Conformational Dynamics of Asparagine at Coiled-Coil Interfaces

Coiled coils (CCs) are among the best-understood protein folds. Nonetheless, there are gaps in our knowledge of CCs. Notably, CCs are likely to be structurally more dynamic than often considered. Here, we explore this in an abundant class of CCs, parallel dimers, focusing on polar asparagine (Asn) residues in the hydrophobic interface. It is well documented that such inclusions discriminate between different CC oligomers, which has been rationalized in terms of whether the Asn can make side-chain hydrogen bonds. Analysis of parallel CC dimers in the Protein Data Bank reveals a variety of Asn side-chain conformations, but not all of these make the expected inter-side-chain hydrogen bond. We probe the structure and dynamics of a <i>de novo</i>-designed coiled-coil homodimer, CC-Di, by multidimensional nuclear magnetic resonance spectroscopy, including model-free dynamical analysis and relaxation–dispersion experiments. We find dynamic exchange on the millisecond time scale between Asn conformers with the side chains pointing into and out of the core. We perform molecular dynamics simulations that are consistent with this, revealing that the side chains are highly dynamic, exchanging between hydrogen-bonded-paired conformations in picoseconds to nanoseconds. Combined, our data present a more dynamic view for Asn at CC interfaces. Although inter-side-chain hydrogen bonding states are the most abundant, Asn is not always buried or engaged in such interactions. Because interfacial Asn residues are key design features for modulating CC stability and recognition, these further insights into how they are accommodated within CC structures will aid their predictive modeling, engineering, and design

Genetic Relations Between the Aves Ridge and the Grenada Back-Arc Basin, East Caribbean Sea

The Grenada Basin separates the active Lesser Antilles Arc from the Aves Ridge, described as a Cretaceous‐Paleocene remnant of the “Great Arc of the Caribbean.” Although various tectonic models have been proposed for the opening of the Grenada Basin, the data on which they rely are insufficient to reach definitive conclusions. This study presents, a large set of deep‐penetrating multichannel seismic reflection data and dredge samples acquired during the GARANTI cruise in 2017. By combining them with published data including seismic reflection data, wide‐angle seismic data, well data and dredges, we refine the understanding of the basement structure, depositional history, tectonic deformation and vertical motions of the Grenada Basin and its margins as follows: (1) rifting occurred during the late Paleocene‐early Eocene in a NW‐SE direction and led to seafloor spreading during the middle Eocene; (2) this newly formed oceanic crust now extends across the eastern Grenada Basin between the latitude of Grenada and Martinique; (3) asymmetrical pre‐Miocene depocenters support the hypothesis that the southern Grenada Basin originally extended beneath the present‐day southern Lesser Antilles Arc and probably partly into the present‐day forearc before the late Oligocene‐Miocene rise of the Lesser Antilles Arc; and (4) the Aves Ridge has subsided along with the Grenada Basin since at least the middle Eocene, with a general subsidence slowdown or even an uplift during the late Oligocene, and a sharp acceleration on its southeastern flank during the late Miocene. Until this acceleration of subsidence, several bathymetric highs remained shallow enough to develop carbonate platforms

Distribution of Hyperpolarized Xenon in the Brain Following Sensory Stimulation: Preliminary MRI Findings

In hyperpolarized xenon magnetic resonance imaging (HP 129Xe MRI), the inhaled spin-1/2 isotope of xenon gas is used to generate the MR signal. Because hyperpolarized xenon is an MR signal source with properties very different from those generated from water-protons, HP 129Xe MRI may yield structural and functional information not detectable by conventional proton-based MRI methods. Here we demonstrate the differential distribution of HP 129Xe in the cerebral cortex of the rat following a pain stimulus evoked in the animal's forepaw. Areas of higher HP 129Xe signal corresponded to those areas previously demonstrated by conventional functional MRI (fMRI) methods as being activated by a forepaw pain stimulus. The percent increase in HP 129Xe signal over baseline was 13–28%, and was detectable with a single set of pre and post stimulus images. Recent innovations in the production of highly polarized 129Xe should make feasible the emergence of HP 129Xe MRI as a viable adjunct method to conventional MRI for the study of brain function and disease

Reference material for radionuclides in sediment IAEA-384 (Fangataufa Lagoon sediment)

Author Posting. © Springer, 2007. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Journal of Radioanalytical and Nuclear Chemistry 273 (2007): 383-393, doi:10.1007/s10967-007-6898-4.A reference material designed for the determination of anthropogenic and natural radionuclides in sediment, IAEA-384 (Fangataufa Lagoon sediment), is described and the results of certification are presented. The material has been certified for 8 radionuclides (40K, 60Co, 155Eu, 230Th, 238U, 238Pu, 239+240Pu and 241Am). Information values are given for 12 radionuclides (90Sr, 137Cs, 210Pb (210Po), 226Ra, 228Ra, 232Th, 234U, 235U, 239Pu, 240Pu and 241Pu). Less reported radionuclides include 228Th, 236U, 239Np and 242Pu. The reference material may be used for quality management of radioanalytical laboratories engaged in the analysis of radionuclides in the environment, as well as for the development and validation of analytical methods and for training purposes. The material is available from IAEA in 100 g units

A phase I study of the nitroimidazole hypoxia marker SR4554 using 19F magnetic resonance spectroscopy

SR4554 is a fluorine-containing 2-nitroimidazole, designed as a hypoxia marker detectable with 19F magnetic resonance spectroscopy (MRS). In an initial phase I study of SR4554, nausea/vomiting was found to be dose-limiting, and 1400 mg m−2 was established as MTD. Preliminary MRS studies demonstrated some evidence of 19F retention in tumour. In this study we investigated higher doses of SR4554 and intratumoral localisation of the 19F MRS signal. Patients had tumours 3 cm in diameter and 4 cm deep. Measurements were performed using 1H/19F surface coils and localised 19F MRS acquisition. SR4554 was administered at 1400 mg m−2, with subsequent increase to 2600 mg m−2 using prophylactic metoclopramide. Spectra were obtained immediately post infusion (MRS no. 1), at 16 h (MRS no. 2) and 20 h (MRS no. 3), based on the SR4554 half-life of 3.5 h determined from a previous study. 19Fluorine retention index (%) was defined as (MRS no. 2/MRS no. 1)*100. A total of 26 patients enrolled at: 1400 (n=16), 1800 (n=1), 2200 (n=1) and 2600 mg m−2 (n=8). SR4554 was well tolerated and toxicities were all grade 1; mean plasma elimination half-life was 3.7±0.9 h. SR4554 signal was seen on both unlocalised and localised MRS no. 1 in all patients. Localised 19F signals were detected at MRS no. 2 in 5 out of 9 patients and 4 out of 5 patients at MRS no. 3. The mean retention index in tumour was 13.6 (range 0.6-43.7) compared with 4.1 (range 0.6-7.3) for plasma samples taken at the same times (P=0.001) suggesting 19F retention in tumour and, therefore, the presence of hypoxia. We have demonstrated the feasibility of using 19F MRS with SR4554 as a potential method of detecting hypoxia. Certain patients showed evidence of 19F retention in tumour, supporting further development of this technique for detection of tumour hypoxia

Genome-wide mapping of cystitis due to Streptococcus agalactiae and Escherichia coli in mice identifies a unique bladder transcriptome that signifies pathogen-specific antimicrobial defense against urinary tract infection

The most common causes of urinary tract infections (UTIs) are Gram-negative pathogens such as Escherichia coli; however, Gram-positive organisms, including Streptococcus agalactiae, or group B streptococcus (GBS), also cause UTI. In GBS infection, UTI progresses to cystitis once the bacteria colonize the bladder, but the host responses triggered in the bladder immediately following infection are largely unknown. Here, we used genome-wide expression profiling to map the bladder transcriptome of GBS UTI in mice infected transurethrally with uropathogenic GBS that was cultured from a 35-year-old women with cystitis. RNA from bladders was applied to Affymetrix Gene-1.0ST microarrays; quantitative reverse transcriptase PCR (qRT-PCR) was used to analyze selected gene responses identified in array data sets. A surprisingly small significant-gene list of 172 genes was identified at 24 h; this compared to 2,507 genes identified in a side-by-side comparison with uropathogenic E. coli (UPEC). No genes exhibited significantly altered expression at 2 h in GBS-infected mice according to arrays despite high bladder bacterial loads at this early time point. The absence of a marked early host response to GBS juxtaposed with broad-based bladder responses activated by UPEC at 2 h. Bioinformatics analyses, including integrative system-level network mapping, revealed multiple activated biological pathways in the GBS bladder transcriptome that regulate leukocyte activation, inflammation, apoptosis, and cytokine-chemokine biosynthesis. These findings define a novel, minimalistic type of bladder host response triggered by GBS UTI, which comprises collective antimicrobial pathways that differ dramatically from those activated by UPEC. Overall, this study emphasizes the unique nature of bladder immune activation mechanisms triggered by distinct uropathogens

Reference Material for Radionuclides in Sediment, IAEA-384 (Fangataufa Lagoon Sediment)

The IAEA Marine Environment Laboratory (IAEA-MEL) in Monaco has conducted intercomparison exercises on radionuclides in marine samples for many years as part of its contribution to the IAEA's program of Analytical Quality Control Services (AQCS). An important part of the AQCS program has been a production of Reference Materials (RMs) and their provision to radioanalytical laboratories. The RMs have been developed for different marine matrices (sediment, water, biota), with accuracy and precision required for the present state of the art of radiometrics and mass spectrometry methods. The RMs have been produced as the final products of world-wide intercomparison exercises organized during last 30 years. A total of 44 intercomparison exercises were undertaken and 39 RMs were produced for radionuclides in the marine environment. All required matrices (seawater, biota, sediment) have been covered with radionuclide concentrations ranging from typical environmental levels to elevated levels affected by discharges from nuclear reprocessing plants. The long-term availability of RMs (over 10 years) requires the use of very specific techniques to collect and pretreat large quantities of material (e.g., in excess of 100 kg) in order to ensure sample stability and homogenization of any analytes of interest. The production of a RM is therefore a long process, covering the identification of needs, sample collection, pre-treatment, homogenization, bottling, distribution to laboratories, evaluation of data, preliminary reporting, additional analyses in expert laboratories, certification of the material, and finally issuing the RM. In this paper we describe a reference material IAEA-384, Fangataufa lagoon sediment, designed for determination of anthropogenic and natural radionuclides in the marine environment. This RM has been prepared with the aim of testing the performance of analytical laboratories to measure the activity of these radionuclides in a sediment sample contaminated by elevated levels of fallout from nuclear weapons tests. Participating laboratories were requested to determine as many radionuclides as possible by radiometric (alpha, beta and gamma-spectrometry) as well as by mass spectrometry methods (e.g., ICPMS - Inductively Coupled Plasma Mass Spectrometry, TIMS - Thermal Ionization Mass Spectrometry, AMS - Accelerator Mass Spectrometry)

Radionuclides As Tracers Of Water Fronts In The South Indian Ocean-Antares Iv Results

ISI Document Delivery No.: 438EA Times Cited: 5 Cited Reference Count: 58 Cited References: Aarkrog A, 1997, J ENVIRON RADIOACTIV, V34, P69, DOI 10.1016/0265-931X(96)00005-7 BAYER R, 1991, MAR CHEM, V35, P123 Belkin IM, 1996, J GEOPHYS RES-OCEANS, V101, P3675, DOI 10.1029/95JC02750 Bhushan R, 2003, DEEP-SEA RES PT II, V50, P2777, DOI 10.1016/S0967-0645(03)00147-4 BOWEN VT, 1980, EARTH PLANET SC LETT, V49, P411, DOI 10.1016/0012-821X(80)90083-7 Broecker W., 1982, TRACERS SEA BROECKER WS, 1986, J GEOPHYS RES-OCEANS, V91, P14331, DOI 10.1029/JC091iC12p14331 CHERRY MI, 1987, MAR BIOL, V96, P441, DOI 10.1007/BF00412529 Coppola L, 2005, DEEP-SEA RES PT I, V52, P51, DOI 10.1016/j.dsr.2004.07.020 Coppola L, 2006, MAR CHEM, V100, P299, DOI 10.1016/j.marchem.2005.10.019 DeMaster DJ, 2002, DEEP-SEA RES PT II, V49, P3155, DOI 10.1016/S0967-0645(02)00076-0 EPSTEIN S, 1953, GEOCHIM COSMOCHIM AC, V4, P213, DOI 10.1016/0016-7037(53)90051-9 FOWLER SW, 1983, DEEP-SEA RES, V30, P1221, DOI 10.1016/0198-0149(83)90081-X Gaillard JF, 1997, DEEP-SEA RES PT II, V44, P951, DOI 10.1016/S0967-0645(97)00003-9 GAMBERONI L, 1982, OCEANOL ACTA, V5, P289 GONFIANTINI R, 1978, NATURE, V271, P534, DOI 10.1038/271534a0 Heinze C, 2002, DEEP-SEA RES PT II, V49, P3105, DOI 10.1016/S0967-0645(02)00074-7 HIROSE K, 2009, PROG OCEANOGR UNPUB Hong GH, 2002, MAR POLLUT BULL, V44, P660, DOI 10.1016/S0025-326X(01)00322-8 Jeffree RA, 1997, ENVIRON SCI TECHNOL, V31, P2584, DOI 10.1021/es9610592 Jia GG, 2000, ANTARCT SCI, V12, P141 KOIDE M, 1982, NATURE, V296, P544, DOI 10.1038/296544a0 KOIDE M, 1981, EARTH PLANET SC LETT, V54, P239, DOI 10.1016/0012-821X(81)90007-8 Labat JP, 2002, DEEP-SEA RES PT I, V49, P735, DOI 10.1016/S0967-0637(01)00076-0 La Rosa JJ, 2001, J RADIOANAL NUCL CH, V248, P765, DOI 10.1023/A:1010661232765 Lee SH, 2005, MAR GEOL, V216, P249, DOI 10.1016/j.margeo.2005.02.013 Lee SH, 2001, J RADIOANAL NUCL CH, V248, P757, DOI 10.1023/A:1010609215926 LIVINGSTON HD, 1983, NATURE, V303, P228, DOI 10.1038/303228a0 Livingston HD, 2001, RADIOACTIV ENVIRONM, V1, P267 Livingston HD, 2002, HEALTH PHYS, V82, P656, DOI 10.1097/00004032-200205000-00012 Livingston HD, 2000, OCEAN COAST MANAGE, V43, P689, DOI 10.1016/S0964-5691(00)00054-5 Mayzaud P, 2002, DEEP-SEA RES PT II, V49, P3169, DOI 10.1016/S0967-0645(02)00077-2 MICHEL E, 1995, PALEOCEANOGRAPHY, V10, P927, DOI 10.1029/95PA00978 Miyake Y., 1988, PAPERS METEOROLOGY G, V39, P95, DOI 10.2467/mripapers.39.95 Mulsow S, 2003, DEEP-SEA RES PT II, V50, P2761, DOI 10.1016/S0967-0645(03)00146-2 NOWLIN WD, 1986, REV GEOPHYS, V24, P469, DOI 10.1029/RG024i003p00469 Park YH, 2002, DEEP-SEA RES PT II, V49, P1823, DOI 10.1016/S0967-0645(02)00014-0 PARK YH, 1991, MAR CHEM, V35, P45 PARK YH, 1993, J GEOPHYS RES-OCEANS, V98, P12361, DOI 10.1029/93JC00938 Perkins R.W., 1980, TRANSURANIC ELEMENTS, P53 Pham MK, 2006, APPL RADIAT ISOTOPES, V64, P1253, DOI 10.1016/j.apradiso.2006.02.032 Pollard RT, 2002, DEEP-SEA RES PT II, V49, P3289, DOI 10.1016/S0967-0645(02)00084-X Povinec PP, 2008, ACTA PHYS SLOVACA, V58, P1, DOI 10.2478/v10155-010-0088-6 POVINEC PP, 2009, PROG OCEANOGR UNPUB Povinec PP, 2005, J ENVIRON RADIOACTIV, V81, P63, DOI 10.1016/j.jenvrad.2004.12.003 Povinec PP, 2003, DEEP-SEA RES PT II, V50, P2751, DOI 10.1016/S0967-0645(03)00145-0 Povinec PP, 2004, J ENVIRON RADIOACTIV, V76, P113, DOI 10.1016/j.jenvrad.2004.03.022 Povinec P. P., 2005, Journal of Radioanalytical and Nuclear Chemistry, V263, DOI 10.1007/s10967-005-0070-9 Povinec PP, 2002, J RADIOANAL NUCL CH, V251, P369, DOI 10.1023/A:1014861620713 Povinec PP, 2003, DEEP-SEA RES PT II, V50, P2607, DOI 10.1016/S0967-0645(03)00138-3 Ragueneau O, 2002, DEEP-SEA RES PT II, V49, P3127, DOI 10.1016/S0967-0645(02)00075-9 ROOS P, 1994, J ENVIRON RADIOACTIV, V24, P235, DOI 10.1016/0265-931X(94)90042-6 SAMIENTO JL, 1984, NATURE, V308, P621 SIEVERS HA, 1984, J GEOPHYS RES-OCEANS, V89, P489, DOI 10.1029/JC089iC06p10489 TALJAARD HA, 1984, CLIMATES OCEANS, P505 VanBeusekom JEE, 1997, DEEP-SEA RES PT II, V44, P987, DOI 10.1016/S0967-0645(96)00105-1 Vintro L. Leon, 1999, Science of the Total Environment, V237-238, P77, DOI 10.1016/S0048-9697(99)00126-6 WEISS W, 1980, EARTH PLANET SC LETT, V49, P435, DOI 10.1016/0012-821X(80)90084-9 Lee, Sang-Han Povinec, Pavel P. Gastaud, Janine Oregioni, Beniamino Coppola, Laurent Jeandel, Catherine 5 SPRINGER DORDRECHT J OCEANOGRAnthropogenic Sr-90, Pu-239,Pu-240 and Am-241 were used as tracers of water mass circulation in the Crozet Basin of the South Indian Ocean, represented by three main water fronts-Agulhas (AF), Subtropical (STF) and Subantarctic (SAF). Higher Sr-90 concentrations observed north of 43A degrees S were due to the influence of AF and STF, which are associated with the south branch of the Subtropical gyre, which acts as a reservoir of radionuclides transported from the North to the South Indian Ocean. On the other hand, the region south of 43A degrees S has been influenced by SAF, bringing to the Crozet Basin Antarctic waters with lower radionuclide concentrations. The Pu-238/Pu-239,Pu-240 activity ratios observed in water and zooplankton samples indicated that, even 35 years after the injection of Pu-238 to the Indian Ocean from the burn-up of the SNAP-9A satellite, the increased levels of Pu-238 in surface water and zooplankton are still well visible. The radionuclide concentrations in seawater and their availability to zooplankton are responsible for the observed Po-210, Pu-239,Pu-240 and Am-241 levels in zooplankton

Controlling the dynamics of the Nek2 leucine zipper by engineering of "kinetic" disulphide bonds

<div><p>Nek2 is a dimeric serine/ threonine protein kinase that belongs to the family of NIMA-related kinases (Neks). Its N-terminal catalytic domain and its C-terminal regulatory region are bridged by a leucine zipper, which plays an important role in the activation of Nek2’s catalytic activity. Unusual conformational dynamics on the intermediary/slow timescale has thwarted all attempts so far to determine the structure of the Nek2 leucine zipper by means of X-ray crystallography and Nuclear Magnetic Resonance (NMR). Disulfide engineering, the strategic placement of non-native disulfide bonds into flexible regions flanking the coiled coil, was used to modulate the conformational exchange dynamics of this important dimerization domain. The resulting reduction in exchange rate leads to substantial improvements of important features in NMR spectra, such as line width, coherence transfer leakage and relaxation. These effects were comprehensively analyzed for the wild type protein, two single disulfide bond-bearing mutants and another double disulfide bonds-carrying mutant. Furthermore, exchange kinetics were measured across a wide temperature range, allowing for a detailed analysis of activation energy (ΔG^‡) and maximal rate constant (k’_ex). For one mutant carrying a disulfide bond at its C-terminus, a full backbone NMR assignment could be obtained for both conformers, demonstrating the benefits of the disulfide engineering. Our study demonstrates the first successful application of ‘kinetic’ disulfide bonds for the purpose of controlling the adverse effects of protein dynamics. Firstly, this provides a promising, robust platform for the full structural and functional investigation of the Nek2 leucine zipper in the future. Secondly, this work broadens the toolbox of protein engineering by disulfide bonds through the addition of a kinetic option in addition to the well-established thermodynamic uses of disulfide bonds.</p></div

Temporal evolution of Cs-137, Np-237, and Pu239+240 and estimated vertical Pu239+240 export in the northwestern Mediterranean Sea

The evolution of Cs-137, Np-237 and Pu239+240 at the DYFAMED station (NW Mediterranean) is discussed in relation to physical processes, downward fluxes of particles, and changes in the main input sources. The data set presented in this study represents the first complete Np-237 vertical profiles (0.12-0.27 mu Bq L-1), and constitutes a baseline measurement to assess future changes. A similar behavior of Cs and Np has been evidenced, confirming that Np behaves conservatively. While the Cs-137 decrease has been driven by its radioactive decay, the vertical distribution of Np-237 has not substantially changed over the last decade. In the absence of recent major inputs, a homogenization of their vertical distribution occurred, partly due to deep convection events that became more intense during the last decade. In contrast, Pu239+240 surface levels in the NW Mediterranean waters have fallen in the past four decades by a factor of 5. This decrease in surface has been balanced by higher concentrations in the deep-water layers. A first estimate of the downward Pu239+240 fluxes in the NW Mediterranean Sea is proposed over more than two decades. This estimation, based on the DYFAMED sediment trap time-series data and published Pu239+240 flux measurements, suggests that sinking particles have accounted for 60-90% of the upper layer (0-200 m) Pu inventory loss over the period 1989-2013. The upper layer residence time of Pu is estimated to be similar to 28 years, twice as long as the residence time estimated for the whole western Mediterranean (similar to 15 years). This difference highlights the slow removal of Pu in the open waters of the NW Mediterranean and confirms that most of the Pu removal occurs along the coastal margin where sedimentation rates are high. (C) 2017 Elsevier B.V. All rights reserved