Ion specific effects in bundling and depolymerization of taxol-stabilized microtubules

Needleman, Daniel J.,Ojeda-Lopez, Miguel A.,Raviv, Uri,Miller, Herbert P.,Li, Youli,Song, Chaeyeon,Feinstein, Stuart C.,Wilson, Leslie,Choi, Myung Chul,Safinya, Cyrus R. The Royal Society of Chemistry 2013 Faraday discussions Vol.166 No.-

<P>Microtubules (MTs) are nanometer scale hollow cylindrical biological polyelectrolytes. They are assembled from α/β-tubulin dimers, which stack to form protofilaments (PFs) with lateral interactions between PFs resulting in the curved MT. In cells, MTs and their assemblies are critical components in a range of functions from providing tracks for the transport of cargo to forming the spindle structure during mitosis. Previous studies have shown that while cations with valence equal to or larger than 3+ tend to assemble tight 3D bundles of taxol-stabilized MTs, certain divalent cations induce relatively loose 2D bundles of different symmetry (D. J. Needleman <I>et al.</I>, <I>Proc. Natl. Acad. Sci. U. S. A.</I>, 2004, <B>101</B>, 16099). Similarly, divalent cations form 2D bundles of DNA adsorbed on cationic membranes (I. Koltover <I>et al.</I>, <I>Proc. Natl. Acad. Sci. U. S. A.</I>, 2000, <B>97</B>, 14046). The bundling behavior for these biological polyelectrolyte systems is qualitatively in agreement with current theory. Here, we present results which show that, unlike the case for DNA adsorbed on cationic membranes, bundling of taxol-stabilized MTs occurs only for certain divalent cations above a critical ion concentration (<I>e.g.</I> Ca<SUP>2+</SUP>, Sr<SUP>2+</SUP>, Ba<SUP>2+</SUP>). Instead, many divalent cations pre-empt the bundling transition and depolymerize taxol-stabilized MTs at a lower counterion concentration. Although previous cryogenic TEM has shown that, in the absence of taxol, Ca<SUP>2+</SUP> depolymerizes MTs assembling in buffers containing GTP (guanosine triphosphate), our finding is surprising given the known stabilizing effects of taxol on GDP (guanosine diphosphate)-MTs. The ion concentration required for MT depolymerization decreases with increasing atomic number for the divalents Mg<SUP>2+</SUP>, Mn<SUP>2+</SUP>, Co<SUP>2+</SUP>, and Zn<SUP>2+</SUP>. GdCl<SUB>3</SUB> (3+) is found to be extremely efficient at MT depolymerization requiring ion concentrations of about 1 mM, while oligolysine (2+), is observed not to depolymerize MTs at concentrations as high as 144 mM. The surprising MT depolymerization results are discussed in the context of divalents either disrupting lateral interactions between PFs (which are strengthened for taxol containing β-tubulin), or interfering with taxol's ability to induce flexibility at the interface between two tubulin dimers in the same PF (which has been recently suggested as a mechanism by which taxol stabilizes MTs post-hydrolysis with the induced flexibility counteracting the kink between GDP-tubulin dimers in a PF).</P>

Paclitaxel suppresses Tau-mediated microtubule bundling in a concentration-dependent manner

Choi, Myung Chul,Chung, Peter J.,Song, Chaeyeon,Miller, Herbert P.,Kiris, E.,Li, Youli,Wilson, Leslie,Feinstein, Stuart C.,Safinya, Cyrus R. Elsevier 2017 Biochimica et biophysica acta, General subjects Vol.1861 No.1

<P><B>Abstract</B></P> <P><B>Background</B></P> <P>Microtubules (MTs) are protein nanotubes comprised of straight protofilaments (PFs), head to tail assemblies of αβ-tubulin heterodimers. Previously, it was shown that Tau, a microtubule-associated protein (MAP) localized to neuronal axons, regulates the average number of PFs in microtubules with increasing inner radius <<I> R</I> <SUB>in</SUB> <SUP>MT</SUP> > observed for increasing Tau/tubulin-dimer molar ratio Φ<SUB>Tau</SUB> at paclitaxel/tubulin-dimer molar ratio Λ<SUB>Ptxl</SUB> =1/1.</P> <P><B>Methods</B></P> <P>We report a synchrotron SAXS and TEM study of the phase behavior of microtubules as a function of varying concentrations of paclitaxel (1/32≤Λ<SUB>Ptxl</SUB> ≤1/4) and Tau (human isoform 3RS, 0≤Φ<SUB>3RS</SUB> ≤1/2) at room temperature.</P> <P><B>Results</B></P> <P>Tau and paclitaxel have opposing regulatory effects on microtubule bundling architectures and microtubule diameter. Surprisingly and in contrast to previous results at Λ<SUB>Ptxl</SUB> =1/1 where microtubule bundles are absent, in the lower paclitaxel concentration regime (Λ<SUB>Ptxl</SUB> ≤1/4), we observe both microtubule doublets and triplets with increasing Tau. Furthermore, increasing paclitaxel concentration (up to Λ<SUB>Ptxl</SUB> =1/1) slightly decreased the average microtubule diameter (by ~1 PF) while increasing Tau concentration (up to Φ<SUB>3RS</SUB> =1/2) significantly increased the diameter (by ~2–3 PFs).</P> <P><B>Conclusions</B></P> <P>The suppression of Tau-mediated microtubule bundling with increasing paclitaxel is consistent with paclitaxel seeding more, but shorter, microtubules by rapidly exhausting tubulin available for polymerization. Microtubule bundles require the aggregate Tau-Tau attractions along the microtubule length to overcome individual microtubule thermal energies disrupting bundles.</P> <P><B>General significance</B></P> <P>Investigating MAP-mediated interactions between microtubules (as it relates to <I>in vivo</I> behavior) requires the elimination or minimization of paclitaxel.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Increasing paclitaxel suppresses Tau-mediated microtubule bundling. </LI> <LI> A length-dependent mechanism for Tau-mediated microtubule bundling is proposed. </LI> <LI> Understanding MAP/microtubule behavior requires elimination of paclitaxel use. </LI> </UL> </P>

A MACHINE-LEARNING METHOD TO INFER FUNDAMENTAL STELLAR PARAMETERS FROM PHOTOMETRIC LIGHT CURVES

Miller, A. A.,Bloom, J. S.,Richards, J. W.,Lee, Y. S.,Starr, D. L.,Butler, N. R.,Tokarz, S.,Smith, N.,Eisner, J. A. IOP Publishing 2015 The Astrophysical journal Vol.798 No.2

<P>A fundamental challenge for wide-field imaging surveys is obtaining follow-up spectroscopic observations: there are >10(9) photometrically cataloged sources, yet modern spectroscopic surveys are limited to similar to fewx10(6) targets. As we approach the Large Synoptic Survey Telescope era, new algorithmic solutions are required to cope with the data deluge. Here we report the development of a machine-learning framework capable of inferring fundamental stellar parameters (T-eff, log g, and [Fe/H]) using photometric-brightness variations and color alone. A training set is constructed from a systematic spectroscopic survey of variables with Hectospec/ Multi-Mirror Telescope. In sum, the training set includes similar to 9000 spectra, for which stellar parameters are measured using the SEGUE Stellar Parameters Pipeline (SSPP). We employed the random forest algorithm to perform a non-parametric regression that predicts Teff, log g, and [Fe/H] from photometric time-domain observations. Our final optimized model produces a cross-validated rms error (RMSE) of 165 K, 0.39 dex, and 0.33 dex for T-eff, log g, and [Fe/H], respectively. Examining the subset of sources for which the SSPP measurements are most reliable, the RMSE reduces to 125 K, 0.37 dex, and 0.27 dex, respectively, comparable to what is achievable via low-resolution spectroscopy. For variable stars this represents a approximate to 12%-20% improvement in RMSE relative to models trained with single-epoch photometric colors. As an application of our method, we estimate stellar parameters for similar to 54,000 known variables. We argue that this method may convert photometric time-domain surveys into pseudo-spectrographic engines, enabling the construction of extremely detailed maps of the Milky Way, its structure, and history.</P>

증례 : 외국문헌초록 / Dithiazanine 에 의한 충증의 치료

Miller J. H.,Anthouy. S. O.,Swartzwclder J. C.,Frye. W. W.,Lampert. R.,박상기 대한내과학회 1959 대한내과학회지 Vol.2 No.1

The impact of incontinence etiology on artificial urinary sphincter outcomes

Adam R. Miller,Brian J. Linder,Laureano J. Rangel,David Y. Yang,Daniel S. Elliott 대한비뇨의학회 2017 Investigative and Clinical Urology Vol.58 No.4

Purpose: To evaluate the impact of incontinence etiology on artificial urinary sphincter (AUS) device outcomes. Materials and Methods: We identified 925 patients who underwent primary AUS placement from 1983 to 2011. The etiology of incontinence was categorized as radical prostatectomy alone, radical prostatectomy with radiation, benign prostate resection, and those with cryotherapy as a salvage prostate cancer treatment. Hazard regression and competing risk analyses were used to determine the association of the etiology of incontinence with device outcomes. Results: The distribution of the 4 etiologies of incontinence included: 598 patients (64.6%) treated with prostatectomy alone, 206 (22.2%) with prostatectomy and pelvic radiation therapy, 104 (11.2%) with benign prostate resection, and 17 (1.8%) with prior cryotherapy. With a median follow-up of 4.9 years (interquartile range, 1.2–8.8 years), there was significant difference in the cumulative incidence of device infection/urethral erosion events between the four etiologies (p=0.003). On multivariable analysis, prior cryotherapy (reference prostatectomy alone; hazard ratio [HR], 3.44; p=0.01), older age (HR, 1.07; p=0.0009) and history of a transient ischemic attack (HR, 2.57; p=0.04) were associated with an increased risk of device infection or erosion. Notably, pelvic radiation therapy with prostatectomy was not associated with an increased risk of device infection or erosion (reference prostatectomy alone, p=0.30). Conclusions: Compared to prostatectomy alone, prior treatment with salvage cryotherapy for recurrent prostate cancer was associated with an increased risk of AUS infection/erosion, whereas radiation (in addition to prostatectomy) was not.

Structural Changes Associated with Delayed Dark Adaptation in Age-Related Macular Degeneration

Lains, I.,Miller, J.B.,Park, D.H.,Tsikata, E.,Davoudi, S.,Rahmani, S.,Pierce, J.,Silva, R.,Chen, T.C.,Kim, I.K.,Vavvas, D.,Miller, J.W.,Husain, D. Published for the American Academy of Ophthalmolog 2017 Ophthalmology Vol.124 No.9

Purpose: To examine the relationship between dark adaptation (DA) and optical coherence tomography (OCT)-based macular morphology in age-related macular degeneration (AMD). Design: Prospective, cross-sectional study. Participants: Patients with AMD and a comparison group (>50 years) without any vitreoretinal disease. Methods: All participants were imaged with spectral-domain OCT and color fundus photographs, and then staged for AMD (Age-related Eye Disease Study system). Both eyes were tested with the AdaptDx (MacuLogix, Middletown, PA) DA extended protocol (20 minutes). A software program was developed to map the DA testing spot (2<SUP>o</SUP> circle, 5<SUP>o</SUP> superior to the fovea) to the OCT B-scans. Two independent graders evaluated the B-scans within this testing spot, as well as the entire macula, recording the presence of several AMD-associated abnormalities. Multilevel mixed-effects models (accounting for correlated outcomes between 2 eyes) were used for analyses. Main Outcome Measures: The primary outcome was rod-intercept time (RIT), defined in minutes, as a continuous variable. For subjects unable to reach RIT within the 20 minutes of testing, the value of 20 was assigned. Results: We included 137 eyes (n = 77 subjects), 72.3% (n = 99 eyes) with AMD and the remainder belonging to the comparison group. Multivariable analysis revealed that even after adjusting for age and AMD stage, the presence of any abnormalities within the DA testing spot (sz = 4.8, P < 0.001), as well as any abnormalities in the macula (sz = 2.4, P = 0.047), were significantly associated with delayed RITs and therefore impaired DA. In eyes with no structural changes within the DA testing spot (n = 76, 55.5%), the presence of any abnormalities in the remaining macula was still associated with delayed RITs (sz = 2.00, P = 0.046). Presence of subretinal drusenoid deposits and ellipsoid zone disruption were a consistent predictor of RIT, whether located within the DA testing spot (P = 0.001 for both) or anywhere in the macula (P < 0.001 for both). Within the testing spot, the presence of classic drusen or serous pigment epithelium detachment was also significantly associated with impairments in DA (P @? 0.018). Conclusions: Our results suggest a significant association between macular morphology evaluated by OCT and time to dark-adapt. Subretinal drusenoid deposits and ellipsoid zone changes seem to be strongly associated with impaired dark adaptation.

Global and regional emission estimates for HCFC-22

Saikawa, E.,Rigby, M.,Prinn, R. G.,Montzka, S. A.,Miller, B. R.,Kuijpers, L. J. M.,Fraser, P. J. B.,Vollmer, M. K.,Saito, T.,Yokouchi, Y.,Harth, C. M.,Mü,hle, J.,Weiss, R. F.,Salameh, P. K.,Kim, J Copernicus GmbH 2012 Atmospheric chemistry and physics Vol.12 No.21

<P>Abstract. HCFC-22 (CHClF2, chlorodifluoromethane) is an ozone-depleting substance (ODS) as well as a significant greenhouse gas (GHG). HCFC-22 has been used widely as a refrigerant fluid in cooling and air-conditioning equipment since the 1960s, and it has also served as a traditional substitute for some chlorofluorocarbons (CFCs) controlled under the Montreal Protocol. A low frequency record on tropospheric HCFC-22 since the late 1970s is available from measurements of the Southern Hemisphere Cape Grim Air Archive (CGAA) and a few Northern Hemisphere air samples (mostly from Trinidad Head) using the Advanced Global Atmospheric Gases Experiment (AGAGE) instrumentation and calibrations. Since the 1990s high-frequency, high-precision, in situ HCFC-22 measurements have been collected at these AGAGE stations. Since 1992, the Global Monitoring Division of the National Oceanic and Atmospheric Administration/Earth System Research Laboratory (NOAA/ESRL) has also collected flasks on a weekly basis from remote sites across the globe and analyzed them for a suite of halocarbons including HCFC-22. Additionally, since 2006 flasks have been collected approximately daily at a number of tower sites across the US and analyzed for halocarbons and other gases at NOAA. All results show an increase in the atmospheric mole fractions of HCFC-22, and recent data show a growth rate of approximately 4% per year, resulting in an increase in the background atmospheric mole fraction by a factor of 1.7 from 1995 to 2009. Using data on HCFC-22 consumption submitted to the United Nations Environment Programme (UNEP), as well as existing bottom-up emission estimates, we first create globally-gridded a priori HCFC-22 emissions over the 15 yr since 1995. We then use the three-dimensional chemical transport model, Model for Ozone and Related Chemical Tracers version 4 (MOZART v4), and a Bayesian inverse method to estimate global as well as regional annual emissions. Our inversion indicates that the global HCFC-22 emissions have an increasing trend between 1995 and 2009. We further find a surge in HCFC-22 emissions between 2005 and 2009 from developing countries in Asia - the largest emitting region including China and India. Globally, substantial emissions continue despite production and consumption being phased out in developed countries currently. </P>

Human Microtubule-Associated-Protein Tau Regulates the Number of Protofilaments in Microtubules: A Synchrotron X-Ray Scattering Study

Choi, M.C.,Raviv, U.,Miller, H.P.,Gaylord, M.R.,Kiris, E.,Ventimiglia, D.,Needleman, D.J.,Kim, M.W.,Wilson, L.,Feinstein, S.C.,Safinya, C.R. Biophysical Society ; Published for the Biophysica 2009 Biophysical journal Vol.97 No.2

Microtubules (MTs), a major component of the eukaryotic cytoskeleton, are 25 nm protein nanotubes with walls comprised of assembled protofilaments built from αβ heterodimeric tubulin. In neural cells, different isoforms of the microtubule-associated-protein (MAP) tau regulate tubulin assembly and MT stability. Using synchrotron small angle x-ray scattering (SAXS), we have examined the effects of all six naturally occurring central nervous system tau isoforms on the assembly structure of taxol-stabilized MTs. Most notably, we found that tau regulates the distribution of protofilament numbers in MTs as reflected in the observed increase in the average radius <R<SUP>MT</SUP>> of MTs with increasing Φ, the tau/tubulin-dimer molar ratio. Within experimental scatter, the change in <R<SUP>MT</SUP>> seems to be isoform independent. Significantly, <R<SUP>MT</SUP>> was observed to rapidly increase for 0 < Φ < 0.2 and saturate for Φ between 0.2-0.5. Thus, a local shape distortion of the tubulin dimer on tau binding, at coverages much less than a monolayer, is spread collectively over many dimers on the scale of protofilaments. This implies that tau regulates the shape of protofilaments and thus the spontaneous curvature C<SUB>o</SUB><SUP>MT</SUP> of MTs leading to changes in the curvature C<SUP>MT</SUP> (=1/R<SUP>MT</SUP>). An important biological implication of these findings is a possible allosteric role for tau where the tau-induced shape changes of the MT surface may effect the MT binding activity of other MAPs present in neurons. Furthermore, the results, which provide insight into the regulation of the elastic properties of MTs by tau, may also impact biomaterials applications requiring radial size-controlled nanotubes.

History of atmospheric SF6 from 1973 to 2008

Rigby, M.,Mü,hle, J.,Miller, B. R.,Prinn, R. G.,Krummel, P. B.,Steele, L. P.,Fraser, P. J.,Salameh, P. K.,Harth, C. M.,Weiss, R. F.,Greally, B. R.,O&,apos,Doherty, S.,Simmonds, P. G.,Vollmer, M Copernicus GmbH 2010 Atmospheric Chemistry and Physics Vol.10 No.21

<P>Abstract. We present atmospheric sulfur hexafluoride (SF6) mole fractions and emissions estimates from the 1970s to 2008. Measurements were made of archived air samples starting from 1973 in the Northern Hemisphere and from 1978 in the Southern Hemisphere, using the Advanced Global Atmospheric Gases Experiment (AGAGE) gas chromatographic-mass spectrometric (GC-MS) systems. These measurements were combined with modern high-frequency GC-MS and GC-electron capture detection (ECD) data from AGAGE monitoring sites, to produce a unique 35-year atmospheric record of this potent greenhouse gas. Atmospheric mole fractions were found to have increased by more than an order of magnitude between 1973 and 2008. The 2008 growth rate was the highest recorded, at 0.29 ± 0.02 pmolmol−1 yr−1. A three-dimensional chemical transport model and a minimum variance Bayesian inverse method was used to estimate annual emission rates using the measurements, with a priori estimates from the Emissions Database for Global Atmospheric Research (EDGAR, version 4). Consistent with the mole fraction growth rate maximum, global emissions during 2008 were also the highest in the 1973-2008 period, reaching 7.4 ± 0.6 Gg yr−1 (1-σ uncertainties) and surpassing the previous maximum in 1995. The 2008 values follow an increase in emissions of 48 ± 20% since 2001. A second global inversion which also incorporated National Oceanic and Atmospheric Administration (NOAA) flask measurements and in situ monitoring site data agreed well with the emissions derived using AGAGE measurements alone. By estimating continent-scale emissions using all available AGAGE and NOAA surface measurements covering the period 2004-2008, with no pollution filtering, we find that it is likely that much of the global emissions rise during this five-year period originated primarily from Asian developing countries that do not report detailed, annual emissions to the United Nations Framework Convention on Climate Change (UNFCCC). We also find it likely that SF6 emissions reported to the UNFCCC were underestimated between at least 2004 and 2005. </P>

Enhancement of thermal neutron attenuation of nano-B₄C, -BN dispersed neutron shielding polymer nanocomposites

Kim, J.,Lee, B.C.,Uhm, Y.R.,Miller, W.H. North Holland Pub. Co 2014 JOURNAL OF NUCLEAR MATERIALS Vol.453 No.1

Nano-sized boron carbide (B<SUB>4</SUB>C) and boron nitride (BN) powder were prepared using ball milling. Micro- and milled nano-powders were melt blended with high density polyethylene (HDPE) using a polymer mixer followed by hot pressing to fabricate sheet composites. The tensile and flexural strengths of HDPE nanocomposites were ~20% higher than their micro counterparts, while those for latter decreased compared to neat HDPE. Thermal neutrons attenuation of the prepared HDPE nanocomposites was evaluated using a monochromatic ~0.025eV neutron beam. Thermal neutron attenuation of the HDPE nanocomposites was greatly enhanced compared to their micro counterparts at the same B-10 areal densities. Monte Carlo n-Particles (MCNP) simulations based on the lattice structure modeling also shows the similar filler size dependent thermal neutron absorption.