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Gornig DC, Maletz R, Ottl P, Warkentin M. Influence of artificial aging: mechanical and physicochemical properties of dental composites under static and dynamic compression. Clin Oral Investig 2021; 26:1491-1504. [PMID: 34453210 PMCID: PMC8817055 DOI: 10.1007/s00784-021-04122-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 08/01/2021] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The aim of the study was to evaluate the influence of filler content, degradation media and time on the mechanical properties of different dental composites after in vitro aging. MATERIALS AND METHODS Specimens (1 mm3) of three commercially available composites (GrandioSO®, Arabesk Top®, Arabesk Flow®) with respect to their filler content were stored in artificial aging media: artificial saliva, ethanol (60%), lactic acid (pH 5) and citric acid (pH 5). Parameters (Vickers microhardness, compressive strength, elastic modulus, water sorption and solubility) were determined in their initial state (control group, n = 3 for microhardness, n = 5 for the other parameters) and after 14, 30, 90 and 180 days (n = 3 for microhardness, n = 5 for the other parameters for each composite group, time point and media). Specimens were also characterized with dynamic-mechanical-thermal analysis (compression tests, F = ± 7 N; f = 0.5 Hz, 1 Hz and 3.3 Hz; t = 0-170 °C). RESULTS Incorporation of fillers with more than 80 w% leads to significantly better mechanical properties under static and dynamic compression tests and a better water sorption behavior, even after chemical degradation. The influence of degradation media and time is of subordinate importance for chemical degradation. CONCLUSION Although the investigated composites have a similar matrix, they showed different degradation behavior. Since dentine and enamel occur only in small layer thickness, a test specimen geometry with very small dimensions is recommended for direct comparison. Moreover, the use of compression tests to determine the mechanical parameters for the development of structure-compatible and functionally adapted composites makes sense as an additional standard. Clinical relevance Preferential use of highly filled composites for occlusal fillings is recommended.
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Affiliation(s)
- D. C. Gornig
- Dres. Irina & Thorsten Brandt, Orthodontic Practice, Wiesbaden, Germany
| | - R. Maletz
- Department of Material Science and Medical Engineering, Faculty of Mechanical Engineering and Marine Technology, University of Rostock, Rostock, Germany
| | - P. Ottl
- Department of Prosthodontics and Material Science, Faculty of Medicine, University of Rostock, Rostock, Germany
| | - M. Warkentin
- Department of Material Science and Medical Engineering, Faculty of Mechanical Engineering and Marine Technology, University of Rostock, Rostock, Germany
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Brenner DR, Yannitsos DH, Warkentin M, Shaw E, Brockton NT, McGregor SE, Town S, Hilsden RJ. Abstract B02: Recreational physical activity, sedentary time and the incidence of colorectal polyps in a screening population for colon cancer. Cancer Epidemiol Biomarkers Prev 2017. [DOI: 10.1158/1538-7755.carisk16-b02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Background: Despite the consistent association between regular recreational moderate to vigorous physical activity (rMVPA) and reduced risk of colorectal cancer (CRC), few studies have examined the effect of physical activity on carcinogenic development by examining colorectal adenomas (polyps). Furthermore, even fewer studies have examined the impact of sedentary behavior/time (ST) on the development of polyps. In this study we examined the associations between rMVPA and ST and the presence, number and type of colorectal polyps in a population undergoing screening for colorectal cancer in Calgary, Alberta, Canada.
Methods: A cross-sectional study of 2,499 individuals undergoing colonoscopy at the Forzani & MacPhail Colon Cancer Screening Centre in Calgary, Canada was conducted. Physical activity levels and ST were characterized using hours of rMVPA, meeting cancer prevention recommendations (≥150 mins/wk of rMVPA) and hours of ST using self-reported data from the Long Form International Physical Activity Questionnaire. Unconditional logistic regression models were used to estimate the crude and adjusted odds ratios (OR) for presence of polyps associated with rMVP and ST.
Results: Crude estimates for meeting cancer prevention guidelines (ORunadj=0.83, 95% CI: 0.70-0.98) and increasing rMVPA (ORunadj=0.75, 95% CI: 0.60-0.93 for 1-3 hrs/wk vs. 0) were associated with lower odds of having ≥1 polyp at screening. Effect estimates were attenuated in adjusted models. Threshold effects were observed for ST with significant associations observed for up to 20 hours/week of sitting time (ORadj per hour sitting=1.05, 95% CI: 1.01-1.09). Associations were strongest for rMVPA among females (ORadj=0.68, 95% CI: 0.48-0.97 for 1-3 hrs/wk vs. 0) and for ST among males (ORadj=1.74, 95% CI: 1.06-2.86 for 14-35hrs/wk of ST vs. 0-14 hrs/wk)
Conclusions: In this large population undergoing colonoscopy screening for colorectal cancer, rMVPA was associated with reduced prevalence of polyps at screening, particularly among females. Even low amounts of regular ST (2-5hrs/day) were associated with the presence of polyps, particularly among males. Strategies aimed at reducing the amount of pre-carcinogenic colon lesions should combine increasing rMVPA and reducing ST.
Citation Format: Darren R. Brenner, Demetra H. Yannitsos, Matthew Warkentin, Eileen Shaw, Nigel T. Brockton, S. Elizabeth McGregor, Susanna Town, Robert J. Hilsden. Recreational physical activity, sedentary time and the incidence of colorectal polyps in a screening population for colon cancer. [abstract]. In: Proceedings of the AACR Special Conference: Improving Cancer Risk Prediction for Prevention and Early Detection; Nov 16-19, 2016; Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2017;26(5 Suppl):Abstract nr B02.
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Affiliation(s)
| | | | | | - Eileen Shaw
- 1Alberta Health Services, Calgary, AB, Canada,
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3
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Kister F, Specht O, Warkentin M, Geis-Gerstorfer J, Rupp F. Peri-implantitis cleaning instrumentation influences the integrity of photoactive nanocoatings. Dent Mater 2017; 33:e69-e78. [DOI: 10.1016/j.dental.2016.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 09/30/2016] [Accepted: 10/09/2016] [Indexed: 01/06/2023]
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Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, Brunger AT, Soltis SM, Lemke H, Gonzalez A, Sauter NK, Cohen AE, van den Bedem H, Thorne RE, Fraser JS. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. eLife 2015; 4. [PMID: 26422513 PMCID: PMC4721965 DOI: 10.7554/elife.07574] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 09/29/2015] [Indexed: 12/14/2022] Open
Abstract
Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences of these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180-–240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function. DOI:http://dx.doi.org/10.7554/eLife.07574.001 Proteins are the workhorses of the cell. The shape that a protein molecule adopts enables it to carry out its role. However, a protein’s shape, or 'conformation', is not static. Instead, a protein can shift between different conformations. This is particularly true for enzymes – the proteins that catalyze chemical reactions. The region of an enzyme where the chemical reaction happens, known as the active site, often has to change its conformation to allow catalysis to proceed. Changes in temperature can also make a protein shift between alternative conformations. Understanding how a protein shifts between conformations gives insight into how it works. A common method for studying protein conformation is X-ray crystallography. This technique uses a beam of X-rays to figure out where the atoms of the protein are inside a crystal made of millions of copies of that protein. At room temperature or biological temperature, X-rays can rapidly damage the protein. Because of this, most crystal structures are determined at very low temperatures to minimize damage. But cooling to low temperatures changes the conformations that the protein adopts, and usually causes fewer conformations to be present. Keedy, Kenner, Warkentin, Woldeyes et al. have used X-ray crystallography from a very low temperature (-173°C or 100 K) to above room temperature (up to 27°C or 300 K) to explore the alternative conformations of an enzyme called cyclophilin A. These alternative conformations include those that have previously been linked to this enzyme’s activity. Starting at a low temperature, parts of the enzyme were seen to shift from having a single conformation to many conformations above a threshold temperature. Unexpectedly, different parts of the enzyme have different threshold temperatures, suggesting that there isn’t a single transition across the whole protein. Instead, it appears the way a protein’s conformation changes in response to temperature is more complex than was previously realized. This result suggests that conformations in different parts of a protein are coupled to each other in complex ways. Keedy, Kenner, Warkentin, Woldeyes et al. then performed X-ray crystallography at room temperature using an X-ray free-electron laser (XFEL). This technique can capture the protein’s structure before radiation damage occurs, and confirmed that the alternative conformations observed were not affected by radiation damage. The combination of X-ray crystallography at multiple temperatures, new analysis methods for identifying and measuring alternative conformations, and XFEL crystallography should help future studies to characterize conformational changes in other proteins. DOI:http://dx.doi.org/10.7554/eLife.07574.002
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Affiliation(s)
- Daniel A Keedy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Lillian R Kenner
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | | | - Rahel A Woldeyes
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Jesse B Hopkins
- Department of Physics, Cornell University, Ithaca, United States
| | - Michael C Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Andrew H Van Benschoten
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Elizabeth L Baxter
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Scott E McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - James M Holton
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - William I Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - S Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Henrik Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Ana Gonzalez
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Henry van den Bedem
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Robert E Thorne
- Department of Physics, Cornell University, Ithaca, United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
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Warkentin M, Hopkins JB, Haber JB, Blaha G, Thorne RE. Temperature-dependent radiation sensitivity and order of 70S ribosome crystals. Acta Crystallogr D Biol Crystallogr 2014; 70:2890-6. [PMID: 25372680 PMCID: PMC4220972 DOI: 10.1107/s1399004714017672] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 08/01/2014] [Indexed: 11/10/2022]
Abstract
All evidence to date indicates that at T = 100 K all protein crystals exhibit comparable sensitivity to X-ray damage when quantified using global metrics such as change in scaling B factor or integrated intensity versus dose. This is consistent with observations in cryo-electron microscopy, and results because nearly all diffusive motions of protein and solvent, including motions induced by radiation damage, are frozen out. But how do the sensitivities of different proteins compare at room temperature, where radiation-induced radicals are free to diffuse and protein and lattice structures are free to relax in response to local damage? It might be expected that a large complex with extensive conformational degrees of freedom would be more radiation sensitive than a small, compact globular protein. As a test case, the radiation sensitivity of 70S ribosome crystals has been examined. At T = 100 and 300 K, the half doses are 64 MGy (at 3 Å resolution) and 150 kGy (at 5 Å resolution), respectively. The maximum tolerable dose in a crystallography experiment depends upon the initial or desired resolution. When differences in initial data-set resolution are accounted for, the former half dose is roughly consistent with that for model proteins, and the 100/300 K half-dose ratio is roughly a factor of ten larger. 70S ribosome crystals exhibit substantially increased resolution at 100 K relative to 300 K owing to cooling-induced ordering and not to reduced radiation sensitivity and slower radiation damage.
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Affiliation(s)
| | | | - Jonah B. Haber
- Physics Department, Cornell University, Ithaca, NY 14853, USA
| | - Gregor Blaha
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
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Hopkins J, Katz A, Meisburger S, Warkentin M, Gillilan R, Pollack L, Thorne R. CryoSAXS as a Method for Measuring Low Resolution Macromolecular Structure. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314095916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Small angle X-ray scattering (SAXS) is an increasingly popular technique for obtaining low resolution structural information from macromolecules and complexes in solution. Biomolecular SAXS signals can rapidly degrade due to radiation damage, so that flow or oscillating cells and large total sample volumes may be required. For particularly sensitive or hard to produce samples, such as of light sensitive proteins, metalloenzymes, and large complexes, and studies where multiple buffer conditions are probed sample consumption may be prohibitive. We describe cryo-cooling of samples to 100 K to prevent X-ray induced radiation damage. We identify SAXS-friendly cryoprotectant conditions that suppress ice formation upon cooling, and compare cryoSAXS profiles obtained in window-free variable-path-length cells with room temperature measurements for a variety of standard molecules. We obtain data sufficient for envelope reconstructions using scattering volumes as small as 20 nL, and find good agreement between cryoSAXS data and known atomic structures. We also discuss work on developing low-volume fixed path-length sample holders for cryoSAXS. Cryo-cooled samples can withstand doses that are 2-3 orders of magnitude higher than typically used for SAXS at room temperature, comparable to those used in cryo-crystallography. While practical challenges remain, cryoSAXS opens the possibility of studies exploiting high brightness X-ray sources and mail-in high-throughput SAXS. This work is funded by the NSF (DBI-1152348).
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Behrend D, Warkentin M, Klüß D, Bader R, Kopp S, Frank M, Mittelmeier W. [Failure analysis as basis for quality assurance strategies in implant technology]. Orthopade 2014; 43:555-60. [PMID: 24816979 DOI: 10.1007/s00132-014-2301-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Implant safety is a topic gaining more and more public interest. Implants are safety relevant medical devices which in the case of failure can lead to life-threatening situations. OBJECTIVES A well-founded failure analysis requires expert knowledge not only of materials and implant design but also a qualified explantation procedure and storage conditions. METHODS A selective literature search was carried out putting the main emphasis on implant failure analysis supplemented with own investigations. RESULTS The reasons for implant breakdown are mostly failures of materials and in the manufacturing process. In some cases false material combinations can lead to tribocorrosion effects under cyclic loading. CONCLUSION The increased level of knowledge gained from complex analyses of failed implants produces valuable evidence for better quality management.
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Affiliation(s)
- D Behrend
- Lehrstuhl Werkstoffe für die Medizintechnik, Universität Rostock, Friedrich-Barnewitz-Str. 4, 18119, Rostock-Warnemünde, Deutschland,
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Kopp S, Behrend D, Kundt G, Ottl P, Frerich B, Warkentin M. Dental implants and immediate loading: Multivariate analysis of success factors. ACTA ACUST UNITED AC 2013; 114:146-54. [DOI: 10.1016/j.revsto.2013.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Accepted: 02/18/2013] [Indexed: 11/24/2022]
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Meisburger SP, Warkentin M, Chen H, Hopkins JB, Gillilan RE, Pollack L, Thorne RE. Breaking the radiation damage limit with Cryo-SAXS. Biophys J 2013; 104:227-36. [PMID: 23332075 DOI: 10.1016/j.bpj.2012.11.3817] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 11/27/2012] [Accepted: 11/29/2012] [Indexed: 11/27/2022] Open
Abstract
Small angle x-ray scattering (SAXS) is a versatile and widely used technique for obtaining low-resolution structures of macromolecules and complexes. SAXS experiments measure molecules in solution, without the need for labeling or crystallization. However, radiation damage currently limits the application of SAXS to molecules that can be produced in microgram quantities; for typical proteins, 10-20 μL of solution at 1 mg/mL is required to accumulate adequate signal before irreversible x-ray damage is observed. Here, we show that cryocooled proteins and nucleic acids can withstand doses at least two orders of magnitude larger than room temperature samples. We demonstrate accurate T = 100 K particle envelope reconstructions from sample volumes as small as 15 nL, a factor of 1000 smaller than in current practice. Cryo-SAXS will thus enable structure determination of difficult-to-express proteins and biologically important, highly radiation-sensitive proteins including light-activated switches and metalloenzymes.
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Affiliation(s)
- Steve P Meisburger
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, USA
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Petersen S, Glock H, Specht O, Kuehl H, Heinitz W, Warkentin M, Behrend D. Dental Ultrasound Diagnostics – a Simulation Study. BIOMED ENG-BIOMED TE 2013; 58 Suppl 1:/j/bmte.2013.58.issue-s1-N/bmt-2013-4338/bmt-2013-4338.xml. [DOI: 10.1515/bmt-2013-4338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Warkentin M, Sethna JP, Thorne RE. Critical droplet theory explains the glass formability of aqueous solutions. Phys Rev Lett 2013; 110:015703. [PMID: 23383808 DOI: 10.1103/physrevlett.110.015703] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Indexed: 05/11/2023]
Abstract
When pure water is cooled at ~10(6) K / s, it forms an amorphous solid (glass) instead of the more familiar crystalline phase. The presence of solutes can reduce this required (or "critical") cooling rate by orders of magnitude. Here, we present critical cooling rates for a variety of solutes as a function of concentration and a theoretical framework for understanding these rates. For all solutes tested, the critical cooling rate is an exponential function of concentration. The exponential's characteristic concentration for each solute correlates with the solute's Stokes radius. A modification of critical droplet theory relates the characteristic concentration to the solute radius and the critical nucleation radius of ice in pure water. This simple theory of ice nucleation and glass formability in aqueous solutions has consequences for general glass-forming systems, and in cryobiology, cloud physics, and climate modeling.
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Affiliation(s)
- Matthew Warkentin
- Physics Department, Cornell University, Ithaca, New York 14853, USA.
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Warkentin M, Hopkins JB, Badeau R, Mulichak AM, Keefe LJ, Thorne RE. Global radiation damage: temperature dependence, time dependence and how to outrun it. J Synchrotron Radiat 2013; 20:7-13. [PMID: 23254651 PMCID: PMC3526918 DOI: 10.1107/s0909049512048303] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 11/25/2012] [Indexed: 05/22/2023]
Abstract
A series of studies that provide a consistent and illuminating picture of global radiation damage to protein crystals, especially at temperatures above ∼200 K, are described. The radiation sensitivity shows a transition near 200 K, above which it appears to be limited by solvent-coupled diffusive processes. Consistent with this interpretation, a component of global damage proceeds on timescales of several minutes at 180 K, decreasing to seconds near room temperature. As a result, data collection times of order 1 s allow up to half of global damage to be outrun at 260 K. Much larger damage reductions near room temperature should be feasible using larger dose rates delivered using microfocused beams, enabling a significant expansion of structural studies of proteins under more nearly native conditions.
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Affiliation(s)
| | | | - Ryan Badeau
- Physics Department, Cornell University, Ithaca, NY 14853, USA
| | | | - Lisa J. Keefe
- IMCA-CAT, Argonne National Laboratory, Argonne, IL 60439, USA
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Hopkins JB, Badeau R, Warkentin M, Thorne RE. Effect of common cryoprotectants on critical warming rates and ice formation in aqueous solutions. Cryobiology 2012; 65:169-78. [PMID: 22728046 PMCID: PMC3500404 DOI: 10.1016/j.cryobiol.2012.05.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 04/25/2012] [Accepted: 05/21/2012] [Indexed: 10/28/2022]
Abstract
Ice formation on warming is of comparable or greater importance to ice formation on cooling in determining survival of cryopreserved samples. Critical warming rates required for ice-free warming of vitrified aqueous solutions of glycerol, dimethyl sulfoxide, ethylene glycol, polyethylene glycol 200 and sucrose have been measured for warming rates of order 10-10⁴ K/s. Critical warming rates are typically one to three orders of magnitude larger than critical cooling rates. Warming rates vary strongly with cooling rates, perhaps due to the presence of small ice fractions in nominally vitrified samples. Critical warming and cooling rate data spanning orders of magnitude in rates provide rigorous tests of ice nucleation and growth models and their assumed input parameters. Current models with current best estimates for input parameters provide a reasonable account of critical warming rates for glycerol solutions at high concentrations/low rates, but overestimate both critical warming and cooling rates by orders of magnitude at lower concentrations and larger rates. In vitrification protocols, minimizing concentrations of potentially damaging cryoprotectants while minimizing ice formation will require ultrafast warming rates, as well as fast cooling rates to minimize the required warming rates.
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Affiliation(s)
| | - Ryan Badeau
- Physics Department, Cornell University, Ithaca, NY 14853 USA
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Warkentin M, Badeau R, Hopkins JB, Thorne RE. Spatial distribution of radiation damage to crystalline proteins at 25-300 K. Acta Crystallogr D Biol Crystallogr 2012; 68:1108-17. [PMID: 22948911 PMCID: PMC3489100 DOI: 10.1107/s0907444912021361] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/10/2012] [Indexed: 11/11/2022]
Abstract
The spatial distribution of radiation damage (assayed by increases in atomic B factors) to thaumatin and urease crystals at temperatures ranging from 25 to 300 K is reported. The nature of the damage changes dramatically at approximately 180 K. Above this temperature the role of solvent diffusion is apparent in thaumatin crystals, as solvent-exposed turns and loops are especially sensitive. In urease, a flap covering the active site is the most sensitive part of the molecule and nearby loops show enhanced sensitivity. Below 180 K sensitivity is correlated with poor local packing, especially in thaumatin. At all temperatures, the component of the damage that is spatially uniform within the unit cell accounts for more than half of the total increase in the atomic B factors and correlates with changes in mosaicity. This component may arise from lattice-level, rather than local, disorder. The effects of primary structure on radiation sensitivity are small compared with those of tertiary structure, local packing, solvent accessibility and crystal contacts.
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Affiliation(s)
| | - Ryan Badeau
- Physics Department, Cornell University, Ithaca, NY 14853, USA
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Warkentin M, Badeau R, Hopkins JB, Mulichak AM, Keefe LJ, Thorne RE. Global radiation damage at 300 and 260 K with dose rates approaching 1 MGy s⁻¹. Acta Crystallogr D Biol Crystallogr 2012; 68:124-33. [PMID: 22281741 DOI: 10.1107/s0907444911052085] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 12/02/2011] [Indexed: 11/10/2022]
Abstract
Global radiation damage to 19 thaumatin crystals has been measured using dose rates from 3 to 680 kGy s⁻¹. At room temperature damage per unit dose appears to be roughly independent of dose rate, suggesting that the timescales for important damage processes are less than ∼1 s. However, at T = 260 K approximately half of the global damage manifested at dose rates of ∼10 kGy s⁻¹ can be outrun by collecting data at 680 kGy s⁻¹. Appreciable sample-to-sample variability in global radiation sensitivity at fixed dose rate is observed. This variability cannot be accounted for by errors in dose calculation, crystal slippage or the size of the data sets in the assay.
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Kmetko J, Warkentin M, Englich U, Thorne RE. Can radiation damage to protein crystals be reduced using small-molecule compounds? Acta Crystallogr D Biol Crystallogr 2011; 67:881-93. [PMID: 21931220 PMCID: PMC3176623 DOI: 10.1107/s0907444911032835] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 08/12/2011] [Indexed: 11/10/2022]
Abstract
Recent studies have defined a data-collection protocol and a metric that provide a robust measure of global radiation damage to protein crystals. Using this protocol and metric, 19 small-molecule compounds (introduced either by cocrystallization or soaking) were evaluated for their ability to protect lysozyme crystals from radiation damage. The compounds were selected based upon their ability to interact with radiolytic products (e.g. hydrated electrons, hydrogen, hydroxyl and perhydroxyl radicals) and/or their efficacy in protecting biological molecules from radiation damage in dilute aqueous solutions. At room temperature, 12 compounds had no effect and six had a sensitizing effect on global damage. Only one compound, sodium nitrate, appeared to extend crystal lifetimes, but not in all proteins and only by a factor of two or less. No compound provided protection at T=100 K. Scavengers are ineffective in protecting protein crystals from global damage because a large fraction of primary X-ray-induced excitations are generated in and/or directly attack the protein and because the ratio of scavenger molecules to protein molecules is too small to provide appreciable competitive protection. The same reactivity that makes some scavengers effective radioprotectors in protein solutions may explain their sensitizing effect in the protein-dense environment of a crystal. A more productive focus for future efforts may be to identify and eliminate sensitizing compounds from crystallization solutions.
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Affiliation(s)
- Jan Kmetko
- Physics Department, Kenyon College, Gambier, OH 43022, USA
| | | | - Ulrich Englich
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
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Warkentin M, Badeau R, Hopkins J, Thorne RE. Dark progression reveals slow timescales for radiation damage between T = 180 and 240 K. Acta Crystallogr D Biol Crystallogr 2011; 67:792-803. [PMID: 21904032 PMCID: PMC3169314 DOI: 10.1107/s0907444911027600] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 07/09/2011] [Indexed: 11/11/2022]
Abstract
Can radiation damage to protein crystals be `outrun' by collecting a structural data set before damage is manifested? Recent experiments using ultra-intense pulses from a free-electron laser show that the answer is yes. Here, evidence is presented that significant reductions in global damage at temperatures above 200 K may be possible using conventional X-ray sources and current or soon-to-be available detectors. Specifically, `dark progression' (an increase in damage with time after the X-rays have been turned off) was observed at temperatures between 180 and 240 K and on timescales from 200 to 1200 s. This allowed estimation of the temperature-dependent timescale for damage. The rate of dark progression is consistent with an Arrhenius law with an activation energy of 14 kJ mol(-1). This is comparable to the activation energy for the solvent-coupled diffusive damage processes responsible for the rapid increase in radiation sensitivity as crystals are warmed above the glass transition near 200 K. Analysis suggests that at T = 300 K data-collection times of the order of 1 s (and longer at lower temperatures) may allow significant reductions in global radiation damage, facilitating structure solution on crystals with liquid solvent. No dark progression was observed below T = 180 K, indicating that no important damage process is slowed through this timescale window in this temperature range.
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Affiliation(s)
| | - Ryan Badeau
- Physics Department, Cornell University, Ithaca, NY 14853, USA
| | - Jesse Hopkins
- Physics Department, Cornell University, Ithaca, NY 14853, USA
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Thorne RE, Warkentin M, Kmetko J, Badeau R, Hopkins JB. Temperature and time dependent studies of radiation damage. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311096097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Soliman ASM, Warkentin M, Apker B, Thorne RE. Development of high-performance X-ray transparent crystallization plates for in situ protein crystal screening and analysis. Acta Crystallogr D Biol Crystallogr 2011; 67:646-56. [PMID: 21697603 DOI: 10.1107/s090744491101883x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 05/17/2011] [Indexed: 11/10/2022]
Abstract
X-ray transparent crystallization plates based upon a novel drop-pinning technology provide a flexible, simple and inexpensive approach to protein crystallization and screening. The plates consist of open cells sealed top and bottom by thin optically, UV and X-ray transparent films. The plates do not need wells or depressions to contain liquids. Instead, protein drops and reservoir solution are held in place by rings with micrometre dimensions that are patterned onto the bottom film. These rings strongly pin the liquid contact lines, thereby improving drop shape and position uniformity, and thus crystallization reproducibility, and simplifying automated image analysis of drop contents. The same rings effectively pin solutions containing salts, proteins, cryoprotectants, oils, alcohols and detergents. Strong pinning by rings allows the plates to be rotated without liquid mixing to 90° for X-ray data collection or to be inverted for hanging-drop crystallization. The plates have the standard SBS format and are compatible with standard liquid-handling robots.
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Warkentin M, Thorne RE. Glass transition in thaumatin crystals revealed through temperature-dependent radiation-sensitivity measurements. Acta Crystallogr D Biol Cryst 2010; 66:1092-100. [PMID: 20944242 PMCID: PMC2954455 DOI: 10.1107/s0907444910035523] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 09/03/2010] [Indexed: 11/10/2022]
Abstract
The temperature-dependence of radiation damage to thaumatin crystals between T = 300 and 100 K is reported. The amount of damage for a given dose decreases sharply as the temperature decreases from 300 to 220 K and then decreases more gradually on further cooling below the protein-solvent glass transition. Two regimes of temperature-activated behavior were observed. At temperatures above ∼200 K the activation energy of 18.0 kJ mol(-1) indicates that radiation damage is dominated by diffusive motions in the protein and solvent. At temperatures below ∼200 K the activation energy is only 1.00 kJ mol(-1), which is of the order of the thermal energy. Similar activation energies describe the temperature-dependence of radiation damage to a variety of solvent-free small-molecule organic crystals over the temperature range T = 300-80 K. It is suggested that radiation damage in this regime is vibrationally assisted and that the freezing-out of amino-acid scale vibrations contributes to the very weak temperature-dependence of radiation damage below ∼80 K. Analysis using the radiation-damage model of Blake and Phillips [Blake & Phillips (1962), Biological Effects of Ionizing Radiation at the Molecular Level, pp. 183-191] indicates that large-scale conformational and molecular motions are frozen out below T = 200 K but become increasingly prevalent and make an increasing contribution to damage at higher temperatures. Possible alternative mechanisms for radiation damage involving the formation of hydrogen-gas bubbles are discussed and discounted. These results have implications for mechanistic studies of proteins and for studies of the protein glass transition. They also suggest that data collection at T ≃ 220 K may provide a viable alternative for structure determination when cooling-induced disorder at T = 100 is excessive.
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Warkentin M, Thorne RE. Slow cooling and temperature-controlled protein crystallography. ACTA ACUST UNITED AC 2009; 11:85-9. [PMID: 20012211 DOI: 10.1007/s10969-009-9074-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 11/23/2009] [Indexed: 11/29/2022]
Abstract
In cryocrystallography, rapid sample cooling is generally deemed essential to prevent solvent crystallization and associated sample damage. We show that by carefully and completely removing all external solvent, many protein crystals can be successfully cooled to T = 100 K at only 0.1 K/s without additional penetrating cryoprotectants. Slow cooling provides an alternative when flash cooling fails, and enables diffraction studies of protein structure and function at all temperatures between T = 300 K and T = 100 K.
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Abstract
Cryoprotectant-free thaumatin crystals have been cooled from 300 to 100 K at a rate of 0.1 K s(-1) - 10(3)-10(4) times slower than in conventional flash cooling - while continuously collecting X-ray diffraction data, so as to follow the evolution of protein lattice and solvent properties during cooling. Diffraction patterns show no evidence of crystalline ice at any temperature. This indicates that the lattice of protein molecules is itself an excellent cryoprotectant, and with sodium potassium tartrate incorporated from the 1.5 M mother liquor ice nucleation rates are at least as low as in a 70% glycerol solution. Crystal quality during slow cooling remains high, with an average mosaicity at 100 K of 0.2 degrees . Most of the mosaicity increase occurs above approximately 200 K, where the solvent is still liquid, and is concurrent with an anisotropic contraction of the unit cell. Near 180 K a crossover to solid-like solvent behavior occurs, and on further cooling there is no additional degradation of crystal order. The variation of B factor with temperature shows clear evidence of a protein dynamical transition near 210 K, and at lower temperatures the slope dB/dT is a factor of 3-6 smaller than has been reported for any other protein. These results establish the feasibility of fully temperature controlled studies of protein structure and dynamics between 300 and 100 K.
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Warkentin M, Stanislavskaia V, Hammes K, Thorne RE. Cryocrystallography in capillaries: critical glycerol concentrations and cooling rates. J Appl Crystallogr 2008; 41:791-797. [PMID: 19529833 DOI: 10.1107/s0021889808018451] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Accepted: 06/17/2008] [Indexed: 11/10/2022] Open
Abstract
Capillary tubes have many advantages over multi-well plates for macromol-ecular crystal growth and handling, including the possibility of in situ structure determination. To obtain complete high-resolution X-ray data sets, cryopreservation protocols must be developed to prevent crystalline ice formation and preserve macromolecular crystal order. The minimum glycerol concentrations required to vitrify aqueous solutions during plunging into liquid nitrogen and liquid propane have been determined for capillary diameters from 3.3 mm to 150 microm. For the smallest diameter, the required glycerol concentrations are 30%(w/v) in nitrogen and 20%(w/v) in propane, corresponding to cooling rates of approximately 800 and approximately 7000 K s(-1), respectively. These concentrations are much larger than are required in current best practice using crystals in loops or on microfabricated mounts. In additon, the relation between the minimum cooling rate for vitrification and glycerol concentration has been estimated; this relation is of fundamental importance in developing rational cryopreservation protocols.
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Abstract
During flash cooling of protein crystals in liquid cryogens, cooling rates are determined by sample size, choice of cooling liquid, and by the thickness of the cold gas layer that forms above the liquid. We describe an experimental protocol for ultra-rapid cooling of protein crystals. This protocol requires no complex apparatus, and yields ice-ring-free diffraction without the use of penetrating cryoprotectants.
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Thorne RE, Kmetko J, Warkentin M, Englich U. Quantifying X-ray radiation damage in protein crystals. Acta Crystallogr A 2007. [DOI: 10.1107/s0108767307098078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Warkentin M, Berejnov V, Husseini NS, Thorne RE. Hyperquenching for protein cryocrystallography. J Appl Crystallogr 2006; 39:805-811. [PMID: 20461232 PMCID: PMC2866519 DOI: 10.1107/s0021889806037484] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Accepted: 09/14/2006] [Indexed: 11/10/2022] Open
Abstract
When samples having volumes characteristic of protein crystals are plunge cooled in liquid nitrogen or propane, most cooling occurs in the cold gas layer above the liquid. By removing this cold gas layer, cooling rates for small samples and modest plunge velocities are increased to 1.5 × 10(4) K s(-1), with increases of a factor of 100 over current best practice possible with 10 μm samples. Glycerol concentrations required to eliminate water crystallization in protein-free aqueous mixtures drop from ∼28% w/v to as low as 6% w/v. These results will allow many crystals to go from crystallization tray to liquid cryogen to X-ray beam without cryoprotectants. By reducing or eliminating the need for cryoprotectants in growth solutions, they may also simplify the search for crystallization conditions and for optimal screens. The results presented here resolve many puzzles, such as why plunge cooling in liquid nitrogen or propane has, until now, not yielded significantly better diffraction quality than gas-stream cooling.
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Affiliation(s)
| | | | - Naji S. Husseini
- Applied and Engineering Physics Department, Cornell University, Ithaca, NY 14853, USA
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Thorne RE, Berejnov V, Warkentin M, Kalinin Y, Husseini N, Alsaeid O. New approaches to cryo- and room-temperature crystallography. Acta Crystallogr A 2006. [DOI: 10.1107/s0108767306099600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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28
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Deutsch JM, Warkentin M. Scaling of polymers in aligned rods. Phys Rev Lett 2005; 95:257802. [PMID: 16384509 DOI: 10.1103/physrevlett.95.257802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Indexed: 05/05/2023]
Abstract
We study the behavior of self-avoiding polymers in a background of infinitely long vertically aligned rods that are either frozen in random positions or free to move horizontally. We find that in both cases the polymer chains are highly elongated, with vertical and horizontal size exponents that differ by a factor of 3. Though these results are different than previous predictions, our results are confirmed by detailed computer simulations.
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Affiliation(s)
- J M Deutsch
- Department of Physics, University of California, Santa Cruz, California 95064, USA
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Bruchovsky N, Klotz LH, Sadar M, Crook JM, Hoffart D, Godwin L, Warkentin M, Gleave ME, Goldenberg SL. Intermittent androgen suppression for prostate cancer: Canadian Prospective Trial and related observations. Mol Urol 2001; 4:191-9;discussion 201. [PMID: 11062374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
The Canadian Prospective Trial of intermittent androgen suppression was a prototype therapeutic initiative started in 1995 for the management of patients in biochemical relapse after radiation for localized prostate cancer. An interim analysis has yielded several observations on the relations between baseline serum prostate specific antigen (PSA), nadir serum PSA, Gleason score, and time off-treatment. In a typical androgen-dependent tumor, the response of serum PSA to androgen withdrawal is biphasic, but with early tumor progression, plateauing of serum PSA is observed. Ligand-independent activation of the androgen receptor, a mechanism subserving the initiation of androgen independence, can be counteracted experimentally with decoy molecules and clinically with nonsteroidal antiandrogens. In some patients, it is possible to lengthen the off-treatment interval by inhibiting the enzyme 5 alpha-reductase, an effect that can be reinforced by lowering serum testosterone with an antigonadotropin. Serial measurements of serum PSA indicate that intermittent androgen suppression engenders a more diverse range of hormone-related responses than previously appreciated. These include: (1) repeated differentiation of tumor with recovery of apoptotic potential; (2) inhibition of tumor growth by rapid restoration of serum testosterone; and (3) restraint of tumor growth by subnormal levels of serum testosterone. These responses are aspects of regulation that should be taken into account when planning long-term treatment of prostate cancer with intermittent androgen suppression.
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Affiliation(s)
- N Bruchovsky
- Department of Cancer Endocrinology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
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