WorldWideScience

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.

    Directory of Open Access Journals (Sweden)

    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

    Energy Technology Data Exchange (ETDEWEB)

    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. Macromolecular contrast agents for MR mammography: current status

    International Nuclear Information System (INIS)

    Macromolecular contrast media (MMCM) encompass a new class of diagnostic drugs that can be applied with dynamic MRI to extract both physiologic and morphologic information in breast lesions. Kinetic analysis of dynamic MMCM-enhanced MR data in breast tumor patients provides useful estimates of tumor blood volume and microvascular permeability, typically increased in cancer. These tumor characteristics can be applied to differentiate benign from malignant lesions, to define the angiogenesis status of cancers, and to monitor tumor response to therapy. The most immediate challenge to the development of MMCM-enhanced mammography is the identification of those candidate compounds that demonstrate the requisite long intravascular distribution and have the high tolerance necessary for clinical use. Potential mammographic applications and limitations of various MMCM, defined by either experimental animal testing or clinical testing in patients, are reviewed in this article. (orig.)

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

    Directory of Open Access Journals (Sweden)

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

    Science.gov (United States)

    Chen, Yanzuo; Huang, Yukun; Qin, Dongdong; Liu, Wenchao; Song, Chao; Lou, Kaiyan; Wang, Wei; Gao, Feng

    2016-01-01

    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. PMID:26964047

  7. MRI macromolecular contrast agents as indicators of changed tumor blood flow

    International Nuclear Information System (INIS)

    Background. A rapid mapping technique derived from dynamic contrast enhanced MRI data was used to identify and characterize reduction of blood flow in fibrosarcoma SA-1 tumors treated either by application of electric pulses or vinblastine. Materials and methods. Tissue permeability surface area product (PS) and fractional blood volume (BV) were calculated on a pixel-by-pixel basis using dynamic MRI intensity data after administration of gadomer- 17 or polylysine-Gd-DTPA; prototypic macromolecular contrast agents designed for blood pool enhancement. PS and BV values of untreated tumors were compared to those of tumors treated by local application of 8 electric pulses (amplitude/distance ratio, 1300 V/cm; duration, 100 μs, frequency, 1 Hz) percutaneously to the tumor or by systemic administration of vinblastine (2.5 mg/kg). Results. Both treatments transiently, but significantly reduced tumor blood flow, application of electric pulses to the tumors being by 40% more effective in reducing tumor blood flow than systemic administration of vinblastine. PS and BV values derived with polylysine-Gd-DTPA-enhanced MRI were lower compared to those with gadomer-17, due to larger molecular size. Interestingly, Gd-DTPA-enhanced MRI did not show any significant changes of PS and BV between untreated and treated tumors. Conclusion. This study demonstrates that dynamic contrast enhanced MRI can be effectively used to qualitatively monitor tumor blood flow, and quantitatively by means of BV and PS. (author)

  8. Correlation of dynamic contrast-enhanced magnetic resonance imaging with histologic tumor grade: comparison of macromolecular and small-molecular contrast media

    International Nuclear Information System (INIS)

    Background. The endothelial integrity of microvessels is disrupted in malignant tumors. Quantitative assays of tumor microvascular characteristics based on dynamic magnetic resonance imaging (MRI) were correlated with histopathologic grade in mammary soft tissue tumors. Materials and methods. A spectrum of tumors, benign through highly malignant, was induced in 33 female rats by administration of N -ethyl-N -nitrosourea (ENU), a potent carcinogen. Dynamic contrast-enhanced MRI was performed using a small-molecular contrast medium [gadopentetate, MW = 0.5 kDa] and a macromolecular contrast medium [albumin-(Gd-DTPA)30, MW = 92 kDa] at an interval of 1-2 days. Permeability surface area product (PS), as estimated by the corresponding endothelial transfer coefficient (KPS), and fractional plasma volume (fPV) were calculated for each tumor and each contrast agent using a two-compartment bi-directional kinetic model. MRI microvascular characteristics were correlated with histopathologic tumor grade. Results. Tumor permeability to macromolecular contrast medium, characterized by KPS, showed a highly positive correlation with tumor grade (r 2 = 0.76, P -10). K PS values were zero for all benign and some low-grade carcinomas, greater than zero in all other carcinomas, and increased in magnitude with higher tumor grade. A considerably smaller but significantly positive correlation was found between fPV and tumor grade using macromolecular contrast medium (r 2 = 0.25, P PS or fPV values and tumor grade was found using gadopentetate (r 2 = 0.01, P > 0.95 and r 2 = 0.03, P > 0.15, respectively). Conclusion. Quantitative tumor microvascular permeability assays generated with macromolecular MRI contrast medium correlate closely with histologic tumor grade. No significant correlation is found using small-molecular gadopentetate. (orig.)

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

    Science.gov (United States)

    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

  10. Permeability to macromolecular contrast media quantified by dynamic MRI correlates with tumor tissue assays of vascular endothelial growth factor (VEGF)

    International Nuclear Information System (INIS)

    Purpose: To correlate dynamic MRI assays of macromolecular endothelial permeability with microscopic area–density measurements of vascular endothelial growth factor (VEGF) in tumors. Methods and material: This study compared tumor xenografts from two different human cancer cell lines, MDA-MB-231 tumors (n = 5), and MDA-MB-435 (n = 8), reported to express respectively higher and lower levels of VEGF. Dynamic MRI was enhanced by a prototype macromolecular contrast medium (MMCM), albumin-(Gd-DTPA)35. Quantitative estimates of tumor microvascular permeability (KPS; μl/min × 100 cm3), obtained using a two-compartment kinetic model, were correlated with immunohistochemical measurements of VEGF in each tumor. Results: Mean KPS was 2.4 times greater in MDA-MB-231 tumors (KPS = 58 ± 30.9 μl/min × 100 cm3) than in MDA-MB-435 tumors (KPS = 24 ± 8.4 μl/min × 100 cm3) (p < 0.05). Correspondingly, the area–density of VEGF in MDA-MB-231 tumors was 2.6 times greater (27.3 ± 2.2%, p < 0.05) than in MDA-MB-435 cancers (10.5 ± 0.5%, p < 0.05). Considering all tumors without regard to cell type, a significant positive correlation (r = 0.67, p < 0.05) was observed between MRI-estimated endothelial permeability and VEGF immunoreactivity. Conclusion: Correlation of MRI assays of endothelial permeability to a MMCM and VEGF immunoreactivity of tumors support the hypothesis that VEGF is a major contributor to increased macromolecular permeability in cancers. When applied clinically, the MMCM-enhanced MRI approach could help to optimize the appropriate application of VEGF-inhibiting therapy on an individual patient basis.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. 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.

  13. Tunable, biodegradable gold nanoparticles as contrast agents for computed tomography and photoacoustic imaging.

    Science.gov (United States)

    Cheheltani, Rabee; Ezzibdeh, Rami M; Chhour, Peter; Pulaparthi, Kumidini; Kim, Johoon; Jurcova, Martina; Hsu, Jessica C; Blundell, Cassidy; Litt, Harold I; Ferrari, Victor A; Allcock, Harry R; Sehgal, Chandra M; Cormode, David P

    2016-09-01

    Gold nanoparticles (AuNP) have been proposed for many applications in medicine. Although large AuNP (>5.5 nm) are desirable for their longer blood circulation and accumulation in diseased tissues, small AuNP (nanoparticles (Au-PCPP) can perform their function as contrast agents, then subsequently break down into harmless byproducts and release the AuNP for swift excretion. Homogeneous Au-PCPP were synthesized using a microfluidic device. The size of the Au-PCPP can be controlled by the amount of polyethylene glycol-polylysine (PEG-PLL) block co-polymer in the formulation. Synthesis of Au-PCPP nanoparticles and encapsulation of AuNP in PCPP were evaluated using transmission electron microscopy and their biocompatibility and biodegradability confirmed in vitro. The Au-PCPP nanoparticles were found to produce strong computed tomography contrast. The UV-Vis absorption peak of Au-PCPP can be tuned into the near infrared region via inclusion of varying amounts of AuNP and controlling the nanoparticle size. In vitro and in vivo experiments demonstrated the potential of Au-PCPP as contrast agents for photoacoustic imaging. Therefore, Au-PCPP nanoparticles have high potency as contrast agents for two imaging modalities, as well as being biocompatible and biodegradable, and thus represent a platform with potential for translation into the clinic. PMID:27322961

  14. 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.

  15. 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.

  16. 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.

  17. 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....

  18. 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.

  19. 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

  20. Teaching macromolecular modeling.

    OpenAIRE

    Harvey, S C; Tan, R K

    1992-01-01

    Training newcomers to the field of macromolecular modeling is as difficult as is training beginners in x-ray crystallography, nuclear magnetic resonance, or other methods in structural biology. In one or two lectures, the most that can be conveyed is a general sense of the relationship between modeling and other structural methods. If a full semester is available, then students can be taught how molecular structures are built, manipulated, refined, and analyzed on a computer. Here we describe...

  1. 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.

  2. 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. PMID:24365328

  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. Biodegradability of dissolved and particulate organic matter in tributaries of contrasting land-use in the Upper Mississippi River

    Science.gov (United States)

    Voss, B.; Wickland, K.; Stets, E.; Aiken, G.; Striegl, R. G.; Stackpoole, S. M.

    2015-12-01

    Recent estimates of significant CO2 efflux from inland waters have spurred interest in respiration of organic matter (OM) as a contributor to regional carbon budgets. Dissolved organic carbon (DOC) has been the focus of many investigations, with numerous studies targeting the structural and environmental controls on degradation rates. Very little is known about the reactivity of riverine particulate OC (POC), which can be composed of a range of materials from freshly fixed photosynthetic organic matter to ancient sedimentary OC. This study examines OC reactivity in two watersheds with contrasting land-use, the highly forested Chippewa River basin in Wisconsin (45% forested, 19% agricultural) and the heavily agricultural Minnesota River basin in Minnesota (3% forested, 72% agricultural). The Minnesota and Chippewa rivers are the largest tributary sources of suspended sediment to the Mississippi River upstream of Iowa, and their distinct land-use features lead to a diversity in carbon sources and loads across a small geographic range. Respiration incubations were conducted on the DOC and POC collected at different seasonal and flow conditions from these two rivers. Optical oxygen measurements were used for non-destructive monitoring of incubations at high temporal frequency. Coupled with traditional DOC loss and CO2 production approaches, these experiments allow for comparison of potential CO2 production from DOC and POC, determination of oxygen:carbon respiratory quotients, and compositional changes in OM (e.g. DOM fluorescence, POM elemental composition). We observed potential CO2 production from POC that was 1x and 3x greater than that of DOC at field concentrations in the Chippewa and Minnesota rivers, respectively, for incubation samples collected in spring of 2015. By linking OM respiration rates to metrics such as land use types and environmental variables, these results can help improve estimates of CO2 efflux from rivers across seasonal and spatial gradients.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  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. 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.

  11. Macromolecular crystallography research at Trombay

    International Nuclear Information System (INIS)

    Neutron diffraction studies of hydrogen positions in small molecules of biological interest at Trombay have provided valuable information that has been used in protein and enzyme structure model-building and in developing hydrogen bond potential functions. The new R-5 reactor is expected to provide higher neutron fluxes and also make possible small-angle neutron scattering studies of large biomolecules and bio-aggregates. In the last few years infrastructure facilities have also been established for macromolecular x-ray crystallography research. Meanwhile, the refinement of carbonic hydrases and lyysozyme structures have been carried out and interesting results obtained on protein dynamics and structure-function relationships. Some interesting presynaptic toxin phospholipases have also taken up for study. (author)

  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. Fractal Dimensions of Macromolecular Structures

    Science.gov (United States)

    Todoroff, Nickolay; Kunze, Jens; Schreuder, Herman; Hessler, Gerhard; Baringhaus, Karl-Heinz; Schneider, Gisbert

    2014-01-01

    Quantifying the properties of macromolecules is a prerequisite for understanding their roles in biochemical processes. One of the less-explored geometric features of macromolecules is molecular surface irregularity, or ‘roughness’, which can be measured in terms of fractal dimension (D). In this study, we demonstrate that surface roughness correlates with ligand binding potential. We quantified the surface roughnesses of biological macromolecules in a large-scale survey that revealed D values between 2.0 and 2.4. The results of our study imply that surface patches involved in molecular interactions, such as ligand-binding pockets and protein-protein interfaces, exhibit greater local fluctuations in their fractal dimensions than ‘inert’ surface areas. We expect approximately 22 % of a protein’s surface outside of the crystallographically known ligand binding sites to be ligandable. These findings provide a fresh perspective on macromolecular structure and have considerable implications for drug design as well as chemical and systems biology. PMID:26213587

  14. 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...

  15. 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...

  16. New pharmaceutical applications for macromolecular binders.

    Science.gov (United States)

    Bertrand, Nicolas; Gauthier, Marc A; Bouvet, Céline; Moreau, Pierre; Petitjean, Anne; Leroux, Jean-Christophe; Leblond, Jeanne

    2011-10-30

    Macromolecular binders consist of polymers, dendrimers, and oligomers with binding properties for endogenous or exogenous substrates. This field, at the frontier of host/guest chemistry and pharmacology, has met a renewed interest in the past decade due to the clinical success of several sequestrants, like sevelamer hydrochloride (Renagel®) or sugammadex (Bridion®). In many instances, multivalent binding by the macromolecular drugs can modify the properties of the substrate, and may prevent it from reaching its site of action and/or trigger a biological response. From small (e.g., ions) to larger substrates (e.g., bacteria and cells), this review presents the state-of-the-art of macromolecular binders and provides detailed illustrative examples of recent developments bearing much promise for future pharmaceutical applications. PMID:21571017

  17. 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...

  18. Protein stabilization by macromolecular crowding through enthalpy rather than entropy.

    Science.gov (United States)

    Senske, Michael; Törk, Lisa; Born, Benjamin; Havenith, Martina; Herrmann, Christian; Ebbinghaus, Simon

    2014-06-25

    The interior of the cell is a densely crowded environment in which protein stability is affected differently than in dilute solution. Macromolecular crowding is commonly understood in terms of an entropic volume exclusion effect based on hardcore repulsions among the macromolecules. We studied the thermal unfolding of ubiquitin in the presence of different cosolutes (glucose, dextran, poly(ethylene glycol), KCl, urea). Our results show that for a correct dissection of the cosolute-induced changes of the free energy into its enthalpic and entropic contributions, the temperature dependence of the heat capacity change needs to be explicitly taken into account. In contrast to the prediction by the excluded volume theory, we observed an enthalpic stabilization and an entropic destabilization for glucose, dextran, and poly(ethylene glycol). The enthalpic stabilization mechanism induced by the macromolecular crowder dextran was similar to the enthalpic stabilization mechanism of its monomeric building block glucose. In the case of poly(ethylene glycol), entropy is dominating over enthalpy leading to an overall destabilization. We propose a new model to classify cosolute effects in terms of their enthalpic contributions to protein stability.

  19. Determining the architectures of macromolecular assemblies

    NARCIS (Netherlands)

    Alber, Frank; Dokudovskaya, Svetlana; Veenhoff, Liesbeth M.; Zhang, Wenzhu; Kipper, Julia; Devos, Damien; Suprapto, Adisetyantari; Karni-Schmidt, Orit; Williams, Rosemary; Chait, Brian T.; Rout, Michael P.; Sali, Andrej

    2007-01-01

    To understand the workings of a living cell, we need to know the architectures of its macromolecular assemblies. Here we show how proteomic data can be used to determine such structures. The process involves the collection of sufficient and diverse high-quality data, translation of these data into s

  20. MR lymphography with macromolecular Gd-DTPA compounds

    International Nuclear Information System (INIS)

    This paper investigates the suitability of macromolecular Gd-DTPA compounds as signal-enhancing lymphographic agents in MR imaging. Two Gd-DTPA polylysin compounds and Gd-DTPA albumin, with molecular weights of 48,000,170,000, and 87,000 daltons, respectively, were tested in rabbits at gadolinium doses of 5 and 15 μmol per animal. Three animals were examined at each dose with T1-weighted sequences. The iliac lymph nodes were imaged prior to and during unilateral endolymphatic infusion into a femoral lymph vessel as well as over a period of 2 hours thereafter. All contrast media showed a homogeneous and pronounced signal enhancement in the lymph nodes during infusion at both doses

  1. Proceedings of biodegradation

    International Nuclear Information System (INIS)

    This book contains the proceedings of Biodegradation. Topics include:biodegradation using the tools of biotechnology, basic science aspects of biodegradation, the physiological characteristics of microorganisms, the use of selective techniques that enhance the process of microbial evolution of biodegradative genes in nature, the genetic characteristics of microorganisms allowing them to biodegrade both natural and synthetic toxic chemicals, the molecular techniques that allow selective assembly of genetic segments form a variety of bacterial strains to a single strain, and methods needed to advance biodegradation research as well as the high-priority chemical problems important to the Department of Defense or to the chemical industry

  2. 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.

  3. 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.

  4. Radiation damage to nucleoprotein complexes in macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Bury, Charles; Garman, Elspeth F.; Ginn, Helen Mary [University of Oxford, South Parks Road, Oxford OX1 3QU (United Kingdom); Ravelli, Raimond B. G. [Maastricht University, PO Box 616, Maastricht 6200 MD (Netherlands); Carmichael, Ian [University of Notre Dame, Notre Dame, IN 46556 (United States); Kneale, Geoff; McGeehan, John E., E-mail: john.mcgeehan@port.ac.uk [University of Portsmouth, King Henry 1st Street, Portsmouth PO1 2DY (United Kingdom)

    2015-01-30

    Quantitative X-ray induced radiation damage studies employing a model protein–DNA complex revealed a striking partition of damage sites. The DNA component was observed to be far more resistant to specific damage compared with the protein. Significant progress has been made in macromolecular crystallography over recent years in both the understanding and mitigation of X-ray induced radiation damage when collecting diffraction data from crystalline proteins. In contrast, despite the large field that is productively engaged in the study of radiation chemistry of nucleic acids, particularly of DNA, there are currently very few X-ray crystallographic studies on radiation damage mechanisms in nucleic acids. Quantitative comparison of damage to protein and DNA crystals separately is challenging, but many of the issues are circumvented by studying pre-formed biological nucleoprotein complexes where direct comparison of each component can be made under the same controlled conditions. Here a model protein–DNA complex C.Esp1396I is employed to investigate specific damage mechanisms for protein and DNA in a biologically relevant complex over a large dose range (2.07–44.63 MGy). In order to allow a quantitative analysis of radiation damage sites from a complex series of macromolecular diffraction data, a computational method has been developed that is generally applicable to the field. Typical specific damage was observed for both the protein on particular amino acids and for the DNA on, for example, the cleavage of base-sugar N{sub 1}—C and sugar-phosphate C—O bonds. Strikingly the DNA component was determined to be far more resistant to specific damage than the protein for the investigated dose range. At low doses the protein was observed to be susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses.

  5. 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.

  6. Automated macromolecular crystal detection system and method

    Science.gov (United States)

    Christian, Allen T.; Segelke, Brent; Rupp, Bernard; Toppani, Dominique

    2007-06-05

    An automated macromolecular method and system for detecting crystals in two-dimensional images, such as light microscopy images obtained from an array of crystallization screens. Edges are detected from the images by identifying local maxima of a phase congruency-based function associated with each image. The detected edges are segmented into discrete line segments, which are subsequently geometrically evaluated with respect to each other to identify any crystal-like qualities such as, for example, parallel lines, facing each other, similarity in length, and relative proximity. And from the evaluation a determination is made as to whether crystals are present in each image.

  7. 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

  8. 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

  9. 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....

  10. Biodegradability of Plastics

    Directory of Open Access Journals (Sweden)

    Yutaka Tokiwa

    2009-08-01

    Full Text Available 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.

  11. Panorama of ancient metazoan macromolecular complexes.

    Science.gov (United States)

    Wan, Cuihong; Borgeson, Blake; Phanse, Sadhna; Tu, Fan; Drew, Kevin; Clark, Greg; Xiong, Xuejian; Kagan, Olga; Kwan, Julian; Bezginov, Alexandr; Chessman, Kyle; Pal, Swati; Cromar, Graham; Papoulas, Ophelia; Ni, Zuyao; Boutz, Daniel R; Stoilova, Snejana; Havugimana, Pierre C; Guo, Xinghua; Malty, Ramy H; Sarov, Mihail; Greenblatt, Jack; Babu, Mohan; Derry, W Brent; Tillier, Elisabeth R; Wallingford, John B; Parkinson, John; Marcotte, Edward M; Emili, Andrew

    2015-09-17

    Macromolecular complexes are essential to conserved biological processes, but their prevalence across animals is unclear. By combining extensive biochemical fractionation with quantitative mass spectrometry, here we directly examined the composition of soluble multiprotein complexes among diverse metazoan models. Using an integrative approach, we generated a draft conservation map consisting of more than one million putative high-confidence co-complex interactions for species with fully sequenced genomes that encompasses functional modules present broadly across all extant animals. Clustering reveals a spectrum of conservation, ranging from ancient eukaryotic assemblies that have probably served cellular housekeeping roles for at least one billion years, ancestral complexes that have accrued contemporary components, and rarer metazoan innovations linked to multicellularity. We validated these projections by independent co-fractionation experiments in evolutionarily distant species, affinity purification and functional analyses. The comprehensiveness, centrality and modularity of these reconstructed interactomes reflect their fundamental mechanistic importance and adaptive value to animal cell systems. PMID:26344197

  12. Macromolecular diffractive imaging using imperfect crystals

    Science.gov (United States)

    Ayyer, Kartik; Yefanov, Oleksandr M.; Oberthür, Dominik; Roy-Chowdhury, Shatabdi; Galli, Lorenzo; Mariani, Valerio; Basu, Shibom; Coe, Jesse; Conrad, Chelsie E.; Fromme, Raimund; Schaffer, Alexander; Dörner, Katerina; James, Daniel; Kupitz, Christopher; Metz, Markus; Nelson, Garrett; Xavier, Paulraj Lourdu; Beyerlein, Kenneth R.; Schmidt, Marius; Sarrou, Iosifina; Spence, John C. H.; Weierstall, Uwe; White, Thomas A.; Yang, Jay-How; Zhao, Yun; Liang, Mengning; Aquila, Andrew; Hunter, Mark S.; Robinson, Joseph S.; Koglin, Jason E.; Boutet, Sébastien; Fromme, Petra; Barty, Anton; Chapman, Henry N.

    2016-02-01

    The three-dimensional structures of macromolecules and their complexes are mainly elucidated by X-ray protein crystallography. A major limitation of this method is access to high-quality crystals, which is necessary to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields information of sufficiently high resolution with which to solve the crystal structure. The observation that crystals with reduced unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks suggests that crystallographic resolution for some macromolecules may be limited not by their heterogeneity, but by a deviation of strict positional ordering of the crystalline lattice. Such displacements of molecules from the ideal lattice give rise to a continuous diffraction pattern that is equal to the incoherent sum of diffraction from rigid individual molecular complexes aligned along several discrete crystallographic orientations and that, consequently, contains more information than Bragg peaks alone. Although such continuous diffraction patterns have long been observed—and are of interest as a source of information about the dynamics of proteins—they have not been used for structure determination. Here we show for crystals of the integral membrane protein complex photosystem II that lattice disorder increases the information content and the resolution of the diffraction pattern well beyond the 4.5-ångström limit of measurable Bragg peaks, which allows us to phase the pattern directly. Using the molecular envelope conventionally determined at 4.5 ångströms as a constraint, we obtain a static image of the photosystem II dimer at a resolution of 3.5 ångströms. This result shows that continuous diffraction can be used to overcome what have long been supposed to be the resolution limits of macromolecular crystallography, using a method that exploits commonly encountered imperfect crystals and enables model-free phasing.

  13. Phylogenetic Diversity in the Macromolecular Composition of Microalgae

    Science.gov (United States)

    Finkel, Zoe V.; Follows, Mick J.; Liefer, Justin D.; Brown, Chris M.; Benner, Ina; Irwin, Andrew J.

    2016-01-01

    The elemental stoichiometry of microalgae reflects their underlying macromolecular composition and influences competitive interactions among species and their role in the food web and biogeochemistry. Here we provide a new estimate of the macromolecular composition of microalgae using a hierarchical Bayesian analysis of data compiled from the literature. The median macromolecular composition of nutrient-sufficient exponentially growing microalgae is 32.2% protein, 17.3% lipid, 15.0% carbohydrate, 17.3% ash, 5.7% RNA, 1.1% chlorophyll-a and 1.0% DNA as percent dry weight. Our analysis identifies significant phylogenetic differences in macromolecular composition undetected by previous studies due to small sample sizes and the large inherent variability in macromolecular pools. The phylogenetic differences in macromolecular composition lead to variations in carbon-to-nitrogen ratios that are consistent with independent observations. These phylogenetic differences in macromolecular and elemental composition reflect adaptations in cellular architecture and biochemistry; specifically in the cell wall, the light harvesting apparatus, and storage pools. PMID:27228080

  14. 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.

  15. 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.

  16. Grey water biodegradability.

    Science.gov (United States)

    Ghunmi, Lina Abu; Zeeman, Grietje; Fayyad, Manar; van Lier, Jules B

    2011-02-01

    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 conditions in the biodegradation test. The maximum aerobic and anaerobic biodegradability and conversion rate for the different COD fractions is determined. The results show that, on average, dormitory grey water COD fractions are 28% suspended, 32% colloidal and 40% dissolved. The studied factors incubation time, inoculum addition and temperature are influencing the determined biodegradability. The maximum biodegradability and biodegradation rate differ between different COD fractions, viz. COD(ss), COD(col) and COD(diss). The dissolved COD fraction is characterised by the lowest degradation rate, both for anaerobic and aerobic conditions. The maximum biodegradability for aerobic and anaerobic conditions is 86 and 70% respectively, whereas the first order conversion rate constant, k₂₀, is 0.119 and 0.005 day⁻¹, respectively. The anaerobic and aerobic conversion rates in relation to temperature can be described by the Arrhenius relation, with temperature coefficients of 1.069 and 1.099, respectively. PMID:20658309

  17. 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.

  18. A Novel Algorithm for Macromolecular Epitope Matching

    Directory of Open Access Journals (Sweden)

    Stanislav Jakuschev

    2009-03-01

    Full Text Available Many macromolecules, namely proteins, show functional substructures or epitopes defined by characteristic spatial arrangements of groups of specific atoms or residues. The identification of such substructures in a set of macromolecular 3D-structures solves an important problem in molecular biology as it allows the assignment of functions to molecular moieties and thus opens the possibility of a mechanistic understanding of molecular function. We have devised an algorithm that models a functional epitope formed by a group of atoms or residues as set of points in cartesian space with associated functional properties. The algorithm searches for similar epitopes in a database of structures by an efficient multistage comparison of distance sets in the epitope and in the structures from the database. The search results in a list of optimal matches and corresponding optimal superpositions of query epitope and matching epitopes from the database. The algorithm is discussed against the background of related approaches, and it is successfully tested in three application scenarios: global match of two homologous proteins, search for an epitope on a homologous protein, and finding matching epitopes in a protein database.

  19. 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.

  20. Macromolecular Crystal Growth by Means of Microfluidics

    Science.gov (United States)

    vanderWoerd, Mark; Ferree, Darren; Spearing, Scott; Monaco, Lisa; Molho, Josh; Spaid, Michael; Brasseur, Mike; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    We have performed a feasibility study in which we show that chip-based, microfluidic (LabChip(TM)) technology is suitable for protein crystal growth. This technology allows for accurate and reliable dispensing and mixing of very small volumes while minimizing bubble formation in the crystallization mixture. The amount of (protein) solution remaining after completion of an experiment is minimal, which makes this technique efficient and attractive for use with proteins, which are difficult or expensive to obtain. The nature of LabChip(TM) technology renders it highly amenable to automation. Protein crystals obtained in our initial feasibility studies were of excellent quality as determined by X-ray diffraction. Subsequent to the feasibility study, we designed and produced the first LabChip(TM) device specifically for protein crystallization in batch mode. It can reliably dispense and mix from a range of solution constituents into two independent growth wells. We are currently testing this design to prove its efficacy for protein crystallization optimization experiments. In the near future we will expand our design to incorporate up to 10 growth wells per LabChip(TM) device. Upon completion, additional crystallization techniques such as vapor diffusion and liquid-liquid diffusion will be accommodated. Macromolecular crystallization using microfluidic technology is envisioned as a fully automated system, which will use the 'tele-science' concept of remote operation and will be developed into a research facility for the International Space Station as well as on the ground.

  1. 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.

  2. 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.

  3. Biodegradation of plastics.

    Science.gov (United States)

    Shimao, M

    2001-06-01

    Widespread studies on the biodegradation of plastics have been carried out in order to overcome the environmental problems associated with synthetic plastic waste. Recent work has included studies of the distribution of synthetic polymer-degrading microorganisms in the environment, the isolation of new microorganisms for biodegradation, the discovery of new degradation enzymes, and the cloning of genes for synthetic polymer-degrading enzymes. PMID:11404101

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. Contrast Materials

    Science.gov (United States)

    ... adverse reaction, you should tell your doctor about: allergies to contrast materials, food, drugs, dyes, preservatives, or animals medications ... These include: previous adverse reactions to iodine-based contrast materials history of ... disease dehydration sickle cell anemia , polycythemia and ...

  13. Effects of macromolecular crowding and osmolyte on human Tau fibrillation.

    Science.gov (United States)

    Wu, Yingying; Teng, Ningning; Li, Sen

    2016-09-01

    Tau fibrillation is reported to be involved in neurodegenerative disorders, such as Alzheimer's disease, in which the natural environment is very crowded in the cells. Understanding the role of crowding environments in regulating Tau fibrillation is of great importance for elucidating the etiology of these diseases. In this experiment, the effects of macromolecular crowding and osmolyte reagents in the crowding environment on Tau fibrillation were studied by thioflavin T binding, SDS-PAGE and TEM assays. Ficoll 70 and Dextran 70 of different concentrations were used as macromolecular crowding reagents inside the cells and showed a strong enhancing effect on the fibrillation of normal and hyperphosphorylated Tau. The enhancing effect of Dextran is stronger than that of Ficoll 70 at the same concentration. In addition, the cellular osmolyte sucrose was found to protect Tau against fibrillation, and inhibit the enhancing effect of macromolecular crowding on Tau fibrillation. A possible model for the fibrillation process of Tau and the effect of macromolecular crowding and osmolyte on this process was proposed based on these experimental results. The information obtained from our study can enhance the understanding of how proteins aggregate and avoid aggregation in crowded physiological environments and might lead to a better understanding of the molecular mechanisms of Alzheimer's disease in vivo. PMID:26683879

  14. Macromolecular crystallography radiation damage research: what’s new?

    OpenAIRE

    Garman, Elspeth F.; Weik, Martin

    2011-01-01

    Radiation damage in macromolecular crystallography has become a mainstream concern over the last ten years. The current status of research into this area is briefly assessed, and the ten new papers published in this issue are set into the context of previous work in the field. Some novel and exciting developments emerging over the last two years are also summarized.

  15. 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 efficie...

  16. 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.

  17. Biodegradation of cyanuric acid.

    Science.gov (United States)

    Saldick, J

    1974-12-01

    Cyanuric acid biodegrades readily under a wide variety of natural conditions, and particularly well in systems of either low or zero dissolved-oxygen level, such as anaerobic activated sludge and sewage, soils, muds, and muddy streams and river waters, as well as ordinary aerated activated sludge systems with typically low (1 to 3 ppm) dissolved-oxygen levels. Degradation also proceeds in 3.5% sodium chloride solution. Consequently, there are degradation pathways widely available for breaking down cyanuric acid discharged in domestic effluents. The overall degradation reaction is merely a hydrolysis; CO(2) and ammonia are the initial hydrolytic breakdown products. Since no net oxidation occurs during this breakdown, biodegradation of cyanuric acid exerts no primary biological oxygen demand. However, eventual nitrification of the ammonia released will exert its usual biological oxygen demand.

  18. 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

  19. 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

  20. 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…

  1. 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.

  2. Macromolecular Brushes as Stabilizers of Hydrophobic Solute Nanoparticles.

    Science.gov (United States)

    Luo, Hanying; Raciti, David; Wang, Chao; Herrera-Alonso, Margarita

    2016-06-01

    Macromolecular brushes bearing poly(ethylene glycol) and poly(d,l-lactide) side chains were used to stabilize hydrophobic solute nanoparticles formed by a rapid change in solvent quality. Unlike linear diblock copolymers with the same hydrophilic and hydrophobic block chemistries, the brush copolymer enabled the formation of ellipsoidal β-carotene nanoparticles, which in cosolvent mixtures developed into rod-like structures, resulting from a combination of Ostwald ripening and particle aggregation. The stabilizing ability of the copolymer was highly dependent on the mobility of the hydrophobic component, influenced by its molecular weight. As shown here, asymmetric amphiphilic macromolecular brushes of this type may be used as hydrophobic drug stabilizers and potentially assist the shape control of nonspherical aggregate morphologies. PMID:27035279

  3. 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.

  4. 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.

  5. Effects of macromolecular chelators on intestinal cadmium absorption in mice

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, O.; Nielsen, J.B.; Bulman, R.A.

    1989-01-01

    Suppression of absorption by macromolecular chelators have been sucessful with several metals. In this paper a series of immobilized chelators ranging from DTPA to S-containing soft bases have been synthetized and investigated for ability to suppress intestinal uptake of /sup 109/Cd/sup 2+/ in mice. Dextran-O-ethyl-mercaptan, xanthates derived from polysaccharides and polyvinyl alcohol, dithiocarbamates of polyethylene imine and aminoethyl cellulose, and DTPA immobilized on aminopropyl silica were all ineffective. DTPA immobilized on aminoethyl cellulose even enhanced the intestinal uptake. The macromolecular chelators were without extensive effect on organ distribution of absorbed cadmium, except for dithiocarbamate immobilized on polyethylene imine, which enhanced the deposition of cadmium in several organs including the brain. Although the results are discouragign, they indicate that desing and synthesis of immobilized vicinal dithio compounds may represent an avenue for development of non-absorbable chelators with high affinity for cadmium.

  6. Integrating Topology and Geometry for Macro-Molecular Simulations

    OpenAIRE

    Moore, Edward L. F.; Peters, Thomas J.; Ferguson, David R.; Neil F Stewart

    2005-01-01

    Emerging macro-molecular simulations, such as supercoiling of DNA and protein unfolding, have an opportunity to profit from two decades of experience with geometric models within computer-aided geometric design (CAGD). For CAGD, static models are often sufficient, while form and function are inextricably related in biochemistry, resulting in greater attention to critical topological characteristics of these dynamic models. The greater emphasis upon dynamic change in macro-...

  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. 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.

  9. 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.

  10. Contrast-enhanced magnetic resonance imaging estimation of altered capillary permeability in experimental mammary carcinomas after x-irradiation

    International Nuclear Information System (INIS)

    Dynamic magnetic resonance imaging (MRI) enhanced with a macromolecular contrast medium, albumin-(Gd-DTPA)35, was used to detect changes in microvascular characteristics in R3230 mammary adenocarcinomas induced by x-irradiation. Tumors were implanted in either flank in nine rats. One of the tumors was exposed to single-dose x-irradiation (30 Gy) 3 days before MRI. The contralateral control tumor was shielded from irradiation. Capillary permeability to macromolecular contrast medium in irradiated tumors was elevated significantly (P -1 cm-3 compared with 0.121 ± .011 mL hr-1 cm-3 for the nonirradiated tumors. This radiation-induced increase in permeability was corroborated using a macromolecular Evans blue-protein complex measured in the same tumors using an invasive spectrophotometric technique. Dynamic MRI-enhanced with macromolecular contrast medium permits noninvasive quantitative estimates of capillary permeability in tumors, with and without x-irradiation. Because the transendothelial permeability for macromolecular solutes likely influences tumoral accumulation of macromolecular chemotherapeutic agents, this noninvasive technique may prove to be clinically useful in tailoring tumor treatment programs which combine radiation and chemotherapy. 51 refs., 4 figs., 1 tab

  11. 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.

  12. 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

  13. 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...

  14. 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.

  15. Impact of synchrotron radiation on macromolecular crystallography: a personal view

    International Nuclear Information System (INIS)

    This article, largely based on personal experiences of the authors, reviews the early history of the application of synchrotron radiation to structural biology, and particularly protein crystallography, to show the tremendous impact that this experimental innovation has had on these disciplines. The introduction of synchrotron radiation sources almost four decades ago has led to a revolutionary change in the way that diffraction data from macromolecular crystals are being collected. Here a brief history of the development of methodologies that took advantage of the availability of synchrotron sources are presented, and some personal experiences with the utilization of synchrotrons in the early days are recalled

  16. 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.

  17. Cardiac voltage-gated calcium channel macromolecular complexes.

    Science.gov (United States)

    Rougier, Jean-Sébastien; Abriel, Hugues

    2016-07-01

    Over the past 20years, a new field of research, called channelopathies, investigating diseases caused by ion channel dysfunction has emerged. Cardiac ion channels play an essential role in the generation of the cardiac action potential. Investigators have largely determined the physiological roles of different cardiac ion channels, but little is known about the molecular determinants of their regulation. The voltage-gated calcium channel Cav1.2 shapes the plateau phase of the cardiac action potential and allows the influx of calcium leading to cardiomyocyte contraction. Studies suggest that the regulation of Cav1.2 channels is not uniform in working cardiomyocytes. The notion of micro-domains containing Cav1.2 channels and different calcium channel interacting proteins, called macro-molecular complex, has been proposed to explain these observations. The objective of this review is to summarize the currently known information on the Cav1.2 macromolecular complexes in the cardiac cell and discuss their implication in cardiac function and disorder. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel. PMID:26707467

  18. Identifying and Visualizing Macromolecular Flexibility in Structural Biology.

    Science.gov (United States)

    Palamini, Martina; Canciani, Anselmo; Forneris, Federico

    2016-01-01

    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.

  19. 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.

  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. 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.

  2. 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.

  3. 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.

  4. Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy.

    Science.gov (United States)

    Stark, Holger; Chari, Ashwin

    2016-02-01

    Single particle cryo-EM has recently developed into a powerful tool to determine the 3D structure of macromolecular complexes at near-atomic resolution, which allows structural biologists to build atomic models of proteins. All technical aspects of cryo-EM technology have been considerably improved over the last two decades, including electron microscopic hardware, image processing software and the ever growing speed of computers. This leads to a more widespread use of the technique, and it can be anticipated that further automation of electron microscopes and image processing tools will soon fully shift the focus away from the technological aspects, onto biological questions that can be answered. In single particle cryo-EM, no crystals of a macromolecule are required. In contrast to X-ray crystallography, this significantly facilitates structure determination by cryo-EM. Nevertheless, a relatively high level of biochemical control is still essential to obtain high-resolution structures by cryo-EM, and it can be anticipated that the success of the cryo-EM technology goes hand in hand with further developments of sample purification and preparation techniques. This will allow routine high-resolution structure determination of the many macromolecular complexes of the cell that until now represent evasive targets for X-ray crystallographers. Here we discuss the various biochemical tools that are currently available and the existing sample purification and preparation techniques for cryo-EM grid preparation that are needed to obtain high-resolution images for structure determination. PMID:26671943

  5. 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.

  6. 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

  7. A loop of coagulation factor VIIa influencing macromolecular substrate specificity

    DEFF Research Database (Denmark)

    Bjelke, Jais R; Persson, Egon; Rasmussen, Hanne B;

    2006-01-01

    . The resulting variant exhibited increased intrinsic activity, concurrent with maturation of the active site, a less accessible N-terminus, and, interestingly, an altered macromolecular substrate specificity reflected in an increased ability to cleave factor IX (FIX) and a decreased rate of FX activation....../Met(298{156})Lys-FVIIa with almost the same activity and specificity profile. We conclude that a lysine residue in position 298{156} of FVIIa requires a hydrophilic environment to be fully accommodated. This position appears critical for substrate specificity among the proteases of the blood coagulation......Coagulation factor VIIa (FVIIa) belongs to a family of proteases being part of the stepwise, self-amplifying blood coagulation cascade. To investigate the impact of the mutation Met(298{156})Lys in FVIIa, we replaced the Gly(283{140})-Met(298{156}) loop with the corresponding loop of factor Xa...

  8. 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.

  9. 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.

  10. Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin

    International Nuclear Information System (INIS)

    The three macromolecular crystallography beamlines BL14.1, BL14.2 and BL14.3 at the BESSY II storage ring at the Helmholtz-Zentrum Berlin are described. 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

  11. 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

  12. Poly (3-Hydroxyalkanoates: Biodegradable Plastics

    Directory of Open Access Journals (Sweden)

    Surbhi Jain

    2013-03-01

    Full Text Available 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 renewable carbon sources. However, their application is limited by high production cost. Polyhydroxyalkanoates (PHAs have attracted research and commercial interests worldwide because they can be used as biodegradable thermoplastics and also because they can be produced from renewable resources. This review will present an overview on synthesis and degradation of polyhydroxyalkanoates (PHAs, development as biodegradable plastics and its potential production from renewable resources such as palm oil products.

  13. Testing biodegradability with standardized methods.

    Science.gov (United States)

    Pagga, U

    1997-12-01

    Laboratory test methods are used by industry laboratories to determine biodegradability, an important parameter for the evaluation of the ecological behaviour of substances. Biodegradability has a key role due to the simple fact that a degradable substance will cause no long term risk in the environment. The great variety of biodegradation processes in the natural environment and in technical plants for treating waste water and solid wastes gave rise to a rather large number of test methods based on different test principles. To guarantee the acceptance of the test results by authorities and customers internationally standardized methods (ISO, OECD) and established quality criteria (GLP, EN 45,000, ISO 9000) are used. PMID:9415981

  14. Petroleum biodegradation in marine environments.

    Science.gov (United States)

    Harayama, S; Kishira, H; Kasai, Y; Shutsubo, K

    1999-08-01

    Petroleum-based products are the major source of energy for industry and daily life. Petroleum is also the raw material for many chemical products such as plastics, paints, and cosmetics. The transport of petroleum across the world is frequent, and the amounts of petroleum stocks in developed countries are enormous. Consequently, the potential for oil spills is significant, and research on the fate of petroleum in a marine environment is important to evaluate the environmental threat of oil spills, and to develop biotechnology to cope with them. Crude oil is constituted from thousands of components which are separated into saturates, aromatics, resins and asphaltenes. Upon discharge into the sea, crude oil is subjected to weathering, the process caused by the combined effects of physical, chemical and biological modification. Saturates, especially those of smaller molecular weight, are readily biodegraded in marine environments. Aromatics with one, two or three aromatic rings are also efficiently biodegraded; however, those with four or more aromatic ring are quite resistant to biodegradation. The asphaltene and resin fractions contain higher molecular weight compounds whose chemical structures have not yet been resolved. The biodegradability of these compounds is not yet known. It is known that the concentrations of available nitrogen and phosphorus in seawater limit the growth and activities of hydrocarbon-degrading microorganisms in a marine environment. In other words, the addition of nitrogen and phosphorus fertilizers to an oil-contaminated marine environment can stimulate the biodegradation of spilled oil. This notion was confirmed in the large-scale operation for bioremediation after the oil spill from the Exxon Valdez in Alaska. Many microorganisms capable of degrading petroleum components have been isolated. However, few of them seem to be important for petroleum biodegradation in natural environments. One group of bacteria belonging to the genus

  15. 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.

  16. Photodegradation of major soil microbial biomolecules is comparable to biodegradation: Insights from infrared and diffusion editing NMR spectroscopies

    Science.gov (United States)

    Spence, Adrian; Kelleher, Brian P.

    2016-03-01

    As a primary decomposition process in terrestrial biosystems, biodegradation has been extensively studied with regard to its impact on soil organic matter transformation. However, the biotransformation of soil microbial biomass (a primary source of soil organic carbon) remains poorly understood, and even less is known about the fate of microbial-derived carbon under photodegradation. Here, we combine infrared and diffusion editing NMR spectroscopies to provide molecular-level information on the photodegradation of major biochemical components in soil microbial biomass and leachates over time. Results indicate a considerable enrichment in aliphatic components, presumably polymethylenic-C [(C-H2)n] and the simultaneous loss of carbohydrate and protein structures in the biomass. An immediate conclusion is that photodegradation increased the conversion of macromolecular carbohydrates and proteins to smaller components. However, further analysis reveals that macromolecular carbohydrates and proteins may be more resistant to photodegradation than initially thought and are found in the leachates. Although attenuated, there is also evidence to suggest that some aliphatic structures persist in the leachates. Overall, the photodegradation pathway reported here is remarkably similar to that of biodegradation, suggesting that under rapidly expanding anthropogenic land disturbances, photodegradation could be an important driver of the transformation of microbial-derived organic matter in terrestrial biosystems.

  17. 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

  18. 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...

  19. 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

  20. 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...

  1. Synthesis of a water-soluble macromolecular light stabilizer containing hindered amine structures

    Institute of Scientific and Technical Information of China (English)

    Wei Ma; Mei Meng; Xue Jiang; Bing-Tao Tang; Shu-Fen Zhang

    2013-01-01

    A novel water-soluble macromolecular light stabilizer was synthesized by grafting 2-chloro-4,6-bis-[(2,2,6,6-tetramethylpiperidin-4-yl)amino]-1,3,5-triazine onto polyvinylamine.The intermediate 2-chloro-4,6-bis-[(2,2,6,6-tetramethylpiperidin-4-yl)amino]-1,3,5-triazine and the obtained macromolecular light stabilizer were characterized by 1H NMR,HRMS,IR and UV spectroscopy.Cotton fabrics dyed with C.I.Reactive Yellow 145,C.l.Reactive Red 195 and C.I.Reactive Blue 19 were finished with the macromolecular light stabilizer,and the lightfastness of the dyes was tested.The results showed that the lightfastness of the reactive dyes was improved by 0.5-1.0 grade after being finished and the macromolecular light stabilizer exhibited good wash fastness and thermal stability.

  2. 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.

  3. Rapid Metal -free Macromolecular Coupling via in situ Nitrile Oxide-Activated Alkene Cycloaddition

    OpenAIRE

    Isaacman, Michael J.; Cui, Weibin; Theogarajan, Luke S.

    2014-01-01

    Nitrile oxide 1,3 dipolar cycloaddition is a simple and powerful coupling methodology. However, the self-dimerization of nitrile oxides has prevented the widespread use of this strategy for macromolecular coupling. By combining an in situ nitrile oxide generation with a highly reactive activated dipolarophile, we have overcome these obstacles and present a metal-free macromolecular coupling strategy for the modular synthesis of several ABA triblock copolymers. Nitrile oxides were generated in...

  4. 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.

  5. 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

  6. JBluIce-EPICS control system for macromolecular crystallography

    International Nuclear Information System (INIS)

    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.

  7. 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.

  8. 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. PMID:26786768

  9. 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.

  10. 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

  11. Macromolecular coal structure as revealed by novel diffusion tests

    Energy Technology Data Exchange (ETDEWEB)

    Peppas, N.A.; Olivares, J.; Drummond, R.; Lustig, S.

    1990-01-01

    The main goal of the present work was the elucidation of the mechanistic characteristics of dynamic transport of various penetrants (solvents) in thin sections of coals by examining their penetrant uptake, front swelling and stress development. An important objective of this work was the study of coal network structure in different thermodynamically compatible penetrants and the analysis of dynamic swelling in terms of present anomalous transport theories. Interferometry/polariscopy, surface image analysis and related techniques were used to quantify the stresses and solvent concentration profiles in these sections. Dynamic and equilibrium swelling behavior were correlated using the polar interaction contributions of the solvent solubility parameters. The penetrant front position was followed in thin coal sections as a function of time. The initial front velocity was calculated for various coals and penetrants. Our penetrant studies with thin coal section from the same coal sample but with different thickness show that within the range of 150 {mu}m to 1500{mu}m the transport mechanism of dimethyl formamide in the macromolecular coal network is non-Fickian. In fact, for the thickest samples the transport mechanism is predominately Case-II whereas in the thinner samples penetrant uptake may be diffusion-controlled. Studies in various penetrants such as acetone, cyclohexane, methanol, methyl ethyl ketone, toluene and methylene chloride indicated that penetrant transport is a non-Fickian phenomenon. Stresses and cracks were observed for transport of methylene chloride. 73 refs., 88 figs., 15 tabs.

  12. 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.

  13. 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.

  14. Polycapillary x-ray optics for macromolecular crystallography

    International Nuclear Information System (INIS)

    Polycapillary x-ray optics have found potential application in many different fields, including antiscatter and magnification in mammography, radiography, x-ray fluorescence, x-ray lithography, and x-ray diffraction techniques. In x-ray diffraction, an optic is used to collect divergent x-rays from a point source and redirect them into a quasi-parallel, or slightly focused beam. Monolithic polycapillary optics have been developed recently for macromolecular crystallography and have already shown considerable gains in diffracted beam intensity over pinhole collimation. Development is being pursued through a series of simulations and prototype optics. Many improvements have been made over the stage 1 prototype reported previously, which include better control over the manufacturing process, reducing the diameter of the output beam, and addition of a slight focusing at the output of the optic to further increase x-ray flux at the sample. The authors report the characteristics and performance of the stage 1 and stage 2 optics

  15. Automated identification of elemental ions in macromolecular crystal structures

    International Nuclear Information System (INIS)

    The solvent-picking procedure in phenix.refine has been extended and combined with Phaser anomalous substructure completion and analysis of coordination geometry to identify and place elemental ions. Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms in phenix.refine have been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy, B factor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed

  16. 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.

  17. Dynamic Contrast Enhanced MRI Assessing the Antiangiogenic Effect of Silencing HIF-1α with Targeted Multifunctional ECO/siRNA Nanoparticles.

    Science.gov (United States)

    Malamas, Anthony S; Jin, Erlei; Gujrati, Maneesh; Lu, Zheng-Rong

    2016-07-01

    Stabilization of hypoxia inducible factor 1α (HIF-1α), a biomarker of hypoxia, in hypoxic tumors mediates a variety of downstream genes promoting tumor angiogenesis and cancer cell survival as well as invasion, and compromising therapeutic outcome. In this study, dynamic contrast enhanced MRI (DCE-MRI) with a biodegradable macromolecular MRI contrast agent was used to noninvasively assess the antiangiogenic effect of RGD-targeted multifunctional lipid ECO/siHIF-1α nanoparticles in a mouse HT29 colon cancer model. The RGD-targeted ECO/siHIF-1α nanoparticles resulted in over 50% reduction in tumor size after intravenous injection at a dose of 2.0 mg of siRNA/kg every 3 days for 3 weeks compared to a saline control. DCE-MRI revealed significant decline in vascularity and over a 70% reduction in the tumor blood flow, permeability-surface area product, and plasma volume fraction vascular parameters in the tumor treated with the targeted ECO/siHIF-1α nanoparticles. The treatment with targeted ECO/siRNA nanoparticles resulted in significant silencing of HIF-1α expression at the protein level, which also significantly suppressed the expression of VEGF, Glut-1, HKII, PDK-1, LDHA, and CAIX, which are all important players in tumor angiogenesis, glycolytic metabolism, and pH regulation. By possessing the ability to elicit a multifaceted effect on tumor biology, silencing HIF-1α with RGD-targeted ECO/siHIF-1α nanoparticles has great promise as a single therapy or in combination with traditional chemotherapy or radiation strategies to improve cancer treatment. PMID:27264671

  18. 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

  19. 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.

  20. Biodegradation of Polycyclic Aromatic Hydrocarbons

    OpenAIRE

    DEMİR, İsmail; DEMİRBAĞ, Zihni

    1999-01-01

    Polycylic aromatic hydrocarbons (PAHs), such as petroleum and petroleum derivatives, are widespread organic pollutants entering the environment, chiefly, through oil spills and incomplete combustion of fossil fuels. Since most PAHs are persist in the environment for a long period of time and bioaccumulate, they cause environmental pollution and effect biological equilibrium dramatically. Biodegradation of some PAHs by microorganisms has been biochemically and genetically investigated. Ge...

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. Macromolecular compositions of phytoplankton in the Amundsen Sea, Antarctica

    Science.gov (United States)

    Kim, Bo Kyung; Lee, Jang Han; Joo, HuiTae; Song, Ho Jung; Yang, Eun Jin; Lee, Sang Hoon; Lee, Sang H.

    2016-01-01

    The biochemical compositions (proteins, carbohydrates, and lipids) of phytoplankton provide useful information for their environmental growth conditions and nutritional status as a basic food source for upper trophic consumers. Concentrations of these compositions were assessed at 100, 30, and 1% light penetration depths within the euphotic zone in the Amundsen Sea, Antarctica, using colorimetric techniques. The major inorganic nutrients were generally abundant throughout the study area. The average chlorophyll a (chl-a) concentration was 49.2 mg m-2 (S.D.=±27.6 mg m-2) and large phytoplankton (>20 μm) accounted for 64.1% of the total chl-a concentration. The biochemical compositions of the phytoplankton were not significantly different among different light depths or productivity stations. The overall compositions of proteins, carbohydrates, and lipids from all stations averaged 65.9% (S.D.=±12.5%), 22.4% (S.D.=±10.9%), and 11.7% (S.D.=±6.5%), respectively. Regardless of dominant phytoplankton species, nitrogen-abundant conditions sustained high protein compositions of phytoplankton in the Amundsen Sea during the cruise period. Based on the macromolecular compositions, the average food material (FM) concentration was 219.4 μg L-1 (S.D.=±151.1 μg L-1) and correlated positively with the primary productivity in the Amundsen Sea. High protein/carbohydrate ratios (>1) and large proportions of proteins suggest that phytoplankton provide nitrogen-sufficient foods to higher trophic consumers through a higher efficiency of protein carbon incorporated into herbivores.

  6. 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.

  7. 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.

  8. 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

  9. 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-P...

  10. 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. PMID:16419620

  11. 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)

  12. 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

  13. 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.

  14. Changing the warm-up transition of macromolecular system at irradiation

    International Nuclear Information System (INIS)

    Full text: The whole complex of characteristics of macromolecular system is defined by its warm-up condition. So for revealing a consequence of irradiating it is necessary study of warm-up turning the molecules of chain construction from the energy of irradiation. As is well known an irradiation is accompanied by suturing or destruction of separate kinetic units. In given work is studied changing a warm-up interval of high-elastic state of macromolecular system depending on energy of irradiating for the reason extrapolation its results to deciding the applied problems of ecological, metabolically processes. Coming from theories free volume and Boltzmann's distribution were determined changing the temperatures of glassing and viscous current. The variable parameter considered models is a mobility factor, which is defined as an attitude radiation energy to energy of Van-der-Waals interactions and hydrogen bonds, where energy of irradiation is taken much less, than energy of chemical bond. Restriction of energy of inter- and intramolecular chemical unbound kinetic units guarantees wholeness of the macromolecular chains that it is required for functional quality conservations. The obtained results show that than more deflection of mobility factor from units, that broader area high-elastic considered model of macromolecular system. Changing a warm-up interval also enough vastly depends on the free member of deciding, which characterizes a condition of polymer before the irradiation. Rendered that the most vulnerable to irradiating is hard chain macromolecular system

  15. 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.

  16. 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.

  17. New Paradigm for Macromolecular Crystallography Experiments at SSRL: Automated Crystal Screening And Remote Data Collection

    Energy Technology Data Exchange (ETDEWEB)

    Soltis, S.M.; Cohen, A.E.; Deacon, A.; Eriksson, T.; Gonzalez, A.; McPhillips, S.; Chui, H.; Dunten, P.; Hollenbeck, M.; Mathews, I.; Miller, M.; Moorhead, P.; Phizackerley, R.P.; Smith, C.; Song, J.; Bedem, H.van dem; Ellis, P.; Kuhn, P.; McPhillips, T.; Sauter, N.; Sharp, K.

    2009-05-26

    Complete automation of the macromolecular crystallography experiment has been achieved at Stanford Synchrotron Radiation Lightsource (SSRL) through the combination of robust mechanized experimental hardware and a flexible control system with an intuitive user interface. These highly reliable systems have enabled crystallography experiments to be carried out from the researchers' home institutions and other remote locations while retaining complete control over even the most challenging systems. A breakthrough component of the system, the Stanford Auto-Mounter (SAM), has enabled the efficient mounting of cryocooled samples without human intervention. Taking advantage of this automation, researchers have successfully screened more than 200 000 samples to select the crystals with the best diffraction quality for data collection as well as to determine optimal crystallization and cryocooling conditions. These systems, which have been deployed on all SSRL macromolecular crystallography beamlines and several beamlines worldwide, are used by more than 80 research groups in remote locations, establishing a new paradigm for macromolecular crystallography experimentation.

  18. Pharmacokinetics and biodegradation of chitosan in rats

    Science.gov (United States)

    Li, Hui; Jiang, Zhiwen; Han, Baoqin; Niu, Shuyi; Dong, Wen; Liu, Wanshun

    2015-10-01

    Chitosan, an excellent biomedical material, has received a widespread in vivo application. In contrast, its metabolism and distribution once being implanted were less documented. In this study, the pharmacokinetics and biodegradation of fluorescein isothiocyanate (FITC) labeled and muscle implantation administrated chitosan in rats were investigated with fluorescence spectrophotometry, histological assay and gel chromatography. After implantation, chitosan was degraded gradually during its distribution to diverse organs. Among the tested organs, liver and kidney were found to be the first two highest in chitosan content, which was followed by heart, brain and spleen. Urinary excretion was believed to be the major pathway of chitosan elimination, yet 80% of chitosan administered to rats was not trackable in their urine. This indicated that the majority of chitosan was degraded in tissues. In average, the molecular weight of the degradation products of chitosan in diverse organs and urine was found to be <65 kDa. This further confirmed the in vivo degradation of chitosan. Our findings provided new evidences for the intensive and safe application of chitosan as a biomedical material.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Biodegradable products by lipase biocatalysis.

    Science.gov (United States)

    Linko, Y Y; Lämsä, M; Wu, X; Uosukainen, E; Seppälä, J; Linko, P

    1998-11-18

    The interest in the applications of biocatalysis in organic syntheses has rapidly increased. In this context, lipases have recently become one of the most studied groups of enzymes. We have demonstrated that lipases can be used as biocatalyst in the production of useful biodegradable compounds. A number of examples are given. 1-Butyl oleate was produced by direct esterification of butanol and oleic acid to decrease the viscosity of biodiesel in winter use. Enzymic alcoholysis of vegetable oils without additional organic solvent has been little investigated. We have shown that a mixture of 2-ethyl-1-hexyl esters can be obtained in a good yield by enzymic transesterification from rapeseed oil fatty acids for use as a solvent. Trimethylolpropane esters were also similarly synthesized as lubricants. Finally, the discovery that lipases can also catalyze ester syntheses and transesterification reactions in organic solvent systems has opened up the possibility of enzyme catalyzed production of biodegradable polyesters. In direct polyesterification of 1,4-butanediol and sebacic acid, polyesters with a mass average molar mass of the order of 56,000 g mol-1 or higher, and a maximum molar mass of about 130,000 g mol-1 were also obtained by using lipase as biocatalyst. Finally, we have demonstrated that also aromatic polyesters can be synthesized by lipase biocatalysis, a higher than 50,000 g mol-1 mass average molar mass of poly(1,6-hexanediyl isophthalate) as an example. PMID:9866859

  9. Corrective Contrast in Russian, in Contrast

    Directory of Open Access Journals (Sweden)

    Katja Jasinskaja

    2011-02-01

    Full Text Available In many languages markers of contrast, such as the English 'but', are also used to express correction: John didn't go to Paris, but to Berlin. The present paper tries to explain this cross-linguistic pattern and represents correction as a special case of contrast. It focuses on the Russian contrastive conjunction 'a' and argues that its corrective uses in combination with negation 'ne ... a' / 'a ne', which are traditionally viewed as a fixed collocation, are in fact co-occurrences of a general contrastive 'a' with constituent negation.

  10. 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.

  11. Dissolved organic carbon in Alaskan boreal forest: Sources, chemical characteristics, and biodegradability

    Science.gov (United States)

    Wickland, K.P.; Neff, J.C.; Aiken, G.R.

    2007-01-01

    The fate of terrestrially-derived dissolved organic carbon (DOC) is important to carbon (C) cycling in both terrestrial and aquatic environments, and recent evidence suggests that climate warming is influencing DOC dynamics in northern ecosystems. To understand what determines the fate of terrestrial DOC, it is essential to quantify the chemical nature and potential biodegradability of this DOC. We examined DOC chemical characteristics and biodegradability collected from soil pore waters and dominant vegetation species in four boreal black spruce forest sites in Alaska spanning a range of hydrologic regimes and permafrost extents (Well Drained, Moderately Well Drained, Poorly Drained, and Thermokarst Wetlands). DOC chemistry was characterized using fractionation, UV-Vis absorbance, and fluorescence measurements. Potential biodegradability was assessed by incubating the samples and measuring CO2 production over 1 month. Soil pore water DOC from all sites was dominated by hydrophobic acids and was highly aromatic, whereas the chemical composition of vegetation leachate DOC varied significantly with species. There was no seasonal variability in soil pore water DOC chemical characteristics or biodegradability; however, DOC collected from the Poorly Drained site was significantly less biodegradable than DOC from the other three sites (6% loss vs. 13-15% loss). The biodegradability of vegetation-derived DOC ranged from 10 to 90% loss, and was strongly correlated with hydrophilic DOC content. Vegetation such as Sphagnum moss and feathermosses yielded DOC that was quickly metabolized and respired. In contrast, the DOC leached from vegetation such as black spruce was moderately recalcitrant. Changes in DOC chemical characteristics that occurred during microbial metabolism of DOC were quantified using fractionation and fluorescence. The chemical characteristics and biodegradability of DOC in soil pore waters were most similar to the moderately recalcitrant vegetation

  12. 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.

  13. Pyelolithotomy by the use of a hydrophilous macromolecular binding material ("pyeloform" pyelotomy).

    Science.gov (United States)

    Nagy, Z; Frang, D; Jávor, A; Götz, F; Szatmári, J; Vizi, L; Kovács, G

    1984-01-01

    The use of a synthetic macromolecular hydrophilous binding material for the extraction of multiple renal calculi (" Pyeloform " pyelotomy) is reported. An account of the results of animal studies in vitro is given and the possibilities of the method in are pointed out. PMID:6724825

  14. Closed Mechanoelectrochemical Cycles of Individual Single-Chain Macromolecular Motors by AFM

    NARCIS (Netherlands)

    Shi, Weiqing; Giannotti, Marina I.; Zhang, Xi; Hempenius, Mark A.; Schönherr, Holger; Vancso, G. Julius

    2007-01-01

    Motor cycles: Mechanoelectrochemical loops of single-chain macromolecular motors based on individual end-grafted poly(ferrocenyldimethylsilane) are shown by AFM to have an efficiency of up to 26 %. Upon oxidation of a prestretched chain, the chain length increases and the force decreases significant

  15. 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

  16. 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.

  17. 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. PMID:19528060

  18. Biodegradation of surfactant bearing wastes

    International Nuclear Information System (INIS)

    In nuclear industry, during decontamination of protective wears and contaminated materials, detergents are employed to bring down the level of radioactive contamination within safe limits. However, the surfactant present in these wastes interferes in the chemical treatment process, reducing the decontamination factor. Biodegradation is an efficient and ecologically safe method for surfactant removal. A surfactant degrading culture was isolated and inoculated separately into simulated effluents containing 1% yeast extract and 5-100 ppm sodium lauryl sulphate (SLS) and 1% yeast extract and 5-100 ppm of commercial detergent respectively. The growth of the bacterial culture and the degradation characteristics of the surfactant in the above effluents were monitored under both dynamic and static conditions. (author). 6 refs., 6 figs., 1 tab

  19. New perspectives in plastic biodegradation.

    Science.gov (United States)

    Sivan, Alex

    2011-06-01

    During the past 50 years new plastic materials, in various applications, have gradually replaced the traditional metal, wood, leather materials. Ironically, the most preferred property of plastics--durability--exerts also the major environmental threat. Recycling has practically failed to provide a safe solution for disposal of plastic waste (only 5% out of 1 trillion plastic bags, annually produced in the US alone, are being recycled). Since the most utilized plastic is polyethylene (PE; ca. 140 million tons/year), any reduction in the accumulation of PE waste alone would have a major impact on the overall reduction of the plastic waste in the environment. Since PE is considered to be practically inert, efforts were made to isolate unique microorganisms capable of utilizing synthetic polymers. Recent data showed that biodegradation of plastic waste with selected microbial strains became a viable solution. PMID:21356588

  20. 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.

  1. 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. PMID:27260524

  2. 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

  3. KinImmerse: Macromolecular VR for NMR ensembles

    OpenAIRE

    Vinson E Claire; Davis Ian W; Chen Vincent B; Zielinski David J; Block Jeremy N; Brady Rachael; Richardson Jane S; Richardson David C

    2009-01-01

    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 prog...

  4. 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.

  5. Biodegradable polymers: Which, when and why?

    Directory of Open Access Journals (Sweden)

    Kotwal V

    2007-01-01

    Full Text Available The plethora of drug therapies and types of drugs demand different formulations, fabrications conditions and release kinetics. No single polymer can satisfy all the requirements. Therefore there have been tremendous advances in area of biodegradable copolymers over the last 30 years. This article reviews current research on biodegradable polymers, focusing their potential as drug carries. The major classes of polymers are briefly discussed with regard to synthesis, properties and biodegradability, and known degradation modes and products are indicated based on studies reported in the literature. A vast majority of biodegradable polymers studied belongs to the polyester family, which includes polyglycolides and polylactides. Other degradable polymers such as polyorthoesters, polyanhydrides and polyphosphazenes are also discussed and their advantages and disadvantages are summarized.

  6. 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.

  7. 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. PMID:17849431

  8. Phyllosphere yeasts rapidly break down biodegradable plastics

    OpenAIRE

    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

    2011-01-01

    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 ...

  9. Biodegradation and toxicological evaluation of lubricant oils

    OpenAIRE

    Ivo Shodji Tamada; Paulo Renato Matos Lopes; Renato Nallin Montagnolli; Ederio Dino Bidoia

    2012-01-01

    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...

  10. Biodegradation of cresol isomers in anoxic aquifers.

    OpenAIRE

    Smolenski, W J; Suflita, J M

    1987-01-01

    The biodegradation of o-, m-, and p-cresol was examined in material obtained from a shallow anaerobic alluvial sand aquifer. The cresol isomers were preferentially metabolized, with p-cresol being the most easily degraded. m-Cresol was more persistent than the para-isomer, and o-cresol persisted for over 90 days. Biodegradation of cresol isomers was favored under sulfate-reducing conditions (SRC) compared with that under methanogenic conditions (MC). Slurries that were acclimated to p-cresol ...

  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. 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.

  13. Cost-effective imprinting combining macromolecular crowding and a dummy template for the fast purification of punicalagin from pomegranate husk extract.

    Science.gov (United States)

    Sun, Guang-Ying; Wang, Chao; Luo, Yu-Qin; Zhao, Yong-Xin; Yang, Jian; Liu, Zhao-Sheng; Aisa, Haji Akber

    2016-05-01

    The combination of molecular crowding and virtual imprinting was employed to develop a cost-effective method to prepare molecularly imprinted polymers. By using linear polymer polystyrene as a macromolecular crowding agent, an imprinted polymer recognizable to punicalagin had been successfully synthesized with punicalin as the dummy template. The resulting punicalin-imprinted polymer presented a remarkable selectivity to punicalagin with an imprinting factor of 3.17 even at extremely low consumption of the template (template/monomer ratio of 1:782). In contrast, the imprinted polymer synthesized without crowding agent, did not show any imprinting effect at so low template amount. The imprinted polymers made by combination of molecular crowding and virtual imprinting can be utilized for the fast separation of punicalagin from pomegranate husk extract after optimizing the protocol of solid-phase extraction with the recovery of 85.3 ± 1.2%. PMID:27027975

  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. 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 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 composition) due, in part, to their location on the landscape.

  16. Biodegradation of microbial and synthetic polyesters by fungi.

    Science.gov (United States)

    Kim, D Y; Rhee, Y H

    2003-05-01

    A variety of biodegradable polyesters have been developed in order to obtain useful biomaterials and to reduce the impact of environmental pollution caused by the large-scale accumulation of non-degradable waste plastics. Polyhydroxyalkanoates, poly(epsilon-caprolactone), poly( l-lactide), and both aliphatic and aromatic polyalkylene dicarboxylic acids are examples of biodegradable polyesters. In general, most aliphatic polyesters are readily mineralized by a number of aerobic and anaerobic microorganisms that are widely distributed in nature. However, aromatic polyesters are more resistant to microbial attack than aliphatic polyesters. The fungal biomass in soils generally exceeds the bacterial biomass and thus it is likely that fungi may play a considerable role in degrading polyesters, just as they predominantly perform the decomposition of organic matter in the soil ecosystem. However, in contrast to bacterial polyester degradation, which has been extensively investigated, the microbiological and environmental aspects of fungal degradation of polyesters are unclear. This review reports recent advances in our knowledge of the fungal degradation of microbial and synthetic polyesters and discusses the ecological importance and contribution of fungi in the biological recycling of waste polymeric materials in the biosphere. PMID:12743758

  17. 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.

  18. (Questions)n on phloem biology. 2. Mass flow, molecular hopping, distribution patterns and macromolecular signalling.

    Science.gov (United States)

    van Bel, Aart J E; Furch, Alexandra C U; Hafke, Jens B; Knoblauch, Michael; Patrick, John W

    2011-10-01

    This review speculates on correlations between mass flow in sieve tubes and the distribution of photoassimilates and macromolecular signals. Since micro- (low-molecular compounds) and macromolecules are withdrawn from, and released into, the sieve-tube sap at various rates, distribution patterns of these compounds do not strictly obey mass-flow predictions. Due to serial release and retrieval transport steps executed by sieve tube plasma membranes, micromolecules are proposed to "hop" between sieve element/companion cell complexes and phloem parenchyma cells under source-limiting conditions (apoplasmic hopping). Under sink-limiting conditions, micromolecules escape from sieve tubes via pore-plasmodesma units and are temporarily stored. It is speculated that macromolecules "hop" between sieve elements and companion cells using plasmodesmal trafficking mechanisms (symplasmic hopping). We explore how differential tagging may influence distribution patterns of macromolecules and how their bidirectional movement could arise. Effects of exudation techniques on the macromolecular composition of sieve-tube sap are discussed. PMID:21889037

  19. PIMADb: A Database of Protein–Protein Interactions in Huge Macromolecular Assemblies

    Science.gov (United States)

    Mathew, Oommen K.; Sowdhamini, Ramanathan

    2016-01-01

    Protein–protein interactions play a very important role in the process of cellular functionality. Intricate details about the interactions between the proteins in a macromolecular assembly are important to understand the function and significance of protein complexes. We are reporting about a database of protein–protein interactions in huge macromolecular assemblies (PIMADb) that records the intrinsic details of 189,532 interchain interactions in 40,049 complexes from the Protein Data Bank. These details include the results of the quantification and analysis of all the interactions in the complex. The availability of interprotomer interaction networks can enable the design of point mutation experiments. PIMADb can be accessed from the URL: http://caps.ncbs.res.in/pimadb PMID:27478368

  20. 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.

  1. 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.

  2. 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.

  3. Drug-Free Macromolecular Therapeutics--A New Paradigm in Polymeric Nanomedicines.

    Science.gov (United States)

    Chu, Te-Wei; Kopeček, Jindřich

    2015-07-01

    This review highlights a unique research area in polymer-based nanomedicine designs. Drug-free macromolecular therapeutics induce apoptosis of malignant cells by the crosslinking of surface non-internalizing receptors. The receptor crosslinking is mediated by the biorecognition of high-fidelity natural binding motifs (such as antiparallel coiled-coil peptides or complementary oligonucleotides) that are grafted to the side chains of polymers or attached to targeting moieties against cell receptors. This approach features the absence of low-molecular-weight cytotoxic compounds. Here, we summarize the rationales, different designs, and advantages of drug-free macromolecular therapeutics. Recent developments of novel therapeutic systems for B-cell lymphomas are discussed, as well as relevant approaches for other diseases. We conclude by pointing out various potential future directions in this exciting new field. PMID:26191406

  4. [Contrast sensitivity in glaucoma].

    Science.gov (United States)

    Bartos, D

    1989-05-01

    Author reports on results of the contrast sensitivity examinations using the Cambridge low-contrast lattice test supplied by Clement Clarke International LTD, in patients with open-angle glaucoma and ocular hypertension. In glaucoma patients there was observed statistically significant decrease of the contrast sensitivity. In patients with ocular hypertension decrease of the contrast sensitivity was in patients affected by corresponding changes of the visual field and of the optical disc. The main advantages of the Cambridge low-contrast lattice test were simplicity, rapidity and precision of its performance. PMID:2743444

  5. A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces

    OpenAIRE

    Y. C. ZHOU; Holst, Michael; McCammon, J. Andrew

    2010-01-01

    In this paper we propose a nonlinear elasticity model of macromolecular conformational change (deformation) induced by electrostatic forces generated by an implicit solvation model. The Poisson-Boltzmann equation for the electrostatic potential is analyzed in a domain varying with the elastic deformation of molecules, and a new continuous model of the electrostatic forces is developed to ensure solvability of the nonlinear elasticity equations. We derive the estimates of electrostatic forces ...

  6. Macromolecularly crowded in vitro microenvironments accelerate the production of extracellular matrix-rich supramolecular assemblies

    OpenAIRE

    Kumar, Pramod; Satyam, Abhigyan; Fan, Xingliang; Rodriguez, Brian J.; et al

    2015-01-01

    Therapeutic strategies based on the principles of tissue engineering by self-assembly put forward the notion that functional regeneration can be achieved by utilising the inherent capacity of cells to create highly sophisticated supramolecular assemblies. However, in dilute ex vivo microenvironments, prolonged culture time is required to develop an extracellular matrix-rich implantable device. Herein, we assessed the influence of macromolecular crowding, a biophysical phenomenon that regulate...

  7. From “Simple” DNA-Protein Interactions to the Macromolecular Machines of Gene Expression

    OpenAIRE

    von Hippel, Peter H.

    2007-01-01

    The physicochemical concepts that underlie our present ideas on the structure and assembly of the “macromolecular machines of gene expression” are developed, starting with the structure and folding of the individual protein and DNA components, the thermodynamics and kinetics of their conformational rearrangements during complex assembly, and the molecular basis of the sequence specificity and recognition interactions of the final assemblies that include the DNA genome. The role of diffusion i...

  8. 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.

  9. Contrast induced nephropathy

    DEFF Research Database (Denmark)

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

    2011-01-01

    PURPOSE: The Contrast Media Safety Committee (CMSC) of the European Society of Urogenital Radiology (ESUR) has updated its 1999 guidelines on contrast medium-induced nephropathy (CIN). AREAS COVERED: Topics reviewed include the definition of CIN, the choice of contrast medium, the prophylactic...... 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....

  10. Contrast induced nephropathy

    DEFF Research Database (Denmark)

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

    2011-01-01

    PURPOSE: The Contrast Media Safety Committee (CMSC) of the European Society of Urogenital Radiology (ESUR) has updated its 1999 guidelines on contrast medium-induced nephropathy (CIN). AREAS COVERED: Topics reviewed include the definition of CIN, the choice of contrast medium, the prophylactic...... 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....

  11. 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.

  12. A smooth and differentiable bulk-solvent model for macromolecular diffraction

    International Nuclear Information System (INIS)

    A new method for modeling the bulk solvent in macromolecular diffraction data based on Babinet’s principle is presented. The proposed models offer the advantage of differentiability with respect to atomic coordinates. Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute–solvent boundary (i.e. the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using R, Rfree and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6 Å) data versus no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography

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

    Science.gov (United States)

    Maximova, Tatiana; Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth; Shehu, Amarda

    2016-04-01

    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. PMID:27124275

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Compressive Phase Contrast Tomography

    OpenAIRE

    Maia, Filipe

    2010-01-01

    When x-rays penetrate soft matter, their phase changes more rapidly than their amplitude. Interference 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 contrast 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-R...

  4. 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....

  5. 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.

  6. 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.

  7. Biodegradable nanoparticles for gene therapy technology

    International Nuclear Information System (INIS)

    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

  8. Petroleum biodegradation and oil spill bioremediation

    International Nuclear Information System (INIS)

    Hydrocarbon-utilizing microorganisms are ubiquitously distributed in the marine environment following oil spills. These microorganisms naturally biodegrade numerous contaminating petroleum hydrocarbons, thereby cleansing the oceans of oil pullutants. Bioremediation, which is accomplished by adding exogenous microbial populations or stimulating indigenous ones, attempts to raise the rates of degradation found naturally to significantly higher rates. Seeding with oil degraders has not been demonstrated to be effective, but addition of nitrogenous fertilizers has been shown to increase rates of petroleum biodegradation. In the case of the Exxon Valdez spill, the largest and most thoroughly studied application of bioremediation, the application of fertilizer (slow release or oleophilic) increased rates of biodegradation 3-5 times. Because of the patchiness of oil, an internally conserved compound, hopane, was critical for demonstrating the efficacy of bioremediation. Multiple regression models showed that the effectiveness of bioremediation depended upon the amount of nitrogen delivered, the concentration of oil, and time. (author)

  9. 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.

  10. Biodegradable Photonic Melanoidin for Theranostic Applications.

    Science.gov (United States)

    Lee, Min-Young; Lee, Changho; Jung, Ho Sang; Jeon, Mansik; Kim, Ki Su; Yun, Seok Hyun; Kim, Chulhong; Hahn, Sei Kwang

    2016-01-26

    Light-absorbing nanoparticles for localized heat generation in tissues have various biomedical applications in diagnostic imaging, surgery, and therapies. Although numerous plasmonic and carbon-based nanoparticles with strong optical absorption have been developed, their clearance, potential cytotoxicity, and long-term safety issues remain unresolved. Here, we show that "generally regarded as safe (GRAS)" melanoidins prepared from glucose and amino acid offer a high light-to-heat conversion efficiency, biocompatibility, biodegradability, nonmutagenicity, and efficient renal clearance, as well as a low cost for synthesis. We exhibit a wide range of biomedical photonic applications of melanoidins, including in vivo photoacoustic mapping of sentinel lymph nodes, photoacoustic tracking of gastrointestinal tracts, photothermal cancer therapy, and photothermal lipolysis. The biodegradation rate and renal clearance of melanoidins are controllable by design. Our results confirm the feasibility of biodegradable melanoidins for various photonic applications to theranostic nanomedicines. PMID:26623481

  11. Dialysis and contrast media

    International Nuclear Information System (INIS)

    In a previous survey we revealed uncertainty among responders about (a) whether or not to perform hemodialysis in patients with severely reduced renal function who had received contrast medium; and (b) when to perform hemodialysis in patients on regular treatment with hemodialysis or continuous ambulatory dialysis who received contrast medium. Therefore, the Contrast Media Safety Committee of The European Society of Urogenital Radiology decided to review the literature and to issue guidelines. The committee performed a Medline search. Based on this, a report and guidelines were prepared. The report was discussed at the Ninth European Symposium on Urogenital Radiology in Genoa, Italy. Hemodialysis and peritoneal dialysis safely remove both iodinated and gadolinium-based contrast media. The effectiveness of hemodialysis depends on many factors including blood and dialysate flow rate, permeability of dialysis membrane, duration of hemodialysis and molecular size, protein binding, hydrophilicity, and electrical charge of the contrast medium. Generally, several hemodialysis sessions are needed to removal all contrast medium, whereas it takes 3 weeks for continuous ambulatory dialysis to remove the agent completely. There is no need to schedule the dialysis in relation to the injection of iodinated or MR contrast media or the injection of contrast agent in relation to the dialysis program. Hemodialysis does not protect poorly functioning kidneys against contrast-medium-induced nephrotoxicity. Simple guidelines are given. (orig.)

  12. Dialysis and contrast media

    Energy Technology Data Exchange (ETDEWEB)

    Morcos, Sameh K. [Department of Diagnostic Imaging, Northern General Hospital, Sheffield Teaching Hospitals NHS Trust, Sheffield S5 7AU (United Kingdom); Thomsen, Henrik S. [Department of Diagnostic Radiology 54E2, Copenhagen University Hospital at Herlev, Herlev Ringvej 75, 2730 Herlev (Denmark); Webb, Judith A.W. [Department of Diagnostic Imaging, St Bartholomew' s Hospital, London EC1A 7BE (United Kingdom)

    2002-12-01

    In a previous survey we revealed uncertainty among responders about (a) whether or not to perform hemodialysis in patients with severely reduced renal function who had received contrast medium; and (b) when to perform hemodialysis in patients on regular treatment with hemodialysis or continuous ambulatory dialysis who received contrast medium. Therefore, the Contrast Media Safety Committee of The European Society of Urogenital Radiology decided to review the literature and to issue guidelines. The committee performed a Medline search. Based on this, a report and guidelines were prepared. The report was discussed at the Ninth European Symposium on Urogenital Radiology in Genoa, Italy. Hemodialysis and peritoneal dialysis safely remove both iodinated and gadolinium-based contrast media. The effectiveness of hemodialysis depends on many factors including blood and dialysate flow rate, permeability of dialysis membrane, duration of hemodialysis and molecular size, protein binding, hydrophilicity, and electrical charge of the contrast medium. Generally, several hemodialysis sessions are needed to removal all contrast medium, whereas it takes 3 weeks for continuous ambulatory dialysis to remove the agent completely. There is no need to schedule the dialysis in relation to the injection of iodinated or MR contrast media or the injection of contrast agent in relation to the dialysis program. Hemodialysis does not protect poorly functioning kidneys against contrast-medium-induced nephrotoxicity. Simple guidelines are given. (orig.)

  13. Enhancement of biodegradability of real textile and dyeing wastewater by electron beam irradiation

    Science.gov (United States)

    He, Shijun; Sun, Weihua; Wang, Jianlong; Chen, Lvjun; Zhang, Youxue; Yu, Jiang

    2016-07-01

    A textile and dyeing wastewater treatment plant is going to be upgraded due to the stringent discharge standards in Jiangsu province, China, and electron beam irradiation is considering to be used. In order to determine the suitable location of the electron accelerator in the process of wastewater treatment plant, the effects of electron beam (EB) irradiation on the biodegradability of various real wastewater samples collecting from the different stages of the wastewater treatment plant, the values of chemical oxygen demand (COD), biochemical oxygen demand (BOD5), and the ratio of BOD5 and COD (BOD5/COD), were compared before and after EB irradiation. During EB irradiation process, color indices and absorbance at 254 nm wavelength (UV254) of wastewater were also determined. The results showed that EB irradiation pre-treatment cannot improve the biodegradability of raw textile and dyeing wastewater, which contains a large amount of biodegradable organic matters. In contrast, as to the final effluent of biological treatment process, EB irradiation can enhance the biodegradability to 224%. Therefore, the promising way is to apply EB irradiation as a post-treatment of the conventional biological process.

  14. Biodegradation of creosote compounds: Comparison of experiments at different scales

    DEFF Research Database (Denmark)

    Broholm, K.; Arvin, Erik

    2001-01-01

    This paper compares the results of biodegradation experiments with creosote compounds performed at different scales. The experiments include field observations, field experiments, large-scale intact laboratory column experiments, model fracture experiments, and batch experiments. Most of the expe...... of the pyrroles on the biodegradation of benzene, and the biodegradation of benzothiophene occurs only in the presence of a primary substrate. The experiments show that some biodegradation processes of organic compounds may be common to different microorganisms....

  15. 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.

  16. 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.

  17. Biodegradable poly lactone-family polymer and their applications in medical field

    International Nuclear Information System (INIS)

    Poly lactone-family polymers such as poly lactide, poly glycolide and polycaprolactone are kind aliphatic polyester. Since they can degrade by hydrolysis reaction under all the ph condition and possess biocompatibility, biodegradability and other good properties, especially they included not peptide bond in their molecules, they are non-antigen and non-immunization, as well as have no-toxicity and no-stimulation. So they are interested biomaterials and very useful in medical field. However the properties of all of the homo-poly lactones can not be changed in a large range, the limited properties result in limited applications of these homo-poly lactones. Based on macromolecular design, a series of copolylactones such as poly(lactide-co-glycolide) (PLGA), poly(glycolide-co-lactide-co-caprolactone) tri- component copolymer (PGLC), tri- and multi-block poly lactide/poly(ethylene oxide) copolymer (TPLE and BPLE), as well as polycaprolactone/poly lactide/poly(ethylene oxide) copolymer (PCEL) et al were synthesized by copolymerization among various lactone monomers or lactone monomers with poly(ethylene glycol). These copolylactones have wide range of degradation life from several months to years and different mechanical properties. After plasma treatment the surface property of the copolylactones were improved further and cell affinity of the copolylactones was improved obviously. The applications of these poly lactone-family polymers in medical field for used as drug carrier in drug delivery system, and as cell scaffold in tissue engineering were discussed

  18. 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.

  19. Biodegradable polymers in clinical use and clinical development

    CERN Document Server

    Domb, Abraham J

    2011-01-01

    The definitive guide to biodegradable polymer science-where we are and what's to come The most comprehensive review of biodegradable polymers already utilized or under development for clinical use, Biodegradable Polymers in Clinical Use and Clinical Development looks at the state of biodegradable polymers now and over the next five years. Implantable molecules that break down within the body over a predetermined period of time, biodegradable polymers have been employed as drug carriers, orthopedic fixation devices, and absorbable sutures. Yet while hundreds of such polymers have been deve

  20. 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

  1. 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.

  2. 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

    2011-01-01

    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. PMID:22126328

  3. 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

  4. 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

  5. Biodegradable Polymeric Microcapsules: Preparation and Properties

    NARCIS (Netherlands)

    Sawalha, H.I.M.; Schroën, C.G.P.H.; Boom, R.M.

    2011-01-01

    Biodegradable polymeric microcapsules can be produced through different methods of which emulsion solvent-evaporation/extraction is frequently used. In this technique, the polymer (often polylactide) is dissolved in a good solvent and is emulsified together with a poor solvent into a nonsolvent phas

  6. 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

  7. Biodegradable synthetic polymers for tissue engineering

    Directory of Open Access Journals (Sweden)

    Gunatillake P. A.

    2003-05-01

    Full Text Available This paper reviews biodegradable synthetic polymers focusing on their potential in tissue engineering applications. The major classes of polymers are briefly discussed with regard to synthesis, properties and biodegradability, and known degradation modes and products are indicated based on studies reported in the literature. A vast majority of biodegradable polymers studied belongs to the polyester family, which includes polyglycolides and polylactides. Some disadvantages of these polymers in tissue engineering applications are their poor biocompatibility, release of acidic degradation products, poor processability and loss of mechanical properties very early during degradation. Other degradable polymers such as polyorthoesters, polyanhydrides, polyphosphazenes, and polyurethanes are also discussed and their advantages and disadvantages summarised. With advancements in tissue engineering it has become necessary to develop polymers that meet more demanding requirements. Recent work has focused on developing injectable polymer compositions based on poly (propylene fumarate and poly (anhydrides to meet these requirements in orthopaedic tissue engineering. Polyurethanes have received recent attention for development of degradable polymers because of their great potential in tailoring polymer structure to achieve mechanical properties and biodegradability to suit a variety of applications.

  8. 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.)

  9. 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. PMID:16740383

  10. 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

  11. Compressive Phase Contrast Tomography

    Energy Technology Data Exchange (ETDEWEB)

    Maia, Filipe; MacDowell, Alastair; Marchesini, Stefano; Padmore, Howard A.; Parkinson, Dula Y.; Pien, Jack; Schirotzek, Andre; Yang, Chao

    2010-09-01

    When x-rays penetrate soft matter, their phase changes more rapidly than their amplitude. Interference 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 contrast 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).

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  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. 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.

  19. 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.

  20. 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.

  1. Improving the biodegradative capacity of subsurface bacteria

    International Nuclear Information System (INIS)

    The continual release of large volumes of synthetic materials into the environment by agricultural and industrial sources over the last few decades has resulted in pollution of the subsurface environment. Cleanup has been difficult because of the relative inaccessibility of the contaminants caused by their wide dispersal in the deep subsurface, often at low concentrations and in large volumes. As a possible solution for these problems, interest in the introduction of biodegradative bacteria for in situ remediation of these sites has increased greatly in recent years (Timmis et al. 1988). Selection of biodegradative microbes to apply in such cleanup is limited to those strains that can survive among the native bacterial and predator community members at the particular pH, temperature, and moisture status of the site (Alexander, 1984). The use of microorganisms isolated from subsurface environments would be advantageous because the organisms are already adapted to the subsurface conditions. The options are further narrowed to strains that are able to degrade the contaminant rapidly, even in the presence of highly recalcitrant anthropogenic waste mixtures, and in conditions that do not require addition of further toxic compounds for the expression of the biodegradative capacity (Sayler et al. 1990). These obstacles can be overcome by placing the genes of well-characterized biodegradative enzymes under the control of promoters that can be regulated by inexpensive and nontoxic external factors and then moving the new genetic constructs into diverse groups of subsurface microbes. ne objective of this research is to test this hypothesis by comparing expression of two different toluene biodegradative enzymatic pathways from two different regulatable promoters in a variety of subsurface isolates

  2. Hydrocarbons biodegradation in unsaturated porous medium

    International Nuclear Information System (INIS)

    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)

  3. Generalized Phase Contrast

    CERN Document Server

    Glückstad, Jesper

    2009-01-01

    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 the restrictive assumptions of conventional Zernike phase contrast analysis and achieves an expanded range of validity beyond weak phase perturbations. The generalized analysis yields design criteria for tuning experimental parameters to achieve optimal performance in terms of accuracy, fidelity and light efficiency. Optimization can address practical issues, such as finding an optimal spatial filter for the chosen application, ...

  4. 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. PMID:16446985

  5. 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.

  6. Relations between functionality and macromolecular properties of alterated coals: the behaviour in solubility and swelling

    Energy Technology Data Exchange (ETDEWEB)

    Kuznetsov, P.N.; Gruber, R.; Bimer, J.; Salbut, P.D.; Djega-Mariadassou, G.; Kruchinin, A.V.; Kuznetsova, L.I. [Institute of Chemistry and Chemico-Metallurgical Processes, Krasnoyarsk (Russian Federation)

    1995-12-31

    Describes the study of the effects of chemical alteration of brown and bituminous coals on the solubility and swelling behaviour. A variety of chemical procedures such as ion-exchange with HCl, O-methylation and reductive methylation, reduction with LiAlH{sub 4} and with K/isopropanol in THF and oxidation with performic acid was applied in order to vary the oxygen functionality, the content of the alkyl substitutes and the proportion of aromatic to hydroaromatic rings. The extent of degradation of the macromolecular structure was evaluated as a function of chemical alteration. 6 refs., 2 tabs.

  7. 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.

  8. Compressive Phase Contrast Tomography

    OpenAIRE

    Maia, F. R. N. C.; MacDowell, A.; Marchesini, S.; Padmore, H. A.; Parkinson, D. Y.; PIEN., J.; Schirotzek, A.; Yang, C

    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...

  9. 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

  10. Biodegradation of Aliphatic-aromatic Coplyester under Thermophilic Conditions

    Directory of Open Access Journals (Sweden)

    Elsayed B. Belal

    2013-11-01

    Full Text Available The biodegradation of poly (tetramethylene adipate-co-tetramethylene terephthalate (BTA-copolyester as synthetic polyester was investigated under thermophilic conditions. Two efficient BTA degrading actinomycetes were isolated from compost at thermophilic phase. These strains were identified as Thermobifida fusca and Thermobispora bispora. The degradation rate for BTA films within 7 days was 17.12 and 16.96 mg/week.cm2 by T. fusca and T. bispora, respectively. The optimum BTA40:60 degradation conditions are obtained as pH7 and 55°C. The both strains exhibited a wider substrate spectrum as they are able to degrade synthetic polyesters (BTA40:60, PCL-S MaterBi ZF03U/A and natural polymers (poly-&beta-hydroxybutyric acid (PHB and carboxymethyl cellulose. It was shown that the extracellular hydrolyases activity from the both strains was induced in the presence of BTA-copolyester, while the presence of additional carbon sources such as glucose or a complex medium suppressed enzyme formation. Tributyrin as triglycerides was degraded by the both crude concentrated BTA-hydrolases. In contrast the enzyme was not capable to depolymerize the natural polymers PHB and carboxymethyl cellulose, although the organism itself degraded both types of polymers. The obtained results showed that the degradation rate with T. fusca BTA40:60-hydrolase was 3.67 mg/day.cm2 and was 3.5 mg/day.cm2 with T. bispora BTA40:60-hydrolase. The pH optimum for BTA-hydrolases was 7 with 20 and 100 mM phosphate buffer and it was 6 with 150 mM citrate buffer. Finally, it could be concluded that actinomycetes and their hydrolases play an outstanding role in recycling of biodegradable plastics under thermophilic phase during composting process.

  11. Gadolinium MRI Contrast Agents Based on Triazine Dendrimers: Relaxivity and In Vivo Pharmacokinetics

    OpenAIRE

    Lim, Jongdoo; Turkbey, Baris; Bernardo, Marcelino; Bryant, L. Henry; Garzoni, Matteo; Pavan, Giovanni M.; Nakajima, Takahito; Choyke, Peter L; Simanek, Eric E; Kobayashi, Hisataka

    2012-01-01

    Four gadolinium (Gd)-based macromolecular contrast agents, G3-(Gd-DOTA)24, G5-(Gd-DOTA)96, G3-(Gd-DTPA)24, and G5-(Gd-DTPA)96, were prepared that varied in the size of dendrimer (generation three and five), the type of chelate group (DTPA or DOTA), and the theoretical number of metallated chelates (24 and 96). Synthesis relied on a dichlorotriazine derivatized with a DOTA or DTPA ligand that was incorporated into the dendrimer and ultimately metallated with Gd ions. Paramagnetic characteristi...

  12. 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.

  13. 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.

  14. 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.

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

    International Nuclear Information System (INIS)

    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 al1 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.1D. Silagy, Y. Demay, and J-F. Agassant, Polym. Eng. Sci., 36, 2614 (1996)

  16. Oral delivery of macromolecular drugs: Where we are after almost 100years of attempts.

    Science.gov (United States)

    Moroz, Elena; Matoori, Simon; Leroux, Jean-Christophe

    2016-06-01

    Since the first attempt to administer insulin orally in humans more than 90years ago, the oral delivery of macromolecular drugs (>1000g/mol) has been rather disappointing. Although several clinical pilot studies have demonstrated that the oral absorption of macromolecules is possible, the bioavailability remains generally low and variable. This article reviews the formulations and biopharmaceutical aspects of orally administered biomacromolecules on the market and in clinical development for local and systemic delivery. The most successful approaches for systemic delivery often involve a combination of enteric coating, protease inhibitors and permeation enhancers in relatively high amounts. However, some of these excipients have induced local or systemic adverse reactions in preclinical and clinical studies, and long-term studies are often missing. Therefore, strategies aimed at increasing the oral absorption of macromolecular drugs should carefully take into account the benefit-risk ratio. In the absence of specific uptake pathways, small and potent peptides that are resistant to degradation and that present a large therapeutic window certainly represent the best candidates for systemic absorption. While we acknowledge the need for systemically delivering biomacromolecules, it is our opinion that the oral delivery to local gastrointestinal targets is currently more promising because of their accessibility and the lacking requirement for intestinal permeability enhancement. PMID:26826437

  17. An Efficient Low Storage and Memory Treatment of Gridded Interaction Fields for Simulations of Macromolecular Association.

    Science.gov (United States)

    Ozboyaci, Musa; Martinez, Michael; Wade, Rebecca C

    2016-09-13

    Computer simulations of molecular systems often make use of regular rectangular grids with equidistant spacing to store information on their molecular interaction fields, e.g., electrostatic potential. These grids provide an easy way to store the data as they do not require any particular specification of the structure of the data. However, such grids may easily become large, and the storage and memory demands may become so high that calculations become infeasible. To overcome this problem, we show here how the data structure DT-Grid can be adapted and applied to efficiently represent macromolecular interaction grids by exploiting the nonuniformity of information on the grid; at the same time, this data structure ensures fast random data access. We demonstrate use of the DT-Grid data structure for potential of mean force and Brownian dynamics simulations of protein-surface binding and macromolecular association with the SDA software. We further demonstrate that the DT-Grid structure enables systems of large size, such as a viral capsid, and high resolution grids to be handled that are beyond current computational feasibility. PMID:27463233

  18. 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.

  19. Oral delivery of macromolecular drugs: Where we are after almost 100years of attempts.

    Science.gov (United States)

    Moroz, Elena; Matoori, Simon; Leroux, Jean-Christophe

    2016-06-01

    Since the first attempt to administer insulin orally in humans more than 90years ago, the oral delivery of macromolecular drugs (>1000g/mol) has been rather disappointing. Although several clinical pilot studies have demonstrated that the oral absorption of macromolecules is possible, the bioavailability remains generally low and variable. This article reviews the formulations and biopharmaceutical aspects of orally administered biomacromolecules on the market and in clinical development for local and systemic delivery. The most successful approaches for systemic delivery often involve a combination of enteric coating, protease inhibitors and permeation enhancers in relatively high amounts. However, some of these excipients have induced local or systemic adverse reactions in preclinical and clinical studies, and long-term studies are often missing. Therefore, strategies aimed at increasing the oral absorption of macromolecular drugs should carefully take into account the benefit-risk ratio. In the absence of specific uptake pathways, small and potent peptides that are resistant to degradation and that present a large therapeutic window certainly represent the best candidates for systemic absorption. While we acknowledge the need for systemically delivering biomacromolecules, it is our opinion that the oral delivery to local gastrointestinal targets is currently more promising because of their accessibility and the lacking requirement for intestinal permeability enhancement.

  20. 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)

  1. 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.

  2. A new paradigm for macromolecular crystallography beamlines derived from high-pressure methodology and results

    Energy Technology Data Exchange (ETDEWEB)

    Fourme, Roger, E-mail: roger.fourme@synchrotron-soleil.fr [Synchrotron SOLEIL, BP 48, Saint Aubin, 91192 Gif-sur-Yvette (France); Girard, Eric [IBS (UMR 5075 CEA-CNRS-UJF-PSB), 41 rue Jules Horowitz, 38027 Grenoble Cedex (France); Dhaussy, Anne-Claire [CRISMAT, ENSICAEN, 6 Boulevard du Maréchal Juin, 14000 Caen (France); Medjoubi, Kadda [Synchrotron SOLEIL, BP 48, Saint Aubin, 91192 Gif-sur-Yvette (France); Prangé, Thierry [LCRB (UMR 8015 CNRS), Université Paris Descartes, Faculté de Pharmacie, 4 avenue de l’Observatoire, 75270 Paris (France); Ascone, Isabella [ENSCP (UMR CNRS 7223), 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); Mezouar, Mohamed [ESRF, BP 220, 38043 Grenoble (France); Kahn, Richard [IBS (UMR 5075 CEA-CNRS-UJF-PSB), 41 rue Jules Horowitz, 38027 Grenoble Cedex (France)

    2011-01-01

    Macromolecular crystallography at high pressure (HPMX) is a mature technique. Shorter X-ray wavelengths increase data collection efficiency on cryocooled crystals. Extending applications and exploiting spin-off of HPMX will require dedicated synchrotron radiation beamlines based on a new paradigm. Biological structures can now be investigated at high resolution by high-pressure X-ray macromolecular crystallography (HPMX). The number of HPMX studies is growing, with applications to polynucleotides, monomeric and multimeric proteins, complex assemblies and even a virus capsid. Investigations of the effects of pressure perturbation have encompassed elastic compression of the native state, study of proteins from extremophiles and trapping of higher-energy conformers that are often of biological interest; measurements of the compressibility of crystals and macromolecules were also performed. HPMX results were an incentive to investigate short and ultra-short wavelengths for standard biocrystallography. On cryocooled lysozyme crystals it was found that the data collection efficiency using 33 keV photons is increased with respect to 18 keV photons. This conclusion was extended from 33 keV down to 6.5 keV by exploiting previously published data. To be fully exploited, the potential of higher-energy photons requires detectors with a good efficiency. Accordingly, a new paradigm for MX beamlines was suggested, using conventional short and ultra-short wavelengths, aiming at the collection of very high accuracy data on crystals under standard conditions or under high pressure. The main elements of such beamlines are outlined.

  3. Errors in macromolecular synthesis after stress : a study of the possible protective role of the small heat shock proteins

    OpenAIRE

    Marin Vinader, L.

    2006-01-01

    The general goal of this thesis was to gain insight in what small heat shock proteins (sHsps) do with respect to macromolecular synthesis during a stressful situation in the cell. It is known that after a non-lethal heat shock, cells are better protected against a subsequent more severe heat shock, a phenomenon known as thermotolerance and attributed to the presence of the heat shock proteins. The question we asked first is whether the error rate in macromolecular synthesis (transcription, RN...

  4. 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...

  5. Working at higher magnifications in scanning electron microscopy with secondary and backscattered electrons on metal coated biological specimens and imaging macromolecular cell membrane structures.

    Science.gov (United States)

    Peters, K R

    1985-01-01

    Membrane structures of macromolecular dimensions were imaged with high resolution secondary electron type I (SE-I) signal contrasts on metal coated biological specimens. The quality of the surface information was strongly dependent on the signal used for microscopy and on the properties of metal films, i.e., thickness, continuity, structure and decoration effects. Films of 10 nm thickness produced so much type II electrons that identical images were obtained with the conventional SE-II and BSE-II signals. In such images, the type I SE signal was so low that only very weak contrasts were recognizable. If the films--continuous or discontinuous--were composed of large metal aggregates (gold and platinum) a strong micro-roughness contrast was produced by the type II signal. At high magnifications (100,000 x) this background signal greatly reduced the S/N ratio of the SE-I signal. A similar effect was previously shown to be produced by the type III background signal. The type II background signal minimized when continuous films of small aggregates (tantalum and chromium) were applied. SE-I contrast dominated in the image if the film thickness was limited to 1 nm. Additionally, it was found that gold and platinum decorated membrane surface structures, less than 20 nm in size, and did not reveal all the topographic information available (size, shape, orientation spacing of small surface features) but merely displayed center-to-center distances. These decoration effects were avoided and extensive topographic information was obtained through surface coating with Ta or Cr. PMID:4095499

  6. 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

  7. 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).

  8. Phase Contrast Imaging

    DEFF Research Database (Denmark)

    1996-01-01

    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 with a si......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...

  9. Contrast image correction method

    Science.gov (United States)

    Schettini, Raimondo; Gasparini, Francesca; Corchs, Silvia; Marini, Fabrizio; Capra, Alessandro; Castorina, Alfio

    2010-04-01

    A method for contrast enhancement is proposed. The algorithm is based on a local and image-dependent exponential correction. The technique aims to correct images that simultaneously present overexposed and underexposed regions. To prevent halo artifacts, the bilateral filter is used as the mask of the exponential correction. Depending on the characteristics of the image (piloted by histogram analysis), an automated parameter-tuning step is introduced, followed by stretching, clipping, and saturation preserving treatments. Comparisons with other contrast enhancement techniques are presented. The Mean Opinion Score (MOS) experiment on grayscale images gives the greatest preference score for our algorithm.

  10. 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.

  11. 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℃.

  12. Biodegradation of Petroleum Hydrocarbons in Soil

    OpenAIRE

    MR Mehrasbi; B Haghighi; M.Shariat; S Naseri; Naddafi, K

    2003-01-01

    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. Dehydrogenas...

  13. Assessment of polymer-based nanocomposites biodegradability

    OpenAIRE

    Machado, A.V.; Araújo, Andreia Isabel Silva; Oliveira, Manuel

    2015-01-01

    The management of solid waste is a growing concern in many countries. Municipal solid waste is a major component of the total solid waste generated by society, and the composting of municipal solid waste has gained some attention even though a composting treatment for it is not yet widespread. It may not be realistic to replace large portions of these plastics with biodegradable materials, and it may be more important to separate plastics unsuitable for the composting process at the generatin...

  14. Biodegradation of hexachlorocyclohexane (HCH) by microorganisms.

    Science.gov (United States)

    Phillips, Theresa M; Seech, Alan G; Lee, Hung; Trevors, Jack T

    2005-08-01

    The organochlorine pesticide Lindane is the gamma-isomer of hexachlorocyclohexane (HCH). Technical grade Lindane contains a mixture of HCH isomers which include not only gamma-HCH, but also large amounts of predominantly alpha-, beta- and delta-HCH. The physical properties and persistence of each isomer differ because of the different chlorine atom orientations on each molecule (axial or equatorial). However, all four isomers are considered toxic and recalcitrant worldwide pollutants. Biodegradation of HCH has been studied in soil, slurry and culture media but very little information exists on in situ bioremediation of the different isomers including Lindane itself, at full scale. Several soil microorganisms capable of degrading, and utilizing HCH as a carbon source, have been reported. In selected bacterial strains, the genes encoding the enzymes involved in the initial degradation of Lindane have been cloned, sequenced, expressed and the gene products characterized. HCH is biodegradable under both oxic and anoxic conditions, although mineralization is generally observed only in oxic systems. As is found for most organic compounds, HCH degradation in soil occurs at moderate temperatures and at near neutral pH. HCH biodegradation in soil has been reported at both low and high (saturated) moisture contents. Soil texture and organic matter appear to influence degradation presumably by sorption mechanisms and impact on moisture retention, bacterial growth and pH. Most studies report on the biodegradation of relatively low (sources or other soil amendments is scattered and inconclusive. More in-depth assessments of amendment effects and evaluation of bioremediation protocols, on a large scale, using soil with high HCH concentrations, are needed.

  15. 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.

  16. Titanate nanotube coatings on biodegradable photopolymer scaffolds

    International Nuclear Information System (INIS)

    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

  17. Biodegradation of ion-exchange media

    International Nuclear Information System (INIS)

    Ion-exchange media, both bead resins and powdered filter media, are used in nuclear power plants to remove radioactivity from process water prior to reuse or environmental discharge. Since the ion- exchange media are made from synthetic hydrocarbon-based polymers, they may be susceptible to damage from biological activity. The purpose of this study was to investigate some of the more basic aspects of biodegradation of ion-exchange media, specifically to evaluate the ability of microorganisms to utilize the ion-exchange media or materials sorbed on them as a food source. The ASTM-G22 test, alone and combined with the Bartha Pramer respirometric method, failed to indicate the biodegradability of the ion-exchange media. The limitation of these methods was that they used a single test organism. In later phases of this study, a mixed microbial culture was grown from resin waste samples obtained from the BNL High Flux Beam Reactor. These microorganisms were used to evaluate the susceptibility of different types of ion-exchange media to biological attack. Qualitative assessments of biodegradability were based on visual observations of culture growths. Greater susceptibility was associated with increased turbidity in solution indicative of bacterial growth, and more luxuriant fungal mycelial growth in solution or directly on the ion-exchange resin beads. 21 refs., 9 figs., 18 tabs

  18. Nanomembranes and Nanofibers from Biodegradable Conducting Polymers

    Directory of Open Access Journals (Sweden)

    Jordi Puiggalí

    2013-09-01

    Full Text Available This review provides a current status report of the field concerning preparation of fibrous mats based on biodegradable (e.g., aliphatic polyesters such as polylactide or polycaprolactone and conducting polymers (e.g., polyaniline, polypirrole or polythiophenes. These materials have potential biomedical applications (e.g., tissue engineering or drug delivery systems and can be combined to get free-standing nanomembranes and nanofibers that retain the better properties of their corresponding individual components. Systems based on biodegradable and conducting polymers constitute nowadays one of the most promising solutions to develop advanced materials enable to cover aspects like local stimulation of desired tissue, time controlled drug release and stimulation of either the proliferation or differentiation of various cell types. The first sections of the review are focused on a general overview of conducting and biodegradable polymers most usually employed and the explanation of the most suitable techniques for preparing nanofibers and nanomembranes (i.e., electrospinning and spin coating. Following sections are organized according to the base conducting polymer (e.g., Sections 4–6 describe hybrid systems having aniline, pyrrole and thiophene units, respectively. Each one of these sections includes specific subsections dealing with applications in a nanofiber or nanomembrane form. Finally, miscellaneous systems and concluding remarks are given in the two last sections.

  19. Macmillan ring-free oil biodegradation project

    International Nuclear Information System (INIS)

    Crude oil processing at the Macmillan Ring-Free Oil Company facility (Macmillan Oil Refinery) began in approximately 1929. Operations produced naphtha, diesel fuel, insulating oil, lubricating oil, and asphalt until approximately 1987. The waste material generated by the process was Resource Conservation and Recovery Act (RCRA) listed waste K048-Dissolved Air Flotation (DAF) float containing volatile and semivolatile organic compounds. On-site unlined surface impoundments used to store DAF and crude oil wastes have periodically overflowed and contaminated two adjacent creeks. A series of extensive site investigation activities in 1992 and 1993 addressed tank and drum, asbestos, lagoon and groundwater contamination at the site. The results of the investigation indicated that the majority of the contamination is contained within 10 lagoons and surrounding soils. Volume calculations indicate that approximately 45,000 cubic yards of contaminated soils and sediments required treatment. A field simulation of biodegradation of these wastes in a land treatment unit was implemented during removal actions. Results of the remedy selection biodegradation assessment provided evidence of a 61 to 96 percent reduction in contaminant concentrations. These concentrations are below land disposal and health risk-based criteria. The technology of biodegradation meets the EPA criteria for inclusion in the potential remedies for the Macmillan Oil Refinery

  20. 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.

  1. Contrast media: future aspects

    Energy Technology Data Exchange (ETDEWEB)

    Weinmann, H.J.; Platzek, J.; Schirmer, H.; Pietsch, H. [Research Labs., Schering AG, Berlin (Germany); Carretero, J.; Harto, J.; Medina, J.; Riefke, B.; Martin, J. [Justesa Imagen SA, Madrid (Spain)

    2005-11-15

    In spite of the dramatic development in CT, there was no major breakthrough in the iodinated contrast media development. New agents based on hybrid between MRI and CT compounds may be a new innovative alternative. This new approach may also open new indications such as radiotherapy. (orig.)

  2. Phonation in Tonal Contrasts

    Science.gov (United States)

    Kuang, Jianjing

    2013-01-01

    Phonation is used in many tonal languages, but how it should be incorporated into tonal systems is not well understood. The purpose of this dissertation thus is to examine the role of phonation in tonal contrasts, and to investigate how phonation and pitch interact in the tonal space. This dissertation presents close studies of tonal contrasts…

  3. Biodegradability evaluation of polymers by ISO 14855-2.

    Science.gov (United States)

    Funabashi, Masahiro; Ninomiya, Fumi; Kunioka, Masao

    2009-10-01

    Biodegradabilities of polymers and their composites in a controlled compost were described. Polycaprolactone (PCL) and poly(lactic acid) (PLA) were employed as biodegradable polymers. Biodegradabilities of PCL and PLA samples in a controlled compost were measured using a Microbial Oxidative Degradation Analyzer (MODA) according to ISO 14855-2. Sample preparation method for biodegradation test according to ISO/DIS 10210 was also described. Effects of sizes and shapes of samples on biodegradability were studied. Reproducibility of biodegradation test of ISO 14855-2 by MODA was confirmed. Validity of sample preparation method for polymer pellets, polymer film, and polymer products of ISO/DIS 10210 for ISO 14855-2 was confirmed. PMID:20111676

  4. 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...

  5. 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.

  6. Strawberry under low-tunnel protected with experimental biodegradable films

    International Nuclear Information System (INIS)

    A research was carried out in order to test innovative biodegradable materials for the protected cultivation of strawberry in Southern Italy. A field test was carried out in order to evaluate the agronomic performances of the biodegradable materials in comparison with non biodegradable LDPE materials. Different kinds of biodegradable black films were used for soil mulching and transparent biodegradable films for the covering of the low tunnels. Climatic data of the site, air temperature and relative humidity inside the low tunnels and soil temperature under the mulching films were gathered during the test. Besides, laboratory radiometric tests were executed on the films in order to evaluate parameters such as the transmissivity in different wavelength ranges. The biodegradable materials showed a high capacity to induce greenhouse effect due to their very low transmissivity in the long wave infrared range. The yield obtained using biodegradable materials was on average 12% higher then the one obtained with traditional films. Concerning the earliness, at the first day of the harvest, the yield obtained with biodegradable materials was 70% higher in comparison with the case of LDPE films. The research showed that the biodegradable materials could be a sustainable alternative to the plastic films based on fossil raw materials

  7. Critical evaluation of biodegradable polymers used in nanodrugs.

    Science.gov (United States)

    Marin, Edgar; Briceño, Maria Isabel; Caballero-George, Catherina

    2013-01-01

    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.

  8. 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.

  9. 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

  10. Critical evaluation of biodegradable polymers used in nanodrugs.

    Science.gov (United States)

    Marin, Edgar; Briceño, Maria Isabel; Caballero-George, Catherina

    2013-01-01

    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. PMID:23990720

  11. 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.

  12. Contrast normalization in colour vision: the effect of luminance contrast on colour contrast detection

    OpenAIRE

    Mullen, Kathy T.; Kim, Yeon Jin; Gheiratmand, Mina

    2014-01-01

    While contrast normalization is well known to occur in luminance vision between overlaid achromatic contrasts, and in colour vision between overlaid colour contrasts, it is unknown whether it transfers between colour and luminance contrast. Here we investigate whether contrast detection in colour vision can be normalized by achromatic contrast, or whether this is a selective process driven only by colour contrast. We use a method of cross-orientation masking, in which colour detection is mask...

  13. Errors in macromolecular synthesis after stress : a study of the possible protective role of the small heat shock proteins

    NARCIS (Netherlands)

    Marin Vinader, L.

    2006-01-01

    The general goal of this thesis was to gain insight in what small heat shock proteins (sHsps) do with respect to macromolecular synthesis during a stressful situation in the cell. It is known that after a non-lethal heat shock, cells are better protected against a subsequent more severe heat shock,

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

    International Nuclear Information System (INIS)

    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

  15. 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.

  16. 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

  17. 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.

  18. CONTRAST SENSITIVITY IN AMBLYOPIA

    Institute of Scientific and Technical Information of China (English)

    1991-01-01

    Contrast sensitivity function(CSF) for sinusoid gratings of varying spatial frequencies was determined for each eye of 21 cases with unilateral amblyopia. The CSF of all amblyopic eyes, except one, showed reduced sensitivity when compared with the non-amblyopic eye of the same person. The curve showed reduction more significantly at middle and high spatial frequencies. The cut-off frequency was shifted toward lower spatial frequencies. The relationship between CSF and various degree of amblyopia was als...

  19. Evaluation of the hazardous impact of landfill leachates by toxicity and biodegradability tests.

    Science.gov (United States)

    Kalcíková, G; Vávrová, M; Zagorc-Koncan, J; Gotvajn, A Zgajnar

    2011-01-01

    The aim of our research was to assess the ecotoxicity and biodegradability of leachates originating from two parts of a municipal landfill before and after biological treatment in the existing treatment plant. Biotests represent important tools for adequate environmental characterization of landfill leachates and could be helpful in reliable assessment and monitoring of the treatment plant efficiency. For ecotoxicity testing of landfill leachate before and after biological treatment, different organisms were chosen: the bacteria Vibrio fischeri, a mixed culture of activated sludge, duckweed Lemna minor, white mustard Sinapis alba, brine shrimp Artemia salina, and water flea Daphnia magna. For assessment of biodegradability, the method for determination of oxygen demand in a closed respirometer was used. The investigated leachates were heavily polluted, and in some cases, effluent limits were exceeded even after treatment. Results indicated that toxicity tests and physico-chemical parameters determined before and after treatment equivalently assess the efficiency of the existing treatment plant. However, the investigated leachates showed higher toxicity to Daphnia magna and especially to Lemna minor in contrast to Vibrio fischeri and Artemia salina (neither was sensitive to any of the leachates). No leachates were readily biodegradable. Experiments confirmed that the battery of toxicity tests should be applied for more comprehensive assessment of landfill leachate treatment and for reliable assessment of the treated leachate's subsequent environmental impact. It was confirmed that treated leachate, in spite of its better physico-chemical characteristics, still represents a potential environmental risk and thus should not be released into the environment. PMID:21970176

  20. Polychromatic diffraction contrast tomography

    International Nuclear Information System (INIS)

    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

  1. 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.

  2. 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

  3. 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.

  4. 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...... of around 32% is measured for a pure yeast cell suspension. Thus, EPS and BSA are "competing" in being transmitted which might explain the lowered BSA transmission in the presence of yeast cells. Additionally, EPS heavily foul the membranes, leading to a 86% permeability drop and a fouling resistance 6...

  5. Whole Cell Imprinting in Sol-Gel Thin Films for Bacterial Recognition in Liquids: Macromolecular Fingerprinting

    Directory of Open Access Journals (Sweden)

    Robert Armon

    2010-03-01

    Full Text Available Thin films of organically modified silica (ORMOSILS produced by a sol-gel method were imprinted with whole cells of a variety of microorganisms in order to develop an easy and specific probe to concentrate and specifically identify these microorganisms in liquids (e.g., water. Microorganisms with various morphology and outer surface components were imprinted into thin sol-gel films. Adsorption of target microorganism onto imprinted films was facilitated by these macromolecular fingerprints as revealed by various microscopical examinations (SEM, AFM, HSEM and CLSM. The imprinted films showed high selectivity toward each of test microorganisms with high adsorption affinity making them excellent candidates for rapid detection of microorganisms from liquids.

  6. Polymer segregation under confinement: Influences of macromolecular crowding and the interaction between the polymer and crowders

    Science.gov (United States)

    Chen, Yuhao; Yu, Wancheng; Wang, Jiajun; Luo, Kaifu

    2015-10-01

    Entropy driven polymer segregation in confinements as a model for chromosome separation in bacteria has attracted wide attention; however, the effects of macromolecular crowding and the interaction between the binding protein and the newly replicated DNA on the segregation dynamics are not clear. Using Langevin dynamics simulations, we investigate the influences of crowders and the attractive interaction between the polymer and a small number of crowders on segregation of two overlapping polymers under a cylindrical confinement. We find that the segregation time increases with increasing the volume fraction of crowders due to the slower chain diffusion in crowded environments. For a fixed volume fraction of crowders, the segregation time decreases with increasing the size of crowders. Moreover, the attractive interaction between the polymer and a small number of crowders can significantly facilitate the chain segregation. These results are important for understanding the chromosome segregation in living cells.

  7. Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes

    Directory of Open Access Journals (Sweden)

    Sadhna Phanse

    2016-03-01

    Full Text Available Our analysis examines the conservation of multiprotein complexes among metazoa through use of high resolution biochemical fractionation and precision mass spectrometry applied to soluble cell extracts from 5 representative model organisms Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Strongylocentrotus purpuratus, and Homo sapiens. The interaction network obtained from the data was validated globally in 4 distant species (Xenopus laevis, Nematostella vectensis, Dictyostelium discoideum, Saccharomyces cerevisiae and locally by targeted affinity-purification experiments. Here we provide details of our massive set of supporting biochemical fractionation data available via ProteomeXchange (PXD002319-PXD002328, PPIs via BioGRID (185267; and interaction network projections via (http://metazoa.med.utoronto.ca made fully accessible to allow further exploration. The datasets here are related to the research article on metazoan macromolecular complexes in Nature [1].

  8. Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes.

    Science.gov (United States)

    Phanse, Sadhna; Wan, Cuihong; Borgeson, Blake; Tu, Fan; Drew, Kevin; Clark, Greg; Xiong, Xuejian; Kagan, Olga; Kwan, Julian; Bezginov, Alexandr; Chessman, Kyle; Pal, Swati; Cromar, Graham; Papoulas, Ophelia; Ni, Zuyao; Boutz, Daniel R; Stoilova, Snejana; Havugimana, Pierre C; Guo, Xinghua; Malty, Ramy H; Sarov, Mihail; Greenblatt, Jack; Babu, Mohan; Derry, W Brent; Tillier, Elisabeth R; Wallingford, John B; Parkinson, John; Marcotte, Edward M; Emili, Andrew

    2016-03-01

    Our analysis examines the conservation of multiprotein complexes among metazoa through use of high resolution biochemical fractionation and precision mass spectrometry applied to soluble cell extracts from 5 representative model organisms Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Strongylocentrotus purpuratus, and Homo sapiens. The interaction network obtained from the data was validated globally in 4 distant species (Xenopus laevis, Nematostella vectensis, Dictyostelium discoideum, Saccharomyces cerevisiae) and locally by targeted affinity-purification experiments. Here we provide details of our massive set of supporting biochemical fractionation data available via ProteomeXchange (PXD002319-PXD002328), PPIs via BioGRID (185267); and interaction network projections via (http://metazoa.med.utoronto.ca) made fully accessible to allow further exploration. The datasets here are related to the research article on metazoan macromolecular complexes in Nature [1]. PMID:26870755

  9. Rasta silanes: new silyl resins with novel macromolecular architecture via living free radical polymerization

    Science.gov (United States)

    Lindsley; Hodges; Filzen; Watson; Geyer

    2000-09-01

    Heating TEMPO-methyl resin with dialkylsilane styrenes affords larger resin beads via living free radical polymerization. The new silyl resins prepared by this solvent-free suspension polymerization protocol have been coined "Rasta silanes". Rasta silanes have a novel macromolecular architecture typified by long straight chain polymers bearing the silanes which emanate from the phenyl rings of a cross-linked polystyrene core. By careful selection of comonomers during the polymerization step, loading capacity, silane spacing, and the relative distance of the silane moieties from the resin core can be controlled. The consistently high-loading Rasta silane resins produced can be easily converted into either a reactive silyl chloride or triflate to subsequently anchor alcohols and phenols to the solid phase. Cleavage from the resin can be mediated by treatment with HF.pyridine, TFA solutions, or TBAF.

  10. Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes.

    Science.gov (United States)

    Goh, Boon Chong; Hadden, Jodi A; Bernardi, Rafael C; Singharoy, Abhishek; McGreevy, Ryan; Rudack, Till; Cassidy, C Keith; Schulten, Klaus

    2016-07-01

    The rise of the computer as a powerful tool for model building and refinement has revolutionized the field of structure determination for large biomolecular systems. Despite the wide availability of robust experimental methods capable of resolving structural details across a range of spatiotemporal resolutions, computational hybrid methods have the unique ability to integrate the diverse data from multimodal techniques such as X-ray crystallography and electron microscopy into consistent, fully atomistic structures. Here, commonly employed strategies for computational real-space structural refinement are reviewed, and their specific applications are illustrated for several large macromolecular complexes: ribosome, virus capsids, chemosensory array, and photosynthetic chromatophore. The increasingly important role of computational methods in large-scale structural refinement, along with current and future challenges, is discussed. PMID:27145875

  11. OCTOPUS: an innovative multimodal diffractometer for neutron macromolecular crystallography across the length scales

    International Nuclear Information System (INIS)

    We propose to construct a novel protein diffractometer at position H112B. The new instrument will deliver major efficiency gains, as well as offering greatly extended flexibility through the option of several easily interchangeable modes of operation. This proposal builds on the demonstrable need to extend ILL's capacity for high resolution structural studies of protein systems, as well as a need to widen the scope of biological crystallography - in particular for monochromatic studies at both high and low resolution. The development will be carried out in close collaboration with structural biologists at the ESRF, and engineered in such a way that the user interface of the instrument (from sample to software) will be transparently identifiable to a large, dynamic, and driven community of European synchrotron X-ray macromolecular crystallographers. (authors)

  12. 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.

  13. 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.

  14. Parallel macromolecular delivery and biochemical/electrochemical interface to cells employing nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    McKnight, Timothy E; Melechko, Anatoli V; Griffin, Guy D; Guillorn, Michael A; Merkulov, Vladimir L; Simpson, Michael L

    2015-03-31

    Systems and methods are described for parallel macromolecular delivery and biochemical/electrochemical interface to whole cells employing carbon nanostructures including nanofibers and nanotubes. A method includes providing a first material on at least a first portion of a first surface of a first tip of a first elongated carbon nanostructure; providing a second material on at least a second portion of a second surface of a second tip of a second elongated carbon nanostructure, the second elongated carbon nanostructure coupled to, and substantially parallel to, the first elongated carbon nanostructure; and penetrating a boundary of a biological sample with at least one member selected from the group consisting of the first tip and the second tip.

  15. 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.

  16. 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.

  17. Application of environmental isotopes in studies of biodegradation of organic contaminants in groundwater

    International Nuclear Information System (INIS)

    -DCE ) and 1,2-dichloroethane (1,2-DCA). In contrast small carbon isotope fractionation occurred during biodegradation of BTEX. Recent studies have shown deuterium can be more sensitive than carbon-13 for BTEX biodegradation studies. An example of microcosm studies is illustrated on Figure 1 that shows concentration and isotope pattern for biodegradation of cis-dichloroethene (cis-DCE) to vinyl chloride (VC) and final product, ethene. As the cis-DCE is transformed to VC, an enrichment trend is observed in the remaining cis-DCE. The formed VC is isotopically lighter than the primary product, but as the VC is transformed, the remaining VC becomes enriched in 13C. The ethene is lighter than the VC and its isotope composition tend to the isotope composition of the primary substrate, cis-DCE, at the end of the experiment. The laboratory results have been confirmed at field sites. This paper will present a state of the art review on the application of environmental isotopes in biodegradation studies of organic contaminants in groundwater. Laboratories and field studies, and potential new applications of environmental isotopes in contaminant hydrogeology will be discussed during this presentation

  18. 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/.

  19. Macromolecular Stabilization by Excluded Cosolutes: Mean Field Theory of Crowded Solutions.

    Science.gov (United States)

    Sapir, Liel; Harries, Daniel

    2015-07-14

    We propose a mean field theory to account for the experimentally determined temperature dependence of protein stabilization that emerges in solutions crowded by preferentially excluded cosolutes. Based on regular solution theory and employing the Flory-Huggins approximation, our model describes cosolutes in terms of their size, and two temperature-dependent microscopic parameters that correspond to macromolecule-cosolute and bulk solution interactions. The theory not only predicts a "depletion force" that can account for the experimentally observed stabilization of protein folding or association in the presence of excluded cosolutes but also predicts the full range of associated entropic and enthalpic components. Remarkably, depending on cosolute identity and in accordance with experiments, the theory describes entropically as well as enthalpically dominated depletion forces, even those disfavored by entropy. This emerging depletion attraction cannot be simply linked to molecular volumes. Instead, the relevant parameter is an effective volume that represents an interplay between solvent, cosolute, and macromolecular interactions. We demonstrate that the apparent depletion free energy is often accompanied by significant yet compensating entropy and enthalpy terms that, although having a net zero contribution to stabilization, can obscure the underlying molecular mechanism. This study underscores the importance of including often-neglected free energy terms that correspond to solvent-cosolute and cosolute-macromolecule interactions, which for most typical cosolutes are expected to be temperature dependent. We propose that experiments specifically aimed at resolving the temperature-dependence of cosolute exclusion from macromolecular surfaces should help reveal the full range of the underlying molecular mechanisms of the depletion force.

  20. 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/. PMID:19020347

  1. Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast

    Science.gov (United States)

    Dong, Biqin; Almassalha, Luay M.; Stypula-Cyrus, Yolanda; Urban, Ben E.; Chandler, John E.; Nguyen, The-Quyen; Sun, Cheng; Zhang, Hao F.; Backman, Vadim

    2016-01-01

    Visualizing the nanoscale intracellular structures formed by nucleic acids, such as chromatin, in nonperturbed, structurally and dynamically complex cellular systems, will help expand our understanding of biological processes and open the next frontier for biological discovery. Traditional superresolution techniques to visualize subdiffractional macromolecular structures formed by nucleic acids require exogenous labels that may perturb cell function and change the very molecular processes they intend to study, especially at the extremely high label densities required for superresolution. However, despite tremendous interest and demonstrated need, label-free optical superresolution imaging of nucleotide topology under native nonperturbing conditions has never been possible. Here we investigate a photoswitching process of native nucleotides and present the demonstration of subdiffraction-resolution imaging of cellular structures using intrinsic contrast from unmodified DNA based on the principle of single-molecule photon localization microscopy (PLM). Using DNA-PLM, we achieved nanoscopic imaging of interphase nuclei and mitotic chromosomes, allowing a quantitative analysis of the DNA occupancy level and a subdiffractional analysis of the chromosomal organization. This study may pave a new way for label-free superresolution nanoscopic imaging of macromolecular structures with nucleotide topologies and could contribute to the development of new DNA-based contrast agents for superresolution imaging. PMID:27535934

  2. Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast.

    Science.gov (United States)

    Dong, Biqin; Almassalha, Luay M; Stypula-Cyrus, Yolanda; Urban, Ben E; Chandler, John E; Nguyen, The-Quyen; Sun, Cheng; Zhang, Hao F; Backman, Vadim

    2016-08-30

    Visualizing the nanoscale intracellular structures formed by nucleic acids, such as chromatin, in nonperturbed, structurally and dynamically complex cellular systems, will help expand our understanding of biological processes and open the next frontier for biological discovery. Traditional superresolution techniques to visualize subdiffractional macromolecular structures formed by nucleic acids require exogenous labels that may perturb cell function and change the very molecular processes they intend to study, especially at the extremely high label densities required for superresolution. However, despite tremendous interest and demonstrated need, label-free optical superresolution imaging of nucleotide topology under native nonperturbing conditions has never been possible. Here we investigate a photoswitching process of native nucleotides and present the demonstration of subdiffraction-resolution imaging of cellular structures using intrinsic contrast from unmodified DNA based on the principle of single-molecule photon localization microscopy (PLM). Using DNA-PLM, we achieved nanoscopic imaging of interphase nuclei and mitotic chromosomes, allowing a quantitative analysis of the DNA occupancy level and a subdiffractional analysis of the chromosomal organization. This study may pave a new way for label-free superresolution nanoscopic imaging of macromolecular structures with nucleotide topologies and could contribute to the development of new DNA-based contrast agents for superresolution imaging. PMID:27535934

  3. 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

  4. 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.

  5. Biodegradable and semi-biodegradable composite hydrogels as bone substitutes: morphology and mechanical characterization.

    Science.gov (United States)

    Sanginario, V; Ginebra, M P; Tanner, K E; Planell, J A; Ambrosio, L

    2006-05-01

    Biodegradable and semi-biodegradable composite hydrogels are proposed as bone substitutes. They consist of an hydrophilic biodegradable polymer (HYAFF 11) as matrix and two ceramic powders (alpha-TCP and HA) as reinforcement. Both components of these composites have been of great interest in biomedical applications due to their excellent biocompatibility and tissue interactions, however they have never been investigated as bone substitute composites. Morphological and mechanical analysis have shown that the two fillers behave in a very different way. In the HYAFF 11/alpha-TCP composite, alpha-TCP is able to hydrolyze in contact with water while in the HYAFF 11 matrix. As a result, the composite sets and hardens, and entangled CDHA crystals are formed in the hydrogel phase and increases in the mechanical properties are obtained. In the HYAFF11/HA composite the ceramic reinforcement acts as inert phase leading to lower mechanical properties. Both mechanical properties and microstructure analysis have demonstrated the possibility to design hydrophilic biodegradable composite structures for bone tissue substitution applications. PMID:16688585

  6. Attenuation contrast between biomolecular and inorganic materials at terahertz frequencies

    Science.gov (United States)

    Chan, T. L. J.; Bjarnason, J. E.; Lee, A. W. M.; Celis, M. A.; Brown, E. R.

    2004-09-01

    Wideband photomixing spectroscopy is used in the present work to contrast the transmission spectra of macromolecules commonly found in biomaterials such as potato starch, wheat flour and cornstarch, and proteins (Cytoplex™), and micromolecules such as sucrose, and inorganic materials such as sodium bicarbonate, and calcium sulfate. Powdered samples were measured at 0.1-0.5THz frequencies. A significant difference in attenuation is found between these samples. At 300GHz starch shows an absorption coefficient of ˜6cm-1 whereas Cytoplex shows 1-3cm-1, while inorganic micromolecules have ˜1cm-1. The absorption in starch increases rapidly with frequency tending to follow a power law α =fn with n typically between 1.5 and 2.0. In contrast, protein materials display a slower dependence on frequency with n between 1.0 and 1.5, and simple molecules show the least n among all three categories. The difference between these ubiquitous macromolecular and micromolecular materials is explained in terms of water content and molecular structure.

  7. 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

  8. Contrastive discourse studies

    OpenAIRE

    Clyne, Michael

    2009-01-01

    Le discours est un aspect essentiel du langage. Mais cet aspect est lié plus étroitement aux valeurs culturelles. Cet article présente les études contrastives du discours, comment elles ont été menées et les difficultés possibles dans les techniques de collection de données. Une typologie comparative des discours peut se développer au-delà de la typologie grammaticale. Parmi les applications du discours contrastif sont la formation interculturelle et l’enseignement des langues étrangères. ...

  9. Mutational interactions between near-UV radiation and DNA damaging agents in Escherichia coli: the role of near-UV-induced modifications in growth and macromolecular synthesis

    International Nuclear Information System (INIS)

    The mutational interactions between near-ultraviolet (334 nm, 365 nm) radiation and DNA damaging agents (far-UV (254 nm) and ethyl-methanesulphonate (EMS)) were studied in strains of Escherichia coli B/r trp thy with different susceptibilities to near-UV-induced growth delay (wild-type, rel and sr). Far-UV induced reversion to tryptophan independence is reduced while forward mutation to streptomycin is enhanced by prior exposure of the rel+ srd+ strains to near-UV radiation. The observed interactions are reduced (rel) or absent (srd) in the two mutant strains as are the corresponding growth and macromolecular synthesis delays normally observed after near-UV treatment. Quantitatively, the degree of interaction induced by near-UV pre-treatment correlates closely with the degree of protein synthesis inhibition. A mechanism is proposed for the contrasting interactions at the two genetic loci based on the different pathways by which pre-mutagenic lesions may be processed. The primary chromophore for the mutational interactions would appear to be 4-thiouracil-containing transfer RNA. (author)

  10. Biodegradable Long-Circulating Polymeric Nanospheres

    Science.gov (United States)

    Gref, Ruxandra; Minamitake, Yoshiharu; Peracchia, Maria Teresa; Trubetskoy, Vladimir; Torchilin, Vladimir; Langer, Robert

    1994-03-01

    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.

  11. 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.)

  12. Development of biodegradable fungicide by radiation

    International Nuclear Information System (INIS)

    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

  13. Development of biodegradable fungicide by radiation

    International Nuclear Information System (INIS)

    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. Sixteen antifungal microbes were isolated and 4 antifungal activity enhanced mutants were induced by using radiation. P. lentimorbus WJ5a17 had 41% higher antifungal activity than the wild type. Two biomaterials related to the antifungal activity from the above mutant were isolated and purified

  14. 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.

  15. 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

  16. 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.

  17. Biodegradation of the Nitramine Explosive CL-20

    OpenAIRE

    Trott, Sandra; Nishino, Shirley F.; Hawari, Jalal; Spain, Jim C.

    2003-01-01

    The cyclic nitramine explosive CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane) was examined in soil microcosms to determine whether it is biodegradable. CL-20 was incubated with a variety of soils. The explosive disappeared in all microcosms except the controls in which microbial activity had been inhibited. CL-20 was degraded most rapidly in garden soil. After 2 days of incubation, about 80% of the initial CL-20 had disappeared. A CL-20-degrading bacterial strain, Agrobact...

  18. 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.

  19. 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)

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. The use of biodegradable mulch films in muskmelon crop production

    Directory of Open Access Journals (Sweden)

    Artur Saraiva

    2012-10-01

    Full Text Available Due to the large amount of mulch films used in agricultural crops and to all the environmental problems related with their disposal, the biodegradable mulch films seems to be the best solution for replacing the conventional polyethylene mulches. The main goal of this work was to evaluate and compare the performance of biodegradable mulch films with the conventional polyethylene ones in muskmelon culture during two years. Beyond fruit productivity and quality, the impact of each plastic in the soil moisture and temperature were also assessed. Taking into account that there are no reported biodegradation studies realized in Portugal, it was also important to verify the biodegradability of this new mulch films under the Portuguese soil conditions. The biodegradable mulch films did not show significant differences in fruit productivity and quality. The biodegradation rate of the mulches tested was not as high as would be expected. From the overall results obtained, biodegradable mulch films appear to be a good solution for the replacement of the conventional polyethylene mulches, however the Research and Development should continue to be done ton improve their biodegradation rate.

  6. 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

  7. [Progress on biodegradation of polylactic acid--a review].

    Science.gov (United States)

    Li, Fan; Wang, Sha; Liu, Weifeng; Chen, Guanjun

    2008-02-01

    Polylactic acid is a high molecular-weight polyester made from renewable resources such as corn or starch. It is a promising biodegradable plastic due to its mechanical properties, biocompatibility and biodegradability. To achieve natural recycling of polylactic acid, relative microorganisms and the underlying mechanisms in the biodegradation has become an important issue in biodegradable materials. Up to date, most isolated microbes capable of degrading polylactic acid belong to actinomycetes. Proteases secreted by these microorganisms are responsible for the degradation. However, subtle differences exist between these polylactic acid degrading enzymes and typical proteases with respect to substrate binding and catalysis. Amino acids relative to catalysis are postulated to be highly plastic allowing their catalytic hydrolysis of polylactic acid. In this paper we reviewed current studies on biodegradation of polylactic acid concerning its microbial, enzymatic reactions and the possible mechanisms. We also discussed the probability of biologically recycling PLA by applying highly efficient strains and enzymes. PMID:18438013

  8. Experimental studies of biodegradation of asphalt by microorganisms

    International Nuclear Information System (INIS)

    On the geological disposal system of the radioactive wastes, the activities of the microorganisms that could degrade the asphalt might be significant for the assessment of the system performance. As the main effects of the biodegradation of the asphalt, the fluctuation of leaching behavior of the nuclides included in asphalt waste has been indicated. In this study, the asphalt biodegradation test was carried out. The microorganism of which asphalt degradation ability was comparatively higher under aerobic condition and anaerobic condition was used. The asphalt biodegradation rate was calculated and it was evaluated whether the asphalt biodegradation in this system could occur. The results show that the asphalt biodegradation rate under anaerobic and high alkali condition will be 300 times lower than under aerobic and neutral pH. (author)

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Biodegradability of industrial textile wastewater - batch tests.

    Science.gov (United States)

    Paździor, Katarzyna; Klepacz-Smółka, Anna; Wrębiak, Julita; Liwarska-Bizukojć, Ewa; Ledakowicz, Stanisław

    2016-01-01

    Following new trends we applied oxygen uptake rate (OUR) tests as well as long-term tests (in two batch bioreactors systems) in order to assess the biodegradability of textile wastewater. Effluents coming from a dyeing factory were divided into two streams which differed in inorganic and organic contaminants loads. Usefulness of the stream division was proved. Biodegradation of the low-loaded stream led to over 97% reduction of biochemical oxygen demand (BOD5) together with 80% reduction of chemical oxygen demand (COD) and total organic carbon (TOC). Most of the controlled parameter values were below the levels allowed by legislation for influents to surface water, whereas the high-loaded stream was so contaminated with recalcitrant organic compounds that despite the reduction of BOD5 by over 95%, COD, TOC, total nitrogen and total phosphorus levels exceeded permissible values. OUR tests were aimed at determination of the following kinetic parameters: maximum specific growth rate (μMax), half-saturation constant, hydrolysis constant and decay coefficient for activated sludge biomass for both types of textile wastewater studied. The values of kinetic parameters will be applied in activated sludge models used for prediction and optimisation of biological treatment of textile wastewater. PMID:27642827

  17. Monitoring Biodegradation of Magnesium Implants with Sensors

    Science.gov (United States)

    Zhao, Daoli; Wang, Tingting; Guo, Xuefei; Kuhlmann, Julia; Doepke, Amos; Dong, Zhongyun; Shanov, Vesselin N.; Heineman, William R.

    2016-04-01

    Magnesium and its alloys exhibit properties such as high strength, light weight, and in vivo corrosion that make them promising candidates for the development of biodegradable metallic implant materials for bone repair, stents and other medical applications. Sensors have been used to monitor the corrosion of magnesium and its alloys by measuring the concentrations of the following corrosion products: magnesium ions, hydroxyl ions and hydrogen gas. The corrosion characterization system with home-made capillary pH and Mg2+ microsensors has been developed for real-time detection of magnesium corrosion in vitro. A hydrogen gas sensor was used to monitor the corrosion of magnesium by measuring the concentration of the hydrogen gas reaction product in vivo. The high permeability of hydrogen through skin allows transdermal monitoring of the biodegradation of a magnesium alloy implanted beneath the skin by detecting hydrogen gas at the skin surface. The sensor was used to map hydrogen concentration in the vicinity of an implanted magnesium alloy.

  18. Modification of Biodegradable Polyesters Using Electron Beam

    International Nuclear Information System (INIS)

    Poly(4-Hydroxybutyrate) P4HB, Poly(butylene succinate-co-adipate) PBSA and Poly(ε-caprolactone) PCL were electron beam (EB)-irradiated. Poly(4-Hydroxybutyrate) 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. (author)

  19. 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.

  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. 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).

  2. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

    Science.gov (United States)

    Foffi, G; Pastore, A; Piazza, F; Temussi, P A

    2013-08-02

    More than 60 years of biochemical and biophysical studies have accustomed us to think of proteins as highly purified entities that act in isolation, more or less freely diffusing until they find their cognate partner to bind to. While in vitro experiments that reproduce these conditions largely remain the only way to investigate the intrinsic properties of molecules, this approach ignores an important factor: in their natural milieu , proteins are surrounded by several other molecules of different chemical nature, and this crowded environment can considerably modify their behaviour. About 40% of the cellular volume on average is occupied by all sorts of molecules. Furthermore, biological macromolecules live and operate in an extremely structured and complex environment within the cell (endoplasmic reticulum, Golgi apparatus, cytoskeletal structures, etc). Hence, to further complicate the picture, the interior of the cell is by no means a simply crowded medium, rather, a most crowded and confining one. In recent times, several approaches have been developed in the attempt to take into account important factors such as the ones mentioned above, at both theoretical and experimental levels, so that this field of research is now emerging as one of the most thriving in molecular and cell biology (see figure 1). [Formula: see text] Figure 1. Left: number of articles containing the word 'crowding' as a keyword limited to the biological and chemical science domains (source: ISI Web of Science). The arrow flags the 2003 'EMBO Workshop on Biological Implications of Macromolecular Crowding' (Embo, 2012). Right: number of citations to articles containing the word 'crowding' limited to the same domains (bars) and an exponential regression curve (source: Elsevier Scopus). To promote the importance of molecular crowding and confinement and provide researchers active in this field an interdisciplinary forum for meeting and exchanging ideas, we recently organized an international

  3. 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

  4. DISTURBANCE OF THE CARDIOMYOCYTE’S MACROMOLECULAR STRUCTURE IN HEART ALLOGRAFTS AS A SIGN OF CHRONIC REJECTION

    Directory of Open Access Journals (Sweden)

    A. G. Kupriyanova

    2012-01-01

    Full Text Available Chronic rejection, especially cardiac allograft vasculopathy, is a major limiting factor for long-term transplant survival. This process affects not only the blood vessels, but also cardiomyocytes. However, there are extremely few reports on the evaluation of their macromolecular structure state. The aim of the study was to evaluate the structural proteins of cardiomyocytes (actin, myosin, troponin I, titin, desmin, vinculin of heart allografts in different periods after the operation (from 6 days to 15 years. Major changes of macromolecular structure were revealed in late period after transplantation (6 months – 15 years. The contribution of humoral immune response in the process of chronic cardiac allograft rejection was observed: in eight of twelve recipients episodes of acute humoral rejection had been repeatedly registered; disorders of the expression of 5 proteins out of 6 characterized were found in recipients with recurrent and persistent antibody-mediated rejection. 

  5. 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.

  6. DISTURBANCE OF THE CARDIOMYOCYTE’S MACROMOLECULAR STRUCTURE IN HEART ALLOGRAFTS AS A SIGN OF CHRONIC REJECTION

    OpenAIRE

    A. G. Kupriyanova; L. V. Beletskaya; I. M. Ilyinsky; V. A. Zaidenov; N. P. Mozeiko; R. S. Saitgareev; A. Y. Kormer; A. M. Golts; V. M. Zakharevich; S. V. Gautier

    2012-01-01

    Chronic rejection, especially cardiac allograft vasculopathy, is a major limiting factor for long-term transplant survival. This process affects not only the blood vessels, but also cardiomyocytes. However, there are extremely few reports on the evaluation of their macromolecular structure state. The aim of the study was to evaluate the structural proteins of cardiomyocytes (actin, myosin, troponin I, titin, desmin, vinculin) of heart allografts in different periods after the operation (from ...

  7. The influence of hyaluronic acid hydrogel crosslinking density and macromolecular diffusivity on human MSC chondrogenesis and hypertrophy

    OpenAIRE

    Bian, Liming; Hou, Chieh; Tous, Elena; Rai, Reena; Mauck, Robert L.; Burdick, Jason A.

    2012-01-01

    Hyaluronic acid (HA) hydrogels formed via photocrosslinking provide stable 3D hydrogel environments that support the chondrogenesis of mesenchymal stem cells (MSCs). Crosslinking density has a significant impact on the physical properties of hydrogels, including their mechanical stiffness and macromolecular diffusivity. Variations in the HA hydrogel crosslinking density can be obtained by either changes in the HA macromer concentration (1, 3, or 5% w/v at 15 min exposure) or the extent of rea...

  8. Impaired Macromolecular Protein Pools in Fronto-Striato-Thalamic Circuits in Type 2 Diabetes Revealed by Magnetization Transfer Imaging

    OpenAIRE

    Yang, Shaolin; Ajilore, Olusola; Wu, Minjie; Lamar, Melissa; Kumar, Anand

    2014-01-01

    Previous research has shown that type 2 diabetes mellitus (T2DM) is associated with white matter microstructural changes, cognitive impairment, and decreased resting-state functional connectivity and spontaneous brain activity. This study used magnetization transfer imaging to examine, for the first time, the integrity of macromolecular protein pools in fronto-striato-thalamic circuits and its clinical and cognitive correlates in patients with T2DM. T2DM patients without mood disorders (n = 2...

  9. 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.

  10. [Biodegradation Coefficients of Typical Pollutants in the Plain Rivers Network].

    Science.gov (United States)

    Feng, Shuai; Li, Xu-yongl; Deng, Jian-cai

    2016-05-15

    Biodegradation is a significant part of pollutant integrated degradation, the process rate of which is represented by the biodegradation coefficient. To investigate the biodegradation law of typical pollutants in the plain rivers network located in the upstream of the Lake Taihu, experiments were conducted in site in September 2015, one order kinetics model was used to measure the biodegradation coefficients for permanganate index, ammonia, total nitrogen and total phosphorus, and influencing factors of the biodegradation coefficients were also analyzed. The results showed that the biodegradation coefficients for permanganate index, ammonia, total nitrogen and total phosphorus were 0.008 3-0.126 4 d⁻¹, 0.002 1-0.213 8 d⁻¹, 0.002 1-0.090 5 d⁻¹ and 0.011 0- 0.152 8 d⁻¹, respectively. The influencing factors of the biodegradation coefficients for permanganate index were permanganate index and pH; those for ammonia were ammonia concentration and pH; those for total nitrogen were inorganic nitrogen concentration, total dissolved solid concentration and nitrite concentration; and those for total phosphorus were background concentration and pH. The research results were of important guiding significance for pollutants removal and ecological restoration of the plain rivers network located in the unstream of the Lake Taihu. PMID:27506025

  11. 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. PMID:23967057

  12. 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.

  13. 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

  14. 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.

  15. 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. PMID:27497351

  16. 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.

  17. 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.

  18. Pedagogical Implications of Contrastive Studies

    Science.gov (United States)

    Marton, Waldemar

    1972-01-01

    Pessimism regarding pedagogical applications of contrastive studies, and reasons therefore, are described. Several misunderstandings believed to contribute to this pessimism, and several areas of controversy concerning uses of contrastive studies, are discussed. See FL 508 197 for availability. (RM)

  19. Purified terephthalic acid wastewater biodegradation and toxicity

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xu-xiang; LUO Xiang; GU Ji-dong; WAN Yu-qiu; CHENG Shu-pei; SUN Shi-lei; ZHU Cheng-jun; LI Wei-xin; ZHANG Xiao-chun; WANG Gui-lin; LU Jian-hua

    2005-01-01

    The biodegradation and toxicity of the purified terephthalic acid(PTA) processing wastewater was researched at NJYZ pilot with the fusant strain Fhhh in the carrier activated sludge process(CASP). Sludge loading rate(SLR) for Fhhh to COD of the wastewater was 1.09 d-1 and to PTA in the wastewater was 0.29 d-1. The results of bioassay at the pilot and calculation with software Ebis3 showed that the 48h-LC50 (median lethal concentration) to Daphnia magna for the PTA concentration in the wastewater was only 1/10 of that for the chemical PTA. There were 5 kinds of benzoate pollutants and their toxicities existing in the wastewater at least. The toxicity parameter value of the pure chemical PTA cannot be used to predicate the PTA wastewater toxicity. The toxicity of the NJYZ PTA wastewater will be discussed in detail in this paper.

  20. 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.

  1. Gas foamed open porous biodegradable polymeric microspheres.

    Science.gov (United States)

    Kim, Taek Kyoung; Yoon, Jun Jin; Lee, Doo Sung; Park, Tae Gwan

    2006-01-01

    Highly open porous biodegradable polymeric microspheres were fabricated for use as injectable scaffold microcarriers for cell delivery. A modified water-in-oil-in-water (W1/O/W2) double emulsion solvent evaporation method was employed for producing the microspheres. The incorporation of an effervescent salt, ammonium bicarbonate, in the primary W1 droplets spontaneously produced carbon dioxide and ammonia gas bubbles during the solvent evaporation process, which not only stabilized the primary emulsion, but also created well inter-connected pores in the resultant microspheres. The porous microspheres fabricated under various gas foaming conditions were characterized. The surface pores became as large as 20 microm in diameter with increasing the concentration of ammonium bicarbonate, being sufficient enough for cell infiltration and seeding. These porous scaffold microspheres could be potentially utilized for cultivating cells in a suspension manner and for delivering the seeded cells to the tissue defect site in an injectable manner. PMID:16023197

  2. 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.

  3. Biodegradation of the nitramine explosive CL-20.

    Science.gov (United States)

    Trott, Sandra; Nishino, Shirley F; Hawari, Jalal; Spain, Jim C

    2003-03-01

    The cyclic nitramine explosive CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane) was examined in soil microcosms to determine whether it is biodegradable. CL-20 was incubated with a variety of soils. The explosive disappeared in all microcosms except the controls in which microbial activity had been inhibited. CL-20 was degraded most rapidly in garden soil. After 2 days of incubation, about 80% of the initial CL-20 had disappeared. A CL-20-degrading bacterial strain, Agrobacterium sp. strain JS71, was isolated from enrichment cultures containing garden soil as an inoculum, succinate as a carbon source, and CL-20 as a nitrogen source. Growth experiments revealed that strain JS71 used 3 mol of nitrogen per mol of CL-20. PMID:12620886

  4. Biodegradation of polyester. Polyester no bunkai sei

    Energy Technology Data Exchange (ETDEWEB)

    Tokiwa, Y. (Agency of Industrial Science and Technology, Tokyo (Japan). Fermentation Research Inst.)

    1991-09-10

    Penicillium sp. 14-3 and penicillium sp. 26-1 can degrade various kinds of polyester. The results of studies made on hydrolysis of polyester by enzyme, hydrolysis of polyester by various kinds of lipase, and degradation of ester type polyurethane by microbes and lipase are introduced. For the improvement of physical properties of aliphatic polyester, aromatic-aliphatic polyester copolymers (CPE) have been synthesized to study the biodegradability. Copolymer in which a number of polyamide (nylon) are alternately introduced (CPAE) to aliphatic polyester has been developed. The result of studies made on the degradability of a blended body of PCL and natural high polymer, and on the collapsibility by lipase of high polymer materials including aliphatic polyamide are introduced. 26 refs., 5 figs., 1 tab.

  5. Lignin biodegradation with laccase-mediator systems

    Directory of Open Access Journals (Sweden)

    Lew Paul Christopher

    2014-03-01

    Full Text Available Lignin has a significant and largely unrealized potential as a source for the sustainable production of fuels and bulk high-value chemicals. It can replace fossil-based oil as a renewable feedstock that would bring about socio-economic and environmental benefits in our transition to a biobased economy. The efficient utilization of lignin however requires its depolymerization to low molecular weight phenolics and aromatics that can then serve as the building blocks for chemical syntheses of high-value products. The ability of laccase to attack and degrade lignin in conjunction with laccase mediators is currently viewed as one of the potential breakthrough applications for lignin valorization. Here we review the recent progress in lignin biodegradation with laccase-mediator systems, and research needs that need to be addressed in this field.

  6. Biodegradable Polyphosphazene Based Peptide-Polymer Hybrids

    Directory of Open Access Journals (Sweden)

    Anne Linhardt

    2016-04-01

    Full Text Available A novel series of peptide based hybrid polymers designed to undergo enzymatic degradation is presented, via macrosubstitution of a polyphosphazene backbone with the tetrapeptide Gly-Phe-Leu-Gly. Further co-substitution of the hybrid polymers with hydrophilic polyalkylene oxide Jeffamine M-1000 leads to water soluble and biodegradable hybrid polymers. Detailed degradation studies, via 31P NMR spectroscopy, dynamic light scattering and field flow fractionation show the polymers degrade via a combination of enzymatic, as well as hydrolytic pathways. The peptide sequence was chosen due to its known property to undergo lysosomal degradation; hence, these degradable, water soluble polymers could be of significant interest for the use as polymer therapeutics. In this context, we investigated conjugation of the immune response modifier imiquimod to the polymers via the tetrapeptide and report the self-assembly behavior of the conjugate, as well as its enzymatically triggered drug release behavior.

  7. Biodegradation and flushing of MBT wastes.

    Science.gov (United States)

    Siddiqui, A A; Richards, D J; Powrie, W

    2013-11-01

    Mechanical-biological treatment (MBT) processes are increasingly being adopted as a means of diverting biodegradable municipal waste (BMW) from landfill, for example to comply with the EU Landfill Directive. However, there is considerable uncertainty concerning the residual pollution potential of such wastes. This paper presents the results of laboratory experiments on two different MBT waste residues, carried out to investigate the remaining potential for the generation of greenhouse gases and the flushing of contaminants from these materials when landfilled. The potential for gas generation was found to be between 8% and 20% of that for raw MSW. Pretreatment of the waste reduced the potential for the release of organic carbon, ammoniacal nitrogen, and heavy metal contents into the leachate; and reduced the residual carbon remaining in the waste after final degradation from ∼320g/kg dry matter for raw MSW to between 183 and 195g/kg dry matter for the MBT wastes. PMID:23973052

  8. Biodegradation of concrete intended for their decontamination

    International Nuclear Information System (INIS)

    The decontamination of sub-structural materials represents a stake of high importance because of the high volume generated. It is agreed then to propose efficient and effective processes. The process of bio-decontamination of the hydraulic binders leans on the mechanisms of biodegradation of concretes, phenomenon characterized in the 40's by an indirect attack of the material by acids stem from the microbial metabolism: sulphuric acid (produced by Thiobacillus), nitric acid (produced by Nitrosomonas and Nitrobacter) and organic acids (produced by fungi). The principle of the bio-decontamination process is to apply those microorganisms on the surface of the contaminated material, in order to damage its surface and to retrieve the radionuclides. One of the multiple approaches of the process is the use of a bio-gel that makes possible the micro-organisms application. (author)

  9. Application of a Biodegradable Lubricant in a Diesel Vehicle

    DEFF Research Database (Denmark)

    Schramm, Jesper

    2003-01-01

    station in Germany. The driving patterns that were applied in these experiments were the FTP and EU test cycles. Since the biodegradability of lubricants changes with age, it was necessary to measure this change by driving the vehicles for a number of kilometers in order to obtain a full picture...... of the environmental impact of implementing biodegradable lubricants. Therefore lubricant samples were taken from the engine crankcase after driving 7500 km on the road. These samples were analyzed in order to evaluate biodegradability of the used lubricant and engine wear. The main findings from the study can...

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Tailoring Phase Behavior and Mechanical Properties in Thermoplastic Elastomers through Block Sequence and Macromolecular Architecture

    Science.gov (United States)

    Burns, Adam; Register, Richard

    2015-03-01

    Block copolymers exhibit unique properties which depend not only on the identities of the constituent blocks but also the block sequence and macromolecular architecture. Thermoplastic elastomers (TPEs) are a prime example. In TPEs the arrangement of glassy end blocks flanking a long rubbery midblock gives rise to a physically cross-linked, elastic solid. Exchanging the glassy blocks for crystalline blocks can improve the processability and solvent resistance, but adversely affects the mechanical performance. The block sequence crystalline-glassy-rubbery-glassy-crystalline has been developed to combine the advantages of both crystalline and glassy blocks. Careful selection of block lengths produces materials in which the order-disorder transition temperature lies below the melting point of the crystalline block, ensuring that the melt will be homogeneous above the melting point. Access to single-phase melts provides a large reduction in viscosity and elasticity over conventional TPEs, which remain microphase-separated in the melt. Inserting the glassy blocks between the crystalline and rubbery blocks produces a vitreous layer surrounding the crystalline domains, which improves the room-temperature mechanical performance. Incorporating the crystalline-glassy-rubbery motif into the arms of star block copolymers adds another level of control. The star architecture introduces a permanent cross-link at the center of the star without appreciably affecting the phase behavior.

  15. 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.

  16. ‘Broken symmetries’ in macromolecular crystallography: phasing from unmerged data

    International Nuclear Information System (INIS)

    Site-specific radiation damage and anisotropy of anomalous scattering can induce intensity differences in symmetry-related reflections. If the data are kept unmerged, these symmetry-breaking effects can become a source of phase information. The space-group symmetry of a crystal structure imposes a point-group symmetry on its diffraction pattern, giving rise to so-called symmetry-equivalent reflections. Instances in macromolecular crystallography are discussed in which the symmetry in reciprocal space is broken, i.e. where symmetry-related reflections are no longer equivalent. Such a situation occurs when the sample suffers from site-specific radiation damage during the X-ray measurements. Another example of broken symmetry arises from the polarization anisotropy of anomalous scattering. In these cases, the genuine intensity differences between symmetry-related reflections can be exploited to yield phase information in the structure-solution process. In this approach, the usual separation of the data merging and phasing steps is abandoned. The data are kept unmerged down to the Harker construction, where the symmetry-breaking effects are explicitly modelled and refined and become a source of supplementary phase information

  17. 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.

  18. 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.

  19. Effects of macromolecular crowding and DNA looping on gene regulation kinetics

    Science.gov (United States)

    Li, Gene-Wei; Berg, Otto G.; Elf, Johan

    2009-04-01

    DNA-binding proteins control how genomes function. The theory of facilitated diffusion explains how DNA-binding proteins can find targets apparently faster than the diffusion limit by using reduced dimensionality-combining three-dimensional (3D) diffusion through cytoplasm with 1D sliding along DNA (refs 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15). However, it does not include a description of macromolecular crowding on DNA as observed in living cells. Here, we show that such a physical constraint to sliding greatly reduces the search speed, in agreement with single-molecule measurements. Interestingly, the generalized theory also reveals significant insights into the design principles of biology. First, it places a hard constraint on the total number of DNA-binding proteins per cell. Remarkably, the number measured for Escherichia coli fits within the optimal range. Secondly, it defines a new role for DNA looping, a ubiquitous topological motif in genomes. DNA looping can speed up the search process by bypassing proteins that block the sliding track close to the target.

  20. 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.

  1. Olfactory nerve transport of macromolecular drugs to the brain. A problem in olfactory impaired patients

    International Nuclear Information System (INIS)

    Nasal administration of macromolecular drugs (including peptides and nanoparticles) has the potential to enable drug delivery system beyond the blood brain barrier (BBB) via olfactory nerve transport. Basic research on drug deliver systems to the brain via nasal administration has been well reported. Insulin-like growth factor-I (IGF-I) is associated with the development and growth of the central nervous system. Clinical application of IGF-I with nasal administration is intended to enable drug delivery to brain through the BBB. Uptake of IGF-I in the olfactory bulb and central nervous system increased according to the dosage of nasally administered IGF-I in normal ICR mice, however IGF-I uptake in the trigeminal nerve remained unchanged. Olfactory nerve transport is important for the delivery of nasally administered IGF-I to the brain in vivo. Because a safe olfactory nerve tracer has not been clinically available, olfactory nerve transport has not been well studied in humans. Nasal thallium-201 (201Tl) administration has been safely used to assess the direct pathway to the brain via the nose in healthy volunteers with a normal olfactory threshold. 201Tl olfactory nerve transport has recently been shown to decrease in patients with hyposmia. The olfactory nerve transport function in patients with olfactory disorders will be determined using 201Tl olfacto-scintigraphy for the exclusion of candidates in a clinical trial to assess the usefulness of nasal administration of IGF-I. (author)

  2. 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.

  3. 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.

  4. 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

  5. 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.

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

    Science.gov (United States)

    Gu, Shaobin; Zhang, Yongzhu; Wu, Ying

    2016-01-01

    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. PMID:27077011

  7. 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.

  8. 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.

  9. About Small Streams and Shiny Rocks: Macromolecular Crystal Growth in Microfluidics

    Science.gov (United States)

    vanderWoerd, Mark; Ferree, Darren; Spearing, Scott; Monaco, Lisa; Molho, Josh; Spaid, Michael; Brasseur, Mike; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    We are developing a novel technique with which we have grown diffraction quality protein crystals in very small volumes, utilizing chip-based, microfluidic ("LabChip") technology. With this technology volumes smaller than achievable with any laboratory pipette can be dispensed with high accuracy. We have performed a feasibility study in which we crystallized several proteins with the aid of a LabChip device. The protein crystals are of excellent quality as shown by X-ray diffraction. The advantages of this new technology include improved accuracy of dispensing for small volumes, complete mixing of solution constituents without bubble formation, highly repeatable recipe and growth condition replication, and easy automation of the method. We have designed a first LabChip device specifically for protein crystallization in batch mode and can reliably dispense and mix from a range of solution constituents. We are currently testing this design. Upon completion additional crystallization techniques, such as vapor diffusion and liquid-liquid diffusion will be accommodated. Macromolecular crystallization using microfluidic technology is envisioned as a fully automated system, which will use the 'tele-science' concept of remote operation and will be developed into a research facility aboard the International Space Station.

  10. 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

    2016-08-01

    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

  11. 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.

  12. SPring-8 BL41XU, a high-flux macromolecular crystallography beamline

    Energy Technology Data Exchange (ETDEWEB)

    Hasegawa, Kazuya [SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan); Shimizu, Nobutaka [SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan); KEK-PF, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Okumura, Hideo; Mizuno, Nobuhiro; Baba, Seiki [SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan); Hirata, Kunio [RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148 (Japan); Takeuchi, Tomoyuki; Yamazaki, Hiroshi; Senba, Yasunori; Ohashi, Haruhiko [SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan); Yamamoto, Masaki [RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148 (Japan); Kumasaka, Takashi, E-mail: kumasaka@spring8.or.jp [SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan)

    2013-11-01

    SPring-8 BL41XU provides a high-flux X-ray beam of size 10–50 µm, and enables high-quality diffraction data to be obtained from various types of protein crystals. Details of this beamline and an upgrade project are described. SPring-8 BL41XU is a high-flux macromolecular crystallography beamline using an in-vacuum undulator as a light source. The X-rays are monochromated by a liquid-nitrogen-cooling Si double-crystal monochromator, and focused by Kirkpatrick–Baez mirror optics. The focused beam size at the sample is 80 µm (H) × 22 µm (V) with a photon flux of 1.1 × 10{sup 13} photons s{sup −1}. A pinhole aperture is used to collimate the beam in the range 10–50 µm. This high-flux beam with variable size provides opportunities not only for micro-crystallography but also for data collection effectively making use of crystal volume. The beamline also provides high-energy X-rays covering 20.6–35.4 keV which allows ultra-high-resolution data to be obtained and anomalous diffraction using the K-edge of Xe and I. Upgrade of BL41XU for more rapid and accurate data collection is proceeding. Here, details of BL41XU are given and an outline of the upgrade project is documented.

  13. 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.

  14. 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. PMID:27594349

  15. 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.

  16. Native gel analysis of macromolecular protein complexes in cultured mammalian cells.

    Science.gov (United States)

    Munawar, Nayla; Olivero, Giorgio; Jerman, Emilia; Doyle, Benjamin; Streubel, Gundula; Wynne, Kieran; Bracken, Adrian; Cagney, Gerard

    2015-11-01

    Native gel electrophoresis enables separation of cellular proteins in their non-denatured state. In experiments aimed at analysing proteins in higher order or multimeric assemblies (i.e. protein complexes) it offers some advantages over rival approaches, particularly as an interface technology with mass spectrometry. Here we separated fractions from HEK293 cells by native electrophoresis in order to survey protein complexes in the cytoplasmic, nuclear and chromatin environments, finding 689 proteins distributed among 217 previously described complexes. As expected, different fractions contained distinct combinations of macromolecular complexes, with subunits of the same complex tending to co-migrate. Exceptions to this observation could often be explained by the presence of subunits shared among different complexes. We investigated one identified complex, the Polycomb Repressor Complex 2 (PRC2), in more detail following affinity purification of the EZH2 subunit. This approach resulted in the identification of all previously reported members of PRC2. Overall, this work demonstrates that the use of native gel electrophoresis as an upstream separating step is an effective approach for analysis of the components and cellular distribution of protein complexes. PMID:26223664

  17. 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

    2016-08-01

    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.

  18. Antibacterial biodegradable Mg-Ag alloys

    Directory of Open Access Journals (Sweden)

    D Tie

    2013-06-01

    Full Text Available The use of magnesium alloys as degradable metals for biomedical applications is a topic of ongoing research and the demand for multifunctional materials is increasing. Hence, binary Mg-Ag alloys were designed as implant materials to combine the favourable properties of magnesium with the well-known antibacterial property of silver. In this study, three Mg-Ag alloys, Mg2Ag, Mg4Ag and Mg6Ag that contain 1.87 %, 3.82 % and 6.00 % silver by weight, respectively, were cast and processed with solution (T4 and aging (T6 heat treatment.The metallurgical analysis and phase identification showed that all alloys contained Mg4Ag as the dominant β phase. After heat treatment, the mechanical properties of all Mg-Ag alloys were significantly improved and the corrosion rate was also significantly reduced, due to presence of silver. Mg(OH2 and MgO present the main magnesium corrosion products, while AgCl was found as the corresponding primary silver corrosion product. Immersion tests, under cell culture conditions, demonstrated that the silver content did not significantly shift the pH and magnesium ion release. In vitro tests, with both primary osteoblasts and cell lines (MG63, RAW 264.7, revealed that Mg-Ag alloys show negligible cytotoxicity and sound cytocompatibility. Antibacterial assays, performed in a dynamic bioreactor system, proved that the alloys reduce the viability of two common pathogenic bacteria, Staphylococcus aureus (DSMZ 20231 and Staphylococcus epidermidis (DSMZ 3269, and the results showed that the killing rate of the alloys against tested bacteria exceeded 90%. In summary, biodegradable Mg-Ag alloys are cytocompatible materials with adjustable mechanical and corrosion properties and show promising antibacterial activity, which indicates their potential as antibacterial biodegradable implant materials.

  19. Biodegradation of carbon nanohorns in macrophage cells

    Science.gov (United States)

    Zhang, Minfang; Yang, Mei; Bussy, Cyrill; Iijima, Sumio; Kostarelos, Kostas; Yudasaka, Masako

    2015-02-01

    With the rapid developments in the medical applications of carbon nanomaterials such as carbon nanohorns (CNHs), carbon nanotubes, and graphene based nanomaterials, understanding the long-term fate, health impact, excretion, and degradation of these materials has become crucial. Herein, the in vitro biodegradation of CNHs was determined using a non-cellular enzymatic oxidation method and two types of macrophage cell lines. Approximately 60% of the CNHs was degraded within 24 h in a phosphate buffer solution containing myeloperoxidase. Furthermore, approximately 30% of the CNHs was degraded by both RAW 264.7 and THP-1 macrophage cells within 9 days. Inflammation markers such as pro-inflammatory cytokines interleukin 6 and tumor necrosis factor α were not induced by exposure to CNHs. However, reactive oxygen species were generated by the macrophage cells after uptake of CNHs, suggesting that these species were actively involved in the degradation of the nanomaterials rather than in an inflammatory pathway induction.With the rapid developments in the medical applications of carbon nanomaterials such as carbon nanohorns (CNHs), carbon nanotubes, and graphene based nanomaterials, understanding the long-term fate, health impact, excretion, and degradation of these materials has become crucial. Herein, the in vitro biodegradation of CNHs was determined using a non-cellular enzymatic oxidation method and two types of macrophage cell lines. Approximately 60% of the CNHs was degraded within 24 h in a phosphate buffer solution containing myeloperoxidase. Furthermore, approximately 30% of the CNHs was degraded by both RAW 264.7 and THP-1 macrophage cells within 9 days. Inflammation markers such as pro-inflammatory cytokines interleukin 6 and tumor necrosis factor α were not induced by exposure to CNHs. However, reactive oxygen species were generated by the macrophage cells after uptake of CNHs, suggesting that these species were actively involved in the degradation of the

  20. Comparing the desorption and biodegradation of low concentrations of phenanthrene sorbed to activated carbon, biochar and compost

    DEFF Research Database (Denmark)

    Marchal, Geoffrey; Smith, Kilian E.C.; Rein, Arno;

    2013-01-01

    ±0.3%, respectively) and compost (1.3±0.21%, similar for all media). Secondly, the mineralization of phenanthrene sorbed to AC, charcoal and compost by Sphingomonas sp. 10-1 (DSM 12247) was determined. In contrast to the amounts desorbed, phenanthrene mineralization was similar for all the soil amendments at about 56......Carbonaceous soil amendments are applied to contaminated soils and sediments to strongly sorb hydrophobic organic contaminants (HOCs) and reduce their freely dissolved concentrations. This limits biouptake and toxicity, but also biodegradation. To investigate whether HOCs sorbed to such amendments...... can be degraded at all, the desorption and biodegradation of low concentrations of 14C-labelled phenanthrene (⩽5μgL−1) freshly sorbed to suspensions of the pure soil amendments activated carbon (AC), biochar (charcoal) and compost were compared. Firstly, the maximum abiotic desorption of phenanthrene...

  1. 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.

  2. 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.

  3. 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. PMID:26212495

  4. 40 CFR 796.3100 - Aerobic aquatic biodegradation.

    Science.gov (United States)

    2010-07-01

    ... compound is desirable. Aniline, sodium citrate, dextrose, phthalic acid and trimellitic acid will exhibit... test medium. Reference compounds which are positive for ultimate biodegradability include: sodium citrate, dextrose, phthalic acid, trimellitic acid, and aniline. (iv) For each test set,...

  5. 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.

  6. BACTERIAL BIODEGRADATION OF PERMETRINA AND CIPERMETRINA PESTICIDES IN CULTURE LOT

    OpenAIRE

    José C. Mendoza; Yazmin S. Perea; Jaime A. Salvador; Janette A. Morales; Gabriela Pérez

    2011-01-01

    The biodegradation of permetrhin and cypermethrin (50 and 100 mg/L) with Pseudomonas putida, Pseudomonas mendocina, Chromobacterium violaceum and Burkholderia cepacia in batch reactors was studied. The strain of Pseudomonas putida and Pseudomonas mendocina showed a greater capability of biodegradation of pesticides, after 5 days, this is of 65% for both pesticides and after the 15 days it practically stays constant, being of until 95% for permetrina to 50 and 100 mg/l and for cipermetrina fr...

  7. Biodegradation of bioaccessible textile azo dyes by Phanerochaete chrysosporium

    OpenAIRE

    Martins, Maria Adosinda; Ferreira, Isabel C.F.R.; Santos, Isabel; Queiroz, Maria João R. P.; Lima, Nelson

    2000-01-01

    Azo dyes are important chemical pollutants of industrial origin. Textile azo dyes with bioaccessible groups for lignin degrading fungi, such as 2-methoxyphenol (guaiacol) and 2,6-dimethoxyphenol (syringol), were synthesised using different aminobenzoic and aminosulphonic acids as diazo components. The inocula of the best biodegradation assays were obtained from a pre-growth medium (PAM), containing one of the synthesised dyes. The results of the dye biodegradation assays were eval...

  8. Comparative study on the biodegradability of morpholinium herbicidal ionic liquids

    OpenAIRE

    Ławniczak, Łukasz; Materna, Katarzyna; Framski, Grzegorz; Szulc, Alicja; Syguda, Anna

    2015-01-01

    This study focused on evaluating the toxicity as well as primary and ultimate biodegradability of morpholinium herbicidal ionic liquids (HILs), which incorporated MCPA, MCPP, 2,4-D or Dicamba anions. The studied HILs were also subjected to determination of surface active properties in order to assess their influence on toxicity and biodegradability. The study was carried out with microbiota isolated from different environmental niches: sediments from river channel, garden soil, drainage trenc...

  9. Biodegradable Nanocomposite Films Based on Sodium Alginate and Cellulose Nanofibrils

    OpenAIRE

    B. Deepa; Eldho Abraham; Pothan, Laly A; Nereida Cordeiro; Marisa Faria; Sabu Thomas

    2016-01-01

    Biodegradable nanocomposite films were prepared by incorporation of cellulose nanofibrils (CNF) into alginate biopolymer using the solution casting method. The effects of CNF content (2.5, 5, 7.5, 10 and 15 wt %) on mechanical, biodegradability and swelling behavior of the nanocomposite films were determined. The results showed that the tensile modulus value of the nanocomposite films increased from 308 to 1403 MPa with increasing CNF content from 0% to 10%; however, it decreased with further...

  10. Biodegradation of the High Explosive Hexanitrohexaazaiso-wurtzitane (CL-20)

    OpenAIRE

    Steve Nicolich; Mohammed Sidhoum; Wendy Balas; Pelin Karakaya; Agamemnon Koutsospyros; Christos Christodoulatos

    2009-01-01

    The aerobic biodegradability of the high explosive CL-20 by activated sludge and the white rot fungus Phanerochaete chrysosporium has been investigated. Although activated sludge is not effective in degrading CL-20 directly, it can mineralize the alkaline hydrolysis products. Phanerochaete chrysosporium degrades CL-20 in the presence of supplementary carbon and nitrogen sources. Biodegradation studies were conducted using various nutrient media under diverse conditions. Variables included the...

  11. Biodegradation of Asphalt Cement-20 by Aerobic Bacteria

    OpenAIRE

    Pendrys, John P.

    1989-01-01

    Seven gram-negative, aerobic bacteria were isolated from a mixed culture enriched for asphalt-degrading bacteria. The predominant genera of these isolates were Pseudomonas, Acinetobacter, Alcaligenes, Flavimonas, and Flavobacterium. The mixed culture preferentially degraded the saturate and naphthene aromatic fractions of asphalt cement-20. A residue remained on the surface which was resistant to biodegradation and protected the underlying asphalt from biodegradation. The most potent asphalt-...

  12. Biodegradability determination of municipal waste: an evaluation of methods

    OpenAIRE

    Godley, Andrew R.; Lewin, Kathy; Graham, Adele; Barker, H.; Smith, Richard

    2004-01-01

    The Environment Agency is required to monitor the diversion of biodegradable municipal waste (BMW) from landfill. Reliable methods are needed to measure the biodegradability of municipal waste, both as mixed municipal waste and as individually separated fractions. An evaluation of several methods was carried out using a variety of organic materials typically found in municipal solid waste. The assessment considered biological and non-biological methods to determine which provid...

  13. Factors influencing crude oil biodegradation by Yarrowia lipolytica

    OpenAIRE

    Tatiana Felix Ferreira; Maria Alice Zarur Coelho; Maria Helena Miguez da Rocha-Leão

    2012-01-01

    Yarrowia lipolytica is unique strictly aerobic yeast with the ability to efficiently degrade hydrophobic substrates such as n-alkenes, fatty acids, glycerol and oils. In the present work, a 2(4) full factorial design was used to investigate the influence of the independent variables of temperature, agitation, initial cell concentration and initial petroleum concentration on crude oil biodegradation. The results showed that all variables studied had significant effects on the biodegradation pr...

  14. Removal of Textile Dyestufes From Wastewater by Adsorptive Biodegradation

    OpenAIRE

    KAPDAN, İlgi KARAPINAR; KARGI, Fikret

    2000-01-01

    Removal of dyestuffs from a synthetic wastewater by adsorptive biodegradation was investigated in this study. The dyestuff adsorption capacities of granular, powdered activated carbon (GAC and PAC) and low-cost adsorbents such as zeolite, wood chips and wood ash were evaluated in order to obtain a low-cost adsorbent for use in an activated sludge unit. Then various activated sludge cultures were tested for biodegradation of a selected dyestuff. An activated sludge unit with the selected activ...

  15. Biodegradation of Para Amino Acetanilide by Halomonas sp. TBZ3

    OpenAIRE

    Hajizadeh, Nader; Sefidi Heris, Youssof; Zununi Vahed, Sepideh; Vallipour, Javad; Hejazi, Mohammad Amin; Golabi, Sayyed Mahdi; Asadpour-Zeynali, Karim; Hejazi, Mohammad Saeid

    2015-01-01

    Background: Aromatic compounds are known as a group of highly persistent environmental pollutants. Halomonas sp. TBZ3 was isolated from the highly salty Urmia Lake of Iran. In this study, characterization of a new Halomonas isolate called Halomonas sp. TBZ3 and its employment for biodegradation of para-amino acetanilide (PAA), as an aromatic environmental pollutant, is described. Objectives: This study aimed to characterize the TBZ3 isolate and to elucidate its ability as a biodegradative age...

  16. Study of the biodegradation in soil of new generation plactics

    OpenAIRE

    Siotto,

    2011-01-01

    The intense use of plastic contributes to increase the amount of municipal waste that are generally disposed in landfill. For some applications and sectors, an important alternative to the conventional plastic materials can be found in the use of the new generation materials: the biodegradable polymers. Their use can be an alternative to landfill disposal and can thus reduce the cost of waste management and the accumulation in the environment. The biodegradable polymers, in fact, are used by ...

  17. Isomer-Specific Biodegradation and Chemical Oxidation of Nonylphenol

    OpenAIRE

    Lu, Zhijiang

    2014-01-01

    Nonylphenol (NP), a well-known environmental estrogen with numerous isomers, is commonly treated as a single compound in the evaluation of its environmental occurrence, fate and transport, treatment removal and toxicity. Recent studies showed that NP isomers exhibited different estrogenicity and biodegradability. However, at present little systematic information is available on its isomer-specific biodegradation and chemical oxidation under natural and engineered conditions.We comprehensively...

  18. Critical evaluation of biodegradable polymers used in nanodrugs

    OpenAIRE

    Marin E; Briceño MI; Caballero-George C

    2013-01-01

    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, ...

  19. Biodegradation and biocompatibility of a degradable chitosan vascular prosthesis

    OpenAIRE

    Kong, Xiaoying; Xu, Wenhua

    2015-01-01

    An instrument made by ourselves was used to fabricate biodegradable chitosan-heparin artificial vascular prosthesis with small internal diameter (2 mm) and different crosslinking degree from biodegradable chitosan, chitosan derivates and heparin. In vivo and in vitro degradation studies, inflammatory analysis and electron microscope scanning of this artificial vascular prosthesis were performed. It was observed that 50% of the prosthesis decomposed in vivo and was replaced by natural tissues....

  20. Assessment of the biodegradability of xanthan in offshore injection water

    OpenAIRE

    Hovland, Beate

    2015-01-01

    The application of biopolymers in EOR operations is considered environmental friendly compared to synthetic polymers. However, microbial degradation of the biopolymers may lead to a deterioration of effect in EOR applications. This thesis is part of an industrial project conducted by UNI Research CIPR for Statoil ASA, were the aim is to assess biodegradation of xanthan at specific oil field conditions. Investigation of the biodegradation of xanthan was perform...

  1. Saponification of fatty slaughterhouse wastes for enhancing anaerobic biodegradability.

    Science.gov (United States)

    Battimelli, Audrey; Carrère, Hélène; Delgenès, Jean-Philippe

    2009-08-01

    The thermochemical pretreatment by saponification of two kinds of fatty slaughterhouse waste--aeroflotation fats and flesh fats from animal carcasses--was studied in order to improve the waste's anaerobic degradation. The effect of an easily biodegradable compound, ethanol, on raw waste biodegradation was also examined. The aims of the study were to enhance the methanisation of fatty waste and also to show a link between biodegradability and bio-availability. The anaerobic digestion of raw waste, saponified waste and waste with a co-substrate was carried out in batch mode under mesophilic and thermophilic conditions. The results showed little increase in the total volume of biogas, indicating a good biodegradability of the raw wastes. Mean biogas volume reached 1200 mL/g VS which represented more than 90% of the maximal theoretical biogas potential. Raw fatty wastes were slowly biodegraded whereas pretreated wastes showed improved initial reaction kinetics, indicating a better initial bio-availability, particularly for mesophilic runs. The effects observed for raw wastes with ethanol as co-substrate depended on the process temperature: in mesophilic conditions, an initial improvement was observed whereas in thermophilic conditions a significant decrease in biodegradability was observed.

  2. 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.

  3. 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.

  4. Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures

    International Nuclear Information System (INIS)

    The maximum-likelihood free-kick target, which calculates model error estimates from the work set and a randomly displaced model, proved superior in the accuracy and consistency of refinement of crystal structures compared with the maximum-likelihood cross-validation target, which calculates error estimates from the test set and the unperturbed model. The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. They utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errors via the random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation of Rfree or may leave it out completely

  5. X-ray detectors for soft X-ray macromolecular crystallography

    International Nuclear Information System (INIS)

    Full text: Modern protein crystallography ultimately makes use of the two-dimensional position - sensitive detectors such as Image Plates and CCD with scintillation convertors coupled with fiber optics for detection of X-Ray diffraction pictures taken from macromolecular crystals. These detectors have high efficiency for 1.5-1.0 A synchrotron radiation, special resolution ∼80-50 μm and large effective area (i.e. Σ 300 mm2 for large MAR Image Plate). Both of these types of detectors lack energy resolution. A major drawback of Image Plates is long read-out time (2.5-4 minutes). CCD based devices permit data collection in a real time, however at present they are much more expensive. One of the novel and very promising trends in protein crystallography is to use soft X-ray synchrotron radiation between 2.2 keV and 6 keV (5.6 to 2.5 A) and there is an urgent need to develop suitable detection system for these kinds of applications. It is to be two- dimensional positional sensitive detector with pitch of about 10 to 20 μm, high efficiency and real-time readout. An active area of the detector is to be at least 20 x 20 mm2. It seems to be the simplest solution to use conventional direct-illumination CCD detectors because absorption length of the 5 A radiation in silicon is about 3 μm. However they lack, for example, energy resolution and optimum solution of the problem has yet to come. (author)

  6. Improving 2D and 3D Skin In Vitro Models Using Macromolecular Crowding.

    Science.gov (United States)

    Benny, Paula; Badowski, Cedric; Lane, E Birgitte; Raghunath, Michael

    2016-01-01

    The glycoprotein family of collagens represents the main structural proteins in the human body, and are key components of biomaterials used in modern tissue engineering. A technical bottleneck is the deposition of collagen in vitro, as it is notoriously slow, resulting in sub-optimal formation of connective tissue and subsequent tissue cohesion, particularly in skin models. Here, we describe a method which involves the addition of differentially-sized sucrose co-polymers to skin cultures to generate macromolecular crowding (MMC), which results in a dramatic enhancement of collagen deposition. Particularly, dermal fibroblasts deposited a significant amount of collagen I/IV/VII and fibronectin under MMC in comparison to controls. The protocol also describes a method to decellularize crowded cell layers, exposing significant amounts of extracellular matrix (ECM) which were retained on the culture surface as evidenced by immunocytochemistry. Total matrix mass and distribution pattern was studied using interference reflection microscopy. Interestingly, fibroblasts, keratinocytes and co-cultures produced cell-derived matrices (CDM) of varying composition and morphology. CDM could be used as "bio-scaffolds" for secondary cell seeding, where the current use of coatings or scaffolds, typically from xenogenic animal sources, can be avoided, thus moving towards more clinically relevant applications. In addition, this protocol describes the application of MMC during the submerged phase of a 3D-organotypic skin co-culture model which was sufficient to enhance ECM deposition in the dermo-epidermal junction (DEJ), in particular, collagen VII, the major component of anchoring fibrils. Electron microscopy confirmed the presence of anchoring fibrils in cultures developed with MMC, as compared to controls. This is significant as anchoring fibrils tether the dermis to the epidermis, hence, having a pre-formed mature DEJ may benefit skin graft recipients in terms of graft stability and

  7. Electrostatic, elastic and hydration-dependent interactions in dermis influencing volume exclusion and macromolecular transport.

    Science.gov (United States)

    Øien, Alf H; Wiig, Helge

    2016-07-01

    Interstitial exclusion refers to the limitation of space available for plasma proteins and other macromolecules based on collagen and negatively charged glycosaminoglycans (GAGs) in the interstitial space. It is of particular importance to interstitial fluid and plasma volume regulation. Here we present a novel mechanical and mathematical model of the dynamic interactions of structural elements within the interstitium of the dermis at the microscopic level that may explain volume exclusion of charged and neutral macroparticles. At this level, the interstitium is considered to consist of elements called extracellular matrix (ECM) cells, again containing two main interacting structural components on a fluid background including anions and cations setting up osmotic forces: one smaller GAG component, having an intrinsic expansive electric force, and one bigger collagen component, having an intrinsic elastic force. Because of size differences, the GAG component interacts with a fraction of the collagen component only at normal hydration. This fraction, however, increases with rising hydration as a consequence of the modeled form of the interaction force between the GAGs and collagen. Collagen is locally displaced at variable degrees as hydration changes. Two models of GAGs are considered, having largely different geometries which demands different, but related, forms of GAG-collagen interaction forces. The effects of variable fixed charges on GAGs and of GAG density in tissue are evaluated taking into account observed volume exclusion properties of charged macromolecules as a function of tissue hydration. The presented models may improve our biophysical understanding of acting forces influencing tissue fluid dynamics. Such knowledge is significant when evaluating the transport of electrically charged and neutral macromolecules into and through the interstitium, and therefore to drug uptake and the therapeutic effects of macromolecular agents. PMID:27079466

  8. 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

  9. Evaluation of the biodegradation of Alaska North Slope oil in microcosms using the biodegradation model BIOB

    Directory of Open Access Journals (Sweden)

    Jagadish eTorlapati

    2014-05-01

    Full Text Available We present the details of a numerical model, BIOB that is capable of simulating the biodegradation of oil entrapped in the sediment. The model uses Monod kinetics to simulate the growth of bacteria in the presence of nutrients and the subsequent consumption of hydrocarbons. The model was used to simulate experimental results of Exxon Valdez oil biodegradation in laboratory columns (Venosa et al. (2010. In that study, samples were collected from three different islands: Eleanor Island (EL107, Knight Island (KN114A, and Smith Island (SM006B, and placed in laboratory microcosms for a duration of 168 days to investigate oil bioremediation through natural attenuation and nutrient amendment. The kinetic parameters of the BIOB model were estimated by fitting to the experimental data using a parameter estimation tool based on Genetic Algorithms (GA. The parameter values of EL107 and KN114A were similar whereas those of SM006B were different from the two other sites; in particular biomass growth at SM006B was four times slower than at the other two islands. Grain size analysis from each site revealed that the specific surface area per unit mass of sediment was considerably lower at SM006B, which suggest that the surface area of sediments is a key control parameter for microbial growth in sediments. Comparison of the BIOB results with exponential decay curves fitted to the data indicated that BIOB provided better fit for KN114A and SM006B in nutrient amended treatments, and for EL107 and KN114A in natural attenuation. In particular, BIOB was able to capture the initial slow biodegradation due to the lag phase in microbial growth. Sensitivity analyses revealed that oil biodegradation at all three locations were sensitive to nutrient concentration whereas SM006B was sensitive to initial biomass concentration due to its slow growth rate. Analyses were also performed to compare the half-lives of individual compounds with the decay rate of the overall PAH.

  10. [Allergy to radiographic contrast media].

    Science.gov (United States)

    Vionnet, Julien; Petitpierre, Stéphanie; Fumeaux, Alexandre; Meuli, Reto; Spertini, Francois; Comte, Denis

    2013-04-17

    Allergy to radiographic contrast media Hypersensitivity reactions to radio-contrast media are common in the daily practice. These products are responsible for immediate ( 1 hour after administration) hypersensitivity reactions. A diagnostic work-up by an allergologist with skin tests and in some cases provocation tests is of value in reducing the risk of recurrent hypersensitivity reactions to iodinated contrast media. A careful selection of the patients is required because the incidence of breakthrough reactions is still concerning, even with proper premedication. Practical recommendations are presented in this article. For gadolinium-based contrast agents, data in the literature is not sufficient for suggesting guidelines. PMID:23667970

  11. Biodegradation and surfactant-mediated biodegradation of diesel fuel by 218 microbial consortia are not correlated to cell surface hydrophobicity

    Energy Technology Data Exchange (ETDEWEB)

    Owsianiak, Mikolaj; Szulc, Alicja; Chrzanowski, Lukasz; Bogacki, Mariusz [Poznan Univ. of Technology (Poland). Inst. of Chemical Technology and Engineering; Cyplik, Pawel; Olejnik-Schmidt, Agniezka K. [Poznan Univ. of Life Sciences (Poland). Dept. of Biotechnology and Food Microbiology; Heipieper, Hermann J. [Helmholtz Centre for Environmental Research - UFZ, Leipzig (Germany). Dept. of Environmental Biotechnology

    2009-09-15

    In this study, we elucidated the role of cell surface hydrophobicity (microbial adhesion to hydrocarbons method, MATH) and the effect of anionic rhamnolipids and nonionic Triton X-100 surfactants on biodegradation of diesel fuel employing 218 microbial consortia isolated from petroleum-contaminated soils. Applied enrichment procedure with floating diesel fuel as a sole carbon source in liquid cultures resulted in consortia of varying biodegradation potential and diametrically different cell surface properties, suggesting that cell surface hydrophobicity is a conserved parameter. Surprisingly, no correlations between cell surface hydrophobicity and biodegradation of diesel fuel were found. Nevertheless, both surfactants altered cell surface hydrophobicity of the consortia in similar manner: increased for the hydrophilic and decreased for the hydrophobic cultures. In addition to this, the surfactants exhibited similar influence on diesel fuel biodegradation: Increase was observed for initially slow-degrading cultures and the opposite for fast degraders. This indicates that in the surfactant-mediated biodegradation, effectiveness of surfactants depends on the specification of microorganisms and not on the type of surfactant. In contrary to what was previously reported for pure strains, cell surface hydrophobicity, as determined by MATH, is not a good descriptor of biodegrading potential for mixed cultures. (orig.)

  12. Biodegradation of chlorpyrifos by bacterial genus Pseudomonas.

    Science.gov (United States)

    Gilani, Razia Alam; Rafique, Mazhar; Rehman, Abdul; Munis, Muhammad Farooq Hussain; Rehman, Shafiq Ur; Chaudhary, Hassan Javed

    2016-02-01

    Chlorpyrifos is an organophosphorus pesticide commonly used in agriculture. It is noxious to a variety of organisms that include living soil biota along with beneficial arthropods, fish, birds, humans, animals, and plants. Exposure to chlorpyrifos may cause detrimental effects as delayed seedling emergence, fruit deformities, and abnormal cell division. Contamination of chlorpyrifos has been found about 24 km from the site of its application. There are many physico-chemical and biological approaches to remove organophosphorus pesticides from the ecosystem, among them most promising is biodegradation. The 3,5,6-trichloro-2-pyridinol (TCP) and diethylthiophosphate (DETP) as primary products are made when chlorpyrifos is degraded by soil microorganisms which further break into nontoxic metabolites as CO(2), H(2)O, and NH(3). Pseudomonas is a diversified genus possessing a series of catabolic pathways and enzymes involved in pesticide degradation. Pseudomonas putida MAS-1 is reported to be more efficient in chlorpyrifos degradation by a rate of 90% in 24 h among Pseudomonas genus. The current review analyzed the comparative potential of bacterial species in Pseudomonas genus for degradation of chlorpyrifos thus, expressing an ecofriendly approach for the treatment of environmental contaminants like pesticides. PMID:26837064

  13. Electrospun biodegradable polymers loaded with bactericide agents

    Directory of Open Access Journals (Sweden)

    Ramaz Katsarava

    2016-03-01

    Full Text Available Development of materials with an antimicrobial activity is fundamental for different sectors, including medicine and health care, water and air treatment, and food packaging. Electrospinning is a versatile and economic technique that allows the incorporation of different natural, industrial, and clinical agents into a wide variety of polymers and blends in the form of micro/nanofibers. Furthermore, the technique is versatile since different constructs (e.g. those derived from single electrospinning, co-electrospinning, coaxial electrospinning, and miniemulsion electrospinning can be obtained to influence the ability to load agents with different characteristics and stability and to modify the release behaviour. Furthermore, antimicrobial agents can be loaded during the electrospinning process or by a subsequent coating process. In order to the mitigate burst release effect, it is possible to encapsulate the selected drug into inorganic nanotubes and nanoparticles, as well as in organic cyclodextrine polysaccharides. In the same way, processes that involve covalent linkage of bactericide agents during surface treatment of electrospun samples may also be considered. The present review is focused on more recent works concerning the electrospinning of antimicrobial polymers. These include chitosan and common biodegradable polymers with activity caused by the specific load of agents such as metal and metal oxide particles, quaternary ammonium compounds, hydantoin compounds, antibiotics, common organic bactericides, and bacteriophages.

  14. Biodegradation of sulfanilic acid by Pseudomonas paucimobilis.

    Science.gov (United States)

    Perei, K; Rákhely, G; Kiss, I; Polyák, B; Kovács, K L

    2001-01-01

    An aerobic bacterium, isolated from a contaminated site, was able to degrade sulfanilic acid (4-aminobenzenesulfonic acid) and was identified as Pseudomonas paucimobilis. The isolate could grow on sulfanilic acid (SA) as its sole carbon and nitrogen source and metabolized the target compound to biomass. The bioconversion capacity depended on the sulfanilic acid concentration; greater than 98% elimination of the hazardous compound was achieved at low (10 mM) sulfanilic acid concentration, and the yield was greater than 70% at 50 mM concentration of the contaminant. The maximum conversion rate was 1.5 mmol sulfanilic acid/h per mg wet cells at 30 degrees C. Ca-alginate-phytagel proved a good matrix for immobilization of P. paucimobilis, with essentially unaltered biodegradation activity. Removal of sulfanilic acid from contaminated industrial waste water was demonstrated. SDS-PAGE analysis of the crude extract revealed novel proteins appearing upon induction with sulfanilic acid and related compounds, which indicated alternative degradation mechanisms involving various inducible enzymes.

  15. Biodegradability enhancement of municipal landfill leachate

    Institute of Scientific and Technical Information of China (English)

    Pi Kewu; Gong Wenqi

    2008-01-01

    The method of enhancing the biodegradability of landfill leachate via air stripping followed by coagulation/ultrafiltration (UF) processes is introduced. In this study, the air stripping process obtained a removal efficiency of 88.6% for ammonia nitrogen (NH3-N), at an air-to-liquid ratio (A/L) of 3 300 (pH=11) and after 18 h of stripping. The single coagulation process increased the BOD (biological oxygen demand)/COD (chemical oxygen demand) ratio by 0.089 with a FeCl3 dosage of 570 mg/L, at pH 7.0, and the single UF process increased the BOD/COD ratio from 0.049 to 0.311. However, the combination of coagulation and UF increased the BOD/COD ratio from 0.049 to 0.423, and the final BOD, COD, NH3-N, and colour of the leachate were 1 023 mg/L, 2 845 mg/L, 145 mg/L, and 2 056, respectively, when a 3 kDa molecular weight cut-off (MWCO) membrane was used at an operating pressure of 0.7 MPa. In the ultrafiltration process, the average solution flux (JⅤ), concentration multiple (MC), and retention rate (R) for the COD were 107.3 L/(m2.h), 6.3, and 84.2%, respectively.

  16. Equilibrium gold nanoclusters quenched with biodegradable polymers.

    Science.gov (United States)

    Murthy, Avinash K; Stover, Robert J; Borwankar, Ameya U; Nie, Golay D; Gourisankar, Sai; Truskett, Thomas M; Sokolov, Konstantin V; Johnston, Keith P

    2013-01-22

    Although sub-100 nm nanoclusters of metal nanoparticles are of interest in many fields including biomedical imaging, sensors, and catalysis, it has been challenging to control their morphologies and chemical properties. Herein, a new concept is presented to assemble equilibrium Au nanoclusters of controlled size by tuning the colloidal interactions with a polymeric stabilizer, PLA(1k)-b-PEG(10k)-b-PLA(1k). The nanoclusters form upon mixing a dispersion of ~5 nm Au nanospheres with a polymer solution followed by partial solvent evaporation. A weakly adsorbed polymer quenches the equilibrium nanocluster size and provides steric stabilization. Nanocluster size is tuned from ~20 to ~40 nm by experimentally varying the final Au nanoparticle concentration and the polymer/Au ratio, along with the charge on the initial Au nanoparticle surface. Upon biodegradation of the quencher, the nanoclusters reversibly and fully dissociate to individual ~5 nm primary particles. Equilibrium cluster size is predicted semiquantitatively with a free energy model that balances short-ranged depletion and van der Waals attractions with longer-ranged electrostatic repulsion, as a function of the Au and polymer concentrations. The close spacings of the Au nanoparticles in the clusters produce strong NIR extinction over a broad range of wavelengths from 650 to 900 nm, which is of practical interest in biomedical imaging. PMID:23230905

  17. Biodegradation of chlorpyrifos by bacterial genus Pseudomonas.

    Science.gov (United States)

    Gilani, Razia Alam; Rafique, Mazhar; Rehman, Abdul; Munis, Muhammad Farooq Hussain; Rehman, Shafiq Ur; Chaudhary, Hassan Javed

    2016-02-01

    Chlorpyrifos is an organophosphorus pesticide commonly used in agriculture. It is noxious to a variety of organisms that include living soil biota along with beneficial arthropods, fish, birds, humans, animals, and plants. Exposure to chlorpyrifos may cause detrimental effects as delayed seedling emergence, fruit deformities, and abnormal cell division. Contamination of chlorpyrifos has been found about 24 km from the site of its application. There are many physico-chemical and biological approaches to remove organophosphorus pesticides from the ecosystem, among them most promising is biodegradation. The 3,5,6-trichloro-2-pyridinol (TCP) and diethylthiophosphate (DETP) as primary products are made when chlorpyrifos is degraded by soil microorganisms which further break into nontoxic metabolites as CO(2), H(2)O, and NH(3). Pseudomonas is a diversified genus possessing a series of catabolic pathways and enzymes involved in pesticide degradation. Pseudomonas putida MAS-1 is reported to be more efficient in chlorpyrifos degradation by a rate of 90% in 24 h among Pseudomonas genus. The current review analyzed the comparative potential of bacterial species in Pseudomonas genus for degradation of chlorpyrifos thus, expressing an ecofriendly approach for the treatment of environmental contaminants like pesticides.

  18. [Biodegradable polyhydroxyalkanoates as carriers for antitumor agents].

    Science.gov (United States)

    Shishatskaia, E I; Zhemchugova, A V; Volova, T G

    2005-01-01

    The possible use of biodegradable polyethers of microbial origin (polyhydroxyalkanoates) as matrices for deposition of daunorubicin (rubomycin), an antitumor anthracycline, was studied. The tablet dosage form of various rubomycin load (from 1 to 60% w/w) was prepared by cold compaction under pressure. The in vitro kinetics of the rubomycin release from the polymer matrix was investigated. It was shown that the rubomycin release to the medium resulted from the drug solution and diffusion within various periods, from tens hours to several weeks and months depending on the load. When the rubomycin load was under 20% w/w the drug release was prolonged and directly proportional to the observation time. When the rubomycin concentration was under 5%, the drug release kinetics corresponded to the type of the zero order reaction with prolonged release without sharp efflux at the initial stage of the observation. The findings showed that the polyhydroxyalkanoates were applicable as matrices for deposition of rubomycin and preparation of drugs with prolonged action.

  19. Biodegradation and flushing of MBT wastes

    Energy Technology Data Exchange (ETDEWEB)

    Siddiqui, A.A., E-mail: aasiddiqui.cv@amu.ac.in [Department of Civil Engineering, Aligarh Muslim University, Aligarh 202002 (India); Richards, D.J.; Powrie, W. [Waste Management Research Group, Faculty of Engineering and the Environment, University of Southampton, Southampton SO17 1BJ (United Kingdom)

    2013-11-15

    Highlights: • Stabilization was achieved for MBT wastes of different degrees of pretreatment. • About 92% reduction in the gas generation compared with raw MSW. • Pretreatment resulted in reduced TOC, nitrogen and heavy metals in leachate. • A large proportion of carbon and nitrogen remained in the waste material. - Abstract: Mechanical–biological treatment (MBT) processes are increasingly being adopted as a means of diverting biodegradable municipal waste (BMW) from landfill, for example to comply with the EU Landfill Directive. However, there is considerable uncertainty concerning the residual pollution potential of such wastes. This paper presents the results of laboratory experiments on two different MBT waste residues, carried out to investigate the remaining potential for the generation of greenhouse gases and the flushing of contaminants from these materials when landfilled. The potential for gas generation was found to be between 8% and 20% of that for raw MSW. Pretreatment of the waste reduced the potential for the release of organic carbon, ammoniacal nitrogen, and heavy metal contents into the leachate; and reduced the residual carbon remaining in the waste after final degradation from ∼320 g/kg dry matter for raw MSW to between 183 and 195 g/kg dry matter for the MBT wastes.

  20. 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)

  1. Drug-laden 3D biodegradable label using QR code for anti-counterfeiting of drugs.

    Science.gov (United States)

    Fei, Jie; Liu, Ran

    2016-06-01

    Wiping out counterfeit drugs is a great task for public health care around the world. The boost of these drugs makes treatment to become potentially harmful or even lethal. In this paper, biodegradable drug-laden QR code label for anti-counterfeiting of drugs is proposed that can provide the non-fluorescence recognition and high capacity. It is fabricated by the laser cutting to achieve the roughness over different surface which causes the difference in the gray levels on the translucent material the QR code pattern, and the micro mold process to obtain the drug-laden biodegradable label. We screened biomaterials presenting the relevant conditions and further requirements of the package. The drug-laden microlabel is on the surface of the troches or the bottom of the capsule and can be read by a simple smartphone QR code reader application. Labeling the pill directly and decoding the information successfully means more convenient and simple operation with non-fluorescence and high capacity in contrast to the traditional methods. PMID:27040262

  2. Polycyclic aromatic hydrocarbon biodegradation and extracellular enzyme secretion in agitated and stationary cultures of Phanerochaete chrysosporium

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The extracellular enzyme secretion and biodegradation of polycyclic aromatic hydrocarbons (PAHs) were studied in agitated and shallow stationary liquid cultures of Phanerochaete chrysosporium. Veratryl alcohol and Tween80 were added to cultures as lignin peroxidase (LiP) and manganese peroxidase (MnP) inducer, respectively. Shallow stationary cultures were suitable for the production of enzyme, whereas agitated cultures enhanced overall biodegradation by facilitating interphase mass transfer of PAH into aqueous phases. The use of a LiP stimulator, veratryl alcohol, did not increase PAH degradation but significantly enhanced LiP activity. In contrast, Tween80 increased both MnP secretion and PAH degradation in shallow stationary cultures. On the other hand, high PAH degradation was observed in agitated cultures in the absence of detectable LiP and MnP activities. The results suggested that extracellular peroxidase activities are not directly related to the PAH degradation, and the increased solubility rather than enzyme activity may be more important in the promotion of PAH degradation.

  3. Hydrogen Isotope Fractionation As a Tool to Identify Aerobic and Anaerobic PAH Biodegradation.

    Science.gov (United States)

    Kümmel, Steffen; Starke, Robert; Chen, Gao; Musat, Florin; Richnow, Hans H; Vogt, Carsten

    2016-03-15

    Aerobic and anaerobic polycyclic aromatic hydrocarbon (PAH) biodegradation was characterized by compound specific stable isotope analysis (CSIA) of the carbon and hydrogen isotope effects of the enzymatic reactions initiating specific degradation pathways, using naphthalene and 2-methylnaphtalene as model compounds. Aerobic activation of naphthalene and 2-methylnaphthalene by Pseudomonas putida NCIB 9816 and Pseudomonas fluorescens ATCC 17483 containing naphthalene dioxygenases was associated with moderate carbon isotope fractionation (εC = -0.8 ± 0.1‰ to -1.6 ± 0.2‰). In contrast, anaerobic activation of naphthalene by a carboxylation-like mechanism by strain NaphS6 was linked to negligible carbon isotope fractionation (εC = -0.2 ± 0.2‰ to -0.4 ± 0.3‰). Notably, anaerobic activation of naphthalene by strain NaphS6 exhibited a normal hydrogen isotope fractionation (εH = -11 ± 2‰ to -47 ± 4‰), whereas an inverse hydrogen isotope fractionation was observed for the aerobic strains (εH = +15 ± 2‰ to +71 ± 6‰). Additionally, isotope fractionation of NaphS6 was determined in an overlaying hydrophobic carrier phase, resulting in more reliable enrichment factors compared to immobilizing the PAHs on the bottle walls without carrier phase. The observed differences especially in hydrogen fractionation might be used to differentiate between aerobic and anaerobic naphthalene and 2-methylnaphthalene biodegradation pathways at PAH-contaminated field sites. PMID:26855125

  4. Controlled release profiles of dipyridamole from biodegradable microspheres on the base of poly(3-hydroxybutyrate.

    Directory of Open Access Journals (Sweden)

    2007-12-01

    Full Text Available Novel biodegradable microspheres on the base of poly(3-hydroxybutyrate (PHB designed for controlled release of antithrombotic drug, namely dipyridamole (DPD, have been kinetically studied. The profiles of release from the microspheres with different diameters 4, 9, 63, and 92 µm present the progression of nonlinear and linear stages. Diffusionkinetic equation describing both linear (PHB hydrolysis and nonlinear (diffusion stages of the DPD release profiles from the spherical subjects has been written down as the sum of two terms: desorption from the homogeneous sphere in accordance with diffusion mechanism and the zero-order release. In contrast to the diffusivity dependence on microsphere size, the constant characteristics (k of linearity are scarcely affected by the diameter of PHB microparticles. The view of the kinetic profiles as well as the low rate of DPD release are in satisfactory agreement with kinetics of weight loss measured in vitro for the PHB films. Taking into account kinetic results, we suppose that the degradation of both films and PHB microspheres is responsible for the linear stage of DPD release profiles. In the nearest future, combination of biodegradable PHB and DPD as a representative of proliferation cell inhibitors will give possibility to elaborate the novel injectable therapeutic system for a local, long-term, antiproliferative action.

  5. Biodegradation: Updating the Concepts of Control for Microbial Cleanup in Contaminated Aquifers

    DEFF Research Database (Denmark)

    Meckenstock, Rainer U.; Elsner, Martin; Griebler, Christian;

    2015-01-01

    Biodegradation is one of the most favored and sustainable means of removing organic pollutants from contaminated aquifers but the major steering factors are still surprisingly poorly understood. Growing evidence questions some of the established concepts for control of biodegradation. Here, we cr...... on the controls of biodegradation in contaminant plumes. These include the plume fringe concept, transport limitations, and transient conditions as currently underestimated processes affecting biodegradation....... critically discuss classical concepts such as the thermodynamic redox zonation, or the use of steady state transport scenarios for assessing biodegradation rates. Furthermore, we discuss if the absence of specific degrader populations can explain poor biodegradation. We propose updated perspectives...

  6. 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.

  7. 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.

  8. SANS contrast variation method applied in experiments on ferrofluids at MURN instrument of IBR-2 reactor

    Science.gov (United States)

    Balasoiu, Maria; Kuklin, Alexander

    2012-03-01

    Separate determination of the nuclear and magnetic contributions to the scattering intensity by means of a contrast variation method applied in a small angle neutron scattering experiment of nonpolarized neutrons in ferrofluids in early 90 's at the MURN instrument is reviewed. The nuclear scattering contribution gives the features of the colloidal particle dimensions, surfactant shell structure and the solvent degree penetration to the macromolecular layer. The magnetic scattering part is compatible to the models where is supposed that the particle surface has a nonmagnetic layer. Details on experimental "Grabcev method" in obtaining separate nuclear and magnetic contributions to the small angle neutron scattering intensity of unpolarized neutrons are emphasized for the case of a high quality ultrastabile benzene-based ferrofluid with magnetite nanoparticles.

  9. Nitrogen limitation in natural populations of cyanobacteria (Spirulina and Oscillatoria spp.) and its effect on macromolecular synthesis

    International Nuclear Information System (INIS)

    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 14C 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

  10. 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...

  11. Mycelium-Like Networks Increase Bacterial Dispersal, Growth, and Biodegradation in a Model Ecosystem at Various Water Potentials.

    Science.gov (United States)

    Worrich, Anja; König, Sara; Miltner, Anja; Banitz, Thomas; Centler, Florian; Frank, Karin; Thullner, Martin; Harms, Hauke; Kästner, Matthias; Wick, Lukas Y

    2016-05-15

    Fungal mycelia serve as effective dispersal networks for bacteria in water-unsaturated environments, thereby allowing bacteria to maintain important functions, such as biodegradation. However, poor knowledge exists on the effects of dispersal networks at various osmotic (Ψo) and matric (Ψm) potentials, which contribute to the water potential mainly in terrestrial soil environments. Here we studied the effects of artificial mycelium-like dispersal networks on bacterial dispersal dynamics and subsequent effects on growth and benzoate biodegradation at ΔΨo and ΔΨm values between 0 and -1.5 MPa. In a multiple-microcosm approach, we used a green fluorescent protein (GFP)-tagged derivative of the soil bacterium Pseudomonas putida KT2440 as a model organism and sodium benzoate as a representative of polar aromatic contaminants. We found that decreasing ΔΨo and ΔΨm values slowed bacterial dispersal in the system, leading to decelerated growth and benzoate degradation. In contrast, dispersal networks facilitated bacterial movement at ΔΨo and ΔΨm values between 0 and -0.5 MPa and thus improved the absolute biodegradation performance by up to 52 and 119% for ΔΨo and ΔΨm, respectively. This strong functional interrelationship was further emphasized by a high positive correlation between population dispersal, population growth, and degradation. We propose that dispersal networks may sustain the functionality of microbial ecosystems at low osmotic and matric potentials. PMID:26944849

  12. Role of microbial adhesion in phenanthrene biodegradation by Pseudomonas fluorescens LP6a

    Science.gov (United States)

    Abbasnezhad, Hassan

    Biodegradation of poorly water soluble hydrocarbons, such as n-alkanes and polycyclic aromatic hydrocarbons (PAHs) is often limited by the low availability of the pollutant to microbes. Adhesion of microorganisms to the oil-water interface can influence this availability. Our approach was to study a range of compounds and mechanisms to promote the adhesion of a hydrophilic PAH degrading bacterium, Pseudomonas fluorescens LP6a, to an oil-water interface and examine the effect on biodegradation of phenanthrene by the bacteria. The cationic surfactants cetylpyridinium chloride (CPC), poly-L-lysine and chlorhexidine gluconate (CHX) and the long chain alcohols 1-dodecanol, 2-dodecanol and farnesol increased the adhesion of P. fluorescens LP6a to n-hexadecane from ca. 30% to ca. 90% of suspended cells adhering. The alcohols also caused a dramatic change in the oil-water contact angle of the cell surface, increasing it from 24° to 104°, whereas the cationic compounds had little effect. In contrast, cationic compounds changed the electrophoretic mobility of the bacteria, reducing the mean zeta potential from --23 to --7 mV in 0.01M potassium phosphate buffer, but the alcohols had no effect on zeta potential. This results illustrate that alcohols acted through altering the cell surface hydrophobicity, whereas cationic surfactants changed the surface charge density. Phenanthrene was dissolved in heptamethylnonane and introduced to the aqueous growth medium, hence forming a two phase system. Introducing 1-dodecanol at concentrations of 217, 820 or 4100 mg/L resulted in comparable increases in phenanthrene biodegradation of about 30% after 120 h incubation with non-induced cultures. After 100 h of incubation with LP6a cultures induced with 2-aminobenzoate, 4.5% of the phenanthrene was mineralized by cultures versus more than 10% by the cultures containing initial 1-dodecanol or 2-dodecanol concentrations of 120 or 160 mg/L. The production and accumulation of metabolites in

  13. Ionic versus nonionic contrast use.

    Science.gov (United States)

    Stolberg, H O; McClennan, B L

    1991-01-01

    It has taken many years of research, development and intense scientific investigation to produce intravascular contrast media. Research on relations between chemical structure, animal toxicity, and water-solubility has produced a number of highly water-soluble, iodinated compounds for use in diagnostic radiology as intravascular contrast agents. The currently used intravascular agents may be classified into four groups according to their chemical structure: 1. Ionic monomers 2. Ionic monoacid dimers 3. Nonionic monomers 4. Nonionic dimers It is the objective of this publication to review the history and development of intravascular contrast media as well as their properties, general effects and clinical use. The four types of contrast media differ significantly in their chemical structure and physico-chemical properties, and these differences determine their osmotoxicity, chemotoxicity, and ion toxicity. We analyze the organ specific toxic effects of intravascular contrast media upon the central nervous system, the cardiovascular system, and the renal system. We also review the secondary effects, clinical manifestations, and the incidence of adverse events associated with different types of contrast. The choice of contrast media has become critical since the introduction of nonionic agents because their toxicological and pharmacological properties differ from those of the ionic agents. The application of basic concepts involved in the use of contrast media in excretory urography, computed tomography, angiography, and angiocardiography is discussed, and the advantages of the use of nonionic contrast agents are outlined. Economic and ethical issues are presented with emphasis upon strategies to reduce the risk associated with the injection of intravascular contrast and to curtail consumption according to rational principles of use. PMID:2049958

  14. 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

  15. 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

  16. Photon-counting single-molecule spectroscopy for studying conformational dynamics and macromolecular interactions

    International Nuclear Information System (INIS)

    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

  17. 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

  18. Biodegradation of methyl parathion by Acinetobacter radioresistens USTB-04

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Biodegradation of methyl parathion (MP), a widely used organophosphorus pesticide, was investigated using a newly isolated bacterium strain Acinetobacter radioresistens USTB-04. MP at an initial concentration of 1200 mg/L could be totally biodegraded by A. radioresistens USTB-04 as the sole carbon source less than 4 d in the presence of phosphate and urea as phosphorus and nitrogen sources, respectively. Biodegradation of MP was also achieved using cell-free extract of A. radioresistens USTB-04. MP at an initial concentration of 130 mg/L was completely biodegraded in 2 h in the presence of cell-free extract with a protein concentration of 148.0mg/L, which was increased with the increase of pH from 5.0 to 8.0. Contrary to published reports, no intermediate or final degradation metabolites of MP could be observed. Thus we suggest that the cleavage of C-C bond on the benzene ring other than P-O bond may be the biodegradation pathway of MP by A. radioresistens USTB-04.

  19. Study on biodegradation process of lignin by FTIR and DSC.

    Science.gov (United States)

    Liu, Yang; Hu, Tianjue; Wu, Zhengping; Zeng, Guangming; Huang, Danlian; Shen, Ying; He, Xiaoxiao; Lai, Mingyong; He, Yibin

    2014-12-01

    The biodegradation process of lignin by Penicillium simplicissimum was studied to reveal the lignin biodegradation mechanisms. The biodegradation products of lignin were detected using Fourier transform infrared spectroscopy (FTIR), UV-Vis spectrophotometer, different scanning calorimeter (DSC), and stereoscopic microscope. The analysis of FTIR spectrum showed the cleavage of various ether linkages (1,365 and 1,110 cm(-1)), oxidation, and demethylation (2,847 cm(-1)) by comparing the different peak values in the corresponding curve of each sample. Moreover, the differences (Tm and ΔHm values) between the DSC curves indirectly verified the FTIR analysis of biodegradation process. In addition, the effects of adding hydrogen peroxide (H2O2) to lignin biodegradation process were analyzed, which indicated that H2O2 could accelerate the secretion of the MnP and LiP and improve the enzymes activity. What is more, lignin peroxidase and manganese peroxidase catalyzed the lignin degradation effectively only when H2O2 was presented.

  20. Biodegradable HEMA-based hydrogels with enhanced mechanical properties.

    Science.gov (United States)

    Moghadam, Mohamadreza Nassajian; Pioletti, Dominique P

    2016-08-01

    Hydrogels are widely used in the biomedical field. Their main purposes are either to deliver biological active agents or to temporarily fill a defect until they degrade and are followed by new host tissue formation. However, for this latter application, biodegradable hydrogels are usually not capable to sustain any significant load. The development of biodegradable hydrogels presenting load-bearing capabilities would open new possibilities to utilize this class of material in the biomedical field. In this work, an original formulation of biodegradable photo-crosslinked hydrogels based on hydroxyethyl methacrylate (HEMA) is presented. The hydrogels consist of short-length poly(2-hydroxyethyl methacrylate) (PHEMA) chains in a star shape structure, obtained by introducing a tetra-functional chain transfer agent in the backbone of the hydrogels. They are cross-linked with a biodegradable N,O-dimethacryloyl hydroxylamine (DMHA) molecule sensitive to hydrolytic cleavage. We characterized the degradation properties of these hydrogels submitted to mechanical loadings. We showed that the developed hydrogels undergo long-term degradation and specially meet the two essential requirements of a biodegradable hydrogel suitable for load bearing applications: enhanced mechanical properties and low molecular weight degradation products. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 104B: 1161-1169, 2016. PMID:26061346