introduction of fillers of natural origin, as saw dust and wood flour, were used to tailor the mechanical properties and the environmental durability of the product. The biodegradable products, which are almost completely manufactured from renewable-based raw materials, look promising for several applications, particularly in agriculture for the additional fertilizing action of PH or in packaging.

  14. Compressive Phase Contrast Tomography

    CERN Document Server

    Maia, F R N C; Marchesini, S; Padmore, H A; Parkinson, D Y; Pien, J; Schirotzek, A; Yang, C; 10.1117/12.861946

    2010-01-01

    When x-rays penetrate soft matter, their phase changes more rapidly than their amplitude. In- terference effects visible with high brightness sources creates higher contrast, edge enhanced images. When the object is piecewise smooth (made of big blocks of a few components), such higher con- trast datasets have a sparse solution. We apply basis pursuit solvers to improve SNR, remove ring artifacts, reduce the number of views and radiation dose from phase contrast datasets collected at the Hard X-Ray Micro Tomography Beamline at the Advanced Light Source. We report a GPU code for the most computationally intensive task, the gridding and inverse gridding algorithm (non uniform sampled Fourier transform).

  15. Comparative study on the biodegradation and biocompatibility of silicate bioceramic coatings on biodegradable magnesium alloy as biodegradable biomaterial

    Science.gov (United States)

    Razavi, M.; Fathi, M. H.; Savabi, O.; Razavi, S. M.; Hashemibeni, B.; Yazdimamaghani, M.; Vashaee, D.; Tayebi, L.

    2014-03-01

    Many clinical cases as well as in vivo and in vitro assessments have demonstrated that magnesium alloys possess good biocompatibility. Unfortunately, magnesium and its alloys degrade too quickly in physiological media. In order to improve the biodegradation resistance and biocompatibility of a biodegradable magnesium alloy, we have prepared three types of coating include diopside (CaMgSi2O6), akermanite (Ca2MgSi2O6) and bredigite (Ca7MgSi4O16) coating on AZ91 magnesium alloy through a micro-arc oxidation (MAO) and electrophoretic deposition (EPD) method. In this research, the biodegradation and biocompatibility behavior of samples were evaluated in vitro and in vivo. The in vitro analysis was performed by cytocompatibility and MTT-assay and the in vivo test was conducted on the implantation of samples in the greater trochanter of adult rabbits. The results showed that diopside coating has the best bone regeneration and bredigite has the best biodegradation resistance compared to others.

  16. Biodegradation of phenol, salicylic acid, benzenesulfonic acid, and iomeprol by Pseudomonas fluorescens in the capillary fringe

    Science.gov (United States)

    Hack, Norman; Reinwand, Christian; Abbt-Braun, Gudrun; Horn, Harald; Frimmel, Fritz H.

    2015-12-01

    Mass transfer and biological transformation phenomena in the capillary fringe were studied using phenol, salicylic acid, benzenesulfonic acid, and the iodinated X-ray contrast agent iomeprol as model organic compounds and the microorganism strain Pseudomonas fluorescens. Three experimental approaches were used: Batch experiments (uniform water saturation and transport by diffusion), in static columns (with a gradient of water saturation and advective transport in the capillaries) and in a flow-through cell (with a gradient of water saturation and transport by horizontal and vertical flow: 2-dimension flow-through microcosm). The reactors employed for the experiments were filled with quartz sand of defined particle size distribution (dp = 200…600 μm, porosity ε = 0.42). Batch experiments showed that phenol and salicylic acid have a high, whereas benzenesulfonic acid and iomeprol have a quite low potential for biodegradation under aerobic conditions and in a matrix nearly close to water saturation. Batch experiments under anoxic conditions with nitrate as electron acceptor revealed that the biodegradation of the model compounds was lower than under aerobic conditions. Nevertheless, the experiments showed that the moisture content was also responsible for an optimized transport in the liquid phase of a porous medium. Biodegradation in the capillary fringe was found to be influenced by both the moisture content and availability of the dissolved substrate, as seen in static column experiments. The gas-liquid mass transfer of oxygen also played an important role for the biological activity. In static column experiments under aerobic conditions, the highest biodegradation was found in the capillary fringe (e.g. βt/β0 (phenol) = 0 after t = 6 d) relative to the zone below the water table and unsaturated zone. The highest biodegradation occurred in the flow-through cell experiment where the height of the capillary fringe was largest.

  17. Biodegradation of phenol, salicylic acid, benzenesulfonic acid, and iomeprol by Pseudomonas fluorescens in the capillary fringe.

    Science.gov (United States)

    Hack, Norman; Reinwand, Christian; Abbt-Braun, Gudrun; Horn, Harald; Frimmel, Fritz H

    2015-12-01

    Mass transfer and biological transformation phenomena in the capillary fringe were studied using phenol, salicylic acid, benzenesulfonic acid, and the iodinated X-ray contrast agent iomeprol as model organic compounds and the microorganism strain Pseudomonas fluorescens. Three experimental approaches were used: Batch experiments (uniform water saturation and transport by diffusion), in static columns (with a gradient of water saturation and advective transport in the capillaries) and in a flow-through cell (with a gradient of water saturation and transport by horizontal and vertical flow: 2-dimension flow-through microcosm). The reactors employed for the experiments were filled with quartz sand of defined particle size distribution (dp=200...600 μm, porosity ε=0.42). Batch experiments showed that phenol and salicylic acid have a high, whereas benzenesulfonic acid and iomeprol have a quite low potential for biodegradation under aerobic conditions and in a matrix nearly close to water saturation. Batch experiments under anoxic conditions with nitrate as electron acceptor revealed that the biodegradation of the model compounds was lower than under aerobic conditions. Nevertheless, the experiments showed that the moisture content was also responsible for an optimized transport in the liquid phase of a porous medium. Biodegradation in the capillary fringe was found to be influenced by both the moisture content and availability of the dissolved substrate, as seen in static column experiments. The gas-liquid mass transfer of oxygen also played an important role for the biological activity. In static column experiments under aerobic conditions, the highest biodegradation was found in the capillary fringe (e.g. βt/β0 (phenol)=0 after t=6 d) relative to the zone below the water table and unsaturated zone. The highest biodegradation occurred in the flow-through cell experiment where the height of the capillary fringe was largest.

  18. Biodegradability of leathers through anaerobic pathway.

    Science.gov (United States)

    Dhayalan, K; Fathima, N Nishad; Gnanamani, A; Rao, J Raghava; Nair, B Unni; Ramasami, T

    2007-01-01

    Leather processing generates huge amounts of both solid and liquid wastes. The management of solid wastes, especially tanned leather waste, is a challenging problem faced by tanners. Hence, studies on biodegradability of leather become imperative. In this present work, biodegradability of untanned, chrome tanned and vegetable tanned leather under anaerobic conditions has been addressed. Two different sources of anaerobes have been used for this purpose. The effect of detanning as a pretreatment method before subjecting the leather to biodegradation has also been studied. It has been found that vegetable tanned leather leads to more gas production than chrome tanned leather. Mixed anaerobic isolates when employed as an inoculum are able to degrade the soluble organics of vegetable tanned material and thus exhibit an increased level of gas production during the initial days, compared to the results of the treatments that received the anaerobic sludge. With chrome tanned materials, there was not much change in the volume of the gas produced from the two different sources. It has been found that detanning tends to improve the biodegradability of both types of leathers.

  19. Natural Biodegradation of Phenolic Compounds in Groundwater

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A combination of field data and theoretical approaches is used to assess the natural attenuation and status of a complex plume of phenolic compounds (phenol, cresols, xylenols) in a deep, consolidated, UK Permo-Triassic sandstone aquifer. Biodegradation of the phenolic compounds at concentrations up to 12500mg·L-1 is occurring under aerobic, NO-3-reducing, Mn/Fe-reducing, SO2-4-reducing and methanogenic conditions in the aquifer, with the accumulation of inorganic and organic metabolites in the plume. An electron and carbon balance for the plume suggests that only 6% of the source term has been degraded in 50 years. The residual contaminant mass in the plume significantly exceeds estimates of electron acceptor inputs, indicating that the plume will grow. Two detailed vertical profiles through the plume show that contaminant distributions are controlled more by source history than by biodegradation processes. Microbiological and mass balance studies show that biodegradation is greatest at the plume fringe where contaminant concentrations are diluted by transverse mixing. Active bacterial populations exist throughout the plume but biodegradation is inhibited in the plume core by high contaminant concentrations. Stable isotope studies show that SO2-4-reduction is particularly sensitive to contaminant concentration. The aquifer is not oxidant-deficient but natural attenuation of the phenolic compounds in this system is limited by toxicity from the pollutant load and the bioavailability of electron acceptors. Natural attenuation of these contaminants will increase only after increased dilution of the plume.

  20. Enhancement of 4-chlorophenol biodegradation using glucose

    Energy Technology Data Exchange (ETDEWEB)

    Tarighian, Alireza; Hill, Gordon; Headley, John [Division of Environmental Engineering, University of Saskatchewan, 105 Maintenance Road, S7N 5C5, Saskatoon, SK (Canada); Pedras, Soledad [Department of Chemistry, University of Saskatchewan, 110 Science Place, S7N 5C9, Saskatoon, SK (Canada)

    2003-03-01

    Toxic, xenobiotic chemicals present challenging problems for the environment since they are normally resistant to biodegradation. Sometimes it is possible to induce biodegradation activity by the use of growth cosubstrates. In this study, pure solutions and binary mixtures of glucose, phenol and 4-chlorophenol have been metabolized in batch cultures by a pure strain of Pseudomonas putida. Following a lag period during which slow growth and low production of biomass occurred, phenol was metabolized according to the Monod model. Glucose was also metabolized according to the Monod model but exponential growth commenced immediately after inoculation with no noticeable lag phase. Biokinetic behavior for growth on a mixture of phenol and glucose paralleled the behavior on individual substrates with simultaneous consumption of both substrates. 4-chlorophenol was not consumed as a sole substrate by Pseudomonas putida but was consumed as a cometabolite with either glucose or phenol acting as the primary growth cosubstrate. Surprisingly, glucose was found to be the superior growth cosubstrate, suggesting that inexpensive sugars can be used to enhance the biodegradation of chlorophenol-contaminated sites. Glucose and the excreted metabolic products of the biodegradation process, including a bright yellow pigment, demonstrated negligible toxicity towards Artemia salina, unlike the phenol and 4-chlorophenol substrates. (orig.)

  1. Transport of nonlinearly biodegradable contaminants in aquifers

    NARCIS (Netherlands)

    Keijzer, H.

    2001-01-01

    This thesis deals with the transport behavior of nonlinearly biodegradable contaminants in aquifers. Such transport occurs during in situ bioremediation which is based on the injection of an electron acceptor or electron donor. The main interests in this thesis are the mutual influences of underlyin

  2. Biodegradable polymersomes for targeted ultrasound imaging

    NARCIS (Netherlands)

    Zhou, W.; Meng, F.; Engbers, G.H.M.; Feijen, J.

    2006-01-01

    Biodegradable polymersomes with a sub-micron size were prepared by using poly(ethylene glycol)–polylactide (PEG–PDLLA) block-copolymers in aqueous media. Air-encapsulated polymersomes could be obtained by a lyophilization/rehydration procedure. Preliminary results showed that these polymersomes were

  3. Biodegradable elastomeric scaffolds for soft tissue engineering

    NARCIS (Netherlands)

    Pego, Ana Paula; Poot, André A.; Grijpma, Dirk W.; Feijen, Jan

    2003-01-01

    Elastomeric copolymers of 1,3-trimethylene carbonate (TMC) and ε-caprolactone (CL) and copolymers of TMC and D,L-lactide (DLLA) have been evaluated as candidate materials for the preparation of biodegradable scaffolds for soft tissue engineering. TMC-DLLA copolymers are amorphous and degrade more r

  4. Neuronal growth and differentiation on biodegradable membranes.

    Science.gov (United States)

    Morelli, Sabrina; Piscioneri, Antonella; Messina, Antonietta; Salerno, Simona; Al-Fageeh, Mohamed B; Drioli, Enrico; De Bartolo, Loredana

    2015-02-01

    Semipermeable polymeric membranes with appropriate morphological, physicochemical and transport properties are relevant to inducing neural regeneration. We developed novel biodegradable membranes to support neuronal differentiation. In particular, we developed chitosan, polycaprolactone and polyurethane flat membranes and a biosynthetic blend between polycaprolactone and polyurethane by phase-inversion techniques. The biodegradable membranes were characterized in order to evaluate their morphological, physicochemical, mechanical and degradation properties. We investigated the efficacy of these different membranes to promote the adhesion and differentiation of neuronal cells. We employed as model cell system the human neuroblastoma cell line SHSY5Y, which is a well-established system for studying neuronal differentiation. The investigation of viability and specific neuronal marker expression allowed assessment that the correct neuronal differentiation and the formation of neuronal network had taken place in vitro in the cells seeded on different biodegradable membranes. Overall, this study provides evidence that neural cell responses depend on the nature of the biodegradable polymer used to form the membranes, as well as on the dissolution, hydrophilic and, above all, mechanical membrane properties. PCL-PU membranes exhibit mechanical properties that improve neurite outgrowth and the expression of specific neuronal markers.

  5. Fabrication of Environmentally Biodegradable Lignin Nanoparticles

    NARCIS (Netherlands)

    Frangville, C.; Rutkevicius, M.; Richter, A.P.; Velev, O.D.; Stoyanov, S.D.; Paunov, V.N.

    2012-01-01

    We developed a method for the fabrication of novel biodegradable nanoparticles (NPs) from lignin which are apparently non-toxic for microalgae and yeast. We compare two alternative methods for the synthesis of lignin NPs which result in particles of very different stability upon change of pH. The fi

  6. Fate and biodegradability of sulfonated aromatic amines

    NARCIS (Netherlands)

    Tan, N.C.G.; Leeuwen, van A.; Voorthuizen, van E.M.; Slenders, P.; Prenafeta, F.X.; Temmink, H.; Lettinga, G.; Field, J.A.

    2005-01-01

    Ten sulfonated aromatic amines were tested for their aerobic and anaerobic biodegradability and toxicity potential in a variety of environmental inocula. Of all the compounds tested, only two aminobenzenesulfonic acid (ABS) isomers, 2- and 4-ABS, were degraded. The observed degradation occurred only

  7. Biodegradation of Guanidinium By Aquatic Microorganisms.

    Science.gov (United States)

    1985-12-01

    Linear Alkylbenzene Sulfonates . Appl. Microbiol. 30:922-929. 21. Pfaender, F.K. and G.W. Bartholomew. 1982. Measurement of Aquatic Biodegradation Rates by...incubation, after which time its disappearance became linear , and it could no longer be detected by the 20th day. Results for an identical water sample

  8. Biodegradation of acetanilide herbicides acetochlor and butachlor in soil.

    Science.gov (United States)

    Ye, Chang-ming; Wang, Xing-jun; Zheng, He-hui

    2002-10-01

    The biodegradation of two acetanilide herbicides, acetochlor and butachlor in soil after other environmental organic matter addition were measured during 35 days laboratory incubations. The herbicides were applied to soil alone, soil-SDBS (sodium dodecylbenzene sulfonate) mixtures and soil-HA (humic acid) mixtures. Herbicide biodegradation kinetics were compared in the different treatment. Biodegradation products of herbicides in soil alone samples were identified by GC/MS at the end of incubation. Addition of SDBS and HA to soil decreased acetochlor biodegradation, but increased butachlor biodegradation. The biodegradation half-life of acetochlor and butachlor in soil alone, soil-SDBS mixtures and soil-HA mixtures were 4.6 d, 6.1 d and 5.4 d and 5.3 d, 4.9 d and 5.3 d respectively. The biodegradation products were hydroxyacetochlor and 2-methyl-6-ethylaniline for acetochlor, and hydroxybutachlor and 2,6-diethylaniline for butachlor.

  9. Development of biodegradable materials; balancing degradability and performance

    Energy Technology Data Exchange (ETDEWEB)

    Mayer, J.M.; Allen, A.L.; Dell, P.A.; McCassie, J.E.; Shupe, A.E.; Stenhouse, P.J. Stenhouse, Welch, E.A.; Kaplan, D.L. [Army Natick Research Development, MA (United States)

    1993-12-31

    The development of biodegradable materials suitable for packaging must take into consideration various performance criteria such as mechanical and barrier properties, as well as rate of biodegradability in given environments. Individual or blended biopolymer films were obtained commercially or blown into film in the laboratory and tested for tensile strength, ultimate elongation and oxygen barrier. These films were then subjected to accelerated marine biodegradation tests as well as simulated marine respirometry. Starch/ethylene vinyl alcohol films exhibited good mechanical and excellent oxygen barrier properties, but were very slow to biodegrade in the simulated and excellent oxygen barrier properties, but were very slow to biodegrade in the simulated marine environment. Polyhydroxyalkanoates had good mechanical properties, average oxygen barrier and good biodegradability. Data indicate that performance and biodegradability of packaging can be tailored to needs by combining individual biopolymers in different proportions in blends and laminates.

  10. Proceedings of a one-week course on exploiting anomalous scattering in macromolecular structure determination (EMBO'07)

    Energy Technology Data Exchange (ETDEWEB)

    Weiss, M.S.; Shepard, W.; Dauter, Z.; Leslie, A.; Diederichs, K.; Evans, G.; Svensson, O.; Schneider, T.; Bricogne, G.; Dauter, Z.; Flensburg, C.; Terwilliger, T.; Lamzin, V.; Leslie, A.; Kabsch, W.; Flensburg, C.; Terwilliger, T.; Lamzin, V.; Read, R.; Panjikar, S.; Pannu, N.S.; Dauter, Z.; Weiss, M.S.; McSweeney, S

    2007-07-01

    This course, which was directed to young scientists, illustrated both theoretical and practical aspects of macromolecular crystal structure solution using synchrotron radiation. Some software dedicated to data collection, processing and analysis were presented. This document gathers only the slides of the presentations.

  11. Force Spectroscopy of Individual Stimulus-Responsive Poly(ferrocenyldimethylsilane) Chains: Towards a Redox-Driven Macromolecular Motor

    NARCIS (Netherlands)

    Zou, Shan; Hempenius, Mark A.; Schönherr, Holger; Vancso, G. Julius

    2006-01-01

    Progress in the development of a redox-driven macromolecular motor and the characterization of its redox-mechanical cycle using electrochemical AFM-based single-molecule force spectroscopy (SMFS) is described. The elasticities of individual neutral and oxidized poly(ferrocenyldimethylsilane) (PFS) m

  12. Lipase-catalyzed Regioselective Synthesis of Vinyl Ester Derivatives of Thiamphenicol: Novel Thiamphenicol Monomers for Preparation of Macromolecular Antibiotic

    Institute of Scientific and Technical Information of China (English)

    Yu Zhen SHI; Zhi Chun CHEN; Na WANG; Qi WU; Xian Fu LIN

    2005-01-01

    Three polymerizable vinyl thiamphenicol esters with different acyl donor carbon chain length (C4, C6, C10) were regioselectivly synthesized by Lipozyme(R) (immobilized from mucor miehei) in acetone at 50 ℃ for 12 h to give 73%, 81%, 63% yield, respectively. The products were valuable monomers for preparation of macromolecular antibiotic.

  13. Macromolecular crowding meets oxygen tension in human mesenchymal stem cell culture - A step closer to physiologically relevant in vitro organogenesis

    Science.gov (United States)

    Cigognini, Daniela; Gaspar, Diana; Kumar, Pramod; Satyam, Abhigyan; Alagesan, Senthilkumar; Sanz-Nogués, Clara; Griffin, Matthew; O'Brien, Timothy; Pandit, Abhay; Zeugolis, Dimitrios I.

    2016-08-01

    Modular tissue engineering is based on the cells’ innate ability to create bottom-up supramolecular assemblies with efficiency and efficacy still unmatched by man-made devices. Although the regenerative potential of such tissue substitutes has been documented in preclinical and clinical setting, the prolonged culture time required to develop an implantable device is associated with phenotypic drift and/or cell senescence. Herein, we demonstrate that macromolecular crowding significantly enhances extracellular matrix deposition in human bone marrow mesenchymal stem cell culture at both 20% and 2% oxygen tension. Although hypoxia inducible factor - 1α was activated at 2% oxygen tension, increased extracellular matrix synthesis was not observed. The expression of surface markers and transcription factors was not affected as a function of oxygen tension and macromolecular crowding. The multilineage potential was also maintained, albeit adipogenic differentiation was significantly reduced in low oxygen tension cultures, chondrogenic differentiation was significantly increased in macromolecularly crowded cultures and osteogenic differentiation was not affected as a function of oxygen tension and macromolecular crowding. Collectively, these data pave the way for the development of bottom-up tissue equivalents based on physiologically relevant developmental processes.

  14. Probing the Interplay of Size, Shape, and Solution Environment in Macromolecular Diffusion Using a Simple Refraction Experiment

    Science.gov (United States)

    Mankidy, Bijith D.; Coutinho, Cecil A.; Gupta, Vinay K.

    2010-01-01

    The diffusion coefficient of polymers is a critical parameter in biomedicine, catalysis, chemical separations, nanotechnology, and other industrial applications. Here, measurement of macromolecular diffusion in solutions is described using a visually instructive, undergraduate-level optical refraction experiment based on Weiner's method. To…

  15. Contrastive topics decomposed

    Directory of Open Access Journals (Sweden)

    Michael Wagner

    2012-12-01

    Full Text Available The analysis of contrastive topics introduced in Büring 1997b and further developed in Büring 2003 relies on distinguishing two types of constituents that introduce alternatives: the sentence focus, which is marked by a FOC feature, and the contrastive topic, which is marked by a CT feature. A non-compositional rule of interpretation that refers to these features is used to derive a topic semantic value, a nested set of sets of propositions. This paper presents evidence for a correlation between the restrictive syntax of nested focus operators and the syntax of contrastive topics, a correlation which is unexpected under this analysis. A compositional analysis is proposed that only makes use of the flatter focus semantic values introduced by focus operators. The analysis aims at integrating insights from the original analysis while at the same time capturing the observed syntactic restrictions. http://dx.doi.org/10.3765/sp.5.8 BibTeX info

  16. Polychromatic diffraction contrast tomography

    Energy Technology Data Exchange (ETDEWEB)

    King, A., E-mail: king@synchrotron-soleil.fr [Synchrotron SOLEIL, Gif-sur-Yvette 91192 (France); Reischig, P. [Xnovo Technology ApS, 4600 Køge (Denmark); Department of Materials Science and Engineering, Delft University of Technology, Delft 2628 CD (Netherlands); Adrien, J. [MATEIS, INSA de Lyon, Villeurbanne 69621 (France); Peetermans, S. [Paul Scherrer Institut, CH-5232 Villigen (Switzerland); Ludwig, W. [MATEIS, INSA de Lyon, Villeurbanne 69621 (France); European Synchrotron Radiation Facility, Grenoble 38043 (France)

    2014-11-15

    This tutorial review introduces the use of polychromatic radiation for 3D grain mapping using X-ray diffraction contrast tomography. The objective is to produce a 3D map of the grain shapes and orientations within a bulk, millimeter-sized polycrystalline sample. The use of polychromatic radiation enables the standard synchrotron X-ray technique to be applied in a wider range of contexts: 1) Using laboratory X-ray sources allows a much wider application of the diffraction contrast tomography technique. 2) Neutron sources allow large samples, or samples containing high Z elements to be studied. 3) Applied to synchrotron sources, smaller samples may be treated, or faster measurements may be possible. Challenges and particularities in the data acquisition and processing, and the limitations of the different variants, are discussed. - Highlights: • We present a tutorial review of polychromatic diffraction contrast tomography techniques. • The use of polychromatic radiation allows the standard synchrotron DCT technique to be extended to a range of other sources. • The characteristics and limitations of all variants of the techniques are derived, discussed and compared. • Examples using laboratory X-ray and cold neutron radiation are presented. • Suggestions for the future development of these techniques are presented.

  17. Biodegradable microparticles with surface dimples as a bi-modal imaging contrast agent.

    Science.gov (United States)

    Kim, Mi Ri; Lim, Yong Taik; Cho, Kuk Young

    2013-03-12

    Fabrication of physically engineered colloids and their application to the biological fields is emerging importance because of their potential to provide an enhanced performance without altering the chemical properties of biomaterials used. A facile approach is reported to fabricate sub-10-μm-sized PLGA microparticle with small dimples covering the surface by droplet imprinting. Optical and magnetic resonance bioimaging agents are easily co-encapsulated inside the microparticles to obtain a bi-modal imaging agent. Cell internalization efficacy of dimpled particles in DC 2.4 cell is enhanced compared with conventional smooth round-shaped colloids. Our result indicates that morphology-controlled microparticles show promise as a cell labeling with improved cell interaction.

  18. Biodegradable Porous Silicon Nanomaterials for Imaging and Treatment of Cancer

    Science.gov (United States)

    Gu, Luo

    Cancer is the second leading cause of death, claiming ˜0.56 million lives in the U.S. every year following heart diseases (˜0.62 million). From 1991 to 2007, mortality associated with heart diseases decreased 39%; by contrast, the death rate of cancer only decreased by 17% in spite of intensive research and improved therapeutics. The stagnation of conventional medicine and the complexity of cancer demand new therapeutic strategies. As an emerging approach, the use of nanomaterials as cancer diagnostic and therapeutic agents has shown promising results due to their unique physical and chemical properties. To date, more than two dozen nanoparticle-based products have been approved for clinical use and they show advantages over conventional therapeutics. However, translation of many other nanomaterials has been impeded due to concerns over toxicity and biodegradability. This dissertation presents the development of biodegradable luminescent porous silicon nanomaterials and their potential applications for imaging and treatment of cancer. After a brief introduction to nanomedicine and the biomedical applications of porous silicon, Chapter 2 presents a method of making silicon nanoparticles with porous structure and intrinsic luminescence (LPSiNPs). The low toxicity and biodegradability of LPSiNPs are demonstrated in vitro with human cancer cells and in vivo with mouse model. The in vivo clearance of intravenously injected LPSiNPs is studied by tracking the emission of the nanoparticles with fluorescence imaging. Chapter 3 presents a diagnostic application of LPSiNPs. Time-gated fluorescence imaging of tumors using LPSiNPs with long emission lifetime is developed. This technique can effectively eliminate interference from short-lived tissue autofluorescence and improve the detection sensitivity. Chapter 4--6 demonstrate the therapeutic applications of porous silicon nanomaterials. In Chapter 4, magnetically-guided delivery of anticancer drug to cancer cells in vitro

  19. Anisotropic contrast optical microscope

    Science.gov (United States)

    Peev, D.; Hofmann, T.; Kananizadeh, N.; Beeram, S.; Rodriguez, E.; Wimer, S.; Rodenhausen, K. B.; Herzinger, C. M.; Kasputis, T.; Pfaunmiller, E.; Nguyen, A.; Korlacki, R.; Pannier, A.; Li, Y.; Schubert, E.; Hage, D.; Schubert, M.

    2016-11-01

    An optical microscope is described that reveals contrast in the Mueller matrix images of a thin, transparent, or semi-transparent specimen located within an anisotropic object plane (anisotropic filter). The specimen changes the anisotropy of the filter and thereby produces contrast within the Mueller matrix images. Here we use an anisotropic filter composed of a semi-transparent, nanostructured thin film with sub-wavelength thickness placed within the object plane. The sample is illuminated as in common optical microscopy but the light is modulated in its polarization using combinations of linear polarizers and phase plate (compensator) to control and analyze the state of polarization. Direct generalized ellipsometry data analysis approaches permit extraction of fundamental Mueller matrix object plane images dispensing with the need of Fourier expansion methods. Generalized ellipsometry model approaches are used for quantitative image analyses. These images are obtained from sets of multiple images obtained under various polarizer, analyzer, and compensator settings. Up to 16 independent Mueller matrix images can be obtained, while our current setup is limited to 11 images normalized by the unpolarized intensity. We demonstrate the anisotropic contrast optical microscope by measuring lithographically defined micro-patterned anisotropic filters, and we quantify the adsorption of an organic self-assembled monolayer film onto the anisotropic filter. Comparison with an isotropic glass slide demonstrates the image enhancement obtained by our method over microscopy without the use of an anisotropic filter. In our current instrument, we estimate the limit of detection for organic volumetric mass within the object plane of ≈49 fg within ≈7 × 7 μm2 object surface area. Compared to a quartz crystal microbalance with dissipation instrumentation, where contemporary limits require a total load of ≈500 pg for detection, the instrumentation demonstrated here improves

  20. Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

    Science.gov (United States)

    Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.; Thiele, Ines; Palsson, Bernhard O.; Saunders, Michael A.

    2017-01-01

    Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many orders of magnitude. Data values also have greatly varying magnitudes. Standard double-precision solvers may return inaccurate solutions or report that no solution exists. Exact simplex solvers based on rational arithmetic require a near-optimal warm start to be practical on large problems (current ME models have 70,000 constraints and variables and will grow larger). We have developed a quadruple-precision version of our linear and nonlinear optimizer MINOS, and a solution procedure (DQQ) involving Double and Quad MINOS that achieves reliability and efficiency for ME models and other challenging problems tested here. DQQ will enable extensive use of large linear and nonlinear models in systems biology and other applications involving multiscale data.

  1. Integration and global analysis of isothermal titration calorimetry data for studying macromolecular interactions.

    Science.gov (United States)

    Brautigam, Chad A; Zhao, Huaying; Vargas, Carolyn; Keller, Sandro; Schuck, Peter

    2016-05-01

    Isothermal titration calorimetry (ITC) is a powerful and widely used method to measure the energetics of macromolecular interactions by recording a thermogram of differential heating power during a titration. However, traditional ITC analysis is limited by stochastic thermogram noise and by the limited information content of a single titration experiment. Here we present a protocol for bias-free thermogram integration based on automated shape analysis of the injection peaks, followed by combination of isotherms from different calorimetric titration experiments into a global analysis, statistical analysis of binding parameters and graphical presentation of the results. This is performed using the integrated public-domain software packages NITPIC, SEDPHAT and GUSSI. The recently developed low-noise thermogram integration approach and global analysis allow for more precise parameter estimates and more reliable quantification of multisite and multicomponent cooperative and competitive interactions. Titration experiments typically take 1-2.5 h each, and global analysis usually takes 10-20 min.

  2. A mixed method for measuring low-frequency acoustic properties of macromolecular materials

    Institute of Scientific and Technical Information of China (English)

    LIU; Hongwei; YAO; Lei; ZHAO; Hong; ZHANG; Jichuan; XUE; Zhaohong

    2006-01-01

    A mixed method for measuring low-frequency acoustic properties of macromolecular materials is presented.The dynamic mechanical parameters of materials are first measured by using Dynamic Mechanical Thermal Apparatus(DMTA) at low frequencies,usually less than 100 Hz; then based on the Principles of Time-Temperature Super position (TTS),these parameters are extended to the frequency range that acousticians are concerned about,usually from hundreds to thousands of hertz; finally the extended dynamic mechanical parameters are transformed into acoustic parameters with the help of acoustic measurement and inverse analysis.To test the feasibility and accuracy,we measure a kind of rubber sample in DMTA and acquire the basic acoustic parameters of the sample by using this method.While applying the basic parameters to calculating characteristics of the sample in acoustic pipe,a reasonable agreement of sound absorption coefficients is obtained between the calculations and measurements in the acoustic pipe.

  3. Phenix - a comprehensive python-based system for macromolecular structure solution

    Energy Technology Data Exchange (ETDEWEB)

    Terwilliger, Thomas C [Los Alamos National Laboratory; Hung, Li - Wei [Los Alamos National Laboratory; Adams, Paul D [UC BERKELEY; Afonine, Pavel V [UC BERKELEY; Bunkoczi, Gabor [UNIV OF CAMBRIDGE; Chen, Vincent B [DUKE UNIV; Davis, Ian [DUKE UNIV; Echols, Nathaniel [LBNL; Headd, Jeffrey J [DUKE UNIV; Grosse Kunstleve, Ralf W [LBNL; Mccoy, Airlie J [UNIV OF CAMBRIDGE; Moriarty, Nigel W [LBNL; Oeffner, Robert [UNIV OF CAMBRIDGE; Read, Randy J [UNIV OF CAMBRIDGE; Richardson, David C [DUKE UNIV; Richardson, Jane S [DUKE UNIV; Zwarta, Peter H [LBNL

    2009-01-01

    Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages, and the repeated use of interactive three-dimensional graphics. Phenix has been developed to provide a comprehensive system for crystallographic structure solution with an emphasis on automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand, and finally the development of a framework that allows a tight integration between the algorithms.

  4. Recent Major Improvements to the ALS Sector 5 MacromolecularCrystallography Beamlines

    Energy Technology Data Exchange (ETDEWEB)

    Morton, Simon A.; Glossinger, James; Smith-Baumann, Alexis; McKean, John P.; Trame, Christine; Dickert, Jeff; Rozales, Anthony; Dauz,Azer; Taylor, John; Zwart, Petrus; Duarte, Robert; Padmore, Howard; McDermott, Gerry; Adams, Paul

    2007-07-01

    Although the Advanced Light Source (ALS) was initially conceived primarily as a low energy (1.9GeV) 3rd generation source of VUV and soft x-ray radiation it was realized very early in the development of the facility that a multipole wiggler source coupled with high quality, (brightness preserving), optics would result in a beamline whose performance across the optimal energy range (5-15keV) for macromolecular crystallography (MX) would be comparable to, or even exceed, that of many existing crystallography beamlines at higher energy facilities. Hence, starting in 1996, a suite of three beamlines, branching off a single wiggler source, was constructed, which together formed the ALS Macromolecular Crystallography Facility. From the outset this facility was designed to cater equally to the needs of both academic and industrial users with a heavy emphasis placed on the development and introduction of high throughput crystallographic tools, techniques, and facilities--such as large area CCD detectors, robotic sample handling and automounting facilities, a service crystallography program, and a tightly integrated, centralized, and highly automated beamline control environment for users. This facility was immediately successful, with the primary Multiwavelength Anomalous Diffraction beamline (5.0.2) in particular rapidly becoming one of the foremost crystallographic facilities in the US--responsible for structures such as the 70S ribosome. This success in-turn triggered enormous growth of the ALS macromolecular crystallography community and spurred the development of five additional ALS MX beamlines all utilizing the newly developed superconducting bending magnets ('superbends') as sources. However in the years since the original Sector 5.0 beamlines were built the performance demands of macromolecular crystallography users have become ever more exacting; with growing emphasis placed on studying larger complexes, more difficult structures, weakly diffracting or

  5. Syntheses of Macromolecular Ruthenium Compounds: A New Approach for the Search of Anticancer Drugs

    Directory of Open Access Journals (Sweden)

    Andreia Valente

    2014-03-01

    Full Text Available The continuous rising of the cancer patient death rate undoubtedly shows the pressure to find more potent and efficient drugs than those in clinical use. These agents only treat a narrow range of cancer conditions with limited success and are associated with serious side effects caused by the lack of selectivity. In this frame, innovative syntheses approaches can decisively contribute to the success of “smart compounds” that might be only selective and/or active towards the cancer cells, sparing the healthy ones. In this scope, ruthenium chemistry is a rising field for the search of proficient metallodrugs by the use of macromolecular ruthenium complexes (dendrimers and dendronized polymers, coordination-cage and protein conjugates, nanoparticles and polymer-“ruthenium-cyclopentadienyl” conjugates that can take advantage of the singularities of tumor cells (vs. healthy cells.

  6. Site-selective electroless nickel plating on patterned thin films of macromolecular metal complexes.

    Science.gov (United States)

    Kimura, Mutsumi; Yamagiwa, Hiroki; Asakawa, Daisuke; Noguchi, Makoto; Kurashina, Tadashi; Fukawa, Tadashi; Shirai, Hirofusa

    2010-12-01

    We demonstrate a simple route to depositing nickel layer patterns using photocross-linked polymer thin films containing palladium catalysts, which can be used as adhesive interlayers for fabrication of nickel patterns on glass and plastic substrates. Electroless nickel patterns can be obtained in three steps: (i) the pattern formation of partially quaterized poly(vinyl pyridine) by UV irradiation, (ii) the formation of macromolecular metal complex with palladium, and (iii) the nickel metallization using electroless plating bath. Metallization is site-selective and allows for a high resolution. And the resulting nickel layered structure shows good adhesion with glass and plastic substrates. The direct patterning of metallic layers onto insulating substrates indicates a great potential for fabricating micro/nano devices.

  7. Phase transitions of macromolecular microsphere composite hydrogels based on the stochastic Cahn–Hilliard equation

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xiao, E-mail: lixiao1228@163.com; Ji, Guanghua, E-mail: ghji@bnu.edu.cn; Zhang, Hui, E-mail: hzhang@bnu.edu.cn

    2015-02-15

    We use the stochastic Cahn–Hilliard equation to simulate the phase transitions of the macromolecular microsphere composite (MMC) hydrogels under a random disturbance. Based on the Flory–Huggins lattice model and the Boltzmann entropy theorem, we develop a reticular free energy suit for the network structure of MMC hydrogels. Taking the random factor into account, with the time-dependent Ginzburg-Landau (TDGL) mesoscopic simulation method, we set up a stochastic Cahn–Hilliard equation, designated herein as the MMC-TDGL equation. The stochastic term in the equation is constructed appropriately to satisfy the fluctuation-dissipation theorem and is discretized on a spatial grid for the simulation. A semi-implicit difference scheme is adopted to numerically solve the MMC-TDGL equation. Some numerical experiments are performed with different parameters. The results are consistent with the physical phenomenon, which verifies the good simulation of the stochastic term.

  8. Functionalization of Planet-Satellite Nanostructures Revealed by Nanoscopic Localization of Distinct Macromolecular Species

    KAUST Repository

    Rossner, Christian

    2016-09-26

    The development of a straightforward method is reported to form hybrid polymer/gold planet-satellite nanostructures (PlSNs) with functional polymer. Polyacrylate type polymer with benzyl chloride in its backbone as a macromolecular tracer is synthesized to study its localization within PlSNs by analyzing the elemental distribution of chlorine. The functionalized nanohybrid structures are analyzed by scanning transmission electron microscopy, electron energy loss spectroscopy, and spectrum imaging. The results show that the RAFT (reversible addition-fragmentation chain transfer) polymers\\' sulfur containing end groups are colocalized at the gold cores, both within nanohybrids of simple core-shell morphology and within higher order PlSNs, providing microscopic evidence for the affinity of the RAFT group toward gold surfaces. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA., Weinheim.

  9. Mix and Inject: Reaction Initiation by Diffusion for Time-Resolved Macromolecular Crystallography

    Directory of Open Access Journals (Sweden)

    Marius Schmidt

    2013-01-01

    Full Text Available Time-resolved macromolecular crystallography unifies structure determination with chemical kinetics, since the structures of transient states and chemical and kinetic mechanisms can be determined simultaneously from the same data. To start a reaction in an enzyme, typically, an initially inactive substrate present in the crystal is activated. This has particular disadvantages that are circumvented when active substrate is directly provided by diffusion. However, then it is prohibitive to use macroscopic crystals because diffusion times become too long. With small micro- and nanocrystals diffusion times are adequately short for most enzymes and the reaction can be swiftly initiated. We demonstrate here that a time-resolved crystallographic experiment becomes feasible by mixing substrate with enzyme nanocrystals which are subsequently injected into the X-ray beam of a pulsed X-ray source.

  10. Phase behaviour of macromolecular liquid crystalline materials. Computational studies at the molecular level

    CERN Document Server

    Stimson, L M

    2003-01-01

    Molecular simulations provide an increasingly useful insight into the static and dynamic characteristics of materials. In this thesis molecular simulations of macro-molecular liquid crystalline materials are reported. The first liquid crystalline material that has been investigated is a side chain liquid crystal polymer (SCLCP). In this study semi-atomistic molecular dynamics simulations have been conducted at a range of temperatures and an aligning potential has been applied to mimic the effect of a magnetic field. In cooling the SCLCP from an isotropic melt, microphase separation was observed yielding a domain structure. The application of a magnetic field to this structure aligns the domains producing a stable smectic mesophase. This is the first study in which mesophases have been observed using an off-lattice model of a SCLCP. The second material that has been investigated is a dendrimer with terminal mesogenic functionalization. Here, a multi-scale approach has been taken with Monte Carlo studies of a s...

  11. PURY: a database of geometric restraints of hetero compounds for refinement in complexes with macromolecular structures.

    Science.gov (United States)

    Andrejasic, Miha; Praaenikar, Jure; Turk, Dusan

    2008-11-01

    The number and variety of macromolecular structures in complex with ;hetero' ligands is growing. The need for rapid delivery of correct geometric parameters for their refinement, which is often crucial for understanding the biological relevance of the structure, is growing correspondingly. The current standard for describing protein structures is the Engh-Huber parameter set. It is an expert data set resulting from selection and analysis of the crystal structures gathered in the Cambridge Structural Database (CSD). Clearly, such a manual approach cannot be applied to the vast and ever-growing number of chemical compounds. Therefore, a database, named PURY, of geometric parameters of chemical compounds has been developed, together with a server that accesses it. PURY is a compilation of the whole CSD. It contains lists of atom classes and bonds connecting them, as well as angle, chirality, planarity and conformation parameters. The current compilation is based on CSD 5.28 and contains 1978 atom classes and 32,702 bonding, 237,068 angle, 201,860 dihedral and 64,193 improper geometric restraints. Analysis has confirmed that the restraints from the PURY database are suitable for use in macromolecular crystal structure refinement and should be of value to the crystallographic community. The database can be accessed through the web server http://pury.ijs.si/, which creates topology and parameter files from deposited coordinates in suitable forms for the refinement programs MAIN, CNS and REFMAC. In the near future, the server will move to the CSD website http://pury.ccdc.cam.ac.uk/.

  12. A 3D image filter for parameter-free segmentation of macromolecular structures from electron tomograms.

    Directory of Open Access Journals (Sweden)

    Rubbiya A Ali

    Full Text Available 3D image reconstruction of large cellular volumes by electron tomography (ET at high (≤ 5 nm resolution can now routinely resolve organellar and compartmental membrane structures, protein coats, cytoskeletal filaments, and macromolecules. However, current image analysis methods for identifying in situ macromolecular structures within the crowded 3D ultrastructural landscape of a cell remain labor-intensive, time-consuming, and prone to user-bias and/or error. This paper demonstrates the development and application of a parameter-free, 3D implementation of the bilateral edge-detection (BLE algorithm for the rapid and accurate segmentation of cellular tomograms. The performance of the 3D BLE filter has been tested on a range of synthetic and real biological data sets and validated against current leading filters-the pseudo 3D recursive and Canny filters. The performance of the 3D BLE filter was found to be comparable to or better than that of both the 3D recursive and Canny filters while offering the significant advantage that it requires no parameter input or optimisation. Edge widths as little as 2 pixels are reproducibly detected with signal intensity and grey scale values as low as 0.72% above the mean of the background noise. The 3D BLE thus provides an efficient method for the automated segmentation of complex cellular structures across multiple scales for further downstream processing, such as cellular annotation and sub-tomogram averaging, and provides a valuable tool for the accurate and high-throughput identification and annotation of 3D structural complexity at the subcellular level, as well as for mapping the spatial and temporal rearrangement of macromolecular assemblies in situ within cellular tomograms.

  13. A 3D image filter for parameter-free segmentation of macromolecular structures from electron tomograms.

    Science.gov (United States)

    Ali, Rubbiya A; Landsberg, Michael J; Knauth, Emily; Morgan, Garry P; Marsh, Brad J; Hankamer, Ben

    2012-01-01

    3D image reconstruction of large cellular volumes by electron tomography (ET) at high (≤ 5 nm) resolution can now routinely resolve organellar and compartmental membrane structures, protein coats, cytoskeletal filaments, and macromolecules. However, current image analysis methods for identifying in situ macromolecular structures within the crowded 3D ultrastructural landscape of a cell remain labor-intensive, time-consuming, and prone to user-bias and/or error. This paper demonstrates the development and application of a parameter-free, 3D implementation of the bilateral edge-detection (BLE) algorithm for the rapid and accurate segmentation of cellular tomograms. The performance of the 3D BLE filter has been tested on a range of synthetic and real biological data sets and validated against current leading filters-the pseudo 3D recursive and Canny filters. The performance of the 3D BLE filter was found to be comparable to or better than that of both the 3D recursive and Canny filters while offering the significant advantage that it requires no parameter input or optimisation. Edge widths as little as 2 pixels are reproducibly detected with signal intensity and grey scale values as low as 0.72% above the mean of the background noise. The 3D BLE thus provides an efficient method for the automated segmentation of complex cellular structures across multiple scales for further downstream processing, such as cellular annotation and sub-tomogram averaging, and provides a valuable tool for the accurate and high-throughput identification and annotation of 3D structural complexity at the subcellular level, as well as for mapping the spatial and temporal rearrangement of macromolecular assemblies in situ within cellular tomograms.

  14. [Biodegradable catheters and urinary stents. When?

    Science.gov (United States)

    Soria, F; Morcillo, E; López de Alda, A; Pastor, T; Sánchez-Margallo, F M

    2016-10-01

    One of the main wishes in the field of urinary catheters and stents is to arm them with biodegradable characteristics because we consider a failure of these devices the need for retrieval, the forgotten catheter syndrome as well as the adverse effects permanent devices cause after fulfilling their aim. The efforts focused in new designs, coatings and biomaterials aim to increase the biocompatibility of theses internal devices. Lately, there have been correct advances to answer the main challenges regarding biodegradable ureteral devices. Thus, modulation of the rate of degradation has been achieved thanks to new biomaterials and the use of copolymers that enable to choose the time of permanence as it is programmed with conventional double J catheters. Biocompatibility has improved with the use of new polymers that adapt better to the urine. Finally, one of the main problems is elimination of degraded fragments and experimentally it has be demonstrated that new designs elicit controlled degradation, from distal to proximal; using stranding and combination of copolymers degradation may be caused by dilution, reducing fragmentation to the last stages of life of the prosthesis. Moreover, it has been demonstrated that biodegradable catheters potentially may cause less urinary tract infection, less encrustation and predictably they will diminish catheter morbidity, since their degradation process reduces adverse effects. Regarding the development of biodegradable urethral stents, it is necessary to find biomaterials that enable maintaining their biomechanical properties in the long term, keeping open the urethral lumen both in patients with BPH and urethral stenosis. Modulation of the time of degradation of the prosthesis has been achieved, but the appearance of urothelial hyperplasia is still a constant in the initial phases after implantation. The development of drug eluting stents, anti-proliferative or anti-inflammatory, as well as biodegradable stents biocoated is a

  15. Contrast Invariant SNR

    DEFF Research Database (Denmark)

    Weiss, Pierre; Escande, Paul; Dong, Yiqiu

    We design an image quality measure independent of local contrast changes, which constitute simple models of illumination changes. Given two images, the algorithm provides the image closest to the first one with the component tree of the second. This problem can be cast as a specific convex progra...... algorithms based on interior point methods. The algorithm has potential applications in change detection, color image processing or image fusion. A Matlab implementation is available at http://www.math.univ-toulouse.fr/_weiss/PageCodes.html....

  16. Facile Fabrication of Water Dispersible Latex Particles with Homogeneous or Chain-Segregated Surface from RAFT Polymerization Using a Mixture of Two Macromolecular Chain Transfer Agents.

    Science.gov (United States)

    Sun, Li; Hong, Liangzhi; Wang, Chaoyang

    2016-04-01

    Water dispersible latex particles with randomly mixed shells or chain segregated surface are synthesized from one-pot reversible addition-fragmentation chain transfer heterogeneous polymerization of benzyl methacrylate (BzMA) using a mixture of poly(glycerol monomethacrylate) (PGMA) and poly(2,3-bis(succinyloxy)propyl methacrylate) (PBSPMA) macromolecular chain transfer agents. In methanol, the two in situ synthesized PGMA-b-PBzMA and PBSPMA-b-PBzMA diblock copolymers coaggregate into spherical micelles, which contain PBzMA core and discrete PGMA and PBSPMA nanodomains on the shell. In contrast, in water-methanol mixture (V/V = 9/1), latex particles with homogeneous distribution of PGMA and PBSPMA polymer chains on the shell are obtained. The reasons leading to formation of latex particles with homogenous or chain-segregated surface are discussed, and polymerization kinetics and physical state of PBSPMA in methanol and water-methanol mixtures are ascribed. These polymeric micelles with patterned functional group on the surface are potentially important for application in supracolloidal hierarchical assemblies and catalysis.

  17. Biodegradable Magnetic Particles for Cellular MRI

    Science.gov (United States)

    Nkansah, Michael Kwasi

    Cell transplantation has the potential to treat numerous diseases and injuries. While magnetic particle-enabled, MRI-based cell tracking has proven useful for visualizing the location of cell transplants in vivo, current formulations of particles are either too weak to enable single cell detection or have non-degradable polymer matrices that preclude clinical translation. Furthermore, the off-label use of commercial agents like Feridex®, Bangs beads and ferumoxytol for cell tracking significantly stunts progress in the field, rendering it needlessly susceptible to market externalities. The recent phasing out of Feridex from the market, for example, heightens the need for a dedicated agent specifically designed for MRI-based cell tracking. To this end, we engineered clinically viable, biodegradable particles of iron oxide made using poly(lactide-co-glycolide) (PLGA) and demonstrated their utility in two MRI-based cell tracking paradigms in vivo. Both micro- and nanoparticles (2.1±1.1 μm and 105±37 nm in size) were highly magnetic (56.7-83.7 wt% magnetite), and possessed excellent relaxometry (r2* relaxivities as high as 614.1 s-1mM-1 and 659.1 s -1mM-1 at 4.7 T respectively). Magnetic PLGA micropartides enabled the in vivo monitoring of neural progenitor cell migration to the olfactory bulb in rat brains over 2 weeks at 11.7 T with ˜2-fold greater contrast-to-noise ratio and ˜4-fold better sensitivity at detecting migrated cells in the olfactory bulb than Bangs beads. Highly magnetic PLGA nanoparticles enabled MRI detection (at 11.7 T) of up to 10 rat mesenchymal cells transplanted into rat brain at 100-μm resolution. Highly magnetic PLGA particles were also shown to degrade by 80% in mice liver over 12 weeks in vivo. Moreover, no adverse effects were observed on cellular viability and function in vitro after labeling a wide range of cells. Magnetically labeled rat mesenchymal and neural stem cells retained their ability to differentiate into multiple

  18. Biodegradability of biodegradable/degradable plastic materials under aerobic and anaerobic conditions.

    Science.gov (United States)

    Mohee, R; Unmar, G D; Mudhoo, A; Khadoo, P

    2008-01-01

    A study was conducted on two types of plastic materials, Mater-Bi Novamont (MB) and Environmental Product Inc. (EPI), to assess their biodegradability under aerobic and anaerobic conditions. For aerobic conditions, organic fractions of municipal solid wastes were composted. For the anaerobic process, anaerobic inoculum from a wastewater treatment plant was used. Cellulose filter papers (CFP) were used as a positive control for both mediums. The composting process was monitored in terms of temperature, moisture and volatile solids and the biodegradation of the samples were monitored in terms of mass loss. Monitoring results showed a biodegradation of 27.1% on a dry basis for MB plastic within a period of 72 days of composting. Biodegradability under an anaerobic environment was monitored in terms of biogas production. A cumulative methane gas production of 245 ml was obtained for MB, which showed good degradation as compared to CFP (246.8 ml). However, EPI plastic showed a cumulative methane value of 7.6 ml for a period of 32 days, which was close to the blank (4.0 ml). The EPI plastic did not biodegrade under either condition. The cumulative carbon dioxide evolution after 32 days was as follows: CFP 4.406 cm3, MB 2.198 cm3 and EPI 1.328 cm3. The cumulative level of CO2 varying with time fitted sigmoid type curves with R2 values of 0.996, 0.996 and 0.995 for CFP, MB and EPI, respectively.

  19. Biodegradation studies of rosin-based polymers.

    Science.gov (United States)

    Satturwar, P M; Mandaogade, P M; Darwhekar, G N; Fulzele, S V; Joshi, S B; Dorle, A K

    2003-07-01

    This study was designed to investigate two rosin-based polymers (R-1 and R-2) for their in vitro and in vivo biodegradation behavior. The in vitro hydrolytic degradation was carried out in buffer solutions of pH 4.4, 7.4, and 10.4 at 37 degrees C. Enzymatic degradation was studied using enzymes lipase, pancreatine, and pectinase. Free films of the two polymers were subcutaneously implanted in rabbits for the in vivo biodegradation. The extent of degradation was determined quantitatively by weight loss and was followed qualitatively by scanning electron microscopy. The extent and the rate of degradation was better in vivo than in vitro. The polymers showed poor enzymatic degradation and a highly pH-dependent hydrolytic degradation.

  20. Hydrocarbon biodegradation in intertidal wetland sediments.

    Science.gov (United States)

    McGenity, Terry J

    2014-06-01

    Intertidal wetlands, primarily salt marsh, mangrove and mudflats, which provide many essential ecosystem services, are under threat on numerous fronts; a situation that is made worse by crude-oil pollution. Microbes are the main vehicle for remediation of such sediments, and new discoveries, such as novel biodegradation pathways, means of accessing oil, multi-species interactions, and community-level responses to oil addition, are helping us to understand, predict and monitor the fate of oil. Despite this, there are many challenges, not least because of the heterogeneity of these ecosystems and the complexity of crude oil. For example, there is growing awareness about the toxicity of the oxygenated products that result from crude-oil weathering, which are difficult to degrade. This review highlights how developments in areas as diverse as systems biology, microbiology, ecology, biogeochemistry and analytical chemistry are enhancing our understanding of hydrocarbon biodegradation and thus bioremediation of oil-polluted intertidal wetlands.

  1. BIODEGRADATION OF REGENERATED CELLULOSE FILMS BY FUNGI

    Institute of Scientific and Technical Information of China (English)

    ZHANG Lina; LIU Haiqing; ZHENG Lianshuang; ZHANG Jiayao; DU Yumin; LIU Weili

    1996-01-01

    The biodegradability of Aspergillus niger (A. niger), Mucor (M-305) and Trichoderma (T-311) strains on regenerated cellulose films in media was investigated. The results showed that T-311 strain isolated from soil adhered on the cellulose film fragments has stronger degradation effect on the cellulose film than A. niger strain. The weights, molecular weights and tensile strengths of the cellulose films in both shake culture and solid media decreased with incubation time, accompanied by producing CO2 and saccharides. HPLC, IR and released CO2 analysis indicated that the biodegradation products of the regenerated cellulose films mainly contain oligosaccharides, cellobiose, glucose, arabinose, erythrose, glycerose,glycerol, ethanal, formaldehyde and organic acid, the end products were CO2 and water.After a month, the films were completely decomposed by fungi in the media at 30℃.

  2. [Development of biodegradable magnesium-based biomaterials].

    Science.gov (United States)

    Zhu, Shengfa; Xu, Li; Huang, Nan

    2009-04-01

    Magnesium is a macroelement which is indispensable to human bodies. As a lightweight metal with high specific strength and favorable biocompatibility, magnesium and its alloys have been introduced in the field of biomedical materials research and have a broad application prospect. It is possible to develop new type of biodegradable medical magnesium alloys by use of the poor corrosion resistance of magnesium. Bioabsorbable magnesium stents implanted in vivo could mechanically support the vessel in a short term, effectly prevent the acute coronary occlusion and in-stent restenosis, and then be gradully biodegraded and completely absorbed in a long term. Osteoconductive bioactivity in magnesium-based alloys could promote the apposition growth of bone tissue. This paper reviews the progress of magnesium and its alloys applied in bone tissue and cardiovascular stents, and the prospect of the future research of magnesium-based biomaterials is discussed.

  3. Biodegradable foam plastics based on castor oil.

    Science.gov (United States)

    Wang, Hong Juan; Rong, Min Zhi; Zhang, Ming Qiu; Hu, Jing; Chen, Hui Wen; Czigány, Tibor

    2008-02-01

    In this work, a simple but effective approach was proposed for preparing biodegradable plastic foams with a high content of castor oil. First of all, castor oil reacted with maleic anhydride to produce maleated castor oil (MACO) without the aid of any catalyst. Then plastic foams were synthesized through free radical initiated copolymerization between MACO and diluent monomer styrene. With changes in MACO/St ratio and species of curing initiator, mechanical properties of MACO foams can be easily adjusted. In this way, biofoams with comparable compressive stress at 25% strain as commercial polyurethane (PU) foams were prepared, while the content of castor oil can be as high as 61 wt %. The soil burial tests further proved that the castor oil based foams kept the biodegradability of renewable resources despite the fact that some petrol-based components were introduced.

  4. Modeling ready biodegradability of fragrance materials.

    Science.gov (United States)

    Ceriani, Lidia; Papa, Ester; Kovarich, Simona; Boethling, Robert; Gramatica, Paola

    2015-06-01

    In the present study, quantitative structure activity relationships were developed for predicting ready biodegradability of approximately 200 heterogeneous fragrance materials. Two classification methods, classification and regression tree (CART) and k-nearest neighbors (kNN), were applied to perform the modeling. The models were validated with multiple external prediction sets, and the structural applicability domain was verified by the leverage approach. The best models had good sensitivity (internal ≥80%; external ≥68%), specificity (internal ≥80%; external 73%), and overall accuracy (≥75%). Results from the comparison with BIOWIN global models, based on group contribution method, show that specific models developed in the present study perform better in prediction than BIOWIN6, in particular for the correct classification of not readily biodegradable fragrance materials.

  5. Starch-based completely biodegradable polymer materials

    Directory of Open Access Journals (Sweden)

    2009-06-01

    Full Text Available Starch is a natural polymer which possesses many unique properties and some shortcoming simultaneously. Some synthetic polymers are biodegradable and can be tailor-made easily. Therefore, by combining the individual advantages of starch and synthetic polymers, starch-based completely biodegradable polymers (SCBP are potential for applications in biomedical and environmental fields. Therefore it received great attention and was extensively investigated. In this paper, the structure and characteristics of starch and some synthetic degradable polymers are briefly introduced. Then, the recent progress about the preparation of SCBP via physical blending and chemical modification is reviewed and discussed. At last, some examples have been presented to elucidate that SCBP are promising materials for various applications and their development is a good solution for reducing the consumption of petroleum resources and environmental problem.

  6. Catechol biodegradation kinetics using Candida parapsilopsis

    OpenAIRE

    Maurício Rigo; Ranulfo Monte Alegre; José Raniere Mazile Vidal Bezerra; Narjara Coelho; Reinaldo Gaspar Bastos

    2010-01-01

    This study evaluated the biodegradation of catechol by a yeast strain of Candida parapsilopsis in standard medium in Erlenmeyer flasks. Results shown that the highest concentration of catechol caused the longer lag period, demonstrating that acclimatized cultures could completely degrade an initial catechol concentration of 910 mg/L within 48 h. Haldane's model validated the experimental data adequately for growth kinetics over the studied catechol concentration ranges of 36 to 910 mg/L. The ...

  7. Kinetics of dimethoate biodegradation in bacterial system

    OpenAIRE

    Manisha DebMandal; Shyamapada Mandal; Nishith Kumar Pal

    2011-01-01

    The present study is an investigation on the kinetics of dimethoate biodegradation and an estimation of residual dimethoate in bacterial culture by spectrophotometry. The methylene chloride extract of the culture medium was used for determination of dimethoate through its reaction with 1 chloro-2, 4 dinitrobenzene to produce methylamine whose absorbance at 505 nm gave an estimation of dimethoate content. The dimethoate standard curve follows Beer’s law at 505 nm with a slope of 0.0129 absorba...

  8. Polymers from plants to develop biodegradable plastics.

    Science.gov (United States)

    Conrad, Udo

    2005-11-01

    Katrin Neumann et al. have recently shown that transgenic tobacco and potato plants can accumulate high levels of cyanophycin, a possible source for poly-aspartate. This work opens the way to the future production of biodegradable plastics using a plant-based production system. Several problems need to be overcome first, such as growth retardation as a result of cyanophycin accumulating in the cytosol, and a co-production system needs to be developed for economical reasons.

  9. Behaviour of biodegradable plastics in composting facilities.

    Science.gov (United States)

    Körner, I; Redemann, K; Stegmann, R

    2005-01-01

    Composting is a preferred treatment strategy for biodegradable plastics (BDPs). In this sense, the collection of BDPs together with organic household wastes is a highly discussed possibility. Under the aspect of the behaviour of BDPs in composting facilities, a telephone survey was carried out with selected composting facility operators. They were interviewed with respect to treated wastes, content of impurities, processes for impurity separation, experiences with biodegradable plastics and assumptions to the behaviour of biodegradable plastics in their facility. Forty percent of the facilities had some experiences with BDPs due to test runs, and also since the occurrence of BDPs in their waste was known. The majority of the operators expressed apprehension regarding an increase of impurities resulting from a combined collection of biowaste and BDPs. In the facilities, measures for the impurity separation from the biowaste were used in common practice - in 33% of the cases, separation of disturbing plastics was done before composting, in 33% after composting, and in 13% before and after composting. The most important separation processes for conventional plastics were sieving and manual sorting. In two cases air classification was also used. When asked about the separation possibility of the conventional but not of the biodegradable plastics in their facilities, the majority of operators were not in a position to comment or they replied that it was not an option. No problems were seen in most cases if the impurity separation follows composting. If impurity separation takes place before composting it was often assumed that the BDPs are mainly separated by sieving. In conclusion, in more than half of the cases, BDPs would not be composted if delivered to a composting facility. Under the actual conditions regarding the collection and the treatment/disposal possibilities, an application of BDPs seems to only be reasonable for clean (i.e., source separated on their own

  10. Fabrication of Biodegradable Polyester Nanocomposites by Electrospinning for Tissue Engineering

    Directory of Open Access Journals (Sweden)

    Zhi-Cai Xing

    2011-01-01

    Full Text Available Recently, nanocomposites have emerged as an efficient strategy to upgrade the structural and functional properties of synthetic polymers. Polyesters have attracted wide attention because of their biodegradability and biocompatibility. A logic consequence has been the introduction of natural extracellular matrix (ECM molecules, organic or inorganic nanostructures to biodegradable polymers to produce nanocomposites with enhanced properties. Consequently, the improvement of the interfacial adhesion between biodegradable polymers and natural ECM molecules or nanostructures has become the key technique in the fabrication of nanocomposites. Electrospinning has been employed extensively in the design and development of tissue engineering scaffolds to generate nanofibrous substrates of synthetic biodegradable polymers and to simulate the cellular microenvironment. In this paper, several types of biodegradable polyester nanocomposites were prepared by electrospinning, with the aim of being used as tissue engineering scaffolds. The combination of biodegradable nanofibrous polymers and natural ECM molecules or nanostructures opens new paradigms for tissue engineering applications.

  11. Titanate nanotube coatings on biodegradable photopolymer scaffolds

    Energy Technology Data Exchange (ETDEWEB)

    Beke, S., E-mail: szabolcs.beke@iit.it [Department of Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova (Italy); Kőrösi, L. [Department of Biotechnology, Nanophage Therapy Center, Enviroinvest Corporation, Kertváros u. 2, H-7632, Pécs (Hungary); Scarpellini, A. [Department of Nanochemistry, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova (Italy); Anjum, F.; Brandi, F. [Department of Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova (Italy)

    2013-05-01

    Rigid, biodegradable photopolymer scaffolds were coated with titanate nanotubes (TNTs) by using a spin-coating method. TNTs were synthesized by a hydrothermal process at 150 °C under 4.7 bar ambient pressure. The biodegradable photopolymer scaffolds were produced by mask-assisted excimer laser photocuring at 308 nm. For scaffold coating, a stable ethanolic TNT sol was prepared by a simple colloid chemical route without the use of any binding compounds or additives. Scanning electron microscopy along with elemental analysis revealed that the scaffolds were homogenously coated by TNTs. The developed TNT coating can further improve the surface geometry of fabricated scaffolds, and therefore it can further increase the cell adhesion. Highlights: ► Biodegradable scaffolds were produced by mask-assisted UV laser photocuring. ► Titanate nanotube deposition was carried out without binding compounds or additives. ► The titanate nanotube coating can further improve the surface geometry of scaffolds. ► These reproducible platforms will be of high importance for biological applications.

  12. Bacterial production of the biodegradable plastics polyhydroxyalkanoates.

    Science.gov (United States)

    Urtuvia, Viviana; Villegas, Pamela; González, Myriam; Seeger, Michael

    2014-09-01

    Petroleum-based plastics constitute a major environmental problem due to their low biodegradability and accumulation in various environments. Therefore, searching for novel biodegradable plastics is of increasing interest. Microbial polyesters known as polyhydroxyalkanoates (PHAs) are biodegradable plastics. Life cycle assessment indicates that PHB is more beneficial than petroleum-based plastics. In this report, bacterial production of PHAs and their industrial applications are reviewed and the synthesis of PHAs in Burkholderia xenovorans LB400 is described. PHAs are synthesized by a large number of microorganisms during unbalanced nutritional conditions. These polymers are accumulated as carbon and energy reserve in discrete granules in the bacterial cytoplasm. 3-hydroxybutyrate and 3-hydroxyvalerate are two main PHA units among 150 monomers that have been reported. B. xenovorans LB400 is a model bacterium for the degradation of polychlorobiphenyls and a wide range of aromatic compounds. A bioinformatic analysis of LB400 genome indicated the presence of pha genes encoding enzymes of pathways for PHA synthesis. This study showed that B. xenovorans LB400 synthesize PHAs under nutrient limitation. Staining with Sudan Black B indicated the production of PHAs by B. xenovorans LB400 colonies. The PHAs produced were characterized by GC-MS. Diverse substrates for the production of PHAs in strain LB400 were analyzed.

  13. Water-curable and biodegradable prepolymers.

    Science.gov (United States)

    Kobayashi, H; Hyon, S H; Ikada, Y

    1991-12-01

    In an attempt to develop biodegradable polymers which can be shaped in situ and adhere to living tissues, we synthesized esterurethane prepolymers which can be cured upon contact with water in living tissues. First, D,L-lactide polymerization or D,L-lactide-epsilon-caprolactone (50:50) copolymerization was carried out using ethylene glycol or poly(ethylene glycol) as initiator to obtain hydroxyl-terminated biodegradable polyesters. They were then reacted with an excess of diisocyanate such as hexamethylene diisocyanate, toluylene diisocyanate, and diphenylmethane diisocyanate to introduce a reactive isocyanate group to both of the end groups of the polyesters. The isocyanate-terminated prepolymers could be cured in the presence of water and the cured polymers were degraded by hydrolysis both in vitro and in vivo. It was found that the presence of appropriate amounts of hydrophilic units in the main chain was essential for giving a high curing rate and a high degradation rate for the biodegradable urethane prepolymers. The tissue responses to the cured polymers were not severe.

  14. Biodegradation of sedimentary organic matter associated with coalbed methane in the Powder River and San Juan Basins, U.S.A.

    Energy Technology Data Exchange (ETDEWEB)

    Formolo, Michael; Petsch, Steven [Department of Geosciences, University of Massachusetts, Amherst, MA, 01003-9297 (United States); Martini, Anna [Department of Geology, Amherst College, Amherst, MA, 01002 (United States)

    2008-10-02

    The Powder River Basin and San Juan Basin, U.S.A., are two of the most productive coalbed methane reserves in the world. Of particular interest is the microbial biodegradation of coal beds associated with this natural gas production. Biogenic methane production is indicated as a significant component to the total gas resources in the San Juan Basin, and as the nearly sole source for the shallow coals of the Powder River Basin. Molecular and isotopic signatures indicate a microbial origin for the gas. Geochemical characteristics of formation waters, such as elevated alkalinity and {sup 13}C-enriched dissolved inorganic carbon (DIC), further support extensive microbial degradation of coal organic matter associated with methanogenesis. Extractable organic matter isolated from coals in both basins point to patterns of hydrocarbon biodegradation in coals restricted to specific depths. To some extent, biodegradation patterns are similar to those observed in methanogenic, biodegraded black shales of the mid-continent of the United States. Specifically, both coals and shales exhibit near-quantitative removal of straight-chain and acyclic isoprenoid hydrocarbons. However, loss of aromatic hydrocarbons in the coals proceeds prior to the extensive removal of the saturated hydrocarbons, in contrast to what is conventionally observed in biodegraded petroleum systems or in black shales. In addition, previous thermal maturation histories in both the Fruitland and Fort Union coalbed methane systems have little impact on more recent hydrocarbon biodegradation. Instead, localized hydrologic conditions and subsurface geology likely play important roles in controlling the extents of biodegradation and methanogenesis. These results suggest that biodegradation of hydrocarbons coupled with methanogenesis may develop regardless of organic matter source across a range of inherited thermal maturities. (author)

  15. Phase Contrast Imaging

    DEFF Research Database (Denmark)

    1996-01-01

    with a simple one-to-one mapping between resolution elements of a spatial phase modulator and resolution elements of the generated intensity pattern is provided. According to the invention a method is provided for synthesizing an intensity pattern with low loss of electromagnetic energy, comprising spatial...... modulation of electromagnetic radiation with a spatial phase mask for modulation of the phase of the incident eletromagnetic radiation by phasor values of individual resolution elements of the spatial phase mask, each phasor value being determined in such a way that the values of the Fourier transformed......The invention relates to a method and a system for synthesizing a prescribed intensity pattern based on phase contrast imaging that is not based on the assumption of prior art methods that the pahase shift phi is less than 1 radian. An improved method based on a simple imaging operation...

  16. Biodegradation of low-density polyethylene (LDPE by mixed culture of Lysinibacillus xylanilyticus and Aspergillus niger in soil.

    Directory of Open Access Journals (Sweden)

    Atefeh Esmaeili

    Full Text Available In this study, two strains of Aspergillus sp. and Lysinibacillus sp. with remarkable abilities to degrade low-density polyethylene (LDPE were isolated from landfill soils in Tehran using enrichment culture and screening procedures. The biodegradation process was performed for 126 days in soil using UV- and non-UV-irradiated pure LDPE films without pro-oxidant additives in the presence and absence of mixed cultures of selected microorganisms. The process was monitored by measuring the microbial population, the biomass carbon, pH and respiration in the soil, and the mechanical properties of the films. The carbon dioxide measurements in the soil showed that the biodegradation in the un-inoculated treatments were slow and were about 7.6% and 8.6% of the mineralisation measured for the non-UV-irradiated and UV-irradiated LDPE, respectively, after 126 days. In contrast, in the presence of the selected microorganisms, biodegradation was much more efficient and the percentages of biodegradation were 29.5% and 15.8% for the UV-irradiated and non-UV-irradiated films, respectively. The percentage decrease in the carbonyl index was higher for the UV-irradiated LDPE when the biodegradation was performed in soil inoculated with the selected microorganisms. The percentage elongation of the films decreased during the biodegradation process. The Fourier transform infra-red (FT-IR, x-ray diffraction (XRD and scanning electron microscopy (SEM were used to determine structural, morphological and surface changes on polyethylene. These analyses showed that the selected microorganisms could modify and colonise both types of polyethylene. This study also confirmed the ability of these isolates to utilise virgin polyethylene without pro-oxidant additives and oxidation pretreatment, as the carbon source.

  17. Biodegradation of low-density polyethylene (LDPE) by mixed culture of Lysinibacillus xylanilyticus and Aspergillus niger in soil.

    Science.gov (United States)

    Esmaeili, Atefeh; Pourbabaee, Ahmad Ali; Alikhani, Hossein Ali; Shabani, Farzin; Esmaeili, Ensieh

    2013-01-01

    In this study, two strains of Aspergillus sp. and Lysinibacillus sp. with remarkable abilities to degrade low-density polyethylene (LDPE) were isolated from landfill soils in Tehran using enrichment culture and screening procedures. The biodegradation process was performed for 126 days in soil using UV- and non-UV-irradiated pure LDPE films without pro-oxidant additives in the presence and absence of mixed cultures of selected microorganisms. The process was monitored by measuring the microbial population, the biomass carbon, pH and respiration in the soil, and the mechanical properties of the films. The carbon dioxide measurements in the soil showed that the biodegradation in the un-inoculated treatments were slow and were about 7.6% and 8.6% of the mineralisation measured for the non-UV-irradiated and UV-irradiated LDPE, respectively, after 126 days. In contrast, in the presence of the selected microorganisms, biodegradation was much more efficient and the percentages of biodegradation were 29.5% and 15.8% for the UV-irradiated and non-UV-irradiated films, respectively. The percentage decrease in the carbonyl index was higher for the UV-irradiated LDPE when the biodegradation was performed in soil inoculated with the selected microorganisms. The percentage elongation of the films decreased during the biodegradation process. The Fourier transform infra-red (FT-IR), x-ray diffraction (XRD) and scanning electron microscopy (SEM) were used to determine structural, morphological and surface changes on polyethylene. These analyses showed that the selected microorganisms could modify and colonise both types of polyethylene. This study also confirmed the ability of these isolates to utilise virgin polyethylene without pro-oxidant additives and oxidation pretreatment, as the carbon source.

  18. "Rational" management of dichlorophenols biodegradation by the microalga Scenedesmus obliquus.

    Science.gov (United States)

    Papazi, Aikaterini; Kotzabasis, Kiriakos

    2013-01-01

    The microalga Scenedesmus obliquus exhibited the ability to biodegrade dichlorophenols (dcps) under specific autotrophic and mixotrophic conditions. According to their biodegradability, the dichlorophenols used can be separated into three distinct groups. Group I (2,4-dcp and 2,6 dcp - no meta-substitution) consisted of quite easily degraded dichlorophenols, since both chloride substituents are in less energetically demanding positions. Group II (2,3-dcp, 2,5-dcp and 3,4-dcp - one meta-chloride) was less susceptible to biodegradation, since one of the two substituents, the meta one, required higher energy for C-Cl-bond cleavage. Group III (3,5-dcp - two meta-chlorides) could not be biodegraded, since both chlorides possessed the most energy demanding positions. In general, when the dcp-toxicity exceeded a certain threshold, the microalga increased the energy offered for biodegradation and decreased the energy invested for biomass production. As a result, the biodegradation per cell volume of group II (higher toxicity) was higher, than group I (lower toxicity) and the biodegradation of dichlorophenols (higher toxicity) was higher than the corresponding monochlorophenols (lower toxicity). The participation of the photosynthetic apparatus and the respiratory mechanism of microalga to biodegrade the group I and the group II, highlighted different bioenergetic strategies for optimal management of the balance between dcp-toxicity, dcp-biodegradability and culture growth. Additionally, we took into consideration the possibility that the intermediates of each dcp-biodegradation pathway could influence differently the whole biodegradation procedures. For this reason, we tested all possible combinations of phenolic intermediates to check cometabolic interactions. The present contribution bring out the possibility of microalgae to operate as "smart" bioenergetic "machines", that have the ability to continuously "calculate" the energy reserves and "use" the most energetically

  19. Degradation of Oxo-Biodegradable Plastic by Pleurotus ostreatus

    OpenAIRE

    José Maria Rodrigues da Luz; Sirlaine Albino Paes; Mateus Dias Nunes; Marliane de Cássia Soares da Silva; Maria Catarina Megumi Kasuya

    2013-01-01

    Growing concerns regarding the impact of the accumulation of plastic waste over several decades on the environmental have led to the development of biodegradable plastic. These plastics can be degraded by microorganisms and absorbed by the environment and are therefore gaining public support as a possible alternative to petroleum-derived plastics. Among the developed biodegradable plastics, oxo-biodegradable polymers have been used to produce plastic bags. Exposure of this waste plastic to ul...

  20. Novel nano-sized MR contrast agent mediates strong tumor contrast enhancement in an oncogene-driven breast cancer model.

    Directory of Open Access Journals (Sweden)

    Per-Olof Eriksson

    Full Text Available The current study was carried out to test the potential of a new nanomaterial (Spago Pix as a macromolecular magnetic MR contrast agent for tumor detection and to verify the presence of nanomaterial in tumor tissue. Spago Pix, synthesized by Spago Nanomedical AB, is a nanomaterial with a globular shape, an average hydrodynamic diameter of 5 nm, and a relaxivity (r1 of approximately 30 (mM Mn-1 s-1 (60 MHz. The material consists of an organophosphosilane hydrogel with strongly chelated manganese (II ions and a covalently attached PEG surface layer. In vivo MRI of the MMTV-PyMT breast cancer model was performed on a 3 T clinical scanner. Tissues were thereafter analyzed for manganese and silicon content using inductively coupled plasma-atomic emission spectroscopy (ICP-AES. The presence of nanomaterial in tumor and muscle tissue was assessed using an anti-PEG monoclonal antibody. MR imaging of tumor-bearing mice (n = 7 showed a contrast enhancement factor of 1.8 (tumor versus muscle at 30 minutes post-administration. Contrast was retained and further increased 2-4 hours after administration. ICP-AES and immunohistochemistry confirmed selective accumulation of nanomaterial in tumor tissue. A blood pharmacokinetics analysis showed that the concentration of Spago Pix gradually decreased over the first hour, which was in good agreement with the time frame in which the accumulation in tumor occurred. In summary, we demonstrate that Spago Pix selectively enhances MR tumor contrast in a clinically relevant animal model. Based on the generally higher vascular leakiness in malignant compared to benign tissue lesions, Spago Pix has the potential to significantly improve cancer diagnosis and characterization by MRI.

  1. Influence of inorganic salt on aerobic biodegradability of dyestuffs

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    this paper, the influence of inorganic salt on aerobic biodegradability of dyestuffs was studied by means of semicontinuous activated sludge method. It was found that: biodegradability of dyestuffs would decrease with the increase of the concentration of NaCl; however, biodegradability in the condition of NaCl = 30 g/L was better than that in the condition of NaCl =15 g/L; in the three NaCl conditions, biodegradability of tasted dyestuffs followed the following order: NaCl= 0 g/L > NaCl= 30g/L>NaCl= 15 g/L.

  2. Biodegradation of flax fiber reinforced poly lactic acid

    Directory of Open Access Journals (Sweden)

    2010-07-01

    Full Text Available Woven and nonwoven flax fiber reinforced poly lactic acid (PLA biocomposites were prepared with amphiphilic additives as accelerator for biodegradation. The prepared composites were buried in farmland soil for biodegradability studies. Loss in weight of the biodegraded composite samples was determined at different time intervals. The surface morphology of the biodegraded composites was studied with scanning electron microscope (SEM. Results indicated that in presence of mandelic acid, the composites showed accelerated biodegradation with 20–25% loss in weight after 50–60 days. On the other hand, in presence of dicumyl peroxide (as additive, biodegradation of the composites was relatively slow as confirmed by only 5–10% loss in weight even after 80–90 days. This was further confirmed by surface morphology of the biodegraded composites. We have attempted to show that depending on the end uses, we can add different amphiphilic additives for delayed or accelerated biodegradability. This work gives us the idea of biodegradation of materials from natural fiber reinforced PLA composites when discarded carelessly in the environment instead of proper waste disposal site.

  3. Silicon microneedles array with biodegradable tips for transdermal drug delivery

    CERN Document Server

    Chen, B; Tay, Francis; Wong, Y T; Iliescu, C

    2008-01-01

    This paper presents the fabrication process, characterization results and basic functionality of silicon microneedles array with biodegradable tips. In order to avoid the main problems related to silicon microneedles : broking of the top part of the needles inside the skin, a simple solution can be fabrication of microneedles array with biodegradable tips. The silicon microneedles array was fabricated by using reactive ion etching while the biodegradable tips were performed using and anodization process that generates selectively porous silicon only on the top part of the skin. The paper presents also the results of in vitro release of calcein using microneedles array with biodegradable tips

  4. In vitro analysis of PDZ-dependent CFTR macromolecular signaling complexes.

    Science.gov (United States)

    Wu, Yanning; Wang, Shuo; Li, Chunying

    2012-08-13

    has been shown to be of functional significance, suggesting that PDZ scaffold proteins may facilitate formation of CFTR macromolecular signaling complexes for specific/selective and efficient signaling in cells(16-18). Multiple biochemical assays have been developed to study CFTR-involving protein interactions, such as co-immunoprecipitation, pull-down assay, pair-wise binding assay, colorimetric pair-wise binding assay, and macromolecular complex assembly assay(16-19,28,29). Here we focus on the detailed procedures of assembling a PDZ motif-dependent CFTR-containing macromolecular complex in vitro, which is used extensively by our laboratory to study protein-protein or domain-domain interactions involving CFTR(16-19,28,29).

  5. Chemiluminescence-imaging detection of DNA on a solid-phase membrane by using a peroxidase-labeled macromolecular probe.

    Science.gov (United States)

    Azam, Md Golam; Yamasuji, Mutsumi; Krawczyk, Tomasz; Shibata, Takayuki; Kabashima, Tsutomu; Kai, Masaaki

    2015-07-01

    We have developed a novel method for sensitive chemiluminescence (CL)-imaging detection of DNA by using a macromolecular probe synthesized by attaching multiple molecules of horseradish peroxidase (HRP) and biotin in dextran backbone. The probe formed a macromolecular assembly by binding to streptavidin which specifically recognized biotinylated complementary DNA, which was hybridized to a target DNA on a solid-phase membrane. This methodology was applied to CL-imaging detection of a synthetic telomere DNA (TTAGGG)10 and human telomere DNA by using the CL probe comprising of dextranT2000 (MW=ca. 2000kDa) bonded to approximately 42 molecules of HRP and 210 molecules of biotin. The human telomere DNA in a small number of buccal mucous cells (ca. 70 cell numbers) of cheek tissue was quantitatively determined by the proposed CL detection method that afforded approximately 10 times higher sensitivity than that of the conventional CL method using commercially available HRP-avidin probe.

  6. 08B1-1: an automated beamline for macromolecular crystallography experiments at the Canadian Light Source.

    Science.gov (United States)

    Fodje, Michel; Grochulski, Pawel; Janzen, Kathryn; Labiuk, Shaunivan; Gorin, James; Berg, Russ

    2014-05-01

    Beamline 08B1-1 is a recently commissioned bending-magnet beamline at the Canadian Light Source. The beamline is designed for automation and remote access. Together with the undulator-based beamline 08ID-1, they constitute the Canadian Macromolecular Crystallography Facility. This paper describes the design, specifications, hardware and software of beamline 08B1-1. A few scientific results using data obtained at the beamline will be highlighted.

  7. A facile metal-free "grafting-from" route from acrylamide-based substrate toward complex macromolecular combs

    KAUST Repository

    Zhao, Junpeng

    2013-01-01

    High-molecular-weight poly(N,N-dimethylacrylamide-co-acrylamide) was used as a model functional substrate to investigate phosphazene base (t-BuP 4)-promoted metal-free anionic graft polymerization utilizing primary amide moieties as initiating sites. The (co)polymerization of epoxides was proven to be effective, leading to macromolecular combs with side chains being single- or double-graft homopolymer, block copolymer and statistical copolymer. © 2013 The Royal Society of Chemistry.

  8. ESTIMATION OF BIODEGRADATION AND BIO-CORROSION OF MATERIALS IN NATURAL ENVIRONMENTS

    Directory of Open Access Journals (Sweden)

    Varchenko E. A.

    2014-12-01

    Full Text Available The article analyzes the problems that arise when evaluating biodegradation of materials, items, structures and products in natural environments.. The causes of biodegradations are revealed

  9. A decade of user operation on the macromolecular crystallography MAD beamline ID14-4 at the ESRF.

    Science.gov (United States)

    McCarthy, Andrew A; Brockhauser, Sandor; Nurizzo, Didier; Theveneau, Pascal; Mairs, Trevor; Spruce, Darren; Guijarro, Matias; Lesourd, Marc; Ravelli, Raimond B G; McSweeney, Sean

    2009-11-01

    ID14-4 at the ESRF is the first tunable undulator-based macromolecular crystallography beamline that can celebrate a decade of user service. During this time ID14-4 has not only been instrumental in the determination of the structures of biologically important molecules but has also contributed significantly to the development of various instruments, novel data collection schemes and pioneering radiation damage studies on biological samples. Here, the evolution of ID14-4 over the last decade is presented, and some of the major improvements that were carried out in order to maintain its status as one of the most productive macromolecular crystallography beamlines are highlighted. The experimental hutch has been upgraded to accommodate a high-precision diffractometer, a sample changer and a large CCD detector. More recently, the optical hutch has been refurbished in order to improve the X-ray beam quality on ID14-4 and to incorporate the most modern and robust optical elements used at other ESRF beamlines. These new optical elements will be described and their effect on beam stability discussed. These studies may be useful in the design, construction and maintenance of future X-ray beamlines for macromolecular crystallography and indeed other applications, such as those planned for the ESRF upgrade.

  10. A decade of user operation on the macromolecular crystallography MAD beamline ID14-4 at the ESRF

    Energy Technology Data Exchange (ETDEWEB)

    McCarthy, Andrew A., E-mail: andrewmc@embl.fr; Brockhauser, Sandor [European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042 Grenoble (France); Unit of Virus Host Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9 (France); Nurizzo, Didier; Theveneau, Pascal; Mairs, Trevor; Spruce, Darren; Guijarro, Matias; Lesourd, Marc [European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38042 Grenoble (France); Ravelli, Raimond B. G. [European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042 Grenoble (France); McSweeney, Sean [European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38042 Grenoble (France)

    2009-11-01

    The improvement of the X-ray beam quality achieved on ID14-4 by the installation of new X-ray optical elements is described. ID14-4 at the ESRF is the first tunable undulator-based macromolecular crystallography beamline that can celebrate a decade of user service. During this time ID14-4 has not only been instrumental in the determination of the structures of biologically important molecules but has also contributed significantly to the development of various instruments, novel data collection schemes and pioneering radiation damage studies on biological samples. Here, the evolution of ID14-4 over the last decade is presented, and some of the major improvements that were carried out in order to maintain its status as one of the most productive macromolecular crystallography beamlines are highlighted. The experimental hutch has been upgraded to accommodate a high-precision diffractometer, a sample changer and a large CCD detector. More recently, the optical hutch has been refurbished in order to improve the X-ray beam quality on ID14-4 and to incorporate the most modern and robust optical elements used at other ESRF beamlines. These new optical elements will be described and their effect on beam stability discussed. These studies may be useful in the design, construction and maintenance of future X-ray beamlines for macromolecular crystallography and indeed other applications, such as those planned for the ESRF upgrade.

  11. The status of the macromolecular crystallography beamlines at the European Synchrotron Radiation Facility

    Science.gov (United States)

    Mueller-Dieckmann, Christoph; Bowler, Matthew W.; Carpentier, Philippe; Flot, David; McCarthy, Andrew A.; Nanao, Max H.; Nurizzo, Didier; Pernot, Petra; Popov, Alexander; Round, Adam; Royant, Antoine; de Sanctis, Daniele; von Stetten, David; Leonard, Gordon A.

    2015-04-01

    The European Synchrotron Radiation Facility (ESRF) is the oldest and most powerful 3rd generation synchrotron in Europe, providing X-rays to more than 40 experimental stations welcoming several thousand researchers per year. A major success story has been the ESRF's facilities for macromolecular crystallography (MX). These are grouped around 3 straight sections: On ID23 canted undulators accommodate ID23-1, a mini-focus tuneable energy end station and ID23-2, the world's first micro-focus beamline dedicated to MX; ID29 houses a single, mini-focus, tuneable energy end station; ID30 will provide three end stations for MX due in operation from mid-2014 to early 2015. Here, one branch of a canted X-ray source feeds two fixed-energy end stations (MASSIF-1, MASSIF-3). The second feeds ID30B, a variable focus, tuneable energy beamline. MASSIF-1 is optimised for automatic high-throughput experiments requiring a relatively large beam size at the sample position, MASSIF-3 is a high-intensity, micro-focus facility designed to complement ID23-2. All end stations are highly automated, equipped with sample mounting robots and large area, fast-readout photon-counting detectors. Experiment control and tracking is achieved via a combination of the MXCuBE2 graphical user interface and the ISPyB database, the former allowing user-friendly control of all beamline components, the latter providing data tracking before, after and during experiments.

  12. A test of macromolecular crystallization in microgravity: large well ordered insulin crystals.

    Science.gov (United States)

    Borgstahl, G E; Vahedi-Faridi, A; Lovelace, J; Bellamy, H D; Snell, E H

    2001-08-01

    Crystals of insulin grown in microgravity on Space Shuttle Mission STS-95 were extremely well ordered and unusually large (many >2 mm). The physical characteristics of six microgravity and six earth-grown crystals were examined by X-ray analysis employing superfine phi slicing and unfocused synchrotron radiation. This experimental setup allowed hundreds of reflections to be precisely examined from each crystal in a short period of time. The microgravity crystals were on average 34 times larger, had sevenfold lower mosaicity, had 54-fold higher reflection peak heights and diffracted to significantly higher resolution than their earth-grown counterparts. A single mosaic domain model could account for the observed reflection profiles in microgravity crystals, whereas data from earth crystals required a model with multiple mosaic domains. This statistically significant and unbiased characterization indicates that the microgravity environment was useful for the improvement of crystal growth and the resultant diffraction quality in insulin crystals and may be similarly useful for macromolecular crystals in general.

  13. RoboDiff: combining a sample changer and goniometer for highly automated macromolecular crystallography experiments

    Science.gov (United States)

    Nurizzo, Didier; Bowler, Matthew W.; Caserotto, Hugo; Dobias, Fabien; Giraud, Thierry; Surr, John; Guichard, Nicolas; Papp, Gergely; Guijarro, Matias; Mueller-Dieckmann, Christoph; Flot, David; McSweeney, Sean; Cipriani, Florent; Theveneau, Pascal; Leonard, Gordon A.

    2016-01-01

    Automation of the mounting of cryocooled samples is now a feature of the majority of beamlines dedicated to macromolecular crystallography (MX). Robotic sample changers have been developed over many years, with the latest designs increasing capacity, reliability and speed. Here, the development of a new sample changer deployed at the ESRF beamline MASSIF-1 (ID30A-1), based on an industrial six-axis robot, is described. The device, named RoboDiff, includes a high-capacity dewar, acts as both a sample changer and a high-accuracy goniometer, and has been designed for completely unattended sample mounting and diffraction data collection. This aim has been achieved using a high level of diagnostics at all steps of the process from mounting and characterization to data collection. The RoboDiff has been in service on the fully automated endstation MASSIF-1 at the ESRF since September 2014 and, at the time of writing, has processed more than 20 000 samples completely automatically. PMID:27487827

  14. The Effect of Attractive Interactions and Macromolecular Crowding on Crystallins Association.

    Directory of Open Access Journals (Sweden)

    Jiachen Wei

    Full Text Available In living systems proteins are typically found in crowded environments where their effective interactions strongly depend on the surrounding medium. Yet, their association and dissociation needs to be robustly controlled in order to enable biological function. Uncontrolled protein aggregation often causes disease. For instance, cataract is caused by the clustering of lens proteins, i.e., crystallins, resulting in enhanced light scattering and impaired vision or blindness. To investigate the molecular origins of cataract formation and to design efficient treatments, a better understanding of crystallin association in macromolecular crowded environment is needed. Here we present a theoretical study of simple coarse grained colloidal models to characterize the general features of how the association equilibrium of proteins depends on the magnitude of intermolecular attraction. By comparing the analytic results to the available experimental data on the osmotic pressure in crystallin solutions, we identify the effective parameters regimes applicable to crystallins. Moreover, the combination of two models allows us to predict that the number of binding sites on crystallin is small, i.e. one to three per protein, which is different from previous estimates. We further observe that the crowding factor is sensitive to the size asymmetry between the reactants and crowding agents, the shape of the protein clusters, and to small variations of intermolecular attraction. Our work may provide general guidelines on how to steer the protein interactions in order to control their association.

  15. Distinct Contribution of Electrostatics, Initial Conformational Ensemble, and Macromolecular Stability in RNA Folding

    Energy Technology Data Exchange (ETDEWEB)

    Laederach,A.; Shcherbakova, I.; Jonikas, M.; Altman, R.; Brenowitz, M.

    2007-01-01

    We distinguish the contribution of the electrostatic environment, initial conformational ensemble, and macromolecular stability on the folding mechanism of a large RNA using a combination of time-resolved 'Fast Fenton' hydroxyl radical footprinting and exhaustive kinetic modeling. This integrated approach allows us to define the folding landscape of the L-21 Tetrahymena thermophila group I intron structurally and kinetically from its earliest steps with unprecedented accuracy. Distinct parallel pathways leading the RNA to its native form upon its Mg2+-induced folding are observed. The structures of the intermediates populating the pathways are not affected by variation of the concentration and type of background monovalent ions (electrostatic environment) but are altered by a mutation that destabilizes one domain of the ribozyme. Experiments starting from different conformational ensembles but folding under identical conditions show that whereas the electrostatic environment modulates molecular flux through different pathways, the initial conformational ensemble determines the partitioning of the flux. This study showcases a robust approach for the development of kinetic models from collections of local structural probes.

  16. Macromolecular depletion modulates the binding of red blood cells to activated endothelial cells.

    Science.gov (United States)

    Yang, Yang; Koo, Stephanie; Lin, Cheryl Shuyi; Neu, Björn

    2010-09-01

    Adhesion of red blood cells (RBCs) to endothelial cells (ECs) is usually insignificant but an enhanced adhesion has been observed in various diseases associated with vascular complications. This abnormal adhesion under pathological conditions such as sickle cell disease has been correlated with increased levels of various plasma proteins but the detailed underlying mechanism(s) remains unclear. Usually it is assumed that the proadhesive effects of plasma proteins originate from ligand interactions cross-linking receptors on adjacent cells, but explicit results detailing binding sites or receptors for some proteins (e.g., fibrinogen) on either RBC or EC surfaces that would support this model are missing. In this study, the authors tested whether there is an alternative mechanism. Their results demonstrate that dextran 2 MDa promotes the adhesion of normal RBCs to thrombin-activated ECs and that this effect becomes more pronounced with increasing thrombin concentration or with prolonged thrombin incubation time. It is concluded that depletion interaction originating from nonadsorbing macromolecules (i.e., dextran) can modulate the adhesion of red blood cells to thrombin-activated EC. This study thereby suggests macromolecular depletion as an alternative mechanism for the adhesion-promoting effects of nonadsorbing plasma proteins. These findings should not only aid in getting a better understanding of diseases associated with vascular complications but should also have many potential applications in biomedical or biotechnological areas that require the control of cell-cell or cell surface interactions.

  17. Optimizing the spatial distribution of dose in X-ray macromolecular crystallography.

    Science.gov (United States)

    Zeldin, Oliver B; Gerstel, Markus; Garman, Elspeth F

    2013-01-01

    X-ray data collection for macromolecular crystallography can lead to highly inhomogeneous distributions of dose within the crystal volume for cases when the crystal is larger than the beam or when the beam is non-uniform (gaussian-like), particularly when crystal rotation is fully taken into account. Here the spatial distribution of dose is quantitatively modelled in order to compare the effectiveness of two dose-spreading data-collection protocols: helical scanning and translational collection. Their effectiveness in reducing the peak dose per unit diffraction is investigated via simulations for four common crystal shapes (cube, plate, long and short needles) and beams with a wide range of full width half maximum values. By inspection of the chosen metric, it is concluded that the optimum strategy is always to use as flat (top-hat) a beam as possible and to either match the beam size in both dimensions to the crystal, or to perform a helical scan with a beam which is narrow along the rotation axis and matched to the crystal size along the perpendicular axis. For crystal shapes where this is not possible, the reduction in peak dose per unit diffraction achieved through dose spreading is quantified and tabulated as a reference for experimenters.

  18. Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection.

    Science.gov (United States)

    Bowler, Matthew W; Guijarro, Matias; Petitdemange, Sebastien; Baker, Isabel; Svensson, Olof; Burghammer, Manfred; Mueller-Dieckmann, Christoph; Gordon, Elspeth J; Flot, David; McSweeney, Sean M; Leonard, Gordon A

    2010-08-01

    Crystals of biological macromolecules often exhibit considerable inter-crystal and intra-crystal variation in diffraction quality. This requires the evaluation of many samples prior to data collection, a practice that is already widespread in macromolecular crystallography. As structural biologists move towards tackling ever more ambitious projects, new automated methods of sample evaluation will become crucial to the success of many projects, as will the availability of synchrotron-based facilities optimized for high-throughput evaluation of the diffraction characteristics of samples. Here, two examples of the types of advanced sample evaluation that will be required are presented: searching within a sample-containing loop for microcrystals using an X-ray beam of 5 microm diameter and selecting the most ordered regions of relatively large crystals using X-ray beams of 5-50 microm in diameter. A graphical user interface developed to assist with these screening methods is also presented. For the case in which the diffraction quality of a relatively large crystal is probed using a microbeam, the usefulness and implications of mapping diffraction-quality heterogeneity (diffraction cartography) are discussed. The implementation of these techniques in the context of planned upgrades to the ESRF's structural biology beamlines is also presented.

  19. Competitive interactions of ligands and macromolecular crowders with maltose binding protein.

    Directory of Open Access Journals (Sweden)

    Andrew C Miklos

    Full Text Available Cellular signaling involves a cascade of recognition events occurring in a complex environment with high concentrations of proteins, polysaccharides, and other macromolecules. The influence of macromolecular crowders on protein binding affinity through hard-core repulsion is well studied, and possible contributions of protein-crowder soft attraction have been implicated recently. Here we present direct evidence for weak association of maltose binding protein (MBP with a polysaccharide crowder Ficoll, and that this association effectively competes with the binding of the natural ligand, maltose. Titration data over wide ranges of maltose and Ficoll concentrations fit well with a three-state competitive binding model. Broadening of MBP (1H-(15N TROSY spectra by the addition of Ficoll indicates weak protein-crowder association, and subsequent recovery of sharp NMR peaks upon addition of maltose indicates that the interactions of the crowder and the ligand with MBP are competitive. We hypothesize that, in the Escherichia coli periplasm, the competitive interactions of polysaccharides and maltose with MBP could allow MBP to shuttle between the peptidoglycan attached to the outer membrane and the ATP-binding cassette transporter in the inner membrane.

  20. Characterization of PEG-Like Macromolecular Coatings on Plasma Modified NiTi Alloy

    Science.gov (United States)

    Yang, Jun; Gao, Jiacheng; Chang, Peng; Wang, Jianhua

    2008-04-01

    A poly (ethylene glycol) (PEG-like) coating was developed to improve the biocompatibility of Nickel-Titanium (NiTi) alloy implants. The PEG-like macromolecular coatings were deposited on NiTi substrates at a room temperature of 298 K through a ECR (electron-cyclotron resonance) cold-plasma enhanced chemical vapor deposition method using tetraglyme (CH3-O-(CH2-CH2-O)4-CH3) as a precursor. A power supply with a frequency of 2.45 GHz was applied to ignite the plasma with Ar(argon) used as the carrier gas. Based on the atomic force microscopy (AFM) studies, a thin smooth coating on NiTi substrates with highly amorphous functional groups on the modified NiTi surfaces were mainly the same accumulated stoichiometric ratio of C and O with PEG. The vitro studies showed that platelet-rich plasma (PRP) adsorption on the modified NiTi alloy surface was significantly reduced. This study indicated that plasma surface modification changes the surface components of NiTi alloy and subsequently improves its biocompatibility.

  1. Characterization of PEG-Like Macromolecular Coatings on Plasma Modified NiTi Alloy

    Institute of Scientific and Technical Information of China (English)

    YANG Jun; GAO Jiacheng; CHANG Peng; WANG Jianhua

    2008-01-01

    A poly(ethylene glycol) (PEG-like) coating was developed to improve the biocompatibility of Nickel-Titanium (NiTi) alloy implants. The PEG-like macromolecular coatings were deposited on NiTi substrates at a room temperature of 298 K through a ECR (electron-cyclotron resonance) cold-plasma .enhanced chemical vapor deposition method using tetraglyme (CH3-O(CH2-CH2-O)4-CH3) as a precursor. A power supply with a frequency of 2.45 GHz was applied to ignite the plasma with Ar(argon) used as the carrier gas. Based on the atomic force microscopy (AFM) studies, a thin smooth coating on NiTi substrates with highly amorphous functional groups on the modified NiTi surfaces were mainly the same accumulated stoichiometric ratio of C and O with PEG. The vitro studies showed that platelet-rich plasma (PRP) adsorption on the modified NiTi alloy surface was significantly reduced. This study indicated that plasma surface modification changes the surface components of NiTi alloy and subsequently improves its biocompatibility.

  2. Effects of sound exposure on the growth and intracellular macromolecular synthesis of E. coli k-12

    Directory of Open Access Journals (Sweden)

    Shaobin Gu

    2016-04-01

    Full Text Available Microbes, as one of the primary producers of the biosphere, play an important role in ecosystems. Exploring the mechanism of adaptation and resistance of microbial population to various environmental factors has come into focus in the fields of modern microbial ecology and molecular ecology. However, facing the increasingly serious problem of acoustic pollution, very few efforts have been put forth into studying the relation of single cell organisms and sound field exposure. Herein, we studied the biological effects of sound exposure on the growth of E. coli K-12 with different acoustic parameters. The effects of sound exposure on the intracellular macromolecular synthesis and cellular morphology of E. coli K-12 were also analyzed and discussed. Experimental results indicated that E. coli K-12 exposed to sound waves owned a higher biomass and a faster specific growth rate compared to the control group. Also, the average length of E. coli K-12 cells increased more than 27.26%. The maximum biomass and maximum specific growth rate of the stimulation group by 8000 Hz, 80dB sound wave was about 1.7 times and 2.5 times that of the control group, respectively. Moreover, it was observed that E. coli K-12 can respond rapidly to sound stress at both the transcriptional and posttranscriptional levels by promoting the synthesis of intracellular RNA and total protein. Some potential mechanisms may be involved in the responses of bacterial cells to sound stress.

  3. FitEM2EM--tools for low resolution study of macromolecular assembly and dynamics.

    Directory of Open Access Journals (Sweden)

    Ziv Frankenstein

    Full Text Available Studies of the structure and dynamics of macromolecular assemblies often involve comparison of low resolution models obtained using different techniques such as electron microscopy or atomic force microscopy. We present new computational tools for comparing (matching and docking of low resolution structures, based on shape complementarity. The matched or docked objects are represented by three dimensional grids where the value of each grid point depends on its position with regard to the interior, surface or exterior of the object. The grids are correlated using fast Fourier transformations producing either matches of related objects or docking models depending on the details of the grid representations. The procedures incorporate thickening and smoothing of the surfaces of the objects which effectively compensates for differences in the resolution of the matched/docked objects, circumventing the need for resolution modification. The presented matching tool FitEM2EMin successfully fitted electron microscopy structures obtained at different resolutions, different conformers of the same structure and partial structures, ranking correct matches at the top in every case. The differences between the grid representations of the matched objects can be used to study conformation differences or to characterize the size and shape of substructures. The presented low-to-low docking tool FitEM2EMout ranked the expected models at the top.

  4. Involvement of lysosomes in the uptake of macromolecular material by bloodstream forms of Trypanosoma brucei.

    Science.gov (United States)

    Opperdoes, F R; Van Roy, J

    1982-09-01

    To investigate whether the lysosomes of Trypanosoma brucei are capable of uptake of macromolecules after internalization by the cell, we used Triton WR-1339, a non-digestible macromolecular compound, which is known to cause a marked decrease in the density of hepatic lysosomes due to massive intralysosomal storage. Intraperitoneal administration of 0.4 g/kg Triton WR-1339 to rats infected with T. brucei led to the development of a large vacuole in the trypanosomes between nucleus and kinetoplast within 22 h. Higher doses (2 g/kg) led to the disappearance of the trypanosomes from the blood and resulted in permanent cures (greater than 100 days). Lysosomes isolated from the trypanosomes of animals treated with a sub-curative dose showed a decrease in equilibrium density of 0.03 g/cm3 in sucrose gradients. These lysosomes were partly damaged as evidenced by a reduction in latency and an increase in the non-sedimentable part of lysosomal enzymes. We conclude that acid proteinase and alpha-mannosidase-containing organelles of T. brucei take up exogenous macromolecules and must therefore be considered as true lysosomes and that Triton WR-1339 acts in T. brucei as a true lysosomotropic drug. Its trypanocidal action probably results from an interference with lysosomal function.

  5. Macromolecular crowding and the steady-state kinetics of malate dehydrogenase.

    Science.gov (United States)

    Poggi, Christopher G; Slade, Kristin M

    2015-01-20

    To understand how macromolecular crowding affects enzyme activity, we quantified the Michaelis-Menten kinetics of mitochondrial malate dehydrogenase (MDH) in the presence of hen egg white (HEW), lysozyme, bovine serum albumin (BSA), gum arabic, poly(vinylpyrrolidone) (PVP), and dextrans of various molecular weights. Although crowding tended to decrease Km and Vmax values, the magnitude depended on the crowding agent, reaction direction, and isozyme (mitochondrial porcine heart or thermophlic TaqMDH from Thermus flavus). Crowding slowed oxaloacetate reduction more significantly than malate oxidation, which may suggest that mitochondrial enzymes have evolved to function optimally under the crowded constraints in which they are immersed. Since direct comparisons of neutral to charged crowders are underrepresented in the literature, we performed these studies and found that neutral crowding agents lowered Vmax values more than charged crowders of similar size. The exception was hen egg white, a mixture of charged proteins that caused the largest observed decreases in both Km and Vmax. Finally, the data provide insight about the mechanism by corroborating MDH subunit dependence.

  6. Proteinase K activity determination with β-galactosidase as sensitive macromolecular substrate.

    Science.gov (United States)

    Ghéczy, Nicolas; Küchler, Andreas; Walde, Peter

    2016-11-15

    Proteinase K from Engyodontium album (proK) is a relatively unspecific serine endopeptidase which is known to attack proteins yet in their native states. If the attacked protein is an enzyme, even a partial hydrolysis by proK may lead to an inactivation of the enzyme, which can be monitored by measuring the loss of catalytic activity of the attacked enzyme. E. coli β-galactosidase (β-Gal) was used in this work as such enzyme. It was found to be a convenient and sensitive macromolecular model substrate for comparing the "native protein-attacking ability" of free and immobilized proK at pH = 7.0 and 23 °C. The β-Gal activity was measured spectrophotometrically with o-nitrophenyl-β-galactopyranoside. Reproducible proK determinations were possible for as little as 4.3 ng proK by using a proK analyte solution of 10 nM. Compared to free proK, immobilized proK was much less efficient in inactivating β-Gal, most likely due to a decreased mobility of immobilized proK and a restricted accessibility of β-Gal to the active site of proK. Worth noting is, that under conditions at which β-Gal was completely inactivated by proK, the activity of hen egg lysozyme, horseradish peroxidase, or Aspergillus sp. glucose oxidase remained unaltered.

  7. SCIENTIFIC PRINCIPLES FOR MODIFICATION OF WATER-SOLUBLE POLYMERS. FORMATION OF MACROMOLECULAR COMPLEXES

    Institute of Scientific and Technical Information of China (English)

    1998-01-01

    The study of nanosecond dynamics of macromolecules with the luminescent methods make it possible to investigate the formation and functioning of polymeric complexes, polymeric conjugates and macromolecular metal complexes, which are widely used for solving many practical tasks. The nanosecond dynamics of macromolecules are a highly sensitive indicator of interpolymer complexes (IPC) formation. It enables us to solve the problems of studying IPC formation and stability and to investigate the interpolymer reactions of exchange and substitution. The investigation of changes in the rotational mobility of globular protein molecules as a whole makes it possible to determine the complex composition and its stability, and to control the course of polymer-protein conjugate formstion reaction. The nanosecond dynamics of polymers interacting with surfacants' ions (S)are the sensitive indicator of the S-polymer complex formation. A method for determining the equilibrium constants of the S-polymer complex formation was developed on the basis of the study of polymer chains mobility. It is established that nanosecond dynamics influences the course of chemical reactions in polymer chains. Moreover, the marked effect of the nanosecond dynamics is also revealed in the study of photophysical processes (the formation of excimers and energy migration of electron excitation) in polymers with photoactive groups. It was found that the efficiency of both processes increases with increasing the mobility of side chains, the carriers of photoactive groups.

  8. Macromolecular scaffolding: the relationship between nanoscale architecture and function in multichromophoric arrays for organic electronics.

    Science.gov (United States)

    Palermo, Vincenzo; Schwartz, Erik; Finlayson, Chris E; Liscio, Andrea; Otten, Matthijs B J; Trapani, Sara; Müllen, Klaus; Beljonne, David; Friend, Richard H; Nolte, Roeland J M; Rowan, Alan E; Samorì, Paolo

    2010-02-23

    The optimization of the electronic properties of molecular materials based on optically or electrically active organic building blocks requires a fine-tuning of their self-assembly properties at surfaces. Such a fine-tuning can be obtained on a scale up to 10 nm by mastering principles of supramolecular chemistry, i.e., by using suitably designed molecules interacting via pre-programmed noncovalent forces. The control and fine-tuning on a greater length scale is more difficult and challenging. This Research News highlights recent results we obtained on a new class of macromolecules that possess a very rigid backbone and side chains that point away from this backbone. Each side chain contains an organic semiconducting moiety, whose position and electronic interaction with neighboring moieties are dictated by the central macromolecular scaffold. A combined experimental and theoretical approach has made it possible to unravel the physical and chemical properties of this system across multiple length scales. The (opto)electronic properties of the new functional architectures have been explored by constructing prototypes of field-effect transistors and solar cells, thereby providing direct insight into the relationship between architecture and function.

  9. A graph theoretical approach for assessing bio-macromolecular complex structural stability.

    Science.gov (United States)

    Del Carpio, Carlos Adriel; Iulian Florea, Mihai; Suzuki, Ai; Tsuboi, Hideyuki; Hatakeyama, Nozomu; Endou, Akira; Takaba, Hiromitsu; Ichiishi, Eiichiro; Miyamoto, Akira

    2009-11-01

    Fast and proper assessment of bio macro-molecular complex structural rigidity as a measure of structural stability can be useful in systematic studies to predict molecular function, and can also enable the design of rapid scoring functions to rank automatically generated bio-molecular complexes. Based on the graph theoretical approach of Jacobs et al. [Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF (2001) Protein flexibility predictions using graph theory. Proteins: Struct Funct Genet 44:150-165] for expressing molecular flexibility, we propose a new scheme to analyze the structural stability of bio-molecular complexes. This analysis is performed in terms of the identification in interacting subunits of clusters of flappy amino acids (those constituting regions of potential internal motion) that undergo an increase in rigidity at complex formation. Gains in structural rigidity of the interacting subunits upon bio-molecular complex formation can be evaluated by expansion of the network of intra-molecular inter-atomic interactions to include inter-molecular inter-atomic interaction terms. We propose two indices for quantifying this change: one local, which can express localized (at the amino acid level) structural rigidity, the other global to express overall structural stability for the complex. The new system is validated with a series of protein complex structures reported in the protein data bank. Finally, the indices are used as scoring coefficients to rank automatically generated protein complex decoys.

  10. Enzyme activity determination on macromolecular substrates by isothermal titration calorimetry: application to mesophilic and psychrophilic chitinases.

    Science.gov (United States)

    Lonhienne, T; Baise, E; Feller, G; Bouriotis, V; Gerday, C

    2001-02-09

    Isothermal titration calorimetry has been applied to the determination of the kinetic parameters of chitinases (EC 3.2.1.14) by monitoring the heat released during the hydrolysis of chitin glycosidic bonds. Experiments were carried out using two different macromolecular substrates: a soluble polymer of N-acetylglucosamine and the insoluble chitin from crab shells. Different experimental temperatures were used in order to compare the thermodependence of the activity of two chitinases from the psychrophile Arthrobacter sp. TAD20 and of chitinase A from the mesophile Serratia marcescens. The method allowed to determine unequivocally the catalytic rate constant k(cat), the activation energy (E(a)) and the thermodynamic activation parameters (DeltaG(#), DeltaH(#), DeltaS(#)) of the chitinolytic reaction on the soluble substrate. The catalytic activity has also been determined on insoluble chitin, which displays an effect of substrate saturation by chitinases. On both substrates, the thermodependence of the activity of the psychrophilic chitinases was lower than that observed with the mesophilic counterpart.

  11. Interaction of wall shear stress magnitude and gradient in the prediction of arterial macromolecular permeability.

    Science.gov (United States)

    LaMack, Jeffrey A; Himburg, Heather A; Li, Xue-Mei; Friedman, Morton H

    2005-04-01

    Large spatial shear stress gradients have anecdotally been associated with early atherosclerotic lesion susceptibility in vivo and have been proposed as promoters of endothelial cell dysfunction in vitro. Here, experiments are presented in which several measures of the fluid dynamic shear stress, including its gradient, at the walls of in vivo porcine iliac arteries, are correlated against the transendothelial macromolecular permeability of the vessels. The fluid dynamic measurements are based on postmortem vascular casts, and permeability is measured from Evans blue dye (EBD) uptake. Time-averaged wall shear stress (WSS), as well as a new parameter termed maximum gradient stress (MGS) that describes the spatial shear stress gradient due to flow acceleration at a given point, are mapped for each artery and compared on a point-by-point basis to the corresponding EBD patterns. While there was no apparent relation between MGS and EBD uptake, a composite parameter, WSS(-0.11) MGS(0.044), was highly correlated with permeability. Notwithstanding the small exponents, the parameter varied widely within the region of interest. The results suggest that sites exposed to low wall shear stresses are more likely to exhibit elevated permeability, and that this increase is exacerbated in the presence of large spatial shear stress gradients.

  12. Temperature sensitivity of soil microbial communities: An application of macromolecular rate theory to microbial respiration

    Science.gov (United States)

    Alster, Charlotte J.; Koyama, Akihiro; Johnson, Nels G.; Wallenstein, Matthew D.; Fischer, Joseph C.

    2016-06-01

    There is compelling evidence that microbial communities vary widely in their temperature sensitivity and may adapt to warming through time. To date, this sensitivity has been largely characterized using a range of models relying on versions of the Arrhenius equation, which predicts an exponential increase in reaction rate with temperature. However, there is growing evidence from laboratory and field studies that observe nonmonotonic responses of reaction rates to variation in temperature, indicating that Arrhenius is not an appropriate model for quantitatively characterizing temperature sensitivity. Recently, Hobbs et al. (2013) developed macromolecular rate theory (MMRT), which incorporates thermodynamic temperature optima as arising from heat capacity differences between isoenzymes. We applied MMRT to measurements of respiration from soils incubated at different temperatures. These soils were collected from three grassland sites across the U.S. Great Plains and reciprocally transplanted, allowing us to isolate the effects of microbial community type from edaphic factors. We found that microbial community type explained roughly 30% of the variation in the CO2 production rate from the labile C pool but that temperature and soil type were most important in explaining variation in labile and recalcitrant C pool size. For six out of the nine soil × inoculum combinations, MMRT was superior to Arrhenius. The MMRT analysis revealed that microbial communities have distinct heat capacity values and temperature sensitivities sometimes independent of soil type. These results challenge the current paradigm for modeling temperature sensitivity of soil C pools and understanding of microbial enzyme dynamics.

  13. Using support vector machines to improve elemental ion identification in macromolecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Morshed, Nader [University of California, Berkeley, CA 94720 (United States); Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Echols, Nathaniel, E-mail: nechols@lbl.gov [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Adams, Paul D., E-mail: nechols@lbl.gov [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); University of California, Berkeley, CA 94720 (United States)

    2015-05-01

    A method to automatically identify possible elemental ions in X-ray crystal structures has been extended to use support vector machine (SVM) classifiers trained on selected structures in the PDB, with significantly improved sensitivity over manually encoded heuristics. In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.

  14. Visualization of X-ray Beam Using CdWO4 Crystal for Macromolecular Crystallography

    Directory of Open Access Journals (Sweden)

    Kazimierz J. Gofron

    2011-12-01

    Full Text Available In synchrotron diffraction experiments, it is typically assumed that the X-ray beam at the sample position is uniform, stable and has dimensions that are controlled by the focus and slits settings. As might be expected, this process is much more complex. We present here an investigation of the properties of a synchrotron X-ray beam at the sample position. The X-ray beam is visualized with a single crystal scintillator that converts X-ray photons into visible light photons, which can be imaged using Structure Biology Center (SBC on-axis and off-axis microscope optics. The X-ray penetration is dependent on the composition of the scintillator (especially the effective Z, and X-ray energy. Several scintillators have been used to visualize X-ray beams. Here we compare CdWO4, PbWO4, Bi4Ge3O12, Y3Al5O12:Ce (YAG:Ce, and Gd2O2S:Tb (phosphor. We determined that scintillator crystals made of CdWO4 and similar high-Z materials are best suited for the energy range (7–20 keV and are most suitable for beam visualization for macromolecular crystallography applications. These scintillators show excellent absorption, optical, and mechanical properties.

  15. IMAGINE: first neutron protein structure and new capabilities for neutron macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Munshi, Parthapratim [ORNL; Myles, Dean A A [ORNL; Robertson, Lee [ORNL; Stoica, Alexandru Dan [ORNL; Crow, Lowell [ORNL; Kovalevskyi, Andrii Y [ORNL; Koritsanszky, Tibor S [ORNL; Chakoumakos, Bryan C [ORNL; Blessing, Robert [Hauptman-Woodward Medical Research Institute; Meilleur, Flora [ORNL

    2013-01-01

    We report the first high resolution neutron protein structure of perdeuterated rubredoxin from Pyrococcus furiosus (PfRd) determined using the new IMAGINE macromolecular neutron crystallography instrument at the Oak Ridge National Laboratory. Neutron diffraction data extending to 1.65 resolution were collected from a relatively small 0.7 mm3 PfRd crystal using 2.5 days (60 h) of beam time. The refined structure contains 371 out of 391, or 95%, of the deuterium atoms of the protein, and 58 solvent molecules. The IMAGINE instrument is designed to provide neutron data at or near atomic resolutions (1.5 ) from crystals with volume < 1.0 mm3 and with unit cell edges < 100 . Beam line features include elliptical focusing mirrors that deliver 3x107 n s-1 cm-2 into a 3.5 x 2.0 mm2 focal spot at the sample position, and variable short and long wavelength cutoff optics that provide automated exchange between multiple wavelength configurations ( min=2.0 , 2.8 , 3.3 - max =3.0 , 4.0 , 4.5 , ~20 ). Notably, the crystal used to collect this PfRd data is 5-10 times smaller than has been previously reported.

  16. Influence of temperature and macromolecular mobility on sorption of TCE on humic acid coated mineral surfaces.

    Science.gov (United States)

    Bell, Katherine Young; LeBoeuf, Eugene J

    2013-01-01

    This study demonstrates differences in sorptive capacity of volatile organic compound (VOC) trichloroethylene (TCE) onto natural organic matter (NOM) coated and uncoated mineral surfaces above and below the NOM glass transition temperature. TCE sorption isotherms for dry NOM-mineral systems below the NOM glass transition temperature (T(g)) demonstrated sorption behavior characteristic of micropore filling, with sorption capacities reduced relative to uncoated mineral matrices. Such differences were not entirely associated with differences in surface areas of the coated and uncoated mineral matrices, but were likely associated with either a blockage of pore space available to the VOC or a kinetic limitation that does not allow the VOC access to the internal porosity of the model soil within the time periods of the experiment. TCE sorption in dry NOM-mineral matrices above the T(g), however, was described in terms of sorption within a more fluid, macromolecular dissolution medium that does not hinder access to mineral surfaces. Such observations have potential important implications for modeling the fate and transport of VOCs in soils and sediment systems.

  17. Synthesis and Self-Assembly of Amphiphilic Triblock Terpolymers with Complex Macromolecular Architecture

    KAUST Repository

    Polymeropoulos, George

    2015-11-25

    Two star triblock terpolymers (PS-b-P2VP-b-PEO)3 and one dendritic-like terpolymer [PS-b-P2VP-b-(PEO)2]3 of PS (polystyrene), P2VP (poly(2-vinylpyridine)), and PEO (poly(ethylene oxide)), never reported before, were synthesized by combining atom transfer radical and anionic polymerizations. The synthesis involves the transformation of the -Br groups of the previously reported Br-terminated 3-arm star diblock copolymers to one or two -OH groups, followed by anionic polymerization of ethylene oxide to afford the star or dendritic structure, respectively. The well-defined structure of the terpolymers was confirmed by static light scattering, size exclusion chromatography, and NMR spectroscopy. The self-assembly in solution and the morphology in bulk of the terpolymers, studied by dynamic light scattering and transmission electron microscopy, respectively, reveal new insights in the phase separation of these materials with complex macromolecular architecture. © 2015 American Chemical Society.

  18. Discovering free energy basins for macromolecular systems via guided multiscale simulation.

    Science.gov (United States)

    Sereda, Yuriy V; Singharoy, Abhishek B; Jarrold, Martin F; Ortoleva, Peter J

    2012-07-26

    An approach for the automated discovery of low free energy states of macromolecular systems is presented. The method does not involve delineating the entire free energy landscape but proceeds in a sequential free energy minimizing state discovery; i.e., it first discovers one low free energy state and then automatically seeks a distinct neighboring one. These states and the associated ensembles of atomistic configurations are characterized by coarse-grained variables capturing the large-scale structure of the system. A key facet of our approach is the identification of such coarse-grained variables. Evolution of these variables is governed by Langevin dynamics driven by thermal-average forces and mediated by diffusivities, both of which are constructed by an ensemble of short molecular dynamics runs. In the present approach, the thermal-average forces are modified to account for the entropy changes following from our knowledge of the free energy basins already discovered. Such forces guide the system away from the known free energy minima, over free energy barriers, and to a new one. The theory is demonstrated for lactoferrin, known to have multiple energy-minimizing structures. The approach is validated using experimental structures and traditional molecular dynamics. The method can be generalized to enable the interpretation of nanocharacterization data (e.g., ion mobility-mass spectrometry, atomic force microscopy, chemical labeling, and nanopore measurements).

  19. Poly(trimethylene carbonate) as an elastic biodegradable film for human embryonic stem cell-derived retinal pigment epithelial cells.

    Science.gov (United States)

    Sorkio, Anni; Haimi, Suvi; Verdoold, Vincent; Juuti-Uusitalo, Kati; Grijpma, Dirk; Skottman, Heli

    2017-01-04

    Human embryonic stem cell-derived retinal pigment epithelial (hESC-RPE) cell therapies show tremendous potential for the treatment of retinal degenerative diseases. A tissue engineering approach, where cells are delivered to the subretinal space on a biodegradable carrier as a sheet, shows great promise for these RPE cell therapies. The aim of the present study was to assess whether a flexible, elastic and biodegradable poly(trimethylene carbonate) (PTMC) film promotes the formation of functional hESC-RPE and performs better than often used biodegradable poly(d,l-lactide) (PDLLA) film. Human ESC-RPE maturation and functionality on PTMC films was assessed by cell proliferation assays, RPE-specific gene and protein expression, phagocytic activity and growth factor secretion. It is demonstrated that the mechanical properties of PTMC films have close resemblance to those of the native Bruch's membrane and support the formation hESC-RPE monolayer in serum-free culture conditions with high degree of functionality. In contrast, use of PDLLA films did not lead to the formation of confluent monolayers of hESC-RPE cells and had unsuitable mechanical properties for retinal application. In conclusion, the present study indicates that flexible and elastic biodegradable PTMC films show potential for retinal tissue engineering applications. Copyright © 2017 John Wiley & Sons, Ltd.

  20. Sociobiology of biodegradation and the role of predatory protozoa in biodegrading communities

    Indian Academy of Sciences (India)

    Tejashree Modak; Shalmali Pradhan; Milind Watve

    2007-06-01

    Predatory protozoa are known to enhance biodegradation by bacteria in a variety of systems including rumen. This is apparently counterintuitive since many protozoa do not themselves produce extracellular degradative enzymes and prey upon bacterial degraders. We propose a mechanism of protozoal enhancement of bacterial biodegradation based on the sociobiology of biodegradation. Since extracellular enzyme production by degraders involves a cost to the bacterial cell, cheaters that do not make the enzyme will have a selective advantage. In the presence of cheaters, degraders that physically attach to water-insoluble substrate will have a selective advantage over free-floating degraders. On the other hand, cheaters will benefit by being free floaters since they consume the solubilized products of extracellular enzymes. Predatory ciliated protozoa are more likely to consume free-floating cheaters. Thus, due to protozoan predation a control is exerted on the cheater population. We illustrate the dynamics of such a system with the help of a computer simulation model. Available data on rumen and other biodegradation systems involving protozoa are compatible with the assumptions and predictions of the model.

  1. Development of aliphatic biodegradable photoluminescent polymers

    Science.gov (United States)

    Yang, Jian; Zhang, Yi; Gautam, Santosh; Liu, Li; Dey, Jagannath; Chen, Wei; Mason, Ralph P.; Serrano, Carlos A.; Schug, Kevin A.; Tang, Liping

    2009-01-01

    None of the current biodegradable polymers can function as both implant materials and fluorescent imaging probes. The objective of this study was to develop aliphatic biodegradable photoluminescent polymers (BPLPs) and their associated cross-linked variants (CBPLPs) for biomedical applications. BPLPs are degradable oligomers synthesized from biocompatible monomers including citric acid, aliphatic diols, and various amino acids via a convenient and cost-effective polycondensation reaction. BPLPs can be further cross-linked into elastomeric cross-linked polymers, CBPLPs. We have shown representatively that BPLP-cysteine (BPLP-Cys) and BPLP-serine (BPLP-Ser) offer advantages over the traditional fluorescent organic dyes and quantum dots because of their preliminarily demonstrated cytocompatibility in vitro, minimal chronic inflammatory responses in vivo, controlled degradability and high quantum yields (up to 62.33%), tunable fluorescence emission (up to 725 nm), and photostability. The tensile strength of CBPLP-Cys film ranged from 3.25 ± 0.13 MPa to 6.5 ± 0.8 MPa and the initial Modulus was in a range of 3.34 ± 0.15 MPa to 7.02 ± 1.40 MPa. Elastic CBPLP-Cys could be elongated up to 240 ± 36%. The compressive modulus of BPLP-Cys (0.6) (1:1:0.6 OD:CA:Cys) porous scaffold was 39.60 ± 5.90 KPa confirming the soft nature of the scaffolds. BPLPs also possess great processability for micro/nano-fabrication. We demonstrate the feasibility of using BPLP-Ser nanoparticles (“biodegradable quantum dots”) for in vitro cellular labeling and noninvasive in vivo imaging of tissue engineering scaffolds. The development of BPLPs and CBPLPs represents a new direction in developing fluorescent biomaterials and could impact tissue engineering, drug delivery, bioimaging. PMID:19506254

  2. Biodegradation of polyester polyurethane by Aspergillus tubingensis.

    Science.gov (United States)

    Khan, Sehroon; Nadir, Sadia; Shah, Zia Ullah; Shah, Aamer Ali; Karunarathna, Samantha C; Xu, Jianchu; Khan, Afsar; Munir, Shahzad; Hasan, Fariha

    2017-03-15

    The xenobiotic nature and lack of degradability of polymeric materials has resulted in vast levels of environmental pollution and numerous health hazards. Different strategies have been developed and still more research is being in progress to reduce the impact of these polymeric materials. This work aimed to isolate and characterize polyester polyurethane (PU) degrading fungi from the soil of a general city waste disposal site in Islamabad, Pakistan. A novel PU degrading fungus was isolated from soil and identified as Aspergillus tubingensis on the basis of colony morphology, macro- and micro-morphology, molecular and phylogenetic analyses. The PU degrading ability of the fungus was tested in three different ways in the presence of 2% glucose: (a) on SDA agar plate, (b) in liquid MSM, and (c) after burial in soil. Our results indicated that this strain of A. tubingensis was capable of degrading PU. Using scanning electron microscopy (SEM), we were able to visually confirm that the mycelium of A. tubingensis colonized the PU material, causing surface degradation and scarring. The formation or breakage of chemical bonds during the biodegradation process of PU was confirmed using Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy. The biodegradation of PU was higher when plate culture method was employed, followed by the liquid culture method and soil burial technique. Notably, after two months in liquid medium, the PU film was totally degraded into smaller pieces. Based on a comprehensive literature search, it can be stated that this is the first report showing A. tubingensis capable of degrading PU. This work provides insight into the role of A. tubingensis towards solving the dilemma of PU wastes through biodegradation.

  3. [Biodegradation of pyridine under UV irradiation].

    Science.gov (United States)

    Fang, Miao-Miao; Yan, Ning; Zhang, Yong-Ming

    2012-02-01

    Pyridine, a complex nitrogen-containing heterocyclic compounds, is usually difficult to degrade by means of single biological method. The internal loop photobiodegradation reactor (ILPBR) was used for degradation of pyridine in batch and continuous experiments following three protocols: photolysis alone (P), biodegradation alone (B), and intimately coupled photolysis and biodegradation (P&B) to investigate the regularity of pyridine degradation. The experimental results indicated that pyridine removal rate by P&B was fastest among three protocols in batch experiment, in which protocol B was faster than P. For initial pyridine concentration of 100 mg L(-1), the pyridine removal rates were respectively 4.95, 10.2 and 14.58 mg (L x h)(-1) corresponding to protocol P, B and P&B. Pyridine degradation kinetic equations were established based on Monod model, and the saturation constants decreased from 1920.4 mg x L(-1) for protocol B to 1094.1 mg x L(-1) for protocol P&B. Protocols P, B and P&B were also used for pyridine degradation in continuous flow and influent pyridine concentration increased from 50 to 300 mg x L(-1), and their average removal rates were respectively 15.8 mg (L x h)(-1) for protocol P, 23.1 mg x (L x h)(-1) for protocol B and 24.9 mg x (L x h)(-1) for protocol P&B, in which the removal rates were higher than that in batch. Experiments suggested that the inhibition of pyridine to biofilm could be relieved due to UV irradiation in process of intimately coupled UV photolysis and biodegradation, and biofilm had kept its bioactivity degrading pyridine and enhanced pyridine removal rates.

  4. The effects of biodegradation on biomarker maturity indicators in sequentially biodegraded oils from Liaohe Basin,China

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    By aid of gas chromatogram/mass spectrometry(GC-MS) ,the distributions and the compositions of biomarkers in a set of sequentially biodegraded oils from Liaohe Basin,China,have been quantitatively analyzed,and it has been found that during the biodegradation process of crude oils,the molecular maturity parameters such as Ts/Tm,homohopane C31 22S/(22S+22R) and sterane C29 20S/(20S+20R) ratios will be affected to different extent. The results show that except homohopane C31 22S/(22S+22R) ratio,Ts/Tm ratio will decrease with increasing biodegradation,but for C29 20S/(20S+20R) ratio,it will almost remain constant in slightly and moderately biodegraded oils,and then will increase quickly in severely biodegraded oils. The main reason is that there are some differences in the ability of resistant biodegradation for different isomer of biomarkers with different stereo configuration,resulting in the fact that destroying rate by bacteria for those biomarkers with weak ability will be higher than those with strong ability in resistant biodegradation. For example,18α(H) -22,29,30-trisnorhopanes(Ts) will be destroyed more quickly than 17α(H) -22,29,30-trisnorshopanres(Tm) ,and 20R isomer is more quickly than 20S isomer for C29 sterane,resulting in the relative ratios changed with increasing biodegradation. Therefore,much more attention should be paid to the biodegradation extent of crude oils and the type of biomarker maturity indicators,when the distributions and the compositions of biomarkers in biodegraded oils are used to determine the maturity of biodegraded oils.

  5. SCREENING OF BACTERIAL PRODUCTS FOR THEIR CRUDE OIL BIODEGRADATION EFFECTIVENESS

    Science.gov (United States)

    Although petroleum hydrocarbons have been known to be biodegradable for decades (1-5), use of microbial cultures to enhance natural biodegradation (bioaugmentation) has met with limited success (6-10). Despite the paucity of controlled field studies demonstrating the effectivene...

  6. Methods for Evaluating the Biodegradability of Environmentally Degradable Polymers

    NARCIS (Netherlands)

    Zee, van der M.

    2014-01-01

    This chapter presents an overview of the current knowledge on experimental methods for monitoring the biodegradability of polymeric materials. The focus is, in particular, on the biodegradation of materials under environmental conditions. Examples of in vivo degradation of polymers used in biomedica

  7. Biodegradable hollow fibres for the controlled release of drugs

    NARCIS (Netherlands)

    Schakenraad, J.M.; Oosterbaan, J.A.; Nieuwenhuis, P.; Molenaar, I.; Olijslager, J.; Potman, W.; Eenink, M.J.D.; Feijen, J.

    1988-01-01

    Biodegradable hollow fibres of poly-l-lactic acid (PLLA) filled with a suspension of the contraceptive hormone levonorgestrel in castor oil were implanted subcutaneously in rats to study the rate of drug release, rate of biodegradation and tissue reaction caused by the implant. The in vivo drug rele

  8. Biodegradation of clofibric acid and identification of its metabolites

    Energy Technology Data Exchange (ETDEWEB)

    Salgado, R. [REQUIMTE/CQFB, Chemistry Department, FCT, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); ESTS-IPS, Escola Superior de Tecnologia de Setubal do Instituto Politecnico de Setubal, Rua Vale de Chaves, Campus do IPS, Estefanilha, 2910-761 Setubal (Portugal); Oehmen, A. [REQUIMTE/CQFB, Chemistry Department, FCT, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); Carvalho, G. [REQUIMTE/CQFB, Chemistry Department, FCT, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); Instituto de Biologia Experimental e Tecnologica (IBET), Av. da Republica (EAN), 2784-505 Oeiras (Portugal); Noronha, J.P. [REQUIMTE/CQFB, Chemistry Department, FCT, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); Reis, M.A.M., E-mail: amr@fct.unl.pt [REQUIMTE/CQFB, Chemistry Department, FCT, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal)

    2012-11-30

    Graphical abstract: Metabolites produced during clofibric acid biodegradation. Highlights: Black-Right-Pointing-Pointer Clofibric acid is biodegradable. Black-Right-Pointing-Pointer Mainly heterotrophic bacteria degraded the clofibric acid. Black-Right-Pointing-Pointer Metabolites of clofibric acid biodegradation were identified. Black-Right-Pointing-Pointer The metabolic pathway of clofibric acid biodegradation is proposed. - Abstract: Clofibric acid (CLF) is the pharmaceutically active metabolite of lipid regulators clofibrate, etofibrate and etofyllinclofibrate, and it is considered both environmentally persistent and refractory. This work studied the biotransformation of CLF in aerobic sequencing batch reactors (SBRs) with mixed microbial cultures, monitoring the efficiency of biotransformation of CLF and the production of metabolites. The maximum removal achieved was 51% biodegradation (initial CLF concentration = 2 mg L{sup -1}), where adsorption and abiotic removal mechanisms were shown to be negligible, showing that CLF is indeed biodegradable. Tests showed that the observed CLF biodegradation was mainly carried out by heterotrophic bacteria. Three main metabolites were identified, including {alpha}-hydroxyisobutyric acid, lactic acid and 4-chlorophenol. The latter is known to exhibit higher toxicity than the parent compound, but it did not accumulate in the SBRs. {alpha}-Hydroxyisobutyric acid and lactic acid accumulated for a period, where nitrite accumulation may have been responsible for inhibiting their degradation. A metabolic pathway for the biodegradation of CLF is proposed in this study.

  9. Nanocomposites with biodegradable polymers synthesis properties and future perspectives

    CERN Document Server

    2011-01-01

    Polymers are used in practically every facet of daily life. Most polymers come from fossil fuels and are not biodegradable, causing long-term environmental hazards. Biodegradable polymers provide an alternative class of materials. Composites of such polymers have high potential within a wide spectrum of applications.

  10. A Sensitive and Biodegradable Pressure Sensor Array for Cardiovascular Monitoring.

    Science.gov (United States)

    Boutry, Clementine M; Nguyen, Amanda; Lawal, Qudus Omotayo; Chortos, Alex; Rondeau-Gagné, Simon; Bao, Zhenan

    2015-11-18

    An array of highly sensitive pressure sensors entirely made of biodegradable materials is presented, designed as a single-use flexible patch for application in cardiovascular monitoring. The high sensitivity in combination with fast response time is unprecedented when compared to recent reports on biodegradable pressure sensors (sensitivity three orders of magnitude higher), as illustrated by pulse wave velocity measurements, toward hypertension detection.

  11. Wet air oxidation induced enhanced biodegradability of distillery effluent.

    Science.gov (United States)

    Malik, S N; Saratchandra, T; Tembhekar, P D; Padoley, K V; Mudliar, S L; Mudliar, S N

    2014-04-01

    The present study reports the feasibility of Wet Air Oxidation (WAO) as a pretreatment option for enhanced biodegradation of complex distillery effluent. Initially, the distillery effluent was pretreated by WAO at different process conditions (pressure, temperature and time) to facilitate enhancement in the biodegradability index (BI = BOD5: COD ratio). The biodegradability of WAO pretreated effluent was evaluated by subjecting it to aerobic biodegradation and anaerobic followed by aerobic biodegradation. Aerobic biodegradation of pretreated effluent with enhanced biodegradability index (BI = 0.4-0.8) showed enhanced COD reduction of up to 67.7%, whereas the untreated effluent (BI = 0.17) indicated poor COD reduction of only 22.5%. Anaerobic followed by aerobic biodegradation of pretreated effluent has shown up to 87.9% COD reduction, while the untreated effluent has shown only 43.1% COD reduction. Bio-kinetic parameters also confirmed the increased rate of bio-oxidation at enhanced BIs. The results indicate that the WAO pretreatment facilitates enhanced bio-oxidation/bio-degradation of complex effluents like the distillery spent wash.

  12. Biodegradable elastomers for biomedical applications and regenerative medicine

    NARCIS (Netherlands)

    Bat, Erhan; Zhang, Zheng; Feijen, Jan; Grijpma, Dirk W.; Poot, Andre A.

    2014-01-01

    Synthetic biodegradable polymers are of great value for the preparation of implants that are required to reside only temporarily in the body. The use of biodegradable polymers obviates the need for a second surgery to remove the implant, which is the case when a nondegradable implant is used. After

  13. Hydrocarbons biodegradation in unsaturated porous medium; Biodegradation des hydrocarbures en milieu poreux insature

    Energy Technology Data Exchange (ETDEWEB)

    Gautier, C

    2007-12-15

    Biological processes are expected to play an important role in the degradation of petroleum hydrocarbons in contaminated soils. However, factors influencing the kinetics of biodegradation are still not well known, especially in the unsaturated zone. To address these biodegradation questions in the unsaturated zone an innovative experimental set up based on a physical column model was developed. This experimental set up appeared to be an excellent tool for elaboration of a structured porous medium, with well defined porous network and adjusted water/oil saturations. Homogeneous repartition of both liquid phases (i.e., aqueous and non aqueous) in the soil pores, which also contain air, was achieved using ceramic membranes placed at the bottom of the soil column. Reproducible interfaces (and connectivity) are developed between gas, and both non mobile water and NAPL phases, depending on the above-defined characteristics of the porous media and on the partial saturations of these three phases (NAPL, water and gas). A respirometric apparatus was coupled to the column. Such experimental set up have been validated with hexadecane in dilution in an HMN phase. This approach allowed detailed information concerning n-hexadecane biodegradation, in aerobic condition, through the profile of the oxygen consumption rate. We have taken benefit of this technique, varying experimental conditions, to determine the main parameters influencing the biodegradation kinetics and compositional evolution of hydrocarbons, under steady state unsaturated conditions and with respect to aerobic metabolism. Impacts of the nitrogen quantity and of three different grain sizes have been examined. Biodegradation of petroleum cut, as diesel cut and middle distillate without aromatic fraction, were, also studied. (author)

  14. Biodegradation of petroleum hydrocarbons in hypersaline environments

    Directory of Open Access Journals (Sweden)

    Luiz Fernando Martins

    2012-09-01

    Full Text Available Literature on hydrocarbon degradation in extreme hypersaline media presents studies that point to a negative effect of salinity increase on hydrocarbonoclastic activity, while several others report an opposite tendency. Based on information available in the literature, we present a discussion on the reasons that justify these contrary results. Despite the fact that microbial ability to metabolize hydrocarbons is found in extreme hypersaline media, indeed some factors are critical for the occurrence of hydrocarbon degradation in such environments. How these factors affect hydrocarbon degradation and their implications for the assessment of hydrocarbon biodegradation in hypersaline environments are presented in this review.

  15. Development of biodegradable fungicide by radiation

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Youngkeun; Kim, Dongsub

    2012-03-15

    To develop the fungicide which is biodegradable and alternative to chemical pesticide that has an side effect of environmental pollution, Mutant induction of the enhanced antifungal activity was studied by using radiation. Characteristics and structure of antifungal biomaterials derived from these mutants were analysed. Two biomaterials related to the antifungal activity from the above mutant were isolated and purified. Microbial pesticide were manufactured in combination of various additives. Antiphytopathogenic effects were proven by field test and it was promising to prevent Chinese cabbage and radish from phytophthora and root rot.

  16. Development of biodegradable fungicide by radiation

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Young Keun; Kim, Dong Sub [KAERI, Daejeon (Korea, Republic of)

    2011-01-15

    To develop the fungicide which is biodegradable and alternative to chemical pesticide that has an side effect of environmental pollution, Mutant induction of the enhanced antifungal activity was studied by using radiation. Characteristics and structure of antifungal biomaterials derived from these mutants were analysed. Two biomaterials related to the antifungal activity from the above mutant were isolated and purified. Microbial pesticide were manufactured in combination of various additives. Antiphytopathogenic effects were proven by pot experiment and It was promising to prevent pepper, Chinese cabbage and radish from anthrax, phytophthora and root rot

  17. Injectable, Biodegradable Hydrogels for Tissue Engineering Applications

    Directory of Open Access Journals (Sweden)

    Huaping Tan

    2010-03-01

    Full Text Available Hydrogels have many different applications in the field of regenerative medicine. Biodegradable, injectable hydrogels could be utilized as delivery systems, cell carriers, and scaffolds for tissue engineering. Injectable hydrogels are an appealing scaffold because they are structurally similar to the extracellular matrix of many tissues, can often be processed under relatively mild conditions, and may be delivered in a minimally invasive manner. This review will discuss recent advances in the field of injectable hydrogels, including both synthetic and native polymeric materials, which can be potentially used in cartilage and soft tissue engineering applications.

  18. Lipase biocatalysis for useful biodegradable products

    Energy Technology Data Exchange (ETDEWEB)

    Linko, Y.Y.; Wang, Zhuo Lin; Uosukainen, E.; Seppaelae, J. [Helsinki Univ. of Technology, Espoo (Finland); Laemsae, M. [Raisio Group Oil Milling Industry, Raisio (Finland)

    1996-12-31

    It was shown that lipases can be used as biocatalysts in the production of useful biodegradable compounds such as 1-butyl oleate by direct esterification of butanol and oleic acid to decrease viscosity of biodiesel in winter use. By enzymic transesterification, a mixture of 2-ethyl-1-hexyl esters from rapeseed oil fatty acids can be obtained in good yields for use as a solvent, and of trimethylolpropane esters for use as a lubricant. Finally, it was demonstrated that polyesters with a mass average molar mass in excess of 75,000 g mol{sup -}1 can be obtained by esterification or transesterification by using lipase as biocatalyst. (author) (3 refs.)

  19. Biosynthesis and biodegradation of wood components

    Energy Technology Data Exchange (ETDEWEB)

    Higuchi, T. (ed.)

    1985-01-01

    A textbook containing 22 chapters by various authors covers the structure of wood, the localization of polysaccharides and lignins in wood cell walls, metabolism and synthetic function of cambial tissue, cell organelles and their function in the biosynthesis of cell wall components, biosynthesis of plant cell wall polysaccharides, lignin, cutin, suberin and associated waxes, phenolic acids and monolignols, quinones, flavonoids, tannins, stilbenes and terpenoid wood extractives, the occurrence of extractives, the metabolism of phenolic acids, wood degradation by micro-organisms and fungi, and biodegradation of cellulose, hemicelluloses, lignin, and aromatic extractives of wood. An index is included.

  20. Biodegradation of petroleum hydrocarbons in hypersaline environments

    Science.gov (United States)

    Martins, Luiz Fernando; Peixoto, Raquel Silva

    2012-01-01

    Literature on hydrocarbon degradation in extreme hypersaline media presents studies that point to a negative effect of salinity increase on hydrocarbonoclastic activity, while several others report an opposite tendency. Based on information available in the literature, we present a discussion on the reasons that justify these contrary results. Despite the fact that microbial ability to metabolize hydrocarbons is found in extreme hypersaline media, indeed some factors are critical for the occurrence of hydrocarbon degradation in such environments. How these factors affect hydrocarbon degradation and their implications for the assessment of hydrocarbon biodegradation in hypersaline environments are presented in this review. PMID:24031900

  1. Biodegradable long-circulating polymeric nanospheres.

    Science.gov (United States)

    Gref, R; Minamitake, Y; Peracchia, M T; Trubetskoy, V; Torchilin, V; Langer, R

    1994-03-18

    Injectable nanoparticulate carriers have important potential applications such as site-specific drug delivery or medical imaging. Conventional carriers, however, cannot generally be used because they are eliminated by the reticulo-endothelial system within seconds or minutes after intravenous injection. To address these limitations, monodisperse biodegradable nanospheres were developed from amphiphilic copolymers composed of two biocompatible blocks. The nanospheres exhibited dramatically increased blood circulation times and reduced liver accumulation in mice. Furthermore, they entrapped up to 45 percent by weight of the drug in the dense core in a one-step procedure and could be freeze-dried and easily redispersed without additives in aqueous solutions.

  2. Biodegradation and mineralization of metolachlor and alachlor by Candida xestobii.

    Science.gov (United States)

    Munoz, Ana; Koskinen, William C; Cox, Lucía; Sadowsky, Michael J

    2011-01-26

    Metolachlor (2-chloro-6'-ethyl-N-(2-methoxy-1-methylethyl)aceto-o-toluidide) is a pre-emergent chloroacetanilide herbicide used to control broadleaf and annual grassy weeds in a variety of crops. The S enantiomer, S-metolachlor, is the most effective form for weed control. Although the degradation of metolachlor in soils is thought to occur primarily by microbial activity, little is known about the microorganisms that carry out this process and the mechanisms by which this occurs. This study examined a silty-clay soil (a Luvisol) from Spain, with 10 and 2 year histories of metolachlor and S-metolachlor applications, respectively, for microorganisms that had the ability to degrade this herbicide. Tis paper reports the isolation and characterization of pure cultures of Candida xestobii and Bacillus simplex that have the ability to use metolachlor as a sole source of carbon for growth. Species assignment was confirmed by morphological and biochemical criteria and by sequence analysis of 18S and 16S rRNA, respectively. High-performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) analyses indicated that C. xestobii degraded 60% of the added metolachlor after 4 days of growth and converted up to 25% of the compound into CO(2) after 10 days. In contrast, B. simplex biodegraded 30% of metolachlor following 5 days of growth in minimal medium. In contrast, moreover, the yeast degraded other acetanilide compounds and 80% of acetochlor (2-chloro-N-ethoxymethyl-6'-ethylaceto-o-toluidide) and alachlor (2-chloro-2',6'-diethyl-N-methoxymethylacetanilide) were degraded after 15 and 41 h of growth, respectively. The results of these studies indicate that microorganisms comprising two main branches of the tree of life have acquired the ability to degrade the same novel chlorinated herbicide that has been recently added to the biosphere.

  3. The Value of Contrast Echocardiography

    Directory of Open Access Journals (Sweden)

    Shannon C. Treiber

    2016-01-01

    Full Text Available Purpose: There is much evidence-based research proving the effectiveness of contrast echocardiography, but there are still questions and concerns about its specific uses. This study tested the effectiveness of contrast echocardiography in defining the left ventricular endocardial border. Methods: From 30 patients, a total of 60 echocardiograms –– 30 with and 30 without use of contrast –– were retrospectively reviewed by four blinded cardiologists with advanced training in echocardiography. No single cardiologist reviewed contrast and noncontrast images of the same patient. Each set of 30 echocardiograms was then studied for wall-motion scoring. Visualization of left ventricular wall segments and a global visualization confidence level of interpretation were recorded. Results: Of all wall segments (N = 510, 91% were visualized in echocardiograms with use of contrast, whereas 75% of the walls were visualized in echocardiograms without contrast (P < 0.001. Of 30 examinations, 17 contrast echocardiograms were read with high confidence compared to 6 without contrast use (P = 0.004. The number of walls visualized with contrast was increased in 18 patients (60%, whereas noncontrast echocardiograms yielded more visualized walls in 6 patients (20%, P = 0.002. Conclusions: This study demonstrates that contrast is valuable to echocardiographic imaging. Its use should be supported throughout echocardiography clinics and encouraged in certain patients for whom resting and stress echocardiography results without contrast often prove uninterpretable.

  4. Enhanced biodegradation of hydrocarbons in soil by microbial biosurfactant, sophorolipid.

    Science.gov (United States)

    Kang, Seok-Whan; Kim, Young-Bum; Shin, Jae-Dong; Kim, Eun-Ki

    2010-03-01

    Effectiveness of a microbial biosurfactant, sophorolipid, was evaluated in washing and biodegradation of model hydrocarbons and crude oil in soil. Thirty percent of 2-methylnaphthalene was effectively washed and solubilized with 10 g/L of sophorolipid with similar or higher efficiency than that of commercial surfactants. Addition of sophorolipid in soil increased biodegradation of model compounds: 2-methylnaphthalene (95% degradation in 2 days), hexadecane (97%, 6 days), and pristane (85%, 6 days). Also, effective biodegradation method of crude oil in soil was observed by the addition of sophorolipid, resulting in 80% biodegradation of saturates and 72% aromatics in 8 weeks. These results showed the potentials of the microbial biosurfactant, sophorolipid, as an effective surfactant for soil washing and as an in situ biodegradation enhancer.

  5. Biodegradation of acetanilide herbicides acetochlor and butachlor in soil

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The biodegradation of two acetanilide herbicides,acetochlor and butachlor in soil after other environmental organicmatters addition were measured during 35 days laboratoryincubations. The herbicides were applied to soil alone, soil-SDBS(sodium dodecylbenzene sulfonate) mixtures and soil-HA (humic acid)mixtures. Herbicide biodegradation kinetics were compared in thedifferent treatment. Biodegradation products of herbicides in soilalone samples were identified by GC/MS at the end of incubation.Addition of SDBS and HA to soil decreased acetochlorbiodegradation, but increased butachlor biodegradation. Thebiodegradation half-life of acetochlor and butachlor in soil alone,soil-SDBS mixtures and soil-HA mixtures were 4.6d, 6.1d, 5.4d, and5.3d, 4.9d, and 5.3d respectively. The biodegradation products werehydroxyacetochlor and 2-methyl-6-ethylaniline for acetochlor, andhydroxybutachlor and 2,6-diethylaniline for butachlor.

  6. Biodegradable plastic agricultural mulches and key features of microbial degradation.

    Science.gov (United States)

    Brodhagen, Marion; Peyron, Mark; Miles, Carol; Inglis, Debra Ann

    2015-02-01

    The development of biodegradable plastic mulch films for use in agriculture has been ongoing for decades. These films consist of mixtures of polymers with various additives. As a result, their physical and chemical properties differ from those of the pure polymers often used for in vitro enzymatic and microbial degradation studies, raising questions about the biodegradation capability of mulch films. Currently, standards exist for the biodegradation of plastics in composting conditions but not in soil. Biodegradation in soil or compost depends on a complex synergy of biological and abiotic degradative processes. This review discusses the physicochemical and structural properties of biodegradable plastic mulches, examines their potential for on-site decomposition in light of site-to-site variance due to environmental and biological conditions, and considers the potential for long-term effects on agroecosystem sustainability and functionality.

  7. Evaluation of Artificial Intelligence Based Models for Chemical Biodegradability Prediction

    Directory of Open Access Journals (Sweden)

    Aleksandar Sabljic

    2004-12-01

    Full Text Available This study presents a review of biodegradability modeling efforts including a detailed assessment of two models developed using an artificial intelligence based methodology. Validation results for these models using an independent, quality reviewed database, demonstrate that the models perform well when compared to another commonly used biodegradability model, against the same data. The ability of models induced by an artificial intelligence methodology to accommodate complex interactions in detailed systems, and the demonstrated reliability of the approach evaluated by this study, indicate that the methodology may have application in broadening the scope of biodegradability models. Given adequate data for biodegradability of chemicals under environmental conditions, this may allow for the development of future models that include such things as surface interface impacts on biodegradability for example.

  8. Critical evaluation of biodegradable polymers used in nanodrugs

    Directory of Open Access Journals (Sweden)

    Marin E

    2013-08-01

    Full Text Available Edgar Marin,1–3 Maria Isabel Briceño,2 Catherina Caballero-George11Unit of Pharmacology, Center of Biodiversity and Drug Discovery, Institute of Scientific Research and High Technology Services, 2Nano Dispersions Technology, Panama, Republic of Panama; 3Department of Biotechnology, Archaria Nagarjuna University, Guntur, IndiaAbstract: Use of biodegradable polymers for biomedical applications has increased in recent decades due to their biocompatibility, biodegradability, flexibility, and minimal side effects. Applications of these materials include creation of skin, blood vessels, cartilage scaffolds, and nanosystems for drug delivery. These biodegradable polymeric nanoparticles enhance properties such as bioavailability and stability, and provide controlled release of bioactive compounds. This review evaluates the classification, synthesis, degradation mechanisms, and biological applications of the biodegradable polymers currently being studied as drug delivery carriers. In addition, the use of nanosystems to solve current drug delivery problems are reviewed.Keywords: biodegradable polymers, nanoparticles, drug delivery, cellular uptake, biomedical applications

  9. Porous Biodegradable Metals for Hard Tissue Scaffolds: A Review

    Directory of Open Access Journals (Sweden)

    A. H. Yusop

    2012-01-01

    Full Text Available Scaffolds have been utilized in tissue regeneration to facilitate the formation and maturation of new tissues or organs where a balance between temporary mechanical support and mass transport (degradation and cell growth is ideally achieved. Polymers have been widely chosen as tissue scaffolding material having a good combination of biodegradability, biocompatibility, and porous structure. Metals that can degrade in physiological environment, namely, biodegradable metals, are proposed as potential materials for hard tissue scaffolding where biodegradable polymers are often considered as having poor mechanical properties. Biodegradable metal scaffolds have showed interesting mechanical property that was close to that of human bone with tailored degradation behaviour. The current promising fabrication technique for making scaffolds, such as computation-aided solid free-form method, can be easily applied to metals. With further optimization in topologically ordered porosity design exploiting material property and fabrication technique, porous biodegradable metals could be the potential materials for making hard tissue scaffolds.

  10. Characterization and aerobic biodegradation of selected monoterpenes

    Energy Technology Data Exchange (ETDEWEB)

    Misra, G.; Pavlostathis, S.G.; Li, J.; Purdue, E.M. [Georgia Institute of Technology, Atlanta, GA (United States)

    1996-12-31

    Monoterpenes are biogenic chemicals and occur in abundance in nature. Large-scale industrial use of these chemicals has recently been initiated in an attempt to replace halogenated solvents and chlorofluorocarbons which have been implicated in the stratospheric depletion of ozone. This study examined four hydrocarbon monoterpenes (d-limonene, {alpha}-pinene, {gamma}-terpinene, and terpinolene) and four alcohols (arbanol, linalool, plinol, and {alpha}-terpineol). Water solubility, vapor pressure, and octanol/water partition coefficients were estimated. Aerobic biodegradability tests were conducted in batch reactors by utilizing forest soil extract and enriched cultures as inoculum. The hydrophobic nature and high volatility of the hydrocarbons restricted the investigation to relatively low aqueous concentrations. Each monoterpene was analyzed with a gas chromatograph equipped with a flame ionization detector after extraction from the aqueous phase with isooctane. Terpene mineralization was tested by monitoring liquid-phase carbon, CO{sub 2} production and biomass growth. All four hydrocarbons and two alcohols readily degraded under aerobic conditions. Plinol resisted degradation in assays using inocula from diverse sources, while arbanol degraded very slowly. The intrinsic biokinetics coefficients for the degradation of d-limonene and {alpha}-terpineol were estimated by using cultures enriched with the respective monoterpenes. Monoterpene biodegradation followed Monod kinetics.

  11. Optimization of low ring polycylic aromatic biodegradation

    Science.gov (United States)

    Othman, N.; Abdul-Talib, S.; Tay, C. C.

    2016-07-01

    Polycyclic aromatic hydrocarbons (PAHs) are recalcitrance and persistence that finally turn into problematic environmental contaminants. Microbial degradation is considered to be the primary mechanism of PAHs removal from the environment due to its organic criteria. This study is carried out to optimize degradation process of low ring PAHs. Bacteria used in this study was isolated from sludge collected from Kolej Mawar, Universiti Teknologi MARA, Shah Alam, Selangor. Working condition namely, substrate concentration, bacteria concentration, pH and temperature were optimized. PAHs in the liquid sample was extracted by using solid phase microextractio equipped with a 7 µm polydimethylsiloxane (PDMS) SPME fibr. Removal of PAHs were assessed by measuring PAHs concentration using GC-FID. Results from the optimization study of biodegradation indicated that maximum rate of PAHs removal occurred at 100 mgL-1 of PAHs, 10% bacteria concentration, pH 7.0 and 30°C. These working condition had proved the effectiveness of using bacteria in biodegradation process of PAHs.

  12. A REVIEW ON BIODEGRADABLE STARCH BASED FILM

    Directory of Open Access Journals (Sweden)

    Hooman Molavi

    2015-04-01

    Full Text Available In recent years, biodegradable edible films have become very important in research related to food, due to their compatibility with the environment and their use in the food packaging industry. Various sources can be used in the production of biopolymers as biodegradable films that include polysaccharides, proteins and lipids. Among the various polysaccharides, starch due to its low price and its abundance in nature is of significant importance. Several factors affect the properties of starch films; such as the source which starch is obtained from, as well as the ratio of constituents of the starch. Starch films have advantages such as low thickness, flexibility and transparency though; there are some downsides to mention, such as the poor mechanical properties and water vapor permeability. Thus, using starch alone to produce the film will led to restrictions on its use. To improve the mechanical properties of starch films and also increases resistance against humidity, several methods can be used; including the starch modifying techniques such as cross linking of starch and combining starch with other natural polymers. Other methods such as the use of lipid in formulations of films to increase the resistance to moisture are possible, but lipids are susceptible to oxidation. Therefore, new approaches are based on the integration of different biopolymers in food packaging.

  13. Endothelial Cellular Responses to Biodegradable Metal Zinc.

    Science.gov (United States)

    Ma, Jun; Zhao, Nan; Zhu, Donghui

    Biodegradable zinc (Zn) metals, a new generation of biomaterials, have attracted much attention due to their excellent biodegradability, bioabsorbability, and adaptability to tissue regeneration. Compared with magnesium (Mg) and iron (Fe), Zn exhibits better corrosion and mechanical behaviors in orthopedic and stent applications. After implantation, Zn containing material will slowly degrade, and Zn ions (Zn(2+)) will be released to the surrounding tissue. For stent applications, the local Zn(2+)concentration near endothelial tissue/cells could be high. However, it is unclear how endothelia will respond to such high concentrations of Zn(2+), which is pivotal to vascular remodeling and regeneration. Here, we evaluated the short-term cellular behaviors of primary human coronary artery endothelial cells (HCECs) exposed to a concentration gradient (0-140 μM) of extracellular Zn(2+). Zn(2+) had an interesting biphasic effect on cell viability, proliferation, spreading, and migration. Generally, low concentrations of Zn(2+) promoted viability, proliferation, adhesion, and migration, while high concentrations of Zn(2+) had opposite effects. For gene expression profiles, the most affected functional genes were related to cell adhesion, cell injury, cell growth, angiogenesis, inflammation, vessel tone, and coagulation. These results provide helpful information and guidance for Zn-based alloy design as well as the controlled release of Zn(2+)in stent and other related medical applications.

  14. Immunological Response to Biodegradable Magnesium Implants

    Science.gov (United States)

    Pichler, Karin; Fischerauer, Stefan; Ferlic, Peter; Martinelli, Elisabeth; Brezinsek, Hans-Peter; Uggowitzer, Peter J.; Löffler, Jörg F.; Weinberg, Annelie-Martina

    2014-04-01

    The use of biodegradable magnesium implants in pediatric trauma surgery would render surgical interventions for implant removal after tissue healing unnecessary, thereby preventing stress to the children and reducing therapy costs. In this study, we report on the immunological response to biodegradable magnesium implants—as an important aspect in evaluating biocompatibility—tested in a growing rat model. The focus of this study was to investigate the response of the innate immune system to either fast or slow degrading magnesium pins, which were implanted into the femoral bones of 5-week-old rats. The main alloying element of the fast-degrading alloy (ZX50) was Zn, while it was Y in the slow-degrading implant (WZ21). Our results demonstrate that degrading magnesium implants beneficially influence the immune system, especially in the first postoperative weeks but also during tissue healing and early bone remodeling. However, rodents with WZ21 pins showed a slightly decreased phagocytic ability during bone remodeling when the degradation rate reached its maximum. This may be due to the high release rate of the rare earth-element yttrium, which is potentially toxic. From our results we conclude that magnesium implants have a beneficial effect on the innate immune system but that there are some concerns regarding the use of yttrium-alloyed magnesium implants, especially in pediatric patients.

  15. Tailoring the biodegradability of porous silicon nanoparticles.

    Science.gov (United States)

    Hon, Nick K; Shaposhnik, Zory; Diebold, Eric D; Tamanoi, Fuyuhiko; Jalali, Bahram

    2012-12-01

    Porous silicon nanoparticles (PSiNPs) are attractive carriers for targeted drug delivery in nanomedicine. For in vivo applications, the biodegradation property of PSiNPs provides a pathway for their safe clearance from the body. Particles sizes of 80-120 nm are of particular interest as they are important for cellular applications, such as drug delivery for cancer therapy, because these nanoparticles can take advantage of the enhanced permeability and retention effect to deliver drug preferentially to tumors with leaky vasculature, yet large enough to avoid renal clearance. However, the biodegradability rate of such particles is often too fast, which limits particle half-life and potentially reduces their in vivo delivery efficiency. In this work, we focus on the degradation of nanoscale particles and study the effect of both thermal oxidation and silica coating on the stability of PSiNPs in phosphate buffered saline solution (a close mimic of a basic biological fluid). Using thermal oxidation, the half-life of PSiNPs can be varied from 10 min up to 3 h. Using silica coating, the half-life can be extended further to 8 h. The particles produced using both these techniques can be functionalized using standard silica surface chemistries developed for applications in drug delivery.

  16. Polymeric Biodegradable Stent Insertion in the Esophagus

    Directory of Open Access Journals (Sweden)

    Kai Yang

    2016-04-01

    Full Text Available Esophageal stent insertion has been used as a well-accepted and effective alternative to manage and improve the quality of life for patients diagnosed with esophageal diseases and disorders. Current stents are either permanent or temporary and are fabricated from either metal or plastic. The partially covered self-expanding metal stent (SEMS has a firm anchoring effect and prevent stent migration, however, the hyperplastic tissue reaction cause stent restenosis and make it difficult to remove. A fully covered SEMS and self-expanding plastic stent (SEPS reduced reactive hyperplasia but has a high migration rate. The main advantage that polymeric biodegradable stents (BDSs have over metal or plastic stents is that removal is not require and reduce the need for repeated stent insertion. But the slightly lower radial force of BDS may be its main shortcoming and a post-implant problem. Thus, strengthening support of BDS is a content of the research in the future. BDSs are often temporarily effective in esophageal stricture to relieve dysphagia. In the future, it can be expect that biodegradable drug-eluting stents (DES will be available to treat benign esophageal stricture, perforations or leaks with additional use as palliative modalities for treating malignant esophageal stricture, as the bridge to surgery or to maintain luminal patency during neoadjuvant chemoradiation.

  17. Modification of Biodegradable Polyesters Using Electron Beam

    Directory of Open Access Journals (Sweden)

    M. Suhartini

    2013-12-01

    Full Text Available Poly(4-Hydroxybutirat P4HB, Poly(butylene succinate-co-adipate PBSA and Poly(-caprolactone PCL were electron beam (EB-irradiated. Poly(4-Hydroxybutirat was irradiated without any polyfunctional monomers (PFM. While PBSA and PCL were irradiated in the presence of polyfunctional monomers such as Trimethallyl isocyanurate (TMAIC, Polyethyleneglycol dimethacrylate (2G, 4G, Trimethylolpropane trimethacrylate (TMPT and Tetramethylolmethane tetraacrylate (A-TMMT at ambient temperature. Aim of the study is to improve the properties of biodegradable polyester. It was pointed out that crosslinking yield of P4HB (6.39% gel was formed at dose of 90 kGy irradiated in vacuum conditions. Radiation degradation promoted, when P4HB was irradiated in air. The optimum crosslinking yield of PCL and PBSA respectively, were formed in the presence of 1% TMAIC at dose of 50 kGy. The biodegradability of the crosslinked PBSA evaluated by soil burial test is slightly retarded by increasing crosslinking yields.

  18. Biodegradable polymer optical fiber (Conference Presentation)

    Science.gov (United States)

    Zhang, Chenji; Kalaba, Surge; Shan, Dingying; Xu, Kaitian; Yang, Jian; Liu, Zhiwen

    2016-10-01

    Biocompatible and even biodegradable polymers have unique advantages in various biomedical applications. Recent years, photonic devices fabricated using biocompatible polymers have been widely studied. In this work, we manufactured an optical fiber using biodegradable polymer POC and POMC. This step index optical fiber is flexible and easy to handle. Light was coupled into this polymer fiber by directly using objective. The fiber has a good light guiding property and an approximate loss of 2db/cm. Due to the two layer structure, our fiber is able to support applications inside biological tissue. Apart from remarkable optical performance, our fiber was also found capable of performing imaging. By measuring the impulse response of this multimode polymer fiber and using the linear inversion algorithm, concept proving experiments were completed. Images input into our fiber were able to be retrieved from the intensity distribution of the light at the output end. Experiment result proves the capability of our optical fiber to be used as a fiber endoscopy no needs to remove.

  19. Role of biodegradation in the removal of pharmaceutically active compounds with different bulk organic matter characteristics through managed aquifer recharge: Batch and column studies

    KAUST Repository

    Maeng, Sungkyu

    2011-10-01

    Natural water treatment systems such as bank filtration have been recognized as providing effective barriers in the multi-barrier approach for attenuation of organic micropollutants for safe drinking water supply. In this study, the role of biodegradation in the removal of selected pharmaceutically active compounds (PhACs) during soil passage was investigated. Batch studies were conducted to investigate the removal of 13 selected PhACs from different water sources with respect to different sources of biodegradable organic matter. Neutral PhACs (phenacetine, paracetamol, and caffeine) and acidic PhACs (ibuprofen, fenoprofen, bezafibrate, and naproxen) were removed with efficiencies greater than 88% from different organic matter water matrices during batch studies (hydraulic retention time (HRT): 60 days). Column experiments were then performed to differentiate between biodegradation and sorption with regard to the removal of selected PhACs. In column studies, removal efficiencies of acidic PhACs (e.g., analgesics) decreased under conditions of limited biodegradable carbon. The removal efficiencies of acidic PhACs were found to be less than 21% under abiotic conditions. These observations were attributed to sorption under abiotic conditions established by a biocide (20 mM sodium azide), which suppresses microbial activity/biodegradation. However, under biotic conditions, the removal efficiencies of these acidic PhACs were found to be greater than 59%. This is mainly attributed to biodegradation. Moreover, the average removal efficiencies of hydrophilic (polar) neutral PhACs (paracetamol, pentoxifylline, and caffeine) with low octanol/water partition coefficients (log K ow less than 1) were low (11%) under abiotic conditions. However, under biotic conditions, removal efficiencies of the neutral PhACs were greater than 98%. In contrast, carbamazepine persisted and was not easily removed under either biotic or abiotic conditions. This study indicates that biodegradation

  20. Temperature Sensitivity as a Microbial Trait Using Parameters from Macromolecular Rate Theory

    Directory of Open Access Journals (Sweden)

    Charlotte Jean Alster

    2016-11-01

    Full Text Available The activity of soil microbial extracellular enzymes is strongly controlled by temperature, yet the degree to which temperature sensitivity varies by microbe and enzyme type is unclear. Such information would allow soil microbial enzymes to be incorporated in a traits-based framework to improve prediction of ecosystem response to global change. If temperature sensitivity varies for specific soil enzymes, then determining the underlying causes of variation in temperature sensitivity of these enzymes will provide fundamental insights for predicting nutrient dynamics belowground. In this study, we characterized how both microbial taxonomic variation as well as substrate type affects temperature sensitivity. We measured β-glucosidase, leucine aminopeptidase, and phosphatase activities at six temperatures: 4, 11, 25, 35, 45, and 60°C, for seven different soil microbial isolates. To calculate temperature sensitivity, we employed two models, Arrhenius, which predicts an exponential increase in reaction rate with temperature, and Macromolecular Rate Theory (MMRT, which predicts rate to peak and then decline as temperature increases. We found MMRT provided a more accurate fit and allowed for more nuanced interpretation of temperature sensitivity in all of the enzyme × isolate combinations tested. Our results revealed that both the enzyme type and soil isolate type explain variation in parameters associated with temperature sensitivity. Because we found temperature sensitivity to be an inherent and variable property of an enzyme, we argue that it can be incorporated as a microbial functional trait, but only when using the MMRT definition of temperature sensitivity. We show that the Arrhenius metrics of temperature sensitivity are overly sensitive to test conditions, with activation energy changing depending on the temperature range it was calculated within. Thus, we propose the use of the MMRT definition of temperature sensitivity for accurate

  1. Temperature Sensitivity as a Microbial Trait Using Parameters from Macromolecular Rate Theory.

    Science.gov (United States)

    Alster, Charlotte J; Baas, Peter; Wallenstein, Matthew D; Johnson, Nels G; von Fischer, Joseph C

    2016-01-01

    The activity of soil microbial extracellular enzymes is strongly controlled by temperature, yet the degree to which temperature sensitivity varies by microbe and enzyme type is unclear. Such information would allow soil microbial enzymes to be incorporated in a traits-based framework to improve prediction of ecosystem response to global change. If temperature sensitivity varies for specific soil enzymes, then determining the underlying causes of variation in temperature sensitivity of these enzymes will provide fundamental insights for predicting nutrient dynamics belowground. In this study, we characterized how both microbial taxonomic variation as well as substrate type affects temperature sensitivity. We measured β-glucosidase, leucine aminopeptidase, and phosphatase activities at six temperatures: 4, 11, 25, 35, 45, and 60°C, for seven different soil microbial isolates. To calculate temperature sensitivity, we employed two models, Arrhenius, which predicts an exponential increase in reaction rate with temperature, and Macromolecular Rate Theory (MMRT), which predicts rate to peak and then decline as temperature increases. We found MMRT provided a more accurate fit and allowed for more nuanced interpretation of temperature sensitivity in all of the enzyme × isolate combinations tested. Our results revealed that both the enzyme type and soil isolate type explain variation in parameters associated with temperature sensitivity. Because we found temperature sensitivity to be an inherent and variable property of an enzyme, we argue that it can be incorporated as a microbial functional trait, but only when using the MMRT definition of temperature sensitivity. We show that the Arrhenius metrics of temperature sensitivity are overly sensitive to test conditions, with activation energy changing depending on the temperature range it was calculated within. Thus, we propose the use of the MMRT definition of temperature sensitivity for accurate interpretation of

  2. The High Mosaicity Illusion: Revealing the True Physical Characteristics of Macromolecular Crystals

    Science.gov (United States)

    Bellamy, Henry; Snell, Edward H.; Borgstahl, Gloria

    2000-01-01

    An experimental system and software have been developed for simultaneously measuring the diffraction resolution and mosaic spread of macromolecular crystals. Hundreds of reflection profiles over a wide resolution range were rapidly measured by using a charge coupled device (CCD) area detector in combination with superfine phi slicing data collection. The contributions of the X-ray beam to the reflection widths were minimized by using a highly-parallel, highly-monochromatic synchrotron source. These contributions and Lorentz effects were evaluated and deconvoluted from the recorded data. Data collection and processing is described. From one degree of superfine phi slice data collected on a crystal of manganese superoxide dismutase the mosaicity of 261 reflections were measured. The average mosaicity was 0.0101 degrees (0.0035) at the full-width-at-half-maximum (FWHM) and ranged from 0.0011 degrees to 0.0188 degrees. Each reflection profile was individually fit with two gaussian profiles with the first gaussian contributing 55% and the second contributing 35% of the reflection. On average, the mosaicity of the first gaussian was 0.0054 degrees (0.0015) and the second was 0.0061 degrees (0.0023). The mosaicity of the crystal was anisotropic with fh, f k, and fl values of 0.0068 degrees, 0.0140 degrees and 0.0046 degrees, respectively at the FWHM. The anisotropic mosaicity analysis indicates that the crystal is the most perfect in the I direction which corresponds to the favored growth direction of the crystal.

  3. Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin.

    Science.gov (United States)

    Mueller, Uwe; Darowski, Nora; Fuchs, Martin R; Förster, Ronald; Hellmig, Michael; Paithankar, Karthik S; Pühringer, Sandra; Steffien, Michael; Zocher, Georg; Weiss, Manfred S

    2012-05-01

    Three macromolecular crystallography (MX) beamlines at the Helmholtz-Zentrum Berlin (HZB) are available for the regional, national and international structural biology user community. The state-of-the-art synchrotron beamlines for MX BL14.1, BL14.2 and BL14.3 are located within the low-β section of the BESSY II electron storage ring. All beamlines are fed from a superconducting 7 T wavelength-shifter insertion device. BL14.1 and BL14.2 are energy tunable in the range 5-16 keV, while BL14.3 is a fixed-energy side station operated at 13.8 keV. All three beamlines are equipped with CCD detectors. BL14.1 and BL14.2 are in regular user operation providing about 200 beam days per year and about 600 user shifts to approximately 50 research groups across Europe. BL14.3 has initially been used as a test facility and was brought into regular user mode operation during the year 2010. BL14.1 has recently been upgraded with a microdiffractometer including a mini-κ goniometer and an automated sample changer. Additional user facilities include office space adjacent to the beamlines, a sample preparation laboratory, a biology laboratory (safety level 1) and high-end computing resources. In this article the instrumentation of the beamlines is described, and a summary of the experimental possibilities of the beamlines and the provided ancillary equipment for the user community is given.

  4. Role of solvent properties of aqueous media in macromolecular crowding effects.

    Science.gov (United States)

    Ferreira, Luisa A; Madeira, Pedro P; Breydo, Leonid; Reichardt, Christian; Uversky, Vladimir N; Zaslavsky, Boris Y

    2016-01-01

    Analysis of the macromolecular crowding effects in polymer solutions show that the excluded volume effect is not the only factor affecting the behavior of biomolecules in a crowded environment. The observed inconsistencies are commonly explained by the so-called soft interactions, such as electrostatic, hydrophobic, and van der Waals interactions, between the crowding agent and the protein, in addition to the hard nonspecific steric interactions. We suggest that the changes in the solvent properties of aqueous media induced by the crowding agents may be the root of these "soft" interactions. To check this hypothesis, the solvatochromic comparison method was used to determine the solvent dipolarity/polarizability, hydrogen-bond donor acidity, and hydrogen-bond acceptor basicity of aqueous solutions of different polymers (dextran, poly(ethylene glycol), Ficoll, Ucon, and polyvinylpyrrolidone) with the polymer concentration up to 40% typically used as crowding agents. Polymer-induced changes in these features were found to be polymer type and concentration specific, and, in case of polyethylene glycol (PEG), molecular mass specific. Similarly sized polymers PEG and Ucon producing different changes in the solvent properties of water in their solutions induced morphologically different α-synuclein aggregates. It is shown that the crowding effects of some polymers on protein refolding and stability reported in the literature can be quantitatively described in terms of the established solvent features of the media in these polymers solutions. These results indicate that the crowding agents do induce changes in solvent properties of aqueous media in crowded environment. Therefore, these changes should be taken into account for crowding effect analysis.

  5. Structure of metaphase chromosomes: a role for effects of macromolecular crowding.

    Directory of Open Access Journals (Sweden)

    Ronald Hancock

    Full Text Available In metaphase chromosomes, chromatin is compacted to a concentration of several hundred mg/ml by mechanisms which remain elusive. Effects mediated by the ionic environment are considered most frequently because mono- and di-valent cations cause polynucleosome chains to form compact ~30-nm diameter fibres in vitro, but this conformation is not detected in chromosomes in situ. A further unconsidered factor is predicted to influence the compaction of chromosomes, namely the forces which arise from crowding by macromolecules in the surrounding cytoplasm whose measured concentration is 100-200 mg/ml. To mimic these conditions, chromosomes were released from mitotic CHO cells in solutions containing an inert volume-occupying macromolecule (8 kDa polyethylene glycol, 10.5 kDa dextran, or 70 kDa Ficoll in 100 µM K-Hepes buffer, with contaminating cations at only low micromolar concentrations. Optical and electron microscopy showed that these chromosomes conserved their characteristic structure and compaction, and their volume varied inversely with the concentration of a crowding macromolecule. They showed a canonical nucleosomal structure and contained the characteristic proteins topoisomerase IIα and the condensin subunit SMC2. These observations, together with evidence that the cytoplasm is crowded in vivo, suggest that macromolecular crowding effects should be considered a significant and perhaps major factor in compacting chromosomes. This model may explain why ~30-nm fibres characteristic of cation-mediated compaction are not seen in chromosomes in situ. Considering that crowding by cytoplasmic macromolecules maintains the compaction of bacterial chromosomes and has been proposed to form the liquid crystalline chromosomes of dinoflagellates, a crowded environment may be an essential characteristic of all genomes.

  6. Prospects for simulating macromolecular surfactant chemistry at the ocean-atmosphere boundary

    Science.gov (United States)

    Elliott, S.; Burrows, S. M.; Deal, C.; Liu, X.; Long, M.; Ogunro, O.; Russell, L. M.; Wingenter, O.

    2014-05-01

    Biogenic lipids and polymers are surveyed for their ability to adsorb at the water-air interfaces associated with bubbles, marine microlayers and particles in the overlying boundary layer. Representative ocean biogeochemical regimes are defined in order to estimate local concentrations for the major macromolecular classes. Surfactant equilibria and maximum excess are then derived based on a network of model compounds. Relative local coverage and upward mass transport follow directly, and specific chemical structures can be placed into regional rank order. Lipids and denatured protein-like polymers dominate at the selected locations. The assigned monolayer phase states are variable, whether assessed along bubbles or at the atmospheric spray droplet perimeter. Since oceanic film compositions prove to be irregular, effects on gas and organic transfer are expected to exhibit geographic dependence as well. Moreover, the core arguments extend across the sea-air interface into aerosol-cloud systems. Fundamental nascent chemical properties including mass to carbon ratio and density depend strongly on the geochemical state of source waters. High surface pressures may suppress the Kelvin effect, and marine organic hygroscopicities are almost entirely unconstrained. While bubble adsorption provides a well-known means for transporting lipidic or proteinaceous material into sea spray, the same cannot be said of polysaccharides. Carbohydrates tend to be strongly hydrophilic so that their excess carbon mass is low despite stacked polymeric geometries. Since sugars are abundant in the marine aerosol, gel-based mechanisms may be required to achieve uplift. Uncertainties distill to a global scale dearth of information regarding two dimensional kinetics and equilibria. Nonetheless simulations are recommended, to initiate the process of systems level quantification.

  7. Prospects for Simulating Macromolecular Surfactant Chemistry at the Ocean-Atmosphere Boundary

    Energy Technology Data Exchange (ETDEWEB)

    Elliott, S.; Burrows, Susannah M.; Deal, C.; Liu, Xiaohong; Long, M.; Ogunro, O.; Russell, Lynn M.; Wingenter, O.

    2014-05-01

    Biogenic lipids and polymers are surveyed for their ability to adsorb at the water-air interfaces associated with bubbles, marine microlayers and particles in the overlying boundary layer. Representative ocean biogeochemical regimes are defined in order to estimate local concentrations for the major macromolecular classes. Surfactant equilibria and maximum excess are then derived based on a network of model compounds. Relative local coverage and upward mass transport follow directly, and specific chemical structures can be placed into regional rank order. Lipids and denatured protein-like polymers dominate at the selected locations. The assigned monolayer phase states are variable, whether assessed along bubbles or at the atmospheric spray droplet perimeter. Since oceanic film compositions prove to be irregular, effects on gas and organic transfer are expected to exhibit geographic dependence as well. Moreover, the core arguments extend across the sea-air interface into aerosol-cloud systems. Fundamental nascent chemical properties including mass to carbon ratio and density depend strongly on the geochemical state of source waters. High surface pressures may suppress the Kelvin effect, and marine organic hygroscopicities are almost entirely unconstrained. While bubble adsorption provides a well-known means for transporting lipidic or proteinaceous material into sea spray, the same cannot be said of polysaccharides. Carbohydrates tend to be strongly hydrophilic so that their excess carbon mass is low despite stacked polymeric geometries. Since sugars are abundant in the marine aerosol, gel-based mechanisms may be required to achieve uplift. Uncertainties in the surfactant logic distill to a global scale dearth of information regarding two dimensional kinetics and equilibria. Nonetheless simulations are recommended, to initiate the process of systems level quantification.

  8. Structure of metaphase chromosomes: a role for effects of macromolecular crowding.

    Science.gov (United States)

    Hancock, Ronald

    2012-01-01

    In metaphase chromosomes, chromatin is compacted to a concentration of several hundred mg/ml by mechanisms which remain elusive. Effects mediated by the ionic environment are considered most frequently because mono- and di-valent cations cause polynucleosome chains to form compact ~30-nm diameter fibres in vitro, but this conformation is not detected in chromosomes in situ. A further unconsidered factor is predicted to influence the compaction of chromosomes, namely the forces which arise from crowding by macromolecules in the surrounding cytoplasm whose measured concentration is 100-200 mg/ml. To mimic these conditions, chromosomes were released from mitotic CHO cells in solutions containing an inert volume-occupying macromolecule (8 kDa polyethylene glycol, 10.5 kDa dextran, or 70 kDa Ficoll) in 100 µM K-Hepes buffer, with contaminating cations at only low micromolar concentrations. Optical and electron microscopy showed that these chromosomes conserved their characteristic structure and compaction, and their volume varied inversely with the concentration of a crowding macromolecule. They showed a canonical nucleosomal structure and contained the characteristic proteins topoisomerase IIα and the condensin subunit SMC2. These observations, together with evidence that the cytoplasm is crowded in vivo, suggest that macromolecular crowding effects should be considered a significant and perhaps major factor in compacting chromosomes. This model may explain why ~30-nm fibres characteristic of cation-mediated compaction are not seen in chromosomes in situ. Considering that crowding by cytoplasmic macromolecules maintains the compaction of bacterial chromosomes and has been proposed to form the liquid crystalline chromosomes of dinoflagellates, a crowded environment may be an essential characteristic of all genomes.

  9. Development of an online UV-visible microspectrophotometer for a macromolecular crystallography beamline.

    Science.gov (United States)

    Shimizu, Nobutaka; Shimizu, Tetsuya; Baba, Seiki; Hasegawa, Kazuya; Yamamoto, Masaki; Kumasaka, Takashi

    2013-11-01

    Measurement of the UV-visible absorption spectrum is a convenient technique for detecting chemical changes of proteins, and it is therefore useful to combine spectroscopy and diffraction studies. An online microspectrophotometer for the UV-visible region was developed and installed on the macromolecular crystallography beamline, BL38B1, at SPring-8. This spectrophotometer is equipped with a difference dispersive double monochromator, a mercury-xenon lamp as the light source, and a photomultiplier as the detector. The optical path is mostly constructed using mirrors, in order to obtain high brightness in the UV region, and the confocal optics are assembled using a cross-slit diaphragm like an iris to eliminate stray light. This system can measure optical densities up to a maximum of 4.0. To study the effect of radiation damage, preliminary measurements of glucose isomerase and thaumatin crystals were conducted in the UV region. Spectral changes dependent on X-ray dose were observed at around 280 nm, suggesting that structural changes involving Trp or Tyr residues occurred in the protein crystal. In the case of the thaumatin crystal, a broad peak around 400 nm was also generated after X-ray irradiation, suggesting the cleavage of a disulfide bond. Dose-dependent spectral changes were also observed in cryo-solutions alone, and these changes differed with the composition of the cryo-solution. These responses in the UV region are informative regarding the state of the sample; consequently, this device might be useful for X-ray crystallography.

  10. Isolation and characterization of macromolecular protein R-Phycoerythrin from Portieria hornemannii.

    Science.gov (United States)

    Senthilkumar, Namasivayam; Suresh, Veeraperumal; Thangam, Ramar; Kurinjimalar, Chidambaram; Kavitha, Ganapathy; Murugan, Pitchai; Kannan, Soundarapandian; Rengasamy, Ramasamy

    2013-04-01

    R-Phycoerythrin (R-PE) is one of the three phycobiliproteins which are extensively used as fluorescent probes, and it is prepared from red macro-algae. This macromolecular protein has gained importance in many biotechnological applications in food science, immunodiagnostic, therapy, cosmetics, protein and cell labeling, and analytical processes. In the present investigation, R-PE was isolated and purified from a red alga Portieria hornemannii. R-PE extracted and purified through ammonium sulfate precipitation (55%) followed by Q-Sepharose column chromatography had yielded a maximum purity of 5.2%. R-PE exhibited a typical "three-peak" with absorption maxima at 499, 545 and 565 nm. CD spectrum of R-PE yielded the following secondary structure data: alpha helix (14.30%), beta helix (28.10%), turn helix (19.20%) and random coil helix (38.40%). The molecular mass of R-PE was 240 kDa under Native-PAGE. Three different subunits such as α, β and γ of 16 kDa, 21 kDa and 39 kDa were segregated under SDS-PAGE. On two dimensional gel electrophoresis, one basic and four acidic subunits were detected. Five different tryptic peptides were assigned under MALDI-TOF. The sequences of N-terminus of R-PE of 10 different amino acids are Met Lys Gln Met Trp Asp Arg Met Val Val. The preparative procedures of the R-PE extraction and purification established based on the experiments exhibit advantages and can offer a reference for R-PE preparation from other marine red macro-alga P. hornemannii.

  11. Room-temperature macromolecular crystallography using a micro-patterned silicon chip with minimal background scattering

    Science.gov (United States)

    Roedig, Philip; Duman, Ramona; Sanchez-Weatherby, Juan; Vartiainen, Ismo; Burkhardt, Anja; Warmer, Martin; David, Christian; Wagner, Armin; Meents, Alke

    2016-01-01

    Recent success at X-ray free-electron lasers has led to serial crystallography experiments staging a comeback at synchrotron sources as well. With crystal lifetimes typically in the millisecond range and the latest-generation detector technologies with high framing rates up to 1 kHz, fast sample exchange has become the bottleneck for such experiments. A micro-patterned chip has been developed from single-crystalline silicon, which acts as a sample holder for up to several thousand microcrystals at a very low background level. The crystals can be easily loaded onto the chip and excess mother liquor can be efficiently removed. Dehydration of the crystals is prevented by keeping them in a stream of humidified air during data collection. Further sealing of the sample holder, for example with Kapton, is not required. Room-temperature data collection from insulin crystals loaded onto the chip proves the applicability of the chip for macromolecular crystallography. Subsequent structure refinements reveal no radiation-damage-induced structural changes for insulin crystals up to a dose of 565.6 kGy, even though the total diffraction power of the crystals has on average decreased to 19.1% of its initial value for the same dose. A decay of the diffracting power by half is observed for a dose of D 1/2 = 147.5 ± 19.1 kGy, which is about 1/300 of the dose before crystals show a similar decay at cryogenic temperatures. PMID:27275143

  12. Experimental study of clay-hydrocarbon interactions relevant to the biodegradation of the Deepwater Horizon oil from the Gulf of Mexico.

    Science.gov (United States)

    Warr, Laurence N; Friese, André; Schwarz, Florian; Schauer, Frieder; Portier, Ralph J; Basirico, Laura M; Olson, Gregory M

    2016-11-01

    Adding clay to marine oil pollution represents a promising approach to enhance bacterial hydrocarbon degradation in nutrient poor waters. In this study, three types of regionally available clays (Ca-bentonite, Fuller's Earth and kaolin) were tested to stimulate the biodegradation of source and weathered oil collected from the Deepwater Horizon spill. The weathered oil showed little biodegradation prior to experimentation and was extensively degraded by bacteria in the laboratory in a similar way as the alkane-rich source oil. For both oils, the addition of natural clay-flakes showed minor enhancement of oil biodegradation compared to the non-clay bearing control, but the clay-oil films did limit evaporation. Only alkanes of a molecular weight (MW) > 420 showed significant reduction by enhanced biodegradation following natural clay treatment. In contrast, all fertilized clay flakes showed major bacterial degradation of the oil, with a 6-10 times reduction in alkane content, and an up to 8 fold increase in the rate of O2 consumption. Compared to the control, such treatment showed particular reduction of longer chained alkanes (MW > 226). The application of natural and fertilized clay flakes also showed selective reduction of PAHs, mainly in the MW range of 200-300, but without significant change in the toxicity indices measured. These results imply that a large variety of clays may be used to boost oil biodegradation by aiding attachment of fertilizing nutrients to the oil.

  13. Contrast-enhanced endoscopic ultrasonography

    DEFF Research Database (Denmark)

    Reddy, Nischita K; Ioncica, Ana Maria; Saftoiu, Adrian;

    2011-01-01

    agents and their use in various endoscopic procedures in the gastrointestinal tract. Various applications of contrast-enhanced endoscopic ultrasonography include differentiating benign from malignant mediastinal lymphadenopathy, assessment of depth of invasion of esophageal, gastric and gall bladder...... sonography to depict tumor neovascularization can be increased by contrast agents. Contrast-enhanced harmonic imaging is a useful aid in identifying the tumor vasculature and studying pancreatic microperfusion. In the future, these techniques could potentially be used to quantify tumor perfusion, to assess...

  14. Biodegradation of 17β-estradiol, estrone, and testosterone in stream sediments

    Science.gov (United States)

    Bradley, P.M.; Chapelle, F.H.; Barber, L.B.; McMahon, P.B.; Gray, J.L.; Kolpin, D.W.

    2009-01-01

    The release of endocrine-disrupting chemicals (EDCs) in wastewater treatment plant (WWTP) effluent poses a significant threat to the ecology of surface water receptors, due to impacts on the hormonal control, sexual development, reproductive success and community structure of the indigenous aquatic organisms and associated wildlife. Among the EDCs commonly observed in WWTP effluent, the natural [e.g., 17??-estradiol (E2) and estrone (E1)] and synthetic [e.g., ethynylestradiol (EE2)] estrogens are particular concerns owing to their high endocrine reactivity in both in vitro and in vivo laboratory models. These reproductive hormones have been identified as the primary cause of estrogenic effects in wastewater effluent, with greater than 95% of the estrogen receptor agonist activity in effluent attributed to this contaminant group. The potentials for in situ biodegradation of 17??-estradiol (E2), estrone (E1), and testosterone (T) were investigated in three, hydrologically-distinct, WWTP-impacted streams in the United States. Relative differences in the mineralization of [4-14C] substrates were assessed in oxic microcosms containing sediment or water-only from locations upstream and downstream of the WWTP outfall in each system. Upstream samples provided insight into the biodegradative potential of sediment microbial communities that were not under the immediate impact of WWTP effluent. Upstream sediment from all three systems demonstrated significant mineralization of the "A" ring of E2, E1 and T, with the potential of T biodegradation consistently greater than of E2 and no systematic difference in the potentials of E2 and E1. Downstream samples provided insight into the impacts of effluent on reproductive hormone biodegradation. Significant "A" ring mineralization was also observed in downstream sediment, with the potentials for E1 and T mineralization being substantially depressed relative to upstream samples. In marked contrast, the potentials for E2

  15. Local Kinetic Measures of Macromolecular Structure Reveal Partitioning Among Multiple Parallel Pathways from the Earliest Steps in the Folding of a Large RNA Molecule

    Energy Technology Data Exchange (ETDEWEB)

    Laederach,A.; Shcherbakova, I.; Liang, M.; Brenowitz, M.; Altman, R.

    2006-01-01

    At the heart of the RNA folding problem is the number, structures, and relationships among the intermediates that populate the folding pathways of most large RNA molecules. Unique insight into the structural dynamics of these intermediates can be gleaned from the time-dependent changes in local probes of macromolecular conformation (e.g. reports on individual nucleotide solvent accessibility offered by hydroxyl radical ({center_dot}OH) footprinting). Local measures distributed around a macromolecule individually illuminate the ensemble of separate changes that constitute a folding reaction. Folding pathway reconstruction from a multitude of these individual measures is daunting due to the combinatorial explosion of possible kinetic models as the number of independent local measures increases. Fortunately, clustering of time progress curves sufficiently reduces the dimensionality of the data so as to make reconstruction computationally tractable. The most likely folding topology and intermediates can then be identified by exhaustively enumerating all possible kinetic models on a super-computer grid. The folding pathways and measures of the relative flux through them were determined for Mg{sup 2+} and Na{sup +}-mediated folding of the Tetrahymena thermophila group I intron using this combined experimental and computational approach. The flux during Mg{sup 2+}-mediated folding is divided among numerous parallel pathways. In contrast, the flux during the Na{sup +}-mediated reaction is predominantly restricted through three pathways, one of which is without detectable passage through intermediates. Under both conditions, the folding reaction is highly parallel with no single pathway accounting for more than 50% of the molecular flux. This suggests that RNA folding is non-sequential under a variety of different experimental conditions even at the earliest stages of folding. This study provides a template for the systematic analysis of the time-evolution of RNA structure

  16. Fuzzy-Contextual Contrast Enhancement.

    Science.gov (United States)

    Parihar, Anil; Verma, Om; Khanna, Chintan

    2017-02-08

    This paper presents contrast enhancement algorithms based on fuzzy contextual information of the images. We introduce fuzzy similarity index and fuzzy contrast factor to capture the neighborhood characteristics of a pixel. A new histogram, using fuzzy contrast factor of each pixel is developed, and termed as the fuzzy dissimilarity histogram (FDH). A cumulative distribution function (CDF) is formed with normalized values of FDH and used as a transfer function to obtain the contrast enhanced image. The algorithm gives good contrast enhancement and preserves the natural characteristic of the image. In order to develop a contextual intensity transfer function, we introduce a fuzzy membership function based on fuzzy similarity index and coefficient of variation of the image. The contextual intensity transfer function is designed using the fuzzy membership function to achieve final contrast enhanced image. The overall algorithm is referred as the fuzzy contextual contrast-enhancement (FCCE) algorithm. The proposed algorithms are compared with conventional and state-of-art contrast enhancement algorithms. The quantitative and visual assessment of the results is performed. The results of quantitative measures are statistically analyzed using t-test. The exhaustive experimentation and analysis show the proposed algorithm efficiently enhances contrast and yields in natural visual quality images.

  17. Degradation of oxo-biodegradable plastic by Pleurotus ostreatus.

    Science.gov (United States)

    da Luz, José Maria Rodrigues; Paes, Sirlaine Albino; Nunes, Mateus Dias; da Silva, Marliane de Cássia Soares; Kasuya, Maria Catarina Megumi

    2013-01-01

    Growing concerns regarding the impact of the accumulation of plastic waste over several decades on the environmental have led to the development of biodegradable plastic. These plastics can be degraded by microorganisms and absorbed by the environment and are therefore gaining public support as a possible alternative to petroleum-derived plastics. Among the developed biodegradable plastics, oxo-biodegradable polymers have been used to produce plastic bags. Exposure of this waste plastic to ultraviolet light (UV) or heat can lead to breakage of the polymer chains in the plastic, and the resulting compounds are easily degraded by microorganisms. However, few studies have characterized the microbial degradation of oxo-biodegradable plastics. In this study, we tested the capability of Pleurotus ostreatus to degrade oxo-biodegradable (D2W) plastic without prior physical treatment, such as exposure to UV or thermal heating. After 45 d of incubation in substrate-containing plastic bags, the oxo-biodegradable plastic, which is commonly used in supermarkets, developed cracks and small holes in the plastic surface as a result of the formation of hydroxyl groups and carbon-oxygen bonds. These alterations may be due to laccase activity. Furthermore, we observed the degradation of the dye found in these bags as well as mushroom formation. Thus, P. ostreatus degrades oxo-biodegradable plastics and produces mushrooms using this plastic as substrate.

  18. Degradation of oxo-biodegradable plastic by Pleurotus ostreatus.

    Directory of Open Access Journals (Sweden)

    José Maria Rodrigues da Luz

    Full Text Available Growing concerns regarding the impact of the accumulation of plastic waste over several decades on the environmental have led to the development of biodegradable plastic. These plastics can be degraded by microorganisms and absorbed by the environment and are therefore gaining public support as a possible alternative to petroleum-derived plastics. Among the developed biodegradable plastics, oxo-biodegradable polymers have been used to produce plastic bags. Exposure of this waste plastic to ultraviolet light (UV or heat can lead to breakage of the polymer chains in the plastic, and the resulting compounds are easily degraded by microorganisms. However, few studies have characterized the microbial degradation of oxo-biodegradable plastics. In this study, we tested the capability of Pleurotus ostreatus to degrade oxo-biodegradable (D2W plastic without prior physical treatment, such as exposure to UV or thermal heating. After 45 d of incubation in substrate-containing plastic bags, the oxo-biodegradable plastic, which is commonly used in supermarkets, developed cracks and small holes in the plastic surface as a result of the formation of hydroxyl groups and carbon-oxygen bonds. These alterations may be due to laccase activity. Furthermore, we observed the degradation of the dye found in these bags as well as mushroom formation. Thus, P. ostreatus degrades oxo-biodegradable plastics and produces mushrooms using this plastic as substrate.

  19. Biodegradability of fluorinated fire-fighting foams in water.

    Science.gov (United States)

    Bourgeois, A; Bergendahl, J; Rangwala, A

    2015-07-01

    Fluorinated fire-fighting foams may be released into the environment during fire-fighting activities, raising concerns due to the potential environmental and health impacts for some fluorinated organics. The current study investigated (1) the biodegradability of three fluorinated fire-fighting foams, and (2) the applicability of current standard measures used to assess biodegradability of fluorinated fire-fighting foams. The biodegradability of three fluorinated fire-fighting foams was evaluated using a 28-day dissolved organic carbon (DOC) Die-Away Test. It was found that all three materials, diluted in water, achieved 77-96% biodegradability, meeting the criteria for "ready biodegradability". Defluorination of the fluorinated organics in the foam during biodegradation was measured using ion chromatography. It was found that the fluorine liberated was 1-2 orders of magnitude less than the estimated initial amount, indicating incomplete degradation of fluorinated organics, and incomplete CF bond breakage. Published biodegradability data may utilize biochemical oxygen demand (BOD), chemical oxygen demand (COD), and total organic carbon (TOC) metrics to quantify organics. COD and TOC of four fluorinated compounds were measured and compared to the calculated carbon content or theoretical oxygen demand. It was found that the standard dichromate-based COD test did not provide an accurate measure of fluorinated organic content. Thus published biodegradability data using COD for fluorinated organics quantification must be critically evaluated for validity. The TOC measurements correlated to an average of 91% of carbon content for the four fluorinated test substances, and TOC is recommended for use as an analytical parameter in fluorinated organics biodegradability tests.

  20. Fully biodegradable coronary stents : progress to date.

    Science.gov (United States)

    Ramcharitar, Steve; Serruys, Patrick W

    2008-01-01

    The limitations of currently available metallic drug-eluting stents have renewed interest in biodegradable stents (BDS). Apart from removing the (offending) foreign material that may potentiate a thrombotic event, BDS have the advantage of avoiding 'full metal jackets,' and thus can preclude subsequent coronary surgery. In addition, they do not interfere with the diagnostic evaluation of non-invasive imaging such as cardiac magnetic resonance and CT. There are now several BDS in development or in clinical trials that incorporate a variety of biodegradable polymer technologies. Two broad categories of materials are generally used: those made from organic biopolymers and those made from corrodible metals. However, to date, none of the materials/stents tested have been able to establish a perfect balance between biocompatibility, the kinetics of degradation needed to maintain mechanical strength to limit recoil, and inflammation. However, studies, such as the ABSORB trial with the everolimus eluting poly-L-lactide stent, which demonstrated comparable restenotic rates with bare metallic stents and a low incidence of major adverse cardiac events (MACE) at 12 months of 3.3%, with only one patient having a non-Q-wave myocardial infarction and no target lesion revascularization, suggest that there has been significant progress with respect to the earlier prototypes. The acute recoil observed could potentially be addressed with the polytyrosine REVA stent currently being evaluated in the RESORB trial, which incorporates a novel locking mechanism within its design. Alternative BDS designs include the combination of an antiproliferative drug with endothelial progenitor cell capturing antibodies to facilitate epithelialization and/or dual eluting having, in addition to the antiproliferative drug, polymeric salicyclic acid to limit inflammation. Compared with biodegradable polymers, there are fewer metals used in the manufacture of BDS. The only metal BDS in trials is the

  1. Perturbation-based Markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of GroEL-GroES.

    Directory of Open Access Journals (Sweden)

    Hsiao-Mei Lu

    2009-10-01

    Full Text Available Large macromolecular assemblies are often important for biological processes in cells. Allosteric communications between different parts of these molecular machines play critical roles in cellular signaling. Although studies of the topology and fluctuation dynamics of coarse-grained residue networks can yield important insights, they do not provide characterization of the time-dependent dynamic behavior of these macromolecular assemblies. Here we develop a novel approach called Perturbation-based Markovian Transmission (PMT model to study globally the dynamic responses of the macromolecular assemblies. By monitoring simultaneous responses of all residues (>8,000 across many (>6 decades of time spanning from the initial perturbation until reaching equilibrium using a Krylov subspace projection method, we show that this approach can yield rich information. With criteria based on quantitative measurements of relaxation half-time, flow amplitude change, and oscillation dynamics, this approach can identify pivot residues that are important for macromolecular movement, messenger residues that are key to signal mediating, and anchor residues important for binding interactions. Based on a detailed analysis of the GroEL-GroES chaperone system, we found that our predictions have an accuracy of 71-84% judged by independent experimental studies reported in the literature. This approach is general and can be applied to other large macromolecular machineries such as the virus capsid and ribosomal complex.

  2. Aging changes of macromolecular synthesis in the digestive organs of mice as revealed by microscopic radioautography and X-ray microanalysis

    Energy Technology Data Exchange (ETDEWEB)

    Nagata, Tetsuji [Shinshu Univ., Matsumoto (Japan). School of Medicine. Dept. of Anatomy and Cell Biology]. E-mail: nagatas@po.cnet.ne.jp

    2002-07-01

    For the purpose of elucidating the aging changes of macromolecular synthesis such as DNA, RNA, proteins, glycoproteins, glycides and lipids in various organ systems of experimental animals, we have studied the digestive organs of aging mice and rats as a series of systematic studies using light and electron microscopic radioautography after incorporations with macromolecular precursors. The experimental animals mainly used were ddY strain mice at various aging groups from embryo to postnatal days 1 and 3, weeks 1 and 2, months 1, 2, 6, 12 up to 2 year senescent stages as well as several groups of adult Wistar rats. The animals were injected with such macromolecular precursors as {sup 3}H - thymidine for DNA, {sup 3}H-uridine for RNA, {sup 3}H-leucine and {sup 3}H proline for proteins, {sup 35}SO{sub 4} for glycoproteins, {sup 3} H-glucosamine for glucides and {sup 3}H-glycerol for lipids. The results demonstrated that these precursors were incorporated into various cell types in the oral cavity, the salivary glands, the esophagus, the stomach, the small and large intestines, the liver and the pancreas at various ages from perinatal to juvenile, mature and senescent stages, showing specific patterns of macromolecular synthesis. It is concluded that these specific patterns of macromolecular synthesis in respective cell types demonstrated the organ specificity of aging of animals. (author)

  3. Biodegradable and biocompatible polymers for tissue engineering application: a review.

    Science.gov (United States)

    Asghari, Fatemeh; Samiei, Mohammad; Adibkia, Khosro; Akbarzadeh, Abolfazl; Davaran, Soodabeh

    2017-03-01

    Since so many years ago, tissue damages that are caused owing to various reasons attract scientists' attention to find a practical way to treat. In this regard, many studies were conducted. Nano scientists also suggested some ways and the newest one is called tissue engineering. They use biodegradable polymers in order to replace damaged structures in tissues to make it practical. Biodegradable polymers are dominant scaffolding materials in tissue engineering field. In this review, we explained about biodegradable polymers and their application as scaffolds.

  4. Contrast discrimination at high contrasts reveals the influence of local light adaptation on contrast processing.

    Science.gov (United States)

    Kingdom, F A; Whittle, P

    1996-03-01

    Previous measurements of contrast discrimination threshold, delta C, as a function of pedestal contrast, C, for sine-wave gratings have shown a power law relationship between delta C and C at suprathreshold levels of C. However, these studies have rarely used contrasts greater than 50%. Whittle (1986), using incremental and decremental patches, found that delta C increased with C only up to about 50%. At higher contrasts it decreased. Since a periodic stimulus can be considered to be composed of increments and decrements, we thought we might find such an inverse U-shaped function for gratings if we used contrasts up to 100%. We tested this for both sine-wave and square-wave stimuli at spatial frequencies from 0.0625 to 8.0 c/deg. We found that for frequencies up to 0.5 c/deg, delta C in nearly all cases 'dipped down' after about C = 50% contrast. At 4.0 and 8.0 c/deg, however, no dip-down occurred. Additional experiments showed that the dip-down was unlikely to be due to cortical long-term adaptation and most likely an effect of localized light adaptation to the dark bars. We argue that the absence of dip-down at high spatial frequencies was mainly due to the attenuation of contrast by the optics of the eye. As for the results of Whittle (1986), a Weber's Law in W = (Lmax-Lmin)/Lmin describes the inverse U-shaped contrast discrimination function well. Two other contrast expressions also linearize the data on log-log plots. We show how some familiar notions about the physiological operation of localized light adaptation can easily account for the form of the contrast discrimination function. Finally we estimate the number of discriminable steps in contrast from detection threshold to maximum contrast for the various spatial frequencies tested.

  5. Contrast enhancement in light microscopy.

    Science.gov (United States)

    Ernst Keller, H; Watkins, Simon

    2013-01-01

    The optical microscope is a fundamental component of an image cytometry system. This unit covers the basic concepts of light microscopy, including Köhler illumination, resolution, contrast, and numerical aperture, and reviews the many types of instruments and techniques for contrast enhancement.

  6. Contrast-enhanced peripheral MRA

    DEFF Research Database (Denmark)

    Nielsen, Yousef W; Thomsen, Henrik S

    2012-01-01

    In the last decade contrast-enhanced magnetic resonance angiography (CE-MRA) has gained wide acceptance as a valuable tool in the diagnostic work-up of patients with peripheral arterial disease. This review presents current concepts in peripheral CE-MRA with emphasis on MRI technique and contrast...

  7. MX1: a bending-magnet crystallography beamline serving both chemical and macromolecular crystallography communities at the Australian Synchrotron.

    Science.gov (United States)

    Cowieson, Nathan Philip; Aragao, David; Clift, Mark; Ericsson, Daniel J; Gee, Christine; Harrop, Stephen J; Mudie, Nathan; Panjikar, Santosh; Price, Jason R; Riboldi-Tunnicliffe, Alan; Williamson, Rachel; Caradoc-Davies, Tom

    2015-01-01

    MX1 is a bending-magnet crystallography beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the energy range from 8 to 18 keV to a focal spot at the sample position of 120 µm FWHM. The beamline endstation and ancillary equipment facilitate local and remote access for both chemical and biological macromolecular crystallography. Here, the design of the beamline and endstation are discussed. The beamline has enjoyed a full user program for the last seven years and scientific highlights from the user program are also presented.

  8. Nitrogen limitation in natural populations of cyanobacteria (Spirulina and Oscillatoria spp. ) and its effect on macromolecular synthesis

    Energy Technology Data Exchange (ETDEWEB)

    van Rijn, J.; Shilo, M.

    1986-08-01

    Natural populations of the cyanobacteria Spirulina species and Oscillatoria species obtained from Israeli fish ponds were limited in growth by nitrogen availability in summer. Physiological indicators for nitrogen limitation, such as phycocyanin, chlorophyll a, and carbohydrate content, did not show clear evidence for nitrogen limited growth, since these organisms are capable of vertical migration from and to the nitrogen-rich bottom. By means of /sup 14/C labeling of the cells under simulated pond conditions followed by cell fractionation into macromolecular compounds, it was found that carbohydrates synthesized at the lighted surface were partially utilized for dark protein synthesis at the bottom of these ponds.

  9. Curcumin suppresses gastric NF-κB activation and macromolecular leakage in Helicobacter pylori-infected rats

    Institute of Scientific and Technical Information of China (English)

    Kawiya; Sintara; Duangporn; Thong-Ngam; Suthiluk; Patumraj; Naruemon; Klaikeaw; Tanittha; Chatsuwan

    2010-01-01

    AIM:To investigate whether curcumin could attenuate nuclear factor(NF)-κB p65 expression and macromolecular leakage in the gastric mucosa of Helicobacter pylori(H.pylori)-infected rats.METHODS:Twenty-five male Sprague-Dawley rats were equally divided into five groups:control rats(Control),control rats supplemented with 600 mg/kg curcumin,H.pylori-infected rats(Hp),H.pylori-infected rats supplemented with 200 mg/kg curcumin(Hp + curIn H.pylori-infected groups,rats were inoculated with H.pylori suspension twi...

  10. Holographic methods in X-ray crystallography. Pt. 4. A fast algorithm and its application to macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Somoza, J.R. [California Univ., Berkeley (United States). Dept. of Chemistry]|[Lawrence Berkeley Lab., CA (United States); Szoeke, H. [Lawrence Livermore National Lab., CA (United States); Goodman, D.M. [Lawrence Livermore National Lab., CA (United States); Beran, P. [Lawrence Livermore National Lab., CA (United States); Truckses, D. [Wisconsin Univ., Madison, WI (United States). Dept. of Biochemistry; Kim, S.H. [California Univ., Berkeley (United States). Dept. of Chemistry]|[Lawrence Berkeley Lab., CA (United States); Szoeke, A. [Lawrence Livermore National Lab., CA (United States)

    1995-09-01

    The holographic method makes use of partially modeled electron density and experimentally measured structure-factor amplitudes to recover electron density corresponding to the unmodeled part of a crystal structure. This paper describes a fast algorithm that makes it possible to apply the holographic method to sizable crystallographic problems. The algorithm uses positivity constraints on the electron density and can incorporate a `target` electron density, making it similar to solvent flattening. The potential for applying the holographic method to macromolecular X-ray crystallography is assessed using both synthetic and experimental data. (orig.).

  11. Comparison of two self-assembled macromolecular prodrug micelles with different conjugate positions of SN38 for enhancing antitumor activity

    Directory of Open Access Journals (Sweden)

    Liu Y

    2015-03-01

    Full Text Available Yi Liu,1 Hongyu Piao,1 Ying Gao,1 Caihong Xu,2 Ye Tian,1 Lihong Wang,1 Jinwen Liu,1 Bo Tang,1 Meijuan Zou,1 Gang Cheng1 1Department of Pharmaceutics, Shenyang Pharmaceutical University, Shenyang, Liaoning Province, People’s Republic of China; 2Department of Food Science, Shenyang Normal University, Shenyang, Liaoning Province, People’s Republic of China Abstract: 7-Ethyl-10-hydroxycamptothecin (SN38, an active metabolite of irinotecan (CPT-11, is a remarkably potent antitumor agent. The clinical application of SN38 has been extremely restricted by its insolubility in water. In this study, we successfully synthesized two macromolecular prodrugs of SN38 with different conjugate positions (chitosan-(C10-OHSN38 and chitosan-(C20-OHSN38 to improve the water solubility and antitumor activity of SN38. These prodrugs can self-assemble into micelles in aqueous medium. The particle size, morphology, zeta potential, and in vitro drug release of SN38 and its derivatives, as well as their cytotoxicity, pharmacokinetics, and in vivo antitumor activity in a xenograft BALB/c mouse model were studied. In vitro, chitosan-(C10-OHSN38 (CS-(10sSN38 and chitosan-(C20-OHSN38 (CS-(20sSN38 were 13.3- and 25.9-fold more potent than CPT-11 in the murine colon adenocarcinoma cell line CT26, respectively. The area under the curve (AUC0–24 of SN38 after intravenously administering CS-(10sSN38 and CS-(20sSN38 to Sprague Dawley rats was greatly improved when compared with CPT-11 (both P<0.01. A larger AUC0–24 of CS-(20sSN38 was observed when compared to CS-(10sSN38 (P<0.05. Both of the novel self-assembled chitosan-SN38 prodrugs demonstrated superior anticancer activity to CPT-11 in the CT26 xenograft BALB/c mouse model. We have also investigated the differences between these macromolecular prodrug micelles with regards to enhancing the antitumor activity of SN38. CS-(20sSN38 exhibited better in vivo antitumor activity than CS-(10sSN38 at a dose of 2.5 mg/kg (P<0

  12. Partial Discharge Degradation of Several Biodegradable Polymers

    Science.gov (United States)

    Fuse, Norikazu; Fujita, Shinjiro; Hirai, Naoshi; Tanaka, Toshikatsu; Kozako, Masahiro; Kohtoh, Masanori; Okabe, Shigemitsu; Ohki, Yoshimichi

    Partial discharge (PD) resistance was examined by applying a constant voltage for four kinds of biodegradable polymers, i.e. poly-L-lactic acid (PLLA), polyethylene terephthalate succinate (PETS), poly ε-caprolactone butylene succinate (PCL-BS), and polybutylene succinate (PBS), and the results were compared with those of low density polyethylene (LDPE) and crosslinked low density polyethylene (XLPE). The PD resistance is determined by the erosion depth and the surface roughness caused by PDs, and is ranked as LDPE ≅ XLPE > PLLA ≅ PETS > PBS > PCL-BS. This means that the sample with a lower permittivity has better PD resistance. Furthermore, observations of the sample surface by a polarization microscope and a laser confocal one reveal that crystalline regions with spherulites are more resistant to PDs than amorphous regions. Therefore, good PD resistance can be achieved by the sample with a high crystallinity and a low permittivity.

  13. Biodegradation of Petroleum Hydrocarbons in Soil

    Directory of Open Access Journals (Sweden)

    MR Mehrasbi

    2003-09-01

    Full Text Available Biodegradation of petroleum hydrocarbons (20 g/kg dw soil was investigated in 3 media, differing in the kind of petroleum fractions. In the laboratory experiments, during 5 months, the activities of petroleum hydrocarbon-degrading microorganisms and dehydrogenase activity of soil was determined. Gas chromatographic analysis showed the biological decontaminations for gas oil, kerosene and synthetic mixture (gas oil, kerosene and furnace oil are 60 %, 36 % and 55 %, respectively. Dehydrogenase activity which was assessed by TTC technique, correlated significantly positive with the numbers of microorganisms. The Spearman rank correlation coefficients(r in contaminated soils with gas oil, kerosene and synthetic mixture were 0.79, 0.80 and 0.69, respectively.

  14. Biodegradable polymeric fiber structures in tissue engineering.

    Science.gov (United States)

    Tuzlakoglu, Kadriye; Reis, Rui L

    2009-03-01

    Tissue engineering offers a promising new approach to create biological alternatives to repair or restore function of damaged or diseased tissues. To obtain three-dimensional tissue constructs, stem or progenitor cells must be combined with a highly porous three-dimensional scaffold, but many of the structures purposed for tissue engineering cannot meet all the criteria required by an adequate scaffold because of lack of mechanical strength and interconnectivity, as well as poor surface characteristics. Fiber-based structures represent a wide range of morphological and geometric possibilities that can be tailored for each specific tissue-engineering application. The present article overviews the research data on tissue-engineering therapies based on the use of biodegradable fiber architectures as a scaffold.

  15. Biodegradation of lignin by Agaricus Bisporus

    Energy Technology Data Exchange (ETDEWEB)

    Vane, C.H.; Abbott, G.D.; Head, I.M. [Univ. of Newcastle upon Tyne (United Kingdom)

    1996-12-31

    The lignolytic activity of Agaricus bisporus will be addressed in this paper. Sound and fungally degraded lignins were characterized by Pyrolysis-Gas Chromatography-Mass Spectrometry (Py-GC-MS), Fourier Transform Infrared Spectroscopy (FnR) and elemental analysis. Fungally degraded lignins displayed increased wt%N, wt%H and wt%O content and decreased wt%C content The FTIR spectrum of decayed lignin showed an increase in the relative intensity of absorption bands assigned to carbonyl and carboxyl functional groups located on the aliphatic side chain and a decrease in absorption bands assigned to aromatic skeletal vibration modes. Semiquantitative Py-GC-MS revealed an 82% decrease in lignin derived pyrolysis products upon biodegradation. No significant increase in pyrolysis products with an oxygenated aliphatic side chain were detected in the fungally degraded lignin however shortening of the aliphatic side chain via cleavage at the {alpha}, {beta} and {gamma} positions was observed.

  16. Aerobic biodegradation of precoagulated cheese whey wastewater.

    Science.gov (United States)

    Rivas, Javier; Prazeres, Ana R; Carvalho, Fatima

    2011-03-23

    Prior to the application of an aerobic biological process, cheese whey wastewater has been pretreated by means of a precipitation stage by adding either NaOH or CaOH2. Both precipitating agents reduce roughly 50% of the raw wastewater chemical oxygen demand (COD). The sludge generated in the prestage shows acceptable settling properties, although solids from the CaOH2-treated effluent are better separated from the liquid bulk than those formed in NaOH-processed wastewater. In both situations, the presedimentation stage renders a supernatant more prone to biodegradation than the untreated effluent. The previous statement is corroborated by the determination of some biological kinetic parameters. Under the operating conditions used in this work, sludge generation after the biological process is reduced to a minimum. The sludge generated shows good settling properties, especially for those experiments in which CaOH2 has previously been added.

  17. Biodegradation of Crystal Violet by Agrobacterium radiobacter

    Institute of Scientific and Technical Information of China (English)

    G.K.Parshetti; S.G.Parshetti; A.A.Telke; D.C.Kalyani; R.A.Doong; S.P.Govindwar

    2011-01-01

    Agrobacterium radiobacter MTCC 8161 completely decolorized the Crystal Violet with 8 hr (10 mg/L) at static anoxic conditions.The decreased decolorization capability by A.radiobacter was observed,when the Crystal Violet concentration was increased from 10 to 100 mg/L.Semi-synthetic medium containing 1% yeast extract and 0.1% NH4Cl has shown 100% decolorization of Crystal Violet within 5 hr.A complete degradation of Crystal Violet by A.radiobacter was observed up to 7 cycles of repeated addition (10 mg/L).When the effect of increasing inoculum concentration on decolorization of Crystal Violet (100 rag/L) was studied,maximum decolorization was observed with 15% inoculum concentration.A significant increase in the activities of laccase (184%) and aminopyrine N-demethylase (300%) in cells obtained after decolorization indicated the involvement of these enzymes in decolorization process.The intermediates formed during the degradation of Crystal Violet were analyzed by gas chromatography and mass spectroscopy (GC/MS).It was detected the presence of N,N,N′,N"-tetramethylpararosaniline,[N,N-dimethylaminophenyl][N-methylaminophenyl] benzophenone,N,N-dimethylaminobenzaldehyde,4-methyl amino phenol and phenol.We proposed the hypothetical metabolic pathway of Crystal Violet biodegradation by A.radiobacter.Phytotoxicity and microbial toxicity study showed that Crystal Violet biodegradation metabolites were less toxic to bacteria (A.radiobacter,P.aurugenosa and A.vinelandii) contributing to soil fertility and for four kinds of plants (Sorghum bicolor,Vigna radiata,Lens culinaris and Triticum aestivum) which are most sensitive,fast growing and commonly used in Indian agriculture.

  18. Asphalts and asphaltenes: Macromolecular structure, precipitation properties, and flow in porous media

    Science.gov (United States)

    Rassamdana, Hossein

    Depending on rock and fluid properties, more than 50% of reservoir oil in place is normally produced by enhanced oil recovery (EOR) methods. Among the EOR techniques, miscible flooding is one of the most efficient and widely-used methods. However, this method can suffer from the formation and precipitation of asphalt aggregates. In addition, asphalt deposition is also a major hindrance to heavy oil production, and even primary recovery operations. Asphalt deposition can alter the reservoir rock properties, fluid saturation distribution, fluid flow properties, and eventually the ultimate oil recovery. The shortage of studies on the macromolecular structure and growth mechanisms of asphalt particles is the main reason for the unsuccessful modeling of their precipitation properties. The equivocal behavior of asphalt under some specific conditions could be the other reason. In this research we look at the problem of asphalt formation, flow, and precipitation from three different angles. We analyze extensive small-angle X-ray and neutron scattering data, precipitation data, and molecular weight distribution measurements, and show that they all suggest conclusively that asphalts and asphaltenes are fractal aggregates, and their growth mechanisms are diffusion-limited particle (DLP) and diffusion-limited cluster-cluster (DLCC) aggregation processes. These results lead us to development of a scaling equation of state for predicting asphalt precipitation properties, such as its onset and amount of precipitation. Another result of our study is an analytical equation for modeling the molecular weight distribution of asphalt and asphaltene aggregates. In addition, asphalt phase behavior in miscible and immiscible injections is studied. The effect of the governing thermodynamic factors, such as the pressure, temperature, and composition of the oil and precipitation agents, on the asphalt aggregation and disaggregation processes are investigated. Finally, a model is developed to

  19. Photon-counting single-molecule spectroscopy for studying conformational dynamics and macromolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Laurence, Ted Alfred

    2002-07-30

    Single-molecule methods have the potential to provide information about conformational dynamics and molecular interactions that cannot be obtained by other methods. Removal of ensemble averaging provides several benefits, including the ability to detect heterogeneous populations and the ability to observe asynchronous reactions. Single-molecule diffusion methodologies using fluorescence resonance energy transfer (FRET) are developed to monitor conformational dynamics while minimizing perturbations introduced by interactions between molecules and surfaces. These methods are used to perform studies of the folding of Chymotrypsin Inhibitor 2, a small, single-domain protein, and of single-stranded DNA (ssDNA) homopolymers. Confocal microscopy is used in combination with sensitive detectors to detect bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract fluorescence resonance energy transfer (FRET) efficiency. Advances in data acquisition and analysis techniques that are providing a more complete picture of the accessible molecular information are discussed. Photon Arrival-time Interval Distribution (PAID) analysis is a new method for monitoring macromolecular interactions by fluorescence detection with simultaneous determination of coincidence, brightness, diffusion time, and occupancy (proportional to concentration) of fluorescently-labeled molecules undergoing diffusion in a confocal detection volume. This method is based on recording the time of arrival of all detected photons, and then plotting the two-dimensional histogram of photon pairs, where one axis is the time interval between each pair of photons 1 and 2, and the second axis is the number of other photons detected in the time interval between photons 1 and 2. PAID is related to Fluorescence Correlation Spectroscopy (FCS) by a collapse of this histogram onto the time interval axis. PAID extends auto- and cross-correlation FCS

  20. Photon-counting single-molecule spectroscopy for studying conformational dynamics and macromolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Laurence, Ted Alfred [Univ. of California, Berkeley, CA (United States)

    2002-01-01

    Single-molecule methods have the potential to provide information about conformational dynamics and molecular interactions that cannot be obtained by other methods. Removal of ensemble averaging provides several benefits, including the ability to detect heterogeneous populations and the ability to observe asynchronous reactions. Single-molecule diffusion methodologies using fluorescence resonance energy transfer (FRET) are developed to monitor conformational dynamics while minimizing perturbations introduced by interactions between molecules and surfaces. These methods are used to perform studies of the folding of Chymotrypsin Inhibitor 2, a small, single-domain protein, and of single-stranded DNA (ssDNA) homopolymers. Confocal microscopy is used in combination with sensitive detectors to detect bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract fluorescence resonance energy transfer (FRET) efficiency. Advances in data acquisition and analysis techniques that are providing a more complete picture of the accessible molecular information are discussed. Photon Arrival-time Interval Distribution (PAID) analysis is a new method for monitoring macromolecular interactions by fluorescence detection with simultaneous determination of coincidence, brightness, diffusion time, and occupancy (proportional to concentration) of fluorescently-labeled molecules undergoing diffusion in a confocal detection volume. This method is based on recording the time of arrival of all detected photons, and then plotting the two-dimensional histogram of photon pairs, where one axis is the time interval between each pair of photons 1 and 2, and the second axis is the number of other photons detected in the time interval between photons 1 and 2. PAID is related to Fluorescence Correlation Spectroscopy (FCS) by a collapse of this histogram onto the time interval axis. PAID extends auto- and cross-correlation FCS

  1. Macromolecular crowding gives rise to microviscosity, anomalous diffusion and accelerated actin polymerization

    Science.gov (United States)

    Rashid, Rafi; Chee, Stella Min Ling; Raghunath, Michael; Wohland, Thorsten

    2015-05-01

    Macromolecular crowding (MMC) has been used in various in vitro experimental systems to mimic in vivo physiology. This is because the crowded cytoplasm of cells contains many different types of solutes dissolved in an aqueous medium. MMC in the extracellular microenvironment is involved in maintaining stem cells in their undifferentiated state (niche) as well as in aiding their differentiation after they have travelled to new locations outside the niche. MMC at physiologically relevant fractional volume occupancies (FVOs) significantly enhances the adipogenic differentiation of human bone marrow-derived mesenchymal stem cells during chemically induced adipogenesis. The mechanism by which MMC produces this enhancement is not entirely known. In the context of extracellular collagen deposition, we have recently reported the importance of optimizing the FVO while minimizing the bulk viscosity. Two opposing properties will determine the net rate of a biochemical reaction: the negative effect of bulk viscosity and the positive effect of the excluded volume, the latter being expressed by the FVO. In this study we have looked more closely at the effect of viscosity on reaction rates. We have used fluorimetry to measure the rate of actin polymerization and fluorescence correlation spectroscopy (FCS) to measure diffusion of various probes in solutions containing the crowder Ficoll at physiological concentrations. Similar to its effect on collagen, Ficoll enhanced the actin polymerization rate despite increasing the bulk viscosity. Our FCS measurements reveal a relatively minor component of anomalous diffusion. In addition, our measurements do suggest that microviscosity becomes relevant in a crowded environment. We ruled out bulk viscosity as a cause of the rate enhancement by performing the actin polymerization assay in glycerol. These opposite effects of Ficoll and glycerol led us to conclude that microviscosity becomes relevant at the length scale of the reacting

  2. Leaching of organic acids from macromolecular organic matter by non-supercritical CO2

    Science.gov (United States)

    Sauer, P.; Glombitza, C.; Kallmeyer, J.

    2012-04-01

    The storage of CO2 in underground reservoirs is discussed controversly in the scientific literature. The worldwide search for suitable storage formations also considers coal-bearing strata. CO2 is already injected into seams for enhanced recovery of coal bed methane. However, the effects of increased CO2 concentration, especially on organic matter rich formations, are rarely investigated. The injected CO2 will dissolve in the pore water, causing a decrease in pH and resulting in acidic formation waters. Huge amounts of low molecular weight organic acids (LMWOAs) are chemically bound to the macromolecular matrix of sedimentary organic matter and may be liberated by hydrolysis, which is enhanced by the acidic porewater. Recent investigations outlined the importance of LMWOAs as a feedstock for microbial life in the subsurface [1]. Therefore, injection of CO2 into coal formations may result in enhanced nutrient supply for subsurface microbes. To investigate the effect of high concentrations of dissolved CO2 on the release of LMWOAs from coal we developed an inexpensive high-pressure high temperature system that allows manipulating the partial pressure of dissolved gases at pressures and temperatures up to 60 MPa and 120° C, respectively. In a reservoir vessel, gases are added to saturate the extraction medium to the desired level. Inside the extraction vessel hangs a flexible and inert PVDF sleeve (polyvinylidene fluoride, almost impermeable for gases), holding the sample and separating it from the pressure fluid. The flexibility of the sleeve allows for subsampling without loss of pressure. Coal samples from the DEBITS-1 well, Waikato Basin, NZ (R0 = 0.29, TOC = 30%). were extracted at 90° C and 5 MPa, either with pure or CO2-saturated water. Subsamples were taken at different time points during the extraction. The extracted LMWOAs such as formate, acetate and oxalate were analysed by ion chromatography. Yields of LMWOAs were higher with pure water than with CO2

  3. Biodegradation of imazapyr in typical soils in Zhejiang Province, China

    Institute of Scientific and Technical Information of China (English)

    WANG Xue-dong; ZHOU Su-mei; WANG Hui-li; FAN De-fang

    2005-01-01

    The degradation of imazapyr in non-sterile and sterile soils from four sampling sites in Zhejiang, China was studied. The results showed that the half-lives of imazapyr in non-sterile soils were in the range of 30 to 45 d, while 81 to 133 d in sterile(by autoclaving) soils.It means the rate constants of imazapyr under non-sterile conditions were 2.3-4.4 times faster than that under sterile(by autoclaving) conditions, evidently indicating that the indigenous microorganisms in soil play an important role in the degradation of imazapyr. The different sterilization methods could result in different degradation rates of imazapyr. The heat of sterilization of soil largely decreased the degradation. However, the sterile treatment of soil by sodium azide had a different effect from that by autoclaving. Further more, the mechanism was also discussed. Biodegradation in four non-sterile soils accounted for 62% to 78% of imazapyr degradation. In contrast,less than 39% of imazapyr degradation was associated with chemical mechanisms. Therefore, the degradation mechanism was predominantly involved in biology including organisms and microorganisms in soil. Two imazapyr-degrading bacterial strains were isolated in enrichment culture technique and they were identified as Pseudomonas fluorescenes biotype Ⅱ (ZJX-5) and Bacillus cereus(ZJX-9),respectively. When added at a concentration of 50 μg/g in mineral salts medium(MSM), ZJX-5 and ZJX-9 could degrade 81 % and 87%imazapyr after 48 h of incubation. For the treatment of incorporation of ZJX-5 or ZJX-9 into soil, the degradation rate enhanced 3-4 fold faster than that for control samples, which showed an important value in quick decontamination of imazapyr in soil.

  4. Vectorization of copper complexes via biocompatible and biodegradable PLGA nanoparticles

    Science.gov (United States)

    Courant, T.; Roullin, V. G.; Cadiou, C.; Delavoie, F.; Molinari, M.; Andry, M. C.; Gafa, V.; Chuburu, F.

    2010-04-01

    A double emulsion-solvent diffusion approach with fully biocompatible materials was used to encapsulate copper complexes within biodegradable nanoparticles, for which the release kinetics profiles have highlighted their potential use for a prolonged circulating administration.

  5. Vectorization of copper complexes via biocompatible and biodegradable PLGA nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Courant, T; Roullin, V G; Andry, M C [Institut de Chimie Moleculaire de Reims, CNRS UMR 6229, UFR Pharmacie Reims, 51 rue Cognacq-Jay, F-51100 Reims (France); Cadiou, C; Chuburu, F [Institut de Chimie Moleculaire de Reims, CNRS UMR 6229, UFR des Sciences Exactes et Naturelles, Batiment 18-Europol' Agro, BP 1039, F-51687 Reims Cedex 2 (France); Delavoie, F [Laboratoire de Microscopie Electronique Analytique, INSERM UMRS 926, 21 rue Clement Ader, F-51685 Reims Cedex 2 (France); Molinari, M [Laboratoire de Microscopies et d' Etudes des Nanostructures, UFR des Sciences, Universite de Reims Champagne-Ardenne, 21 rue Clement Ader, F-51685 Reims Cedex 2 (France); Gafa, V, E-mail: gaelle.roullin@univ-reims.fr, E-mail: francoise.chuburu@univ-reims.fr [EA4303 ' Inflammation et Immunite de l' Epithelium Respiratoire' , IFR53, UFR de Pharmacie, Universite de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, F-51100 Reims (France)

    2010-04-23

    A double emulsion-solvent diffusion approach with fully biocompatible materials was used to encapsulate copper complexes within biodegradable nanoparticles, for which the release kinetics profiles have highlighted their potential use for a prolonged circulating administration.

  6. Fade to Green: A Biodegradable Stack of Microbial Fuel Cells.

    Science.gov (United States)

    Winfield, Jonathan; Chambers, Lily D; Rossiter, Jonathan; Stinchcombe, Andrew; Walter, X Alexis; Greenman, John; Ieropoulos, Ioannis

    2015-08-24

    The focus of this study is the development of biodegradable microbial fuel cells (MFCs) able to produce useful power. Reactors with an 8 mL chamber volume were designed using all biodegradable products: polylactic acid for the frames, natural rubber as the cation-exchange membrane and egg-based, open-to-air cathodes coated with a lanolin gas diffusion layer. Forty MFCs were operated in various configurations. When fed with urine, the biodegradable stack was able to power appliances and was still operational after six months. One useful application for this truly sustainable MFC technology includes onboard power supplies for biodegradable robotic systems. After operation in remote ecological locations, these could degrade harmlessly into the surroundings to leave no trace when the mission is complete.

  7. Vectorization of copper complexes via biocompatible and biodegradable PLGA nanoparticles.

    Science.gov (United States)

    Courant, T; Roullin, V G; Cadiou, C; Delavoie, F; Molinari, M; Andry, M C; Gafa, V; Chuburu, F

    2010-04-23

    A double emulsion-solvent diffusion approach with fully biocompatible materials was used to encapsulate copper complexes within biodegradable nanoparticles, for which the release kinetics profiles have highlighted their potential use for a prolonged circulating administration.

  8. Biodegradable kinetics of plastics under controlled composting conditions.

    Science.gov (United States)

    Leejarkpai, Thanawadee; Suwanmanee, Unchalee; Rudeekit, Yosita; Mungcharoen, Thumrongrut

    2011-06-01

    This study models and evaluates the kinetics of C-CO(2) evolution during biodegradation of plastic materials including Polyethylene (PE), PE/starch blend (PE/starch), microcrystalline cellulose (MCE), and Polylactic acid (PLA). The aerobic biodegradation under controlled composting conditions was monitorated according to ISO 14855-1, 2004. The kinetics model was based on first order reaction in series with a flat lag phase. A non-linear regression technique was used to analyze the experimental data. SEM studies of the morphology of the samples before and after biodegradation testing were used to confirm the biodegradability of plastics and the accuracy of the model. The work showed that MCE and PLA produced the high amounts of C-CO(2) evolution, which gave readily hydrolysable carbon values of 55.49% and 40.17%, respectively with readily hydrolysis rates of 0.338 day(-1) and 0.025 day(-1), respectively. Whereas, a lower amount of C-CO(2) evolution was found in PE/starch, which had a high concentration of moderately hydrolysable carbon of 97.74% and a moderate hydrolysis rate of 0.00098 day(-1). The mineralization rate of PLA was 0.500 day(-1) as a lag phase was observed at the beginning of the biodegradability test. No lag phase was observed in the biodegradability testing of the PE/starch and MCE. The mineralization rates of the PE/starch and MCE were found to be 1.000 day(-1), and 1.234 day(-1), respectively. No C-CO(2) evolution was observed during biodegradability testing of PE, which was used for reference as a non-biodegradable plastics sample.

  9. Electro-Fenton pretreatment for the improvement of tylosin biodegradability

    OpenAIRE

    Ferrag-Siagh, Fatiha; Fourcade, Florence; Soutrel, Isabelle; Aït-Amar, Hamid; Djelal, Hayet; Amrane, Abdelatif

    2014-01-01

    International audience; The feasibility of an electro-Fenton process to treat tylosin (TYL), a non-biodegradable antibiotic, was examined in a discontinuous electrochemical cell with divided cathodic and anodic compartments. Only 15 min electrolysis was needed for total tylosin degradation using a carbon felt cathode and a platinum anode; while 6 h electrolysis was needed to achieve high oxidation and mineralization yields, 96 and 88 % respectively. Biodegradability improvement was shown sinc...

  10. Improvement of Landfill Leachate Biodegradability with Ultrasonic Process

    OpenAIRE

    Mahvi Amirhossein; Roodbari Aliakbar; Nabizadeh Nodehi Ramin; Naseri Simin; Dehghani Mohammadhadii; Alimohammadi Mahmood

    2012-01-01

    Leachate from mature landfills is typically characterized by high ammonium (NH4+) content, low biodegradability (low BOD5/COD ratio) and high fraction of refractory and large organic molecules such as humic and fulvic acids. Mature leachate effluents are known to contain recalcitrant and/or non-biodegradable organic substances and biological processes are not efficient in these cases. A promising alternative to complete oxidation of biorecalcitrant leachate is the use of ultrasonic process as...

  11. A facile method to prepare superparamagnetic iron oxide and hydrophobic drug-encapsulated biodegradable polyurethane nanoparticles

    Science.gov (United States)

    Cheng, Kuo-Wei; Hsu, Shan-hui

    2017-01-01

    Superparamagnetic iron oxide nanoparticles (SPIO NPs) have a wide range of biomedical applications such as in magnetic resonance imaging, targeting, and hyperthermia therapy. Aggregation of SPIO NPs can occur because of the hydrophobic surface and high surface energy of SPIO NPs. Here, we developed a facile method to encapsulate SPIO NPs in amphiphilic biodegradable polymer. Anionic biodegradable polyurethane nanoparticles (PU NPs) with ~35 nm size and different chemistry were prepared by waterborne processes. SPIO NPs were synthesized by chemical co-precipitation. SPIO NPs were then added to the aqueous dispersion of PU NPs, followed by application of high-frequency (~20 kHz) ultrasonic vibration for 3 min. This method rendered SPIO-PU hybrid NPs (size ~110 nm) suspended in water. SPIO-PU hybrid NPs contained ~50–60 wt% SPIO and retained the superparamagnetic property (evaluated by a magnetometer) as well as high contrast in magnetic resonance imaging. SPIO-PU NPs also showed the ability to provide cell hyperthermic treatment. Using the same ultrasonic method, hydrophobic drug (Vitamin K3 [VK3]) or (9-(methylaminomethyl) anthracene [MAMA]) could also be encapsulated in PU NPs. The VK3-PU or MAMA-PU hybrid NPs had ~35 nm size and different release profiles for PUs with different chemistry. The encapsulation efficiency for VK3 and MAMA was high (~95%) without burst release. The encapsulation mechanism may be attributed to the low glass transition temperature (Tg) and good mechanical compliance of PU NPs. The new encapsulation method involving waterborne biodegradable PU NPs is simple, rapid, and effective to produce multimodular NP carriers. PMID:28280341

  12. A facile method to prepare superparamagnetic iron oxide and hydrophobic drug-encapsulated biodegradable polyurethane nanoparticles

    Directory of Open Access Journals (Sweden)

    Cheng K

    2017-03-01

    Full Text Available Kuo-Wei Cheng, Shan-hui Hsu Institute of Polymer Science and Engineering, College of Engineering, National Taiwan University, Taipei, Taiwan, Republic of China Abstract: Superparamagnetic iron oxide nanoparticles (SPIO NPs have a wide range of biomedical applications such as in magnetic resonance imaging, targeting, and hyperthermia therapy. Aggregation of SPIO NPs can occur because of the hydrophobic surface and high surface energy of SPIO NPs. Here, we developed a facile method to encapsulate SPIO NPs in amphiphilic biodegradable polymer. Anionic biodegradable polyurethane nanoparticles (PU NPs with ~35 nm size and different chemistry were prepared by waterborne processes. SPIO NPs were synthesized by chemical co-precipitation. SPIO NPs were then added to the aqueous dispersion of PU NPs, followed by application of high-frequency (~20 kHz ultrasonic vibration for 3 min. This method rendered SPIO-PU hybrid NPs (size ~110 nm suspended in water. SPIO-PU hybrid NPs contained ~50–60 wt% SPIO and retained the superparamagnetic property (evaluated by a magnetometer as well as high contrast in magnetic resonance imaging. SPIO-PU NPs also showed the ability to provide cell hyperthermic treatment. Using the same ultrasonic method, hydrophobic drug (Vitamin K3 [VK3] or (9-(methylaminomethylanthracene [MAMA] could also be encapsulated in PU NPs. The VK3-PU or MAMA-PU hybrid NPs had ~35 nm size and different release profiles for PUs with different chemistry. The encapsulation efficiency for VK3 and MAMA was high (~95% without burst release. The encapsulation mechanism may be attributed to the low glass transition temperature (Tg and good mechanical compliance of PU NPs. The new encapsulation method involving waterborne biodegradable PU NPs is simple, rapid, and effective to produce multimodular NP carriers. Keywords: superparamagnetic iron oxide, polyurethane, drug release, hybrid nanoparticles

  13. Macromolecular structures probed by combining single-shot free-electron laser diffraction with synchrotron coherent X-ray imaging.

    Science.gov (United States)

    Gallagher-Jones, Marcus; Bessho, Yoshitaka; Kim, Sunam; Park, Jaehyun; Kim, Sangsoo; Nam, Daewoong; Kim, Chan; Kim, Yoonhee; Noh, Do Young; Miyashita, Osamu; Tama, Florence; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Tono, Kensuke; Kohmura, Yoshiki; Yabashi, Makina; Hasnain, S Samar; Ishikawa, Tetsuya; Song, Changyong

    2014-05-02

    Nanostructures formed from biological macromolecular complexes utilizing the self-assembly properties of smaller building blocks such as DNA and RNA hold promise for many applications, including sensing and drug delivery. New tools are required for their structural characterization. Intense, femtosecond X-ray pulses from X-ray free-electron lasers enable single-shot imaging allowing for instantaneous views of nanostructures at ambient temperatures. When combined judiciously with synchrotron X-rays of a complimentary nature, suitable for observing steady-state features, it is possible to perform ab initio structural investigation. Here we demonstrate a successful combination of femtosecond X-ray single-shot diffraction with an X-ray free-electron laser and coherent diffraction imaging with synchrotron X-rays to provide an insight into the nanostructure formation of a biological macromolecular complex: RNA interference microsponges. This newly introduced multimodal analysis with coherent X-rays can be applied to unveil nano-scale structural motifs from functional nanomaterials or biological nanocomplexes, without requiring a priori knowledge.

  14. SYNTHESIS OF STYRYL-CAPPED POLYPROPYLENE via METALLOCENE-MEDIATED COORDINATION POLYMERIZATION: APPLY TO POLYPROPYLENE MACROMOLECULAR ENGINEERING

    Institute of Scientific and Technical Information of China (English)

    Hua-hua Huang; Chuan-hui Zhang; Ya-wei Qin; Hui Niu; Jin-yong Dong

    2013-01-01

    In this paper,we review our recent progress in the synthesis and application of styryl-capped polypropylene (PP-tSt),an excellent reactive polyolefin that is both convenient and efficient in synthesis and facile and versatile in application for preparing advanced polypropylene materials via macromolecular engineering.The synthesis of PP-t-St is made possible by a unique chain transfer reaction coordinated by a bis-styrenic molecule,such as 1,4-divinylbenzene (DVB) and 1,2-bis(4-vinylphenyl)ethane (BVPE),and hydrogen in typical C2-symmetric metallocene (e.g.rac-Me2Si(2-Me-4-Ph-Ind)2ZrC12,in association with methylaluminocene,MAO) catalyzed propylene polymerization.The regio-selective 2,1-insertion of the styrenic double bond in DVB or BVPE into the overwhelmingly 1,2-fashioned Zr-PP propagating chain enables substantial dormancy of the catalyst active site,which triggers selective hydrogen chain transfer that,with the formed Zr-H species ultimately saturated by the insertion of propylene monomer,results in an exclusive capping of the afforded PP chains by styryl group at the termination end.With a highly reactive styryl group at chain end,PP-t-St has been used as a facile building block in PP macromolecular engineering together with the employment of state-of-the-art synthetic polymer chemistry to fabricate broad types of new polypropylene architectures.

  15. Mass distributions of a macromolecular assembly based on electrospray ionization mass spectrometric masses of the constituent subunits

    Indian Academy of Sciences (India)

    Leonid Hanin; Brian Green; Franck Zal; Serge Vinogradov

    2003-09-01

    Macromolecular assemblies containing multiple protein subunits and having masses in the megadalton (MDa) range are involved in most of the functions of a living cell. Because of variation in the number and masses of subunits, macromolecular assemblies do not have a unique mass, but rather a mass distribution. The giant extracelular erythrocruorins (Ers), ∼ 3.5 MDa, comprized of at least 180 polypeptide chains, are one of the best characterized assemblies. Three-dimensional reconstructions from cryoelectron microscopic images show them to be hexagonal bilayer complexes of 12 subassemblies, each comprised of 12 globin chains, anchored to a subassembly of 36 nonglobin linker chains. We have calculated the most probable mass distributions for Lumbricus and Riftia assemblies and their globin and linker subassemblies, based on the Lumbricus Er stoichiometry and using accurate subunit masses obtained by electrospray ionization mass spectrometry. The expected masses of Lumbricus and Riftia Ers are 3.517 MDa and 3.284 MDa, respectively, with a possible variation of ∼ 9% due to the breadth of the mass distributions. The Lumbricus Er mass is in astonishingly good agreement with the mean of 23 known masses, 3.524 ± 0.481 MDa.

  16. Slowed Diffusion and Excluded Volume Both Contribute to the Effects of Macromolecular Crowding on Alcohol Dehydrogenase Steady-State Kinetics.

    Science.gov (United States)

    Schneider, Samuel H; Lockwood, Schuyler P; Hargreaves, Dominique I; Slade, David J; LoConte, Micaela A; Logan, Bridget E; McLaughlin, Erin E; Conroy, Michael J; Slade, Kristin M

    2015-09-29

    To understand the consequences of macromolecular crowding, studies have largely employed in vitro experiments with synthetic polymers assumed to be both pure and "inert". These polymers alter enzyme kinetics by excluding volume that would otherwise be available to the enzymes, substrates, and products. Presented here is evidence that other factors, in addition to excluded volume, must be considered in the interpretation of crowding studies with synthetic polymers. Dextran has a weaker effect on the Michaelis-Menten kinetic parameters of yeast alcohol dehydrogenase (YADH) than its small molecule counterpart, glucose. For glucose, the decreased Vmax values directly correlate with slower translational diffusion and the decreased Km values likely result from enhanced substrate binding due to YADH stabilization. Because dextran is unable to stabilize YADH to the same extent as glucose, this polymer's ability to decrease Km is potentially due to the nonideality of the solution, a crowding-induced conformational change, or both. Chronoamperometry reveals that glucose and dextran have surprisingly similar ferricyanide diffusion coefficients. Thus, the reduction in Vmax values for glucose is partially offset by an additional macromolecular crowding effect with dextran. Finally, this is the first report that supplier-dependent impurities in dextran affect the kinetic parameters of YADH. Taken together, our results reveal that caution should be used when interpreting results obtained with inert synthetic polymeric agents, as additional effects from the underlying monomer need to be considered.

  17. Upgrade of IMCA-CAT Bending Magnet Beamline 17-BM for Macromolecular Crystallography at the Advanced Photon Source

    Energy Technology Data Exchange (ETDEWEB)

    Koshelev, I.; Huang, R.; Graber, T.; Meron, M.; Muir, J.L.; Lavender, W.; Battaile, K.; Mulichak, A.M.; Keefe, L.J. (UC)

    2007-05-15

    Pharmaceutical research depends on macromolecular crystallography as a tool in drug design and development. To solve the de novo three-dimensional atomic structure of a protein, it is essential to know the phases of the X-rays scattered by a protein crystal. Experimental phases can be obtained from multiwavelength anomalous dispersion (MAD) experiments. Dedicated to macromolecular crystallography, the IMCA-CAT bending magnet beamline at sector 17 of the Advanced Photon Source (APS) was upgraded to provide the energy resolution required to successfully perform synchrotron radiation-based MAD phasing of protein crystal structures. A collimating mirror was inserted into the beam path upstream of a double-crystal monochromator, thus increasing the monochromatic beam throughput in a particular bandwidth without sacrificing the energy resolution of the system. The beam is focused horizontally by a sagittally bent crystal and vertically by a cylindrically bent mirror, delivering a beam at the sample of 130 {micro}m (vertically) x 250 {micro}m (horizontally) FWHM. As a result of the upgrade, the beamline now operates with an energy range of 7.5 x 17.5 keV, delivers 8 x 10{sup +11} photons/sec at 12.398 keV at the sample, and has an energy resolution of {delta}E/E = 1.45 x 10{sup -4} at 10 keV, which is suitable for MAD experiments.

  18. Preclinical imaging and translational animal models of cancer for accelerated clinical implementation of nanotechnologies and macromolecular agents.

    Science.gov (United States)

    De Souza, Raquel; Spence, Tara; Huang, Huang; Allen, Christine

    2015-12-10

    The majority of animal models of cancer have performed poorly in terms of predicting clinical performance of new therapeutics, which are most often first evaluated in patients with advanced, metastatic disease. The development and use of metastatic models of cancer may enhance clinical translatability of preclinical studies focused on the development of nanotechnology-based drug delivery systems and macromolecular therapeutics, potentially accelerating their clinical implementation. It is recognized that the development and use of such models are not without challenge. Preclinical imaging tools offer a solution by allowing temporal and spatial characterization of metastatic lesions. This paper provides a review of imaging methods applicable for evaluation of novel therapeutics in clinically relevant models of advanced cancer. An overview of currently utilized models of oncology in small animals is followed by image-based development and characterization of visceral metastatic cancer models. Examples of imaging tools employed for metastatic lesion detection, evaluation of anti-tumor and anti-metastatic potential and biodistribution of novel therapies, as well as the co-development and/or use of imageable surrogates of response, are also discussed. While the focus is on development of macromolecular and nanotechnology-based therapeutics, examples with small molecules are included in some cases to illustrate concepts and approaches that can be applied in the assessment of nanotechnologies or macromolecules.

  19. A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules.

    Science.gov (United States)

    Shan, Hong; Wang, Zihao; Zhang, Fa; Xiong, Yong; Yin, Chang-Cheng; Sun, Fei

    2016-01-01

    Single particle analysis, which can be regarded as an average of signals from thousands or even millions of particle projections, is an efficient method to study the three-dimensional structures of biological macromolecules. An intrinsic assumption in single particle analysis is that all the analyzed particles must have identical composition and conformation. Thus specimen heterogeneity in either composition or conformation has raised great challenges for high-resolution analysis. For particles with multiple conformations, inaccurate alignments and orientation parameters will yield an averaged map with diminished resolution and smeared density. Besides extensive classification approaches, here based on the assumption that the macromolecular complex is made up of multiple rigid modules whose relative orientations and positions are in slight fluctuation around equilibriums, we propose a new method called as local optimization refinement to address this conformational heterogeneity for an improved resolution. The key idea is to optimize the orientation and shift parameters of each rigid module and then reconstruct their three-dimensional structures individually. Using simulated data of 80S/70S ribosomes with relative fluctuations between the large (60S/50S) and the small (40S/30S) subunits, we tested this algorithm and found that the resolutions of both subunits are significantly improved. Our method provides a proof-of-principle solution for high-resolution single particle analysis of macromolecular complexes with dynamic conformations.

  20. Integration of imaging into clinical practice to assess the delivery and performance of macromolecular and nanotechnology-based oncology therapies.

    Science.gov (United States)

    Spence, Tara; De Souza, Raquel; Dou, Yannan; Stapleton, Shawn; Reilly, Raymond M; Allen, Christine

    2015-12-10

    Functional and molecular imaging has become increasingly used to evaluate interpatient and intrapatient tumor heterogeneity. Imaging allows for assessment of microenvironment parameters including tumor hypoxia, perfusion and proliferation, as well as tumor metabolism and the intratumoral distribution of specific molecular markers. Imaging information may be used to stratify patients for targeted therapies, and to define patient populations that may benefit from alternative therapeutic approaches. It also provides a method for non-invasive monitoring of treatment response at earlier time-points than traditional cues, such as tumor shrinkage. Further, companion diagnostic imaging techniques are becoming progressively more important for development and clinical implementation of targeted therapies. Imaging-based companion diagnostics are likely to be essential for the validation and FDA approval of targeted nanotherapies and macromolecular medicines. This review describes recent clinical advances in the use of functional and molecular imaging to evaluate the tumor microenvironment. Additionally, this article focuses on image-based assessment of distribution and anti-tumor effect of nano- and macromolecular systems.