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Sample records for macromolecular contrast medium

  1. Monitoring blood-brain barrier status in a rat model of glioma receiving therapy: dual injection of low-molecular-weight and macromolecular MR contrast media.

    PubMed

    Lemasson, Benjamin; Serduc, Raphaël; Maisin, Cécile; Bouchet, Audrey; Coquery, Nicolas; Robert, Philippe; Le Duc, Géraldine; Troprès, Irène; Rémy, Chantal; Barbier, Emmanuel L

    2010-11-01

    To evaluate the sequential injection of a low-molecular-weight (gadoterate meglumine [Gd-DOTA], 0.5 kDa) and a macromolecular (P846, 3.5 kDa) contrast media in monitoring the effect of antitumor therapies (antiangiogenic therapy and/or microbeam radiation therapy [MRT]) on healthy brain tissue and implanted tumors. Animal use was compliant with official French guidelines and was assessed by the local Internal Evaluation Committee for Animal Welfare and Rights. Eighty male rats bearing 9L gliosarcoma were randomized into four groups: untreated, antiangiogenic (sorafenib) therapy, MRT, and both treatments. Magnetic resonance (MR) imaging was performed 1 day before and 1, 5, and 8 days after the start of the treatment. At all time points, vascular integrity to a macromolecular contrast medium (P846) and, 11 minutes 30 seconds later, to low-molecular-weight contrast medium (Gd-DOTA) was evaluated by using a dynamic contrast material-enhanced MR imaging approach. To quantify vessel wall integrity, areas under the signal intensity curves were computed for each contrast medium. Unpaired t tests and one-way analysis of variance were used for statistical analyses. Tumor vessels receiving antiangiogenic therapy became less permeable to the macromolecular contrast medium, but their permeability to the low-molecular-weight contrast medium remained unchanged. Healthy double-irradiated vessels became permeable to the low-molecular-weight contrast medium but not to the macromolecular contrast medium. Antiangiogenic therapy and MRT generate different effects on the extravasation of contrast medium in tumoral and healthy tissues. This study indicates that the use of a low-molecular-weight contrast medium and a macromolecular contrast medium provides complementary information and suggests that the use of two contrast media within the same MR imaging session is feasible. © RSNA, 2010.

  2. 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.

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

    PubMed Central

    Daldrup-Link, Heike E.; Mohanty, Suchismita; Ansari, Celina; 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

  4. Incompatibility of Contrast Medium and Trisodium Citrate

    SciTech Connect

    Delcour, Christian Bruninx, Guy

    2013-02-15

    To test the compatibility of trisodium citrate, a catheter lock solution, with iodinated contrast medium. Iohexol, iobitridol, iodixanol, ioxaglate, ioxithalamate, iomeprol, and iopromide were tested. In all tests, 2 ml of contrast medium were mixed with 2 ml of trisodium citrate solution. Iodixanol and ioxaglate provoked a highly viscous gluelike precipitation when mixed with trisodium citrate. A brief transient precipitate was observed with iohexol, iomeprol, and ioxithalamate. Permanent precipitation occurred with iobitridol and iopromide. One must be aware of the potential for precipitation when contrast medium is mixed with trisodium citrate solution. Before trisodium citrate solution is injected, the catheter should be thoroughly flushed with saline if a contrast medium has previously been injected through it.

  5. Polydisulfide Manganese(II) Complexes as Non-Gadolinium Biodegradable Macromolecular MRI Contrast Agents

    PubMed Central

    Ye, Zhen; Jeong, Eun-Kee; Wu, Xueming; Tan, Mingqian; Yin, Shouyu; Lu, Zheng-Rong

    2011-01-01

    Purpose To develop safe and effective manganese(II) based biodegradable macromolecular MRI contrast agents. Materials and Methods In this study, we synthesized and characterized two polydisulfide manganese(II) complexes, Mn-DTPA cystamine copolymers and Mn-EDTA cystamine copolymers, as new biodegradable macromolecular MRI contrast agents. The contrast enhancement of the two manganese based contrast agents were evaluated in mice bearing MDA-MB-231 human breast carcinoma xenografts, in comparison with MnCl2. Results The T1 and T2 relaxivities were 4.74 and 10.38 mM−1s−1 per manganese at 3T for Mn-DTPA cystamine copolymers (Mn=30.50 kDa) and 6.41 and 9.72 mM−1s−1 for Mn-EDTA cystamine copolymers (Mn= 61.80 kDa). Both polydisulfide Mn(II) complexes showed significant liver, myocardium and tumor enhancement. Conclusion The manganese based polydisulfide contrast agents have a potential to be developed as alternative non-gadolinium contrast agents for MR cancer and myocardium imaging. PMID:22031457

  6. Hytrast: A New Contrast Medium for Bronchography

    PubMed Central

    Misener, F. J.; Quinlan, J. J.; Hiltz, J. E.

    1965-01-01

    In 1962 Hytrast, an aqueous suspension containing 50% w/v of combined iodine as a mixture of N-(2,3-dihydroxypropyl)-3,5-diiodopyridone-4 and 3,5-diiodopyridone-4, was introduced as a contrast medium for bronchography. Extensive clinical trials had suggested that this agent was superior to products usually employed for this purpose. At the Nova Scotia Sanatorium, Hytrast was used as a bronchographic contrast medium in 31 consecutive cases. For comparison purposes, the records of the first 50 patients in whom another contrast medium, Dionosil Oily, was used were reviewed. In all cases the contrast medium was introduced through a catheter passed into the bronchus with the aid of a laryngeal mirror, after local anesthesia was induced by pontocaine 2%. Experience in this limited number of cases was at variance with most published results. Hytrast was more irritating than Dionosil Oily, had a greater tendency to produce alveolarization, caused more frequent undesirable sequelae, and was retained in the lung for prolonged periods. PMID:14264971

  7. 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

  8. A new macromolecular paramagnetic MR contrast agent binds to activated human platelets.

    PubMed

    Chaubet, Frédéric; Bertholon, Isabelle; Serfaty, Jean-Michel; Bazeli, Ramin; Alsaid, Hasan; Jandrot-Perrus, Martine; Zahir, Charaf; Even, Pascale; Bachelet, Laure; Touat, Ziad; Lancelot, Eric; Corot, Claire; Canet-Soulas, Emmanuelle; Letourneur, Didier

    2007-07-01

    A new functionalized macromolecular magnetic resonance (MR) contrast agent has been developed from a carboxymethyldextran-Gd(DOTA) devoid of biospecificity. The functionalized contrast agent was synthesized in order to mimic PSGL-1, the main ligand of P-selectin, a glycoprotein mainly expressed on the surface of activated platelets. The starting compound, CM1, was first carboxymethylated by monochloroacetic acid leading to a series of 10 derivatives varying in their carboxymethyl content. CM8 derivative, with a degree of substitution in carboxymethyl of 0.84, was chosen for subsequent fluorolabeling and sulfation to give CM8FS. CM8FS has an average number molecular weight of 27 000 +/- 500 g/mol, a hydrodynamic radius of 5.7 +/- 0.2 nm and a high relaxivity (r(1) = 11.2/mM (Gd)/s at 60 MHz). Flow cytometry experiments on whole human blood or on isolated platelets evidenced in vitro a preferential binding of CM8FS on TRAP-activated human platelets. Interestingly, CM8FS did not bind to other blood cells or to resting platelets. Pellets of TRAP-activated human platelets have also been imaged in tubes with a 1.5 T MR imager. A MR signal was observed for activated platelets incubated with CM8FS. Altogether, these in vitro results evidenced the recognition of activated human platelets by a fluorescent paramagnetic contrast agent grafted with carboxyl and sulfate groups. This biomimetic approach associated with the versatile macromolecular platform appears promising for the development of new contrast agents for molecular imaging of activated platelets in cardiovascular diseases such as atherosclerosis and aneurysms.

  9. 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.

  10. Contrast medium enhanced susceptibility imaging signal mechanism; should we use contrast medium?

    PubMed

    Aydın, Ömer; Büyükkaya, Ramazan; Hakyemez, Bahattin

    2017-01-01

    Intracranial lesions exhibit clear contrast enhancement in T1-weighted imaging, but the mechanism whereby contrast-enhanced susceptibility-weighted imaging (CE-SWI) generates signals remains unclear. Contrast enhancement patterns cannot be reliably predicted. To explore the mechanism of CE-SWI contrast enhancement. Fifty-five patients were retrospectively enrolled. All of the imaging employed a clinical 3T magnetic resonance imaging (MRI) system fitted with a 32-channel head coil. Minimum-intensity projection reformatted images were evaluated. Intracranial lesions and brain parenchymal intensities were explored using SWI and CE-SWI. signal intensity rates were calculated by dividing the lesional intensity by the white matter intensity, after which the SWI and CE-SWI signal intensity rate were compared. Two observers independently performed intralesional susceptibility signal analysis. After contrast medium administration, malignant and extra-axial tumors exhibited obvious contrast enhancement on CE-SWI (P < 0.001 and P = 0.013, respectively). The signal intensity of white matter was significantly reduced. The signal intensity rates rose significantly in the benign, malignant, and extra-axial groups (P < 0.001). Between-radiologist agreement in terms of intralesional susceptibility signal assessment was strong (kappa = 0.8, P < 0.001). Contrast media can either reduce or increase SWI signal intensities. The dual contrast feature of CE-SWI can be useful when exploring intracranial disorders. © The Foundation Acta Radiologica 2016.

  11. 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.

  12. Autopsy case of delayed anaphylactic shock due to contrast medium.

    PubMed

    Nagai, Yayoi; Tanaka, Yuko; Nakazato, Yoichi; Sugawara, Nobuyuki; Arai, Miho; Okada, Etsuko; Koyama, Yoshinari; Hinohara, Hiroshi; Yamamoto, Koujirou; Kurabayashi, Masahiko; Nojima, Yoshihisa; Ishikawa, Osamu

    2012-10-01

    We report an autopsy case of delayed anaphylactic shock due to contrast medium. A 17-year-old Japanese man underwent angiography using non-ionic contrast medium under the suspected diagnosis of Buerger's disease. Initial symptoms appeared 6 h after the administration of the contrast medium, and death was confirmed 11 h later. Considering the clinical course and the results of the autopsy, we concluded that the direct cause of the patient's death was severe acute circulatory failure due to a delayed allergic reaction to the contrast medium. The reported incidence of serious delayed reactions or biphasic reactions to non-ionic contrast medium is extremely low; however, we should be aware of such rare adverse reactions. © 2012 Japanese Dermatological Association.

  13. Anaphylactic Shock Following Nonionic Contrast Medium during Caudal Epidural Injection.

    PubMed

    Lee, Sang Hyun; Park, Jae Woo; Hwang, Byeong Mun

    2015-10-01

    Caudal epidural injection is a common intervention in patients with low back pain and sciatica. Even though the complications of fluoroscopically directed epidural injections are less frequent than in blind epidural injections, complications due to contrast media can occur. We report a case of anaphylactic shock immediately after injection of an intravenous nonionic contrast medium (iohexol) during the caudal epidural injection for low back pain and sciatica in a patient without a previous allergic history to ionic contrast media (ioxitalamate). Five minutes after the dye was injected, the patient began to experience dizziness, and the systolic blood pressure dropped to 60 mmHg. Subsequently, the patient exhibited a mild drowsy mental state. About 30 minutes after the subcutaneous injection of 0.2 mg epinephrine, the systolic blood pressure increased to 90 mmHg. The patient recovered without any sequela. Life-threatening complications after injection of intravenous contrast medium require immediate treatment.

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

    NASA Astrophysics Data System (ADS)

    Wang, Jianxin Steven

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

  16. Synthesis and evaluation of a polydisulfide with Gd-DOTA monoamide side chains as a biodegradable macromolecular contrast agent for MR blood pool imaging.

    PubMed

    Ye, Zhen; Wu, Xueming; Tan, Mingqian; Jesberger, Jack; Grisworld, Mark; Lu, Zheng-Rong

    2013-01-01

    Macromolecular Gd(III)-based contrast agents are effective for contrast-enhanced blood pool and cancer MRI in preclinical studies. However, their clinical applications are impeded by potential safety concerns associated with slow excretion and prolonged retention of these agents in the body. To minimize the safety concerns of macromolecular Gd contrast agents, we have developed biodegradable macromolecular Gd contrast agents based on polydisulfide Gd(III) complexes. In this study, we designed and synthesized a new generation of the polydisulfide Gd(III) complexes containing a macrocyclic Gd(III) chelate, Gd-DOTA monoamide, to improve the in vivo kinetic inertness of the Gd(III) chelates. (N6-Lysyl)lysine-(Gd-DOTA) monoamide and 3-(2-carboxyethyldisulfanyl)propanoic acid copolymers (GODC) were synthesized by copolymerization of (N6-lysyl)lysine DOTA monoamide and dithiobis(succinimidylpropionate), followed by complexation with Gd(OAc)3. The GODC had an apparent molecular weight of 26.4 kDa and T1 relaxivity of 8.25 mM(-1) s(-1) per Gd at 1.5 T. The polymer chains of GODC were readily cleaved by L-cysteine and the chelates had high kinetic stability against transmetallation in the presence of an endogenous metal ion Zn(2+). In vivo MRI study showed that GODC produced strong and prolonged contrast enhancement in the vasculature and tumor periphery of mice with breast tumor xenografts. GODC is a promising biodegradable macromolecular MRI contrast agent with high kinetic stability for MR blood pool imaging.

  17. 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.

  18. Human pharmacokinetics of iohexol. A new nonionic contrast medium

    SciTech Connect

    Olsson, B.; Aulie, A.; Sveen, K.; Andrew, E.

    1983-03-01

    The pharmacokinetics of iohexol, a new nonionic, water-soluble contrast medium, have been determined after intravenous injection in 20 healthy volunteers, at four different dose levels (125-500 mg I/kg). The apparent volume of distribution was 0.27 1/kg, indicating distribution in the extracellular water. The biologic half-life was 121 minutes, comparable with that of other intravascular contrast media. Iohexol was excreted completely unmetabolized in the urine, with a 100% recovery 24 hours after injection. A comparison of iohexol and chromium-51 (/sup 51/Cr)-EDTA clearances indicates that iohexol is mainly excreted by glomerular filtration. The /sup 51/Cr-EDTA clearance was the same when injected separately and concomitantly with iohexol, indicating that glomerular filtration rate is not affected by iohexol. No dose dependency was observed in the investigated parameters t1/2 alpha, t1/2 beta, Vd, ClT or ClR. Iohexol pharmacokinetics are in correspondence with previously reported data on intravascular contrast media.

  19. In vivo monitoring of sorafenib therapy effects on experimental prostate carcinomas using dynamic contrast-enhanced MRI and macromolecular contrast media

    PubMed Central

    Schwarz, Bettina; Paprottka, Philipp M.; Sourbron, Steven; von Einem, Jobst C.; Dietrich, Olaf; Hinkel, Rabea; Clevert, Dirk A.; Bruns, Christiane J.; Reiser, Maximilian F.; Nikolaou, Konstantin; Wintersperger, Bernd J.

    2013-01-01

    Abstract Purpose: To investigate dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) with macromolecular contrast media (MMCM) to monitor the effects of the multikinase inhibitor sorafenib on subcutaneous prostate carcinomas in rats with immunohistochemical validation. Materials and methods: Copenhagen rats, implanted with prostate carcinoma allografts, were randomized to the treatment group (n = 8) or the control group (n = 8). DCE-MRI with albumin-(Gd-DTPA)35 was performed at baseline and after 1 week using a clinical 3-Tesla system. The treatment group received sorafenib, 10 mg/kg body weight daily. Kinetic analysis yielded quantitative parameters of tumor endothelial permeability–surface area product (PS; ml/100 ml/min) and fractional blood volume (Vb, %). Tumors were harvested on day 7 for immunohistochemical analysis. Results: In sorafenib-treated tumors, PS (0.62 ± 0.20 vs 0.08 ± 0.09 ml/100 ml/min; P < 0.01) and Vb (5.1 ± 1.0 vs 0.56 ± 0.48%; P < 0.01) decreased significantly from day 0 to day 7. PS showed a highly significant inverse correlation with tumor cell apoptosis (TUNEL; r = −0.85, P < 0.001). Good, significant correlations of PS were also observed with tumor cell proliferation (Ki-67; r = 0.67, P < 0.01) and tumor vascularity (RECA-1; r = 0.72, P < 0.01). MRI-assayed fractional blood volume Vb showed a highly significant correlation with tumor vascularity (RECA-1; r = 0.87, P < 0.001) and tumor cell proliferation (Ki-67; r = 0.82, P < 0.01). Conclusion: Results of DCE-MRI with MMCM demonstrated good, significant correlations with the immunohistochemically assessed antiangiogenic, antiproliferative, and proapoptotic effects of a 1-week, daily treatment course of sorafenib on experimental prostate carcinoma allografts. PMID:24380871

  20. 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

  1. Effects of contrast medium on radiation-induced chromosome aberrations

    SciTech Connect

    Matsubara, S.; Suzuki, S.; Suzuki, H.; Kuwabara, Y.; Okano, T.

    1982-07-01

    The effects of contrast material (meglumine iothalamate) on radiation-induced chromosome aberrations were investigated in studies on the lymphocytes of patients who had undergone diagnostic radiography and in in vitro experiments with diagnostic x rays and /sup 60/Co gamma rays. Chromosome and chromatid aberrations were found to increase significantly with increasing concentrations of contrast material that were added at irradiation. However, the aberrations were not associated with elevation of the ratio of dicentric and ring chromosomes to the number of cells with unstable chromosome aberrations at the first mitosis. Lymphocytes irradiated in the absence of contrast material did not show an increase in chromosome-type aberrations when the agent was given in increasing concentrations during subsequent incubation, but there were greater numbers of chromatid gaps and breaks. When lymphocytes were exposed to 400 R (103.2 mC/kg) of /sup 60/Co gamma rays, the presence of contrast agent did not increase the yield of dicentric and ring chromosomes, but induced a marked delay in cell proliferation, especially in lymphocytes with more heavily damaged chromosomes. In additional examination, the contrast agent itself induced sister chromatid exchanges in lymphocytes.

  2. 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

  3. Macromolecular therapeutics.

    PubMed

    Yang, Jiyuan; Kopeček, Jindřich

    2014-09-28

    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.

  4. Brain tumor enhancement in magnetic resonance imaging at 3 tesla: intraindividual comparison of two high relaxivity macromolecular contrast media with a standard extracellular gd-chelate in a rat brain tumor model.

    PubMed

    Fries, Peter; Runge, Val M; Bücker, Arno; Schürholz, Hellmut; Reith, Wolfgang; Robert, Philippe; Jackson, Carney; Lanz, Titus; Schneider, Günther

    2009-04-01

    The aim of this study was to evaluate lesion enhancement (LE) and contrast-to-noise ratio (CNR) properties of P846, a new intermediate sized, high relaxivity Gd-based contrast agent at 3 Tesla in a rat brain glioma model, and to compare this contrast agent with a high relaxivity, macromolecular compound (P792), and a standard extracellular Gd-chelate (Gd-DOTA). Seven rats with experimental induced brain glioma were evaluated using 3 different contrast agents, with each MR examination separated by at least 24 hours. The time between injections assured sufficient clearance of the agent from the tumor, before the next examination. P792 (Gadomelitol, Guerbet, France) and P846 (a new compound from Guerbet Research) are macromolecular and high relaxivity contrast agents with no protein binding, and were compared with the extracellular agent Gd-DOTA (Dotarem, Guerbet, France). T1w gradient echo sequences (TR/TE 200 milliseconds/7.38 milliseconds, flip angle = 90 degrees , acquisition time: 1:42 minutes:sec, voxel size: 0.2 x 0.2 x 2.0 mm, FOV = 40 mm, acquisition matrix: 256 x 256) were acquired before and at 5 consecutive time points after each intravenous contrast injection in the identical slice orientation, using a dedicated 4-channel head array animal coil. The order of contrast media injection was randomized, with however Gd-DOTA used either as the first or second contrast agent. Contrast agent dose was adjusted to compensate for the different T1 relaxivities of the 3 agents. Signal-to-noise ratio, CNR, and LE were evaluated using region-of-interest analysis. A veterinary histopathologist confirmed the presence of a glioma in each subject, after completion of the imaging study. P792 showed significantly less LE as compared with Gd-DOTA within the first 7 minutes after contrast agent injection (P < 0.05) with, however, reaching comparable LE values at 9 minutes after injection (P = 0.07). However, P792 provided significantly less CNR as compared with Gd-DOTA (P < 0

  5. Zero Contrast Coronary Intervention Using Intravascular Ultrasound Guidance in a Patient with Allergy to Contrast Medium.

    PubMed

    Nagaoka, Masakazu; Tsumuraya, Naoko; Nie, Masaki; Ikari, Yuji

    2016-09-20

    The occurrence of allergy to iodinated contrast in certain patients may prevent the use of percutaneous coronary intervention (PCI) in such cases. We present a 53-year-old male with a history of allergic reaction to iodinated contrast who successfully underwent intravascular ultrasound (IVUS) guided PCI. Stent size was determined based on IVUS. After PCI, stent expansion and a lack of edge dissection or incomplete apposition were confirmed by IVUS. Thus, PCI without contrast injection under IVUS may be feasible in selected patients with allergy to iodinated contrast.

  6. Quantitative dynamic contrast enhanced MRI of experimental synovitis in the rabbit knee: comparison of macromolecular blood pool agents vs. Gadolinium-DOTA.

    PubMed

    Watrin-Pinzano, Astrid; Loeuille, Damien; Goebel, Jean-Christophe; Lapicque, Françoise; Walter, Fredéric; Robert, Philippe; Netter, Patrick; Corot, Claire; Gillet, Pierre; Blum, Alain

    2008-01-01

    The purpose of this study was to assess 2 Gd-based macromolecular intravascular contrast agents (P792, rapid clearance blood pool agent (rBPA) and P717, slow clearance blood pool agent (sBPA)) compared to Gd-DOTA (representative extracellular non specific agent) in MR imaging of knee rabbit experimental synovitis. Quantitative dynamic contrast enhanced MRI (qDCE-MRI) after intravascular injection of a low molecular weight contrast agent of 0.56 kDa (Gd-DOTA) and 2 high-molecular-weight contrast agents of 6.47 kDa (P792) and 52 kDa (P717) was performed in rabbits with carrageenan-induced synovitis of the right knee. P792 and P717 provided a progressive and persistent enhancement of arthritic synovial tissue while Gd-DOTA provided an early and rapidly declining enhancement with a concomitant diffusion in synovial fluid, thus limitating delineation of synovial pannus. P792 allowed acquisition of high-quality MR arthrograms, due to both a better diffusion in synovial pannus (vs. P717) and a concomitant restricted diffusion into the synovial fluid (vs. Gd-DOTA). In fact, experimental rabbit synovitis represent a specific entity that favors the T1 effect of high-molecular-weight agents, and especially rBPA P792, entrapped in synovial pannus, without diffusion in the synovial fluid. Due to this lack of arthrographic effect, P792 accumulation could be specifically sequentially analyzed by qDCE-MRI for detecting, characterizing and monitoring synovial vascular permeability changes during mono- or polysynovitis.

  7. Macromolecular recognition.

    PubMed

    Deremble, Cyril; Lavery, Richard

    2005-04-01

    Computational methods are being developed both to detect the binding surfaces of individual macromolecules and to predict the structure of binary macromolecular complexes. Speeding up and refining this process has required work on search algorithms, molecular representations and interaction potentials. Although backbone flexibility and solvent effects continue to pose problems, encouraging results have been obtained for both protein-protein and protein-DNA complexes.

  8. Nephrogenic systemic fibrosis and gadolinium-based contrast media: updated ESUR Contrast Medium Safety Committee guidelines.

    PubMed

    Thomsen, Henrik S; Morcos, Sameh K; Almén, Torsten; Bellin, Marie-France; Bertolotto, Michele; Bongartz, Georg; Clement, Olivier; Leander, Peter; Heinz-Peer, Gertraud; Reimer, Peter; Stacul, Fulvio; van der Molen, Aart; Webb, Judith A W

    2013-02-01

    To update the guidelines of the Contrast Media Safety Committee (CMSC) of the European Society of Urogenital Radiology (ESUR) on nephrogenic systemic fibrosis and gadolinium-based contrast media. Topics reviewed include the history, clinical features and prevalence of nephrogenic systemic fibrosis and the current understanding of its pathophysiology. The risk factors for NSF are discussed and prophylactic measures are recommended. The stability of the different gadolinium-based contrast media and the potential long-term effects of gadolinium in the body have also been reviewed.

  9. In the eye of the storm: iodinated contrast medium induced thyroid storm presenting as cardiopulmonary arrest.

    PubMed

    Alkhuja, Samer; Pyram, Ronald; Odeyemi, Olutunde

    2013-01-01

    The administration of iodinated contrast medium may lead to excess free thyroid hormone release and cause thyroid storm. A woman presented to the emergency department with dyspnea, hemoptysis, and intermittent bilateral lower extremities edema. Physical examination revealed mildly enlarged thyroid. Patient underwent a computed tomography scan of the chest with intravenous iodinated contrast medium to rule out pulmonary embolism, the patient developed a thyroid storm second to iodinated contrast medium injection. Proper treatment was provided and the patient had a good outcome. We present this case of an unusual presentation of a thyroid storm with cardiac arrest. This case illustrates that evaluating thyroid function tests in patients with an enlarged thyroid prior to the administration of iodinated contrast medium could prevent the development of thyroid storm.

  10. 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. Copyright © 2015 John Wiley & Sons, Ltd.

  11. Power port contrast medium flushing and trapping: impact of temperature, an in vitro experimental study

    PubMed Central

    Guiffant, Gérard; Durussel, Jean Jacques; Flaud, Patrice; Royon, Laurent; Marcy, Pierre Yves; Merckx, Jacques

    2013-01-01

    Purpose The use of totally implantable venous access devices (TIVADs) certified as “high pressure resistant” or “power port” has begun to spread worldwide as a safe procedure for power contrast injection. Owing to the thermo-rheological properties of the contrast media, the primary aim of this work is to present an in vitro experimental impact study concerning the impact of the temperature level on flushing efficiency after contrast medium injection. Moreover, we report experimental data that confirms the role of needle bevel orientation. The secondary aim is to answer the following questions: Is there significant device contrast medium trapping after contrast medium injection? Is saline flushing efficient? And, finally, is it safe to inject contrast medium through an indwelled port catheter? Results The experimental results show that in addition to hydrodynamics, temperature is a key parameter for the efficiency of device flushing after contrast medium injection. It appears that this is the case when the cavity is incompletely rinsed after three calibrated flushing volumes of 10 mL saline solution, even by using the Huber needle bevel opposite to the port exit. This leads to a potentially important trapped volume of contrast medium in the port, and consequently to the possibility of subsequent salt precipitates and long term trisubstituted benzene nuclei delivery that might impair the solute properties, which may be further injected via the power port later on. Conclusion We thus suggest, in TIVADS patients, the use of a temporary supplementary intravenous line rather than the port to perform contrast medium injections in daily radiology routine practice. PMID:24043959

  12. 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.

  13. Is Contrast Medium Osmolality a Causal Factor for Contrast-Induced Nephropathy?

    PubMed Central

    Bucher, Andreas M.; De Cecco, Carlo N.; Schoepf, U. Joseph; Meinel, Felix G.; Krazinski, Aleksander W.; Spearman, James V.; McQuiston, Andrew D.; Wang, Rui; Bucher, Judith; Vogl, Thomas J.; Katzberg, Richard W.

    2014-01-01

    The exact pathophysiology of contrast-induced nephropathy (CIN) is not fully clarified, yet the osmotic characteristics of contrast media (CM) have been a significant focus in many investigations of CIN. Osmotic effects of CM specific to the kidney include transient decreases in blood flow, filtration fraction, and glomerular filtration rate. Potentially significant secondary effects include an osmotically induced diuresis with a concomitant dehydrating effect. Clinical experiences that have compared the occurrence of CIN between the various classes of CM based on osmolality have suggested a much less than anticipated advantage, if any, with a lower osmolality. Recent animal experiments actually suggest that induction of a mild osmotic diuresis in association with iso-osmolar agents tends to offset potentially deleterious renal effects of high viscosity-mediated intratubular CM stagnation. PMID:24800254

  14. Contrast medium administration in the elderly patient: is advancing age an independent risk factor for contrast nephropathy after angiographic procedures?

    PubMed

    Detrenis, Simona; Meschi, Michele; Bertolini, Laura; Savazzi, Giorgio

    2007-02-01

    Contrast medium-induced nephropathy (CMIN) is the third leading cause of hospital-acquired acute renal dysfunction. Even if the number of patients over 75 years of age undergoing diagnostic and/or interventional procedures and requiring administration of contrast medium (CM) is growing constantly, at present there is no definitive consensus regarding the role of advancing age and related morphologic or functional renal changes as an independent risk factor for CMIN. The authors review the evidence from recent medical literature on the definition, pathophysiology, and clinical presentation of CMIN as well as therapeutic approaches to its prophylaxis. Attention is focused on advancing age as a preexisting physiologic condition that is, per se, able to predispose the patient to CM-induced renal impairment, assuming that every elderly patient is potentially at risk for CMIN.

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

    PubMed

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

    2015-10-01

    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. 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. 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. 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.

  16. The effect of oil and water-soluble contrast medium in hysterosalpingography on thyroid function.

    PubMed

    So, Shuhei; Yamaguchi, Wakasa; Tajima, Hiroko; Nakayama, Takeshi; Tamura, Naoaki; Kanayama, Naohiro; Tawara, Fumiko

    2017-09-01

    Hysterosalpingography (HSG) using iodinated contrast medium is X-ray diagnostic test that examines the inside of the uterus and fallopian tubes in infertile women. In this study, we compared thyroid function (thyroid stimulating hormone: TSH and free-T4: FT4 levels) after HSG with an oil-soluble contrast medium (OSCM) and a water-soluble contrast medium (WSCM). One hundred and sixty-four and 94 patients with normal thyroid function received HSG with OSCM and WSCM, respectively. Approximately 25% of the women in the OSCM group developed subclinical hypothyroidism (SCH), whereas only less than 10% of the patients in the WSCM group developed SCH. Our data clearly indicate that WSCM is safe for thyroid function in women who plan to get pregnant.

  17. 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

  18. 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

  19. 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

  20. Thyroid function in very low birthweight infants after intravenous administration of the iodinated contrast medium iopromide

    PubMed Central

    Dembinski, J; Arpe, V; Kroll, M; Hieronimi, G; Bartmann, P

    2000-01-01

    BACKGROUND—Thyroid function disorders have often been observed in preterm infants after intravenous administration of iodinated contrast medium. The effect on thyroid function depends on the dosage, but the choice of the contrast medium may be equally important, as there are appreciable pharmacological differences between them.
METHOD—Thyroid function was analysed in 20 very low birthweight infants of gestational age less than 30 weeks after injection of iopromide, a monomeric non-ionic iodinated contrast medium. Levels of free thyroxine and thyroid stimulating hormone were compared with those in 26 control infants.
RESULTS—Free thyroxine levels in all study infants ranged from 9.0 to 25.7 pmol/l (days 14-21) and 9.0 to 23.2 pmol/l (days 35-49), and thyroid stimulating hormone levels ranged from 0.13 to 0.26mU/l (days 14-21) and 0.26 to 11.11 mU/l (days 35-49). These levels were not altered after injection of iopromide.
CONCLUSION—The risk of transient hypothyroidism or hyperthyrotropinaemia may be reduced with the use of iopromide compared with other contrast media.

 PMID:10794789

  1. [CT study of the cervical spine with intravenous administration of the contrast medium].

    PubMed

    Magnaldi, S; Pozzi-Mucelli, R S; Cova, M A; De Morpurgo, P

    1989-04-01

    Computed tomography (CT) without contrast medium is largely applied to the study of intervertebral disk pathology in the lumbar spine, but has not been widely accepted in the cervical spine, due to technical and anatomical limitations. For these reasons many neuroradiologists still prefer myelography or myelo-CT. CT may yield better results if combined with iv contrast medium injection, which allows a better visualization of disk herniation. This technique is aimed at enhancing the density of the venous plexus which is located close to the intervertebral disk, the vertebral bodies and the neural foramina. A better contrast enhancement is thus obtained between the disk and the spinal cord. The authors' experience is based on 61 patients who underwent contrast enhanced CT; in 22 cases myelography and myelo-CT were also performed. The authors describe their technique and the most frequent CT findings of disk herniation: the typical finding includes a focal hypodensity surrounded by a linear blush, due to a posteriorly dislocated epidural vein. The posterior linear blush alone may be present in few cases. Contrast-enhanced CT is very useful in the study of disk pathology of the cervical spine, even when compared with myelography and myelo-CT, due the increase in the density of epidural plexus it allows. However, the technique must be very accurate if the same results as those of myelo-CT are to be obtained.

  2. 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

  3. Relationship between ventral lumbar disc protrusion and contrast medium leakage during sympathetic nerve block.

    PubMed

    Tazawa, Toshiharu; Kamiya, Yoshinori; Takamori, Mina; Ogawa, Ken-Ichi; Goto, Takahisa

    2015-02-01

    Ventral disc protrusions have been neglected because they are asymptomatic. Lumbar sympathetic nerve block (LSNB) is one of the clinical choices for refractory low back pain treatment. Leakage of the contrast medium may occur and lead to complications, especially when using a neurolytic agent. In this study, we retrospectively reviewed the magnetic resonance images (MRIs) of 52 consecutive patients with refractory low back pain due to lumbar spinal canal stenosis who underwent LSNB, and graded ventral disc protrusion at the L1/2 to L5/S1 vertebral discs on a three-point scale (grade 0 = no protrusion, grade 1 = protrusion without migration, grade 2 = protrusion with migration). We also determined if there was leakage of contrast medium in LSNB. Ventral disc protrusion was observed in all patients, and 75 % (39/52) had grade 2 protrusion in the L1/2-L3/4 vertebral discs. Moreover, the incidence of contrast medium leakage was significantly higher at the vertebrae that had grade 2 protrusion than at those with less protrusion. We revealed a higher incidence of ventral disc protrusion of the lumbar vertebrae than previously reported, and that the incidence of leakage in LSNB increased when ventral disc protrusion was present. To avoid complications, attention should be paid to ventral disc protrusions before performing LSNB.

  4. 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.

  5. Evaluation of two methods for topical application of contrast medium to the pharyngeal and laryngeal region of horses.

    PubMed

    Colbath, Aimée C; Valdés-Martínez, Alejandro; Leise, Britta S; Hackett, Eileen S

    2017-09-01

    OBJECTIVE To determine the pharyngeal and laryngeal distribution of radiopaque contrast medium administered orally or via nasopharyngeal catheter to standing horses. ANIMALS 5 healthy adult horses. PROCEDURES A crossover study was conducted. Radiopaque contrast medium (12 mL) was administered orally and via nasopharyngeal catheter to each horse. Pharyngeal and laryngeal distribution of contrast medium was determined by examination of radiographs obtained immediately after administration of contrast medium, compared with those obtained before administration. Regional distribution of contrast medium was graded. Endoscopic examination of the nasopharynx, laryngopharynx, and larynx was performed to confirm radiographic results. RESULTS Examination of radiographs obtained after nasopharyngeal administration revealed contrast medium in the nasopharynx (n = 5), oropharynx (2), laryngopharynx (3), and larynx (5) of the 5 horses. Examination of radiographs obtained after oral administration revealed contrast medium in the oropharynx (n = 4) and larynx (1) of the 5 horses. Endoscopic examination confirmed radiographic findings and was found to be sensitive for detection of contrast medium in the laryngopharynx, whereby detection rates were higher for both administration methods. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that medication administered by use of a nasopharyngeal catheter will result in topical distribution within the nasopharynx, including the dorsal surface of the soft palate, and larynx, although distribution should be evaluated in horses with clinical airway disease to confirm these findings. Oral administration did not result in consistently detectable topical laryngeal distribution but could be used for selected conditions (eg, palatitis).

  6. Relative diffusion of paramagnetic metal complexes of MRI contrast agents in an isotropic hydrogel medium.

    PubMed

    Weerakoon, Bimali Sanjeevani; Osuga, Toshiaki

    2017-03-01

    The observation of molecular diffusion by means of magnetic resonance imaging (MRI) is significant in the evaluation of the metabolic activity of living tissues. Series of MRI examinations were conducted on a diffusion model to study the behaviour of the diffusion process of different-molecular-weight (MW) paramagnetic MRI contrast agents in an isotropic agar hydrogel medium. The model consisted of a solidified 1 % agar gel with an initial concentration of 0.5 mmol/L contrast solution layered on top of the gel. The diffusion process was monitored at pre-determined time intervals of immediately, 1, 6, 9, 23, and 48 h after introduction of the contrast agents onto the agar gel with a T1-weighted spin-echo (SE) pulse sequence. Three types of paramagnetic contrast agents, Gd-DTPA with a MW of 547.57 g/mol, Prohance with a MW of 558.69 g/mol and MnCl2 with a MW of 125.84 g/mol, resulted in an approximate average diffusional displacement ratio of 1:1:2 per hour, respectively, within 48 h of the experiment. Therefore, the results of this study supported the hypothesis that the rate of the diffusion process of MRI contrast agents in the agar hydrogel medium is inversely related to their MWs. However, more repetitions are necessary under various types of experimental conditions and also with various types of contrast media of different MWs for further confirmation and validation of these results.

  7. Intraoperative ultrasound with contrast medium in resective pancreatic surgery: a pilot study.

    PubMed

    Spinelli, Antonino; Del Fabbro, Daniele; Sacchi, Matteo; Zerbi, Alessandro; Torzilli, Guido; Lutman, Fabio R; Laghi, Luigi; Malesci, Alberto; Montorsi, Marco

    2011-11-01

    The introduction of contrast-enhanced ultrasound has been a major innovation in liver and pancreatic imaging. Previous studies have validated its intraoperative use during liver surgery, while there is a lack of data regarding its use during pancreatic surgery. The purpose of the present study was to prospectively evaluate the possible role of contrast-enhanced intraoperative ultrasound (CEIOUS) during resective pancreatic surgery for primary lesion characterization and intraoperative staging. Thirty-four patients (70% males, mean age 67.9 years) were selected for pancreatic surgery between October 2006 and July 2009. All patients underwent intraoperative ultrasound with intravenous injection of 4.8 mL sulfur-hexafluoride microbubbles. Location of the primary tumor, relation to the main vessels, contrast medium uptake modalities, presence of liver metastases, and multifocal pancreatic involvement were evaluated. The majority of operations were pancreatoduodenectomies (70.6%) performed for pancreatic ductal adenocarcinoma (64.7%). Additional lesions were detected by ultrasound in six patients (17.6%: liver metastases in four patients, a hemangioma in one patient, and a further pancreatic lesion in one patient). In five of these patients (5/34, 14.7%) surgical management was modified by these findings. All these new findings were diagnosed before injection of contrast medium, except for a metastasis from a neuroendocrine tumor; the characterization of the hemangioma was possible only after contrast injection. Intraoperative findings regarding location of primary tumor, relation to the main vessels, and lesion characterization did not differ from those obtained with preoperative imaging. In our experience intraoperative ultrasound is a valid technique for intraoperative staging prior to pancreatic resection; it is unclear whether, in pancreatic surgery, the addition of contrast enhancement adds any benefit to traditional intraoperative ultrasound.

  8. 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

  9. Assessment of renal vasoconstriction in vivo after intra-arterial administration of the isosmotic contrast medium iodixanol compared to the low-osmotic contrast medium iopamidol.

    PubMed

    Treitl, Marcus; Rupprecht, Harald; Wirth, Stefan; Korner, Markus; Reiser, Maximilian; Rieger, Johannes

    2009-05-01

    Low-osmotic contrast media (LOCM) such as iopamidol are known to increase the renal resistance index (RRI). The aim of our study was to evaluate in vivo the different effects of intra-arterial administration of LOCM in comparison to isosmotic contrast medium (IOCM) such as iodixanol on the human RRI. Twenty patients (16 males, 4 females; 66 years on average) with normal renal function (mean creatinine 1.0 mg/dl) had digital subtraction angiography (DSA) of the abdominal and lower-limb arteries. Ten patients received LOCM, and 10 patients IOCM (150 ml on average, 20 ml/s). The RRI was assessed by an experienced nephrologist with duplex ultrasound from 15 min before until 30 min after the first injection with delays of 1-5 min. The basic value of the RRI and differential RRI were calculated. The basic value of the RRI was 0.69 in the LOCM group and 0.71 in the IOCM group. After LOCM a significant increase of the RRI to 0.73 on average (P < or = 0.001) 2 min after the first injection was found, whereas IOCM did not result in a significant change of the RRI (RRI remained 0.71 on average, P > or = 0.1). In the LOCM group, the RRI returned to the basic value after 30 min (+/-2.3 min). Intra-arterial administration of IOCM had no influence on renal vascular resistance as expressed by the RRI, unlike LOCM, which induced a highly significant increase of the RRI for up to 30 min.

  10. Automated contrast medium monitoring system for computed tomography--Intra-institutional audit.

    PubMed

    Lauretti, Dario Luca; Neri, Emanuele; Faggioni, Lorenzo; Paolicchi, Fabio; Caramella, Davide; Bartolozzi, Carlo

    2015-12-01

    The aim of this study was to analyze the usage and the data recorded by a RIS-PACS-connected contrast medium (CM) monitoring system (Certegra(®), Bayer Healthcare, Leverkusen, Germany) over 19 months of CT activity. The system used was connected to two dual syringe power injectors (each associated with a 16-row and a high definition 64-row multidetector CT scanner, respectively), allowing to manage contrast medium injection parameters and to send and retrieve CT study-related information via RIS/PACS for any scheduled contrast-enhanced CT examination. The system can handle up to 64 variables and can be accessed via touchscreen by CT operators as well as via a web interface by registered users with three different hierarchy levels. Data related to CM injection parameters (i.e. iodine concentration, volume and flow rate of CM, iodine delivery rate and iodine dose, CM injection pressure, and volume and flow rate of saline), patient weight and height, and type of CT study over a testing period spanning from 1 June 2013 to 10 January 2015 were retrieved from the system. Technical alerts occurred for each injection event (such as system disarm due to technical failure, disarm due to operator's stop, incomplete filling of patient data fields, or excessively high injection pressure), as well as interoperability issues related to data sending and receiving to/from the RIS/PACS were also recorded. During the testing period, the CM monitoring system generated a total of 8609 reports, of which 7629 relative to successful injection events (88.6%). 331 alerts were generated, of which 40 resulted in injection interruption and 291 in CM flow rate limitation due to excessively high injection pressure (>325 psi). Average CM volume and flow rate were 93.73 ± 17.58 mL and 3.53 ± 0.89 mL/s, and contrast injection pressure ranged between 5 and 167 psi. A statistically significant correlation was found between iodine concentration and peak IDR (rs=0.2744, p<0.0001), as well as between

  11. Iodinated contrast medium as an aid to gallstone dissolution with methyl tert-butyl ether: in vitro study.

    PubMed

    Zhou, J; Lee, S H; Rawat, B; Fache, J S; Maciejewska, U; Burhenne, H J

    1990-05-01

    Methyl tert-butyl ether (MTBE) floats on bile, whereas gallstones sink. Therefore, stones and MTBE are separated by a layer of bile. This study investigates the effect of contrast medium on flotation of gallstones in bile and its role in stone and fragment dissolution with MTBE. Fresh human gallstones, both calcified and noncalcified, from different patients were tested in vitro for flotation in bile, with and without addition of contrast medium. All gallstones or fragments sank in bile before the introduction of contrast medium. Noncalcified stones floated when the contrast medium-bile volume ratio was 1:6 or more, while double this amount of contrast medium was required to float calcified stones. Fragments did dissolve somewhat in MTBE in the presence of bile alone, but when contrast medium was added, almost complete dissolution occurred. This is thought to be due to increased contact between the fragments and MTBE, both floating on the contrast medium-bile mixture. Contrast material may be a useful adjuvant in gallstone dissolution therapy with MTBE in vivo.

  12. Vascular extravasation of contrast medium in radiological examinations: University of California San Diego Health System Experience.

    PubMed

    Niv, Galia; Costa, Matthew; Kicak, Patricia; Richman, Katherine

    2014-06-01

    Extravasation is a well-recognized complication estimated to be between 0.1% and 0.9% of contrast medium administrations. According to the UC San Diego (UCSD) health system policy, all contrast medium extravasation (CME) reports are reviewed by the department of Risk Management, and the appropriate action is taken. Despite this strategy, a decrease in the incidence of CME could not be demonstrated. The aims of this study were to determine the frequency, management, and outcome of CME in UC San Diego patients and to assess the knowledge regarding CME among radiology technologists based on policy and guidelines. The secondary aim was to assess the manual ability of the radiology technologists in the performance of the procedure. The study has 2 parts; the first was retrospective, including data collection and interpretation of all radiology procedures using intravenous contrast medium injection between January 1, 2010, and September 30, 2011, and the second was prospective, including proactive observations and knowledge questionnaire. There were 83 (0.48%) cases of CME of 17,200 patients, 54 women (0.64%) and 29 men (0.33%), P = 0.005. The patients with CME were older, and their cannula was inserted in other departments than Radiology Department, P < 0.000. There was a gap between the high theoretical knowledge that was found in the knowledge questionnaire and its implementation that was demonstrated in the proactive observation. Our data demonstrate that sex, age, and where the cannula was inserted are predictive factors for CME. We believe that CME could be prevented by proper educational program and establishment of efficient strategy.

  13. Enhancement of temporal contrast of high-power laser pulses in an anisotropic medium with cubic nonlinearity

    SciTech Connect

    Kuz'mina, M S; Khazanov, E A

    2015-05-31

    We consider the methods for enhancing the temporal contrast of super-high-power laser pulses, based on the conversion of radiation polarisation in a medium with cubic nonlinearity. For a medium with weak birefringence and isotropic nonlinearity, we propose a new scheme to enhance the temporal contrast. For a medium with anisotropic nonlinearity, the efficiency of the temporal contrast optimisation is shown to depend not only on the spatial orientation of the crystal and B-integral, but also on the type of the crystal lattice symmetry. (extreme light fields and their applications)

  14. Extensive exfoliative dermatitis induced by non-ionic contrast medium Iodixanol (Visipaque) used during percutaneous coronary intervention.

    PubMed

    Choi, Cheol Ung; Rha, Seung-Woon; Suh, Soon Yong; Kim, Jin Won; Kim, Eung Ju; Park, Chang Gyu; Seo, Hong Seog; Oh, Dong Joo

    2008-02-29

    We report a case of extensive exfoliative dermatitis in a patient appearing 3 days after intracoronary administration of non-ionic contrast medium Iodixanol (Visipaque) during the primary percutaneous coronary intervention. The patient presented with acute myocardial infarction and has never exposed to any X-ray contrast medium. The patient was successfully treated with corticosteroid, antihistamines and antibiotics for the prevention of secondary bacterial infection. The patient was recovered 8 days after the anti-allergic medical management. This case can be a rare example of late-onset allergic reaction to a non-ionic contrast medium Iodixanol presented with extensive exfoliative dermatitis.

  15. Multiple doses of contrast medium from a single container: bacteriological studies.

    PubMed

    Tress, B M; Hellyar, A G; Pennington, J; Thomson, K R; Desmond, P M; Martinkus, J; Lavan, J J

    1994-05-01

    Preparations of Iopromide (Ultravist 370; Schering Pty Ltd, Sydney, NSW, Australia), brain/heart infusion broth (BHI; positive growth control) and distilled water (negative control) were inoculated with 10(3) to 10(4) Pseudomonas aeruginosa, Escherichia coli or Staphylococcus aureus cells and incubated at 37 degrees C. Slow decreases (up to one log) were observed in each organism's count in Iopromide and distilled water at room temperature and in S. aureus and E. coli in Iopromide and distilled water at 35 degrees C until 6-8 h, when counts stabilized. BHI cultures showed logarithmic increases. P. aeruginosa counts increased (half log over 8 h) in Ultravist at 37 degrees C. Radiology laboratories were shown to have similar airborne bacterial loads to operating theatres. Samples from repeatedly entered Iopromide bottles showed no contamination. Multiple intravenous doses from a single bottle of non-ionic contrast medium can safely be used as a cost-saving measure provided scrupulous attention is paid to aseptic preparation. Unused decanted contrast medium should be discarded after 4 h.

  16. Potential harmful effect of iodinated intravenous contrast medium on the clinical course of mild acute pancreatitis.

    PubMed

    Carmona-Sánchez, R; Uscanga, L; Bezaury-Rivas, P; Robles-Díaz, G; Suazo-Barahona, J; Vargas-Vorácková, F

    2000-11-01

    A worse clinical outcome might be expected in patients with acute pancreatitis (AP) who receive intravenous contrast medium for a nondynamic contrast-enhanced computed tomographic (CECT) study early during hospital admission. Cohort analytic study. Tertiary care center. Of 126 patients with mild AP, 52 patients underwent CECT to establish AP diagnosis (group 1), and the remaining 74 did not (group 2). Survival and development of local or systemic complications during the hospital stay. Potential confounders were demographic, clinical, and biochemical data, as well as therapeutic measures. The Atlanta classification was used to define local and systemic complications. Mean age, etiology of AP, prognostic score on admission, and pharmacologic treatment were similar between groups. Local and systemic complications were more frequently observed in patients who underwent CECT (odds ratio, 11.4; 95% confidence interval, 2.0-64.8; P =.008). Six patients, all in group 1, developed a pancreatic abscess (odds ratio, 20.8; P =.004). In 5 of them, a second CECT showed more severe AP changes. The association between CECT and abscess development was more apparent in patients with a body mass index of 25 or more and/or nasogastric suction. Six patients in group 1 and 1 in group 2 had systemic complications (odds ratio, 9. 5; P =.01). There were no deaths. The observed increased incidence of local and systemic complications in patients with mild AP who undergo CECT, particularly in those with a body mass index of 25 or more, suggests a potentially harmful effect of intravenous contrast medium. Until this issue is clarified, it seems reasonable to restrict the use of dynamic CECT to patients with severe AP, protracted clinical course, or suspected local septic complication.

  17. Analytical optimization of digital subtraction mammography with contrast medium using a commercial unit

    SciTech Connect

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

    2008-12-15

    Contrast-medium-enhanced digital mammography (CEDM) is an image subtraction technique which might help unmasking lesions embedded in very dense breasts. Previous works have stated the feasibility of CEDM and the imperative need of radiological optimization. This work presents an extension of a former analytical formalism to predict contrast-to-noise ratio (CNR) in subtracted mammograms. The goal is to optimize radiological parameters available in a clinical mammographic unit (x-ray tube anode/filter combination, voltage, and loading) by maximizing CNR and minimizing total mean glandular dose (D{sub gT}), simulating the experimental application of an iodine-based contrast medium and the image subtraction under dual-energy nontemporal, and single- or dual-energy temporal modalities. Total breast-entrance air kerma is limited to a fixed 8.76 mGy (1 R, similar to screening studies). Mathematical expressions obtained from the formalism are evaluated using computed mammographic x-ray spectra attenuated by an adipose/glandular breast containing an elongated structure filled with an iodinated solution in various concentrations. A systematic study of contrast, its associated variance, and CNR for different spectral combinations is performed, concluding in the proposal of optimum x-ray spectra. The linearity between contrast in subtracted images and iodine mass thickness is proven, including the determination of iodine visualization limits based on Rose's detection criterion. Finally, total breast-entrance air kerma is distributed between both images in various proportions in order to maximize the figure of merit CNR{sup 2}/D{sub gT}. Predicted results indicate the advantage of temporal subtraction (either single- or dual-energy modalities) with optimum parameters corresponding to high-voltage, strongly hardened Rh/Rh spectra. For temporal techniques, CNR was found to depend mostly on the energy of the iodinated image, and thus reduction in D{sub gT} could be achieved if the

  18. The association between use of metformin and change in serum CO2 level after administration of contrast medium.

    PubMed

    Kim, S K; Jung, J; Jung, J H; Kim, K Y; Baek, J-H; Hahm, J R

    2016-06-01

    To evaluate the changes in serum creatinine and total CO2 levels in patients receiving metformin during administration of contrast medium. Patient records from January 2012 to December 2012 after the administration of contrast medium were reviewed retrospectively. A total of 924 patients were included for the final analysis. Of them, 105 received metformin during contrast medium administration, 112 were taking other oral hypoglycaemic agents, and 707 patients were not diabetic (controls). No significant change in total CO2 levels was detected (p=0.678). Metabolic acidosis was present in 33 (31.4%) metformin users, 31 (28.6%) other oral hypoglycaemic agent users, and 153 (21.6%) control patients. In the present logistic regression analysis, age, baseline levels of creatinine, and total CO2 levels were associated with metabolic acidosis after contrast medium exposure. These data indicate the presence of a coexisting risk factor, other than metformin use, associated with metabolic acidosis after contrast medium exposure. No relationship was found between the use of metformin and metabolic acidosis during contrast medium exposure. Copyright © 2016 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

  19. Tools of the trade for CTA: MDCT scanners and contrast medium injection protocols.

    PubMed

    Hallett, Richard L; Fleischmann, Dominik

    2006-12-01

    The introduction of multi-detector row computed tomography (MDCT) scanners in 1998 ushered in new advances in CT angiography (CTA). The subsequent expansion of MDCT scanner capabilities, coupled with advances in understanding of contrast medium (CM) dynamics, has further improved the clinical availability and consistency of CTA. We will review recent advances in CT scanner technology and discuss early CM dynamics. Specifically, we describe an approach tailored to the available scanner technology and to patient size aimed at providing consistently robust CTA studies across all vascular territories. A rational method to design combined CTA scan/injection protocols to facilitate this goal will be described. Our current experience with a simplified protocol for CTA with 64-MDCT will also be explained.

  20. Bilateral Renal Fornix Rupture Following Intraarterial Contrast Medium Application for Infrarenal Aortic Stent Placement

    SciTech Connect

    Niggemann, Pascal Brehmer, Bernhard; Schuermann, Karl

    2006-02-15

    A 74-year-old male claudicant who had a significant abdominal aortic stenosis was hydrated before aortic stent placement because of an elevated creatinine level. During the intervention the patient experienced acute abdominal pain with vomiting. No vascular cause was detected. Due to persistant pain, plain radiography and an abdominal CT scan were performed a few hours after the procedure. Images revealed a bilateral renal fornix rupture with a large retroperitoneal fluid collection. The patient was treated conservatively with ureteral double-J placement and percutaneous nephrostomy. The further course was uneventful and the patient was discharged 2 weeks later free of symptoms. Renal fornix rupture is a very rare complication after contrast medium application that can be treated without surgery.

  1. Elimination of non-ionic contrast medium by hemodialysis in patients with impaired renal function.

    PubMed

    Horiuchi, K; Yoshida, K; Tsuboi, N; Akimoto, M; Tajima, H; Kumazaki, T

    1999-10-01

    The elimination rate of iohexol, a non-ionic contrast medium, from the blood by hemodialysis, and the elimination rate of iohexol by a dialyzer were studied in 15 patients with chronic renal dysfunction who required angiography or enhanced CT. The elimination rate of iohexol was 19.8% at 15 min after the start of hemodialysis, 30.6% after 30 min, 44.2% after 1 hour, 62.1% after 2 hours and 72.9% after 3 hours. The dialyzer elimination rate was maintained at about 75% from 1 to 3 hours after the start of hemodialysis. If only about 70% of iohexol in the blood needs to be eliminated, hemodialysis for 3 hours with a blood flow rate of 120 ml/min and a dialysate flow of 500 ml/min using a 0.7 m2 cellulose triacetate membrane is sufficient.

  2. Coronary MR angiography: experimental results with a monomer-stabilized blood pool contrast medium.

    PubMed

    Taupitz, Matthias; Schnorr, Jörg; Wagner, Susanne; Abramjuk, Claudia; Pilgrimm, Herbert; Kivelitz, Dietmar; Schink, Tania; Hansel, Jörg; Laub, Gerhard; Hünigen, Hanna; Hamm, Bernd

    2002-01-01

    To evaluate the signal-enhancing characteristics of monomer-coated very small superparamagnetic iron oxide (SPIO) particles used as a blood pool contrast medium for magnetic resonance (MR) angiography in the coronary arteries. The particles used in this study were coated with citrate as the monomer (VSOP-C91). The particles have a total diameter of 7 nm and show the following relaxivities at 0.47 T: T1, 19 L/mmol. sec(-1); T2, 29 L/mmol. sec(-1). Fifteen cardiac MR examinations were performed at 1.5 T in five pigs. Images were acquired from immediately to 35 minutes (equilibrium phase) after intravenous injection of gadopentetate dimeglumine, gadobenate dimeglumine, and the very small SPIO particles (n = 5 for each substance). Immediately after administration of gadopentetate dimeglumine, gadobenate dimeglumine, and the very small SPIO particles, respectively, increases in the signal-to-noise ratio in blood were 94%, 103%, and 102% and in myocardium were 83%, 83%, and 29% (P <.05, very small SPIO particles versus the low-molecular-weight gadolinium-based compounds). Differences in the blood-to-myocardium contrast-to-noise ratio and visualization of the coronary arteries and their branches were also significant. VSOP-C91 significantly improves visualization of the coronary arteries at MR angiography from immediately to 35 minutes after injection.

  3. In vitro evaluation of contrast medium concentration and depth effects on the radiographic appearance of specific canine urolith mineral types.

    PubMed

    Weichselbaum, R C; Feeney, D A; Jessen, C R; Osborne, C A; Dunphy, E D; Bartges, J W

    1998-01-01

    Nine pure mineral types of canine uroliths (bladder or urethral origin only) identified in a chronologic sample from the Minnesota Urolith Center were compared to sequential dilutions of iodinated radiographic contrast medium in vitro. The uroliths studied were those composed of 100% magnesium ammonium phosphate, calcium oxalate monohydrate, calcium oxalate dihydrate, calcium phosphate appatite, calcium hydrogen phosphate dihydrate (brushite), ammonium acid urate, sodium acid urate, cystine, and silica. The radiopacity of the uroliths was classified as radiolucent, isopaque, or radiopaque, as compared to the radiopacity of the contrast medium solutions in which they were placed, using 2.0 mm and 5.0 mm depths in petri dishes radiographed using a table-top technique. A statistically significant relationship was found between the effective atomic number of the uroliths and the effective atomic number of the contrast medium solutions to which they were compared for the endpoints of isopacity, first lucency (in increasing iodine concentration sequence), and optimal visualization of internal architecture. In general, uroliths isopaque or radiolucent in contrast medium solutions weaker than 23.5 mgI2/ml are most likely ammonium acid urate or sodium acid urate. Uroliths isopaque or radiolucent in contrast medium solutions between 23.5 mgI2/ml and 44.4 mgI2/ml are probably magnesium ammonium phosphate, cystine, or silica. Uroliths that remained radiopaque in solutions stronger than 44.4 mgI2/ml, and particularly those radiopaque in contrast medium solutions stronger than 80 mgI2/ml, almost always contained calcium. This relative opacity assessment is proposed for use in double contrast cystography as an aid in differentiating urolith mineral types clinically to facilitate appropriate use of medical protocols to dissolve uroliths or to prevent their growth or recurrence.

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

    PubMed

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

    2005-05-16

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

  5. Thyroid function after hysterosalpingography using an oil-soluble iodinated contrast medium.

    PubMed

    Mekaru, Keiko; Kamiyama, Shigeru; Masamoto, Hitoshi; Sakumoto, Kaoru; Aoki, Yoichi

    2008-09-01

    The objective of the present study was to evaluate the effect of an oil-soluble iodinated contrast medium (lipiodol) for hysterosalpingography (HSG) on thyroid function. In 214 of 528 women with infertility examined by HSG using lipiodol between 1996 and 2006 at our institution, serum free thyroxine (FT4) and thyrotropin-stimulating hormone (TSH) were measured before and several months after HSG. The average age of the women was 34.5 +/- 4.6 years and their average infertility period was 2.9 +/- 2.5 years (mean+/-standard deviation). The 214 patients were divided into three groups based on the results of thyroid function before HSG: 180 in euthyroid, 28 in subclinical hypothyroidism and 13 in subclinical hyperthyroidism. The number of patients in the subclinical hypothyroidism group who developed hypothyroidism after HSG (ten of 28) was significantly higher than that of the euthyroid group (four of 180). Thyroid hormone replacement was required in three patients from the subclinical hypothyroidism group 1, 2 and 5 months after HSG. We conclude that thyroid function should be monitored closely after HSG using lipiodol to detect the development of hypothyroidism, particularly in patients with subclinical hypothyroidism, and TSH and FT4 measurements should be performed before HSG to identify patients at risk for hypothyroidism.

  6. Contrasting metabolic effects of medium- versus long-chain fatty acids in skeletal muscle.

    PubMed

    Montgomery, Magdalene K; Osborne, Brenna; Brown, Simon H J; Small, Lewin; Mitchell, Todd W; Cooney, Gregory J; Turner, Nigel

    2013-12-01

    Dietary intake of long-chain fatty acids (LCFAs) plays a causative role in insulin resistance and risk of diabetes. Whereas LCFAs promote lipid accumulation and insulin resistance, diets rich in medium-chain fatty acids (MCFAs) have been associated with increased oxidative metabolism and reduced adiposity, with few deleterious effects on insulin action. The molecular mechanisms underlying these differences between dietary fat subtypes are poorly understood. To investigate this further, we treated C2C12 myotubes with various LCFAs (16:0, 18:1n9, and 18:2n6) and MCFAs (10:0 and 12:0), as well as fed mice diets rich in LCFAs or MCFAs, and investigated fatty acid-induced changes in mitochondrial metabolism and oxidative stress. MCFA-treated cells displayed less lipid accumulation, increased mitochondrial oxidative capacity, and less oxidative stress than LCFA-treated cells. These changes were associated with improved insulin action in MCFA-treated myotubes. MCFA-fed mice exhibited increased energy expenditure, reduced adiposity, and better glucose tolerance compared with LCFA-fed mice. Dietary MCFAs increased respiration in isolated mitochondria, with a simultaneous reduction in reactive oxygen species generation, and subsequently low oxidative damage. Collectively our findings indicate that in contrast to LCFAs, MCFAs increase the intrinsic respiratory capacity of mitochondria without increasing oxidative stress. These effects potentially contribute to the beneficial metabolic actions of dietary MCFAs.

  7. Contrasting metabolic effects of medium- versus long-chain fatty acids in skeletal muscle[S

    PubMed Central

    Montgomery, Magdalene K.; Osborne, Brenna; Brown, Simon H. J.; Small, Lewin; Mitchell, Todd W.; Cooney, Gregory J.; Turner, Nigel

    2013-01-01

    Dietary intake of long-chain fatty acids (LCFAs) plays a causative role in insulin resistance and risk of diabetes. Whereas LCFAs promote lipid accumulation and insulin resistance, diets rich in medium-chain fatty acids (MCFAs) have been associated with increased oxidative metabolism and reduced adiposity, with few deleterious effects on insulin action. The molecular mechanisms underlying these differences between dietary fat subtypes are poorly understood. To investigate this further, we treated C2C12 myotubes with various LCFAs (16:0, 18:1n9, and 18:2n6) and MCFAs (10:0 and 12:0), as well as fed mice diets rich in LCFAs or MCFAs, and investigated fatty acid-induced changes in mitochondrial metabolism and oxidative stress. MCFA-treated cells displayed less lipid accumulation, increased mitochondrial oxidative capacity, and less oxidative stress than LCFA-treated cells. These changes were associated with improved insulin action in MCFA-treated myotubes. MCFA-fed mice exhibited increased energy expenditure, reduced adiposity, and better glucose tolerance compared with LCFA-fed mice. Dietary MCFAs increased respiration in isolated mitochondria, with a simultaneous reduction in reactive oxygen species generation, and subsequently low oxidative damage. Collectively our findings indicate that in contrast to LCFAs, MCFAs increase the intrinsic respiratory capacity of mitochondria without increasing oxidative stress. These effects potentially contribute to the beneficial metabolic actions of dietary MCFAs. PMID:24078708

  8. [Two cases of elderly patients with ruptured AVM with contrast medium extravasation during cerebral angiography].

    PubMed

    Ueda, Y; Urakawa, M; Kawakami, N

    2001-12-01

    Two cases are reported of elderly patients who experienced intracranial extravasation of contrast medium (CM) during carotid angiography (CAG) for ruptured cerebral arteriovenous malformations (AVM). The first patient, an 87-year-old male with no history of hypertension, was admitted immediately following a loss of consciousness after swimming in a pool. CT scan revealed a large intracranial hematoma in the left frontal lobe. CAG performed 1 hour after his arrival revealed a small AVM, fed by the left anterior cerebral artery with concomitant extravasation of CM. The patient's condition subsequently deteriorated and he died the following day. The second patient, a 71-year-old female, was admitted to our hospital in a comatose state after complaining of a severe headache. CT scan revealed a right parietal lobe hemorrhage extending into the ventricles. CAG was performed and demonstrated a small AVM in the right parietal lobe with extravasation of CM. Following emergency removal of the hematoma and AVM, the patient regained consciousness although some motor deficits persisted. A literature review revealed that only 6 cases of CM extravasation with ruptured AVM have been previously reported. The 4 previous cases involved patients 9, 15, 33 and 66-year-old, the younger three of which had a good outcome. The patients reported here were much older, and had a much less favorable outcome. Thus, AVM with CM extravasation may have a better prognosis in younger individuals.

  9. Transformation of the X-ray contrast medium iopromide in soil and biological wastewater treatment.

    PubMed

    Schulz, Manoj; Löffler, Dirk; Wagner, Manfred; Ternes, Thomas A

    2008-10-01

    In water/soil systems, the iodinated contrast medium iopromide was quantitatively biotransformed into several transformation products (TPs). Twelve TPs were identified via HPLC-UV and LC tandem MS. The chemical structures of the TPs were elucidated via fragmentation in MS2 and MS3 of LC tandem MS with a linear ion trap and 1H and 13C NMR analyses. All TPs exhibited transformations at the side chains containing either carboxylic moieties and/or primary and secondary amide moieties, while the triiodoisophthalic acid structure remained unaltered. A transformation pathway was proposed based on the sequence of TP formation in aerobic batch experiments. Additionally, the occurrence of iopromide TPs was investigated in native water samples. All TPs identified were found in municipal WWTP effluents because of their formation during biological wastewater treatment with maximum concentrations of up to 3.7 +/- 0.9 microg/L (TP 819). Predominantly, those TPs were present at higher concentrations in WWTP effluents which were formed at the beginning of the transformation pathway. Furthermore, four TPs formed at the end of the transformation pathway (TP 759, 701A/B, and 643) were also found in bank filtrate up to 0.050 microg/L and in groundwater of an wastewater irrigation area up to 4.6 microg/L.

  10. Aggravation of Pre-Existing Atrioventricular Block, Wenckebach Type, Provoked by Application of X-Ray Contrast Medium

    SciTech Connect

    Brodmann, Marianne Seinost, Gerald; Stark, Gerhard; Pilger, Ernst

    2006-12-15

    Background. Significant bradycardia followed by cardiac arrest related to single bolus administration of X-ray contrast medium into a peripheral artery has not, to our knowledge, been described in the literature. Methods and Results. While performing a percutaneous transluminal angioplasty of the left superficial femoral artery in a 68-year old patient with a pre-existing atrioventricular (AV) block, Wenckebach type, he developed an AV block III after a single bolus injection of intra-arterial X-ray contrast medium. Conclusion. We believe that application of contrast medium causes a transitory ischemia in the obstructed vessel and therefore elevation of endogenous adenosine. In the case of a previously damaged AV node this elevation of endogenous adenosine may be responsible for the development of a short period of third-degree AV block.

  11. Effects of contrast medium injection technique on attenuation values of adrenal glands in healthy dogs during contrast-enhanced computed tomography.

    PubMed

    Blaser, Alexandra; Dennler, Matthias; Mosing, Martina; Gent, Thomas C; Santner, Guido; Imhasly, Sandro; Boretti, Felicitas S; Reusch, Claudia E; Kircher, Patrick; Sieber-Ruckstuhl, Nadja S

    2016-02-01

    To assess the effects of 3 contrast medium injection techniques on attenuation values for canine adrenal glands during contrast-enhanced CT. 9 healthy Beagles. 3 protocols were evaluated in a randomized cross-over design study: 700 mg of iodine/kg at a constant injection rate over 20 seconds (full-dose constant rate), the same dose at a rate following an exponential decay curve over 20 seconds (full-dose decelerated rate), and 350 mg of iodine/kg at a constant injection rate over 10 seconds (half-dose constant rate). Multislice CT images were obtained before and at predetermined time points after the start of contrast medium injection. Median peak attenuation values were 129, 133, and 87 Hounsfield units with the full-dose constant rate, full-dose decelerated rate, and half-dose constant rate injection protocols, respectively. Peak attenuation differed significantly between the full-dose constant rate and half-dose constant rate injection protocols and between the full-dose decelerated rate and half-dose constant rate injection protocols. Median time to peak attenuation did not differ significantly among injection methods and was 30, 23, and 15 seconds for the full-dose constant rate, full-dose decelerated rate, and half-dose constant rate injections, respectively. The dose of contrast medium and the timing of postinjection CT scanning were main determinants of peak attenuation for adrenal glands in healthy dogs; effects of the 3 injection protocols on attenuation were minor. The exponentially decelerated injection method was subjectively complex. A constant injection protocol delivering 700 mg of iodine/kg over 20 seconds, with scans obtained approximately 30 seconds after starting contrast medium injection, provided images with maximum adrenal gland attenuation values.

  12. Macromolecular Nanostructured Materials

    NASA Astrophysics Data System (ADS)

    Ueyama, Norikazu; Harada, Akira

    This book presents a detailed account of the synthesis, characterization and application of organic and inorganic macromolecular nanostructured materials. These materials consist of simple organic compounds, inorganic complexes and polymers, and display unique properties such as electrical conductivity ranging from semiconducting to superconducting. Also described in the book are the roles of these materials in electrodeposition and gas deposition, as photosensitizers, magnets, macromolecular metal catalysts, sol-gel hybrids, and in biomineralization.

  13. [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

  14. Hepatic contrast medium enhancement at computed tomography and its correlation with various body size measures.

    PubMed

    Svensson, Anders; Nouhad, Jallo; Cederlund, Kerstin; Aspelin, Peter; Nyman, Ulf; Björk, Jonas; Torkel, Brismar B

    2012-07-01

    When the same dose of iodine is given to all patients when performing abdominal computed tomography (CT) there may be a wide inter-individual variation in contrast medium (CM) enhancement of the liver. To evaluate if any of the measures body height (BH), body mass index (BMI), lean body mass (LBM), ideal body weight (IBW), and body surface area (BSA) correlated better than body weight (BW) with hepatic enhancement, and to compare the enhancement when using iodixanol and iomeprol. One hundred patients referred for standard three-phase CT examination of abdomen were enrolled. Body weight and height were measured at the time of the CT examination. Forty grams of iodine (iodixanol 320 mg I/mL or iomeprol 400 mg I/mL) was injected at a rate of 1.6 g-I/s, followed by a 50 mL saline flush. The late arterial phase was determined by using a semi-automatic smart prep technique with a scan delay of 20 s. The hepatic parenchymal phase started automatically 25 s after the late arterial phase. CM concentration was estimated by placement of regions of interest in aorta (native and late arterial phase) and in liver (native and parenchymal phase). BW (r = -0.51 and -0.64), LBM (r = -0.54 and -0.59), and BSA (r = -0.54 and -0.65) showed the best correlation coefficients with aortic and hepatic parenchymal enhancement, respectively, without any significant differences between the measures. Comparing iodixanol and iomeprol there was no significant difference in aortic enhancement. The liver enhancement was significantly higher (P < 0.05) using iodixanol than iomeprol. To achieve a consistent hepatic enhancement, CM dose may simply be adjusted to body weight instead of using more complicated calculated parameters based on both weight and height.

  15. Establishment of the intracranial hemodynamic model based on contrast medium and clinical applications

    PubMed Central

    Cheng, Yaoer; He, Wen

    2016-01-01

    Abstract Ischemic cerebrovascular diseases are one of the most common vascular diseases in aged people and CT perfusion (CTP) is a very popular tool to detect the ischemic changes in brain vascular. The present study aims to establish a novel intracranial hemodynamic model to simulate anterior cerebral artery blood flow, and compare the actual and simulated hemodynamic parameters of healthy people and patients with carotid stenosis or occlusion. A mathematical model of the intracranial hemodynamic was generated using MATLAB software, and data from patients with or without infarct disease (57 and 44 cases, respectively) were retrospectively collected to test the new model. The actual time-density curve (TDC) of anterior cerebral artery was obtained from the original intracranial CTP data, and simulated TDC was calculated from our intracranial hemodynamic model. All model parameters were adjusted according to patients’ sex, height, and weight. Time to peak enhancement (TTP), maximum enhancement (ME), and mean transit time (MTT) were selected to evaluate the status of hemodynamics. In healthy people, there were no significant differences of TTP and ME between actual and simulated curves. For patients with infarct symptoms, ME was significantly decreased in actual data compared with simulated curve, while there was no obvious difference of TTP between actual and simulated data. Moreover, MTT was delayed in infarct patients compared with healthy people. Our group generated a computer-based, physiologic model to simulate intracranial hemodynamics. The model successfully simulated anterior cerebral artery hemodynamics in normal healthy people and showed noncompliant ME and MTT in infarct patients, reflecting their abnormal cerebral hemodynamic status. The digital model is reliable and may help optimize the protocol of contrast medium enhancement in intracranial CT, and provide a solid tool to study intracranial hemodynamics. PMID:27930555

  16. Establishment of the intracranial hemodynamic model based on contrast medium and clinical applications.

    PubMed

    Cheng, Yaoer; He, Wen

    2016-12-01

    Ischemic cerebrovascular diseases are one of the most common vascular diseases in aged people and CT perfusion (CTP) is a very popular tool to detect the ischemic changes in brain vascular. The present study aims to establish a novel intracranial hemodynamic model to simulate anterior cerebral artery blood flow, and compare the actual and simulated hemodynamic parameters of healthy people and patients with carotid stenosis or occlusion.A mathematical model of the intracranial hemodynamic was generated using MATLAB software, and data from patients with or without infarct disease (57 and 44 cases, respectively) were retrospectively collected to test the new model. The actual time-density curve (TDC) of anterior cerebral artery was obtained from the original intracranial CTP data, and simulated TDC was calculated from our intracranial hemodynamic model. All model parameters were adjusted according to patients' sex, height, and weight. Time to peak enhancement (TTP), maximum enhancement (ME), and mean transit time (MTT) were selected to evaluate the status of hemodynamics.In healthy people, there were no significant differences of TTP and ME between actual and simulated curves. For patients with infarct symptoms, ME was significantly decreased in actual data compared with simulated curve, while there was no obvious difference of TTP between actual and simulated data. Moreover, MTT was delayed in infarct patients compared with healthy people.Our group generated a computer-based, physiologic model to simulate intracranial hemodynamics. The model successfully simulated anterior cerebral artery hemodynamics in normal healthy people and showed noncompliant ME and MTT in infarct patients, reflecting their abnormal cerebral hemodynamic status. The digital model is reliable and may help optimize the protocol of contrast medium enhancement in intracranial CT, and provide a solid tool to study intracranial hemodynamics.

  17. Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin.

    PubMed

    Spokevicius, Antanas V; Tibbits, Josquin; Rigault, Philippe; Nolin, Marc-Alexandre; Müller, Caroline; Merchant, Andrew

    2017-04-07

    Climatic and edaphic conditions over geological timescales have generated enormous diversity of adaptive traits and high speciation within the genus Eucalyptus (L. Hér.). Eucalypt species occur from high rainfall to semi-arid zones and from the tropics to latitudes as high as 43°S. Despite several morphological and metabolomic characterizations, little is known regarding gene expression differences that underpin differences in tolerance to environmental change. Using species of contrasting taxonomy, morphology and physiology (E. globulus and E. cladocalyx), this study combines physiological characterizations with 'second-generation' sequencing to identify key genes involved in eucalypt responses to medium-term water limitation. One hundred twenty Million high-quality HiSeq reads were created from 14 tissue samples in plants that had been successfully subjected to a water deficit treatment or a well-watered control. Alignment to the E. grandis genome saw 23,623 genes of which 468 exhibited differential expression (FDR < 0.01) in one or both ecotypes in response to the treatment. Further analysis identified 80 genes that demonstrated a significant species-specific response of which 74 were linked to the 'dry' species E. cladocalyx where 23 of these genes were uncharacterised. The majority (approximately 80%) of these differentially expressed genes, were expressed in stem tissue. Key genes that differentiated species responses were linked to photoprotection/redox balance, phytohormone/signalling, primary photosynthesis/cellular metabolism and secondary metabolism based on plant metabolic pathway network analysis. These results highlight a more definitive response to water deficit by a 'dry' climate eucalypt, particularly in stem tissue, identifying key pathways and associated genes that are responsible for the differences between 'wet' and 'dry' climate eucalypts. This knowledge provides the opportunity to further investigate and understand the mechanisms and

  18. Reduction of vascular and permeable regions in solid tumors detected by macromolecular contrast magnetic resonance imaging after treatment with antiangiogenic agent TNP-470.

    PubMed

    Bhujwalla, Zaver M; Artemov, Dmitri; Natarajan, Kshama; Solaiyappan, Meiyappan; Kollars, Peggy; Kristjansen, Paul E G

    2003-01-01

    The availability of noninvasive techniques to detect the effects of antiangiogenic agents is critically important for optimizing treatment of cancer with these agents. Magnetic resonance imaging (MRI) is one such noninvasive technique that is routinely used clinically. In this study, we have evaluated the use of MRI of the intravascular contrast agent albumin-GdDTPA to detect the effects of the antiangiogenic agent TNP-470 on the vascular volume and permeability of the MatLyLu prostate cancer model. TNP-470-treated tumors demonstrated a significant decrease of vascular volume, as well as a significant reduction in vascular and permeable regions, compared with volume-matched control tumors. Although the fractional volume of permeable regions in the tumor decreased, the average value of tumor permeability did not decrease significantly. This was attributable to increase in permeability in some regions of the tumor. These regions were mostly associated with low vascular volume. ELISA assays of control and treated MatLyLu tumors also detected a significant increase of vascular endothelial growth factor in the TNP-470-treated tumors. MRI detected significant changes in tumor vascular characteristics after treatment with TNP-470.

  19. Intense femtosecond laser driven collimated fast electron transport in a dielectric medium-role of intensity contrast.

    PubMed

    Dey, Indranuj; Adak, Amitava; Singh, Prashant Kumar; Shaikh, Moniruzzaman; Chatterjee, Gourab; Sarkar, Deep; Lad, Amit D; Kumar, G Ravindra

    2016-12-12

    Ultra-high intensity (> 1018 W/cm2), femtosecond (~30 fs) laser induced fast electron transport in a transparent dielectric has been studied for two laser systems having three orders of magnitude different peak to pedestal intensity contrast, using ultrafast time-resolved shadowgraphy. Use of a 400 nm femtosecond pulse as a probe enables the exclusive visualization of the dynamics of highest density electrons (> 7 × 1021 cm-3) observed so far. High picosecond contrast (~109) results in greater coupling of peak laser energy to the plasma electrons, enabling long (~1 mm), collimated (divergence angle ~2°) transport of fast electrons inside the dielectric medium at relativistic speeds (~0.66c). In comparison, the laser system with a contrast of ~106 has a large pre-plasma, limiting the coupling of laser energy to the solid and yielding limited fast electron injection into the dielectric. In the lower contrast case, bulk of the electrons expand as a cloud inside the medium with an order of magnitude lower speed than that of the fast electrons obtained with the high contrast laser. The expansion speed of the plasma towards vacuum is similar for the two contrasts.

  20. 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.

  1. 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

  2. Penetration of subarachnoid contrast medium into rabbit spinal cord. Comparison between metrizamide and iohexol

    SciTech Connect

    Holtas, S.; Morris, T.W.; Ekholm, S.E.; Isaac, L.; Fonte, D.

    1986-02-01

    The penetration into rabbit spinal cord of two nonionic contrast media, iohexol and metrizamide, and a reference tracer, technetium DTPA, were compared. The spinal subarachnoid space was perfused for 4 hours with a CSF solution to which technetium DTPA and either iohexol or metrizamide had been added. The contrast media and technetium DTPA concentrations reached a plateau level in CSF outflow within 80 minutes. The contrast media concentrations in CSF were higher than the technetium DTPA (P less than .001). In the cord tissue, technetium DTPA reached higher concentrations than the contrast media (P less than .001), and iohexol reached higher concentrations relative to technetium DTPA than metrizamide (P less than .001). The mean contrast media distribution volumes in the thoracic cord were 13% (iohexol) and 12% (metrizamide). The smaller distribution volume observed for metrizamide could be related to the larger effective size of associated metrizamide molecules or an interference with diffusion perhaps related to binding to glucose carriers.

  3. 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)

  4. 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

  5. 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

  6. Echocolor Power Doppler with contrast medium to evaluate vascularization in lesions of the soft tissues of the limbs.

    PubMed

    De Marchi, A; De Petro, P; Faletti, C; Brach del Prever, E M; Gino, G; Albertini, U; Piana, R; Marone, S; Mellano, D; Linari, A; Forni, M; Bertoldo, U; Comandone, A; Boglione, A; Brach del Prever, A

    2003-01-01

    Echocolor Power Doppler with contrast medium forms a non-invasive vascular image; the purpose of the study is to evaluate the effectiveness in differentiating benign and malignant tumors in the soft tissues of the limbs. Echocolor Power Doppler with contrast medium was used to study 80 patients with swelling in the soft tissues of the limbs: there were 54 benign lesions, 22 sarcomas, and 4 aggressive desmoid fibromatoses. Were identified 4 patterns of wash-in and wash-out curves that could be correlated to the histological diagnosis: type I was present in 85% of benign lesions, type III in 91% of malignant lesions and in 3.7% of the benign ones, type II in aggressive fibromatoses, anomalous type in 4 benign lesions and 2 sarcomas; the curve was absent in 2 benign lesions. Power Doppler Echocolor with contrast medium can become a useful method to be associated with traditional imaging methods in the differential diagnosis of swelling of the soft tissues of the limbs.

  7. Contrast medium injection optimisation in spiral CT for the diagnosis of pulmonary embolism.

    PubMed

    Gattoni, Filippo; Tagliaferri, Beatrice; Scali, Paolo; Brioschi, Sonia; Boioli, Faustino

    2003-01-01

    Spiral CT, normally a highly accurate diagnostic method to diagnose pulmonary embolism, has its weak point in the synchronisation of contrast medium (CM) injection and the start of the acquisition, essential to obtain optimal vascular enhancement. The aim of this paper is to introduce a method to control the CM injection based on the enhancement of blood vessels in the diagnosis of pulmonary embolism. The CARE bolus software pilots an electronic trigger that first monitors the CM passage, then starts the acquisition procedure when the intensity of enhancement reaches a pre-set value. Our spiral CT has a 6-second scan delay between the trigger's "go-ahead" and the start of the acquisition. During this interval, the CM reaches the pulmonary venous system, enhancing it and making the diagnosis of pulmonary embolism more difficult. This problem was overcome by injecting a slow bolus (30 ml; 1.5 ml/s flow rate) before the CM that triggers the start of the scan when the CM is only present in the pulmonary arteries. We examined 80 patients (36 men, 44 women, mean age 66.9, age range 18 to 89 years). All patients were examined for clinically, radiographically or scintigraphically suspected pulmonary embolism. We evaluated the enhancement of pulmonary arteries on a scale from 0 (poor) to 10 (excellent), image quality (excellent, fair, poor), the examination time and patient tolerance. The results were compared with those obtained in a group of 80 patients studied with CARE bolus without a timing bolus. Monitor scans were performed with the ROI that triggers the sequence centred on the right heart (trigger value set at 30/35 HU). There were no diagnostic artefacts caused by the enhancement of pulmonary veins due the timing bolus. The average time per procedure was less than 30 min and the time needed to reach the trigger value was 15 sec (range: 10-24 sec). The average volume of CM injected was 130 ml (timing bolus: 30 ml, scan bolus: 100 ml). There were no adverse events to

  8. Effects of contrast medium on radiation-induced chromosome aberrations. [X-ray; /sup 60/Co

    SciTech Connect

    Matsubara, S.; Suzuki, S.; Suzuki, H.; Kuwabara, Y.; Okano, T.

    1982-07-01

    The effects of contrast material (meglumine iothalamate) on radiation-induced chromosome aberrations were investigated in studies on the lymphocytes of patients who had undergone diagnostic radiography and in vitro experiments with diagnostic x rays and /sup 60/Co ..gamma.. rays. Chromosome and chromatic aberrations were found to increase significantly with increasing concentrations of contrast material that were added at irradiation. However, the aberrations were not associated with elevation of the ratio of dicentric and ring chromosomes to the number of cells with unstable chromosome aberrations at the first mitosis. Lymphocytes irradiated in the absence of contrast material did not show an increase in chromosome-type aberrations when the agent was given in increasing concentrations during subsequent incubation, but there were greater numbers of chromatid gaps and breaks. When lymphocytes were exposed to 400 R (103.2 mC/kg) of /sup 60/Co ..gamma.. rays, the presence of contrast agent did not increase the yield of dicentric and ring chromosomes, but induced a marked delay in cell proliferation, especially in lymphocytes with more heavily damaged chromosomes. In additional examination, the contrast agent itself induced sister chromatid exchanges in lymphocytes.

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

    PubMed Central

    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

  10. 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.

  11. 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.

  12. Blueprinting macromolecular electronics.

    PubMed

    Palma, Carlos-Andres; Samorì, Paolo

    2011-06-01

    Recently, by mastering either top-down or bottom-up approaches, tailor-made macromolecular nano-objects with semiconducting properties have been fabricated. These engineered nanostructures for organic electronics are based on conjugated systems predominantly made up of sp²-hybridized carbon, such as graphene nanoribbons. Here, we describe developments in a selection of these nanofabrication techniques, which include graphene carving, stimulus-induced synthesis of conjugated polymers and surface-assisted synthesis. We also assess their potential to reproduce chemically and spatially precise molecular arrangements, that is, molecular blueprints. In a broad context, the engineering of a molecular blueprint represents the fabrication of an integrated all-organic macromolecular electronic circuit. In this Perspective, we suggest chemical routes, as well as convergent on-surface synthesis and microfabrication approaches, for the ultimate goal of bringing the field closer to technology.

  13. Indirect lymph node lymphangiography using an iodine-based contrast medium and projection radiography following submucosal injection in a rabbit model.

    PubMed

    Dietrich, A; Wuttke, M; Walter, F; De Leon, I; Kloeppel, R; Schoenfelder, M

    2002-11-01

    This study investigated the possibility of local lymph node detection and lymphatic mapping following submucosal injection of an iodine-based contrast medium. We established a contrast medium (oil/water emulsion on iodine basis) with a particle size of mainly 1.7+/-0.1 micro m. Ten rabbits received rectal submucosal injections of the contrast medium and underwent repeated projection radiography. Passage of the contrast medium into lymphatic vessels and storage in lymph nodes was seen in all ten animals. The best contrast was achieved within 24 and 48 h after injection. Lymph nodes were still seen in eight cases with the final radiograph on day 14. There were no clinical side effects observed. Injection sites showed mild signs of inflammation in histological examinations. Pathological signs were not detectable in lymph nodes containing the contrast media. This method appears useful when investigating local lymph nodes following submucosal injection due to its passage into lymphatic vessels and storage in lymph nodes.

  14. 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.

  15. 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.

  16. Premedication of patients for prior urticarial reaction to iodinated contrast medium.

    PubMed

    Kolbe, Amy B; Hartman, Robert P; Hoskin, Tanya L; Carter, Rickey E; Maddox, Daniel E; Hunt, Christopher H; Hesley, Gina K

    2014-04-01

    The purpose of this study was to determine whether premedication of patients with a history of urticaria after low osmolality contrast media (LOCM) results in fewer subsequent reactions, and if a benefit is seen, to determine which premedication regimen results in the fewest reactions. The subsequent contrast enhanced studies of patients who experienced urticaria after intravenous LOCM between 2002 and 2009 were reviewed to determine whether an additional reaction occurred. Patients undergoing subsequent studies received either no premedication, or premedication with diphenhydramine alone, corticosteroid alone, or corticosteroid plus diphenhydramine. Reactions occurring without premedication were termed repeat reactions and reactions occurring after premedication were termed breakthrough reactions. Fifty patients with a history of urticaria after LOCM met the inclusion criteria and underwent 133 subsequent contrast enhanced studies. Repeat reactions occurred in 7.6% (5/66) of subsequent studies in patients receiving no premedication. Breakthrough reactions occurred in 8% (2/25), 46% (12/26), and 44% (7/16) of subsequent studies in patients receiving premedication with diphenhydramine, corticosteroid, and corticosteroid plus diphenhydramine, respectively. All subsequent reactions consisted of urticaria as the most severe manifestation; no hemodynamic instability or respiratory compromise occurred. In multivariate analysis, premedication with corticosteroid was significantly associated with higher rate of breakthrough reaction relative to no premedication (OR 14.3, 95% CI: 4.1-50.4), as was premedication with corticosteroid plus diphenhydramine (OR 8.3, 95% CI: 1.8-37.9). The results suggest that premedication of patients with a history of urticaria after LOCM may not be necessary.

  17. Effect and distribution of contrast medium after injection into the anterior suprachoroidal space in ex vivo eyes.

    PubMed

    Seiler, Gabriela S; Salmon, Jacklyn H; Mantuo, Rebecca; Feingold, Steven; Dayton, Paul A; Gilger, Brian C

    2011-07-29

    To determine the effects and posterior distribution of injections made into the anterior suprachoroidal space (SCS). The anterior SCS of adult porcine and canine ex vivo eyes was cannulated. Latex injections and high frequency ultrasound (50 MHz) was used to image the effect and distension of the SCS. Flow characteristics and percentage maximal distribution of microbubble contrast injection into the SCS were assessed by 2D and 3D ultrasound. Mean (SD) distension of the SCS with PBS increased from 1.57 (0.48) mm after injection of 250 μL to 3.28 (0.57) mm with 1000 μL PBS. Eyes injected at physiologic IOP had no significant difference in SCS distension. In real-time 2D ultrasound, the contrast agent flowed from the injection site to the opposite ventral anterior SCS and the posterior SCS. Contrast arrived at the opposite and posterior SCS 7.8 (4.6) and 7.7 (4.6) seconds after injection, respectively. In sagittal images, contrast was visible in 24.0%to 27.2% of the SCS; in 10 of 12 eyes, contrast reached the posterior pole of the eye. In 3D images, contrast medium occupied 39.0% to 52.1% of the entire SCS. These results suggest that the SCS can expand, in a dose-dependent manner, to accommodate various volumes of fluid and that it is possible to image the SCS with ultrasound contrast. The authors' hypothesis that a single anterior SCS injection can reach the ocular posterior segment was supported. Further development of SCS injections for treatment of the ocular posterior segment is warranted.

  18. Direct cardiac effects of an ionic and a non-ionic contrast medium in dogs.

    PubMed

    Palik, I; Szente, A; Köszeghy, G A; Koltai, M Z; Kiss, V; Pogátsa, G

    1986-11-01

    Direct cardiac effects of ionic diatrizoate (Uromiro) and non-ionic iopamidol (Iopamiro) were investigated in "in situ" heart-lung preparation of 19 vagotomized dogs. Diatrizoate was found to induce considerably greater alteration in plasma osmolality and subsequent dehydration of the myocardium compared with iopamidol. Myocardial dehydration resulted in a decrease of left ventricular compliance and in that of cardiac performance. Diatrizoate was shown to influence the myocardium not only by its hyperosmolarity but also by a direct action. Heart rate was reduced by both contrast media.

  19. Highlighting cancer cells with macromolecular probes

    NASA Astrophysics Data System (ADS)

    Tang, Sicheng; Zhang, Yang; Thapaliya, Ek Raj; Brown, Adrienne S.; Wilson, James N.; Raymo, Françisco M.

    2017-02-01

    Conventional fluorophore-ligand constructs for the detection of cancer cells generally produce relatively weak signals with modest contrast. The inherently low brightness accessible per biding event with the pairing of a single organic fluorophore to a single ligand as well as the contribution of unbound probes to background fluorescence are mainly responsible for these limitations. Our laboratories identified a viable structural design to improve both brightness and contrast. It is based on the integration of activatable fluorophores and targeting ligands within the same macromolecular construct. The chromophoric components are engineered to emit bright fluorescence exclusively in acidic environments. The targeting agents are designed to bind complementary receptors overexpressed on the surface of cancer cells and allow internalization of the macromolecules into acidic organelles. As a result of these properties, our macromolecular probes switch their intense emission on exclusively in the intracellular space of target cells with minimal background fluorescence from the extracellular matrix. In fact, these operating principles translate into a 170-fold enhancement in brightness, relative to equivalent but isolated chromophoric components, and a 3-fold increase in contrast, relative to model but non-activatable fluorophores. Thus, our macromolecular probes might ultimately evolve into valuable analytical tools to highlight cancer cells with optimal signal-to-noise ratios in a diversity of biomedical applications.

  20. Monomer-coated very small superparamagnetic iron oxide particles as contrast medium for magnetic resonance imaging: preclinical in vivo characterization.

    PubMed

    Wagner, Susanne; Schnorr, Jorg; Pilgrimm, Herbert; Hamm, Bernd; Taupitz, Matthias

    2002-04-01

    Preclinical in-vivo characterization of a newly developed MR contrast medium consisting of very small superparamagnetic iron oxide particles (VSOP) coated with citrate (VSOP-C184). VSOP-C184 (core diameter: 4 nm; total diameter: 8.6 nm; relaxivities in water at 0.94 T (T1) 20.1 and (T2) 37.1 l/[mmol*sec]) was investigated to determine its pharmacokinetics, efficacy, acute single dose toxicity, repeated dose toxicity, and genotoxicity. The plasma elimination half-life at 0.045 mmol Fe/kg was 21.3 +/- 5.5 minutes in rats and 36.1 +/- 4.2 minutes in pigs, resulting in a T1-relaxation time of plasma of < 100 milliseconds for 30 minutes in pigs. The particles are mainly cleared via the phagocytosing system of the liver. MR angiography at a dose of 0.045 mmol Fe/kg shows an excellent depiction of the thoracic and abdominal vasculature in rats and of the coronary arteries in pigs. The LD50 in mice is > 17.9 mmol Fe/kg. A good tolerance and safety profile was found. The experiments indicate, that VSOP-C184 may be a well tolerated and safe contrast medium for MR imaging that can be effectively used for MR angiography including visualization of the coronary arteries.

  1. 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.

  2. 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

  3. Practical macromolecular cryocrystallography.

    PubMed

    Pflugrath, J W

    2015-06-01

    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.

  4. 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.

  5. Annealing macromolecular crystals.

    PubMed

    Hanson, B Leif; Bunick, Gerard J

    2007-01-01

    The process of crystal annealing has been used to improve the quality of diffraction from crystals that would otherwise be discarded for displaying unsatisfactory diffraction after flash cooling. Although techniques and protocols vary, macromolecular crystals are annealed by warming the flash-cooled crystal, then flash cooling it again. To apply macromolecular crystal annealing, a flash-cooled crystal displaying unacceptably high mosaicity or diffraction from ice is removed from the goniometer and immediately placed in cryoprotectant buffer. The crystal is incubated in the buffer at either room temperature or the temperature at which the crystal was grown. After about 3 min, the crystal is remounted in the loop and flash cooled. In situ annealing techniques, where the cold stream is diverted and the crystal allowed to warm on the loop prior to flash cooling, are variations of annealing that appears to work best when large solvent channels are not present in the crystal lattice or the solvent content of the crystal is relatively low.

  6. Comparison of single- and dual-tracer pharmacokinetic modeling of dynamic contrast-enhanced MRI data using low, medium, and high molecular weight contrast agents.

    PubMed

    Orth, Robert C; Bankson, James; Price, Roger; Jackson, Edward F

    2007-10-01

    Pharmacokinetic parameters corresponding to perfused microvascular volume determined from dynamic contrast-enhanced (DCE) MRI data were compared to immunohistochemical measures of microvascular density (MVD) and perfused microvascular density. DCE MRI data from human mammary tumors (MDA-MB-435) implanted in nude mice using low (Gd-DTPA, MW approximately equal 0.6 kDa), medium (Gadomer-17, MW(eff) approximately equal 35 kDa), and high (PG-Gd-DTPA, MW approximately equal 220 kDa) molecular weight contrast agents were analyzed with single- and dual-tracer pharmacokinetic models. MVD values were determined by two manual counting methods, "hot spot" and summed region of interest (SROI). Pharmacokinetic parameters determined using the single-tracer model (Gd-DTPA [n = 15] and Gadomer-17 [n = 13]) did not correlate with MVD measures using either manual counting method. For dual-tracer studies (Gadomer-17/Gd-DTPA [n = 15] and PG-Gd-DTPA/Gd-DTPA [n = 13]), pharmacokinetic parameters demonstrated a statistically significant correlation with MVD determined by the SROI method, but not the "hot spot" method. Ten mice successfully underwent intravital FITC-labeled lectin perfusion with the hemisphere of highest lectin labeling correlating with pharmacokinetic parameter values in 9 of 10 tumors (single-tracer Gd-DTPA [n = 2], single-tracer Gadomer-17 [n = 3], and dual-tracer Gadomer-17/Gd-DTPA [n = 5]). This study demonstrates that dual-tracer DCE MRI studies yield pharmacokinetic parameters that correlate with immunohistochemical measures of MVD.

  7. Intravenous contrast ultrasound examination using contrast-tuned imaging (CnTI) and the contrast medium SonoVue for discrimination between benign and malignant adnexal masses with solid components.

    PubMed

    Testa, A C; Timmerman, D; Van Belle, V; Fruscella, E; Van Holsbeke, C; Savelli, L; Ferrazzi, E; Leone, F P G; Marret, H; Tranquart, F; Exacoustos, C; Nazzaro, G; Bokor, D; Magri, F; Van Huffel, S; Ferrandina, G; Valentin, L

    2009-12-01

    To determine whether intravenous contrast ultrasound examination is superior to gray-scale or power Doppler ultrasound for discrimination between benign and malignant adnexal masses with complex ultrasound morphology. In an international multicenter study, 134 patients with an ovarian mass with solid components or a multilocular cyst with more than 10 cyst locules, underwent a standardized transvaginal ultrasound examination followed by contrast examination using the contrast-tuned imaging technique and intravenous injection of the contrast medium SonoVue(R). Time intensity curves were constructed, and peak intensity, area under the intensity curve, time to peak, sharpness and half wash-out time were calculated. The sensitivity and specificity with regard to malignancy were calculated and receiver-operating characteristics (ROC) curves were drawn for gray-scale, power Doppler and contrast variables and for pattern recognition (subjective assignment of a certainly benign, probably benign, uncertain or malignant diagnosis, using gray-scale and power Doppler ultrasound findings). The gold standard was the histological diagnosis of the surgically removed tumors. After exclusions (surgical removal of the mass > 3 months after the ultrasound examination, technical problems), 72 adnexal masses with solid components were used in our statistical analyses. The values for peak contrast signal intensity and area under the contrast signal intensity curve in malignant tumors were significantly higher than those in borderline tumors and benign tumors, while those for the benign and borderline tumors were similar. The area under the ROC curve of the best contrast variable with regard to diagnosing borderline or invasive malignancy (0.84) was larger than that of the best gray-scale (0.75) and power Doppler ultrasound variable (0.79) but smaller than that of pattern recognition (0.93). Findings on ultrasound contrast examination differed between benign and malignant tumors but there

  8. Myocardial rupture associated with bolus injection of contrast medium during computed tomographic study in a patient with acute myocardial infarction: a rare but lethal complication.

    PubMed

    Lai, Vincent; Hau, K C; Lau, H Y; Chan, W C

    2009-08-01

    Well-documented potential cardiovascular complications associated with the use of contrast media include bradycardia, hypotension, arrhythmia, and conduction disturbances. Rupture of the myocardium after acute myocardial infarction is a known cause of death, but has yet to be recognised as a potential complication of the use of a bolus injection of contrast medium. On the contrary, contrast-enhanced computed tomographic studies have been performed widely for the diagnosis and evaluation of myocardial infarction. We report a case of complicated myocardial rupture after a single bolus injection of contrast medium during a computed tomographic study in an elderly woman with acute myocardial infarction, which led to cardiac tamponade and rapid death. Although rare, this should alert us to the need for cautious use of contrast medium in patients with acute myocardial infarction.

  9. 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.

  10. Clinical analysis of contributors to the delayed gallbladder opacification following the use of water-soluble contrast medium

    PubMed Central

    Ku, Ming-Chang; Kok, Victor C; Lee, Ming-Yung; Hsu, Soa-Min; Lee, Pei-Yu; Chang, Che-Wei; Tyan, Yeu-Sheng; Juan, Chi-Wen

    2016-01-01

    Objectives Gallbladder opacification (GBO) on computed tomography (CT) imaging may obscure certain pathological or emergent conditions in the gallbladder, such as neoplasms, stones, and hemorrhagic cholecystitis. This study aimed to investigate the clinical contributing factors that could predict the presence of delayed GBO determined by CT. Methods This study retrospectively evaluated 243 consecutive patients who received enhanced CT or intravenous pyelography imaging and then underwent abdominal CT imaging within 5 days. According to the interval between imaging, the patients were divided into group A (1 day), group B (2 or 3 days), and group C (4 or 5 days). Three radiologists evaluated CT images to determine GBO. Fisher’s exact test and multivariate backward stepwise elimination logistic regression were performed. Results Positive GBO was significantly associated with the interval between imaging studies, contrast type, contrast volume, renal function, and hypertransaminasemia (P<0.05). Multivariate backward stepwise elimination logistic regression analysis of the three groups identified contrast type and hypertransaminasemia as independent predictors of GBO in group B patients (odds ratio [OR], 13.52, 95% confidence interval [CI], 1.72–106.38 and OR, 3.43, 95% CI, 1.31–8.98, respectively; P<0.05). Hypertransaminasemia was the only independent predictor of GBO in group C patients with an OR of 7.2 (95% CI, 1.62–31.73). Hypertransaminasemia was noted in three patients (100%) who initially underwent imaging 5 days prior to GBO. Conclusion Delayed GBO on CT imaging may be associated with laboratory hypertransaminasemia, particularly in patients receiving contrast medium over a period of ≥4 days. A detailed clinical history, physical examination, and further workup are of paramount importance for investigating the underlying cause behind the hypertransaminasemia. PMID:27660453

  11. Continuum of Vasodilator Stress From Rest to Contrast Medium to Adenosine Hyperemia for Fractional Flow Reserve Assessment.

    PubMed

    Johnson, Nils P; Jeremias, Allen; Zimmermann, Frederik M; Adjedj, Julien; Witt, Nils; Hennigan, Barry; Koo, Bon-Kwon; Maehara, Akiko; Matsumura, Mitsuaki; Barbato, Emanuele; Esposito, Giovanni; Trimarco, Bruno; Rioufol, Gilles; Park, Seung-Jung; Yang, Hyoung-Mo; Baptista, Sérgio B; Chrysant, George S; Leone, Antonio M; Berry, Colin; De Bruyne, Bernard; Gould, K Lance; Kirkeeide, Richard L; Oldroyd, Keith G; Pijls, Nico H J; Fearon, William F

    2016-04-25

    This study compared the diagnostic performance with adenosine-derived fractional flow reserve (FFR) ≤0.8 of contrast-based FFR (cFFR), resting distal pressure (Pd)/aortic pressure (Pa), and the instantaneous wave-free ratio (iFR). FFR objectively identifies lesions that benefit from medical therapy versus revascularization. However, FFR requires maximal vasodilation, usually achieved with adenosine. Radiographic contrast injection causes submaximal coronary hyperemia. Therefore, intracoronary contrast could provide an easy and inexpensive tool for predicting FFR. We recruited patients undergoing routine FFR assessment and made paired, repeated measurements of all physiology metrics (Pd/Pa, iFR, cFFR, and FFR). Contrast medium and dose were per local practice, as was the dose of intracoronary adenosine. Operators were encouraged to perform both intracoronary and intravenous adenosine assessments and a final drift check to assess wire calibration. A central core lab analyzed blinded pressure tracings in a standardized fashion. A total of 763 subjects were enrolled from 12 international centers. Contrast volume was 8 ± 2 ml per measurement, and 8 different contrast media were used. Repeated measurements of each metric showed a bias <0.005, but a lower SD (less variability) for cFFR than resting indexes. Although Pd/Pa and iFR demonstrated equivalent performance against FFR ≤0.8 (78.5% vs. 79.9% accuracy; p = 0.78; area under the receiver-operating characteristic curve: 0.875 vs. 0.881; p = 0.35), cFFR improved both metrics (85.8% accuracy and 0.930 area; p < 0.001 for each) with an optimal binary threshold of 0.83. A hybrid decision-making strategy using cFFR required adenosine less often than when based on either Pd/Pa or iFR. cFFR provides diagnostic performance superior to that of Pd/Pa or iFR for predicting FFR. For clinical scenarios or health care systems in which adenosine is contraindicated or prohibitively expensive, cFFR offers a universal technique to

  12. 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.

  13. Investigations into the environmental fate and effects of iopromide (ultravist), a widely used iodinated X-ray contrast medium.

    PubMed

    Steger-Hartmann, Thomas; Länge, Reinhard; Schweinfurth, Hermann; Tschampel, Matthias; Rehmann, Irmgard

    2002-01-01

    lodinated X-ray contrast media are pharmaceuticals which are biologically inert and metabolically stable during their passage through the body and are excreted almost completely within a day into waste water. They are not readily biodegradable. However, in a test system simulating sewage treatment, we were able to show that the model compound iopromide (N,N'-bis(2,3-dihydroxypropyl)-2,4,6-triiodo-5-methoxyacetylamino-N-methyliso-phthalamide) was amenable to primary degradation. The resulting degradation product (5-amino-N'N'-bis(2,3-dihydroxypropyl)-2,4,6-triiodo-N-methyliso-phthalamide) showed a faster photolysis than the parent compound. Additionally this product was further degraded in a test system simulating surface water conditions. Short-term toxicity of the primary degradation product was low, i.e. no effects on any of various aquatic species could be found even at concentrations of 1 gl(-1). Additionally no chronic toxicity of the degradation product was observed in an early-life stage test with zebrafish at the highest tested concentration of 100mgl(-1). Based on the results from model systems a degradation pathway for iopromide is postulated. Though further work showing the transferability of the laboratory results to environmental conditions is necessary the presently available information on the environmental fate and effects of iopromide and its degradation products do not provide evidence of a risk for aquatic life caused by the introduction of this contrast medium into waste water.

  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. Assessment of errors caused by X-ray scatter and use of contrast medium when using CT-based attenuation correction in PET.

    PubMed

    Ay, Mohammad Reza; Zaidi, Habib

    2006-11-01

    Quantitative image reconstruction in positron emission tomography (PET) requires an accurate attenuation map of the object under study for the purpose of attenuation correction. Current dual-modality PET/CT systems offer significant advantages over stand-alone PET, including decreased overall scanning time and increased accuracy in lesion localisation and detectability. However, the contamination of CT data with scattered radiation and misclassification of contrast medium with high-density bone in CT-based attenuation correction (CTAC) are known to generate artefacts in the attenuation map and thus the resulting PET images. The purpose of this work was to quantitatively measure the impact of scattered radiation and contrast medium on the accuracy of CTAC. Our recently developed MCNP4C-based Monte Carlo X-ray CT simulator for modelling both fan- and cone-beam CT scanners and the Eidolon dedicated 3D PET Monte Carlo simulator were used to generate realigned PET/CT data sets. The impact of X-ray scattered radiation on the accuracy of CTAC was investigated through simulation of a uniform cylindrical water phantom for both a commercial fan-beam multi-slice and a prototype cone-beam flat panel detector-based CT scanner. The influence of contrast medium was studied by simulation of a cylindrical phantom containing different concentrations of contrast medium. Moreover, an experimental study using an anthropomorphic striatal phantom was conducted for quantitative evaluation of errors arising from the presence of contrast medium by calculating the apparent recovery coefficient (ARC) in the presence of different concentrations of contrast medium. The analysis of attenuation correction factors (ACFs) for the simulated cylindrical water phantom in both fan- and cone-beam CT scanners showed that the contamination of CT data with scattered radiation in the absence of scatter removal causes underestimation of the true ACFs, namely by 7.3% and 28.2% in the centre for the two

  16. Potentials and limitations of low-concentration contrast medium (150 mg iodine/ml) in CT pulmonary angiography.

    PubMed

    Radon, M R; Kaduthodil, M J; Jagdish, J; Matthews, S; Hill, C; Bull, M J; Morcos, S K

    2011-01-01

    To assess the feasibility of producing diagnostic multidetector computed tomography (MDCT) pulmonary angiography with low iodine concentration contrast media (150 mg iodine/ml) in patients with suspected acute pulmonary embolism. Ninety-five randomized patients underwent MDCT (64 row) pulmonary angiography with 100ml iopromide either at low concentration (LC) of 150 mg iodine/ml (n=45) or high concentration (HC) of 300 mg iodine/ml (n=50), delivered at the rate of 5 ml/s via a power injector. Two experienced radiologists, blinded to the concentration used, subjectively assessed the diagnostic quality and confidence using a four-point scale [1=poor (not diagnostic), 2=satisfactory, 3=good, 4=excellent]. Attenuation values (in HU) were measured in the main proximal branches of the pulmonary arteries. The median diagnostic quality score for both observers was 3.5 (interquartile range 3-4) in the HC group and 2.5 (interquartile range 1.5-3) in the LC group (p<0.01). The median diagnostic confidence score for both observers was 4 (interquartile range 3-4) in the HC group and 3 (interquartile range 1.5-4) in the LC group (p<0.01). Both observers rated examinations as diagnostic in 69% of cases in the LC group, compared with 96% of cases in the HC group. Good interobserver agreement was found in both groups (K value 0.72 in the LC group and 0.73 in the HC). Obesity, poor scan timing, and dilution by venous return of non-opacified blood were the main reasons for a reduction in diagnostic quality of examinations in the LC group. Despite a 50% reduction of contrast medium dose in comparison to the standard technique, 150 mg iodine/ml can produce diagnostic MDCT pulmonary angiogram studies in the absence of obesity or high cardiac output and hyper-dynamic pulmonary circulation. Reducing the dose of contrast media would minimize the risk of contrast nephropathy in patients at risk of this complication, particularly those suffering from congestive heart failure in whom

  17. Effect of the surface potential of the hemodialysis membrane and the electrical charge of the gadolinium contrast medium on dialyzability.

    PubMed

    Okada, Susumu; Inoue, Kohei; Kijima, Tetsuji; Katagiri, Kiwayo; Kumazaki, Tatsuo

    2003-02-01

    To search for methods of improving the excretion of injected gadolinium contrast medium (GdCM) in hemodialysis (HD) patients, we investigated the effect of the surface potential of HD membranes and the electrical charge of GdCM on the dialyzability of GdCM. Ionic (Gd-DTPA) or non-ionic (Gd-DO3A) GdCM solutions were dialyzed using a clinical HD unit. Two types of HD membranes, AN69 with a surface potential and PMMA without, were used. GdCM clearance was then calculated. Gd-DTPA clearance was significantly higher for PMMA membranes than for AN69 membranes. Gd-DO3A clearance was slightly higher for AN69 membranes than for PMMA membranes. The difference in Gd-DTPA and Gd-DO3A clearance values was not significant when PMMA membranes were used. These data indicate that non-ionic GdCM is preferable to ionic GdCM in patients receiving dialysis through an electrically positive membrane. Either ionic or non-ionic GdCM can be used when a normal dialysis membrane is being used.

  18. 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.

  19. 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

  20. Evaluation of the dark-medium objective lens in counting asbestos fibers by phase-contrast microscopy.

    PubMed

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

    2015-06-01

    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 the

  1. 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.

  2. Solvent isotope effect on macromolecular dynamics in E. coli.

    PubMed

    Jasnin, Marion; Tehei, Moeava; Moulin, Martine; Haertlein, Michael; Zaccai, Giuseppe

    2008-06-01

    Elastic incoherent neutron scattering was used to explore solvent isotope effects on average macromolecular dynamics in vivo. Measurements were performed on living E. coli bacteria containing H2O and D2O, respectively, close to physiological conditions of temperature. Global macromolecular flexibility, expressed as mean square fluctuation (MSF) values, and structural resilience in a free energy potential, expressed as a mean effective force constant, [Symbol: see text]k'[Symbol: see text], were extracted in the two solvent conditions. They referred to the average contribution of all macromolecules inside the cell, mostly dominated by the internal motions of the protein fraction. Flexibility and resilience were both found to be smaller in D2O than in H2O. A difference was expected because the driving forces behind macromolecular stabilization and dynamics are different in H2O and D2O. In D2O, the hydrophobic effect is known to be stronger than in H2O: it favours the burial of non-polar surfaces as well as their van der Waals' packing in the macromolecule cores. This may lead to the observed smaller MSF values. In contrast, in H2O, macromolecules would present more water-exposed surfaces, which would give rise to larger MSF values, in particular at the macromolecular surface. The smaller [Symbol: see text]k'[Symbol: see text] value suggested a larger entropy content in the D2O case due to increased sampling of macromolecular conformational substates.

  3. Transmucosal macromolecular drug delivery.

    PubMed

    Prego, C; García, M; Torres, D; Alonso, M J

    2005-01-03

    Mucosal surfaces are the most common and convenient routes for delivering drugs to the body. However, macromolecular drugs such as peptides and proteins are unable to overcome the mucosal barriers and/or are degraded before reaching the blood stream. Among the approaches explored so far in order to optimize the transport of these macromolecules across mucosal barriers, the use of nanoparticulate carriers represents a challenging but promising strategy. The present paper aims to compare the characteristics and potential of nanostructures based on the mucoadhesive polysaccharide chitosan (CS). These are CS nanoparticles, CS-coated oil nanodroplets (nanocapsules) and CS-coated lipid nanoparticles. The characteristics and behavior of CS nanoparticles and CS-coated lipid nanoparticles already reported [A. Vila, A. Sanchez, M. Tobio, P. Calvo, M.J. Alonso, Design of biodegradable particles for protein delivery, J. Control. Rel. 78 (2002) 15-24; R. Fernandez-Urrusuno, P. Calvo, C. Remunan-Lopez, J.L. Vila-Jato, M.J. Alonso, Enhancement of nasal absorption of insulin using chitosan nanoparticles, Pharm. Res. 16 (1999) 1576-1581; M. Garcia-Fuentes, D. Torres, M.J. Alonso, New surface-modified lipid nanoparticles as delivery vehicles for salmon calcitonin (submitted for publication).] are compared with those of CS nanocapsules originally reported here. The three types of systems have a size in the nanometer range and a positive zeta potential that was attributed to the presence of CS on their surface. They showed an important capacity for the association of peptides such as insulin, salmon calcitonin and proteins, such as tetanus toxoid. Their mechanism of interaction with epithelia was investigated using the Caco-2 model cell line. The results showed that CS-coated systems caused a concentration-dependent reduction in the transepithelial resistance of the cell monolayer. Moreover, within the range of concentrations investigated, these systems were internalized in the

  4. Intravenous injection of high and medium concentrations of computed tomography contrast media and related heat sensation, local pain, and adverse reactions.

    PubMed

    Masui, Takayuki; Katayama, Motoyuki; Kobayashi, Shigeru; Sakahara, Harumi

    2005-01-01

    To evaluate the incidence of acute adverse reactions and degrees of heat sensation and local pain after intravenous injection of high and medium concentrations of iodinated contrast medium for computed tomography (CT). A prospective study was performed involving 729 patients who underwent contrast CT scans. High-concentration (370 mgI/mL) and medium-concentration (300 mgI/mL) iodinated contrast medium was assigned to 342 patients (group H, aged 20-90 years, mean = 59.8 years) and to 387 patients (group M, aged 20-95 years, mean = 61.7 years), respectively. An injection rate of contrast medium (1, 2, or 4 mL/s) at a base volume of 2 mL/kg of body weight was selected according to the protocols for the evaluated diseases and regions. Each patient was assessed for heat sensation and local pain at the injection site using a visual analog scale (ranging from none for 0 to severe for 10). Acute adverse reactions were recorded when they occurred. There were no significant differences in patient background factors, including age, sex, history of prior adverse reactions, and allergies, between the 2 groups. The score for heat sensation was significantly higher in group H than in group M (4.46 +/- 2.44 vs. 3.44 +/- 2.45; P < 0.0001 for heat sensation). The data did not show a higher incidence of adverse reactions in group H than in group M (5 [1.46%] of 342 patients vs. 2 [0.52%] of 387 patients; P = 0.26) or a higher score for local pain in group H than in group M (0.98 +/- 1.70 vs. 0.88 +/- 1.49; P = 0.66), respectively. High and medium concentrations of iodinated contrast medium can be used for CT study with comparable safety profiles even though heat sensation produced by the high-concentration CM is greater than that produced by the medium-concentration CM.

  5. 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

  6. Rotation-Induced Macromolecular Spooling of DNA

    NASA Astrophysics Data System (ADS)

    Shendruk, Tyler N.; Sean, David; Berard, Daniel J.; Wolf, Julian; Dragoman, Justin; Battat, Sophie; Slater, Gary W.; Leslie, Sabrina R.

    2017-07-01

    Genetic information is stored in a linear sequence of base pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we discover that rotation-induced macromolecular spooling of DNA around a rotating microwire can monotonically order genomic bases, overcoming this challenge. We use single-molecule fluorescence microscopy to directly visualize long DNA strands deforming and elongating in shear flow near a rotating microwire, in agreement with numerical simulations. While untethered DNA is observed to elongate substantially, in agreement with our theory and numerical simulations, strong extension of DNA becomes possible by introducing tethering. For the case of tethered polymers, we show that increasing the rotation rate can deterministically spool a substantial portion of the chain into a fully stretched, single-file conformation. When applied to DNA, the fraction of genetic information sequentially ordered on the microwire surface will increase with the contour length, despite the increased entropy. This ability to handle long strands of DNA is in contrast to modern DNA sample preparation technologies for sequencing and mapping, which are typically restricted to comparatively short strands, resulting in challenges in reconstructing the genome. Thus, in addition to discovering new rotation-induced macromolecular dynamics, this work inspires new approaches to handling genomic-length DNA strands.

  7. 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

  8. [CT evaluation of extravascular perfusion of contrast medium and its potential to a new method of diagnosis: an experimental study using macro, micro-molecular contrast media].

    PubMed

    Sako, M; Sugimoto, K; Matsumoto, S; Hirota, S; Fujita, Y; Hasegawa, Y; Kuwata, Y; Tomita, M; Murakami, T; Kono, M

    1994-03-25

    To evaluate the dynamics of extravascular perfusion, dynamic CT with two different molecular sized contrast media was performed on VX2 tumor of rabbit. The first dynamic CT was performed with a bolus injection of iopamidol (IP:120 mgI/ml, 5 ml). After ascertaining that the tumor attenuation had returned to the pre-contrast level, the second dynamic CT was performed on the same slice with bolus injection of iodoethylated starch (IES:120 mgI/ml). The time-density (T-D) curves of the same tumor area on the images obtained by two contrast media were compared. The T-D curve with IP showed definitely higher level than that with IES. This occurrence can be explained that IP, 13 A in size, has higher permeability distributing not only in the intravascular space, but also into the extravascular space. On the other hand, IES, 200 A in size, will stay mostly in the intravascular space. From this, we consider that the attenuation difference between the two curves will be an indicator for the dynamics of extravascular perfusion, suggesting to become a new method for CT diagnosis.

  9. [Significance of a nonionic renographic contrast medium (Iopamidol 300) in the roentgen diagnosis of the kidneys and urinary tract in children].

    PubMed

    Schneider, K; Fendel, H

    1984-10-01

    The ionic contrast media used so far have been associated with considerable risks in infants and children. The high osmolality of these media did not always permit a dosage sufficient for kidney imaging in the nephrographic and in the pyelographic phase. The new non-ionic contrast media have largely reduced these risks so that their general application in infants and young children should be recommended. Intravenous urographies using the non-ionic contrast medium Iopamidol 300 (Solutrast 300) were performed in 195 children aged one day to 12 years. Good to superior urograms were obtained in 85% of the investigations. No adverse reactions caused by the osmolality of the contrast media had been observed in spite of the relative high dosage. As a result of their low osmolality and non-ionic property a safe application of high doses was possible.

  10. Medium-dependent control of the bacterial growth rate.

    PubMed

    Ehrenberg, Måns; Bremer, Hans; Dennis, Patrick P

    2013-04-01

    By combining results from previous studies of nutritional up-shifts we here re-investigate how bacteria adapt to different nutritional environments by adjusting their macromolecular composition for optimal growth. We demonstrate that, in contrast to a commonly held view the macromolecular composition of bacteria does not depend on the growth rate as an independent variable, but on three factors: (i) the genetic background (i.e. the strain used), (ii) the physiological history of the bacteria used for inoculation of a given growth medium, and (iii) the kind of nutrients in the growth medium. These factors determine the ribosome concentration and the average rate of protein synthesis per ribosome, and thus the growth rate. Immediately after a nutritional up-shift, the average number of ribosomes in the bacterial population increases exponentially with time at a rate which eventually is attained as the final post-shift growth rate of all cell components. After a nutritional up-shift from one minimal medium to another minimal medium of higher nutritional quality, ribosome and RNA polymerase syntheses are co-regulated and immediately increase by the same factor equal to the increase in the final growth rate. However, after an up-shift from a minimal medium to a medium containing all 20 amino acids, RNA polymerase and ribosome syntheses are no longer coregulated; a smaller rate of synthesis of RNA polymerase is compensated by a gradual increase in the fraction of free RNA polymerase, possibly due to a gradual saturation of mRNA promoters. We have also analyzed data from a recent publication, in which it was concluded that the macromolecular composition in terms of RNA/protein and RNA/DNA ratios is solely determined by the effector molecule ppGpp. Our analysis indicates that this is true only in special cases and that, in general, medium adaptation also depends on factors other than ppGpp.

  11. Effects of Intra-Arterial and Intravenous Iso-Osmolar Contrast Medium (Iodixanol) on the Risk of Contrast-Induced Acute Kidney Injury: A Meta-Analysis

    PubMed Central

    McCullough, Peter A.; Brown, Jeremiah R.

    2011-01-01

    Background The iso-osmolar contrast agent iodixanol may be associated with a lower incidence of contrast-induced acute kidney injury (CI-AKI) than low-osmolar contrast media (LOCM), but previous meta-analyses have yielded mixed results. Objectives: To compare the incidence of CI-AKI between iodixanol and LOCM. Methods Studies were identified from literature searches to December 2009, clinicaltrials.gov, and conference abstracts from the past 2 years including 2010. Only prospective, randomized comparisons between iodixanol and LOCM with CI-AKI [increase in serum creatinine (sCr) ≥0.5 mg/dl or ≥25% from baseline, as defined in the trial] as a primary and/or secondary endpoint and a Jadad score ≥2 were included. A random-effects model was used to obtain pooled relative risks (RRs) for CI-AKI in analyses based on route of administration [intra-arterial (IA) or intravenous (IV)], definition of CI-AKI, and timing of sCr measurements. Results 145 potential articles were identified, of which 25 were included in the meta-analysis. Following IA administration (n = 19), the RR for CI-AKI (≥0.5 mg/dl definition) with iodixanol, compared with LOCM, was 0.462 [95% confidence interval (CI): 0.272–0.786, p = 0.004, 15 studies]. Using the ≥25% definition, there was a lower incidence of CI-AKI with iodixanol versus LOCM, but the difference was not statistically significant (RR: 0.577, 95% CI: 0.297–1.12, p = 0.104, 11 studies). In the IV trials, there was no significant difference in the incidence of CI-AKI using either definition (≥0.5 mg/dl definition: RR: 0.967, 95% CI: 0.188–4.972, p = 0.968, 3 trials; ≥25% definition: RR: 0.656, 95% CI: 0.316–1.360, p = 0.257, 4 trials). Conclusions IA but not IV administration of iodixanol is associated with a significantly lower risk of CI-AKI than LOCM. PMID:22164156

  12. Pedal angiography in peripheral arterial occlusive disease: first-pass i.v. contrast-enhanced MR angiography with blood pool contrast medium versus intraarterial digital subtraction angiography.

    PubMed

    Kos, Sebastian; Reisinger, Clemens; Aschwanden, Markus; Bongartz, Georg M; Jacob, Augustinus L; Bilecen, Deniz

    2009-03-01

    The purpose of this study was to prospectively evaluate first-pass i.v. gadofosveset-enhanced MR angiography in patients with peripheral arterial occlusive disease for visualization of the pedal arteries and stenosis or occlusion of those arteries with intraarterial digital subtraction angiography as the reference standard. Twenty patients with peripheral arterial occlusive disease (nine women, 11 men; age-range 58-83 years) were prospectively enrolled. Gadofosveset first-pass contrast-enhanced MR angiography was performed with a 1.5-T system, a dedicated foot coil, and cuff compression to the calf. Arterial segments were assessed for degree of arterial stenosis, arterial visibility, diagnostic utility, and venous contamination. Detection of vessel stenosis or occlusion was evaluated in comparison with findings at digital subtraction angiography. The unpaired Student's t test was used to test arterial visibility with the two techniques. First-pass MR angiography with gadofosveset had good diagnostic utility in 83.9% of all segments and no venous contamination in 96.8% of all segments. There was no difference between the performance of intraarterial digital subtraction angiography and that of i.v. contrast-enhanced MR angiography in arterial visibility overall (p = 0.245) or in subgroup analysis of surgical arterial bypass targets (p = 0.202). The overall sensitivity, specificity, and accuracy of i.v. gadofosveset-enhanced MR angiography for characterization of clinically significant stenosis and occlusion were 91.4%, 96.1%, and 93.9%. In the subgroup analysis, the sensitivity, specificity, and accuracy were 85.5%, 96.5%, and 92.1%. Gadofosveset-enhanced MR angiography of the pedal arteries in patients with peripheral arterial occlusive disease has arterial visibility equal to that of digital subtraction angiography and facilitates depiction of clinically significant stenosis and occlusion.

  13. The influence of buoyancy contrasts on miscible source sink flows in a porous medium with thermal inertia

    NASA Astrophysics Data System (ADS)

    Nigam, Mats S.; Woods, Andrew W.

    We investigate the displacement of one fluid through an inclined porous sheet by the injection of a second fluid of different density. Using numerical simulation we explore the role of the density contrast between the injected and the reservoir fluid on the displacement process, in the cases where the density contrast originates from either compositional contrasts and/or temperature contrasts between the fluids. In the case where the density contrast originates from compositional differences between the fluids, the density front moves with the fluid fluid front, and gravity may accelerate or decelerate the time for the injected liquid to reach the sink. In the case where the density contrast originates from a temperature contrast between the injected fluid and the reservoir fluid, then the density front follows the thermal front. Therefore, owing to thermal inertia, it lags behind the fluid fluid front. This has a quantitative impact on the time required for the injected liquid to reach the sink. If there are both thermal and compositional contrasts between the injected and reservoir fluid, then the thermal and compositional fronts become decoupled in space. The two fronts may lead to complementary or opposing density changes; the different cases lead to vastly different patterns of displacement and time at which the injected liquid reaches the sink, even if the net change in density between reservoir and the injected fluid is the same. We discuss the implications of these phenomena for water injection in sub-surface hydrocarbon and geothermal reservoirs. In an Appendix, we note how a viscosity across both the thermal front and the fluid fluid front can also lead to a rich spectrum of flow patterns, especially if one front is stable and the other unstable to viscous instability.

  14. Risk of contrast-medium-induced nephropathy in high-risk patients undergoing MDCT--a pooled analysis of two randomized trials.

    PubMed

    Thomsen, Henrik S; Morcos, Sameh K

    2009-04-01

    The incidence of contrast-medium-induced nephropathy (CIN) following intravenous (IV) CM administration of contrast media to renally impaired patients undergoing multidetector computed tomography (MDCT) is not well characterized. Our objective was to investigate the incidence of CIN in patients with glomerular filtration rate (GFR) <60 ml/min undergoing contrast-enhanced MDCT examinations and to compare the rates of CIN following the IV administration of low-osmolar contrast media (LOCM, iopamidol and iomeprol) and an iso-osmolar contrast medium (IOCM, iodixanol). A total of 301 adult patients with moderate-to-severe renal failure received a similar IV contrast dose (40 gI). Serum creatinine (SCr) was measured at screening, baseline and 48-72 +/- 6 h after the MDCT examination. Primary CIN outcome was an increase in SCr >or=0.5 mg/dl (>or=44.2 micromol/l) from baseline. The CIN rates were 2.3% in the total population, 0.6% when GFR >40 ml/min, 4.6% when GFR <40 ml/min and 7.8% in patients with GFR <30 ml/min. The incidence of CIN was significantly higher after iodixanol than after LOCM (seven patients, 4.7% following IOCM, no CIN cases following the LOCM; p = 0.007). Significant differences in favor of the LOCM were also observed in patients with GFR <40 ml/min and GFR <30 ml/min. Following the IV administration of nonionic contrast agents in patients with moderate-to-severe renal insufficiency, the risk of significant CIN seems to be low. The IOCM iodixanol caused a higher rate of CIN than the LOCM iopamidol and iomeprol, especially in high-risk patients. Differences in osmolality between these LOCM and iodixanol do not play a role in the genesis of CIN.

  15. Radiation damage in macromolecular cryocrystallography.

    PubMed

    Ravelli, Raimond B G; Garman, Elspeth F

    2006-10-01

    X-ray radiation damage to cryocooled ( approximately 100 K) macromolecular crystals has emerged as a general problem, especially since the advent of third generation synchrotron undulator sources. Interest in understanding the physical and chemical phenomena behind the observed effects is growing rapidly. The specific structural damage seen in electron density maps has to be accounted for when studying intermediates, and can sometimes be related to biological function. Radiation damage induces non-isomorphism, thus hampering traditional phasing methods. However, specific damage can also be used to obtain phases. With an increased knowledge of expected crystal lifetime, beamline characteristics and types of damage, macromolecular crystallographers might soon be able to account for radiation damage in data collection, processing and phasing.

  16. Effect of low-osmolar contrast medium iopromide and iso-osmolar iodixanol on DNA fragmentation in renal tubular cell culture.

    PubMed

    Ludwig, Ulla; Connemann, Julia; Keller, Frieder

    2013-12-01

    Intravascular administration of iodinated contrast media continues to be a common cause of hospital-acquired acute kidney injury. Accumulating evidence suggests that radiocontrast agent-induced nephrotoxicity is associated with increased oxidative stress, which leads to renal tissue damage with DNA fragmentation. We therefore tested whether an iso-osmolar contrast medium (iodixanol) causes less oxidative DNA damage to renal tubular cells than a low-osmolar contrast medium (iopromide). HK-2 cells (human proximal renal tubular cell line) were incubated at different time points (10 min-2 h) with increasing concentrations (20-120 mg/ml iodine) of iodixanol or of iopromide. Oxidative DNA damage to renal tubular cells was measured by alkaline comet assay (single-cell gel electrophoresis). Both iso- and low-osmolar contrast agents induced time- and concentration-dependent DNA fragmentation. DNA fragmentation was maximal at 2 h with 120 mg/ml iodine for iopromide (32 ± 27 tail moments) and iodixanol (46 ± 41 tail moments); both were significantly different from the control value with 3.15 ± 1.6 tail moments (Student's t test; p < 0.001). After 1 and 2 h and for all concentrations, iodixanol produced significantly higher DNA fragmentation than iopromide (ANOVA for 1 h p = 0.039 and 2 h p = 0.025, respectively). We were able to demonstrate for the first time that an iso-osmolar contrast medium induced even greater oxidative stress and DNA damage than a low-osmolar agent in HK-2 cells. This could provide an explanation for the nephrotoxicity that also is observed with iodixanol in clinical practice.

  17. Nonlinear image blending for dual-energy MDCT of the abdomen: can image quality be preserved if the contrast medium dose is reduced?

    PubMed

    Mileto, Achille; Ramirez-Giraldo, Juan Carlos; Marin, Daniele; Alfaro-Cordoba, Marcela; Eusemann, Christian D; Scribano, Emanuele; Blandino, Alfredo; Mazziotti, Silvio; Ascenti, Giorgio

    2014-10-01

    The objective of this study was to compare the image quality of a dual-energy nonlinear image blending technique at reduced load of contrast medium with a simulated 120-kVp linear blending technique at a full dose during portal venous phase MDCT of the abdomen. Forty-five patients (25 men, 20 women; mean age, 65.6 ± 9.7 [SD] years; mean body weight, 74.9 ± 12.4 kg) underwent contrast-enhanced single-phase dual-energy CT of the abdomen by a random assignment to one of three different contrast medium (iomeprol 400) dose injection protocols: 1.3, 1.0, or 0.65 mL/kg of body weight. The contrast-to-noise ratio (CNR) and noise at the portal vein, liver, aorta, and kidney were compared among the different datasets using the ANOVA. Three readers qualitatively assessed all datasets in a blinded and independent fashion. Nonlinear blended images at a 25% reduced dose allowed a significant improvement in CNR (p < 0.05 for all comparisons), compared with simulated 120-kVp linear blended images at a full dose. No statistically significant difference existed in CNR and noise between the nonlinear blended images at a 50% reduced dose and the simulated 120-kVp linear blended images at a full dose. Nonlinear blended images at a 50% reduced dose were considered in all cases to have acceptable image quality. The dual-energy nonlinear image blending technique allows reducing the dose of contrast medium up to 50% during portal venous phase imaging of the abdomen while preserving image quality.

  18. Influence of osmolarity of contrast medium and saline flush on computed tomography angiography: comparison of monomeric and dimeric iodinated contrast media with different iodine concentrations at an identical iodine delivery rate.

    PubMed

    Kishimoto, Miori; Doi, Shoko; Shimizu, Junichiro; Lee, Ki-Ja; Iwasaki, Toshiroh; Miyake, Yoh-Ichi; Yamada, Kazutaka

    2010-10-01

    To evaluate the influence of osmolarity of iodinated contrast media and saline flush on the contrast effect in thoracic computed tomography angiography (CTA) at an identical iodine delivery rate (IDR). Seven beagles were used in a cross-over experiment. The contrast media used were iohexol 350 mgI/ml (IOH350; osmolarity 844 mmol/kg) and iodixanol 320 mgI/ml (IDX320; osmolarity 290 mmol/kg). Each contrast medium was administered to groups with and without saline flush at 40.0 mgI/kg/s for all experiments. Dynamic CT scanning was performed at the ninth thoracic vertebra level. The peak value, area under the curve (AUC), and time to peak (TTP) were calculated from the time attenuation curves of the pulmonary artery and aorta. There was no significant difference between IOH350 and IDX320 with or without saline flush in the peak values for the pulmonary artery and aorta. AUC was significantly higher in groups with saline flush for both contrast media and arteries (p<0.05) with no significant difference between contrast media. TTP was significantly longer in groups with saline flush than without saline flush for both contrast media and arteries (p<0.05), with no significant difference between contrast media. There were no significant differences in the contrast effects of monomeric IOH350 and dimeric IDX320 in thoracic CTA when used at an identical IDR. Moreover, saline flush prolonged the peak duration at 600 mgI/kg. Copyright © 2009 Elsevier Ireland Ltd. All rights reserved.

  19. Advantages of T2 Weighted Three Dimensional and T1 Weighted Three Dimensional Contrast Medium Enhanced Magnetic Resonance Urography in Examination of the Child Population

    PubMed Central

    Sehic, Adnan; Julardzija, Fuad; Vegar-Zubovic, Sandra; Sefic-Pasic, Irmina

    2017-01-01

    Aim: The aim of this study is to prove the advantages of combined use of T2 weighted three dimensional (T2 W 3D) and T1 weighted three dimensional contrast medium enhanced (T1 W 3D CE) magnetic resonance (MR) urography in displaying urinary tract in child population. Material and methods: Total of 120 patients were included in the study, 71 (59%) male patients and 49 (41%) female patients. The study was conducted on the Radiology clinic, University of Sarajevo Clinical Center, during the period from February to November 2016. Patients were examined on the 1.5T and 3T MRI, with standard protocol which includes T2 W 3D and T1 W 3D contrast medium enhanced MR urography. In the post procesing quantitative measurement of signal intensity and evaluation of the display quality in the area of renal pelvis, middle of ureter and the mouth of the ureter were done. Measurement was concluded on Syngo software B13. Results: Analyzing the acquired data and statistically processing them we got results which have shown higher signal intensity of measured structures on T1 W 3D contrast medium enhanced MR urography on the level p<0.01 and p<0.05 compared to T2 W 3D MR urography in patients that had normal dynamics of contrast medium secretion. However, in kidneys with decreased function, T2 W 3D MR urography provided higher signal intensity and better display compared to T1 W 3D contrast medium enhanced MR urography on the level p<0.05 and p<0.01. Conclusion: T2 W3D MR urography is useful in imaging nonfunctional kidney as well as in patients prone to allergic reactions, where as T1 W3D CE MR urography is at an advantage over T2 W 3D MR urography in imaging the kidney functionality, kidney dynamics measurement, it provides higher MRI signal intensity required for clear 3D reconstructions. PMID:28484293

  20. Can low-dose CT with iterative reconstruction reduce both the radiation dose and the amount of iodine contrast medium in a dynamic CT study of the liver?

    PubMed

    Takahashi, Hiroto; Okada, Masahiro; Hyodo, Tomoko; Hidaka, Syojiro; Kagawa, Yuki; Matsuki, Mitsuru; Tsurusaki, Masakatsu; Murakami, Takamichi

    2014-04-01

    To investigate whether low-dose dynamic CT of the liver with iterative reconstruction can reduce both the radiation dose and the amount of contrast medium. This study was approved by our institutional review board. 113 patients were randomly assigned to one of two groups. Group A/group B (fifty-eight/fifty-five patients) underwent liver dynamic CT at 120/100 kV, with 0/40% adaptive statistical iterative reconstruction (ASIR), with a contrast dose of 600/480 mg I/kg, respectively. Radiation exposure was estimated based on the manufacturer's phantom data. The enhancement value of the hepatic parenchyma, vessels and the tumor-to-liver contrast of hepatocellular carcinomas (HCCs) were compared between two groups. Two readers independently assessed the CT images of the hepatic parenchyma and HCCs. The mean CT dose indices: 6.38/4.04 mGy, the dose-length products: 194.54/124.57 mGy cm, for group A/group B. The mean enhancement value of the hepatic parenchyma and the tumor-to-liver contrast of HCCs with diameters greater than 1cm in the post-contrast all phases did not differ significantly between two groups (P>0.05). The enhancement values of vessels in group B were significantly higher than that in group A in the delayed phases (P<0.05). Two reader's confidence levels for the hepatic parenchyma in the delayed phases and HCCs did not differ significantly between the groups (P>0.05). Low-dose dynamic CT with ASIR can reduce both the radiation dose and the amount of contrast medium without image quality degradation, compared to conventional dynamic CT without ASIR. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  1. Should the dose of contrast medium be determined solely on the basis of body weight regardless of the patient's sex?

    PubMed

    Tanaka, Junji; Kozawa, Eito; Inoue, Kaiji; Okamoto, Yasumasa; Toya, Masahito; Sato, Youichi

    2011-06-01

    The aim of this study was to evaluate prospectively the difference in contrast enhancement of liver parenchyma between male and female subjects when the total amount of contrast material is determined by the total body weight (TBW). Computed tomography of the abdomen was performed with a total amount of iodine of 597 ± 3.9 mg I/kg (mean ± SD) over a mean ± SD total injection time of 30 ± 0.26 s. Postcontrast attenuation during the portal venous phase was measured in the liver parenchyma, portal vein, and aorta. These values were summed for each and compared to those obtained before contrast injection. A total of 565 consecutive patients without a history of underlying liver/heart disease, including 297 male and 268 female subjects (age 16-92 years, mean 67 years) were scanned and analyzed using a two-tailed t-test. The difference between precontrast and the portal venous phase in the male subjects was 315.4 ± 40.5 HU (mean ± SD), and that in female subjects was 358.6 ± 44.8 HU. This difference was statistically significant (P < 0.0001). The contrast enhancement in females was 13.7% higher than that in males when the amount of iodine administered was based on the TBW. The difference can presumably be attributed to the difference in fat and muscle components. This result suggests that the amount of contrast material used in females should be reduced according to this difference.

  2. The growth of filaments under macromolecular confinement using scaling theory.

    PubMed

    Zhu, Lin; Pan, Wei; Lu, Xi; Li, Desheng; Zhao, Jiang; Liang, Dehai

    2015-11-14

    Quantitatively describing macromolecular confinement is still a challenge. Using the assembly of DNA tiles in a polyacrylamide network as a model, we studied the effect of macromolecular confinement on the growth of the filament by scaling theory. The results show that the confinement regulates the morphology, the initial growth rate v, and the eventual length of the filament Nm. The initial growth rate is dependent on the medium viscosity η as ν∝η(-0.94), and the filament adjusts its length in the given confined space as Nm∝ (ξ/Rg)(1.8), with ξ being the mesh size of the polyacrylamide solution and Rg being the radius of gyration of polyacrylamide.

  3. Influence of the X-ray beam quality on the dose increment in CT with iodinated contrast medium.

    PubMed

    Amato, Ernesto; Asero, Grazia; Leotta, Salvatore; Auditore, Lucrezia; Salamone, Ignazio; Mannino, Giovanni; Privitera, Salvatore; Gueli, Anna

    2016-01-01

    In computed tomography (CT), the image contrast is given by the difference in X-ray attenuation in the various tissues of the patient and contrast media are used to enhance image contrast in anatomic regions characterized by similar attenuation coefficients. Aim of the present work is to enlarge the range of applicability of the method previously introduced for organ dosimetry in contrast-enhanced CT, by studying the effects of X-ray beam quality on the parameters of the model. Furthermore, an experimental method for the evaluation of the attenuation properties of iodinated solutions is proposed. Monte Carlo simulations of anthropomorphic phantoms were carried out to determine a bi-parametrical (a and b) analytical relationship between iodine concentration and dose increase in organs of interest as a function of the tube kilo-voltage peak potential (kVp) and filtration. Experimental measurements of increments in Hounsfield Units (HU) were conducted in several CT scanners, at all the kVp available, in order to determine the parameter γ which relates the HU increment with the iodine mass fraction. A cylindrical phantom that can be filled with iodine solutions provided with an axial housing for a pencil ionization chamber was designed and assembled in order to measure the attenuation properties of iodine solutions under irradiation of a CT scanner and to obtain a further validation of Monte Carlo simulations. The simulation-derived parameters of the model, a and b, are only slightly dependent upon the tube kilo-voltage peak potential and filtration, while such scanner-dependent features influence mainly the experimentally-derived γ parameter. Relative dose variations registered by the ionization chamber inside the iodine-filled cylindrical phantom decrease when the X-ray mean energy increases, and reaches about 50% for 10 mg/ml of iodine. The dosimetric method for contrast-enhanced CT can be applied to all CT scanners by adopting average simulative parameters and

  4. Application of flash dual-source CT at low radiation dose and low contrast medium dose in triple-rule-out (tro) examination.

    PubMed

    Chen, Hong-Liang; Chen, Tian-Wu; Qiu, Li-Hua; Diao, Xian-Ming; Zhang, Chao; Chen, Li

    2015-01-01

    To evaluate the clinical imaging capacity of FLASH dual-source CT at low radiation dose and low contrast medium dose in thoracic aorta, pulmonary artery & vein and coronary artery. One hundred and eight patients of thoracalgia were randomly divided into two groups; 60 cases (group A) received dual-source CT scan in flash model at 100 KV and contrast medium dose of 74 ml combined with digital subtraction angiography (DSA) examination; 48 cases (group B) received retrospectively. ECG-triggered high-pitch spiral acquisition at 120 KV and contrast medium dose of 101 ml. Several image reconstruction techniques were adopted for coronary artery, pulmonary artery and aorta. The imaging quality and the diagnostic value of this technique were evaluated. Coronary artery stenosis of group A was compared against the results of DSA examination. The scan time in group A was obviously shorter than that of group B, i.e., t=0.7±0.1 s in group A and t=7.7±1.7 s in group A. The image reconstruction phase of coronary artery was 70.4±15.6% in group A, and the systolic phase accounted for 13.3% of the optimal reconstruction phase. Compared with group B, the radiation dose of group A decreased obviously, i.e. ED=2.7±0.7 mSv for group A and ED=21.6±6.0 mSv for group B. Moreover, less contrast agent was consumed in group A than in group B, which was 74 ml in group A and 101 ml in group B. The image quality of aorta and pulmonary artery & vein was grade 1 for all cases in group A, which was the same as with group B. The coronary artery images of group A had better quality, with score of 2.9±0.1. Of 780 segments, only 2 segments could be effectively diagnosed, showing no statistically significant differences from group B (P>0.05). The coronary artery stenosis revealed by dual-source CT for group A was not significantly different from that by DSA (P>0.05). FLASH dual-source CT scan at reduced radiation dose and reduced contrast medium dose used for triple-rule-out (TRO) examination

  5. Application of flash dual-source CT at low radiation dose and low contrast medium dose in triple-rule-out (tro) examination

    PubMed Central

    Chen, Hong-Liang; Chen, Tian-Wu; Qiu, Li-Hua; Diao, Xian-Ming; Zhang, Chao; Chen, Li

    2015-01-01

    Objective: To evaluate the clinical imaging capacity of FLASH dual-source CT at low radiation dose and low contrast medium dose in thoracic aorta, pulmonary artery & vein and coronary artery. Method: One hundred and eight patients of thoracalgia were randomly divided into two groups; 60 cases (group A) received dual-source CT scan in flash model at 100 KV and contrast medium dose of 74 ml combined with digital subtraction angiography (DSA) examination; 48 cases (group B) received retrospectively. ECG-triggered high-pitch spiral acquisition at 120 KV and contrast medium dose of 101 ml. Several image reconstruction techniques were adopted for coronary artery, pulmonary artery and aorta. The imaging quality and the diagnostic value of this technique were evaluated. Coronary artery stenosis of group A was compared against the results of DSA examination. Results: The scan time in group A was obviously shorter than that of group B, i.e., t=0.7±0.1 s in group A and t=7.7±1.7 s in group A. The image reconstruction phase of coronary artery was 70.4±15.6% in group A, and the systolic phase accounted for 13.3% of the optimal reconstruction phase. Compared with group B, the radiation dose of group A decreased obviously, i.e. ED=2.7±0.7 mSv for group A and ED=21.6±6.0 mSv for group B. Moreover, less contrast agent was consumed in group A than in group B, which was 74 ml in group A and 101 ml in group B. The image quality of aorta and pulmonary artery & vein was grade 1 for all cases in group A, which was the same as with group B. The coronary artery images of group A had better quality, with score of 2.9±0.1. Of 780 segments, only 2 segments could be effectively diagnosed, showing no statistically significant differences from group B (P>0.05). The coronary artery stenosis revealed by dual-source CT for group A was not significantly different from that by DSA (P>0.05). Conclusion: FLASH dual-source CT scan at reduced radiation dose and reduced contrast medium dose used for

  6. Barium sulfate aspiration: Severe chemical pneumonia induced by a massive reflux of contrast medium during small bowel barium enema.

    PubMed

    Zhang, Lin; Yang, Yi; Zhang, Ji; Zhou, Xiaowei; Dong, Hongmei; Zhou, Yiwu

    2015-08-01

    Barium contrast radiography is a conventional procedure aimed at revealing lesions of the alimentary tract using barium sulfate on X-ray irradiation. Although it is widely used in clinics, adverse effects and complications are observed, such as anaphylaxis, granuloma, fecalithes, abdomen-leaking, embolism, bacterial contamination, and aspiration. We report a case of death due to a massive barium sulfate aspiration resulted from an air-barium double contrast enema radiography. A 25-year-old female patient was hospitalized with symptoms of abdominal distention, nausea, vomiting and diarrhea for three days. A progressive respiratory distress presented only 1h after a small bowel air-barium double contrast enema. The patient died 11h later. The result of autopsy revealed the cause of death to be severe chemical pneumonitis induced by gastric fluid which was aspirated into her lungs. Barium sulfate is generally recognized to be chemically inert for the respiratory system, but a mixture of barium sulfate with gastric contents is fatal. Here we intend to suggest that, when determining the potential cause of death, medical examiners should consider a patient's status quo as well as the possible adverse effects and complications caused by the barium sulfate preparation during gastrointestinal radiography.

  7. Demonstration of liver metastases on postmortem whole body CT angiography following inadvertent systemic venous infusion of the contrast medium.

    PubMed

    O'Donnell, Chris; Hislop-Jambrich, Jacqueline; Woodford, Noel; Baker, Melissa

    2012-03-01

    An 86-year-old woman was hospitalized for breathlessness and a large right-sided pleural effusion. Approximately 1 h after thoracentesis, she developed a hemothorax resulting in hypotension and death. Routine postmortem CT scanning showed a large volume right hemothorax and a markedly enlarged liver. In an attempt to determine the origin of bleeding prior to autopsy, a postmortem CT angiogram was performed. Following inadvertent cannulation of the left long saphenous vein and infusion of ∼1,700 mL of a polyethylene glycol 200 and iodine-based radiographic contrast solution into systemic veins using a mechanical pump, CT scanning revealed a dense hepatic "parenchogram" containing multiple large, filling defects indicative of metastases. These were confirmed at autopsy. Microscopic evaluation of the liver using hematoxylin and eosin staining showed marked histological artifact characterized by centrilobular sinusoidal expansion although histology of the adenocarcinoma metastases was typical and apparently unaffected by the contrast solution. Postmortem CT angiography using an aqueous radiographic contrast agent in the so-called venous phase seems to be useful for the identification of hepatic parenchymal metastatic disease although it does cause histological artifact.

  8. Computed tomography pulmonary angiography using a 20% reduction in contrast medium dose delivered in a multiphasic injection.

    PubMed

    Chen, Mitchell; Mattar, Gaith; Abdulkarim, Jamal A

    2017-03-28

    To evaluate the feasibility of reducing the dose of iodinated contrast agent in computed tomography pulmonary angiography (CTPA). One hundred and twenty-seven patients clinically suspected of having pulmonary embolism underwent spiral CTPA, out of whom fifty-seven received 75 mL and the remaining seventy a lower dose of 60 mL of contrast agent. Both doses were administered in a multiphasic injection. A minimum opacification threshold of 250 Hounsfield units (HU) in the main pulmonary artery is used for assessing the technical adequacy of the scans. Mean opacification was found to be positively correlated to patient age (Pearson's correlation 0.4255, P < 0.0001) and independent of gender (male:female, 425.6 vs 450.4, P = 0.34). When age is accounted for, the study and control groups did not differ significantly in their mean opacification in the main (436.8 vs 437.9, P = 0.48), left (416.6 vs 419.8, P = 0.45) or the right pulmonary arteries (417.3 vs 423.5, P = 0.40). The number of sub-optimally opacified scans (the mean opacification in the main pulmonary artery < 250 HU) did not differ significantly between the study and control groups (7 vs 10). A lower dose of iodine contrast at 60 mL can be feasibly used in CTPA without resulting in a higher number of sub-optimally opacified scans.

  9. Computed tomography pulmonary angiography using a 20% reduction in contrast medium dose delivered in a multiphasic injection

    PubMed Central

    Chen, Mitchell; Mattar, Gaith; Abdulkarim, Jamal A

    2017-01-01

    AIM To evaluate the feasibility of reducing the dose of iodinated contrast agent in computed tomography pulmonary angiography (CTPA). METHODS One hundred and twenty-seven patients clinically suspected of having pulmonary embolism underwent spiral CTPA, out of whom fifty-seven received 75 mL and the remaining seventy a lower dose of 60 mL of contrast agent. Both doses were administered in a multiphasic injection. A minimum opacification threshold of 250 Hounsfield units (HU) in the main pulmonary artery is used for assessing the technical adequacy of the scans. RESULTS Mean opacification was found to be positively correlated to patient age (Pearson’s correlation 0.4255, P < 0.0001) and independent of gender (male:female, 425.6 vs 450.4, P = 0.34). When age is accounted for, the study and control groups did not differ significantly in their mean opacification in the main (436.8 vs 437.9, P = 0.48), left (416.6 vs 419.8, P = 0.45) or the right pulmonary arteries (417.3 vs 423.5, P = 0.40). The number of sub-optimally opacified scans (the mean opacification in the main pulmonary artery < 250 HU) did not differ significantly between the study and control groups (7 vs 10). CONCLUSION A lower dose of iodine contrast at 60 mL can be feasibly used in CTPA without resulting in a higher number of sub-optimally opacified scans. PMID:28396728

  10. Low-dose triple-rule-out using 320-row-detector volume MDCT--less contrast medium and lower radiation exposure.

    PubMed

    Durmus, Tahir; Rogalla, Patrik; Lembcke, Alexander; Mühler, Matthias R; Hamm, Bernd; Hein, Patrick A

    2011-07-01

    To investigate image quality of triple-rule-out (TRO) computed tomography (CT) using a 320-row-detector CT system with substantially reduced contrast medium volume at 100 kV. Forty-six consecutive patients with noncritical, acute chest pain underwent 320-row-detector CT using a two-step TRO protocol consisting of a non-spiral, non-gated chest CT acquisition (150 mA) followed by a non-spiral, electrocardiography-gated cardiac acquisition (200-500 mA based on body mass index (BMI)). Data were acquired using a biphasic injection protocol with a total iodinated contrast medium volume of 60 ml (370 mg/ml). Vessel attenuation and effective doses were recorded. Image quality was scored independently by two readers. Mean attenuation was 584 ± 114 Hounsfield units (HU) in the ascending aorta, 335 ± 63HU in the aortic arch, 658 ± 136HU in the pulmonary trunk, and 521 ± 97HU and 549 ± 102HU in the right and left coronary artery, respectively. In all but one patient, attenuation and image quality allowed accurate visualization of the pulmonary arteries, thoracic aorta, and coronary arteries in a single examination. Ninety-six percent of all coronary artery segments were rated diagnostic. Radiation exposure ranged between 2.0 and 3.3 mSv. Using 320-row-detector CT the investigated low-dose TRO protocol resulted in excellent opacification and image quality with substantial reduction of contrast medium volume compared to recently published TRO protocols.

  11. Myelography in achondroplasia: value of a lateral C1-2 puncture and non-ionic, water-soluble contrast medium

    SciTech Connect

    Suss, R.A.; Udvarhelyi, G.B.; Wang, H.; Kumar, A.J.; Zinreich, S.J.; Rosenbaum, A.E.

    1983-10-01

    Because of technical difficulties and diagnostic limitations encountered with other myelographic techniques in patients with achondroplasia, the authors employed a lateral C1-2 puncture and non-ionic, water-soluble contrast medium in 18 achondroplastic patients with spinal compression (21 procedures). This technique proved most appropriate for identifying the upper limit of degenerative osteophytes causing exacerbation of congenital spinal stenosis, which is crucial in planning decompressive surgery. A potentially important additional finding was the presence of degenerative lower cervical spine disease in the majority of patients. There were no serious complications. The authors recommend this technique as safe and effective in achondroplastic patients with severe congenital spinal stenosis.

  12. Computed tomography (CT) of the lungs of the dog using a helical CT scanner, intravenous iodine contrast medium and different CT windows.

    PubMed

    Cardoso, L; Gil, F; Ramírez, G; Teixeira, M A; Agut, A; Rivero, M A; Arencibia, A; Vázquez, J M

    2007-10-01

    The aim of this study was to determine the accuracy of helical computed tomography (CT) for visualizing pulmonary parenchyma and associated formations in normal dogs. CT scan was performed by using intravenous contrast medium and by applying different types of CT windows: soft tissue and lung windows, and high-resolution computed tomography of the lung. This technique allowed, especially with lung window types, a good view of the parenchyma, bronchial tree, vascular structures and pleural cavity. The selected images, with high anatomical quality and tissue contrast, may be a reference for future clinical studies of this organ. Thus, helical CT is a promising non-invasive method of diagnosing a wide variety of pulmonary diseases in dogs.

  13. 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

  14. Data Mining of Macromolecular Structures.

    PubMed

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

    2016-01-01

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

  15. Macromolecular Diffusion in Polymer Nanocomposites

    NASA Astrophysics Data System (ADS)

    Gam, Sangah; Meth, Jeff; Zane, Steve; Winey, Karen; Clarke, Nigel; Composto, Russell

    2011-03-01

    Macromolecular diffusion in crowded systems is important in biological and engineered systems. We have studied macromolecular diffusion through a model polymer nanocomposite (PNC) containing phenyl grafted silica nanoparticles (NPs), randomly distributed in a polystyrene matrix. Over a wide range of NP loading and tracer molecular weight (M), the scaling of the diffusion coefficient with M is in excellent agreement with the entropic barrier model (EBM) previously used to describe diffusion of DNA through confined media (e.g., gels and nanopores). To investigate the effect of NP size, diffusion was measured in PNC's with silica NPs having diameters of 28 and 12 nm. The normalized diffusion coefficients (D / D0) plotted against the interparticle separation relative to probe size (i.e., ID/ 2 Rg) collapse on a master curve. Diffusion in a poly(methyl methacrylate):silica NP system was also investigated to understand how attractive interactions (i.e., enthalpy) perturb motion relative to the polystyrene and phenyl-silica NP system which is athermal. Finally, a flux-based model is proposed and compared with experimental results.

  16. Atomic force microscopy imaging of macromolecular complexes.

    PubMed

    Santos, Sergio; Billingsley, Daniel; Thomson, Neil

    2013-01-01

    This chapter reviews amplitude modulation (AM) AFM in air and its applications to high-resolution imaging and interpretation of macromolecular complexes. We discuss single DNA molecular imaging and DNA-protein interactions, such as those with topoisomerases and RNA polymerase. We show how relative humidity can have a major influence on resolution and contrast and how it can also affect conformational switching of supercoiled DNA. Four regimes of AFM tip-sample interaction in air are defined and described, and relate to water perturbation and/or intermittent mechanical contact of the tip with either the molecular sample or the surface. Precise control and understanding of the AFM operational parameters is shown to allow the user to switch between these different regimes: an interpretation of the origins of topographical contrast is given for each regime. Perpetual water contact is shown to lead to a high-resolution mode of operation, which we term SASS (small amplitude small set-point) imaging, and which maximizes resolution while greatly decreasing tip and sample wear and any noise due to perturbation of the surface water. Thus, this chapter provides sufficient information to reliably control the AFM in the AM AFM mode of operation in order to image both heterogeneous samples and single macromolecules including complexes, with high resolution and with reproducibility. A brief introduction to AFM, its versatility and applications to biology is also given while providing references to key work and general reviews in the field.

  17. The Gd3+ complex of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid mono(p-isothiocyanatoanilide) conjugated to inulin: a potential stable macromolecular contrast agent for MRI.

    PubMed

    Granato, Luigi; Laurent, Sophie; Vander Elst, Luce; Djanashvili, Kristina; Peters, Joop A; Muller, Robert N

    2011-01-01

    Reaction of DOTA-NCSA [1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid mono(p-isothiocyanatoanilide)] with O-(aminopropyl)inulin (degree of polymerization 25) provided a chelate that formed a kinetically extremely stable Gd(3+) complex. No transmetalation was observed with Zn(2+). The conjugate has a relaxivity of 21.7 s(-1) mM(-1) at 20 MHz and 37 °C, and each molecule of the inulin carries on average 35 Gd(3+) ions. The parameters governing the relaxivity of this material and of a low-molecular-weight model compound prepared by conjugation of DOTA-NCSA and propylamine were evaluated by investigation of their water (1)H longitudinal relaxation rate enhancements at different magnetic fields (NMRD) and by studying variable temperature (17)O NMR data. The high relaxivity of the inulin conjugate can be ascribed to the efficient slowing down of the molecular tumbling by this carrier. The rotational correlation time at 37 °C of this material is 1460 ps, whereas that of the model compound is 84 ps. Furthermore, both complexes do not interact significantly with human serum albumin, as shown by their NMRD profiles, and do not undergo transmetallation by zinc ions. The inulin conjugate thus has potential for application as a contrast agent for MRI, particularly as a blood pool agent. Copyright © 2011 John Wiley & Sons, Ltd.

  18. Magnetic resonance imaging of liver metastases: experimental comparison of anionic and conventional superparamagnetic iron oxide particles with a hepatobiliary contrast medium during dynamic and uptake phases.

    PubMed

    Kaufels, Nicola; Korn, Ronny; Wagner, Susanne; Schink, Tania; Hamm, Bernd; Taupitz, Matthias; Schnorr, Jörg

    2008-07-01

    To assess the contrast-enhancing effects of citrate-coated superparamagnetic iron oxide particles (VSOP-C184) in a rat liver tumor model using dynamic and delayed magnetic resonance imaging in comparison to carboxydextran-coated particles (ferucarbotran) and a hepatobiliary contrast medium (gadobenate dimeglumine). A total of 32 male rats with liver tumors (CC-531 colorectal carcinoma) were examined at 1.5 T with a T1-weighted dynamic series (3D gradient echo sequence) and T1-weighted and T2*-weighted images (2D gradient echo sequences) before and 15 and 90 minutes after injection. VSOP-C184 was investigated at doses of 0.015, 0.045, and 0.06 mmol Fe/kg, ferucarbotran at 0.015 mmol Fe/kg, and gadobenate dimeglumine at 0.025, 0.05, and 0.1 mmol Gd/kg. Liver-tumor contrast-to-noise ratio (CNR) was calculated and statistically compared. T1-weighted dynamic images: VSOP-C184 has significantly higher CNR values at a dose of 0,015 mmol Fe/kg than ferucarbotran at the same dose (P = 0.001). VSOP-C184 produces a significantly higher CNR at a dose of 0.045 mmol Fe/kg than gadobenate dimeglumine at a dose of 0.05 mmol Gd/kg (P = 0.019). At a dose of 0.06 mmol Fe/kg, the CNR for VSOP-C184 is significantly lower than that of gadobenate dimeglumine (0.1 mmol Gd/kg) (P = 0.005).T2-weighted delayed images: CNR values of VSOP-C184 are similar to those of ferucarbotran and are significantly higher than those of gadobenate dimeglumine (P < 0.05). On T1-weighted magnetic resonance imaging of liver tumors VSOP-C184 produces a high contrast comparable to that of a hepatobiliary contrast medium in addition to its contrast-enhancing effect in T2-weighted imaging.

  19. 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

  20. [Study of low radiation exposure dose and low contrast medium dose in coronary CT angiography with High-pitch spiral acquisition mode of dual source CT].

    PubMed

    Dai, Yingyu; Guo, Liang; Dai, Qichun; Liu, Yonghao; Ma, Xinxing

    2014-08-05

    To evaluate the feasibility of low radiation exposure and low contrast medium volume for coronary CT angiography with High- pitch spiral acquisition mode of dual source CT. 135 patients whose BMI <23 kg/m² and heart rates <65 bpm selected from 291 patients diagnosed of suspected CHD at our institution from September 2013 to February 2014 were randomly divided into 3 groups before CCTA, and there were 45 patients in each group. 80 kV , Iodixanol (320 mgI/ml) and sinogram affirmed iterative reconstruction (SAFIRE) were used in A group. 80 kV , Iopamidol (370 mgI/ml) and SAFIRE were used in B group. 100 kV, Iodixanol and filtered back projection (FBP) were used in C group. Two radiologists assessed image quality with 5-piont scale subjectively and double-blind. Independent-Sample Test was used to analyze statistical significance of image quality including signal to noise ratio(SNR) and contrast to noise ratio (CNR) between A and B group or between A and C group. At the same time, Contrast medium dose statistical significance between A and B group and mean effective Radiation dose (ED)statistical significance between A and C were analyzed by the same way. There were no significant difference of image quality including SNR and CNR of aortic root (AO), left main coronary artery (LM), left anterior descending artery (LAD), circumflex coronary artery (CX) and right coronary artery (RCA) Between A and B group (P = non-significant for all comparison), whereas Iodine in taken of A group decreased 14% (17 600 mg vs 20 350 mg). There were no significant difference of image quality including SNR and CNR of AO, LM, LAD, CX and RCA Between A and C group (P = non-significant for all comparison), whereas mean ED of A group decreased 50% (0.41 ± 0.05 mSv vs 0.79 ± 0.15 mSv). The double low dose application which use High-pitch spiral mode, 80 kV, SAFIRE, and Iodixanol (320 mgI/ml) can be used in those patients whose BMI <23 kg/m² and heart rates <65 bpm to reduce the burden of

  1. How good is the turbid medium-based approach for accounting for light partitioning in contrasted grass--legume intercropping systems?

    PubMed

    Barillot, Romain; Louarn, Gaëtan; Escobar-Gutiérrez, Abraham J; Huynh, Pierre; Combes, Didier

    2011-10-01

    Most studies dealing with light partitioning in intercropping systems have used statistical models based on the turbid medium approach, thus assuming homogeneous canopies. However, these models could not be directly validated although spatial heterogeneities could arise in such canopies. The aim of the present study was to assess the ability of the turbid medium approach to accurately estimate light partitioning within grass-legume mixed canopies. Three contrasted mixtures of wheat-pea, tall fescue-alfalfa and tall fescue-clover were sown according to various patterns and densities. Three-dimensional plant mock-ups were derived from magnetic digitizations carried out at different stages of development. The benchmarks for light interception efficiency (LIE) estimates were provided by the combination of a light projective model and plant mock-ups, which also provided the inputs of a turbid medium model (SIRASCA), i.e. leaf area index and inclination. SIRASCA was set to gradually account for vertical heterogeneity of the foliage, i.e. the canopy was described as one, two or ten horizontal layers of leaves. Mixtures exhibited various and heterogeneous profiles of foliar distribution, leaf inclination and component species height. Nevertheless, most of the LIE was satisfactorily predicted by SIRASCA. Biased estimations were, however, observed for (1) grass species and (2) tall fescue-alfalfa mixtures grown at high density. Most of the discrepancies were due to vertical heterogeneities and were corrected by increasing the vertical description of canopies although, in practice, this would require time-consuming measurements. The turbid medium analogy could be successfully used in a wide range of canopies. However, a more detailed description of the canopy is required for mixtures exhibiting vertical stratifications and inter-/intra-species foliage overlapping. Architectural models remain a relevant tool for studying light partitioning in intercropping systems that exhibit

  2. How good is the turbid medium-based approach for accounting for light partitioning in contrasted grass–legume intercropping systems?

    PubMed Central

    Barillot, Romain; Louarn, Gaëtan; Escobar-Gutiérrez, Abraham J.; Huynh, Pierre; Combes, Didier

    2011-01-01

    Background and Aims Most studies dealing with light partitioning in intercropping systems have used statistical models based on the turbid medium approach, thus assuming homogeneous canopies. However, these models could not be directly validated although spatial heterogeneities could arise in such canopies. The aim of the present study was to assess the ability of the turbid medium approach to accurately estimate light partitioning within grass–legume mixed canopies. Methods Three contrasted mixtures of wheat–pea, tall fescue–alfalfa and tall fescue–clover were sown according to various patterns and densities. Three-dimensional plant mock-ups were derived from magnetic digitizations carried out at different stages of development. The benchmarks for light interception efficiency (LIE) estimates were provided by the combination of a light projective model and plant mock-ups, which also provided the inputs of a turbid medium model (SIRASCA), i.e. leaf area index and inclination. SIRASCA was set to gradually account for vertical heterogeneity of the foliage, i.e. the canopy was described as one, two or ten horizontal layers of leaves. Key Results Mixtures exhibited various and heterogeneous profiles of foliar distribution, leaf inclination and component species height. Nevertheless, most of the LIE was satisfactorily predicted by SIRASCA. Biased estimations were, however, observed for (1) grass species and (2) tall fescue–alfalfa mixtures grown at high density. Most of the discrepancies were due to vertical heterogeneities and were corrected by increasing the vertical description of canopies although, in practice, this would require time-consuming measurements. Conclusions The turbid medium analogy could be successfully used in a wide range of canopies. However, a more detailed description of the canopy is required for mixtures exhibiting vertical stratifications and inter-/intra-species foliage overlapping. Architectural models remain a relevant tool for

  3. Collagen macromolecular drug delivery systems

    SciTech Connect

    Gilbert, D.L.

    1988-01-01

    The objective of this study was to examine collagen for use as a macromolecular drug delivery system by determining the mechanism of release through a matrix. Collagen membranes varying in porosity, crosslinking density, structure and crosslinker were fabricated. Collagen characterized by infrared spectroscopy and solution viscosity was determined to be pure and native. The collagen membranes were determined to possess native vs. non-native quaternary structure and porous vs. dense aggregate membranes by electron microscopy. Collagen monolithic devices containing a model macromolecule (inulin) were fabricated. In vitro release rates were found to be linear with respect to t{sup {1/2}} and were affected by crosslinking density, crosslinker and structure. The biodegradation of the collagen matrix was also examined. In vivo biocompatibility, degradation and {sup 14}C-inulin release rates were evaluated subcutaneously in rats.

  4. Solvent diffusion outside macromolecular surfaces

    NASA Astrophysics Data System (ADS)

    Lindahl, Erik; Edholm, Olle

    1998-01-01

    The effect of the inhomogeneous environment upon solvent molecules close to a macromolecular surface is evaluated from a molecular-dynamics simulation of a protein, myoglobin, in water solution. The simulation is analyzed in terms of a mean-field potential from the protein upon the water molecules and spatially varying translational diffusion coefficients for solvent molecules in directions parallel and perpendicular to the protein surface. The diffusion coefficients can be obtained from the slope of the average-square displacements vs time, as well as from the integral of the velocity autocorrelation functions. It is shown that the former procedure gives a lot of ambiguities due to the variation of the slope of the curve with time. The latter, however, after analytic correction for the contribution from algebraic long-time tails, furnish a much more reliable alternative.

  5. Visual automated macromolecular model building.

    PubMed

    Langer, Gerrit G; Hazledine, Saul; Wiegels, Tim; Carolan, Ciaran; Lamzin, Victor S

    2013-04-01

    Automated model-building software aims at the objective interpretation of crystallographic diffraction data by means of the construction or completion of macromolecular models. Automated methods have rapidly gained in popularity as they are easy to use and generate reproducible and consistent results. However, the process of model building has become increasingly hidden and the user is often left to decide on how to proceed further with little feedback on what has preceded the output of the built model. Here, ArpNavigator, a molecular viewer tightly integrated into the ARP/wARP automated model-building package, is presented that directly controls model building and displays the evolving output in real time in order to make the procedure transparent to the user.

  6. Intra-arterial and intravenous applications of Iosimenol 340 injection, a new non-ionic, dimeric, iso-osmolar radiographic contrast medium: phase 2 experience

    PubMed Central

    Laniado, Michael; Hosten, Norbert; Kelsch, Bettina; Hogstrom, Barry

    2015-01-01

    Background Iosimenol 340 injection is a new, dimeric, iso-osmolar, iodinated contrast medium for X-ray angiography. Purpose To compare the safety and efficacy of iosimenol injection to iodixanol injection in two randomized, controlled phase 2 trials. Material and Methods One hundred and forty-four adult patients were enrolled in the two trials, one for evaluation during arteriography and the other for evaluation during computed tomography. Safety was compared by assessing adverse events, vital signs, ECGs, and laboratory parameters. Efficacy was assessed as X-ray attenuation in the computed tomography (CT) trial and as the quality of contrast enhancement in the arteriography trial. Results There were no statistically significant differences in terms of safety or efficacy between the two contrast media. Both were well tolerated upon intravenous as well as intra-arterial injection. The most common adverse event was a feeling of warmth (observed in 35.1% of the patients with Iosimenol injection and 44.3% with iodixanol injection). Conclusion Iosimenol upon intravenous as well as upon intra-arterial injection exhibits a safety profile and shows an efficacy similar to that of iodixanol. PMID:24938661

  7. In vivo magnetic resonance imaging of atherosclerotic lesions with a newly developed Evans blue-DTPA-gadolinium contrast medium in apolipoprotein-E-deficient mice.

    PubMed

    Yasuda, Satoshi; Ikuta, Kenjiro; Uwatoku, Toyokazu; Oi, Keiji; Abe, Kohtaro; Hyodo, Fuminori; Yoshimitsu, Kengo; Sugimura, Kohtaro; Utsumi, Hideo; Katayama, Yoshiki; Shimokawa, Hiroaki

    2008-01-01

    Magnetic resonance imaging (MRI) contrast agents that specifically detect atherosclerotic plaque may be useful for the noninvasive detection of the plaque. We have recently developed a new contrast agent, Evans blue-DTPA-gadolinium (EB-DTPA-Gd), which selectively accumulates vascular lesions with endothelial removal. In this study, we examined whether EB-DTPA-Gd is also useful for in vivo imaging of atherosclerotic plaques. We used male apolipoprotein-E-deficient (ApoE-/-) mice of different ages (3, 6 and 12 months old) and age-matched male wild-type mice. After a single intravenous administration of EB-DTPA-Gd (160 microM/kg body weight), MRI T(1) signal was obtained in vivo. Increased signal intensity in the aortic wall was noted within 10-20 min after intravenous injection of EB-DTPA-Gd and was maintained for 30 min. The MRI enhancement in the aorta of ApoE-/- mice was increased in accordance with age, whereas no such enhancement was noted in wild-type mice. Histological examination demonstrated that there was a topological correlation between the site of MRI enhancement and that of atherosclerotic plaque. These results indicate that EB-DTPA-Gd is a useful MRI contrast medium for the in vivo detection of atherosclerotic plaques. Copyright (c) 2007 S. Karger AG, Basel.

  8. CT pulmonary angiography using a reduced volume of high-concentration iodinated contrast medium and multiphasic injection to achieve dose reduction.

    PubMed

    Goble, E W; Abdulkarim, J A

    2014-01-01

    To evaluate whether a reduced volume of a higher-concentration iodinated contrast medium delivered with a multiphasic injection could be used in computed tomography pulmonary angiography (CTPA) to achieve a reduction in dose without adversely affecting image quality. The CTPA images were retrospectively evaluated of 69 patients who received 100 ml of 300 mg iodine/ml ioversol, injected at constant rate of 5 ml/s and 70 patients who received 75 ml of 350 mg iodine/ml ioversol contrast medium delivered using a multiphasic injection protocol (starting at 5 ml/s and reducing exponentially). The degree of opacification in the proximal pulmonary arteries was measured in Hounsfield units. The groups did not differ in terms of age, sex distribution, or weight. The mean iodine dose was lower in the 75 ml of 350 mg iodine/ml group (26.25 versus 29.5 g, p < 0.0001). Mean opacification did not differ significantly between the 75 ml of 350 mg iodine/ml and 100 ml of 300 mg iodine/ml groups in the main pulmonary artery (365 versus 331, p = 0.055) although it was significantly higher in the 75 ml group in the right (352 versus 315, p = 0.024) and left pulmonary arteries (347 versus 312, p = 0.028). Opacification correlated positively with age and negatively with weight (p < 0.001) and when these effects had been accounted for, the differences in opacification were not statistically significant in the main (p = 0.23), right (p = 0.11), or left pulmonary arteries (p = 0.13). The number of suboptimally opacified studies (opacification of less than 250 HU in main pulmonary artery) did not differ between the groups (12 versus 13, p = 0.83). A reduction in iodine dose can be achieved without adversely affecting pulmonary arterial enhancement in CTPA by administering a smaller volume of high-concentration contrast medium using a multiphasic injection protocol. Copyright © 2013 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

  9. 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.; Curreri, Peter A. (Technical Monitor)

    2002-01-01

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

  10. 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.; Curreri, Peter A. (Technical Monitor)

    2002-01-01

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

  11. Phase I clinical evaluation of citrate-coated monocrystalline very small superparamagnetic iron oxide particles as a new contrast medium for magnetic resonance imaging.

    PubMed

    Taupitz, Matthias; Wagner, Susanne; Schnorr, Jörg; Kravec, Irina; Pilgrimm, Herbert; Bergmann-Fritsch, Henrike; Hamm, Bernd

    2004-07-01

    To evaluate the safety and pharmacokinetics of a newly developed MR contrast medium consisting of very small superparamagnetic iron oxide particles (VSOP) coated with citrate (VSOP-C184) in a clinical phase I trial. A total of 18 healthy subjects received either VSOP-C184 (core diameter: 4 nm; total diameter: 7 +/- 0.15 nm; relaxivities in water at 0.47 T (T1) 18.7 and (T2) 30 L/(mmol*seconds)) at doses of 0.015, 0.045, or 0.075 mmol Fe/kg (n = 5 per dose) or placebo (n = 1 per dose) as intravenous injections. Physical status and vital parameters were recorded, blood samples were collected for clinical chemistry and relaxometry (0.94 T), and urinalyses were performed before and for up to 2 weeks after administration. No serious adverse events occurred. The most pronounced adverse events occurred in 2 subjects of the highest dose group 45-50 minutes after injection. These were a drop in blood pressure and a drop in oxygen saturation, which were considered to be possibly drug-related and rapidly resolved without medication. Otherwise, no relevant changes in vital and laboratory parameters were observed. The parameters of iron metabolism exhibited short-term, dose-related changes. The injection of VSOP-C184 decreased T1 relaxation time of blood below 100 milliseconds for 18 minutes after a dose of 0.045 mmol [corrected] Fe/kg and for 60 minutes after 0.075 mmol [corrected] Fe/kg. The favorable data on the safety, tolerability, and efficacy of VSOP-C184 justify further clinical phase II and III trials as a contrast medium for MRI.

  12. Automated data collection for macromolecular crystallography.

    PubMed

    Winter, Graeme; McAuley, Katherine E

    2011-09-01

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

  13. 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.

  14. Macromolecular crowding: Macromolecules friend or foe.

    PubMed

    Mittal, Shruti; Chowhan, Rimpy Kaur; Singh, Laishram Rajendrakumar

    2015-09-01

    Cellular interior is known to be densely crowded due to the presence of soluble and insoluble macromolecules, which altogether occupy ~40% of the total cellular volume. This results in altered biological properties of macromolecules. Macromolecular crowding is observed to have both positive and negative effects on protein folding, structure, stability and function. Significant data has been accumulated so far on both the aspects. However, most of the review articles so far have focused on the positive aspect of macromolecular crowding and not much attention has been paid on the deleterious aspect of crowding on macromolecules. In order to have a complete knowledge of the effect of macromolecular crowding on proteins and enzymes, it is important to look into both the aspects of crowding to determine its precise role under physiological conditions. To fill the gap in the understanding of the effect of macromolecular crowding on proteins and enzymes, this review article focuses on the deleterious influence of crowding on macromolecules. Macromolecular crowding is not always good but also has several deleterious effects on various macromolecular properties. Taken together, the properties of biological macromolecules in vivo appears to be finely regulated by the nature and level of the intracellular crowdedness in order to perform their biological functions appropriately. The information provided here gives an understanding of the role played by the nature and level of cellular crowdedness in intensifying and/or alleviating the burden of various proteopathies. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. 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.

  16. New generation of monomer-stabilized very small superparamagnetic iron oxide particles (VSOP) as contrast medium for MR angiography: preclinical results in rats and rabbits.

    PubMed

    Taupitz, M; Schnorr, J; Abramjuk, C; Wagner, S; Pilgrimm, H; Hünigen, H; Hamm, B

    2000-12-01

    The purpose of this study was to evaluate the signal enhancement characteristics of very small superparamagnetic iron oxide particles (VSOP)-C63, a new monomer-coated, iron oxide-based magnetic resonance (MR) blood pool contrast medium with a very small particle size and optimized physical properties. Equilibrium MR angiography (MRA) of rats (thoracic and abdominal vessels) was performed at 1.5 T with a three-dimensional gradient-recalled echo (3D GRE) technique (TR/TE 6.6/2.3 msec, flip angle 25 degrees ) before and after (every 3-5 minutes up to 50 minutes) i.v. injection of VSOP-C63 [dosages: 15, 30, 45, 60, 75, and 90 micromol Fe/kg; diameter: 8 nm; relaxivities at 0.47 T: R1 = 30 l/(mmol * s); R2 = 39 l/(mmol * s)]. First-pass MRA images (3D-GRE, TR/TE 4.5/1.7 msec, flip angle 25 degrees ) were obtained with 45 micromol Fe/kg VSOP-C63 in comparison with 0.2 mmol Gd/kg of gadolinium diethylene triamine pentaacetic acid (Gd DTPA; before and every 5 seconds p.i.). MRA (3D GRE, TR/TE 4.5/1.7 msec, flip angle 25 degrees) of coronary vessels in rabbits was performed after i.v. injection of 45 micromol Fe/kg of VSOP-C63. In rats maximal S/N ratio in thoracic and abdominal arteries directly after i.v. injection of VSOP-C63 was 25 +/- 1, 43 +/- 2, 49 +/- 4, 57 +/- 3, 64 +/- 3, and 63 +/- 3 for the different dosages. Blood half-life was dose dependent (15 +/- 2, 20 +/- 3, 29 +/- 6, 37 +/- 5, 61 +/- 16, and 86 +/- 21 minutes). At a dose of 30 micromol Fe/kg even small intrarenal arteries were sharply delineated. First-pass MRA showed no significant difference in the S/N ratio between Gd-DTPA (71.5 +/- 11.5) and VSOP-C63 (65.1 +/- 18. 3). The proximal segments of the coronary arteries in rabbits were clearly depicted at a dose of 45 micromol Fe/kg. The monomer-coated, iron oxide-based contrast medium VSOP-C63 exhibits favorable properties as a blood pool agent for both equilibrium and first-pass MRA. J. Magn. Reson. Imaging 2000;12:905-911. Copyright 2000 Wiley-Liss, Inc.

  17. Molecular Control of Macromolecular Properties

    NASA Astrophysics Data System (ADS)

    Holcombe, Thomas Wesley, III

    Molecular level control over macromolecules has been at the heart of human advancement, long before Hermann Staudinger coined the term Makromolekule. From the development of primitive pharmaceuticals to the advanced materials that sent Man into outer-space, We have been tinkering with God's paint since our inception. The work described herein primarily involves advances concerning poly-aromatic macromolecules for use in future electronic applications, particularly that of organic photovoltaics. There is a final chapter, however, that gives the reader a taste of how some molecular level changes can be directly visualized with modern microscopy techniques. Chapter 1 provides a very brief introduction to conjugated polymers and molecular level control over macromolecular properties. Chapters 2--4 introduces the concept of polymer substitution as a means by which to control and improve charge generation in organic photovoltaic devices. Chapters 5 and 6 show how these polymers can take on larger, defined structures, yet are still beholden to intrinsic molecular properties---such as regioregularity, a fancy word for the regularity of the position in which two aromatic rings are joined together. Chapter 7 re-examines the role of polymer substitution on photovoltaic performance, this time with an emphasis on homo-polymer packing rather than electron transfer at the donor/acceptor interface. Finally, Chapter 8 visualizes how controlling the environment about a single metal atom can lead directly to a cyclic polyolefin. Individually, these advances do not yield any breakthroughs noticeable to a general audience; collectively, they sit atop a mountain of human knowledge, waiting to provide a stepping stone for the next generation.

  18. The Preinterventional Cystatin-Creatinine-Ratio: A Prognostic Marker for Contrast Medium-Induced Acute Kidney Injury and Long-Term All-Cause Mortality.

    PubMed

    Lüders, Florian; Meyborg, Matthias; Malyar, Nasser; Reinecke, Holger

    2015-01-01

    Contrast medium-induced acute kidney injury (CI-AKI) is an important iatrogenic complication following the injection of iodinated contrast media. The level of serum creatinine (SCr) is the currently accepted 'gold standard' to diagnose CI-AKI. Cystatin C (CyC) has been detected as a more sensitive marker for renal dysfunction. Both have their limitations. The role of the preinterventional CyC-SCr ratio for evaluating the risk for CI-AKI and long-term all-cause mortality was retrospectively analyzed in the prospective single-center 'Dialysis-versus-Diuresis trial'. CI-AKI was defined and staged according to the Acute Kidney Injury Network classification. Three hundred and seventy-three patients were included (average age 67.4 ± 10.2 years, 16.4% women, 29.2% with diabetes mellitus, mean baseline glomerular filtration rate 56.3 ± 20.2 ml/min/1.73 m(2) [as estimated by Chronic Kidney Disease Epidemiology Collaboration Serum Creatinine Cystatin C equation], 5.1% ejection fraction <35%). A total of 79 patients (21.2%) developed CI-AKI after elective heart catheterization, and 65 patients (17.4%) died during follow-up. Multivariate analyses by logistic regression confirmed that the preinterventional CyC-SCr ratio is independently associated with CI-AKI (OR 9.423, 95% CI 1.494-59.436, p = 0.017). Also, the Cox regression model found a high significant association between preinterventional CyC-SCr ratio and long-term all-cause mortality (mean follow-up 649 days, hazards ratio 4.096, 95% CI 1.625-10.329, p = 0.003). The preinterventional CyC-SCr ratio is independently associated with CI-AKI and highly significant associated with long-term mortality after heart catheterization. © 2015 S. Karger AG, Basel.

  19. Improving optical transmission and image contrast in medium and high performance optical systems using weighted average angle of incidence techniques to optimize coatings

    NASA Astrophysics Data System (ADS)

    Harder, James A.; Sprague, Michaelene

    2008-10-01

    Designers of medium and high performance optical systems often overlook a very simple technique that can improve the system transmission and image contrast, as well as reduce scattering within the system. The resulting improvement in the optical collection efficiency can be used to increase performance or be traded off to realize improvements in other areas (i.e. aperture size, weight, etc.). The technique is based on the observation that many (if not most) anti-reflection coatings specified for lens surfaces, are specified at a normal angle of incidence. Since most of the energy incident on a typical lens impinges at angles other than the normal, the efficiency of an anti-reflection coating at any surface might be improved by using an approach based on weighted average angles of the incident radiation. This paper describes one approach to calculate weighted average coating angles for a optical systems. The optical transmissions are estimated, when the respective coatings are specified at the normal angle of incidence and at an angle based on the incident ray geometry. The measured transmission of two (otherwise identical) aspheric lenses, one coated using a standard SLAR coating specified at a normal incidence angle and the other coated using a standard SLAR coating specified at optimized incidence angles are presented.

  20. 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.

  1. 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

  2. Variable effects of soman on macromolecular secretion by ferret trachea

    SciTech Connect

    McBride, R.K.; Zwierzynski, D.J.; Stone, K.K.; Culp, D.J.; Marin, M.G. )

    1991-01-01

    The purpose of this study was to examine the effect of the anticholinesterase agent, soman, on macromolecular secretion by ferret trachea, in vitro. We mounted pieces of ferret trachea in Ussing-type chambers. Secreted sulfated macromolecules were radiolabeled by adding 500 microCi of {sup 35}SO{sub 4} to the submucosal medium and incubating for 17 hr. Soman added to the submucosal side produced a concentration-dependent increase in radiolabeled macromolecular release with a maximal secretory response (mean +/- SD) of 202 +/- 125% (n = 8) relative to the basal secretion rate at a concentration of 10{sup {minus} 7} M. The addition of either 10{sup {minus}6} M pralidoxime (acetylcholinesterase reactivator) or 10{sup {minus}6} M atropine blocked the response to 10{sup {minus}7} M soman. At soman concentrations greater than 10{sup {minus}7} M, secretion rate decreased and was not significantly different from basal secretion. Additional experiments utilizing acetylcholine and the acetylcholinesterase inhibitor, physostigmine, suggest that inhibition of secretion by high concentrations of soman may be due to a secondary antagonistic effect of soman on muscarinic receptors.

  3. Pre-operative Simulation of the Appropriate C-arm Position Using Computed Tomography Post-processing Software Reduces Radiation and Contrast Medium Exposure During EVAR Procedures.

    PubMed

    Stahlberg, E; Planert, M; Panagiotopoulos, N; Horn, M; Wiedner, M; Kleemann, M; Barkhausen, J; Goltz, J P

    2017-02-01

    The aim was to evaluate the feasibility and efficacy of a new method for pre-operative calculation of an appropriate C-arm position for iliac bifurcation visualisation during endovascular aortic repair (EVAR) procedures by using three dimensional computed tomography angiography (CTA) post-processing software. Post-processing software was used to simulate C-arm angulations in two dimensions (oblique, cranial/caudal) for appropriate visualisation of distal landing zones at the iliac bifurcation during EVAR. Retrospectively, 27 consecutive EVAR patients (25 men, mean ± SD age 73 ± 7 years) were identified; one group of patients (NEW; n = 12 [23 iliac bifurcations]) was compared after implementation of the new method with a group of patients who received a historic method (OLD; n = 15 [23 iliac bifurcations]), treated with EVAR before the method was applied. In the OLD group, a median of 2.0 (interquartile range [IQR] 1-3) digital subtraction angiography runs were needed per iliac bifurcation versus 1.0 (IQR 1-1) runs in the NEW group (p = .007). The median dose area products per iliac bifurcation were 11951 mGy*cm(2) (IQR 7308-16663 mGy*cm(2)) for the NEW, and 39394 mGy*cm(2) (IQR 19066-53702 mGy*cm(2)) for the OLD group, respectively (p = .001). The median volume of contrast per iliac bifurcation was 13.0 mL (IQR: 13-13 mL) in the NEW and 26 mL (IQR 13-39 mL) in the OLD group (p = .007). Pre-operative simulation of the appropriate C-arm angulation in two dimensions using dedicated computed tomography angiography post-processing software is feasible and significantly reduces radiation and contrast medium exposure. Copyright © 2016 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved.

  4. 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.

  5. Contrast medium-induced nephrotoxicity risk assessment in adult inpatients: a comparison of serum creatinine level- and estimated glomerular filtration rate-based screening methods.

    PubMed

    Davenport, Matthew S; Khalatbari, Shokoufeh; Cohan, Richard H; Ellis, James H

    2013-10-01

    To compare serum creatinine (SCr) level- and estimated glomerular filtration rate (eGFR)-based screening methods for identifying adult inpatients at risk for contrast medium-induced nephrotoxicity (CIN). Institutional review board approval was obtained; informed consent was waived for this HIPAA-compliant retrospective study. Computed tomographic examinations performed during 10 years in adult inpatients with stable renal function were identified (n = 28 390). The proportion of inpatients meeting various eGFR (≥60, <60, <45, <30, 30-44, 45-59 mL/min/1.73 m(2)) and SCr (<1.5, ≥1.5, ≥1.6, ≥1.7, ≥1.8, ≥1.9, ≥2.0 mg/dL) thresholds were contrasted with each other and with published guidelines (≥2.0 mg/dL [SCr] and <45 mL/min/1.73 m(2) [eGFR]) using McNemar and binomial tests. Most inpatients were considered low risk for CIN with commonly used thresholds: 92.6% (26 285 of 28 390) had SCr <1.5 mg/dL; 91.3% (25 922 of 28 390) had eGFR of ≥45 mL/min/1.73 m(2). Using SCr threshold of ≥1.5 mg/dL, identified inpatients had the following eGFRs: 19.6% (413 of 2105), 45-59 mL/min/1.73 m(2); 51.1% (1075 of 2105), 30-44 mL/min/1.73 m(2); 28.6% (603 of 2105), <30 mL/min/1.73 m(2); and 0.7% (14 of 2105), ≥60 mL/min/1.73 m(2) . Using SCr threshold of ≥2.0 mg/dL, identified inpatients had the following eGFRs: 100% (658 of 658), <45 mL/min/1.73 m(2); 74.6% (491 of 658), <30 mL/min/1.73 m(2). Threshold of SCr ≥2.0 mg/dL could not be used to identify eGFR <30 mL/min/1.73 m(2) in 0.4% (112 of 28 390) and <45 mL/min/1.73 m(2) in 6.4% (1810 of 28 390) of all inpatients. Using eGFR <45 mL/min/1.73 m(2) instead of SCr of ≥1.5 mg/dL would result in a significant but small increase in identified inpatients (8.7% [2468 of 28 390; 95% confidence interval: 8.4%, 9.0%] vs 7.4% [2105 of 28 390; 95% confidence interval: 7.1%, 7.7%]; P < .0001). Screening using eGFR <45 mL/min/1.73 m(2) instead of common SCr thresholds would significantly increase the number of inpatients

  6. A comparison of ionic versus nonionic contrast medium during primary percutaneous transluminal coronary angioplasty for acute myocardial infarction (GUSTO IIb). Global Use of Strategies to Open Occluded Coronary Arteries in Acute Coronary Syndromes.

    PubMed

    Batchelor, W B; Granger, C B; Kleiman, N S; Phillips, H R; Ellis, S G; Betriu, A; Criger, D A; Stebbins, A L; Topol, E J; Califf, R M

    2000-03-15

    The clinical impact of contrast medium selection during primary percutaneous transluminal coronary angioplasty for acute myocardial infarction (AMI) has not been studied. We compared the clinical outcomes of patients who received ionic versus nonionic low osmolar contrast medium in the setting of primary percutaneous transluminal coronary angioplasty for AMI in the second Global Use of Strategies to Open Occluded Coronary Arteries in Acute Coronary Syndromes (GUSTO IIb) trial. Univariable and multivariable analyses were performed to assess the relation between contrast medium selection and clinical outcome (death, reinfarction, or refractory ischemia) at 30 days. Although baseline clinical and angiographic characteristics were generally similar between the 2 groups, patients who received ionic, low osmolar contrast were less likely to have been enrolled at a US site (23% vs 43%, p = 0.001) and less likely to have occlusion of the left anterior descending coronary artery (34% vs 47%, p = 0.03) or a history of prior AMI (8% vs 16%, p = 0.02). The triple composite end point of death, reinfarction, or refractory ischemia occurred less frequently in the ionic group, both in the hospital (4.4% vs 11%, p = 0.018) and at 30 days (5.5% vs 11%, p = 0.044). Although the trend favoring ionic contrast persisted, the differences were no longer statistically significant after adjustment for imbalances in baseline characteristics using a risk model developed from the study sample (n = 454, adjusted odds ratio for ionic contrast 0.48 [0.22 to 1.02], p = 0.055), and using a model developed from the entire GUSTO IIb study cohort (n = 12,142, adjusted odds ratio for ionic contrast 0.50 [0.23 to 1.06], p = 0.072). The results of this observational study warrant further elucidation by a randomized study design in this setting.

  7. Macromolecular Imaging Agents Containing Lanthanides: Can Conceptual Promise Lead to Clinical Potential?

    PubMed Central

    Bryson, Joshua; Reineke, Jeffrey W.; Reineke, Theresa M.

    2012-01-01

    Macromolecular magnetic resonance imaging (MRI) contrast agents are increasingly being used to improve the resolution of this noninvasive diagnostic technique. All clinically-approved T1 contrast agents are small molecule chelates of gadolinium [Gd(III)] that affect bound water proton relaxivity. Both the small size and monomeric nature of these agents ultimately limits the image resolution enhancement that can be achieved for both contrast enhancement and pharmacokinetic/biodistribution reasons. The multimeric nature of macromolecules, such as polymers, dendrimers, and noncovalent complexes of small molecule agents with proteins, have been shown to significantly increase the image contrast and resolution due to their large size and ability to incorporate multiple Gd(III) chlelation sites. Also, macromolecular agents are advantageous as they have the ability to be designed to be nontoxic, hydrophilic, easily purified, aggregation-resistant, and have controllable three-dimensional macromolecular structure housing the multiple lanthanide chelation sites. For these reasons, large molecule diagnostics have the ability to significantly increase the relaxivity of water protons within the targeted tissues and thus the image resolution for many diagnostic applications. The FDA approval of a contrast agent that consists of a reversible, non-covalent coupling of a small Gd(III) chelate with serum albumin for blood pool imaging (marketed under the trade names of Vasovist and Ablivar) proved to be one of the first diagnostic agent to capitalize on these benefits from macromolecular association in humans. However, much research and development is necessary to optimize the safety of these unique agents for in vivo use and potential clinical development. To this end, recent work in the field of polymer, dendrimer, and noncovalent complex-based imaging agents are reviewed herein and the future outlook of this field is discussed. PMID:23467737

  8. 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

  9. 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.

  10. Selection and evolution in macromolecular systems.

    PubMed

    Demetrius, L

    1983-08-21

    The notion of a quasi-species represents the ensemble of macromolecular sequences derived by the mechanism of mutation and replication from a single wild type. In Eigen (1971) and Eigen & Schuster (1979), the deterministic evolution of this ensemble under constant environmental conditions is given in terms of continuous models which describe the dynamics of the distribution of polynucleotides. This paper starts from a discrete model of macromolecular evolution and introduces the notion of a genealogy in order to study the dynamics of the quasi-species in constant and variable environments. We introduce, in terms of these genealogies, the notions of entropy and adaptive value of a quasi-species and the notion of capacity of the environment. We discuss the significance of these indices as measures of selective value and we analyse the conditions under which these measures coincide with the growth rate of the quasi-species.

  11. In situ macromolecular crystallography using microbeams.

    PubMed

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

    2012-05-01

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

  12. The structural dynamics of macromolecular processes

    PubMed Central

    Russel, Daniel; Lasker, Keren; Phillips, Jeremy; Schneidman-Duhovny, Dina; Velázquez-Muriel, Javier A.; Sali, Andrej

    2009-01-01

    Summary Dynamic processes involving macromolecular complexes are essential to cell function. These processes take place over a wide variety of length scales from nanometers to micrometers, and over time scales from nanoseconds to many minutes. As a result, information from a variety of different experimental and computational approaches is required. We review the relevant sources of information and introduce a framework for integrating the data to produce representations of dynamic processes. PMID:19223165

  13. Macromolecular extraction based on contour evolution

    NASA Astrophysics Data System (ADS)

    Wang, Zhaobin; Guo, Miao; Zhu, Ying; Yang, Lizhen; Ma, Yi-de

    2013-03-01

    Detecting the region of interest plays an important role in the field of image processing and analysis. For the microscopic image of plant embryo slice, region of interest usually indicates various cells or macromolecules. Combining contour evolution theory and pulse coupled neural network, we propose a new method of macromolecular detection and extraction for biological microscopic image. Some existing methods are compared with the proposed method. Experimental results show the proposed method has the better performance than existing methods.

  14. 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).

  15. Macromolecular nanotheranostics for multimodal anticancer therapy

    NASA Astrophysics Data System (ADS)

    Huis in't Veld, Ruben; Storm, Gert; Hennink, Wim E.; Kiessling, Fabian; Lammers, Twan

    2011-10-01

    Macromolecular carrier materials based on N-(2-hydroxypropyl)methacrylamide (HPMA) are prototypic and well-characterized drug delivery systems that have been extensively evaluated in the past two decades, both at the preclinical and at the clinical level. Using several different imaging agents and techniques, HPMA copolymers have been shown to circulate for prolonged periods of time, and to accumulate in tumors both effectively and selectively by means of the Enhanced Permeability and Retention (EPR) effect. Because of this, HPMA-based macromolecular nanotheranostics, i.e. formulations containing both drug and imaging agents within a single formulation, have been shown to be highly effective in inducing tumor growth inhibition in animal models. In patients, however, as essentially all other tumor-targeted nanomedicines, they are generally only able to improve the therapeutic index of the attached active agent by lowering its toxicity, and they fail to improve the efficacy of the intervention. Bearing this in mind, we have recently reasoned that because of their biocompatibility and their beneficial biodistribution, nanomedicine formulations might be highly suitable systems for combination therapies. In the present manuscript, we briefly summarize several exemplary efforts undertaken in this regard in our labs in the past couple of years, and we show that long-circulating and passively tumor-targeted macromolecular nanotheranostics can be used to improve the efficacy of radiochemotherapy and of chemotherapy combinations.

  16. Surface oxidation of gold nanoparticles supported on a glassy carbon electrode in sulphuric acid medium: contrasts with the behaviour of 'macro' gold.

    PubMed

    Wang, Ying; Laborda, Eduardo; Crossley, Alison; Compton, Richard G

    2013-03-07

    Consecutive electro-oxidation and reduction cycling of gold macroelectrodes in sulphuric acid medium is a widely-used cleaning and calibration procedure. In this paper this method is applied to electrodeposited nanoparticles revealing significant differences in the electro-oxidation process and the cleaning effectiveness. This suggests a higher density of surface defects on the nanoparticles.

  17. Coal chemistry for mechanical engineers: from macromolecular thermodynamics to reservoir simulation

    SciTech Connect

    Vyacheslav Romanov

    2007-06-15

    In pilot trials and commercial scale field demonstrations of CO{sub 2} 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 CO{sub 2} dissolution in the macromolecular network of the coal matrix can be incorporated into geomechanical models. 96 refs., 4 figs.

  18. 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.

  19. Efficient Cryoprotection of Macromolecular Crystals using Vapor Diffusion of Volatile Alcohols

    PubMed Central

    Farley, Christopher; Juers, Douglas H.

    2014-01-01

    Macromolecular X-ray crystallography, usually done at cryogenic temperature to limit radiation damage, often requires liquid cryoprotective soaking that can be labor intensive and damaging to crystals. Here we describe a method for cryoprotection that uses vapor diffusion of volatile cryoprotective agents into loop-mounted crystals. The crystal is mounted into a vial containing a small volume of an alcohol-based cryosolution. After a short incubation with the looped crystal sitting in the cryosolution vapor, the crystal is transferred directly from the vial into the cooling medium. Effective for several different protein crystals, the approach obviates the need for liquid soaking and opens up a heretofore underutilized class of cryoprotective agents for macromolecular crystallography. PMID:25286441

  20. 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

  1. 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

  2. A public database of macromolecular diffraction experiments.

    PubMed

    Grabowski, Marek; Langner, Karol M; Cymborowski, Marcin; Porebski, Przemyslaw J; Sroka, Piotr; Zheng, Heping; Cooper, David R; Zimmerman, Matthew D; Elsliger, Marc André; Burley, Stephen K; Minor, Wladek

    2016-11-01

    The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences. However, there remains no mandate for public disclosure of the original diffraction data. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata. IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability. The resource, which is accessible via the web portal at http://www.proteindiffraction.org, can be searched using various criteria. All data are available for unrestricted access and download. The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallographic studies of biological macromolecules. The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics

  3. Crystallization of macromolecular complexes:. stoichiometric variation screening

    NASA Astrophysics Data System (ADS)

    Stura, Enrico A.; Graille, Marc; Taussig, Michael J.; Sutton, Brian; Gore, Michael G.; Silverman, Gregg J.; Charbonnier, Jean-Baptiste

    2001-11-01

    Theoretically a crystal may contain both complexed and uncomplexed molecules simultaneously in the same lattice. Since we seldom screen for such possibilities, such occurrences are only rarely reported. Here we propose that stoichiometry should be one of the parameters to be screened in the crystallization of macromolecular complexes. By allowing for non-biologically significant stoichiometries, we may increase the chances of crystallizing a macromolecular complex and of selecting arrangements which crystallize better or yield more ordered crystals. Although biological forces tend to be stronger than lattice-building interactions, in the crystal the latter will dominate numerically. By allowing for a varied stoichiometry we permit a wider selection of lattice-building contacts and increase the probability of crystallization. From these theoretical considerations we have developed methodology compatible with classical solubility screening and other well-established crystallization principles. We discuss this technique, stoichiometric variation screening (SVS), as part of a multicomponent system for the enhancement of crystallization of macromolecular complexes. We present this technique as an extension of reverse screening and illustrate the complementarity in the methodology. We present two examples of the use of SVS: the complexes between an immunoglobulin Fab fragment and two bacterial proteins, namely the D domain of protein A from Staphylococcus aureus (SpA) and a single domain of protein L from Peptostreptococcus magnus (PpL). In the first example there are 3 Fab molecules and only 2 SpA D domains (domD) (2 complexed and 1 unliganded Fab), in the second 2 Fabs and only 1 PpL domain (1 complexed and 1 unliganded Fab). SVS has the added and unique advantage that in the same crystal we have information on both the unliganded and complexed states under precisely identical conditions: one structure, two answers. Together with a combinatorial method for complex

  4. 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.

  5. The degree of macromolecular crowding in the cytoplasm and nucleoplasm of mammalian cells is conserved.

    PubMed

    Guigas, Gernot; Kalla, Claudia; Weiss, Matthias

    2007-10-30

    Macromolecular crowding provides the cytoplasm and the nucleoplasm with strongly viscoelastic properties and renders the diffusion of soluble proteins in both fluids anomalous. Here, we have determined the nanoscale viscoelasticity of the cytoplasm and the nucleoplasm in different mammalian cell lines. In contrast to the cell-specific response on the macroscale the nanoscale viscoelasticity (i.e. the behavior on length scales about 100-fold smaller than the cell size) only showed minor variations between different cell types. Similarly, the associated anomalous diffusion properties varied only slightly. Our results indicate a conserved state of macromolecular crowding in both compartments for a variety of mammalian cells with the cytoplasm being somewhat more crowded than the nucleus.

  6. 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.

  7. EIGER detector: application in macromolecular crystallography

    PubMed Central

    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

    2016-01-01

    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

  8. 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.

  9. 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.

  10. Effects of macromolecular crowding on nuclear size.

    PubMed

    Rosania, G R; Swanson, J A

    1995-05-01

    The concentration of macromolecules inside cells is high, and the resultant crowding of cytoplasm can be expected to affect many interactions involving macromolecular assemblies. Here, we have examined the effect of solute size and concentration on nuclear volume in saponin-permeabilized macrophages. Nuclei swelled in the presence of small solutes and shrank reversibly in the presence of larger permeant solutes. Remarkably, the smallest solutes capable of shrinking the nucleus were not excluded by the pores in the nuclear envelope. Indeed, nuclei shrank in the presence of such solutes even after the nuclear envelope had been sheared mechanically or permeabilized with detergent. Nuclei extracted with 1% Triton X-100 shrank in the presence of very high concentrations of small solute molecules (30% w/v) as well as in lower concentrations of larger solutes. Consistent with a macromolecular crowding effect, changes in nuclear volume were dependent on solute size and not simply dependent on the colligative properties of solutes or the exclusion of solutes by the nuclear envelope. Solute size-dependent changes in nuclear volume were independent of the chemical nature of the solutes and of the activity of the ions in the buffer. Together, these observations indicate that high concentrations of macromolecules such as those found inside cells can influence the size of the nucleus by directly affecting nuclear structure.

  11. Macromolecular recognition in the Protein Data Bank

    PubMed Central

    Janin, Joël; Rodier, Francis; Chakrabarti, Pinak; Bahadur, Ranjit P.

    2007-01-01

    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 Å2 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. PMID:17164520

  12. MolSurfer: A macromolecular interface navigator.

    PubMed

    Gabdoulline, Razif R; Wade, Rebecca C; Walther, Dirk

    2003-07-01

    We describe the current status of the Java molecular graphics tool, MolSurfer. MolSurfer has been designed to assist the analysis of the structures and physico-chemical properties of macromolecular interfaces. MolSurfer provides a coupled display of two-dimensional (2D) maps of the interfaces generated with the ADS software and a three-dimensional (3D) view of the macromolecular structure in the Java PDB viewer, WebMol. The interfaces are analytically defined and properties such as electrostatic potential or hydrophobicity are projected on to them. MolSurfer has been applied previously to analyze a set of 39 protein-protein complexes, with structures available from the Protein Data Bank (PDB). A new application, described here, is the visualization of 75 interfaces in structures of protein-DNA and protein-RNA complexes. Another new feature is that the MolSurfer web server is now able to compute and map Poisson-Boltzmann electrostatic potentials of macromolecules onto interfaces. The MolSurfer web server is available at http://projects.villa-bosch.de/mcm/software/molsurfer.

  13. 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

  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.

  15. Dominance hierarchies, diversity and species richness of vascular plants in an alpine meadow: contrasting short and medium term responses to simulated global change

    PubMed Central

    Little, Chelsea J.; Jägerbrand, Annika K.; Molau, Ulf

    2014-01-01

    We studied the impact of simulated global change on a high alpine meadow plant community. Specifically, we examined whether short-term (5 years) responses are good predictors for medium-term (7 years) changes in the system by applying a factorial warming and nutrient manipulation to 20 plots in Latnjajaure, subarctic Sweden. Seven years of experimental warming and nutrient enhancement caused dramatic shifts in dominance hierarchies in response to the nutrient and the combined warming and nutrient enhancement treatments. Dominance hierarchies in the meadow moved from a community being dominated by cushion plants, deciduous, and evergreen shrubs to a community being dominated by grasses, sedges, and forbs. Short-term responses were shown to be inconsistent in their ability to predict medium-term responses for most functional groups, however, grasses showed a consistent and very substantial increase in response to nutrient addition over the seven years. The non-linear responses over time point out the importance of longer-term studies with repeated measurements to be able to better predict future changes. Forecasted changes to temperature and nutrient availability have implications for trophic interactions, and may ultimately influence the access to and palatability of the forage for grazers. Depending on what anthropogenic change will be most pronounced in the future (increase in nutrient deposits, warming, or a combination of them both), different shifts in community dominance hierarchies may occur. Generally, this study supports the productivity–diversity relationship found across arctic habitats, with community diversity peaking in mid-productivity systems and degrading as nutrient availability increases further. This is likely due the increasing competition in plant–plant interactions and the shifting dominance structure with grasses taking over the experimental plots, suggesting that global change could have high costs to biodiversity in the Arctic. PMID

  16. Dominance hierarchies, diversity and species richness of vascular plants in an alpine meadow: contrasting short and medium term responses to simulated global change.

    PubMed

    Alatalo, Juha M; Little, Chelsea J; Jägerbrand, Annika K; Molau, Ulf

    2014-01-01

    We studied the impact of simulated global change on a high alpine meadow plant community. Specifically, we examined whether short-term (5 years) responses are good predictors for medium-term (7 years) changes in the system by applying a factorial warming and nutrient manipulation to 20 plots in Latnjajaure, subarctic Sweden. Seven years of experimental warming and nutrient enhancement caused dramatic shifts in dominance hierarchies in response to the nutrient and the combined warming and nutrient enhancement treatments. Dominance hierarchies in the meadow moved from a community being dominated by cushion plants, deciduous, and evergreen shrubs to a community being dominated by grasses, sedges, and forbs. Short-term responses were shown to be inconsistent in their ability to predict medium-term responses for most functional groups, however, grasses showed a consistent and very substantial increase in response to nutrient addition over the seven years. The non-linear responses over time point out the importance of longer-term studies with repeated measurements to be able to better predict future changes. Forecasted changes to temperature and nutrient availability have implications for trophic interactions, and may ultimately influence the access to and palatability of the forage for grazers. Depending on what anthropogenic change will be most pronounced in the future (increase in nutrient deposits, warming, or a combination of them both), different shifts in community dominance hierarchies may occur. Generally, this study supports the productivity-diversity relationship found across arctic habitats, with community diversity peaking in mid-productivity systems and degrading as nutrient availability increases further. This is likely due the increasing competition in plant-plant interactions and the shifting dominance structure with grasses taking over the experimental plots, suggesting that global change could have high costs to biodiversity in the Arctic.

  17. Fabrication of potential macromolecular prodrugs of aspirin and diclofenac with dextran.

    PubMed

    Hussain, Muhammad Ajaz; Hassan, Zahid; Haseeb, Muhammad Tahir; Iqbal, Mohammad Saeed; Sher, Muhammad; Tahir, Muhammad Nawaz; Tremel, Wolfgung; Bashir, Sajid; Ahmad, Riaz

    2011-10-01

    Aspirin and diclofenac conjugates with dextran were synthesized as potential macromolecular prodrugs under homogeneous reaction conditions by using 4-methyl-benzenesulfonyl chloride as an acylating agent in the presence of triethylamine as a base. Highly pure conjugates with good yields were synthesized by this acylation method. All of the products were found soluble in aqueous medium as well as in dimethylsulfoxide and N,N-dimethylacetamide. The UV/Vis spectrophotometry has indicated the incorporation of drugs in conjugates and extent of substitution of drug onto dextran polymer. Covalent attachment of the drug onto the drug carrier polymer (dextran) was verified by (1)H NMR and Fourier transform infrared (FTIR) spectroscopic analysis. The prodrugs were analysed by powder X-ray diffraction (XRD) measurements. Phase changes were noticed by powder XRD for all macromolecular prodrugs indicating the change of state of matter towards more crystallinity. Therefore, fabricated macromolecular prodrugs are potential candidates to show better pharmacokinetic profile. All of the products were thoroughly characterized by using different spectroscopic techniques.

  18. [Comparative microangiographic and histological study of hepatic metastases. Possible implications in the phenomena of contrast medium uptake in x-ray computed tomography of the neoplastic liver].

    PubMed

    Tshibwabwa-Tumba, E; Marchal, G; Pylyser, K; Verbeken, E; Goddeeris, P; Baert, A L; Lauweryns, J

    1984-10-01

    A comparative study using microangiographic and histologic techniques was realized in 43 metastatic livers, totaling 109 lesions. Three different types of tumor vascularization could be recognized. In 30 lesions, residual vessels could be identified. They constitute the only vascular elements in most of the hypervascular lesions studied. On histology, these vessels corresponded to preserved hepatic arterial branches and portal radicles. 79 lesions appeared hypervascular. In 51 lesions, hypervascularity was due to tortuous irregular vessels, corresponding at microscopy to dysplastic capillaries clearly lined with endothelial cells. On the contrary, in 28 metastases, microangiographies showed amorphous contrast uptake. In these cases the contrast was found in large intercellular spaces without endothelial lining, suggesting free interstitial circulation. These observations suggest that the morphology and the dynamic of CT in liver metastases must be influenced by the arterial or portal venous nature of the different vessels. Furthermore, the extravascular diffusion should be function of the type of tumor circulation. If this circulation is confined to real vessels, diffusion will be function of the structure of the walls of these vessels. On the contrary, if the intratumoral circulation is of the free interstitial type, diffusion will be absent and mixing will occur because of the continuity of vascular and interstitial spaces.

  19. Macromolecular Synthesis and Thymineless Death in Mycoplasma laidlawii B1

    PubMed Central

    Smith, Douglas W.; Hanawalt, Philip C.

    1968-01-01

    The relationships between macromolecular synthesis and viability have been studied in the pleuropneumonia-like organism Mycoplasma laidlawii B adapted to a semidefined grwoth medium. This organism exhibited an absolute growth requirement for the nucleosides uridine and thymidine, a partial requirement for guanosine and deoxyguanosine, but no requirement for adenosine, deoxyadenosine, cytosine, and deoxycytosine. Cytosine and deoxycytosine partially satisfied the requirement for uridine. Loss in viability resulted from thymidine deprivation, but not from a deficiency in other growth requirements. This phenomenon of thymineless death in a mycoplasma is similar in many respects to that reported in other bacterial systems. Chloramphenicol specifically inhibited protein synthesis and allowed deoxyribonucleic acid synthesis to proceed to only about 40% of that normally produced per generation period, while causing less inhibition of ribonucleic acid synthesis. Protein synthesis inhibition permitted thymineless death to a survival level of less than 0.5%, but ribonucleic acid synthesis inhibition resulted in a higher (10%) survival level. These results are consistent with previously noted aspects of thymineless death in Escherichia coli strains, which suggest that thymineless death is coupled to ribonucleic acid synthesis. PMID:4881702

  20. Renal cortical retention of contrast medium on delayed CT and nephropathy following transcatheter arterial chemoembolisation in patients with high serum creatinine level.

    PubMed

    Yamazaki, H; Oi, H; Matshushita, M; Inoue, T; Nakamura, H; Inoue, T

    2002-11-01

    The aim of this study was to investigate the prevalence of renal cortical retention (RCR) of contrast media seen on delayed CT, and nephropathy following transarterial chemoembolisation (TACE) in high-risk patients. The findings of 18 patients with abnormally high serum creatinine levels who underwent TACE were reviewed. Nephropathy was defined as an increase in serum creatinine level of more than 44 micromol l(-1), or more than 25%, on day 1, 3, 7 or 14. RCR was defined as mild (CT value >50) or severe (CT value >100). RCR was seen in 16 cases (89%) and in seven cases (39%) of post-TACE nephropathy. Patients without severe RCR did not develop nephropathy post-TACE, whereas 50% of those with such retention did (p=0.19). Delayed CT appears to have the potential as an early detector of nephropathy post-TACE in high-risk patients.

  1. Induction of Upregulation and Downregulation of the T-Cell Activation Marker CD98 in Patients Undergoing Contrast-Enhanced CT with Iodinated Non-Ionic Dimeric Contrast Medium

    PubMed Central

    Schild, Hans H.

    2009-01-01

    Objective This study was designed to determine prospectively the expression of the multifunctional CD98 protein in peripheral white blood cells in patients receiving iodinated contrast media (CM) for a computed tomography (CT) examination. Materials and Methods In 12 adult patients that received non-ionic dimeric CM (iosimenol or iodixanol), the expression of CD98 was analyzed from samples of peripheral white blood cells obtained prior to, one hour, and 24 hours after CM injection by the use of flow cytometry analysis and the use of the direct immunofluorescence technique. Results Overall, expression of CD98 was significantly downregulated 24 hours after CM injection (51.9%±10.8% vs. 38.8%±16.9%; p < 0.04). Patients that received iosimenol exhibited a more pronounced but not significant decrease of CD98 expression both one hour and 24 hours after CM injection. In an analysis of specific patient responses, CD98 downregulation occurred in eight patients. In two patients, CD98 was upregulated, and in the remaining two patients, expression remained unchanged. No patient acquired an adverse CM reaction. Conclusion This is the first demonstration that CM may be a regulator of CD98 expression. To determine if upregulation is associated with an increased risk for the acquisition of an adverse CM-induced hypersensitivity reaction and if downregulation is associated without a risk for the acquisition of an adverse CM-induced hypersensitivity reaction, further studies with a larger population of patients are required. PMID:19182504

  2. Macromolecular recognition and macroscopic interactions by cyclodextrins.

    PubMed

    Harada, Akira; Takashima, Yoshinori

    2013-10-01

    Herein macromolecular recognition by cyclodextrins (CDs) is summarized. Recognition of macromolecules by CDs is classified as main-chain recognition or side-chain recognition. We found that CDs form inclusion complexes with various polymers with high selectivity. Polyrotaxanes in which many CDs are entrapped in a polymer chain were prepared. Tubular polymers were prepared from the polyrotaxanes. CDs were found to recognize side-chains of polymers selectively. CD host polymers were found to form gels with guest polymers in water. These gels showed self-healing properties. When azobenzene was used as a guest, the gel showed sol-gel transition by photoirradiation. When ferrocene was used, redox-responsive gels were obtained. Macroscopic self-assembly through molecular recognition has been discovered. Photoswitchable gel association and dissociation have been observed.

  3. 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

  4. Nitric Oxide Release Part I. Macromolecular Scaffolds

    PubMed Central

    Riccio, Daniel A.; Schoenfisch, Mark H.

    2012-01-01

    Summary The roles of nitric oxide (NO) in physiology and pathophysiology merit the use of NO as a therapeutic for certain biomedical applications. Unfortunately, limited NO payloads, too rapid NO release, and the lack of targeted NO delivery have hindered the clinical utility of NO gas and low molecular weight NO donor compounds. A wide-variety of NO-releasing macromolecular scaffolds has thus been developed to improve NO’s pharmacological potential. In this tutorial review, we provide an overview of the most promising NO release scaffolds including protein, organic, inorganic, and hybrid organic-inorganic systems. The NO release vehicles selected for discussion were chosen based on their enhanced NO storage, tunable NO release characteristics, and potential as therapeutics. PMID:22362355

  5. Quantum diffusive dynamics of macromolecular transitions

    NASA Astrophysics Data System (ADS)

    Beccara, S. a.; Garberoglio, G.; Faccioli, P.

    2011-07-01

    We study the role of quantum fluctuations of atomic nuclei in the real-time dynamics of non-equilibrium macro-molecular transitions. To this goal we introduce an extension of the dominant reaction pathways formalism, in which the quantum corrections to the classical overdamped Langevin dynamics are rigorously taken into account to order ℏ2. We first illustrate our approach in simple cases, and compare with the results of the instanton theory. Then we apply our method to study the C7eq → C7ax transition of alanine dipeptide. We find that the inclusion of quantum fluctuations can significantly modify the reaction mechanism for peptides. For example, the energy difference which is overcome along the most probable pathway is reduced by as much as 50%.

  6. 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.

  7. The spliceosome: a flexible, reversible macromolecular machine

    PubMed Central

    Hoskins, Aaron A.; Moore, Melissa J.

    2012-01-01

    With more than a hundred individual RNA and protein parts and a highly dynamic assembly and disassembly pathway, the spliceosome is arguably the most complicated macromolecular machine in the eukaryotic cell. This complexity has made kinetic and mechanistic analysis of splicing incredibly challenging. Yet recent technological advances are now providing tools for understanding this process in much greater detail. Ranging from genome-wide analyses of splicing and creation of an orthogonal spliceosome in vivo, to purification of active spliceosomes and observation of single molecules in vitro, such new experimental approaches are yielding significant insight into the inner workings of this remarkable machine. These experiments are rewriting the textbooks, with a new picture emerging of a dynamic, malleable machine heavily influenced by the identity of its pre-mRNA substrate. PMID:22480731

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. Macromolecular Prodrugs of Ribavirin: Structure-Function Correlation as Inhibitors of Influenza Infectivity.

    PubMed

    Riber, Camilla Frich; Hinton, Tracey M; Gajda, Paulina; Zuwala, Kaja; Tolstrup, Martin; Stewart, Cameron; Zelikin, Alexander N

    2017-01-03

    The requirement for new antiviral therapeutics is an ever present need. Particularly lacking are broad spectrum antivirals that have low toxicity. We develop such agents based on macromolecular prodrugs whereby both the polymer chain and the drug released from the polymer upon cell entry have antiviral effects. Specifically, macromolecular prodrugs were designed herein based on poly(methacrylic acid) and ribavirin. Structure-function parameter space was analyzed via the synthesis of 10 polymer compositions varied by molar mass and drug content. Antiviral activity was tested in cell culture against both low and high pathogenic strains of influenza. Lead compounds were successfully used to counter infectivity of influenza in chicken embryos. The lead composition with the highest activity against influenza was also active against another respiratory pathogen, respiratory syncytial virus, providing opportunity to potentially treat infection by the two pathogens with one antiviral agent. In contrast, structure-function activity against the herpes simplex virus was drastically different, revealing limitations of the broad spectrum antiviral agents based on macromolecular prodrugs.

  14. Feasibility of low-dose contrast medium high pitch CT angiography for the combined evaluation of coronary, head and neck arteries.

    PubMed

    Wang, Zhiwei; Chen, Yu; Wang, Yining; Xue, Huadan; Jin, Zhengyu; Kong, Lingyan; Cao, Jian; Li, Shuo

    2014-01-01

    To evaluate the image quality and radiation dose of combined heart, head, and neck CT angiography (CTA) using prospectively electrocardiography (ECG)-triggered high-pitch spiral scan protocol, compared with single coronary CTA. 151 consecutive patients were prospectively included and randomly divided into three groups. Group 1 (n = 47) underwent combined heart, neck, and head CTA using prospectively ECG-triggered high-pitch spiral (Flash) scan protocol with a single-phase intravenous injection of iodinated contrast and saline flush; Group 2 (n = 51) underwent single coronary CTA with Flash scan protocol; and Group 3 (n = 53) underwent single coronary CTA with prospective sequence scan protocol. All patients were examined on a dual source CT (Definition FLASH). The image quality was determined for each CT study. Patients of scanning protocol Group 1, 2, and 3 showed no significant differences in age, sex, heart rates, and BMI. Evaluation of coronary artery image quality showed comparable results in the three scanning protocol groups on a per patient-based analysis. In group 1, image quality was found to be sufficient to be diagnostic in all arterial segments of carotid arteries. The mean dose-length product (DLP) for group 1 was 256.3±24.5 mGy×cm and was significantly higher in comparison with group 2 (93.4±19.9 mGy×cm; p < 0.001). However, there was no significant difference of DLP between group 1 and group 3 (254.1±69.9 mGy×cm). The combined heart, neck, and head arteries scan using prospectively electrocardiography (ECG)-triggered high-pitch spiral scan protocol in 1 single examination resulted in an excellent opacification of the aorta, the carotid arteries, and the coronary arteries and provided a good image quality with low radiation dose.

  15. 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

  16. 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

  17. Gadolinium/terbium hybrid macromolecular complexes for bimodal imaging of atherothrombosis

    NASA Astrophysics Data System (ADS)

    Nghĩa, Nguyen Tráeng; Tinet, Eric; Ettori, Dominique; Beilvert, Anne; Pavon-Djavid, Graciela; Maire, Murielle; Ou, Phalla; Tualle, Jean-Michel; Chaubet, Frédéric

    2017-07-01

    We developed a fluorescence imaging microscope system intended for the localization within artery slices of a gadolinium-based macromolecular biospecific magnetic resonance (MR) contrast agent used for the visualization of atherothrombosis. As the contrast agent is not initially fluorescent, we substitute some gadolinium ions for terbium ions to make them fluorescent while preserving their chemical characteristics. A long fluorescence emission time constant enables us to have a suitable signal-to-noise ratio, despite a low intensity, using pulsed illumination and time-gated imaging. Images of rat arteries show that the contrast agent is indeed localized on the specific regions of the tissues. We currently have a tool that allows us to understand and optimize the MR contrast agent.

  18. 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.

  19. 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.

  20. Comparative evaluation of modified canal staining and clearing technique, cone-beam computed tomography, peripheral quantitative computed tomography, spiral computed tomography, and plain and contrast medium-enhanced digital radiography in studying root canal morphology.

    PubMed

    Neelakantan, Prasanna; Subbarao, Chandana; Subbarao, Chandragiri V

    2010-09-01

    This study investigated the accuracy of cone-beam computed tomography (CBCT), peripheral quantitative computed tomography (pQCT), spiral computed tomography (SCT), plain (plain digi), and contrast medium-enhanced digital radiographs (contrast digi) in studying root canal morphology. The root canal anatomy was analyzed in 95 teeth using CBCT, pQCT, SCT, plain digi, and contrast digi. After flushing out the radiopaque dye, access cavities were sealed, and the teeth were subject to the modified canal staining and clearing technique. The number of root canals (Vertucci classification and Gulabivala's additional classes) was calculated by three calibrated endodontists and two maxillofacial radiologists. Erroneous or unsuccessful identifications of root canals were statistically analyzed by one-way analysis of variance (p = 0.05). The modified canal staining and clearing technique identified an average of 1.8 root canals per mandibular central incisor, 2.3 per maxillary first premolar, 3.9 per maxillary first molar, 3.8 per maxillary and mandibular second molar, and 4.3 per mandibular first molar. CBCT and pQCT were erroneous in 0.29% and 2.05% cases, whereas SCT, contrast digi, and plain digi were unsuccessful in 15.58%, 14.7%, and 23.8%, respectively. There was a significant difference between all the methods (p < 0.05) in the unsuccessful identification of root canals except between CBCT and modified canal staining and clearing technique where there was no significant difference (p > 0.05). CBCT and pQCT were as accurate as the modified canal staining and tooth clearing technique in identifying root canal systems. Copyright 2010 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  1. An upper limit for macromolecular crowding effects

    PubMed Central

    2011-01-01

    Background Solutions containing high macromolecule concentrations are predicted to affect a number of protein properties compared to those properties in dilute solution. In cells, these macromolecular crowders have a large range of sizes and can occupy 30% or more of the available volume. We chose to study the stability and ps-ns internal dynamics of a globular protein whose radius is ~2 nm when crowded by a synthetic microgel composed of poly(N-isopropylacrylamide-co-acrylic acid) with particle radii of ~300 nm. Results Our studies revealed no change in protein rotational or ps-ns backbone dynamics and only mild (~0.5 kcal/mol at 37°C, pH 5.4) stabilization at a volume occupancy of 70%, which approaches the occupancy of closely packing spheres. The lack of change in rotational dynamics indicates the absence of strong crowder-protein interactions. Conclusions Our observations are explained by the large size discrepancy between the protein and crowders and by the internal structure of the microgels, which provide interstitial spaces and internal pores where the protein can exist in a dilute solution-like environment. In summary, microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects. PMID:21627822

  2. 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.

  3. Macromolecular components of tomato fruit pectin.

    PubMed

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

    1989-10-01

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

  4. The solvent component of macromolecular crystals

    SciTech Connect

    Weichenberger, Christian X.; Kantardjieff, Katherine; Rupp, Bernhard

    2015-04-30

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

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

    PubMed Central

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

    2016-01-01

    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

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. Determining contrast medium dose and rate on basis of lean body weight: does this strategy improve patient-to-patient uniformity of hepatic enhancement during multi-detector row CT?

    PubMed

    Ho, Lisa M; Nelson, Rendon C; Delong, David M

    2007-05-01

    To prospectively evaluate the use of lean body weight (LBW) as the main determinant of the volume and rate of contrast material administration during multi-detector row computed tomography of the liver. This HIPAA-compliant study had institutional review board approval. All patients gave written informed consent. Four protocols were compared. Standard protocol involved 125 mL of iopamidol injected at 4 mL/sec. Total body weight (TBW) protocol involved 0.7 g iodine per kilogram of TBW. Calculated LBW and measured LBW protocols involved 0.86 g of iodine per kilogram and 0.92 g of iodine per kilogram calculated or measured LBW for men and women, respectively. Injection rate used for the three experimental protocols was determined proportionally on the basis of the calculated volume of contrast material. Postcontrast attenuation measurements during portal venous phase were obtained in liver, portal vein, and aorta for each group and were summed for each patient. Patient-to-patient enhancement variability in same group was measured with Levene test. Two-tailed t test was used to compare the three experimental protocols with the standard protocol. Data analysis was performed in 101 patients (25 or 26 patients per group), including 56 men and 45 women (mean age, 53 years). Average summed attenuation values for standard, TBW, calculated LBW, and measured LBW protocols were 419 HU +/- 50 (standard deviation), 443 HU +/- 51, 433 HU +/- 50, and 426 HU +/- 33, respectively (P = not significant for all). Levene test results for summed attenuation data for standard, TBW, calculated LBW, and measured LBW protocols were 40 +/- 29, 38 +/- 33 (P = .83), 35 +/- 35 (P = .56), and 26 +/- 19 (P = .05), respectively. By excluding highly variable but poorly perfused adipose tissue from calculation of contrast medium dose, the measured LBW protocol may lessen patient-to-patient enhancement variability while maintaining satisfactory hepatic and vascular enhancement.

  11. Macromolecular Antioxidants and Dietary Fiber in Edible Seaweeds.

    PubMed

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

    2017-02-01

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

  12. RECENT ADVANCES IN MACROMOLECULAR HYDRODYNAMIC MODELING

    PubMed Central

    Aragon, Sergio R.

    2010-01-01

    The modern implementation of the boundary element method (S.R. Aragon, J. Comput. Chem. 25(2004)1191–12055) has ushered unprecedented accuracy and precision for the solution of the Stokes equations of hydrodynamics with stick boundary conditions. This article begins by reviewing computations with the program BEST of smooth surface objects such as ellipsoids, the dumbbell, and cylinders that demonstrate that the numerical solution of the integral equation formulation of hydrodynamics yields very high precision and accuracy. When BEST is used for macromolecular computations, the limiting factor becomes the definition of the molecular hydrodynamic surface and the implied effective solvation of the molecular surface. Studies on 49 different proteins, ranging in molecular weight from 9 to over 400 kDa, have shown that a model using a 1.1 A thick hydration layer describes all protein transport properties very well for the overwhelming majority of them. In addition, this data implies that the crystal structure is an excellent representation of the average solution structure for most of them. In order to investigate the origin of a handful of significant discrepancies in some multimeric proteins (over −20% observed in the intrinsic viscosity), the technique of Molecular Dynamics simulation (MD) has been incorporated into the research program. A preliminary study of dimeric α-chymotrypsin using approximate implicit water MD is presented. In addition I describe the successful validation of modern protein force fields, ff03 and ff99SB, for the accurate computation of solution structure in explicit water simulation by comparison of trajectory ensemble average computed transport properties with experimental measurements. This work includes small proteins such as lysozyme, ribonuclease and ubiquitin using trajectories around 10 ns duration. We have also studied a 150 kDa flexible monoclonal IgG antibody, trastuzumab, with multiple independent trajectories encompassing over

  13. Polysaccharide-based micro/nanohydrogels for delivering macromolecular therapeutics.

    PubMed

    Ganguly, Kuntal; Chaturvedi, Kiran; More, Uttam A; Nadagouda, Mallikarjuna N; Aminabhavi, Tejraj M

    2014-11-10

    Increased interest in developing novel micro/nanohydrogel based formulations for delivering macromolecular therapeutics has led to multiple choices of biodegradable and biocompatible natural polymers. This interest is largely due to the availability of large number of highly pure recombinant proteins and peptides with tunable properties as well as RNA interference technology that are used in treating some of the deadly diseases that were difficult to be treated by the conventional approaches. The majority of marketed drugs that are now available are in the form of injectables that pose limited patient compliance and convenience. On the other hand, micro/nanotechnology based macromolecular delivery formulations offer many alternative routes of administration and advantages with improved patient compliance and efficient or targeted delivery of intracellular therapeutics to the site of action. This review outlines and critically evaluates the research findings on micro and nano-carrier polymeric hydrogels for the delivery of macromolecular therapeutics.

  14. Macromolecular crystallography beamline X25 at the NSLS.

    PubMed

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

    2014-05-01

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

  15. 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

  16. Electrostatics in the self-assembly of macromolecular surfactants

    NASA Astrophysics Data System (ADS)

    Mendes, E.; Schädler, V.; Marques, C. M.; Lindner, P.; Wiesner, U.

    1997-12-01

    We report on a small-angle neutron scattering (SANS) study of dilute solutions of neutral and charged polystyrene-polyisoprene (PS-b-PI) diblock copolymers in dimethyl acetamide (DMAc), a polar selective solvent for PS. This is a model macromolecular surfactant system: the low glass temperature of the PI block ensures that thermodynamic equilibrium can be attained; the ionic character of the copolymers is provided by a single sulfonate group at the free chain end of the PI block. The crossover from ionic to non-ionic behaviour is investigated by addition of salt. The results are compared to theoretical predictions for micellization of these model macromolecular systems.

  17. Crystallization of macromolecular complexes: combinatorial complex crystallization

    NASA Astrophysics Data System (ADS)

    Stura, Enrico A.; Graille, Marc; Charbonnier, Jean-Baptiste

    2001-11-01

    The usefulness of antibody complexation, as a way of increasing the chances of crystallization needs to be re-evaluated after many antibody complexes have been crystallized and their structure determined. It is somewhat striking that among these, only a small number is a complex with a large protein antigen. The problem is that the effort of raising, cleaving and purifying an Fab is rewarded only by an extra chance of getting crystals; depending on the relative likelihood of crystallization of the complexed and uncomplexed protein. The example of the complex between HIV gp120, CD4 and an Fab fragment from a neutralizing antibody suggests that further complexation of an antigen-antibody complex with a third protein could, by increasing the number of possible combinations, improve the likelihood of crystallization. We propose the use of Ig-binding proteins as a way of extending the method from HIV gp120 to all proteins for which there are monoclonal antibodies. We discuss this technique, combinatorial complex crystallization (CCC), as part of a multi-component system for the enhancement of crystallization of macromolecular complexes. The method makes use of single Ig-binding domains from Staphylococcus aureus protein A (SpA), Peptostreptococcus magnus protein L (PpL) and the streptococcal protein G (SpG). The generality of the method depends on the ability of these domains to interact with a large repertoire of antibodies without affecting antigen binding. There is strong evidence to suggest that these Ig-binding domains bind outside the antigen-combining site of the antibody without perturbing antigen binding. It is clear from the crystal structure of the single SpG domain complexed with an Fab that the interaction involves mainly the immunoglobulin CH1 domain, a region not involved in antigen recognition. We have recently determined the structure of the complex between a human Fab and the domain D from SpA and found that steric hindrance is unlikely even for large

  18. 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

  19. Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion

    PubMed Central

    Golkaram, Mahdi; Hellander, Stefan; Drawert, Brian; Petzold, Linda R.

    2016-01-01

    We seek to elucidate the role of macromolecular crowding in transcription and translation. It is well known that stochasticity in gene expression can lead to differential gene expression and heterogeneity in a cell population. Recent experimental observations by Tan et al. have improved our understanding of the functional role of macromolecular crowding. It can be inferred from their observations that macromolecular crowding can lead to robustness in gene expression, resulting in a more homogeneous cell population. We introduce a spatial stochastic model to provide insight into this process. Our results show that macromolecular crowding reduces noise (as measured by the kurtosis of the mRNA distribution) in a cell population by limiting the diffusion of transcription factors (i.e. removing the unstable intermediate states), and that crowding by large molecules reduces noise more efficiently than crowding by small molecules. Finally, our simulation results provide evidence that the local variation in chromatin density as well as the total volume exclusion of the chromatin in the nucleus can induce a homogenous cell population. PMID:27893768

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

    SciTech Connect

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

    2006-03-28

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

  1. 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.

  2. Insights into the disparate action of osmolytes and macromolecular crowders on amyloid formation

    PubMed Central

    Sukenik, Shahar

    2012-01-01

    It is widely recognized that amyloid formation sensitively responds to conditions set by myriad cellular solutes. These cosolutes include two important classes: macromolecular crowders and compatible osmolytes. We have recently found that addition of macromolecular PEG only slightly affects fibril formation of a model peptide in vitro. Polyol osmolytes, in contrast, lengthen the lag time for aggregation, and lead to larger fibril mass at equilibrium. To further hypothesize on the molecular underpinnings of the disparate effect of the two cosolute classes, we have further analyzed the experiments using an available kinetic mechanism describing fibril aggregation. Model calculations suggest that all cosolutes similarly lengthen the time required for nucleation, possibly due to their excluded volume effect. However, PEGs may in addition promote fibril fragmentation, leading to lag times that are overall almost unvaried. Moreover, polyols effectively slow the monomer-fibril detachment rates, thereby favoring additional fibril formation. Our analysis provides first hints that cosolutes act not only by changing association or dissociation rates, but potentially also by directing the formation of fibrils of varied morphologies with different mechanical properties. Although additional experiments are needed to unambiguously resolve the action of excluded cosolutes on amyloid formation, it is becoming clear that these compounds are important to consider in the search for ways to modulate fibril formation. PMID:22453174

  3. A new parallel method for molecular dynamics simulation of macromolecular systems

    SciTech Connect

    Plimpton, S.; Hendrickson, B.

    1994-08-01

    Short-range molecular dynamics simulations of molecular systems are commonly parallelized by replicated-data methods, where each processor stores a copy of all atom positions. This enables computation of bonded 2-, 3-, and 4-body forces within the molecular topology to be partitioned among processors straightforwardly. A drawback to such methods is that the inter-processor communication scales as N, the number of atoms, independent of P, the number of processors. Thus, their parallel efficiency falls off rapidly when large numbers of processors are used. In this paper a new parallel method called force-decomposition for simulating macromolecular or small-molecule systems is presented. Its memory and communication costs scale as N/{radical}P, allowing larger problems to be run faster on greater numbers of processors. Like replicated-data techniques, and in contrast to spatial-decomposition approaches, the new method can be simply load-balanced and performs well even for irregular simulation geometries. The implementation of the algorithm in a prototypical macromolecular simulation code ParBond is also discussed. On a 1024-processor Intel Paragon, ParBond runs a standard benchmark simulation of solvated myoglobin with a parallel efficiency of 61% and at 40 times the speed of a vectorized version of CHARMM running on a single Cray Y-MP processor.

  4. Code generation through annotation of macromolecular structure data.

    PubMed

    Biggs, J; Pu, C; Bourne, P

    1997-01-01

    The maintenance of software which uses a rapidly evolving data annotation scheme is time consuming and expensive. At the same time without current software the annotation scheme itself becomes limited and is less likely to be widely adopted. A solution to this problem has been developed for the macromolecular Crystallographic Information File (mmCIF) annotation scheme. The approach could be generalized for a variety of annotation schemes used or proposed for molecular biology data. mmCIF provides a highly structured and complete annotation for describing NMR and X-ray crystallographic data and the resulting macromolecular structures. This annotation is maintained in the mmCIF dictionary which currently contains over 3,200 terms. A major challenge is to maintain code for converting between mmCIF and Protein Data Bank (PDB) annotations while both continue to evolve. The solution has been to define a simple domain specific language (DSL) which is added to the extensive annotation already found in the mmCIF dictionary. The DSL calls specific mapping modules for each category of data item in the mmCIF dictionary. Adding or changing the mapping between PDB and mmCIF items of data is straightforward since data categories (and hence mapping modules) correspond to elements of macromolecular structure familiar to the experimentalist. Each time a change is made to the macromolecular annotation the appropriate change is made to the easily located and modifiable mapping modules. A code generator is then called which reads the mapping modules and creates a new executable for performing the data conversion. In this way code is easily kept current by individuals with limited programming skill, but who have an understanding of macromolecular structure and details of the annotation scheme. Most important, the conversion process becomes part of the global dictionary and is not open to a variety of interpretations by different research groups writing code based on dictionary contents

  5. Combined Effects of Agitation, Macromolecular Crowding, and Interfaces on Amyloidogenesis*

    PubMed Central

    Lee, Chiu Fan; Bird, Sarah; Shaw, Michael; Jean, Létitia; Vaux, David J.

    2012-01-01

    Amyloid formation and accumulation is a hallmark of protein misfolding diseases and is associated with diverse pathologies including type II diabetes and Alzheimer's disease (AD). In vitro, amyloidogenesis is widely studied in conditions that do not simulate the crowded and viscous in vivo environment. A high volume fraction of most biological fluids is occupied by various macromolecules, a phenomenon known as macromolecular crowding. For some amyloid systems (e.g. α-synuclein) and under shaking condition, the excluded volume effect of macromolecular crowding favors aggregation, whereas increased viscosity reduces the kinetics of these reactions. Amyloidogenesis can also be catalyzed by hydrophobic-hydrophilic interfaces, represented by the air-water interface in vitro and diverse heterogeneous interfaces in vivo (e.g. membranes). In this study, we investigated the effects of two different crowding polymers (dextran and Ficoll) and two different experimental conditions (with and without shaking) on the fibrilization of amyloid-β peptide, a major player in AD pathogenesis. Specifically, we demonstrate that, during macromolecular crowding, viscosity dominates over the excluded volume effect only when the system is spatially non homogeneous (i.e. an air-water interface is present). We also show that the surfactant activity of the crowding agents can critically influence the outcome of macromolecular crowding and that the structure of the amyloid species formed may depend on the polymer used. This suggests that, in vivo, the outcome of amyloidogenesis may be affected by both macromolecular crowding and spatial heterogeneity (e.g. membrane turn-over). More generally, our work suggests that any factors causing changes in crowding may be susceptibility factors in AD. PMID:22988239

  6. Functionalized biopolymers as soluble macromolecular chelating agents.

    PubMed

    Giraudi, G; Baggiani, C; Giovannoli, C; Anfossi, L; Tozzi, C; Vanni, A

    2001-01-01

    Two different conjugates of bovine serum albumin (BSA) with lysine and a derivative of imidazole have been synthesized to obtain watersoluble macromolecules with binding properties against bivalent transition metal ions. Syntheses have been carried out using the 60 aminogroups or the 99 carboxylic groups on BSA for the coupling reactions, with such molar ratios able to produce highly substituted BSA. The skill of each conjugate to bind metal ions in aqueous medium was studied through the use of titration curves with some metal ions, characterized by a good affinity for the free ligand. Both the conjugates allow us to recover a high number of metal ions per protein molecule, close to the number of ligand molecules on the BSA surface in the case of the lysine conjugate, whereas in the case of the imidazole conjugate M3L complexes are performed.

  7. Contrast Materials

    MedlinePlus

    ... veins of the body, including vessels in the brain, neck, chest, abdomen, pelvis and legs soft tissues of the body, including the muscles, fat and skin brain breast Microbubble Contrast Materials Microbubble contrast materials are ...

  8. Contrast Materials

    MedlinePlus

    ... of page Side effects and adverse and allergic reactions Barium Sulfate Contrast Materials You should tell your ... You are at greater risk of an adverse reaction to barium-sulfate contrast materials if: you have ...

  9. 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.

  10. Toll-like receptor signalling through macromolecular protein complexes.

    PubMed

    Bryant, Clare E; Symmons, Martyn; Gay, Nicholas J

    2015-02-01

    The molecular mechanisms by which pattern recognition receptors (PRRs) signal are increasingly well understood. Toll-like receptor 4 (TLR4) signals through two separate pairs of adaptor proteins Mal/MyD88 and Tram/Trif. Structural studies have revealed a common theme for PRR signalling in that their signalling proteins form large macromolecular complexes which are thought to form the active signalling complex. The first of these to be characterised was the MyD88 signalling complex Myddosome. Many questions remain unanswered however. In particular it is unclear whether these signalling complexes form within the living cell, how many of each signalling protein is within the intracellular Myddosome and whether the stoichiometry can vary in a ligand-dependent manner. In this review we will discuss what is known about the macromolecular complexes thought to be important for TLR4 signalling. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. 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.

  12. Macromolecular metamorphosis via stimulus-induced transformations of polymer architecture

    NASA Astrophysics Data System (ADS)

    Sun, Hao; Kabb, Christopher P.; Dai, Yuqiong; Hill, Megan R.; Ghiviriga, Ion; Bapat, Abhijeet P.; Sumerlin, Brent S.

    2017-08-01

    Macromolecular architecture plays a pivotal role in determining the properties of polymers. When designing polymers for specific applications, it is not only the size of a macromolecule that must be considered, but also its shape. In most cases, the topology of a polymer is a static feature that is inalterable once synthesized. Using reversible-covalent chemistry to prompt the disconnection of chemical bonds and the formation of new linkages in situ, we report polymers that undergo dramatic topological transformations via a process we term macromolecular metamorphosis. Utilizing this technique, a linear amphiphilic block copolymer or hyperbranched polymer undergoes 'metamorphosis' into comb, star and hydrophobic block copolymer architectures. This approach was extended to include a macroscopic gel which transitioned from a densely and covalently crosslinked network to one with larger distances between the covalent crosslinks when heated. These architectural transformations present an entirely new approach to 'smart' materials.

  13. Maintaining network security: how macromolecular structures cross the peptidoglycan layer.

    PubMed

    Scheurwater, Edie M; Burrows, Lori L

    2011-05-01

    Peptidoglycan plays a vital role in bacterial physiology, maintaining cell shape and resisting cellular lysis from high internal turgor pressures. Its integrity is carefully maintained by controlled remodeling during growth and division by the coordinated activities of penicillin-binding proteins, lytic transglycosylases, and N-acetylmuramyl-l-alanine amidases. However, its small pore size (∼2 nm) and covalently closed structure make it a formidable barrier to the assembly of large macromolecular cell-envelope-spanning complexes involved in motility and secretion. Here, we review the strategies used by Gram-negative bacteria to assemble such macromolecular complexes across the peptidoglycan layer, while preserving its essential structural role. In addition, we discuss evidence that suggests that peptidoglycan can be integrated into cell-envelope-spanning complexes as a structural and functional extension of their architecture.

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

    PubMed

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

    2014-02-01

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

  15. 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.

  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. Branched Macromolecular Architectures for Degradable, Multifunctional Phosphorus-Based Polymers.

    PubMed

    Henke, Helena; Brüggemann, Oliver; Teasdale, Ian

    2017-02-01

    This feature article briefly highlights some of the recent advances in polymers in which phosphorus is an integral part of the backbone, with a focus on the preparation of functional, highly branched, soluble polymers. A comparison is made between the related families of materials polyphosphazenes, phosphazene/phosphorus-based dendrimers and polyphosphoesters. The work described herein shows this to be a rich and burgeoning field, rapidly catching up with organic chemistry in terms of the macromolecular synthetic control and variety of available macromolecular architectures, whilst offering unique property combinations not available with carbon backbones, such as tunable degradation rates, high multi-valency and facile post-polymerization functionalization. As an example of their use in advanced applications, we highlight some investigations into their use as water-soluble drug carriers, whereby in particular the degradability in combination with multivalent nature has made them useful materials, as underlined by some of the recent studies in this area.

  18. Temperature-dependent macromolecular X-ray crystallography

    SciTech Connect

    Weik, Martin Colletier, Jacques-Philippe

    2010-04-01

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

  19. Enhancement of scleral macromolecular permeability with prostaglandins.

    PubMed Central

    Weinreb, R N

    2001-01-01

    PURPOSE: It is proposed that the sclera is a metabolically active and pharmacologically responsive tissue. These studies were undertaken to determine whether prostaglandin exposure can enhance scleral permeability to high-molecular-weight substances. METHODS: Topical prostaglandin F2 alpha (PGF2 alpha) was administered to monkeys to determine if this altered the amount of scleral matrix metalloproteinases (MMPs). Experiments also were performed to determine whether the prostaglandin F (FP) receptor and gene transcripts are expressed in normal human sclera. Permeability of organ-cultured human sclera following prostaglandin exposure then was studied and the amount of MMP released into the medium measured. Finally, the permeability of human sclera to basic fibroblast growth factor (FGF-2) was determined following prostaglandin exposure. RESULTS: Topical prostaglandin administration that reduced scleral collagen also increased scleral MMP-1, MMP-2, and MMP-3 by 63 +/- 35%, 267 +/- 210%, and 729 +/- 500%, respectively. FP receptor protein was localized in scleral fibroblasts, and FP receptor gene transcript was identified in sclera. Exposure to prostaglandin F2 alpha, 17-phenyltrinor, PGF2 alpha, or latanoprost acid increased scleral permeability by up to 124%, 183%, or 213%, respectively. In these cultures, MMP-1, MMP-2, and MMP-3 were increased by up to 37%, 267%, and 96%, respectively. Finally, transscleral absorption of FGF-2 was increased by up to 126% with scleral exposure to latanoprost. CONCLUSIONS: These studies demonstrate that the sclera is metabolically active and pharmacologically responsive to prostaglandins. Further, they demonstrate the feasibility of cotreatment with prostaglandin to enhance transscleral delivery of peptides, such as growth factors and high-molecular-weight substances, to the posterior segment of the eye. PMID:11797317

  20. Third-generation Dual-source CT for Head and Neck CT Angiography with 70 kV Tube Voltage and 20-25 ml Contrast Medium in Patients With Body Weight Lower than 75 kg.

    PubMed

    Chen, Yu; Zhu, Yuanli; Xue, Huadan; Wang, Yun; Li, Yumei; Zhang, Zhuhua; Jin, Zhengyu

    2017-02-20

    Objective To investigate the image quality of head and neck CT angiography (CTA)using the third-generation dual-source CT combined with 70 kV tube voltage and 20-25 ml contrast medium (CM),and evaluate the effects of venous artifacts arising from the CM on the ipsilateral side of injection. Methods Totally 40 consecutive patients with suspected vascular diseases and body weight lower than 75 kg prospectively underwent head and neck CTA examination using the third-generation dual-source CT. CTA was performed with a third-generation dual-source CT system. Patients were randomly divived into 70 kV group (n=20)and 100 kV group (n=20). The 70 kV group used 20-25 ml CM and advanced modeled iterative reconstruction technique,and the 100 kV group used 40 ml CM and filtered back projection. Venous artifacts and CM residues were evaluated by a 3-point scale (1=excellent,3=poor),respectively. Results The effective dose of 70 kV group decreased 58% compared to 100 kV group (t=-18.14,P<0.001).In the 70 kV group,16 patients (80.0%)presented with venous artifacts and six of them (37.5%,6/16)affected the adjacent arteries. In the 100 kV group,19 patients (95.0%)presented with venous artifacts,and seven of them (36.8%,7/19)affected the adjacent arteries (Z=-0.878,P=0.380). In the 70 kV group,13 patients (65.0%)presented with obvious CM residues and two of them (15.3%,2/13)prolonged into the superior vena cava (SVC). In the 100 kV group,19 patients(95.0%)presented with obvious CM residues,and thirteen of them(68.4%,13/19)prolonged into the SVC (Z=-3.654,P<0.001). Conclusion Compared with the 100 kV,the third-generation dual-source CT for head and neck CTA,combined with 70 kV and 20-25 ml CM,can remarkably decrease the radiation dose,along with reduced CM residues and comparable venous artifacts.

  1. Short-Term High-Dose Vitamin E to Prevent Contrast Medium-Induced Acute Kidney Injury in Patients With Chronic Kidney Disease Undergoing Elective Coronary Angiography: A Randomized Placebo-Controlled Trial.

    PubMed

    Rezaei, Yousef; Khademvatani, Kamal; Rahimi, Behzad; Khoshfetrat, Mehran; Arjmand, Nasim; Seyyed-Mohammadzad, Mir-Hossein

    2016-03-15

    Contrast medium-induced acute kidney injury (CIAKI) is a leading cause of acquired renal impairment. The effects of antioxidants have been conflicting regarding the prevention of CIAKI. We performed a study of vitamin E use to decrease CIAKI in patients undergoing elective coronary angiography. In a placebo-controlled randomized trial at 2 centers in Iran, 300 patients with chronic kidney disease-defined as estimated glomerular filtration rate <60 mL/min per 1.73 m(2)-were randomized 1:1 to receive 0.9% saline infusion 12 hours prior to and after intervention combined with 600 mg vitamin E 12 hours before plus 400 mg vitamin E 2 hours before coronary angiography or to receive placebo. The primary end point was the development of CIAKI, defined as an increase ≥0.5 mg/dL or ≥25% in serum creatinine that peaked within 72 hours. Based on an intention-to-treat analysis, CIAKI developed in 10 (6.7%) and 21 (14.1%) patients in the vitamin E and placebo groups, respectively (P=0.037). Change in white blood cell count from baseline to peak value was greater in the vitamin E group compared with the placebo group (-500 [-1500 to 200] versus 100 [-900 to 600]×10(3)/mL, P=0.001). In multivariate analysis, vitamin E (odds ratio 0.408, 95% CI 0.170-0.982, P=0.045) and baseline Mehran score (odds ratio 1.257, 95% CI 1.007-1.569; P=0.043) predicted CIAKI. Prophylactic short-term high-dose vitamin E combined with 0.9% saline infusion is superior to placebo for prevention of CIAKI in patients undergoing elective coronary angiography. URL: https://www.clinicaltrials.gov/. Unique identifier: NCT02070679. © 2016 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

  2. 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

  3. 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

  4. Ultrashort Laser Pulse Induced Electromagnetic Stress on Biological Macromolecular Systems.

    DTIC Science & Technology

    1979-11-01

    ULTRASHORT LASER PULSE INDUCED ~~~~~ ELECTROMAGNET IC STRESS ON BIOLOGICAL MACROMOLECULAR SYSTEMS Adam P. Bruckner , Ph.D. ( i~iiCJ. Michael ...AFSC, Brooks Air Force Base, Texas. Dr. John Taboada (RZL) was the Laboratory Project Scientjst..in...Charge When U.S. Goverrijie~t drawings...available to the general public , including foreignnations. Thi s technical report has been reviewed and is approved for publ i-cation. OHN TABOADA , Ph.D

  5. Fast native-SAD phasing for routine macromolecular structure determination.

    PubMed

    Weinert, Tobias; Olieric, Vincent; Waltersperger, Sandro; Panepucci, Ezequiel; Chen, Lirong; Zhang, Hua; Zhou, Dayong; Rose, John; Ebihara, Akio; Kuramitsu, Seiki; Li, Dianfan; Howe, Nicole; Schnapp, Gisela; Pautsch, Alexander; Bargsten, Katja; Prota, Andrea E; Surana, Parag; Kottur, Jithesh; Nair, Deepak T; Basilico, Federica; Cecatiello, Valentina; Pasqualato, Sebastiano; Boland, Andreas; Weichenrieder, Oliver; Wang, Bi-Cheng; Steinmetz, Michel O; Caffrey, Martin; Wang, Meitian

    2015-02-01

    We describe a data collection method that uses a single crystal to solve X-ray structures by native SAD (single-wavelength anomalous diffraction). We solved the structures of 11 real-life examples, including a human membrane protein, a protein-DNA complex and a 266-kDa multiprotein-ligand complex, using this method. The data collection strategy is suitable for routine structure determination and can be implemented at most macromolecular crystallography synchrotron beamlines.

  6. 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

  7. 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

  8. Comparison of the iron oxide-based blood-pool contrast medium VSOP-C184 with gadopentetate dimeglumine for first-pass magnetic resonance angiography of the aorta and renal arteries in pigs.

    PubMed

    Schnorr, Jörg; Wagner, Susanne; Abramjuk, Claudia; Wojner, Ines; Schink, Tania; Kroencke, Thomas J; Schellenberger, Eyk; Hamm, Bernd; Pilgrimm, Herbert; Taupitz, Matthias

    2004-09-01

    VSOP-C184 at a dose of 0.045 mmol Fe/kg has been shown to be an efficient blood pool contrast medium for equilibrium magnetic resonance angiography (MRA) that can be administered as a bolus. The present study was performed to determine whether VSOP-C184 is also suitable for first-pass MRA. Fifteen MRA examinations at 1.5 T were performed in minipigs using a fast 3D fast low-angle shot (FLASH) sequence (repetition time = 4.5 ms, echo time = 1.7 ms, excitation angle = 25 degrees, matrix 256, body phased-array coil). The citrate-stabilized iron oxide preparation VSOP-C184 was investigated (total particle diameter: 7.0 +/- 0.15 nm; core size: 4 nm) and compared with gadopentetate dimeglumine (Gd-DTPA). The following doses were tested: VSOP-C184: 0.015, 0.025, and 0.035 mmol Fe/kg; Gd-DTPA: 0.1 and 0.2 mmol Gd/kg; n = 3 examinations/dose. Data were analyzed quantitatively (signal enhancement (ENH) and vessel edge definition (VED)) and qualitatively. First-pass MRA using the 3 doses of VSOP-C184 yielded the following ENH: aorta: 9.4 +/- 2.6; 12.31 +/- 1.2; 16.53 +/- 1.7; renal arteries: 7.6 +/- 2.2; 9.9 +/- 1.0; 13.2 +/- 0.5. The values for the 2 doses of Gd-DTPA were aorta: 12.9 +/- 1.0; 16.8 +/- 2.2; renal arteries: 11.2 +/- 1.23; 11.3 +/- 1.7. VED for the 3 doses of VSOP-C184 was aorta: 106.3 +/- 31.0; 135.3 +/- 58.8; 141.3 +/- 71.0; renal arteries: 102.2 +/- 24.3; 146.8 +/- 63.0; 126.9 +/- 37.6 and for the 2 doses of Gd-DTPA, aorta: 157.2 +/- 47.8; 164.2 +/- 36.8; renal arteries: 165.9 +/- 30.4; 170.3 +/- 38.2 respectively. The differences between VSOP-C184 and Gd-DTPA are clinically not relevant and statistically not significant (p > or = .05). Qualitative evaluation of image quality, contrast, and delineation of vessels showed the results obtained with VSOP-C184 at doses of 0.025 and 0.035 mmol Fe/kg to be similar to those of Gd-DTPA at 0.1 and 0.2 mmol Gd/kg. VSOP-C184 is suitable for first-pass MRA at doses of 0.025 and 0.035 mmol Fe/kg and thus, in addition to

  9. Macromolecular amplification of binding response in superaptamer hydrogels.

    PubMed

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

    2013-05-08

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

  10. Polybivalency and disordered proteins in ordering macromolecular assemblies.

    PubMed

    Barbar, Elisar; Nyarko, Afua

    2015-01-01

    Intrinsically disordered proteins (IDPs) are prevalent in macromolecular assemblies and are thought to mediate protein recognition in complex regulatory processes and signaling pathways. The formation of a polybivalent scaffold is a key process by which IDPs drive early steps in macromolecular assemblies. Three intrinsically disordered proteins, IC, Swallow and Nup159, are core components, respectively, of cytoplasmic dynein, bicoid mRNA localization apparatus, and nuclear pore complexes. In all three systems, the hub protein LC8 recognizes on the IDP, short linear motifs that are fully disordered in the apo form, but adopt a β-strand when bound to LC8. The IDP/LC8 complex forms a bivalent scaffold primed to bind additional bivalent ligands. Scaffold formation also promotes self-association and/or higher order organization of the IDP components at a site distant from LC8 binding. Rigorous thermodynamic analyses imply that association of additional bivalent ligands is driven by entropic effects where the first binding event is weak but subsequent binding of additional ligands occurs with higher affinity. Here, we review specific examples of macromolecular assemblies in which polybivalency of aligned IDP duplexes not only enhances binding affinity and results in formation of a stable complex but also compensates unfavorable steric and enthalpic interactions. We propose that polybivalent scaffold assembly involving IDPs and LC8-like proteins is a general process in the cell biology of a class of multi-protein structures that are stable yet fine-tuned for diverse cellular requirements.

  11. 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.

  12. Macromolecular target prediction by self-organizing feature maps.

    PubMed

    Schneider, Gisbert; Schneider, Petra

    2017-03-01

    Rational drug discovery would greatly benefit from a more nuanced appreciation of the activity of pharmacologically active compounds against a diverse panel of macromolecular targets. Already, computational target-prediction models assist medicinal chemists in library screening, de novo molecular design, optimization of active chemical agents, drug re-purposing, in the spotting of potential undesired off-target activities, and in the 'de-orphaning' of phenotypic screening hits. The self-organizing map (SOM) algorithm has been employed successfully for these and other purposes. Areas covered: The authors recapitulate contemporary artificial neural network methods for macromolecular target prediction, and present the basic SOM algorithm at a conceptual level. Specifically, they highlight consensus target-scoring by the employment of multiple SOMs, and discuss the opportunities and limitations of this technique. Expert opinion: Self-organizing feature maps represent a straightforward approach to ligand clustering and classification. Some of the appeal lies in their conceptual simplicity and broad applicability domain. Despite known algorithmic shortcomings, this computational target prediction concept has been proven to work in prospective settings with high success rates. It represents a prototypic technique for future advances in the in silico identification of the modes of action and macromolecular targets of bioactive molecules.

  13. 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

  14. 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.

  15. Cryo-electron tomography for structural characterization of macromolecular complexes.

    PubMed

    Cope, Julia; Heumann, John; Hoenger, Andreas

    2011-08-01

    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 matter 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 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.

  16. 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

  17. VQLM: A visual query language for macromolecular structural databases

    SciTech Connect

    Cohen, D.; Dickinson, B.; Salem, H.

    1994-12-31

    Databases of macromolecular structures allow researchers to identify general principles of molecular behavior. They do this by providing a variety of data obtained under a number of different experimental conditions. Many new tools have been developed recently to aid in exploratory analysis of structural data. However, some queries of interest still require considerable manual filtering of data. In particular, studies attempting to make generalizations about complex arrangements of atoms or building blocks in macro-molecular structures cannot be approached directly with existing tools. Such studies are frequently carried out on only a few structures or else require a labor-intensive process. To address this problem, we have developed a visual language, VQLM (Visual Query Language for Macromolecules). A query is formulated in this language by drawing an abstract picture of sub-structures to be searched for in the database and specifying constraints on the objects in them. To illustrate the usefulness of our language, we show how to encode a number of queries that were found scientifically interesting in the published literature in molecular biology. VQLM relies on VQL, a new database language, as its underlying engine for database retrieval and computation. We believe that VQLM will make macromolecular structural data more accessible to scientists, enabling faster and deeper data analysis.

  18. 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…

  19. Contrastive Analysis.

    ERIC Educational Resources Information Center

    James, Carl

    Contrastive analysis is viewed as an interlinguistic, bidirectional phenomenon which is concerned with both the form and function of language. As such, contrastive analysis must view language psycholinguistically and sociolinguistically as a system to be both described and acquired. Due to the need for a psychological component in the analysis,…

  20. 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.

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

    PubMed

    Iwasa, Janet H

    2015-04-01

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

  2. Cryo-Electron Microscopy of Biological Macromolecular Structures

    NASA Astrophysics Data System (ADS)

    Yonekura, Koji

    There are many huge macromolecular complexes in living organisms. They are often hard to crystallize because of their size, complexity and heterogeneity. Cryo-electron microscopy (cryo-EM) is a suitable method to analyze the structures of such biological macromolecules, because it can be applied to various forms of samples, e.g. two-dimensional crystal, helical assembly, spherical virus, dispersed particle, cell organelle and cell, although attainable resolution depends on the system. In this review, I introduce these techniques and examples of the structure analysis, and briefly review the perspective of cryo-EM.

  3. 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.

  4. A General Method for Modeling Macromolecular Shape in Solution

    PubMed Central

    Harding, Stephen E.

    1987-01-01

    A general method for modeling macromolecular shape in solution is described involving measurements of viscosity, radius of gyration, and the second thermodynamic virial coefficient. The method, which should be relatively straightforward to apply, does not suffer from uniqueness problems, involves shape functions that are independent of hydration, and models the gross conformation of the macromolecule in solution as a general triaxial ellipsoid. The method is illustrated by application to myosin, and the relevance and applicability of ellipsoid modeling to biological structures is discussed. PMID:19431695

  5. Cryosalts: suppression of ice formation in macromolecular crystallography.

    PubMed

    Rubinson, K A; Ladner, J E; Tordova, M; Gilliland, G L

    2000-08-01

    Quality data collection for macromolecular cryocrystallography requires suppressing the formation of crystalline or microcrystalline ice that may result from flash-freezing crystals. Described here is the use of lithium formate, lithium chloride and other highly soluble salts for forming ice-ring-free aqueous glasses upon cooling from ambient temperature to 100 K. These cryosalts are a new class of cryoprotectants that are shown to be effective with a variety of commonly used crystallization solutions and with proteins crystallized under different conditions. The influence of cryosalts on crystal mosaicity and diffraction resolution is comparable with or superior to traditional organic cryoprotectants.

  6. 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.

  7. Oligoethylenimine-grafted chitosan as enhanced T1 contrast agent for in vivo targeted tumor MRI.

    PubMed

    Tong, Xiaoyan; Liu, Min; Zhang, Kunchi; Cao, Yi; Dong, Jingjin; Jiang, Bin; Lu, Bo; Zheng, Hua; Zhang, Hailu; Pei, Renjun

    2016-07-01

    To synthesize and characterize an effective macromolecular magnetic resonance imaging (MRI) contrast agent based on oligoethylenimine-grafted chitosan with targeting capability. In this study we synthesized and characterized oligoethylenimine-grafted chitosan copolymers, followed by conjugating with Gd-DTPA and folic acid. The toxicity was evaluated by WST assay, and in vitro MRI studies were performed in comparison with Gd-DTPA. Finally, the contrast enhancement of the new macromolecular MRI contrast agent was then evaluated in the mice bearing KB xenografts. Compared to Gd-DTPA (4.3 mM(-1) s(-1) ), this macromolecular contrast agent (mCA) exhibited much higher T1 relaxivity (14.4 mM(-1) s(-1) ), up to 3.3 times higher. Meanwhile, the WST assay illustrated that the viability of KB cells remained at 90% even when the Gd concentration was 1 mM. During the in vivo study, the image contrast produced by FA-mCA was higher than one produced by mCA, up to 2.5 times higher. Our results showed this macromolecular contrast agent has potential for developing sensitive and biocompatible MRI probe with targeting capability. J. Magn. Reson. Imaging 2016;44:23-29. © 2015 Wiley Periodicals, Inc.

  8. Protein-ion binding process on finite macromolecular concentration. A Poisson-Boltzmann and Monte Carlo study.

    PubMed

    de Carvalho, Sidney Jurado; Fenley, Márcia O; da Silva, Fernando Luís Barroso

    2008-12-25

    Electrostatic interactions are one of the key driving forces for protein-ligands complexation. Different levels for the theoretical modeling of such processes are available on the literature. Most of the studies on the Molecular Biology field are performed within numerical solutions of the Poisson-Boltzmann Equation and the dielectric continuum models framework. In such dielectric continuum models, there are two pivotal questions: (a) how the protein dielectric medium should be modeled, and (b) what protocol should be used when solving this effective Hamiltonian. By means of Monte Carlo (MC) and Poisson-Boltzmann (PB) calculations, we define the applicability of the PB approach with linear and nonlinear responses for macromolecular electrostatic interactions in electrolyte solution, revealing some physical mechanisms and limitations behind it especially due the raise of both macromolecular charge and concentration out of the strong coupling regime. A discrepancy between PB and MC for binding constant shifts is shown and explained in terms of the manner PB approximates the excess chemical potentials of the ligand, and not as a consequence of the nonlinear thermal treatment and/or explicit ion-ion interactions as it could be argued. Our findings also show that the nonlinear PB predictions with a low dielectric response well reproduce the pK shifts calculations carried out with an uniform dielectric model. This confirms and completes previous results obtained by both MC and linear PB calculations.

  9. 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

  10. Identifying and Visualizing Macromolecular Flexibility in Structural Biology

    PubMed Central

    Palamini, Martina; Canciani, Anselmo; Forneris, Federico

    2016-01-01

    Structural biology comprises a variety of tools to obtain atomic resolution data for the investigation of macromolecules. Conventional structural methodologies including crystallography, NMR and electron microscopy often do not provide sufficient details concerning flexibility and dynamics, even though these aspects are critical for the physiological functions of the systems under investigation. However, the increasing complexity of the molecules studied by structural biology (including large macromolecular assemblies, integral membrane proteins, intrinsically disordered systems, and folding intermediates) continuously demands in-depth analyses of the roles of flexibility and conformational specificity involved in interactions with ligands and inhibitors. The intrinsic difficulties in capturing often subtle but critical molecular motions in biological systems have restrained the investigation of flexible molecules into a small niche of structural biology. Introduction of massive technological developments over the recent years, which include time-resolved studies, solution X-ray scattering, and new detectors for cryo-electron microscopy, have pushed the limits of structural investigation of flexible systems far beyond traditional approaches of NMR analysis. By integrating these modern methods with powerful biophysical and computational approaches such as generation of ensembles of molecular models and selective particle picking in electron microscopy, more feasible investigations of dynamic systems are now possible. Using some prominent examples from recent literature, we review how current structural biology methods can contribute useful data to accurately visualize flexibility in macromolecular structures and understand its important roles in regulation of biological processes. PMID:27668215

  11. 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

  12. 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

    2016-09-08

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

  13. 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.

  14. On the calculation of absolute macromolecular binding free energies

    PubMed Central

    Luo, Hengbin; Sharp, Kim

    2002-01-01

    The standard framework for calculating the absolute binding free energy of a macromolecular association reaction A + B → AB with an association constant KAB is to equate chemical potentials of the species on the left- and right-hand sides of this reaction and evaluate the chemical potentials from theory. This theory involves (usually hidden) assumptions about what constitutes the bound species, AB, and where the contribution of the solvent appears. We present here an alternative derivation that can be traced back to Bjerrum, in which the expectation value of KAB is obtained directly through the statistical mechanical method of evaluating its ensemble (Boltzmann-weighted) average. The generalized Bjerrum approach more clearly delineates: (i) the different contributions to binding; (ii) the origin of the much-discussed and somewhat controversial association entropy term; and (iii) where the solvent contribution appears. This approach also allows approximations required for practical evaluation of the binding constant in complex macromolecular systems, to be introduced in a well defined way. We provide an example, with application to test cases that illustrate a range of binding behavior. PMID:12149474

  15. Structural and functional assessment of APOBEC3G macromolecular complexes.

    PubMed

    Polevoda, Bogdan; McDougall, William M; Bennett, Ryan P; Salter, Jason D; Smith, Harold C

    2016-09-01

    There are eleven members in the human APOBEC family of proteins that are evolutionarily related through their zinc-dependent cytidine deaminase domains. The human APOBEC gene clusters arose on chromosome 6 and 22 through gene duplication and divergence to where current day APOBEC proteins are functionally diverse and broadly expressed in tissues. APOBEC serve enzymatic and non enzymatic functions in cells. In both cases, formation of higher-order structures driven by APOBEC protein-protein interactions and binding to RNA and/or single stranded DNA are integral to their function. In some circumstances, these interactions are regulatory and modulate APOBEC activities. We are just beginning to understand how macromolecular interactions drive processes such as APOBEC subcellular compartmentalization, formation of holoenzyme complexes, gene targeting, foreign DNA restriction, anti-retroviral activity, formation of ribonucleoprotein particles and APOBEC degradation. Protein-protein and protein-nucleic acid cross-linking methods coupled with mass spectrometry, electrophoretic mobility shift assays, glycerol gradient sedimentation, fluorescence anisotropy and APOBEC deaminase assays are enabling mapping of interacting surfaces that are essential for these functions. The goal of this methods review is through example of our research on APOBEC3G, describe the application of cross-linking methods to characterize and quantify macromolecular interactions and their functional implications. Given the homology in structure and function, it is proposed that these methods will be generally applicable to the discovery process for other APOBEC and RNA and DNA editing and modifying proteins.

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

    PubMed

    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

    2015-07-01

    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.

  17. 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

  18. 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

  19. Preparation of macromolecular complexes for cryo-electron microscopy.

    PubMed

    Grassucci, Robert A; Taylor, Derek J; Frank, Joachim

    2007-01-01

    This protocol describes the preparation of frozen-hydrated single-particle specimens of macromolecular complexes. First, it describes how to create a grid surface coated with holey carbon by first inducing holes in a Formvar film to act as a template for the holey carbon that is stable under cryo-electron microscopy (cryo-EM) conditions and is sample-friendly. The protocol then describes the steps required to deposit the homogeneous sample on the grid and to plunge-freeze the grid into liquid ethane at the temperature of liquid nitrogen, so that it is suitable for cryo-EM visualization. It takes 4-5 h to make several hundred holey carbon grids and about 1 h to make the frozen-hydrated grids. The time required for sample purification varies from hours to days, depending on the sample and the specific procedure required. A companion protocol details how to collect cryo-EM data using an FEI Tecnai transmission electron microscope that can subsequently be processed to obtain a three-dimensional reconstruction of the macromolecular complex.

  20. The Phenix software for automated determination of macromolecular structures.

    PubMed

    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

    2011-09-01

    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 favor 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.

  1. 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.

  2. REFMAC5 for the refinement of macromolecular crystal structures.

    PubMed

    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

    2011-04-01

    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.

  3. Identifying and Visualizing Macromolecular Flexibility in Structural Biology.

    PubMed

    Palamini, Martina; Canciani, Anselmo; Forneris, Federico

    2016-01-01

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

  4. Outrunning free radicals in room-temperature macromolecular crystallography

    SciTech Connect

    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

    2012-06-15

    A systematic increase in lifetime is observed in room-temperature protein and virus crystals through the use of reduced exposure times and a fast detector. 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 A{sub 2A} 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.

  5. Rhamnolipids as epithelial permeability enhancers for macromolecular therapeutics.

    PubMed

    Perinelli, Diego Romano; Vllasaliu, Driton; Bonacucina, Giulia; Come, Benedetta; Pucciarelli, Stefania; Ricciutelli, Massimo; Cespi, Marco; Itri, Rosangela; Spinozzi, Francesco; Palmieri, Giovanni Filippo; Casettari, Luca

    2017-10-01

    The use of surfactants as drug permeability enhancers across epithelial barriers remains a challenge. Although many studies have been performed in this field using synthetic surfactants, the possibility of employing surfactants produced by bacteria (the so called biosurfactants") has not been completely explored. Among them, one of the most well characterized class of biosurfactants are rhamnolipids. The aim of the study was to investigate the effect of rhamnolipids on the epithelial permeability of fluorescein isothiocyanate-labelled dextrans 4kDa and 10kDa (named FD4 and FD10, respectively) as model for macromolecular drugs, across Caco-2 and Calu-3monolayers. These cell lines were selected as an in vitro model for the oral and respiratory administration of drugs. Before performing permeability studies, rhamnolipids mixture was analysed in terms of chemical composition and quantification through mass analysis and HPLC. Cytotoxicity and transepithelial electrical resistance (TEER) studies were also conducted using Caco-2 and Calu-3 cell lines. A dose-dependent effect of rhamnolipids on TEER and FD4 or FD10 permeability across both cell lines was observed at relatively safe concentrations. Overall, results suggest the possibility of using rhamnolipids as absorption enhancers for macromolecular drugs through a reversible tight junction opening (paracellular route), despite more investigations are required to confirm their mechanism of action in term of permeability. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. 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.

  7. Production of macromolecular chloramines by chlorine-transfer reactions.

    PubMed

    Bedner, Mary; MacCrehan, William A; Helz, George R

    2004-03-15

    Chlorination of treated wastewaters is undertaken to prevent dispersal of human pathogens into the environment. Except in well-nitrified effluents, the primary agents in chlorination, Cl2(g) or NaOCl(aq), are short-lived and quickly transfer oxidative chlorine to secondary agents (N-chloramines), which then participate in the disinfection process. Maturation of residual chlorine resulting from chlorine-transfer reactions is still poorly characterized. Using gel permeation and reversed-phase liquid chromatography combined with a novel, oxidant-specific detector, unanticipated trends during the maturation of residual chlorine in wastewater are identified. Within 2 min after addition of NaOCl, and continuing for several hours at least, significant amounts of oxidative chlorine are transferred to secondary agents that are moderately to strongly hydrophobic and to agents that have high relative molecular masses (Mr 1300-25000). It is hypothesized that hydrophobic stabilization of organic chloramines (RNHCl(o)) thermodynamically drives these transfers, making macromolecular chloramines the ultimate oxidative chlorine carriers. Macromolecular chloramines are expected to be sluggish oxidants, as observed in their reduction by sulfite, and are expected to be poor disinfectants. If transfer of oxidative chlorine to high Mr components occurs widely at treatment plants, then this phenomenon offers a new, physicochemical explanation for the well-known impotency of organic chloramines in wastewater disinfection.

  8. Ab initio solution of macromolecular crystal structures without direct methods.

    PubMed

    McCoy, Airlie J; Oeffner, Robert D; Wrobel, Antoni G; Ojala, Juha R M; Tryggvason, Karl; Lohkamp, Bernhard; Read, Randy J

    2017-04-04

    The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure. Instead, likelihood-based methods allow a continuum of applications depending predictably on the quality of the model and the resolution of the data. Unexpectedly, our understanding of the signal-to-noise ratio in molecular replacement leads to the finding that, with data to sufficiently high resolution, fragments as small as single atoms of elements usually found in proteins can yield ab initio solutions of macromolecular structures, including some that elude traditional direct methods.

  9. Critical review and perspective of macromolecularly imprinted polymers.

    PubMed

    Kryscio, David R; Peppas, Nicholas A

    2012-02-01

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

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

    PubMed

    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.

  11. 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

  12. Development of Methodologies for Structure Determination of Biological Macromolecular Assemblies Using Synchrotron Radiation and Its Applications

    NASA Astrophysics Data System (ADS)

    Nakagawa, Atsushi

    Synchrotron radiation contributed to the recent progress in protein crystallography. High brilliance and small divergence synchrotron radiation X-ray beam is indispensable to collect diffraction data from crystals of biological macromolecular assemblies. Recent advance on methodologies and technologies on protein crystallography including synchrotron radiation allows us to solve huge biological macromolecular assemblies, such as large virus particles.

  13. [A short infusion or a bolus injection of contrast medium in i.v. urography. Comparative density measurements in the kidney pelvic-caliceal system using sequential computed tomography].

    PubMed

    Kaltenborn, H; Klose, P; Klose, K; Schmiedel, E

    1993-06-01

    The rate of contrast injection during i.v. urography may vary considerably (bolus injection or drip infusion). The effect of 5 rates of injection (6, 12, 18, 36 and 72 ml/min) on the contrast density in the renal collecting system was examined over a period of 30 minutes. Measurements showed an inter-individual difference of more than 200% in each group. The intra-individual variations for different rates of injection were very slight; individual concentration in the kidney for a given dose depends only slightly on the rate of injection. There is no statistically significant improvement in contrast values as a result of a bolus injection. The reduced incidence of side effects justifies the use of bolus injections but pressure injections are unnecessary from a diagnostic point view.

  14. Macromolecular crowding directs extracellular matrix organization and mesenchymal stem cell behavior.

    PubMed

    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.

  15. 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

  16. 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

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

    PubMed

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

    2014-08-01

    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.

  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. Topological Polymer Chemistry Designing Complex Macromolecular Graph Constructions.

    PubMed

    Tezuka, Yasuyuki

    2017-08-22

    The precision design of topologically intriguing macromolecular architectures has continuously been an attractive challenge in polymer science and polymer materials engineering. A class of multicyclic polymer topologies, including three subclasses of spiro, bridged, and fused forms, are particularly unique not only from a topological geometry viewpoint but also from their biochemical relevance to programmed folding structures. In this Account, we describe recent progress in constructing this class of macromolecules, in particular by means of an electrostatic self-assembly and covalent fixation (ESA-CF) protocol, in which ion-paired polymer self-assemblies are employed as key intermediates. All three dicyclic constructions having either 8 (spiro), manacle (bridged), or θ (fused) forms, as well as a tricyclic trefoil (spiro) graph, have been constructed by the ESA-CF process. Moreover, a triply fused-tetracyclic macromolecular K3,3 graph has been constructed using a uniform-size dendritic polymer precursor having six cyclic ammonium salt end groups carrying two units of a trifunctional carboxylate counteranion. Remarkably, the K3,3 graph is known in topological geometry as a prototypical nonplanar graph and has been identified as topologically equivalent to some multicyclic polypeptides (cyclotides) produced through the intramolecular S-S bridging with cysteine residues. A series of single cyclic (ring) polymers having one, two, and even three designated functional groups at the prescribed positions along their cyclic backbone segment (kyklo-telechelics) have also been obtained by the ESA-CF protocol. And in conjunction with a tandem alkyne-azide addition (i.e., click) and an olefin metathesis (i.e., clip) reaction, the precision design of complex multicyclic macromolecular architectures has been achieved. Thus, a series of tri-, tetra-, and even hexacyclic polymer topologies of spiro- and bridged-forms and three doubly fused-tricycle (β-, γ-, and δ-graph) forms

  20. Ferrimagnetic susceptibility contrast agents.

    PubMed

    Bach-Gansmo, T

    1993-01-01

    Contrast agents based on superparamagnetic particles have been in clinical development for more than 5 years, and the complexity of their effects is still not elucidated. The relaxivities are frequently used to give an idea of their efficacy, but these parameters can only be used if they are concentration independent. For large superparamagnetic systems, the evolution of the transverse magnetization is biexponential, after an initial loss of magnetization. Both these characteristics of large superparamagnetic systems should lead to prudence in using the relaxivities as indicators of contrast medium efficacy. Susceptibility induced artefacts have been associated with the use of superparamagnetic contrast agents since the first imaging evaluation took place. The range of concentrations where good contrast effect was achieved without inducing artefacts, as well as blurring and metal artefacts were evaluated. The influence of motion on the induction of artefacts was studied, and compared to the artefacts induced by a paramagnetic agent subject to motion. With a suitable concentration of a negative contrast agent, a signal void could be achieved in the region prone to motion, and no artefacts were induced. If the concentration was too high, a displacement of the region close to the contrast agent was observed. The artefacts occurred in a volume surrounding the contrast agent, i.e., also outside the imaging plane. In comparison a positive, paramagnetic contrast agent induced heavy artefacts in the phase encoding direction, appearing as both high intensity regions and black holes, in a mosaic pattern. Clinical trials of the oral contrast agent OMP for abdominal MR imaging showed this agent to be safe and efficacious. OMP increased the diagnostic efficacy of abdominal MR imaging in 2 of 3 cases examined, with a significant decrease in motion artefacts. Susceptibility contrast agents may also be of use in the evaluation of small lesions in the liver. Particulate material

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

    PubMed

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

    2017-02-01

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

  2. 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.

  3. The analysis of macromolecular interactions by sedimentation equilibrium

    PubMed Central

    Ghirlando, Rodolfo

    2010-01-01

    The study of macromolecular interactions by sedimentation equilibrium is a highly technical method that requires great care in both the experimental design and data analysis. The complexity of the interacting system that can be analyzed is only limited by the ability to deconvolute the exponential contributions of each of the species to the overall concentration gradient. This is achieved in part through the use of multi-signal data collection and the implementation of soft mass conservation. We illustrate the use of these constraints in SEDPHAT through the study of an A + B + B ⇌ AB + B ⇌ ABB system and highlight some of the technical challenges that arise. We show that both the multi-signal analysis and mass conservation result in a precise and robust data analysis and discuss improvements that can be obtained through the inclusion of data from other methods such as sedimentation velocity and isothermal titration calorimetry. PMID:21167941

  4. Spontaneous and specific activation of chemical bonds in macromolecular fluids.

    PubMed

    Park, Insun; Shirvanyants, David; Nese, Alper; Matyjaszewski, Krzysztof; Rubinstein, Michael; Sheiko, Sergei S

    2010-09-08

    Mechanical activation of chemical bonds typically involves the application of external forces, which implies a broad distribution of bond tensions. We demonstrate that controlling the flow profile of a macromolecular fluid generates and delineates mechanical force concentration, enabling a hierarchical activation of chemical bonds on different length scales from the macroscopic to the molecular. Bond tension is spontaneously generated within brushlike macromolecules as they spread on a solid substrate. The molecular architecture creates an uneven distribution of tension in the covalent bonds, leading to spatially controlled bond scission. By controlling the flow rate and the gradient of the film pressure, one can sever the flowing macromolecules with high precision. Specific chemical bonds are activated within distinct macromolecules located in a defined area of a thin film. Furthermore, the flow-controlled loading rate enables quantitative analysis of the bond activation parameters.

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

    PubMed Central

    Joosten, Robbie P.; Soueidan, Hayssam; Wessels, Lodewyk F. A.; Perrakis, Anastassis

    2013-01-01

    Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found that a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature. PMID:24311569

  6. 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

  7. 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.

  8. Reciprocal Space Mapping of Macromolecular Crystals in the Home Laboratory

    NASA Technical Reports Server (NTRS)

    Snell, Edward H.; Fewster, P. F.; Andrew, Norman; Boggon, T. J.; Judge, Russell A.; Pusey, Marc A.

    1999-01-01

    Reciprocal space mapping techniques are used widely by the materials science community to provide physical information about their crystal samples. We have used similar methods at synchrotron sources to look at the quality of macromolecular crystals produced both on the ground and under microgravity conditions. The limited nature of synchrotron time has led us to explore the use of a high resolution materials research diffractometer to perform similar measurements in the home laboratory. Although the available intensity is much reduced due to the beam conditioning necessary for high reciprocal space resolution, lower resolution data can be collected in the same detail as the synchrotron source. Experiments can be optimized at home to make most benefit from the synchrotron time available. Preliminary results including information on the mosaicity and the internal strains from reciprocal space maps will be presented.

  9. Detecting stoichiometry of macromolecular complexes in live cells using FRET.

    PubMed

    Ben-Johny, Manu; Yue, Daniel N; Yue, David T

    2016-12-06

    The stoichiometry of macromolecular interactions is fundamental to cellular signalling yet challenging to detect from living cells. Fluorescence resonance energy transfer (FRET) is a powerful phenomenon for characterizing close-range interactions whereby a donor fluorophore transfers energy to a closely juxtaposed acceptor. Recognizing that FRET measured from the acceptor's perspective reports a related but distinct quantity versus the donor, we utilize the ratiometric comparison of the two to obtain the stoichiometry of a complex. Applying this principle to the long-standing controversy of calmodulin binding to ion channels, we find a surprising Ca(2+)-induced switch in calmodulin stoichiometry with Ca(2+) channels-one calmodulin binds at basal cytosolic Ca(2+) levels while two calmodulins interact following Ca(2+) elevation. This feature is curiously absent for the related Na channels, also potently regulated by calmodulin. Overall, our assay adds to a burgeoning toolkit to pursue quantitative biochemistry of dynamic signalling complexes in living cells.

  10. Revealing the macromolecular targets of complex natural products.

    PubMed

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

    2014-12-01

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

  11. 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.

  12. Cooperative Macromolecular Disassembly via the Heat Shock Chaperone Hsc70

    NASA Astrophysics Data System (ADS)

    Puchalla, Jason; Krantz, Kelly; Austin, Robert; Rye, Hays

    2008-03-01

    Many essential cellular functions depend on the assembly and disassembly of macromolecular complexes. A general class of protein known as molecular chaperones regulates several of these processes. How can complex protein structure be quickly and efficiently disassembled by the action of a small number of these proteins? One such example is that of clathrin: a ubiquitous coat protein that stabilizes vesicular trafficking by forming a scaffold onto the membrane surface. This scaffold must be removed before the vesicle can deliver its cargo. We report on the cooperative disassembly of yeast-derived GFP-labeled clathrin baskets via its interaction with Hsc70. We exploit the highest signal-to-noise light bursts from single fluorescent baskets transiting a confocal excitation spot to recursively determine the brightness and size distribution of the baskets during the uncoating process. This minimal uncoating system demonstrates the ability of a surprisingly simple protein system to facilitate rapid structural changes through cooperative action.

  13. 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

  14. Detecting stoichiometry of macromolecular complexes in live cells using FRET

    PubMed Central

    Ben-Johny, Manu; Yue, Daniel N.; Yue, David T.

    2016-01-01

    The stoichiometry of macromolecular interactions is fundamental to cellular signalling yet challenging to detect from living cells. Fluorescence resonance energy transfer (FRET) is a powerful phenomenon for characterizing close-range interactions whereby a donor fluorophore transfers energy to a closely juxtaposed acceptor. Recognizing that FRET measured from the acceptor's perspective reports a related but distinct quantity versus the donor, we utilize the ratiometric comparison of the two to obtain the stoichiometry of a complex. Applying this principle to the long-standing controversy of calmodulin binding to ion channels, we find a surprising Ca2+-induced switch in calmodulin stoichiometry with Ca2+ channels—one calmodulin binds at basal cytosolic Ca2+ levels while two calmodulins interact following Ca2+ elevation. This feature is curiously absent for the related Na channels, also potently regulated by calmodulin. Overall, our assay adds to a burgeoning toolkit to pursue quantitative biochemistry of dynamic signalling complexes in living cells. PMID:27922011

  15. Studying macromolecular complex stoichiometries by peptide‐based mass spectrometry

    PubMed Central

    Wohlgemuth, Ingo; Lenz, Christof

    2015-01-01

    A majority of cellular functions are carried out by macromolecular complexes. A host of biochemical and spectroscopic methods exists to characterize especially protein/protein complexes, however there has been a lack of a universal method to determine protein stoichiometries. Peptide‐based MS, especially as a complementary method to the MS analysis of intact protein complexes, has now been developed to a point where it can be employed to assay protein stoichiometries in a routine manner. While the experimental demands are still significant, peptide‐based MS has been successfully applied to analyze stoichiometries for a variety of protein complexes from very different biological backgrounds. In this review, we discuss the requirements especially for targeted MS acquisition strategies to be used in this context, with a special focus on the interconnected experimental aspects of sample preparation, protein digestion, and peptide stability. In addition, different strategies for the introduction of quantitative peptide standards and their suitability for different scenarios are compared. PMID:25546807

  16. Femtosecond light-induced macromolecular self-assembly

    NASA Astrophysics Data System (ADS)

    Rebane, Aleksander; Mikhaylov, Alexander

    2016-09-01

    We report femtosecond light-induced macromolecular self-assembly (FLIMSA), which is observed when a high peak intensity femtosecond laser beam propagates through aqueous solution of pseudoisocyanine iodide (PIC) J-aggregates and induces the formation of 0.1 - 1.0 mm-size tube-like structure surrounding the laser beam, while at the same time allowing the beam to continue propagating without obstruction or scattering. The FLIMSA material is morphologically heterogeneous and gel-like and is formed at the margins rather than at the center of the beam. As a potential explanation of this effect we assume that the FLIMSA is induced by the high photon flux gradient characteristic of the femtosecond laser beam periphery. This hypothesis is corroborated by control experiments, where J-aggregate samples were illuminated with nanosecond laser sources with a varying pulse duration, power- and beam shape characteristics, but where no FLIMSA formation was observed.

  17. Revealing the macromolecular targets of complex natural products

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  18. 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.

  19. 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.

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

    PubMed

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

    2017-02-08

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

  1. Enhancement of Biological Reactions on Cell Surfaces via Macromolecular Crowding

    PubMed Central

    Chapanian, Rafi; Kwan, David H.; Constantinescu, Iren; Shaikh, Fathima A.; Rossi, Nicholas A.A.; Withers, Stephen G.; Kizhakkedathu, Jayachandran N.

    2016-01-01

    The reaction of macromolecules such as enzymes and antibodies with cell surfaces is often an inefficient process, requiring large amounts of expensive reagent. Here we report a general method based on macromolecular crowding with a range of neutral polymers to enhance such reactions, using red blood cells (RBCs) as a model system. Rates of conversion of Type A and B red blood cells to universal O type by removal of antigenic carbohydrates with selective glycosidases are increased up to 400-fold in the presence of crowders. Similar enhancements are seen for antibody binding. We further explore the factors underlying these enhancements using confocal microscopy and fluorescent recovery after bleaching (FRAP) techniques with various fluorescent protein fusion partners. Increased cell-surface concentration due to volume exclusion, along with two-dimensionally confined diffusion of enzymes close to the cell surface, appear to be the major contributing factors. PMID:25140641

  2. 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.

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

    DOE PAGES

    Ng, Joseph D.; Baird, James K.; Coates, Leighton; ...

    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

  4. 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.

  5. 129 Xe NMR Relaxation-Based Macromolecular Sensing

    SciTech Connect

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

    2016-07-29

    A 129Xe NMR relaxation-based sensing approach is reported on 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.

  6. In-vacuum long-wavelength macromolecular crystallography.

    PubMed

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

    2016-03-01

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

  7. Associative Pattern Recognition Through Macro-molecular Self-Assembly

    NASA Astrophysics Data System (ADS)

    Zhong, Weishun; Schwab, David J.; Murugan, Arvind

    2017-05-01

    We show that macro-molecular self-assembly can recognize and classify high-dimensional patterns in the concentrations of N distinct molecular species. Similar to associative neural networks, the recognition here leverages dynamical attractors to recognize and reconstruct partially corrupted patterns. Traditional parameters of pattern recognition theory, such as sparsity, fidelity, and capacity are related to physical parameters, such as nucleation barriers, interaction range, and non-equilibrium assembly forces. Notably, we find that self-assembly bears greater similarity to continuous attractor neural networks, such as place cell networks that store spatial memories, rather than discrete memory networks. This relationship suggests that features and trade-offs seen here are not tied to details of self-assembly or neural network models but are instead intrinsic to associative pattern recognition carried out through short-ranged interactions.

  8. 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.

  9. 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.

  10. 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

  11. Bulk-solvent correction in large macromolecular structures.

    PubMed

    Rees, Bernard; Jenner, Lasse; Yusupov, Marat

    2005-09-01

    The estimation of the bulk-solvent contribution to the diffraction of a macromolecular crystal makes use of a solvent mask which delimits the bulk-solvent regions in the crystal. It is shown that the way this mask is usually defined in CNS contains a bias which can lead to absurd results in the case of very large structures, where the calculations can only be made on relatively coarse grids. A modified procedure is described and applied to 70S ribosome data at 5.5 A resolution. The B factor affecting the bulk solvent is also discussed. Even in this case of very high and widely variable atomic B factors, it seems sufficient to consider a constant and isotropic B factor for the bulk solvent. This is initially set to the average value of the atomic B factor, but can be refined.

  12. E-MSD: the European Bioinformatics Institute Macromolecular Structure Database

    PubMed Central

    Boutselakis, H.; Dimitropoulos, D.; Fillon, J.; Golovin, A.; Henrick, K.; Hussain, A.; Ionides, J.; John, M.; Keller, P. A.; Krissinel, E.; McNeil, P.; Naim, A.; Newman, R.; Oldfield, T.; Pineda, J.; Rachedi, A.; Copeland, J.; Sitnov, A.; Sobhany, S.; Suarez-Uruena, A.; Swaminathan, J.; Tagari, M.; Tate, J.; Tromm, S.; Velankar, S.; Vranken, W.

    2003-01-01

    The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool. PMID:12520052

  13. 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

  14. [Progress in researches on synthetic antimicrobial macromolecular polymers].

    PubMed

    Wei, Gang; Yang, Lihua; Chu, Liangyin

    2010-08-01

    Broad-spectrum antimicrobial peptides provide a new way to address the urgent growing problem of bacterial resistance. However, the limited natural resources and the high cost of extraction and purification of natural antimicrobial peptides can not meet the requirements of clinical application. In order to solve this problem, researchers have utilized two basic common structural features (amphiphilic and cationic) for designing and preparing synthetic antimicrobial macromolecular polymers. During the last decade, several kinds of amphiphilic polymers, including arylamide oligomers, phenylene ethynylenes, polymethacrylates, polynorbornenes as well as nylon-3 polymers have been synthesized. In this paper, the structures, antibacterial activities and selectivities of these polymers are reviewed, and the effects of molecular size, polarity and ratio of hydrophobic groups, positive charge density on antibacterial activity and selectivity are also summarized.

  15. 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.

  16. Macromolecular structure and aggregation states of Helicobacter pylori urease.

    PubMed Central

    Austin, J W; Doig, P; Stewart, M; Trust, T J

    1991-01-01

    Urease purified from Helicobacter pylori by differential ultracentrifugation and fast pressure liquid chromatography was composed of subunits with apparent molecular weights (MrS) of 66,000 and 30,000. Electron microscopy of this purified material demonstrated that it formed disc-shaped macromolecular aggregates that were approximately 13 nm in diameter and 3 nm thick. Images of both negatively stained and shadowed preparations indicated that the discs tended to stack to form pairs and then these pairs further aggregated to form four-disc stacks. This stacking of subunits explains the heterogeneity observed previously in the molecular weight of urease preparations. In some negatively stained preparations there were also some smaller (approximately 8-nm-diameter) annular units present, which may represent individual urease units or possibly an aggregate of one of the two subunits from which urease is constructed. Images PMID:1885543

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

    PubMed Central

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

    2015-01-01

    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

  18. 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.

  19. Reciprocal Space Mapping of Macromolecular Crystals in the Home Laboratory

    NASA Technical Reports Server (NTRS)

    Snell, Edward H.; Fewster, P. F.; Andrew, Norman; Boggon, T. J.; Judge, Russell A.; Pusey, Marc A.

    1999-01-01

    Reciprocal space mapping techniques are used widely by the materials science community to provide physical information about their crystal samples. We have used similar methods at synchrotron sources to look at the quality of macromolecular crystals produced both on the ground and under microgravity conditions. The limited nature of synchrotron time has led us to explore the use of a high resolution materials research diffractometer to perform similar measurements in the home laboratory. Although the available intensity is much reduced due to the beam conditioning necessary for high reciprocal space resolution, lower resolution data can be collected in the same detail as the synchrotron source. Experiments can be optimized at home to make most benefit from the synchrotron time available. Preliminary results including information on the mosaicity and the internal strains from reciprocal space maps will be presented.

  20. Conformational States of macromolecular assemblies explored by integrative structure calculation.

    PubMed

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

    2013-09-03

    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.

  1. Radiation damage to nucleoprotein complexes in macromolecular crystallography

    DOE PAGES

    Bury, Charles; Garman, Elspeth F.; Ginn, Helen Mary; ...

    2015-01-30

    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. 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 themore » same controlled conditions. 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. We observed the protein at low doses and found that they were susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses.« less

  2. 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.

  3. Macromolecular crystal growth experiments on International Microgravity Laboratory--1.

    PubMed Central

    Day, J.; McPherson, A.

    1992-01-01

    Macromolecular crystal growth experiments, using satellite tobacco mosaic virus (STMV) and canavalin from jack beans as samples, were conducted on a US Space Shuttle mission designated International Microgravity Laboratory--1 (IML-1), flown January 22-29, 1992. Parallel experiments using identical samples were carried out in both a vapor diffusion-based device (PCG) and a liquid-liquid diffusion-based instrument (CRYOSTAT). The experiments in each device were run at 20-22 degrees C and at colder temperatures. Crystals were grown in virtually every trial, but the characteristics of the crystals were highly dependent on the crystallization technique employed and the temperature experience of the sample. In general, very good results, based on visual inspection of the crystals, were obtained in both PCG and CRYOSTAT. Unusually impressive results were, however, achieved for STMV in the CRYOSTAT instrument. STMV crystals grown in microgravity by liquid-liquid diffusion were more than 10-fold greater in total volume than any STMV crystals previously grown in the laboratory. X-ray diffraction data collected from eight STMV crystals grown in CRYOSTAT demonstrated a substantial improvement in diffraction quality over the entire resolution range when compared to data from crystals grown on Earth. In addition, the extent of the diffraction pattern for the STMV crystals grown in space extended to 1.8 A resolution, whereas the best crystals that were ever grown under conditions of Earth's gravity produced data limited to 2.3 A resolution. Other observations indicate that the growth of macromolecular crystals is indeed influenced by the presence or absence of gravity. These observations further suggest, consistent with earlier results, that the elimination of gravity provides a more favorable environment for such processes. PMID:1303744

  4. Radiation damage to nucleoprotein complexes in macromolecular crystallography

    SciTech Connect

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

    2015-01-30

    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. 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. 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. We observed the protein at low doses and found that they were susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses.

  5. Contrast cystography.

    PubMed

    Essman, Stephanie C

    2005-02-01

    Cystography is a radiographic study performed to aid in evaluation of the urinary bladder for extramural, mural, or intraluminal lesions. These lesions may primarily involve the urinary bladder or may be an extension of disease from adjacent organs. Cystography is easy to perform with relatively few complications. Different types of cystography (positive versus negative contrast) may be used depending on the type of information that the clinician hopes to obtain. Although a valuable technique, it is important to correlate the findings on cystography with other clinical information to arrive at the final diagnosis.

  6. Towards an efficient compression of 3D coordinates of macromolecular structures

    PubMed Central

    Valasatava, Yana; Bradley, Anthony R.; Rose, Alexander S.; Duarte, Jose M.; Prlić, Andreas

    2017-01-01

    The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format. PMID:28362865

  7. Towards an efficient compression of 3D coordinates of macromolecular structures.

    PubMed

    Valasatava, Yana; Bradley, Anthony R; Rose, Alexander S; Duarte, Jose M; Prlić, Andreas; Rose, Peter W

    2017-01-01

    The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format.

  8. Heading toward Macromolecular and Nanosized Bioresponsive MRI Probes for Successful Functional Imaging.

    PubMed

    Angelovski, Goran

    2017-09-19

    track neurotransmitter flux have also been recently reported, allowing the study of brain function in an unprecedented manner. Nevertheless, wider SCA utilization in vivo has not yet been achieved. There are a few reasons for this disparity between their nominal potential and practical usage, with one of the major reasons being the low sensitivity of the MRI technique. Subsequently, the production of detectable signal change can be achieved using higher concentrations of the bioresponsive probe; however, the biocompatibility of these probes then starts to play an important role. An elegant solution to these practical challenges has been found with the integration of multiple small-sized SCAs into macromolecular and nanosized probes. In such case, the multivalent SCAs are able to circumvent the sensitivity issue, thus enhancing the MR signal and desired contrast changes. Moreover, they prolong the probe tissue retention time, while often reducing their toxicity. Finally, with altered size and properties, they allow for exploitation of mechanisms that induce the contrast change which is not possible with small-sized SCAs. To this end, this Account also discusses the current approaches that aim to develop macromolecular and nanosized SCAs suitable for practical MRI applications. With these, further progress of this exciting field is affirmed, with remarkable results expected in the near future on both the probe preparation and their utilization in functional molecular imaging.

  9. Rheo-NMR Studies of an Enzymatic Reaction: Evidence of a Shear-Stable Macromolecular System

    PubMed Central

    Edwards, Patrick J.B.; Kakubayashi, Motoko; Dykstra, Robin; Pascal, Steven M.; Williams, Martin A.K.

    2010-01-01

    Abstract Understanding the effects of shear forces on biopolymers is key to understanding how biological systems function. Although currently there is good agreement between theoretical predictions and experimental measurements of the behavior of DNA and large multimeric proteins under shear flow, applying the same arguments to globular proteins leads to the prediction that they should only exhibit shear-induced conformational changes at extremely large shear rates. Nevertheless, contradictory experimental evidence continues to appear, and the effect of shear on these biopolymers remains contentious. Here, a custom-built rheo-NMR cell was used to investigate whether shear flow modifies enzyme action compared with that observed quiescently. Specifically, 1H NMR was used to follow the kinetics of the liberation of methanol from the methylesterified polysaccharide pectin by pectinmethylesterase enzymes. Two different demethylesterifying enzymes, known to have different action patterns, were used. In all experiments performed, Couette flows with shear rates of up to 1570 s−1 did not generate detectable differences in the rate of methanol liberation compared to unsheared samples. This study provides evidence for a shear-stable macromolecular system consisting of a largely β-sheet protein and a polysaccharide, in line with current theoretical predictions, but in contrast to some other experimental work on other proteins. PMID:20441763

  10. Neutron Spectroscopy as a Probe of Macromolecular Structure and Dynamics under Extreme Spatial Confinement

    NASA Astrophysics Data System (ADS)

    Barroso-Bujans, F.; Fernandez-Alonso, F.; Colmenero, J.

    2014-11-01

    We illustrate the use of high-resolution neutron spectroscopy to explore the extreme spatial confinement of soft matter in nanostructured materials. Two well-defined limits are considered, involving either intercalation or interfacial adsorption of the ubiquitous polymer poly(ethylene oxide) in graphite-oxide-based hosts. Vibrational modes associated with the confined macromolecular phase undergo dramatic changes over a broad range of energy transfers, from those associated with intermolecular modes in the Terahertz frequency range (1 THz = 33 cm-1), to those characteristic of strong chemical bonds above 2000 cm-1. We also consider the effects of polymer chain size and chemical composition of the host material. Variation of the degree of oxidation and exfoliation of graphite oxide leads to two distinct cases, namely: (i) subnanometer two-dimensional confinement; and (ii) surface immobilization. Case (i) is characterised by significant changes to conformational and collective vibrational modes of the polymer as a consequence of a preferentially planar trans-trans-trans chain conformation, whereas case (ii) leads to a substantial increase in the population of gauche conformers. Macroscopically, case (i) translates into the complete suppression of crystallization and glassy behaviour. In contrast, case (ii) exhibits well-defined glass and melting transitions associated with the confined phase, yet at significantly lower temperatures than those of the bulk.

  11. Fourier transform infrared microspectroscopy reveals that tissue culture conditions affect the macromolecular phenotype of human embryonic stem cells.

    PubMed

    Cao, Julie; Ng, Elizabeth S; McNaughton, Don; Stanley, Edouard G; Elefanty, Andrew G; Tobin, Mark J; Heraud, Philip

    2013-07-21

    We employed Fourier transform infrared (FTIR) microspectroscopy to investigate the effects of different tissue culture environments on the FTIR spectra of undifferentiated human embryonic stem cells (hESCs) and their differentiated progeny. First we tested whether there were any possible spectral artifacts resulting from the use of transflectance measurements by comparing them with transmission measurements and found no evidence of these concluding that the lack of any differences resulted from the homogeneity of the dried cytospun cellular monolayers. We found that hESCs that were enzymatically passaged onto mouse embryonic fibroblasts (MEFs) in KOSR based hESC medium, hESCs enzymatically passaged onto Matrigel in mTESR medium and hESCs mechanically passaged onto MEFs in KOSR-based hESC medium, possessed unique FTIR spectroscopic signatures that reflect differences in their macromolecular chemistry. Further, these spectroscopic differences persisted even upon differentiation towards mesendodermal lineages. Our results suggest that FTIR microspectroscopy is a powerful, objective, measurement modality that complements existing methods for studying the phenotype of hESCs and their progeny, particularly changes induced by the cellular environment.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  13. ProteoPlex: stability optimization of macromolecular complexes by sparse-matrix screening of chemical space.

    PubMed

    Chari, Ashwin; Haselbach, David; Kirves, Jan-Martin; Ohmer, Juergen; Paknia, Elham; Fischer, Niels; Ganichkin, Oleg; Möller, Vanessa; Frye, Jeremiah J; Petzold, Georg; Jarvis, Marc; Tietzel, Michael; Grimm, Clemens; Peters, Jan-Michael; Schulman, Brenda A; Tittmann, Kai; Markl, Jürgen; Fischer, Utz; Stark, Holger

    2015-09-01

    Molecular machines or macromolecular complexes are supramolecular assemblies of biomolecules with a variety of functions. Structure determination of these complexes in a purified state is often tedious owing to their compositional complexity and the associated relative structural instability. To improve the stability of macromolecular complexes in vitro, we present a generic method that optimizes the stability, homogeneity and solubility of macromolecular complexes by sparse-matrix screening of their thermal unfolding behavior in the presence of various buffers and small molecules. The method includes the automated analysis of thermal unfolding curves based on a biophysical unfolding model for complexes. We found that under stabilizing conditions, even large multicomponent complexes reveal an almost ideal two-state unfolding behavior. We envisage an improved biochemical understanding of purified macromolecules as well as a substantial boost in successful macromolecular complex structure determination by both X-ray crystallography and cryo-electron microscopy.

  14. Macromolecular Crowding Enhances Catalytic Efficiency and Stability of α-Amylase

    PubMed Central

    Yadav, Jay Kant

    2013-01-01

    In the present study an attempt was made to investigate the macromolecular crowding effect on functional attributes of α-amylase. High concentrations of sugar based cosolvents, (e.g., trehalose, sucrose, sorbitol, and glycerol) were used to mimic the macromolecular crowding environment (of cellular milieu) under in vitro conditions. To assess the effect of macromolecular crowding, the activity and structural properties of the enzyme were evaluated in the presence of different concentrations of the above cosolvents. Based on the results it is suggested that the macromolecular crowding significantly improves the catalytic efficiency of the enzyme with marginal change in the structure. Out of four cosolvents examined, trehalose was found to be the most effective in consistently enhancing thermal stability of the enzyme. Moreover, the relative effectiveness of the above cosolvents was found to be dependent on their concentration used. PMID:25969780

  15. Macromolecular crowding for tailoring tissue-derived fibrillated matrices.

    PubMed

    Magno, Valentina; Friedrichs, Jens; Weber, Heather M; Prewitz, Marina C; Tsurkan, Mikhail V; Werner, Carsten

    2017-06-01

    Tissue-derived fibrillated matrices can be instrumental for the in vitro reconstitution of multiphasic extracellular microenvironments. However, despite of several advantages, the obtained scaffolds so far offer a rather narrow range of materials characteristics only. In this work, we demonstrate how macromolecular crowding (MMC) - the supplementation of matrix reconstitution media with synthetic or natural macromolecules in ways to create excluded volume effects (EVE) - can be employed for tailoring important structural and biophysical characteristics of kidney-derived fibrillated matrices. Porcine kidneys were decellularized, ground and the obtained extracellular matrix (ECM) preparations were reconstituted under varied MMC conditions. We show that MMC strongly influences the fibrillogenesis kinetics and impacts the architecture and the elastic modulus of the reconstituted matrices, with diameters and relative alignment of fibrils increasing at elevated concentrations of the crowding agent Ficoll400, a nonionic synthetic polymer of sucrose. Furthermore, we demonstrate how MMC modulates the distribution of key ECM molecules within the reconstituted matrix scaffolds. As a proof of concept, we compared different variants of kidney-derived fibrillated matrices in cell culture experiments referring to specific requirements of kidney tissue engineering approaches. The results revealed that MMC-tailored matrices support the morphogenesis of human umbilical vein endothelial cells (HUVECs) into capillary networks and of murine kidney stem cells (KSCs) into highly branched aggregates. The established methodology is concluded to provide generally applicable new options for tailoring tissue-specific multiphasic matrices in vitro. Tissue-derived fibrillated matrices can be instrumental for the in vitro reconstitution of multiphasic extracellular microenvironments. However, despite of several advantages, the obtained scaffolds so far offer a rather narrow range of materials

  16. The Macromolecular Neutron Diffractometer MaNDi at the Spallation Neutron Source

    DOE PAGES

    Coates, Leighton; Cuneo, Matthew J.; Frost, Matthew J.; ...

    2015-07-18

    The Macromolecular Neutron Diffractometer (MaNDi) is located on beamline 11B of the Spallation Neutron Source at Oak Ridge National Laboratory. Moreover, the instrument is a neutron time-of-flight wavelength-resolved Laue diffractometer optimized to collect diffraction data from single crystals. Finally, the instrument has been designed to provide flexibility in several instrumental parameters, such as beam divergence and wavelength bandwidth, to allow data collection from a range of macromolecular systems.

  17. The Macromolecular Neutron Diffractometer MaNDi at the Spallation Neutron Source

    SciTech Connect

    Coates, Leighton; Cuneo, Matthew J.; Frost, Matthew J.; He, Junhong; Weiss, Kevin L.; McFeeters, Hana; Tomanicek, Stephen J.; Vandavasi, Venu Gopal; Langan, Paul; Iverson, Erik B.

    2015-07-18

    The Macromolecular Neutron Diffractometer (MaNDi) is located on beamline 11B of the Spallation Neutron Source at Oak Ridge National Laboratory. Moreover, the instrument is a neutron time-of-flight wavelength-resolved Laue diffractometer optimized to collect diffraction data from single crystals. Finally, the instrument has been designed to provide flexibility in several instrumental parameters, such as beam divergence and wavelength bandwidth, to allow data collection from a range of macromolecular systems.

  18. The assay and partial characterization of macromolecular heparin depolymerase activity in rat small intestine.

    PubMed

    Young, E; Horner, A A

    1979-06-15

    Homogenates of rat small intestine can depolymerize macromolecular rat skin heparin (RS heparin) to products similar in size to commercial heparin [Horner (1972) Proc. Natl. Acad. Sci. U.S.A. 69, 3469--3473]. This activity is attributed to an enzyme provisionally named 'macromolecular heparin depolymerase'. An assay for macromolecular heparin depolymerase activity in rat small intestine has been developed, based on the action of the enzyme on 35S-labelled macromolecular RS heparin. The depolymerized products are separated into two peaks by gel chromatography through columns of Bio-Gel A-15m. The amount of label in the second peak, expressed as a percentage of the total radioactivity, is the index of enzyme activity. The pH optimum was found to be 6.0 and the temperature optimum 45 degrees C. The enzyme was shown to be most stable in 50mM-Tris/maleate buffer containing 1 mM-EDTA. Macromolecular heparin depolymerase activity measured as a function of time and substrate concentration produced curves typical of an enzymic reaction. Evidence was obtained demonstrating that the activity did not originate from bacteria in the intestine. Macromolecular heparin depolymerase activity was increased by dilution and storage at 7 degrees C for 24 h. This suggests that homogenates of rat small intestine contain an unstable inhibitor of the enzyme.

  19. The assay and partial characterization of macromolecular heparin depolymerase activity in rat small intestine.

    PubMed Central

    Young, E; Horner, A A

    1979-01-01

    Homogenates of rat small intestine can depolymerize macromolecular rat skin heparin (RS heparin) to products similar in size to commercial heparin [Horner (1972) Proc. Natl. Acad. Sci. U.S.A. 69, 3469--3473]. This activity is attributed to an enzyme provisionally named 'macromolecular heparin depolymerase'. An assay for macromolecular heparin depolymerase activity in rat small intestine has been developed, based on the action of the enzyme on 35S-labelled macromolecular RS heparin. The depolymerized products are separated into two peaks by gel chromatography through columns of Bio-Gel A-15m. The amount of label in the second peak, expressed as a percentage of the total radioactivity, is the index of enzyme activity. The pH optimum was found to be 6.0 and the temperature optimum 45 degrees C. The enzyme was shown to be most stable in 50mM-Tris/maleate buffer containing 1 mM-EDTA. Macromolecular heparin depolymerase activity measured as a function of time and substrate concentration produced curves typical of an enzymic reaction. Evidence was obtained demonstrating that the activity did not originate from bacteria in the intestine. Macromolecular heparin depolymerase activity was increased by dilution and storage at 7 degrees C for 24 h. This suggests that homogenates of rat small intestine contain an unstable inhibitor of the enzyme. PMID:39552

  20. Macromolecular crystallography with a large format CMOS detector

    SciTech Connect

    Nix, Jay C.

    2016-07-27

    Recent advances in CMOS technology have allowed the production of large surface area detectors suitable for macromolecular crystallography experiments [1]. The Molecular Biology Consortium (MBC) Beamline 4.2.2 at the Advanced Light Source in Berkeley, CA, has installed a 2952 x 2820 mm RDI CMOS-8M detector with funds from NIH grant S10OD012073. The detector has a 20nsec dead pixel time and performs well with shutterless data collection strategies. The sensor obtains sharp point response and minimal optical distortion by use of a thin fiber-optic plate between the phosphor and sensor module. Shutterless data collections produce high-quality redundant datasets that can be obtained in minutes. The fine-sliced data are suitable for processing in standard crystallographic software packages (XDS, HKL2000, D*TREK, MOSFLM). Faster collection times relative to the previous CCD detector have resulted in a record number of datasets collected in a calendar year and de novo phasing experiments have resulted in publications in both Science and Nature [2,3]. The faster collections are due to a combination of the decreased overhead requirements of shutterless collections combined with exposure times that have decreased by over a factor of 2 for images with comparable signal to noise of the NOIR-1 detector. The overall increased productivity has allowed the development of new beamline capabilities and data collection strategies.

  1. Macromolecular Crystallography and Structural Biology Databases at NIST.

    PubMed

    Gilliland, G L

    2001-01-01

    In the late 1970s, macromolecular crystallography at NIST began with collaboration between NIST and NIH to establish a single-crystal neutron diffractometer. This instrument was constructed and employed to solve a number of crystal structures: bovine ribonuclease A, bovine-ribonuclease-uridine vanadate complex, and porcine insulin. In the mid 1980s a Biomolecular Structure Group was created establishing NIST capabilities in biomolecular singe-crystal x-ray diffraction. The group worked on a variety of structural problems until joining the NIST/UMBI Center for Advanced Research in Biotechnology (CARB) in 1987. Crystallographic studies at CARB were then focused on protein engineering efforts that included among others chymosin, subtilisin BPN', interleukin 1β, and glutathione S-transferase. Recently, the structural biology efforts have centered on enzymes in the chorismate metabolic pathways involved in amino acid biosynthesis and in structural genomics that involves determining the structures of "hypothetical" proteins to aid in assigning function. In addition to crystallographic studies, structural biology database activities began with the formal establishment of the Biological Macro-molecule Crystallization Database in 1989. Later, in 1997, NIST in partnership with Rutgers and UCSD formed the Research Collaboratory for Structural Bioinformatics that successfully acquired the Protein Data Bank. The NIST efforts in these activities have focused on data uniformity, establishing and maintaining the physical archive, and working with the NMR community.

  2. Reciprocal Space Mapping of Macromolecular Crystals in the Laboratory

    NASA Technical Reports Server (NTRS)

    Snell, Edward H.; Boggon, T. J.; Fewster, P. F.; Siddons, D. P.; Stojanof, V.; Pusey, M. L.

    1998-01-01

    The technique of reciprocal space mapping applied to the physical measurement of macromolecular crystals will be described. This technique uses a triple axis diffractometer setup whereby the monochromator is the first crystal, the sample is the second and the third crystal (of the same material as the monochromator) analyzes the diffracted beam. The geometry is such that it is possible to separate mosaic volume effects from lattice strain effects. The deconvolution of the instrument parameters will also be addressed. Results from measurements at Brookhaven National Synchrotron Radiation Source carried out on microgravity and ground-grown crystals will be presented. The required beam characteristics for reciprocal space mapping are also ideal for topographic studies and the first topographs ever recorded from microgravity protein crystal samples will be shown. We are now working on a system which will enable reciprocal space mapping, mosaicity and topography studies to be carried out in the home laboratory. This system uses a rotating anode X-ray source to provide an intense beam then a Bartels double crystal, four reflection monochromator to provide the spectral and geometric beam conditioning necessary such that the instrument characteristics do not mask the measurement. This is coupled to a high precision diffractometer and sensitive detector. Commissioning data and first results from the system will be presented.

  3. Use of Capillaries for Macromolecular Crystallization in a Cryogenic Dewar

    NASA Technical Reports Server (NTRS)

    Ciszak, Ewa; Hammons, Aaron S.; Hong, Young Soo

    2002-01-01

    The enhanced gaseous nitrogen (EGN) dewar is a cryogenic dry shipper with a sealed cylinder inserted inside along with a temperature monitoring device, and is intended for macromolecular crystallization experiments on the International Space Station. Within the dewar, each crystallization experiment is contained as a solution within a plastic capillary tube. The standard procedure for loading samples in these tubes has involved rapid freezing of the precipitant and biomolecular solution, e.g., protein, directly in liquid nitrogen; this method, however, often resulted in uncontrolled formation of air voids, These air pockets, or bubbles, can lead to irreproducible crystallization results. A novel protocol has been developed to prevent formation of bubbles, and this has been tested in the laboratory as well as aboard the International Space Station during a 42-day long mission of July/August 2001. The gain or loss of mass from solutions within the plastic capillaries revealed that mass transport occurred among separated tubes, and that this mass transport was dependent upon the hygroscopic character of the solution contained in any given tube. The surface area of the plastic capillary tube also related to the observed mass transport. Furthermore, the decreased mass of solutions of-protein correlated to observed formation of protein crystals.

  4. Use of Capillaries for Macromolecular Crystallization in a Cryogenic Dewar

    NASA Technical Reports Server (NTRS)

    Ciszak, Ewa; Hammons, Aaron S.; Hong, Young Soo; Curreri, Peter A. (Technical Monitor)

    2001-01-01

    The Enhanced Gaseous Nitrogen (EGN) Dewar is a cryogenic dry shipper with a sealed cylinder inserted inside along with a temperature-monitoring device, and is intended for macromolecular crystallization experiments on the International Space Station. Within the Dewar, each crystallization experiment is contained as a solution within a plastic capillary. The standard procedure for loading samples in these tubes has involved rapid freezing of the precipitant and biomolecule solution directly in liquid nitrogen; this method, however, often results in uncontrolled formation of air voids. These air pockets, or bubbles, then can lead to irreproducible crystallization results. A novel protocol has been developed to prevent formation of bubbles, and this has been tested in the laboratory as well as aboard the International Space Station during a 42-day long mission of July/August of 2001. Furthermore, gain or loss of mass from solutions within the capillaries revealed that mass transport amongst separated tubes occurred, and that this mass transport was determined by the hygroscopic character of a solution contained in any given tube. The sample volume and the surface area of the plastic capillary tube also related to the observed mass transport.

  5. Translation calibration of inverse-kappa goniometers in macromolecular crystallography.

    PubMed

    Brockhauser, Sandor; White, Kristopher I; McCarthy, Andrew A; Ravelli, Raimond B G

    2011-05-01

    Precise and convenient crystal reorientation is of experimental importance in macromolecular crystallography (MX). The development of multi-axis goniometers, such as the ESRF/EMBL mini-κ, necessitates the corresponding development of calibration procedures that can be used for the setup, maintenance and troubleshooting of such devices. While traditional multi-axis goniometers require all rotation axes to intersect the unique point of the sample position, recently developed miniaturized instruments for sample reorientation in MX are not as restricted. However, the samples must always be re-centred following a change in orientation. To overcome this inconvenience and allow the use of multi-axis goniometers without the fundamental restriction of having all axes intersecting in the same point, an automatic translation correction protocol has been developed for such instruments. It requires precise information about the direction and location of the rotation axes. To measure and supply this information, a general, easy-to-perform translation calibration (TC) procedure has also been developed. The TC procedure is routinely performed on most MX beamlines at the ESRF and some results are presented for reference.

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

    PubMed

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

    2014-02-26

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

  7. JBluIce-EPICS control system for macromolecular crystallography.

    PubMed

    Stepanov, Sergey; Makarov, Oleg; Hilgart, Mark; Pothineni, Sudhir Babu; Urakhchin, Alex; Devarapalli, Satish; Yoder, Derek; Becker, Michael; Ogata, Craig; Sanishvili, Ruslan; Venugopalan, Nagarajan; Smith, Janet L; Fischetti, Robert F

    2011-03-01

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

  8. 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

  9. Dynamic-covalent macromolecular stars with boronic ester linkages.

    PubMed

    Bapat, Abhijeet P; Roy, Debashish; Ray, Jacob G; Savin, Daniel A; Sumerlin, Brent S

    2011-12-14

    Macromolecular stars containing reversible boronic ester linkages were prepared by an arm-first approach by reacting well-defined boronic acid-containing block copolymers with multifunctional 1,2/1,3-diols. Homopolymers of 3-acrylamidophenylboronic acid (APBA) formed macroscopic dynamic-covalent networks when cross-linked with multifunctional diols. On the other hand, adding the diol cross-linkers to block copolymers of poly(N,N-dimethylacrylamide (PDMA))-b-poly(APBA) led to nanosized multiarm stars with boronic ester cores and PDMA coronas. The assembly of the stars under a variety of conditions was considered. The dynamic-covalent nature of the boronic ester cross-links allowed the stars to reconfigure their covalent structure in the presence of monofunctional diols that competed for bonding with the boronic acid component. Therefore, the stars could be induced to dissociate via competitive exchange reactions. The star formation-dissociation process was shown to be repeatable over multiple cycles. © 2011 American Chemical Society

  10. 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

  11. Present status of SPring-8 macromolecular crystallography beamlines

    SciTech Connect

    Kawano, Yoshiaki; Hirata, Kunio; Ueno, Go; Hikima, Takaaki; Murakami, Hironori; Maeda, Daisuke; Nisawa, Atsushi; Yamamoto, Masaki; Shimizu, Nobutaka; Baba, Seiki; Hasegawa, Kazuya; Makino, Masatomo; Mizuno, Nobuhiro; Hoshino, Takeshi; Ito, Ren; Wada, Izumi; Kumasaka, Takashi

    2010-06-23

    Seven beamlines are operated for macromolecular crystallography (MX) at SPring-8. The three undulator beamlines are developed for cutting edge target and four bending-magnet beamlines are developed for high throughput MX. The undulator beamline, BL41XU that provides the most brilliant beam, is dedicated to obtain high quality data even from small-size and weakly-diffracting crystals. The minimum beam size at sample position is achieved to 10 {mu}m diameter using a pin-hole collimator. Its photon flux at wavelength {lambda} = 1.0 A is 2.8x10{sup 11} photons/sec. This small beam coupled with irradiation point scanning method is quite useful to take diffraction dataset from small crystals by suppressing the radiation damage. These advanced technologies made a number of difficult protein structure analysis possible, (i.e. Sodium-potassium ATPase). The bending-magnet beamlines BL26B1/B2 and BL38B1 provide automatic data collection exploiting the high mobility of the beam. The beamline operation software 'BSS', sample auto-changer 'SPACE' and web-based data management software 'D-Cha' have made the automatic data collection possible. The 'Mail-in data collection system' that accepts distant users samples via courier service have made users possible to collect diffraction data without visiting SPring-8. The structural genomics research is promoted by these beamlines.

  12. Macromolecular Crystallography and Structural Biology Databases at NIST

    PubMed Central

    Gilliland, Gary L.

    2001-01-01

    In the late 1970s, macromolecular crystallography at NIST began with collaboration between NIST and NIH to establish a single-crystal neutron diffractometer. This instrument was constructed and employed to solve a number of crystal structures: bovine ribonuclease A, bovine-ribonuclease-uridine vanadate complex, and porcine insulin. In the mid 1980s a Biomolecular Structure Group was created establishing NIST capabilities in biomolecular singe-crystal x-ray diffraction. The group worked on a variety of structural problems until joining the NIST/UMBI Center for Advanced Research in Biotechnology (CARB) in 1987. Crystallographic studies at CARB were then focused on protein engineering efforts that included among others chymosin, subtilisin BPN', interleukin 1β, and glutathione S-transferase. Recently, the structural biology efforts have centered on enzymes in the chorismate metabolic pathways involved in amino acid biosynthesis and in structural genomics that involves determining the structures of “hypothetical” proteins to aid in assigning function. In addition to crystallographic studies, structural biology database activities began with the formal establishment of the Biological Macro-molecule Crystallization Database in 1989. Later, in 1997, NIST in partnership with Rutgers and UCSD formed the Research Collaboratory for Structural Bioinformatics that successfully acquired the Protein Data Bank. The NIST efforts in these activities have focused on data uniformity, establishing and maintaining the physical archive, and working with the NMR community. PMID:27500071

  13. JBluIce-EPICS control system for macromolecular crystallography.

    SciTech Connect

    Stepanov, S.; Makarov, O.; Hilgart, M.; Pothineni, S.; Urakhchin, A.; Devarapalli, S.; Yoder, D.; Becker, M.; Ogata, C.; Sanishvili, R.; Nagarajan, V.; Smith, J. L.; Fischetti, R. F.

    2011-01-01

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

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

    PubMed Central

    Helliwell, John R.; Mitchell, Edward P.

    2015-01-01

    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

  15. 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.

  16. Present status of SPring-8 macromolecular crystallography beamlines

    NASA Astrophysics Data System (ADS)

    Kawano, Yoshiaki; Shimizu, Nobutaka; Baba, Seiki; Hasegawa, Kazuya; Makino, Masatomo; Mizuno, Nobuhiro; Hoshino, Takeshi; Ito, Ren; Wada, Izumi; Hirata, Kunio; Ueno, Go; Hikima, Takaaki; Murakami, Hironori; Maeda, Daisuke; Nisawa, Atsushi; Kumasaka, Takashi; Yamamoto, Masaki

    2010-06-01

    Seven beamlines are operated for macromolecular crystallography (MX) at SPring-8. The three undulator beamlines are developed for cutting edge target and four bending-magnet beamlines are developed for high throughput MX. The undulator beamline, BL41XU that provides the most brilliant beam, is dedicated to obtain high quality data even from small-size and weakly-diffracting crystals. The minimum beam size at sample position is achieved to 10 μm diameter using a pin-hole collimator. Its photon flux at wavelength λ = 1.0 Å is 2.8×1011 photons/sec. This small beam coupled with irradiation point scanning method is quite useful to take diffraction dataset from small crystals by suppressing the radiation damage. These advanced technologies made a number of difficult protein structure analysis possible, (i.e. Sodium-potassium ATPase). The bending-magnet beamlines BL26B1/B2 and BL38B1 provide automatic data collection exploiting the high mobility of the beam. The beamline operation software "BSS," sample auto-changer "SPACE" and web-based data management software "D-Cha" have made the automatic data collection possible. The "Mail-in data collection system" that accepts distant users samples via courier service have made users possible to collect diffraction data without visiting SPring-8. The structural genomics research is promoted by these beamlines.

  17. 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.

  18. Macromolecular coal structure as revealed by novel diffusion tests

    SciTech Connect

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

    1990-01-01

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

  19. On macromolecular refinement at subatomic resolution with interatomic scatterers

    PubMed Central

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

    2007-01-01

    A study of the accurate electron-density distribution in molecular crystals at subatomic resolution (better than ∼1.0 Å) requires more detailed models than those based on independent spherical atoms. A tool that is conventionally used in small-molecule crystallography is the multipolar model. Even at upper resolution limits of 0.8–1.0 Å, the number of experimental data is insufficient for 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 data sets gave results that were comparable in quality with the results of multipolar refinement and superior to those for conventional models. Applications to several data sets of both small molecules and macromolecules are shown. These refinements were performed using the general-purpose macromolecular refinement module phenix.refine of the PHENIX package. PMID:18007035

  20. Macromolecular crystallization in microgravity generated by a superconducting magnet.

    PubMed

    Wakayama, N I; Yin, D C; Harata, K; Kiyoshi, T; Fujiwara, M; Tanimoto, Y

    2006-09-01

    About 30% of the protein crystals grown in space yield better X-ray diffraction data than the best crystals grown on the earth. The microgravity environments provided by the application of an upward magnetic force constitute excellent candidates for simulating the microgravity conditions in space. Here, we describe a method to control effective gravity and formation of protein crystals in various levels of effective gravity. Since 2002, the stable and long-time durable microgravity generated by a convenient type of superconducting magnet has been available for protein crystal growth. For the first time, protein crystals, orthorhombic lysozyme, were grown at microgravity on the earth, and it was proved that this microgravity improved the crystal quality effectively and reproducibly. The present method always accompanies a strong magnetic field, and the magnetic field itself seems to improve crystal quality. Microgravity is not always effective for improving crystal quality. When we applied this microgravity to the formation of cubic porcine insulin and tetragonal lysozyme crystals, we observed no dependence of effective gravity on crystal quality. Thus, this kind of test will be useful for selecting promising proteins prior to the space experiments. Finally, the microgravity generated by the magnet is compared with that in space, considering the cost, the quality of microgravity, experimental convenience, etc., and the future use of this microgravity for macromolecular crystal growth is discussed.

  1. Specific ion effects on macromolecular interactions in Escherichia coli extracts.

    PubMed

    Kyne, Ciara; Ruhle, Brian; Gautier, Virginie W; Crowley, Peter B

    2015-03-01

    Protein characterization in situ remains a major challenge for protein science. Here, the interactions of ΔTat-GB1 in Escherichia coli cell extracts were investigated by NMR spectroscopy and size exclusion chromatography (SEC). ΔTat-GB1 was found to participate in high molecular weight complexes that remain intact at physiologically-relevant ionic strength. This observation helps to explain why ΔTat-GB1 was not detected by in-cell NMR spectroscopy. Extracts pre-treated with RNase A had a different SEC elution profile indicating that ΔTat-GB1 predominantly interacted with RNA. The roles of biological and laboratory ions in mediating macromolecular interactions were studied. Interestingly, the interactions of ΔTat-GB1 could be disrupted by biologically-relevant multivalent ions. The most effective shielding of interactions occurred in Mg(2+) -containing buffers. Moreover, a combination of RNA digestion and Mg(2+) greatly enhanced the NMR detection of ΔTat-GB1 in cell extracts.

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

    PubMed

    Karavassili, Fotini; Margiolaki, Irene

    2016-01-01

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

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

    PubMed

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

    2012-06-01

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

  4. Reciprocal Space Mapping of Macromolecular Crystals in the Laboratory

    NASA Technical Reports Server (NTRS)

    Snell, Edward H.; Boggon, T. J.; Fewster, P. F.; Siddons, D. P.; Stojanof, V.; Pusey, M. L.

    1998-01-01

    The technique of reciprocal space mapping applied to the physical measurement of macromolecular crystals will be described. This technique uses a triple axis diffractometer setup whereby the monochromator is the first crystal, the sample is the second and the third crystal (of the same material as the monochromator) analyzes the diffracted beam. The geometry is such that it is possible to separate mosaic volume effects from lattice strain effects. The deconvolution of the instrument parameters will also be addressed. Results from measurements at Brookhaven National Synchrotron Radiation Source carried out on microgravity and ground-grown crystals will be presented. The required beam characteristics for reciprocal space mapping are also ideal for topographic studies and the first topographs ever recorded from microgravity protein crystal samples will be shown. We are now working on a system which will enable reciprocal space mapping, mosaicity and topography studies to be carried out in the home laboratory. This system uses a rotating anode X-ray source to provide an intense beam then a Bartels double crystal, four reflection monochromator to provide the spectral and geometric beam conditioning necessary such that the instrument characteristics do not mask the measurement. This is coupled to a high precision diffractometer and sensitive detector. Commissioning data and first results from the system will be presented.

  5. Automated identification of elemental ions in macromolecular crystal structures

    SciTech Connect

    Echols, Nathaniel Morshed, Nader; Afonine, Pavel V.; McCoy, Airlie J.; Read, Randy J.; Terwilliger, Thomas C.; Adams, Paul D.

    2014-04-01

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

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

    SciTech Connect

    Joosten, Robbie P.; Soueidan, Hayssam; Wessels, Lodewyk F. A.; Perrakis, Anastassis

    2013-12-01

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

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

    PubMed

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

    2016-01-01

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  10. A MACROMOLECULAR REPEATING UNIT OF MITOCHONDRIAL STRUCTURE AND FUNCTION

    PubMed Central

    Fernández-Morán, H.; Oda, T.; Blair, P. V.; Green, D. E.

    1964-01-01

    A repeating particle associated with the cristae and the inner membrane of the external envelope has been recognized and characterized in beef heart mitochondria by correlated electron microscopic and biochemical studies. Many thousands (ca. 104 to 105) of these particles, disposed in regular arrays, are present in a single mitochondrion. The repeating particle, called the elementary particle (EP), consists of three parts: (1) a spherical or polyhedral head piece (80 to 100 A in diameter); (2) a cylindrical stalk (about 50 A long and 30 to 40 A wide); and (3) a base piece (40 x 110 A). The base pieces of the elementary particles form an integral part of the outer dense layers of the cristae. The elementary particles can be seen in electron micrographs of mitochondria in situ, of isolated mitochondria, and of submitochondrial particles with a complete electron transfer chain. Negative staining with phosphotungstate is only one of several techniques that can be used for reproducible demonstration of the repeating particles and underlying subunit organization of mitochondrial membranes. A particulate unit containing a complete electron transfer chain can be isolated from beef heart mitochondria. The isolated unit approximates in size that of the elementary particle in situ. The molecular weight of the particle in situ is calculated to be 1.3 x 106. Evidence is presented for identifying the isolated unit with the elementary particle visualized in situ. The elementary particle of the mitochondrion is believed to be a prototype of a class of functional particles or macromolecular assemblies of similar size found in association with membranes generally. PMID:14195622

  11. JBluIce–EPICS control system for macromolecular crystallography

    PubMed Central

    Stepanov, Sergey; Makarov, Oleg; Hilgart, Mark; Pothineni, Sudhir Babu; Urakhchin, Alex; Devarapalli, Satish; Yoder, Derek; Becker, Michael; Ogata, Craig; Sanishvili, Ruslan; Venugopalan, Nagarajan; Smith, Janet L.; Fischetti, Robert F.

    2011-01-01

    The trio of macromolecular crystallography beamlines constructed by the General Medicine and Cancer Institutes Collaborative Access Team (GM/CA-CAT) in Sector 23 of the Advanced Photon Source (APS) have been in growing demand owing to their outstanding beam quality and capacity to measure data from crystals of only a few micrometres in size. To take full advantage of the state-of-the-art mechanical and optical design of these beamlines, a significant effort has been devoted to designing fast, convenient, intuitive and robust beamline controls that could easily accommodate new beamline developments. The GM/CA-CAT beamline controls are based on the power of EPICS for distributed hardware control, the rich Java graphical user interface of Eclipse RCP and the task-oriented philosophy as well as the look and feel of the successful SSRL BluIce graphical user interface for crystallography. These beamline controls feature a minimum number of software layers, the wide use of plug-ins that can be written in any language and unified motion controls that allow on-the-fly scanning and optimization of any beamline com­ponent. This paper describes the ways in which BluIce was combined with EPICS and converted into the Java-based JBluIce, discusses the solutions aimed at streamlining and speeding up operations and gives an overview of the tools that are provided by this new open-source control system for facilitating crystallo­graphic experiments, especially in the field of microcrystallo­graphy. PMID:21358048

  12. Polyion complex micelle MRI contrast agents from poly(ethylene glycol)-b-poly(l-lysine) block copolymers having Gd-DOTA; preparations and their control of T(1)-relaxivities and blood circulation characteristics.

    PubMed

    Shiraishi, Kouichi; Kawano, Kumi; Maitani, Yoshie; Yokoyama, Masayuki

    2010-12-01

    The current study synthesized macromolecular magnetic resonance imaging (MRI) contrast agents constituted of the poly(ethylene glycol)-b-poly(L-lysine) block copolymer (PEG-P(Lys)). A chelate group, 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA), was attached to the primary amino group of the block copolymer in desired contents. Gd-DOTA-based macromolecular contrast agents were prepared from PEG-P(Lys) having DOTA (PEG-P(Lys-DOTA) and Gd(III) ions. All of the PEG-P(Lys) block copolymers having gadolinium ions (PEG-P(Lys-DOTA-Gd)) showed higher T(1) relaxivity (per gadolinium), r(1)=5.6-7.3mM(-1)s(-1), than that of a low-molecular-weight gadolinium-chelate, diethylenetriaminepentaacetic acid-gadolinium(III) (Gd-DTPA) at 9.4T. The study prepared the polyion complex (PIC) micelles from the amino groups of the lysine units and an oppositely charged polyanion, poly(methacrylic acid) or dextran sulfate, in an aqueous medium. In contrast, the fully DOTA-attached PEG-P(Lys-DOTA-Gd) formed a PIC with a polycation. Compared with partially DOTA-attached cationic PEG-P(Lys-DOTA-Gd), this PIC micelle yielded a forty percent decrease of r(1). This r(1) decrease was considered to result from a change in the accessibility of water molecules to gadolinium ions in the micelles' inner core. The r(1) was decreased upon formation of the PIC micelle, and this change proved that our concept worked in vitro. Blood-circulation characteristics of PIC micelles were controlled by means of changing the molecular weight of the counter anion. The PIC micelles accumulated in tumor tissues, and MRI study showed T1W image of axial slice of tumor area was significantly enhanced at 24h after the injection.

  13. Leaching of organic acids from macromolecular organic matter by non-supercritical CO2

    NASA Astrophysics Data System (ADS)

    Sauer, P.; Glombitza, C.; Kallmeyer, J.

    2012-04-01

    The storage of CO2 in underground reservoirs is discussed controversly in the scientific literature. The worldwide search for suitable storage formations also considers coal-bearing strata. CO2 is already injected into seams for enhanced recovery of coal bed methane. However, the effects of increased CO2 concentration, especially on organic matter rich formations, are rarely investigated. The injected CO2 will dissolve in the pore water, causing a decrease in pH and resulting in acidic formation waters. Huge amounts of low molecular weight organic acids (LMWOAs) are chemically bound to the macromolecular matrix of sedimentary organic matter and may be liberated by hydrolysis, which is enhanced by the acidic porewater. Recent investigations outlined the importance of LMWOAs as a feedstock for microbial life in the subsurface [1]. Therefore, injection of CO2 into coal formations may result in enhanced nutrient supply for subsurface microbes. To investigate the effect of high concentrations of dissolved CO2 on the release of LMWOAs from coal we developed an inexpensive high-pressure high temperature system that allows manipulating the partial pressure of dissolved gases at pressures and temperatures up to 60 MPa and 120° C, respectively. In a reservoir vessel, gases are added to saturate the extraction medium to the desired level. Inside the extraction vessel hangs a flexible and inert PVDF sleeve (polyvinylidene fluoride, almost impermeable for gases), holding the sample and separating it from the pressure fluid. The flexibility of the sleeve allows for subsampling without loss of pressure. Coal samples from the DEBITS-1 well, Waikato Basin, NZ (R0 = 0.29, TOC = 30%). were extracted at 90° C and 5 MPa, either with pure or CO2-saturated water. Subsamples were taken at different time points during the extraction. The extracted LMWOAs such as formate, acetate and oxalate were analysed by ion chromatography. Yields of LMWOAs were higher with pure water than with CO2

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

    NASA Astrophysics Data System (ADS)

    Bergasa-Caceres, Fernando; Rabitz, Herschel A.

    2013-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  16. Contribution of Macromolecular Antioxidants to Dietary Antioxidant Capacity: A Study in the Spanish Mediterranean Diet.

    PubMed

    Pérez-Jiménez, Jara; Díaz-Rubio, M Elena; Saura-Calixto, Fulgencio

    2015-12-01

    Epidemiological and clinical studies show that diets with a high antioxidant capacity, such us those rich in plant food and beverages, are associated with significant decreases in the overall risk of cardiovascular disease or colorectal cancer. Current studies on dietary antioxidants and dietary antioxidant capacity focus exclusively on low molecular weight or soluble antioxidants (vitamins C and E, phenolic compounds and carotenoids), ignoring macromolecular antioxidants. These are polymeric phenolic compounds or polyphenols and carotenoids linked to plant food macromolecules that yield bioavailable metabolites by the action of the microbiota with significant effects either local and/or systemic after absorption. This study determined the antioxidant capacity of the Spanish Mediterranean diet including for the first time both soluble and macromolecular antioxidants. Antioxidant capacity and consumption data of the 54 most consumed plant foods and beverages were used. Results showed that macromolecular antioxidants are the major dietary antioxidants, contributing a 61% to the diet antioxidant capacity (8000 μmol Trolox, determined by ABTS method). The antioxidant capacity data for foods and beverages provided here may be used to estimate the dietary antioxidant capacity in different populations, where similar contributions of macromolecular antioxidants may be expected, and also to design antioxidant-rich diets. Including macromolecular antioxidants in mechanistic, intervention and observational studies on dietary antioxidants may contribute to a better understanding of the role of antioxidants in nutrition and health.

  17. PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.

    PubMed

    Velankar, Sameer; van Ginkel, Glen; Alhroub, Younes; Battle, Gary M; Berrisford, John M; Conroy, Matthew J; Dana, Jose M; Gore, Swanand P; Gutmanas, Aleksandras; Haslam, Pauline; Hendrickx, Pieter M S; Lagerstedt, Ingvar; Mir, Saqib; Fernandez Montecelo, Manuel A; Mukhopadhyay, Abhik; Oldfield, Thomas J; Patwardhan, Ardan; Sanz-García, Eduardo; Sen, Sanchayita; Slowley, Robert A; Wainwright, Michael E; Deshpande, Mandar S; Iudin, Andrii; Sahni, Gaurav; Salavert Torres, Jose; Hirshberg, Miriam; Mak, Lora; Nadzirin, Nurul; Armstrong, David R; Clark, Alice R; Smart, Oliver S; Korir, Paul K; Kleywegt, Gerard J

    2016-01-04

    The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    PubMed

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

    2017-02-01

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

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

    SciTech Connect

    Chen, Julian C.-H.; Unkefer, Clifford Jay

    2017-01-01

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

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

    PubMed

    Chen, Julian C-H; Unkefer, Clifford J

    2017-01-01

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

  1. PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

    PubMed Central

    Velankar, Sameer; van Ginkel, Glen; Alhroub, Younes; Battle, Gary M.; Berrisford, John M.; Conroy, Matthew J.; Dana, Jose M.; Gore, Swanand P.; Gutmanas, Aleksandras; Haslam, Pauline; Hendrickx, Pieter M. S.; Lagerstedt, Ingvar; Mir, Saqib; Fernandez Montecelo, Manuel A.; Mukhopadhyay, Abhik; Oldfield, Thomas J.; Patwardhan, Ardan; Sanz-García, Eduardo; Sen, Sanchayita; Slowley, Robert A.; Wainwright, Michael E.; Deshpande, Mandar S.; Iudin, Andrii; Sahni, Gaurav; Salavert Torres, Jose; Hirshberg, Miriam; Mak, Lora; Nadzirin, Nurul; Armstrong, David R.; Clark, Alice R.; Smart, Oliver S.; Korir, Paul K.; Kleywegt, Gerard J.

    2016-01-01

    The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the ‘best structures’ for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data. PMID:26476444

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

    DOE PAGES

    Chen, Julian C.-H.; Unkefer, Clifford Jay

    2017-01-01

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

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

    PubMed Central

    Chen, Julian C.-H.

    2017-01-01

    The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002–2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallo­graphy in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s. PMID:28250943

  4. Synthesis and characterization of macromolecular layers grafted to polymer surfaces

    NASA Astrophysics Data System (ADS)

    Burtovyy, Oleksandr

    The composition and behavior of surfaces and interfaces play a pivotal role in dictating the overall efficiency of the majority of polymeric materials and devices. Surface properties of the materials can be altered using surface modification techniques. It is necessary to highlight that successful methods of surface modification should affect only the upper layer of the polymer material without changing bulk properties. The processes must introduce new functionalities to the surface, optimize surface roughness, lubrication, hydrophobicity, hydrophilicity, adhesion, conductivity, and/or biocompatibility. Research presented in this dissertation is dedicated to the synthesis, characterization, and application of thin macromolecular layers anchored to polymer substrates. Specifically, attachment of functional polymers via a "grafting to" approach has been extensively studied using PET and nylon model substrates. First, poly(glycidyl methacrylate) was used to introduce permanent functionalities to the model substrates by anchoring it to model films. Then, three different functional polymers were grafted on top of the previous layer. As one part of this study, the temperature and time dependence of grafting functional layers were studied. The surface coverage by hydrophobic polymer was determined from experimental data and predicted by a model. In general, the model has a high degree of predictive capability. Next, surface modification of polymeric fibers and membranes is presented as an important application of the polymer thin layers targeted in the study. Specifically, the procedures developed for surface modification of model substrates was employed for modification of PET, nylon, and cotton fabrics as well as PET track-etched membranes. Since epoxy groups are highly reactive in various chemical reactions, the approach becomes virtually universal, allowing both various surfaces and end-functionalized macromolecules to be used in the grafted layer synthesis. PET

  5. Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways

    PubMed Central

    Seyler, Sean L.; Kumar, Avishek; Thorpe, M. F.; Beckstein, Oliver

    2015-01-01

    Diverse classes of proteins function through large-scale conformational changes and various sophisticated computational algorithms have been proposed to enhance sampling of these macromolecular transition paths. Because such paths are curves in a high-dimensional space, it has been difficult to quantitatively compare multiple paths, a necessary prerequisite to, for instance, assess the quality of different algorithms. We introduce a method named Path Similarity Analysis (PSA) that enables us to quantify the similarity between two arbitrary paths and extract the atomic-scale determinants responsible for their differences. PSA utilizes the full information available in 3N-dimensional configuration space trajectories by employing the Hausdorff or Fréchet metrics (adopted from computational geometry) to quantify the degree of similarity between piecewise-linear curves. It thus completely avoids relying on projections into low dimensional spaces, as used in traditional approaches. To elucidate the principles of PSA, we quantified the effect of path roughness induced by thermal fluctuations using a toy model system. Using, as an example, the closed-to-open transitions of the enzyme adenylate kinase (AdK) in its substrate-free form, we compared a range of protein transition path-generating algorithms. Molecular dynamics-based dynamic importance sampling (DIMS) MD and targeted MD (TMD) and the purely geometric FRODA (Framework Rigidity Optimized Dynamics Algorithm) were tested along with seven other methods publicly available on servers, including several based on the popular elastic network model (ENM). PSA with clustering revealed that paths produced by a given method are more similar to each other than to those from another method and, for instance, that the ENM-based methods produced relatively similar paths. PSA applied to ensembles of DIMS MD and FRODA trajectories of the conformational transition of diphtheria toxin, a particularly challenging example, showed that

  6. Macromolecular properties and polymeric structure of canine tracheal mucins.

    PubMed Central

    Shankar, V; Virmani, A K; Naziruddin, B; Sachdev, G P

    1991-01-01

    Two high-Mr mucus glycoproteins (mucins), CTM-A and CTM-B, were highly purified from canine tracheal pouch secretions, and their macromolecular properties as well as polymeric structure were investigated. On SDS/composite-gel electrophoresis, a diffuse band was observed for each mucin. Polyacrylamide-gel electrophoresis using 6% gels also showed the absence of low-Mr contaminants in the mucins. Comparison of chemical and amino acid compositions revealed significant differences between the two mucins. Using a static-laser-light-scattering technique, CTM-A and CTM-B were found to have weight-average Mr values of about 11.0 x 10(6) and 1.4 x 10(6) respectively. Both mucins showed concentration-dependent aggregation in buffer containing 6 M-guanidine hydrochloride. Under similar experimental conditions, reduced-alkylated CTM-A had an Mr of 5.48 x 10(6) and showed no concentration-dependent aggregation. Hydrophobic properties of the mucins, investigated by the fluorescent probe technique using mansylphenylalanine as the probe, showed the presence of a large number of low-affinity (KD approx. 10(5) M) binding sites. These sites appeared to be located on the non-glycosylated regions of the protein core, since Pronase digestion of the mucins almost completely eliminated probe binding. Reduction of disulphide bonds of CTM-A and CTM-B did not significantly alter the probe-binding properties. Also, addition of increasing NaCl concentrations (0.03-1.0 M) to the buffer caused only a small change in the hydrophobic properties of native and reduced-alkylated mucins. CTM-A was deglycosylated, without notable in the hydrophobic properties of native and reduced-alkylated mucins. CTM-A was deglycosylated, without notable degradation, using a combination of chemical and enzymic methods. On SDS/PAGE the protein core was estimated to have an Mr of approx. 60,000. On the basis of the protein and carbohydrate contents of the major mucin CTM-A, the mucin monomer was calculated to have an

  7. Non-contact luminescence lifetime cryothermometry for macromolecular crystallography

    PubMed Central

    Mykhaylyk, V. B.; Kraus, H.

    2017-01-01

    Temperature is a very important parameter when aiming to minimize radiation damage to biological samples during experiments that utilize intense ionizing radiation. A novel technique for remote, non-contact, in situ monitoring of the protein crystal temperature has been developed for the new I23 beamline at the Diamond Light Source, a facility dedicated to macromolecular crystallography (MX) with long-wavelength X-rays. The temperature is derived from the temperature-dependent decay time constant of luminescence from a minuscule scintillation sensor (<0.05 mm3) located in very close proximity to the sample under test. In this work the underlying principle of cryogenic luminescence lifetime thermometry is presented, the features of the detection method and the choice of temperature sensor are discussed, and it is demonstrated how the temperature monitoring system was integrated within the viewing system of the endstation used for the visualization of protein crystals. The thermometry system was characterized using a Bi4Ge3O12 crystal scintillator that exhibits good responsivity of the decay time constant as a function of temperature over a wide range (8–270 K). The scintillation sensor was calibrated and the uncertainty of the temperature measurements over the primary operation temperature range of the beamline (30–150 K) was assessed to be ±1.6 K. It has been shown that the temperature of the sample holder, measured using the luminescence sensor, agrees well with the expected value. The technique was applied to characterize the thermal performance of different sample mounts that have been used in MX experiments at the I23 beamline. The thickness of the mount is shown to have the greatest impact upon the temperature distribution across the sample mount. Altogether, these tests and findings demonstrate the usefulness of the thermometry system in highlighting the challenges that remain to be addressed for the in-vacuum MX experiment to become a reliable

  8. Non-contact luminescence lifetime cryothermometry for macromolecular crystallography.

    PubMed

    Mykhaylyk, V B; Wagner, A; Kraus, H

    2017-05-01

    Temperature is a very important parameter when aiming to minimize radiation damage to biological samples during experiments that utilize intense ionizing radiation. A novel technique for remote, non-contact, in situ monitoring of the protein crystal temperature has been developed for the new I23 beamline at the Diamond Light Source, a facility dedicated to macromolecular crystallography (MX) with long-wavelength X-rays. The temperature is derived from the temperature-dependent decay time constant of luminescence from a minuscule scintillation sensor (<0.05 mm(3)) located in very close proximity to the sample under test. In this work the underlying principle of cryogenic luminescence lifetime thermometry is presented, the features of the detection method and the choice of temperature sensor are discussed, and it is demonstrated how the temperature monitoring system was integrated within the viewing system of the endstation used for the visualization of protein crystals. The thermometry system was characterized using a Bi4Ge3O12 crystal scintillator that exhibits good responsivity of the decay time constant as a function of temperature over a wide range (8-270 K). The scintillation sensor was calibrated and the uncertainty of the temperature measurements over the primary operation temperature range of the beamline (30-150 K) was assessed to be ±1.6 K. It has been shown that the temperature of the sample holder, measured using the luminescence sensor, agrees well with the expected value. The technique was applied to characterize the thermal performance of different sample mounts that have been used in MX experiments at the I23 beamline. The thickness of the mount is shown to have the greatest impact upon the temperature distribution across the sample mount. Altogether, these tests and findings demonstrate the usefulness of the thermometry system in highlighting the challenges that remain to be addressed for the in-vacuum MX experiment to become a reliable and

  9. Towards a compact and precise sample holder for macromolecular crystallography.

    PubMed

    Papp, Gergely; Rossi, Christopher; Janocha, Robert; Sorez, Clement; Lopez-Marrero, Marcos; Astruc, Anthony; McCarthy, Andrew; Belrhali, Hassan; Bowler, Matthew W; Cipriani, Florent

    2017-10-01

    Most of the sample holders currently used in macromolecular crystallography offer limited storage density and poor initial crystal-positioning precision upon mounting on a goniometer. This has now become a limiting factor at high-throughput beamlines, where data collection can be performed in a matter of seconds. Furthermore, this lack of precision limits the potential benefits emerging from automated harvesting systems that could provide crystal-position information which would further enhance alignment at beamlines. This situation provided the motivation for the development of a compact and precise sample holder with corresponding pucks, handling tools and robotic transfer protocols. The development process included four main phases: design, prototype manufacture, testing with a robotic sample changer and validation under real conditions on a beamline. Two sample-holder designs are proposed: NewPin and miniSPINE. They share the same robot gripper and allow the storage of 36 sample holders in uni-puck footprint-style pucks, which represents 252 samples in a dry-shipping dewar commonly used in the field. The pucks are identified with human- and machine-readable codes, as well as with radio-frequency identification (RFID) tags. NewPin offers a crystal-repositioning precision of up to 10 µm but requires a specific goniometer socket. The storage density could reach 64 samples using a special puck designed for fully robotic handling. miniSPINE is less precise but uses a goniometer mount compatible with the current SPINE standard. miniSPINE is proposed for the first implementation of the new standard, since it is easier to integrate at beamlines. An upgraded version of the SPINE sample holder with a corresponding puck named SPINEplus is also proposed in order to offer a homogenous and interoperable system. The project involved several European synchrotrons and industrial companies in the fields of consumables and sample-changer robotics. Manual handling of mini

  10. Contrast Adaptation Contributes to Contrast-Invariance of Orientation Tuning of Primate V1 Cells

    PubMed Central

    Nowak, Lionel G.; Barone, Pascal

    2009-01-01

    Background Studies in rodents and carnivores have shown that orientation tuning width of single neurons does not change when stimulus contrast is modified. However, in these studies, stimuli were presented for a relatively long duration (e. g., 4 seconds), making it possible that contrast adaptation contributed to contrast-invariance of orientation tuning. Our first purpose was to determine, in marmoset area V1, whether orientation tuning is still contrast-invariant with the stimulation duration is comparable to that of a visual fixation. Methodology/Principal Findings We performed extracellular recordings and examined orientation tuning of single-units using static sine-wave gratings that were flashed for 200 msec. Sixteen orientations and three contrast levels, representing low, medium and high values in the range of effective contrasts for each neuron, were randomly intermixed. Contrast adaptation being a slow phenomenon, cells did not have enough time to adapt to each contrast individually. With this stimulation protocol, we found that the tuning width obtained at intermediate contrast was reduced to 89% (median), and that at low contrast to 76%, of that obtained at high contrast. Therefore, when probed with briefly flashed stimuli, orientation tuning is not contrast-invariant in marmoset V1. Our second purpose was to determine whether contrast adaptation contributes to contrast-invariance of orientation tuning. Stationary gratings were presented, as previously, for 200 msec with randomly varying orientations, but the contrast was kept constant within stimulation blocks lasting >20 sec, allowing for adaptation to the single contrast in use. In these conditions, tuning widths obtained at low contrast were still significantly less than at high contrast (median 85%). However, tuning widths obtained with medium and high contrast stimuli no longer differed significantly. Conclusions/Significance Orientation tuning does not appear to be contrast-invariant when

  11. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7.

    PubMed

    Langer, Gerrit; Cohen, Serge X; Lamzin, Victor S; Perrakis, Anastassis

    2008-01-01

    ARP/wARP is a software suite to build macromolecular models in X-ray crystallography electron density maps. Structural genomics initiatives and the study of complex macromolecular assemblies and membrane proteins all rely on advanced methods for 3D structure determination. ARP/wARP meets these needs by providing the tools to obtain a macromolecular model automatically, with a reproducible computational procedure. ARP/wARP 7.0 tackles several tasks: iterative protein model building including a high-level decision-making control module; fast construction of the secondary structure of a protein; building flexible loops in alternate conformations; fully automated placement of ligands, including a choice of the best-fitting ligand from a 'cocktail'; and finding ordered water molecules. All protocols are easy to handle by a nonexpert user through a graphical user interface or a command line. The time required is typically a few minutes although iterative model building may take a few hours.

  12. Self-organization in macromolecular systems: the notion of adaptive value.

    PubMed

    Demetrius, L

    1984-10-01

    Self-organization in macromolecular systems refers to the transition from a random assembly of interacting oligomers to a system of stable heteropolymers. The concept of adaptive value describes the correlation between environmental variability and the variability in replication and mutation rates of the interacting oligomers. This paper describes a model of self-organization in macromolecular systems based on the concept of adaptive value. The equilibrium states of a set of interacting polymers are described by states that maximize the adaptive value. The analytic basis for this notion of equilibrium, which is called the adaptive value principle, is given and this principle is invoked to explain two examples of macromolecular self-assembly.

  13. New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection

    PubMed Central

    Soltis, S. Michael; Cohen, Aina E.; Deacon, Ashley; Eriksson, Thomas; González, Ana; McPhillips, Scott; Chui, Hsui; Dunten, Pete; Hollenbeck, Michael; Mathews, Irimpan; Miller, Mitch; Moorhead, Penjit; Phizackerley, R. Paul; Smith, Clyde; Song, Jinhu; van dem Bedem, Henry; Ellis, Paul; Kuhn, Peter; McPhillips, Timothy; Sauter, Nicholas; Sharp, Kenneth; Tsyba, Irina; Wolf, Guenter

    2008-01-01

    Complete automation of the macromolecular crystallography experiment has been achieved at SSRL through the combination of robust mechanized experimental hardware and a flexible control system with an intuitive user interface. These highly reliable systems have enabled crystallography experiments to be carried out from the researchers’ home institutions and other remote locations while retaining complete control over even the most challenging systems. A breakthrough component of the system, the Stanford Auto-Mounter (SAM), has enabled the efficient mounting of cryocooled samples without human intervention. Taking advantage of this automation, researchers have successfully screened more than 200 000 samples to select the crystals with the best diffraction quality for data collection as well as to determine optimal crystallization and cryocooling conditions. These systems, which have been deployed on all SSRL macromolecular crystallography beamlines and several beamlines worldwide, are used by more than 80 research groups in remote locations, establishing a new paradigm for macromolecular crystallo­graphy experimentation. PMID:19018097

  14. Label-free in vivo Raman microspectroscopic imaging of the macromolecular architecture of oocytes.

    PubMed

    Heraud, Philip; Marzec, Katarzyna Maria; Zhang, Qing-Hua; Yuen, Wai Shan; Carroll, John; Wood, Bayden R

    2017-08-21

    Confocal Raman spectroscopy (CRS) can provide information about oocyte competency through measurement of changes in the macromolecular architecture during oocyte development and maturation. Hitherto most spectroscopic studies have been limited to fixed oocytes due to the inherent difficulties working with live cells. Here we report the first three-dimensional images of living murine oocytes using CRS. We show that fixation induces significant changes in the macromolecular chemistry compared to living oocytes. A band at 1602 cm(-1), assigned to a marker for mitochondria function was found in living oocytes but absent from fixed oocytes providing an in vivo marker. Fixation resulted in significant changes in protein and nucleic acid bands and the spatial distribution of organelles. Raman imaging of Metaphase I and II (MI, MII) and germinal vesicle stage oocytes showed changes in nuclear organisation and cytoplasm macromolecular architecture during these development and maturation stages related to changes in chromosome condensation, mitochondria aggregation and lipid droplet numbers.

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

    PubMed

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

    2016-01-11

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

  16. Visualizing Macromolecular Complexes with In Situ Liquid Scanning Transmission Electron Microscopy

    SciTech Connect

    Evans, James E.; Jungjohann, K. L.; Wong, Peony C. K.; Chiu, Po-Lin; Dutrow, Gavin H.; Arslan, Ilke; Browning, Nigel D.

    2012-11-01

    A central focus of biological research is understanding the structure/function relationship of macromolecular protein complexes. Yet conventional transmission electron microscopy techniques are limited to static observations. Here we present the first direct images of purified macromolecular protein complexes using in situ liquid scanning transmission electron microscopy. Our results establish the capability of this technique for visualizing the interface between biology and nanotechnology with high fidelity while also probing the interactions of biomolecules within solution. This method represents an important advancement towards allowing future high-resolution observations of biological processes and conformational dynamics in real-time.

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

    PubMed Central

    Bastard, Karine; Saladin, Adrien; Prévost, Chantal

    2011-01-01

    Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA. We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success. PMID:21541061

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

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

    PubMed

    Bastard, Karine; Saladin, Adrien; Prévost, Chantal

    2011-02-22

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

  20. Visualizing macromolecular complexes with in situ liquid scanning transmission electron microscopy.

    PubMed

    Evans, James E; Jungjohann, Katherine L; Wong, Peony C K; Chiu, Po-Lin; Dutrow, Gavin H; Arslan, Ilke; Browning, Nigel D

    2012-11-01

    A central focus of biological research is understanding the structure/function relationship of macromolecular protein complexes. Yet conventional transmission electron microscopy techniques are limited to static observations. Here we present the first direct images of purified macromolecular protein complexes using in situ liquid scanning transmission electron microscopy. Our results establish the capability of this technique for visualizing the interface between biology and nanotechnology with high fidelity while also probing the interactions of biomolecules within solution. This method represents an important advancement towards allowing future high-resolution observations of biological processes and conformational dynamics in real-time. Published by Elsevier Ltd.

  1. Host responses and metabolic profiles of wood components in Dutch elm hybrids with a contrasting tolerance to Dutch elm disease

    PubMed Central

    Ďurkovič, Jaroslav; Kačík, František; Olčák, Dušan; Kučerová, Veronika; Krajňáková, Jana

    2014-01-01

    Background and Aims Changes occurring in the macromolecular traits of cell wall components in elm wood following attack by Ophiostoma novo-ulmi, the causative agent of Dutch elm disease (DED), are poorly understood. The purpose of this study was to compare host responses and the metabolic profiles of wood components for two Dutch elm (Ulmus) hybrids, ‘Groeneveld’ (a susceptible clone) and ‘Dodoens’ (a tolerant clone), that have contrasting survival strategies upon infection with the current prevalent strain of DED. Methods Ten-year-old plants of the hybrid elms were inoculated with O. novo-ulmi ssp. americana × novo-ulmi. Measurements were made of the content of main cell wall components and extractives, lignin monomer composition, macromolecular traits of cellulose and neutral saccharide composition. Key Results Upon infection, medium molecular weight macromolecules of cellulose were degraded in both the susceptible and tolerant elm hybrids, resulting in the occurrence of secondary cell wall ruptures and cracks in the vessels, but rarely in the fibres. The 13C nuclear magnetic resonance spectra revealed that loss of crystalline and non-crystalline cellulose regions occurred in parallel. The rate of cellulose degradation was influenced by the syringyl:guaiacyl ratio in lignin. Both hybrids commonly responded to the medium molecular weight cellulose degradation with the biosynthesis of high molecular weight macromolecules of cellulose, resulting in a significant increase in values for the degree of polymerization and polydispersity. Other responses of the hybrids included an increase in lignin content, a decrease in relative proportions of d-glucose, and an increase in proportions of d-xylose. Differential responses between the hybrids were found in the syringyl:guaiacyl ratio in lignin. Conclusions In susceptible ‘Groeneveld’ plants, syringyl-rich lignin provided a far greater degree of protection from cellulose degradation than in ‘Dodoens’, but

  2. Macromolecular crowding gives rise to microviscosity, anomalous diffusion and accelerated actin polymerization

    NASA Astrophysics Data System (ADS)

    Rashid, Rafi; Chee, Stella Min Ling; Raghunath, Michael; Wohland, Thorsten

    2015-05-01

    Macromolecular crowding (MMC) has been used in various in vitro experimental systems to mimic in vivo physiology. This is because the crowded cytoplasm of cells contains many different types of solutes dissolved in an aqueous medium. MMC in the extracellular microenvironment is involved in maintaining stem cells in their undifferentiated state (niche) as well as in aiding their differentiation after they have travelled to new locations outside the niche. MMC at physiologically relevant fractional volume occupancies (FVOs) significantly enhances the adipogenic differentiation of human bone marrow-derived mesenchymal stem cells during chemically induced adipogenesis. The mechanism by which MMC produces this enhancement is not entirely known. In the context of extracellular collagen deposition, we have recently reported the importance of optimizing the FVO while minimizing the bulk viscosity. Two opposing properties will determine the net rate of a biochemical reaction: the negative effect of bulk viscosity and the positive effect of the excluded volume, the latter being expressed by the FVO. In this study we have looked more closely at the effect of viscosity on reaction rates. We have used fluorimetry to measure the rate of actin polymerization and fluorescence correlation spectroscopy (FCS) to measure diffusion of various probes in solutions containing the crowder Ficoll at physiological concentrations. Similar to its effect on collagen, Ficoll enhanced the actin polymerization rate despite increasing the bulk viscosity. Our FCS measurements reveal a relatively minor component of anomalous diffusion. In addition, our measurements do suggest that microviscosity becomes relevant in a crowded environment. We ruled out bulk viscosity as a cause of the rate enhancement by performing the actin polymerization assay in glycerol. These opposite effects of Ficoll and glycerol led us to conclude that microviscosity becomes relevant at the length scale of the reacting

  3. Macromolecular crowding gives rise to microviscosity, anomalous diffusion and accelerated actin polymerization.

    PubMed

    Rashid, Rafi; Chee, Stella Min Ling; Raghunath, Michael; Wohland, Thorsten

    2015-04-30

    Macromolecular crowding (MMC) has been used in various in vitro experimental systems to mimic in vivo physiology. This is because the crowded cytoplasm of cells contains many different types of solutes dissolved in an aqueous medium. MMC in the extracellular microenvironment is involved in maintaining stem cells in their undifferentiated state (niche) as well as in aiding their differentiation after they have travelled to new locations outside the niche. MMC at physiologically relevant fractional volume occupancies (FVOs) significantly enhances the adipogenic differentiation of human bone marrow-derived mesenchymal stem cells during chemically induced adipogenesis. The mechanism by which MMC produces this enhancement is not entirely known. In the context of extracellular collagen deposition, we have recently reported the importance of optimizing the FVO while minimizing the bulk viscosity. Two opposing properties will determine the net rate of a biochemical reaction: the negative effect of bulk viscosity and the positive effect of the excluded volume, the latter being expressed by the FVO. In this study we have looked more closely at the effect of viscosity on reaction rates. We have used fluorimetry to measure the rate of actin polymerization and fluorescence correlation spectroscopy (FCS) to measure diffusion of various probes in solutions containing the crowder Ficoll at physiological concentrations. Similar to its effect on collagen, Ficoll enhanced the actin polymerization rate despite increasing the bulk viscosity. Our FCS measurements reveal a relatively minor component of anomalous diffusion. In addition, our measurements do suggest that microviscosity becomes relevant in a crowded environment. We ruled out bulk viscosity as a cause of the rate enhancement by performing the actin polymerization assay in glycerol. These opposite effects of Ficoll and glycerol led us to conclude that microviscosity becomes relevant at the length scale of the reacting

  4. Effects of macromolecular crowding on the inhibition of virus assembly and virus-cell receptor recognition.

    PubMed

    Rincón, Verónica; Bocanegra, Rebeca; Rodríguez-Huete, Alicia; Rivas, Germán; Mateu, Mauricio G

    2011-02-02

    Biological fluids contain a very high total concentration of macromolecules that leads to volume exclusion by one molecule to another. Theory and experiment have shown that this condition, termed macromolecular crowding, can have significant effects on molecular recognition. However, the influence of molecular crowding on recognition events involving virus particles, and their inhibition by antiviral compounds, is virtually unexplored. Among these processes, capsid self-assembly during viral morphogenesis and capsid-cell receptor recognition during virus entry into cells are receiving increasing attention as targets for the development of new antiviral drugs. In this study, we have analyzed the effect of macromolecular crowding on the inhibition of these two processes by peptides. Macromolecular crowding led to a significant reduction in the inhibitory activity of: 1), a capsid-binding peptide and a small capsid protein domain that interfere with assembly of the human immunodeficiency virus capsid, and 2), a RGD-containing peptide able to block the interaction between foot-and-mouth disease virus and receptor molecules on the host cell membrane (in this case, the effect was dependent on the conditions used). The results, discussed in the light of macromolecular crowding theory, are relevant for a quantitative understanding of molecular recognition processes during virus infection and its inhibition.

  5. Macromolecular cross-linked enzyme aggregates (M-CLEAs) of α-amylase.

    PubMed

    Nadar, Shamraja S; Muley, Abhijeet B; Ladole, Mayur R; Joshi, Pranoti U

    2016-03-01

    Macromolecular cross-linked enzyme aggregates (M-CLEAs) of α-amylase were prepared by precipitation and subsequent cross-linking. The non-toxic, biodegradable, biocompatible, renewable polysaccharide based macromolecular cross-linkers viz. agar, chitosan, dextran, and gum arabic were used as a substitute for traditional glutaraldehyde to augment activity recovery toward macromolecular substrate. Macromolecular cross-linkers were prepared by periodate mediated controlled oxidation of polysaccharides. The effects of precipitating agent, concentration and different cross-linkers on activity recovery of α-amylase CLEAs were investigated. α-Amylase aggregated with ammonium sulphate and cross-linked by dextran showed 91% activity recovery, whereas glutaraldehyde CLEAs (G-CLEAs) exhibited 42% activity recovery. M-CLEAs exhibited higher thermal stability in correlation with α-amylase and G-CLEAs. Moreover, dextran and chitosan M-CLEAs showed same affinity for starch hydrolysis as of free α-amylase. The changes in secondary structures revealed the enhancements in structural and conformational rigidity attributed by cross-linkers. Finally, after five consecutive cycles dextran M-CLEAs retained 1.25 times higher initial activity than G-CLEAs. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. The status of beam lines for macromolecular crystallography at the Siberia-2 storage ring

    SciTech Connect

    Kusev, S.V.; Raiko, V.I.; Skuratovskii, I.Y. )

    1992-01-01

    An overview is presented of the x-ray optics of the four macromolecular crystallography beam lines under construction at the storage ring SIBERIA-2, Moscow. The four workstations are to utilize isomorphous replacement, anomalous dispersion, reflections energy profile, and the Laue technique. The instrumentation details, the results of ray-tracing analysis, and the use of an area detector are discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2005-10-01

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

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

    PubMed Central

    Homouz, Dirar; Stagg, Loren; Wittung-Stafshede, Pernilla; Cheung, Margaret S.

    2009-01-01

    Abstract Protein dynamics in cells may be different from those in dilute solutions in vitro, because the environment in cells is highly concentrated with other macromolecules. This volume exclusion because of macromolecular crowding is predicted to affect both equilibrium and kinetic processes involving protein conformational changes. To quantify macromolecular crowding effects on protein folding mechanisms, we investigated the folding energy landscape of an α/β protein, apoflavodoxin, in the presence of inert macromolecular crowding agents, using in silico and in vitro approaches. By means of coarse-grained molecular simulations and topology-based potential interactions, we probed the effects of increased volume fractions of crowding agents (ϕc) as well as of crowding agent geometry (sphere or spherocylinder) at high ϕc. Parallel kinetic folding experiments with purified Desulfovibro desulfuricans apoflavodoxin in vitro were performed in the presence of Ficoll (sphere) and Dextran (spherocylinder) synthetic crowding agents. In conclusion, we identified the in silico crowding conditions that best enhance protein stability, and discovered that upon manipulation of the crowding conditions, folding routes experiencing topological frustrations can be either enhanced or relieved. Our test-tube experiments confirmed that apoflavodoxin's time-resolved folding path is modulated by crowding agent geometry. Macromolecular crowding effects may be a tool for the manipulation of protein-folding and function in living cells. PMID:19167312

  9. SPring-8 BL44XU, beamline designed for structure analysis of large biological macromolecular assemblies

    SciTech Connect

    Higashiura, Akifumi Yamashita, Eiki; Yoshimura, Masato; Hasegawa, Kazuya; Furukawa, Yukito; Kumasaka, Takashi; Tsukihara, Tomitake; Nakagawa, Atsushi

    2016-07-27

    Beamline BL44XU at SPring-8 is operated by the Institute for Protein Research of Osaka University. The beamline is designed for X-ray crystallography of large biological macromolecular assemblies. Here we show its detailed performances, results, and the ongoing upgrade plans.

  10. MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures

    PubMed Central

    Pavelka, Antonín; Valasatava, Yana; Prlić, Andreas

    2017-01-01

    Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualization and analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow to transfer, parse, and hard to incorporate into third-party software tools. Here, we present a new binary and compressed data representation, the MacroMolecular Transmission Format, MMTF, as well as software implementations in several languages that have been developed around it, which address these issues. We describe the new format and its APIs and demonstrate that it is several times faster to parse, and about a quarter of the file size of the current standard format, PDBx/mmCIF. As a consequence of the new data representation, it is now possible to visualize structures with millions of atoms in a web browser, keep the whole PDB archive in memory or parse it within few minutes on average computers, which opens up a new way of thinking how to design and implement efficient algorithms in structural bioinformatics. The PDB archive is available in MMTF file format through web services and data that are updated on a weekly basis. PMID:28574982

  11. The interplay of intrinsic disorder and macromolecular crowding on α-synuclein fibril formation

    NASA Astrophysics Data System (ADS)

    Shirai, Nobu C.; Kikuchi, Macoto

    2016-02-01

    α-synuclein (α-syn) is an intrinsically disordered protein which is considered to be one of the causes of Parkinson's disease. This protein forms amyloid fibrils when in a highly concentrated solution. The fibril formation of α-syn is induced not only by increases in α-syn concentration but also by macromolecular crowding. In order to investigate the coupled effect of the intrinsic disorder of α-syn and macromolecular crowding, we construct a lattice gas model of α-syn in contact with a crowding agent reservoir based on statistical mechanics. The main assumption is that α-syn can be expressed as coarse-grained particles with internal states coupled with effective volume; and disordered states are modeled by larger particles with larger internal entropy than other states. Thanks to the simplicity of the model, we can exactly calculate the number of conformations of crowding agents, and this enables us to prove that the original grand canonical ensemble with a crowding agent reservoir is mathematically equivalent to a canonical ensemble without crowding agents. In this expression, the effect of macromolecular crowding is absorbed in the internal entropy of disordered states; it is clearly shown that the crowding effect reduces the internal entropy. Based on Monte Carlo simulation, we provide scenarios of crowding-induced fibril formation. We also discuss the recent controversy over the existence of helically folded tetramers of α-syn, and suggest that macromolecular crowding is the key to resolving the controversy.

  12. Type IV kerogens as analogues for organic macromolecular materials in aqueously altered carbonaceous chondrites.

    PubMed

    Matthewman, Richard; Martins, Zita; Sephton, Mark A

    2013-04-01

    Understanding the processes involved in the evolution of organic matter in the early Solar System requires extensive experimental work. The scientifically valuable carbonaceous chondrites are principal targets for organic analyses, but these meteorites are rare. Meteoritic analog materials available in larger quantities, on which experiments can be performed, would be highly beneficial. The bulk of the organic inventory of carbonaceous chondrites is made up of solvent-insoluble macromolecular material. This high-molecular-weight entity provides a record of thermal and aqueous parent-body alteration of precursor organic structures present at the birth of the Solar System. To identify an effective analogue for this macromolecular material, we analyzed a series of terrestrial kerogens by pyrolysis-gas chromatography-mass spectrometry. Type I and II kerogens are unsuitable analogues owing to their highly aliphatic nature. Type III kerogens show some similarities to meteoritic macromolecular materials but display a substantial biological heritage. Type IV kerogens, in this study derived from Mesozoic paleosols and produced by the reworking and oxidation of organic matter, represent an effective analogue. Some isomeric differences exist between meteoritic macromolecular materials and type IV kerogens, and stepped pyrolysis indicates variations in thermal stability. In addition to being a suitable material for novel experimentation, type IV kerogens also have the potential to aid in the optimization of instruments for deployment on Mars.

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

    NASA Astrophysics Data System (ADS)

    Bergasa-Caceres, Fernando; Rabitz, Herschel A.

    2014-01-01

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

  14. Hypersensitivity to contrast media and dyes.

    PubMed

    Brockow, Knut; Sánchez-Borges, Mario

    2014-08-01

    This article updates current knowledge on hypersensitivity reactions to diagnostic contrast media and dyes. After application of a single iodinated radiocontrast medium (RCM), gadolinium-based contrast medium, fluorescein, or a blue dye, a hypersensitivity reaction is not a common finding; however, because of the high and still increasing frequency of those procedures, patients who have experienced severe reactions are nevertheless frequently encountered in allergy departments. Evidence on allergologic testing and management is best for iodinated RCM, limited for blue dyes, and insufficient for fluorescein. Skin tests can be helpful in the diagnosis of patients with hypersensitivity reactions to these compounds.