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Sample records for macromolecular contrast medium

  1. Macromolecular and Dendrimer Based Magnetic Resonance Contrast Agents

    PubMed Central

    Bumb, Ambika; Brechbiel, Martin W.; Choyke, Peter

    2010-01-01

    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. PMID:20590365

  2. Chlorotoxin-modified macromolecular contrast agent for MRI tumor diagnosis.

    PubMed

    Huang, Rongqin; Han, Liang; Li, Jianfeng; Liu, Shuhuan; Shao, Kun; Kuang, Yuyang; Hu, Xing; Wang, Xuxia; Lei, Hao; Jiang, Chen

    2011-08-01

    Clinical diagnosis of cancers using magnetic resonance imaging (MRI) is highly dependent on contrast agents, especially for brain tumors which contain blood-brain barrier (BBB) at the early stage. However, currently mostly used low molecular weight contrast agents such as Gd-DTPA suffer from rapid renal clearance, non-specificity, and low contrast efficiency. The aim of this paper is to investigate the potential of a macromolecular MRI contrast agent based on dendrigraft poly-l-lysines (DGLs), using chlorotoxin (CTX) as a tumor-specific ligand. The contrast agent using CTX-modified conjugate as the main scaffold and Gd-DTPA as the payload was successfully synthesized. The results of fluorescent microscopy showed that the modification of CTX could markedly enhance the cellular uptake in C6 glioma and liver tumor cell lines, but not in normal cell line. Significantly increased accumulation of CTX-modified conjugate within glioma and liver tumor was further demonstrated in tumor-bearing nude mice using in vivo imaging system. The MRI results showed that the signal enhancement of mice treated with CTX-modified contrast reached peak level at 5 min for both glioma and liver tumor, 144.97% ± 19.54% and 158.69% ± 12.41%, respectively, significantly higher than that of unmodified counterpart and commercial control. And most importantly, the signal enhancement of CTX-modified contrast agent maintained much longer compared to that of controls, which might be useful for more exact diagnosis for tumors. CTX-modified dendrimer-based conjugate might be applied as an efficient MRI contrast agent for targeted and accurate tumor diagnosis. This finding is especially important for tumors such as brain glioma which is known hard to be diagnosed due to the presence of BBB. PMID:21531455

  3. Tumor Characterization with Dynamic Contrast Enhanced Magnetic Resonance Imaging and Biodegradable Macromolecular Contrast Agents in Mice

    PubMed Central

    Wu, Xueming; Feng, Yi; Jeong, Eun-Kee; Emerson, Lyska; Lu, Zheng-Rong

    2009-01-01

    Purpose To investigate the efficacy of polydisulfide-based biodegradable macromolecular contrast agents of different degradability and molecular weight for tumor characterization based on angiogenesis using dynamic contrast enhanced MRI (DCE-MRI). Methods Biodegradable macromolecular MRI contrast agents, GDCC and GDCP, with molecular weight of 20 and 70 KDa were evaluated for tumor characterization. The DCE-MRI studies were performed in nude mice bearing MDA PCa 2b and PC-3 human prostate tumor xenografts. Tumor angiogenic kinetic parameters, endothelium transfer coefficient (Ktrans) and fractional tumor plasma volume (fPV), were calculated from the DCE-MRI data using a two-compartment model. Results There was no significant difference in the fPV values between two tumor models estimated with the same agent except for GDCC-70. The Ktrans values in both tumor models decreased with increasing molecular weight of the agents. GDCC-70 showed a higher Ktrans values than GDCP-70 due to high degradability of the former in both tumor models (p < 0.05). The Ktrans values of MDA PCa 2b tumors were significantly higher than those of PC-3 tumors estimated by Gd(DTPA-BMA), GDCC-20, GDCC-70, GDCP-70, and albumin-(Gd-DTPA) (p < 0.05). Conclusions The polydisulfide based biodegradable macromolecular MRI contrast agents are promising in tumor characterization with dynamic contrast enhanced MRI. PMID:19597972

  4. A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography.

    PubMed

    Chatake, Toshiyuki; Fujiwara, Satoru

    2016-01-01

    A difference in the neutron scattering length between hydrogen and deuterium leads to a high density contrast in neutron Fourier maps. In this study, a technique for determining the deuterium/hydrogen (D/H) contrast map in neutron macromolecular crystallography is developed and evaluated using ribonuclease A. The contrast map between the D2O-solvent and H2O-solvent crystals is calculated in real space, rather than in reciprocal space as performed in previous neutron D/H contrast crystallography. The present technique can thus utilize all of the amplitudes of the neutron structure factors for both D2O-solvent and H2O-solvent crystals. The neutron D/H contrast maps clearly demonstrate the powerful detectability of H/D exchange in proteins. In fact, alternative protonation states and alternative conformations of hydroxyl groups are observed at medium resolution (1.8 Å). Moreover, water molecules can be categorized into three types according to their tendency towards rotational disorder. These results directly indicate improvement in the neutron crystal structure analysis. This technique is suitable for incorporation into the standard structure-determination process used in neutron protein crystallography; consequently, more precise and efficient determination of the D-atom positions is possible using a combination of this D/H contrast technique and standard neutron structure-determination protocols. PMID:26894536

  5. Alk5 inhibition increases delivery of macromolecular and protein-bound contrast agents to tumors

    PubMed Central

    Daldrup-Link, Heike E.; Mohanty, Suchismita; Ansari, Celina; Lenkov, Olga; Shaw, Aubie; Ito, Ken; Hong, Su Hyun; Hoffmann, Matthias; Pisani, Laura; Boudreau, Nancy; Gambhir, Sanjiv Sam; Coussens, Lisa M.

    2016-01-01

    Limited transendothelial permeability across tumor microvessels represents a significant bottleneck in the development of tumor-specific diagnostic agents and theranostic drugs. Here, we show an approach to increase transendothelial permeability of macromolecular and nanoparticle-based contrast agents via inhibition of the type I TGF-β receptor, activin-like kinase 5 (Alk5), in tumors. Alk5 inhibition significantly increased tumor contrast agent delivery and enhancement on imaging studies, while healthy organs remained relatively unaffected. Imaging data correlated with significantly decreased tumor interstitial fluid pressure, while tumor vascular density remained unchanged. This immediately clinically translatable concept involving Alk5 inhibitor pretreatment prior to an imaging study could be leveraged for improved tumor delivery of macromolecular and nanoparticle-based imaging probes and, thereby, facilitate development of more sensitive imaging tests for cancer diagnosis, enhanced tumor characterization, and personalized, image-guided therapies. PMID:27182558

  6. Preclinical evaluation of biodegradable macromolecular contrast agents for magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Feng, Yi

    Macromolecular contrast agents have been shown to be superior to small molecular weight contrast agents for MRI in blood pool imaging, tumor diagnosis and grading. However, none has been approved by the FDA because they circulate in the bloodstream much longer than small molecular weight contrast agents and result in high tissue accumulation of toxic Gd(III) ions. Biodegradable macromolecular contrast agents (BMCA) were invented to alleviate the toxic accumulation. They have a cleavable disulfide bond based backbone that can be degraded in vivo and excreted out of the body via renal filtration. Furthermore, the side chain of the backbone can be modified to achieve various degradation rates. Three BMCA, (Gd-DTPA)-cystamine copolymers (GDCC), Gd-DTPA cystine copolymers (GDCP), and Gd-DTPA cystine diethyl ester copolymers (GDCEP), were evaluated as blood pool contrast agents in a rat model. They have excellent blood pool enhancement, preferred pharmacokinetics, and only minimal long-term tissue retention of toxic Gd(III) ions. GDCC and GDCP, the lead agents with desired degradation rates, with molecular weights of 20 KDa and 70 KDa, were chosen for dynamic contrast enhanced MRI (DCE-MRI) to differentiate human prostate tumor models of different malignancy and growth rates. GDCC and GDCP could differentiate these tumor models, providing more accurate estimations of plasma volume, flow leakage rate, and permeability surface area product than a small molecular weight contrast agent Gd-DTPA-BMA when compared to the prototype macromolecular contrast agent albumin-Gd-DTPA. GDCC was favored for its neutral charge side chain and reasonable uptake rate by the tumors. GDCC with a molecular weight of 40 KDa (GDCC-40, above the renal filtration cutoff size) was used to assess the efficacy of two photothermal therapies (interstitial and indocyanine green enhanced). GDCC-40 provided excellent tumor enhancement shortly after its injection. Acute tumor response (4 hr) after therapies

  7. Contrast Medium-Induced Acute Kidney Injury

    PubMed Central

    Sadat, Umar; Usman, Ammara; Boyle, Jonathan R.; Hayes, Paul D.; Solomon, Richard J.

    2015-01-01

    Contrast medium-induced acute kidney injury (CI-AKI) is a predominant cause of hospital-acquired renal insufficiency. With an increasing number of contrast medium-enhanced radiological procedures being performed in a rapidly increasing ageing population in the Western world, it is imperative that more attention is given to understand the aetiology of CI-AKI to devise novel diagnostic methods and to formulate effective prophylactic and therapeutic regimens to reduce its incidence and its associated morbidity and mortality. This article presents high-yield information on the above-mentioned aspects of CI-AKI, primarily based on results of randomised controlled trials, meta-analyses, systematic reviews and international consensus guidelines. PMID:26195974

  8. Contrast medium usage reduction in abdominal computed tomography by using high-iodinated concentration contrast medium

    NASA Astrophysics Data System (ADS)

    Suwannasri, A.; Kaewlai, R.; Asavaphatiboon, S.

    2016-03-01

    This study was to determine if administration of a low volume high-concentration iodinated contrast medium can preserve image quality in comparison with regular-concentration intravenous contrast medium in patient undergoing contrast-enhancement abdominal computed tomography (CT). Eighty-four patients were randomly divided into 3 groups of similar iodine delivery rate; A: 1.2 cc/kg of iomeprol-400, B: 1.0 cc/kg of iomeprol-400 and C: 1.5 cc/kg of ioversol-350. Contrast enhancement of the liver parenchyma, pancreas and aorta was quantitatively measured in Hounsfield units and qualitative assessed by a radiologist. T-test was used to evaluate contrast enhancement, and Chi-square test was used to evaluate qualitative image assessment, at significance level of 0.05 with 95% confidence intervals. There were no statistically significant differences in contrast enhancement of liver parenchyma and pancreas between group A and group C in both quantitative and qualitative analyses. Group C showed superior vascular enhancement to group A and B on quantitative analysis.

  9. [Lethal reaction after contrast medium administration].

    PubMed

    Risgaard, Ole; Søe, Charlotte Krabbe; Zejden, Anna

    2008-04-21

    A 49-year-old healthy woman was admitted after a horse-riding accident. On arrival to the emergency department she complained of lower abdominal pain. A CT-scan of the abdomen with non ionic contrast media (iomeprol, 150 ml 4 ml/s) was conducted. The patient died nine hours later due to an anaphylactoid reaction to radio contrast media. The autopsy showed pulmonary oedema and pleural effusion, but did not show any sign of trauma. Early interventions with appropriate therapy had no effect on the fatal outcome. PMID:18462629

  10. A neutral polydisulfide containing Gd(III) DOTA monoamide as a redox-sensitive biodegradable macromolecular MRI contrast agent.

    PubMed

    Ye, Zhen; Zhou, Zhuxian; Ayat, Nadia; Wu, Xueming; Jin, Erlei; Shi, Xiaoyue; Lu, Zheng-Rong

    2016-01-01

    This work aims to develop safe and effective gadolinium (III)-based biodegradable macromolecular MRI contrast agents for blood pool and cancer imaging. A neutral polydisulfide containing macrocyclic Gd-DOTA monoamide (GOLS) was synthesized and characterized. In addition to studying the in vitro degradation of GOLS, its kinetic stability was also investigated in an in vivo model. The efficacy of GOLS for contrast-enhanced MRI was examined with female BALB/c mice bearing 4T1 breast cancer xenografts. The pharmacokinetics, biodistribution, and metabolism of GOLS were also determined in mice. GOLS has an apparent molecular weight of 23.0 kDa with T1 relaxivities of 7.20 mM(-1) s(-1) per Gd at 1.5 T, and 6.62 mM(-1) s(-1) at 7.0 T. GOLS had high kinetic inertness against transmetallation with Zn(2+) ions, and its polymer backbone was readily cleaved by L-cysteine. The agent showed improved efficacy for blood pool and tumor MR imaging. The structural effect on biodistribution and in vivo chelation stability was assessed by comparing GOLS with Gd(HP-DO3A), a negatively charged polydisulfide containing Gd-DOTA monoamide GODC, and a polydisulfide containing Gd-DTPA-bisamide (GDCC). GOLS showed high in vivo chelation stability and minimal tissue deposition of gadolinium. The biodegradable macromolecular contrast agent GOLS is a promising polymeric contrast agent for clinical MR cardiovascular imaging and cancer imaging. PMID:26218648

  11. The use of a radiopaque contrast medium in endodontic radiography.

    PubMed

    Shearer, A C; Wasti, F; Wilson, N H

    1996-03-01

    A series of in vitro studies were carried out to investigate the use and application of a radiopaque contrast medium in conventional periapical dental radiography for the diagnosis and evaluation of root canal systems. The water-soluble radiopaque contrast medium was introduced into the root canals of 30 first permanent maxillary and 30 first permanent mandibular molar teeth. The radiographic images of these teeth with and without radiopaque contrast medium in the root canal systems were compared and contrasted. Further comparisons were made with the same teeth rendered transparent. The results indicate that by standardizing the diagnostic criteria the inter-examiner reliability was in good agreement; it was independent of the radiographic technique used. The validity of the radiographs was enhanced by the use of the radiopaque contrast medium. The results confirm that, with the use of a radiopaque contrast medium, images of root canal systems are easier to read and interpret than plain radiographic images of root canal systems. The use of radiopaque contrast medium in endodontic radiography may be a valuable aid in the diagnosis and evaluation of root canal systems. This system would complement rather than replace plain radiography. PMID:9206431

  12. Accuracy of digital videodensitometry in quantitating contrast medium concentration.

    PubMed

    Yang, X M; Manninen, H; Ji, H X; Vainio, P; Soimakallio, S

    1994-07-01

    To evaluate the accuracy of digital videodensitometric technique in directly quantitating concentration of contrast medium, iohexol 300 mg I/ml was injected into a 2-mm-diameter plastic tube, in which clean water was circulated at a 190 ml/min flow, for digital subtraction angiography. Altogether 27 injections were performed with 3, 4 and 5 ml volumes at 3-, 4- and 5-ml/s flows of the contrast medium. A time-density curve was achieved by selecting a "vessel" region of interest (ROI) and a background ROI. Then, a frame corresponding to the maximum opacification of the contrast medium could be calculated. Finally, the average density and the time to peak density of the contrast medium were obtained. The average density was statistically higher (p < 0.01) with 5 ml/s flow than with 4- and 3-ml/s flows. Times to peak density reduced as injection flows or volumes increased. The results support the conclusion that digital videodensitometric technique is an accurate method for quantitation of contrast medium concentration during angiography. The angiographic opacification may be improved by injecting the iodine contrast medium with higher flows or larger volumes. PMID:8011389

  13. Dynamic Contrast-Enhanced MRI Using a Macromolecular MR Contrast Agent (P792): Evaluation of Antivascular Drug Effect in a Rabbit VX2 Liver Tumor Model

    PubMed Central

    Park, Hee Sun; Lee, Jeong Min; Kim, Young Il; Woo, Sungmin; Yoon, Jung Hwan; Choi, Jin-Young; Choi, Byung Ihn

    2015-01-01

    Objective 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. Materials and Methods 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. Results 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. Conclusion 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. PMID:26357497

  14. Contrast-Medium-Enhanced Digital Mammography: Contrast vs. Iodine Concentration Phantom Calibration

    SciTech Connect

    Rosado-Mendez, I.; Brandan, M. E.; Villasenor, Y.; Benitez-Bribiesca, L.

    2008-08-11

    This work deals with the application of the contrast-medium-enhanced digital subtraction mammography technique in order to calibrate the contrast level in subtracted phantom images as function of iodine concentration to perform dynamic studies of the contrast-medium uptake in the breast. Previously optimized dual-energy temporal subtraction modalities were used (a) to determine radiological parameters for a dynamic clinical study composed of 1 mask+3 post-contrast images limiting the total mean glandular dose to 2.5 mGy, and (b) to perform a contrast vs iodine concentration calibration using a custom-made phantom. Calculated exposure values were applied using a commercial full-field digital mammography unit. Contrast in subtracted phantom images (one mask and one post-CM) is linear as function of iodine concentration, although the sensitivity (contrast per iodine concentration) decreases beyond 8 mg/mL. This calibration seems to apply only to thin and normal thickness breasts.

  15. Targeting cancer chemotherapeutic agents by use of lipiodol contrast medium

    SciTech Connect

    Konno, T. )

    1990-11-01

    Arterially administered Lipiodol Ultrafluid contrast medium selectively remained in various malignant solid tumors because of the difference in time required for the removal of Lipiodol contrast medium from normal capillaries and tumor neovasculature. Although blood flow was maintained in the tumor, even immediately after injection Lipiodol contrast medium remained in the neovasculature of the tumor. To target anti-cancer agents to tumors by using Lipiodol contrast medium as a carrier, the characteristics of the agents were examined. Anti-cancer agents had to be soluble in Lipiodol, be stable in it, and separate gradually from it so that the anti-cancer agents would selectively remain in the tumor. These conditions were found to be necessary on the basis of the measurement of radioactivity in VX2 tumors implanted in the liver of 16 rabbits that received arterial injections of 14C-labeled doxorubicin. Antitumor activities and side effects of arterial injections of two types of anti-cancer agents were compared in 76 rabbits with VX2 tumors. Oily anti-cancer agents that had characteristics essential for targeting were compared with simple mixtures of anti-cancer agents with Lipiodol contrast medium that did not have these essential characteristics. Groups of rabbits that received oily anti-cancer agents responded significantly better than groups that received simple mixtures, and side effects were observed more frequently in the groups that received the simple mixtures. These results suggest that targeting of the anti-cancer agent to the tumor is important for treatment of solid malignant tumors.

  16. Transient oxygen desaturation following radiographic contrast medium administration.

    PubMed

    Neagley, S R; Vought, M B; Weidner, W A; Zwillich, C W

    1986-06-01

    To determine if angiography results in arterial oxygen desaturation, we prospectively studied 40 clinically stable patients undergoing arterial angiography. Arterial oxygen saturation (Sao2) was monitored before, during, and for at least three minutes after contrast medium injection. The mean (+/- SEM) Sao2 was 94.2% +/- 0.39% before injection and fell to 92.6% +/- 0.66% following injection. Eleven patients (28%) demonstrated a decrease in Sao2 of more than 3%, with six (15%) having a postinjection Sao2 of less than 90%. To determine if the vascular route of injected contrast medium influenced the subsequent level of oxygenation, we similarly evaluated the Sao2 of 20 consecutive patients undergoing venous angiography. The Sao2 was 94.2% +/- 0.33% before contrast medium injection and fell to 92.5% +/- 0.78% following injection. Six patients (30%) experienced a fall in Sao2 of more than 3%, with four (20%) having a postinjection Sao2 of less than 90%. We conclude that arterial oxygen desaturation occurs frequently in patients undergoing angiography. PMID:3718095

  17. INTRAARTERIAL INJECTION OF IODINATED CONTRAST MEDIUM FOR CONTRAST ENHANCED COMPUTED TOMOGRAPHY OF THE EQUINE HEAD.

    PubMed

    Carmalt, James L; Montgomery, James

    2015-01-01

    Minimizing the volume of contrast administered for contrast-enhanced computed tomography (CT) of the equine head is desirable for reducing costs and risks of adverse reactions, however evidence-based studies on the effects of varying volumes on image quality are currently lacking. The objective of the current study was to determine whether low-volume intraarterial administration of contrast medium would result in an equivalent image quality and tissue attenuation vs. high-volume intravenous bolus administration. A prospective cross-over experimental design was used in a sample of six horses. After anesthetic induction, the right carotid artery was exposed surgically and catheterized. Four CT scans of the cranium were performed for each horse: baseline, immediately following intraarterial contrast injection, five-min postinjection (return to baseline) and a final scan after intravenous contrast administration. Soft tissue attenuation in predetermined regions of interest (ROI); and length, width, and height measurements of the pituitary gland were recorded at each time point. Horses were euthanized and measurements of the pituitary gland were repeated postmortem. No adverse reactions to contrast administration were observed. Intraarterial and intravenous administration of contrast medium resulted in significantly greater soft tissue enhancement of some brain ROI's and the pituitary gland vs. baseline values. Pituitary gland measurements made on postcontrast CT images did not differ from those obtained during postmortem examination. Findings indicated that low-dose intraarterial administration of contrast material in the equine head resulted in comparable soft tissue enhancement vs. high volume intravenous administration. PMID:25782997

  18. Reduction of iodinated contrast medium in CT: feasibility study

    NASA Astrophysics Data System (ADS)

    Nasirudin, Radin A.; Mei, Kai; Kopp, Felix K.; Penchev, Petar; Rummeny, Ernst J.; Fiebich, Martin; Noël, Peter B.

    2015-03-01

    In CT, the magnitude of enhancement is proportional to the amount of contrast medium (CM) injected. However, high doses of iodinated CM pose health risks, ranging from mild side effects to serious complications such as contrast-induced nephropathy (CIN). This work presents a method that enables the reduction of CM dosage, without affecting the diagnostic image quality. The technique proposed takes advantage of the additional spectral information provided by photon-counting CT systems. In the first step, we apply a material decomposition technique on the projection data to discriminate iodine from other materials. Then, we estimated the noise of the decomposed image by calculating the Cramér-Rao lower bound of the parameter estimator. Next, we iteratively reconstruct the iodine-only image by using the decomposed image and the estimation of noise as an input into a maximum-likelihood iterative reconstruction algorithm. Finally, we combine the iodine-only image with the original image to enhance the contrast of low iodine concentrations. The resulting reconstructions show a notably improved contrast in the final images. Quantitatively, the combined image has a significantly improved CNR, while the measured concentrations are closer to the actual concentrations of the iodine. The preliminary results from our technique show the possibility of reducing the clinical dosage of iodine, without affecting the diagnostic image quality.

  19. Speckle contrast diffuse correlation tomography of complex turbid medium flow

    SciTech Connect

    Huang, Chong; Irwin, Daniel; Lin, Yu; Shang, Yu; He, Lian; Kong, Weikai; Yu, Guoqiang; Luo, Jia

    2015-07-15

    Purpose: Developed herein is a three-dimensional (3D) flow contrast imaging system leveraging advancements in the extension of laser speckle contrast imaging theories to deep tissues along with our recently developed finite-element diffuse correlation tomography (DCT) reconstruction scheme. This technique, termed speckle contrast diffuse correlation tomography (scDCT), enables incorporation of complex optical property heterogeneities and sample boundaries. When combined with a reflectance-based design, this system facilitates a rapid segue into flow contrast imaging of larger, in vivo applications such as humans. Methods: A highly sensitive CCD camera was integrated into a reflectance-based optical system. Four long-coherence laser source positions were coupled to an optical switch for sequencing of tomographic data acquisition providing multiple projections through the sample. This system was investigated through incorporation of liquid and solid tissue-like phantoms exhibiting optical properties and flow characteristics typical of human tissues. Computer simulations were also performed for comparisons. A uniquely encountered smear correction algorithm was employed to correct point-source illumination contributions during image capture with the frame-transfer CCD and reflectance setup. Results: Measurements with scDCT on a homogeneous liquid phantom showed that speckle contrast-based deep flow indices were within 12% of those from standard DCT. Inclusion of a solid phantom submerged below the liquid phantom surface allowed for heterogeneity detection and validation. The heterogeneity was identified successfully by reconstructed 3D flow contrast tomography with scDCT. The heterogeneity center and dimensions and averaged relative flow (within 3%) and localization were in agreement with actuality and computer simulations, respectively. Conclusions: A custom cost-effective CCD-based reflectance 3D flow imaging system demonstrated rapid acquisition of dense boundary

  20. MACROMOLECULAR THERAPEUTICS

    PubMed Central

    Yang, Jiyuan; Kopeček, Jindřich

    2014-01-01

    This review covers water-soluble polymer-drug conjugates and macromolecules that possess biological activity without attached low molecular weight drugs. The main design principles of traditional and backbone degradable polymer-drug conjugates as well as the development of a new paradigm in nanomedicines – (low molecular weight) drug-free macromolecular therapeutics are discussed. To address the biological features of cancer, macromolecular therapeutics directed to stem/progenitor cells and the tumor microenvironment are deliberated. Finally, the future perspectives of the field are briefly debated. PMID:24747162

  1. Dual Energy CT Angiography of Peripheral Arterial Disease: Feasibility of Using Lower Contrast Medium Volume

    PubMed Central

    Almutairi, Abdulrahman; Sun, Zhonghua; Poovathumkadavi, Abduljaleel; Assar, Tarek

    2015-01-01

    Objective One of the main drawbacks associated with Dual Energy Computed Tomography Angiography (DECTA) is the risk of developing contrast medium-induced nephropathy (CIN). The aim of the present study was firstly, to design an optimal CT imaging protocol by determining the feasibility of using a reduced contrast medium volume in peripheral arterial DECTA, and secondly, to compare the results with those obtained from using routine contrast medium volume. Methods Thirty four patients underwent DECTA for the diagnosis of peripheral arterial disease. They were randomly divided into two groups: Group 1 (routine contrast volume group) with n = 17, injection rate 4–5 ml/s, and 1.5 ml/kg of contrast medium, and Group 2 ((low contrast volume group), with n = 17, injection rate 4–5ml/s, and contrast medium volume 0.75 ml/kg. A fast kilovoltage—switching 64-slice CT scanner in the dual-energy mode was employed for the study. A total of 6 datasets of monochromatic images at 50, 55, 60, 65, 70 and 75 keV levels were reconstructed with adaptive statistical iterative reconstruction (ASIR) at 50%. A 4-point scale was the tool for qualitative analysis of results. The two groups were compared and assessed quantitatively for image quality on the basis of signal-to-noise ratio (SNR) and contrast-to-noise-ratio (CNR). Radiation and contrast medium doses were also compared. Results The overall mean CT attenuation and mean noise for all lower extremity body parts was significantly lower for the low volume contrast group (p<0.001), and varied significantly between groups (p = 0.001), body parts (p<0.001) and keVs (p<0.001). The interaction between group body parts was significant with CT attenuation and CNR (p = 0.002 and 0.003 respectively), and marginally significant with SNR (p = 0.047), with minimal changes noticed between the two groups. Group 2 (low contrast volume group) displayed the lowest image noise between 65 and 70 keV, recorded the highest SNR and CNR at 65 keV, and

  2. Contrast medium induced changes in granulocyte adherence in vitro and during angiography.

    PubMed

    Lang, E V; Lasser, E C

    1988-01-01

    The effect of ioxaglate and diatrizoate on per cent granulocyte adherence to nylon fibers was investigated in blood to which contrast medium was added in vitro and in blood from patients undergoing angiography. Very high concentrations of contrast medium, added to blood in vitro, directly abolished granulocyte adherence to nylon fibers. Intraaortic bolus injections of ioxaglate, but not of saline, transiently increased granulocyte concentrations in the femoral vein. Fractional granulocyte adherence to nylon fibers increased significantly above the baseline when angiographic dosages of contrast medium were diluted by circulation within the human body. On the other hand, dilute concentrations of contrast medium had no effect on per cent granulocyte adherence when added to whole blood in vitro. This indicates that the increased adherence produced in vivo is an indirect effect, which, usually, cannot be simulated in vitro. PMID:3166881

  3. Multi-modal magnetic resonance imaging and histology of vascular function in xenografts using macromolecular contrast agent hyperbranched polyglycerol (HPG-GdF).

    PubMed

    Baker, Jennifer H E; McPhee, Kelly C; Moosvi, Firas; Saatchi, Katayoun; Häfeli, Urs O; Minchinton, Andrew I; Reinsberg, Stefan A

    2016-01-01

    Macromolecular gadolinium (Gd)-based contrast agents are in development as blood pool markers for MRI. HPG-GdF is a 583 kDa hyperbranched polyglycerol doubly tagged with Gd and Alexa 647 nm dye, making it both MR and histologically visible. In this study we examined the location of HPG-GdF in whole-tumor xenograft sections matched to in vivo DCE-MR images of both HPG-GdF and Gadovist. Despite its large size, we have shown that HPG-GdF extravasates from some tumor vessels and accumulates over time, but does not distribute beyond a few cell diameters from vessels. Fractional plasma volume (fPV) and apparent permeability-surface area product (aPS) parameters were derived from the MR concentration-time curves of HPG-GdF. Non-viable necrotic tumor tissue was excluded from the analysis by applying a novel bolus arrival time (BAT) algorithm to all voxels. aPS derived from HPG-GdF was the only MR parameter to identify a difference in vascular function between HCT116 and HT29 colorectal tumors. This study is the first to relate low and high molecular weight contrast agents with matched whole-tumor histological sections. These detailed comparisons identified tumor regions that appear distinct from each other using the HPG-GdF biomarkers related to perfusion and vessel leakiness, while Gadovist-imaged parameter measures in the same regions were unable to detect variation in vascular function. We have established HPG-GdF as a biocompatible multi-modal high molecular weight contrast agent with application for examining vascular function in both MR and histological modalities. PMID:26268906

  4. Syringomyelia caused by intrathecal remnants of oil-based contrast medium.

    PubMed

    Kubota, Mayumi; Shin, Masahiro; Taniguchi, Makoto; Terao, Toru; Nakauchi, Jun; Takahashi, Hiroshi

    2008-02-01

    Oily contrast medium had been in use since the early 19th century as a radiographic agent for detecting spinal lesions and spinal cord tumors until the late 20th century. At that point computed tomography scanning and magnetic resonance imaging, or other hydrophilic contrast medium substituted for it. Adverse effects of oil-based dye, both acute and chronic, had been reported since the middle of the 20th century. In this paper the authors report the case of syringomyelia that seemed to be caused mainly by remaining oily contrast medium for 44 years. Syringomyelia secondary to adhesive arachnoiditis caused by oily contrast medium after a long period of time is well known. In the present case, however, surgery revealed only mild arachnoiditis at the level of syringomyelia as well as both solid and liquid remnants of contrast medium. Generally, cerebrospinal fluid (CSF) blockage due to an arachnoid adhesion is considered to cause syringomyelia following adhesive arachnoiditis. The authors speculated that in the present case syringomyelia was induced by a mechanism different from that in the previously reported cases; the oily contrast medium itself seems to have induced the functional block of CSF and impaired the buffer system of the intrathecal pressure. No reports on thoracic adhesive arachnoiditis and syringomyelia caused by oil-based dye referred to this mechanism in reviewing the literature. PMID:18248289

  5. [1st experience with Solutrast, a new contrast medium for myelography].

    PubMed

    Thun, F

    1983-01-01

    Following a brief survey of myelographic results with aqueous contrast media, the article reports on the results obtained in 150 myelographies with the new contrast medium Lopamidol = Solutrast. This substance was found to be very well tolerated, involving low risk, and is suitable for examining the entire vertebral canal. The image quality is faultless. PMID:6823535

  6. Optical tracking of contrast medium bolus to optimize bolus shape and timing in dynamic computed tomography

    NASA Astrophysics Data System (ADS)

    Eisa, Fabian; Brauweiler, Robert; Peetz, Alexander; Hupfer, Martin; Nowak, Tristan; Kalender, Willi A.

    2012-05-01

    One of the biggest challenges in dynamic contrast-enhanced CT is the optimal synchronization of scan start and duration with contrast medium administration in order to optimize image contrast and to reduce the amount of contrast medium. We present a new optically based approach, which was developed to investigate and optimize bolus timing and shape. The time-concentration curve of an intravenously injected test bolus of a dye is measured in peripheral vessels with an optical sensor prior to the diagnostic CT scan. The curves can be used to assess bolus shapes as a function of injection protocols and to determine contrast medium arrival times. Preliminary results for phantom and animal experiments showed the expected linear behavior between dye concentration and absorption. The kinetics of the dye was compared to iodinated contrast medium and was found to be in good agreement. The contrast enhancement curves were reliably detected in three mice with individual bolus shapes and delay times of 2.1, 3.5 and 6.1 s, respectively. The optical sensor appears to be a promising approach to optimize injection protocols and contrast enhancement timing and is applicable to all modalities without implying any additional radiation dose. Clinical tests are still necessary.

  7. Assessment of the Early Effects of 5,6-Dimethylxanthenone-4-Acetic Acid Using Macromolecular Contrast Media-Enhanced Magnetic Resonance Imaging: Ectopic Versus Orthotopic Tumors

    SciTech Connect

    Seshadri, Mukund Bellnier, David A.; Cheney, Richard T.

    2008-11-15

    Purpose: To investigate the early effects of a vascular disrupting agent (VDA) in ectopic and orthotopic tumors by using macromolecular contrast media (MMCM)-enhanced magnetic resonance imaging (MMCM-MRI). Methods and Materials: The MMCM-MRI of ectopic and orthotopic MCA205 murine fibrosarcomas was performed using the intravascular contrast agent albumin-(gadopentetate dimeglumine){sub 35}. Change in longitudinal relaxation rate ({delta}R1) was measured 24 hours after treatment with 5,6-dimethylxanthenone-4-acetic acid (DMXAA; 30 mg/kg) and used to compute tumor vascular volume and permeability. Correlative histologic and immunohistochemical evaluation was carried out, along with measurement of tumor necrosis factor {alpha} and vascular endothelial growth factor levels in whole tumor extracts using the enzyme-linked immunosorbent assay. Results: Orthotopic tumors showed higher vascular volume (p < 0.05) than ectopic tumors before treatment. Twenty-four hours after DMXAA treatment, a significant (p < 0.0001), but differential, decrease in {delta}R1 (70% in ectopic and 50% in orthotopic tumors) was observed compared with baseline estimates. Consistent with this observation, greater levels of tumor necrosis factor {alpha}, an important mediator of the antivascular activity of DMXAA, were measured in ectopic tumors 3 hours posttreatment compared with orthotopic tumors (p < 0.05). Immunohistochemical (CD31) and histologic (hematoxylin and eosin) sections of ectopic and orthotopic tumors showed highly tumor-selective vascular damage after treatment with the presence of viable surrounding normal tissue. Conclusions: The MMCM-MRI provided early quantitative estimates of change in tumor perfusion after VDA treatment that showed good correlation with cytokine induction. Differences in the response of ectopic and orthotopic tumors highlight the influence of the host microenvironment in modulating the activity of VDAs.

  8. Intravenous contrast medium aggravates the impairment of pancreatic microcirculation in necrotizing pancreatitis in the rat.

    PubMed Central

    Schmidt, J; Hotz, H G; Foitzik, T; Ryschich, E; Buhr, H J; Warshaw, A L; Herfarth, C; Klar, E

    1995-01-01

    BACKGROUND: Previous reports demonstrated that radiographic contrast medium, as used in contrast-enhanced computed tomography, increases acinar necrosis and mortality in experimental pancreatitis. The authors studied the possibility that these changes may be related to an additional impairment of pancreatic microcirculation. METHODS: Fifty Wistar rats had acute pancreatitis induced by intraductal glycodeoxycholic acid (10 mmol/L for 10 min) and intravenous cerulein (5 micrograms/kg/hr for 6 hrs). After rehydration (16 mL/kg), pancreatic capillary perfusion was quantified by means of intravital microscopy at baseline before intravenous infusion of contrast medium (n = 25) or saline (n = 25), and 30 and 60 minutes thereafter. In addition to total capillary flow, capillaries were categorized as high- or low-flow (> or < 1.6 nL/min). RESULTS: Pancreatic capillary flow did not change in either high- or low-flow capillaries after saline infusion. However, contrast medium infusion induced a significant decrease of total capillary flow (p < 0.001). Analysis according to the relative flow rate revealed that this was primarily because of a significant additional reduction of perfusion in low-flow capillaries (p < 0.0001). Furthermore, complete capillary stasis was observed in 15.9 +/- 3.4% after contrast medium as compared with 3.2 +/- 1.2% after saline infusion (p < 0.006). CONCLUSION: Radiographic contrast medium aggravates the impairment of pancreatic microcirculation in experimental necrotizing pancreatitis. PMID:7717779

  9. Successful management of contrast medium extravasation injury through stellate ganglion block and intra-arterial nitroglycerin.

    PubMed

    Lee, Chien-Ching; Chuang, Chia-Chun; Liou, Jing-Yang; Hsieh, Ying-Chou; Tsou, Mei-Yung; Chen, Kwok-Hon

    2011-09-01

    We describe the successful management of extravasation injury to the left hand by contrast medium with stellate ganglion block and intra-arterial nitroglycerin in a patient which befell during contrast-enhanced imaging. The incidence of contrast-medium extravasation injury is increasing because of the convenience and availability of contrast-enhanced imaging and ease of injection access. Extravasation of contrast medium may results in severe pain, erythema, cyanosis, and edema or even skin necrosis, which is largely related to the ionization, osmolarity, and volume of the contrast medium. The conservative treatment is often adequate in small amount extravasation, but if the extravasation is overwhelming further energetic management is mandatory. A 29-year-old man was brought to our emergency because of diffuse abdominal pain and he was arranged to receive intravenous contrast media enhanced abdominal computed tomography for diagnosis. Ruptured appendicitis with abscess formation was suspected; then the patient underwent emergent appendectomy and drainage of the abscess. However, severe swelling and cyanotic change that radiated from the intravenous catheter insertion site in every direction over the entire dorsum of the left hand were noted after the surgery. Contrast-medium extravasation injury was highly contemplated and a left stellate ganglion block was performed immediately for relief of symptoms. The consulting surgeon ruled out compartment syndrome, but advised emergent left upper limb arteriography, which revealed signs of vasospasm with high intravascular pressure of the left distal ulnar and radial arteries; thus nitroglycerin was injected into left distal ulnar and radial arteries for relief of vasospasm. The clinical symptoms were improved after the above managements and the patient was discharged 7 days later without any sequela. PMID:21982175

  10. Liver-specific magnetic resonance contrast medium in the evaluation of chronic liver disease

    PubMed Central

    dos Reis, Marcio Augusto Correia Rodrigues; Baroni, Ronaldo Hueb

    2015-01-01

    ABSTRACT The hepatobiliary-specific contrast medium (gadoxetic acid – Primovist®) is primarily used to improve detection and characterization of focal hepatic lesions, such as in chronic liver disease patients with suspected hepatocellular carcinoma. Since the contrast medium is selectively taken up by functioning hepatocytes in the late hepatobiliary phase, it helps to detect typical hepatocellular carcinoma, which show low signal intensity on this phase. This imaging feature also assists in differentiating regenerative/dysplastic nodules from early hepatocellular carcinomas (with over 90% accuracy), as well as hypervascular hepatocellular carcinomas from arterial pseudo-enhancement foci. Future perspectives include its use in quantification of hepatic function and fibrosis. PMID:26154554

  11. Carbon dioxide contrast medium for endovascular treatment of ilio-femoral occlusive disease

    PubMed Central

    de Almeida Mendes, Cynthia; de Arruda Martins, Alexandre; Teivelis, Marcelo Passos; Kuzniec, Sergio; Varella, Andrea Yasbek Monteiro; Fioranelli, Alexandre; Wolosker, Nelson

    2015-01-01

    OBJECTIVES: Compare the use of carbon dioxide contrast medium with iodine contrast medium for the endovascular treatment of ilio-femoral occlusive disease in patients without contraindications to iodine. MATERIALS AND METHODS: From August 2012 to August 2014, 21 consecutive patients with ilio-femoral occlusive disease who were eligible for endovascular treatment and lacked contraindications to either iodine contrast or carbon dioxide were randomized into the carbon dioxide or iodine groups and subjected to ilio-femoral angioplasty. We analyzed the feasibility of the procedures, the surgical and clinical outcomes, the procedure lengths, the endovascular material costs, the contrast costs and the quality of the angiographic images in each group. RESULTS: No conversions to open surgery and no contrast media related complications were noted in either group. A post-operative femoral pulse was present in 88.9% of the iodine group and 80% of the carbon dioxide group. No differences in procedure length, endovascular material cost or renal function variation were noted between the groups. Four patients in the carbon dioxide group required iodine supplementation to complete the procedure. Contrast media expenses were reduced in the carbon dioxide group. Regarding angiographic image quality, 82% of the carbon dioxide images were graded as either good or fair by observers. CONCLUSIONS: The use of carbon dioxide contrast medium is a good option for ilio-femoral angioplasty in patients without contraindications to iodine and is not characterized by differences in endovascular material costs, procedure duration and surgical outcomes. In addition, carbon dioxide has lower contrast expenses compared with iodine. PMID:26598079

  12. A method to evaluate the dose increase in CT with iodinated contrast medium

    SciTech Connect

    Amato, Ernesto; Lizio, Domenico; Settineri, Nicola; Di Pasquale, Andrea; Salamone, Ignazio; Pandolfo, Ignazio

    2010-08-15

    Purpose: The objective of this study is to develop a method to calculate the relative dose increase when a computerized tomography scan (CT) is carried out after administration of iodinated contrast medium, with respect to the same CT scan in absence of contrast medium. Methods: A Monte Carlo simulation in GEANT4 of anthropomorphic neck and abdomen phantoms exposed to a simplified model of CT scanner was set up in order to calculate the increase of dose to thyroid, liver, spleen, kidneys, and pancreas as a function of the quantity of iodine accumulated; a series of experimental measurements of Hounsfield unit (HU) increment for known concentrations of iodinated contrast medium was carried out on a Siemens Sensation 16 CT scanner in order to obtain a relationship between the increment in HU and the relative dose increase in the organs studied. The authors applied such a method to calculate the average dose increase in three patients who underwent standard CT protocols consisting of one native scan in absence of contrast, followed by a contrast-enhanced scan in venous phase. Results: The authors validated their GEANT4 Monte Carlo simulation by comparing the resulting dose increases for iodine solutions in water with the ones presented in literature and with their experimental data obtained through a Roentgen therapy unit. The relative dose increases as a function of the iodine mass fraction accumulated and as a function of the Hounsfield unit increment between the contrast-enhanced scan and the native scan are presented. The data shown for the three patients exhibit an average relative dose increase between 22% for liver and 74% for kidneys; also, spleen (34%), pancreas (28%), and thyroid (48%) show a remarkable average increase. Conclusions: The method developed allows a simple evaluation of the dose increase when iodinated contrast medium is used in CT scans, basing on the increment in Hounsfield units observed on the patients' organs. Since many clinical protocols

  13. Low contrast medium and radiation dose for hepatic computed tomography perfusion of rabbit VX2 tumor

    PubMed Central

    Zhang, Cai-Yuan; Cui, Yan-Fen; Guo, Chen; Cai, Jing; Weng, Ya-Fang; Wang, Li-Jun; Wang, Deng-Bin

    2015-01-01

    AIM: To evaluate the feasibility of low contrast medium and radiation dose for hepatic computed tomography (CT) perfusion of rabbit VX2 tumor. METHODS: Eleven rabbits with hepatic VX2 tumor underwent perfusion CT scanning with a 24-h interval between a conventional tube potential (120 kVp) protocol with 350 mgI/mL contrast medium and filtered back projection, and a low tube potential (80 kVp) protocol with 270 mgI/mL contrast medium with iterative reconstruction. Correlation and agreement among perfusion parameters acquired by the conventional and low dose protocols were assessed for the viable tumor component as well as whole tumor. Image noise and tumor-to-liver contrast to noise ratio during arterial and portal venous phases were evaluated. RESULTS: A 38% reduction in contrast medium dose (360.1 ± 13.3 mgI/kg vs 583.5 ± 21.5 mgI/kg, P < 0.001) and a 73% decrease in radiation dose (1898.5 mGy • cm vs 6951.8 mGy • cm) were observed. Interestingly, there was a strong positive correlation in hepatic arterial perfusion (r = 0.907, P < 0.001; r = 0.879, P < 0.001), hepatic portal perfusion (r = 0.819, P = 0.002; r = 0.831, P = 0.002), and hepatic blood flow (r = 0.945, P < 0.001; r = 0.930, P < 0.001) as well as a moderate correlation in hepatic perfusion index (r = 0.736, P = 0.01; r = 0.636, P = 0.035) between the low dose protocol with iterative reconstruction and the conventional protocol for the viable tumor component and the whole tumor. These two imaging protocols provided a moderate but acceptable agreement for perfusion parameters and similar tumor-to-liver CNR during arterial and portal venous phases (5.63 ± 2.38 vs 6.16 ± 2.60, P = 0.814; 4.60 ± 1.27 vs 5.11 ± 1.74, P = 0.587). CONCLUSION: Compared with the conventional protocol, low contrast medium and radiation dose with iterative reconstruction has no significant influence on hepatic perfusion parameters for rabbits VX2 tumor. PMID:25954099

  14. Object reconstruction in scattering medium using multiple elliptical polarized speckle contrast projections and optical clearing agents

    NASA Astrophysics Data System (ADS)

    Moshe, Tomer; Firer, Michael A.; Abookasis, David

    2015-05-01

    In this paper, we present a hybrid method for improving the imaging quality of objects obscured within a scattering environment by combining multiple elliptical polarized speckle contrast projections with the use of optical clearing agents (OCAs). Elliptically polarized light enables the probing of subsurface volumes, where OCAs decrease light scattering while increasing photons' penetration depth through the medium. Experiments were conducted on object sample and prostate cancer cells embedded within ex vivo biological samples (chicken breasts) in reflection configuration. After immersion with OCAs, the medium was irradiated with an elliptically polarized laser beam and multiple polarized speckled images obtained from a lens array were first converted to speckled contrast images and then processed using a self-deconvolution shift-and-add algorithm. The conversion to contrast images and multiple perspectives acquisition was found to emphasize contrast. Analysis of image quality indicated improvement in object visualization by the combination of elliptical polarization and OCAs. This enhanced imaging strategy may advance the development of improved methods in biomedicine field, specifically biomedical tomography.

  15. Efficacy of coronary fractional flow reserve using contrast medium compared to adenosine

    PubMed Central

    Tanboğa, Ibrahim Halil; Aksakal, Enbiya; Aksu, Uğur; Gulcu, Oktay; Birdal, Oğuzhan; Arısoy, Arif; Kalaycı, Arzu; Ulusoy, Fatih Rifat; Sevimli, Serdar

    2016-01-01

    Introduction Coronary fractional flow reserve (FFR) is recommended as the gold standard method in evaluating intermediate coronary stenoses. However, there are significant debates concerning the agents and the timing of the measurement. Aim To compare the contrast medium induced Pd/Pa ratio (CMR) with the FFR. Material and methods We enrolled 28 consecutive patients with 34 intermediate lesions who underwent coronary FFR measurement by intracoronary (i.c.) adenosine. After baseline Pd/Pa was calculated, a single contrast medium (Iomeron) injection of 6 ml (3 ml/s) was performed manually. Within 10 s after the contrast medium injection, the CMR was calculated. Bolus injection of i.c. adenosine was performed to induce maximal hyperemia (from 60 µg to 600 µg), and when it was ≤ 0.80, the intermediate lesion was considered as significant. Results After bolus i.c. adenosine, 12 lesions of 34 (35.3%) were identified as significant. The CMR value was 0.86 ±0.06 (range: 0.71–0.97). There were no significant differences between FFR and CMR values (p = 0.108). A substantial positive correlation between adenosine and contrast values was detected (0.886 and p < 0.001). Good agreement in Bland-Altman analysis was revealed (mean bias was 0.027, 95% confidence interval 0.038–0.092). Receiver operating characteristics curve analysis showed 90.9% sensitivity and 91.7% specificity for a cut-off value of 0.85 for the CMR compared to FFR (≤ 0.80). Conclusions Our study showed that measuring the CMR is a feasible method compared to FFR. The CMR may be used in situations where adenosine cannot be administered. PMID:27625683

  16. A method to remove the projection error in triple-energy radiography with contrast medium

    NASA Astrophysics Data System (ADS)

    Baldazzi, G.; Lanconelli, N.; Masetti, S.; Fiaschetti, M.; Maccagnani, M.; Roma, L.; Rossi, P. L.; Levi, G.; Sbarra, C.

    2009-10-01

    The density-map reconstruction of a radiological contrast medium is affected by noise arising from the background lack of homogeneity (the so-called "projection error") if images of the medium are collected starting from quasi-monochromatic X-ray beams. This noise, especially for a dual-energy reconstruction algorithm, becomes more significant than the statistical fluctuations of the photon-transmitted flux, dramatically reducing the accuracy and the sensitivity of the reconstruction. In this work, we investigate the efficacy of the triple-energy technique, which is based on the simultaneous acquisition of three monochromatic images of the same target injected with contrast medium. A theoretical analysis allows to estimate the sensitivity and the accuracy of the reconstructed density map compared with the dual-energy one (i.e., the density map reconstructed acquiring only two monochromatic images). To validate the theory, a set of experimental measurements was performed: results show that triple energy drastically reduces the projection errors (from 10 to 60 times smaller than the dual-energy one), making it negligible with respect to the statistical noise.

  17. Imaging Quality Evaluation of Low Tube Voltage Coronary CT Angiography Using Low Concentration Contrast Medium

    PubMed Central

    Zhang, Zaixian; Wang, Qingguo; Zheng, Linfeng; Feng, Yan; Zhou, Zhiguo; Zhang, Guixiang; Li, Kangan

    2015-01-01

    Purpose To compare the image quality of prospectively ECG-gated low voltage coronary computed tomography angiography (CTA) with an administration of low concentration contrast medium. Method and Materials A total of 101 patients, each with a heart rate below 65 beats per minute (BPM), underwent a prospectively ECG-gated axial scan in CT coronary angiography on a 64-slice CT scanner. All patients were allocated in three groups (group A: n=31, 80kVp, 300 mgI/ml; group B: n=34, 100kVp, 300 mgI/ml; group C: n=36, 120kVp, 370 mgI/ml). The CT attenuation values of aortic root (AR), left main coronary artery (LMA), right main coronary artery (RMA) and chest subcutaneous fat tissue were measured. The contrast-to-noise ratio (CNR) of AR, LMA and RMA were calculated according to the formulas below. The values of computed tomography dose index (CTDI) and dose-length product (DLP) were recorded. Image quality was assessed on a 5-point scale. The results were compared using the one-way ANOVA and rank sum tests. Results The values of CNR and SNR for vessels in group A and group B were not significantly different from group C (each p > 0.05). The effective radiation dose in group A (1.51±0.70 mSv) and group B (2.59±1.24 mSv) were both lower than group C (4.92±2.82 mSv) (each p < 0.05). There was no significant difference among the image quality scores of group A (4.10±0.41), group B (3.90±0.48) and group C (4.04±0.36) (each P > 0.05). Conclusion Low tube voltage coronary CT angiography using low concentration contrast medium does not affect the imaging quality for assessing the coronary arteries compared with high voltage coronary CT angiography using high concentration contrast medium. Meanwhile low concentration contrast medium allowed 47-69% of radiation dose reduction. PMID:25811785

  18. The effect of bilipolinum (Adipiodon), an iodine contrast medium on erythrocyte enzymes.

    PubMed

    Kwiatkowska, J; Kwiatkowska, D; Dawiskiba, J

    1980-01-01

    Bilipolinum (Adipiodon), iodine contrast medium used in cholangiography, showed an inhibitory effect on the activity of human erythrocyte phosphohexoseisomerase, phosphofructokinase, aldolase and glucose-6-phosphate dehydrogenase. The addition of glucose metabolites (glucose-6-phosphate, fructose-6-phosphate, fructose-1,6-bis-phosphate, pyruvate and lactate) abolished the inhibitory effect of Bilipolinum. In the presence of Bilipolinum purified erythrocyte phosphofructokinase showed a decreased affinity towards substrate, modified allosteric properties and reduced stability at pH below 7.5. Purified erythrocyte glucose-6-phosphate dehydrogenase was also affected by Bilipolinum and its affinity for NADP was decreased. Testing of erythrocyte enzymes in the evaluation of toxicity of iodine contrast media is discussed. PMID:6452104

  19. Real-time contrast medium detection in x-ray images by mathematical morphology operators

    NASA Astrophysics Data System (ADS)

    Ly, Dieu Sang; Beucher, Serge; Bilodeau, Michel

    2015-11-01

    This paper proposes a solution to contrast agent (CA) detection in angiograms by considering x-ray images as intensity images and applying mathematical morphology operators. We present two detection approaches, one based on the intensity infimum and the other based on the dual reconstruction. The evaluation using several data sets shows that both techniques are able to detect the presence of the contrast medium volume. Moreover, the dual reconstruction-based method is proven to be faster in processing time and more effective than the intensity infimum-based method in distinguishing the intensity change at the same location from the displacement of the same region. In addition, we show how to track the CA passage through a region of interest by observing the intensity evolution in successive submasks.

  20. High-Pitch Coronary CT Angiography at 70 kVp With Low Contrast Medium Volume

    PubMed Central

    Zhang, Long Jiang; Qi, Li; De Cecco, Carlo N.; Zhou, Chang Sheng; Spearman, James V.; Schoepf, U. Joseph; Lu, Guang Ming

    2014-01-01

    Abstract The purpose of this article is to evaluate image quality and radiation dose of prospectively electrocardiogram (ECG)-triggered high-pitch coronary computed tomography angiography (CCTA) at 70 kVp and 30 mL contrast medium. One hundred fifty patients with a heart rate ≤70 beats per minute (bpm) underwent CCTA using a second-generation dual-source computed tomography (CT) scanner and were randomized into 3 groups according to tube voltage and contrast medium volume (370 mg/mL iodine concentration) (100 kVp group, 100 kVp/60 mL, n = 55; 80 kVp group, 80 kVp/60 mL, n = 44; 70 kVp group, 70 kVp/30 mL, n = 51). Objective and subjective image quality along with the effect of heart rate (HR) and body mass index (BMI) was evaluated and compared between the groups. Radiation dose was estimated for each patient. CT attenuation and image noise were higher in the 80 and 70 kVp groups than in the 100 kVp group (all P < 0.001). Signal-to-noise ratios (SNRs) and contrast-to-noise ratios (CNRs) were lower in the 70 kVp group than in the 80 and 100 kVp groups (all P < 0.05). There was no difference for subjective image quality between the groups (P > 0.05). HR did not affect subjective image quality (all P > 0.05), while patients with BMI <23 kg/m2 had higher image quality than patients with BMI ≥23 kg/m2 (P < 0.05). Compared with the 100 kVp group, the radiation dose of the 70 kVp group was reduced by 75%. In conclusion, prospectively ECG-triggered high-pitch 70 kVp/30 mL CCTA can obtain diagnostic image quality with lower radiation dose in selected patients with BMI <23 kg/m2 compared with 80/100 kVp/60 mL CCTA. PMID:25396334

  1. [Preclinical evaluation of iotrolan as a contrast medium for angiography and urography].

    PubMed

    Miyazawa, T; Murayama, C; Uchimoto, R; Fritz-Zieroth, B

    1992-09-25

    Efficacy and tolerability of iotrolan, a nonionic isotonic dimer, as a contrast medium for angiography and urography were investigated in animals. In the arteriography of rabbit femur, the efficacy of iotrolan 280 mgI/ml was as good as iopamidol 300 mgI/ml and better than meglumine diatrizoate 306 mgI/ml. In rat urography, the efficacy of iotrolan 280 mgI/ml was better than both iopamidol 370 mgI/ml and iohexol 350 mgI/ml. Vascular pain was less with iotrolan 280 mgI/ml than with iohexol 300 mgI/ml in rats. Effect of iotrolan on the pulmo-cardiovascular parameters, arterial pO2, hematocrit and plasma osmolality was less than iopamidol and diatrizoate in rabbits. Iotrolan induced no renal dysfunction and diuresis where iopamidol induced diuresis in rats. Effect of iotrolan on the blood coagulation was similar to nonionic monomers and less than diatrizoate in rabbits. Because of its isotonicity, iotrolan induced little water shift in the blood vessel and urinary tract, which would result in good efficacy and tolerability. These results suggest that iotrolan is superior to ionic and nonionic monomers for angiography and urography. PMID:1437534

  2. Removal of the iodinated X-ray contrast medium diatrizoate by anaerobic transformation.

    PubMed

    Redeker, Maria; Wick, Arne; Meermann, Björn; Ternes, Thomas A

    2014-09-01

    The iodinated X-ray contrast medium diatrizoate is known to be very persistent in current wastewater treatment as well as in environmental compartments. In this study, the potential of anaerobic processes in soils, sediments, and during wastewater treatment to remove and transform diatrizoate was investigated. In anaerobic batch experiments with soil and sediment seven biologically formed transformation products (TPs) as well as the corresponding transformation pathway were identified. The TPs resulted from successive deiodinations and deacetylations. The final TP 3,5-diaminobenzoic acid (DABA) was stable under anaerobic conditions. However, DABA was further transformed under air atmosphere, indicating the potential for the mineralization of diatrizoate by combining anaerobic and aerobic conditions. With the development of a methodology using complementary liquid chromatography-electrospray ionization-tandem mass spectrometry and liquid chromatography-inductively coupled plasma-mass spectrometry techniques, all identified TPs were quantified and the mass balance could be closed without having authentic standards for four of the TPs available. The detection and quantification of diatrizoate TPs in groundwater, in technical wetlands with anaerobic zones, and in a pilot wastewater treatment plant established for anaerobic treatment highlights the transferability and up-scaling of the results attained by laboratory experiments to environmental conditions. PMID:25140788

  3. Breviscapine attenuatted contrast medium-induced nephropathy via PKC/Akt/MAPK signalling in diabetic mice

    PubMed Central

    Jiang, Wenbin; Li, Zhengwei; Zhao, Wei; Chen, Hao; Wu, Youyang; Wang, Yi; Shen, Zhida; He, Jialin; Chen, Shengyu; Zhang, Jiefang; Fu, Guosheng

    2016-01-01

    Contrast medium-induced nephropathy (CIN) remains a major cause of iatrogenic, drug-induced renal injury. Recent studies reveal that Breviscapine can ameliorate diabetic nephropathy in mice. Yet it remains unknown if Breviscapine could reduce CIN in diabetic mice. In this study, male C57/BL6J mice were randomly divided into 7 groups: control, diabetes mellitus, CIN, diabetes mellitus+CIN, diabetes mellitus+Breviscapine, CIN+Breviscapine and diabetes mellitus+CIN+Breviscapine. Model of CIN was induced by tail intravenous administration of iopromide and model of diabetes mellitus was induced by Streptozotocin intraperitoneally. Breviscapine was administered intragastrically for 4 weeks. Renal function parameters, kidney histology, markers of renal fibrosis, phosphorylation of protein kinase C/Akt/mitogen activated protein kinases were measured by western blot. We found out that diabetes mellitus aggravated CIN damage. Renal histological analysis showed Breviscapine reduced of renal fibrosis and tubular damage. Breviscapine was also shown markedly to ameliorate CIN fibrotic markers expression, reduced proteinuria and serum creatinine. Furthermore, Breviscapine decreased phosphorylation of PKCβII, Akt, JNK1/2 and p38. Therefore, Breviscapine treatment could ameliorate the development of CIN in diabetic mice, which was partly attributed to its suppression of renal fibrosis via phosphorylation of PKCβII/Akt/JNK1/2/p38 signalling. PMID:27158329

  4. [General pharmacological study of iodixanol, a new non-ionic isotonic contrast medium].

    PubMed

    Takasuna, K; Kasai, Y; Kitano, Y; Mori, K; Kobayashi, R; Makino, M; Hagiwara, T; Hirohashi, M; Nomura, M; Algate, D R

    1995-10-01

    The general pharmacological study of iodixanol, a non-ionic isotonic contrast medium, was conducted. 1) Iodixanol administered intravenously over a dose range of 320 to 3,200 mgI/kg had little or no effect on the general behavior, spontaneous locomotor activity, hexobarbital sleeping time, pain response, electroshock- or pentylenetetrazol-induced convulsion (mouse), EEG or body temperature (rabbit), gastrointestinal propulsion (mouse) or skeletal muscle contraction (rabbit). Iodixanol had no specific interaction with acetylcholine, histamine, serotonin, nicotin, BaCl2 (ileum), methacholine (trachea), isoprenaline (atrium) or oxytocin (pregnant uterus), nor had any effect on spontaneous contractility (atrium and uterus), or transmural electrostimulation-induced contractility (vas deferens) at concentrations of < or = 3.2 x 10(-3) gI/ml in vitro. Iodixanol had no effect on the cardiovascular system of dog, except that it increased femoral blood flow and respiratory rate at doses of > or = 1,000 mgI/kg. Iodixanol at 3,200 mgI/kg i.v. reduced urine output with a decrease in Na+ and Cl- excretion, whereas at 320 mgI/kg i.v., it slightly increased urine output (rat). 2) Injections of iodixanol into the cerebroventricular (0.96, 9.6 mgI/mouse and 3.2, 32 mgI/rat), left ventricular (1,920, 6,400 mgI/dog) or coronary artery (640, 1,920 mgI/dog) had no conspicuous effect on the central nervous system or the cardiovascular system, respectively. There was no marked difference among iodixanol, iohexol and iopamidol in this respect. Vascular pain during injection into the femoral artery (300-320 mgI/guinea pig) appeared to be less intense with iodixanol, compared with the other contrast media iohexol and iopamidol. These results suggest that intravenous injection of iodixanol is relatively free from pharmacological activity, and effects of iodixanol on the central nervous system (intracerebroventricular injection) and cardiovascular system (intra-left ventricular and -coronary

  5. Fox baiting against Echinococcus multilocularis: contrasted achievements among two medium size cities.

    PubMed

    Comte, S; Raton, V; Raoul, F; Hegglin, D; Giraudoux, P; Deplazes, P; Favier, S; Gottschek, D; Umhang, G; Boué, F; Combes, B

    2013-08-01

    In Europe, most cities are currently colonized by red foxes (Vulpes vulpes), which are considered to be the main definitive host of the zoonotic cestode Echinococcus multilocularis. The risk of transmission to humans is of particular concern where high fox populations overlap with high human populations. The distribution of baits containing praziquantel has successfully reduced the infection pressure in rural areas and in small plots within large cities. The purpose of this study was to assess its efficiency in two medium size cities (less than 100,000 inhabitants) in areas of high human alveolar echinococcosis incidence. From August 2006 to March 2009, 14 baiting campaigns of praziquantel treatment were run in Annemasse and Pontarlier (Eastern France), each of which encompassed 33 km(2), with a density of 40 baits/km(2). The bait consumption appeared to be lower in strictly urban context compared to suburban areas (78.9% vs. 93.4%) and lower in Annemasse than in Pontarlier (82.2% vs. 89.5%). During our study, the prevalence of E. multilocularis, as assessed by EM-ELISA on fox faeces collected in the field in Annemasse, was lower within the treated area than in the rural control area. A "before/during" treatment comparison revealed a significant decrease of spring prevalence from 13.3% to 2.2%. No significant change in prevalence was detected in Pontarlier (stable prevalence: 9.1%) where the contamination of the treated area followed the temporal trend observed in the control area. There, a greater resilience of the parasite's life cycle, probably due to a strong pressure of recontamination from outside the treated area, may have counteracted the prophylaxis treatment. These contrasted outcomes suggest that the frequency of fox anthelmintic treatment should be adapted to the local situation. PMID:23642656

  6. A novel foam fluid negative contrast medium for clear visualization of the colon wall in CT imaging.

    PubMed

    Wei, Xiaohui; Zhu, Jiong; Gong, Hongxia; Xu, Jianrong; Xu, Yuhong

    2011-01-01

    Computed tomography (CT) imaging is a valuable tool for the diagnosis of colorectal diseases. However, the colonic wall depiction in 2D CT images is usually poor because of the low contrast between the colonic wall and the luminal content. In order to improve the visualization of the colonic wall and any abnormality on its surface, we report in this paper the development of an oil-free foam fluid negative contrast medium for improved CT imaging of the colon. The foam fluid negative contrast medium was prepared by dispersing and stabilizing microbubbles in a polymeric solution. The stabilities of both the individual bubbles and the foam fluid system were optimized by incorporating bovine serum albumin and gluconolactone as the stabilization agent. The medium had a mean X-ray density of -120 Hounsfield units (close to that of the extraluminal tissues), and enabled clear 2D visualization of the colonic wall in both ex vivo and in vivo imaging studies. The measured colonic wall thicknesses at different segments in a beagle dog based on the 2D CT images obtained with the negative contrast medium accurately reflected the anatomical values, as compared with the values based on air-contrasted images. In vivo study of a simulated polyps pig model demonstrated sensitive detection of 11 out of 12 polyps with the smallest one 2 mm in diameter. We believe this new and safe foam fluid negative medium would enable the implementation of CT imaging as a convenient and useful tool for diagnosis of colon cancer, especially in the elderly population. PMID:22144024

  7. [Oral magnetic particles as an MR contrast medium for the gastrointestinal tract].

    PubMed

    Rinck, P A; Myhr, G; Smevik, O; Børseth, A

    1992-12-01

    The authors summarise their experience of four clinical studies with a negative oral contrast agent for magnetic resonance imaging of the abdomen and pelvis. 140 patients were enrolled in the studies. These were partly comparative studies pre- and post-contrast, partly at 0.5 and 1.5 T, partly pre-injection and post-injection of glucagon. All patients received 800 ml of a suspension of oral magnetic particles "OMP". The distribution of this contrast agent was homogeneous throughout the entire GI tract. A complete or partial signal void was observed in all patients in T1, T2-, and intermediately weighted images. Generally, diagnostic information was higher after contrast. Artifacts caused by peristalsis and movement of the diaphragm were fewer after contrast. After contrast metallic artifacts were observed in a minority of patients. Adverse events after contrast were minimal; they included nausea and vomiting. PMID:1457787

  8. Contrast evaluation of the polarimetric images of different targets in turbid medium: possible sources of systematic errors

    NASA Astrophysics Data System (ADS)

    Novikova, T.; Bénière, A.; Goudail, F.; De Martino, A.

    2010-04-01

    Subsurface polarimetric (differential polarization, degree of polarization or Mueller matrix) imaging of various targets in turbid media shows image contrast enhancement compared with total intensity measurements. The image contrast depends on the target immersion depth and on both target and background medium optical properties, such as scattering coefficient, absorption coefficient and anisotropy. The differential polarization image contrast is usually not the same for circularly and linearly polarized light. With linearly and circularly polarized light we acquired the orthogonal state contrast (OSC) images of reflecting, scattering and absorbing targets. The targets were positioned at various depths within the container filled with polystyrene particle suspension in water. We also performed numerical Monte Carlo modelling of backscattering Mueller matrix images of the experimental set-up. Quite often the dimensions of container, its shape and optical properties of container walls are not reported for similar experiments and numerical simulations. However, we found, that depending on the photon transport mean free path in the scattering medium, the above mentioned parameters, as well as multiple target design could all be sources of significant systematic errors in the evaluation of polarimetric image contrast. Thus, proper design of experiment geometry is of prime importance in order to remove the sources of possible artefacts in the image contrast evaluation and to make a correct choice between linear and circular polarization of the light for better target detection.

  9. Contrast medium administration and image acquisition parameters in renal CT angiography: what radiologists need to know

    PubMed Central

    Saade, Charbel; Deeb, Ibrahim Alsheikh; Mohamad, Maha; Al-Mohiy, Hussain; El-Merhi, Fadi

    2016-01-01

    Over the last decade, exponential advances in computed tomography (CT) technology have resulted in improved spatial and temporal resolution. Faster image acquisition enabled renal CT angiography to become a viable and effective noninvasive alternative in diagnosing renal vascular pathologies. However, with these advances, new challenges in contrast media administration have emerged. Poor synchronization between scanner and contrast media administration have reduced the consistency in image quality with poor spatial and contrast resolution. Comprehensive understanding of contrast media dynamics is essential in the design and implementation of contrast administration and image acquisition protocols. This review includes an overview of the parameters affecting renal artery opacification and current protocol strategies to achieve optimal image quality during renal CT angiography with iodinated contrast media, with current safety issues highlighted. PMID:26728701

  10. Improvement of the optical imaging of objects in a strongly scattering medium by means of contrast-enhancing dyes

    SciTech Connect

    Vorob'ev, Nikolai S; Smirnov, A V; Podgaetskii, Vitalii M; Tereshchenko, Sergei A; Tomilova, Larisa G

    1999-12-31

    The problem of enhancing the contrast of optical images in a strongly scattering medium by means of luminescent and absorbing dyes, topical in laser tomography, is examined. Preparations based on diphthalocyanine compounds were selected on the grounds of their tropism and resistance to the action of heat and light. Images with enhanced contrast in model scattering media (an aqueous solution of milk and margarine) were obtained in the IR region of the spectrum using the radiation of a picosecond neodymium laser. (laser applications and other topics in quantum electronics)

  11. Contrast medium accumulation and washout in canine brain tumors and irradiated normal brain: a CT study of kinetics

    SciTech Connect

    Fike, J.R.; Cann, C.E.

    1984-04-01

    Kinetics of an iodinated contrast medium were evaluated quantitatively as a function of time up to one hour after intravenous infusion in the brains of dogs with experimentally induced radiation damage and dogs with spontaneous brain tumor. Radiation damage was characterized by an increase in iodine accumulation soon after the infusion, while tumor concentration of iodine either showed no change or decreased with time. These results suggest that contrast kinetic studies may be useful in differentiating radiation damage to normal brain tissue from a malignant brain tumor.

  12. Importance of extracolonic findings at IV contrast medium-enhanced CT colonography versus those at non-enhanced CT colonography.

    PubMed

    Spreng, Adrian; Netzer, Peter; Mattich, Joerg; Dinkel, Hans-Peter; Vock, Peter; Hoppe, Hanno

    2005-10-01

    To compare the clinical importance of extracolonic findings at intravenous (IV) contrast-enhanced CT colonography versus those at non-enhanced CT colonography. IV contrast medium-enhanced (n=72) and non-enhanced (n=30) multidetector CT colonography was performed in 102 symptomatic patients followed by conventional colonoscopy on the same day. The impact of extracolonic findings on further work up and treatment was assessed by a review of patient records. Extracolonic findings were divided into two groups: either leading to further work up respectively having an impact on therapy or not. A total of 303 extracolonic findings were detected. Of those, 71% (215/303) were found on IV contrast-enhanced CT, and 29% (88/303) were found on non-enhanced CT colonography. The extracolonic findings in 25% (26/102) of all patients led to further work up or had an impact on therapy. Twenty-two of these patients underwent CT colonography with IV contrast enhancement, and four without. The percentage of extracolonic findings leading to further work up or having an impact on therapy was higher for IV contrast-enhanced (31%; 22/72) than for non-enhanced (13%; 4/30) CT scans (P=0.12). IV contrast-enhanced CT colonography produced more extracolonic findings than non-enhanced CT colonography. A substantially greater proportion of findings on IV contrast-enhanced CT colonography led to further work up and treatment than did non-enhanced CT colonography. PMID:15965661

  13. Estimation of shear velocity contrast for dipping or anisotropic medium from transmitted Ps amplitude variation with ray-parameter

    NASA Astrophysics Data System (ADS)

    Kumar, Prakash

    2015-12-01

    Amplitude versus offset analysis of P to P reflection is often used in exploration seismology for hydrocarbon exploration. In the present work, the feasibility to estimate crustal velocity structure from transmitted P to S wave amplitude variation with ray-parameter has been investigated separately for dipping layer and anisotropy medium. First, for horizontal and isotropic medium, the approximation of P-to-s conversion is used that is expressed as a linear form in terms of slowness. Next, the intercept of the linear regression has been used to estimate the shear wave velocity contrast (δβ) across an interface. The formulation holds good for isotropic and horizontal layer medium. Application of such formula to anisotropic medium or dipping layer data may lead to erroneous estimation of δβ. In order to overcome this problem, a method has been proposed to compensate the SV-amplitude using shifted version of SH-amplitude, and subsequently transforming SV amplitudes equivalent to that from isotropic or horizontal layer medium as the case may be. Once this transformation has been done, δβ can be estimated using isotropic horizontal layer formula. The shifts required in SH for the compensation are π/2 and π/4 for dipping layer and anisotropic medium, respectively. The effectiveness of the approach has been reported using various synthetic data sets. The methodology is also tested on real data from HI-CLIMB network in Himalaya, where the presence of dipping Moho has already been reported. The result reveals that the average shear wave velocity contrast across the Moho is larger towards the Indian side compared to the higher Himalayan and Tibetan regions.

  14. Macromolecular Crystallization in Microgravity

    NASA Technical Reports Server (NTRS)

    Snell, Edward H.; Helliwell, John R.

    2004-01-01

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

  15. Does iodinated contrast medium amplify DNA damage during exposure to radiation.

    PubMed

    Riley, Peter

    2015-01-01

    There is a recognized increased risk of cancer following exposure of humans to ionizing radiation; this is felt to be most likely due to damage to DNA strands during exposure. Damage to DNA strands can be demonstrated microscopically following exposure to X-rays, and new evidence is emerging that this effect may be compounded by administration of iodinated contrast agents. PMID:26234959

  16. Thromboelastographic Changes Following Nonionic Contrast Medium Injection During Transfemoral Angiography in Patients with Peripheral Arterial Occlusive Disease

    SciTech Connect

    Shankar, V.K. Handa, A.; Philips-Hughes, J.; Boardman, P.; Uberoi, R.; Hands, L.J.

    2006-12-15

    Background/Purpose. Patients with peripheral arterial occlusive disease (PAOD) are known to be systemically hypercoagulable and there is concern that exposing them to contrast media during angiography may exacerbate that thrombotic tendency. Many in vitro studies in which blood is exposed to contrast media suggest that nonionic contrast medium (NICM) has a weaker anticoagulant effect than ionic contrast medium (ICM) and some studies suggest that NICM can lead to activation of coagulation thus increasing the risk of thrombotic events where it is employed. We have looked at the changes in coagulation adjacent to the site of contrast injection/potential angioplasty to determine the magnitude of change locally. Methods. We measured changes in the coagulability of aortic blood samples immediately before and within 2 min after injection of the last bolus of iohexol (NICM) prior to any intervention procedure in 30 patients with PAOD. Samples were analyzed using thromboelastography (TEG) to identify changes in the coagulability of the aortic blood samples. Results. TEG tracings of samples taken from the aorta after injection of NICM showed a significant increase in R time (time to fibrin formation) (p = 0.036) and in k time (dynamics of clot formation) (p = 0.028) and a reduction in Angle (decreased acceleration of fibrin build-up) (p = 0.013), Maximal amplitude (MA) (reduced ultimate clot strength) (p = 0.018) and Coagulation Index (CI) (p = 0.032). Conclusion. These changes in TEG parameters show that the local effect of NICM is a reduction in coagulation activity rather than the activation suggested by some previous studies.

  17. Nanotoxic Profiling of Novel Iron Oxide Nanoparticles Functionalized with Perchloric Acid and SiPEG as a Radiographic Contrast Medium

    PubMed Central

    Mohamed, Muhamad Idham; Mohammad, Mohd Khairul Amran; Abdul Razak, Hairil Rashmizal; Abdul Razak, Khairunisak; Md Saad, Wan Mazlina

    2015-01-01

    Emerging syntheses and findings of new metallic nanoparticles (MNPs) have become an important aspect in various fields including diagnostic imaging. To date, iodine has been utilized as a radiographic contrast medium. However, the raise concern of iodine threats on iodine-intolerance patient has led to search of new contrast media with lower toxic level. In this animal modeling study, 14 nm iron oxide nanoparticles (IONPs) with silane-polyethylene glycol (SiPEG) and perchloric acid have been assessed for toxicity level as compared to conventional iodine. The nanotoxicity of IONPs was evaluated in liver biochemistry, reactive oxygen species production (ROS), lipid peroxidation mechanism, and ultrastructural evaluation using transmission electron microscope (TEM). The hematological analysis and liver function test (LFT) revealed that most of the liver enzymes were significantly higher in iodine-administered group as compared to those in normal and IONPs groups (P < 0.05). ROS production assay and lipid peroxidation indicator, malondialdehyde (MDA), also showed significant reductions in comparison with iodine group (P < 0.05). TEM evaluation yielded the aberration of nucleus structure of iodine-administered group as compared to those in control and IONPs groups. This study has demonstrated the less toxic properties of IONPs and it may postulate that IONPs are safe to be applied as radiographic contrast medium. PMID:26075217

  18. Nanotoxic profiling of novel iron oxide nanoparticles functionalized with perchloric acid and SiPEG as a radiographic contrast medium.

    PubMed

    Mohamed, Muhamad Idham; Mohammad, Mohd Khairul Amran; Abdul Razak, Hairil Rashmizal; Abdul Razak, Khairunisak; Saad, Wan Mazlina Md

    2015-01-01

    Emerging syntheses and findings of new metallic nanoparticles (MNPs) have become an important aspect in various fields including diagnostic imaging. To date, iodine has been utilized as a radiographic contrast medium. However, the raise concern of iodine threats on iodine-intolerance patient has led to search of new contrast media with lower toxic level. In this animal modeling study, 14 nm iron oxide nanoparticles (IONPs) with silane-polyethylene glycol (SiPEG) and perchloric acid have been assessed for toxicity level as compared to conventional iodine. The nanotoxicity of IONPs was evaluated in liver biochemistry, reactive oxygen species production (ROS), lipid peroxidation mechanism, and ultrastructural evaluation using transmission electron microscope (TEM). The hematological analysis and liver function test (LFT) revealed that most of the liver enzymes were significantly higher in iodine-administered group as compared to those in normal and IONPs groups (P < 0.05). ROS production assay and lipid peroxidation indicator, malondialdehyde (MDA), also showed significant reductions in comparison with iodine group (P < 0.05). TEM evaluation yielded the aberration of nucleus structure of iodine-administered group as compared to those in control and IONPs groups. This study has demonstrated the less toxic properties of IONPs and it may postulate that IONPs are safe to be applied as radiographic contrast medium. PMID:26075217

  19. Misleading changes of the signal intensity on opposed-phase MRI after injection of contrast medium

    SciTech Connect

    Heywang-Koebrunner, S.H.; Hoefer, H.; Spielmann, R.P.

    1996-03-01

    The effect of opposed-phase imaging on the interpretation of MR contrast studies is highlighted. A model calculation is performed. It demonstrates the change of signal intensity of an average tumor before and after application of Gd-DTPA on an in-phase and an opposed-phase image, depending on the percentage of fat within the voxels. The effect is then demonstrated, using a small cotton stick soaked with water or a solution of contrast agent representing a tumor before and after i.v. application of Gd-DTPA. If an average enhancing tumor, which is surrounded by fat, occupies less than 50-60% of the slice thickness, it becomes undetectable on opposed-phase images. The reason is that due to signal cancellation on the the opposed image, no signal change or even signal decrease results, while signal increase is visible on the in-phase image. In those areas of the body where significant partial volume of a tumor with fat may occur (such as for breast tumors growing along ducts, which are surrounded by fat), severe errors can result. Therefore we explicitly warn from using opposed-image sequences for MR contrast studies. 14 ref.s, 4 figs.

  20. Practical macromolecular cryocrystallography

    SciTech Connect

    Pflugrath, J. W.

    2015-05-27

    Current methods, reagents and experimental hardware for successfully and reproducibly flash-cooling macromolecular crystals to cryogenic temperatures for X-ray diffraction data collection are reviewed. Cryocrystallography is an indispensable technique that is routinely used for single-crystal X-ray diffraction data collection at temperatures near 100 K, where radiation damage is mitigated. Modern procedures and tools to cryoprotect and rapidly cool macromolecular crystals with a significant solvent fraction to below the glass-transition phase of water are reviewed. Reagents and methods to help prevent the stresses that damage crystals when flash-cooling are described. A method of using isopentane to assess whether cryogenic temperatures have been preserved when dismounting screened crystals is also presented.

  1. Automated macromolecular crystallization screening

    DOEpatents

    Segelke, Brent W.; Rupp, Bernhard; Krupka, Heike I.

    2005-03-01

    An automated macromolecular crystallization screening system wherein a multiplicity of reagent mixes are produced. A multiplicity of analysis plates is produced utilizing the reagent mixes combined with a sample. The analysis plates are incubated to promote growth of crystals. Images of the crystals are made. The images are analyzed with regard to suitability of the crystals for analysis by x-ray crystallography. A design of reagent mixes is produced based upon the expected suitability of the crystals for analysis by x-ray crystallography. A second multiplicity of mixes of the reagent components is produced utilizing the design and a second multiplicity of reagent mixes is used for a second round of automated macromolecular crystallization screening. In one embodiment the multiplicity of reagent mixes are produced by a random selection of reagent components.

  2. High-contrast 3D microscopic imaging of deep layers in a biological medium

    NASA Astrophysics Data System (ADS)

    Faridian, Ahmad; Pedrini, Giancarlo; Osten, Wolfgang

    2014-03-01

    Multilayer imaging of biological specimens is a demanding field of research, but scattering is one of the major obstacles in imaging the internal layers of a specimen. Although in many studies the biological object is assumed to be a weak scatterer, this condition is hardly satisfied for sub-millimeter sized organisms. The scattering medium is inhomogeneously distributed inside the specimen. Therefore, the scattering which occurs in the upper layers of a given internal layer of interest is different from the lower layers. That results in a different amount of collectable information for a specific point in the layer from each view. An opposed view dark-field digital holographic microscope (DHM) has been implemented in this work to collect the information concurrently from both views and increase the image quality. Implementing a DHM system gives the possibility to perform digital refocusing process and obtain multilayer images from each side without depth scanning of the object. The results have been presented and discussed here for a Drosophila embryo.

  3. Microgravity and Macromolecular Crystallography

    NASA Technical Reports Server (NTRS)

    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.

  4. Practical macromolecular cryocrystallography

    PubMed Central

    Pflugrath, J. W.

    2015-01-01

    Cryocrystallography is an indispensable technique that is routinely used for single-crystal X-ray diffraction data collection at temperatures near 100 K, where radiation damage is mitigated. Modern procedures and tools to cryoprotect and rapidly cool macromolecular crystals with a significant solvent fraction to below the glass-transition phase of water are reviewed. Reagents and methods to help prevent the stresses that damage crystals when flash-cooling are described. A method of using isopentane to assess whether cryogenic temperatures have been preserved when dismounting screened crystals is also presented. PMID:26057787

  5. Macromolecular character of amber

    SciTech Connect

    Wert, C.A.; Weller, M.; Schlee, D.; Ledbetter, H.

    1989-03-15

    Measurements are reported of anelastic and dielectric loss of various ambers and copals. They show spectra typical of synthetic polymers. This similarity permits description of the macromolecular character of amber which was not possible from previous studies of chemical composition. Measurements on amber of several origins and geological ages show generally similar character, but also differences in detail. These may be caused by differences in chemistry of the original resin and the geological age and history of the amber, reflecting differences in degree of polymerization. Also reported are elastic constants measured at high frequency.

  6. [Manganese DPDP as a contrast medium for MR tomography of focal liver lesions. Tolerance and image quality in 20 patients].

    PubMed

    Kopp, A F; Laniado, M; Aicher, K P; Grönewäller, E F; Claussen, C D

    1992-12-01

    Twenty patients with focal liver lesions (18 metastases, 1 hepatocellular carcinoma, 1 cholangiocarcinoma) were given manganese DPDP as part of a multicentric phase II study of paramagnetic hepatobiliary MR contrast media. 5 mumol/kg manganese DPDP were injected into 10 patients in a concentration of 50 mumol/ml or 10 mumol/ml (3 ml/min). Blood pressure, pulse rate, ECG, respiratory rate, body temperature, blood and serum parameters and the patients' subjective feelings were recorded. MRI was performed with 1.5 T using T1- and T2-weighted sequences. 6 patients reported 8 side effects (flushing, feeling of warmth, metallic taste); 7 of these were produced by the 50 mumol concentration. Two hours after injection there was a significant reduction in alkaline phosphatase which was no longer present after 24 hours. On T1-weighted images manganese DPDP resulted in marked improvement in the contrast difference between the lesions and the liver parenchyma which resulted in a marked increase in the signal to noise ratio. Comparing the two concentrations, better results were obtained by the lower concentration. Extrahepatic uptake was found in the gallbladder, duodenum, pancreas, kidneys, gastric mucosa and myocardium. Manganese DPDP in a concentration of 10 mumol/ml and a dose of 5 mumol/kg is a well tolerated contrast medium which improves the demonstration of focal liver lesions in view of its distribution and uptake. The mechanisms for the transitory side effects require further studies. PMID:1457788

  7. Contrast Medium Induced Nephropathy after Endovascular Stent Graft Placement: An Examination of Its Prevalence and Risk Factors

    PubMed Central

    Kawatani, Yohei; Nakamura, Yoshitsugu; Mochida, Yoshihiko; Yamauchi, Naoya; Hayashi, Yujiro; Taneichi, Tetsuyoshi; Ito, Yujiro; Kurobe, Hirotsugu; Suda, Yuji; Hori, Takaki

    2016-01-01

    Endovascular stent graft placement has become a major treatment for thoracic and abdominal aneurysms. While endovascular therapy is less invasive than open surgery, it involves the use of a contrast medium. Contrast media can cause renal impairment, a condition termed as contrast-induced nephropathy (CIN). This study sought to evaluate the incidence and risk factors of CIN following endovascular stent graft placement for aortic aneurysm repair. The study included 167 consecutive patients who underwent endovascular stent graft placement in our hospital from October 2013 to June 2014. CIN was diagnosed using the European Society of Urogenital Radiology criteria. Patients with and without CIN were compared. Chi-squared tests, t-tests, and multivariate logistic regression analyses were performed. Thirteen patients (7.8%) developed CIN. Left ventricular dysfunction and intraoperative blood transfusion were significantly more frequent in the CIN group (P = 0.017 and P = 0.032, resp.). Multivariate analysis showed that left ventricular dysfunction had the strongest influence on CIN development (odds ratio 9.34, P = 0.018, and 95% CI = 1.46–59.7). Patients with CIN also experienced longer ICU and hospital stays. Measures to improve renal perfusion flow should be considered for patients with left ventricular dysfunction who are undergoing endovascular stent graft placement. PMID:27069685

  8. Quantitative analysis applied to contrast medium extravasation by using the computed-tomography number within the region of interest

    NASA Astrophysics Data System (ADS)

    Lee, Jae-Seung; Im, In-Chul; Kim, Moon-Jib; Goo, Eun-Hoe; Kim, Sun-Ju; Kim, Kwang; Kwak, Byung-Joon

    2014-02-01

    The present study was carried out to present a method to analyze extravasation quantitatively by measuring the computed tomography (CT) number after determining the region of interest (ROI) in the CT images obtained from patients suspected of extravasation induced by contrast medium auto-injection. To achieve this, we divided the study subjects into a group of patients who incurred extravasation and a group of patients who underwent routine scans without incurring extravasation. The CT numbers at IV sites were obtained as reference values, and CT numbers at extravasation sites and hepatic portal veins, respectively, were obtained as relative values. Thereupon, the predicted time for extravasation ( T EP ) and the predicted ratio for extravasation ( R EP ) of an extravasation site were obtained and analyzed quantitatively. In the case of extravasation induced by a dual auto-injector, the values of the CT numbers were confirmed to be lower and the extravasation site to be enlarged when compared to the extravasation induced by a single autoinjector. This is because the physiological saline introduced after the injection of the contrast agent diluted the concentration of the extravasated contrast agent. Additionally, the T EP caused by the auto-injector was about 40 seconds, and we could perform a precise quantitative assessment of the site suspected of extravasation. In conclusion, the dual auto-injection method, despite its advantage of reducing the volume of contrast agent and improving the quality of images for patients with good vascular integrity, was judged to be likely to increase the risk of extravasation and aggravate outcomes for patients with poor vascular integrity by enlarging extravasation sites.

  9. Case Report: Atrial Fibrillation After Intravenous Administration of Iodinated Contrast Medium in a Patient With Hepatocellular Carcinoma.

    PubMed

    Maimone, Sergio; Filomia, Roberto; Saitta, Carlo; Raimondo, Giovanni; Squadrito, Giovanni

    2015-09-01

    We describe the case of a 73-year-old woman with liver cirrhosis and hepatocellular carcinoma (HCC) who developed 2 distinct episodes of paroxystic atrial fibrillation (AF) each of which occurred 1 to 4 hours after iodine medium contrast-enhanced computed tomography. Sinus rhythm was restored by amiodarone therapy after the first AF episode and by electrical cardioversion after the second one. A careful clinical, biochemical, and instrumental examination showed that the patient had subclinical hyperthyroidism and moderate mitral insufficiency with mild atrial enlargement.Thus, the coexistence of both subclinical disthyroidism and of cardiac anatomical alterations may have predisposed the patient to AF that in fact occurred when exogenous iodine administration triggered a hyperthyroidism status. PMID:26334896

  10. Case Report: Atrial Fibrillation After Intravenous Administration of Iodinated Contrast Medium in a Patient With Hepatocellular Carcinoma

    PubMed Central

    Maimone, Sergio; Filomia, Roberto; Saitta, Carlo; Raimondo, Giovanni; Squadrito, Giovanni

    2015-01-01

    Abstract We describe the case of a 73-year-old woman with liver cirrhosis and hepatocellular carcinoma (HCC) who developed 2 distinct episodes of paroxystic atrial fibrillation (AF) each of which occurred 1 to 4 hours after iodine medium contrast-enhanced computed tomography. Sinus rhythm was restored by amiodarone therapy after the first AF episode and by electrical cardioversion after the second one. A careful clinical, biochemical, and instrumental examination showed that the patient had subclinical hyperthyroidism and moderate mitral insufficiency with mild atrial enlargement. Thus, the coexistence of both subclinical disthyroidism and of cardiac anatomical alterations may have predisposed the patient to AF that in fact occurred when exogenous iodine administration triggered a hyperthyroidism status. PMID:26334896

  11. Phantom study to evaluate contrast-medium-enhanced digital subtraction mammography with a full-field indirect-detection system

    SciTech Connect

    Palma, B. A.; Rosado-Mendez, I.; Villasenor, Y.; Brandan, M. E.

    2010-02-15

    This phantom study simulates contrast-medium-enhanced digital subtraction mammography (CEDM) and compares subtracted image quality and total mean glandular dose for two alternative spectral combinations available in a GE Senographe DS mammography unit. The first choice takes advantage of large iodine attenuation at low photon energies and uses traditionally available spectra (anode/filter combinations Mo/Mo at 25 kV and Rh/Rh at 40 kV, ''Mo25-Rh40''). The second choice, selected from a previous analytical optimization, includes harder spectra obtained by adding external filtration to traditional beams (Rh/Rh at 34 kV and Rh/Rh+5 mm of Al at 45 kV, ''Rh34-Rh45H''). Individual images of a custom-made phantom containing tubes of various diameters filled with water- or iodine-based contrast agent were acquired with both spectral combinations. The total breast entrance air kerma, considering subtraction of two images, was limited to 8.76 mGy (1 R). The results were compared to predictions obtained through an analytical formalism that assumes noise of stochastic origin. Individual images were evaluated and subtracted under five combinations of temporal and dual-energy modalities. Signal variance analysis in individual raw images showed important contributions of nonstochastic origin, associated with the software applied to raw images, the curved geometry, and strong attenuation of the phantom cylindrical iodine-filled tubes, causing experimental SNR to vary from 2.2 to 0.8 times the predictions from low to high values of SNR. Iodine contrast in the subtracted images was found to be mainly defined by the spectra, independent of exposure, and linearly dependent on the iodine mass thickness. The highest contrast was obtained with the combined dual-energy temporal subtraction with Rh34-Rh45H, its value was 7% larger than the highest value measured with Mo25-Rh40. As expected, temporal modalities (single and dual energy, any spectral choice) led to higher contrast

  12. Teaching macromolecular modeling.

    PubMed

    Harvey, S C; Tan, R K

    1992-12-01

    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 a one-semester modeling course that combines lectures, discussions, and a laboratory using a commercial modeling package. In the laboratory, students carry out prescribed exercises that are coordinated to the lectures, and they complete a term project on a modeling problem of their choice. The goal is to give students an understanding of what kinds of problems can be attacked by molecular modeling methods and which problems are beyond the current capabilities of those methods. PMID:1489919

  13. Macromolecular crystal growing system

    NASA Technical Reports Server (NTRS)

    Snyder, Robert S. (Inventor); Herren, Blair J. (Inventor); Carter, Daniel C. (Inventor); Yost, Vaughn H. (Inventor); Bugg, Charles E. (Inventor); Delucas, Lawrence J. (Inventor); Suddath, Fred L. (Inventor)

    1991-01-01

    A macromolecular crystal growing system especially designed for growing crystals in the low gravity of space as well as the gravity of earth includes at least one tray assembly, a carrier assembly which receives the tray, and a refrigeration-incubation module in which the carrier assembly is received. The tray assembly includes a plurality of sealed chambers with a plastic syringe and a plug means for the double tip of the syringe provided therein. Ganging mechanisms operate the syringes and plugs simultaneously in a precise and smooth operation. Preferably, the tray assemblies are mounted on ball bearing slides for smooth operation in inserting and removing the tray assemblies into the carrier assembly. The plugging mechanism also includes a loading control mechanism. A mechanism for leaving a syringe unplugged is also provided.

  14. Dose perturbations due to contrast medium and air in MammoSite registered treatment: An experimental and Monte Carlo study

    SciTech Connect

    Cheng, C.-W.; Mitra, R.; Allen Li, X.; Das, Indra J.

    2005-07-15

    In the management of early breast cancer, a partial breast irradiation technique called MammoSite registered (Proxima Therapeutic Inc., Alpharetta, GA) has been advocated in recent years. In MammoSite, a balloon implanted at the surgical cavity during tumor excision is filled with a radio-opaque solution, and radiation is delivered via a high dose rate brachytherapy source situated at the center of the balloon. Frequently air may be introduced during placement of the balloon and/or injection of the contrast solution into the balloon. The purpose of this work is to quantify as well as to understand dose perturbations due to the presence of a high-Z contrast medium and/or an air bubble with measurements and Monte Carlo calculations. In addition, the measured dose distribution is compared with that obtained from a commercial treatment planning system (Nucletron PLATO system). For a balloon diameter of 42 mm, the dose variation as a function of distance from the balloon surface is measured for various concentrations of a radio-opaque solution (in the range 5%-25% by volume) with a small volume parallel plate ion chamber and a micro-diode detector placed perpendicular to the balloon axis. Monte Carlo simulations are performed to provide a basic understanding of the interaction mechanism and the magnitude of dose perturbation at the interface near balloon surface. Our results show that the radio-opaque concentration produces dose perturbation up to 6%. The dose perturbation occurs mostly within the distances <1 mm from the balloon surface. The Plato system that does not include heterogeneity correction may be sufficient for dose planning at distances {>=}10 mm from the balloon surface for the iodine concentrations used in the MammoSite procedures. The dose enhancement effect near the balloon surface (<1 mm) due to the higher iodine concentration is not correctly predicted by the Plato system. The dose near the balloon surface may be increased by 0.5% per cm{sup 3} of air

  15. A study on quantitative analyses before and after injection of contrast medium in spine examinations performed by using diffusion weighted image

    NASA Astrophysics Data System (ADS)

    Cho, Jae-Hwan; Lee, Hae-Kag; Kim, Yong-Kyun; Dong, Kyung-Rae; Chung, Woon-Kwan; Joo, Kyu-Ji

    2013-02-01

    This study examined the changes in the signal-to-noise ratio (SNR), the contrast-to-noise ratio (CNR) and the apparent diffusion coefficient (ADC) of metastatic cancer in the lumbar region by using diffusion weighted image taken with a 1.5 T (Tesla) magnetic resonance (MR) scanner before and after injecting a contrast medium. The study enrolled 30 healthy people and 30 patients with metastatic spine cancer from patients who underwent a lumbar MRI scan from January 2011 to October 2012. A 1.5 T MR scanner was used to obtain the diffusion weighted images (DWIs) before and after injecting the contrast medium. In the group with metastatic spine cancer, the SNR and the CNR were measured in three parts among the L1-L5 lumbar vertebrae, which included the part with metastatic spine cancer, the area of the spine with spine cancer, and the area of spine under the region with cancer. In the acquired ADC map image, the SNRs and the ADCs of the three parts were measured in ADC map images. Among the healthy subjects, the measurements were conducted for the lumbar regions of L3-L5. According to the results, in the group with metastatic spine cancer, the SNR in the DWI before the contrast medium had been injected was lowest in the part with spine cancer. In the DWI after the contrast medium had been injected, the SNR and the CNR were increased in all three parts. In the ADC map image after the contrast medium had been injected, the SNR decreased in all three parts compared to the SNR before the contrast had been injected. The ADC after had been injected the contrast medium was decreased in all three parts compared to that before the contrast medium had been injected. In the healthy group, the SNR was increased in the L3-L5 lumbar regions in the DWI. In the ADC map image, the SNR in all the three parts was decreased in the DWI after injecting the contrast medium had been injected. The ADC in the ADC map image was also decreased in all three parts.

  16. Cell-Free Protein Expression under Macromolecular Crowding Conditions

    PubMed Central

    Ge, Xumeng; Luo, Dan; Xu, Jianfeng

    2011-01-01

    Background Cell-free protein expression (CFPE) comprised of in vitro transcription and translation is currently manipulated in relatively dilute solutions, in which the macromolecular crowding effects present in living cells are largely ignored. This may not only affect the efficiency of protein synthesis in vitro, but also limit our understanding of the functions and interactions of biomolecules involved in this fundamental biological process. Methodology/Principal Findings Using cell-free synthesis of Renilla luciferase in wheat germ extract as a model system, we investigated the CFPE under macromolecular crowding environments emulated with three different crowding agents: PEG-8000, Ficoll-70 and Ficoll-400, which vary in chemical properties and molecular size. We found that transcription was substantially enhanced in the macromolecular crowding solutions; up to 4-fold increase in the mRNA production was detected in the presence of 20% (w/v) of Ficoll-70. In contrast, translation was generally inhibited by the addition of each of the three crowding agents. This might be due to PEG-induced protein precipitation and non-specific binding of translation factors to Ficoll molecules. We further explored a two-stage CFPE in which transcription and translation was carried out under high then low macromolecular crowding conditions, respectively. It produced 2.2-fold higher protein yield than the coupled CFPE control. The macromolecular crowding effects on CFPE were subsequently confirmed by cell-free synthesis of an approximately two-fold larger protein, Firefly luciferase, under macromolecular crowding environments. Conclusions/Significance Three macromolecular crowding agents used in this research had opposite effects on transcription and translation. The results of this study should aid researchers in their choice of macromolecular crowding agents and shows that two-stage CFPE is more efficient than coupled CFPE. PMID:22174874

  17. Conventional versus storage phosphor-plate digital images to visualize the root canal system contrasted with a radiopaque medium.

    PubMed

    Naoum, Hani J; Chandler, Nicholas P; Love, Robert M

    2003-05-01

    The pulp tissue was removed from 20 mandibular first molar teeth using 2.5% NaOCl irrigation and hand files. The dried canals were infused with radiopaque contrast medium. Standardized conventional and Digora digital images were obtained of each tooth positioned in a dried mandible at 0- and 30-degree horizontal angulations. Three evaluators rated the image clarity of the 0- and 30-degree original, enhanced, three-dimensional, zoom, and reverse digital image modes as superior, equal, or inferior to corresponding 0- and 30-degree conventional radiographs. The ratings were compared using the Wilcoxon signed rank test. The original, three-dimensional, zoom, or reverse digital images were inferior to the conventional radiographs for clarity of canal anatomy. The enhanced digital images were not always inferior to the conventional radiographs and were the only images superior to the original digital images. Overall, evaluators rated the image clarity of root canal anatomy on conventional radiographs better than on Digora images. However, factors in the experimental design may have contributed to this result. PMID:12775009

  18. [Consciousness Impairment and Left Hemiparesis due to Contrast Medium in the Coil Embolization of Unruptured Large Right Middle Cerebral Artery Aneurysm:A Case Report].

    PubMed

    Nakajima, Nobuhiko; Koyanagi, Masaomi; Kobayashi, Tamaki; Enatsu, Rei; Oda, Masashi; Saiki, Masaaki

    2016-05-01

    Neurological deficits following coil embolization of anterior circulation aneurysms due to the toxicity of contrast medium are rare. Here, we describe a patient with mild consciousness impairment and left hemiparesis following coil embolization of a large right middle cerebral artery aneurysm without evidence of ischemia or hemorrhage, who recovered completely with conservative treatment. The patient's clinical course and radiological findings led us to conclude that the neurological deficits were due to the toxic effect of contrast medium used during the coil embolization. PMID:27166842

  19. SU-C-12A-03: The Impact of Contrast Medium On Radiation Dose in CT: A Systematic Evaluation Across 58 Patient Models

    SciTech Connect

    Sahbaee, P; Samei, E; Segars, W

    2014-06-01

    Purpose: To assess the effect of contrast medium on radiation dose as a function of time via Monte Carlo simulation from the liver CT scan across a library of 5D XCAT models Methods: A validated Monte Carlo simulation package (PENELOPE) was employed to model a CT system (LightSpeed 64 VCT, GE Healthcare). The radiation dose was estimated from a common abdomen CT examination. The dose estimation was performed on a library of adult extended cardiac-torso (5D XCAT) phantoms (35 male, 23 female, mean age 51.5 years, mean weight 80.2 kg). The 5D XCAT models were created based on patient-specific iodine concentration-time results from our computational contrast medium propagation model for different intravenous injection protocols. To enable a dynamic estimation of radiation dose, each organ in the model was assigned to its own time-concentration curve via the PENELOPE package, material.exe. Using the Monte Carlo, for each scan time point after the injection, 80 million photons were initiated and tracked through the phantoms. Finally, the dose to the liver was tallied from the deposited energy. Results: Monte Carlo simulation results of radiation dose delivered to the liver from the XCAT models indicated up to 30% increase in dose for different time after the administration of contrast medium. Conclusion: The contrast enhancement is employed in over 60% of imaging modalities, which not only remarkably affects the CT image quality, but also increases the radiation dose by as much as 70%. The postinjection multiple acquisition in several enhanced CT protocols, makes the radiation dose increment through the use of contrast medium, an inevitable factor in optimization of these protocols. The relationship between radiation dose and injected contrast medium as a function of time studied in this work allows optimization of contrast administration for vulnerable individuals.

  20. LASER APPLICATIONS AND OTHER TOPICS IN QUANTUM ELECTRONICS: Improvement of the optical imaging of objects in a strongly scattering medium by means of contrast-enhancing dyes

    NASA Astrophysics Data System (ADS)

    Vorob'ev, Nikolai S.; Podgaetskii, Vitalii M.; Smirnov, A. V.; Tereshchenko, Sergei A.; Tomilova, Larisa G.

    1999-12-01

    The problem of enhancing the contrast of optical images in a strongly scattering medium by means of luminescent and absorbing dyes, topical in laser tomography, is examined. Preparations based on diphthalocyanine compounds were selected on the grounds of their tropism and resistance to the action of heat and light. Images with enhanced contrast in model scattering media (an aqueous solution of milk and margarine) were obtained in the IR region of the spectrum using the radiation of a picosecond neodymium laser.

  1. Evaluation of the Dark-Medium Objective Lens in Counting Asbestos Fibers by Phase-Contrast Microscopy

    PubMed Central

    Lee, Eun Gyung; Nelson, John H.; Kashon, Michael L.; Harper, Martin

    2015-01-01

    A Japanese round-robin study revealed that analysts who used a dark-medium (DM) objective lens reported higher fiber counts from American Industrial Hygiene Association (AIHA) Proficiency Analytical Testing (PAT) chrysotile samples than those using a standard objective lens, but the cause of this difference was not investigated at that time. The purpose of this study is to determine any major source of this difference by performing two sets of round-robin studies. For the first round-robin study, 15 AIHA PAT samples (five each of chrysotile and amosite generated by water-suspended method, and five chrysotile generated by aerosolization method) were prepared with relocatable cover slips and examined by nine laboratories. A second round-robin study was then performed with six chrysotile field sample slides by six out of nine laboratories who participated in the first round-robin study. In addition, two phase-shift test slides to check analysts’ visibility and an eight-form diatom test plate to compare resolution between the two objectives were examined. For the AIHA PAT chrysotile reference slides, use of the DM objective resulted in consistently higher fiber counts (1.45 times for all data) than the standard objective (P-value < 0.05), regardless of the filter generation (water-suspension or aerosol) method. For the AIHA PAT amosite reference and chrysotile field sample slides, the fiber counts between the two objectives were not significantly different. No statistically significant differences were observed in the visibility of blocks of the test slides between the two objectives. Also, the DM and standard objectives showed no pattern of differences in viewing the fine lines and/or dots of each species images on the eight-form diatom test plate. Among various potential factors that might affect the analysts’ performance of fiber counts, this study supports the greater contrast caused by the different phase plate absorptions as the main cause of high counts for

  2. Use of computed tomography-lymphangiography with direct injection of water-soluble contrast medium to identify the origin of chylous ascites.

    PubMed

    Otake, Kohei; Uchida, Keiichi; Inoue, Mikihiro; Koike, Yuhki; Narushima, Mitsunaga; Kusunoki, Masato

    2015-01-01

    Contrast lymphangiography is a useful technique to determine the site of lymphatic leakage in the patient with chylous ascites. Conventional lymphangiography with lipid-soluble contrast material carries the disadvantage of complications, such as oil emboli and lymphedema. The authors report a successful case of computed tomography (CT)-lymphangiography with direct injection of water-soluble contrast medium into a lower limb lymphatic vessel to determine the site of lymphatic leakage in a pediatric patient with refractory primary chylous ascites. The patient subsequently underwent laparoscopic ligation of the leaking site and recovered well. This novel technique offers superior potential for preoperative assessment and the planning of laparoscopic repair. PMID:26993687

  3. Contrast Medium Exposure During Computed Tomography and Risk of Development of End-Stage Renal Disease in Patients With Chronic Kidney Disease

    PubMed Central

    Hsieh, Ming-Shun; Chiu, Chien-Shan; How, Chorng-Kuang; Chiang, Jen-Huai; Sheu, Meei-Ling; Chen, Wen-Chi; Lin, Hsuan-Jen; Hsieh, Vivian Chia-Rong; Hu, Sung-Yuan

    2016-01-01

    Abstract The aim of the study was to investigate the long-term association between contrast medium exposure during computed tomography (CT) and the subsequent development of end-stage renal disease (ESRD) in patients with chronic kidney disease (CKD). We conducted a population-based cohort study using Taiwan's National Health Insurance Research Database. A total of 7100 patients with nonadvanced CKD who underwent contrast medium-enhanced CT were identified and served as the study cohort. To avoid selection bias, we used the propensity score to match 7100 nonadvanced CKD patients, who underwent noncontrast medium-enhanced CT to serve as the comparison cohort. The age, sex, index year, and frequency of undergoing CTs were also matched between the study and comparison cohorts. Participants were followed until a new diagnosis of ESRD or December 31, 2011. Hazard ratios (HRs) with 95% confidence interval (95% CI) were calculated using the Cox proportional hazards regression. Contrast medium exposure was not identified as a risk factor for developing ESRD in nonadvanced CKD patients after confounders adjustment (adjusted HR = 0.91; 95% CI, 0.66–1.26; P = 0.580). We further divided the patients who underwent CTs with contrast medium use into ≤1 exposure per year on average, >1 and <2 exposure per year on average, and ≥2 exposure per year on average. After adjusting for confounders, we identified a much higher risk for developing ESRD in the 2 groups of >1 and <2 exposure per year on average and ≥2 exposure per year on average (adjusted HR = 8.13; 95% CI, 5.57–11.87 and adjusted HR = 12.08; 95% CI, 7.39–19.75, respectively) compared with the patients who underwent CTs without contrast medium use. This long-term follow-up study demonstrated that contrast medium exposure was not associated with an increased risk of ESRD development in nonadvanced CKD patients. PMID:27100424

  4. MO-E-17A-02: Incorporation of Contrast Medium Dynamics in Anthropomorphic Phantoms: The Advent of 5D XCAT Models

    SciTech Connect

    Sahbaee, P; Samei, E; Segars, W

    2014-06-15

    Purpose: To develop a unique method to incorporate the dynamics of contrast-medium propagation into the anthropomorphic phantom, to generate a five-dimensional (5D) patient model for multimodality imaging studies. Methods: A compartmental model of blood circulation network within the body was embodied into an extended cardiac-torso (4D-XCAT) patient model. To do so, a computational physiologic model of the human cardiovascular system was developed which includes a series of compartments representing heart, vessels, and organs. Patient-specific cardiac output and blood volume were used as inputs influenced by the weight, height, age, and gender of the patient's model. For a given injection protocol and given XCAT model, the contrast-medium transmission within the body was described by a series of mass balance differential equations, the solutions to which provided the contrast enhancement-time curves for each organ; thereby defining the tissue materials including the contrastmedium within the XCAT model. A library of time-dependent organ materials was then defined. Each organ in each voxelized 4D-XCAT phantom was assigned to a corresponding time-varying material to create the 5D-XCAT phantom in which the fifth dimension is blood/contrast-medium within the temporal domain. Results: The model effectively predicts the time-varying concentration behavior of various contrast-medium administration in each organ for different patient models as function of patient size (weight/height) and different injection protocol factors (injection rate and pattern, iodine concentration or volume). The contrast enhanced XCAT patient models was developed based on the concentration of iodine as a function of time after injection. Conclusion: Majority of medical imaging systems take advantage of contrast-medium administration in terms of better image quality, the effect of which was ignored in previous optimization studies. The study enables a comprehensive optimization of contrast

  5. Drug eruption caused by the nonionic contrast medium iohexol. "Recall-like phenomenon" appearing on an area previously affected by herpes zoster.

    PubMed

    Matsumura, Takumi; Watanabe, Hideaki; Batchelor, Jonathan; Sueki, Hirohiko; Iijima, Masafumi

    2006-10-01

    We report a case of "recall-like phenomenon" caused by nonionic contrast medium. A 62-year-old woman suffering from postherpetic neuralgia developed erythematous plaques 12 h after an intercostal nerve block under X-ray guidance using iohexol (Omnipaque) as contrast medium. The erythematous plaques were preferentially located in the sites where she had experienced herpes zoster 4 months previously. The lesions cleared spontaneously leaving no pigmentation. Both patch testing and intradermal testing with iohexol and ioversol were positive. We postulate that local immunological changes in the skin, such as an increased number and/or accelerated activity of Langerhans cells and mast cells in the herpes zoster lesions, were responsible for this phenomenon. This "recall-like phenomenon", occurring preferentially in skin previously affected by herpes zoster, could facilitate understanding of the pathology of drug eruptions. PMID:17040501

  6. [Anaphylactic shock from an iodine contrast medium: role of the allergy check-up in one case].

    PubMed

    Halna du Fretay, X; Gaillet, G; Hoarau, C; Blanchard-Lemoine, B

    2012-12-01

    Anaphylactoid reactions to iodine contrast media are rare but serious, possibly life-threatening and calling an appropriate and urgent care. The physiopathological mechanism of these reactions remains to be fully elucidated. This reaction is still mostly called "pseudoallergic" in the literature. However, recent papers emphasise that a true allergic process is more frequent than previously expected. They also insist on the interest of running allergy tests including skin testing. We report the case of an anaphylactic shock to iodine contrast media, occurring during coronary angiography. We performed an allergy check-up and found the culprit allergen. We also evidenced a cross-reaction to another contrast media from the similar group. On the other hand, there was no reaction to contrast media of other types. With these results, another coronary angiography could be performed without any adverse event. When hypersensitivity reactions to iodine contrast media occur, it is mandatory to perform a complete allergy check-up. This will help determine the precise mechanism of the reaction and find the culprit allergen. PMID:23102513

  7. Blackberry (Rubus spp.): a pH-dependent oral contrast medium for gastrointestinal tract images by magnetic resonance imaging.

    PubMed

    Espinosa, María G; Sosa, Modesto; De León-Rodríguez, Luis M; Córdova, Teodoro; Bernal-Alvarado, Jesus; Avila-Rodríguez, Mario; Reyes-Aguilera, Jose A; Ortíz, Juan J; Barrios, Fernando A

    2006-02-01

    In this study, seven fruits have been tested on their magnetic properties, paramagnetic metal content and contrast enhancement in magnetic resonance imaging (MRI) of phantom and in vivo. Magnetic susceptibility was determined for the fruit pulps, as well as the contents of paramagnetic metals; iron, manganese and copper. The total content of these metals was 4.3, 8.6, 11.1, 10.9, 12.3, 8.3 and 29.3 mg/kg of fruit for plum, blueberry, apple (red), pineapple, beet, grape, blackberry, respectively, and with magnetic susceptibility of -2.29+/-0.07, -2.43+/-0.07, -2.13+/-0.07, -1.84+/-0.02, -1.75+/-0.01, -1.78+/-0.06, -2.18+/-0.07 SI, respectively. T(1)- and T(2)-weighted MR images were performed for the seven fruits and water (chi= -9.98 x 10(-3) SI) and in one subject. While there was no correlation between the magnetic susceptibility and contrast enhancement, there is a correlation with the total paramagnetic metal content determined with contrast enhancement in MRI. Thus, blackberry (Rubus spp.) contrast enhancement was the highest among the fruits in T(1)-weighted images. Furthermore, this fruit's contrast enhancement shows to be pH-dependent. These characteristics and the wide availability of the Rubus spp. suggest that it should be implemented as an oral contrast agent in images by MR to assess the function of the gastric section of the GI tract. Furthermore, it has the advantage of being a natural meal, so that it can be well tolerated by the patients and use as much as it is needed without side effects. PMID:16455409

  8. Macromolecular Crowding Modulates Actomyosin Kinetics.

    PubMed

    Ge, Jinghua; Bouriyaphone, Sherry D; Serebrennikova, Tamara A; Astashkin, Andrei V; Nesmelov, Yuri E

    2016-07-12

    Actomyosin kinetics is usually studied in dilute solutions, which do not reflect conditions in the cytoplasm. In cells, myosin and actin work in a dense macromolecular environment. High concentrations of macromolecules dramatically reduce the amount of free space available for all solutes, which results in an effective increase of the solutes' chemical potential and protein stabilization. Moreover, in a crowded solution, the chemical potential depends on the size of the solute, with larger molecules experiencing a larger excluded volume than smaller ones. Therefore, since myosin interacts with two ligands of different sizes (actin and ATP), macromolecular crowding can modulate the kinetics of individual steps of the actomyosin ATPase cycle. To emulate the effect of crowding in cells, we studied actomyosin cycle reactions in the presence of a high-molecular-weight polymer, Ficoll70. We observed an increase in the maximum velocity of the actomyosin ATPase cycle, and our transient-kinetics experiments showed that virtually all individual steps of the actomyosin cycle were affected by the addition of Ficoll70. The observed effects of macromolecular crowding on the myosin-ligand interaction cannot be explained by the increase of a solute's chemical potential. A time-resolved Förster resonance energy transfer experiment confirmed that the myosin head assumes a more compact conformation in the presence of Ficoll70 than in a dilute solution. We conclude that the crowding-induced myosin conformational change plays a major role in the changed kinetics of actomyosin ATPase. PMID:27410745

  9. Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform

    PubMed Central

    Xu, Dong; Zhang, Yang

    2009-01-01

    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. PMID:19956577

  10. Facile Preparation of a Macromolecular Benzophenone Photoinitiator

    NASA Astrophysics Data System (ADS)

    Huang, Qinghua; Gu, Lingling; Bai, Xiongxiong; Cheng, Chuanjie

    2014-08-01

    Photoinitiators play important roles in the preparation of photo-cured resins. Macromolecular as well as reactive photoinitiators have attracted much attention both in industry and in academia due to the disadvantages of conventional small molecular photoinitiators such as volatility and mobility. A macromolecular benzophenone photoinitiator was designed and efficiently synthesized in this study. Hydroxyl-containing Michler's ketone was firstly synthesized in 82% yield, followed by reacting with toluene di-isocyanate (TDI) to prepare polyurethanetype macromolecular benzophenone photoinitiator.

  11. [Color-coded duplex sonography and ultrasound contrast medium in the study of peripheral arteries--initial clinical experiences].

    PubMed

    Fobbe, F; Ohnesorge, I; Reichel, M; Dollinger, P; Schürmann, R; Wolf, K J

    1992-08-01

    Ultrasound contrast agents (US-CA) amplify reflected sound waves. Most substances used as contrast agents are destroyed when passing the lungs. SH U 508 is a new US-CA that can pass the lungs without impairment after peripheral intravenous application. In a clinical trial of this US-CA, we investigated its effect on the visualization of blood movement in peripheral arteries by color-coded Duplex sonography (CCDS). The leg arteries of 20 patients with severe chronic arterial occlusion were examined by CCDS (QAD I and Platinum) after i.v. application of the US-CA. After passage of the pulmonary capillaries, the US-CA amplified blood flow signals in the arterial system in a dose-dependent manner with both systems used. Undesired side-effects were not observed. The amplification produced by appropriate concentrations of the US-CA markedly improved the visualization of blood movement. Further studies are required to determine the optimal dosage and application technique as well as the indication for using this US-CA. PMID:1411473

  12. Low kV settings CT angiography (CTA) with low dose contrast medium volume protocol in the assessment of thoracic and abdominal aorta disease: a feasibility study

    PubMed Central

    Talei Franzesi, C; Fior, D; Bonaffini, P A; Minutolo, O; Sironi, S

    2015-01-01

    Objective: To assess the diagnostic quality of low dose (100 kV) CT angiography (CTA), by using ultra-low contrast medium volume (30 ml), for thoracic and abdominal aorta evaluation. Methods: 67 patients with thoracic or abdominal vascular disease underwent multidetector CT study using a 256 slice scanner, with low dose radiation protocol (automated tube current modulation, 100 kV) and low contrast medium volume (30 ml; 4 ml s−1). Density measurements were performed on ascending, arch, descending thoracic aorta, anonymous branch, abdominal aorta, and renal and common iliac arteries. Radiation dose exposure [dose–length product (DLP)] was calculated. A control group of 35 patients with thoracic or abdominal vascular disease were evaluated with standard CTA protocol (automated tube current modulation, 120 kV; contrast medium, 80 ml). Results: In all patients, we correctly visualized and evaluated main branches of the thoracic and abdominal aorta. No difference in density measurements was achieved between low tube voltage protocol (mean attenuation value of thoracic aorta, 304 HU; abdominal, 343 HU; renal arteries, 331 HU) and control group (mean attenuation value of thoracic aorta, 320 HU; abdominal, 339; renal arteries, 303 HU). Radiation dose exposure in low tube voltage protocol was significantly different between thoracic and abdominal low tube voltage studies (490 and 324 DLP, respectively) and the control group (thoracic DLP, 1032; abdomen, DLP 1078). Conclusion: Low-tube-voltage protocol may provide a diagnostic performance comparable with that of the standard protocol, decreasing radiation dose exposure and contrast material volume amount. Advances in knowledge: Low-tube-voltage-setting protocol combined with ultra-low contrast agent volume (30 ml), by using new multidetector-row CT scanners, represents a feasible diagnostic tool to significantly reduce the radiation dose delivered to patients and to preserve renal function

  13. Analytical model for macromolecular partitioning during yeast cell division

    PubMed Central

    2014-01-01

    Background Asymmetric cell division, whereby a parent cell generates two sibling cells with unequal content and thereby distinct fates, is central to cell differentiation, organism development and ageing. Unequal partitioning of the macromolecular content of the parent cell — which includes proteins, DNA, RNA, large proteinaceous assemblies and organelles — can be achieved by both passive (e.g. diffusion, localized retention sites) and active (e.g. motor-driven transport) processes operating in the presence of external polarity cues, internal asymmetries, spontaneous symmetry breaking, or stochastic effects. However, the quantitative contribution of different processes to the partitioning of macromolecular content is difficult to evaluate. Results Here we developed an analytical model that allows rapid quantitative assessment of partitioning as a function of various parameters in the budding yeast Saccharomyces cerevisiae. This model exposes quantitative degeneracies among the physical parameters that govern macromolecular partitioning, and reveals regions of the solution space where diffusion is sufficient to drive asymmetric partitioning and regions where asymmetric partitioning can only be achieved through additional processes such as motor-driven transport. Application of the model to different macromolecular assemblies suggests that partitioning of protein aggregates and episomes, but not prions, is diffusion-limited in yeast, consistent with previous reports. Conclusions In contrast to computationally intensive stochastic simulations of particular scenarios, our analytical model provides an efficient and comprehensive overview of partitioning as a function of global and macromolecule-specific parameters. Identification of quantitative degeneracies among these parameters highlights the importance of their careful measurement for a given macromolecular species in order to understand the dominant processes responsible for its observed partitioning. PMID

  14. Physical modelling of a surface-wave survey over a laterally varying granular medium with property contrasts and velocity gradients

    NASA Astrophysics Data System (ADS)

    Bergamo, Paolo; Bodet, Ludovic; Socco, Laura Valentina; Mourgues, Régis; Tournat, Vincent

    2014-04-01

    Laboratory experiments using laser-based ultrasonic techniques can be used to simulate seismic surveys on highly controlled small-scale physical models of the subsurface. Most of the time, such models consist in assemblies of homogeneous and consolidated materials. To enable the physical modelling of unconsolidated, heterogeneous and porous media, the use of granular materials is suggested here. We describe a simple technique to build a two-layer physical model characterized by lateral variations, strong property contrasts and velocity gradients. We use this model to address the efficiency of an innovative surface-wave processing technique developed to retrieve 2-D structures from a limited number of receivers. A step by step inversion procedure of the extracted dispersion curves yields accurate results so that the 2-D structure of the physical model is satisfactorily reconstructed. The velocity gradients within each layer are accurately retrieved as well, confirming current theoretical and experimental studies regarding guided surface acoustic modes in unconsolidated granular media.

  15. Use of postmortem coronary computed tomography angiography with water-insoluble contrast medium to detect stenosis of the left anterior descending artery in a case of sudden death.

    PubMed

    Takahashi, Yoichiro; Sano, Rie; Takahashi, Keiko; Kominato, Yoshihiko; Takei, Hiroyuki; Kobayashi, Susumu; Shimada, Takehiro; Tokue, Hiroyuki; Awata, Sachiko; Hirasawa, Satoshi

    2016-03-01

    A 40-year-old man was found dead on a sidewalk in an expressway parking area one hour after he had entered the area on a motorcycle. A medicolegal autopsy was performed to reveal the cause of this sudden and unexpected death. Postmortem coronary CT angiography after introduction of 5% gelatin-barium emulsion as a radiopaque contrast medium into the heart demonstrated a significant arterial luminal filling defect in the left anterior descending (LAD) coronary artery. Macroscopic and microscopic examinations revealed that a thrombus had become deposited on ruptured plaque within the LAD artery, and that a small amount of the contrast medium was present between the thrombus and the vessel endothelium. These histological findings were consistent with incomplete occlusion of the LAD artery in the 3D reconstructed image. The cause of death in this case was definitively determined to be ischemic heart disease. Postmortem angiography played a role in screening of a vascular lesion that was subsequently verified by histology to have been responsible for sudden and unexpected death. PMID:26980254

  16. Electromagnetic induction in a conductive strip in a medium of contrasting conductivity: application to VLF and MT above molten dykes

    NASA Astrophysics Data System (ADS)

    Davis, Paul M.

    2014-11-01

    Very low frequency (VLF) electromagnetic waves that penetrate conductive magma-filled dykes generate secondary fields on the surface that can be used to invert for dyke properties. The model used for the interpretation calculates currents induced in a conductive strip by an inducing field that decays exponentially with depth due to the conductivity of the surrounding medium. The differential equations are integrated to give an inhomogeneous Fredholm equation of the second kind with a kernel consisting of a modified Bessel function of the second kind. Numerical methods are typically used to solve for the induced currents in the strip. In this paper, we apply a modified Galerkin-Chebyshev method, which involves separating the kernel into source and field spectra and integrating the source terms to obtain a matrix equation for the unknown coefficients. The incident wave is expressed as a Chebyshev series. The modified Bessel function is separated into a logarithmic singularity and a non-singular remainder, both of which are expanded in complex Chebyshev polynomials. The Chebyshev coefficients for the remainder are evaluated using a fast Fourier transform, while the logarithmic term and incident field have analytic series. The deconvolution then involves a matrix inversion. The results depend on the ratio of strip-size to skin-depth. For infinite skin-depth and a singular conductivity distribution given by τ_0 a/√{a^2 - z^2 } (where τ0 is the conductance, a is the half-length and z the distance from the centre), Parker gives an analytic solution. We present a similar analytic series solution for the finite skin-depth case, where the size to skin depth ratio is small. Results are presented for different ratios of size to skin depth that can be compared with numerical solutions. We compare full-space and half-space solutions. A fit of the model to VLF data taken above a magma filled dykes in Hawaii and Mt Etna demonstrates that while properties such as depth to top

  17. How can macromolecular crowding inhibit biological reactions? The enhanced formation of DNA nanoparticles

    PubMed Central

    Hou, Sen; Trochimczyk, Piotr; Sun, Lili; Wisniewska, Agnieszka; Kalwarczyk, Tomasz; Zhang, Xuzhu; Wielgus-Kutrowska, Beata; Bzowska, Agnieszka; Holyst, Robert

    2016-01-01

    In contrast to the already known effect that macromolecular crowding usually promotes biological reactions, solutions of PEG 6k at high concentrations stop the cleavage of DNA by HindIII enzyme, due to the formation of DNA nanoparticles. We characterized the DNA nanoparticles and probed the prerequisites for their formation using multiple techniques such as fluorescence correlation spectroscopy, dynamic light scattering, fluorescence analytical ultracentrifugation etc. In >25% PEG 6k solution, macromolecular crowding promotes the formation of DNA nanoparticles with dimensions of several hundreds of nanometers. The formation of DNA nanoparticles is a fast and reversible process. Both plasmid DNA (2686 bp) and double-stranded/single-stranded DNA fragment (66bp/nt) can form nanoparticles. We attribute the enhanced nanoparticle formation to the depletion effect of macromolecular crowding. This study presents our idea to enhance the formation of DNA nanoparticles by macromolecular crowding, providing the first step towards a final solution to efficient gene therapy. PMID:26903405

  18. How can macromolecular crowding inhibit biological reactions? The enhanced formation of DNA nanoparticles.

    PubMed

    Hou, Sen; Trochimczyk, Piotr; Sun, Lili; Wisniewska, Agnieszka; Kalwarczyk, Tomasz; Zhang, Xuzhu; Wielgus-Kutrowska, Beata; Bzowska, Agnieszka; Holyst, Robert

    2016-01-01

    In contrast to the already known effect that macromolecular crowding usually promotes biological reactions, solutions of PEG 6k at high concentrations stop the cleavage of DNA by HindIII enzyme, due to the formation of DNA nanoparticles. We characterized the DNA nanoparticles and probed the prerequisites for their formation using multiple techniques such as fluorescence correlation spectroscopy, dynamic light scattering, fluorescence analytical ultracentrifugation etc. In >25% PEG 6k solution, macromolecular crowding promotes the formation of DNA nanoparticles with dimensions of several hundreds of nanometers. The formation of DNA nanoparticles is a fast and reversible process. Both plasmid DNA (2686 bp) and double-stranded/single-stranded DNA fragment (66bp/nt) can form nanoparticles. We attribute the enhanced nanoparticle formation to the depletion effect of macromolecular crowding. This study presents our idea to enhance the formation of DNA nanoparticles by macromolecular crowding, providing the first step towards a final solution to efficient gene therapy. PMID:26903405

  19. Quantum chemistry of macromolecular shape

    NASA Astrophysics Data System (ADS)

    Mezey, Paul G.

    Some of the new developments in the quantum-chemical study of macromolecular shapes are reviewed, with special emphasis on the additive fuzzy electron density fragmentation methods and on the algebraic-topological shape group analysis of global and local shape features of fuzzy three-dimensional bodies of electron densities of macromolecules. Earlier applications of these methods to actual macromolecules are reviewed, including studies on the anticancer drug taxol, the proteins bovine insulin and HIV protease, and other macromolecules. The results of test calculations establishing the accuracy of these methods are also reviewed. The spherically weighted affine transformation technique is described and proposed for the deformation of electron densities approximating the changes occurring in small conformational displacements of atomic nuclei in macromolecules.

  20. Statistical mechanics of macromolecular complexation

    NASA Astrophysics Data System (ADS)

    Nakamura, Issei

    The self-assembly of macromolecules through molecular association has attracted long-standing attention in soft-condensed matter physics. The hierarchical formation from small-scale building blocks into larger-scale complex structures often leads to very rich phase behavior controlled by various ambient conditions. The understanding and control of the phase behavior of self-assembling systems require detailed knowledge about the entropy and enthalpy contributions to the free energy of the system. However, this knowledge is limited at the present time because a comprehensive theoretical description of molecular association is still lacking. In this thesis, four tales of achievements in developing theories of macromolecular complexation are presented. (1) We begin with an analytically solvable model of the self-assembly of rigid macromolecules with surface adsorption. A generic understanding of the driving force and the role of entropy is obtained from the exact solutions. (2) We move on to further development of the theory in order to study the complexation between polymers and ionic molecules. The extension of the first model to chain-like molecules is performed using a well-established method in polymer physics, the self-consistent field theory (SCFT) of polymers. We also discuss gelation in this system within the scope of mean-filed approximations. (3) Then, a ladder-like polymer-polymer complexation is studied. Unconventional phase diagrams are predicted from the modified SCFT, indicating a large effect of variations in entropy due to the complexation on bulk properties. (4) Finally, the kinetic aspect of macromolecular binding reactions is discussed.

  1. A Versatile Microparticle-Based Immunoaggregation Assay for Macromolecular Biomarker Detection and Quantification

    PubMed Central

    Wu, Haiyan; Han, Yu; Yang, Xi; Chase, George G.; Tang, Qiong; Lee, Chen-Jung; Cao, Bin; Zhe, Jiang; Cheng, Gang

    2015-01-01

    The rapid, sensitive and low-cost detection of macromolecular biomarkers is critical in clinical diagnostics, environmental monitoring, research, etc. Conventional assay methods usually require bulky, expensive and designated instruments and relative long assay time. For hospitals and laboratories that lack immediate access to analytical instruments, fast and low-cost assay methods for the detection of macromolecular biomarkers are urgently needed. In this work, we developed a versatile microparticle (MP)-based immunoaggregation method for the detection and quantification of macromolecular biomarkers. Antibodies (Abs) were firstly conjugated to MP through streptavidin-biotin interaction; the addition of macromolecular biomarkers caused the aggregation of Ab-MPs, which were subsequently detected by an optical microscope or optical particle sizer. The invisible nanometer-scale macromolecular biomarkers caused detectable change of micrometer-scale particle size distributions. Goat anti-rabbit immunoglobulin and human ferritin were used as model biomarkers to demonstrate MP-based immunoaggregation assay in PBS and 10% FBS to mimic real biomarker assay in the complex medium. It was found that both the number ratio and the volume ratio of Ab-MP aggregates caused by biomarker to all particles were directly correlated to the biomarker concentration. In addition, we found that the detection range could be tuned by adjusting the Ab-MP concentration. We envision that this novel MP-based immunoaggregation assay can be combined with multiple detection methods to detect and quantify macromolecular biomarkers at the nanogram per milliliter level. PMID:25658837

  2. High-pitch coronary CT angiography at 70 kVp with low contrast medium volume: comparison of 80 and 100 kVp high-pitch protocols.

    PubMed

    Zhang, Long Jiang; Qi, Li; De Cecco, Carlo N; Zhou, Chang Sheng; Spearman, James V; Schoepf, U Joseph; Lu, Guang Ming

    2014-11-01

    The purpose of this article is to evaluate image quality and radiation dose of prospectively electrocardiogram (ECG)-triggered high-pitch coronary computed tomography angiography (CCTA) at 70 kVp and 30 mL contrast medium.One hundred fifty patients with a heart rate ≤70 beats per minute (bpm) underwent CCTA using a second-generation dual-source computed tomography (CT) scanner and were randomized into 3 groups according to tube voltage and contrast medium volume (370 mg/mL iodine concentration) (100 kVp group, 100 kVp/60 mL, n = 55; 80 kVp group, 80 kVp/60 mL, n = 44; 70 kVp group, 70 kVp/30 mL, n = 51). Objective and subjective image quality along with the effect of heart rate (HR) and body mass index (BMI) was evaluated and compared between the groups. Radiation dose was estimated for each patient.CT attenuation and image noise were higher in the 80 and 70 kVp groups than in the 100 kVp group (all P < 0.001). Signal-to-noise ratios (SNRs) and contrast-to-noise ratios (CNRs) were lower in the 70 kVp group than in the 80 and 100 kVp groups (all P < 0.05). There was no difference for subjective image quality between the groups (P > 0.05). HR did not affect subjective image quality (all P > 0.05), while patients with BMI <23 kg/m had higher image quality than patients with BMI ≥23 kg/m (P < 0.05). Compared with the 100 kVp group, the radiation dose of the 70 kVp group was reduced by 75%.In conclusion, prospectively ECG-triggered high-pitch 70 kVp/30 mL CCTA can obtain diagnostic image quality with lower radiation dose in selected patients with BMI <23 kg/m compared with 80/100 kVp/60 mL CCTA. PMID:25396334

  3. Fractal Dimensions of Macromolecular Structures

    PubMed Central

    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

  4. Quantifying macromolecular conformational transition pathways

    NASA Astrophysics Data System (ADS)

    Seyler, Sean; Kumar, Avishek; Thorpe, Michael; Beckstein, Oliver

    2015-03-01

    Diverse classes of proteins function through large-scale conformational changes that are challenging for computer simulations. A range of fast path-sampling techniques have been used to generate transitions, but it has been difficult to compare paths from (and assess the relative strengths of) different methods. We introduce a comprehensive method (pathway similarity analysis, PSA) for quantitatively characterizing and comparing macromolecular pathways. The Hausdorff and Fréchet metrics (known from computational geometry) are used to quantify the degree of similarity between polygonal curves in configuration space. A strength of PSA is its use of the full information available from the 3 N-dimensional configuration space trajectory without requiring additional specific knowledge about the system. We compare a sample of eleven different methods for the closed-to-open transitions of the apo enzyme adenylate kinase (AdK) and also apply PSA to an ensemble of 400 AdK trajectories produced by dynamic importance sampling MD and the Geometrical Pathways algorithm. We discuss the method's potential to enhance our understanding of transition path sampling methods, validate them, and help guide future research toward deeper physical insights into conformational transitions.

  5. Ordered macromolecular structures in ferrofluid mixtures

    SciTech Connect

    Hayter, J.B.; Pynn, R.; Charles, S.; Skjeltorp, A.T.; Trewhella, J.; Stubbs, G.; Timmins, P.

    1989-04-03

    We have observed ordering of dilute dispersions of spherical and cylindrical macromolecules in magnetized ferrofluids. The order results from structural correlations between macromolecular and ferrofluid particles rather than from macroscopic magnetostatic effects. We have aligned elongated macromolecules by this technique and have obtained anisotropic neutron-diffraction patterns, which reflect the internal structure of the macromolecules. The method provides a tool for orienting suspended macromolecular assemblies which are not amenable to conventional alignment techniques.

  6. Feasibility of low-concentration iodinated contrast medium with lower-tube-voltage dual-source CT aortography using iterative reconstruction: comparison with automatic exposure control CT aortography.

    PubMed

    Shin, Hee Jeong; Kim, Song Soo; Lee, Jae-Hwan; Park, Jae-Hyeong; Jeong, Jin-Ok; Jin, Seon Ah; Shin, Byung Seok; Shin, Kyung-Sook; Ahn, Moonsang

    2016-06-01

    To evaluate the feasibility of low-concentration contrast medium (CM) for vascular enhancement, image quality, and radiation dose on computed tomography aortography (CTA) using a combined low-tube-voltage and iterative reconstruction (IR) technique. Ninety subjects underwent dual-source CT (DSCT) operating in dual-source, high-pitch mode. DSCT scans were performed using both high-concentration CM (Group A, n = 50; Iomeprol 400) and low-concentration CM (Group B, n = 40; Iodixanol 270). Group A was scanned using a reference tube potential of 120 kVp and 120 reference mAs under automatic exposure control with IR. Group B was scanned using low-tube-voltage (80 or 100 kVp if body mass index ≥25 kg/m(2)) at a fixed current of 150 mAs, along with IR. Images of the two groups were compared regarding attenuation, image noise, signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), iodine load, and radiation dose in various locations of the CTA. In comparison between Group A and Group B, the average mean attenuation (454.73 ± 86.66 vs. 515.96 ± 101.55 HU), SNR (25.28 ± 4.34 vs. 31.29 ± 4.58), and CNR (21.83 ± 4.20 vs. 27.55 ± 4.81) on CTA in Group B showed significantly greater values and significantly lower image noise values (18.76 ± 2.19 vs. 17.48 ± 3.34) than those in Group A (all Ps < 0.05). Homogeneous contrast enhancement from the ascending thoracic aorta to the infrarenal abdominal aorta was significantly superior in Group B (P < 0.05). Low-concentration CM and a low-tube-voltage combination technique using IR is a feasible method, showing sufficient contrast enhancement and image quality. PMID:26621755

  7. A database of macromolecular motions.

    PubMed Central

    Gerstein, M; Krebs, W

    1998-01-01

    We describe a database of macromolecular motions meant to be of general use to the structural community. The database, which is accessible on the World Wide Web with an entry point at http://bioinfo.mbb.yale.edu/MolMovDB , attempts to systematize all instances of protein and nucleic acid movement for which there is at least some structural information. At present it contains >120 motions, most of which are of proteins. Protein motions are further classified hierarchically into a limited number of categories, first on the basis of size (distinguishing between fragment, domain and subunit motions) and then on the basis of packing. Our packing classification divides motions into various categories (shear, hinge, other) depending on whether or not they involve sliding over a continuously maintained and tightly packed interface. In addition, the database provides some indication about the evidence behind each motion (i.e. the type of experimental information or whether the motion is inferred based on structural similarity) and attempts to describe many aspects of a motion in terms of a standardized nomenclature (e.g. the maximum rotation, the residue selection of a fixed core, etc.). Currently, we use a standard relational design to implement the database. However, the complexity and heterogeneity of the information kept in the database makes it an ideal application for an object-relational approach, and we are moving it in this direction. Specifically, in terms of storing complex information, the database contains plausible representations for motion pathways, derived from restrained 3D interpolation between known endpoint conformations. These pathways can be viewed in a variety of movie formats, and the database is associated with a server that can automatically generate these movies from submitted coordinates. PMID:9722650

  8. A Model for Macromolecular Crystallization

    NASA Technical Reports Server (NTRS)

    Pusey, Marc L.; Whitaker, Ann F. (Technical Monitor)

    2001-01-01

    Macromolecular crystallization is a complex process. involving a system which typically has 5 or more components (macromolecule, water, buffer + counter ion, and precipitant). Whereas small molecules have only several well defined contacts in the crystal lattice, macromolecules generally have 10's or even 100's of contacts between molecules. These can range from hydrogen bonds (direct or water-mediated), through van der Waals, hydrophobic, salt bridges, and ion-mediated contacts. The latter interactions are stronger and require some specificity in the molecular alignment, while the others are weaker, more prevalent, and more promiscuous, i.e., can often be readily broken and reformed between other sites. Formation of a consistent, ordered, 3D structure may be impossible in the absence of any or presence of too many strong interactions. Further complicating the process is the inherent structural asymmetry of monomeric single chain macromolecules. The process of crystal nucleation and growth involves the ordered assembly of growth units into a defined 3D lattice. We suggest that for many macromolecules, particularly those that are monomeric, this involves a preliminary solution-phase assembly process into a growth unit having some symmetry prior to addition to the lattice, recapitulating the initial stages of the nucleation process. If this model is correct then fluids and crystal growth models assuming a strictly monodisperse nutrient solution need to be revised. Experimental evidence, based upon face growth rate, AFM, and fluorescence energy transfer data, for a postulated model of the nucleation of tetragonal lysozyme crystals and how it transitions into crystal growth will be presented.

  9. Macromolecular complexes in crystals and solutions

    PubMed Central

    Krissinel, Evgeny

    2011-01-01

    This paper presents a discussion of existing methods for the analysis of macromolecular interactions and complexes in crystal packing. Typical situations and conditions where wrong answers may be obtained in the course of ordinary procedures are presented and discussed. The more general question of what the relationship is between natural (in-solvent) and crystallized assemblies is discussed and researched. A computational analysis suggests that weak interactions with K d ≥ 100 µM have a considerable chance of being lost during the course of crystallization. In such instances, crystal packing misrepresents macromolecular complexes and interactions. For as many as 20% of protein dimers in the PDB the likelihood of misrepresentation is estimated to be higher than 50%. Given that weak macromolecular interactions play an important role in many biochemical processes, these results suggest that a complementary noncrystallographic study should be always conducted when inferring structural aspects of weakly bound complexes. PMID:21460456

  10. The design of macromolecular crystallography diffraction experiments

    SciTech Connect

    Evans, Gwyndaf Axford, Danny; Owen, Robin L.

    2011-04-01

    Thoughts about the decisions made in designing macromolecular X-ray crystallography experiments at synchrotron beamlines are presented. The measurement of X-ray diffraction data from macromolecular crystals for the purpose of structure determination is the convergence of two processes: the preparation of diffraction-quality crystal samples on the one hand and the construction and optimization of an X-ray beamline and end station on the other. Like sample preparation, a macromolecular crystallography beamline is geared to obtaining the best possible diffraction measurements from crystals provided by the synchrotron user. This paper describes the thoughts behind an experiment that fully exploits both the sample and the beamline and how these map into everyday decisions that users can and should make when visiting a beamline with their most precious crystals.

  11. Effects of macromolecular crowding on genetic networks.

    PubMed

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

    2011-12-21

    The intracellular environment is crowded with proteins, DNA, and other macromolecules. Under physiological conditions, macromolecular crowding can alter both molecular diffusion and the equilibria of bimolecular reactions and therefore is likely to have a significant effect on the function of biochemical networks. We propose a simple way to model the effects of macromolecular crowding on biochemical networks via an appropriate scaling of bimolecular association and dissociation rates. We use this approach, in combination with kinetic Monte Carlo simulations, to analyze the effects of crowding on a constitutively expressed gene, a repressed gene, and a model for the bacteriophage λ genetic switch, in the presence and absence of nonspecific binding of transcription factors to genomic DNA. Our results show that the effects of crowding are mainly caused by the shift of association-dissociation equilibria rather than the slowing down of protein diffusion, and that macromolecular crowding can have relevant and counterintuitive effects on biochemical network performance. PMID:22208186

  12. New pharmaceutical applications for macromolecular binders.

    PubMed

    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

  13. Macromolecular engineering by atom transfer radical polymerization.

    PubMed

    Matyjaszewski, Krzysztof; Tsarevsky, Nicolay V

    2014-05-01

    This Perspective presents recent advances in macromolecular engineering enabled by ATRP. They include the fundamental mechanistic and synthetic features of ATRP with emphasis on various catalytic/initiation systems that use parts-per-million concentrations of Cu catalysts and can be run in environmentally friendly media, e.g., water. The roles of the major components of ATRP--monomers, initiators, catalysts, and various additives--are explained, and their reactivity and structure are correlated. The effects of media and external stimuli on polymerization rates and control are presented. Some examples of precisely controlled elements of macromolecular architecture, such as chain uniformity, composition, topology, and functionality, are discussed. Syntheses of polymers with complex architecture, various hybrids, and bioconjugates are illustrated. Examples of current and forthcoming applications of ATRP are covered. Future challenges and perspectives for macromolecular engineering by ATRP are discussed. PMID:24758377

  14. Effects of Macromolecular Crowding on Genetic Networks

    PubMed Central

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

    2011-01-01

    The intracellular environment is crowded with proteins, DNA, and other macromolecules. Under physiological conditions, macromolecular crowding can alter both molecular diffusion and the equilibria of bimolecular reactions and therefore is likely to have a significant effect on the function of biochemical networks. We propose a simple way to model the effects of macromolecular crowding on biochemical networks via an appropriate scaling of bimolecular association and dissociation rates. We use this approach, in combination with kinetic Monte Carlo simulations, to analyze the effects of crowding on a constitutively expressed gene, a repressed gene, and a model for the bacteriophage λ genetic switch, in the presence and absence of nonspecific binding of transcription factors to genomic DNA. Our results show that the effects of crowding are mainly caused by the shift of association-dissociation equilibria rather than the slowing down of protein diffusion, and that macromolecular crowding can have relevant and counterintuitive effects on biochemical network performance. PMID:22208186

  15. Chemical oscillations in closed macromolecular systems.

    PubMed Central

    Di Cera, E; Phillipson, P E; Wyman, J

    1988-01-01

    A cycle of irreversible, first-order, autocatalytic reactions among different states of a polyfunctional macromolecule, subject to the conservation of mass, can display stable chemical oscillations. This introduces a class of nonlinear dynamic models for energy transduction in closed macromolecular systems. PMID:3413066

  16. Contrast Medium Exposure During Computed Tomography and Risk of Development of End-Stage Renal Disease in Patients With Chronic Kidney Disease: A Nationwide Population-Based, Propensity Score-Matched, Longitudinal Follow-Up Study.

    PubMed

    Hsieh, Ming-Shun; Chiu, Chien-Shan; How, Chorng-Kuang; Chiang, Jen-Huai; Sheu, Meei-Ling; Chen, Wen-Chi; Lin, Hsuan-Jen; Hsieh, Vivian Chia-Rong; Hu, Sung-Yuan

    2016-04-01

    The aim of the study was to investigate the long-term association between contrast medium exposure during computed tomography (CT) and the subsequent development of end-stage renal disease (ESRD) in patients with chronic kidney disease (CKD).We conducted a population-based cohort study using Taiwan's National Health Insurance Research Database. A total of 7100 patients with nonadvanced CKD who underwent contrast medium-enhanced CT were identified and served as the study cohort. To avoid selection bias, we used the propensity score to match 7100 nonadvanced CKD patients, who underwent noncontrast medium-enhanced CT to serve as the comparison cohort. The age, sex, index year, and frequency of undergoing CTs were also matched between the study and comparison cohorts. Participants were followed until a new diagnosis of ESRD or December 31, 2011. Hazard ratios (HRs) with 95% confidence interval (95% CI) were calculated using the Cox proportional hazards regression.Contrast medium exposure was not identified as a risk factor for developing ESRD in nonadvanced CKD patients after confounders adjustment (adjusted HR = 0.91; 95% CI, 0.66-1.26; P = 0.580). We further divided the patients who underwent CTs with contrast medium use into ≤1 exposure per year on average, >1 and <2 exposure per year on average, and ≥2 exposure per year on average. After adjusting for confounders, we identified a much higher risk for developing ESRD in the 2 groups of >1 and <2 exposure per year on average and ≥2 exposure per year on average (adjusted HR = 8.13; 95% CI, 5.57-11.87 and adjusted HR = 12.08; 95% CI, 7.39-19.75, respectively) compared with the patients who underwent CTs without contrast medium use.This long-term follow-up study demonstrated that contrast medium exposure was not associated with an increased risk of ESRD development in nonadvanced CKD patients. PMID:27100424

  17. The role of gadoxetic acid as a paramagnetic contrast medium in the characterization and detection of focal liver lesions: a review

    PubMed Central

    Bormann, Renata Lilian; da Rocha, Eduardo Lima; Kierzenbaum, Marcelo Longo; Pedrassa, Bruno Cheregati; Torres, Lucas Rios; D'Ippolito, Giuseppe

    2015-01-01

    Recent studies have demonstrated that the use of paramagnetic hepatobiliary contrast agents in the acquisition of magnetic resonance images remarkably improves the detection and differentiation of focal liver lesions, as compared with extracellular contrast agents. Paramagnetic hepatobiliary contrast agents initially show the perfusion of the lesions, as do extracellular agents, but delayed contrast-enhanced images can demonstrate contrast uptake by functional hepatocytes, providing further information for a better characterization of the lesions. Additionally, this intrinsic characteristic increases the accuracy in the detection of hepatocellular carcinomas and metastases, particularly the small-sized ones. Recently, a hepatobiliary contrast agent called gadolinium ethoxybenzyl dimeglumine, that is simply known as gadoxetic acid, was approved by the National Health Surveillance Agency for use in humans. The authors present a literature review and a practical approach of magnetic resonance imaging utilizing gadoxetic acid as contrast agent, based on patients' images acquired during their initial experiment. PMID:25798007

  18. [Measurement of glomerular filtration rate (GFR) after administration of iodine contrast medium with the Renalyzer PRX90 in healthy cats and cats with kidney diseases].

    PubMed

    Meyer-Lindenberg, A; Westhoff, A; Wohlsein, P; Pohlenz, J; Nolte, I

    1998-09-01

    In the present study, the measurement of the glomerular filtration rate (GFR) in the cat with the aid of an iodine contrast medium clearance with the renalyzer PRX90 is introduced. Investigations on the accuracy of measurement showed that even repeated measurement of plasma samples after two days of storage at room temperature yielded reproducible clearance results. Also, partial dilution of the plasma sample (2 ml with 1 ml Aqua bidest.) to reduce the volume of blood withdrawn still produced reliable results. Further dilution of the plasma volume (1 ml with 2 ml Aqua bidest.) however did not allow for accurate measurements. A total of 59 cats of different age and sex were included in the study. 31 cats had healthy kidneys with urea and creatinine values within the reference range, unchanged urine findings and physiologic urine protein patterns (SDS-PAGE). These cats served as reference group. The GFR reference value ascertained for these animals was 2.1 ml/min/kg BW (mean = 3.45 ml/min/kg with s = +/- 1.0 ml/min/kg). 28 cats had elevated values of urea and creatinine in the blood, as well as partially changed urine findings. For further diagnosis of renal disease, separation of urine proteins was done with the SDS-PAGE in the PhastSystem, which in all cases yielded a pathologic urine protein pattern. In 11 cases the renal disease could be further confirmed by histological investigation. GFR in these patients was clearly lowered compared with healthy cats, with measured values between 0 and 1.8 ml/min/kg. It can be concluded that the renalyzer allows reliable determination of the GFR also in the cat. To what extent measurement of the GFR is also helpful to diagnose nephropathies in the stage of compensation needs to be further investigated. In cats with high grade uremia and a GFR below 1 ml/min however, an exact calculation is not possible, since the accuracy of measurement within this range is inadequate. Thus, in severe disease no correct assessment is possible

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

    PubMed

    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. PMID:24888734

  20. Ultrasonic Imaging of the Electroacoustic Effect in Macromolecular Gels

    PubMed Central

    Wen, Han; Balaban, Robert S.

    2010-01-01

    The electroacoustic effect occurs in electrolytes and colloidal suspensions. It describes the phenomenon in which a voltage applied to the sample produces an acoustic signal or vice versa. The basic mechanism is that charged particles in the sample have various mobilities due to different masses and viscosities. Under an external voltage they respond differently to the electrical force. This results in an overall acoustic vibration. The electroacoustic effect has been the basis for many measurement tools of solutions and other materials. In this note a method to image macromolecular gel samples using the electroacoustic effect at ultrasound frequencies is presented. Radio-frequency electrical excitation produces ultrasonic signal due to spatial changes in the electroacoustic sonic amplitude of the sample, which is used to construct an image similar to ultrasonography. This method is demonstrated in agar gel and eggwhite protein phantoms. The image contrast mechanism is also discussed. PMID:10197349

  1. In situ macromolecular crystallography using microbeams

    PubMed Central

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

    2012-01-01

    Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side-stepped. Using a dedicated goniometer installed on the microfocus macromolecular crystallography beamline I24 at Diamond Light Source, crystals have been studied in situ with an intense and flexible microfocus beam, allowing weakly diffracting samples to be assessed without a manual crystal-handling step but with good signal to noise, despite the background scatter from the plate. A number of case studies are reported: the structure solution of bovine enterovirus 2, crystallization screening of membrane proteins and complexes, and structure solution from crystallization hits produced via a high-throughput pipeline. These demonstrate the potential for in situ data collection and structure solution with microbeams. PMID:22525757

  2. Macromolecular transport in synapse to nucleus communication.

    PubMed

    Panayotis, Nicolas; Karpova, Anna; Kreutz, Michael R; Fainzilber, Mike

    2015-02-01

    Local signaling events at synapses or axon terminals must be communicated to the nucleus to elicit transcriptional responses. The lengths of neuronal processes pose a significant challenge for such intracellular communication. This challenge is met by mechanisms ranging from rapid signals encoded in calcium waves to slower macromolecular signaling complexes carried by molecular motors. Here we summarize recent findings on macromolecular signaling from the synapse to the nucleus, in comparison to those employed in injury signaling along axons. A number of common themes emerge, including combinatorial signal encoding by post-translational mechanisms such as differential phosphorylation and proteolysis, and conserved roles for importins in coordinating signaling complexes. Neurons may integrate ionic flux with motor-transported signals as a temporal code for synaptic plasticity signaling. PMID:25534890

  3. Growth and Dissolution of Macromolecular Markov Chains

    NASA Astrophysics Data System (ADS)

    Gaspard, Pierre

    2016-07-01

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

  4. Stochastic dynamics of macromolecular-assembly networks.

    NASA Astrophysics Data System (ADS)

    Saiz, Leonor; Vilar, Jose

    2006-03-01

    The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current computational methods strongly limited for understanding how the physical interactions between cellular components give rise to systemic properties of cells. Here we present a stochastic approach to study the dynamics of networks formed by macromolecular complexes in terms of the molecular interactions of their components [1]. Exploiting key thermodynamic concepts, this approach makes it possible to both estimate reaction rates and incorporate the resulting assembly dynamics into the stochastic kinetics of cellular networks. As prototype systems, we consider the lac operon and phage λ induction switches, which rely on the formation of DNA loops by proteins [2] and on the integration of these protein-DNA complexes into intracellular networks. This cross-scale approach offers an effective starting point to move forward from network diagrams, such as those of protein-protein and DNA-protein interaction networks, to the actual dynamics of cellular processes. [1] L. Saiz and J.M.G. Vilar, submitted (2005). [2] J.M.G. Vilar and L. Saiz, Current Opinion in Genetics & Development, 15, 136-144 (2005).

  5. Radiation damage to nucleoprotein complexes in macromolecular crystallography

    PubMed Central

    Bury, Charles; Garman, Elspeth F.; Ginn, Helen Mary; Ravelli, Raimond B. G.; Carmichael, Ian; Kneale, Geoff; McGeehan, John E.

    2015-01-01

    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 N1—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. PMID:25723923

  6. Development of macromolecular prodrug for rheumatoid arthritis☆

    PubMed Central

    Yuan, Fang; Quan, Ling-dong; Cui, Liao; Goldring, Steven R.; Wang, Dong

    2012-01-01

    Rheumatoid arthritis (RA) is a chronic autoimmune disease that is considered to be one of the major public health problems worldwide. The development of therapies that target tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and co-stimulatory pathways that regulate the immune system have revolutionized the care of patients with RA. Despite these advances, many patients continue to experience symptomatic and functional impairment. To address this issue, more recent therapies that have been developed are designed to target intracellular signaling pathways involved in immunoregulation. Though this approach has been encouraging, there have been major challenges with respect to off-target organ side effects and systemic toxicities related to the widespread distribution of these signaling pathways in multiple cell types and tissues. These limitations have led to an increasing interest in the development of strategies for the macromolecularization of anti-rheumatic drugs, which could target them to the inflamed joints. This approach enhances the efficacy of the therapeutic agent with respect to synovial inflammation, while markedly reducing non-target organ adverse side effects. In this manuscript, we provide a comprehensive overview of the rational design and optimization of macromolecular prodrugs for treatment of RA. The superior and the sustained efficacy of the prodrug may be partially attributed to their Extravasation through Leaky Vasculature and subsequent Inflammatory cell-mediated Sequestration (ELVIS) in the arthritic joints. This biologic process provides a plausible mechanism, by which macromolecular prodrugs preferentially target arthritic joints and illustrates the potential benefits of applying this therapeutic strategy to the treatment of other inflammatory diseases. PMID:22433784

  7. Coal Chemistry for Mechanical Engineers: From Macromolecular Thermodynamics to Reservoir Simulation

    SciTech Connect

    Romanov, V.

    2007-05-01

    In pilot trials and commercial scale field demonstrations of CO2 storage in coal seams, quite often unexpected problems with coal swelling around injector and reducing injection efficiency (e.g., Allison unit in the San Juan Basin, RECOPOL in Poland, Hokkaido project in Japan, etc.) can stall or even terminate the site development. To avoid the costly mistakes with the prospective site evaluation, the state of the art in reservoir modeling needs to be improved by taking into account coal properties at the macromolecular level. The current models are based on the rock mechanics, which ignores decades of experimental and theoretical studies of interaction between coal and injected fluids. A pseudopolymer approach is introduced to the modelers as a viable alternative, especially, at medium to high fluid pressures. Further, it is discussed how the thermodynamics of CO2 dissolution in the macromolecular network of the coal matrix can be incorporated into geomechanical models.

  8. Fock spaces for modeling macromolecular complexes

    NASA Astrophysics Data System (ADS)

    Kinney, Justin

    Large macromolecular complexes play a fundamental role in how cells function. Here I describe a Fock space formalism for mathematically modeling these complexes. Specifically, this formalism allows ensembles of complexes to be defined in terms of elementary molecular ``building blocks'' and ``assembly rules.'' Such definitions avoid the massive redundancy inherent in standard representations, in which all possible complexes are manually enumerated. Methods for systematically computing ensembles of complexes from a list of components and interaction rules are described. I also show how this formalism readily accommodates coarse-graining. Finally, I introduce diagrammatic techniques that greatly facilitate the application of this formalism to both equilibrium and non-equilibrium biochemical systems.

  9. Automated macromolecular crystal detection system and method

    DOEpatents

    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.

  10. Multiscale macromolecular simulation: role of evolving ensembles.

    PubMed

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

    2012-10-22

    Multiscale analysis provides an algorithm for the efficient simulation of macromolecular assemblies. This algorithm involves the coevolution of a quasiequilibrium probability density of atomic configurations and the Langevin dynamics of spatial coarse-grained variables denoted order parameters (OPs) characterizing nanoscale system features. In practice, implementation of the probability density involves the generation of constant OP ensembles of atomic configurations. Such ensembles are used to construct thermal forces and diffusion factors that mediate the stochastic OP dynamics. Generation of all-atom ensembles at every Langevin time step is computationally expensive. Here, multiscale computation for macromolecular systems is made more efficient by a method that self-consistently folds in ensembles of all-atom configurations constructed in an earlier step, history, of the Langevin evolution. This procedure accounts for the temporal evolution of these ensembles, accurately providing thermal forces and diffusions. It is shown that efficiency and accuracy of the OP-based simulations is increased via the integration of this historical information. Accuracy improves with the square root of the number of historical timesteps included in the calculation. As a result, CPU usage can be decreased by a factor of 3-8 without loss of accuracy. The algorithm is implemented into our existing force-field based multiscale simulation platform and demonstrated via the structural dynamics of viral capsomers. PMID:22978601

  11. Macromolecular recognition in the Protein Data Bank

    SciTech Connect

    Janin, Joël; Rodier, Francis; Chakrabarti, Pinak

    2007-01-01

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

  12. Multiscale Macromolecular Simulation: Role of Evolving Ensembles

    PubMed Central

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

    2013-01-01

    Multiscale analysis provides an algorithm for the efficient simulation of macromolecular assemblies. This algorithm involves the coevolution of a quasiequilibrium probability density of atomic configurations and the Langevin dynamics of spatial coarse-grained variables denoted order parameters (OPs) characterizing nanoscale system features. In practice, implementation of the probability density involves the generation of constant OP ensembles of atomic configurations. Such ensembles are used to construct thermal forces and diffusion factors that mediate the stochastic OP dynamics. Generation of all-atom ensembles at every Langevin timestep is computationally expensive. Here, multiscale computation for macromolecular systems is made more efficient by a method that self-consistently folds in ensembles of all-atom configurations constructed in an earlier step, history, of the Langevin evolution. This procedure accounts for the temporal evolution of these ensembles, accurately providing thermal forces and diffusions. It is shown that efficiency and accuracy of the OP-based simulations is increased via the integration of this historical information. Accuracy improves with the square root of the number of historical timesteps included in the calculation. As a result, CPU usage can be decreased by a factor of 3-8 without loss of accuracy. The algorithm is implemented into our existing force-field based multiscale simulation platform and demonstrated via the structural dynamics of viral capsomers. PMID:22978601

  13. EIGER detector: application in macromolecular crystallography.

    PubMed

    Casanas, Arnau; Warshamanage, Rangana; Finke, Aaron D; Panepucci, Ezequiel; Olieric, Vincent; Nöll, Anne; Tampé, Robert; Brandstetter, Stefan; Förster, Andreas; Mueller, Marcus; Schulze-Briese, Clemens; Bunk, Oliver; Wang, Meitian

    2016-09-01

    The development of single-photon-counting detectors, such as the PILATUS, has been a major recent breakthrough in macromolecular crystallography, enabling noise-free detection and novel data-acquisition modes. The new EIGER detector features a pixel size of 75 × 75 µm, frame rates of up to 3000 Hz and a dead time as low as 3.8 µs. An EIGER 1M and EIGER 16M were tested on Swiss Light Source beamlines X10SA and X06SA for their application in macromolecular crystallography. The combination of fast frame rates and a very short dead time allows high-quality data acquisition in a shorter time. The ultrafine ϕ-slicing data-collection method is introduced and validated and its application in finding the optimal rotation angle, a suitable rotation speed and a sufficient X-ray dose are presented. An improvement of the data quality up to slicing at one tenth of the mosaicity has been observed, which is much finer than expected based on previous findings. The influence of key data-collection parameters on data quality is discussed. PMID:27599736

  14. Magnetic macromolecular cross linked enzyme aggregates (CLEAs) of glucoamylase.

    PubMed

    Nadar, Shamraja S; Rathod, Virendra K

    2016-02-01

    This work illustrates the preparation of magnetic macromolecular glucoamylase CLEAs using dialdehydic pectin, as a cross linker instead of traditional glutaraldehyde. The effect of precipitators type and amount, cross linker concentration, cross linking time and amount of amino functionalized magnetic nanoparticles (AFMNs) on glucoamylase activity was studied. Glucoamylase magnetic macromolecular CLEAs prepared by precipitation in presence of AFMNs by ammonium sulfate were subsequently cross linked by dialdehydic pectin. After cross-linked by pectin, 95.4% activity recovery was achieved in magnetic macromolecular CLEAs, whereas in case of glutaraldehyde cross linker, 85.3% activity recovery was achieved. Magnetic macromolecular CLEAs showed 2.91 and 1.27 folds higher thermal stability as compared to free and magnetic glutaraldehyde CLEAs. In kinetics study, magnetic macromolecular CLEAs retained same Km values, whereas magnetic glutaraldehyde CLEAs showed higher Km value than free enzyme. The porous structure of magnetic macromolecular CLEAs was not only enhanced mass transfer toward macromolecular substrates, but also showed compression resistance for 5 consecutive cycles which was checked in terms of effectiveness factor. At the end, in reusability study; magnetic macromolecular CLEAs were retained 84% activity after 10(th) cycle without leaching of enzyme which is 22% higher than traditional magnetic CLEAs. PMID:26777253

  15. The design of macromolecular crystallography diffraction experiments

    PubMed Central

    Evans, Gwyndaf; Axford, Danny; Owen, Robin L.

    2011-01-01

    The measurement of X-ray diffraction data from macro­molecular crystals for the purpose of structure determination is the convergence of two processes: the preparation of diffraction-quality crystal samples on the one hand and the construction and optimization of an X-ray beamline and end station on the other. Like sample preparation, a macromolecular crystallography beamline is geared to obtaining the best possible diffraction measurements from crystals provided by the synchrotron user. This paper describes the thoughts behind an experiment that fully exploits both the sample and the beamline and how these map into everyday decisions that users can and should make when visiting a beamline with their most precious crystals. PMID:21460444

  16. Panorama of ancient metazoan macromolecular complexes.

    PubMed

    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

  17. Simulation and display of macromolecular complexes

    NASA Technical Reports Server (NTRS)

    Nir, S.; Garduno, R.; Rein, R.; Macelroy, R. D.

    1977-01-01

    In association with an investigation of the interaction of proteins with DNA and RNA, an interactive computer program for building, manipulating, and displaying macromolecular complexes has been designed. The system provides perspective, planar, and stereoscopic views on the computer terminal display, as well as views for standard and nonstandard observer locations. The molecule or its parts may be rotated and/or translated in any direction; bond connections may be added or removed by the viewer. Molecular fragments may be juxtaposed in such a way that given bonds are aligned, and given planes and points coincide. Another subroutine provides for the duplication of a given unit such as a DNA or amino-acid base.

  18. A new method for mapping macromolecular topography.

    PubMed

    Mezei, Mihaly

    2003-03-01

    A new method, using circular variance, is introduced for mapping macromolecular topography. Circular variance, generally used to measures angular spread, can be used to characterize of molecular structures based on a simple idea. It will be shown that the circular variance of vectors drawn from some origin to a set of points is well correlated with the degree to which that origin is inside/outside the chosen points. In addition, it has continuous derivatives that are also easy to compute. This concept will be shown to be useful for: (i) distinguishing between atoms near the surface of a macromolecule and those in either the deep interior or remote exterior; (ii) identifying invaginations (even shallow ones); and (iii) detecting linker regions that interconnect two domains. PMID:12543141

  19. Macromolecular crowding explains overflow metabolism in cells

    PubMed Central

    Vazquez, Alexei; Oltvai, Zoltán N.

    2016-01-01

    Overflow metabolism is a metabolic phenotype of cells characterized by mixed oxidative phosphorylation (OxPhos) and fermentative glycolysis in the presence of oxygen. Recently, it was proposed that a combination of a protein allocation constraint and a higher proteome fraction cost of energy generation by OxPhos relative to fermentation form the basis of overflow metabolism in the bacterium, Escherichia coli. However, we argue that the existence of a maximum or optimal macromolecular density is another essential requirement. Here we re-evaluate our previous theory of overflow metabolism based on molecular crowding following the proteomic fractions formulation. We show that molecular crowding is a key factor in explaining the switch from OxPhos to overflow metabolism. PMID:27484619

  20. Macromolecular diffractive imaging using imperfect crystals.

    PubMed

    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

    2016-02-11

    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. PMID

  1. Macromolecular diffractive imaging using imperfect crystals

    PubMed Central

    Ayyer, Kartik; Yefanov, Oleksandr; 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; Lourdu Xavier, Paulraj; 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.

    2016-01-01

    The three-dimensional structures of macromolecules and their complexes are predominantly elucidated by X-ray protein crystallography. A major limitation is access to high-quality crystals, to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields sufficiently high-resolution information that the crystal structure can be solved. The observation that crystals with shrunken unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks1,2 hints that crystallographic resolution for some macromolecules may be limited not by their heterogeneity but rather 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, equal to the incoherent sum of diffraction from rigid single molecular complexes aligned along several discrete crystallographic orientations and hence with an increased information content3. Although such continuous diffraction patterns have long been observed—and are of interest as a source of information about the dynamics of proteins4 —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 Å limit of measurable Bragg peaks, which allows us to directly phase5 the pattern. With the molecular envelope conventionally determined at 4.5 Å as a constraint, we then obtain a static image of the photosystem II dimer at 3.5 Å resolution. This result shows that continuous diffraction can be used to overcome long-supposed resolution limits of macromolecular crystallography, with a method that puts great value in commonly encountered imperfect crystals and opens up the possibility for model-free phasing6,7. PMID:26863980

  2. Macromolecular diffractive imaging using imperfect crystals

    NASA Astrophysics Data System (ADS)

    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.

  3. Follow-up of endovascular aortic aneurysm repair: Preliminary validation of digital tomosynthesis and contrast enhanced ultrasound in detection of medium- to long-term complications

    PubMed Central

    Mazzei, Maria Antonietta; Guerrini, Susanna; Mazzei, Francesco Giuseppe; Cioffi Squitieri, Nevada; Notaro, Dario; de Donato, Gianmarco; Galzerano, Giuseppe; Sacco, Palmino; Setacci, Francesco; Volterrani, Luca; Setacci, Carlo

    2016-01-01

    AIM: To validate the feasibility of digital tomosynthesis of the abdomen (DTA) combined with contrast enhanced ultrasound (CEUS) in assessing complications after endovascular aortic aneurysm repair (EVAR) by using computed tomography angiography (CTA) as the gold standard. METHODS: For this prospective study we enrolled 163 patients (123 men; mean age, 65.7 years) referred for CTA for EVAR follow-up. CTA, DTA and CEUS were performed at 1 and 12 mo in all patients, with a maximum time interval of 2 d. RESULTS: Among 163 patients 33 presented complications at CTA. DTA and CTA correlated for the presence of complications in 32/33 (96.96%) patients and for the absence of complications in 127/130 (97.69%) patients; the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy of DTA were 97%, 98%, 91%, 99%, and 98%, respectively. CEUS and CTA correlated for the presence of complications in 19/33 (57.57%) patients and for the absence of complications in 129/130 (99.23%) patients; the sensitivity, specificity, PPV, NPV and accuracy of CEUS were 58%, 99%, 95%, 90%, and 91%, respectively. Sensitivity, specificity and accuracy of combining DTA and CEUS together in detecting EVAR complications were 77%, 98% and 95%, respectively. CONCLUSION: Combining DTA and CEUS in EVAR follow-up has the potential to limit the use of CTA only in doubtful cases. PMID:27247719

  4. Phylogenetic Diversity in the Macromolecular Composition of Microalgae.

    PubMed

    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

  5. Phylogenetic Diversity in the Macromolecular Composition of Microalgae

    PubMed Central

    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

  6. The use of a mini-κ goniometer head in macromolecular crystallography diffraction experiments

    SciTech Connect

    Brockhauser, Sandor; Ravelli, Raimond B. G.; McCarthy, Andrew A.

    2013-07-01

    Hardware and software solutions for MX data-collection strategies using the EMBL/ESRF miniaturized multi-axis goniometer head are presented. Most macromolecular crystallography (MX) diffraction experiments at synchrotrons use a single-axis goniometer. This markedly contrasts with small-molecule crystallography, in which the majority of the diffraction data are collected using multi-axis goniometers. A novel miniaturized κ-goniometer head, the MK3, has been developed to allow macromolecular crystals to be aligned. It is available on the majority of the structural biology beamlines at the ESRF, as well as elsewhere. In addition, the Strategy for the Alignment of Crystals (STAC) software package has been developed to facilitate the use of the MK3 and other similar devices. Use of the MK3 and STAC is streamlined by their incorporation into online analysis tools such as EDNA. The current use of STAC and MK3 on the MX beamlines at the ESRF is discussed. It is shown that the alignment of macromolecular crystals can result in improved diffraction data quality compared with data obtained from randomly aligned crystals.

  7. Fluid Physics and Macromolecular Crystal Growth in Microgravity

    NASA Technical Reports Server (NTRS)

    Helliwell, John R.; Snell, Edward H.; Chayen, Naomi E.; Judge, Russell A.; Boggon, Titus J.; Pusey, M. L.; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    The first protein crystallization experiment in microgravity was launched in April, 1981 and used Germany's Technologische Experimente unter Schwerelosigkeit (TEXUS 3) sounding rocket. The protein P-galactosidase (molecular weight 465Kda) was chosen as the sample with a liquid-liquid diffusion growth method. A sliding device brought the protein, buffer and salt solution into contact when microgravity was reached. The sounding rocket gave six minutes of microgravity time with a cine camera and schlieren optics used to monitor the experiment, a single growth cell. In microgravity a strictly laminar diffusion process was observed in contrast to the turbulent convection seen on the ground. Several single crystals, approx 100micron in length, were formed in the flight which were of inferior but of comparable visual quality to those grown on the ground over several days. A second experiment using the same protocol but with solutions cooled to -8C (kept liquid with glycerol antifreeze) again showed laminar diffusion. The science of macromolecular structural crystallography involves crystallization of the macromolecule followed by use of the crystal for X-ray diffraction experiments to determine the three dimensional structure of the macromolecule. Neutron protein crystallography is employed for elucidation of H/D exchange and for improved definition of the bound solvent (D20). The structural information enables an understanding of how the molecule functions with important potential for rational drug design, improved efficiency of industrial enzymes and agricultural chemical development. The removal of turbulent convection and sedimentation in microgravity, and the assumption that higher quality crystals will be produced, has given rise to the growing number of crystallization experiments now flown. Many experiments can be flown in a small volume with simple, largely automated, equipment - an ideal combination for a microgravity experiment. The term "protein crystal growth

  8. Macromolecular Crystal Growth by Means of Microfluidics

    NASA Technical Reports Server (NTRS)

    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.

  9. Miniaturized kappa goniometer for macromolecular crystallography

    SciTech Connect

    Rosenbaum, G.; Westbrook, E. M.

    1997-07-01

    A goniometer with kappa geometry has been designed and built specifically for macromolecular crystallography. The main feature is a miniaturized kappa stage made possible by the small weight of specimen and specimen holder. The design goal was to: 1) eliminate interference between stage and area detector for specimen-to-detector distances of 100 mm and more; 2) minimize the sphere of confusion on expectation of dealing with very small crystals at third generation sources; 3) minimize the solid angle of shadow and inaccessible positioning of the sample due to interference of the stage with other objects in the sample area; 4) achieve a rotation speed of 10 degree/s at 0.5% constancy and 0.4 s acceleration time for 0.05 s exposures of 0.2 degree fine slice frames every 2 seconds, and 5) to achieve precise synchronization between rotation angle and shutter opening and closing. The kappa stage is mounted on a commercial high precision rotary table, designed for use in both horizontal and vertical orientation. This table provides the high precision rotation for data acquisition. The required crisp response and constant speed is delivered by a high output direct drive DC-motor, controlled by a closed-loop controller using feedback from a precision angular encoder. The kappa- and phi-motions are used for sample positioning only and are driven by miniature DC-motors equipped with integral encoders.

  10. Miniaturized kappa goniometer for macromolecular crystallography

    SciTech Connect

    Rosenbaum, G.; Westbrook, E.M.

    1997-07-01

    A goniometer with kappa geometry has been designed and built specifically for macromolecular crystallography. The main feature is a miniaturized kappa stage made possible by the small weight of specimen and specimen holder. The design goal was to: 1) eliminate interference between stage and area detector for specimen-to-detector distances of 100 mm and more; 2) minimize the sphere of confusion on expectation of dealing with very small crystals at third generation sources; 3) minimize the solid angle of shadow and inaccessible positioning of the sample due to interference of the stage with other objects in the sample area; 4) achieve a rotation speed of 10 degree/s at 0.5{percent} constancy and 0.4 s acceleration time for 0.05 s exposures of 0.2 degree fine slice frames every 2 seconds, and 5) to achieve precise synchronization between rotation angle and shutter opening and closing. The kappa stage is mounted on a commercial high precision rotary table, designed for use in both horizontal and vertical orientation. This table provides the high precision rotation for data acquisition. The required crisp response and constant speed is delivered by a high output direct drive DC-motor, controlled by a closed-loop controller using feedback from a precision angular encoder. The kappa- and phi-motions are used for sample positioning only and are driven by miniature DC-motors equipped with integral encoders.{copyright} {ital 1997 American Institute of Physics.}

  11. Neutron Laue diffraction in macromolecular crystallography

    NASA Astrophysics Data System (ADS)

    Myles, D. A. A.; Bon, C.; Langan, P.; Cipriani, F.; Castagna, J. C.; Lehmann, M. S.; Wilkinson, C.

    The time scales required for conventional neutron diffraction analysis of biological single crystals at, or near, atomic resolution are prohibitive - such studies are rarely performed. Laue (white beam) diffraction can provide a more rapid and efficient survey of reciprocal space, maximising the flux at the sample and stimulating large numbers of reflections simultaneously. A LAue DIffractometer (LADI), designed specifically for macromolecular crystallography, has been installed on a cold neutron guide at ILL. The detector comprises a large Gd 2O 3-doped neutron-sensitive image plate (400 × 800 mm) mounted on a cylindrical camera (318 mm diameter) that is read in phonographic mode after exposure. Detector response has been evaluated and performance indicators are given. Narrow (Quasi-Laue) band-passes (d/ gl/ λ = 8-20%) are often required for large unit-cell biological crystals in order to reduce reflection overlap and incoherent background. Laue and Quasi-Laue data have now been collected for a number of proteins and other biological crystals. Recent results are presented and future prospects reviewed.

  12. Environmentally responsive MRI contrast agents

    PubMed Central

    Davies, Gemma-Louise; Kramberger, Iris; Davis, Jason J.

    2015-01-01

    Biomedical imaging techniques can provide a vast amount of anatomical information, enabling diagnosis and the monitoring of disease and treatment profile. MRI uniquely offers convenient, non-invasive, high resolution tomographic imaging. A considerable amount of effort has been invested, across several decades, in the design of non toxic paramagnetic contrast agents capable of enhancing positive MRI signal contrast. Recently, focus has shifted towards the development of agents capable of specifically reporting on their local biochemical environment, where a switch in image contrast is triggered by a specific stimulus/biochemical variable. Such an ability would not only strengthen diagnosis but also provide unique disease-specific biochemical insight. This feature article focuses on recent progress in the development of MRI contrast switching with molecular, macromolecular and nanoparticle-based agents. PMID:24040650

  13. Phase sensitive x-ray diffraction imaging of defects in biological macromolecular crystals

    NASA Technical Reports Server (NTRS)

    Hu, Z. W.; Lai, B.; Chu, Y. S.; Cai, Z.; Mancini, D. C.; Thomas, B. R.; Chernov, A. A.

    2001-01-01

    Conventional x-ray diffraction topography is currently used to map defects in the bulk of protein crystals, but the lack of sufficient contrast is frequently a limiting factor. We experimentally demonstrate that this barrier can be circumvented using a method that combines phase sensitive and diffraction imaging principles. Details of defects revealed in tetragonal lysozyme and cubic ferritin crystals are presented and discussed. The approach enabling the detection of the phase changes of diffracted x rays should prove to be useful in the study of defect structures in a broad range of biological macromolecular crystals.

  14. Benefits and Limitations of Low-kV Macromolecular Imaging of Frozen-Hydrated Biological Samples.

    PubMed

    Majorovits, Endre; Angert, Isabel; Kaiser, Ute; Schröder, Rasmus R

    2016-02-23

    Object contrast is one of the most important parameters of macromolecular imaging. Low-voltage transmission electron microscopy has shown an increased atom contrast for carbon materials, indicating that amplitude contrast contributions increase at a higher rate than phase contrast and inelastic scattering. Here, we studied image contrast using ice-embedded tobacco mosaic virus particles as test samples at 20-80 keV electron energy. The particles showed the expected increase in contrast for lower energies, but at the same time the 2.3-nm-resolution measure decayed more rapidly. We found a pronounced signal loss below 60 keV, and therefore we conclude that increased inelastic scattering counteracts increased amplitude contrast. This model also implies that as long as the amplitude contrast does not increase with resolution, beam damage and multiple scattering will always win over increased contrast at the lowest energies. Therefore, we cannot expect that low-energy imaging of conventionally prepared samples would provide better data than state-of-the-art 200-300 keV imaging. PMID:26910420

  15. JBlulce Data Acquisition Software for Macromolecular Crystallography

    Energy Science and Technology Software Center (ESTSC)

    2010-06-01

    JBlulce (Java Beam Line Universal Integrated Configuration Environment is a data acquisition software for macromolecular crystallography conforming user interface of the SSRL Blulce that has become a de-factor standard in the field. Besides this interface conformity, JBlulce is a unique system in terms of architecture, speec, capability and osftware implementation. It features only two software layers, the JBlulce clients and the EPICS servers, as compared to three layers present in Blulc and most of similarmore » systems. This layers reduction provides a faster communication with hardware and an easier access to advanced hardware capabilities like on-the-fly scanning. Then JBlulc clients are designed to operate in parallel with the other beamline controls which streamlines the tasks performed by staff such as beamline preparation, maitenance, audting and user assistance. Another distinction is the deployment of multiple plugins that can be written in any programming languag thus involving more staff into the development. further on, JBlulce makes use of unified motion controls allowing for easy scanning and optimizing of any beamline component. Finally, the graphic interface is implemented in Java making full use of rich Java libraries and Jave IDE for debugging. to compare, Blulce user interface is implemented with aging Tcl/tk language providing very restricted capabilities. JBlulce makes full use of the industrial power and wide drivers selection of EPICS in controlling hardware; all hardware commuication is routed via multiple EPICS servers residing on local area network. JBlulce also includes several EPICS State Notation servers aimed at making hardware communication more robust. Besides using EPICS for controlling hardware, JBlulce extensively uses EPICS databases for efficien communications between multiple instances of JBlulce clients and JBlulce pplugins that can run in parallel on different computers. All of the above makes JBlulce one of the biggest

  16. JBlulce Data Acquisition Software for Macromolecular Crystallography

    SciTech Connect

    2010-06-01

    JBlulce (Java Beam Line Universal Integrated Configuration Environment is a data acquisition software for macromolecular crystallography conforming user interface of the SSRL Blulce that has become a de-factor standard in the field. Besides this interface conformity, JBlulce is a unique system in terms of architecture, speec, capability and osftware implementation. It features only two software layers, the JBlulce clients and the EPICS servers, as compared to three layers present in Blulc and most of similar systems. This layers reduction provides a faster communication with hardware and an easier access to advanced hardware capabilities like on-the-fly scanning. Then JBlulc clients are designed to operate in parallel with the other beamline controls which streamlines the tasks performed by staff such as beamline preparation, maitenance, audting and user assistance. Another distinction is the deployment of multiple plugins that can be written in any programming languag thus involving more staff into the development. further on, JBlulce makes use of unified motion controls allowing for easy scanning and optimizing of any beamline component. Finally, the graphic interface is implemented in Java making full use of rich Java libraries and Jave IDE for debugging. to compare, Blulce user interface is implemented with aging Tcl/tk language providing very restricted capabilities. JBlulce makes full use of the industrial power and wide drivers selection of EPICS in controlling hardware; all hardware commuication is routed via multiple EPICS servers residing on local area network. JBlulce also includes several EPICS State Notation servers aimed at making hardware communication more robust. Besides using EPICS for controlling hardware, JBlulce extensively uses EPICS databases for efficien communications between multiple instances of JBlulce clients and JBlulce pplugins that can run in parallel on different computers. All of the above makes JBlulce one of the biggest and most

  17. Macromolecular Topography Leaps into the Digital Age

    NASA Technical Reports Server (NTRS)

    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.

  18. Macromolecular networks and intelligence in microorganisms

    PubMed Central

    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

  19. Macromolecular networks and intelligence in microorganisms.

    PubMed

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

    2014-01-01

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

  20. Macromolecular synthesis after a nutritional shift-up of Bacillus subtilis.

    PubMed

    Murakami, S; Murakami, S; Yamaguchi, K; Yoshikawa, H

    1976-06-15

    Effects of amino acids of macromolecular synthesis in Bacillus subtilis were studied. Two mutants, CRK4001 and NIG45, that were selected as slow growers in rich media were proved to be useful to analyse early events occurring after addition of amino acids to exponentially growing cells in a glucose-salts medium (nutritional shift-up). In a wild type strain, the rate of stable RNA (sRNA: essentially ribosomal RNA) synthesis increased 2.3 fold shortly after the shift-up to the rate characteristic of the post-shift steady state growth. In contrast,sRNA synthesis in the mutant strains responded to the shift-up in two steps. Thus, shortly after the shift the rate of sRNA synthesis increased 2.2 fold as in the wild type but this increased level was maintained temporarily for 60 min and suddenly decreased to the post-shift steady state rate (1.4 fold increase). On the other hand, rates of DNA synthesis increased some 30 min after the shift directly to the post-shift steady state rates in all strains. Ratios of an origin to a terminus marker (purA/metB) began to increase exponentially to reach maximum values at 60 min after the shift, indicating that initiation of DNA replication occurred at frequencies characteristic of respective post-shift growth rates soon after the shift. These results revealed that the initial increase in the rate of sRNA synthesis and the frequency of initation of DNA replication after nutritional shift are not related to each other and are independently affected by amino acids. In concert with these findings, the increase in sRNA synthesis was not affected by inhibition of DNA synthesis for the first 60 min after the shift, while it was completely prevented by puromycin and choramphenicol. Protein synthesis for 10 min after the shift was sufficient to fully change the sRNA synthesis rate by amino acids. PMID:820961

  1. Contrast studies.

    PubMed

    Anderson, Susan M

    2006-01-01

    Contrast media plays an important role in imaging soft tissues and organs. Though contrast imaging is considered safe, radiologic technologists can improve the safety of contrast examinations by reviewing institutional safety procedures, safe practices for different methods of contrast administration and possible complications. The need for efficient communication and attention to detail during contrast procedures is essential for patient safety. PMID:16998193

  2. Macromolecular NMR spectroscopy for the non-spectroscopist: beyond macromolecular solution structure determination.

    PubMed

    Bieri, Michael; Kwan, Ann H; Mobli, Mehdi; King, Glenn F; Mackay, Joel P; Gooley, Paul R

    2011-03-01

    A strength of NMR spectroscopy is its ability to monitor, on an atomic level, molecular changes and interactions. In this review, which is intended for non-spectroscopist, we describe major uses of NMR in protein science beyond solution structure determination. After first touching on how NMR can be used to quickly determine whether a mutation induces structural perturbations in a protein, we describe the unparalleled ability of NMR to monitor binding interactions over a wide range of affinities, molecular masses and solution conditions. We discuss the use of NMR to measure the dynamics of proteins at the atomic level and over a wide range of timescales. Finally, we outline new and expanding areas such as macromolecular structure determination in multicomponent systems, as well as in the solid state and in vivo. PMID:21214861

  3. Effects of Macromolecular Crowding on the Mechanical Unfolding of Ubiquitin

    NASA Astrophysics Data System (ADS)

    Peng, Haibo; Lin, Fan-Chi; Yuan, Jian-Min; Yang, Guoliang; Chyan, Chia-Lin

    2004-03-01

    Macromolecular crowding exists in all living cells and affects protein folding, rates of diffusion, and amyloid formation. Although the biophysical theory of macromolecular crowding by thermodynamics and statistical thermodynamics approaches has been well developed, the effect of crowding on protein stability and kinetics has not received sufficient attention experimentally. We have carried out experiments to characterize the effects of macromolecular crowding on the mechanical force-induced unfolding and refolding of individual protein molecules of ubiquitin. To facilitate the mechanical unfolding experiments, polymers of ubiquitin molecules were synthesized. Using the atomic force microscope, we determined that, as the concentration of the crowding agents (dextran) increases from zero to 300 g/l, the average unfolding force of ubiquitin increase from 228 pN to 296 pN with a pulling speed of 1000 nm/s and in neutral pH. This result suggests that the unfolding rate of ubiquitin is reduced due to molecular crowding.

  4. Unexpected effects of macromolecular crowding on protein stability.

    PubMed

    Benton, Laura A; Smith, Austin E; Young, Gregory B; Pielak, Gary J

    2012-12-11

    Most theories about macromolecular crowding focus on two ideas: the macromolecular nature of the crowder and entropy. For proteins, the volume excluded by the crowder favors compact native states over expanded denatured states, enhancing protein stability by decreasing the entropy of unfolding. We tested these ideas with the widely used crowding agent Ficoll-70 and its monomer, sucrose. Contrary to expectations, Ficoll and sucrose have approximately the same stabilizing effect on chymotrypsin inhibitor 2. Furthermore, the stabilization is driven by enthalpy, not entropy. These results point to the need for carefully controlled studies and more sophisticated theories for understanding crowding effects. PMID:23167542

  5. A macromolecular prodrug strategy for combinatorial drug delivery.

    PubMed

    Li, Nan-Nan; Lin, Jiantao; Gao, Di; Zhang, Li-Ming

    2014-03-01

    A novel macromolecular prodrug strategy was developed for the combinatorial delivery of two poorly water-soluble drugs, dexamethasone and doxorubicin. In this work, dexamethasone was firstly conjugated onto a water-soluble modified polysaccharide by an acid-labile hydrazone linkage. The resultant macromolecular prodrug had an amphiphilic character and could self-assemble into spherical polymeric micelles in aqueous system. With these micelles, doxorubicin was then encapsulated into their hydrophobic cores. For the conjugated dexamethasone and encapsulated doxorubicin, they could exhibit independent and acid-sensitive release characteristics. For the doxorubicin-loaded prodrug micelles, they were easily be internalized by living cells and showed obvious antitumor activity. PMID:24407691

  6. Macromolecular crystallography beamline X25 at the NSLS

    PubMed Central

    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.

    2014-01-01

    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. PMID:24763654

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

    PubMed

    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

  8. Macromolecular Pt(IV) Prodrugs from Poly(organo)phosphazenes.

    PubMed

    Henke, Helena; Kryeziu, Kushtrim; Banfić, Jelena; Theiner, Sarah; Körner, Wilfried; Brüggemann, Oliver; Berger, Walter; Keppler, Bernhard K; Heffeter, Petra; Teasdale, Ian

    2016-08-01

    The preparation of novel macromolecular prodrugs via the conjugation of two platinum(IV) complexes to suitably functionalized poly(organo)phosphazenes is presented. The inorganic/organic polymers provide carriers with controlled dimensions due to the use of living cationic polymerization and allow the preparation of conjugates with excellent aqueous solubility but long-term hydrolytic degradability. The macromolecular Pt(IV) prodrugs are designed to undergo intracellular reduction and simultaneous release from the macromolecular carrier to present the active Pt(II) drug derivatives. In vitro investigations show a significantly enhanced intracellular uptake of Pt for the macromolecular prodrugs when compared to small molecule Pt complexes, which is also reflected in an increase in cytotoxicity. Interestingly, drug-resistant sublines also show a significantly smaller resistance against the conjugates compared to clinically established platinum drugs, indicating that an alternative uptake route of the Pt(IV) conjugates might also be able to overcome acquired resistance against Pt(II) drugs. In vivo studies of a selected conjugate show improved tumor shrinkage compared to the respective Pt(IV) complex. PMID:27169668

  9. Impact of Synchrotron Radiation on Macromolecular Crystallography: a Personal View

    SciTech Connect

    Dauter, Z.; Jaskolski, M; Wlodawer, A

    2010-01-01

    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.

  10. Macromolecular Pt(IV) Prodrugs from Poly(organo)phosphazenes

    PubMed Central

    Banfić, Jelena; Theiner, Sarah; Körner, Wilfried; Brüggemann, Oliver; Berger, Walter; Keppler, Bernhard K.; Heffeter, Petra; Teasdale, Ian

    2016-01-01

    The preparation of novel macromolecular prodrugs via the conjugation of two platinum(IV) complexes to suitably functionalized poly(organo)phosphazenes is presented. The inorganic/organic polymers provide carriers with controlled dimensions due to the use of living cationic polymerization and allow the preparation of conjugates with excellent aqueous solubility but long-term hydrolytic degradability. The macromolecular Pt(IV) prodrugs are designed to undergo intracellular reduction and simultaneous release from the macromolecular carrier to present the active Pt(II) drug derivatives. In vitro investigations show a significantly enhanced intracellular uptake of Pt for the macromolecular prodrugs when compared to small molecule Pt complexes, which is also reflected in an increase in cytotoxicity. Interestingly, drug-resistant sublines also show a significantly smaller resistance against the conjugates compared to clinically established platinum drugs, indicating that an alternative uptake route of the Pt(IV) conjugates might also be able to overcome acquired resistance against Pt(II) drugs. In vivo studies of a selected conjugate show improved tumor shrinkage compared to the respective Pt(IV) complex. PMID:27169668

  11. Crystallography & NMR system: A new software suite for macromolecular structure determination.

    PubMed

    Brünger, A T; Adams, P D; Clore, G M; DeLano, W L; Gros, P; Grosse-Kunstleve, R W; Jiang, J S; Kuszewski, J; Nilges, M; Pannu, N S; Read, R J; Rice, L M; Simonson, T; Warren, G L

    1998-09-01

    A new software suite, called Crystallography & NMR System (CNS), has been developed for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contrast to existing structure-determination programs, the architecture of CNS is highly flexible, allowing for extension to other structure-determination methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical structure: a high-level hypertext markup language (HTML) user interface, task-oriented user input files, module files, a symbolic structure-determination language (CNS language), and low-level source code. Each layer is accessible to the user. The novice user may just use the HTML interface, while the more advanced user may use any of the other layers. The source code will be distributed, thus source-code modification is possible. The CNS language is sufficiently powerful and flexible that many new algorithms can be easily implemented in the CNS language without changes to the source code. The CNS language allows the user to perform operations on data structures, such as structure factors, electron-density maps, and atomic properties. The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallographic procedures for phasing, density modification and refinement. User-friendly task-oriented input files are available for nearly all aspects of macromolecular structure determination by X-ray crystallography and solution NMR. PMID:9757107

  12. Iodinated Contrast Medium Exposure During Computed Tomography Increase the Risk of Subsequent Development of Thyroid Disorders in Patients Without Known Thyroid Disease: A Nationwide Population-Based, Propensity Score-Matched, Longitudinal Follow-Up Study.

    PubMed

    Hsieh, Ming-Shun; Chiu, Chien-Shan; Chen, Wen-Chi; Chiang, Jen-Huai; Lin, Shih-Yi; Lin, Meng-Yu; Chang, Shih-Liang; Sheu, Meei-Ling; Hu, Sung-Yuan

    2015-12-01

    To investigate the association between iodinated contrast medium (ICM) exposure during computed tomography (CT) and the subsequent development of thyroid disorders in patients without known thyroid disease in Taiwan, an iodine-sufficient area. We conducted a population-based cohort study by using data from 1996 to 2012 in the Taiwan National Health Insurance Research Database. A total of 33,426 patients who underwent ICM-enhanced CT were included as the study cohort. To avoid selection bias, we used propensity score and matched for the index year (defined as the year of first ICM exposure) to retrieve 33,426 patients as the comparison cohort. No patients in the 2 cohorts had any known thyroid disease before the index year. Patients with a history of amiodarone treatment or coronary angiography and those with <1 year follow-up were excluded. Participants were followed until a new diagnosis of thyroid disorder or December 31, 2011. Hazard ratios (HRs) with 95% confidence interval (95% CI) were calculated using the Cox proportional hazards regression. An association was identified between ICM exposure and the subsequent development of thyroid disorders after adjustment for potential confounders (adjusted HR = 1.17; 95% CI: 1.07-1.29; P = 0.001). Male patients and patients' ages ≥40 years in the ICM-exposure cohort had a higher adjusted HR for developing thyroid disorders than did those in the non-ICM-exposure cohort. Hypothyroidism had the highest adjusted HR (HR = 1.37; 95% CI: 1.06-1.78; P < 0.05) among all thyroid disorders and had a higher risk of development or detection during >0.5-year post-ICM exposure compared with that during ≤0.5-year post-ICM exposure (HR = 1.26; 95% CI: 1.01-1.58; P < 0.05). Repeated ICM exposure increased the risk of thyroid disorders in patients who accepted >1 time of ICM per year on average compared with those who accepted ≤1 time per year on average (adjusted HR = 3.04; 95% CI: 2.47-3.73; P < 0

  13. Macromolecular structure of cellulose studied by second-harmonic generation imaging microscopy

    NASA Astrophysics Data System (ADS)

    Brown, R. Malcom; Millard, Andrew C.; Campagnola, Paul J.

    2003-11-01

    The macromolecular structure of purified cellulose samples is studied by second-harmonic generation (SHG) imaging microscopy. We show that the SHG contrast in both Valonia and Acetobacter cellulose strongly resembles that of collagen from animal tissues, both in terms of morphology and polarization anisotropy. Polarization analysis shows that microfibrils in each lamella are highly aligned and ordered and change directions by 90° in adjacent lamellae. The angular dependence of the SHG intensity fits well to a cos2 θ distribution, which is characteristic of the electric dipole interaction. Enzymatic degradation of Valonia fibers by cellulase is followed in real time by SHG imaging and results in exponential decay kinetics, showing that SHG imaging microscopy is ideal for monitoring dynamics in biological systems.

  14. Contrastive Lexicology.

    ERIC Educational Resources Information Center

    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…

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

    PubMed

    DiPasquale, Stephen A; Byrne, Mark E

    2016-08-01

    This brief review analyzes recent developments in the field of living/controlled polymerization and the potential of this technique for creating imprinted polymers with highly structured architecture with macromolecular memory. As a result, it is possible to engineer polymers at the molecular level with increased homogeneity relating to enhanced template binding and transport. Only recently has living/controlled polymerization been exploited to decrease heterogeneity and substantially improve the efficiency of the imprinting process for both highly and weakly crosslinked imprinted polymers. Living polymerization can be utilized to create imprinted networks that are vastly more efficient than similar polymers produced using conventional free radical polymerization, and these improvements increase the role that macromolecular memory can play in the design and engineering of new drug delivery and sensing platforms. PMID:27322505

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

    SciTech Connect

    Wright, P.E.

    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.

  17. Macromolecular Brushes as Stabilizers of Hydrophobic Solute Nanoparticles.

    PubMed

    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

  18. Stochastic reaction–diffusion algorithms for macromolecular crowding

    NASA Astrophysics Data System (ADS)

    Sturrock, Marc

    2016-06-01

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

  19. Crystallization with oils: a new dimension in macromolecular crystal growth

    NASA Astrophysics Data System (ADS)

    Chayen, Naomi E.

    1999-01-01

    The crystal growth of biological macromolecules is a complicated process involving numerous parameters. This paper presents an approach which employs the use of oil as a major aid to crystal growth, and which has opened up a new dimension in the field of macromolecular crystallization. The presence of oil is a parameter which can contribute to the accuracy, the cleanliness and to the increase in the reproducibility of the experiments. Furthermore, the oil has a role in the protection of the trials during the course of their duration and in maintaining the stability of the resulting crystals. The use of oil also applies to the crystallization of membrane proteins. The results of a wide range of experiments which exploit the presence of oil to abet macromolecular crystal growth using both vapour diffusion and microbatch are presented.

  20. DOT2: Macromolecular docking with improved biophysical models.

    PubMed

    Roberts, Victoria A; Thompson, Elaine E; Pique, Michael E; Perez, Martin S; Ten Eyck, L F

    2013-07-30

    Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here, we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate an infinitive complete list of favorable candidate configurations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome. PMID:23695987

  1. DOT2: Macromolecular Docking With Improved Biophysical Models

    PubMed Central

    Roberts, Victoria A.; Thompson, Elaine E.; Pique, Michael E.; Perez, Martin S.; Eyck, Lynn Ten

    2015-01-01

    Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate a complete list of favorable candidate configu-rations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions, and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome. PMID:23695987

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

    PubMed Central

    Dauter, Zbigniew; Jaskolski, Mariusz; Wlodawer, Alexander

    2010-01-01

    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. PMID:20567074

  3. Comprehensive objective maps of macromolecular conformations by quantitative SAXS analysis

    PubMed Central

    Hura, Greg L.; Budworth, Helen; Dyer, Kevin N.; Rambo, Robert P.; Hammel, Michal

    2013-01-01

    Comprehensive perspectives of macromolecular conformations are required to connect structure to biology. Here we present a small angle X-ray scattering (SAXS) Structural Similarity Map (SSM) and Volatility of Ratio (VR) metric providing comprehensive, quantitative and objective (superposition-independent) perspectives on solution state conformations. We validate VR and SSM utility on human MutSβ, a key ABC ATPase and chemotherapeutic target, by revealing MutSβ DNA sculpting and identifying multiple conformational states for biological activity. PMID:23624664

  4. A strategy for dissecting the architectures of native macromolecular assemblies

    PubMed Central

    Shi, Yi; Pellarin, Riccardo; Fridy, Peter C.; Fernandez-Martinez, Javier; Thompson, Mary K.; Li, Yinyin; Wang, Qing Jun; Sali, Andrej; Rout, Michael P.; Chait, Brian T.

    2015-01-01

    Despite the central role of large multi-protein complexes in many biological processes, it remains challenging to elucidate their structures and particularly problematic to define the structures of native macromolecular assemblies, which are often of low abundance. Here, we present a strategy for isolating such complexes and for extracting distance restraints that allow the determination of their molecular architectures. The method was optimized to allow facile use of the extensive global resources of GFP-tagged transgenic cells and animals. PMID:26436480

  5. A 3D cellular context for the macromolecular world

    PubMed Central

    Patwardhan, Ardan; Ashton, Alun; Brandt, Robert; Butcher, Sarah; Carzaniga, Raffaella; Chiu, Wah; Collinson, Lucy; Doux, Pascal; Duke, Elizabeth; Ellisman, Mark H; Franken, Erik; Grünewald, Kay; Heriche, Jean-Karim; Koster, Abraham; Kühlbrandt, Werner; Lagerstedt, Ingvar; Larabell, Carolyn; Lawson, Catherine L; Saibil, Helen R; Sanz-García, Eduardo; Subramaniam, Sriram; Verkade, Paul; Swedlow, Jason R; Kleywegt, Gerard J

    2015-01-01

    We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community. PMID:25289590

  6. Cryo-Electron Tomography for Structural Characterization of Macromolecular Complexes

    PubMed Central

    Cope, Julia; Heumann, John; Hoenger, Andreas

    2011-01-01

    Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological material embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as the relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions. PMID:21842467

  7. Application of complex macromolecular architectures for advanced microelectronic materials.

    PubMed

    Hedrick, James L; Magbitang, Teddie; Connor, Eric F; Glauser, Thierry; Volksen, Willi; Hawker, Craig J; Lee, Victor Y; Miller, Robert D

    2002-08-01

    The distinctive features of well-defined, three-dimensional macromolecules with topologies designed to enhance solubility and amplify end-group functionality facilitated nanophase morphologies in mixtures with organosilicates and ultimately nanoporous organosilicate networks. Novel macromolecular architectures including dendritic and star-shaped polymers and organic nanoparticles were prepared by a modular approach from several libraries of building blocks including various generations of dendritic initiators and dendrons, selectively placed to amplify functionality and/or arm number, coupled with living polymerization techniques. Mixtures of an organosilicate and the macromolecular template were deposited, cured, and the phase separation of the organic component, organized the vitrifying organosilicate into nanostructures. Removal of the sacrificial macromolecular template, also denoted as porogen, by thermolysis, yielded the desired nanoporous organosilicate, and the size scale of phase separation was strongly dependent on the chain topology. These materials were designed for use as interlayer, ultra-low dielectric insulators for on-chip applications with dielectric constant values as low as 1.5. The porogen design, chemistry and role of polymer architecture on hybrid and pore morphology will be emphasized. PMID:12203311

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

    NASA Astrophysics Data System (ADS)

    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. What Macromolecular Crowding Can Do to a Protein

    PubMed Central

    Kuznetsova, Irina M.; Turoverov, Konstantin K.; Uversky, Vladimir N.

    2014-01-01

    The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area. PMID:25514413

  10. International summer school on macromolecular crystallographic computing. Final report

    SciTech Connect

    1998-08-01

    The School was the seventh in a series of International Union of Crystallography (IUCr) Crystallographic Symposia. The format of the School was formal lectures in the morning, tutorials in the afternoon, and software demonstrations and more lectures in the evening. The full program which left both the organizers and attendees exhausted, reflects the current state of excitement in the field of macromolecular structure determination using the technique of X-ray crystallography. The new and improved technologies and techniques described in these Proceedings are contributing to that growth and at the same time, as pointed out in the paper given by Sussman, creating challenges for the Protein Data Bank (PDB). As the School progressed, the authors were struck by the similarities to events which took place in small molecule crystallography beginning some 20 to 25 years ago. Growth then was fueled by the advent of new algorithms, affordable computer hardware, and good software. So it is today for macromolecular crystallography, but with the added bonus of the Internet which is changing how scientist conduct their research. Flack presented this view as part of his on-going contribution to how crystallographers use the Internet. After presentations discussing structures en masse they returned to the more traditional mode of presentation which parallels the determination of a single macromolecular structure: data collection -- phasing -- model building and visualization -- refinement.

  11. Contrast Materials

    MedlinePlus

    ... or other reactions to contrast materials are rare, radiology departments are well-equipped to deal with them. ... is given. However, both the American College of Radiology (ACR) and the European Society of Urogenital Radiology ...

  12. A role for macromolecular crowding effects in the assembly and function of compartments in the nucleus.

    PubMed

    Hancock, Ronald

    2004-06-01

    The mechanisms which cause macromolecules to form discrete compartments within the nucleus are not understood. Here, two ubiquitous compartments, nucleoli, and PML bodies, are shown to disassemble when K562 cell nuclei expand in medium of low monovalent cation concentration; their major proteins dispersed as seen by immunofluorescence and immunoelectron microscopy, and nucleolar transcript elongation fell by approximately 85%. These compartments reassembled and nucleolar transcription recovered in the same medium after adding inert, penetrating macromolecules (8 kDa polyethylene glycol (PEG), or 10.5 kDa dextran) to 12% w/v, showing that disassembly was not caused by the low cation concentration. These responses satisfy the criteria for crowding or volume exclusion effects which occur in concentrated mixtures of macromolecules; upon expansion the macromolecular concentration within the nucleus falls, and can be restored by PEG or dextran. These observations, together with evidence of a high concentration of macromolecules in the nucleus (in the range of 100mg/ml) which must cause strong crowding forces, suggest strongly that these forces play an essential role in driving the formation, and maintaining the function of nuclear compartments. This view is consistent with their dynamic and mobile nature and can provide interpretations of several unexplained observations in nuclear biology. PMID:15099570

  13. Aspiration of Barium Contrast

    PubMed Central

    Fuentes Santos, Cristina; Steen, Bárbara

    2014-01-01

    The aspiration of barium contrast is a rare complication that may occur during studies of the digestive tract. Barium is an inert material that can cause anywhere from an asymptomatic mechanical obstruction to serious symptoms of respiratory distress that can result in patient death. We present the case of a 79-year-old male patient in whom we observed the presence of contrast medium residue in the lung parenchyma as an incidental finding during hospitalization. When the patient's medical file was reviewed, images were found of a barium swallow study that the patient had undergone months earlier, and we were able to observe the exact moment of the aspiration of the contrast material. The patient had been asymptomatic since the test. PMID:25309769

  14. Contrast lipocryolysis

    PubMed Central

    Pinto, Hernán; Melamed, Graciela

    2014-01-01

    Alternative crystal structures are possible for all lipids and each different crystal structure is called a polymorphic form. Inter-conversion between polymorphisms would imply the possibility of leaning crystal formation toward the most effective polymorphism for adipocyte destruction. Food industry has been tempering lipids for decades. Tempering technology applied to lipocryolysis gave birth to “contrast lipocryolysis”, which involves pre- and post-lipocryolysis fat layer heating as part of a specific tempering protocol. In this study, we evaluated the skinfold thickness of 10 subjects after a single contrast lipocryolysis session and witnessed important and fast reductions. PMID:25068088

  15. Thermodynamic signatures in macromolecular interactions involving conformational flexibility.

    PubMed

    Menzel, Anja; Neumann, Piotr; Schwieger, Christian; Stubbs, Milton T

    2014-07-01

    The energetics of macromolecular interactions are complex, particularly where protein flexibility is involved. Exploiting serendipitous differences in the plasticity of a series of closely related trypsin variants, we analyzed the enthalpic and entropic contributions accompanying interaction with L45K-eglin C. Binding of the four variants show significant differences in released heat, although the affinities vary little, in accordance with the principle of enthalpy-entropy compensation. Binding of the most disordered variant is almost entirely enthalpically driven, with practically no entropy change. As structures of the complexes reveal negligible differences in protein-inhibitor contacts, we conclude that solvent effects contribute significantly to binding affinities. PMID:25003391

  16. Bringing single-molecule spectroscopy to macromolecular protein complexes

    PubMed Central

    Joo, Chirlmin; Fareh, Mohamed; Kim, V. Narry

    2013-01-01

    Single-molecule fluorescence spectroscopy offers real-time, nanometer-resolution information. Over the past two decades, this emerging single-molecule technique has been rapidly adopted to investigate the structural dynamics and biological functions of proteins. Despite this remarkable achievement, single-molecule fluorescence techniques must be extended to macromolecular protein complexes that are physiologically more relevant for functional studies. In this review, we present recent major breakthroughs for investigating protein complexes within cell extracts using single-molecule fluorescence. We outline the challenges, future prospects and potential applications of these new single-molecule fluorescence techniques in biological and clinical research. PMID:23200186

  17. Biophysical Highlights from 54 Years of Macromolecular Crystallography

    PubMed Central

    Richardson, Jane S.; Richardson, David C.

    2014-01-01

    The United Nations has declared 2014 the International Year of Crystallography, and in commemoration, this review features a selection of 54 notable macromolecular crystal structures that have illuminated the field of biophysics in the 54 years since the first excitement of the myoglobin and hemoglobin structures in 1960. Chronological by publication of the earliest solved structure, each illustrated entry briefly describes key concepts or methods new at the time and key later work leveraged by knowledge of the three-dimensional atomic structure. PMID:24507592

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

    SciTech Connect

    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.

  19. Visualizing Proteins and Macromolecular Complexes by Negative Stain EM: from Grid Preparation to Image Acquisition

    PubMed Central

    Booth, David S.; Avila-Sakar, Agustin; Cheng, Yifan

    2011-01-01

    Single particle electron microscopy (EM), of both negative stained or frozen hydrated biological samples, has become a versatile tool in structural biology 1. In recent years, this method has achieved great success in studying structures of proteins and macromolecular complexes 2, 3. Compared with electron cryomicroscopy (cryoEM), in which frozen hydrated protein samples are embedded in a thin layer of vitreous ice 4, negative staining is a simpler sample preparation method in which protein samples are embedded in a thin layer of dried heavy metal salt to increase specimen contrast 5. The enhanced contrast of negative stain EM allows examination of relatively small biological samples. In addition to determining three-dimensional (3D) structure of purified proteins or protein complexes 6, this method can be used for much broader purposes. For example, negative stain EM can be easily used to visualize purified protein samples, obtaining information such as homogeneity/heterogeneity of the sample, formation of protein complexes or large assemblies, or simply to evaluate the quality of a protein preparation. In this video article, we present a complete protocol for using an EM to observe negatively stained protein sample, from preparing carbon coated grids for negative stain EM to acquiring images of negatively stained sample in an electron microscope operated at 120kV accelerating voltage. These protocols have been used in our laboratory routinely and can be easily followed by novice users. PMID:22215030

  20. Mechanisms, kinetics, impurities and defects: consequences in macromolecular crystallization

    PubMed Central

    McPherson, Alexander; Kuznetsov, Yurii G.

    2014-01-01

    The nucleation and growth of protein, nucleic acid and virus crystals from solution are functions of underlying kinetic and thermodynamic parameters that govern the process, and these are all supersaturation-dependent. While the mechanisms of macromolecular crystal growth are essentially the same as for conventional crystals, the underlying parameters are vastly different, in some cases orders of magnitude lower, and this produces very different crystallization processes. Numerous physical features of macromolecular crystals are of serious interest to X-ray diffractionists; the resolution limit and mosaicity, for example, reflect the degree of molecular and lattice order. The defect structure of crystals has an impact on their response to flash-cooling, and terminal crystal size is dependent on impurity absorption and incorporation. The variety and extent of these issues are further unique to crystals of biological macromolecules. All of these features are amenable to study using atomic force microscopy, which provides direct images at the nanoscale level. Some of those images are presented here. PMID:24699728

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

    PubMed

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

    2016-01-01

    Bioactive macromolecular peptides and oligonucleotides have significant therapeutic potential. However, due to their size, they have no ability to enter the cytoplasm of cells. Peptide/Protein transduction domains (PTDs), also called cell-penetrating peptides (CPPs), can promote uptake of macromolecules via endocytosis. However, overcoming the rate-limiting step of endosomal escape into the cytoplasm remains a major challenge. Hydrophobic amino acid R groups are known to play a vital role in viral escape from endosomes. Here we utilize a real-time, quantitative live cell split-GFP fluorescence complementation phenotypic assay to systematically analyze and optimize a series of synthetic endosomal escape domains (EEDs). By conjugating EEDs to a TAT-PTD/CPP spilt-GFP peptide complementation assay, we were able to quantitatively measure endosomal escape into the cytoplasm of live cells via restoration of GFP fluorescence by intracellular molecular complementation. We found that EEDs containing two aromatic indole rings or one indole ring and two aromatic phenyl groups at a fixed distance of six polyethylene glycol (PEG) units from the TAT-PTD-cargo significantly enhanced cytoplasmic delivery in the absence of cytotoxicity. EEDs address the critical rate-limiting step of endosomal escape in delivery of macromolecular biologic peptide, protein and siRNA therapeutics into cells. PMID:27604151

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

    PubMed Central

    Waltersperger, Sandro; Olieric, Vincent; Pradervand, Claude; Glettig, Wayne; Salathe, Marco; Fuchs, Martin R.; Curtin, Adrian; Wang, Xiaoqiang; Ebner, Simon; Panepucci, Ezequiel; Weinert, Tobias; Schulze-Briese, Clemens; Wang, Meitian

    2015-01-01

    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. PMID:26134792

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

    PubMed Central

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

    2016-01-01

    Bioactive macromolecular peptides and oligonucleotides have significant therapeutic potential. However, due to their size, they have no ability to enter the cytoplasm of cells. Peptide/Protein transduction domains (PTDs), also called cell-penetrating peptides (CPPs), can promote uptake of macromolecules via endocytosis. However, overcoming the rate-limiting step of endosomal escape into the cytoplasm remains a major challenge. Hydrophobic amino acid R groups are known to play a vital role in viral escape from endosomes. Here we utilize a real-time, quantitative live cell split-GFP fluorescence complementation phenotypic assay to systematically analyze and optimize a series of synthetic endosomal escape domains (EEDs). By conjugating EEDs to a TAT-PTD/CPP spilt-GFP peptide complementation assay, we were able to quantitatively measure endosomal escape into the cytoplasm of live cells via restoration of GFP fluorescence by intracellular molecular complementation. We found that EEDs containing two aromatic indole rings or one indole ring and two aromatic phenyl groups at a fixed distance of six polyethylene glycol (PEG) units from the TAT-PTD-cargo significantly enhanced cytoplasmic delivery in the absence of cytotoxicity. EEDs address the critical rate-limiting step of endosomal escape in delivery of macromolecular biologic peptide, protein and siRNA therapeutics into cells. PMID:27604151

  4. The Phenix Software for Automated Determination of Macromolecular Structures

    PubMed Central

    Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor; Chen, Vincent B.; Echols, Nathaniel; Headd, Jeffrey J.; Hung, Li-Wei; Jain, Swati; Kapral, Gary J.; Grosse Kunstleve, Ralf W.; McCoy, Airlie J.; Moriarty, Nigel W.; Oeffner, Robert D.; Read, Randy J.; Richardson, David C.; Richardson, Jane S.; Terwilliger, Thomas C.; Zwart, Peter H.

    2011-01-01

    X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favour of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface. PMID:21821126

  5. REFMAC5 for the refinement of macromolecular crystal structures

    PubMed Central

    Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A.; Pannu, Navraj S.; Steiner, Roberto A.; Nicholls, Robert A.; Winn, Martyn D.; Long, Fei; Vagin, Alexei A.

    2011-01-01

    This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement tools such as secondary-structure restraints, restraints to known homologous structures, automatic global and local NCS restraints, ‘jelly-body’ restraints and the use of novel long-range restraints on atomic displacement parameters (ADPs) based on the Kullback–Leibler divergence. REFMAC5 additionally offers TLS parameterization and, when high-resolution data are available, fast refinement of anisotropic ADPs. Refinement in the presence of twinning is performed in a fully automated fashion. REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography. PMID:21460454

  6. Enzymes as Green Catalysts for Precision Macromolecular Synthesis.

    PubMed

    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. PMID:26791937

  7. Cardiac voltage-gated calcium channel macromolecular complexes.

    PubMed

    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

  8. The macromolecular crystallography facility at the advanced light source

    NASA Astrophysics Data System (ADS)

    Earnest, Thomas; Padmore, Howard; Cork, Carl; Behrsing, Rolf; Kim, Sung-Hou

    1996-10-01

    Synchrotron radiation offers several advantages over the use of rotating anode sources for biological crystallography, which allow for the collection of higher-resolution data, substantially more rapid data collection, phasing by multiwavelength anomalous diffraction (MAD) techniques, and time-resolved experiments using polychromatic radiation (Laue diffraction). The use of synchrotron radiation is often necessary to record useful data from crystals which diffract weakly or have very large unit cells. The high brightness and stability characteristics of the advanced light source (ALS) at Lawrence Berkeley National Laboratory, along with the low emittance and long straight sections to accommodate insertion devices present in third generation synchrotrons like the ALS, lead to several advantages in the field of macromolecular crystallography. We are presently constructing a macromolecular crystallography facility at the ALS which is optimized for user-friendliness and high-throughput data collection, with advanced capabilities for MAD and Laue experiments. The X-rays will be directed to three branchlines. A well-equipped support lab will be available for biochemistry, crystal mounting and sample storage, as well as computer hardware and software available, along with staff support, allowing for the complete processing of data on site.

  9. Preparation of phenylboronate affinity rigid monolith with macromolecular porogen.

    PubMed

    Li, Xiang-Jie; Jia, Man; Zhao, Yong-Xin; Liu, Zhao-Sheng; Akber Aisa, Haji

    2016-03-18

    Boronate-affinity monolithic column was first prepared via polystyrene (PS) as porogen in this work. The monolithic polymer was synthetized using 4-vinylphenylboronic acid (4-VPBA) as functional monomer, ethylene glycol dimethacrylate (EDMA) as crosslinker monomer, and a mixture of PS solution in tetrahydrofuran, the linear macromolecular porogen, and toluene as porogen. Isoquercitrin (ISO) and hyperoside (HYP), isomer diol flavonoid glycosides, can be baseline separated on the poly(VPBA-co-EDMA) monolith. The effect of polymerization variables on the selectivity factor, e.g., the ratio of monomer to crosslinker (M/C), the amount of PS and the molecular weight of macromolecular porogen was investigated. The surface properties of the monolithic polymer were characterized by scanning electron microscopy and nitrogen adsorption. The best polymerization condition was the M/C ratio of 7:3, and the PS concentration of 40 mg/ml. The poly(VPBA-co-EDMA) polymer was also applied to extract cis-diol flavonoid glycosides from the crude extraction of cotton flower. After treated by poly(VPBA-co-EDMA) for solid phase extraction, high purity ISO and HYP (>99.96%) can be obtained with recovery of 83.7% and 78.6%, respectively. PMID:26896914

  10. Crosslinked macromolecular structures in bituminous coals: Theoretical and experimental considerations

    NASA Astrophysics Data System (ADS)

    Lucht, Lucy M.; Peppas, Nicolaos A.

    1981-02-01

    Ample evidence from physicochemical experiments suggests that bituminous coals can be described as highly crosslinked and entangled networks of macromolecular chains of irregular structure. Theoretically these structures can be analyzed by statistical mechanical models considering non-Gaussian distribution of the macro-molecular chains along with departure from the Flory theories of crosslinked macromolecules. The models of Kovac (1978) and Peppas and Lucht (1979) have been developed in order to describe non-extractable coal matrices and their behavior during swelling in appropriate swelling agents. The molecular weight between cross-links Mc and the crosslinking density ρx can be determined for various solvents and equilibrium swelling ratios. Few experimental data are available to which these models can be applied. Thus, in view of these new theoretical models, experimental research must be directed towards the reexamination of extraction and swelling behavior of bituminous coals. Some of the important parameters to be determined for characterization of the physical structure of coals include the thermodynamic interaction parameter χ, the crosslinking parameters Mc and ρx and the molecular weight distribution of the extractable coal portion.

  11. Design and application of PDBlib, a C++ macromolecular class library.

    PubMed

    Chang, W; Shindyalov, I N; Pu, C; Bourne, P E

    1994-12-01

    PDBlib is an extensible object-oriented class library written in C++ for representing the three-dimensional structure of biological macromolecules. The software design strategy, features of many of the 129 classes currently distributed with the library, and two sample applications which use the library are described. Version 1.0 of the library represents the structural features of proteins, DNA, RNA and complexes thereof, at a level of detail on a par with that which can be parsed from a Protein Data Bank (PDB) entry. However, the memory-resident representation of the macromolecule is independent of the PDB entry and can be obtained from other sources, e.g. relational and object-oriented databases. PDBlib classes are organized into four categories: (i) classes that model the macromolecule; (ii) classes that enhance the extensibility of the library; (iii) classes that provide navigation facilities of the object-oriented macromolecular structure representation; and (iv) a class that loads a PDB file into the memory-resident object-oriented representation. A number of general-purpose procedures that return features of this representation and that are relevant to all biological disciplines are included in (i). The library has been used to develop PDBtool, a prototype structure verification tool, and PDBview, a structure rendering tool that requires no specialized graphics hardware and software. Current work centers on making the macromolecular structures represented by PDBlib persistent using a commercial object-oriented database and providing an additional class library, MMQLlib, to query those structures. PMID:7704656

  12. Bioelectrochemical activity of an electroactive macromolecular weight coenzyme derivative

    NASA Astrophysics Data System (ADS)

    Liu, Pu; Zheng, Haitao; Nie, Pingping; Wei, Yaotian; Feng, Zhenchao; Sun, Tao

    2009-07-01

    As coenzyme utilized by more than hundreds of dehydrogenases, the efficient immobilization and regeneration of nicotinamide adenine dinucleotide (NAD+) are of great importance and have practical applications in industrial, analytical and biomedical field. In this paper, an electroactive macromolecular weight coenzyme derivative (PEI-DHBNAD) was prepared by attaching both NAD+ and 3,4-dihydroxybenzaldehyde (3,4-DHB) to a water-soluble polyelectrolyte, poly(ethylenimine) (PEI). The functional polymer exhibited both electrochemical properties of catechol unites and coenzymatic activity of NAD moieties. The macromolecular NAD analogue showed a substantial degree of efficiency relative to free NAD+ with alcohol dehydrogenase (ADH) and glucose-6-phophate dehydrogenase (G6PDH), and a litter higher Michaelis-Menton constant (Km) was obtained for the coenzyme derivative than free NAD+. The bioelectrochemical properties of PEI-DHB-NAD were investigated by using G6PDH as the model enzyme, and both of them were retained on electrode surface by ultrafiltration membrane. The modified electrode showed typical response to substrate without the addition of free coenzyme, which indicated that PEI-DHB-NAD can carry out the electron transfer between electrode and NAD-dependent dehydrogenase. The utilization of polymer-based PEI-DHB-NAD is convenient for the immobilization of both electron mediator and coenzyme, and offers a practical approach for the construction of reagentless biosensors.

  13. Comparison of two self-assembled macromolecular prodrug micelles with different conjugate positions of SN38 for enhancing antitumor activity

    PubMed Central

    Liu, Yi; Piao, Hongyu; Gao, Ying; Xu, Caihong; Tian, Ye; Wang, Lihong; Liu, Jinwen; Tang, Bo; Zou, Meijuan; Cheng, Gang

    2015-01-01

    7-Ethyl-10-hydroxycamptothecin (SN38), an active metabolite of irinotecan (CPT-11), is a remarkably potent antitumor agent. The clinical application of SN38 has been extremely restricted by its insolubility in water. In this study, we successfully synthesized two macromolecular prodrugs of SN38 with different conjugate positions (chitosan-(C10-OH)SN38 and chitosan-(C20-OH)SN38) to improve the water solubility and antitumor activity of SN38. These prodrugs can self-assemble into micelles in aqueous medium. The particle size, morphology, zeta potential, and in vitro drug release of SN38 and its derivatives, as well as their cytotoxicity, pharmacokinetics, and in vivo antitumor activity in a xenograft BALB/c mouse model were studied. In vitro, chitosan-(C10-OH)SN38 (CS-(10s)SN38) and chitosan-(C20-OH) SN38 (CS-(20s)SN38) were 13.3- and 25.9-fold more potent than CPT-11 in the murine colon adenocarcinoma cell line CT26, respectively. The area under the curve (AUC)0–24 of SN38 after intravenously administering CS-(10s)SN38 and CS-(20s)SN38 to Sprague Dawley rats was greatly improved when compared with CPT-11 (both P<0.01). A larger AUC0–24 of CS-(20s)SN38 was observed when compared to CS-(10s)SN38 (P<0.05). Both of the novel self-assembled chitosan-SN38 prodrugs demonstrated superior anticancer activity to CPT-11 in the CT26 xenograft BALB/c mouse model. We have also investigated the differences between these macromolecular prodrug micelles with regards to enhancing the antitumor activity of SN38. CS-(20s)SN38 exhibited better in vivo antitumor activity than CS-(10s)SN38 at a dose of 2.5 mg/kg (P<0.05). In conclusion, both macromolecular prodrug micelles improved the in vivo conversion rate and antitumor activity of SN38, but the prodrug in which C20-OH was conjugated to macromolecular materials could be a more promising platform for SN38 delivery. PMID:25848251

  14. Macromolecular Crowding Directs Extracellular Matrix Organization and Mesenchymal Stem Cell Behavior

    PubMed Central

    Zeiger, Adam S.; Loe, Felicia C.; Li, Ran; Raghunath, Michael; Van Vliet, Krystyn J.

    2012-01-01

    Microenvironments of biological cells are dominated in vivo by macromolecular crowding and resultant excluded volume effects. This feature is absent in dilute in vitro cell culture. Here, we induced macromolecular crowding in vitro by using synthetic macromolecular globules of nm-scale radius at physiological levels of fractional volume occupancy. We quantified the impact of induced crowding on the extracellular and intracellular protein organization of human mesenchymal stem cells (MSCs) via immunocytochemistry, atomic force microscopy (AFM), and AFM-enabled nanoindentation. Macromolecular crowding in extracellular culture media directly induced supramolecular assembly and alignment of extracellular matrix proteins deposited by cells, which in turn increased alignment of the intracellular actin cytoskeleton. The resulting cell-matrix reciprocity further affected adhesion, proliferation, and migration behavior of MSCs. Macromolecular crowding can thus aid the design of more physiologically relevant in vitro studies and devices for MSCs and other cells, by increasing the fidelity between materials synthesized by cells in vivo and in vitro. PMID:22649562

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

    PubMed Central

    Wei, Jiachen; Dobnikar, Jure; Curk, Tine; Song, Fan

    2016-01-01

    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. PMID:26954357

  16. Analysis of the size dependence of macromolecular crowding shows that smaller is better

    PubMed Central

    Sharp, Kim A.

    2015-01-01

    The aqueous milieu inside cells contains as much as 30–40% dissolved protein and RNA by volume. This large concentration of macromolecules is expected to cause significant deviations from solution ideality. In vivo biochemical reaction rates and equilibria might differ significantly from those measured in the majority of in vitro experiments that are performed at much lower macromolecule concentrations. Consequently crowding, a nonspecific phenomenon believed to arise from the large excluded volume of these macromolecules, has been studied extensively by experimental and theoretical methods. However, the relevant theory has not been applied consistently. When the steric effects of macromolecular crowders and small molecules like water and ions are treated on an equal footing, the effect of the macromolecules is opposite to that commonly believed. Large molecules are less effective at crowding than water and ions. There is also a surprisingly weak dependence on crowder size. Molecules of medium size, ∼5 Å radius, have the same effect as much larger macromolecules like proteins and RNA. These results require a reassessment of observed high-concentration effects and of strategies to mimic in vivo conditions with in vitro experiments. PMID:26080429

  17. Improved reproducibility of unit-cell parameters in macromolecular cryocrystallography by limiting dehydration during crystal mounting

    PubMed Central

    Farley, Christopher; Burks, Geoffry; Siegert, Thomas; Juers, Douglas H.

    2014-01-01

    In macromolecular cryocrystallography unit-cell parameters can have low reproducibility, limiting the effectiveness of combining data sets from multiple crystals and inhibiting the development of defined repeatable cooling protocols. Here, potential sources of unit-cell variation are investigated and crystal dehydration during loop-mounting is found to be an important factor. The amount of water lost by the unit cell depends on the crystal size, the loop size, the ambient relative humidity and the transfer distance to the cooling medium. To limit water loss during crystal mounting, a threefold strategy has been implemented. Firstly, crystal manipulations are performed in a humid environment similar to the humidity of the crystal-growth or soaking solution. Secondly, the looped crystal is transferred to a vial containing a small amount of the crystal soaking solution. Upon loop transfer, the vial is sealed, which allows transport of the crystal at its equilibrated humidity. Thirdly, the crystal loop is directly mounted from the vial into the cold gas stream. This strategy minimizes the exposure of the crystal to relatively low humidity ambient air, improves the reproducibility of low-temperature unit-cell parameters and offers some new approaches to crystal handling and cryoprotection. PMID:25084331

  18. Multiphoton excitation and photodynamic activity of macromolecular derivatized mTHPC

    NASA Astrophysics Data System (ADS)

    Schneider, Marc; Graschew, Georgi; Roelofs, Theo A.; Balanos, Evangelos; Rakowsky, Stefan; Sinn, Hanns-joerg; Schlag, Peter M.

    2000-03-01

    Multiphoton excitation of photosensitizers in photodynamic therapy constitutes a promising approach, because of the increasing tissue penetration for longer wavelength of illumination. In this contribution the photodynamic activity of polyethylene glycol macromolecular derivatized mTHPC upon two-photon excitation is established. To test the photo- activity of the photosensitizer, human colon carcinoma cells, HCT-116, were incubated with 2 (mu) g/ml of mTHPC- CMPEG4 in the nutrition medium. Subsequent pulsed laser irradiation at 784 nm focused down on growing cell monolayers restricts cell vitality clearly within 24 hours after irradiation. To investigate whether an anoxic or euoxic energy transfer mechanism is involved, a uric acid assay was performed to test for the generation of singlet oxygen. Upon single-photon excitation mTHPC-CMPEG4 in TriPEG decomposed uric acid via the generation of singlet oxygen. Using femtosecond pulsed laser irradiation no decomposition of the uric acid was found, implying an anoxic energy transfer mechanism after tow-photon excitation. However, at present, we cannot exclude local hyperthermic effects in the cells containing the photosensitizer to contribute to the photodynamic activity upon two-photon excitation.

  19. Macromolecular Crystallization in Microfluidics for the International Space Station

    NASA Technical Reports Server (NTRS)

    Monaco, Lisa A.; Spearing, Scott

    2003-01-01

    At NASA's Marshall Space Flight Center, the Iterative Biological Crystallization (IBC) project has begun development on scientific hardware for macromolecular crystallization on the International Space Station (ISS). Currently ISS crystallization research is limited to solution recipes that were prepared on the ground prior to launch. The proposed hardware will conduct solution mixing and dispensing on board the ISS, be fully automated, and have imaging functions via remote commanding from the ground. Utilizing microfluidic technology, IBC will allow for on orbit iterations. The microfluidics LabChip(R) devices that have been developed, along with Caliper Technologies, will greatly benefit researchers by allowing for precise fluid handling of nano/pico liter sized volumes. IBC will maximize the amount of science return by utilizing the microfluidic approach and be a valuable tool to structural biologists investigating medically relevant projects.

  20. The promise of macromolecular crystallization in microfluidic chips

    NASA Technical Reports Server (NTRS)

    van der Woerd, Mark; Ferree, Darren; Pusey, Marc

    2003-01-01

    Microfluidics, or lab-on-a-chip technology, is proving to be a powerful, rapid, and efficient approach to a wide variety of bioanalytical and microscale biopreparative needs. The low materials consumption, combined with the potential for packing a large number of experiments in a few cubic centimeters, makes it an attractive technique for both initial screening and subsequent optimization of macromolecular crystallization conditions. Screening operations, which require a macromolecule solution with a standard set of premixed solutions, are relatively straightforward and have been successfully demonstrated in a microfluidics platform. Optimization methods, in which crystallization solutions are independently formulated from a range of stock solutions, are considerably more complex and have yet to be demonstrated. To be competitive with either approach, a microfluidics system must offer ease of operation, be able to maintain a sealed environment over several weeks to months, and give ready access for the observation and harvesting of crystals as they are grown.

  1. (129)Xe NMR Relaxation-Based Macromolecular Sensing.

    PubMed

    Gomes, Muller D; Dao, Phuong; Jeong, Keunhong; Slack, Clancy C; Vassiliou, Christophoros C; Finbloom, Joel A; Francis, Matthew B; Wemmer, David E; Pines, Alexander

    2016-08-10

    We report a (129)Xe NMR relaxation-based sensing approach that exploits changes in the bulk xenon relaxation rate induced by slowed tumbling of a cryptophane-based sensor upon target binding. The amplification afforded by detection of the bulk dissolved xenon allows sensitive detection of targets. The sensor comprises a xenon-binding cryptophane cage, a target interaction element, and a metal chelating agent. Xenon associated with the target-bound cryptophane cage is rapidly relaxed and then detected after exchange with the bulk. Here we show that large macromolecular targets increase the rotational correlation time of xenon, increasing its relaxation rate. Upon binding of a biotin-containing sensor to avidin at 1.5 μM concentration, the free xenon T2 is reduced by a factor of 4. PMID:27472048

  2. Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement

    PubMed Central

    Leaver-Fay, Andrew; O’Meara, Matthew J.; Tyka, Mike; Jacak, Ron; Song, Yifan; Kellogg, Elizabeth H.; Thompson, James; Davis, Ian W.; Pache, Roland A.; Lyskov, Sergey; Gray, Jeffrey J.; Kortemme, Tanja; Richardson, Jane S.; Havranek, James J.; Snoeyink, Jack; Baker, David; Kuhlman, Brian

    2013-01-01

    Accurate energy functions are critical to macromolecular modeling and design. We describe new tools for identifying inaccuracies in energy functions and guiding their improvement, and illustrate the application of these tools to improvement of the Rosetta energy function. The feature analysis tool identifies discrepancies between structures deposited in the PDB and low energy structures generated by Rosetta; these likely arise from inaccuracies in the energy function. The optE tool optimizes the weights on the different components of the energy function by maximizing the recapitulation of a wide range of experimental observations. We use the tools to examine three proposed modifications to the Rosetta energy function: improving the unfolded state energy model (reference energies), using bicubic spline interpolation to generate knowledge based torisonal potentials, and incorporating the recently developed Dunbrack 2010 rotamer library (Shapovalov and Dunbrack, 2011). PMID:23422428

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

    PubMed

    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. PMID:25849493

  4. Outrunning free radicals in room-temperature macromolecular crystallography

    PubMed Central

    Owen, Robin L.; Axford, Danny; Nettleship, Joanne E.; Owens, Raymond J.; Robinson, James I.; Morgan, Ann W.; Doré, Andrew S.; Lebon, Guillaume; Tate, Christopher G.; Fry, Elizabeth E.; Ren, Jingshan; Stuart, David I.; Evans, Gwyndaf

    2012-01-01

    A significant increase in the lifetime of room-temperature macromolecular crystals is reported through the use of a high-brilliance X-ray beam, reduced exposure times and a fast-readout detector. This is attributed to the ability to collect diffraction data before hydroxyl radicals can propagate through the crystal, fatally disrupting the lattice. Hydroxyl radicals are shown to be trapped in amorphous solutions at 100 K. The trend in crystal lifetime was observed in crystals of a soluble protein (immunoglobulin γ Fc receptor IIIa), a virus (bovine enterovirus serotype 2) and a membrane protein (human A2A adenosine G-protein coupled receptor). The observation of a similar effect in all three systems provides clear evidence for a common optimal strategy for room-temperature data collection and will inform the design of future synchrotron beamlines and detectors for macro­molecular crystallography. PMID:22751666

  5. In-vacuum long-wavelength macromolecular crystallography

    PubMed Central

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

    2016-01-01

    Structure solution based on the weak anomalous signal from native (protein and DNA) crystals is increasingly being attempted as part of synchrotron experiments. Maximizing the measurable anomalous signal by collecting diffraction data at longer wavelengths presents a series of technical challenges caused by the increased absorption of X-rays and larger diffraction angles. A new beamline at Diamond Light Source has been built specifically for collecting data at wavelengths beyond the capability of other synchrotron macromolecular crystallography beamlines. Here, the theoretical considerations in support of the long-wavelength beamline are outlined and the in-vacuum design of the endstation is discussed, as well as other hardware features aimed at enhancing the accuracy of the diffraction data. The first commissioning results, representing the first in-vacuum protein structure solution, demonstrate the promising potential of the beamline. PMID:26960130

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

    NASA Technical Reports Server (NTRS)

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

    2005-01-01

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

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

    SciTech Connect

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

    2015-03-30

    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. We report that these include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.

  8. Cryo electron microscopy to determine the structure of macromolecular complexes.

    PubMed

    Carroni, Marta; Saibil, Helen R

    2016-02-15

    Cryo-electron microscopy (cryo-EM) is a structural molecular and cellular biology technique that has experienced major advances in recent years. Technological developments in image recording as well as in processing software make it possible to obtain three-dimensional reconstructions of macromolecular assemblies at near-atomic resolution that were formerly obtained only by X-ray crystallography or NMR spectroscopy. In parallel, cryo-electron tomography has also benefitted from these technological advances, so that visualization of irregular complexes, organelles or whole cells with their molecular machines in situ has reached subnanometre resolution. Cryo-EM can therefore address a broad range of biological questions. The aim of this review is to provide a brief overview of the principles and current state of the cryo-EM field. PMID:26638773

  9. On macromolecular refinement at subatomic resolution withinteratomic scatterers

    SciTech Connect

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

    2007-11-09

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

  10. Macromolecular therapeutics in cancer treatment: the EPR effect and beyond.

    PubMed

    Maeda, Hiroshi

    2012-12-10

    In this review, I have discussed various issues of the cancer drug targeting primarily related to the EPR (enhanced permeability and retention) effect, which utilized nanomedicine or macromolecular drugs. The content goes back to the development of the first polymer-protein conjugate anticancer agent SMANCS and development of the arterial infusion in Lipiodol formulation into the tumor feeding artery (hepatic artery for hepatoma). The brief account on the EPR effect and its definition, factors involved, heterogeneity, and various methods of augmentation of the EPR effect, which showed remarkably improved clinical outcomes are also discussed. Various obstacles involved in drug developments and commercialization are also discussed through my personal experience and recollections. PMID:22595146

  11. Macromolecular crowding increases structural content of folded proteins.

    PubMed

    Perham, Michael; Stagg, Loren; Wittung-Stafshede, Pernilla

    2007-10-30

    Here we show that increased amount of secondary structure is acquired in the folded states of two structurally-different proteins (alpha-helical VlsE and alpha/beta flavodoxin) in the presence of macromolecular crowding agents. The structural content of flavodoxin and VlsE is enhanced by 33% and 70%, respectively, in 400 mg/ml Ficoll 70 (pH 7, 20 degrees C) and correlates with higher protein-thermal stability. In the same Ficoll range, there are only small effects on the unfolded-state structures of the proteins. This is the first in vitro assessment of crowding effects on the native-state structures at physiological conditions. Our findings imply that for proteins with low intrinsic stability, the functional structures in vivo may differ from those observed in dilute buffers. PMID:17919600

  12. Conformational States of Macromolecular Assemblies Explored by Integrative Structure Calculation

    PubMed Central

    Thalassinos, Konstantinos; Pandurangan, Arun Prasad; Xu, Min; Alber, Frank; Topf, Maya

    2013-01-01

    Summary A detailed description of macromolecular assemblies in multiple conformational states can be very valuable for understanding cellular processes. At present, structural determination of most assemblies in different biologically relevant conformations cannot be achieved by a single technique and thus requires an integrative approach that combines information from multiple sources. Different techniques require different computational methods to allow efficient and accurate data processing and analysis. Here, we summarize the latest advances and future challenges in computational methods that help the interpretation of data from two techniques—mass spectrometry and three-dimensional cryo-electron microscopy (with focus on alignment and classification of heterogeneous subtomograms from cryo-electron tomography). We evaluate how new developments in these two broad fields will lead to further integration with atomic structures to broaden our picture of the dynamic behavior of assemblies in their native environment. PMID:24010709

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

    DOE PAGESBeta

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

    2015-03-30

    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 themore » growth of crystals to significant dimensions that are now relevant to NMC are revisited. We report that these include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.« less

  14. Size-exclusion chromatography system for macromolecular interaction analysis

    DOEpatents

    Stevens, Fred J.

    1988-01-01

    A low pressure, microcomputer controlled system employing high performance liquid chromatography (HPLC) allows for precise analysis of the interaction of two reversibly associating macromolecules such as proteins. Since a macromolecular complex migrates faster than its components during size-exclusion chromatography, the difference between the elution profile of a mixture of two macromolecules and the summation of the elution profiles of the two components provides a quantifiable indication of the degree of molecular interaction. This delta profile is used to qualitatively reveal the presence or absence of significant interaction or to rank the relative degree of interaction in comparing samples and, in combination with a computer simulation, is further used to quantify the magnitude of the interaction in an arrangement wherein a microcomputer is coupled to analytical instrumentation in a novel manner.

  15. Metabolomics reveals elevated macromolecular degradation in periodontal disease.

    PubMed

    Barnes, V M; Ciancio, S G; Shibly, O; Xu, T; Devizio, W; Trivedi, H M; Guo, L; Jönsson, T J

    2011-11-01

    Periodontitis is a chronic inflammatory disease characterized by tissue destruction. In the diseased oral environment, saliva has primarily been considered to act as a protectant by lubricating the tissue, mineralizing the bones, neutralizing the pH, and combating microbes. To understand the metabolic role that saliva plays in the diseased state, we performed untargeted metabolomic profiling of saliva from healthy and periodontitic individuals. Several classes of biochemicals, including dipeptide, amino acid, carbohydrate, lipids, and nucleotide metabolites, were altered, consistent with increased macromolecular degradation of proteins, triacylglycerol, glycerolphospholipids, polysaccharides, and polynucleotides in the individuals with periodontal disease. These changes partially reflected the enhanced host-bacterial interactions in the diseased state as supported by increased levels of bacterially modified amino acids and creatine metabolite. More importantly, the increased lipase, protease, and glycosidase activities associated with periodontitis generated a more favorable energy environment for oral bacteria, potentially exacerbating the disease state. PMID:21856966

  16. Macromolecular neutron crystallography at the Protein Crystallography Station (PCS)

    PubMed Central

    Kovalevsky, Andrey; Fisher, Zoe; Johnson, Hannah; Mustyakimov, Marat; Waltman, Mary Jo; Langan, Paul

    2010-01-01

    The Protein Crystallography Station (PCS) at Los Alamos Neutron Science Center is a high-performance beamline that forms the core of a capability for neutron macromolecular structure and function determination. Neutron diffraction is a powerful technique for locating H atoms and can therefore provide unique information about how biological macro­molecules function and interact with each other and smaller molecules. Users of the PCS have access to neutron beam time, deuteration facilities, the expression of proteins and the synthesis of substrates with stable isotopes and also support for data reduction and structure analysis. The beamline exploits the pulsed nature of spallation neutrons and a large electronic detector in order to collect wavelength-resolved Laue patterns using all available neutrons in the white beam. The PCS user facility is described and highlights from the user program are presented. PMID:21041938

  17. Macromolecular Crystallization with Microfluidic Free-Interface Diffusion

    SciTech Connect

    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.

  18. Macromolecular structure analysis and effective liquefaction pretreatment. Final report

    SciTech Connect

    Suuberg, E.M.; Yun, Y.; Lilly, W.D.; Leung, K.; Gates, T.; Otake, Y.; Deevi, S.C.

    1994-07-01

    This project was concerned with characterizing the changes in coal macromolecular structure, that are of significance for liquefaction pretreatments of coal. The macromolecular structure of the insoluble portion of coal is difficult to characterize. Techniques that do so indirectly (based upon, for example, NMR and FTIR characterizations of atomic linkages) are not particularly sensitive for this purpose. Techniques that characterize the elastic structure (such as solvent swelling) are much more sensitive to subtle changes in the network structure. It is for this reason that we focused upon these techniques. The overall objective involved identifying pretreatments that reduce the crosslinking (physical or chemical) of the network structure, and thus lead to materials that can be handled to a greater extent by traditional liquid-phase processing techniques. These techniques tend to be inherently more efficient at producing desirable products. This report is divided into seven chapters. Chapter II summarizes the main experimental approaches used throughout the project, and summarizes the main findings on the Argonne Premium coal samples. Chapter III considers synergistic effects of solvent pairs. It is divided into two subsections. The first is concerned with mixtures of CS{sub 2} with electron donor solvents. The second subsection is concerned with aromatic hydrocarbon - alcohol or hydrocarbon - alcohol mixtures, as might be of interest for preliquefaction delivery of catalysts into bituminous coals. Chapter IV deals with questions of how oxidation might influence the results that are obtained. Chapter V briefly details what conclusions may be drawn concerning the elastic behavior of coals, and the effects of thermal treatments on this behavior. Chapter VI is concerned with theories to describe the action of solvents that are capable of dissociating non-covalent crosslinks. Finally, Chapter VII discusses the practical implications of the study.

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

    PubMed

    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

  20. Characterization of Macromolecular Flocculants Produced by Phormidium sp. Strain J-1 and by Anabaenopsis circularis PCC 6720

    PubMed Central

    Bar-Or, Y.; Shilo, M.

    1987-01-01

    Several benthic cyanobacteria were found to produce significant amounts of extracellular flocculants. The macromolecular flocculants produced by Phormidium sp. strain J-1 and Anabaenopsis circularis PCC 6720 were characterized. The Phormidium flocculant is a sulfated heteropolysaccharide to which fatty acids and protein are bound. The polysaccharide backbone is composed of uronic acids, rhamnose, mannose, and galactose. The A. circularis flocculant is also an acidic polysaccharide containing keto acid residues and neutral sugars, but to which no fatty acids, proteins, or sulfates are linked. Both flocculants could be recovered from growth medium by precipitation with cetyltrimethylammonium bromide and were found to bind the cationic dye Alcian-blue in a linear proportion to their concentration in solution. The latter property was used to quantify flocculant concentrations in culture supernatants and natural water samples and to compute their anion densities. PMID:16347442

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

    PubMed

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

    2013-08-01

    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

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

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

    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). Figure 1. 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 conference

  3. Macromolecular crowding-assisted fabrication of liquid-crystalline imprinted polymers.

    PubMed

    Zhang, Chen; Zhang, Jing; Huang, Yan-Ping; Liu, Zhao-Sheng

    2015-04-01

    A macromolecular crowding-assisted liquid-crystalline molecularly imprinted monolith (LC-MIM) was prepared successfully for the first time. The imprinted stationary phase was synthesized with polymethyl methacrylate (PMMA) or polystyrene (PS) as the crowding agent, 4-cyanophenyl dicyclohexyl propylene (CPCE) as the liquid-crystal monomer, and hydroquinidine as the pseudo-template for the chiral separation of cinchona alkaloids in HPLC. A low level of cross-linker (26%) has been found to be sufficient to achieve molecular recognition on the crowding-assisted LC-MIM due to the physical cross-linking of mesogenic groups in place of chemical cross-linking, and baseline separation of quinidine and quinine could be achieved with good resolution (R(s) = 2.96), selectivity factor (α = 2.16), and column efficiency (N = 2650 plates/m). In contrast, the LC-MIM prepared without crowding agents displayed the smallest diastereoselectivity (α = 1.90), while the crowding-assisted MIM with high level of cross-linker (80%) obtained the greatest selectivity factor (α = 7.65), but the lowest column efficiency (N = 177 plates/m). PMID:25701416

  4. Hierarchical amplification of macromolecular helicity of dynamic helical poly(phenylacetylene)s composed of chiral and achiral phenylacetylenes in dilute solution, liquid crystal, and two-dimensional crystal.

    PubMed

    Ohsawa, Sousuke; Sakurai, Shin-ichiro; Nagai, Kanji; Banno, Motonori; Maeda, Katsuhiro; Kumaki, Jiro; Yashima, Eiji

    2011-01-12

    Optically active poly(phenylacetylene) copolymers consisting of optically active and achiral phenylacetylenes bearing L-alanine decyl esters (1L) and 2-aminoisobutylic acid decyl esters (Aib) as the pendant groups (poly(1L(m)-co-Aib(n))) with various compositions were synthesized by the copolymerization of the optically active 1L with achiral Aib using a rhodium catalyst, and their chiral amplification of the macromolecular helicity in a dilute solution, a lyotropic liquid crystalline (LC) state, and a two-dimensional (2D) crystal on the substrate was investigated by measuring the circular dichroism of the copolymers, mesoscopic cholesteric twist in the LC state (cholesteric helical pitch), and high-resolution atomic force microscopy (AFM) images of the self-assembled 2D helix-bundles of the copolymer chains. We found that the macromolecular helicity of poly(1L(m)-co-Aib(n))s could be hierarchically amplified in the order of the dilute solution, LC state, and 2D crystal. In sharp contrast, almost no chiral amplification of the macromolecular helicity was observed for the homopolymer mixtures of 1L and Aib in the LC state and 2D crystal on graphite. PMID:21141965

  5. Biodegradable Iodinated Polydisulfides as Contrast Agents for CT Angiography

    PubMed Central

    Jin, Erlei; Zheng-Rong, Lu

    2014-01-01

    Current clinical CT contrast agents are mainly small molecular iodinated compounds, which often suffer from short blood pool retention for more comprehensive cardiovascular CT imaging and may cause contrast-induced nephropathy. In this work, we prepared polydisulfides containing a traditional iodinated CT contrast agent in order to optimize the pharmacokinetics of the agent and improve its safety. Initially acting as a macromolecular agent and achieving sharp blood vessel delineation, the polydisulfides can be reduced by endogenous thiols via disulfide-thiol exchange reaction to oligomers that can be readily excreted via renal filtration. Short polyethylene glycol (PEG) chain was also introduced to the polymers to further modify the in vivo properties of the agents. Strong and prolonged vascular enhancement has been generated with two new agents in mice (5–10 times higher blood pool enhancement than iodinaxol). The polydisulfide agents gradually degraded and excreted via renal filtration. The gradual excretion process could prevent contrast induced nephropathy. These results suggest that the biodegradable macromolecular CT contrast agents are promising safe and effective blood contrast agents for CT angiography and image-guided interventions. PMID:24768156

  6. Contrast-Enhanced Digital Mammography and Angiogenesis

    SciTech Connect

    Rosado-Mendez, I.; Palma, B. A.; Villasenor, Y.; Benitez-Bribiesca, L.; Brandan, M. E.

    2007-11-26

    Angiogenesis could be a means for pouring contrast media around tumors. In this work, optimization of radiological parameters for contrast-enhanced subtraction techniques in mammography has been performed. A modification of Lemacks' analytical formalism was implemented to model the X-ray absorption in the breast with contrast medium and detection by a digital image receptor. Preliminary results of signal-to-noise ratio analysis show the advantage of subtracting two images taken at different energies, one prior and one posterior to the injection of contrast medium. Preliminary experimental results using a custom-made phantom have shown good agreement with calculations. A proposal is presented for the clinical application of the optimized technique, which aims at finding correlations between angiogenesis indicators and dynamic variables of contrast medium uptake.

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

    PubMed

    Helliwell, John R; Mitchell, Edward P

    2015-03-01

    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. PMID:25866664

  8. Evaluating the stoichiometry of macromolecular complexes using multisignal sedimentation velocity

    PubMed Central

    Padrick, Shae B.; Brautigam, Chad A.

    2011-01-01

    Gleaning information regarding the molecular physiology of macromolecular complexes requires knowledge of their component stoichiometries. In this work, a relatively new means of analyzing sedimentation velocity (SV) data from the analytical ultracentrifuge is examined in detail. The method depends on collecting concentration profile data simultaneously using multiple signals, like Rayleigh interferometry and UV spectrophotometry. If the cosedimenting components of a complex are spectrally distinguishable, continuous sedimentation-coefficient distributions specific for each component can be calculated to reveal the molar ratio of the complex’s components. When combined with the hydrodynamic information available from the SV data, a stoichiometry can be derived. Herein, the spectral properties of sedimenting species are systematically explored to arrive at a predictive test for whether a set of macromolecules can be spectrally resolved in a multisignal SV (MSSV) experiment. Also, a graphical means of experimental design and criteria to judge the success of the spectral discrimination in MSSV are introduced. A detailed example of the analysis of MSSV experiments is offered, and the possibility of deriving equilibrium association constants from MSSV analyses is explored. Finally, successful implementations of MSSV are reviewed. PMID:21256217

  9. Quantitative influence of macromolecular crowding on gene regulation kinetics

    PubMed Central

    Tabaka, Marcin; Kalwarczyk, Tomasz; Hołyst, Robert

    2014-01-01

    We introduce macromolecular crowding quantitatively into the model for kinetics of gene regulation in Escherichia coli. We analyse and compute the specific-site searching time for 180 known transcription factors (TFs) regulating 1300 operons. The time is between 160 s (e.g. for SoxS Mw = 12.91 kDa) and 1550 s (e.g. for PepA6 of Mw = 329.28 kDa). Diffusion coefficients for one-dimensional sliding are between for large proteins up to for small monomers or dimers. Three-dimensional diffusion coefficients in the cytoplasm are 2 orders of magnitude larger than 1D sliding coefficients, nevertheless the sliding enhances the binding rates of TF to specific sites by 1–2 orders of magnitude. The latter effect is due to ubiquitous non-specific binding. We compare the model to experimental data for LacI repressor and find that non-specific binding of the protein to DNA is activation- and not diffusion-limited. We show that the target location rate by LacI repressor is optimized with respect to microscopic rate constant for association to non-specific sites on DNA. We analyse the effect of oligomerization of TFs and DNA looping effects on searching kinetics. We show that optimal searching strategy depends on TF abundance. PMID:24121687

  10. The Promise of Macromolecular Crystallization in Micro-fluidic Chips

    NASA Technical Reports Server (NTRS)

    vanderWoerd, Mark; Ferree, Darren; Pusey, Marc

    2003-01-01

    Micro-fluidics, or lab on a chip technology, is proving to be a powerful, rapid, and efficient approach to a wide variety of bio-analytical and microscale bio-preparative needs. The low materials consumption, combined with the potential for packing a large number of experiments in a few cubic centimeters, makes it an attractive technique for both initial screening and subsequent optimization of macromolecular crystallization conditions. Screening operations, which require equilibrating macromolecule solution with a standard set of premixed solutions, are relatively straightforward and have been successfully demonstrated in a micro-fluidics platform. More complex optimization methods, where crystallization solutions are independently formulated from a range of stock solutions, are considerably more complex and have yet to be demonstrated. To be competitive with either approach, a micro-fluidics system must offer ease of operation, be able to maintain a sealed environment over several weeks to months, and give ready access for the observation of crystals as they are grown.