A sorting nexin 17-binding domain within the LRP1 cytoplasmic tail mediates receptor recycling through the basolateral sorting endosome.

PubMed

Farfán, Pamela; Lee, Jiyeon; Larios, Jorge; Sotelo, Pablo; Bu, Guojun; Marzolo, María-Paz

2013-07-01

Sorting nexin 17 (SNX17) is an adaptor protein present in early endosomal antigen 1 (EEA1)-positive sorting endosomes that promotes the efficient recycling of low-density lipoprotein receptor-related protein 1 (LRP1) to the plasma membrane through recognition of the first NPxY motif in the cytoplasmic tail of this receptor. The interaction of LRP1 with SNX17 also regulates the basolateral recycling of the receptor from the basolateral sorting endosome (BSE). In contrast, megalin, which is apically distributed in polarized epithelial cells and localizes poorly to EEA1-positive sorting endosomes, does not interact with SNX17, despite containing three NPxY motifs, indicating that this motif is not sufficient for receptor recognition by SNX17. Here, we identified a cluster of 32 amino acids within the cytoplasmic domain of LRP1 that is both necessary and sufficient for SNX17 binding. To delineate the function of this SNX17-binding domain, we generated chimeric proteins in which the SNX17-binding domain was inserted into the cytoplasmic tail of megalin. This insertion mediated the binding of megalin to SNX17 and modified the cell surface expression and recycling of megalin in non-polarized cells. However, the polarized localization of chimeric megalin was not modified in polarized Madin-Darby canine kidney cells. These results provide evidence regarding the molecular and cellular mechanisms underlying the specificity of SNX17-binding receptors and the restricted function of SNX17 in the BSE. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Pre- and post-remediation characterization of acid-generating fluvial tailings material

USGS Publications Warehouse

Smith, Kathleen S.; Walton-Day, Katherine; Hoal, Karin O.; Driscoll, Rhonda L.; Pietersen, K.

2012-01-01

The upper Arkansas River south of Leadville, Colorado, USA, contains deposits of fluvial tailings from historical mining operations in the Leadville area. These deposits are potential non-point sources of acid and metal contamination to surface- and groundwater systems. We are investigating a site that recently underwent in situ remediation treatment with lime, fertilizer, and compost. Pre- and post-remediation fluvial tailings material was collected from a variety of depths to examine changes in mineralogy, acid generation, and extractable nutrients. Results indicate sufficient nutrient availability in the post-remediation near-surface material, but pyrite and acid generation persist below the depth of lime and fertilizer addition. Mineralogical characterization performed using semi-quantitative X-ray diffraction and quantitative SEM-based micro-mineralogy (Mineral Liberation Analysis, MLA) reveal formation of gypsum, jarosite, and complex coatings surrounding mineral grains in post-remediation samples.

Ubiquitination of the Dishevelled DIX domain blocks its head-to-tail polymerization

PubMed Central

Madrzak, Julia; Fiedler, Marc; Johnson, Christopher M.; Ewan, Richard; Knebel, Axel; Bienz, Mariann; Chin, Jason W.

2015-01-01

Dishevelled relays Wnt signals from the plasma membrane to different cytoplasmic effectors. Its signalling activity depends on its DIX domain, which undergoes head-to-tail polymerization to assemble signalosomes. The DIX domain is ubiquitinated in vivo at multiple lysines, which can be antagonized by various deubiquitinases (DUBs) including the CYLD tumour suppressor that attenuates Wnt signalling. Here, we generate milligram quantities of pure human Dvl2 DIX domain mono-ubiquitinated at two lysines (K54 and K58) by genetically encoded orthogonal protection with activated ligation (GOPAL), to investigate their effect on DIX polymerization. We show that the ubiquitination of DIX at K54 blocks its polymerization in solution, whereas DIX58-Ub remains oligomerization-competent. DUB profiling identified 28 DUBs that cleave DIX-ubiquitin conjugates, half of which prefer, or are specific for, DIX54-Ub, including Cezanne and CYLD. These DUBs thus have the potential to promote Dvl polymerization and signalosome formation, rather than antagonize it as previously thought for CYLD. PMID:25907794

Assessment of Phytostabilization Success in Metalliferous Acid Mine Tailings

NASA Astrophysics Data System (ADS)

Wang, Y.; Root, R. A.; Hammond, C.; Amistadi, M. K.; Maier, R. M.; Chorover, J.

2014-12-01

Legacy mine tailings are a significant source of metal(loid)s due to wind and water erosion, especially in the arid southwest, and exposure to fugative dusts presents a health risk to surrounding populations. Compost assisted phytostabilization has been implemented to reduce off site emissions at the Iron King Mine U.S. Superfund Site in central Arizona, concurrent with a greenhouse mesocosm study for detailed study of subsurface mechanisms. Quantification of plant available toxic metal(loid)s in the amended tailings was accessed with a targeted single extraction of diethylenetriaminepentaactic acid (DTPA). Greenhouse mesocosms (1m dia, 0.4 m deep), run in triplicate, mimicked field treatments with: i) tailings only control (TO), ii) tailings plus 15 wt% compost (TC), iii) TC + quailbush seeds (TCA), and iv) TC + buffalo grass seeds (TCB). Core samples collected at 3-month intervals for 1 year were dissected by depth (10 cm each) for analysis. DTPA results indicated that compost treated samples decreased plant availability of Al, As, Cd, Cu, Fe, and Pb but increased Mn and Zn compared with TO. TCB decreased plant available metal(loid)s at all depths, whereas TCA plant available Al, As, Cd, Cu, Fe, Mn and Zn increased in the deeper 20-30cm and 30-40 cm relative to TCB. Samples from the greenhouse were compared to tailings from both the field site and tailings impacted soils used to grow vegetables. Mineral transformations and metal complexation, in the pre- and post-extracted tailings were analyzed by synchrotron transmission XRD and FTIR spectroscopy. The temporal change in plant available metal(loid)s in response to phytostabilization indicates mineralogical alteration that improves soil quality by reducing plant available metal(loid)s. These results will aid in the understanding and efficacy of phytostabilization as a means of remediating and reducing toxicity on mine tailings as well as providing information on health risk management in the region.

Structure and function of the interacting domains of Spire and Fmn-family formins.

PubMed

Vizcarra, Christina L; Kreutz, Barry; Rodal, Avital A; Toms, Angela V; Lu, Jun; Zheng, Wei; Quinlan, Margot E; Eck, Michael J

2011-07-19

Evidence for cooperation between actin nucleators is growing. The WH2-containing nucleator Spire and the formin Cappuccino interact directly, and both are essential for assembly of an actin mesh during Drosophila oogenesis. Their interaction requires the kinase noncatalytic C-lobe domain (KIND) domain of Spire and the C-terminal tail of the formin. Here we describe the crystal structure of the KIND domain of human Spir1 alone and in complex with the tail of Fmn2, a mammalian ortholog of Cappuccino. The KIND domain is structurally similar to the C-lobe of protein kinases. The Fmn2 tail is coordinated in an acidic cleft at the base of the domain that appears to have evolved via deletion of a helix from the canonical kinase fold. Our functional analysis of Cappuccino reveals an unexpected requirement for its tail in actin assembly. In addition, we find that the KIND/tail interaction blocks nucleation by Cappuccino and promotes its displacement from filament barbed ends providing insight into possible modes of cooperation between Spire and Cappuccino.

IEDA: Making Small Data BIG Through Interdisciplinary Partnerships Among Long-tail Domains

NASA Astrophysics Data System (ADS)

Lehnert, K. A.; Carbotte, S. M.; Arko, R. A.; Ferrini, V. L.; Hsu, L.; Song, L.; Ghiorso, M. S.; Walker, D. J.

2014-12-01

The Big Data world in the Earth Sciences so far exists primarily for disciplines that generate massive volumes of observational or computed data using large-scale, shared instrumentation such as global sensor networks, satellites, or high-performance computing facilities. These data are typically managed and curated by well-supported community data facilities that also provide the tools for exploring the data through visualization or statistical analysis. In many other domains, especially those where data are primarily acquired by individual investigators or small teams (known as 'Long-tail data'), data are poorly shared and integrated, lacking a community-based data infrastructure that ensures persistent access, quality control, standardization, and integration of data, as well as appropriate tools to fully explore and mine the data within the context of broader Earth Science datasets. IEDA (Integrated Earth Data Applications, www.iedadata.org) is a data facility funded by the US NSF to develop and operate data services that support data stewardship throughout the full life cycle of observational data in the solid earth sciences, with a focus on the data management needs of individual researchers. IEDA builds on a strong foundation of mature disciplinary data systems for marine geology and geophysics, geochemistry, and geochronology. These systems have dramatically advanced data resources in those long-tail Earth science domains. IEDA has strengthened these resources by establishing a consolidated, enterprise-grade infrastructure that is shared by the domain-specific data systems, and implementing joint data curation and data publication services that follow community standards. In recent years, other domain-specific data efforts have partnered with IEDA to take advantage of this infrastructure and improve data services to their respective communities with formal data publication, long-term preservation of data holdings, and better sustainability. IEDA hopes to

Replication-coupled chromatin assembly of newly synthesized histones: distinct functions for the histone tail domains.

PubMed

Ejlassi-Lassallette, Aïda; Thiriet, Christophe

2012-02-01

The maintenance of the genome during replication requires the assembly of nucleosomes with newly synthesized histones. Achieving the deposition of newly synthesized histones in chromatin implies their transport from the cytoplasm to the nucleus at the replication sites. Several lines of evidence have revealed critical functions of the histone tail domains in these conserved cellular processes. In this review, we discuss the role of the amino termini of the nucleosome building blocks, H2A/H2B and H3/H4, in different model systems. The experimental data showed that H2A/H2B tails and H3/H4 tails display distinct functions in nuclear import and chromatin assembly. Furthermore, we describe recent studies exploiting the unique properties of the slime mold, Physarum polycephalum , that have advanced understanding of the function of the highly conserved replication-dependent diacetylation of H4.

Kinetic Study on the Removal of Iron from Gold Mine Tailings by Citric Acid

NASA Astrophysics Data System (ADS)

Mashifana, T.; Mavimbela, N.; Sithole, N.

2018-03-01

The Gold mining generates large volumes of tailings, with consequent disposal and environmental problems. Iron tends to react with sulphur to form pyrite and pyrrhotite which then react with rain water forming acid rain. The study focuses on the removal of iron (Fe) from Gold Mine tailings; Fe was leached using citric acid as a leaching reagent. Three parameters which have an effect on the removal of Fe from the gold mine tailings, namely; temperature (25 °C and 50 °C), reagent concentration (0.25 M, 0.5 M, 0.75 M and 1 M) and solid loading ratio (20 %, 30 % and 40 %) were investigated. It was found that the recovery of Fe from gold mine tailings increased with increasing temperature and reagent concentration, but decreased with increasing solid loading ratio. The optimum conditions for the recovery of Fe from gold mine tailings was found to be at a temperature of 50 ºC, reagent concentration of 1 M and solid loading of 20 %. Three linear kinetic models were investigated and Prout-Tompkins kinetic model was the best fit yielding linear graphs with the highest R2 values.

The H3-H4 N-Terminal Tail Domains Are the Primary Mediators of Transcription Factor IIIA Access to 5S DNA within a Nucleosome

PubMed Central

Vitolo, Joseph M.; Thiriet, Christophe; Hayes, Jeffrey J.

2000-01-01

Reconstitution of a DNA fragment containing a Xenopus borealis somatic type 5S rRNA gene into a nucleosome greatly restricts the binding of transcription factor IIIA (TFIIIA) to its cognate DNA sequence within the internal promoter of the gene. Removal of all core histone tail domains by limited trypsin proteolysis or acetylation of the core histone tails significantly relieves this inhibition and allows TFIIIA to exhibit high-affinity binding to nucleosomal DNA. Since only a single tail or a subset of tails may be primarily responsible for this effect, we determined whether removal of the individual tail domains of the H2A-H2B dimer or the H3-H4 tetramer affects TFIIIA binding to its cognate DNA site within the 5S nucleosome in vitro. The results show that the tail domains of H3 and H4, but not those of H2A and/or H2B, directly modulate the ability of TFIIIA to bind nucleosomal DNA. In vitro transcription assays carried out with nucleosomal templates lacking individual tail domains show that transcription efficiency parallels the binding of TFIIIA. In addition, we show that the stoichiometry of core histones within the 5S DNA-core histone-TFIIIA triple complex is not changed upon TFIIIA association. Thus, TFIIIA binding occurs by displacement of H2A-H2B–DNA contacts but without complete loss of the dimer from the nucleoprotein complex. These data, coupled with previous reports (M. Vettese-Dadey, P. A. Grant, T. R. Hebbes, C. Crane-Robinson, C. D. Allis, and J. L. Workman, EMBO J. 15:2508–2518, 1996; L. Howe, T. A. Ranalli, C. D. Allis, and J. Ausio, J. Biol. Chem. 273:20693–20696, 1998), suggest that the H3/H4 tails are the primary arbiters of transcription factor access to intranucleosomal DNA. PMID:10688663

Oil sands thickened froth treatment tailings exhibit acid rock drainage potential during evaporative drying.

PubMed

Kuznetsov, Petr; Kuznetsova, Alsu; Foght, Julia M; Siddique, Tariq

2015-02-01

Bitumen extraction from oil sands ores after surface mining produces different tailings waste streams: 'froth treatment tailings' are enriched in pyrite relative to other streams. Tailings treatment can include addition of organic polymers to produce thickened tailings (TT). TT may be further de-watered by deposition into geotechnical cells for evaporative drying to increase shear strength prior to reclamation. To examine the acid rock drainage (ARD) potential of TT, we performed predictive analyses and laboratory experiments on material from field trials of two types of thickened froth treatment tailings (TT1 and TT2). Acid-base accounting (ABA) of initial samples showed that both TT1 and TT2 initially had net acid-producing potential, with ABA values of -141 and -230 t CaCO₃ equiv. 1000 t(-1) of TT, respectively. In long-term kinetic experiments, duplicate ~2-kg samples of TT were incubated in shallow trays and intermittently irrigated under air flow for 459 days to simulate evaporative field drying. Leachates collected from both TT samples initially had pH~6.8 that began decreasing after ~50 days (TT2) or ~250 days (TT1), stabilizing at pH~2. Correspondingly, the redox potential of leachates increased from 100-200 mV to 500-580 mV and electrical conductivity increased from 2-5 dS m(-1) to 26 dS m(-1), indicating dissolution of minerals during ARD. The rapid onset and prolonged ARD observed with TT2 is attributed to its greater pyrite (13.4%) and lower carbonate (1.4%) contents versus the slower onset of ARD in TT1 (initially 6.0% pyrite and 2.5% carbonates). 16S rRNA gene pyrosequencing analysis revealed rapid shift in microbial community when conditions became strongly acidic (pH~2) favoring the enrichment of Acidithiobacillus and Sulfobacillus bacteria in TT. This is the first report showing ARD potential of TT and the results have significant implications for effective management of pyrite-enriched oil sands tailings streams/deposits. Copyright © 2014

Peptides derived from human galectin-3 N-terminal tail interact with its carbohydrate recognition domain in a phosphorylation-dependent manner

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berbís, M. Álvaro; André, Sabine; Cañada, F. Javier

2014-01-03

Highlights: •Galectin-3 is composed of a carbohydrate recognition domain and an N-terminal tail. •Synthetic peptides derived from the tail are shown to interact with the CRD. •This interaction is modulated by Ser- and Tyr-phosphorylation of the peptides. -- Abstract: Galectin-3 (Gal-3) is a multi-functional effector protein that functions in the cytoplasm and the nucleus, as well as extracellularly following non-classical secretion. Structurally, Gal-3 is unique among galectins with its carbohydrate recognition domain (CRD) attached to a rather long N-terminal tail composed mostly of collagen-like repeats (nine in the human protein) and terminating in a short non-collagenous terminal peptide sequence uniquemore » in this lectin family and not yet fully explored. Although several Ser and Tyr sites within the N-terminal tail can be phosphorylated, the physiological significance of this post-translational modification remains unclear. Here, we used a series of synthetic (phospho)peptides derived from the tail to assess phosphorylation-mediated interactions with {sup 15}N-labeled Gal-3 CRD. HSQC-derived chemical shift perturbations revealed selective interactions at the backface of the CRD that were attenuated by phosphorylation of Tyr 107 and Tyr 118, while phosphorylation of Ser 6 and Ser 12 was essential. Controls with sequence scrambling underscored inherent specificity. Our studies shed light on how phosphorylation of the N-terminal tail may impact on Gal-3 function and prompt further studies using phosphorylated full-length protein.« less

Separation of Main and Tail Rotor Noise Sources from Ground-Based Acoustic Measurements Using Time-Domain De-Dopplerization

NASA Technical Reports Server (NTRS)

Greenwood, Eric II; Schmitz, Fredric H.

2009-01-01

A new method of separating the contributions of helicopter main and tail rotor noise sources is presented, making use of ground-based acoustic measurements. The method employs time-domain de-Dopplerization to transform the acoustic pressure time-history data collected from an array of ground-based microphones to the equivalent time-history signals observed by an array of virtual inflight microphones traveling with the helicopter. The now-stationary signals observed by the virtual microphones are then periodically averaged with the main and tail rotor once per revolution triggers. The averaging process suppresses noise which is not periodic with the respective rotor, allowing for the separation of main and tail rotor pressure time-histories. The averaged measurements are then interpolated across the range of directivity angles captured by the microphone array in order to generate separate acoustic hemispheres for the main and tail rotor noise sources. The new method is successfully applied to ground-based microphone measurements of a Bell 206B3 helicopter and demonstrates the strong directivity characteristics of harmonic noise radiation from both the main and tail rotors of that helicopter.

Structural and Functional Studies of gpX of Escherichia coli Phage P2 Reveal a Widespread Role for LysM Domains in the Baseplates of Contractile-Tailed Phages

PubMed Central

Fatehi Hassanabad, Mostafa; Chang, Tom; Pirani, Nawaz; Bona, Diane; Edwards, Aled M.

2013-01-01

A variety of bacterial pathogenicity determinants, including the type VI secretion system and the virulence cassettes from Photorhabdus and Serratia, share an evolutionary origin with contractile-tailed myophages. The well-characterized Escherichia coli phage P2 provides an excellent system for studies related to these systems, as its protein composition appears to represent the “minimal” myophage tail. In this study, we used nuclear magnetic resonance (NMR) spectroscopy to determine the solution structure of gpX, a 68-residue tail baseplate protein. Although the sequence and structure of gpX are similar to those of LysM domains, which are a large family associated with peptidoglycan binding, we did not detect a peptidoglycan-binding activity for gpX. However, bioinformatic analysis revealed that half of all myophages, including all that possess phage T4-like baseplates, encode a tail protein with a LysM-like domain, emphasizing a widespread role for this domain in baseplate function. While phage P2 gpX comprises only a single LysM domain, many myophages display LysM domain fusions with other tail proteins, such as the DNA circulation protein found in Mu-like phages and gp53 of T4-like phages. Electron microscopy of P2 phage particles with an incorporated gpX-maltose binding protein fusion revealed that gpX is located at the top of the baseplate, near the junction of the baseplate and tail tube. gpW, the orthologue of phage T4 gp25, was also found to localize to this region. A general colocalization of LysM-like domains and gpW homologues in diverse phages is supported by our bioinformatic analysis. PMID:24097944

Microbial diversity at the moderate acidic stage in three different sulfidic mine tailings dumps generating acid mine drainage.

PubMed

Korehi, Hananeh; Blöthe, Marco; Schippers, Axel

2014-11-01

In freshly deposited sulfidic mine tailings the pH is alkaline or circumneutral. Due to pyrite or pyrrhotite oxidation the pH is dropping over time to pH values <3 at which acidophilic iron- and sulfur-oxidizing prokaryotes prevail and accelerate the oxidation processes, well described for several mine waste sites. The microbial communities at the moderate acidic stage in mine tailings are only scarcely studied. Here we investigated the microbial diversity via 16S rRNA gene sequence analysis in eight samples (pH range 3.2-6.5) from three different sulfidic mine tailings dumps in Botswana, Germany and Sweden. In total 701 partial 16S rRNA gene sequences revealed a divergent microbial community between the three sites and at different tailings depths. Proteobacteria and Firmicutes were overall the most abundant phyla in the clone libraries. Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospira occurred less frequently. The found microbial communities were completely different to microbial communities in tailings at

Low molecular weight carboxylic acids in oxidizing porphyry copper tailings.

PubMed

Dold, Bernhard; Blowes, David W; Dickhout, Ralph; Spangenberg, Jorge E; Pfeifer, Hans-Rudolf

2005-04-15

The distribution of low molecular weight carboxylic acids (LMWCA) was investigated in pore water profiles from two porphyry copper tailings impoundments in Chile (Piuquenes at La Andina and Cauquenes at El Teniente mine). The objectives of this study were (1) to determine the distribution of LMWCA, which are interpreted to be the metabolic byproducts of the autotroph microbial community in this low organic carbon system, and (2) to infer the potential role of these acids in cycling of Fe and other elements in the tailings impoundments. The speciation and mobility of iron, and potential for the release of H+ via hydrolysis of the ferric iron, are key factors in the formation of acid mine drainage in sulfidic mine wastes. In the low-pH oxidation zone of the Piuquenes tailings, Fe(III) is the dominant iron species and shows high mobility. LMWCA, which occur mainly between the oxidation front down to 300 cm below the tailings surface at both locations (e.g., max concentrations of 0.12 mmol/L formate, 0.17 mmol/L acetate, and 0.01 mmol/L pyruvate at Piuquenes and 0.14 mmol/L formate, 0.14 mmol/L acetate, and 0.006 mmol/L pyruvate at Cauquenes), are observed at the same location as high Fe concentrations (up to 71.2 mmol/L Fe(II) and 16.1 mmol/L Fe(III), respectively). In this zone, secondary Fe(III) hydroxides are depleted. Our data suggest that LMWCA may influence the mobility of iron in two ways. First, complexation of Fe(III), through formation of bidentate Fe(III)-LMWCA complexes (e.g., pyruvate, oxalate), may enhance the dissolution of Fe(III) (oxy)hydroxides or may prevent precipitation of Fe(III) (oxy)hydroxides. Soluble Fe(III) chelate complexes which may be mobilized downward and convert to Fe(II) by Fe(III) reducing bacteria. Second, monodentate LMWCA (e.g., acetate and formate) can be used by iron-reducing bacteria as electron donors (e.g., Acidophilum spp.), with ferric iron as the electron acceptor. These processes may, in part, explain the low abundances

Impact of the Motor and Tail Domains of Class III Myosins on Regulating the Formation and Elongation of Actin Protrusions*

PubMed Central

Quintero, Omar A.; Weck, Meredith L.; Unrath, William C.; Gallagher, James W.; Cui, Runjia; Kachar, Bechara; Tyska, Matthew J.; Yengo, Christopher M.

2016-01-01

Class III myosins (MYO3A and MYO3B) are proposed to function as transporters as well as length and ultrastructure regulators within stable actin-based protrusions such as stereocilia and calycal processes. MYO3A differs from MYO3B in that it contains an extended tail domain with an additional actin-binding motif. We examined how the properties of the motor and tail domains of human class III myosins impact their ability to enhance the formation and elongation of actin protrusions. Direct examination of the motor and enzymatic properties of human MYO3A and MYO3B revealed that MYO3A is a 2-fold faster motor with enhanced ATPase activity and actin affinity. A chimera in which the MYO3A tail was fused to the MYO3B motor demonstrated that motor activity correlates with formation and elongation of actin protrusions. We demonstrate that removal of individual exons (30–34) in the MYO3A tail does not prevent filopodia tip localization but abolishes the ability to enhance actin protrusion formation and elongation in COS7 cells. Interestingly, our results demonstrate that MYO3A slows filopodia dynamics and enhances filopodia lifetime in COS7 cells. We also demonstrate that MYO3A is more efficient than MYO3B at increasing formation and elongation of stable microvilli on the surface of cultured epithelial cells. We propose that the unique features of MYO3A, enhanced motor activity, and an extended tail with tail actin-binding motif, allow it to play an important role in stable actin protrusion length and ultrastructure maintenance. PMID:27582493

Crystal structures of the coil 2B fragment and the globular tail domain of human lamin B1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruan, Jianbin; Xu, Chao; Bian, Chuanbing

2012-07-18

We present here the crystal structures of human lamin B1 globular tail domain and coiled 2B domain, which adopt similar folds to Ig-like domain and coiled-coil domain of lamin A, respectively. Despite the overall similarity, we found an extra intermolecular disulfide bond in the lamin B1 coil 2B domain, which does not exist in lamin A/C. In addition, the structural analysis indicates that interactions at the lamin B1 homodimer interface are quite different from those of lamin A/C. Thus our research not only reveals the diversely formed homodimers among lamin family members, but also sheds light on understanding the importantmore » roles of lamin B1 in forming the nuclear lamina matrix.« less

TAIL1: an isthmin-like gene, containing type 1 thrombospondin-repeat and AMOP domain, mapped to ARVD1 critical region.

PubMed

Rossi, Valeria; Beffagna, Giorgia; Rampazzo, Alessandra; Bauce, Barbara; Danieli, Gian Antonio

2004-06-23

Isthmins represent a novel family of vertebrate secreted proteins containing one copy of the thrombospondin type 1 repeat (TSR), which in mammals is shared by several proteins with diverse biological functions, including cell adhesion, angiogenesis, and patterning of developing nervous system. We have determined the genomic organization of human TAIL1 (thrombospondin and AMOP containing isthmin-like 1), a novel isthmin-like gene encoding a protein that contains a TSR and a C-terminal AMOP domain (adhesion-associated domain in MUC4 and other proteins), characteristic of extracellular proteins involved in adhesion processes. TAIL1 gene encompasses more than 24.4 kb. Analysis of the DNA sequence surrounding the putative transcriptional start region revealed a TATA-less promoter located in a CpG island. Several consensus binding sites for the transcription factors Sp1 and MZF-1 were identified in this promoter region. In humans, TAIL1 gene is located on chromosome 14q24.3 within ARVD1 (arrhythmogenic right ventricular dysplasia/cardiomyopathy, type 1) critical region; preliminary evidence suggests that it is expressed in several tissues, showing multiple alternative splicing.

[Experimental study on acid mine drainage treatment using mine tailings of Xiangsi Valley, Tongling, China].

PubMed

Zhang, Nan; Chen, Tian-Hu; Zhou, Yue-Fei; Li, Shao-Jie; Jin, Jie; Wang, Yan-Ming

2012-04-01

Mine tailings in Xiangsi Valley, Tongling, China, is a typical skarn-type tailing with high contents of carbonates. This study designed dynamic leaching experiments to investigate the efficiency of this tailing under the acid mine drainage treatment. During 80 d trial period, the physical and chemical properties of influents were fixed and the effluents were monitored. After the trial, the speciation of Fe, Cu and Zn in solid was analyzed. The results showed that during the trial period, pH value maintained above 7.5. Moreover, the concentrations of Cu, Zn, Fe ions in effluents kept below 0.1, 0.4 and 1 mg x L(-1), respectively. In addition, the permeability coefficient of experimental column kept decreasing during the experimental period (from 0.23 cm x s(-1) to 0.10 cm x s(-1)). Five-step sequential extraction method was employed to study the distribution of elements at different depths. The results showed that Cu2+, Zn2+ were removed mainly through sorption and precipitation. This study indicates that Tongling skarn mine tailings have strong acid neutralization as well as heavy metal binding capacities. Therefore, the authors suggest that this mine tailing, which used to be waste, has a potential in AMD control and treatment.

Nutritional restriction and acid-base balance in white-tailed deer

USGS Publications Warehouse

DelGiudice, G.D.; Mech, L.D.; Seal, U.S.

1994-01-01

We examined the effect of progressive nutritional restriction on acid-base balance in seven captive, adult white-tailed deer (Odocoileus virginianus) from 4 February to 5 May 1988 in north central Minnesota (USA). Metabolic acidosis was indicated by low mean blood pH (7.25 to 7.33) in deer throughout the study. Mean urinary pH values declined (P = 0.020) from a mean (+SE) baseline of 8.3 +0.1 to 6.7 + 0.3 as restriction progressed. Acidemia and aciduria were associated with significant variations in mean blood CO2 (P = 0.006) and pO2 (P = 0.032), serum potassium (P = 0.004) concentrations, and with a significant (P = 0.104) handling date times group interaction in urinary potassium:creatinine values. Mean bicarbonate:carbonic acid ratios were consistently below 20:1 during nutritional restriction. Mean packed cell volume increased (P = 0.019) and serum total protein decreased (P = 0.001); thus there was evidence for progressive dehydration and net protein catabolism, respectively. Blood pCO2, serum sodium, and urinary sodium:creatinine were stable throughout the study. We propose that acidosis and aciduria are metabolic complications associated with nutritional restriction of white-tailed deer.

Acid production potentials of massive sulfide minerals and lead-zinc mine tailings: a medium-term study.

PubMed

Çelebi, Emin Ender; Öncel, Mehmet Salim; Kobya, Mehmet

2018-01-01

Weathering of sulfide minerals is a principal source of acid generation. To determine acid-forming potentials of sulfide-bearing materials, two basic approaches named static and kinetic tests are available. Static tests are short-term, and easily undertaken within a few days and in a laboratory. In contrast, kinetic tests are long-term procedures and mostly carried out on site. In this study, experiments were conducted over a medium-term period of 2 months, not as short as static tests and also not as long as kinetic tests. As a result, pH and electrical conductivity oscillations as a function of time, acid-forming potentials and elemental contents of synthetically prepared rainwater leachates of massive sulfides and sulfide-bearing lead-zinc tailings from abandoned and currently used deposition areas have been determined. Although the lowest final pH of 2.70 was obtained in massive pyrite leachate, massive chalcopyrite leachate showed the highest titrable acidity of 1.764 g H 2 SO 4 /L. On the other hand, a composite of currently deposited mine tailings showed no acidic characteristic with a final pH of 7.77. The composite abandoned mine tailing leachate had a final pH of 6.70, close to the final pH of massive galena and sphalerite leachates, and produced a slight titrable acidity of 0.130 g H 2 SO 4 /L.

Metabolomics method to comprehensively analyze amino acids in different domains.

PubMed

Gu, Haiwei; Du, Jianhai; Carnevale Neto, Fausto; Carroll, Patrick A; Turner, Sally J; Chiorean, E Gabriela; Eisenman, Robert N; Raftery, Daniel

2015-04-21

Amino acids play essential roles in both metabolism and the proteome. Many studies have profiled free amino acids (FAAs) or proteins; however, few have connected the measurement of FAA with individual amino acids in the proteome. In this study, we developed a metabolomics method to comprehensively analyze amino acids in different domains, using two examples of different sample types and disease models. We first examined the responses of FAAs and insoluble-proteome amino acids (IPAAs) to the Myc oncogene in Tet21N human neuroblastoma cells. The metabolic and proteomic amino acid profiles were quite different, even under the same Myc condition, and their combination provided a better understanding of the biological status. In addition, amino acids were measured in 3 domains (FAAs, free and soluble-proteome amino acids (FSPAAs), and IPAAs) to study changes in serum amino acid profiles related to colon cancer. A penalized logistic regression model based on the amino acids from the three domains had better sensitivity and specificity than that from each individual domain. To the best of our knowledge, this is the first study to perform a combined analysis of amino acids in different domains, and indicates the useful biological information available from a metabolomics analysis of the protein pellet. This study lays the foundation for further quantitative tracking of the distribution of amino acids in different domains, with opportunities for better diagnosis and mechanistic studies of various diseases.

Regulation of lipid droplet and membrane biogenesis by the acidic tail of the phosphatidate phosphatase Pah1p

PubMed Central

Karanasios, Eleftherios; Barbosa, Antonio Daniel; Sembongi, Hiroshi; Mari, Muriel; Han, Gil-Soo; Reggiori, Fulvio; Carman, George M.; Siniossoglou, Symeon

2013-01-01

Lipins are evolutionarily conserved phosphatidate phosphatases that perform key functions in phospholipid, triglyceride, and membrane biogenesis. Translocation of lipins on membranes requires their dephosphorylation by the Nem1p-Spo7p transmembrane phosphatase complex through a poorly understood mechanism. Here we identify the carboxy-terminal acidic tail of the yeast lipin Pah1p as an important regulator of this step. Deletion or mutations of the tail disrupt binding of Pah1p to the Nem1p-Spo7p complex and Pah1p membrane translocation. Overexpression of Nem1p-Spo7p drives the recruitment of Pah1p in the vicinity of lipid droplets in an acidic tail–dependent manner and induces lipid droplet biogenesis. Genetic analysis shows that the acidic tail is essential for the Nem1p-Spo7p–dependent activation of Pah1p but not for the function of Pah1p itself once it is dephosphorylated. Loss of the tail disrupts nuclear structure, INO1 gene expression, and triglyceride synthesis. Similar acidic sequences are present in the carboxy-terminal ends of all yeast lipin orthologues. We propose that acidic tail–dependent binding and dephosphorylation of Pah1p by the Nem1p-Spo7p complex is an important determinant of its function in lipid and membrane biogenesis. PMID:23657815

Determination of acid forming potential of massive sulfide minerals and the tailings situated in lead/zinc mining district of Balya (NW Turkey)

NASA Astrophysics Data System (ADS)

Çelebi, E. Ender; Öncel, M. Salim

2016-12-01

Weathering of sulfide minerals is a major source of acid production in nature and especially in mining territories. Pyrite is not the only principal mineral that generates acid drainage: other sulfide minerals (sphalerite, galena, chalcopyrite, etc.) may also be responsible for acid production. In addition to massive sulfide minerals, sulfide-bearing mine tailings may also produce acid drainage due to oxidation and hydrolysis reactions in waste dumps. The lead/zinc (Pb/Zn) mining region in Balya and Balıkesir, in Turkey, has operated mines intensively since the 1860s; so that characterization of the sulfide minerals and tailings situated and formed around the mining site is of great importance to secure a sustainable environment. For this purpose, acid production and neutralization potentials of massive sulfide ores of the region, and in the Pb/Zn process facility mine tailings from ten different points of tailings dam, have been determined by applied conventional Acid-Base Accounting (ABA) and Net Acid Generation (NAG) static tests after chemical and mineralogical analysis. The NAG pH and net acid production potential (NAPP) values were compared on a chart in order to classify the samples as either acid generating or non-acid generating. According to the comparisons, the sulfide minerals were classified as potentially acid forming (PAF). Massive pyrite had the highest NAPP and NAG pH value of 1966.6 kg H2SO4/ton and 1.91, respectively and the galena had the lowest NAPP value of 558.9 kg H2SO4/ton. However, the sphalerite NAG leachate pH value of 4.30 was the highest in sulfide minerals so that the sphalerite plotted near the uncertainty reference border in the PAF zone. In the mine tailings, NAPP values of 105.9 kg H2SO4/ton on average and the NAG pH values of over 7.5 were determined. In addition to these tests, water leaching (agitation test) was carried out on tailings in order to generate more information. The tailings did not generate acidic leachates as

Spatial and Temporal Analysis of the Microbial Community in the Tailings of a Pb-Zn Mine Generating Acidic Drainage ▿ †

PubMed Central

Huang, Li-Nan; Zhou, Wen-Hua; Hallberg, Kevin B.; Wan, Cai-Yun; Li, Jie; Shu, Wen-Sheng

2011-01-01

Analysis of spatial and temporal variations in the microbial community in the abandoned tailings impoundment of a Pb-Zn mine revealed distinct microbial populations associated with the different oxidation stages of the tailings. Although Acidithiobacillus ferrooxidans and Leptospirillum spp. were consistently present in the acidic tailings, acidophilic archaea, mostly Ferroplasma acidiphilum, were predominant in the oxidized zones and the oxidation front, indicating their importance to generation of acid mine drainage. PMID:21705549

Response of key soil parameters during compost-assisted phytostabilization in extremely acidic tailings: effect of plant species.

PubMed

Solís-Dominguez, Fernando A; White, Scott A; Hutter, Travis Borrillo; Amistadi, Mary Kay; Root, Robert A; Chorover, Jon; Maier, Raina M

2012-01-17

Phytostabilization of mine tailings acts to mitigate both eolian dispersion and water erosion events which can disseminate barren tailings over large distances. This technology uses plants to establish a vegetative cover to permanently immobilize contaminants in the rooting zone, often requiring addition of an amendment to assist plant growth. Here we report the results of a greenhouse study that evaluated the ability of six native plant species to grow in extremely acidic (pH ∼ 2.5) metalliferous (As, Pb, Zn: 2000-3000 mg kg(-1)) mine tailings from Iron King Mine Humboldt Smelter Superfund site when amended with a range of compost concentrations. Results revealed that three of the six plant species tested (buffalo grass, mesquite, and catclaw acacia) are good candidates for phytostabilization at an optimum level of 15% compost (w/w) amendment showing good growth and minimal shoot accumulation of metal(loid)s. A fourth candidate, quailbush, also met all criteria except for exceeding the domestic animal toxicity limit for shoot accumulation of zinc. A key finding of this study was that the plant species that grew most successfully on these tailings significantly influenced key tailings parameters; direct correlations between plant biomass and both increased tailings pH and neutrophilic heterotrophic bacterial counts were observed. We also observed decreased iron oxidizer counts and decreased bioavailability of metal(loid)s mainly as a result of compost amendment. Taken together, these results suggest that the phytostabilization process reduced tailings toxicity as well as the potential for metal(loid) mobilization. This study provides practical information on plant and tailings characteristics that is critically needed for successful implementation of assisted phytostabilization on acidic, metalliferous mine tailings sites.

Response of Key Soil Parameters During Compost-Assisted Phytostabilization in Extremely Acidic Tailings: Effect of Plant Species

PubMed Central

Solís-Dominguez, Fernando A.; White, Scott A.; Hutter, Travis Borrillo; Amistadi, Mary Kay; Root, Robert A.; Chorover, Jon; Maier, Raina M.

2012-01-01

Phytostabilization of mine tailings acts to mitigate both eolian dispersion and water erosion events which can disseminate barren tailings over large distances. This technology uses plants to establish a vegetative cover to permanently immobilize contaminants in the rooting zone, often requiring addition of an amendment to assist plant growth. Here we report the results of a greenhouse study that evaluated the ability of six native plant species to grow in extremely acidic (pH ~ 2.5) metalliferous (As, Pb, Zn: 2000–3000 mg kg−1) mine tailings from Iron King Mine Humboldt Smelter Superfund site when amended with a range of compost concentrations. Results revealed that three of the six plant species tested (buffalo grass, mesquite, and catclaw acacia) are good candidates for phytostabilization at an optimum level of 15% compost (w/w) amendment showing good growth and minimal shoot accumulation of metal(loid)s. A fourth candidate, quailbush, also met all criteria except for exceeding the domestic animal toxicity limit for shoot accumulation of zinc. A key finding of this study was that the plant species that grew most successfully on these tailings significantly influenced key tailings parameters; direct correlations between plant biomass and both increased tailings pH and neutrophilic heterotrophic bacterial counts were observed. We also observed decreased iron oxidizer counts and decreased bioavailability of metal(loid)s mainly as a result of compost amendment. Taken together, these results suggest that the phytostabilization process reduced tailings toxicity as well as the potential for metal(loid) mobilization. This study provides practical information on plant and tailings characteristics that is critically needed for successful implementation of assisted phytostabilization on acidic, metalliferous mine tailings sites. PMID:22191663

Metabolism of branched-chain amino acids in leg muscles from tail-cast suspended intact and adrenalectomized rats

NASA Technical Reports Server (NTRS)

Jaspers, Stephen R.; Henriksen, Erik; Jacob, Stephan; Tischler, Marc E.

1989-01-01

The effects of muscle unloading, adrenalectomy, and cortisol treatment on the metabolism of branched-chain amino acids in the soleus and extensor digitorum longus of tail-cast suspended rats were investigated using C-14-labeled lucine, isoleucine, and valine in incubation studies. It was found that, compared to not suspended controls, the degradation of branched-chain amino acids in hind limb muscles was accelerated in tail-cast suspended rats. Adrenalectomy was found to abolish the aminotransferase flux and to diminish the dehydrogenase flux in the soleus. The data also suggest that cortisol treatment increases the rate of metabolism of branched-chain amino acids at the dehydrogenase step.

Efficient inhibition of heavy metal release from mine tailings against acid rain exposure by triethylenetetramine intercalated montmorillonite (TETA-Mt).

PubMed

Gong, Beini; Wu, Pingxiao; Huang, Zhujian; Li, Yuanyuan; Yang, Shanshan; Dang, Zhi; Ruan, Bo; Kang, Chunxi

2016-11-15

The potential application of triethylenetetramine intercalated montmorillonite (TETA-Mt) in mine tailings treatment and AMD (acid mine drainage) remediation was investigated with batch experiments. The structural and morphological characteristics of TETA-Mt were analyzed with XRD, FTIR, DTG-TG and SEM. The inhibition efficiencies of TETA-Mt against heavy metal release from mine tailings when exposed to acid rain leaching was examined and compared with that of triethylenetetramine (TETA) and Mt. Results showed that the overall inhibition by TETA-Mt surpassed that by TETA or Mt for various heavy metal ions over an acid rain pH range of 3-5.6 and a temperature range of 25-40°C. When mine tailings were exposed to acid rain of pH 4.8 (the average rain pH of the mining site where the mine tailings were from), TETA-Mt achieved an inhibition efficiency of over 90% for Cu(2+), Zn(2+), Cd(2+) and Mn(2+) release, and 70% for Pb(2+) at 25°C. It was shown that TETA-Mt has a strong buffering capacity. Moreover, TETA-Mt was able to adsorb heavy metal ions and the adsorption process was fast, suggesting that coordination was mainly responsible. These results showed the potential of TETA-Mt in AMD mitigation, especially in acid rain affected mining area. Copyright © 2016 Elsevier B.V. All rights reserved.

Pollution in acid mine drainage from mine tailings in Svalbard Norwegian Arctic

NASA Astrophysics Data System (ADS)

Holm, E. B.; Brandvik, P. J.; Steinnes, E.

2003-05-01

Throughout the summer season of 2000 samples of acid mine drainage (AMD) were collected from areas below tailing deposits from the coal mining in Svalbard, Norwegian Arctic. The water was analysed for pH, oxygen, conductivity, 9 sulfate and various metals. Oxygen, pH and conductivity were measured by standard electrodes, sulphate was determined gravimetrically and metals were determined by flame/graphite furnace AAS. The AMD was found to contain heavy metals and sulphate in high concentrations, causing damage to the local tundra vegetation. Large spatial variation however was observed in pH (2.5-9.5) as well as in metal concentrations in the AMD, indicating strongly inhomogeneous distribution of sulphide minerais in the tailing deposits.

Structural and functional properties of the N transcriptional activation domain of thyroid transcription factor-1: similarities with the acidic activation domains.

PubMed Central

Tell, G; Perrone, L; Fabbro, D; Pellizzari, L; Pucillo, C; De Felice, M; Acquaviva, R; Formisano, S; Damante, G

1998-01-01

The thyroid transcription factor 1 (TTF-1) is a tissue-specific transcription factor involved in the development of thyroid and lung. TTF-1 contains two transcriptional activation domains (N and C domain). The primary amino acid sequence of the N domain does not show any typical characteristic of known transcriptional activation domains. In aqueous solution the N domain exists in a random-coil conformation. The increase of the milieu hydrophobicity, by the addition of trifluoroethanol, induces a considerable gain of alpha-helical structure. Acidic transcriptional activation domains are largely unstructured in solution, but, under hydrophobic conditions, folding into alpha-helices or beta-strands can be induced. Therefore our data indicate that the inducibility of alpha-helix by hydrophobic conditions is a property not restricted to acidic domains. Co-transfections experiments indicate that the acidic domain of herpes simplex virus protein VP16 (VP16) and the TTF-1 N domain are interchangeable and that a chimaeric protein, which combines VP16 linked to the DNA-binding domain of TTF-1, undergoes the same regulatory constraints that operate for the wild-type TTF-1. In addition, we demonstrate that the TTF-1 N domain possesses two typical properties of acidic activation domains: TBP (TATA-binding protein) binding and ability to activate transcription in yeast. Accordingly, the TTF-1 N domain is able to squelch the activity of the p65 acidic domain. Altogether, these structural and functional data suggest that a non-acidic transcriptional activation domain (TTF-1 N domain) activates transcription by using molecular mechanisms similar to those used by acidic domains. TTF-1 N domain and acidic domains define a family of proteins whose common property is to activate transcription through the use of mechanisms largely conserved during evolutionary development. PMID:9425125

Effect of Interferon, Polyacrylic Acid, and Polymethacrylic Acid on Tail Lesions in Mice Infected with Vaccinia Virus

PubMed Central

De Clercq, E.; De Somer, P.

1968-01-01

Intravenous inoculation of mice with vaccinia virus produced characteristic lesions of the tail surface which were suppressed by intraperitoneal administration of interferon and polyacrylic acid (PAA). Polymethacrylic acid (PMAA) stimulated the formation of vaccinia virus lesions. For full activity, both interferon and PAA must be given prior to infection. PAA was still significantly effective at small dose levels (3 mg/kg) and achieved protection for at least 4 weeks. Protection increased with increasing molecular weight of the polymer. The mode of action of PAA is discussed. PMID:5676405

Investigation of the possibility of copper recovery from the flotation tailings by acid leaching.

PubMed

Antonijević, M M; Dimitrijević, M D; Stevanović, Z O; Serbula, S M; Bogdanovic, G D

2008-10-01

The flotation tailings pond of the Bor Copper Mine poses a great ecological problem not only for the town of Bor but also for the surrounding soils and watercourses. Since the old flotation tailings contain about 0.2% of copper on the average, we investigated their leaching with sulphuric acid in the absence and presence of an oxidant. The aim was to determine the leaching kinetics of copper and iron as affected by various factors such as: the pH value of the leach solution, stirring speed, pulp density, particle size, concentration of ferric ions, temperature and time for leaching. The average copper and iron recovery obtained was from 60% to 70% and from 2% to 3%, respectively. These results indicate that the old flotation tailings pond represents an important source of secondary raw material for the extraction of copper and that it should be valorized rather than land reclamation. At the end of the paper, a mechanism of dissolution of copper and iron minerals from the tailings was described.

Mediator Recruitment to Heat Shock Genes Requires Dual Hsf1 Activation Domains and Mediator Tail Subunits Med15 and Med16*

PubMed Central

Kim, Sunyoung; Gross, David S.

2013-01-01

The evolutionarily conserved Mediator complex is central to the regulation of gene transcription in eukaryotes because it serves as a physical and functional interface between upstream regulators and the Pol II transcriptional machinery. Nonetheless, its role appears to be context-dependent, and the detailed mechanism by which it governs the expression of most genes remains unknown. Here we investigate Mediator involvement in HSP (heat shock protein) gene regulation in the yeast Saccharomyces cerevisiae. We find that in response to thermal upshift, subunits representative of each of the four Mediator modules (Head, Middle, Tail, and Kinase) are rapidly, robustly, and selectively recruited to the promoter regions of HSP genes. Their residence is transient, returning to near-background levels within 90 min. Hsf1 (heat shock factor 1) plays a central role in recruiting Mediator, as indicated by the fact that truncation of either its N- or C-terminal activation domain significantly reduces Mediator occupancy, whereas removal of both activation domains abolishes it. Likewise, ablation of either of two Mediator Tail subunits, Med15 or Med16, reduces Mediator recruitment to HSP promoters, whereas deletion of both abolishes it. Accompanying the loss of Mediator, recruitment of RNA polymerase II is substantially diminished. Interestingly, Mediator antagonizes Hsf1 occupancy of non-induced promoters yet facilitates enhanced Hsf1 association with activated ones. Collectively, our observations indicate that Hsf1, via its dual activation domains, recruits holo-Mediator to HSP promoters in response to acute heat stress through cooperative physical and/or functional interactions with the Tail module. PMID:23447536

Efficient degradation of Acid Orange 7 in aqueous solution by iron ore tailing Fenton-like process.

PubMed

Zheng, Jianming; Gao, Zhanqi; He, Huan; Yang, Shaogui; Sun, Cheng

2016-05-01

An effective method based on iron ore tailing Fenton-like process was studied for removing an azo dye, Acid Orange 7 (AO7) in aqueous solution. Five tailings were characterized by X-ray fluorescence spectroscope (XFS), Brunner-Emmet-Teller (BET) measurement, and Scanning Electron Microscope (SEM). The result of XFS showed that Fe, Si and Ca were the most abundant elements and some toxic heavy metals were also present in the studied tailings. The result of BET analysis indicated that the studied tailings had very low surface areas (0.64-5.68 m(2) g(-1)). The degradation efficiencies of AO7 were positively correlated with the content of iron oxide and cupric oxide, and not related with the BET surface area of the tailings. The co-existing metal elements, particularly Cu, might accelerate the heterogeneous Fenton-like reaction. The effects of other parameters on heterogeneous Fenton-like degradation of AO7 by a converter slag iron tailing (tailing E) which contains highest iron oxide were also investigated. The tailing could be reused 10 times without significant decrease of the catalytic capacity. Very low amount of iron species and almost undetectable toxic elements were leached in the catalytic degradation of AO7 by the tailing E. The reaction products were identified by gas chromatography-mass spectrometry and a possible pathway of AO7 degradation was proposed. This study not only provides an effective method for removing azo dyes in polluted water by employing waste tailings as Fenton-like catalysts, but also uses waste tailings as the secondary resource. Copyright © 2016 Elsevier Ltd. All rights reserved.

Enriching acid rock drainage related microbial communities from surface-deposited oil sands tailings.

PubMed

Dean, Courtney; Xiao, Yeyuan; Roberts, Deborah J

2016-10-01

Little is known about the microbial communities native to surface-deposited pyritic oil sands tailings, an environment where acid rock drainage (ARD) could occur. The goal of this study was to enrich sulfur-oxidizing organisms from these tailings and determine whether different populations exist at pH levels 7, 4.5, and 2.5. Using growth-based methods provides model organisms for use in the future to predict potential activities and limitations of these organisms and to develop possible control methods. Thiosulfate-fed enrichment cultures were monitored for approximately 1 year. The results showed that the enrichments at pH 4.5 and 7 were established quicker than at pH 2.5. Different microbial community structures were found among the 3 pH environments. The sulfur-oxidizing microorganisms identified were most closely related to Halothiobacillus neapolitanus, Achromobacter spp., and Curtobacterium spp. While microorganisms related to Chitinophagaceae and Acidocella spp. were identified as the only possible iron-oxidizing and -reducing microbes. These results contribute to the general knowledge of the relatively understudied microbial communities that exist in pyritic oil sands tailings and indicate these communities may have a potential role in ARD generation, which may have implications for future tailings management.

Identification of Carbohydrate-Binding Domains in the Attachment Proteins of Type 1 and Type 3 Reoviruses

PubMed Central

Chappell, James D.; Duong, Joy L.; Wright, Benjamin W.; Dermody, Terence S.

2000-01-01

The reovirus attachment protein, ς1, is responsible for strain-specific patterns of viral tropism in the murine central nervous system and receptor binding on cultured cells. The ς1 protein consists of a fibrous tail domain proximal to the virion surface and a virion-distal globular head domain. To better understand mechanisms of reovirus attachment to cells, we conducted studies to identify the region of ς1 that binds cell surface carbohydrate. Chimeric and truncated ς1 proteins derived from prototype reovirus strains type 1 Lang (T1L) and type 3 Dearing (T3D) were expressed in insect cells by using a baculovirus vector. Assessment of expressed protein susceptibility to proteolytic cleavage, binding to anti-ς1 antibodies, and oligomerization indicates that the chimeric and truncated ς1 proteins are properly folded. To assess carbohydrate binding, recombinant ς1 proteins were tested for the capacity to agglutinate mammalian erythrocytes and to bind sialic acid presented on glycophorin, the cell surface molecule bound by type 3 reovirus on human erythrocytes. Using a panel of two wild-type and ten chimeric and truncated ς1 proteins, the sialic acid-binding domain of type 3 ς1 was mapped to a region of sequence proposed to form the more amino terminal of two predicted β-sheet structures in the tail. This unit corresponds to morphologic region T(iii) observed in computer-processed electron micrographs of ς1 protein purified from virions. In contrast, the homologous region of T1L ς1 sequence was not implicated in carbohydrate binding; rather, sequences in the distal portion of the tail known as the neck were required. Results of these studies demonstrate that a functional receptor-binding domain, which uses sialic acid as its ligand, is contained within morphologic region T(iii) of the type 3 ς1 tail. Furthermore, our findings indicate that T1L and T3D ς1 proteins contain different arrangements of receptor-binding domains. PMID:10954547

Identification of carbohydrate-binding domains in the attachment proteins of type 1 and type 3 reoviruses.

PubMed

Chappell, J D; Duong, J L; Wright, B W; Dermody, T S

2000-09-01

The reovirus attachment protein, sigma1, is responsible for strain-specific patterns of viral tropism in the murine central nervous system and receptor binding on cultured cells. The sigma1 protein consists of a fibrous tail domain proximal to the virion surface and a virion-distal globular head domain. To better understand mechanisms of reovirus attachment to cells, we conducted studies to identify the region of sigma1 that binds cell surface carbohydrate. Chimeric and truncated sigma1 proteins derived from prototype reovirus strains type 1 Lang (T1L) and type 3 Dearing (T3D) were expressed in insect cells by using a baculovirus vector. Assessment of expressed protein susceptibility to proteolytic cleavage, binding to anti-sigma1 antibodies, and oligomerization indicates that the chimeric and truncated sigma1 proteins are properly folded. To assess carbohydrate binding, recombinant sigma1 proteins were tested for the capacity to agglutinate mammalian erythrocytes and to bind sialic acid presented on glycophorin, the cell surface molecule bound by type 3 reovirus on human erythrocytes. Using a panel of two wild-type and ten chimeric and truncated sigma1 proteins, the sialic acid-binding domain of type 3 sigma1 was mapped to a region of sequence proposed to form the more amino terminal of two predicted beta-sheet structures in the tail. This unit corresponds to morphologic region T(iii) observed in computer-processed electron micrographs of sigma1 protein purified from virions. In contrast, the homologous region of T1L sigma1 sequence was not implicated in carbohydrate binding; rather, sequences in the distal portion of the tail known as the neck were required. Results of these studies demonstrate that a functional receptor-binding domain, which uses sialic acid as its ligand, is contained within morphologic region T(iii) of the type 3 sigma1 tail. Furthermore, our findings indicate that T1L and T3D sigma1 proteins contain different arrangements of receptor

Requirement for the E1 Helicase C-Terminal Domain in Papillomavirus DNA Replication In Vivo.

PubMed

Bergvall, Monika; Gagnon, David; Titolo, Steve; Lehoux, Michaël; D'Abramo, Claudia M; Melendy, Thomas; Archambault, Jacques

2016-01-06

The papillomavirus (PV) E1 helicase contains a conserved C-terminal domain (CTD), located next to its ATP-binding site, whose function in vivo is still poorly understood. The CTD is comprised of an alpha helix followed by an acidic region (AR) and a C-terminal extension termed the C-tail. Recent biochemical studies on bovine papillomavirus 1 (BPV1) E1 showed that the AR and C-tail regulate the oligomerization of the protein into a double hexamer at the origin. In this study, we assessed the importance of the CTD of human papillomavirus 11 (HPV11) E1 in vivo, using a cell-based DNA replication assay. Our results indicate that combined deletion of the AR and C-tail drastically reduces DNA replication, by 85%, and that further truncation into the alpha-helical region compromises the structural integrity of the E1 helicase domain and its interaction with E2. Surprisingly, removal of the C-tail alone or mutation of highly conserved residues within the domain still allows significant levels of DNA replication (55%). This is in contrast to the absolute requirement for the C-tail reported for BPV1 E1 in vitro and confirmed here in vivo. Characterization of chimeric proteins in which the AR and C-tail from HPV11 E1 were replaced by those of BPV1 indicated that while the function of the AR is transferable, that of the C-tail is not. Collectively, these findings define the contribution of the three CTD subdomains to the DNA replication activity of E1 in vivo and suggest that the function of the C-tail has evolved in a PV type-specific manner. While much is known about hexameric DNA helicases from superfamily 3, the papillomavirus E1 helicase contains a unique C-terminal domain (CTD) adjacent to its ATP-binding site. We show here that this CTD is important for the DNA replication activity of HPV11 E1 in vivo and that it can be divided into three functional subdomains that roughly correspond to the three conserved regions of the CTD: an alpha helix, needed for the structural

Requirement for the E1 Helicase C-Terminal Domain in Papillomavirus DNA Replication In Vivo

PubMed Central

Bergvall, Monika; Gagnon, David; Titolo, Steve; Lehoux, Michaël; D'Abramo, Claudia M.

2016-01-01

ABSTRACT The papillomavirus (PV) E1 helicase contains a conserved C-terminal domain (CTD), located next to its ATP-binding site, whose function in vivo is still poorly understood. The CTD is comprised of an alpha helix followed by an acidic region (AR) and a C-terminal extension termed the C-tail. Recent biochemical studies on bovine papillomavirus 1 (BPV1) E1 showed that the AR and C-tail regulate the oligomerization of the protein into a double hexamer at the origin. In this study, we assessed the importance of the CTD of human papillomavirus 11 (HPV11) E1 in vivo, using a cell-based DNA replication assay. Our results indicate that combined deletion of the AR and C-tail drastically reduces DNA replication, by 85%, and that further truncation into the alpha-helical region compromises the structural integrity of the E1 helicase domain and its interaction with E2. Surprisingly, removal of the C-tail alone or mutation of highly conserved residues within the domain still allows significant levels of DNA replication (55%). This is in contrast to the absolute requirement for the C-tail reported for BPV1 E1 in vitro and confirmed here in vivo. Characterization of chimeric proteins in which the AR and C-tail from HPV11 E1 were replaced by those of BPV1 indicated that while the function of the AR is transferable, that of the C-tail is not. Collectively, these findings define the contribution of the three CTD subdomains to the DNA replication activity of E1 in vivo and suggest that the function of the C-tail has evolved in a PV type-specific manner. IMPORTANCE While much is known about hexameric DNA helicases from superfamily 3, the papillomavirus E1 helicase contains a unique C-terminal domain (CTD) adjacent to its ATP-binding site. We show here that this CTD is important for the DNA replication activity of HPV11 E1 in vivo and that it can be divided into three functional subdomains that roughly correspond to the three conserved regions of the CTD: an alpha helix, needed

Evaluation of pyritic mine tailings as a plant growth substrate.

PubMed

Roseby, Stuart J; Kopittke, Peter M; Mulligan, David R; Menzies, Neal W

2017-10-01

At the Kidston gold mine, Australia, the direct establishment of vegetation on tailings was considered as an alternative to the use of a waste rock cover. The tailings acid/base account was used to predict plant growth limitation by acidity, and thus methods capable of identifying tailings that would acidify to pH 4.5 or lower were sought. Total S was found to be poorly correlated with acid-generating sulfide, and total C was poorly correlated with acid-neutralizing carbonate, precluding the use of readily determined total S and C as predictors of net acid generation. Therefore, the selected approach used assessment of sulfide content as a predictor of acid generation, and carbonate content as a measure of the acid-neutralizing capacity available at pH 5 and above. Using this approach, the majority of tailings (67%) were found to be non-acid generating. However, areas of potentially acid-generating tailings were randomly distributed across the dam, and could only be located by intensive sampling. The limitations imposed by the large sample numbers, and costly analysis of sulfide and carbonate, make it impractical to identify and ameliorate acid-generating areas prior to vegetation establishment. However, as only a small proportion of the tailings will acidify, a strategy of re-treating acid areas following oxidation is suggested. The findings of the present study will assist in the selection of appropriate methods for the prediction of net acid generation, particularly where more conservative measurements are required to allow vegetation to be established directly in tailings. Copyright © 2017 Elsevier Ltd. All rights reserved.

The neurofilament middle molecular mass subunit carboxyl-terminal tail domains is essential for the radial growth and cytoskeletal architecture of axons but not for regulating neurofilament transport rate

PubMed Central

Rao, Mala V.; Campbell, Jabbar; Yuan, Aidong; Kumar, Asok; Gotow, Takahiro; Uchiyama, Yasuo; Nixon, Ralph A.

2003-01-01

The phosphorylated carboxyl-terminal “tail” domains of the neurofilament (NF) subunits, NF heavy (NF-H) and NF medium (NF-M) subunits, have been proposed to regulate axon radial growth, neurofilament spacing, and neurofilament transport rate, but direct in vivo evidence is lacking. Because deletion of the tail domain of NF-H did not alter these axonal properties (Rao, M.V., M.L. Garcia, Y. Miyazaki, T. Gotow, A. Yuan, S. Mattina, C.M. Ward, N.S. Calcutt, Y. Uchiyama, R.A. Nixon, and D.W. Cleveland. 2002. J. Cell Biol. 158:681–693), we investigated possible functions of the NF-M tail domain by constructing NF-M tail–deleted (NF-MtailΔ) mutant mice using an embryonic stem cell–mediated “gene knockin” approach that preserves normal ratios of the three neurofilament subunits. Mutant NF-MtailΔ mice exhibited severely inhibited radial growth of both motor and sensory axons. Caliber reduction was accompanied by reduced spacing between neurofilaments and loss of long cross-bridges with no change in neurofilament protein content. These observations define distinctive functions of the NF-M tail in regulating axon caliber by modulating the organization of the neurofilament network within axons. Surprisingly, the average rate of axonal transport of neurofilaments was unaltered despite these substantial effects on axon morphology. These results demonstrate that NF-M tail–mediated interactions of neurofilaments, independent of NF transport rate, are critical determinants of the size and cytoskeletal architecture of axons, and are mediated, in part, by the highly phosphorylated tail domain of NF-M. PMID:14662746

Regulation of receptor-type protein tyrosine phosphatases by their C-terminal tail domains.

PubMed

Barnea, Maayan; Olender, Tsviya; Bedford, Mark T; Elson, Ari

2016-10-15

Protein tyrosine phosphatases (PTPs) perform specific functions in vivo, despite being vastly outnumbered by their substrates. Because of this and due to the central roles PTPs play in regulating cellular function, PTP activity is regulated by a large variety of molecular mechanisms. We review evidence that indicates that the divergent C-terminal tail sequences (C-terminal domains, CTDs) of receptor-type PTPs (RPTPs) help regulate RPTP function by controlling intermolecular associations in a way that is itself subject to physiological regulation. We propose that the CTD of each RPTP defines an 'interaction code' that helps determine molecules it will interact with under various physiological conditions, thus helping to regulate and diversify PTP function. © 2016 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

The cytoplasmic tail of L-selectin interacts with the adaptor-protein complex AP-1 subunit μ1A via a novel basic binding motif

PubMed Central

Tikhonova, Irina G.; Ivetic, Aleksandar; Schu, Peter

2017-01-01

L-selectin regulates leukocyte adhesion and rolling along the endothelium. Proteins binding to the cytoplasmic tail of L-selectin regulate L-selectin functions. We used L-selectin cytoplasmic tail peptide pulldown assays combined with high sensitivity liquid chromatography/mass spectrometry to identify novel L-selectin tail-binding proteins. Incubation of the L-selectin tail with cell extracts from phorbol 12-myristate 13-acetate-stimulated Raw 264.7 macrophages resulted in the binding of μ1A of the clathrin-coated vesicle AP-1 complex. Furthermore, full-length GST-μ1A and the GST-μ1A C-terminal domain, but not the GST-μ1A N-terminal domain, bind to L-selectin tail peptide, and the intracellular pool of L-selectin colocalizes with AP-1 at the trans-Golgi network. We identified a novel basic protein motif consisting of a cluster of three dibasic residues (356RR357, 359KK360, and 362KK363) in the membrane-proximal domain of the L-selectin tail as well as a doublet of aspartic acid residues (369DD370) in the membrane-distal end of the L-selectin tail involved in μ1A binding. Stimulation of Raw 264.7 macrophages with PMA augmented the amount of μ1A associated with anti-L-selectin immunoprecipitates. However, full-length GST-μ1A did not bind to the phospho-L-selectin tail or phospho-mimetic S364D L-selectin tail. Accordingly, we propose that phosphorylation of μ1A is required for interaction with the L-selectin tail and that L-selectin tail phosphorylation may regulate this interaction in vivo. Molecular docking of the L-selectin tail to μ1A was used to identify the μ1A surface domain binding the L-selectin tail and to explain how phosphorylation of the L-selectin tail abrogates μ1A interaction. Our findings indicate that L-selectin is transported constitutively by the AP-1 complex, leading to the formation of a trans-Golgi network reserve pool and that phosphorylation of the L-selectin tail blocks AP-1-dependent retrograde transport of L-selectin. PMID

The cytoplasmic tail of L-selectin interacts with the adaptor-protein complex AP-1 subunit μ1A via a novel basic binding motif.

PubMed

Dib, Karim; Tikhonova, Irina G; Ivetic, Aleksandar; Schu, Peter

2017-04-21

L-selectin regulates leukocyte adhesion and rolling along the endothelium. Proteins binding to the cytoplasmic tail of L-selectin regulate L-selectin functions. We used L-selectin cytoplasmic tail peptide pulldown assays combined with high sensitivity liquid chromatography/mass spectrometry to identify novel L-selectin tail-binding proteins. Incubation of the L-selectin tail with cell extracts from phorbol 12-myristate 13-acetate-stimulated Raw 264.7 macrophages resulted in the binding of μ1A of the clathrin-coated vesicle AP-1 complex. Furthermore, full-length GST-μ1A and the GST-μ1A C-terminal domain, but not the GST-μ1A N-terminal domain, bind to L-selectin tail peptide, and the intracellular pool of L-selectin colocalizes with AP-1 at the trans -Golgi network. We identified a novel basic protein motif consisting of a cluster of three dibasic residues ( 356 RR 357 , 359 KK 360 , and 362 KK 363 ) in the membrane-proximal domain of the L-selectin tail as well as a doublet of aspartic acid residues ( 369 DD 370 ) in the membrane-distal end of the L-selectin tail involved in μ1A binding. Stimulation of Raw 264.7 macrophages with PMA augmented the amount of μ1A associated with anti-L-selectin immunoprecipitates. However, full-length GST-μ1A did not bind to the phospho-L-selectin tail or phospho-mimetic S364D L-selectin tail. Accordingly, we propose that phosphorylation of μ1A is required for interaction with the L-selectin tail and that L-selectin tail phosphorylation may regulate this interaction in vivo Molecular docking of the L-selectin tail to μ1A was used to identify the μ1A surface domain binding the L-selectin tail and to explain how phosphorylation of the L-selectin tail abrogates μ1A interaction. Our findings indicate that L-selectin is transported constitutively by the AP-1 complex, leading to the formation of a trans -Golgi network reserve pool and that phosphorylation of the L-selectin tail blocks AP-1-dependent retrograde transport of L

Inferring Selection on Amino Acid Preference in Protein Domains

PubMed Central

Durbin, Richard

2009-01-01

Models that explicitly account for the effect of selection on new mutations have been proposed to account for “codon bias” or the excess of “preferred” codons that results from selection for translational efficiency and/or accuracy. In principle, such models can be applied to any mutation that results in a preferred allele, but in most cases, the fitness effect of a specific mutation cannot be predicted. Here we show that it is possible to assign preferred and unpreferred states to amino acid changing mutations that occur in protein domains. We propose that mutations that lead to more common amino acids (at a given position in a domain) can be considered “preferred alleles” just as are synonymous mutations leading to codons for more abundant tRNAs. We use genome-scale polymorphism data to show that alleles for preferred amino acids in protein domains occur at higher frequencies in the population, as has been shown for preferred codons. We show that this effect is quantitative, such that there is a correlation between the shift in frequency of preferred alleles and the predicted fitness effect. As expected, we also observe a reduction in the numbers of polymorphisms and substitutions at more important positions in domains, consistent with stronger selection at those positions. We examine the derived allele frequency distribution and polymorphism to divergence ratios of preferred and unpreferred differences and find evidence for both negative and positive selections acting to maintain protein domains in the human population. Finally, we analyze a model for selection on amino acid preferences in protein domains and find that it is consistent with the quantitative effects that we observe. PMID:19095755

Role of the Acidic Tail of High Mobility Group Protein B1 (HMGB1) in Protein Stability and DNA Bending

PubMed Central

Belgrano, Fabricio S.; de Abreu da Silva, Isabel C.; Bastos de Oliveira, Francisco M.; Fantappié, Marcelo R.; Mohana-Borges, Ronaldo

2013-01-01

High mobility group box (HMGB) proteins are abundant nonhistone proteins found in all eukaryotic nuclei and are capable of binding/bending DNA. The human HMGB1 is composed of two binding motifs, known as Boxes A and B, are L-shaped alpha-helix structures, followed by a random-coil acidic tail that consists of 30 Asp and Glu residues. This work aimed at evaluating the role of the acidic tail of human HMGB1 in protein stability and DNA interactions. For this purpose, we cloned, expressed and purified HMGB1 and its tailless form, HMGB1ΔC, in E. coli strain. Tryptophan fluorescence spectroscopy and circular dichroism (CD) experiments clearly showed an increase in protein stability promoted by the acidic tail under different conditions, such as the presence of the chemical denaturant guanidine hydrochloride (Gdn.HCl), high temperature and low pH. Folding intermediates found at low pH for both proteins were denatured only in the presence of chemical denaturant, thus showing a relatively high stability. The acidic tail did not alter the DNA-binding properties of the protein, although it enhanced the DNA bending capability from 76° (HMGB1ΔC) to 91° (HMGB1), as measured using the fluorescence resonance energy transfer technique. A model of DNA bending in vivo was proposed, which might help to explain the interaction of HMGB1 with DNA and other proteins, i.e., histones, and the role of that protein in chromatin remodeling. PMID:24255708

Quantitative Microbial Community Analysis of Three Different Sulfidic Mine Tailing Dumps Generating Acid Mine Drainage▿

PubMed Central

Kock, Dagmar; Schippers, Axel

2008-01-01

The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 109 cells g−1 dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general. PMID:18586975

Quantitative microbial community analysis of three different sulfidic mine tailing dumps generating acid mine drainage.

PubMed

Kock, Dagmar; Schippers, Axel

2008-08-01

The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 10(9) cells g(-1) dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general.

PDZ Binding Domains, Structural Disorder and Phosphorylation: A Menage-a-trois Tailing Dcp2 mRNA Decapping Enzymes.

PubMed

Gunawardana, Dilantha

2016-01-01

Diverse cellular activities are mediated through the interaction of protein domains and their binding partners. One such protein domain widely distributed in the higher metazoan world is the PDZ domain, which facilitates abundant protein-protein interactions. The PDZ domain-PDZ binding domain interaction has been implicated in several pathologies including Alzheimer's disease, Parkinson's disease and Down syndrome. PDZ domains bind to C-terminal peptides/proteins which have either of the following combinations: S/T-X-hydrophobic-COOH for type I, hydrophobic-Xhydrophobic- COOH for type II, and D/E-X-hydrophobic-COOH for type III, although hydrophobicity in the termini form the key characteristic of the PDZ-binding domains. We identified and characterized a Dcp2 type mRNA decapping enzyme from Arabidopsis thaliana, a protein containing a putative PDZ-binding domain using mutagenesis and protein biochemistry. Now we are using bioinformatics to study the Cterminal end of mRNA decapping enzymes from complex metazoans with the aim of (1) identifying putative PDZ-binding domains (2) Correlating structural disorder with PDZ binding domains and (3) Demonstrating the presence of phosphorylation sites in C-terminal extremities of Dcp2 type mRNA decapping enzymes. It is proposed here that the trinity of PDZbinding domains, structural disorder and phosphorylation-susceptible sites are a feature of the Dcp2 family of decapping enzymes and perhaps is a wider trick in protein evolution where scaffolding/tethering is a requirement for localization and function. It is critical though laboratory-based supporting evidence is sought to back-up this bioinformatics exploration into tail regions of mRNA decapping enzymes.

Geochemical characterisation of seepage and drainage water quality from two sulphide mine tailings impoundments: Acid mine drainage versus neutral mine drainage

USGS Publications Warehouse

Heikkinen, P.M.; Raisanen, M.L.; Johnson, R.H.

2009-01-01

Seepage water and drainage water geochemistry (pH, EC, O2, redox, alkalinity, dissolved cations and trace metals, major anions, total element concentrations) were studied at two active sulphide mine tailings impoundments in Finland (the Hitura Ni mine and Luikonlahti Cu mine/talc processing plant). The data were used to assess the factors influencing tailings seepage quality and to identify constraints for water treatment. Changes in seepage water quality after equilibration with atmospheric conditions were evaluated based on geochemical modelling. At Luikonlahti, annual and seasonal changes were also studied. Seepage quality was largely influenced by the tailings mineralogy, and the serpentine-rich, low sulphide Hitura tailings produced neutral mine drainage with high Ni. In contrast, drainage from the high sulphide, multi-metal tailings of Luikonlahti represented typical acid mine drainage with elevated contents of Zn, Ni, Cu, and Co. Other factors affecting the seepage quality included weathering of the tailings along the seepage flow path, process water input, local hydrological settings, and structural changes in the tailings impoundment. Geochemical modelling showed that pH increased and some heavy metals were adsorbed to Fe precipitates after net alkaline waters equilibrated with the atmosphere. In the net acidic waters, pH decreased and no adsorption occurred. A combination of aerobic and anaerobic treatments is proposed for Hitura seepages to decrease the sulphate and metal loading. For Luikonlahti, prolonged monitoring of the seepage quality is suggested instead of treatment, since the water quality is still adjusting to recent modifications to the tailings impoundment.

Crystallogenesis of bacteriophage P22 tail accessory factor gp26 at acidic and neutral pH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cingolani, Gino, E-mail: cingolag@upstate.edu; Andrews, Dewan; Casjens, Sherwood

2006-05-01

The crystallogenesis of bacteriophage P22 tail-fiber gp26 is described. To study possible pH-induced conformational changes in gp26 structure, native trimeric gp26 has been crystallized at acidic pH (4.6) and a chimera of gp26 fused to maltose-binding protein (MBP-gp26) has been crystallized at neutral and alkaline pH (7-10). Gp26 is one of three phage P22-encoded tail accessory factors essential for stabilization of viral DNA within the mature capsid. In solution, gp26 exists as an extended triple-stranded coiled-coil protein which shares profound structural similarities with class I viral membrane-fusion protein. In the cryo-EM reconstruction of P22 tail extracted from mature virions, gp26more » forms an ∼220 Å extended needle structure emanating from the neck of the tail, which is likely to be brought into contact with the cell’s outer membrane when the viral DNA-injection process is initiated. To shed light on the potential role of gp26 in cell-wall penetration and DNA injection, gp26 has been crystallized at acidic, neutral and alkaline pH. Crystals of native gp26 grown at pH 4.6 diffract X-rays to 2.0 Å resolution and belong to space group P2{sub 1}, with a dimer of trimeric gp26 molecules in the asymmetric unit. To study potential pH-induced conformational changes in the gp26 structure, a chimera of gp26 fused to maltose-binding protein (MBP-gp26) was generated. Hexagonal crystals of MBP-gp26 were obtained at neutral and alkaline pH using the high-throughput crystallization robot at the Hauptman–Woodward Medical Research Institute, Buffalo, NY, USA. These crystals diffract X-rays to beyond 2.0 Å resolution. Structural analysis of gp26 crystallized at acidic, neutral and alkaline pH is in progress.« less

Elongation of the Poly-γ-glutamate Tail of F420 Requires Both Domains of the F420:γ-Glutamyl Ligase (FbiB) of Mycobacterium tuberculosis*

PubMed Central

Bashiri, Ghader; Rehan, Aisyah M.; Sreebhavan, Sreevalsan; Baker, Heather M.; Baker, Edward N.; Squire, Christopher J.

2016-01-01

Cofactor F420 is an electron carrier with a major role in the oxidoreductive reactions of Mycobacterium tuberculosis, the causative agent of tuberculosis. A γ-glutamyl ligase catalyzes the final steps of the F420 biosynthesis pathway by successive additions of l-glutamate residues to F420-0, producing a poly-γ-glutamate tail. The enzyme responsible for this reaction in archaea (CofE) comprises a single domain and produces F420-2 as the major species. The homologous M. tuberculosis enzyme, FbiB, is a two-domain protein and produces F420 with predominantly 5–7 l-glutamate residues in the poly-γ-glutamate tail. The N-terminal domain of FbiB is homologous to CofE with an annotated γ-glutamyl ligase activity, whereas the C-terminal domain has sequence similarity to an FMN-dependent family of nitroreductase enzymes. Here we demonstrate that full-length FbiB adds multiple l-glutamate residues to F420-0 in vitro to produce F420-5 after 24 h; communication between the two domains is critical for full γ-glutamyl ligase activity. We also present crystal structures of the C-terminal domain of FbiB in apo-, F420-0-, and FMN-bound states, displaying distinct sites for F420-0 and FMN ligands that partially overlap. Finally, we discuss the features of a full-length structural model produced by small angle x-ray scattering and its implications for the role of N- and C-terminal domains in catalysis. PMID:26861878

Life Cycle Characterization of Sulfolobus Monocaudavirus 1, an Extremophilic Spindle-Shaped Virus with Extracellular Tail Development

PubMed Central

Uldahl, Kristine B.; Jensen, Signe B.; Bhoobalan-Chitty, Yuvaraj; Martínez-Álvarez, Laura; Papathanasiou, Pavlos

2016-01-01

ABSTRACT We provide here, for the first time, insights into the initial infection stages of a large spindle-shaped archaeal virus and explore the following life cycle events. Our observations suggest that Sulfolobus monocaudavirus 1 (SMV1) exhibits a high adsorption rate and that virions adsorb to the host cells via three distinct attachment modes: nosecone association, body association, and body/tail association. In the body/tail association mode, the entire virion, including the tail(s), aligns to the host cell surface and the main body is greatly flattened, suggesting a possible fusion entry mechanism. Upon infection, the intracellular replication cycle lasts about 8 h, at which point the virions are released as spindle-shaped tailless particles. Replication of the virus retarded host growth but did not cause lysis of the host cells. Once released from the host and at temperatures resembling that of its natural habitat, SMV1 starts developing one or two tails. This exceptional property of undergoing a major morphological development outside, and independently of, the host cell has been reported only once before for the related Acidianus two-tailed virus. Here, we show that SMV1 can develop tails of more than 900 nm in length, more than quadrupling the total virion length. IMPORTANCE Very little is known about the initial life cycle stages of viruses infecting hosts of the third domain of life, Archaea. This work describes the first example of an archaeal virus employing three distinct association modes. The virus under study, Sulfolobus monocaudavirus 1, is a representative of the large spindle-shaped viruses that are frequently found in acidic hot springs. The results described here will add valuable knowledge about Archaea, the least studied domain in the virology field. PMID:27053548

Life Cycle Characterization of Sulfolobus Monocaudavirus 1, an Extremophilic Spindle-Shaped Virus with Extracellular Tail Development.

PubMed

Uldahl, Kristine B; Jensen, Signe B; Bhoobalan-Chitty, Yuvaraj; Martínez-Álvarez, Laura; Papathanasiou, Pavlos; Peng, Xu

2016-06-15

We provide here, for the first time, insights into the initial infection stages of a large spindle-shaped archaeal virus and explore the following life cycle events. Our observations suggest that Sulfolobus monocaudavirus 1 (SMV1) exhibits a high adsorption rate and that virions adsorb to the host cells via three distinct attachment modes: nosecone association, body association, and body/tail association. In the body/tail association mode, the entire virion, including the tail(s), aligns to the host cell surface and the main body is greatly flattened, suggesting a possible fusion entry mechanism. Upon infection, the intracellular replication cycle lasts about 8 h, at which point the virions are released as spindle-shaped tailless particles. Replication of the virus retarded host growth but did not cause lysis of the host cells. Once released from the host and at temperatures resembling that of its natural habitat, SMV1 starts developing one or two tails. This exceptional property of undergoing a major morphological development outside, and independently of, the host cell has been reported only once before for the related Acidianus two-tailed virus. Here, we show that SMV1 can develop tails of more than 900 nm in length, more than quadrupling the total virion length. Very little is known about the initial life cycle stages of viruses infecting hosts of the third domain of life, Archaea This work describes the first example of an archaeal virus employing three distinct association modes. The virus under study, Sulfolobus monocaudavirus 1, is a representative of the large spindle-shaped viruses that are frequently found in acidic hot springs. The results described here will add valuable knowledge about Archaea, the least studied domain in the virology field. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Crystallographic Insights into the Autocatalytic Assembly Mechanism of a Bacteriophage Tail Spike

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiang, Ye; Leiman, Petr G.; Li, Long

2010-02-03

The tailed bacteriophage phi29 has 12 'appendages' (gene product 12, gp12) attached to its neck region that participate in host cell recognition and entry. In the cell, monomeric gp12 undergoes proteolytic processing that releases the C-terminal domain during assembly into trimers. We report here crystal structures of the protein before and after catalytic processing and show that the C-terminal domain of gp12 is an 'autochaperone' that aids trimerization. We also show that autocleavage of the C-terminal domain is a posttrimerization event that is followed by a unique ATP-dependent release. The posttranslationally modified N-terminal part has three domains that function tomore » attach the appendages to the phage, digest the cell wall teichoic acids, and bind irreversibly to the host, respectively. Structural and sequence comparisons suggest that some eukaryotic and bacterial viruses as well as bacterial adhesins might have a similar maturation mechanism as is performed by phi29 gp12 for Bacillus subtilis.« less

Curvature-induced domain wall pinning

NASA Astrophysics Data System (ADS)

Yershov, Kostiantyn V.; Kravchuk, Volodymyr P.; Sheka, Denis D.; Gaididei, Yuri

2015-09-01

It is shown that a local bend of a nanowire is a source of pinning potential for a transversal head-to-head (tail-to-tail) domain wall. Eigenfrequency of the domain wall free oscillations at the pinning potential and the effective friction are determined as functions of the curvature and domain wall width. The pinning potential originates from the effective curvature-induced Dzyaloshinsky-like term in the exchange energy. The theoretical results are verified by means of micromagnetic simulations for the case of parabolic shape of the wire bend.

A plasma membrane localization signal in the HIV-1 envelope cytoplasmic domain prevents localization at sites of vesicular stomatitis virus budding and incorporation into VSV virions.

PubMed

Johnson, J E; Rodgers, W; Rose, J K

1998-11-25

Previous studies showed that the HIV-1 envelope (Env) protein was not incorporated into vesicular stomatitis virus (VSV) virions unless its cytoplasmic tail was replaced with that of the VSV glycoprotein (G). To determine whether the G tail provided a positive incorporation signal for Env, or if sequences in the Env tail prevented incorporation, we generated mutants of Env with its 150-amino-acid tail shortened to 29, 10, or 3 amino acids (Envtr mutants). Cells infected with VSV recombinants expressing these proteins or an Env-G tail hybrid showed similar amounts of Env protein at the surface. The Env-G tail hybrid or the Envtr3 mutant were incorporated at the highest levels into budding VSV virions. In contrast, the Envtr29 or Envtr10 mutants were incorporated poorly. These results defined a signal preventing incorporation within the 10 membrane-proximal amino acids of the Env tail. Confocal microscopy revealed that this signal functioned by causing localization of human immunodeficiency virus type 1 Env to plasma membrane domains distinct from the VSV budding sites, where VSV proteins were concentrated. Copyright 1998 Academic Press.

G-protein-coupled receptors for neurotransmitter amino acids: C-terminal tails, crowded signalosomes.

PubMed Central

El Far, Oussama; Betz, Heinrich

2002-01-01

G-protein-coupled receptors (GPCRs) represent a superfamily of highly diverse integral membrane proteins that transduce external signals to different subcellular compartments, including nuclei, via trimeric G-proteins. By differential activation of diffusible G(alpha) and membrane-bound G(beta)gamma subunits, GPCRs might act on both cytoplasmic/intracellular and plasma-membrane-bound effector systems. The coupling efficiency and the plasma membrane localization of GPCRs are regulated by a variety of interacting proteins. In this review, we discuss recently disclosed protein interactions found with the cytoplasmic C-terminal tail regions of two types of presynaptic neurotransmitter receptors, the group III metabotropic glutamate receptors and the gamma-aminobutyric acid type-B receptors (GABA(B)Rs). Calmodulin binding to mGluR7 and other group III mGluRs may provide a Ca(2+)-dependent switch for unidirectional (G(alpha)) versus bidirectional (G(alpha) and G(beta)gamma) signalling to downstream effector proteins. In addition, clustering of mGluR7 by PICK1 (protein interacting with C-kinase 1), a polyspecific PDZ (PSD-95/Dlg1/ZO-1) domain containing synaptic organizer protein, sheds light on how higher-order receptor complexes with regulatory enzymes (or 'signalosomes') could be formed. The interaction of GABA(B)Rs with the adaptor protein 14-3-3 and the transcription factor ATF4 (activating transcription factor 4) suggests novel regulatory pathways for G-protein signalling, cytoskeletal reorganization and nuclear gene expression: processes that may all contribute to synaptic plasticity. PMID:12006104

The B7-1 Cytoplasmic Tail Enhances Intracellular Transport and Mammalian Cell Surface Display of Chimeric Proteins in the Absence of a Linear ER Export Motif

PubMed Central

Lin, Yi-Chieh; Chen, Bing-Mae; Lu, Wei-Cheng; Su, Chien-I; Prijovich, Zeljko M.; Chung, Wen-Chuan; Wu, Pei-Yu; Chen, Kai-Chuan; Lee, I-Chiao; Juan, Ting-Yi; Roffler, Steve R.

2013-01-01

Membrane-tethered proteins (mammalian surface display) are increasingly being used for novel therapeutic and biotechnology applications. Maximizing surface expression of chimeric proteins on mammalian cells is important for these applications. We show that the cytoplasmic domain from the B7-1 antigen, a commonly used element for mammalian surface display, can enhance the intracellular transport and surface display of chimeric proteins in a Sar1 and Rab1 dependent fashion. However, mutational, alanine scanning and deletion analysis demonstrate the absence of linear ER export motifs in the B7 cytoplasmic domain. Rather, efficient intracellular transport correlated with the presence of predicted secondary structure in the cytoplasmic tail. Examination of the cytoplasmic domains of 984 human and 782 mouse type I transmembrane proteins revealed that many previously identified ER export motifs are rarely found in the cytoplasmic tail of type I transmembrane proteins. Our results suggest that efficient intracellular transport of B7 chimeric proteins is associated with the structure rather than to the presence of a linear ER export motif in the cytoplasmic tail, and indicate that short (less than ~ 10-20 amino acids) and unstructured cytoplasmic tails should be avoided to express high levels of chimeric proteins on mammalian cells. PMID:24073236

Magnetic domain wall gratings for magnetization reversal tuning and confined dynamic mode localization.

PubMed

Trützschler, Julia; Sentosun, Kadir; Mozooni, Babak; Mattheis, Roland; McCord, Jeffrey

2016-08-04

High density magnetic domain wall gratings are imprinted in ferromagnetic-antiferromagnetic thin films by local ion irradiation by which alternating head-to-tail-to-head-to-tail and head-to-head-to-tail-to-tail spatially overlapping domain wall networks are formed. Unique magnetic domain processes result from the interaction of anchored domain walls. Non-linear magnetization response is introduced by the laterally distributed magnetic anisotropy phases. The locally varying magnetic charge distribution gives rise to localized and guided magnetization spin-wave modes directly constrained by the narrow domain wall cores. The exchange coupled multiphase material structure leads to unprecedented static and locally modified dynamic magnetic material properties.

Magnetic domain wall gratings for magnetization reversal tuning and confined dynamic mode localization

NASA Astrophysics Data System (ADS)

Trützschler, Julia; Sentosun, Kadir; Mozooni, Babak; Mattheis, Roland; McCord, Jeffrey

2016-08-01

High density magnetic domain wall gratings are imprinted in ferromagnetic-antiferromagnetic thin films by local ion irradiation by which alternating head-to-tail-to-head-to-tail and head-to-head-to-tail-to-tail spatially overlapping domain wall networks are formed. Unique magnetic domain processes result from the interaction of anchored domain walls. Non-linear magnetization response is introduced by the laterally distributed magnetic anisotropy phases. The locally varying magnetic charge distribution gives rise to localized and guided magnetization spin-wave modes directly constrained by the narrow domain wall cores. The exchange coupled multiphase material structure leads to unprecedented static and locally modified dynamic magnetic material properties.

Dietary quality, fecal nitrogen and 2,6 diaminopimelic acid in black-tailed deer in northern California

Treesearch

John G. Kie; Timothy S. Burton

1984-01-01

Range managers need easily measured indices of dietary quality to ensure high quality forage for deer. Levels of fecal nitrogen and fecal 2,6 diaminopimelic acid, which have been suggested as such indices, were monitored for two herds of black-tailed deer (Odocoileus hemionus columbianus) in northern California. Both values were highest in summer...

A basic domain in the histone H2B N-terminal tail is important for nucleosome assembly by FACT

PubMed Central

Mao, Peng; Kyriss, McKenna N. M.; Hodges, Amelia J.; Duan, Mingrui; Morris, Robert T.; Lavine, Mark D.; Topping, Traci B.; Gloss, Lisa M.; Wyrick, John J.

2016-01-01

Nucleosome assembly in vivo requires assembly factors, such as histone chaperones, to bind to histones and mediate their deposition onto DNA. In yeast, the essential histone chaperone FACT (FAcilitates Chromatin Transcription) functions in nucleosome assembly and H2A–H2B deposition during transcription elongation and DNA replication. Recent studies have identified candidate histone residues that mediate FACT binding to histones, but it is not known which histone residues are important for FACT to deposit histones onto DNA during nucleosome assembly. In this study, we report that the histone H2B repression (HBR) domain within the H2B N-terminal tail is important for histone deposition by FACT. Deletion of the HBR domain causes significant defects in histone occupancy in the yeast genome, particularly at HBR-repressed genes, and a pronounced increase in H2A–H2B dimers that remain bound to FACT in vivo. Moreover, the HBR domain is required for purified FACT to efficiently assemble recombinant nucleosomes in vitro. We propose that the interaction between the highly basic HBR domain and DNA plays an important role in stabilizing the nascent nucleosome during the process of histone H2A–H2B deposition by FACT. PMID:27369377

Hydrogen-bond rich ionic liquids with hydroxyl cationic tails

NASA Astrophysics Data System (ADS)

Deng, Li; Shi, Rui; Wang, Yanting; Ou-Yang, Zhong-Can

2013-02-01

To investigate if the amphiphilic feature exhibited in ionic liquids (ILs) with nonpolar cationic tails still exists in ILs with polar tails, by performing molecular dynamics simulations for 1-(8-hydroxyoctyl)-3-methyl-imidazolium nitrate (COH) and 1-octyl-3-methyl-imidazolium nitrate (C8), we found that, in COH, cationic tail groups can no longer aggregate to form separated nonpolar tail domains, instead hydroxyl groups form a rich number of hydrogen bonds with other groups, indicating that the hydroxyl substituent changes the IL system from an amphiphilic liquid to a polar liquid. Due to the large amount of hydrogen bonds, COH has slower dynamics than C8.

Insights into the phosphoregulation of beta-secretase sorting signal by the VHS domain of GGA1.

PubMed

Shiba, Tomoo; Kametaka, Satoshi; Kawasaki, Masato; Shibata, Masahiro; Waguri, Satoshi; Uchiyama, Yasuo; Wakatsuki, Soichi

2004-06-01

BACE (beta-site amyloid precursor protein cleaving enzyme, beta-secretase) is a type-I membrane protein which functions as an aspartic protease in the production of beta-amyloid peptide, a causative agent of Alzheimer's disease. Its cytoplasmic tail has a characteristic acidic-cluster dileucine motif recognized by the VHS domain of adaptor proteins, GGAs (Golgi-localizing, gamma-adaptin ear homology domain, ARF-interacting). Here we show that BACE is colocalized with GGAs in the trans-Golgi network and peripheral structures, and phosphorylation of a serine residue in the cytoplasmic tail enhances interaction with the VHS domain of GGA1 by about threefold. The X-ray crystal structure of the complex between the GGA1-VHS domain and the BACE C-terminal peptide illustrates a similar recognition mechanism as mannose 6-phosphate receptors except that a glutamine residue closes in to fill the gap created by the shorter BACE peptide. The serine and lysine of the BACE peptide point their side chains towards the solvent. However, phosphorylation of the serine affects the lysine side chain and the peptide backbone, resulting in one additional hydrogen bond and a stronger electrostatic interaction with the VHS domain, hence the reversible increase in affinity.

Sulfide oxidation and acid mine drainage formation within two active tailings impoundments in the Golden Quadrangle of the Apuseni Mountains, Romania.

PubMed

Sima, Mihaela; Dold, Bernhard; Frei, Linda; Senila, Marin; Balteanu, Dan; Zobrist, Jurg

2011-05-30

Sulfidic mine tailings have to be classified as one of the major source of hazardous materials leading to water contamination. This study highlights the processes leading to sulfide oxidation and acid mine drainage (AMD) formation in the active stage of two tailings impoundments located in the southern part of the Apuseni Mountains, in Romania, a well-known region for its long-term gold-silver and metal mining activity. Sampling was undertaken when both impoundments were still in operation in order to assess their actual stage of oxidation and long-term behavior in terms of the potential for acid mine drainage generation. Both tailings have high potential for AMD formation (2.5 and 3.7 wt.% of pyrite equivalent, respectively) with lesser amount of carbonates (5.6 and 3.6 wt.% of calcite equivalent) as neutralization potential (ABA=-55.6 and -85.1 tCaCO(3)/1000 t ) and showed clear signs of sulfide oxidation yet during operation. Sequential extraction results indicate a stronger enrichment and mobility of elements in the oxidized tailings: Fe as Fe(III) oxy-hydroxides and oxides (transformation from sulfide minerals, leaching in oxidation zone), Ca mainly in water soluble and exchangeable form where gypsum and calcite are dissolved and higher mobility of Cu for Ribita and Pb for Mialu. Two processes leading to the formation of mine drainage at this stage could be highlighted (1) a neutral Fe(II) plume forming in the impoundment with ferrihydrite precipitation at its outcrop and (2) acid mine drainage seeping in the unsaturated zone of the active dam, leading to the formation of schwertmannite at its outcrop. Copyright © 2011 Elsevier B.V. All rights reserved.

Single molecule FRET observation of kinesin-1’s head-tail interaction on microtubule

PubMed Central

Aoki, Takahiro; Tomishige, Michio; Ariga, Takayuki

2013-01-01

Kinesin-1 (conventional kinesin) is a molecular motor that transports various cargo such as endoplasmic reticulum and mitochondria in cells. Its two head domains walk along microtubule by hydrolyzing ATP, while the tail domains at the end of the long stalk bind to the cargo. When a kinesin is not carrying cargo, its motility and ATPase activity is inhibited by direct interactions between the tail and head. However, the mechanism of this tail regulation is not well understood. Here, we apply single molecule fluorescence resonance energy transfer (smFRET) to observe this interaction in stalk-truncated kinesin. We found that kinesin with two tails forms a folding conformation and dissociates from microtubules, whereas kinesin with one tail remains bound to the micro-tubule and is immobile even in the presence of ATP. We further investigated the head-tail interaction as well as head-head coordination on the microtubule at various nucleotide conditions. From these results, we propose a two-step inhibition model for kinesin motility. PMID:27493553

The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome

PubMed Central

Morrison, Emma A; Bowerman, Samuel; Sylvers, Kelli L

2018-01-01

Histone tails harbor a plethora of post-translational modifications that direct the function of chromatin regulators, which recognize them through effector domains. Effector domain/histone interactions have been broadly studied, but largely using peptide fragments of histone tails. Here, we extend these studies into the nucleosome context and find that the conformation adopted by the histone H3 tails is inhibitory to BPTF PHD finger binding. Using NMR spectroscopy and MD simulations, we show that the H3 tails interact robustly but dynamically with nucleosomal DNA, substantially reducing PHD finger association. Altering the electrostatics of the H3 tail via modification or mutation increases accessibility to the PHD finger, indicating that PTM crosstalk can regulate effector domain binding by altering nucleosome conformation. Together, our results demonstrate that the nucleosome context has a dramatic impact on signaling events at the histone tails, and highlights the importance of studying histone binding in the context of the nucleosome. PMID:29648537

Thermodynamic Linkage Between Calmodulin Domains Binding Calcium and Contiguous Sites in the C-Terminal Tail of CaV1.2

PubMed Central

Evans, T. Idil Apak; Hell, Johannes; Shea, Madeline A.

2011-01-01

Calmodulin (CaM) binding to the intracellular C-terminal tail (CTT) of the cardiac L-type Ca2+ channel (CaV1.2) regulates Ca2+ entry by recognizing sites that contribute to negative feedback mechanisms for channel closing. CaM associates with CaV1.2 under low resting [Ca2+], but is poised to change conformation and position when intracellular [Ca2+] rises. CaM binding Ca2+, and the domains of CaM binding the CTT are linked thermodynamic functions. To better understand regulation, we determined the energetics of CaM domains binding to peptides representing pre-IQ sites A1588, and C1614 and the IQ motif studied as overlapping peptides IQ1644 and IQ′1650 as well as their effect on calcium binding. (Ca2+)4-CaM bound to all four peptides very favorably (Kd ≤ 2 nM). Linkage analysis showed that IQ1644–1670 bound with a Kd ~1 pM. In the pre-IQ region, (Ca2+)2-N-domain bound preferentially to A1588, while (Ca2+)2-C-domain preferred C1614. When bound to C1614, calcium binding in the N-domain affected the tertiary conformation of the C-domain. Based on the thermodynamics, we propose a structural mechanism for calcium-dependent conformational change in which the linker between CTT sites A and C buckles to form an A-C hairpin that is bridged by calcium-saturated CaM. PMID:21757287

Structure of the SANT domain from the Xenopus chromatin remodeling factor ISWI

DOE Office of Scientific and Technical Information (OSTI.GOV)

Horton, John R.; Elgar, Stuart J.; Khan, Seema I.

2008-09-17

The SANT (Swi3, Ada2, N-Cor, and TFIIIB) module was first described as a putative DNA-binding domain with strong similarity to the helix-turn-helix DNA binding domain of Myb-related proteins. The X-ray structure of the C-terminal one third portion of the ATPase ISWI of Drosophila melangoaster, containing both SANT and SLIDE (SANT-Like ISWI Domain), confirmed the overall helix-turn-helix structural architecture of SANT as well as SLIDE. However, the DNA-contacting residues in Myb are not conserved in SANT and the structurally corresponding residues in the ISWI SANT domain are acidic, and therefore incompatible with DNA interaction. Recent studies suggested that SANT domains mightmore » be a histone-tail-binding module, including the DNA binding SANT domain of c-Myb. Here they present the X-ray structure of Xenopus laevis ISWI SANT domain, derived from limited proteolysis of a C-terminal fragment of ISWI protein.« less

Tip-induced domain structures and polarization switching in ferroelectric amino acid glycine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seyedhosseini, E., E-mail: Seyedhosseini@ua.pt; Ivanov, M.; Bdikin, I.

2015-08-21

Bioorganic ferroelectrics and piezoelectrics are becoming increasingly important in view of their intrinsic compatibility with biological environment and biofunctionality combined with strong piezoelectric effect and a switchable polarization at room temperature. Here, we study tip-induced domain structures and polarization switching in the smallest amino acid β-glycine, representing a broad class of non-centrosymmetric amino acids. We show that β-glycine is indeed a room-temperature ferroelectric and polarization can be switched by applying a bias to non-polar cuts via a conducting tip of atomic force microscope (AFM). Dynamics of these in-plane domains is studied as a function of an applied voltage and pulsemore » duration. The domain shape is dictated by polarization screening at the domain boundaries and mediated by growth defects. Thermodynamic theory is applied to explain the domain propagation induced by the AFM tip. Our findings suggest that the properties of β-glycine are controlled by the charged domain walls which in turn can be manipulated by an external bias.« less

Golgi retention of a trans-Golgi membrane protein, galactosyltransferase, requires cysteine and histidine residues within the membrane-anchoring domain.

PubMed

Aoki, D; Lee, N; Yamaguchi, N; Dubois, C; Fukuda, M N

1992-05-15

Galactosyltransferase (GT; UDPgalactose:beta-D-N-acetylglucosaminide beta-1,4-galactosyltransferase, EC 2.4.1.22) is a type II membrane-anchored protein composed of a short N-terminal cytoplasmic tail, a signal/membrane-anchoring domain, and a stem region followed by a large catalytic domain including the C terminus. To identify the peptide segment and key amino acid residues that are critical for Golgi localization of GT, the expression vector pGT-hCG was designed to encode the entire GT molecule fused to the C-terminal region of human chorionic gonadotropin alpha subunit (hCG alpha) as a reporter. COS-1 cells transfected with pGT-hCG expressed the chimera in the Golgi region, as detected by immunofluorescence microscopy using anti-hCG antibodies. Two deletion mutants, delta tail and delta stem, which are lacking most of the N-terminal cytoplasmic tail or 10 amino acids immediately after the membrane-anchoring domain, were localized in the Golgi. Replacement mutations of the membrane-anchoring domain of GT showed that the second quarter of the transmembrane domain or Cys29-Ala30-Leu31-His32-Leu33 is necessary for GT to be retained in the Golgi. Furthermore, the point mutants Cys29----Ser29 and His32----Leu32 were partially transported to the plasma membrane, whereas an Ala30-Leu31----Phe30-Gly31 mutant was localized in the Golgi. Finally, a double mutant, Cys29/His32----Ser29/Leu32, was found to be transported efficiently to the plasma membrane. The signal-anchoring domain of the transferrin receptor, a type II plasma membrane protein, was then replaced by portions of the GT transmembrane domain. Although the Cys-Xaa-Xaa-His sequence by itself cannot retain the transferrin receptor in the Golgi, the cytoplasmic half of the transmembrane domain of GT was partially capable of retaining the transferrin receptor in the Golgi. These results suggest that the cytoplasmic (or N-terminal) half of the transmembrane domain of GT contributes to the Golgi retention signal and

Golgi retention of a trans-Golgi membrane protein, galactosyltransferase, requires cysteine and histidine residues within the membrane-anchoring domain.

PubMed Central

Aoki, D; Lee, N; Yamaguchi, N; Dubois, C; Fukuda, M N

1992-01-01

Galactosyltransferase (GT; UDPgalactose:beta-D-N-acetylglucosaminide beta-1,4-galactosyltransferase, EC 2.4.1.22) is a type II membrane-anchored protein composed of a short N-terminal cytoplasmic tail, a signal/membrane-anchoring domain, and a stem region followed by a large catalytic domain including the C terminus. To identify the peptide segment and key amino acid residues that are critical for Golgi localization of GT, the expression vector pGT-hCG was designed to encode the entire GT molecule fused to the C-terminal region of human chorionic gonadotropin alpha subunit (hCG alpha) as a reporter. COS-1 cells transfected with pGT-hCG expressed the chimera in the Golgi region, as detected by immunofluorescence microscopy using anti-hCG antibodies. Two deletion mutants, delta tail and delta stem, which are lacking most of the N-terminal cytoplasmic tail or 10 amino acids immediately after the membrane-anchoring domain, were localized in the Golgi. Replacement mutations of the membrane-anchoring domain of GT showed that the second quarter of the transmembrane domain or Cys29-Ala30-Leu31-His32-Leu33 is necessary for GT to be retained in the Golgi. Furthermore, the point mutants Cys29----Ser29 and His32----Leu32 were partially transported to the plasma membrane, whereas an Ala30-Leu31----Phe30-Gly31 mutant was localized in the Golgi. Finally, a double mutant, Cys29/His32----Ser29/Leu32, was found to be transported efficiently to the plasma membrane. The signal-anchoring domain of the transferrin receptor, a type II plasma membrane protein, was then replaced by portions of the GT transmembrane domain. Although the Cys-Xaa-Xaa-His sequence by itself cannot retain the transferrin receptor in the Golgi, the cytoplasmic half of the transmembrane domain of GT was partially capable of retaining the transferrin receptor in the Golgi. These results suggest that the cytoplasmic (or N-terminal) half of the transmembrane domain of GT contributes to the Golgi retention signal and

Guidelines for the Use of Protein Domains in Acidic Phospholipid Imaging.

PubMed

Platre, Matthieu Pierre; Jaillais, Yvon

2016-01-01

Acidic phospholipids are minor membrane lipids but critically important for signaling events. The main acidic phospholipids are phosphatidylinositol phosphates (PIPs also known as phosphoinositides), phosphatidylserine (PS), and phosphatidic acid (PA). Acidic phospholipids are precursors of second messengers of key signaling cascades or are second messengers themselves. They regulate the localization and activation of many proteins, and are involved in virtually all membrane trafficking events. As such, it is crucial to understand the subcellular localization and dynamics of each of these lipids within the cell. Over the years, several techniques have emerged in either fixed or live cells to analyze the subcellular localization and dynamics of acidic phospholipids. In this chapter, we review one of them: the use of genetically encoded biosensors that are based on the expression of specific lipid binding domains (LBDs) fused to fluorescent proteins. We discuss how to design such sensors, including the criteria for selecting the lipid binding domains of interest and to validate them. We also emphasize the care that must be taken during data analysis as well as the main limitations and advantages of this approach.

Determination of thermodynamic and transport parameters of naphthenic acids and organic process chemicals in oil sand tailings pond water.

PubMed

Wang, Xiaomeng; Robinson, Lisa; Wen, Qing; Kasperski, Kim L

2013-07-01

Oil sand tailings pond water contains naphthenic acids and process chemicals (e.g., alkyl sulphates, quaternary ammonium compounds, and alkylphenol ethoxylates). These chemicals are toxic and can seep through the foundation of the tailings pond to the subsurface, potentially affecting the quality of groundwater. As a result, it is important to measure the thermodynamic and transport parameters of these chemicals in order to study the transport behavior of contaminants through the foundation as well as underground. In this study, batch adsorption studies and column experiments were performed. It was found that the transport parameters of these chemicals are related to their molecular structures and other properties. The computer program (CXTFIT) was used to further evaluate the transport process in the column experiments. The results from this study show that the transport of naphthenic acids in a glass column is an equilibrium process while the transport of process chemicals seems to be a non-equilibrium process. At the end of this paper we present a real-world case study in which the transport of the contaminants through the foundation of an external tailings pond is calculated using the lab-measured data. The results show that long-term groundwater monitoring of contaminant transport at the oil sand mining site may be necessary to avoid chemicals from reaching any nearby receptors.

Elp3 and RlmN: A tale of two mitochondrial tail-anchored radical SAM enzymes in Toxoplasma gondii.

PubMed

Padgett, Leah R; Lentini, Jenna M; Holmes, Michael J; Stilger, Krista L; Fu, Dragony; Sullivan, William J

2018-01-01

Radical S-adenosylmethionine (rSAM) enzymes use a 5'-deoxyadensyl 5'-radical to methylate a wide array of diverse substrates including proteins, lipids and nucleic acids. One such enzyme, Elongator protein-3 (TgElp3), is an essential protein in Toxoplasma gondii, a protozoan parasite that can cause life-threatening opportunistic disease. Unlike Elp3 homologues which are present in all domains of life, TgElp3 localizes to the outer mitochondrial membrane (OMM) via a tail-anchored trafficking mechanism in Toxoplasma. Intriguingly, we identified a second tail-anchored rSAM domain containing protein (TgRlmN) that also localizes to the OMM. The transmembrane domain (TMD) on Toxoplasma Elp3 and RlmN homologues is required for OMM localization and has not been seen beyond the chromalveolates. Both TgElp3 and TgRlmN contain the canonical rSAM amino acid sequence motif (CxxxCxxC) necessary to form the 4Fe-4S cluster required for tRNA modifications. In E. coli, RlmN is responsible for the 2-methlyadenosine (m2A) synthesis at purine 37 in tRNA while in S. cerevisiae, Elp3 is necessary for the formation of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) at the wobble tRNA position. To investigate why these two rSAM enzymes localize to the mitochondrion in Toxoplasma, and whether or not TgRlmN and TgElp3 possess tRNA methyltransferase activity, a series of mutational and biochemical studies were performed. Overexpression of either TgElp3 or TgRlmN resulted in a significant parasite replication defect, but overexpression was tolerated if either the TMD or rSAM domain was mutated. Furthermore, we show the first evidence that Toxoplasma tRNAGlu contains the mcm5s2U modification, which is the putative downstream product generated by TgElp3 activity.

Lysines in the RNA Polymerase II C-Terminal Domain Contribute to TAF15 Fibril Recruitment.

PubMed

Janke, Abigail M; Seo, Da Hee; Rahmanian, Vahid; Conicella, Alexander E; Mathews, Kaylee L; Burke, Kathleen A; Mittal, Jeetain; Fawzi, Nicolas L

2018-05-01

Many cancer-causing chromosomal translocations result in transactivating protein products encoding FET family (FUS, EWSR1, TAF15) low-complexity (LC) domains fused to a DNA binding domain from one of several transcription factors. Recent work demonstrates that higher-order assemblies of FET LC domains bind the carboxy-terminal domain of the large subunit of RNA polymerase II (RNA pol II CTD), suggesting FET oncoproteins may mediate aberrant transcriptional activation by recruiting RNA polymerase II to promoters of target genes. Here we use nuclear magnetic resonance (NMR) spectroscopy and hydrogel fluorescence microscopy localization and fluorescence recovery after photobleaching to visualize atomic details of a model of this process, interactions of RNA pol II CTD with high-molecular weight TAF15 LC assemblies. We report NMR resonance assignments of the intact degenerate repeat half of human RNA pol II CTD alone and verify its predominant intrinsic disorder by molecular simulation. By measuring NMR spin relaxation and dark-state exchange saturation transfer, we characterize the interaction of RNA pol II CTD with amyloid-like hydrogel fibrils of TAF15 and hnRNP A2 LC domains and observe that heptads far from the acidic C-terminal tail of RNA pol II CTD bind TAF15 fibrils most avidly. Mutation of CTD lysines in heptad position 7 to consensus serines reduced the overall level of TAF15 fibril binding, suggesting that electrostatic interactions contribute to complex formation. Conversely, mutations of position 7 asparagine residues and truncation of the acidic tail had little effect. Thus, weak, multivalent interactions between TAF15 fibrils and heptads throughout RNA pol II CTD collectively mediate complex formation.

Manganese ore tailing: optimization of acid leaching conditions and recovery of soluble manganese.

PubMed

Santos, Olívia de Souza Heleno; Carvalho, Cornélio de Freitas; Silva, Gilmare Antônia da; Santos, Cláudio Gouvêa Dos

2015-01-01

Manganese recovery from industrial ore processing waste by means of leaching with sulfuric acid was the objective of this study. Experimental conditions were optimized by multivariate experimental design approaches. In order to study the factors affecting leaching, a screening step was used involving a full factorial design with central point for three variables in two levels (2(3)). The three variables studied were leaching time, concentration of sulfuric acid and sample amount. The three factors screened were shown to be relevant and therefore a Doehlert design was applied to determine the best working conditions for leaching and to build the response surface. By applying the best leaching conditions, the concentrations of 12.80 and 13.64 %w/w of manganese for the global sample and for the fraction -44 + 37 μm, respectively, were found. Microbeads of chitosan were tested for removal of leachate acidity and recovering of soluble manganese. Manganese recovery from the leachate was 95.4%. Upon drying the leachate, a solid containing mostly manganese sulfate was obtained, showing that the proposed optimized method is efficient for manganese recovery from ore tailings. Copyright © 2014 Elsevier Ltd. All rights reserved.

Eicosapentaenoic acid reduces membrane fluidity, inhibits cholesterol domain formation, and normalizes bilayer width in atherosclerotic-like model membranes.

PubMed

Mason, R Preston; Jacob, Robert F; Shrivastava, Sandeep; Sherratt, Samuel C R; Chattopadhyay, Amitabha

2016-12-01

Cholesterol crystalline domains characterize atherosclerotic membranes, altering vascular signaling and function. Omega-3 fatty acids reduce membrane lipid peroxidation and subsequent cholesterol domain formation. We evaluated non-peroxidation-mediated effects of eicosapentaenoic acid (EPA), other TG-lowering agents, docosahexaenoic acid (DHA), and other long-chain fatty acids on membrane fluidity, bilayer width, and cholesterol domain formation in model membranes. In membranes prepared at 1.5:1 cholesterol-to-phospholipid (C/P) mole ratio (creating pre-existing domains), EPA, glycyrrhizin, arachidonic acid, and alpha linolenic acid promoted the greatest reductions in cholesterol domains (by 65.5%, 54.9%, 46.8%, and 45.2%, respectively) compared to controls; other treatments had modest effects. EPA effects on cholesterol domain formation were dose-dependent. In membranes with 1:1 C/P (predisposing domain formation), DHA, but not EPA, dose-dependently increased membrane fluidity. DHA also induced cholesterol domain formation without affecting temperature-induced changes in-bilayer unit cell periodicity relative to controls (d-space; 57Å-55Å over 15-30°C). Together, these data suggest simultaneous formation of distinct cholesterol-rich ordered domains and cholesterol-poor disordered domains in the presence of DHA. By contrast, EPA had no effect on cholesterol domain formation and produced larger d-space values relative to controls (60Å-57Å; p<0.05) over the same temperature range, suggesting a more uniform maintenance of lipid dynamics despite the presence of cholesterol. These data indicate that EPA and DHA had different effects on membrane bilayer width, membrane fluidity, and cholesterol crystalline domain formation; suggesting omega-3 fatty acids with differing chain length or unsaturation may differentially influence membrane lipid dynamics and structural organization as a result of distinct phospholipid/sterol interactions. Copyright © 2016. Published by

Pharmacokinetics of a single intramuscular injection of ceftiofur crystalline-free acid in red-tailed hawks (Buteo jamaicensis).

PubMed

Sadar, Miranda J; Hawkins, Michelle G; Byrne, Barbara A; Cartoceti, Andrew N; Keel, Kevin; Drazenovich, Tracy L; Tell, Lisa A

2015-12-01

To determine the pharmacokinetics and adverse effects at the injection site of ceftiofur crystalline-free acid (CCFA) following IM administration of 1 dose to red-tailed hawks (Buteo jamaicensis). 7 adult nonreleasable healthy red-tailed hawks. In a randomized crossover study, CCFA (10 or 20 mg/kg) was administered IM to each hawk and blood samples were obtained. After a 2-month washout period, administration was repeated with the opposite dose. Muscle biopsy specimens were collected from the injection site 10 days after each sample collection period. Pharmacokinetic data were calculated. Minimum inhibitory concentrations of ceftiofur for various bacterial isolates were assessed. Mean peak plasma concentrations of ceftiofur-free acid equivalent were 6.8 and 15.1 μg/mL for the 10 and 20 mg/kg doses, respectively. Mean times to maximum plasma concentration were 6.4 and 6.7 hours, and mean terminal half-lives were 29 and 50 hours, respectively. Little to no muscle inflammation was identified. On the basis of a target MIC of 1 μg/mL and target plasma ceftiofur concentration of 4 μg/mL, dose administration frequencies for infections with gram-negative and gram-positive organisms were estimated as every 36 and 45 hours for the 10 mg/kg dose and every 96 and 120 hours for the 20 mg/kg dose, respectively. Study results suggested that CCFA could be administered IM to red-tailed hawks at 10 or 20 mg/kg to treat infections with ceftiofur-susceptible bacteria. Administration resulted in little to no inflammation at the injection site. Additional studies are needed to evaluate effects of repeated CCFA administration.

Importance of the short cytoplasmic domain of the feline immunodeficiency virus transmembrane glycoprotein for fusion activity and envelope glycoprotein incorporation into virions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Celma, Cristina C.P.; Paladino, Monica G.; Gonzalez, Silvia A.

2007-09-30

The mature form of the envelope (Env) glycoprotein of lentiviruses is a heterodimer composed of the surface (SU) and transmembrane (TM) subunits. Feline immunodeficiency virus (FIV) possesses a TM glycoprotein with a cytoplasmic tail of approximately 53 amino acids which is unusually short compared with that of the other lentiviral glycoproteins (more than 100 residues). To investigate the relevance of the FIV TM cytoplasmic domain to Env-mediated viral functions, we characterized the biological properties of a series of Env glycoproteins progressively shortened from the carboxyl terminus. All the mutant Env proteins were efficiently expressed in feline cells and processed intomore » the SU and TM subunits. Deletion of 5 or 11 amino acids from the TM C-terminus did not significantly affect Env surface expression, fusogenic activity or Env incorporation into virions, whereas removal of 17 or 23 residues impaired Env-mediated cell-to-cell fusion. Further truncation of the FIV TM by 29 residues resulted in an Env glycoprotein that was poorly expressed at the cell surface, exhibited only 20% of the wild-type Env fusogenic capacity and was inefficiently incorporated into virions. Remarkably, deletion of the TM C-terminal 35 or 41 amino acids restored or even enhanced Env biological functions. Indeed, these mutant Env glycoproteins bearing cytoplasmic domains of 18 or 12 amino acids were found to be significantly more fusogenic than the wild-type Env and were efficiently incorporated into virions. Interestingly, truncation of the TM cytoplasmic domain to only 6 amino acids did not affect Env incorporation into virions but abrogated Env fusogenicity. Finally, removal of the entire TM cytoplasmic tail or deletion of as many as 6 amino acids into the membrane-spanning domain led to a complete loss of Env functions. Our results demonstrate that despite its relatively short length, the FIV TM cytoplasmic domain plays an important role in modulating Env-mediated viral

Measles virus fusion machinery activated by sialic acid binding globular domain.

PubMed

Talekar, Aparna; Moscona, Anne; Porotto, Matteo

2013-12-01

Paramyxoviruses, including the human pathogen measles virus (MV) and the avian Newcastle disease virus (NDV), enter host cells through fusion of the viral envelope with the target cell membrane. This fusion is driven by the concerted action of two viral envelope glycoproteins: the receptor binding protein and the fusion protein (F). The MV receptor binding protein (hemagglutinin [H]) attaches to proteinaceous receptors on host cells, while the receptor binding protein of NDV (hemagglutinin-neuraminidase [HN]) interacts with sialic acid-containing receptors. The receptor-bound HN/H triggers F to undergo conformational changes that render it competent to mediate fusion of the viral and cellular membranes. The mechanism of fusion activation has been proposed to be different for sialic acid-binding viruses and proteinaceous receptor-binding viruses. We report that a chimeric protein containing the NDV HN receptor binding region and the MV H stalk domain can activate MV F to fuse, suggesting that the signal to the stalk of a protein-binding receptor binding molecule can be transmitted from a sialic acid binding domain. By engineering the NDV HN globular domain to interact with a proteinaceous receptor, the fusion activation signal was preserved. Our findings are consistent with a unified mechanism of fusion activation, at least for the Paramyxovirinae subfamily, in which the receptor binding domains of the receptor binding proteins are interchangeable and the stalk determines the specificity of F activation.

Solution structure of the C-terminal X domain of the measles virus phosphoprotein and interaction with the intrinsically disordered C-terminal domain of the nucleoprotein.

PubMed

Gely, Stéphane; Lowry, David F; Bernard, Cédric; Jensen, Malene R; Blackledge, Martin; Costanzo, Stéphanie; Bourhis, Jean-Marie; Darbon, Hervé; Daughdrill, Gary; Longhi, Sonia

2010-01-01

In this report, the solution structure of the nucleocapsid-binding domain of the measles virus phosphoprotein (XD, aa 459-507) is described. A dynamic description of the interaction between XD and the disordered C-terminal domain of the nucleocapsid protein, (N(TAIL), aa 401-525), is also presented. XD is an all alpha protein consisting of a three-helix bundle with an up-down-up arrangement of the helices. The solution structure of XD is very similar to the crystal structures of both the free and bound form of XD. One exception is the presence of a highly dynamic loop encompassing XD residues 489-491, which is involved in the embedding of the alpha-helical XD-binding region of N(TAIL). Secondary chemical shift values for full-length N(TAIL) were used to define the precise boundaries of a transient helical segment that coincides with the XD-binding domain, thus shedding light on the pre-recognition state of N(TAIL). Titration experiments with unlabeled XD showed that the transient alpha-helical conformation of N(TAIL) is stabilized upon binding. Lineshape analysis of NMR resonances revealed that residues 483-506 of N(TAIL) are in intermediate exchange with XD, while the 475-482 and 507-525 regions are in fast exchange. The N(TAIL) resonance behavior in the titration experiments is consistent with a complex binding model with more than two states.

Thermo-mechanical properties and microfabric of fly ash-stabilized gold tailings.

PubMed

Lee, Joon Kyu; Shang, Julie Q; Jeong, Sangseom

2014-07-15

This paper studies the changes in thermal conductivity, temperature, and unconfined compressive strength of gold tailings and fly ash mixtures during the curing period of 5 days. The microfabric of the cured mixtures was investigated with mercury intrusion porosimetry (MIP). The mixture samples were prepared at their maximum dry unit weight and optimum moisture content. Effect of adding fly ash to gold tailings (i.e., 0, 20, and 40% of the dry weight of tailings) was examined, and a comparison was made on samples prepared at the same fly ash content by replacing gold tailings with humic acid (i.e., gold tailings and humic acid ratios of 100:0, 90:10, and 80:20 by weight) or by varying pore fluid chemistry (i.e., water and salt solutions of 1M NaCl and CaCl2). The results show that the initial thermal conductivity of the samples is sensitive to the mixture proportion and a declination in the thermal conductivity is observed due to hydration of fly ash and evaporation. Inclusion of fly ash and salts into gold tailings improves the unconfined compressive strength but the presence of humic acid in samples leads to the decrease of the strength. MIP results reveal the pore structure changes associated with the packing states of the samples that reflect the influential factors considered. Copyright © 2014 Elsevier B.V. All rights reserved.

The Tail-Elicited Tail Withdrawal Reflex of "Aplysia" Is Mediated Centrally at Tail Sensory-Motor Synapses and Exhibits Sensitization across Multiple Temporal Domains

ERIC Educational Resources Information Center

Philips, Gary T.; Sherff, Carolyn M.; Menges, Steven A.; Carew, Thomas J.

2011-01-01

The defensive withdrawal reflexes of "Aplysia californica" have provided powerful behavioral systems for studying the cellular and molecular basis of memory formation. Among these reflexes the (T-TWR) has been especially useful. In vitro studies examining the monosynaptic circuit for the T-TWR, the tail sensory-motor (SN-MN) synapses, have…

Use of cemented paste backfill in arsenic-rich tailings

NASA Astrophysics Data System (ADS)

Hamberg, Roger; Maurice, Christian; Alakangas, Lena

2015-04-01

Gold is extracted by cyanide leaching from inclusions in arsenopyrite from a mine in the north of Sweden. The major ore mineral assemblage consists of pyrrhotite and arsenopyrite-loellingite. Effluents from the gold extraction were treated with Fe2(SO4)3, with the aim to form stable As-bearing Fe-precipitates (FEP). The use of the method called cemented paste backfill (CPB) is sometimes suggested for the management of tailings. In CPB, tailings are commonly mixed with low proportions (3 - 7 %) of cement and backfilled into underground excavated area. To reduce costs, amendments such as granulated blast furnace slag (GBFS), biofuel fly ash (BFA) and cement kiln dust (CKD) are used for partial replacement of cement in CPB due to their pozzolanic and alkaline properties. The objective for this study was to evaluate the leaching behaviour of As in CPB-mixtures with low proportions (1 - 3 %) of BFA and ordinary cement and unmodified tailings. The selection of CPB-recipies was made based on technical and economical criterias to adress the demands deriving from the mining operations. Speciation of the As in ore and tailings samples revealed that mining processes have dissolved the majority of the arsenopyrite in the ore, causing secondary As phases to co-precipitate with newly formed FEP:s. Tank leaching tests (TLT) and weathering cells (WCT) were used to compare leaching behaviour in a monolithic mass contra a crushed material. Quantification of the presumed benefit of CPB was made by calculation of the cumulative leaching of As. Results from the leaching tests (TLT and WCT) showed that the inclusion of As-rich tailings into a cementitious matrix increased leaching of As. This behaviour could partially be explained by an increase of pH. The addition of alkaline binder materials to tailings increased As leaching due to the relocation of desorbed As from FEPs into less acid-tolerant species such as Ca-arsenates and cementitious As-phases. Unmodified tailings generated an

Phytotoxicity and naphthenic acid dissipation from oil sands fine tailings treatments planted with the emergent macrophyte Phragmites australis.

PubMed

Armstrong, Sarah A; Headley, John V; Peru, Kerry M; Mikula, Randy J; Germida, James J

2010-01-01

During reclamation the water associated with the runoff or groundwater flushing from dry stackable tailings technologies may become available to the reclaimed environment within an oil sands lease. Here we evaluate the performance of the emergent macrophyte, common reed (Phragmites australis), grown in chemically amended mature fine tailings (MFT) and simulated runoff/seepage water from different MFT drying treatments. The present study also investigated the phytotoxicity of the concentration of oil sands naphthenic acids (NAs) in different MFT drying chemical treatments, in both planted and unplanted systems. We demonstrate that although growth was reduced, the emergent macrophyte common reed was capable of growing in diluted unamended MFT runoff, as well as in diluted runoff from MFT amended with either 0.25% lime and gypsum or 0.5% gypsum. Common reed can thus assist in the dewatering process of oil sands MFT. However, simulated runoff or seepage waters from chemically amended and dried MFT were phytotoxic, due to combined levels of salts, naphthenic acids and pH. Phytoremediation of runoff water/ground water seepage from dry-land applied MFT will thus require pre-treatment in order to make conditions more favorable for plant growth.

The measles virus N(TAIL)-XD complex: an illustrative example of fuzziness.

PubMed

Longhi, Sonia

2012-01-01

In this chapter, I focus on the biochemical and structural characterization of the complex between the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (N(TAIL)) and the C-terminal X domain (XD) of the viral phosphoprotein (P). I summarize the main experimental data available so far pointing out the prevalently disordered nature of N(TAIL) even after complex formation and the role of the flexible C-terminal appendage in the binding reaction. I finally discuss the possible functional role of these residual disordered regions within the complex in terms of their ability to capture other regulatory, binding partners.

Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parent, Kristin N., E-mail: kparent@msu.edu; Tang, Jinghua; Cardone, Giovanni

CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the “HK97-fold” shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain (“I-domain”), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphologymore » of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently. - Highlights: • Asymmetric and symmetric three-dimensional reconstructions of phage CUS-3 are presented. • CUS-3 major capsid protein has a conserved I-domain, which is found in all three categories of “P22-like phage”. • CUS-3 has very different tailspike receptor binding domain from those of P22 and Sf6. • The CUS-3 tailspike likely was acquired by horizontal gene transfer.« less

Trace metal mobilization from oil sands froth treatment thickened tailings exhibiting acid rock drainage.

PubMed

Kuznetsova, Alsu; Kuznetsov, Petr; Foght, Julia M; Siddique, Tariq

2016-11-15

Froth treatment thickened tailings (TT) are a waste product of bitumen extraction from surface-mined oil sands ores. When incubated in a laboratory under simulated moist oxic environmental conditions for ~450d, two different types of TT (TT1 and TT2) exhibited the potential to generate acid rock drainage (ARD) by producing acid leachate after 250 and 50d, respectively. We report here the release of toxic metals from TT via ARD, which could pose an environmental threat if oil sands TT deposits are not properly managed. Trace metal concentrations in leachate samples collected periodically revealed that Mn and Sr were released immediately even before the onset of ARD. Spikes in Co and Ni concentrations were observed both pre-ARD and during active ARD, particularly in TT1. For most elements measured (Fe, Cr, V, As, Cu, Pb, Zn, Cd, and Se), leaching was associated with ARD production. Though equivalent acidification (pH2) was achieved in leachate from both TT types, greater metal release was observed from TT2 where concentrations reached 10,000ppb for Ni, 5000ppb for Co, 3000ppb for As, 2000ppb for V, and 1000ppb for Cr. Generally, metal concentrations decreased in leachate with time during ARD and became negligible by the end of incubation (~450d) despite appreciable metals remaining in the leached TT. These results suggest that using TT for land reclamation purposes or surface deposition for volume reduction may unfavorably impact the environment, and warrants application of appropriate strategies for management of pyrite-enriched oil sands tailings streams. Copyright © 2016 Elsevier B.V. All rights reserved.

The Effect of Lactic Acid Bacteria-fermented Soybean Milk Products on Carrageenan-induced Tail Thrombosis in Rats

PubMed Central

KAMIYA, Seitaro; OGASAWARA, Masayoshi; ARAKAWA, Masayuki; HAGIMORI, Masayori

2013-01-01

Thrombosis is characterized by congenital and acquired procatarxis. Lactic acid bacteria-fermented soybean milk products (FS-LAB) inhibit hepatic lipid accumulation and prevent atherosclerotic plaque formation. However, the therapeutic efficacy of FS-LAB against thrombosis has yet to be investigated. In this study, FS-LAB were administered subcutaneously into the tails of rats, with the subsequent intravenous administration of κ-carrageenan 12 hr after the initial injection. In general, administration of κ-carrageenan induces thrombosis. The length of the infarcted tail regions was significantly shorter in the rats administered a single-fold or double-fold concentration of the FS-LAB solution compared with the region in control rats. Therefore, FS-LAB exhibited significant antithrombotic effects. Our study is the first to characterize the properties of FS-LAB and, by testing their efficacy on an in vivo rat model of thrombosis, demonstrate the potency of their antithrombotic effect. PMID:24936368

Inhibition of acid mine drainage and immobilization of heavy metals from copper flotation tailings using a marble cutting waste

NASA Astrophysics Data System (ADS)

Tozsin, Gulsen

2016-01-01

Acid mine drainage (AMD) with high concentrations of sulfates and metals is generated by the oxidation of sulfide bearing wastes. CaCO3-rich marble cutting waste is a residual material produced by the cutting and polishing of marble stone. In this study, the feasibility of using the marble cutting waste as an acid-neutralizing agent to inhibit AMD and immobilize heavy metals from copper flotation tailings (sulfide- bearing wastes) was investigated. Continuous-stirring shake-flask tests were conducted for 40 d, and the pH value, sulfate content, and dissolved metal content of the leachate were analyzed every 10 d to determine the effectiveness of the marble cutting waste as an acid neutralizer. For comparison, CaCO3 was also used as a neutralizing agent. The average pH value of the leachate was 2.1 at the beginning of the experiment ( t = 0). In the experiment employing the marble cutting waste, the pH value of the leachate changed from 6.5 to 7.8, and the sulfate and iron concentrations decreased from 4558 to 838 mg/L and from 536 to 0.01 mg/L, respectively, after 40 d. The marble cutting waste also removed more than 80wt% of heavy metals (Cd, Cr, Cu, Ni, Pb, and Zn) from AMD generated by copper flotation tailings.

Comparative analysis of barophily-related amino acid content in protein domains of Pyrococcus abyssi and Pyrococcus furiosus.

PubMed

Yafremava, Liudmila S; Di Giulio, Massimo; Caetano-Anollés, Gustavo

2013-01-01

Amino acid substitution patterns between the nonbarophilic Pyrococcus furiosus and its barophilic relative P. abyssi confirm that hydrostatic pressure asymmetry indices reflect the extent to which amino acids are preferred by barophilic archaeal organisms. Substitution patterns in entire protein sequences, shared protein domains defined at fold superfamily level, domains in homologous sequence pairs, and domains of very ancient and very recent origin now provide further clues about the environment that led to the genetic code and diversified life. The pyrococcal proteomes are very similar and share a very early ancestor. Relative amino acid abundance analyses showed that biases in the use of amino acids are due to their shared fold superfamilies. Within these repertoires, only two of the five amino acids that are preferentially barophilic, aspartic acid and arginine, displayed this preference significantly and consistently across structure and in domains appearing in the ancestor. The more primordial asparagine, lysine and threonine displayed a consistent preference for nonbarophily across structure and in the ancestor. Since barophilic preferences are already evident in ancient domains that are at least ~3 billion year old, we conclude that barophily is a very ancient trait that unfolded concurrently with genetic idiosyncrasies in convergence towards a universal code.

Plant Growth-Promoting Bacteria for Phytostabilization of Mine Tailings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grandlic, C.J.; Mendez, M.O.; Chorover, J.

2009-05-19

Eolian dispersion of mine tailings in arid and semiarid environments is an emerging global issue for which economical remediation alternatives are needed. Phytostabilization, the revegetation of these sites with native plants, is one such alternative. Revegetation often requires the addition of bulky amendments such as compost which greatly increases cost. We report the use of plant growth-promoting bacteria (PGPB) to enhance the revegetation of mine tailings and minimize the need for compost amendment. Twenty promising PGPB isolates were used as seed inoculants in a series of greenhouse studies to examine revegetation of an extremely acidic, high metal content tailings samplemore » previously shown to require 15% compost amendment for normal plant growth. Several isolates significantly enhanced growth of two native species, quailbush and buffalo grass, in tailings. In this study, PGPB/compost outcomes were plant specific; for quailbush, PGPB were most effective in combination with 10% compost addition while for buffalo grass, PGPB enhanced growth in the complete absence of compost. Results indicate that selected PGPB can improve plant establishment and reduce the need for compost amendment. Further, PGPB activities necessary for aiding plant growth in mine tailings likely include tolerance to acidic pH and metals.« less

SIALIC ACIDS AND AUTOIMMUNE DISEASE

PubMed Central

Mahajan, Vinay S.; Pillai, Shiv

2016-01-01

summary An important underlying mechanism that contributes to autoimmunity is the loss of inhibitory signaling in the immune system. Sialic acid-recognizing Ig superfamily lectins or Siglecs are a family of cell surface proteins largely expressed in hematopoietic cells. The majority of Siglecs are inhibitory receptors expressed in immune cells that bind to sialic acid containing ligands and recruit SH2-domain containing tyrosine phosphatases to their cytoplasmic tails. They deliver inhibitory signals that can contribute to the constraining of immune cells and thus protect the host from autoimmunity. The inhibitory functions of CD22/Siglec-2 and Siglec-G and their contributions to tolerance and autoimmunity, primarily in the B lymphocyte context, are considered in some detail in this review. The relevance to autoimmunity and unregulated inflammation of modified sialic acids, enzymes that modify sialic acid, and other sialic acid binding proteins are also reviewed. PMID:26683151

The Lipid domain Phase diagram in a Dipalmitoyl-PC/Docosahaexnoic Acid-PE/Cholesterol System

NASA Astrophysics Data System (ADS)

Lor, Chai; Hirst, Linda

2011-03-01

Lipid domains in bilayer membrane and polyunsaturated fatty acids (PUFAs) are thought to play an important role in cellular activities. In particular, lipids containing docosahaexnoic acid are an interesting class of PUFAs due to their health benefits. In this project, we perform oxidation measurements of DHA-PE to determine the rate of oxidation in combination with antioxidants. A ternary diagram of DPPC/DHA-PE/cholesterol is mapped out to identify phase separation phenomena using atomic force microscope (AFM). Fluorescence microscopy is also used to image lipid domains in a flat bilayer with fluorescent labels. As expected, we observe the phase, shape, and size of lipid domains changes with varying composition. Moreover, we find that the roughness of the domains changes possibly due to overpacking of cholesterol in domains. This model study provides further understanding of the role of cholesterol in the bilayer membrane leading towards a better understanding of cell membranes. NSF award # DMR 0852791, ``CAREER: Self-Assembly of Polyunsaturated Lipids and Cholesterol In The Cell Membrane.''

Structure of bacteriophage T4 fibritin: a segmented coiled coil and the role of the C-terminal domain.

PubMed

Tao, Y; Strelkov, S V; Mesyanzhinov, V V; Rossmann, M G

1997-06-15

Oligomeric coiled-coil motifs are found in numerous protein structures; among them is fibritin, a structural protein of bacteriophage T4, which belongs to a class of chaperones that catalyze a specific phage-assembly process. Fibritin promotes the assembly of the long tail fibers and their subsequent attachment to the tail baseplate; it is also a sensing device that controls the retraction of the long tail fibers in adverse environments and, thus, prevents infection. The structure of fibritin had been predicted from sequence and biochemical analyses to be mainly a triple-helical coiled coil. The determination of its structure at atomic resolution was expected to give insights into the assembly process and biological function of fibritin, and the properties of modified coiled-coil structures in general. The three-dimensional structure of fibritin E, a deletion mutant of wild-type fibritin, was determined to 2.2 A resolution by X-ray crystallography. Three identical subunits of 119 amino acid residues form a trimeric parallel coiled-coil domain and a small globular C-terminal domain about a crystallographic threefold axis. The coiled-coil domain is divided into three segments that are separated by insertion loops. The C-terminal domain, which consists of 30 residues from each subunit, contains a beta-propeller-like structure with a hydrophobic interior. The residues within the C-terminal domain make extensive hydrophobic and some polar intersubunit interactions. This is consistent with the C-terminal domain being important for the correct assembly of fibritin, as shown earlier by mutational studies. Tight interactions between the C-terminal residues of adjacent subunits counteract the latent instability that is suggested by the structural properties of the coiled-coil segments. Trimerization is likely to begin with the formation of the C-terminal domain which subsequently initiates the assembly of the coiled coil. The interplay between the stabilizing effect of the C

Lysophosphatidic acids are new substrates for the phosphatase domain of soluble epoxide hydrolase.

PubMed

Oguro, Ami; Imaoka, Susumu

2012-03-01

Soluble epoxide hydrolase (sEH) is a bifunctional enzyme that has a C-terminus epoxide hydrolase domain and an N-terminus phosphatase domain. The endogenous substrates of epoxide hydrolase are known to be epoxyeicosatrienoic acids, but the endogenous substrates of the phosphatase activity are not well understood. In this study, to explore the substrates of sEH, we investigated the inhibition of the phosphatase activity of sEH toward 4-methylumbelliferyl phosphate by using lecithin and its hydrolyzed products. Although lecithin itself did not inhibit the phosphatase activity, the hydrolyzed lecithin significantly inhibited it, suggesting that lysophospholipid or fatty acid can inhibit it. Next, we investigated the inhibition of phosphatase activity by lysophosphatidyl choline, palmitoyl lysophosphatidic acid, monopalmitoyl glycerol, and palmitic acid. Palmitoyl lysophosphatidic acid and fatty acid efficiently inhibited phosphatase activity, suggesting that lysophosphatidic acids (LPAs) are substrates for the phosphatase activity of sEH. As expected, palmitoyl, stearoyl, oleoyl, and arachidonoyl LPAs were efficiently dephosphorylated by sEH (Km, 3-7 μM; Vmax, 150-193 nmol/min/mg). These results suggest that LPAs are substrates of sEH, which may regulate physiological functions of cells via their metabolism.

Direct observation of charged domain walls in hybrid improper ferroelectric (Ca,Sr)3Ti2O7

NASA Astrophysics Data System (ADS)

Kurushima, Kousuke; Yoshimoto, Wataru; Ishii, Yui; Cheong, Sang-Wook; Mori, Shigeo

2017-10-01

We investigated ferroelectric (FE) domain wall structures including “charged domain walls” of hybrid improper FE (Ca,Sr)3Ti2O7 at the subatomic resolution by dark-field transmission electron microscopy (TEM) and high-resolution state-of-the-art aberration-corrected high-angle annular-dark-field (HAADF) scanning transmission electron microscopy (STEM). Dark-field TEM and high-resolution HAADF-STEM images obtained in the FE phase of single crystals of Ca2.46Sr0.54Ti2O7 revealed the formation of abundant charged domain walls with the head-to-head and tail-to-tail configurations in the FE domain structure, in addition to the FE 180° domain structure. The charged domain walls with the head-to-head and tail-to-tail FE polarizations exist stably and can be characterized as the unique double arc-type displacement of Ca/Sr ions in a unit cell without charge accumulation.

Metal leaching in mine tailings: short-term impact of biochar and wood ash amendments.

PubMed

Beauchemin, Suzanne; Clemente, Joyce S; MacKinnon, Ted; Tisch, Bryan; Lastra, Rolando; Smith, Derek; Kwong, John

2015-01-01

Biochar is perceived as a promising amendment to reclaim degraded, metal-contaminated lands. The objective of this study was to compare the potential of biochar and wood ash amendments to reduce metal(loid) leaching in mine tailings. A 2-mo leaching experiment was conducted in duplicate on acidic and alkaline tailings, each mixed with 5 wt.% of one of the following amendments: three wood-derived, fast-pyrolysis biochars (OC > 57 wt.%) and two wood ash materials (organic carbon [OC] ≤ 16 wt.%); a control test with no carbon input was also added. The columns were leached with water after 1, 2, 4, 8, 16, 32, and 64 d, and the leachates were monitored for dissolved metals, OC, and pH. For the acidic and alkaline tailings, the most significant impact on metal mobility was observed with wood ash materials due to their greater neutralization potential (>15% CaCO eq.) compared with biochar (≤3.3% CaCO eq.). An increase of 1 pH unit in the wood ash-treated alkaline tailings led to an undesirable mobilization of As and Se. The addition of biochar did not significantly reduce the leaching of the main contaminants (Cu and Ni in the acidic tailings and As in the alkaline tailings) over 2 mo. The Se attenuation noted in some biochar-treated acid tailings may be mainly due to a slight alkaline effect rather than Se removal by biochar, given the low capacity for the fresh biochars to retain Se under acidic conditions (pH 4.5). The increased loss of dissolved OC in the biochar-amended systems was of short duration and was not associated with metal(loid) mobilization. Copyright © Her Majesty the Queen in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada.

Spectral induced polarization (SIP) response of mine tailings.

PubMed

Placencia-Gómez, Edmundo; Parviainen, Annika; Slater, Lee; Leveinen, Jussi

2015-02-01

Mine tailings impoundments are a source of leachates known as acid mine drainage (AMD) which can pose a contamination risk for surrounding surface and groundwater. Methodologies which can help management of this environmental issue are needed. We carried out a laboratory study of the spectral induced polarization (SIP) response of tailings from the Haveri Au-Cu mine, SW Finland. The primary objectives were, (1) to determine possible correlations between SIP parameters and textural properties associated with oxidative-weathering mechanisms, mineralogical composition and metallic content, and (2) to evaluate the effects of the pore water chemistry on SIP parameters associated with redox-inactive and redox-active electrolytes varying in molar concentration, conductivity and pH. The Haveri tailings exhibit well defined relaxation spectra between 100 and 10,000Hz. The relaxation magnitudes are governed by the in-situ oxidative-weathering conditions on sulphide mineral surfaces contained in the tailings, and decrease with the oxidation degree. The oxidation-driven textural variation in the tailings results in changes to the frequency peak of the phase angle, the imaginary conductivity and chargeability, when plotted versus the pore water conductivity. In contrast, the real and the formation electrical conductivity components show a single linear dependence on the pore water conductivity. The increase of the pore water conductivity (dominated by the increase of ions concentration in solution) along with a transition to acidic conditions shifts the polarization peak towards higher frequencies. These findings show the unique sensitivity of the SIP method to potentially discriminate AMD discharges from reactive oxidation zones in tailings, suggesting a significant advantage for monitoring threatened aquifers. Copyright © 2014 Elsevier B.V. All rights reserved.

Spectral induced polarization (SIP) response of mine tailings

NASA Astrophysics Data System (ADS)

Placencia-Gómez, Edmundo; Parviainen, Annika; Slater, Lee; Leveinen, Jussi

2015-02-01

Mine tailings impoundments are a source of leachates known as acid mine drainage (AMD) which can pose a contamination risk for surrounding surface and groundwater. Methodologies which can help management of this environmental issue are needed. We carried out a laboratory study of the spectral induced polarization (SIP) response of tailings from the Haveri Au-Cu mine, SW Finland. The primary objectives were, (1) to determine possible correlations between SIP parameters and textural properties associated with oxidative-weathering mechanisms, mineralogical composition and metallic content, and (2) to evaluate the effects of the pore water chemistry on SIP parameters associated with redox-inactive and redox-active electrolytes varying in molar concentration, conductivity and pH. The Haveri tailings exhibit well defined relaxation spectra between 100 and 10,000 Hz. The relaxation magnitudes are governed by the in-situ oxidative-weathering conditions on sulphide mineral surfaces contained in the tailings, and decrease with the oxidation degree. The oxidation-driven textural variation in the tailings results in changes to the frequency peak of the phase angle, the imaginary conductivity and chargeability, when plotted versus the pore water conductivity. In contrast, the real and the formation electrical conductivity components show a single linear dependence on the pore water conductivity. The increase of the pore water conductivity (dominated by the increase of ions concentration in solution) along with a transition to acidic conditions shifts the polarization peak towards higher frequencies. These findings show the unique sensitivity of the SIP method to potentially discriminate AMD discharges from reactive oxidation zones in tailings, suggesting a significant advantage for monitoring threatened aquifers.

Effects of three low-molecular-weight organic acids (LMWOAs) and pH on the mobilization of arsenic and heavy metals (Cu, Pb, and Zn) from mine tailings.

PubMed

Wang, Suiling; Mulligan, Catherine N

2013-02-01

Natural organic acids may play an important role in influencing the mobility of toxic contaminants in the environment. The mobilization of arsenic (As) and heavy metals from an oxidized Pb-Zn mine tailings sample in the presence of three low-molecular-weight organic acids, aspartic acid, cysteine, and succinic acid, was investigated at a mass ratio of 10 mg organic additive/g mine tailings in this study. The effect of pH was also evaluated. The mine tailings sample, containing elevated levels of As (2,180 mg/kg), copper (Cu, 1,100 mg/kg), lead (Pb, 12,860 mg/kg), and zinc (Zn, 5,075 mg/kg), was collected from Bathurst, New Brunswick, Canada. It was found that the organic additives inhibited As and heavy metal mobilization under acidic conditions (at pH 3 or 5), but enhanced it under neutral to alkaline conditions (at pH above 7) through forming aqueous organic complexes. At pH 11, As, Cu, Pb, and Zn were mobilized mostly by the organic additives, 45, 46, 1,660, and 128 mg/kg by aspartic acid, 31, 28, 1,040, and 112 mg/kg by succinic acid, and 53, 38, 2,020, and 150 mg/kg by cysteine, respectively, whereas those by distilled water were 6, 16, 260, and 52 mg/kg, respectively. It was also found that the mobilization of As and the heavy metals was closely correlated, and both were closely correlated to Fe mobilization. Arsenic mobilization by the three LMWOAs was found to be consistent with the order of the stability of Fe-, Cu-, Pb-, and Zn-organic ligand complexes. The organic acids might be used potentially in the natural attenuation and remediation of As and heavy metal-contaminated sites.

Structure of a double ubiquitin-like domain in the talin head: a role in integrin activation

PubMed Central

Goult, Benjamin T; Bouaouina, Mohamed; Elliott, Paul R; Bate, Neil; Patel, Bipin; Gingras, Alexandre R; Grossmann, J Günter; Roberts, Gordon C K; Calderwood, David A; Critchley, David R; Barsukov, Igor L

2010-01-01

Talin is a 270-kDa protein that activates integrins and couples them to cytoskeletal actin. Talin contains an N-terminal FERM domain comprised of F1, F2 and F3 domains, but it is atypical in that F1 contains a large insert and is preceded by an extra domain F0. Although F3 contains the binding site for β-integrin tails, F0 and F1 are also required for activation of β1-integrins. Here, we report the solution structures of F0, F1 and of the F0F1 double domain. Both F0 and F1 have ubiquitin-like folds joined in a novel fixed orientation by an extensive charged interface. The F1 insert forms a loop with helical propensity, and basic residues predicted to reside on one surface of the helix are required for binding to acidic phospholipids and for talin-mediated activation of β1-integrins. This and the fact that basic residues on F2 and F3 are also essential for integrin activation suggest that extensive interactions between the talin FERM domain and acidic membrane phospholipids are required to orientate the FERM domain such that it can activate integrins. PMID:20150896

Binding of aldolase and glyceraldehyde-3-phosphate dehydrogenase to the cytoplasmic tails of Plasmodium falciparum merozoite duffy binding-like and reticulocyte homology ligands.

PubMed

Pal-Bhowmick, Ipsita; Andersen, John; Srinivasan, Prakash; Narum, David L; Bosch, Jürgen; Miller, Louis H

2012-01-01

Invasion of erythrocytes by Plasmodium falciparum requires a connection between the cytoplasmic tail of the parasite's ligands for its erythrocyte receptors and the actin-myosin motor of the parasite. For the thromobospondin-related anonymous protein (TRAP) ligand on Plasmodium sporozoites, aldolase forms this connection and requires tryptophan and negatively charged amino acids in the ligand's cytoplasmic tail. Because of the importance of the Duffy binding-like (DBL) and the reticulocyte homology (RH) ligand families in erythrocyte binding and merozoite invasion, we characterized the ability of their cytoplasmic tails to bind aldolase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), both of which bind actin. We tested the binding of the cytoplasmic peptides of the two ligand families to aldolase and GAPDH. Only the cytoplasmic peptides of some RH ligands showed strong binding to aldolase, and the binding depended on the presence of an aromatic amino acid (phenylalanine or tyrosine), rather than tryptophan, in the context of negatively charged amino acids. The binding was confirmed by surface plasmon resonance analysis and was found to represent affinity similar to that seen with TRAP. An X-ray crystal structure of aldolase at 2.5 Å in the presence of RH2b peptide suggested that the binding site location was near the TRAP-binding site. GAPDH bound to some of the cytoplasmic tails of certain RH and DBL ligands in an aromatic amino acid-dependent manner. Thus, the connection between Plasmodium merozoite ligands and erythrocyte receptors and the actin motor can be achieved through the activity of either aldolase or GAPDH by mechanisms that do not require tryptophan but, rather, other aromatic amino acids. IMPORTANCE The invasion of the Plasmodium merozoite into erythrocytes is a critical element in malaria pathogenesis. It is important to understand the molecular details of this process, as this machinery can be a target for both vaccine and drug development

Plant growth-promoting bacteria for phytostabilization of mine tailings.

PubMed

Grandlic, Christopher J; Mendez, Monica O; Chorover, Jon; Machado, Blenda; Maier, Raina M

2008-03-15

Eolian dispersion of mine tailings in arid and semiarid environments is an emerging global issue for which economical remediation alternatives are needed. Phytostabilization, the revegetation of these sites with native plants, is one such alternative. Revegetation often requires the addition of bulky amendments such as compost which greatly increases cost. We report the use of plant growth-promoting bacteria (PGPB) to enhance the revegetation of mine tailings and minimize the need for compost amendment. Twenty promising PGPB isolates were used as seed inoculants in a series of greenhouse studies to examine revegetation of an extremely acidic, high metal contenttailings sample previously shown to require 15% compost amendment for normal plant growth. Several isolates significantly enhanced growth of two native species, quailbush and buffalo grass, in tailings. In this study, PGPB/compost outcomes were plant specific; for quailbush, PGPB were most effective in combination with 10% compost addition while for buffalo grass, PGPB enhanced growth in the complete absence of compost. Results indicate that selected PGPB can improve plant establishment and reduce the need for compost amendment. Further, PGPB activities necessary for aiding plant growth in mine tailings likely include tolerance to acidic pH and metals.

Functional map of arrestin-1 at single amino acid resolution.

PubMed

Ostermaier, Martin K; Peterhans, Christian; Jaussi, Rolf; Deupi, Xavier; Standfuss, Jörg

2014-02-04

Arrestins function as adapter proteins that mediate G protein-coupled receptor (GPCR) desensitization, internalization, and additional rounds of signaling. Here we have compared binding of the GPCR rhodopsin to 403 mutants of arrestin-1 covering its complete sequence. This comprehensive and unbiased mutagenesis approach provides a functional dimension to the crystal structures of inactive, preactivated p44 and phosphopeptide-bound arrestins and will guide our understanding of arrestin-GPCR complexes. The presented functional map quantitatively connects critical interactions in the polar core and along the C tail of arrestin. A series of amino acids (Phe375, Phe377, Phe380, and Arg382) anchor the C tail in a position that blocks binding of the receptor. Interaction of phosphates in the rhodopsin C terminus with Arg29 controls a C-tail exchange mechanism in which the C tail of arrestin is released and exposes several charged amino acids (Lys14, Lys15, Arg18, Lys20, Lys110, and Lys300) for binding of the phosphorylated receptor C terminus. In addition to this arrestin phosphosensor, our data reveal several patches of amino acids in the finger (Gln69 and Asp73-Met75) and the lariat loops (L249-S252 and Y254) that can act as direct binding interfaces. A stretch of amino acids at the edge of the C domain (Trp194-Ser199, Gly337-Gly340, Thr343, and Thr345) could act as membrane anchor, binding interface for a second rhodopsin, or rearrange closer to the central loops upon complex formation. We discuss these interfaces in the context of experimentally guided docking between the crystal structures of arrestin and light-activated rhodopsin.

The basic amino acids in the coiled-coil domain of CIN85 regulate its interaction with c-Cbl and phosphatidic acid during epidermal growth factor receptor (EGFR) endocytosis.

PubMed

Zheng, Xiudan; Zhang, Jing; Liao, Kan

2014-07-08

During EGFR internalization CIN85 bridges EGFR-Cbl complex, endocytic machinery and fusible membrane through the interactions of CIN85 with c-Cbl, endophilins and phosphatidic acid. These protein-protein and protein-lipid interactions are mediated or regulated by the positively charged C-terminal coiled-coil domain of CIN85. However, the details of CIN85-lipid interaction remain unknown. The present study suggested a possible electric interaction between the negative charge of phosphatidic acid and the positive charge of basic amino acids in coiled-coil domain. Mutations of the basic amino acids in the coiled-coil domain, especially K645, K646, R648 and R650, into neutral amino acid alanine completely blocked the interaction of CIN85 with c-Cbl or phosphatidic acid. However, they did not affect CIN85-endophilin interaction. In addition, CIN85 was found to associate with the internalized EGFR endosomes. It interacted with several ESCRT (Endosomal Sorting Complex Required for Transport) component proteins for ESCRT assembly on endosomal membrane. Mutations in the coiled-coil domain (deletion of the coiled-coil domain or point mutations of the basic amino acids) dissociated CIN85 from endosomes. These mutants bound the ESCRT components in cytoplasm to prevent them from assembly on endosomal membrane and inhibited EGFR sorting for degradation. As an adaptor protein, CIN85 interacts with variety of partners through several domains. The positive charges of basic amino acids in the coiled-coil domain are not only involved in the interaction with phosphatidic acid, but also regulate the interaction of CIN85 with c-Cbl. CIN85 also interacts with ESCRT components for protein sorting in endosomes. These CIN85-protein and CIN85-lipid interactions enable CIN85 to link EGFR-Cbl endocytic complex with fusible membrane during EGFR endocytosis and subsequently to facilitate ESCRT formation on endosomal membrane for EGFR sorting and degradation.

Traveling waves and their tails in locally resonant granular systems

DOE PAGES

Xu, H.; Kevrekidis, P. G.; Stefanov, A.

2015-04-22

In the present study, we revisit the theme of wave propagation in locally resonant granular crystal systems, also referred to as mass-in-mass systems. We use three distinct approaches to identify relevant traveling waves. In addition, the first consists of a direct solution of the traveling wave problem. The second one consists of the solution of the Fourier tranformed variant of the problem, or, more precisely, of its convolution reformulation (upon an inverse Fourier transform) in real space. Finally, our third approach will restrict considerations to a finite domain, utilizing the notion of Fourier series for important technical reasons, namely themore » avoidance of resonances, which will be discussed in detail. All three approaches can be utilized in either the displacement or the strain formulation. Typical resulting computations in finite domains result in the solitary waves bearing symmetric non-vanishing tails at both ends of the computational domain. Importantly, however, a countably infinite set of anti-resonance conditions is identified for which solutions with genuinely rapidly decaying tails arise.« less

Traveling waves and their tails in locally resonant granular systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, H.; Kevrekidis, P. G.; Stefanov, A.

In the present study, we revisit the theme of wave propagation in locally resonant granular crystal systems, also referred to as mass-in-mass systems. We use three distinct approaches to identify relevant traveling waves. In addition, the first consists of a direct solution of the traveling wave problem. The second one consists of the solution of the Fourier tranformed variant of the problem, or, more precisely, of its convolution reformulation (upon an inverse Fourier transform) in real space. Finally, our third approach will restrict considerations to a finite domain, utilizing the notion of Fourier series for important technical reasons, namely themore » avoidance of resonances, which will be discussed in detail. All three approaches can be utilized in either the displacement or the strain formulation. Typical resulting computations in finite domains result in the solitary waves bearing symmetric non-vanishing tails at both ends of the computational domain. Importantly, however, a countably infinite set of anti-resonance conditions is identified for which solutions with genuinely rapidly decaying tails arise.« less

Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings.

PubMed

Chen, Lin-Xing; Li, Jin-Tian; Chen, Ya-Ting; Huang, Li-Nan; Hua, Zheng-Shuang; Hu, Min; Shu, Wen-Sheng

2013-09-01

In an attempt to link the microbial community composition and function in mine tailings to the generation of acid mine drainage, we simultaneously explored the geochemistry and microbiology of six tailings collected from a lead/zinc mine, i.e. primary tailings (T1), slightly acidic tailings (T2), extremely acidic tailings (T3, T4 and T5) and orange-coloured oxidized tailings (T6). Geochemical results showed that the six tailings (from T1 to T6) likely represented sequential stages of the acidification process of the mine tailings. 16S rRNA pyrosequencing revealed a contrasting microbial composition between the six tailings: Proteobacteria-related sequences dominated T1-T3 with relative abundance ranging from 56 to 93%, whereas Ferroplasma-related sequences dominated T4-T6 with relative abundance ranging from 28 to 58%. Furthermore, metagenomic analysis of the microbial communities of T2 and T6 indicated that the genes encoding key enzymes for microbial carbon fixation, nitrogen fixation and sulfur oxidation in T2 were largely from Thiobacillus and Acidithiobacillus, Methylococcus capsulatus, and Thiobacillus denitrificans respectively; while those in T6 were mostly identified in Acidithiobacillus and Leptospirillum, Acidithiobacillus and Leptospirillum, and Acidithiobacillus respectively. The microbial communities in T2 and T6 harboured more genes suggesting diverse metabolic capacities for sulfur oxidation/heavy metal detoxification and tolerating low pH respectively. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails.

PubMed

Benleulmi, Mohamed S; Matysiak, Julien; Robert, Xavier; Miskey, Csaba; Mauro, Eric; Lapaillerie, Delphine; Lesbats, Paul; Chaignepain, Stéphane; Henriquez, Daniel R; Calmels, Christina; Oladosu, Oyindamola; Thierry, Eloïse; Leon, Oscar; Lavigne, Marc; Andreola, Marie-Line; Delelis, Olivier; Ivics, Zoltán; Ruff, Marc; Gouet, Patrice; Parissi, Vincent

2017-11-28

Stable insertion of the retroviral DNA genome into host chromatin requires the functional association between the intasome (integrase·viral DNA complex) and the nucleosome. The data from the literature suggest that direct protein-protein contacts between integrase and histones may be involved in anchoring the intasome to the nucleosome. Since histone tails are candidates for interactions with the incoming intasomes we have investigated whether they could participate in modulating the nucleosomal integration process. We show here that histone tails are required for an optimal association between HIV-1 integrase (IN) and the nucleosome for efficient integration. We also demonstrate direct interactions between IN and the amino-terminal tail of human histone H4 in vitro. Structure/function studies enabled us to identify amino acids in the carboxy-terminal domain of IN that are important for this interaction. Analysis of the nucleosome-binding properties of catalytically active mutated INs confirmed that their ability to engage the nucleosome for integration in vitro was affected. Pseudovirus particles bearing mutations that affect the IN/H4 association also showed impaired replication capacity due to altered integration and re-targeting of their insertion sites toward dynamic regions of the chromatin with lower nucleosome occupancy. Collectively, our data support a functional association between HIV-1 IN and histone tails that promotes anchoring of the intasome to nucleosomes and optimal integration into chromatin.

Lysophosphatidic acids are new substrates for the phosphatase domain of soluble epoxide hydrolase[S

PubMed Central

Oguro, Ami; Imaoka, Susumu

2012-01-01

Soluble epoxide hydrolase (sEH) is a bifunctional enzyme that has a C-terminus epoxide hydrolase domain and an N-terminus phosphatase domain. The endogenous substrates of epoxide hydrolase are known to be epoxyeicosatrienoic acids, but the endogenous substrates of the phosphatase activity are not well understood. In this study, to explore the substrates of sEH, we investigated the inhibition of the phosphatase activity of sEH toward 4-methylumbelliferyl phosphate by using lecithin and its hydrolyzed products. Although lecithin itself did not inhibit the phosphatase activity, the hydrolyzed lecithin significantly inhibited it, suggesting that lysophospholipid or fatty acid can inhibit it. Next, we investigated the inhibition of phosphatase activity by lysophosphatidyl choline, palmitoyl lysophosphatidic acid, monopalmitoyl glycerol, and palmitic acid. Palmitoyl lysophosphatidic acid and fatty acid efficiently inhibited phosphatase activity, suggesting that lysophosphatidic acids (LPAs) are substrates for the phosphatase activity of sEH. As expected, palmitoyl, stearoyl, oleoyl, and arachidonoyl LPAs were efficiently dephosphorylated by sEH (Km, 3–7 μM; Vmax, 150–193 nmol/min/mg). These results suggest that LPAs are substrates of sEH, which may regulate physiological functions of cells via their metabolism. PMID:22217705

Mineralogy and Geochemical Processes of Carbonate Mineral-rich Sulfide Mine Tailings, Zimapan, Mexico

NASA Astrophysics Data System (ADS)

McClure, R. J.; Deng, Y.; Loeppert, R.; Herbert, B. E.; Carrillo, R.; Gonzalez, C.

2009-12-01

Mining for silver, lead, zinc, and copper in Zimapan, Hidalgo State, Mexico has been ongoing since 1576. High concentrations of heavy metals have been found in several mine tailing heaps in the Zimapan area, with concentrations of arsenic observed as high as 28,690 mg/kg and levels of Pb as high as 2772 mg/kg. Unsecured tailings heaps and associated acid mine drainage has presented tremendous problems to revegetation, water quality, and dust emission control in the Zimapan area. Although acid mine drainage problems related to weathering of sulfide minerals have been extensively studied and are well known, the weathering products of sulfides in areas with a significant presence of carbonate minerals and their effect on the mobility of heavy metals warrant further study. Carbonate minerals are expected to neutralize sulfuric acid produced from weathering of sulfide minerals, however, in the Zimapan area localized areas of pH as low as 1.8 were observed within carbonate mineral-rich tailing heaps. The objectives of this study are to characterize (1) the heavy metal-containing sulfide minerals in the initial tailing materials, (2) the intermediate oxidation products of sulfide minerals within the carbonate-rich tailings, (3) chemical species of heavy metals within pH gradients between 1.8 and 8.2, the approximate natural pH of limestone, and (4) the mobility of soluble and colloidal heavy metals and arsenic within the carbonate-rich tailings. Representative mine tailings and their intermediate oxidation products have been sampled from the Zimapan area. Mineralogical characterization will be conducted with X-ray diffraction, infrared spectroscopy, electron microscopes and microprobes, and chemical methods. Chemical species will be extracted by selective dissolution methods. Preliminary results have identified calcite as the dominant mineral in the tailing heaps with a pH of 7, suggesting non-equilibrium with the acidic weathering products. Other minerals identified in

Identification of Extracellular Domain Residues Required for Epithelial Na+ Channel Activation by Acidic pH

PubMed Central

Collier, Daniel M.; Peterson, Zerubbabel J.; Blokhin, Ilya O.; Benson, Christopher J.; Snyder, Peter M.

2012-01-01

A growing body of evidence suggests that the extracellular domain of the epithelial Na+ channel (ENaC) functions as a sensor that fine tunes channel activity in response to changes in the extracellular environment. We previously found that acidic pH increases the activity of human ENaC, which results from a decrease in Na+ self-inhibition. In the current work, we identified extracellular domain residues responsible for this regulation. We found that rat ENaC is less sensitive to pH than human ENaC, an effect mediated in part by the γ subunit. We identified a group of seven residues in the extracellular domain of γENaC (Asp-164, Gln-165, Asp-166, Glu-292, Asp-335, His-439, and Glu-455) that, when individually mutated to Ala, decreased proton activation of ENaC. γE455 is conserved in βENaC (Glu-446); mutation of this residue to neutral amino acids (Ala, Cys) reduced ENaC stimulation by acidic pH, whereas reintroduction of a negative charge (by MTSES modification of Cys) restored pH regulation. Combination of the seven γENaC mutations with βE446A generated a channel that was not activated by acidic pH, but inhibition by alkaline pH was intact. Moreover, these mutations reduced the effect of pH on Na+ self-inhibition. Together, the data identify eight extracellular domain residues in human β- and γENaC that are required for regulation by acidic pH. PMID:23060445

Stabilization of Nucleosomes by Histone Tails and by FACT Revealed by spFRET Microscopy

PubMed Central

Valieva, Maria E.; Gerasimova, Nadezhda S.; Kudryashova, Kseniya S.; Kozlova, Anastasia L.; Kirpichnikov, Mikhail P.; Hu, Qi; Botuyan, Maria Victoria; Mer, Georges; Feofanov, Alexey V.; Studitsky, Vasily M.

2017-01-01

A correct chromatin structure is important for cell viability and is tightly regulated by numerous factors. Human protein complex FACT (facilitates chromatin transcription) is an essential factor involved in chromatin transcription and cancer development. Here FACT-dependent changes in the structure of single nucleosomes were studied with single-particle Förster resonance energy transfer (spFRET) microscopy using nucleosomes labeled with a donor-acceptor pair of fluorophores, which were attached to the adjacent gyres of DNA near the contact between H2A-H2B dimers. Human FACT and its version without the C-terminal domain (CTD) and the high mobility group (HMG) domain of the structure-specific recognition protein 1 (SSRP1) subunit did not change the structure of the nucleosomes, while FACT without the acidic C-terminal domains of the suppressor of Ty 16 (Spt16) and the SSRP1 subunits caused nucleosome aggregation. Proteolytic removal of histone tails significantly disturbed the nucleosome structure, inducing partial unwrapping of nucleosomal DNA. Human FACT reduced DNA unwrapping and stabilized the structure of tailless nucleosomes. CTD and/or HMG domains of SSRP1 are required for this FACT activity. In contrast, previously it has been shown that yeast FACT unfolds (reorganizes) nucleosomes using the CTD domain of SSRP1-like Pol I-binding protein 3 subunit (Pob3). Thus, yeast and human FACT complexes likely utilize the same domains for nucleosome reorganization and stabilization, respectively, and these processes are mechanistically similar. PMID:28067802

Stabilization of Nucleosomes by Histone Tails and by FACT Revealed by spFRET Microscopy.

PubMed

Valieva, Maria E; Gerasimova, Nadezhda S; Kudryashova, Kseniya S; Kozlova, Anastasia L; Kirpichnikov, Mikhail P; Hu, Qi; Botuyan, Maria Victoria; Mer, Georges; Feofanov, Alexey V; Studitsky, Vasily M

2017-01-06

A correct chromatin structure is important for cell viability and is tightly regulated by numerous factors. Human protein complex FACT (facilitates chromatin transcription) is an essential factor involved in chromatin transcription and cancer development. Here FACT-dependent changes in the structure of single nucleosomes were studied with single-particle Förster resonance energy transfer (spFRET) microscopy using nucleosomes labeled with a donor-acceptor pair of fluorophores, which were attached to the adjacent gyres of DNA near the contact between H2A-H2B dimers. Human FACT and its version without the C-terminal domain (CTD) and the high mobility group (HMG) domain of the structure-specific recognition protein 1 (SSRP1) subunit did not change the structure of the nucleosomes, while FACT without the acidic C-terminal domains of the suppressor of Ty 16 (Spt16) and the SSRP1 subunits caused nucleosome aggregation. Proteolytic removal of histone tails significantly disturbed the nucleosome structure, inducing partial unwrapping of nucleosomal DNA. Human FACT reduced DNA unwrapping and stabilized the structure of tailless nucleosomes. CTD and/or HMG domains of SSRP1 are required for this FACT activity. In contrast, previously it has been shown that yeast FACT unfolds (reorganizes) nucleosomes using the CTD domain of SSRP1-like Pol I-binding protein 3 subunit (Pob3). Thus, yeast and human FACT complexes likely utilize the same domains for nucleosome reorganization and stabilization, respectively, and these processes are mechanistically similar.

Rapid oxidation of sulfide mine tailings by reaction with potassium ferrate.

PubMed

Murshed, Mohamed; Rockstraw, David A; Hanson, Adrian T; Johnson, Michael

2003-01-01

The chemistry of sulfide mine tailings treated with potassium ferrate (K2FeO4) in aqueous slurry has been investigated. The reaction system is believed to parallel a geochemical oxidation in which ferrate ion replaces oxygen. This chemical system utilized in a pipeline (as a plug flow reactor) may have application eliminating the potential for tailings to leach acid while recovering the metal from the tailings. Elemental analyses were performed using an ICP spectrometer for the aqueous phase extract of the treated tailings; and an SEM-EDX for the tailing solids. Solids were analyzed before and after treatments were applied. ICP shows that as the mass ratio of ferrate ion to tailings increases, the concentration of metals in the extract solution increases; while EDX indicates a corresponding decrease in sulfur content of the tailing solids. The extraction of metal and reduction in sulfide content is significant. The kinetic timeframe is on the order of minutes.

Essential role for SUN5 in anchoring sperm head to the tail

PubMed Central

Wang, Lina; Ouyang, Ying-Chun; Dong, Ming-Zhe; Liu, Chao; Zhao, Haichao; Cui, Xiuhong; Ma, Dongyuan; Zhang, Zhiguo; Yang, Xiaoyu; Guo, Yueshuai; Liu, Feng; Yuan, Li

2017-01-01

SUN (Sad1 and UNC84 domain containing)-domain proteins are reported to reside on the nuclear membrane playing distinct roles in nuclear dynamics. SUN5 is a new member of the SUN family, with little knowledge regarding its function. Here, we generated Sun5−/− mice and found that male mice were infertile. Most Sun5-null spermatozoa displayed a globozoospermia-like phenotype but they were actually acephalic spermatozoa. Additional studies revealed that SUN5 was located in the neck of the spermatozoa, anchoring sperm head to the tail, and without functional SUN5 the sperm head to tail coupling apparatus was detached from nucleus during spermatid elongation. Finally, we found that healthy heterozygous offspring could be obtained via intracytoplasmic injection of Sun5-mutated sperm heads for both male mice and patients. Our studies reveal the essential role of SUN5 in anchoring sperm head to the tail and provide a promising way to treat this kind of acephalic spermatozoa-associated male infertility. PMID:28945193

The basic amino acids in the coiled-coil domain of CIN85 regulate its interaction with c-Cbl and phosphatidic acid during epidermal growth factor receptor (EGFR) endocytosis

PubMed Central

2014-01-01

Background During EGFR internalization CIN85 bridges EGFR-Cbl complex, endocytic machinery and fusible membrane through the interactions of CIN85 with c-Cbl, endophilins and phosphatidic acid. These protein-protein and protein-lipid interactions are mediated or regulated by the positively charged C-terminal coiled-coil domain of CIN85. However, the details of CIN85-lipid interaction remain unknown. The present study suggested a possible electric interaction between the negative charge of phosphatidic acid and the positive charge of basic amino acids in coiled-coil domain. Results Mutations of the basic amino acids in the coiled-coil domain, especially K645, K646, R648 and R650, into neutral amino acid alanine completely blocked the interaction of CIN85 with c-Cbl or phosphatidic acid. However, they did not affect CIN85-endophilin interaction. In addition, CIN85 was found to associate with the internalized EGFR endosomes. It interacted with several ESCRT (Endosomal Sorting Complex Required for Transport) component proteins for ESCRT assembly on endosomal membrane. Mutations in the coiled-coil domain (deletion of the coiled-coil domain or point mutations of the basic amino acids) dissociated CIN85 from endosomes. These mutants bound the ESCRT components in cytoplasm to prevent them from assembly on endosomal membrane and inhibited EGFR sorting for degradation. Conclusions As an adaptor protein, CIN85 interacts with variety of partners through several domains. The positive charges of basic amino acids in the coiled-coil domain are not only involved in the interaction with phosphatidic acid, but also regulate the interaction of CIN85 with c-Cbl. CIN85 also interacts with ESCRT components for protein sorting in endosomes. These CIN85-protein and CIN85-lipid interactions enable CIN85 to link EGFR-Cbl endocytic complex with fusible membrane during EGFR endocytosis and subsequently to facilitate ESCRT formation on endosomal membrane for EGFR sorting and degradation. PMID

Functional map of arrestin-1 at single amino acid resolution

PubMed Central

Ostermaier, Martin K.; Peterhans, Christian; Jaussi, Rolf; Deupi, Xavier; Standfuss, Jörg

2014-01-01

Arrestins function as adapter proteins that mediate G protein-coupled receptor (GPCR) desensitization, internalization, and additional rounds of signaling. Here we have compared binding of the GPCR rhodopsin to 403 mutants of arrestin-1 covering its complete sequence. This comprehensive and unbiased mutagenesis approach provides a functional dimension to the crystal structures of inactive, preactivated p44 and phosphopeptide-bound arrestins and will guide our understanding of arrestin–GPCR complexes. The presented functional map quantitatively connects critical interactions in the polar core and along the C tail of arrestin. A series of amino acids (Phe375, Phe377, Phe380, and Arg382) anchor the C tail in a position that blocks binding of the receptor. Interaction of phosphates in the rhodopsin C terminus with Arg29 controls a C-tail exchange mechanism in which the C tail of arrestin is released and exposes several charged amino acids (Lys14, Lys15, Arg18, Lys20, Lys110, and Lys300) for binding of the phosphorylated receptor C terminus. In addition to this arrestin phosphosensor, our data reveal several patches of amino acids in the finger (Gln69 and Asp73–Met75) and the lariat loops (L249–S252 and Y254) that can act as direct binding interfaces. A stretch of amino acids at the edge of the C domain (Trp194–Ser199, Gly337–Gly340, Thr343, and Thr345) could act as membrane anchor, binding interface for a second rhodopsin, or rearrange closer to the central loops upon complex formation. We discuss these interfaces in the context of experimentally guided docking between the crystal structures of arrestin and light-activated rhodopsin. PMID:24449856

Cocrystal structure of the ICAP1 PTB domain in complex with a KRIT1 peptide

PubMed Central

Liu, Weizhi; Boggon, Titus J.

2013-01-01

Integrin cytoplasmic domain-associated protein-1 (ICAP1) is a suppressor of integrin activation and directly binds to the cytoplasmic tail of β1 integrins; its binding suppresses integrin activation by competition with talin. Krev/Rap1 interaction trapped-1 (KRIT1) releases ICAP1 suppression of integrin activation by sequestering ICAP1 away from integrin cytoplasmic tails. Here, the cocrystal structure of the PTB domain of ICAP1 in complex with a 29-­amino-acid fragment (residues 170–198) of KRIT1 is presented to 1.7 Å resolution [the resolution at which 〈I/σ(I)〉 = 2.9 was 1.83 Å]. In previous studies, the structure of ICAP1 with integrin β1 was determined to 3.0 Å resolution and that of ICAP1 with the N-terminal portion of KRIT1 (residues 1–­198) was determined to 2.54 Å resolution; therefore, this study provides the highest resolution structure yet of ICAP1 and allows further detailed analysis of the interaction of ICAP1 with its minimal binding region in KRIT1. PMID:23695561

Bile acids modulate signaling by functional perturbation of plasma membrane domains.

PubMed

Zhou, Yong; Maxwell, Kelsey N; Sezgin, Erdinc; Lu, Maryia; Liang, Hong; Hancock, John F; Dial, Elizabeth J; Lichtenberger, Lenard M; Levental, Ilya

2013-12-13

Eukaryotic cell membranes are organized into functional lipid and protein domains, the most widely studied being membrane rafts. Although rafts have been associated with numerous plasma membrane functions, the mechanisms by which these domains themselves are regulated remain undefined. Bile acids (BAs), whose primary function is the solubilization of dietary lipids for digestion and absorption, can affect cells by interacting directly with membranes. To investigate whether these interactions affected domain organization in biological membranes, we assayed the effects of BAs on biomimetic synthetic liposomes, isolated plasma membranes, and live cells. At cytotoxic concentrations, BAs dissolved synthetic and cell-derived membranes and disrupted live cell plasma membranes, implicating plasma membrane damage as the mechanism for BA cellular toxicity. At subtoxic concentrations, BAs dramatically stabilized domain separation in Giant Plasma Membrane Vesicles without affecting protein partitioning between coexisting domains. Domain stabilization was the result of BA binding to and disordering the nonraft domain, thus promoting separation by enhancing domain immiscibility. Consistent with the physical changes observed in synthetic and isolated biological membranes, BAs reorganized intact cell membranes, as evaluated by the spatial distribution of membrane-anchored Ras isoforms. Nanoclustering of K-Ras, related to nonraft membrane domains, was enhanced in intact plasma membranes, whereas the organization of H-Ras was unaffected. BA-induced changes in Ras lateral segregation potentiated EGF-induced signaling through MAPK, confirming the ability of BAs to influence cell signal transduction by altering the physical properties of the plasma membrane. These observations suggest general, membrane-mediated mechanisms by which biological amphiphiles can produce their cellular effects.

Voltage-sensing domain mode shift is coupled to the activation gate by the N-terminal tail of hERG channels.

PubMed

Tan, Peter S; Perry, Matthew D; Ng, Chai Ann; Vandenberg, Jamie I; Hill, Adam P

2012-09-01

Human ether-a-go-go-related gene (hERG) potassium channels exhibit unique gating kinetics characterized by unusually slow activation and deactivation. The N terminus of the channel, which contains an amphipathic helix and an unstructured tail, has been shown to be involved in regulation of this slow deactivation. However, the mechanism of how this occurs and the connection between voltage-sensing domain (VSD) return and closing of the gate are unclear. To examine this relationship, we have used voltage-clamp fluorometry to simultaneously measure VSD motion and gate closure in N-terminally truncated constructs. We report that mode shifting of the hERG VSD results in a corresponding shift in the voltage-dependent equilibrium of channel closing and that at negative potentials, coupling of the mode-shifted VSD to the gate defines the rate of channel closure. Deletion of the first 25 aa from the N terminus of hERG does not alter mode shifting of the VSD but uncouples the shift from closure of the cytoplasmic gate. Based on these observations, we propose the N-terminal tail as an adaptor that couples voltage sensor return to gate closure to define slow deactivation gating in hERG channels. Furthermore, because the mode shift occurs on a time scale relevant to the cardiac action potential, we suggest a physiological role for this phenomenon in maximizing current flow through hERG channels during repolarization.

Effects of plant growth-promoting bacteria isolated from copper tailings on plants in sterilized and non-sterilized tailings.

PubMed

Liu, Weiqiu; Yang, Chao; Shi, Si; Shu, Wensheng

2014-02-01

Ten strains of Cu-tolerant bacteria with potential plant growth-promoting ability were isolated by selecting strains with the ability to use 1-aminocyclopropane-1-carboxylate as a sole nitrogen source (designated ACC-B) or fix nitrogen (designated FLN-B) originating from the rhizosphere of plants growing on copper tailings. All 10 strains proved to have intrinsic ability to produce indole acetic acid and siderophores, and most of them could mobilize insoluble phosphate. In addition, a greenhouse study showed that ACC-B, FLN-B and a mixture of both had similar, potent ability to stimulate growth of Pennisetum purpureum, Medicago sativa and Oenothera erythrosepala plants grown on sterilized tailings. For instance, above-ground biomass of P. purpureum was 278-357% greater after 60d growth on sterilized tailings in their presence. They could also significantly promote the growth of the plants grown on non-sterilized tailings, though the growth-promoting effects were much weaker. So, strategies for using of the plant growth-promoting bacteria in the practice of phytoremediation deserve further studies to get higher growth-promoting efficiency. Copyright © 2013 Elsevier Ltd. All rights reserved.

Hydroxycinnamic acid-derived polymers constitute the polyaromatic domain of suberin

NASA Technical Reports Server (NTRS)

Bernards, M. A.; Lopez, M. L.; Zajicek, J.; Lewis, N. G.

1995-01-01

Suberin is an abundant, complex, intractable, plant cell wall polymeric network that forms both protective and wound-healing layers. Its function is, therefore, critical to the survival of all vascular plants. Its chemical structure and biosynthesis are poorly defined, although it is known to consist of both aromatic and aliphatic domains. While the composition of the aliphatic component has been fairly well characterized, that of the phenolic component has not. Using a combination of specific carbon-13 labeling techniques, and in situ solid state 13C NMR spectroscopic analysis, we now provide the first direct evidence for the nature of the phenolic domain of suberin and report here that it is almost exclusively comprised of a covalently linked, hydroxycinnamic acid-derived polymeric matrix.

Growth of Quailbush in Acidic, Metalliferous Desert Mine Tailings: Effect of Azospirillum brasilense Sp6 on Biomass Production and Rhizosphere Community Structure

PubMed Central

de-Bashan, Luz E.; Hernandez, Juan-Pablo; Nelson, Karis N.; Bashan, Yoav

2010-01-01

Mine tailing deposits in semiarid and arid environments frequently remain devoid of vegetation due to the toxicity of the substrate and the absence of a diverse soil microbial community capable of supporting seed germination and plant growth. The contribution of the plant growth promoting bacterium (PGPB) Azospirillum brasilense Sp6 to the growth of quailbush in compost-amended, moderately acidic, high-metal content mine tailings using an irrigation-based reclamation strategy was examined along with its influence on the rhizosphere bacterial community. Sp6 inoculation resulted in a significant (2.2-fold) increase in plant biomass production. The data suggest that the inoculum successfully colonized the root surface and persisted throughout the 60-day experiment in both the rhizosphere, as demonstrated by excision and sequencing of the appropriate denaturing gradient gel electrophoresis (DGGE) band, and the rhizoplane, as indicated by fluorescent in situ hybridization of root surfaces. Changes in rhizosphere community structure in response to Sp6 inoculation were evaluated after 15, 30, and 60 days using DGGE analysis of 16S rRNA polymerase chain reaction amplicons. A comparison of DGGE profiles using canonical correspondence analysis revealed a significant treatment effect (Sp6-inoculated vs. uninoculated plants vs. unplanted) on bacterial community structure at 15, 30, and 60 days (p<0.05). These data indicate that in an extremely stressed environment such as acid mine tailings, an inoculated plant growth promoting bacterium not only can persist and stimulate plant growth but also can directly or indirectly influence rhizobacterial community development. PMID:20632001

TACN-based cationic lipids with amino acid backbone and double tails: materials for non-viral gene delivery.

PubMed

Wang, Bing; Yi, Wen-Jing; Zhang, Ji; Zhang, Qin-Fang; Xun, Miao-Miao; Yu, Xiao-Qi

2014-04-01

Cationic lipids have become an efficient type of non-viral vectors for gene delivery. In this Letter, four cationic lipids containing 1,4,7-triazacyclononane (TACN) headgroup, glutamic/aspartic acid backbone and dioleyl tails were designed and synthesized. The TACN headgroup gives these lipids excellent pH buffering capacities, which were higher than branched 25 kDa PEI. Cationic liposomes prepared from these lipids and DOPE showed good DNA affinity, and full DNA condensation was found at N/P ratio of 3 via agarose gel electrophoresis. The lipoplexes were characterized by dynamic light scattering (DLS) assay, which gave proper particle sizes and zeta-potentials for transfection. In vitro gene transfection results in two cell lines reveal that TAN (with aspartic acid and amide bond in the structure) shows the best transfection efficiency, which is close to commercially available transfection agent Lipofectamine 2000. Copyright © 2014 Elsevier Ltd. All rights reserved.

Significance of Microbial Communities and Interactions in Safeguarding Reactive Mine Tailings by Ecological Engineering▿†

PubMed Central

N̆ancucheo, Ivan; Johnson, D. Barrie

2011-01-01

Pyritic mine tailings (mineral waste generated by metal mining) pose significant risk to the environment as point sources of acidic, metal-rich effluents (acid mine drainage [AMD]). While the accelerated oxidative dissolution of pyrite and other sulfide minerals in tailings by acidophilic chemolithotrophic prokaryotes has been widely reported, other acidophiles (heterotrophic bacteria that catalyze the dissimilatory reduction of iron and sulfur) can reverse the reactions involved in AMD genesis, and these have been implicated in the “natural attenuation” of mine waters. We have investigated whether by manipulating microbial communities in tailings (inoculating with iron- and sulfur-reducing acidophilic bacteria and phototrophic acidophilic microalgae) it is possible to mitigate the impact of the acid-generating and metal-mobilizing chemolithotrophic prokaryotes that are indigenous to tailing deposits. Sixty tailings mesocosms were set up, using five different microbial inoculation variants, and analyzed at regular intervals for changes in physicochemical and microbiological parameters for up to 1 year. Differences between treatment protocols were most apparent between tailings that had been inoculated with acidophilic algae in addition to aerobic and anaerobic heterotrophic bacteria and those that had been inoculated with only pyrite-oxidizing chemolithotrophs; these differences included higher pH values, lower redox potentials, and smaller concentrations of soluble copper and zinc. The results suggest that empirical ecological engineering of tailing lagoons to promote the growth and activities of iron- and sulfate-reducing bacteria could minimize their risk of AMD production and that the heterotrophic populations could be sustained by facilitating the growth of microalgae to provide continuous inputs of organic carbon. PMID:21965397

Rapid screening of fatty acid alkyl esters in olive oils by time domain reflectometry.

PubMed

Berardinelli, Annachiara; Ragni, Luigi; Bendini, Alessandra; Valli, Enrico; Conte, Lanfranco; Guarnieri, Adriano; Toschi, Tullia Gallina

2013-11-20

The main aim of the present research is to assess the possibility of quickly screening fatty acid alkyl esters (FAAE) in olive oils using time domain reflectometry (TDR) and partial least-squares (PLS) multivariate statistical analysis. Eighteen virgin olive oil samples with fatty acid alkyl ester contents and fatty acid ethyl ester/methyl ester ratios (FAEE/FAME) ranging from 3 to 100 mg kg(-1) and from 0.3 to 2.6, respectively, were submitted to tests with time domain resolution of 1 ps. The results obtained in test set validation demonstrated that this new and fast analytical approach is able to predict FAME, FAEE, and FAME + FAEE contents with R(2) values of 0.905, 0.923, and 0.927, respectively. Further measurements on mixtures between olive oil and FAAE standards confirmed that the prediction is based on a direct influence of fatty acid alkyl esters on the TDR signal. The suggested technique appeared potentially suitable for monitoring one of the most important quality attribute of the olive oil in the extraction process.

Study on immobilization and migration of nuclide u in superficial soil of uranium tailings pond

NASA Astrophysics Data System (ADS)

Chang, Zhe; Zhou, Shukui

2017-05-01

The uranium tailings in southern China was used as the object of study to study the fixation and migration characteristics of nuclide U in shallow tailings. The results showed that the precipitation of tailings in the tailings soil was not linearly related to the depth during the acid rain leaching process. Tailings soil in the role of fixatives, when the lime as a fixative, the tailings of different soil uranium in 20 days after the re-precipitation. However, when lime and ammonium phosphate were used as fixing agents, the cumulative precipitation of U had a significant effect, and the migration of uranium was inhibited.

Near-tail reconnection as the cause of cometary tail disconnections

NASA Technical Reports Server (NTRS)

Russell, C. T.; Saunders, M. A.; Phillips, J. L.; Fedder, J. A.

1986-01-01

In a cometary tail disconnection event the plasma tail appears to separate from the coma and to accelerate away from it. As this occurs a new tail begins to form. It is proposed that these disconnections arise in a manner analogous to geomagnetic substorms, i.e., by the formation of a strongly reconnecting region in the near tail that forms a magnetic island in the coma and ejects the plasma tail by strengthening the magnetic 'slingshot' within the tail. This reconnection process may be triggered by several different processes, such as interplanetary shocks or variations in the Alfven Mach number.

Two Cytoplasmic Acylation Sites and an Adjacent Hydrophobic Residue, but No Other Conserved Amino Acids in the Cytoplasmic Tail of HA from Influenza A Virus Are Crucial for Virus Replication

PubMed Central

Siche, Stefanie; Brett, Katharina; Möller, Lars; Kordyukova, Larisa V.; Mintaev, Ramil R.; Alexeevski, Andrei V.; Veit, Michael

2015-01-01

Recruitment of the matrix protein M1 to the assembly site of the influenza virus is thought to be mediated by interactions with the cytoplasmic tail of hemagglutinin (HA). Based on a comprehensive sequence comparison of all sequences present in the database, we analyzed the effect of mutating conserved residues in the cytosol-facing part of the transmembrane region and cytoplasmic tail of HA (A/WSN/33 (H1N1) strain) on virus replication and morphology of virions. Removal of the two cytoplasmic acylation sites and substitution of a neighboring isoleucine by glutamine prevented rescue of infectious virions. In contrast, a conservative exchange of the same isoleucine, non-conservative exchanges of glycine and glutamine, deletion of the acylation site at the end of the transmembrane region and shifting it into the tail did not affect virus morphology and had only subtle effects on virus growth and on the incorporation of M1 and Ribo-Nucleoprotein Particles (RNPs). Thus, assuming that essential amino acids are conserved between HA subtypes we suggest that, besides the two cytoplasmic acylation sites (including adjacent hydrophobic residues), no other amino acids in the cytoplasmic tail of HA are indispensable for virus assembly and budding. PMID:26670246

The Influence of Ionic Environment and Histone Tails on Columnar Order of Nucleosome Core Particles

PubMed Central

Berezhnoy, Nikolay V.; Liu, Ying; Allahverdi, Abdollah; Yang, Renliang; Su, Chun-Jen; Liu, Chuan-Fa; Korolev, Nikolay; Nordenskiöld, Lars

2016-01-01

The nucleosome core particle (NCP) is the basic building block of chromatin. Nucleosome-nucleosome interactions are instrumental in chromatin compaction, and understanding NCP self-assembly is important for understanding chromatin structure and dynamics. Recombinant NCPs aggregated by multivalent cations form various ordered phases that can be studied by x-ray diffraction (small-angle x-ray scattering). In this work, the effects on the supramolecular structure of aggregated NCPs due to lysine histone H4 tail acetylations, histone H2A mutations (neutralizing the acidic patch of the histone octamer), and the removal of histone tails were investigated. The formation of ordered mainly hexagonal columnar NCP phases is in agreement with earlier studies; however, the highly homogeneous recombinant NCP systems used in this work display a more compact packing. The long-range order of the NCP columnar phase was found to be abolished or reduced by acetylation of the H4 tails, acidic patch neutralization, and removal of the H3 and H2B tails. Loss of nucleosome stacking upon removal of the H3 tails in combination with other tails was observed. In the absence of the H2A tails, the formation of an unknown highly ordered phase was observed. PMID:27119633

Mechanics of biomimetic systems propelled by actin comet tails

NASA Astrophysics Data System (ADS)

Kang, Hyeran; Tambe, Dhananjay; Shenoy, Vivek; Tang, Jay

2009-03-01

The motility of intracellular bacterial pathogens such as Listeria monocytogenes is driven by filamentous actin comet tails in a variety of trajectories. Here, we present the in vitro study on the actin-based movements using spherical beads of different sizes coated with VCA protein, a partial domain of N-Wasp, in platelet extracts. Long term two-dimensional trajectories of the spherical beads motility show characteristic difference than those observed for bacteria, which have both elongated shape and asymmetric expression of the polymerization inducing enzyme. The trajectories also vary sensitively with the bead size and shape. These results provide a useful test to our new analytical model including the rotation of the bead relative to the tail.

Unfurling of the band 4.1, ezrin, radixin, moesin (FERM) domain of the merlin tumor suppressor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yogesha, S.D.; Sharff, Andrew J.; Giovannini, Marco

The merlin-1 tumor suppressor is encoded by the Neurofibromatosis-2 (Nf2) gene and loss-of-function Nf2 mutations lead to nervous system tumors in man and to several tumor types in mice. Merlin is an ERM (ezrin, radixin, moesin) family cytoskeletal protein that interacts with other ERM proteins and with components of cell-cell adherens junctions (AJs). Merlin stabilizes the links of AJs to the actin cytoskeleton. Thus, its loss destabilizes AJs, promoting cell migration and invasion, which in Nf2{sup +/-} mice leads to highly metastatic tumors. Paradoxically, the 'closed' conformation of merlin-1, where its N-terminal four-point-one, ezrin, radixin, moesin (FERM) domain binds tomore » its C-terminal tail domain, directs its tumor suppressor functions. Here we report the crystal structure of the human merlin-1 head domain when crystallized in the presence of its tail domain. Remarkably, unlike other ERM head-tail interactions, this structure suggests that binding of the tail provokes dimerization and dynamic movement and unfurling of the F2 motif of the FERM domain. We conclude the 'closed' tumor suppressor conformer of merlin-1 is in fact an 'open' dimer whose functions are disabled by Nf2 mutations that disrupt this architecture.« less

The structure of the Myo4p globular tail and its function in ASH1 mRNA localization.

PubMed

Heuck, Alexander; Fetka, Ingrid; Brewer, Daniel N; Hüls, Daniela; Munson, Mary; Jansen, Ralf-Peter; Niessing, Dierk

2010-05-03

Type V myosin (MyoV)-dependent transport of cargo is an essential process in eukaryotes. Studies on yeast and vertebrate MyoV showed that their globular tails mediate binding to the cargo complexes. In Saccharomyces cerevisiae, the MyoV motor Myo4p interacts with She3p to localize asymmetric synthesis of HO 1 (ASH1) mRNA into the bud of dividing cells. A recent study showed that localization of GFP-MS2-tethered ASH1 particles does not require the Myo4p globular tail, challenging the supposed role of this domain. We assessed ASH1 mRNA and Myo4p distribution more directly and found that their localization is impaired in cells expressing globular tail-lacking Myo4p. In vitro studies further show that the globular tail together with a more N-terminal linker region is required for efficient She3p binding. We also determined the x-ray structure of the Myo4p globular tail and identify a conserved surface patch important for She3p binding. The structure shows pronounced similarities to membrane-tethering complexes and indicates that Myo4p may not undergo auto-inhibition of its motor domain.

Conformational analysis of the partially disordered measles virus N(TAIL)-XD complex by SDSL EPR spectroscopy.

PubMed

Kavalenka, Aleh; Urbancic, Iztok; Belle, Valérie; Rouger, Sabrina; Costanzo, Stéphanie; Kure, Sandra; Fournel, André; Longhi, Sonia; Guigliarelli, Bruno; Strancar, Janez

2010-03-17

To characterize the structure of dynamic protein systems, such as partly disordered protein complexes, we propose a novel approach that relies on a combination of site-directed spin-labeled electron paramagnetic resonance spectroscopy and modeling of local rotation conformational spaces. We applied this approach to the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (N(TAIL)) both free and in complex with the X domain (XD, aa 459-507) of the viral phosphoprotein. By comparing measured and modeled temperature-dependent restrictions of the side-chain conformational spaces of 12 SL cysteine-substituted N(TAIL) variants, we showed that the 490-500 region of N(TAIL) is prestructured in the absence of the partner, and were able to quantitatively estimate, for the first time to our knowledge, the extent of the alpha-helical sampling of the free form. In addition, we showed that the 505-525 region of N(TAIL) conserves a significant degree of freedom even in the bound form. The latter two findings provide a mechanistic explanation for the reported rather high affinity of the N(TAIL)-XD binding reaction. Due to the nanosecond timescale of X-band EPR spectroscopy, we were also able to monitor the disordering in the 488-525 region of N(TAIL), in particular the unfolding of the alpha-helical region when the temperature was increased from 281 K to 310 K. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Effect of Arbuscular Mycorrhizal Fungi on Plant Biomass and the Rhizosphere Microbial Community Structure of Mesquite Grown in Acidic Lead/Zinc Mine Tailings

PubMed Central

Solís-Domínguez, Fernando A.; Valentín-Vargas, Alexis; Chorover, Jon; Maier, Raina M.

2011-01-01

Mine tailings in arid and semi-arid environments are barren of vegetation and subject to eolian dispersion and water erosion. Revegetation is a cost-effective strategy to reduce erosion processes and has wide public acceptance. A major cost of revegetation is the addition of amendments, such as compost, to allow plant establishment. In this paper we explore whether arbuscular mycorrhizal fungi (AMF) can help support plant growth in tailings at a reduced compost concentration. A greenhouse experiment was performed to determine the effects of three AMF inocula on biomass, shoot accumulation of heavy metals, and changes in the rhizosphere microbial community structure of the native plant Prosopis juliflora (mesquite). Plants were grown in an acidic lead/zinc mine tailings amended with 10% (w/w) compost amendment, which is slightly sub-optimal for plant growth in these tailings. After two months, AMF-inoculated plants showed increased dry biomass and root length (p < 0.05) and effective AMF colonization compared to controls grown in uninoculated compost-amended tailings. Mesquite shoot tissue lead and zinc concentrations did not exceed domestic animal toxicity limits regardless of whether AMF inoculation was used. The rhizosphere microbial community structure was assessed using denaturing gradient gel electrophoresis (DGGE) profiles of the small subunit RNA gene for bacteria and fungi. Canonical correspondence analysis (CCA) of DGGE profiles showed that the rhizosphere fungal community structure at the end of the experiment was significantly different from the community structure in the tailings, compost, and AMF inocula prior to planting. Further, CCA showed that AMF inoculation significantly influenced the development of both the fungal and bacterial rhizosphere community structures after two months. The changes observed in the rhizosphere microbial community structure may be either a direct effect of the AMF inocula, caused by changes in plant physiology induced by

The structure of the regulatory domain of the adenylyl cyclase Rv1264 from Mycobacterium tuberculosis with bound oleic acid.

PubMed

Findeisen, Felix; Linder, Jürgen U; Schultz, Anita; Schultz, Joachim E; Brügger, Britta; Wieland, Felix; Sinning, Irmgard; Tews, Ivo

2007-06-22

The universal secondary messenger cAMP is produced by adenylyl cyclases (ACs). Most bacterial and all eukaryotic ACs belong to class III of six divergent classes. A class III characteristic is formation of the catalytic pocket at a dimer interface and the presence of additional regulatory domains. Mycobacterium tuberculosis possesses 15 class III ACs, including Rv1264, which is activated at acidic pH due to pH-dependent structural transitions of the Rv1264 dimer. It has been shown by X-ray crystallography that the N-terminal regulatory and C-terminal catalytic domains of Rv1264 interact in completely different ways in the active and inhibited states. Here, we report an in-depth structural and functional analysis of the regulatory domain of Rv1264. The 1.6 A resolution crystal structure shows the protein in a tight, disk-shaped dimer, formed around a helical bundle, and involving a protein chain crossover. To understand pH regulation, we determined structures at acidic and basic pH values and employed structure-based mutagenesis in the holoenzyme to elucidate regulation using an AC activity assay. It has been shown that regulatory and catalytic domains must be linked in a single protein chain. The new studies demonstrate that the length of the linker segment is decisive for regulation. Several amino acids on the surface of the regulatory domain, when exchanged, altered the pH-dependence of AC activity. However, these residues are not conserved amongst a number of related ACs. The closely related mycobacterial Rv2212, but not Rv1264, is strongly activated by the addition of fatty acids. The structure resolved the presence of a deeply embedded fatty acid, characterised as oleic acid by mass spectrometry, which may serve as a hinge. From these data, we conclude that the regulatory domain is a structural scaffold used for distinct regulatory purposes.

In situ biodegradation of naphthenic acids in oil sands tailings pond water using indigenous algae-bacteria consortium.

PubMed

Mahdavi, Hamed; Prasad, Vinay; Liu, Yang; Ulrich, Ania C

2015-01-01

In this study, the biodegradation of total acid-extractable organics (TAOs), commonly called naphthenic acids (NAs), was investigated. An indigenous microbial culture containing algae and bacteria was taken from the surface of a tailings pond and incubated over the course of 120days. The influence of light, oxygen and the presence of indigenous algae and bacteria, and a diatom (Navicula pelliculosa) on the TAO removal rate were elucidated. The highest biodegradation rate was observed with bacteria growth only (without light exposure) with a half-life (t(1/2)) of 203days. The algae-bacteria consortium enhanced the detoxification process, however, bacterial biomass played the main role in toxicity reduction. Principal component analysis (PCA) conducted on FT-IR spectra, identified functional groups and bonds (representing potential markers for biotransformation of TAOs) as follows: hydroxyl, carboxyl and amide groups along with CH, arylH, arylOH and NH bonds. Copyright © 2015 Elsevier Ltd. All rights reserved.

The MDM2 RING Domain and Central Acidic Domain Play Distinct Roles in MDM2 Protein Homodimerization and MDM2-MDMX Protein Heterodimerization*

PubMed Central

Leslie, Patrick L.; Ke, Hengming; Zhang, Yanping

2015-01-01

The oncoprotein murine double minute 2 (MDM2) is an E3 ligase that plays a prominent role in p53 suppression by promoting its polyubiquitination and proteasomal degradation. In its active form, MDM2 forms homodimers as well as heterodimers with the homologous protein murine double minute 4 (MDMX), both of which are thought to occur through their respective C-terminal RING (really interesting new gene) domains. In this study, using multiple MDM2 mutants, we show evidence suggesting that MDM2 homo- and heterodimerization occur through distinct mechanisms because MDM2 RING domain mutations that inhibit MDM2 interaction with MDMX do not affect MDM2 interaction with WT MDM2. Intriguingly, deletion of a portion of the MDM2 central acidic domain selectively inhibits interaction with MDM2 while leaving intact the ability of MDM2 to interact with MDMX and to ubiquitinate p53. Further analysis of an MDM2 C-terminal deletion mutant reveals that the C-terminal residues of MDM2 are required for both MDM2 and MDMX interaction. Collectively, our results suggest a model in which MDM2-MDMX heterodimerization requires the extreme C terminus and proper RING domain structure of MDM2, whereas MDM2 homodimerization requires the extreme C terminus and the central acidic domain of MDM2, suggesting that MDM2 homo- and heterodimers utilize distinct MDM2 domains. Our study is the first to report mutations capable of separating MDM2 homo- and heterodimerization. PMID:25809483

The MDM2 RING domain and central acidic domain play distinct roles in MDM2 protein homodimerization and MDM2-MDMX protein heterodimerization.

PubMed

Leslie, Patrick L; Ke, Hengming; Zhang, Yanping

2015-05-15

The oncoprotein murine double minute 2 (MDM2) is an E3 ligase that plays a prominent role in p53 suppression by promoting its polyubiquitination and proteasomal degradation. In its active form, MDM2 forms homodimers as well as heterodimers with the homologous protein murine double minute 4 (MDMX), both of which are thought to occur through their respective C-terminal RING (really interesting new gene) domains. In this study, using multiple MDM2 mutants, we show evidence suggesting that MDM2 homo- and heterodimerization occur through distinct mechanisms because MDM2 RING domain mutations that inhibit MDM2 interaction with MDMX do not affect MDM2 interaction with WT MDM2. Intriguingly, deletion of a portion of the MDM2 central acidic domain selectively inhibits interaction with MDM2 while leaving intact the ability of MDM2 to interact with MDMX and to ubiquitinate p53. Further analysis of an MDM2 C-terminal deletion mutant reveals that the C-terminal residues of MDM2 are required for both MDM2 and MDMX interaction. Collectively, our results suggest a model in which MDM2-MDMX heterodimerization requires the extreme C terminus and proper RING domain structure of MDM2, whereas MDM2 homodimerization requires the extreme C terminus and the central acidic domain of MDM2, suggesting that MDM2 homo- and heterodimers utilize distinct MDM2 domains. Our study is the first to report mutations capable of separating MDM2 homo- and heterodimerization. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Roles for the Cytoplasmic Tails of the Fusion and Hemagglutinin-Neuraminidase Proteins in Budding of the Paramyxovirus Simian Virus 5

PubMed Central

Waning, David L.; Schmitt, Anthony P.; Leser, George P.; Lamb, Robert A.

2002-01-01

The efficient release of many enveloped viruses from cells involves the coalescence of viral components at sites of budding on the plasma membrane of infected cells. This coalescence is believed to require interactions between the cytoplasmic tails of surface glycoproteins and the matrix (M) protein. For the paramyxovirus simian virus 5 (SV5), the cytoplasmic tail of the hemagglutinin-neuraminidase (HN) protein has been shown previously to be important for normal virus budding. To investigate a role for the cytoplasmic tail of the fusion (F) protein in virus assembly and budding, we generated a series of F cytoplasmic tail-truncated recombinant viruses. Analysis of these viruses in tissue culture indicated that the cytoplasmic tail of the F protein was dispensable for normal virus replication and budding. To investigate further the requirements for assembly and budding of SV5, we generated two double-mutant recombinant viruses that lack 8 amino acids of the predicted 17-amino-acid HN protein cytoplasmic tail in combination with truncation of either 10 or 18 amino acids from the predicted 20-amino-acid F protein cytoplasmic tail. Both of the double mutant recombinant viruses displayed a replication defect in tissue culture and a budding defect, the extent of which was dependant on the length of the remaining F cytoplasmic tail. Taken together, this work and our earlier data on virus-like particle formation (A. P. Schmitt, G. P. Leser, D. L. Waning, and R. A. Lamb, J. Virol. 76:3953-3964, 2002) suggest a redundant role for the cytoplasmic tails of the HN and F proteins in virus assembly and budding. PMID:12186912

Remarkable alkaline stability of an engineered protein A as immunoglobulin affinity ligand: C domain having only one amino acid substitution

PubMed Central

Minakuchi, Kazunobu; Murata, Dai; Okubo, Yuji; Nakano, Yoshiyuki; Yoshida, Shinichi

2013-01-01

Protein A affinity chromatography is the standard purification process for the capture of therapeutic antibodies. The individual IgG-binding domains of protein A (E, D, A, B, C) have highly homologous amino acid sequences. From a previous report, it has been assumed that the C domain has superior resistance to alkaline conditions compared to the other domains. We investigated several properties of the C domain as an IgG-Fc capture ligand. Based on cleavage site analysis of a recombinant protein A using a protein sequencer, the C domain was found to be the only domain to have neither of the potential alkaline cleavage sites. Circular dichroism (CD) analysis also indicated that the C domain has good physicochemical stability. Additionally, we evaluated the amino acid substitutions at the Gly-29 position of the C domain, as the Z domain (an artificial B domain) acquired alkaline resistance through a G29A mutation. The G29A mutation proved to increase the alkaline resistance of the C domain, based on BIACORE analysis, although the improvement was significantly smaller than that observed for the B domain. Interestingly, a number of other amino acid mutations at the same position increased alkaline resistance more than did the G29A mutation. This result supports the notion that even a single mutation on the originally alkali-stable C domain would improve its alkaline stability. An engineered protein A based on this C domain is expected to show remarkable performance as an affinity ligand for immunoglobulin. PMID:23868198

RNA-binding proteins with basic-acidic dipeptide (BAD) domains self-assemble and aggregate in Alzheimer's disease.

PubMed

Bishof, Isaac; Dammer, Eric B; Duong, Duc M; Kundinger, Sean; Gearing, Marla; Lah, James J; Levey, Allan I; Seyfried, Nicholas T

2018-05-25

U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and other RNA-binding proteins (RBPs) are mislocalized to cytoplasmic neurofibrillary tau aggregates in Alzheimer's disease (AD), yet the co-aggregation mechanisms are incompletely understood. U1-70K harbors two disordered low-complexity domains (LC1 and LC2) that are necessary for aggregation in AD brain extracts. The LC1 domain contains highly repetitive basic (R/K) and acidic (D/E) residues, referred to as a basic-acidic dipeptide (BAD) domain. We report here that this domain shares many of the properties of the Q/N-rich LC domains in RBPs that also aggregate in neurodegenerative disease. These properties included self-assembly into oligomers and localization to nuclear granules. Co-immunoprecipitations of recombinant U1-70K and deletions lacking the LC domain(s) followed by quantitative proteomic analyses were used to resolve functional classes of U1-70K-interacting proteins that depend on the BAD domain for their interaction. Within this interaction network, we identified a class of RBPs with BAD domains nearly identical to that found in U1-70K. Two members of this class, LUC7L3 and RBM25, required their respective BAD domains for reciprocal interactions with U1-70K and nuclear granule localization. Strikingly, a significant proportion of RBPs with BAD domains had elevated insolubility in the AD brain proteome. Furthermore, we show that the BAD domain of U1-70K can interact with tau from AD brains, but not from other tauopathies. These findings highlight a mechanistic role for BAD domains in stabilizing RBP interactions and in potentially mediating co-aggregation with pathological, AD-specific tau isoforms. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Expression of dehydratase domains from a polyunsaturated fatty acid synthase increases the production of fatty acids in Escherichia coli.

PubMed

Oyola-Robles, Delise; Rullán-Lind, Carlos; Carballeira, Néstor M; Baerga-Ortiz, Abel

2014-02-05

Increasing the production of fatty acids by microbial fermentation remains an important step toward the generation of biodiesel and other portable liquid fuels. In this work, we report an Escherichia coli strain engineered to overexpress a fragment consisting of four dehydratase domains from the polyunsaturated fatty acid (PUFA) synthase enzyme complex from the deep-sea bacterium, Photobacterium profundum. The DH1-DH2-UMA enzyme fragment was excised from its natural context within a multi-enzyme PKS and expressed as a stand-alone protein. Fatty acids were extracted from the cell pellet, esterified with methanol and quantified by GC-MS analysis. Results show that the E. coli strain expressing the DH tetradomain fragment was capable of producing up to a 5-fold increase (80.31 mg total FA/L culture) in total fatty acids over the negative control strain lacking the recombinant enzyme. The enhancement in production was observed across the board for all the fatty acids that are typically made by E. coli. The overexpression of the DH tetradomain did not affect E. coli cell growth, thus showing that the observed enhancement in fatty acid production was not a result of effects associated with cell density. The observed enhancement was more pronounced at lower temperatures (3.8-fold at 16 °C, 3.5-fold at 22 °C and 1.5-fold at 30 °C) and supplementation of the media with 0.4% glycerol did not result in an increase in fatty acid production. All these results taken together suggest that either the dehydration of fatty acid intermediates are a limiting step in the E. coli fatty acid biosynthesis machinery, or that the recombinant dehydratase domains used in this study are also capable of catalyzing thioester hydrolysis of the final products. The enzyme in this report is a new tool which could be incorporated into other existing strategies aimed at improving fatty acid production in bacterial fermentations toward accessible biodiesel precursors. Copyright © 2013 Elsevier Inc

Predicting arsenic concentrations in porewaters of buried uranium mill tailings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Langmuir, D.; Mahoney, J.; MacDonald, A.

The proposed JEB Tailings Management Facility (TMF) to be emplaced below the groundwater table in northern Saskatchewan, Canada, will contain uranium mill tailings from McClean Lake, Midwest and Cigar Lake ore bodies, which are high in arsenic (up to 10%) and nickel (up to 5%). A serious concern is the possibility that high arsenic and nickel concentrations may be released from the buried tailings, contaminating adjacent groundwaters and a nearby lake. Laboratory tests and geochemical modeling were performed to examine ways to reduce the arsenic and nickel concentrations in TMF porewaters so as to minimize such contamination from tailings buriedmore » for 50 years and longer. The tests were designed to mimic conditions in the mill neutralization circuit (3 hr tests at 25 C), and in the TMF after burial (5--49 day aging tests). The aging tests were run at 50, 25 and 4 C (the temperature in the TMF). In order to optimize the removal of arsenic by adsorption and precipitation, ferric sulfate was added to tailings raffinates having Fe/As ratios of less than 3--5. The acid raffinates were then neutralized by addition of slaked lime to nominal pH values of 7, 8, or 9. Analysis and modeling of the test results showed that with slaked lime addition to acid tailings raffinates, relatively amorphous scorodite (ferric arsenate) precipitates near pH 1, and is the dominant form of arsenate in slake limed tailings solids except those high in Ni and As and low in Fe, in which cabrerite-annabergite (Ni, Mg, Fe(II) arsenate) may also precipitate near pH 5--6. In addition to the arsenate precipitates, smaller amounts of arsenate are also adsorbed onto tailings solids. The aging tests showed that after burial of the tailings, arsenic concentrations may increase with time from the breakdown of the arsenate phases (chiefly scorodite). However, the tests indicate that the rate of change decreases and approaches zero after 72 hrs at 25 C, and may equal zero at all times in the TMF at 4

Mine tailings composition in a historic site: implications for ecological restoration.

PubMed

Courtney, R

2013-02-01

Ecological restoration, using tolerant plant species and nutrient additions, is a low-cost option to decrease environmental risks associated with mine tailings. An attempt was previously made to establish such a vegetation cover on an abandoned tailings facility in Southern Ireland. Historically, the tailings site has been prone to dusting and is a potential source of contamination to the surrounding environment. The site was examined to determine the success of the previous restoration plan used to revegetate the site and to determine its suitability for further restoration. Three distinct floristic areas were identified (grassland, poor grassland and bare area) based on herbage compositions and elemental analysis. Surface and subsurface samples were taken to characterise tailings from within these areas of the tailings site. The pH of bare surface tailings (pH, 2.7) was significantly more acidic (p < 0.5) than in other areas. Additionally, negligible net neutralising potential resulted in the tailings being hostile to plant growth. Total metal concentrations in tailings were high (c. 10,000 mg kg(-1) for Pb and up to 20,000 mg kg(-1) for Zn). DTPA-extractable Zn and Pb were 16 and 11 % of the total amount, respectively. Metal content in grasses growing on some areas of the tailings were elevated and demonstrated the inability of the tailings to support sustainable plant growth. Due to the inherently hostile characteristics of these areas, future restoration work will employ capping with a barrier layer.

In-situ study of beneficial utilization of coal fly ash in reactive mine tailings.

PubMed

Lee, Joon Kyu; Shang, Julie Q; Wang, Hongliu; Zhao, Cheng

2014-03-15

Oxidation of reactive mine tailings and subsequent generation of acid mine drainage (AMD) have been long recognized as the largest environmental concern for the mining industry. Laboratory studies on utilization of coal fly ash in management of reactive mine tailings have shown reducing water and oxygen infiltration into tailings matrix, thus preventing oxidation of sulphide minerals and acid generation. However, few data from field studies to evaluate the performance of co-placement of mine tailings and fly ash (CMF hereafter) are reported in the open literature. This paper documents the construction and instrumentation of three CMF systems on the Musselwhite mine located in Ontario, Canada and presents results of 3-year real time monitoring. The field data indicates that the CMFs reduced the ingress of water due to cementation generated by hydration of fly ash. It was also found that the electrical conductivity of leachate from CMFs decreased in the early stage of co-placement, compared to the control. With further study, the principle and approach demonstrated in this paper can be adopted as a sustainable technology in the mine tailings management. Copyright © 2014 Elsevier Ltd. All rights reserved.

Identification of amino acids in the tetratricopeptide repeat and C-terminal domains of protein phosphatase 5 involved in autoinhibition and lipid activation.

PubMed

Kang, H; Sayner, S L; Gross, K L; Russell, L C; Chinkers, M

2001-09-04

Protein phosphatase 5 (PP5) exhibits low basal activity due to the autoinhibitory properties of its N-terminal and C-terminal domains but can be activated approximately 40-fold in vitro by polyunsaturated fatty acids. To identify residues involved in regulating PP5 activity, we performed scanning mutagenesis of its N-terminal tetratricopeptide repeat (TPR) domain and deletion mutagenesis of its C-terminal domain. Mutating residues in a groove of the TPR domain that binds to heat shock protein 90 had no effect on basal phosphatase activity. Mutation of Glu-76, however, whose side chain projects away from this groove, resulted in a 10-fold elevation of basal activity without affecting arachidonic acid-stimulated activity. Thus, the interface of the TPR domain involved in PP5 autoinhibition appears to be different from that involved in heat shock protein 90 binding. We also observed a 10-fold elevation of basal phosphatase activity upon removing the C-terminal 13 amino acids of PP5, with a concomitant 50% decrease in arachidonic acid-stimulated activity. These two effects were accounted for by two distinct amino acid deletions: deleting the four C-terminal residues (496-499) of PP5 had no effect on its activity, but removing Gln-495 elevated basal activity 10-fold. Removal of a further three amino acids had no additional effect, but deleting Asn-491 resulted in a 50% reduction in arachidonic acid-stimulated activity. Thus, Glu-76 in the TPR domain and Gln-495 at the C-terminus were implicated in maintaining the low basal activity of PP5. While the TPR domain alone has been thought to mediate fatty acid activation of PP5, our data suggest that Asn-491, near its C-terminus, may also be involved in this process.

Distinct roles for extracellular and intracellular domains in neuroligin function at inhibitory synapses.

PubMed

Nguyen, Quynh-Anh; Horn, Meryl E; Nicoll, Roger A

2016-11-02

Neuroligins (NLGNs) are postsynaptic cell adhesion molecules that interact trans-synaptically with neurexins to mediate synapse development and function. NLGN2 is only at inhibitory synapses while NLGN3 is at both excitatory and inhibitory synapses. We found that NLGN3 function at inhibitory synapses in rat CA1 depends on the presence of NLGN2 and identified a domain in the extracellular region that accounted for this functional difference between NLGN2 and 3 specifically at inhibitory synapses. We further show that the presence of a cytoplasmic tail (c-tail) is indispensible, and identified two domains in the c-tail that are necessary for NLGN function at inhibitory synapses. These domains point to a gephyrin-dependent mechanism that is disrupted by an autism-associated mutation at R705 and a gephyrin-independent mechanism reliant on a putative phosphorylation site at S714. Our work highlights unique and separate roles for the extracellular and intracellular regions in specifying and carrying out NLGN function respectively.

Interactions between the PDZ domains of Bazooka (Par-3) and phosphatidic acid: in vitro characterization and role in epithelial development.

PubMed

Yu, Cao Guo; Harris, Tony J C

2012-09-01

Bazooka (Par-3) is a conserved polarity regulator that organizes molecular networks in a wide range of cell types. In epithelia, it functions as a plasma membrane landmark to organize the apical domain. Bazooka is a scaffold protein that interacts with proteins through its three PDZ (postsynaptic density 95, discs large, zonula occludens-1) domains and other regions. In addition, Bazooka has been shown to interact with phosphoinositides. Here we show that the Bazooka PDZ domains interact with the negatively charged phospholipid phosphatidic acid immobilized on solid substrates or in liposomes. The interaction requires multiple PDZ domains, and conserved patches of positively charged amino acid residues appear to mediate the interaction. Increasing or decreasing levels of diacylglycerol kinase or phospholipase D-enzymes that produce phosphatidic acid-reveal a role for phosphatidic acid in Bazooka embryonic epithelial activity but not its localization. Mutating residues implicated in phosphatidic acid binding revealed a possible role in Bazooka localization and function. These data implicate a closer connection between Bazooka and membrane lipids than previously recognized. Bazooka polarity landmarks may be conglomerates of proteins and plasma membrane lipids that modify each other's activities for an integrated effect on cell polarity.

Tail gut cyst.

PubMed

Rao, G Mallikarjuna; Haricharan, P; Ramanujacharyulu, S; Reddy, K Lakshmi

2002-01-01

The tail gut is a blind extension of the hindgut into the tail fold just distal to the cloacal membrane. Remnants of this structure may form tail gut cyst. We report a 14-year-old girl with tail gut cyst that presented as acute abdomen. The patient recovered after cyst excision.

Telling tails: selective pressures acting on investment in lizard tails.

PubMed

Fleming, Patricia A; Valentine, Leonie E; Bateman, Philip W

2013-01-01

Caudal autotomy is a common defense mechanism in lizards, where the animal may lose part or all of its tail to escape entrapment. Lizards show an immense variety in the degree of investment in a tail (i.e., length) across species, with tails of some species up to three or four times body length (snout-vent length [SVL]). Additionally, body size and form also vary dramatically, including variation in leg development and robustness and length of the body and tail. Autotomy is therefore likely to have fundamentally different effects on the overall body form and function in different species, which may be reflected directly in the incidence of lost/regenerating tails within populations or, over a longer period, in terms of relative tail length for different species. We recorded data (literature, museum specimens, field data) for relative tail length (n=350 species) and the incidence of lost/regenerating tails (n=246 species). We compared these (taking phylogeny into account) with intrinsic factors that have been proposed to influence selective pressures acting on caudal autotomy, including body form (robustness, body length, leg development, and tail specialization) and ecology (foraging behavior, physical and temporal niches), in an attempt to identify patterns that might reflect adaptive responses to these different factors. More gracile species have relatively longer tails (all 350 spp., P < 0.001; also significant for five of the six families tested separately), as do longer (all species, P < 0.001; Iguanidae, P < 0.05; Lacertidae, P < 0.001; Scindidae, P < 0.001), climbing (all species, P < 0.05), and diurnal (all species, P < 0.01; Pygopodidae, P < 0.01) species; geckos without specialized tails (P < 0.05); or active-foraging skinks (P < 0.05). We also found some relationships with the data for caudal autotomy, with more lost/regenerating tails for nocturnal lizards (all 246 spp., P < 0.01; Scindidae, P < 0.05), larger skinks (P < 0.05), climbing geckos (P < 0

Nuclear localization and transactivation by Vitis CBF transcription factors are regulated by combinations of conserved amino acid domains.

PubMed

Carlow, Chevonne E; Faultless, J Trent; Lee, Christine; Siddiqua, Mahbuba; Edge, Alison; Nassuth, Annette

2017-09-01

The highly conserved CBF pathway is crucial in the regulation of plant responses to low temperatures. Extensive analysis of Arabidopsis CBF proteins revealed that their functions rely on several conserved amino acid domains although the exact function of each domain is disputed. The question was what functions similar domains have in CBFs from other, overwintering woody plants such as Vitis, which likely have a more involved regulation than the model plant Arabidopsis. A total of seven CBF genes were cloned and sequenced from V. riparia and the less frost tolerant V. vinifera. The deduced species-specific amino acid sequences differ in only a few amino acids, mostly in non-conserved regions. Amino acid sequence comparison and phylogenetic analysis showed two distinct groups of Vitis CBFs. One group contains CBF1, CBF2, CBF3 and CBF8 and the other group contains CBF4, CBF5 and CBF6. Transient transactivation assays showed that all Vitis CBFs except CBF5 activate via a CRT or DRE promoter element, whereby Vitis CBF3 and 4 prefer a CRT element. The hydrophobic domains in the C-terminal end of VrCBF6 were shown to be important for how well it activates. The putative nuclear localization domain of Vitis CBF1 was shown to be sufficient for nuclear localization, in contrast to previous reports for AtCBF1, and also important for transactivation. The latter highlights the value of careful analysis of domain functions instead of reliance on computer predictions and published data for other related proteins. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Characterization of Emergent Data Networks Among Long-Tail Data

NASA Astrophysics Data System (ADS)

Elag, Mostafa; Kumar, Praveen; Hedstrom, Margaret; Myers, James; Plale, Beth; Marini, Luigi; McDonald, Robert

2014-05-01

Data curation underpins data-driven scientific advancements. It manages the information flux across multiple users throughout data life cycle as well as increases data sustainability and reusability. The exponential growth in data production spanning across the Earth Science involving individual and small research groups, which is termed as log-tail data, increases the data-knowledge latency among related domains. It has become clear that an advanced framework-agnostic metadata and ontologies for long-tail data is required to increase their visibility to each other, and provide concise and meaningful descriptions that reveal their connectivity. Despite the advancement that has been achieved by various sophisticated data management models in different Earth Science disciplines, it is not always straightforward to derive relationships among long-tail data. Semantic data clustering algorithms and pre-defined logic rules that are oriented toward prediction of possible data relationships, is one method to address these challenges. Our work advances the connectivity of related long-tail data by introducing the design for an ontology-based knowledge management system. In this work, we present the system architecture, its components, and illustrate how it can be used to scrutinize the connectivity among datasets. To demonstrate the capabilities of this "data network" prototype, we implemented this approach within the Sustainable Environment Actionable Data (SEAD) environment, an open-source semantic content repository that provides a RDF database for long-tail data, and show how emergent relationships among datasets can be identified.

The Globular Tail Domain of Myosin-5a Functions as a Dimer in Regulating the Motor Activity.

PubMed

Zhang, Wen-Bo; Yao, Lin-Lin; Li, Xiang-Dong

2016-06-24

Myosin-5a contains two heavy chains, which are dimerized via the coiled-coil regions. Thus, myosin-5a comprises two heads and two globular tail domains (GTDs). The GTD is the inhibitory domain that binds to the head and inhibits its motor function. Although the two-headed structure is essential for the processive movement of myosin-5a along actin filaments, little is known about the role of GTD dimerization. Here, we investigated the effect of GTD dimerization on its inhibitory activity. We found that the potent inhibitory activity of the GTD is dependent on its dimerization by the preceding coiled-coil regions, indicating synergistic interactions between the two GTDs and the two heads of myosin-5a. Moreover, we found that alanine mutations of the two conserved basic residues at N-terminal extension of the GTD not only weaken the inhibitory activity of the GTD but also enhance the activation of myosin-5a by its cargo-binding protein melanophilin (Mlph). These results are consistent with the GTD forming a head to head dimer, in which the N-terminal extension of the GTD interacts with the Mlph-binding site in the counterpart GTD. The Mlph-binding site at the GTD-GTD interface must be exposed prior to the binding of Mlph. We therefore propose that the inhibited Myo5a is equilibrated between the folded state, in which the Mlph-binding site is buried, and the preactivated state, in which the Mlph-binding site is exposed, and that Mlph is able to bind to the Myo5a in preactivated state and activates its motor function. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Synthesis of stereoarray isotope labeled (SAIL) lysine via the "head-to-tail" conversion of SAIL glutamic acid.

PubMed

Terauchi, Tsutomu; Kamikawai, Tomoe; Vinogradov, Maxim G; Starodubtseva, Eugenia V; Takeda, Mitsuhiro; Kainosho, Masatsune

2011-01-07

A stereoarray isotope labeled (SAIL) lysine, (2S,3R,4R,5S,6R)-[3,4,5,6-(2)H(4);1,2,3,4,5,6-(13)C(6);2,6-(15)N(2)]lysine, was synthesized by the "head-to-tail" conversion of SAIL-Glu, (2S,3S,4R)-[3,4-(2)H(2);1,2,3,4,5-(13)C(5);2-(15)N]glutamic acid, with high stereospecificities for all five chiral centers. With the SAIL-Lys in hand, the unambiguous simultaneous stereospecific assignments were able to be established for each of the prochiral protons within the four methylene groups of the Lys side chains in proteins.

The pH sensibility of actin-bundling LIM proteins is governed by the acidic properties of their C-terminal domain.

PubMed

Moes, Danièle; Hoffmann, Céline; Dieterle, Monika; Moreau, Flora; Neumann, Katrin; Papuga, Jessica; Furtado, Angela Tavares; Steinmetz, André; Thomas, Clément

2015-08-19

Actin-bundling Arabidopsis LIM proteins are subdivided into two subfamilies differing in their pH sensitivity. Widely-expressed WLIMs are active under low and high physiologically-relevant pH conditions, whereas pollen-enriched PLIMs are inactivated by pH values above 6.8. By a domain swapping approach we identified the C-terminal (Ct) domain of PLIMs as the domain responsible for pH responsiveness. Remarkably, this domain conferred pH sensitivity to LIM proteins, when provided "in trans" (i.e., as a single, independent, peptide), indicating that it operates through the interaction with another domain. An acidic 6xc-Myc peptide functionally mimicked the Ct domain of PLIMs and efficiently inhibited LIM actin bundling activity under high pH conditions. Together, our data suggest a model where PLIMs are regulated by an intermolecular interaction between their acidic Ct domain and another, yet unidentified, domain. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Direct Interactions with the Integrin β1 Cytoplasmic Tail Activate the Abl2/Arg Kinase*

PubMed Central

Simpson, Mark A.; Bradley, William D.; Harburger, David; Parsons, Maddy; Calderwood, David A.; Koleske, Anthony J.

2015-01-01

Integrins are heterodimeric α/β extracellular matrix adhesion receptors that couple physically to the actin cytoskeleton and regulate kinase signaling pathways to control cytoskeletal remodeling and adhesion complex formation and disassembly. β1 integrins signal through the Abl2/Arg (Abl-related gene) nonreceptor tyrosine kinase to control fibroblast cell motility, neuronal dendrite morphogenesis and stability, and cancer cell invasiveness, but the molecular mechanisms by which integrin β1 activates Arg are unknown. We report here that the Arg kinase domain interacts directly with a lysine-rich membrane-proximal segment in the integrin β1 cytoplasmic tail, that Arg phosphorylates the membrane-proximal Tyr-783 in the β1 tail, and that the Arg Src homology domain then engages this phosphorylated region in the tail. We show that these interactions mediate direct binding between integrin β1 and Arg in vitro and in cells and activate Arg kinase activity. These findings provide a model for understanding how β1-containing integrins interact with and activate Abl family kinases. PMID:25694433

Common amino acid domain among endopolygalacturonases of ascomycete fungi.

PubMed Central

Keon, J P; Waksman, G

1990-01-01

The endopolygalacturonase (EC 3.2.1.15) enzymes produced in vitro by three ascomycete fungi, Aspergillus niger, Sclerotinia sclerotiorum, and Colletotrichum lindemuthianum were studied by using thin-layer isoelectric focusing and activity stain overlay techniques. The polygalacturonases from A. niger and S. sclerotiorum consisted of numerous isoforms, whereas the endopolygalacturonase from C. lindemuthianum consisted of a single protein species. The most abundant endopolygalacturonase isoform produced by each of these organisms was purified and characterized. Biochemical parameters, including molecular weight, isoelectric point, kinetic parameters, temperature and pH optima, and thermal stability, were determined. Considerable differences in physical and chemical properties were demonstrated among these fungal polygalacturonases. Antibodies raised against individual proteins exhibited little cross-reaction, suggesting that these enzymes differ structurally as well as biochemically. In contrast, the analysis of the N-terminal amino acid sequences of the three proteins showed extensive homology, particularly in a region labeled domain 1 in which 84% of the amino acids were conserved. Images PMID:2403258

Geochemical and mineralogical characterization of a neutral, low-sulfide/high-carbonate tailings impoundment, Markušovce, eastern Slovakia.

PubMed

Hiller, Edgar; Petrák, Marián; Tóth, Roman; Lalinská-Voleková, Bronislava; Jurkovič, L'ubomír; Kučerová, Gabriela; Radková, Anežka; Sottník, Peter; Vozár, Jaroslav

2013-11-01

Tailings deposits generated from mining activities represent a potential risk for the aquatic environment through the release of potentially toxic metals and metalloids occurring in a variety of minerals present in the tailings. Physicochemical and mineralogical characteristics of tailings such as total concentrations of chemical elements, pH, ratio of acid-producing to acid-neutralizing minerals, and primary and secondary mineral phases are very important factors that control the actual release of potentially toxic metals and metalloids from the tailings to the environment. The aims of this study are the determination of geochemical and mineralogical characteristics of tailings deposited in voluminous impoundment situated near the village of Markušovce (eastern Slovakia) and identification of the processes controlling the mobility of selected toxic metals (Cu, Hg) and metalloids (As, Sb). The studied tailings have unique features in comparison with the other tailings investigated previously because of the specific mineral assemblage primarily consisting of barite, siderite, quartz, and minor sulfides. To meet the aims, samples of the tailings were collected from 3 boreholes and 15 excavated pits and subjected to bulk geochemical analyses (i.e., determination of chemical composition, pH, Eh, acid generation, and neutralization potentials) combined with detailed mineralogical characterization using optical microscopy, X-ray diffraction (XRD), electron microprobe analysis (EMPA), and micro-X-ray diffraction (μ-XRD). Additionally, the geochemical and mineralogical factors controlling the transfer of potentially toxic elements from tailings to waters were also determined using short-term batch test (European norm EN 12457), sampling of drainage waters and speciation-equilibrium calculations performed with PHREEQC. The tailings mineral assemblage consists of siderite, barite, quartz, and dolomite. Sulfide minerals constitute only a minor proportion of the tailings

Elemental mobility in sulfidic mine tailings reclaimed with paper mill by-products as sealing materials.

PubMed

Jia, Yu; Stahre, Nanna; Mäkitalo, Maria; Maurice, Christian; Öhlander, Björn

2017-09-01

Sealing layers made of two alkaline paper mill by-products, fly ash and green liquor dregs, were placed on top of 50-year-old sulfide-containing tailings as a full-scale remediation approach. The performance and effectiveness of the sealing layers with high water content for an oxygen barrier and low hydraulic conductivity for a sealing layer in preventing the formation of acid rock drainage were evaluated 5 years after the remediation. The leaching behavior of the covered tailings was studied using batch leaching tests (L/S ratio 10 L/kg). The leaching results revealed that, in general, the dregs- and ash-covered tailings released relatively lower concentrations of many elements contained in acid rock drainage compared to those from the uncovered tailings. A change in the chemical composition and mineralogical state of the tailings was observed for the tailings beneath the covers. The increase in pH caused by the alkaline materials promoted metal precipitation. Geochemical modeling using PHREEQC confirmed most of the geochemical changes of the covered tailings. Both the ash and dregs showed potential to function as sealing materials in terms of their geochemical properties. However, mobilization of Zn and Ni from the lower part of the dregs-covered tailings was observed. The same phenomenon was observed for the lower part of the ash-covered tailings. Ash showed advantages over dregs as a cover material; based on geochemical studies, the ash immobilized more elements than the dregs did. Lysimeters were installed below the sealing layers, and infiltrating water chemistry and hydrology were studied to monitor the amount and quality of the leachate percolating through.

Aromatic amino acids in the cellulose binding domain of Penicillium crustosum endoglucanase EGL1 differentially contribute to the cellulose affinity of the enzyme

PubMed Central

Xiong, Wei; Chen, Fang-Yuan; Xu, Li; Han, Zheng-Gang

2017-01-01

The cellulose binding domain (CBD) of cellulase binding to cellulosic materials is the initiation of a synergistic action on the enzymatic hydrolysis of the most abundant renewable biomass resources in nature. The binding of the CBD domain to cellulosic substrates generally relies on the interaction between the aromatic amino acids structurally located on the flat face of the CBD domain and the glucose rings of cellulose. In this study, we found the CBD domain of a newly cloned Penicillium crustosum endoglucanase EGL1, which was phylogenetically related to Aspergillus, Fusarium and Rhizopus, and divergent from the well-characterized Trichoderma reeseis cellulase CBD domain, contain two conserved aromatic amino acid-rich regions, Y451-Y452 and Y477-Y478-Y479, among which three amino acids Y451, Y477, and Y478 structurally sited on a flat face of this domain. Cellulose binding assays with green fluorescence protein as the marker, adsorption isotherm assays and an isothermal titration calorimetry assays revealed that although these three amino acids participated in this process, the Y451-Y452 appears to contribute more to the cellulose binding than Y477-Y478-Y479. Further glycine scanning mutagenesis and structural modelling revealed that the binding between CBD domain and cellulosic materials might be multi-amino-acids that participated in this process. The flexible poly-glucose molecule could contact Y451, Y477, and Y478 which form the contacting flat face of CBD domain as the typical model, some other amino acids in or outside the flat face might also participate in the interaction. Thus, it is possible that the conserved Y451-Y452 of CBD might have a higher chance of contacting the cellulosic substrates, contributing more to the affinity of CBD than the other amino acids. PMID:28475645

Extensive analysis of milk fatty acids in two fat-tailed sheep breeds during lactation.

PubMed

Payandeh, S; Kafilzadeh, F; Juárez, M; de la Fuente, M A; Ghadimi, D; Marín, A L Martínez

2016-12-01

The profile of fatty acids (FA) in the milk fat of two Iranian fat-tailed sheep breeds, Sanjabi and Mehraban, was compared during lactation. Eight ewes of each breed, balanced in parity and carrying one foetus, were selected before parturition. Ewes were kept separated in individual pens during the experimental period, under the same management practices and fed the same diet, in order to eliminate any confounding effects on milk FA profile. Milk was sampled at biweekly intervals up to 10 weeks of lactation, starting 2 weeks after parturition. More than 100 FA were determined in milk fat by means of gas chromatography. The milk fat of Sanjabi ewes contained more cis-9 18:1, that of Mehraban ewes was richer in 10:0, 12:0 and 14:0, and no differences were found for 16:0 and 18:0. No breed differences were found for most branched-chain FA. Mehraban ewes showed a higher presence of vaccenic and rumenic acids in their milk fat. The milk fat of Sanjabi ewes had a lower atherogenicity index and n-6/n-3 FA ratio. The contents of several FA showed time-dependent changes, so breed differences were more apparent or disappeared as lactation progressed. The milk fat of Sanjabi ewes showed a better FA profile from the human health point of view.

WHIM syndrome caused by a single amino acid substitution in the carboxy-tail of chemokine receptor CXCR4

PubMed Central

Liu, Qian; Chen, Haoqian; Ojode, Teresa; Gao, Xiangxi; Anaya-O'Brien, Sandra; Turner, Nicholas A.; Ulrick, Jean; DeCastro, Rosamma; Kelly, Corin; Cardones, Adela R.; Gold, Stuart H.; Hwang, Eugene I.; Wechsler, Daniel S.; Malech, Harry L.; Murphy, Philip M.

2012-01-01

WHIM syndrome is a rare, autosomal dominant, immunodeficiency disorder so-named because it is characterized by warts, hypogammaglobulinemia, infections, and myelokathexis (defective neutrophil egress from the BM). Gain-of-function mutations that truncate the C-terminus of the chemokine receptor CXCR4 by 10-19 amino acids cause WHIM syndrome. We have identified a family with autosomal dominant inheritance of WHIM syndrome that is caused by a missense mutation in CXCR4, E343K (1027G → A). This mutation is also located in the C-terminal domain, a region responsible for negative regulation of the receptor. Accordingly, like CXCR4R334X, the most common truncation mutation in WHIM syndrome, CXCR4E343K mediated approximately 2-fold increased signaling in calcium flux and chemotaxis assays relative to wild-type CXCR4; however, CXCR4E343K had a reduced effect on blocking normal receptor down-regulation from the cell surface. Therefore, in addition to truncating mutations in the C-terminal domain of CXCR4, WHIM syndrome may be caused by a single charge-changing amino acid substitution in this domain, E343K, that results in increased receptor signaling. PMID:22596258

Structure of the bacteriophage T4 long tail fiber receptor-binding tip

PubMed Central

Bartual, Sergio G.; Otero, José M.; Garcia-Doval, Carmela; Llamas-Saiz, Antonio L.; Kahn, Richard; Fox, Gavin C.; van Raaij, Mark J.

2010-01-01

Bacteriophages are the most numerous organisms in the biosphere. In spite of their biological significance and the spectrum of potential applications, little high-resolution structural detail is available on their receptor-binding fibers. Here we present the crystal structure of the receptor-binding tip of the bacteriophage T4 long tail fiber, which is highly homologous to the tip of the bacteriophage lambda side tail fibers. This structure reveals an unusual elongated six-stranded antiparallel beta-strand needle domain containing seven iron ions coordinated by histidine residues arranged colinearly along the core of the biological unit. At the end of the tip, the three chains intertwine forming a broader head domain, which contains the putative receptor interaction site. The structure reveals a previously unknown beta-structured fibrous fold, provides insights into the remarkable stability of the fiber, and suggests a framework for mutations to expand or modulate receptor-binding specificity. PMID:21041684

Ferulic acid inhibits neuro-inflammation in mice exposed to chronic unpredictable mild stress.

PubMed

Liu, Ya-Min; Shen, Ji-Duo; Xu, Li-Ping; Li, Han-Bing; Li, Yu-Cheng; Yi, Li-Tao

2017-04-01

Ferulic acid is a hydroxycinnamic acid that widely presents in plant cell wall components. It has been demonstrated that ferulic acid can attenuate depressive-like behaviors in both forced swimming test and tail suspension test. Considering that depression is an inflammatory related mental disease, our present study was aimed to investigate the role of ferulic acid in the regulation of microglia activation, pro-inflammatory cytokines, nuclear factor kappa B (NF-κB) and nucleotide binding and oligomerization domain-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome in mice exposed to chronic unpredictable mild stress (CUMS). Our results firstly showed that decreased sucrose preference and increased immobility time were completely reversed by administration with ferulic acid and fluoxetine for four weeks. Then, we found that CUMS significantly caused interleukin-1β (IL-1β), interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) up-regulation, microglia, NF-κB signaling and NLRP3 inflammasome activation in the prefrontal cortex. On the contrary, these activated inflammatory response induced by CUMS were reversed by ferulic acid and fluoxetine as well, suggesting that anti-inflammatory related mechanism was involved in the antidepressant-like effects of ferulic acid in stressed mice. Copyright © 2017 Elsevier B.V. All rights reserved.

The PR-Set7 binding domain of Riz1 is required for the H4K20me1-H3K9me1 trans-tail 'histone code' and Riz1 tumor suppressor function.

PubMed

Congdon, Lauren M; Sims, Jennifer K; Tuzon, Creighton T; Rice, Judd C

2014-04-01

PR-Set7/Set8/KMT5a is the sole histone H4 lysine 20 monomethyltransferase (H4K20me1) in metazoans and is essential for proper cell division and genomic stability. We unexpectedly discovered that normal cellular levels of monomethylated histone H3 lysine 9 (H3K9me1) were also dependent on PR-Set7, but independent of its catalytic activity. This observation suggested that PR-Set7 interacts with an H3K9 monomethyltransferase to establish the previously reported H4K20me1-H3K9me1 trans-tail 'histone code'. Here we show that PR-Set7 specifically and directly binds the C-terminus of the Riz1/PRDM2/KMT8 tumor suppressor and demonstrate that the N-terminal PR/SET domain of Riz1 preferentially monomethylates H3K9. The PR-Set7 binding domain was required for Riz1 nuclear localization and maintenance of the H4K20me1-H3K9me1 trans-tail 'histone code'. Although Riz1 can function as a repressor, Riz1/H3K9me1 was dispensable for the repression of genes regulated by PR-Set7/H4K20me1. Frameshift mutations resulting in a truncated Riz1 incapable of binding PR-Set7 occur frequently in various aggressive cancers. In these cancer cells, expression of wild-type Riz1 restored tumor suppression by decreasing proliferation and increasing apoptosis. These phenotypes were not observed in cells expressing either the Riz1 PR/SET domain or PR-Set7 binding domain indicating that Riz1 methyltransferase activity and PR-Set7 binding domain are both essential for Riz1 tumor suppressor function.

Clipping of arginine-methylated histone tails by JMJD5 and JMJD7

PubMed Central

Liu, Haolin; Wang, Chao; Lee, Schuyler; Deng, Yu; Wither, Matthew; Oh, Sangphil; Ning, Fangkun; Dege, Carissa; Zhang, Qianqian; Liu, Xinjian; Johnson, Aaron M.; Zang, Jianye; Janknecht, Ralf; Hansen, Kirk; Marrack, Philippa; Li, Chuan-Yuan; Kappler, John W.; Hagman, James; Zhang, Gongyi

2017-01-01

Two of the unsolved, important questions about epigenetics are: do histone arginine demethylases exist, and is the removal of histone tails by proteolysis a major epigenetic modification process? Here, we report that two orphan Jumonji C domain (JmjC)-containing proteins, JMJD5 and JMJD7, have divalent cation-dependent protease activities that preferentially cleave the tails of histones 2, 3, or 4 containing methylated arginines. After the initial specific cleavage, JMJD5 and JMJD7, acting as aminopeptidases, progressively digest the C-terminal products. JMJD5-deficient fibroblasts exhibit dramatically increased levels of methylated arginines and histones. Furthermore, depletion of JMJD7 in breast cancer cells greatly decreases cell proliferation. The protease activities of JMJD5 and JMJD7 represent a mechanism for removal of histone tails bearing methylated arginine residues and define a potential mechanism of transcription regulation. PMID:28847961

Factors affecting the transformation of a pyritic tailing: scaled-up column tests.

PubMed

García, C; Ballester, A; González, F; Blázquez, M L

2005-02-14

Two different methods for predicting the quality of the water draining from a pyritic tailing are compared; for this, a static test (ABA test) and a kinetic test in large columns were chosen. The different results obtained in the two experimental set-ups show the necessity of being careful in selecting both the adequate predictive method and the conclusions and extrapolations derived from them. The tailing chosen for the weathering tests (previously tested in shake flasks and in small weathering columns) was a pyritic residue produced in a flotation plant of complex polymetallic sulphides (Huelva, Spain). The ABA test was a modification of the conventional ABA test reported in bibliography. The modification consisted in the soft conditions employed in the digestion phase. For column tests, two identical methacrylate columns (150 cm high and 15 cm diameter) were used to study the chemical and microbiological processes controlling the leaching of pyrite. The results obtained in the two tests were very different. The static test predicted a strong potential acidity for the tailing. On the contrary, pH value in the effluents draining from the columns reached values of only 5 units, being the concentration of metals (<600 mg/L) and sulphate ions (<17,000 mg/L) very small and far from the values of a typical acid mine drainage. In consequence, the static test may oversize the potential acidity of the tailing; whereas large columns may be saturated in water, displacing the oxygen and inhibiting the microbial activity necessary to catalyse mineral oxidation.

Vertical gradients in carbon flow and methane production in a sulfate-rich oil sands tailings pond.

PubMed

Stasik, Sebastian; Wendt-Potthoff, Katrin

2016-12-01

Oil sands tailings ponds are primary storage basins for tailings produced during oil sands processing in Alberta (Canada). Due to microbial metabolism, methane production contributes to greenhouse gas emissions, but positively affects tailings densification, which is relevant for operational water re-use. Depending on the age and depth of tailings, the activity of sulfate-reducing bacteria (SRB) may control methanogenesis due to the competition for substrates. To assess the depth-related impact of sulfate reduction on CH 4 emissions, original tailings of two vicinal pond profiles were incubated in anoxic microcosms with/without molybdate as selective inhibitor of microbial sulfate reduction. Integrating methane production rates, considerable volumes of CH 4 emissions (∼5.37 million L d -1 ) may be effectively prevented by the activity of SRB in sulfidic tailings between 3.5 and 7.5 m. To infer metabolic potentials controlling methanogenic pathways, a set of relevant organic acids (acetate, formate, propionate, butyrate, lactate) was added to part of the microcosms. Generally, organic acid transformation shifted with depth, with highest rates (305-446 μmol L -1  d -1 ) measured in fresh tailings at 5.5-7.5 m. In all depths, a transient accumulation of acetate revealed its importance as key intermediate during organic matter decomposition. SRB dominated the transformation of acetate, butyrate and propionate, but were not essential for lactate and formate turnover. Acetate as methanogenic substrate was important only at 13.5 m. At 1-7.5 m, methanogenesis significantly increased in presence of organic acids, most likely due to the syntrophic oxidation of acetate to CO 2 by SRB and subsequent conversion to CH 4 . Copyright © 2016 Elsevier Ltd. All rights reserved.

Optimization of digestion parameters for analysing the total sulphur of mine tailings by inductively coupled plasma optical emission spectrometry.

PubMed

Alam, Raquibul; Shang, Julie Q; Cheng, Xiangrong

2012-05-01

The oxidation of sulphidic mine tailings and consequent acid generation poses challenges for the environment. Accurate and precise analysis of sulphur content is necessary for impact assessment and management of mine tailings. Here, the authors aim at developing a rapid and easy digestion procedure, which may analyse and measure the total amount of sulphur in mine tailings by using inductively coupled plasma. For evaluating effects of several variables, the researchers used a univariate (analysis of variance (ANOVA)) strategy and considered factors such as composition of the acid mixture, heating time, and refluxing device to optimize the performance. To do the experiment, the researchers have used two certified reference materials (KZK-1 and RTS-2) and samples of tailings from Musselwhite mine. ANOVA result shows that heating time is the most influencing factor on acid digestion of the reference materials whereas in case of a digestion of tailings sample, hydrochloric acid proved to be the most significant parameter. Satisfactory results between the measured and referenced values are found for all experiments. It is found that the aqua regia (1 ml HNO(3) + 3 ml HCl) digestion of 0.1 g of samples after only 40 min of heating at 95°C produced fast, safe, and accurate analytical results with a recovery of 97% for the selected reference materials.

Multiple-interactions among EMILIN1 and EMILIN2 N- and C-terminal domains.

PubMed

Bot, Simonetta; Andreuzzi, Eva; Capuano, Alessandra; Schiavinato, Alvise; Colombatti, Alfonso; Doliana, Roberto

2015-01-01

EMILIN1 and EMILIN2 belong to a family of extracellular matrix glycoproteins characterized by the N-terminal cysteine-rich EMI domain, a long segment with high probabilty for coiled-coil structure formation and a C-terminal gC1q domain. To study EMILIN1 and EMILIN2 interaction and assembly we have applied qualitative and quantitative two hybrid systems using constructs corresponding to the gC1q and EMI domains. The identified interactions were further confirmed in yeast extracts of co-transfected cells followed by co-immunoprecipitation. The data indicated that gC1q domains are able to self-interact as well as to interact one each other and with the EMI domains, but no self interactions were detected between the EMI domains. Furthermore EMILINs interactions were studied in 293-EBNA cells co-transfected with full lenght EMILIN1 and EMILIN2 constructs. Specific antibodies were able to co-immunoprecipitate EMILINs, indicating that also full-lenght proteins can give rise to non-covalent homo- and hetero-multimers even if reduced and alkylated before mixing. Immunofluorescence analysis on mouse cell cultures and tissues sections with specific antibodies showed co-distribution of EMILIN1 and EMILIN2. Thus, we can hypothesize that EMILINs multimers are formed by head-to-tail interaction between C-terminal and N-terminal domains of EMILIN1 and/or EMILIN2 but also by tail-to-tail interaction between gC1q domains. These multiple interactions may regulate homo-typic and/or hetero-typic linear and eventually lateral branching assemblies of EMILIN1 and EMILIN2 in tissues. Copyright © 2014. Published by Elsevier B.V.

Distinct roles for extracellular and intracellular domains in neuroligin function at inhibitory synapses

PubMed Central

Nguyen, Quynh-Anh; Horn, Meryl E; Nicoll, Roger A

2016-01-01

Neuroligins (NLGNs) are postsynaptic cell adhesion molecules that interact trans-synaptically with neurexins to mediate synapse development and function. NLGN2 is only at inhibitory synapses while NLGN3 is at both excitatory and inhibitory synapses. We found that NLGN3 function at inhibitory synapses in rat CA1 depends on the presence of NLGN2 and identified a domain in the extracellular region that accounted for this functional difference between NLGN2 and 3 specifically at inhibitory synapses. We further show that the presence of a cytoplasmic tail (c-tail) is indispensible, and identified two domains in the c-tail that are necessary for NLGN function at inhibitory synapses. These domains point to a gephyrin-dependent mechanism that is disrupted by an autism-associated mutation at R705 and a gephyrin-independent mechanism reliant on a putative phosphorylation site at S714. Our work highlights unique and separate roles for the extracellular and intracellular regions in specifying and carrying out NLGN function respectively. DOI: http://dx.doi.org/10.7554/eLife.19236.001 PMID:27805570

Interactions between the PDZ domains of Bazooka (Par-3) and phosphatidic acid: in vitro characterization and role in epithelial development

PubMed Central

Yu, Cao Guo; Harris, Tony J. C.

2012-01-01

Bazooka (Par-3) is a conserved polarity regulator that organizes molecular networks in a wide range of cell types. In epithelia, it functions as a plasma membrane landmark to organize the apical domain. Bazooka is a scaffold protein that interacts with proteins through its three PDZ (postsynaptic density 95, discs large, zonula occludens-1) domains and other regions. In addition, Bazooka has been shown to interact with phosphoinositides. Here we show that the Bazooka PDZ domains interact with the negatively charged phospholipid phosphatidic acid immobilized on solid substrates or in liposomes. The interaction requires multiple PDZ domains, and conserved patches of positively charged amino acid residues appear to mediate the interaction. Increasing or decreasing levels of diacylglycerol kinase or phospholipase D—enzymes that produce phosphatidic acid—reveal a role for phosphatidic acid in Bazooka embryonic epithelial activity but not its localization. Mutating residues implicated in phosphatidic acid binding revealed a possible role in Bazooka localization and function. These data implicate a closer connection between Bazooka and membrane lipids than previously recognized. Bazooka polarity landmarks may be conglomerates of proteins and plasma membrane lipids that modify each other's activities for an integrated effect on cell polarity. PMID:22833561

REAR PROFILE OF TAIL FROM SECOND LEVEL OF TAIL DOCK ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

REAR PROFILE OF TAIL FROM SECOND LEVEL OF TAIL DOCK STAND, SHOWING AIRCRAFT NUMBER (319), HORIZONTAL STABILIZER, TAIL CONE AND COOLING CTS FOR THE AUXILIARY POWER UNIT (APU), MECHANIC PAUL RIDEOUT IS LOWERING THE BALANCE PANELS ON THE STABILIZERS FOR LUBRICATION AND INSPECTION. - Greater Buffalo International Airport, Maintenance Hangar, Buffalo, Erie County, NY

A hybrid pareto mixture for conditional asymmetric fat-tailed distributions.

PubMed

Carreau, Julie; Bengio, Yoshua

2009-07-01

In many cases, we observe some variables X that contain predictive information over a scalar variable of interest Y , with (X,Y) pairs observed in a training set. We can take advantage of this information to estimate the conditional density p(Y|X = x). In this paper, we propose a conditional mixture model with hybrid Pareto components to estimate p(Y|X = x). The hybrid Pareto is a Gaussian whose upper tail has been replaced by a generalized Pareto tail. A third parameter, in addition to the location and spread parameters of the Gaussian, controls the heaviness of the upper tail. Using the hybrid Pareto in a mixture model results in a nonparametric estimator that can adapt to multimodality, asymmetry, and heavy tails. A conditional density estimator is built by modeling the parameters of the mixture estimator as functions of X. We use a neural network to implement these functions. Such conditional density estimators have important applications in many domains such as finance and insurance. We show experimentally that this novel approach better models the conditional density in terms of likelihood, compared to competing algorithms: conditional mixture models with other types of components and a classical kernel-based nonparametric model.

Ketoacylsynthase Domains of a Polyunsaturated Fatty Acid Synthase in Thraustochytrium sp. Strain ATCC 26185 Can Effectively Function as Stand-Alone Enzymes in Escherichia coli.

PubMed

Xie, Xi; Meesapyodsuk, Dauenpen; Qiu, Xiao

2017-05-01

Thraustochytrium sp. strain ATCC 26185 accumulates a high level of docosahexaenoic acid (DHA), a nutritionally important ω-3 very-long-chain polyunsaturated fatty acid (VLCPUFA) synthesized primarily by polyunsaturated fatty acid (PUFA) synthase, a type I polyketide synthase-like megaenzyme. The PUFA synthase in this species comprises three large subunits, each with multiple catalytic domains. It was hypothesized that among these domains, ketoacylsynthase (KS) domains might be critical for catalyzing the condensation of specific unsaturated acyl-acyl carrier proteins (ACPs) with malonyl-ACP, thereby retaining double bonds in an extended acyl chain. To investigate the functions of these putative KS domains, two segment sequences from subunit A (KS-A) and subunit B (KS-B) of the PUFA synthase were dissected and then expressed as stand-alone enzymes in Escherichia coli The results showed that both KS-A and KS-B domains could complement the defective phenotypes of both E. coli fabB and fabF mutants. Overexpression of these domains in wild-type E. coli led to increases in total fatty acid production. KS-B produced a higher ratio of unsaturated fatty acids (UFAs) to saturated fatty acids (SFAs), while KS-A could improve the overall production of fatty acids more effectively, particularly for the production of SFAs, implying that KS-A is more comparable to FabF, while KS-B is more similar to FabB in catalytic functions. Successful complementation and functional expression of the embedded KS domains in E. coli are the first step forward in studying the molecular mechanism of the PUFA synthase for the biosynthesis of VLCPUFAs in Thraustochytrium IMPORTANCE Very-long-chain polyunsaturated fatty acids (VLCPUFAs) are important for human health. They can be biosynthesized in either an aerobic pathway or an anaerobic pathway in nature. However, abundant VLCPUFAs in marine microorganisms are primarily synthesized by polyunsaturated fatty acid (PUFA) synthase, a megaenzyme with

Ketoacylsynthase Domains of a Polyunsaturated Fatty Acid Synthase in Thraustochytrium sp. Strain ATCC 26185 Can Effectively Function as Stand-Alone Enzymes in Escherichia coli

PubMed Central

Xie, Xi; Meesapyodsuk, Dauenpen

2017-01-01

ABSTRACT Thraustochytrium sp. strain ATCC 26185 accumulates a high level of docosahexaenoic acid (DHA), a nutritionally important ω-3 very-long-chain polyunsaturated fatty acid (VLCPUFA) synthesized primarily by polyunsaturated fatty acid (PUFA) synthase, a type I polyketide synthase-like megaenzyme. The PUFA synthase in this species comprises three large subunits, each with multiple catalytic domains. It was hypothesized that among these domains, ketoacylsynthase (KS) domains might be critical for catalyzing the condensation of specific unsaturated acyl-acyl carrier proteins (ACPs) with malonyl-ACP, thereby retaining double bonds in an extended acyl chain. To investigate the functions of these putative KS domains, two segment sequences from subunit A (KS-A) and subunit B (KS-B) of the PUFA synthase were dissected and then expressed as stand-alone enzymes in Escherichia coli. The results showed that both KS-A and KS-B domains could complement the defective phenotypes of both E. coli fabB and fabF mutants. Overexpression of these domains in wild-type E. coli led to increases in total fatty acid production. KS-B produced a higher ratio of unsaturated fatty acids (UFAs) to saturated fatty acids (SFAs), while KS-A could improve the overall production of fatty acids more effectively, particularly for the production of SFAs, implying that KS-A is more comparable to FabF, while KS-B is more similar to FabB in catalytic functions. Successful complementation and functional expression of the embedded KS domains in E. coli are the first step forward in studying the molecular mechanism of the PUFA synthase for the biosynthesis of VLCPUFAs in Thraustochytrium. IMPORTANCE Very-long-chain polyunsaturated fatty acids (VLCPUFAs) are important for human health. They can be biosynthesized in either an aerobic pathway or an anaerobic pathway in nature. However, abundant VLCPUFAs in marine microorganisms are primarily synthesized by polyunsaturated fatty acid (PUFA) synthase, a

The carbon chain-selective adenylation enzyme TamA: the missing link between fatty acid and pyrrole natural product biosynthesis.

PubMed

Marchetti, Piera M; Kelly, Van; Simpson, Joanna P; Ward, Mairi; Campopiano, Dominic J

2018-04-18

The marine bacterium Pseudoalteromonas tunicata produces the bipyrrole antibiotic tambjamine YP1. This natural product is built from common amino acid and fatty acid building blocks in a biosynthetic pathway that is encoded in the tam operon which contains 19 genes. The exact role that each of these Tam proteins plays in tambjamine biosynthesis is not known. Here, we provide evidence that TamA initiates the synthesis and controls the chain length of the essential tambjamine fatty amine tail. Sequence analysis suggests the unusual TamA is comprised of an N-terminal adenylation (ANL) domain fused to a C-terminal acyl carrier protein (ACP). Mass spectrometry analysis of recombinant TamA revealed the surprising presence of bound C11 and C12 acyl-adenylate intermediates. Acylation of the ACP domain was observed upon attachment of the phosphopantetheine (4'-PP) arm to the ACP. We also show that TamA can transfer fatty acids ranging in chain length from C6-C13 to an isolated ACP domain. Thus TamA bridges the gap between primary and secondary metabolism by linking fatty acid and pyrrole biosynthetic pathways.

Three-dimensional hydrogeological modeling to assess the elevated-water-table technique for controlling acid generation from an abandoned tailings site in Quebec, Canada

NASA Astrophysics Data System (ADS)

Ethier, Marie-Pier; Bussière, Bruno; Broda, Stefan; Aubertin, Michel

2018-01-01

The Manitou Mine sulphidic-tailings storage facility No. 2, near Val D'Or, Canada, was reclaimed in 2009 by elevating the water table and applying a monolayer cover made of tailings from nearby Goldex Mine. Previous studies showed that production of acid mine drainage can be controlled by lowering the oxygen flux through Manitou tailings with a water table maintained at the interface between the cover and reactive tailings. Simulations of different scenarios were performed using numerical hydrogeological modeling to evaluate the capacity of the reclamation works to maintain the phreatic surface at this interface. A large-scale numerical model was constructed and calibrated using 3 years of field measurements. This model reproduced the field measurements, including the existence of a western zone on the site where the phreatic level targeted is not always met during the summer. A sensitivity analysis was performed to assess the response of the model to varying saturated hydraulic conductivities, porosities, and grain-size distributions. Higher variations of the hydraulic heads, with respect to the calibrated scenario results, were observed when simulating a looser or coarser cover material. Long-term responses were simulated using: the normal climatic data, data for a normal climate with a 2-month dry spell, and a simplified climate-change case. Environmental quality targets were reached less frequently during summer for the dry spell simulation as well as for the simplified climate-change scenario. This study illustrates how numerical simulations can be used as a key tool to assess the eventual performance of various mine-site reclamation scenarios.

Three-dimensional hydrogeological modeling to assess the elevated-water-table technique for controlling acid generation from an abandoned tailings site in Quebec, Canada

NASA Astrophysics Data System (ADS)

Ethier, Marie-Pier; Bussière, Bruno; Broda, Stefan; Aubertin, Michel

2018-06-01

The Manitou Mine sulphidic-tailings storage facility No. 2, near Val D'Or, Canada, was reclaimed in 2009 by elevating the water table and applying a monolayer cover made of tailings from nearby Goldex Mine. Previous studies showed that production of acid mine drainage can be controlled by lowering the oxygen flux through Manitou tailings with a water table maintained at the interface between the cover and reactive tailings. Simulations of different scenarios were performed using numerical hydrogeological modeling to evaluate the capacity of the reclamation works to maintain the phreatic surface at this interface. A large-scale numerical model was constructed and calibrated using 3 years of field measurements. This model reproduced the field measurements, including the existence of a western zone on the site where the phreatic level targeted is not always met during the summer. A sensitivity analysis was performed to assess the response of the model to varying saturated hydraulic conductivities, porosities, and grain-size distributions. Higher variations of the hydraulic heads, with respect to the calibrated scenario results, were observed when simulating a looser or coarser cover material. Long-term responses were simulated using: the normal climatic data, data for a normal climate with a 2-month dry spell, and a simplified climate-change case. Environmental quality targets were reached less frequently during summer for the dry spell simulation as well as for the simplified climate-change scenario. This study illustrates how numerical simulations can be used as a key tool to assess the eventual performance of various mine-site reclamation scenarios.

Organic acids on the growth, anatomical structure, biochemical parameters and heavy metal accumulation of Iris lactea var. chinensis seedling growing in Pb mine tailings.

PubMed

Han, Yu-Lin; Huang, Su-Zhen; Yuan, Hai-Yan; Zhao, Jiu-Zhou; Gu, Ji-Guang

2013-08-01

The effect of citric acid (CA) and ethylene diamine tetraacetic acid (EDTA) on the growth, anatomical structure, physiological responses and lead (Pb) accumulation of Iris lactea var. chinensis seedling growing in Pb mine tailings for 30 days were studied. Results showed that the dry weights (DW) of roots decreased significantly under both levels of CA. The DWs of leaves and roots treated with 2 mmol/kg EDTA decreased significantly and were 23 and 54 %, respectively, lower than those of the control. The tolerant indexes of I. lactea var. chinensis under all treatments of organic acids were lower than control. The root tip anatomical structure was little affected under the treatments of 2 mmol/kg CA and 2 mmol/kg EDTA compared with control. However, the formation of photosynthesizing cells was inhibited by the treatment of 2 mmol/kg EDTA. The concentrations of chlorophyll a, chlorophyll b and total carotenoids in the leaves treated with 2 mmol/kg EDTA significantly decreased. Higher CA level and lower EDTA level could trigger the synthesis of ascorbic acid and higher level of EDTA could trigger the synthesis of glutathione. CA and EDTA could promote Pb accumulation of I. lactea var. chinensis and Pb concentration in the leaves and roots at 2 mmol/kg EDTA treatment increased significantly and reached to 160.44 and 936.08 μg/g DW, respectively, and 1.8 and 1.6 times higher than those of the control. The results indicated that I. lactea var. chinensis could be used to remediate Pb tailing and the role of EDTA in promoting Pb accumulation was better than CA did.

Alanine substitution of conserved residues in the cytoplasmic tail of herpes simplex virus gB can enhance or abolish cell fusion activity and viral entry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruel, Nancy; Zago, Anna; Spear, Patricia G.

2006-03-01

Herpes simplex virus (HSV) glycoprotein B (gB) is one of the four viral glycoproteins required for viral entry and cell fusion and is highly conserved among herpesviruses. Mutants of HSV type 2 gB were generated by substituting conserved residues in the cytoplasmic tail with alanine or by deleting 41 amino acids from the C-terminus. Some of the mutations abolished cell fusion activity and also prevented transport of gB to the cell surface, identifying residues in the gB cytoplasmic tail that are critical for intracellular transport of this glycoprotein. These mutations also prevented production of infectious virus, possibly because the mutantmore » forms of gB were not transported to the site of envelopment. Other mutations, particularly the deletion, significantly enhanced cell fusion activity. These mutations, as well as others described previously, identify regions of the gB cytoplasmic domain that modulate cell fusion activity.« less

Quantitative analyses of tartaric acid based on terahertz time domain spectroscopy

NASA Astrophysics Data System (ADS)

Cao, Binghua; Fan, Mengbao

2010-10-01

Terahertz wave is the electromagnetic spectrum situated between microwave and infrared wave. Quantitative analysis based on terahertz spectroscopy is very important for the application of terahertz techniques. But how to realize it is still under study. L-tartaric acid is widely used as acidulant in beverage, and other food, such as soft drinks, wine, candy, bread and some colloidal sweetmeats. In this paper, terahertz time-domain spectroscopy is applied to quantify the tartaric acid. Two methods are employed to process the terahertz spectra of different samples with different content of tartaric acid. The first one is linear regression combining correlation analysis. The second is partial least square (PLS), in which the absorption spectra in the 0.8-1.4THz region are used to quantify the tartaric acid. To compare the performance of these two principles, the relative error of the two methods is analyzed. For this experiment, the first method does better than the second one. But the first method is suitable for the quantitative analysis of materials which has obvious terahertz absorption peaks, while for material which has no obvious terahertz absorption peaks, the second one is more appropriate.

Characterization and assessment of potential environmental risk of tailings stored in seven impoundments in the Aries river basin, Western Romania

PubMed Central

2013-01-01

Background The objective of this study was to examine the potential environmental risk of tailings resulted after precious and base metal ores processing, stored in seven impoundments located in the Aries river basin, Romania. The tailings were characterized by mineralogical and elemental composition, contamination indices, acid rock drainage generation potential and water leachability of hazardous/priority hazardous metals and ions. Multivariate statistical methods were used for data interpretation. Results Tailings were found to be highly contaminated with several hazardous/priority hazardous metals (As, Cu, Cd, Pb), and pose potential contamination risk for soil, sediments, surface and groundwater. Two out of the seven studied impoundments does not satisfy the criteria required for inert wastes, shows acid rock drainage potential and thus can contaminate the surface and groundwater. Three impoundments were found to be highly contaminated with As, Pb and Cd, two with As and other two with Cu. The tailings impoundments were grouped based on the enrichment factor, geoaccumulation index, contamination factor and contamination degree of 7 hazardous/priority hazardous metals (As, Cd, Cr, Cu, Ni, Pb, Zn) considered typical for the studied tailings. Principal component analysis showed that 47% of the elemental variability was attributable to alkaline silicate rocks, 31% to acidic S-containing minerals, 12% to carbonate minerals and 5% to biogenic elements. Leachability of metals and ions was ascribed in proportion of 61% to silicates, 11% to acidic minerals and 6% to the organic matter. A variability of 18% was attributed to leachability of biogenic elements (Na, K, Cl-, NO3-) with no potential environmental risk. Pattern recognition by agglomerative hierarchical clustering emphasized the grouping of impoundments in agreement with their contamination degree and acid rock drainage generation potential. Conclusions Tailings stored in the studied impoundments were found to

The Abl SH2-kinase linker naturally adopts a conformation competent for SH3 domain binding.

PubMed

Chen, Shugui; Brier, Sébastien; Smithgall, Thomas E; Engen, John R

2007-04-01

The core of the Abelson tyrosine kinase (c-Abl) is structurally similar to Src-family kinases where SH3 and SH2 domains pack against the backside of the kinase domain in the down-regulated conformation. Both kinase families depend upon intramolecular association of SH3 with the linker joining the SH2 and kinase domains for suppression of kinase activity. Hydrogen deuterium exchange (HX) and mass spectrometry (MS) were used to probe intramolecular interaction of the c-Abl SH3 domain with the linker in recombinant constructs lacking the kinase domain. Under physiological conditions, the c-Abl SH3 domain undergoes partial unfolding, which is stabilized by ligand binding, providing a unique assay for SH3:linker interaction in solution. Using this approach, we observed dynamic association of the SH3 domain with the linker in the absence of the kinase domain. Truncation of the linker before W254 completely prevented cis-interaction with SH3, while constructs containing amino acids past this point showed SH3:linker interactions. The observation that the Abl linker sequence exhibits SH3-binding activity in the absence of the kinase domain is unique to Abl and was not observed with Src-family kinases. These results suggest that SH3:linker interactions may have a more prominent role in Abl regulation than in Src kinases, where the down-regulated conformation is further stabilized by a second intramolecular interaction between the C-terminal tail and the SH2 domain.

Kinase Associated-1 Domains Drive MARK/PAR1 Kinases to Membrane Targets by Binding Acidic Phospholipids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moravcevic, Katarina; Mendrola, Jeannine M.; Schmitz, Karl R.

Phospholipid-binding modules such as PH, C1, and C2 domains play crucial roles in location-dependent regulation of many protein kinases. Here, we identify the KA1 domain (kinase associated-1 domain), found at the C terminus of yeast septin-associated kinases (Kcc4p, Gin4p, and Hsl1p) and human MARK/PAR1 kinases, as a membrane association domain that binds acidic phospholipids. Membrane localization of isolated KA1 domains depends on phosphatidylserine. Using X-ray crystallography, we identified a structurally conserved binding site for anionic phospholipids in KA1 domains from Kcc4p and MARK1. Mutating this site impairs membrane association of both KA1 domains and intact proteins and reveals the importancemore » of phosphatidylserine for bud neck localization of yeast Kcc4p. Our data suggest that KA1 domains contribute to coincidence detection, allowing kinases to bind other regulators (such as septins) only at the membrane surface. These findings have important implications for understanding MARK/PAR1 kinases, which are implicated in Alzheimer's disease, cancer, and autism.« less

The PDZ domain of the guanine nucleotide exchange factor PDZGEF directs binding to phosphatidic acid during brush border formation.

PubMed

Consonni, Sarah V; Brouwer, Patricia M; van Slobbe, Eleonora S; Bos, Johannes L

2014-01-01

PDZGEF is a guanine nucleotide exchange factor for the small G protein Rap. It was recently found that PDZGEF contributes to establishment of intestinal epithelial polarity downstream of the kinase Lkb1. By binding to phosphatidic acid enriched at the apical membrane, PDZGEF locally activates Rap2a resulting in induction of brush border formation via a pathway that includes the polarity players TNIK, Mst4 and Ezrin. Here we show that the PDZ domain of PDZGEF is essential and sufficient for targeting PDZGEF to the apical membrane of polarized intestinal epithelial cells. Inhibition of PLD and consequently production of phosphatidic acid inhibitis targeting of PDZGEF to the plasma membrane. Furthermore, localization requires specific positively charged residues within the PDZ domain. We conclude that local accumulation of PDZGEF at the apical membrane during establishment of epithelial polarity is mediated by electrostatic interactions between positively charged side chains in the PDZ domain and negatively charged phosphatidic acid.

The PDZ Domain of the Guanine Nucleotide Exchange Factor PDZGEF Directs Binding to Phosphatidic Acid during Brush Border Formation

PubMed Central

Consonni, Sarah V.; Brouwer, Patricia M.; van Slobbe, Eleonora S.; Bos, Johannes L.

2014-01-01

PDZGEF is a guanine nucleotide exchange factor for the small G protein Rap. It was recently found that PDZGEF contributes to establishment of intestinal epithelial polarity downstream of the kinase Lkb1. By binding to phosphatidic acid enriched at the apical membrane, PDZGEF locally activates Rap2a resulting in induction of brush border formation via a pathway that includes the polarity players TNIK, Mst4 and Ezrin. Here we show that the PDZ domain of PDZGEF is essential and sufficient for targeting PDZGEF to the apical membrane of polarized intestinal epithelial cells. Inhibition of PLD and consequently production of phosphatidic acid inhibitis targeting of PDZGEF to the plasma membrane. Furthermore, localization requires specific positively charged residues within the PDZ domain. We conclude that local accumulation of PDZGEF at the apical membrane during establishment of epithelial polarity is mediated by electrostatic interactions between positively charged side chains in the PDZ domain and negatively charged phosphatidic acid. PMID:24858808

Differential Occurrence of Interactions and Interaction Domains in Proteins Containing Homopolymeric Amino Acid Repeats

PubMed Central

Pelassa, Ilaria; Fiumara, Ferdinando

2015-01-01

Homopolymeric amino acids repeats (AARs), which are widespread in proteomes, have often been viewed simply as spacers between protein domains, or even as “junk” sequences with no obvious function but with a potential to cause harm upon expansion as in genetic diseases associated with polyglutamine or polyalanine expansions, including Huntington disease and cleidocranial dysplasia. A growing body of evidence indicates however that at least some AARs can form organized, functional protein structures, and can regulate protein function. In particular, certain AARs can mediate protein-protein interactions, either through homotypic AAR-AAR contacts or through heterotypic contacts with other protein domains. It is still unclear however, whether AARs may have a generalized, proteome-wide role in shaping protein-protein interaction networks. Therefore, we have undertaken here a bioinformatics screening of the human proteome and interactome in search of quantitative evidence of such a role. We first identified the sets of proteins that contain repeats of any one of the 20 amino acids, as well as control sets of proteins chosen at random in the proteome. We then analyzed the connectivity between the proteins of the AAR-containing protein sets and we compared it with that observed in the corresponding control networks. We find evidence for different degrees of connectivity in the different AAR-containing protein networks. Indeed, networks of proteins containing polyglutamine, polyglutamate, polyproline, and other AARs show significantly increased levels of connectivity, whereas networks containing polyleucine and other hydrophobic repeats show lower degrees of connectivity. Furthermore, we observed that numerous protein-protein, -nucleic acid, and -lipid interaction domains are significantly enriched in specific AAR protein groups. These findings support the notion of a generalized, combinatorial role of AARs, together with conventional protein interaction domains, in

Characterization of calmodulin binding domains in TRPV2 and TRPV5 C-tails.

PubMed

Holakovska, Blanka; Grycova, Lenka; Bily, Jan; Teisinger, Jan

2011-02-01

The transient receptor potential channels TRPV2 and TRPV5 belong to the vanilloid TRP subfamily. TRPV2 is highly similar to TRPV1 and shares many common properties with it. TRPV5 (and also its homolog TRPV6) is a rather distinct member of the TRPV subfamily. It is distant for being strictly Ca(2+)-selective and features quite different properties from the rest of the TRPV subfamily. It is known that TRP channels are regulated by calmodulin in a calcium-dependent manner. In our study we identified a calmodulin binding site on the C-termini of TRPV2 (654-683) and TRPV5 (587-616) corresponding to the consensus CaM binding motif 1-5-10. The R679 and K681 single mutants of TRPV2 caused a 50% decrease in binding affinity and a double mutation of K661/K664 of the same peptide lowered the binding affinity by up to 75%. A double mutation of R606/K607 and triple mutation of R594/R606/R610 in TRPV5 C-terminal peptide resulted in the total loss of binding affinity to calmodulin. These results demonstrate that the TRPV2 C-tail and TRPV5 C-tail contain calmodulin binding sites and that the basic residues are strongly involved in TRP channel binding to calmodulin.

Vegetation successfully prevents oxidization of sulfide minerals in mine tailings.

PubMed

Li, Yang; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

2016-07-15

The oxidization of metal sulfide in tailings causes acid mine drainage. However, it remains unclear whether vegetation prevents the oxidization of metal sulfides. The oxidization characteristics and microbial indices of the tailings in the presence of various plant species were investigated to explore the effects of vegetation on the oxidization of sulfide minerals in tailings. The pH, reducing sulfur, free iron oxides (Fed), chemical oxygen consumption (COC) and biological oxygen consumption (BOC) were measured. Key iron- and sulfur-oxidizing bacteria (Acidithiobacillus spp., Leptospirillum spp. and Thiobacillus spp.) were quantified using real-time PCR. The results indicate that vegetation growing on tailings can effectively prevent the oxidization of sulfide minerals in tailings. A higher pH and reducing-sulfur content and lower Fed were observed in the 0-30 cm depth interval in the presence of vegetation compared to bare tailings (BT). The COC gradually decreased with depth in all of the soil profiles; specifically, the COC rapidly decreased in the 10-20 cm interval in the presence of vegetation but gradually decreased in the BT profiles. Imperata cylindrica (IC) and Chrysopogon zizanoides (CZ) profiles contained the highest BOC in the 10-20 cm interval. The abundance of key iron- and sulfur-oxidizing bacteria in the vegetated tailings were significantly lower than in the BT; in particular, IC was associated with the lowest iron- and sulfur-oxidizing bacterial abundance. In conclusion, vegetation successfully prevented the oxidization of sulfide minerals in the tailings, and Imperata cylindrica is the most effective in reducing the number of iron- and sulfur-oxidizing bacteria and helped to prevent the oxidization of sulfide minerals in the long term. Copyright © 2016 Elsevier Ltd. All rights reserved.

Treatment impacts on temporal microbial community dynamics during phytostabilization of acid-generating mine tailings in semiarid regions.

PubMed

Valentín-Vargas, Alexis; Neilson, Julia W; Root, Robert A; Chorover, Jon; Maier, Raina M

2018-03-15

Direct revegetation, or phytostabilization, is a containment strategy for contaminant metals associated with mine tailings in semiarid regions. The weathering of sulfide ore-derived tailings frequently drives acidification that inhibits plant establishment resulting in materials prone to wind and water dispersal. The specific objective of this study was to associate pyritic mine waste acidification, characterized through pore-water chemistry analysis, with dynamic changes in microbial community diversity and phylogenetic composition, and to evaluate the influence of different treatment strategies on the control of acidification dynamics. Samples were collected from a highly instrumented one-year mesocosm study that included the following treatments: 1) unamended tailings control; 2) tailings amended with 15% compost; and 3) the 15% compost-amended tailings planted with Atriplex lentiformis. Tailings samples were collected at 0, 3, 6 and 12months and pore water chemistry was monitored as an indicator of acidification and weathering processes. Results confirmed that the acidification process for pyritic mine tailings is associated with a temporal progression of bacterial and archaeal phylotypes from pH sensitive Thiobacillus and Thiomonas to communities dominated by Leptospirillum and Ferroplasma. Pore-water chemistry indicated that weathering rates were highest when Leptospirillum was most abundant. The planted treatment was most successful in disrupting the successional evolution of the Fe/S-oxidizing community. Plant establishment stimulated growth of plant-growth-promoting heterotrophic phylotypes and controlled the proliferation of lithoautotrophic Fe/S-oxidizers. The results suggest the potential for eco-engineering a microbial inoculum to stimulate plant establishment and inhibit proliferation of the most efficient Fe/S-oxidizing phylotypes. Copyright © 2017 Elsevier B.V. All rights reserved.

The role of cassiterite controlling arsenic mobility in an abandoned stanniferous tailings impoundment at Llallagua, Bolivia.

PubMed

Romero, Francisco Martín; Canet, Carles; Alfonso, Pura; Zambrana, Rubén N; Soto, Nayelli

2014-05-15

The surface water contamination by potentially toxic elements (PTE) leached from mine tailings is a major environmental concern. However, the formation of insoluble solid phases can control the mobility of PTE, with subsequent decrease of the risk that tailings suppose to the environment. We characterized the tailings from a tin inactive mine in Llallagua, Bolivia in order to assess the risk for surface water quality. These tailings contain high concentrations of PTE, with up to 94,344 mg/kg Fe, 9,135 mg/kg Sn, 4,606 mg/kg As, 1,362 mg/kg Cu, 1,220 mg/kg Zn, 955 mg/kg Pb and 151 mg/kg Cd. Oxidation of sulfide minerals in these tailings generates acid leachates (pH=2.5-3.5), rich in SO4(2-) and dissolved PTE, thereby releasing contaminants to the surface waters. Nevertheless, the concentrations of dissolved Sn, As and Pb in acid leachates are low (Sn<0.01 mg/L; As=0.25-2.55 mg/L; Pb<0.05 mg/L). This indicates that, for the most part, Sn, As and Pb are being retained by the solid phases in the impoundment, so that these elements are not reaching the surface waters. Fe-bearing cassiterite-an insoluble and weathering-resistant oxide mineral-is abundant in the studied tailing deposits; it should be the main solid phase controlling Sn and As mobility in the impoundment. Additionally, jarosite and plumbojarosite, identified among the secondary minerals, could also play an important role controlling the mobility of As and Pb. Taking into account (a) the low solubility constants of cassiterite (Ksp=10(-64.2)), jarosite (Ksp=10(-11)) and plumbojarosite (Ksp=10(-28.66)), and (b) the stability of these minerals under acidic conditions, we can conclude that they control the long-term fate of Sn, As and Pb in the studied tailings. Copyright © 2014 Elsevier B.V. All rights reserved.

The Association of Myosin IB with Actin Waves in Dictyostelium Requires Both the Plasma Membrane-Binding Site and Actin-Binding Region in the Myosin Tail

PubMed Central

Brzeska, Hanna; Pridham, Kevin; Chery, Godefroy; Titus, Margaret A.; Korn, Edward D.

2014-01-01

F-actin structures and their distribution are important determinants of the dynamic shapes and functions of eukaryotic cells. Actin waves are F-actin formations that move along the ventral cell membrane driven by actin polymerization. Dictyostelium myosin IB is associated with actin waves but its role in the wave is unknown. Myosin IB is a monomeric, non-filamentous myosin with a globular head that binds to F-actin and has motor activity, and a non-helical tail comprising a basic region, a glycine-proline-glutamine-rich region and an SH3-domain. The basic region binds to acidic phospholipids in the plasma membrane through a short basic-hydrophobic site and the Gly-Pro-Gln region binds F-actin. In the current work we found that both the basic-hydrophobic site in the basic region and the Gly-Pro-Gln region of the tail are required for the association of myosin IB with actin waves. This is the first evidence that the Gly-Pro-Gln region is required for localization of myosin IB to a specific actin structure in situ. The head is not required for myosin IB association with actin waves but binding of the head to F-actin strengthens the association of myosin IB with waves and stabilizes waves. Neither the SH3-domain nor motor activity is required for association of myosin IB with actin waves. We conclude that myosin IB contributes to anchoring actin waves to the plasma membranes by binding of the basic-hydrophobic site to acidic phospholipids in the plasma membrane and binding of the Gly-Pro-Gln region to F-actin in the wave. PMID:24747353

Omega-3 fatty acids are oxygenated at the n-7 carbon by the lipoxygenase domain of a fusion protein in the cyanobacterium Acaryochloris marina

PubMed Central

Gao, Benlian; Boeglin, William E.; Brash, Alan R.

2009-01-01

Lipoxygenases (LOX) are found in most organisms that contain polyunsaturated fatty acids, usually existing as individual genes although occasionally encoded as a fusion protein with a catalase-related hemoprotein. Such a fusion protein occurs in the cyanobacterium Acaryochloris marina and herein we report the novel catalytic activity of its LOX domain. The full-length protein and the C-terminal LOX domain were expressed in Escherichia coli, and the catalytic activities characterized by UV, HPLC, GC-MS, and CD. All omega-3 polyunsaturates were oxygenated by the LOX domain at the n-7 position and with R stereospecificity: α-linolenic and the most abundant fatty acid in A. marina, stearidonic acid (C18.4ω3), are converted to the corresponding 12R-hydroperoxides, eicosapentaenoic acid to its 14R-hydroperoxide, and docosahexaenoic acid to its 16R-hydroperoxide. Omega-6 polyunsaturates were oxygenated at the n-10 position, forming 9R-hydroperoxy-octadecadienoic acid from linoleic acid and 11R-hydroperoxy-eicosatetraenoic acid from arachidonic acid. The metabolic transformation of stearidonic acid by the full-length fusion protein entails its 12R oxygenation with subsequent conversion by the catalase-related domain to a novel allene epoxide, a likely precursor of cyclopentenone fatty acids or other signaling molecules (Gao et al, J. Biol. Chem. 284:22087-98, 2009). Although omega-3 fatty acids and lipoxygenases are of widespread occurrence, this appears to be the first description of a LOX-catalyzed oxygenation that specifically utilizes the terminal pentadiene of omega-3 fatty acids. PMID:19786119

A Tale of Two Tails: Exploring Stellar Populations in the Tidal Tails of NGC 3256

NASA Astrophysics Data System (ADS)

Rodruck, Michael; Charlton, Jane C.; Konstantopoulos, Iraklis

2016-01-01

Galaxy interactions can inject material into the intergalactic medium via violent gravitational dynamics, often visualized in tidal tails. The composition of these tails has remained a mystery, as previous studies have focused on detecting tidal features, rather than the composite material itself. We have developed an observing program using deep, multiband imaging to probe the chaotic regions of tidal tails in search for an underlying stellar population. NGC 3256's twin tidal tails serve as a case study for this new technique. Our results show color values of u - g = 1.15 and r - i = 0.08 for the Western tail, and u - g = 1.33 and r - i = 0.22 for the Eastern tail, corresponding to discrepant ages between the tails of approximately 320 Myr and 785 Myr, respectively. With the interaction age of the system measured at 400 Myr, we find the stellar light in Western tail to be dominated by disrupted star clusters formed during and after the interaction, whereas the light from the Eastern tail is dominated by a 10 Gyr population originating from the host galaxies. We fit the Eastern tail color to a Mixed Stellar Population (MSP) model comprised 94% by mass of a 10 Gyr stellar population, and 6% of a 309 Myr population. We find 52% of the bolometric flux originating from this 10 Gyr population. We also detect a blue to red color gradient in each tail, running from galactic center to tail tip. In addition to tidal tail light, we detect 29 star cluster candidates (SCCs) in the Western tail and 19 in the Eastern, with mean ages of 282 Myr and 98 Myr respectively. Interestingly, we find an excess of very blue SCCs in the Eastern tail as compared to the Western tail, marking a recent, small episode of star formation.

The frantic play of the concealed HIV envelope cytoplasmic tail

PubMed Central

2013-01-01

Lentiviruses have unusually long envelope (Env) cytoplasmic tails, longer than those of other retroviruses. Whereas the Env ectodomain has received much attention, the gp41 cytoplasmic tail (gp41-CT) is one of the least studied parts of the virus. It displays relatively high conservation compared to the rest of Env. It has been long established that the gp41-CT interacts with the Gag precursor protein to ensure Env incorporation into the virion. The gp41-CT contains distinct motifs and domains that mediate both intensive Env intracellular trafficking and interactions with numerous cellular and viral proteins, optimizing viral infectivity. Although they are not fully understood, a multiplicity of interactions between the gp41-CT and cellular factors have been described over the last decade; these interactions illustrate how Env expression and incorporation into virions is a finely tuned process that has evolved to best exploit the host system with minimized genetic information. This review addresses the structure and topology of the gp41-CT of lentiviruses (mainly HIV and SIV), their domains and believed functions. It also considers the cellular and viral proteins that have been described to interact with the gp41-CT, with a particular focus on subtype-related polymorphisms. PMID:23705972

Introductory tail-flick of the Jacky dragon visual display: signal efficacy depends upon duration.

PubMed

Peters, Richard A; Evans, Christopher S

2003-12-01

Many animal signals have introductory components that alert receivers. Examples from the acoustic and visual domains show that this effect is often achieved with high intensity, a simple structure and a short duration. Quantitative analyses of the Jacky dragon Amphibolurus muricatus visual display reveal a different design: the introductory tail-flick has a lower velocity than subsequent components of the signal, but a longer duration. Here, using a series of video playback experiments with a digitally animated tail, we identify the properties responsible for signal efficacy. We began by validating the use of the computer-generated tail, comparing the responses to digital video footage of a lizard tail-flick with those to a precisely matched 3-D animation (Experiment 1). We then examined the effects of variation in stimulus speed, acceleration, duration and period by expanding and compressing the time scale of the sequence (Experiment 2). The results identified several variables that might mediate recognition. Two follow-up studies assessed the importance of tail-flick amplitude (Experiment 3), movement speed and signal duration (Experiment 4). Lizard responses to this array of stimuli reveal that duration is the most important characteristic of the tail-flick, and that intermittent signalling has the same effect as continuous movement. We suggest that signal design may reflect a trade-off between efficacy and cost.

Mobilization of radionuclides from uranium mill tailings and related waste materials in anaerobic environments

USGS Publications Warehouse

Landa, E.R.

2003-01-01

Specific extraction studies in our laboratory have shown that iron and manganese oxide- and alkaline earth sulfate minerals are important hosts of radium in uranium mill tailings. Iron- and sulfate-reducing bacteria may enhance the release of radium (and its analog barium) from uranium mill tailings, oil field pipe scale [a major technologically enhanced naturally occurring radioactive material (TENORM) waste], and jarosite (a common mineral in sulfuric acid processed-tailings). These research findings are reviewed and discussed in the context of nuclear waste forms (such as barium sulfate matrices), radioactive waste management practices, and geochemical environments in the Earth's surficial and shallow subsurface regions.

Historic mills and mill tailings as potential sources of contamination in and near the Humboldt River basin, northern Nevada. Chapter D.

USGS Publications Warehouse

Nash, J. Thomas; Stillings, Lisa L.

2003-01-01

Reconnaissance field studies of 40 mining districts in and near the Humboldt River basin have identified 83 mills and associated tailings impoundments and several other kinds of mineral-processing facilities (smelters, mercury retorts, heap-leach pads) related to historic mining. The majority of the mills and tailings sites are not recorded in the literature. All tailings impoundments show evidence of substantial amounts of erosion. At least 11 tailings dams were breached by flood waters, carrying fluvial tailings 1 to 15 km down canyons and across alluvial fans. Most of the tailings sites are dry most of the year, but some are near streams. Tailings that are wet for part of the year do not appear to be reacting significantly with those waters because physical factors such as clay layers and hard-pan cement appear to limit permeability and release of metals to surface waters. The major impact of mill tailings on surface- water quality may be brief flushes of runoff during storm events that carry acid and metals released from soluble mineral crusts. Small ephemeral ponds and puddles that tend to collect in trenches and low areas on tailings impoundments tend to be acidic and extremely enriched in metals, in part through cycles of evaporation. Ponded water that is rich in salts and metals could be acutely toxic to unsuspecting animals. Rare extreme storms have the potential to cause catastrophic failure of tailings impoundments, carry away metals in stormwaters, and transport tailings as debris flows for 1 to 15 km. In most situations these stormwaters and transported tailings could impact wildlife but probably would impact few or no people or domes-tic water wells. Because all identified historic tailings sites are several kilometers or more from the Humboldt River and major tributaries, tailings probably have no measurable impact on water quality in the main stem of the Humboldt River.

Domain-to-domain coupling in voltage-sensing phosphatase.

PubMed

Sakata, Souhei; Matsuda, Makoto; Kawanabe, Akira; Okamura, Yasushi

2017-01-01

Voltage-sensing phosphatase (VSP) consists of a transmembrane voltage sensor and a cytoplasmic enzyme region. The enzyme region contains the phosphatase and C2 domains, is structurally similar to the tumor suppressor phosphatase PTEN, and catalyzes the dephosphorylation of phosphoinositides. The transmembrane voltage sensor is connected to the phosphatase through a short linker region, and phosphatase activity is induced upon membrane depolarization. Although the detailed molecular characteristics of the voltage sensor domain and the enzyme region have been revealed, little is known how these two regions are coupled. In addition, it is important to know whether mechanism for coupling between the voltage sensor domain and downstream effector function is shared among other voltage sensor domain-containing proteins. Recent studies in which specific amino acid sites were genetically labeled using a fluorescent unnatural amino acid have enabled detection of the local structural changes in the cytoplasmic region of Ciona intestinalis VSP that occur with a change in membrane potential. The results of those studies provide novel insight into how the enzyme activity of the cytoplasmic region of VSP is regulated by the voltage sensor domain.

Domain-to-domain coupling in voltage-sensing phosphatase

PubMed Central

Sakata, Souhei; Matsuda, Makoto; Kawanabe, Akira; Okamura, Yasushi

2017-01-01

Voltage-sensing phosphatase (VSP) consists of a transmembrane voltage sensor and a cytoplasmic enzyme region. The enzyme region contains the phosphatase and C2 domains, is structurally similar to the tumor suppressor phosphatase PTEN, and catalyzes the dephosphorylation of phosphoinositides. The transmembrane voltage sensor is connected to the phosphatase through a short linker region, and phosphatase activity is induced upon membrane depolarization. Although the detailed molecular characteristics of the voltage sensor domain and the enzyme region have been revealed, little is known how these two regions are coupled. In addition, it is important to know whether mechanism for coupling between the voltage sensor domain and downstream effector function is shared among other voltage sensor domain-containing proteins. Recent studies in which specific amino acid sites were genetically labeled using a fluorescent unnatural amino acid have enabled detection of the local structural changes in the cytoplasmic region of Ciona intestinalis VSP that occur with a change in membrane potential. The results of those studies provide novel insight into how the enzyme activity of the cytoplasmic region of VSP is regulated by the voltage sensor domain. PMID:28744425

Susceptibility to virus-cell fusion at the plasma membrane is reduced through expression of HIV gp41 cytoplasmic domains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malinowsky, Katharina; Department of Virology, University of Heidelberg, Im Neuenheimer Feld 324, D-69120 Heidelberg; Luksza, Julia

2008-06-20

The cytoplasmic tail of the HIV transmembrane protein plays an important role in viral infection. In this study we analyzed the role of retroviral cytoplasmic tails in modulating the cytoskeleton and interfering with virus-cell fusion. HeLaP4 cells expressing different HIV cytoplasmic tail constructs showed reduced acetylated tubulin levels whereas the cytoplasmic tail of MLV did not alter microtubule stability indicating a unique function for the lentiviral cytoplasmic tail. The effect on tubulin is mediated through the membrane proximal region of the HIV cytoplasmic tail and was independent of membrane localization. Site-directed mutagenesis identified three motifs in the HIV-2 cytoplasmic tailmore » required to effect the reduction in acetylated tubulin. Both the Yxx{phi} domain and amino acids 21 to 45 of the HIV-2 cytoplasmic tail need to be present to change the level of acetylated tubulin in transfected cells. T-cells stably expressing one HIV-2 cytoplasmic tail derived construct showed also a reduction in acetylated tubulin thus confirming the importance of this effect not only for HeLaP4 and 293T cells. Challenge experiments using transiently transfected HeLaP4 cells and T cells stably expressing an HIV cytoplasmic tail construct revealed both reduced virus-cell fusion and replication of HIV-1{sub NL4.3} compared to control cells. In the virus-cell fusion assay only virions pseudotyped with either HIV or MLV envelopes showed reduced fusion efficiency, whereas VSV-G pseudotyped virions where not affected by the expression of HIV derived cytoplasmic tail constructs, indicating that fusion at the plasma but not endosomal membrane is affected. Overexpression of human histone-deacetylase 6 (HDAC6) and constitutively active RhoA resulted in a reduction of acetylated tubulin and reduced virus-cell fusion as significant as that observed following expression of HIV cytoplasmic tail constructs. Inhibition of HDAC6 showed a strong increase in acetylated tubulin and

A Tail of Two Sites: A Bipartite Mechanism for Recognition of Notch Ligands by Mind Bomb E3 Ligases

PubMed Central

McMillan, Brian J.; Schnute, Björn; Ohlenhard, Nadja; Zimmerman, Brandon; Miles, Laura; Beglova, Natalia; Klein, Thomas; Blacklow, Stephen C.

2015-01-01

Summary Mind bomb (Mib) proteins are large, multi-domain E3 ligases that promote ubiquitination of the cytoplasmic tails of Notch ligands. This ubiquitination step marks the ligand proteins for epsin-dependent endocytosis, which is critical for in vivo Notch receptor activation. We present here crystal structures of the substrate recognition domains of Mib1, both in isolation and in complex with peptides derived from Notch ligands. The structures, in combination with biochemical, cellular and in vivo assays, show that Mib1 contains two independent substrate recognition domains that engage two distinct epitopes from the cytoplasmic tail of the ligand Jagged1, one in the intracellular membrane proximal region and the other near the C-terminus. Together, these studies provide new insights into the mechanism of ubiquitin transfer by Mind bomb E3 ligases, illuminate a key event in ligand-induced activation of Notch receptors, and identify a potential new target for therapeutic modulation of Notch signal transduction in disease. PMID:25747658

A Tail of Two Sites: A Bipartite Mechanism for Recognition of Notch Ligands by Mind Bomb E3 Ligases

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMillan, Brian J.; Schnute, Björn; Ohlenhard, Nadja

Mind bomb (Mib) proteins are large, multi-domain E3 ligases that promote ubiquitination of the cytoplasmic tails of Notch ligands. This ubiquitination step marks the ligand proteins for epsin-dependent endocytosis, which is critical for in vivo Notch receptor activation. Here we present crystal structures of the substrate recognition domains of Mib1, both in isolation and in complex with peptides derived from Notch ligands. The structures, in combination with biochemical, cellular, and in vivo assays, show that Mib1 contains two independent substrate recognition domains that engage two distinct epitopes from the cytoplasmic tail of the ligand Jagged1, one in the intracellular membranemore » proximal region and the other near the C terminus. Together, these studies provide insights into the mechanism of ubiquitin transfer by Mind bomb E3 ligases, illuminate a key event in ligand-induced activation of Notch receptors, and identify a potential target for therapeutic modulation of Notch signal transduction in disease.« less

A Tail of Two Sites: A Bipartite Mechanism for Recognition of Notch Ligands by Mind Bomb E3 Ligases

DOE PAGES

McMillan, Brian J.; Schnute, Björn; Ohlenhard, Nadja; ...

2015-03-05

Mind bomb (Mib) proteins are large, multi-domain E3 ligases that promote ubiquitination of the cytoplasmic tails of Notch ligands. This ubiquitination step marks the ligand proteins for epsin-dependent endocytosis, which is critical for in vivo Notch receptor activation. Here we present crystal structures of the substrate recognition domains of Mib1, both in isolation and in complex with peptides derived from Notch ligands. The structures, in combination with biochemical, cellular, and in vivo assays, show that Mib1 contains two independent substrate recognition domains that engage two distinct epitopes from the cytoplasmic tail of the ligand Jagged1, one in the intracellular membranemore » proximal region and the other near the C terminus. Together, these studies provide insights into the mechanism of ubiquitin transfer by Mind bomb E3 ligases, illuminate a key event in ligand-induced activation of Notch receptors, and identify a potential target for therapeutic modulation of Notch signal transduction in disease.« less

The C-terminal domains of NF-H and NF-M subunits maintain axonal neurofilament content by blocking turnover of the stationary neurofilament network.

PubMed

Rao, Mala V; Yuan, Aidong; Campbell, Jabbar; Kumar, Asok; Nixon, Ralph A

2012-01-01

Newly synthesized neurofilaments or protofilaments are incorporated into a highly stable stationary cytoskeleton network as they are transported along axons. Although the heavily phosphorylated carboxyl-terminal tail domains of the heavy and medium neurofilament (NF) subunits have been proposed to contribute to this process and particularly to stability of this structure, their function is still obscure. Here we show in NF-H/M tail deletion [NF-(H/M)(tailΔ)] mice that the deletion of both of these domains selectively lowers NF levels 3-6 fold along optic axons without altering either rates of subunit synthesis or the rate of slow axonal transport of NF. Pulse labeling studies carried out over 90 days revealed a significantly faster rate of disappearance of NF from the stationary NF network of optic axons in NF-(H/M)(tailΔ) mice. Faster NF disappearance was accompanied by elevated levels of NF-L proteolytic fragments in NF-(H/M)(tailΔ) axons. We conclude that NF-H and NF-M C-terminal domains do not normally regulate NF transport rates as previously proposed, but instead increase the proteolytic resistance of NF, thereby stabilizing the stationary neurofilament cytoskeleton along axons.

The C-Terminal Domains of NF-H and NF-M Subunits Maintain Axonal Neurofilament Content by Blocking Turnover of the Stationary Neurofilament Network

PubMed Central

Rao, Mala V.; Yuan, Aidong; Campbell, Jabbar; Kumar, Asok; Nixon, Ralph A.

2012-01-01

Newly synthesized neurofilaments or protofilaments are incorporated into a highly stable stationary cytoskeleton network as they are transported along axons. Although the heavily phosphorylated carboxyl-terminal tail domains of the heavy and medium neurofilament (NF) subunits have been proposed to contribute to this process and particularly to stability of this structure, their function is still obscure. Here we show in NF-H/M tail deletion [NF-(H/M)tailΔ] mice that the deletion of both of these domains selectively lowers NF levels 3–6 fold along optic axons without altering either rates of subunit synthesis or the rate of slow axonal transport of NF. Pulse labeling studies carried out over 90 days revealed a significantly faster rate of disappearance of NF from the stationary NF network of optic axons in NF-(H/M)tailΔ mice. Faster NF disappearance was accompanied by elevated levels of NF-L proteolytic fragments in NF-(H/M)tailΔ axons. We conclude that NF-H and NF-M C-terminal domains do not normally regulate NF transport rates as previously proposed, but instead increase the proteolytic resistance of NF, thereby stabilizing the stationary neurofilament cytoskeleton along axons. PMID:23028520

A molecular dynamics simulation study of amino acid selectivity of LeuRS editing domain from Thermus thermophilus.

PubMed

Rayevsky, Alexey; Sharifi, Mohsen; Tukalo, Michael

2018-06-18

The accuracy of protein synthesis is provided by the editing functions of aminoacyl-tRNA synthetases (aaRSs), a mechanism that eliminates misactivated amino acids or mischarged tRNAs. Despite research efforts, some molecular bases of these mechanisms are still unclear. The post-transfer editing pathway of leucyl-tRNA synthetase (LeuRS) carried out in a special insertion domain (the Connective Polypeptide 1 or CP1), as editing domain. Recently, it was shown by in vivo studies and was supported by mutagenesis, and the kinetics approaches that the CP1 domain of LeuRS has discriminatory power for different substrates. The goal of this work is to investigate the structural basis for amino acid recognition of LeuRS post-transfer editing processes with molecular dynamics (MD) simulation method. To pursue this aim, the molecular modeling studies on Thermus thermophiles LeuRS (LeuRSTT) with two post-transfer substrates (norvalyl-tRNA Leu and isoleucyl-tRNA Leu ) was performed. Our results revealed that post-transfer substrate norvalyl-tRNA Leu is more favorable. Moreover, the MD simulations show that branched side chain of Ile-A76 cannot allow water molecules to get close, which leads to a significant decrease in the rate of hydrolysis. Finally, the study showed that site mutation Asp347Ala has elucidated a number of fine structural differences in the binding mode of two post-transfer substrates to the active centre of LeuRS editing domain and two conserved threonines, namely Thr247 and Thr248, are responsible for the amino acid selection through the interaction with substrates. Copyright © 2018 Elsevier Inc. All rights reserved.

Wind-tunnel Investigation of End-plate Effects of Horizontal Tails on a Vertical Tail Compared with Available Theory

NASA Technical Reports Server (NTRS)

Murray, Harry E

1946-01-01

A vertical-tail model with stub fuselage was tested in combination with various simulated horizontal tails to determine the effect of horizontal-tail span and location on the aerodynamic characteristics of the vertical tail. Available theoretical data on end-plate effects were collected and presented in the form most suitable for design purposes. Reasonable agreement was obtained between the measured and theoretical end-plate effects of horizontal tails on vertical tails, and the data indicated that the end-plate effect was determined more by the location of the horizontal tail than by the span of the horizontal tail. The horizontal tail gave most end-plate effect when located near either tip of the vertical tail and, when located near the base of the vertical tail, the end-plate effect was increased by moving the horizontal tail rearward.

Pretreatment of cyanided tailings by catalytic ozonation with Mn2+/O3.

PubMed

Li, Yulong; Li, Dengxin; Li, Jiebing; wang, Jin; Hussain, Asif; Ji, Hao; Zhai, Yijie

2015-02-01

The increasing amount of cyanided tailings produced as a by-product has gained significant attention in recent years because of the rapid development of the gold industry and extensive exploitation of gold mineral resources. The effective use of these secondary resources is becoming an important and urgent problem for all environmental protection staff. Manganese-catalyzed ozonation for the pre-oxidation of cyanided tailings was studied and the effects of Mn2+ dosage, initial sulfuric acid concentration, ozone volume flow, temperature and agitation speed on pretreatment were examined. The optimum reaction conditions were observed to be: ore pulp density 2.5%, agitation speed 700 r/min, temperature 60°C, Mn2+ dosage 40 g/L, ozone volume flow 80 L/hr, initial sulfuric acid concentration 1 mol/L, and reaction time 6 hr. Under these conditions, the leaching rate of Fe and weight loss could reach 94.85% and 48.89% respectively. The leaching process of cyanided tailings by Mn2+/O3 was analyzed, and it was found that the leaching of pyrite depends on synergetic oxidation by high-valent manganese and O3, in which the former played an important part. Copyright © 2014. Published by Elsevier B.V.

Feature-based classification of amino acid substitutions outside conserved functional protein domains.

PubMed

Gemovic, Branislava; Perovic, Vladimir; Glisic, Sanja; Veljkovic, Nevena

2013-01-01

There are more than 500 amino acid substitutions in each human genome, and bioinformatics tools irreplaceably contribute to determination of their functional effects. We have developed feature-based algorithm for the detection of mutations outside conserved functional domains (CFDs) and compared its classification efficacy with the most commonly used phylogeny-based tools, PolyPhen-2 and SIFT. The new algorithm is based on the informational spectrum method (ISM), a feature-based technique, and statistical analysis. Our dataset contained neutral polymorphisms and mutations associated with myeloid malignancies from epigenetic regulators ASXL1, DNMT3A, EZH2, and TET2. PolyPhen-2 and SIFT had significantly lower accuracies in predicting the effects of amino acid substitutions outside CFDs than expected, with especially low sensitivity. On the other hand, only ISM algorithm showed statistically significant classification of these sequences. It outperformed PolyPhen-2 and SIFT by 15% and 13%, respectively. These results suggest that feature-based methods, like ISM, are more suitable for the classification of amino acid substitutions outside CFDs than phylogeny-based tools.

Speciation and leachability of copper in mine tailings from porphyry copper mining: influence of particle size.

PubMed

Hansen, Henrik K; Yianatos, Juan B; Ottosen, Lisbeth M

2005-09-01

Mine tailing from the El Teniente-Codelco copper mine situated in VI Region of Chile was analysed in order to evaluate the mobility and speciation of copper in the solid material. Mine tailing was sampled after the rougher flotation circuits, and the copper content was measured to 1150 mg kg (-1) dry matter. This tailing was segmented into fractions of different size intervals: 0-38, 38-45, 45-53, 53-75, 75-106, 106-150, 150-212, and >212 microm, respectively. Copper content determination, sequential chemical extraction, and desorption experiments were carried out for each size interval in order to evaluate the speciation of copper. It was found that the particles of smallest size contained 50-60% weak acid leachable copper, whereas only 32% of the copper found in largest particles could be leached in weak acid. Copper oxides and carbonates were the dominating species in the smaller particles, and the larger particles contained considerable amounts of sulphides.

Mineralogical and geochemical characterization of arsenic in an abandoned mine tailings of Korea.

PubMed

Ahn, Joo Sung; Park, Young Seog; Kim, Ju-Yong; Kim, Kyoung-Woong

2005-04-01

The mineralogical and chemical characteristics of As solid phases in arsenic-rich mine tailings from the Nakdong As-Bi mine in Korea was investigated. The tailings generated from the ore roasting process contained 4.36% of As whereas the concentration was up to 20.2% in some tailings from the cyanidation process for the Au extraction. Thin indurated layers and other secondary precipitates had formed at the surfaces of the tailings piles and the As contents of the hardened layers varied from 2.87 to 16.0%. Scorodite and iron arsenate (Fe3AsO7) were the primary As-bearing crystalline minerals. Others such as arsenolamprite, bernardite and titanium oxide arsenate were also found. The amorphous As-Fe phases often showed framboidal aggregates and gel type textures with desiccation cracks. Sequential extraction results also showed that 55.7-91.1% of the As in tailings were NH(4)-oxalate extractable As, further confirmed the predominance of amorphous As-Fe solid phases. When the tailings were equilibrated with de-ionized water, the solution exhibited extremely acidic conditions (pH 2.01-3.10) and high concentrations of dissolved As (up to 29.5 mg L(-1)), indicating high potentials for As to be released during rainfall events. The downstream water was affected by drainage from tailings and contained 12.7-522 microg L(-1) of As. The amorphous As-Fe phases in tailings have not entirely been stabilized through the long term natural weathering processes. To remediate the environmental harms they had caused, anthropogenic interventions to stabilize or immobilize As in the tailings pile should be explored.

The Tail Suspension Test

PubMed Central

Terrillion, Chantelle E.; Piantadosi, Sean C.; Bhat, Shambhu; Gould, Todd D.

2012-01-01

The tail-suspension test is a mouse behavioral test useful in the screening of potential antidepressant drugs, and assessing of other manipulations that are expected to affect depression related behaviors. Mice are suspended by their tails with tape, in such a position that it cannot escape or hold on to nearby surfaces. During this test, typically six minutes in duration, the resulting escape oriented behaviors are quantified. The tail-suspension test is a valuable tool in drug discovery for high-throughput screening of prospective antidepressant compounds. Here, we describe the details required for implementation of this test with additional emphasis on potential problems that may occur and how to avoid them. We also offer a solution to the tail climbing behavior, a common problem that renders this test useless in some mouse strains, such as the widely used C57BL/6. Specifically, we prevent tail climbing behaviors by passing mouse tails through a small plastic cylinder prior to suspension. Finally, we detail how to manually score the behaviors that are manifested in this test. PMID:22315011

Deficiency of a Retinal Dystrophy Protein, Acyl-CoA Binding Domain-containing 5 (ACBD5), Impairs Peroxisomal β-Oxidation of Very-long-chain Fatty Acids*

PubMed Central

Yagita, Yuichi; Shinohara, Kyoko; Abe, Yuichi; Nakagawa, Keiko; Al-Owain, Mohammed; Alkuraya, Fowzan S.; Fujiki, Yukio

2017-01-01

Acyl-CoA binding domain-containing 5 (ACBD5) is a peroxisomal protein that carries an acyl-CoA binding domain (ACBD) at its N-terminal region. The recent identification of a mutation in the ACBD5 gene in patients with a syndromic form of retinal dystrophy highlights the physiological importance of ACBD5 in humans. However, the underlying pathogenic mechanisms and the precise function of ACBD5 remain unclear. We herein report that ACBD5 is a peroxisomal tail-anchored membrane protein exposing its ACBD to the cytosol. Using patient-derived fibroblasts and ACBD5 knock-out HeLa cells generated via genome editing, we demonstrate that ACBD5 deficiency causes a moderate but significant defect in peroxisomal β-oxidation of very-long-chain fatty acids (VLCFAs) and elevates the level of cellular phospholipids containing VLCFAs without affecting peroxisome biogenesis, including the import of membrane and matrix proteins. Both the N-terminal ACBD and peroxisomal localization of ACBD5 are prerequisite for efficient VLCFA β-oxidation in peroxisomes. Furthermore, ACBD5 preferentially binds very-long-chain fatty acyl-CoAs (VLC-CoAs). Together, these results suggest a direct role of ACBD5 in peroxisomal VLCFA β-oxidation. Based on our findings, we propose that ACBD5 captures VLC-CoAs on the cytosolic side of the peroxisomal membrane so that the transport of VLC-CoAs into peroxisomes and subsequent β-oxidation thereof can proceed efficiently. Our study reclassifies ACBD5-related phenotype as a novel peroxisomal disorder. PMID:27899449

Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage [psi]29 tail

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiang, Ye; Morais, Marc C.; Cohen, Daniel N.

2009-08-28

The small bacteriophage {phi}29 must penetrate the {approx}250-{angstrom} thick external peptidoglycan cell wall and cell membrane of the Gram-positive Bacillus subtilis, before ejecting its dsDNA genome through its tail into the bacterial cytoplasm. The tail of bacteriophage {phi}29 is noncontractile and {approx}380 {angstrom} long. A 1.8-{angstrom} resolution crystal structure of gene product 13 (gp13) shows that this tail protein has spatially well separated N- and C-terminal domains, whose structures resemble lysozyme-like enzymes and metallo-endopeptidases, respectively. CryoEM reconstructions of the WT bacteriophage and mutant bacteriophages missing some or most of gp13 shows that this enzyme is located at the distal endmore » of the {phi}29 tail knob. This finding suggests that gp13 functions as a tail-associated, peptidoglycan-degrading enzyme able to cleave both the polysaccharide backbone and peptide cross-links of the peptidoglycan cell wall. Comparisons of the gp13{sup -} mutants with the {phi}29 mature and emptied phage structures suggest the sequence of events that occur during the penetration of the tail through the peptidoglycan layer.« less

A Chimeric Kinesin-1 Head/Kinesin-5 Tail Motor Switches between Diffusive and Processive Motility

PubMed Central

Thiede, Christina; Lakämper, Stefan; Wessel, Alok D.; Kramer, Stefanie; Schmidt, Christoph F.

2013-01-01

Homotetrameric kinesin-5 motors are essential for chromosome separation and assembly of the mitotic spindle. These kinesins bind between two microtubules (MTs) and slide them apart, toward the spindle poles. This process must be tightly regulated in mitosis. In in vitro assays, Eg5 moves diffusively on single MTs and switches to a directed mode between MTs. How allosteric communication between opposing motor domains works remains unclear, but kinesin-5 tail domains may be involved. Here we present a single-molecule fluorescence study of a tetrameric kinesin-1 head/kinesin-5 tail chimera, DK4mer. This motor exhibited fast processive motility on single MTs interrupted by pauses. Like Eg5, DK4mer diffused along MTs with ADP, and slid antiparallel MTs apart with ATP. In contrast to Eg5, diffusive and processive periods were clearly distinguishable. This allowed us to measure transition rates among states and for unbinding as a function of buffer ionic strength. These data, together with results from controls using tail-less dimers, indicate that there are two modes of interaction with MTs, separated by an energy barrier. This result suggests a scheme of motor regulation that involves switching between two bound states, possibly allosterically controlled by the opposing tetramer end. Such a scheme is likely to be relevant for the regulation of native kinesin-5 motors. PMID:23442865

Hyaluronic acid in the tail and limb of amphibians and lizards recreates permissive embryonic conditions for regeneration due to its hygroscopic and immunosuppressive properties.

PubMed

Alibardi, Lorenzo

2017-12-01

The present review focuses on the role of hyaluronate (hyaluronic acid; HA) during limb and tail regeneration in amphibians and lizards mainly in relation to cells of the immune system. This non-sulfated glycosaminoglycan (GAG) increases in early stages of wound healing and blastema formation, like during limb or tail embryogenesis, when the immune system is still immature. The formation of a regenerating blastema occurs by the accumulation of mesenchymal cells displaying embryonic-like antigens and HA. This GAG adsorbs large amount of water and generates a soft tissue over 80% hydrated where mesenchymal and epithelial cells can move and interact, an obligatory passage for organ regeneration. GAGs and HA in particular rise to a high amount and coat plasma membranes of blastema cells forming a shield that likely impedes to the circulating immune cells to elicit an immune reaction against the embryonic-like antigens present on blastema cells. The evolution of limb-tail regeneration in amphibians dates back to the Devonian-Carboniferous, while tail regeneration in lizards is a more recent evolution process, possibly occurred since the Jurassic, which is unique among amniotes. Both processes are associated with the reactivation of proliferating embryonic programs that involve the upregulation of genes for Wnt, non-coding RNAs, and HA synthesis in an immune-suppress organ, the regenerative blastema. Failure of maintaining a lasting HA synthesis for the formation of a highly hydrated blastema leads to scarring, the common healing process of amniotes equipped with an efficient immune system. The study of amphibian and lizard regeneration indicates that attempts to stimulate organ regeneration in other vertebrates require the induction of a highly hydrated and immune-depressed, HA-rich environment, similar to the extracellular environment present during development. © 2017 Wiley Periodicals, Inc.

In vivo functional analysis of polyglutamic acid domains in recombinant bone sialoprotein.

PubMed

Wazen, Rima M; Tye, Coralee E; Goldberg, Harvey A; Hunter, Graeme K; Smith, Charles E; Nanci, Antonio

2007-01-01

Bone sialoprotein (BSP) is an anionic phosphoprotein expressed in mineralizing connective tissues that binds to hydroxyapatite and nucleates its formation in vitro. Two polyglutamic acid regions (poly [E]) are believed to participate in these activities. The aim of this study was to evaluate the contribution of these acidic regions to the binding of prokaryote recombinant BSP (prBSP(E)) within an actual in vivo environment. Full-length prBSP(E) and prBSP(E) in which the poly [E] domains were replaced by polyalanine (prBSP(A)) were tagged with dinitrophenol (DNP). Tagged preparations comprised intact molecules and some fragmented forms. They were infused through a surgically created hole in the bone of rat hemimandibles and detected using immunogold labeling with anti-DNP antibodies. prBSP(E)-DNP was consistently immunodetected along exposed mineralized bone surfaces and osteocyte canaliculi at the surgical site. Few gold particles were observed on these surfaces when prBSP(A)-DNP was infused. Quantitative analyses showed significant differences in labeling between prBSP(E)-DNP (5.04 +/- 0.73 particles/micro m2) and prBSP(A)-DNP (1.37 +/- 0.35 particles/micro m2). These results indicate that poly [E] domains influence binding of prBSP(E) to surfaces presenting a mixture of mineral and proteins bathed by tissue fluids and suggest that they may similarly mediate the interaction of native BSP in the bone environment.

Two amino acid residues confer different binding affinities of Abelson family kinase SRC homology 2 domains for phosphorylated cortactin.

PubMed

Gifford, Stacey M; Liu, Weizhi; Mader, Christopher C; Halo, Tiffany L; Machida, Kazuya; Boggon, Titus J; Koleske, Anthony J

2014-07-11

The closely related Abl family kinases, Arg and Abl, play important non-redundant roles in the regulation of cell morphogenesis and motility. Despite similar N-terminal sequences, Arg and Abl interact with different substrates and binding partners with varying affinities. This selectivity may be due to slight differences in amino acid sequence leading to differential interactions with target proteins. We report that the Arg Src homology (SH) 2 domain binds two specific phosphotyrosines on cortactin, a known Abl/Arg substrate, with over 10-fold higher affinity than the Abl SH2 domain. We show that this significant affinity difference is due to the substitution of arginine 161 and serine 187 in Abl to leucine 207 and threonine 233 in Arg, respectively. We constructed Abl SH2 domains with R161L and S187T mutations alone and in combination and find that these substitutions are sufficient to convert the low affinity Abl SH2 domain to a higher affinity "Arg-like" SH2 domain in binding to a phospho-cortactin peptide. We crystallized the Arg SH2 domain for structural comparison to existing crystal structures of the Abl SH2 domain. We show that these two residues are important determinants of Arg and Abl SH2 domain binding specificity. Finally, we expressed Arg containing an "Abl-like" low affinity mutant Arg SH2 domain (L207R/T233S) and find that this mutant, although properly localized to the cell periphery, does not support wild type levels of cell edge protrusion. Together, these observations indicate that these two amino acid positions confer different binding affinities and cellular functions on the distinct Abl family kinases. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Uncovering a role for the tail of the Dictyostelium discoideum SadA protein in cell-substrate adhesion.

PubMed

Kowal, Anthony S; Chisholm, Rex L

2011-05-01

Previous work from our laboratory showed that the Dictyostelium discoideum SadA protein plays a central role in cell-substrate adhesion. SadA null cells exhibit a loss of adhesion, a disrupted actin cytoskeleton, and a cytokinesis defect. How SadA mediates these phenotypes is unknown. This work addresses the mechanism of SadA function, demonstrating an important role for the C-terminal cytoplasmic tail in SadA function. We found that a SadA tailless mutant was unable to rescue the sadA adhesion deficiency, and overexpression of the SadA tail domain reduced adhesion in wild-type cells. We also show that SadA is closely associated with the actin cytoskeleton. Mutagenesis studies suggested that four serine residues in the tail, S924/S925 and S940/S941, may regulate association of SadA with the actin cytoskeleton. Glutathione S-transferase pull-down assays identified at least one likely interaction partner of the SadA tail, cortexillin I, a known actin bundling protein. Thus, our data demonstrate an important role for the carboxy-terminal cytoplasmic tail in SadA function and strongly suggest that a phosphorylation event in this tail regulates an interaction with cortexillin I. Based on our data, we propose a model for the function of SadA.

Acid sphingomyelinase possesses a domain homologous to its activator proteins: saposins B and D.

PubMed Central

Ponting, C. P.

1994-01-01

An N-terminal region of the acid sphingomyelinase sequence (residues 89-165) is shown to be homologous to saposin-type sequences. By analogy with the known functions of saposins, this sphingomyelinase saposin-type domain may possess lipid-binding and/or sphingomyelinase-activator properties. This finding may prove to be important in the understanding of Niemann-Pick disease, which results from sphingomyelinase deficiency. PMID:8003971

The Carboxyl Tail of Connexin32 Regulates Gap Junction Assembly in Human Prostate and Pancreatic Cancer Cells*

PubMed Central

Katoch, Parul; Mitra, Shalini; Ray, Anuttoma; Kelsey, Linda; Roberts, Brett J.; Wahl, James K.; Johnson, Keith R.; Mehta, Parmender P.

2015-01-01

Connexins, the constituent proteins of gap junctions, are transmembrane proteins. A connexin (Cx) traverses the membrane four times and has one intracellular and two extracellular loops with the amino and carboxyl termini facing the cytoplasm. The transmembrane and the extracellular loop domains are highly conserved among different Cxs, whereas the carboxyl termini, often called the cytoplasmic tails, are highly divergent. We have explored the role of the cytoplasmic tail of Cx32, a Cx expressed in polarized and differentiated cells, in regulating gap junction assembly. Our results demonstrate that compared with the full-length Cx32, the cytoplasmic tail-deleted Cx32 is assembled into small gap junctions in human pancreatic and prostatic cancer cells. Our results further document that the expression of the full-length Cx32 in cells, which express the tail-deleted Cx32, increases the size of gap junctions, whereas the expression of the tail-deleted Cx32 in cells, which express the full-length Cx32, has the opposite effect. Moreover, we show that the tail is required for the clustering of cell-cell channels and that in cells expressing the tail-deleted Cx32, the expression of cell surface-targeted cytoplasmic tail alone is sufficient to enhance the size of gap junctions. Our live-cell imaging data further demonstrate that gap junctions formed of the tail-deleted Cx32 are highly mobile compared with those formed of full-length Cx32. Our results suggest that the cytoplasmic tail of Cx32 is not required to initiate the assembly of gap junctions but for their subsequent growth and stability. Our findings suggest that the cytoplasmic tail of Cx32 may be involved in regulating the permeability of gap junctions by regulating their size. PMID:25548281

The carboxyl tail of connexin32 regulates gap junction assembly in human prostate and pancreatic cancer cells.

PubMed

Katoch, Parul; Mitra, Shalini; Ray, Anuttoma; Kelsey, Linda; Roberts, Brett J; Wahl, James K; Johnson, Keith R; Mehta, Parmender P

2015-02-20

Connexins, the constituent proteins of gap junctions, are transmembrane proteins. A connexin (Cx) traverses the membrane four times and has one intracellular and two extracellular loops with the amino and carboxyl termini facing the cytoplasm. The transmembrane and the extracellular loop domains are highly conserved among different Cxs, whereas the carboxyl termini, often called the cytoplasmic tails, are highly divergent. We have explored the role of the cytoplasmic tail of Cx32, a Cx expressed in polarized and differentiated cells, in regulating gap junction assembly. Our results demonstrate that compared with the full-length Cx32, the cytoplasmic tail-deleted Cx32 is assembled into small gap junctions in human pancreatic and prostatic cancer cells. Our results further document that the expression of the full-length Cx32 in cells, which express the tail-deleted Cx32, increases the size of gap junctions, whereas the expression of the tail-deleted Cx32 in cells, which express the full-length Cx32, has the opposite effect. Moreover, we show that the tail is required for the clustering of cell-cell channels and that in cells expressing the tail-deleted Cx32, the expression of cell surface-targeted cytoplasmic tail alone is sufficient to enhance the size of gap junctions. Our live-cell imaging data further demonstrate that gap junctions formed of the tail-deleted Cx32 are highly mobile compared with those formed of full-length Cx32. Our results suggest that the cytoplasmic tail of Cx32 is not required to initiate the assembly of gap junctions but for their subsequent growth and stability. Our findings suggest that the cytoplasmic tail of Cx32 may be involved in regulating the permeability of gap junctions by regulating their size. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Multiple C-terminal tail Ca2+/CaMs regulate CaV1.2 function but do not mediate channel dimerization

PubMed Central

Kim, Eun Young; Rumpf, Christine H; Van Petegem, Filip; Arant, Ryan J; Findeisen, Felix; Cooley, Elizabeth S; Isacoff, Ehud Y; Minor, Daniel L

2010-01-01

Interactions between voltage-gated calcium channels (CaVs) and calmodulin (CaM) modulate CaV function. In this study, we report the structure of a Ca2+/CaM CaV1.2 C-terminal tail complex that contains two PreIQ helices bridged by two Ca2+/CaMs and two Ca2+/CaM–IQ domain complexes. Sedimentation equilibrium experiments establish that the complex has a 2:1 Ca2+/CaM:C-terminal tail stoichiometry and does not form higher order assemblies. Moreover, subunit-counting experiments demonstrate that in live cell membranes CaV1.2s are monomers. Thus, contrary to previous proposals, the crystallographic dimer lacks physiological relevance. Isothermal titration calorimetry and biochemical experiments show that the two Ca2+/CaMs in the complex have different properties. Ca2+/CaM bound to the PreIQ C-region is labile, whereas Ca2+/CaM bound to the IQ domain is not. Furthermore, neither of lobes of apo-CaM interacts strongly with the PreIQ domain. Electrophysiological studies indicate that the PreIQ C-region has a role in calcium-dependent facilitation. Together, the data show that two Ca2+/CaMs can bind the CaV1.2 tail simultaneously and indicate a functional role for Ca2+/CaM at the C-region site. PMID:20953164

Multiple C-terminal tail Ca(2+)/CaMs regulate Ca(V)1.2 function but do not mediate channel dimerization.

PubMed

Kim, Eun Young; Rumpf, Christine H; Van Petegem, Filip; Arant, Ryan J; Findeisen, Felix; Cooley, Elizabeth S; Isacoff, Ehud Y; Minor, Daniel L

2010-12-01

Interactions between voltage-gated calcium channels (Ca(V)s) and calmodulin (CaM) modulate Ca(V) function. In this study, we report the structure of a Ca(2+)/CaM Ca(V)1.2 C-terminal tail complex that contains two PreIQ helices bridged by two Ca(2+)/CaMs and two Ca(2+)/CaM-IQ domain complexes. Sedimentation equilibrium experiments establish that the complex has a 2:1 Ca(2+)/CaM:C-terminal tail stoichiometry and does not form higher order assemblies. Moreover, subunit-counting experiments demonstrate that in live cell membranes Ca(V)1.2s are monomers. Thus, contrary to previous proposals, the crystallographic dimer lacks physiological relevance. Isothermal titration calorimetry and biochemical experiments show that the two Ca(2+)/CaMs in the complex have different properties. Ca(2+)/CaM bound to the PreIQ C-region is labile, whereas Ca(2+)/CaM bound to the IQ domain is not. Furthermore, neither of lobes of apo-CaM interacts strongly with the PreIQ domain. Electrophysiological studies indicate that the PreIQ C-region has a role in calcium-dependent facilitation. Together, the data show that two Ca(2+)/CaMs can bind the Ca(V)1.2 tail simultaneously and indicate a functional role for Ca(2+)/CaM at the C-region site.

Simulation of pyrite oxidation in fresh mine tailings under near-neutral conditions.

PubMed

Alakangas, Lena; Lundberg, Angela; Nason, Peter

2012-08-01

Sulphidic residual products from ore processing may produce acid rock drainage, when exposed to oxygen and water. Predictions of the magnitude of ARD and sulphide oxidation rates are of great importance in mine planning because they can be used to minimize or eliminate ARD and the associated economic and environmental costs. To address the lack of field data of sulphide oxidation rate in fresh sulphide-rich tailings under near-neutral conditions, determination and simulation of the rate was performed in pilot-scale at Kristineberg, northern Sweden. The quality of the drainage water was monitored, along with oxygen and carbon dioxide concentrations. The chemical composition of the solid tailings was also determined. The field data were compared to predictions from simulations of pyrite oxidation using a 1-D numerical model. The simulations' estimates of the amount of Fe and S released over a seven year period (52 kg and 178 kg, respectively) were in reasonably good agreement with those obtained by analysing the tailings (34 kg and 155 kg, respectively). The discrepancy is probably due to the formation of secondary precipitates such as iron hydroxides and gypsum; which are not accounted for in the model. The observed mass transport of Fe and S (0.05 and 1.0 kg per year, respectively) was much lower than expected on the basis of the simulations and the core data. Neutralization reactions involving carbonates in the tailings result in a near-neutral pH at all depths except at the oxidation front (pH < 5), indicating that the dissolution of carbonates was too slow for the acid to be neutralized, which instead neutralized deeper down in the tailings. This was also indicated by the reduced abundance of solid Ca at greater depths and the high levels of carbon dioxide both of which are consistent with the dissolution of carbonates. It could be concluded that the near-neutral pH in the tailings has no decreasing effect on the rate of sulphide oxidation, but does reduce the

cAMP regulates DEP domain-mediated binding of the guanine nucleotide exchange factor Epac1 to phosphatidic acid at the plasma membrane.

PubMed

Consonni, Sarah V; Gloerich, Martijn; Spanjaard, Emma; Bos, Johannes L

2012-03-06

Epac1 is a cAMP-regulated guanine nucleotide exchange factor for the small G protein Rap. Upon cAMP binding, Epac1 undergoes a conformational change that results in its release from autoinhibition. In addition, cAMP induces the translocation of Epac1 from the cytosol to the plasma membrane. This relocalization of Epac1 is required for efficient activation of plasma membrane-located Rap and for cAMP-induced cell adhesion. This translocation requires the Dishevelled, Egl-10, Pleckstrin (DEP) domain, but the molecular entity that serves as the plasma membrane anchor and the possible mechanism of regulated binding remains elusive. Here we show that Epac1 binds directly to phosphatidic acid. Similar to the cAMP-induced Epac1 translocation, this binding is regulated by cAMP and requires the DEP domain. Furthermore, depletion of phosphatidic acid by inhibition of phospholipase D1 prevents cAMP-induced translocation of Epac1 as well as the subsequent activation of Rap at the plasma membrane. Finally, mutation of a single basic residue within a polybasic stretch of the DEP domain, which abolishes translocation, also prevents binding to phosphatidic acid. From these results we conclude that cAMP induces a conformational change in Epac1 that enables DEP domain-mediated binding to phosphatidic acid, resulting in the tethering of Epac1 at the plasma membrane and subsequent activation of Rap.

TIDAL TAILS OF MINOR MERGERS. II. COMPARING STAR FORMATION IN THE TIDAL TAILS OF NGC 2782

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knierman, Karen A.; Scowen, Paul; Veach, Todd

2013-09-10

The peculiar spiral NGC 2782 is the result of a minor merger with a mass ratio {approx}4: 1 occurring {approx}200 Myr ago. This merger produced a molecular and H I-rich, optically bright eastern tail and an H I-rich, optically faint western tail. Non-detection of CO in the western tail by Braine et al. suggested that star formation had not yet begun. However, deep UBVR and H{alpha} narrowband images show evidence of recent star formation in the western tail, though it lacks massive star clusters and cluster complexes. Using Herschel PACS spectroscopy, we discover 158 {mu}m [C II] emission at themore » location of the three most luminous H{alpha} sources in the eastern tail, but not at the location of the even brighter H{alpha} source in the western tail. The western tail is found to have a normal star formation efficiency (SFE), but the eastern tail has a low SFE. The lack of CO and [C II] emission suggests that the western tail H II region may have a low carbon abundance and be undergoing its first star formation. The western tail is more efficient at forming stars, but lacks massive clusters. We propose that the low SFE in the eastern tail may be due to its formation as a splash region where gas heating is important even though it has sufficient molecular and neutral gas to make massive star clusters. The western tail, which has lower gas surface density and does not form high-mass star clusters, is a tidally formed region where gravitational compression likely enhances star formation.« less

Identification of acidic and aromatic residues in the Zta activation domain essential for Epstein-Barr virus reactivation.

PubMed

Deng, Z; Chen, C J; Zerby, D; Delecluse, H J; Lieberman, P M

2001-11-01

Epstein-Barr virus (EBV) lytic cycle transcription and DNA replication require the transcriptional activation function of the viral immediate-early protein Zta. We describe a series of alanine substitution mutations in the Zta activation domain that reveal two functional motifs based on amino acid composition. Alanine substitution of single or paired hydrophobic aromatic amino acid residues resulted in modest transcription activation defects, while combining four substitutions of aromatic residues (F22/F26/W74/F75) led to more severe transcription defects. Substitution of acidic amino acid residue E27, D35, or E54 caused severe transcription defects on most viral promoters. Promoter- and cell-specific defects were observed for some substitution mutants. Aromatic residues were required for Zta interaction with TFIIA-TFIID and the CREB-binding protein (CBP) and for stimulation of CBP histone acetyltransferase activity in vitro. In contrast, acidic amino acid substitution mutants interacted with TFIIA-TFIID and CBP indistinguishably from the wild type. The nuclear domain 10 (ND10) protein SP100 was dispersed by most Zta mutants, but acidic residue mutations led to reduced, while aromatic substitution mutants led to increased SP100 nuclear staining. Acidic residue substitution mutants had more pronounced defects in transcription activation of endogenous viral genes in latently infected cells and for viral replication, as measured by the production of infectious virus. One mutant, K12/F13, was incapable of stimulating EBV lytic replication but had only modest transcription defects. These results indicate that Zta stimulates viral reactivation through two nonredundant structural motifs, one of which interacts with general transcription factors and coactivators, and the other has an essential but as yet not understood function in lytic transcription.

THE NARROW X-RAY TAIL AND DOUBLE Hα TAILS OF ESO 137-002 IN A3627

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, B.; Lin, X. B.; Kong, X.

2013-11-10

We present the analysis of a deep Chandra observation of a ∼2 L{sub *} late-type galaxy, ESO 137-002, in the closest rich cluster A3627. The Chandra data reveal a long (∼>40 kpc) and narrow tail with a nearly constant width (∼3 kpc) to the southeast of the galaxy, and a leading edge ∼1.5 kpc from the galaxy center on the upstream side of the tail. The tail is most likely caused by the nearly edge-on stripping of ESO 137-002's interstellar medium (ISM) by ram pressure, compared to the nearly face-on stripping of ESO 137-001 discussed in our previous work. Spectralmore » analysis of individual regions along the tail shows that the gas throughout it has a rather constant temperature, ∼1 keV, very close to the temperature of the tails of ESO 137-001, if the same atomic database is used. The derived gas abundance is low (∼0.2 solar with the single-kT model), an indication of the multiphase nature of the gas in the tail. The mass of the X-ray tail is only a small fraction (<5%) of the initial ISM mass of the galaxy, suggesting that the stripping is most likely at an early stage. However, with any of the single-kT, double-kT, and multi-kT models we tried, the tail is always 'over-pressured' relative to the surrounding intracluster medium (ICM), which could be due to the uncertainties in the abundance, thermal versus non-thermal X-ray emission, or magnetic support in the ICM. The Hα data from the Southern Observatory for Astrophysical Research show a ∼21 kpc tail spatially coincident with the X-ray tail, as well as a secondary tail (∼12 kpc long) to the east of the main tail diverging at an angle of ∼23° and starting at a distance of ∼7.5 kpc from the nucleus. At the position of the secondary Hα tail, the X-ray emission is also enhanced at the ∼2σ level. We compare the tails of ESO 137-001 and ESO 137-002, and also compare the tails to simulations. Both the similarities and differences of the tails pose challenges to the simulations. Several

Spectral narrowing and spin echo for localized carriers with heavy-tailed L evy distribution of hopping times

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yue, Z.; Mkhitaryan, Vagharsh; Raikh, M. E.

2016-02-02

We study analytically the free induction decay and the spin echo decay originating from the localized carriers moving between the sites which host random magnetic fields. Due to disorder in the site positions and energies, the on-site residence times, , are widely spread according to the L evy distribution. The power-law tail ∝ τ -1-∝ in the distribution of does not affect the conventional spectral narrowing for α > 2, but leads to a dramatic acceleration of the free induction decay in the domain 2 > α > 1. The next abrupt acceleration of the decay takes place as becomesmore » smaller than 1. In the latter domain the decay does not follow a simple-exponent law. To capture the behavior of the average spin in this domain, we solve the evolution equation for the average spin using the approach different from the conventional approach based on the Laplace transform. Unlike the free induction decay, the tail in the distribution of the residence times leads to the slow decay of the spin echo. The echo is dominated by realizations of the carrier motion for which the number of sites, visited by the carrier, is minimal.« less

Automatic early warning of tail biting in pigs: 3D cameras can detect lowered tail posture before an outbreak

PubMed Central

Jack, Mhairi; Futro, Agnieszka; Talbot, Darren; Zhu, Qiming; Barclay, David; Baxter, Emma M.

2018-01-01

Tail biting is a major welfare and economic problem for indoor pig producers worldwide. Low tail posture is an early warning sign which could reduce tail biting unpredictability. Taking a precision livestock farming approach, we used Time-of-flight 3D cameras, processing data with machine vision algorithms, to automate the measurement of pig tail posture. Validation of the 3D algorithm found an accuracy of 73.9% at detecting low vs. not low tails (Sensitivity 88.4%, Specificity 66.8%). Twenty-three groups of 29 pigs per group were reared with intact (not docked) tails under typical commercial conditions over 8 batches. 15 groups had tail biting outbreaks, following which enrichment was added to pens and biters and/or victims were removed and treated. 3D data from outbreak groups showed the proportion of low tail detections increased pre-outbreak and declined post-outbreak. Pre-outbreak, the increase in low tails occurred at an increasing rate over time, and the proportion of low tails was higher one week pre-outbreak (-1) than 2 weeks pre-outbreak (-2). Within each batch, an outbreak and a non-outbreak control group were identified. Outbreak groups had more 3D low tail detections in weeks -1, +1 and +2 than their matched controls. Comparing 3D tail posture and tail injury scoring data, a greater proportion of low tails was associated with more injured pigs. Low tails might indicate more than just tail biting as tail posture varied between groups and over time and the proportion of low tails increased when pigs were moved to a new pen. Our findings demonstrate the potential for a 3D machine vision system to automate tail posture detection and provide early warning of tail biting on farm. PMID:29617403

Determination of the reaction rate coefficient of sulphide mine tailings deposited under water.

PubMed

Awoh, Akué Sylvette; Mbonimpa, Mamert; Bussière, Bruno

2013-10-15

The efficiency of a water cover to limit dissolved oxygen (DO) availability to underlying acid-generating mine tailings can be assessed by calculating the DO flux at the tailings-water interface. Fick's equations, which are generally used to calculate this flux, require knowing the effective DO diffusion coefficient (Dw) and the reaction (consumption) rate coefficient (Kr) of the tailings, or the DO concentration profile. Whereas Dw can be accurately estimated, few studies have measured the parameter Kr for submerged sulphide tailings. The objective of this study was to determine Kr for underwater sulphide tailings in a laboratory experiment. Samples of sulphide mine tailings (an approximately 6 cm layer) were placed in a cell under a water cover (approximately 2 cm) maintained at constant DO concentration. Two tailings were studied: TA1 with high sulphide content (83% pyrite) and TA2 with low sulphide content (2.8% pyrite). DO concentration was measured with a microelectrode at various depths above and below the tailings-water interface at 1 mm intervals. Results indicate that steady-state condition was rapidly attained. As expected, a diffusive boundary layer (DBL) was observed in all cases. An iterative back-calculation process using the numerical code POLLUTEv6 and taking the DBL into account provided the Kr values used to match calculated and experimental concentration profiles. Kr obtained for tailings TA1 and TA2 was about 80 d(-1) and 6.5 d(-1), respectively. For comparison purposes, Kr obtained from cell tests on tailings TA1 was lower than Kr calculated from the sulphate production rate obtained from shake-flask tests. Steady-state DO flux at the water-tailings interface was then calculated with POLLUTEv6 using tailings characteristics Dw and Kr. For the tested conditions, DO flux ranged from 608 to 758 mg O2/m(2)/d for tailings TA1 and from 177 to 221 mg O2/m(2)/d for tailings TA2. The impact of placing a protective layer of inert material over

Nesting habitat relationships of sympatric Crested Caracaras, Red-tailed Hawks, and White-tailed Hawks in South Texas

USGS Publications Warehouse

Actkinson, M.A.; Kuvlesky, W.P.; Boal, C.W.; Brennan, L.A.; Hernandez, F.

2007-01-01

We quantified nesting-site habitats for sympatric White-tailed Hawks (Buteo albicaudatus) (n = 40), Red-tailed Hawks (B. jamaicensis) (n = 39), and Crested Caracaras (Caracara cheriway) (n = 24) in the Coastal Sand Plain of south Texas. White-tailed Hawks and Crested Caracara nest sites occurred in savannas, whereas Red-tailed Hawk nest sites occurred in woodlands on the edge of savannas. White-tailed Hawk nest sites were in shrubs and trees that were shorter (3.5 ?? 1.0 m) and had smaller canopy diameters (5.5 ?? 2.1 m) than those of Red-tailed Hawks (10.1 ?? 2.0 m, 13.7 ?? 5.8 m) and Crested Caracaras (5.6 ?? 1.7 m, 8.5 ?? 3.5 m). Red-tailed Hawk nest sites had higher woody densities (15.7 ?? 9.6 plants) and more woody cover (84 ?? 19%) than those of White-tailed Hawks (5.6 ?? 5.8 plants, 20 ?? 21%) and Crested Caracaras (9.9 ?? 6.7 plants, 55 ?? 34%). Crested Caracara nest sites were in dense, multi-branched shrubs composed of more living material (97 ?? 3%) than those of White-tailed (88 ?? 18%) and Red-tailed hawks (88 ?? 18%). Nest sites of White-tailed Hawks, Red-tailed Hawks, and Crested Caracaras were similar to random samples from the surrounding habitat indicating that preferred nesting habitat was available for each of these species at least within 60 m of active nest sites. Nest tree height, along with woody plant and native grass cover best discriminated nest sites among the three raptor species. There was no overlap at Red-tailed and White-tailed hawk nest sites in vegetation structure, while Crested Caracara nests were in habitat intermediate between the two other species. Partitioning of nesting habitat may be how these raptor species co-exist at the broader landscape scale of our study area in the Coastal Sand Plain of Texas.

Tail Buffeting

NASA Technical Reports Server (NTRS)

Abdrashitov, G.

1943-01-01

An approximate theory of buffeting is here presented, based on the assumption of harmonic disturbing forces. Two cases of buffeting are considered: namely, for a tail angle of attack greater and less than the stalling angle, respectively. On the basis of the tests conducted and the results of foreign investigators, a general analysis is given of the nature of the forced vibrations the possible load limits on the tail, and the methods of elimination of buffeting.

Multivariate statistical characterization of charged and uncharged domain walls in multiferroic hexagonal YMnO3 single crystal visualized by a spherical aberration-corrected STEM.

PubMed

Matsumoto, Takao; Ishikawa, Ryo; Tohei, Tetsuya; Kimura, Hideo; Yao, Qiwen; Zhao, Hongyang; Wang, Xiaolin; Chen, Dapeng; Cheng, Zhenxiang; Shibata, Naoya; Ikuhara, Yuichi

2013-10-09

A state-of-the-art spherical aberration-corrected STEM was fully utilized to directly visualize the multiferroic domain structure in a hexagonal YMnO3 single crystal at atomic scale. With the aid of multivariate statistical analysis (MSA), we obtained unbiased and quantitative maps of ferroelectric domain structures with atomic resolution. Such a statistical image analysis of the transition region between opposite polarizations has confirmed atomically sharp transitions of ferroelectric polarization both in antiparallel (uncharged) and tail-to-tail 180° (charged) domain boundaries. Through the analysis, a correlated subatomic image shift of Mn-O layers with that of Y layers, exhibiting a double-arc shape of reversed curvatures, have been elucidated. The amount of image shift in Mn-O layers along the c-axis is statistically significant as small as 0.016 nm, roughly one-third of the evident image shift of 0.048 nm in Y layers. Interestingly, a careful analysis has shown that such a subatomic image shift in Mn-O layers vanishes at the tail-to-tail 180° domain boundaries. Furthermore, taking advantage of the annular bright field (ABF) imaging technique combined with MSA, the tilting of MnO5 bipyramids, the very core mechanism of multiferroicity of the material, is evaluated.

Research on Long Tail Recommendation Algorithm

NASA Astrophysics Data System (ADS)

Hu, Xuezhi; Zhang, Chuang; Wu, Ming; Zeng, Yang

2017-10-01

Most recommendation systems in the major electronic commerce platforms are influenced by the long tail effect more or less. There are sufficient researches of how to assess recommendation effect while no criteria to evaluate long tail recommendation rate. In this study, we first discussed the existing problems of recommending long tail products through specific experiments. Then we proposed a long tail evaluation criteria and compared the performance in long tail recommendation between different models.

A Tale of Tails: Dissecting the Enhancing Effect of Tailed Primers in Real-Time PCR

PubMed Central

Vandenbussche, Frank; Mathijs, Elisabeth; Lefebvre, David; De Clercq, Kris; Van Borm, Steven

2016-01-01

Non-specific tail sequences are often added to the 5’-terminus of primers to improve the robustness and overall performance of diagnostic assays. Despite the widespread use of tailed primers, the underlying working mechanism is not well understood. To address this problem, we conducted a detailed in vitro and in silico analysis of the enhancing effect of primer tailing on 2 well-established foot-and-mouth disease virus (FMDV) RT-qPCR assays using an FMDV reference panel. Tailing of the panFMDV-5UTR primers mainly affected the shape of the amplification curves. Modelling of the raw fluorescence data suggested a reduction of the amplification efficiency due to the accumulation of inhibitors. In depth analysis of PCR products indeed revealed the rapid accumulation of forward-primer derived artefacts. More importantly, tailing of the forward primer delayed artefacts formation and concomitantly restored the sigmoidal shape of the amplification curves. Our analysis also showed that primer tailing can alter utilisation patterns of degenerate primers and increase the number of primer variants that are able to participate in the reaction. The impact of tailed primers was less pronounced in the panFMDV-3D assay with only 5 out of 50 isolates showing a clear shift in Cq values. Sequence analysis of the target region of these 5 isolates revealed several mutations in the inter-primer region that extend an existing hairpin structure immediately downstream of the forward primer binding site. Stabilisation of the forward primer with either a tail sequence or cationic spermine units restored the sensitivity of the assay, which suggests that the enhancing effect in the panFMDV-3D assay is due to a more efficient extension of the forward primer. ur results show that primer tailing can alter amplification through various mechanisms that are determined by both the assay and target region. These findings expand our understanding of primer tailing and should enable a more targeted and

Alternative waste residue materials for passive in situ prevention of sulfide-mine tailings oxidation: a field evaluation.

PubMed

Nason, Peter; Johnson, Raymond H; Neuschütz, Clara; Alakangas, Lena; Öhlander, Björn

2014-02-28

Novel solutions for sulfide-mine tailings remediation were evaluated in field-scale experiments on a former tailings repository in northern Sweden. Uncovered sulfide-tailings were compared to sewage-sludge biosolid amended tailings over 2 years. An application of a 0.2m single-layer sewage-sludge amendment was unsuccessful at preventing oxygen ingress to underlying tailings. It merely slowed the sulfide-oxidation rate by 20%. In addition, sludge-derived metals (Cu, Ni, Fe, and Zn) migrated and precipitated at the tailings-to-sludge interface. By using an additional 0.6m thick fly-ash sealing layer underlying the sewage sludge layer, a solution to mitigate oxygen transport to the underlying tailings and minimize sulfide-oxidation was found. The fly-ash acted as a hardened physical barrier that prevented oxygen diffusion and provided a trap for sludge-borne metals. Nevertheless, the biosolid application hampered the application, despite the advances in the effectiveness of the fly-ash layer, as sludge-borne nitrate leached through the cover system into the underlying tailings, oxidizing pyrite. This created a 0.3m deep oxidized zone in 6-years. This study highlights that using sewage sludge in unconventional cover systems is not always a practical solution for the remediation of sulfide-bearing mine tailings to mitigate against sulfide weathering and acid rock drainage formation. Copyright © 2014 Elsevier B.V. All rights reserved.

Alternative waste residue materials for passive in situ prevention of sulfide-mine tailings oxidation: A field evaluation

USGS Publications Warehouse

Nason, Peter; Johnson, Raymond H.; Neuschutz, Clara; Alakangas, Lena; Ohlander, Bjorn

2014-01-01

Novel solutions for sulfide-mine tailings remediation were evaluated in field-scale experiments on a former tailings repository in northern Sweden. Uncovered sulfide-tailings were compared to sewage-sludge biosolid amended tailings over 2 years. An application of a 0.2 m single-layer sewage-sludge amendment was unsuccessful at preventing oxygen ingress to underlying tailings. It merely slowed the sulfide-oxidation rate by 20%. In addition, sludge-derived metals (Cu, Ni, Fe, and Zn) migrated and precipitated at the tailings-to-sludge interface. By using an additional 0.6 m thick fly-ash sealing layer underlying the sewage sludge layer, a solution to mitigate oxygen transport to the underlying tailings and minimize sulfide-oxidation was found. The fly-ash acted as a hardened physical barrier that prevented oxygen diffusion and provided a trap for sludge-borne metals. Nevertheless, the biosolid application hampered the application, despite the advances in the effectiveness of the fly-ash layer, as sludge-borne nitrate leached through the cover system into the underlying tailings, oxidizing pyrite. This created a 0.3 m deep oxidized zone in 6-years. This study highlights that using sewage sludge in unconventional cover systems is not always a practical solution for the remediation of sulfide-bearing mine tailings to mitigate against sulfide weathering and acid rock drainage formation.

Identification of distinct SET/TAF-Ibeta domains required for core histone binding and quantitative characterisation of the interaction.

PubMed

Karetsou, Zoe; Emmanouilidou, Anastasia; Sanidas, Ioannis; Liokatis, Stamatis; Nikolakaki, Eleni; Politou, Anastasia S; Papamarcaki, Thomais

2009-04-09

The assembly of nucleosomes to higher-order chromatin structures is finely tuned by the relative affinities of histones for chaperones and nucleosomal binding sites. The myeloid leukaemia protein SET/TAF-Ibeta belongs to the NAP1 family of histone chaperones and participates in several chromatin-based mechanisms, such as chromatin assembly, nucleosome reorganisation and transcriptional activation. To better understand the histone chaperone function of SET/TAF-Ibeta, we designed several SET/TAF-Ibeta truncations, examined their structural integrity by circular Dichroism and assessed qualitatively and quantitatively the histone binding properties of wild-type protein and mutant forms using GST-pull down experiments and fluorescence spectroscopy-based binding assays. Wild type SET/TAF-Ibeta binds to histones H2B and H3 with Kd values of 2.87 and 0.15 microM, respectively. The preferential binding of SET/TAF-Ibeta to histone H3 is mediated by its central region and the globular part of H3. On the contrary, the acidic C-terminal tail and the amino-terminal dimerisation domain of SET/TAF-Ibeta, as well as the H3 amino-terminal tail, are dispensable for this interaction. This type of analysis allowed us to assess the relative affinities of SET/TAF-Ibeta for different histones and identify the domains of the protein required for effective histone recognition. Our findings are consistent with recent structural studies of SET/TAF-Ibeta and can be valuable to understand the role of SET/TAF-Ibeta in chromatin function.

Runaway tails in magnetized plasmas

NASA Technical Reports Server (NTRS)

Moghaddam-Taaheri, E.; Vlahos, L.; Rowland, H. L.; Papadopoulos, K.

1985-01-01

The evolution of a runaway tail driven by a dc electric field in a magnetized plasma is analyzed. Depending on the strength of the electric field and the ratio of plasma to gyrofrequency, there are three different regimes in the evolution of the tail. The tail can be (1) stable with electrons accelerated to large parallel velocities, (2) unstable to Cerenkov resonance because of the depletion of the bulk and the formation of a positive slope, (3) unstable to the anomalous Doppler resonance instability driven by the large velocity anisotropy in the tail. Once an instability is triggered (Cerenkov or anomalous Doppler resonance) the tail relaxes into an isotropic distribution. The role of a convection type loss term is also discussed.

Histone Code Modulation by Oncogenic PWWP-Domain Protein in Breast Cancers

DTIC Science & Technology

2010-06-01

athanogene 4 * DDHD2 DDHD domain containing 2 * PPAPDC1B phosphatidic acid phosphatase type 2 domain containing 1B * WHSC1L1 Wolf-Hirschhorn syndrome...from alternative splicing of exon 10. The WHSC1L1 long isoform encodes a 1437 amino acid protein containing 2 PWWP domains, 2 PHD-type zinc finger...motifs, a TANG2 domain, an AWS domain and a SET domain. The short isoform encodes a 645 amino acid protein containing a PWWP domain only. Our western

Amino acid substitutions affecting aspartic acid 605 and valine 606 decrease the interaction strength between the influenza virus RNA polymerase PB2 '627' domain and the viral nucleoprotein.

PubMed

Hsia, Ho-Pan; Yang, Yin-Hua; Szeto, Wun-Chung; Nilsson, Benjamin E; Lo, Chun-Yeung; Ng, Andy Ka-Leung; Fodor, Ervin; Shaw, Pang-Chui

2018-01-01

The influenza virus RNA genome is transcribed and replicated in the context of the viral ribonucleoprotein (vRNP) complex by the viral RNA polymerase. The nucleoprotein (NP) is the structural component of the vRNP providing a scaffold for the viral RNA. In the vRNP as well as during transcription and replication the viral polymerase interacts with NP but it is unclear which parts of the polymerase and NP mediate these interactions. Previously the C-terminal '627' domain (amino acids 538-693) of PB2 was shown to interact with NP. Here we report that a fragment encompassing amino acids 146-185 of NP is sufficient to mediate this interaction. Using NMR chemical shift perturbation assays we show that amino acid region 601 to 607 of the PB2 '627' domain interacts with this fragment of NP. Substitutions of these PB2 amino acids resulted in diminished RNP activity and surface plasmon resonance assays showed that amino acids D605 was essential for the interaction with NP and V606 may also play a partial role in the interaction. Collectively these results reveal a possible interaction surface between NP and the PB2 subunit of the RNA polymerase complex.

Chromaticity effects on head-tail instabilities for broadband impedance using two particle model, Vlasov analysis, and simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chin, Yong Ho; Chao, Alexander Wu; Blaskiewicz, Michael M.

Effects of the chromaticity on head-tail instabilities for broadband impedances are comprehensively studied, using the two particle model, the Vlasov analysis and computer simulations. We show both in the two particle model and the Vlasov analysis with the trapezoidal (semiconstant) wake model that we can derive universal contour plots for the growth factor as a function of the two dimensionless parameters: the wakefield strength, Υ, and the difference of the betatron phase advances between the head and the tail, χ. They reveal how the chromaticity affects strong head-tail instabilities and excites head-tail instabilities. We also apply the LEP (Large Electron-Positronmore » Collider) broadband resonator model to the Vlasov approach and find that the results are in very good agreement with those of the trapezoidal wake model. The theoretical findings are also reinforced by the simulation results. In conclusion, the trapezoidal wake model turns out to be a very useful tool since it significantly simplifies the time domain analysis and provides well-behaved impedance at the same time.« less

Chromaticity effects on head-tail instabilities for broadband impedance using two particle model, Vlasov analysis, and simulations

DOE PAGES

Chin, Yong Ho; Chao, Alexander Wu; Blaskiewicz, Michael M.; ...

2017-07-28

Effects of the chromaticity on head-tail instabilities for broadband impedances are comprehensively studied, using the two particle model, the Vlasov analysis and computer simulations. We show both in the two particle model and the Vlasov analysis with the trapezoidal (semiconstant) wake model that we can derive universal contour plots for the growth factor as a function of the two dimensionless parameters: the wakefield strength, Υ, and the difference of the betatron phase advances between the head and the tail, χ. They reveal how the chromaticity affects strong head-tail instabilities and excites head-tail instabilities. We also apply the LEP (Large Electron-Positronmore » Collider) broadband resonator model to the Vlasov approach and find that the results are in very good agreement with those of the trapezoidal wake model. The theoretical findings are also reinforced by the simulation results. In conclusion, the trapezoidal wake model turns out to be a very useful tool since it significantly simplifies the time domain analysis and provides well-behaved impedance at the same time.« less

Solution structure of the tandem acyl carrier protein domains from a polyunsaturated fatty acid synthase reveals beads-on-a-string configuration.

PubMed

Trujillo, Uldaeliz; Vázquez-Rosa, Edwin; Oyola-Robles, Delise; Stagg, Loren J; Vassallo, David A; Vega, Irving E; Arold, Stefan T; Baerga-Ortiz, Abel

2013-01-01

The polyunsaturated fatty acid (PUFA) synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP) domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect) and in structural stabilization of the multidomain protein (synergistic effect). While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS) revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of multiple ACP

Solution Structure of the Tandem Acyl Carrier Protein Domains from a Polyunsaturated Fatty Acid Synthase Reveals Beads-on-a-String Configuration

PubMed Central

Trujillo, Uldaeliz; Vázquez-Rosa, Edwin; Oyola-Robles, Delise; Stagg, Loren J.; Vassallo, David A.; Vega, Irving E.; Arold, Stefan T.; Baerga-Ortiz, Abel

2013-01-01

The polyunsaturated fatty acid (PUFA) synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP) domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect) and in structural stabilization of the multidomain protein (synergistic effect). While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS) revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of multiple ACP

Membrane Association of the PTEN Tumor Suppressor: Electrostatic Interaction with Phos-phatidylserine-Containing Bilayers and Regulatory Role of the C-Terminal Tail

PubMed Central

Shenoy, Siddharth S.; Nanda, Hirsh; Lösche, Mathias

2012-01-01

The phosphatidylinositolphosphate phosphatase PTEN is the second most frequently mutated protein in human tumors. Its membrane association, allosteric activation and membrane dissociation are poorly understood. We recently reported PTEN binding affinities to membranes of different compositions and a preliminary investigation of the protein-membrane complex with neutron reflectometry (NR). Here we use NR to validate molecular dynamics (MD) simulations of the protein and study conformational differences of the protein in solution and on anionic membranes. NR shows that full-length PTEN binds to such membranes roughly in the conformation and orientation suggested by the crystal structure of a truncated PTEN protein, in contrast with a recently presented model which suggested that membrane binding depends critically on the SUMOylation of the CBR3 loop of PTEN’s C2 domain. Our MD simulations confirm that PTEN is peripherally bound to the bilayer surface and show slight differences of the protein structure in solution and in the membrane-bound state, where the protein body flattens against the bilayer surface. PTEN’s C2 domain binds phosphatidylserine (PS) tightly through its CBR3 loop, and its phosphatase domain also forms electrostatic interactions with PS. NR and MD results show consistently that PTEN’s unstructured, anionic C-terminal tail is repelled from the bilayer surface. In contrast, this tail is tightly tugged against the C2 domain in solution, partially obstructing the membrane-binding interface of the protein. Arresting the C-terminal tail in this conformation by phosphorylation may provide a control mechanism for PTEN’s membrane binding and activity. PMID:23073177

Direct experimental observation of mesoscopic fluorous domains in fluorinated room temperature ionic liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lo Celso, F.; Yoshida, Y.; Castiglione, F.

Fluorinated room temperature ionic liquids (FRTILs) represent a class of solvent media that are attracting great attention due to their IL-specific properties as well as features stemming from their fluorous nature. Medium-to-long fluorous tails constitute a well-defined apolar moiety in the otherwise polar environment. Similarly to the case of alkyl tails, such chains are expected to result in the formation of self-assembled fluorous domains. So far, however, no direct experimental observation has been made of the existence of such structural heterogeneities on the nm scale. We report here the first experimental evidence of the existence of mesoscopic spatial segregation ofmore » fluorinated domains, on the basis of highly complementary X-ray and neutron scattering data sets (highlighting the importance of the latter probe) and NMR spectroscopy. Data are interpreted using atomistic molecular dynamics simulations, emphasizing the existence of a self-assembly mechanism that delivers segregated fluorous domains, where preferential solubilisation of fluorinated compounds can occur, thus paving the way for several smart applications.« less

Identification of novel phosphatidic acid binding domain on sphingosine kinase 1 of Arabidopsis thaliana.

PubMed

Pandit, Shatakshi; Dalal, Vikram; Mishra, Girish

2018-07-01

Phosphatidic acid (PA) is an important lipid signaling molecule which interacts with Arabidopsis thaliana Sphingosine kinase1 (AtSPHK1) during several abiotic stresses particularly drought stress as a result of Abscisic acid (ABA) signaling in guard cells. PA molecules respond by generating lipid signal and/or by binding and translocating target proteins to membrane. However, site of interaction and role of PA binding to AtSPHK1 is not clear yet. Owing to the importance of AtSPHK1 during stress signaling it is imperative to decipher the site of PA interaction with AtSPHK1. To identify the PA binding region of AtSPHK1, various deletion fragments from N-terminal and C-terminal region were prepared. Results from protein lipid overlay assay using various truncated proteins of AtSPHK1 suggested the involvement of N-terminal region, between 110 and 205 amino acids, in binding with PA. In-silico analyses performed to build homologous structure of AtSPHK1 revealed that PA docking occurs in the hydrophobic cavity of DAG-Kinase domain. Deletion of amino acids 182 VSGDGI 187 perturbed PA-AtSPHK1 binding, indicating an essential role of these six amino acids in PA-AtSPHK1 binding. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

New insights into the targeting of a sub-set of tail-anchored proteins to the outer mitochondrial membrane

USDA-ARS?s Scientific Manuscript database

Tail-anchored (TA) proteins are a unique class of functionally diverse membrane proteins that are defined by their single C-terminal membrane-spanning domain and their ability to insert post-translationally into specific organelles with an Nout-Cin orientation. The molecular mechanisms by which TA p...

Miniature protein ligands for EVH1 domains: Interplay between affinity, specificity, and cell motility⊥

PubMed Central

Holtzman, Jennifer H.; Woronowicz, Kamil; Golemi-Kotra, Dasantila; Schepartz, Alanna

2008-01-01

Dynamic rearrangements of the actin cytoskeleton power cell motility in contexts ranging from intracellular microbial pathogenesis to axon guidance. The Ena/VASP family proteins--Mena, VASP, and Evl--are believed to control cell motility by serving as a direct link between signaling events and the actin cytoskeleton. Our lab has previously reported a novel miniature protein, pGolemi, which binds with high affinity to the EVH1 domain of Mena (Mena1-112) but not to those of VASP (VASP1-115) or Evl (Evl1-115) and also causes an unusual defect in actin-driven L. monocytogenes motility. Here, we use scanning mutagenesis to examine the effects of single amino acid changes within pGolemi on EVH1 domain affinity and specificity, miniature protein secondary structure, and L. monocytogenes motility. The data suggest that pGolemi contains the expected aPP-like fold and binds Mena1-112 in a manner highly analogous to the proline-rich repeat region of L. monocytogenes ActA protein. Residues throughout pGolemi contribute to both EVH1 domain affinity and paralog specificity. Moreover, the affinities of pGolemi variants for Mena1-112 correlate with selectivity against the EVH1 domains of VASP and Evl. In L. monocytogenes motility assays, speed and speed variability correlate strongly with EVH1 paralog specificity, suggesting that the Ena/VASP paralogs do not play equivalent roles in the process of L. monocytogenes actin tail maturation. PMID:17973491

Asparagine-linked oligosaccharides present on a non-consensus amino acid sequence in the CH1 domain of human antibodies.

PubMed

Valliere-Douglass, John F; Kodama, Paul; Mujacic, Mirna; Brady, Lowell J; Wang, Wes; Wallace, Alison; Yan, Boxu; Reddy, Pranhitha; Treuheit, Michael J; Balland, Alain

2009-11-20

We report that N-linked oligosaccharide structures can be present on an asparagine residue not adhering to the consensus site motif NX(S/T), where X is not proline, described in the literature. We have observed oligosaccharides on a non-consensus asparaginyl residue in the C(H)1 constant domain of IgG1 and IgG2 antibodies. The initial findings were obtained from characterization of charge variant populations evident in a recombinant human antibody of the IgG2 subclass. HPLC-MS results indicated that cation-exchange chromatography acidic variant populations were enriched in antibody with a second glycosylation site, in addition to the well documented canonical glycosylation site located in the C(H)2 domain. Subsequent tryptic and chymotryptic peptide map data indicated that the second glycosylation site was associated with the amino acid sequence TVSWN(162)SGAL in the C(H)1 domain of the antibody. This highly atypical modification is present at levels of 0.5-2.0% on most of the recombinant antibodies that have been tested and has also been observed in IgG1 antibodies derived from human donors. Site-directed mutagenesis of the C(H)1 domain sequence in a recombinant-human IgG1 antibody resulted in an increase in non-consensus glycosylation to 3.15%, a greater than 4-fold increase over the level observed in the wild type, by changing the -1 and +1 amino acids relative to the asparagine residue at position 162. We believe that further understanding of the phenomenon of non-consensus glycosylation can be used to gain fundamental insights into the fidelity of the cellular glycosylation machinery.

Bioprocessing-Based Approach for Bitumen/Water/Fines Separation and Hydrocarbon Recovery from Oil Sands Tailings

DOE PAGES

Brigmon, Robin L.; Berry, Christopher J.; Wade, Arielle; ...

2016-05-04

Oil sands are a major source of oil, but their industrial processing generates tailings ponds that are an environmental hazard. The main concerns are mature fine tailings (MFT) composed of residual hydrocarbons, water, and fine clay. Tailings ponds include toxic contaminants such as heavy metals, and toxic organics including naphthenics. Naphthenic acids and polyaromatic hydrocarbons (PAHs) degrade very slowly and pose a long-term threat to surface and groundwater, as they can be transported in the MFT. Research into improved technologies that would enable densification and settling of the suspended particles is ongoing. In batch tests, BioTiger™, a microbial consortium thatmore » can metabolize PAHs, demonstrated improved oil sands tailings settling from a Canadian tailings pond. Results also showed, depending on the timing of the measurements, lower suspended solids and turbidity. Elevated total organic carbon was observed in the first 48 hours in the BioTiger™-treated columns and then decreased in overlying water. Oil sands tailings mixed with BioTiger™ showed a two-fold reduction in suspended solids within 24 hours as compared to abiotic controls. The tailings treated with BioTiger™ increased in microbial densities three orders of magnitude from 8.5 × 105 CFU/mL to 1.2 × 108 CFU/mL without any other carbon or energy source added, indicating metabolism of hydrocarbons and other available nutrients. Results demonstrated that bioaugmentation of BioTiger™ increased separation of organic carbon from particles in oil sands and enhanced settling with tailings with improved water quality.« less

The new idea of transporting tailings-logs in tailings slurry pipeline and the innovation of technology of mining waste-fill method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin Yu; Wang Fuji; Tao Yan

2000-07-01

This paper introduced a new idea of transporting mine tailings-logs in mine tailings-slurry pipeline and a new technology of mine cemented filing of tailings-logs with tailings-slurry. The hydraulic principles, the compaction of tailings-logs and the mechanic function of fillbody of tailings-logs cemented by tailings-slurry have been discussed.

Membrane association of the PTEN tumor suppressor: electrostatic interaction with phosphatidylserine-containing bilayers and regulatory role of the C-terminal tail.

PubMed

Shenoy, Siddharth S; Nanda, Hirsh; Lösche, Mathias

2012-12-01

The phosphatidylinositolphosphate phosphatase PTEN is the second most frequently mutated protein in human tumors. Its membrane association, allosteric activation and membrane dissociation are poorly understood. We recently reported PTEN binding affinities to membranes of different compositions (Shenoy et al., 2012, PLoS ONE 7, e32591) and a preliminary investigation of the protein-membrane complex with neutron reflectometry (NR). Here we use NR to validate molecular dynamics (MD) simulations of the protein and study conformational differences of the protein in solution and on anionic membranes. NR shows that full-length PTEN binds to such membranes roughly in the conformation and orientation suggested by the crystal structure of a truncated PTEN protein, in contrast with a recently presented model which suggested that membrane binding depends critically on the SUMOylation of the CBR3 loop of PTEN's C2 domain. Our MD simulations confirm that PTEN is peripherally bound to the bilayer surface and show slight differences of the protein structure in solution and in the membrane-bound state, where the protein body flattens against the bilayer surface. PTEN's C2 domain binds phosphatidylserine (PS) tightly through its CBR3 loop, and its phosphatase domain also forms electrostatic interactions with PS. NR and MD results show consistently that PTEN's unstructured, anionic C-terminal tail is repelled from the bilayer surface. In contrast, this tail is tightly tugged against the C2 domain in solution, partially obstructing the membrane-binding interface of the protein. Arresting the C-terminal tail in this conformation by phosphorylation may provide a control mechanism for PTEN's membrane binding and activity. Copyright © 2012 Elsevier Inc. All rights reserved.

Adaptation and detoxification mechanisms of Vetiver grass (Chrysopogon zizanioides) growing on gold mine tailings.

PubMed

Melato, F A; Mokgalaka, N S; McCrindle, R I

2016-01-01

Vetiver grass (Chrysopogon zizanioides) was investigated for its potential use in the rehabilitation of gold mine tailings, its ability to extract and accumulate toxic metals from the tailings and its metal tolerant strategies. Vetiver grass was grown on gold mine tailings soil, in a hothouse, and monitored for sixteen weeks. The mine tailings were highly acidic and had high electrical conductivity. Vetiver grass was able to grow and adapt well on gold mine tailings. The results showed that Vetiver grass accumulated large amounts of metals in the roots and restricted their translocation to the shoots. This was confirmed by the bioconcentration factor of Zn, Cu, and Ni of >1 and the translocation factor of <1 for all the metals. This study revealed the defense mechanisms employed by Vetiver grass against metal stress that include: chelation of toxic metals by phenolics, glutathione S-tranferase, and low molecular weight thiols; sequestration and accumulation of metals within the cell wall that was revealed by the scanning electron microscopy that showed closure of stomata and thickened cell wall and was confirmed by high content of cell wall bound phenolics. Metal induced reactive oxygen species are reduced or eliminated by catalase, superoxide dismutase and peroxidase dismutase.

Pb uptake and toxicity to Iris halophila tested on Pb mine tailing materials.

PubMed

Han, Yulin; Zhang, Lili; Yang, Yongheng; Yuan, Haiyan; Zhao, Jiuzhou; Gu, Jiguang; Huang, Suzhen

2016-07-01

Pb tolerant mechanisms, plant physiological response and Pb sub-cellular localization in the root cells of Iris halophila were studied in sand culture and the Pb mine tailings. Results showed that the activities of superoxide dismutase (SOD) and peroxidase (POD) in the underground parts and the activity of catalase (CAT) in the aboveground and underground parts increased as Pb level was enhanced. Glutathione (GSH) and ascorbic acid (AsA) contents increased by Pb treatments. Pb deposits were found in the middle cell walls or along the inner side of epibiotic protoplasm of some cells which accumulated a large quantity of Pb and died. The dry weights (DWs) of aboveground parts under all Pb tailings treatments decreased insignificantly, while the DW of the underground parts growing in the pure Pb tailings decreased significantly. Pb, Cu, Cd, and Zn contents increased significantly as the levels of Pb tailings were enhanced and Pb contents in the aboveground and underground parts reached 64.75 and 751.75 μg/g DW, respectively, at pure Pb tailings treatment. The results indicated that I. halophila is a promising plant in the phytoremediation of Pb contaminated environment. Some antioxidant enzymes, antioxidants and compartmentalization of Pb were played major roles in Pb tolerance of I. halophila. Copyright © 2016 Elsevier Ltd. All rights reserved.

A cell-free stock of simian-human immunodeficiency virus that causes AIDS in pig-tailed macaques has a limited number of amino acid substitutions in both SIVmac and HIV-1 regions of the genome and has offered cytotropism.

PubMed

Stephens, E B; Mukherjee, S; Sahni, M; Zhuge, W; Raghavan, R; Singh, D K; Leung, K; Atkinson, B; Li, Z; Joag, S V; Liu, Z Q; Narayan, O

1997-05-12

We have examined both the sequence changes in the LTR, gag, vif, vpr, vpx, tat, rev, vpu, env, and nef genes and the cell tropism of a cell-free stock of chimeric simian-human immunodeficiency virus (SHIV) isolated from the cerebrospinal fluid of a pig-tailed macaque (PNb) that developed AIDS. This virus (SHIVKU-1) is highly pathogenic when inoculated into other macaques. DNA sequence analysis of PCR-amplified products revealed a total of 5 nucleotide changes in the LTR while vif had 2 consensus amino acid changes. The gag, vif, and vpx had no consensus amino acid substitutions, whereas vpr had 1 consensus substitution. The tat and rev genes of the HXB2 region of SHIVKU-1 had 2 and 1 consensus amino acid changes, respectively. The vpu gene of the HXB2 region of SHIV, which originally had an ACG at the beginning of the gene, reverted to an initiation ATG codon and in addition contained a consensus amino acid substitution at position 69 of this protein. As expected, the majority of the nucleotide substitutions were found in the env and nef genes. Thirteen and 5 amino acid changes were predicted for the corresponding Env and Nef proteins, respectively. In addition, one-third of the env gene clones isolated from the SHIVKU-1 stock had a 5-amino-acid deletion in the V4 region. Using three independent assays, we determined that the changes in the SHIVKU-1 were associated with an increase in the efficiency of replication in macrophages. The strikingly few consensus changes in the virus suggest that conversion of this virus to one capable of causing AIDS in pig-tailed macaques was associated with relatively few changes in the viral envelope and/or accessory genes. These results will provide the basis for the development of a pathogenic, molecular clone of SHIV capable of causing AIDS in pig-tailed macaques.

Identification of amino acids in the human tetherin transmembrane domain responsible for HIV-1 Vpu interaction and susceptibility.

PubMed

Kobayashi, Tomoko; Ode, Hirotaka; Yoshida, Takeshi; Sato, Kei; Gee, Peter; Yamamoto, Seiji P; Ebina, Hirotaka; Strebel, Klaus; Sato, Hironori; Koyanagi, Yoshio

2011-01-01

Tetherin, also known as BST-2/CD317/HM1.24, is an antiviral cellular protein that inhibits the release of HIV-1 particles from infected cells. HIV-1 viral protein U (Vpu) is a specific antagonist of human tetherin that might contribute to the high virulence of HIV-1. In this study, we show that three amino acid residues (I34, L37, and L41) in the transmembrane (TM) domain of human tetherin are critical for the interaction with Vpu by using a live cell-based assay. We also found that the conservation of an additional amino acid at position 45 and two residues downstream of position 22, which are absent from monkey tetherins, are required for the antagonism by Vpu. Moreover, computer-assisted structural modeling and mutagenesis studies suggest that an alignment of these four amino acid residues (I34, L37, L41, and T45) on the same helical face in the TM domain is crucial for the Vpu-mediated antagonism of human tetherin. These results contribute to the molecular understanding of human tetherin-specific antagonism by HIV-1 Vpu.

Membrane re-modelling by BAR domain superfamily proteins via molecular and non-molecular factors.

PubMed

Nishimura, Tamako; Morone, Nobuhiro; Suetsugu, Shiro

2018-04-17

Lipid membranes are structural components of cell surfaces and intracellular organelles. Alterations in lipid membrane shape are accompanied by numerous cellular functions, including endocytosis, intracellular transport, and cell migration. Proteins containing Bin-Amphiphysin-Rvs (BAR) domains (BAR proteins) are unique, because their structures correspond to the membrane curvature, that is, the shape of the lipid membrane. BAR proteins present at high concentration determine the shape of the membrane, because BAR domain oligomers function as scaffolds that mould the membrane. BAR proteins co-operate with various molecular and non-molecular factors. The molecular factors include cytoskeletal proteins such as the regulators of actin filaments and the membrane scission protein dynamin. Lipid composition, including saturated or unsaturated fatty acid tails of phospholipids, also affects the ability of BAR proteins to mould the membrane. Non-molecular factors include the external physical forces applied to the membrane, such as tension and friction. In this mini-review, we will discuss how the BAR proteins orchestrate membrane dynamics together with various molecular and non-molecular factors. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Trapping and Injecting Single Domain Walls in Magnetic Wire by Local Fields

NASA Astrophysics Data System (ADS)

Vázquez, Manuel; Basheed, G. A.; Infante, Germán; Del Real, Rafael P.

2012-01-01

A single domain wall (DW) moves at linearly increasing velocity under an increasing homogeneous drive magnetic field. Present experiments show that the DW is braked and finally trapped at a given position when an additional antiparallel local magnetic field is applied. That position and its velocity are further controlled by suitable tuning of the local field. In turn, the parallel local field of small amplitude does not significantly affect the effective wall speed at long distance, although it generates tail-to-tail and head-to-head pairs of walls moving along opposite directions when that field is strong enough.

Protein cold adaptation strategy via a unique seven-amino acid domain in the icefish (Chionodraco hamatus) PEPT1 transporter

PubMed Central

Rizzello, Antonia; Romano, Alessandro; Kottra, Gabor; Acierno, Raffaele; Storelli, Carlo; Verri, Tiziano; Daniel, Hannelore; Maffia, Michele

2013-01-01

Adaptation of organisms to extreme environments requires proteins to work at thermodynamically unfavorable conditions. To adapt to subzero temperatures, proteins increase the flexibility of parts of, or even the whole, 3D structure to compensate for the lower thermal kinetic energy available at low temperatures. This may be achieved through single-site amino acid substitutions in regions of the protein that undergo large movements during the catalytic cycle, such as in enzymes or transporter proteins. Other strategies of cold adaptation involving changes in the primary amino acid sequence have not been documented yet. In Antarctic icefish (Chionodraco hamatus) peptide transporter 1 (PEPT1), the first transporter cloned from a vertebrate living at subzero temperatures, we came upon a unique principle of cold adaptation. A de novo domain composed of one to six repeats of seven amino acids (VDMSRKS), placed as an extra stretch in the cytosolic COOH-terminal region, contributed per se to cold adaptation. VDMSRKS was in a protein region uninvolved in transport activity and, notably, when transferred to the COOH terminus of a warm-adapted (rabbit) PEPT1, it conferred cold adaptation to the receiving protein. Overall, we provide a paradigm for protein cold adaptation that relies on insertion of a unique domain that confers greater affinity and maximal transport rates at low temperatures. Due to its ability to transfer a thermal trait, the VDMSRKS domain represents a useful tool for future cell biology or biotechnological applications. PMID:23569229

Central Limit Theorems for Linear Statistics of Heavy Tailed Random Matrices

NASA Astrophysics Data System (ADS)

Benaych-Georges, Florent; Guionnet, Alice; Male, Camille

2014-07-01

We show central limit theorems (CLT) for the linear statistics of symmetric matrices with independent heavy tailed entries, including entries in the domain of attraction of α-stable laws and entries with moments exploding with the dimension, as in the adjacency matrices of Erdös-Rényi graphs. For the second model, we also prove a central limit theorem of the moments of its empirical eigenvalues distribution. The limit laws are Gaussian, but unlike the case of standard Wigner matrices, the normalization is the one of the classical CLT for independent random variables.

Exploring Mercury Tail

NASA Image and Video Library

2008-08-26

As the MESSENGER spacecraft approached Mercury, the UVVS field of view was scanned across the planet's exospheric "tail," which is produced by the solar wind pushing Mercury's exosphere (the planet's extremely thin atmosphere) outward. This figure, recently published in Science magazine, shows a map of the distribution of sodium atoms as they stream away from the planet (see PIA10396); red and yellow colors represent a higher abundance of sodium than darker shades of blue and purple, as shown in the colored scale bar, which gives the brightness intensity in units of kiloRayleighs. The escaping atoms eventually form a comet-like tail that extends in the direction opposite that of the Sun for many planetary radii. The small squares outlined in black correspond to individual measurements that were used to create the full map. These measurements are the highest-spatial-resolution observations ever made of Mercury's tail. In less than six weeks, on October 6, 2008, similar measurements will be made during MESSENGER's second flyby of Mercury. Comparing the measurements from the two flybys will provide an unprecedented look at how Mercury's dynamic exosphere and tail vary with time. Date Acquired: January 14, 2008. http://photojournal.jpl.nasa.gov/catalog/PIA11076

Si-based technologies for reduction of the pollutant leaching from landfills and mine tails.

PubMed

Bocharnikova, E; Matichenkov, V; Jiang, J; Yuejin, C

2017-07-01

Monosilicic and polysilicic acids were shown to react with different types of the pollutants. The direction of these reactions can be managed by changing the monosilicic and polysilicic acid concentration in soil or water media. The objective of this study was to determine the effect of Si-treated calcium metallurgical slag and battery slag on the As, Se, Cd, Pb, Ni, Cr, and Hg mobility and bioavailability in mine tailings (Xikuangshan mine, Hunan, China). The results of column experiment showed that the Si-activated slags reduced leaching of As, Se, Cd, Pb, Ni, Cr, and Hg by 13-89% and transformed them into plant-unavailable forms. The greenhouse test has demonstrated that the Si-treated slags provided reinforced plant resistance to heavy metal toxicity and reduced pollutants in barley and pea leaves. Si-treated local solid slags could be used for creating the biogeochemical barriers on the pollutant streams from landfills or mine tailings sites.

Nucleic acid sequences encoding D1 and D1/D2 domains of human coxsackievirus and adenovirus receptor (CAR)

DOEpatents

Freimuth, Paul I.

2010-04-06

The invention provides recombinant human CAR (coxsackievirus and adenovirus receptor) polypeptides which bind adenovirus. Specifically, polypeptides corresponding to adenovirus binding domain D1 and the entire extracellular domain of human CAR protein comprising D1 and D2 are provided. In another aspect, the invention provides nucleic acid sequences encoding these domains and expression vectors for producing the domains and bacterial cells containing such vectors. The invention also includes an isolated fusion protein comprised of the D1 polypeptide fused to a polypeptide which facilitates folding of D1 when expressed in bacteria. The functional D1 domain finds application in a therapeutic method for treating a patient infected with a CAR D1-binding virus, and also in a method for identifying an antiviral compound which interferes with viral attachment. The invention also provides a method for specifically targeting a cell for infection by a virus which binds to D1.

The ATPase domain of the large terminase protein, gp17, from bacteriophage T4 binds DNA: implications to the DNA packaging mechanism.

PubMed

Alam, Tanfis I; Rao, Venigalla B

2008-03-07

Translocation of double-stranded DNA into a preformed capsid by tailed bacteriophages is driven by powerful motors assembled at the special portal vertex. The motor is thought to drive processive cycles of DNA binding, movement, and release to package the viral genome. In phage T4, there is evidence that the large terminase protein, gene product 17 (gp17), assembles into a multisubunit motor and translocates DNA by an inchworm mechanism. gp17 consists of two domains; an N-terminal ATPase domain (amino acids 1-360) that powers translocation of DNA, and a C-terminal nuclease domain (amino acids 361-610) that cuts concatemeric DNA to generate a headful-size viral genome. While the functional motifs of ATPase and nuclease have been well defined and the ATPase atomic structure has been solved, the DNA binding motif(s) responsible for viral DNA recognition, cutting, and translocation are unknown. Here we report the first evidence for the presence of a double-stranded DNA binding activity in the gp17 ATPase domain. Binding to DNA is sensitive to Mg(2+) and salt, but not the type of DNA used. DNA fragments as short as 20 bp can bind to the ATPase but preferential binding was observed to DNA greater than 1 kb. A high molecular weight ATPase-DNA complex was isolated by gel filtration, suggesting oligomerization of ATPase following DNA interaction. DNA binding was not observed with the full-length gp17, or the C-terminal nuclease domain. The small terminase protein, gp16, inhibited DNA binding, which was further accentuated by ATP. The presence of a DNA binding site in the ATPase domain and its binding properties implicate a role in the DNA packaging mechanism.

Tail-scope: Using friends to estimate heavy tails of degree distributions in large-scale complex networks

NASA Astrophysics Data System (ADS)

Eom, Young-Ho; Jo, Hang-Hyun

2015-05-01

Many complex networks in natural and social phenomena have often been characterized by heavy-tailed degree distributions. However, due to rapidly growing size of network data and concerns on privacy issues about using these data, it becomes more difficult to analyze complete data sets. Thus, it is crucial to devise effective and efficient estimation methods for heavy tails of degree distributions in large-scale networks only using local information of a small fraction of sampled nodes. Here we propose a tail-scope method based on local observational bias of the friendship paradox. We show that the tail-scope method outperforms the uniform node sampling for estimating heavy tails of degree distributions, while the opposite tendency is observed in the range of small degrees. In order to take advantages of both sampling methods, we devise the hybrid method that successfully recovers the whole range of degree distributions. Our tail-scope method shows how structural heterogeneities of large-scale complex networks can be used to effectively reveal the network structure only with limited local information.

Interaction between the C-terminal domains of measles virus nucleoprotein and phosphoprotein: a tight complex implying one binding site.

PubMed

Blocquel, David; Habchi, Johnny; Costanzo, Stéphanie; Doizy, Anthony; Oglesbee, Michael; Longhi, Sonia

2012-10-01

The intrinsically disordered C-terminal domain (N(TAIL) ) of the measles virus (MeV) nucleoprotein undergoes α-helical folding upon binding to the C-terminal X domain (XD) of the phosphoprotein. The N(TAIL) region involved in binding coupled to folding has been mapped to a conserved region (Box2) encompassing residues 489-506. In the previous studies published in this journal, we obtained experimental evidence supporting a K(D) for the N(TAIL) -XD binding reaction in the nM range and also showed that an additional N(TAIL) region (Box3, aa 517-525) plays a role in binding to XD. In striking contrast with these data, studies published in this journal by Kingston and coworkers pointed out a much less stable complex (K(D) in the μM range) and supported lack of involvement of Box3 in complex formation. The objective of this study was to critically re-evaluate the role of Box3 in N(TAIL) -XD binding. Since our previous studies relied on N(TAIL) -truncated forms possessing an irrelevant Flag sequence appended at their C-terminus, we, herein, generated an N(TAIL) devoid of Box3 and any additional C-terminal residues, as well as a form encompassing only residues 482-525. We then used isothermal titration calorimetry to characterize the binding reactions between XD and these N(TAIL) forms. Results effectively argue for the presence of a single XD-binding site located within Box2, in agreement with the results by Kingston et al., while providing clear experimental support for a high-affinity complex. Altogether, the present data provide mechanistic insights into the replicative machinery of MeV and clarify a hitherto highly debated point. Copyright © 2012 The Protein Society.

Modeling Multiple Risks: Hidden Domain of Attraction

DTIC Science & Technology

2012-01-01

improve joint tail probability approximation but the deficiency can be remedied by a more general approach which we call hidden domain of attraction ( HDA ...HRV is a special case of HDA . If the distribution of X does not have MRV but (1.2) still holds, we may retrieve the MRV setup by transforming the...potential advantage in some circumstances of the notion of HDA is that it does not require that we transform components. Performing such transformations on

Highly acidic C-terminal domain of pp32 is required for the interaction with histone chaperone, TAF-Ibeta.

PubMed

Lee, In-Seon; Oh, Sang-Min; Kim, Sung-Mi; Lee, Dong-Seok; Seo, Sang-Beom

2006-12-01

We have previously reported that INHAT (inhibitor of acetyltransferases) complex subunits, TAF (template activating factor)-Ialpha, TAF-Ibeta and pp32 can inhibit histone acetylation and HAT (histone acetyltransferase)-dependent transcription by binding to histones. Evidences are accumulating that INHAT complex subunits have important regulatory roles in various cellular activities such as replication, transcription, and apoptosis etc. However, how these subunits interact each other remains largely unknown. Using immunoprecipitation (IP) and protein-protein interaction assays with TAF-Ibeta and pp32 deletion mutant proteins, we identify INHAT complex subunits, TAF-Ibeta and pp32 interaction requires highly acidic C-terminal domain of pp32. We also show that the interaction between the INHAT complex subunits is stronger in the presence of histones. In this study, we report that the synergistic inhibition of HAT-mediated transcription by TAF-Ibeta and pp32 is dependent on the highly acidic C-terminal domain of pp32.

Does climate have heavy tails?

NASA Astrophysics Data System (ADS)

Bermejo, Miguel; Mudelsee, Manfred

2013-04-01

When we speak about a distribution with heavy tails, we are referring to the probability of the existence of extreme values will be relatively large. Several heavy-tail models are constructed from Poisson processes, which are the most tractable models. Among such processes, one of the most important are the Lévy processes, which are those process with independent, stationary increments and stochastic continuity. If the random component of a climate process that generates the data exhibits a heavy-tail distribution, and if that fact is ignored by assuming a finite-variance distribution, then there would be serious consequences (in the form, e.g., of bias) for the analysis of extreme values. Yet, it appears that it is an open question to what extent and degree climate data exhibit heavy-tail phenomena. We present a study about the statistical inference in the presence of heavy-tail distribution. In particular, we explore (1) the estimation of tail index of the marginal distribution using several estimation techniques (e.g., Hill estimator, Pickands estimator) and (2) the power of hypothesis tests. The performance of the different methods are compared using artificial time-series by means of Monte Carlo experiments. We systematically apply the heavy tail inference to observed climate data, in particular we focus on time series data. We study several proxy and directly observed climate variables from the instrumental period, the Holocene and the Pleistocene. This work receives financial support from the European Commission (Marie Curie Initial Training Network LINC, No. 289447, within the 7th Framework Programme).

Identification of distinct SET/TAF-Iβ domains required for core histone binding and quantitative characterisation of the interaction

PubMed Central

Karetsou, Zoe; Emmanouilidou, Anastasia; Sanidas, Ioannis; Liokatis, Stamatis; Nikolakaki, Eleni; Politou, Anastasia S; Papamarcaki, Thomais

2009-01-01

Background The assembly of nucleosomes to higher-order chromatin structures is finely tuned by the relative affinities of histones for chaperones and nucleosomal binding sites. The myeloid leukaemia protein SET/TAF-Iβ belongs to the NAP1 family of histone chaperones and participates in several chromatin-based mechanisms, such as chromatin assembly, nucleosome reorganisation and transcriptional activation. To better understand the histone chaperone function of SET/TAF-Iβ, we designed several SET/TAF-Iβ truncations, examined their structural integrity by circular Dichroism and assessed qualitatively and quantitatively the histone binding properties of wild-type protein and mutant forms using GST-pull down experiments and fluorescence spectroscopy-based binding assays. Results Wild type SET/TAF-Iβ binds to histones H2B and H3 with Kd values of 2.87 and 0.15 μM, respectively. The preferential binding of SET/TAF-Iβ to histone H3 is mediated by its central region and the globular part of H3. On the contrary, the acidic C-terminal tail and the amino-terminal dimerisation domain of SET/TAF-Iβ, as well as the H3 amino-terminal tail, are dispensable for this interaction. Conclusion This type of analysis allowed us to assess the relative affinities of SET/TAF-Iβ for different histones and identify the domains of the protein required for effective histone recognition. Our findings are consistent with recent structural studies of SET/TAF-Iβ and can be valuable to understand the role of SET/TAF-Iβ in chromatin function. PMID:19358706

The Tail of BPM

NASA Astrophysics Data System (ADS)

Kruba, Steve; Meyer, Jim

Business process management suites (BPMS's) represent one of the fastest growing segments in the software industry as organizations automate their key business processes. As this market matures, it is interesting to compare it to Chris Anderson's 'Long Tail.' Although the 2004 "Long Tail" article in Wired magazine was primarily about the media and entertainment industries, it has since been applied (and perhaps misapplied) to other markets. Analysts describe a "Tail of BPM" market that is, perhaps, several times larger than the traditional BPMS product market. This paper will draw comparisons between the concepts in Anderson's article (and subsequent book) and the BPM solutions market.

Uncovering a Role for the Tail of the Dictyostelium discoideum SadA Protein in Cell-Substrate Adhesion ▿ †

PubMed Central

Kowal, Anthony S.; Chisholm, Rex L.

2011-01-01

Previous work from our laboratory showed that the Dictyostelium discoideum SadA protein plays a central role in cell-substrate adhesion. SadA null cells exhibit a loss of adhesion, a disrupted actin cytoskeleton, and a cytokinesis defect. How SadA mediates these phenotypes is unknown. This work addresses the mechanism of SadA function, demonstrating an important role for the C-terminal cytoplasmic tail in SadA function. We found that a SadA tailless mutant was unable to rescue the sadA adhesion deficiency, and overexpression of the SadA tail domain reduced adhesion in wild-type cells. We also show that SadA is closely associated with the actin cytoskeleton. Mutagenesis studies suggested that four serine residues in the tail, S924/S925 and S940/S941, may regulate association of SadA with the actin cytoskeleton. Glutathione S-transferase pull-down assays identified at least one likely interaction partner of the SadA tail, cortexillin I, a known actin bundling protein. Thus, our data demonstrate an important role for the carboxy-terminal cytoplasmic tail in SadA function and strongly suggest that a phosphorylation event in this tail regulates an interaction with cortexillin I. Based on our data, we propose a model for the function of SadA. PMID:21441344

Ultrasound-assisted extraction for total sulphur measurement in mine tailings.

PubMed

Khan, Adnan Hossain; Shang, Julie Q; Alam, Raquibul

2012-10-15

A sample preparation method for percentage recovery of total sulphur (%S) in reactive mine tailings based on ultrasound-assisted digestion (USAD) and inductively coupled plasma-optical emission spectroscopy (ICP-OES) was developed. The influence of various methodological factors was screened by employing a two-level and three-factor (2(3)) full factorial design and using KZK-1, a sericite schist certified reference material (CRM), to find the optimal combination of studied factors and %S. Factors such as the sonication time, temperature and acid combination were studied, with the best result identified as 20 min of sonication, 80°C temperature and 1 ml of HNO(3):1 ml of HCl, which can achieve 100% recovery for the selected CRM. Subsequently a fraction of the 2(3) full factorial design was applied to mine tailings. The percentage relative standard deviation (%RSD) for the ultrasound method is less than 3.0% for CRM and less than 6% for the mine tailings. The investigated method was verified by X-ray diffraction analysis. The USAD method compared favorably with existing methods such as hot plate assisted digestion method, X-ray fluorescence and LECO™-CNS method. Copyright © 2012 Elsevier B.V. All rights reserved.

Cingulin Contains Globular and Coiled-Coil Domains and Interacts with Zo-1, Zo-2, Zo-3, and Myosin

PubMed Central

Cordenonsi, Michelangelo; D'Atri, Fabio; Hammar, Eva; Parry, David A.D.; Kendrick-Jones, John; Shore, David; Citi, Sandra

1999-01-01

We characterized the sequence and protein interactions of cingulin, an M r 140–160-kD phosphoprotein localized on the cytoplasmic surface of epithelial tight junctions (TJ). The derived amino acid sequence of a full-length Xenopus laevis cingulin cDNA shows globular head (residues 1–439) and tail (1,326–1,368) domains and a central α-helical rod domain (440–1,325). Sequence analysis, electron microscopy, and pull-down assays indicate that the cingulin rod is responsible for the formation of coiled-coil parallel dimers, which can further aggregate through intermolecular interactions. Pull-down assays from epithelial, insect cell, and reticulocyte lysates show that an NH2-terminal fragment of cingulin (1–378) interacts in vitro with ZO-1 (K d ∼5 nM), ZO-2, ZO-3, myosin, and AF-6, but not with symplekin, and a COOH-terminal fragment (377–1,368) interacts with myosin and ZO-3. ZO-1 and ZO-2 immunoprecipitates contain cingulin, suggesting in vivo interactions. Full-length cingulin, but not NH2-terminal and COOH-terminal fragments, colocalizes with endogenous cingulin in transfected MDCK cells, indicating that sequences within both head and rod domains are required for TJ localization. We propose that cingulin is a functionally important component of TJ, linking the submembrane plaque domain of TJ to the actomyosin cytoskeleton. PMID:10613913

The effect of intact talin and talin tail fragment on actin filament dynamics and structure depends on pH and ionic strength.

PubMed

Goldmann, W H; Hess, D; Isenberg, G

1999-03-01

We employed quasi-elastic light scattering and electron microscopy to investigate the influence of intact talin and talin tail fragment on actin filament dynamics and network structure. Using these methods, we confirm previous reports that intact talin induces cross-linking as well as filament shortening on actin networks. We now show that the effect of intact talin as well as talin tail fragment on actin networks is controlled by pH and ionic strength. At pH 7.5, actin filament dynamics in the presence of intact talin and talin tail fragment are characterized by a rapid decay of the dynamic structure factor and by a square root power law for the stretched exponential decay which is in contrast with the theory for pure actin solutions. At pH 6 and low ionic strength, intact talin cross-links actin filaments more tightly than talin tail fragment. Talin head fragment showed no effect on actin networks, indicating that the actin binding sites reside probably exclusively within the tail domain.

Active tails enhance arboreal acrobatics in geckos

PubMed Central

Jusufi, Ardian; Goldman, Daniel I.; Revzen, Shai; Full, Robert J.

2008-01-01

Geckos are nature's elite climbers. Their remarkable climbing feats have been attributed to specialized feet with hairy toes that uncurl and peel in milliseconds. Here, we report that the secret to the gecko's arboreal acrobatics includes an active tail. We examine the tail's role during rapid climbing, aerial descent, and gliding. We show that a gecko's tail functions as an emergency fifth leg to prevent falling during rapid climbing. A response initiated by slipping causes the tail tip to push against the vertical surface, thereby preventing pitch-back of the head and upper body. When pitch-back cannot be prevented, geckos avoid falling by placing their tail in a posture similar to a bicycle's kickstand. Should a gecko fall with its back to the ground, a swing of its tail induces the most rapid, zero-angular momentum air-righting response yet measured. Once righted to a sprawled gliding posture, circular tail movements control yaw and pitch as the gecko descends. Our results suggest that large, active tails can function as effective control appendages. These results have provided biological inspiration for the design of an active tail on a climbing robot, and we anticipate their use in small, unmanned gliding vehicles and multisegment spacecraft. PMID:18347344

Molecular basis for TPR domain-mediated regulation of protein phosphatase 5.

PubMed

Yang, Jing; Roe, S Mark; Cliff, Matthew J; Williams, Mark A; Ladbury, John E; Cohen, Patricia T W; Barford, David

2005-01-12

Protein phosphatase 5 (Ppp5) is a serine/threonine protein phosphatase comprising a regulatory tetratricopeptide repeat (TPR) domain N-terminal to its phosphatase domain. Ppp5 functions in signalling pathways that control cellular responses to stress, glucocorticoids and DNA damage. Its phosphatase activity is suppressed by an autoinhibited conformation maintained by the TPR domain and a C-terminal subdomain. By interacting with the TPR domain, heat shock protein 90 (Hsp90) and fatty acids including arachidonic acid stimulate phosphatase activity. Here, we describe the structure of the autoinhibited state of Ppp5, revealing mechanisms of TPR-mediated phosphatase inhibition and Hsp90- and arachidonic acid-induced stimulation of phosphatase activity. The TPR domain engages with the catalytic channel of the phosphatase domain, restricting access to the catalytic site. This autoinhibited conformation of Ppp5 is stabilised by the C-terminal alphaJ helix that contacts a region of the Hsp90-binding groove on the TPR domain. Hsp90 activates Ppp5 by disrupting TPR-phosphatase domain interactions, permitting substrate access to the constitutively active phosphatase domain, whereas arachidonic acid prompts an alternate conformation of the TPR domain, destabilising the TPR-phosphatase domain interface.

Crystallization and preliminary X-ray diffraction analysis of the sialic acid-binding domain (VP8*) of porcine rotavirus strain CRW-8

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scott, Stacy A.; Holloway, Gavan; Coulson, Barbara S.

2005-06-01

The sialic acid-binding domain (VP8*) component of the porcine CRW-8 rotavirus spike protein has been overexpressed in E. coli, purified and co-crystallized with an N-acetylneuraminic acid derivative. X-ray diffraction data have been collected to 2.3 Å, which has enabled determination of the structure by molecular replacement. Rotavirus recognition and attachment to host cells involves interaction with the spike protein VP4 that projects outwards from the surface of the virus particle. An integral component of these spikes is the VP8* domain, which is implicated in the direct recognition and binding of sialic acid-containing cell-surface carbohydrates and facilitates subsequent invasion by themore » virus. The expression, purification, crystallization and preliminary X-ray diffraction analysis of VP8* from porcine CRW-8 rotavirus is reported. Diffraction data have been collected to 2.3 Å resolution, enabling the determination of the VP8* structure by molecular replacement.« less

Important Role for the Transmembrane Domain of Severe Acute Respiratory Syndrome Coronavirus Spike Protein during Entry

PubMed Central

Broer, Rene; Boson, Bertrand; Spaan, Willy; Cosset, François-Loïc; Corver, Jeroen

2006-01-01

The spike protein (S) of severe acute respiratory syndrome coronavirus (SARS-CoV) is responsible for receptor binding and membrane fusion. It contains a highly conserved transmembrane domain that consists of three parts: an N-terminal tryptophan-rich domain, a central domain, and a cysteine-rich C-terminal domain. The cytoplasmic tail of S has previously been shown to be required for assembly. Here, the roles of the transmembrane and cytoplasmic domains of S in the infectivity and membrane fusion activity of SARS-CoV have been studied. SARS-CoV S-pseudotyped retrovirus (SARSpp) was used to measure S-mediated infectivity. In addition, the cell-cell fusion activity of S was monitored by a Renilla luciferase-based cell-cell fusion assay. Svsv-cyt, an S chimera with a cytoplasmic tail derived from vesicular stomatitis virus G protein (VSV-G), and Smhv-tmdcyt, an S chimera with the cytoplasmic and transmembrane domains of mouse hepatitis virus, displayed wild-type-like activity in both assays. Svsv-tmdcyt, a chimera with the cytoplasmic and transmembrane domains of VSV-G, was impaired in the SARSpp and cell-cell fusion assays, showing 3 to 25% activity compared to the wild type, depending on the assay and the cells used. Examination of the oligomeric state of the chimeric S proteins in SARSpp revealed that Svsv-tmdcyt trimers were less stable than wild-type S trimers, possibly explaining the lowered fusogenicity and infectivity. PMID:16415007

Identification of an Amino Acid Domain Encoded by the Capsid Protein Gene of Porcine Circovirus Type 2 that Modulates Viral Protein Distribution During Replication

USDA-ARS?s Scientific Manuscript database

Previous work showed that distinct amino acid motifs are encoded by the Rep, Cap and ORF3 genes of two subgroups of porcine circoviruses (PCV), PCV2a and PCV2b. At a specific location of the gene, a certain amino acid residue or sequence is preferred. Specifically, two amino acid domains located in ...

Affinity Map of Bromodomain Protein 4 (BRD4) Interactions with the Histone H4 Tail and the Small Molecule Inhibitor JQ1*

PubMed Central

Jung, Marie; Philpott, Martin; Müller, Susanne; Schulze, Jessica; Badock, Volker; Eberspächer, Uwe; Moosmayer, Dieter; Bader, Benjamin; Schmees, Norbert; Fernández-Montalván, Amaury; Haendler, Bernard

2014-01-01

Bromodomain protein 4 (BRD4) is a member of the bromodomain and extra-terminal domain (BET) protein family. It binds to acetylated histone tails via its tandem bromodomains BD1 and BD2 and forms a complex with the positive transcription elongation factor b, which controls phosphorylation of RNA polymerase II, ultimately leading to stimulation of transcription elongation. An essential role of BRD4 in cell proliferation and cancer growth has been reported in several recent studies. We analyzed the binding of BRD4 BD1 and BD2 to different partners and showed that the strongest interactions took place with di- and tetra-acetylated peptides derived from the histone 4 N-terminal tail. We also found that several histone 4 residues neighboring the acetylated lysines significantly influenced binding. We generated 10 different BRD4 BD1 mutants and analyzed their affinities to acetylated histone tails and to the BET inhibitor JQ1 using several complementary biochemical and biophysical methods. The impact of these mutations was confirmed in a cellular environment. Altogether, the results show that Trp-81, Tyr-97, Asn-140, and Met-149 play similarly important roles in the recognition of acetylated histones and JQ1. Pro-82, Leu-94, Asp-145, and Ile-146 have a more differentiated role, suggesting that different kinds of interactions take place and that resistance mutations compatible with BRD4 function are possible. Our study extends the knowledge on the contribution of individual BRD4 amino acids to histone and JQ1 binding and may help in the design of new BET antagonists with improved pharmacological properties. PMID:24497639

Acidic Residues Control the Dimerization of the N-terminal Domain of Black Widow Spiders’ Major Ampullate Spidroin 1

NASA Astrophysics Data System (ADS)

Bauer, Joschka; Schaal, Daniel; Eisoldt, Lukas; Schweimer, Kristian; Schwarzinger, Stephan; Scheibel, Thomas

2016-09-01

Dragline silk is the most prominent amongst spider silks and comprises two types of major ampullate spidroins (MaSp) differing in their proline content. In the natural spinning process, the conversion of soluble MaSp into a tough fiber is, amongst other factors, triggered by dimerization and conformational switching of their helical amino-terminal domains (NRN). Both processes are induced by protonation of acidic residues upon acidification along the spinning duct. Here, the structure and monomer-dimer-equilibrium of the domain NRN1 of Latrodectus hesperus MaSp1 and variants thereof have been investigated, and the key residues for both could be identified. Changes in ionic composition and strength within the spinning duct enable electrostatic interactions between the acidic and basic pole of two monomers which prearrange into an antiparallel dimer. Upon naturally occurring acidification this dimer is stabilized by protonation of residue E114. A conformational change is independently triggered by protonation of clustered acidic residues (D39, E76, E81). Such step-by-step mechanism allows a controlled spidroin assembly in a pH- and salt sensitive manner, preventing premature aggregation of spider silk proteins in the gland and at the same time ensuring fast and efficient dimer formation and stabilization on demand in the spinning duct.

Yeast peroxisomal multifunctional enzyme: (3R)-hydroxyacyl-CoA dehydrogenase domains A and B are required for optimal growth on oleic acid.

PubMed

Qin, Y M; Marttila, M S; Haapalainen, A M; Siivari, K M; Glumoff, T; Hiltunen, J K

1999-10-01

The yeast peroxisomal (3R)-hydroxyacyl-CoA dehydrogenase/2-enoyl-CoA hydratase 2 (multifunctional enzyme type 2; MFE-2) has two N-terminal domains belonging to the short chain alcohol dehydrogenase/reductase superfamily. To investigate the physiological roles of these domains, here called A and B, Saccharomyces cerevisiae fox-2 cells (devoid of Sc MFE-2) were taken as a model system. Gly(16) and Gly(329) of the S. cerevisiae A and B domains, corresponding to Gly(16), which is mutated in the human MFE-2 deficiency, were mutated to serine and cloned into the yeast expression plasmid pYE352. In oleic acid medium, fox-2 cells transformed with pYE352:: ScMFE-2(aDelta) and pYE352::ScMFE-2(bDelta) grew slower than cells transformed with pYE352::ScMFE-2, whereas cells transformed with pYE352::ScMFE-2(aDeltabDelta) failed to grow. Candida tropicalis MFE-2 with a deleted hydratase 2 domain (Ct MFE- 2(h2Delta)) and mutational variants of the A and B domains (Ct MFE- 2(h2DeltaaDelta), Ct MFE- 2(h2DeltabDelta), and Ct MFE- 2(h2DeltaaDeltabDelta)) were overexpressed and characterized. All proteins were dimers with similar secondary structure elements. Both wild type domains were enzymatically active, with the B domain showing the highest activity with short chain and the A domain with medium and long chain (3R)-hydroxyacyl-CoA substrates. The data show that the dehydrogenase domains of yeast MFE-2 have different substrate specificities required to allow the yeast to propagate optimally on fatty acids as the carbon source.

NMR assignment of a PDZ domain in complex with a HPV51 E6 derived N-terminally pyroglutamic acid modified peptide.

PubMed

Mischo, André; Ohlenschläger, Oliver; Ramachandran, Ramadurai; Görlach, Matthias

2013-04-01

The resonance assignment of an amino-terminal pyroglutamic acid containing peptide derived from the E6 protein of human papillomavirus (HPV) type 51 in complex with PDZ domain 2 of hDlg/SAP-97 is reported. The assignments include (1)H, (13)C and (15)N resonances for the protein and peptide in the complex and all of the peptide's pyroglutamic acid nuclei.

Comparison of the breeding biology of sympatric red-tailed Hawks, White-tailed Hawks, and Crested Caracaras in south Texas

USGS Publications Warehouse

Actkinson, M.A.; Kuvlesky, W.P.; Boal, C.W.; Brennan, L.A.; Hernandez, F.

2009-01-01

We compared the breeding biology of sympatric nesting Red-tailed Hawks (Buteo jamaicensis), White-tailed Hawks (Buteo albicaudatus), and Crested Caracaras (Caracara cheriway) in south Texas during 2003 and 2004. We monitored 46 breeding attempts by Red-tailed Hawks, 56 by White-tailed Hawks, and 27 by Crested Caracaras. Observed nesting success was similar for Red-tailed Hawks (62%) and Crested Caracaras (61%), but lower for White-tailed Hawks (51%). Daily survival rates (0.99) were the same for all three species. Red-tailed Hawks and White-tailed Hawks both fledged 1.13 young per nesting pair and Crested Caracaras fledged 1.39 young per nesting pair. All three species nested earlier in 2004 than in 2003; in addition, the overall nesting density of these three species almost doubled from 2003 (1.45 pairs/km2) to 2004 (2.71 pairs/km2). Estimated productivity of all three species was within the ranges reported from other studies. Given extensive and progressive habitat alteration in some areas of south Texas, and the limited distributions of White-tailed Hawks and Crested Caracaras, the presence of large ranches managed for free-range cattle production and hunting leases likely provides important habitat and may be key areas for conservation of these two species. ?? 2009 The Raptor Research Foundation, Inc.

The Amino Acid Specificity for Activation of Phenylalanine Hydroxylase Matches the Specificity for Stabilization of Regulatory Domain Dimers

PubMed Central

2016-01-01

Liver phenylalanine hydroxylase is allosterically activated by phenylalanine. The structural changes that accompany activation have not been identified, but recent studies of the effects of phenylalanine on the isolated regulatory domain of the enzyme support a model in which phenylalanine binding promotes regulatory domain dimerization. Such a model predicts that compounds that stabilize the regulatory domain dimer will also activate the enzyme. Nuclear magnetic resonance spectroscopy and analytical ultracentrifugation were used to determine the ability of different amino acids and phenylalanine analogues to stabilize the regulatory domain dimer. The abilities of these compounds to activate the enzyme were analyzed by measuring their effects on the fluorescence change that accompanies activation and on the activity directly. At concentrations of 10–50 mM, d-phenylalanine, l-methionine, l-norleucine, and (S)-2-amino-3-phenyl-1-propanol were able to activate the enzyme to the same extent as 1 mM l-phenylalanine. Lower levels of activation were seen with l-4-aminophenylalanine, l-leucine, l-isoleucine, and 3-phenylpropionate. The ability of these compounds to stabilize the regulatory domain dimer agreed with their ability to activate the enzyme. These results support a model in which allosteric activation of phenylalanine hydroxylase is linked to dimerization of regulatory domains. PMID:26252467

Environmental factors influencing the structural dynamics of soil microbial communities during assisted phytostabilization of acid-generating mine tailings: a mesocosm experiment.

PubMed

Valentín-Vargas, Alexis; Root, Robert A; Neilson, Julia W; Chorover, Jon; Maier, Raina M

2014-12-01

Compost-assisted phytostabilization has recently emerged as a robust alternative for reclamation of metalliferous mine tailings. Previous studies suggest that root-associated microbes may be important for facilitating plant establishment on the tailings, yet little is known about the long-term dynamics of microbial communities during reclamation. A mechanistic understanding of microbial community dynamics in tailings ecosystems undergoing remediation is critical because these dynamics profoundly influence both the biogeochemical weathering of tailings and the sustainability of a plant cover. Here we monitor the dynamics of soil microbial communities (i.e. bacteria, fungi, archaea) during a 12-month mesocosm study that included 4 treatments: 2 unplanted controls (unamended and compost-amended tailings) and 2 compost-amended seeded tailings treatments. Bacterial, fungal and archaeal communities responded distinctively to the revegetation process and concurrent changes in environmental conditions and pore water chemistry. Compost addition significantly increased microbial diversity and had an immediate and relatively long-lasting buffering-effect on pH, allowing plants to germinate and thrive during the early stages of the experiment. However, the compost buffering capacity diminished after six months and acidification took over as the major factor affecting plant survival and microbial community structure. Immediate changes in bacterial communities were observed following plant establishment, whereas fungal communities showed a delayed response that apparently correlated with the pH decline. Fluctuations in cobalt pore water concentrations, in particular, had a significant effect on the structure of all three microbial groups, which may be linked to the role of cobalt in metal detoxification pathways. The present study represents, to our knowledge, the first documentation of the dynamics of the three major microbial groups during revegetation of compost

Environmental Factors Influencing the Structural Dynamics of Soil Microbial Communities During Assisted Phytostabilization of Acid-Generating Mine Tailings: a Mesocosm Experiment

PubMed Central

Valentín-Vargas, Alexis; Root, Robert A.; Neilson, Julia W; Chorover, Jon; Maier, Raina M.

2014-01-01

Compost-assisted phytostabilization has recently emerged as a robust alternative for reclamation of metalliferous mine tailings. Previous studies suggest that root-associated microbes may be important for facilitating plant establishment on the tailings, yet little is known about the long-term dynamics of microbial communities during reclamation. A mechanistic understanding of microbial community dynamics in tailings ecosystems undergoing remediation is critical because these dynamics profoundly influence both the biogeochemical weathering of tailings and the sustainability of a plant cover. Here we monitor the dynamics of soil microbial communities (i.e. bacteria, fungi, archaea) during a 12-month mesocosm study that included 4 treatments: 2 unplanted controls (unamended and compost-amended tailings) and 2 compost-amended seeded tailings treatments. Bacterial, fungal and archaeal communities responded distinctively to the revegetation process and concurrent changes in environmental conditions and pore water chemistry. Compost addition significantly increased microbial diversity and had an immediate and relatively long-lasting buffering-effect on pH, allowing plants to germinate and thrive during the early stages of the experiment. However, the compost buffering capacity diminished after six months and acidification took over as the major factor affecting plant survival and microbial community structure. Immediate changes in bacterial communities were observed following plant establishment, whereas fungal communities showed a delayed response that apparently correlated with the pH decline. Fluctuations in cobalt pore water concentrations, in particular, had a significant effect on the structure of all three microbial groups, which may be linked to the role of cobalt in metal detoxification pathways. The present study represents, to our knowledge, the first documentation of the dynamics of the three major microbial groups during revegetation of compost

Identification of Amino Acids in the Human Tetherin Transmembrane Domain Responsible for HIV-1 Vpu Interaction and Susceptibility▿ †

PubMed Central

Kobayashi, Tomoko; Ode, Hirotaka; Yoshida, Takeshi; Sato, Kei; Gee, Peter; Yamamoto, Seiji P.; Ebina, Hirotaka; Strebel, Klaus; Sato, Hironori; Koyanagi, Yoshio

2011-01-01

Tetherin, also known as BST-2/CD317/HM1.24, is an antiviral cellular protein that inhibits the release of HIV-1 particles from infected cells. HIV-1 viral protein U (Vpu) is a specific antagonist of human tetherin that might contribute to the high virulence of HIV-1. In this study, we show that three amino acid residues (I34, L37, and L41) in the transmembrane (TM) domain of human tetherin are critical for the interaction with Vpu by using a live cell-based assay. We also found that the conservation of an additional amino acid at position 45 and two residues downstream of position 22, which are absent from monkey tetherins, are required for the antagonism by Vpu. Moreover, computer-assisted structural modeling and mutagenesis studies suggest that an alignment of these four amino acid residues (I34, L37, L41, and T45) on the same helical face in the TM domain is crucial for the Vpu-mediated antagonism of human tetherin. These results contribute to the molecular understanding of human tetherin-specific antagonism by HIV-1 Vpu. PMID:21068238

Wheat glutenin: the "tail" of the 1By protein subunits.

PubMed

Nunes-Miranda, Júlio D; Bancel, Emmanuelle; Viala, Didier; Chambon, Christophe; Capelo, José L; Branlard, Gérard; Ravel, Catherine; Igrejas, Gilberto

2017-10-03

Gluten-forming storage proteins play a major role in the viscoelastic properties of wheat dough through the formation of a continuous proteinaceous network. The high-molecular-weight glutenin subunits represent a functionally important subgroup of gluten proteins by promoting the formation of large glutenin polymers through interchain disulphide bonds between glutenin subunits. Here, we present evidences that y-type glutenin subunits encoded at the Glu-B1 locus are prone to proteolytic processing at the C-terminus tail, leading to the loss of the unique cysteine residue present at the C-terminal domain. Results obtained by intact mass measurement and immunochemistry for each proteoform indicate that the proteolytic cleavage appears to occur at the carboxyl-side of two conserved asparagine residues at the C-terminal domain start. Hence, we hypothesize that the responsible enzymes are a class of cysteine endopeptidases - asparaginyl endopeptidases - described in post-translational processing of other storage proteins in wheat. Biological significance The reported study provides new insights into wheat storage protein maturation. In view of the importance of gluten proteins on dough viscoelastic properties and end-product quality, the reported C-terminal domain cleavage of high-molecular-weight glutenin subunits is of particular interest, since this domain possesses a unique conserved cysteine residue which is assumed to participate in gluten polymerization. Copyright © 2017 Elsevier B.V. All rights reserved.

Ecotoxicity of Mine Tailings: Unrehabilitated Versus Rehabilitated.

PubMed

Maboeta, M S; Oladipo, O G; Botha, S M

2018-05-01

Earthworms are bioindicators of soil pollution. The ecotoxicity of tailings from selected gold mines in South Africa was investigated utilizing Eisenia andrei bioassays and biomarkers. Samples were obtained from unrehabilitated, rehabilitated and naturally vegetated sites. Biomass, neutral red retention time (NRRT), survival and reproduction were assessed using standardized protocols. Earthworm biomass, NRRT and reproductive success in rehabilitated tailings (comparable to naturally vegetated site) were significantly higher (p < 0.05) than in unrehabilitated tailings. In addition, significantly lower (p < 0.05) body tissue concentrations of As, Cd, Co, Cu and Ni contents were found in the rehabilitated tailings compared to the unrehabilitated. Further, significantly lower (p < 0.05) soil Mn and Zn concentrations were obtained in unrehabilitated tailings than the rehabilitated and naturally vegetated sites. Overall, reduced ecotoxicity effects were confirmed in rehabilitated compared to unrehabilitated tailings. This suggests that rehabilitation as a post-mining restorative strategy has strong positive influence on mine tailings.

Effect of desliming of sulphide-rich mill tailings on the long-term strength of cemented paste backfill.

PubMed

Ercikdi, Bayram; Baki, Hakan; İzki, Muhammet

2013-01-30

This paper presents the effect of desliming on the short- and long-term strength, stability and rheological properties of cemented paste backfill (CPB) produced from two different mill tailings. A 28-day unconfined compressive strength (UCS) of ≥1.0 MPa and the maintenance of stability over 224 days of curing were selected as the design criteria for the evaluation of paste backfill performance. Desliming induced some changes in the physical, chemical, mineralogical and rheological properties of the tailings. CPB mixture of the deslimed tailings achieved the required consistency at a lower water to cement ratio. The short-term UCSs of CPB samples of the deslimed tailings were found to be 30-100% higher than those samples of the reference tailings at all the binder dosages and curing times. CPB samples of the deslimed tailings achieved the long-term stability at relatively low binder dosages (e.g. 5 wt% c.f. ≥6.1% for the reference tailings). It was also estimated that desliming could allow a 13.4-23.1% reduction in the binder consumption depending apparently on the inherent characteristics of the tailings. Over the curing period, generation of sulphate and acid by the oxidation of pyrite present in the tailings was also monitored to correlate with the strength losses observed in the long term. Scanning electron microscope (SEM) and Mercury Intrusion Porosimetry (MIP) analyses provided an insight into the microstructure of CPB and the formation of secondary mineral phases (i.e. gypsum) confirming the beneficial effect of desliming. These findings suggest that desliming can be suitably exploited for CPB of sulphide-rich mill tailings to improve the strength and stability particularly in the long term and to reduce binder consumption. Copyright © 2012 Elsevier Ltd. All rights reserved.

Compaction and binding properties of the intrinsically disordered C-terminal domain of Henipavirus nucleoprotein as unveiled by deletion studies.

PubMed

Blocquel, David; Habchi, Johnny; Gruet, Antoine; Blangy, Stéphanie; Longhi, Sonia

2012-01-01

Henipaviruses are recently emerged severe human pathogens within the Paramyxoviridae family. Their genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that recruits the polymerase complex via the phosphoprotein (P). We have previously shown that in Henipaviruses the N protein possesses an intrinsically disordered C-terminal domain, N(TAIL), which undergoes α-helical induced folding in the presence of the C-terminal domain (P(XD)) of the P protein. Using computational approaches, we previously identified within N(TAIL) four putative molecular recognition elements (MoREs) with different structural propensities, and proposed a structural model for the N(TAIL)-P(XD) complex where the MoRE encompassing residues 473-493 adopt an α-helical conformation at the P(XD) surface. In this work, for each N(TAIL) protein, we designed four deletion constructs bearing different combinations of the predicted MoREs. Following purification of the N(TAIL) truncated proteins from the soluble fraction of E. coli, we characterized them in terms of their conformational, spectroscopic and binding properties. These studies provided direct experimental evidence for the structural state of the four predicted MoREs, and showed that two of them have clear α-helical propensities, with the one spanning residues 473-493 being strictly required for binding to P(XD). We also showed that Henipavirus N(TAIL) and P(XD) form heterologous complexes, indicating that the P(XD) binding regions are functionally interchangeable between the two viruses. By combining spectroscopic and conformational analyses, we showed that the content in regular secondary structure is not a major determinant of protein compaction.

Covalent and non-covalent curcumin loading in acid-responsive polymeric micellar nanocarriers

NASA Astrophysics Data System (ADS)

Gao, Min; Chen, Chao; Fan, Aiping; Zhang, Ju; Kong, Deling; Wang, Zheng; Zhao, Yanjun

2015-07-01

Poor aqueous solubility, potential degradation, rapid metabolism and elimination lead to low bioavailability of pleiotropic impotent curcumin. Herein, we report two types of acid-responsive polymeric micelles where curcumin was encapsulated via both covalent and non-covalent modes for enhanced loading capacity and on-demand release. Biodegradable methoxy poly(ethylene glycol)-poly(lactic acid) copolymer (mPEG-PLA) was conjugated with curcumin via a hydrazone linker, generating two conjugates differing in architecture (single-tail versus double-tail) and free curcumin was encapsulated therein. The two micelles exhibited similar hydrodynamic size at 95 ± 3 nm (single-tail) and 96 ± 3 nm (double-tail), but their loading capacities differed significantly at 15.0 ± 0.5% (w/w) (single-tail) and 4.8 ± 0.5% (w/w) (double-tail). Under acidic sink conditions (pH 5.0 and 6.0), curcumin displayed a faster release from the single-tail nanocarrier, which was correlated to a low IC50 of 14.7 ± 1.6 (μg mL-1) compared to the value of double-tail micelle (24.9 ± 1.3 μg mL-1) in HeLa cells. The confocal imaging and flow cytometry analysis demonstrated a superior capability of single-tail micelle for intracellular curcumin delivery, which was a consequence of the higher loading capacity and lower degree of mPEG surface coverage. In conclusion, the dual loading mode is an effective means to increase the drug content in the micellar nanocarriers whose delivery efficiency is highly dependent on its polymer-drug conjugate architecture. This strategy offers an alternative nanoplatform for intracellularly delivering impotent hydrophobic agents (i.e. curcumin) in an efficient stimuli-triggered way, which is valuable for the enhancement of curcumin’s efficacy in managing a diverse range of disorders.

Assessing Risks of Mine Tailing Dam Failures

NASA Astrophysics Data System (ADS)

Concha Larrauri, P.; Lall, U.

2017-12-01

The consequences of tailings dam failures can be catastrophic for communities and ecosystems in the vicinity of the dams. The failure of the Fundão tailings dam at the Samarco mine in 2015 killed 19 people with severe consequences for the environment. The financial and legal consequences of a tailings dam failure can also be significant for the mining companies. For the Fundão tailings dam, the company had to pay 6 billion dollars in fines and twenty-one executives were charged with qualified murder. There are tenths of thousands of active, inactive, and abandoned tailings dams in the world and there is a need to better understand the hazards posed by these structures to downstream populations and ecosystems. A challenge to assess the risks of tailings dams in a large scale is that many of them are not registered in publicly available databases and there is little information about their current physical state. Additionally, hazard classifications of tailings dams - common in many countries- tend to be subjective, include vague parameter definitions, and are not always updated over time. Here we present a simple methodology to assess and rank the exposure to tailings dams using ArcGIS that removes subjective interpretations. The method uses basic information such as current dam height, storage volume, topography, population, land use, and hydrological data. A hazard rating risk was developed to compare the potential extent of the damage across dams. This assessment provides a general overview of what in the vicinity of the tailings dams could be affected in case of a failure and a way to rank tailings dams that is directly linked to the exposure at any given time. One hundred tailings dams in Minas Gerais, Brazil were used for the test case. This ranking approach could inform the risk management strategy of the tailings dams within a company, and when disclosed, it could enable shareholders and the communities to make decisions on the risks they are taking.

Active Tails Enhance Arboreal Acrobatics in Geckos

DTIC Science & Technology

2008-03-18

the secret to the gecko s arboreal acrobatics includes an active tail. We examine the tail s role during rapid climbing, aerial descent, and gliding. We show that a gecko s tail functions as an emergency fifth leg to prevent falling during rapid climbing. A response initiated by slipping causes the tail tip to push against the vertical surface, thereby preventing pitch-back of the head and upper body. When pitch-back cannot be prevented, geckos avoid falling by placing their tail in a posture similar to a bicycle s kickstand. Should a gecko fall with its back to the

A cis-prenyltransferase from Methanosarcina acetivorans catalyzes both head-to-tail and nonhead-to-tail prenyl condensation.

PubMed

Ogawa, Takuya; Emi, Koh-Ichi; Koga, Kazushi; Yoshimura, Tohru; Hemmi, Hisashi

2016-06-01

Cis-prenyltransferase usually consecutively catalyzes the head-to-tail condensation reactions of isopentenyl diphosphate to allylic prenyl diphosphate in the production of (E,Z-mixed) polyprenyl diphosphate, which is the precursor of glycosyl carrier lipids. Some recently discovered homologs of the enzyme, however, catalyze the nonhead-to-tail condensation reactions between allylic prenyl diphosphates. In this study, we characterize a cis-prenyltransferase homolog from a methanogenic archaeon, Methanosarcina acetivorans, to obtain information on the biosynthesis of the glycosyl carrier lipids within it. This enzyme catalyzes both head-to-tail and nonhead-to-tail condensation reactions. The kinetic analysis shows that the main reaction of the enzyme is consecutive head-to-tail prenyl condensation reactions yielding polyprenyl diphosphates, while the chain lengths of the major products seem shorter than expected for the precursor of glycosyl carrier lipids. On the other hand, a subsidiary reaction of the enzyme, i.e., nonhead-to-tail condensation between dimethylallyl diphosphate and farnesyl diphosphate, gives a novel diterpenoid compound, geranyllavandulyl diphosphate. © 2016 Federation of European Biochemical Societies.

Molecular Mechanisms of SH2- and PTB-Domain-Containing Proteins in Receptor Tyrosine Kinase Signaling

PubMed Central

Wagner, Melany J.; Stacey, Melissa M.; Liu, Bernard A.; Pawson, Tony

2013-01-01

Intracellular signaling is mediated by reversible posttranslational modifications (PTMs) that include phosphorylation, ubiquitination, and acetylation, among others. In response to extracellular stimuli such as growth factors, receptor tyrosine kinases (RTKs) typically dimerize and initiate signaling through phosphorylation of their cytoplasmic tails and downstream scaffolds. Signaling effectors are recruited to these phosphotyrosine (pTyr) sites primarily through Src homology 2 (SH2) domains and pTyr-binding (PTB) domains. This review describes how these conserved domains specifically recognize pTyr residues and play a major role in mediating precise downstream signaling events. PMID:24296166

Molecular mechanisms of SH2- and PTB-domain-containing proteins in receptor tyrosine kinase signaling.

PubMed

Wagner, Melany J; Stacey, Melissa M; Liu, Bernard A; Pawson, Tony

2013-12-01

Intracellular signaling is mediated by reversible posttranslational modifications (PTMs) that include phosphorylation, ubiquitination, and acetylation, among others. In response to extracellular stimuli such as growth factors, receptor tyrosine kinases (RTKs) typically dimerize and initiate signaling through phosphorylation of their cytoplasmic tails and downstream scaffolds. Signaling effectors are recruited to these phosphotyrosine (pTyr) sites primarily through Src homology 2 (SH2) domains and pTyr-binding (PTB) domains. This review describes how these conserved domains specifically recognize pTyr residues and play a major role in mediating precise downstream signaling events.

[Preparation and characterization of monoclonal antibodies against Micrococcus luteus Rpf domain].

PubMed

Fan, Ai-lin; Shi, Chang-hong; Su, Ming-quan; Ma, Jing; Bai, Yin-lan; Cheng, Xiao-dong; Xu, Zhi-kai; Hao, Xiao-ke

2008-05-01

To express Micrococcus luteus Rpf domain in prokaryotic cells and prepare monoclonal antibodies against Rpf domain. The gene encoding Micrococcus luteus Rpf domain was amplified from genome of Micrococcus luteus by polymerase chain reaction(PCR), and inserted into cloning vector pUC-19. After sequenced, Micrococcus luteus Rpf domain gene was subcloned into the expression vector pPro-EXHT and transfected into E.coli DH5alpha. After induced by IPTG, the bacteria controlled by T7 promoter expressed the fused Micrococcus luteus Rpf domain protein with a hexahistidine tail at its N-terminal and the target protein was purified under denaturing conditions. Using this protein as antigen to immunize the BALB/c mice and prepare monoclonal antibodies against Micrococcus luteus Rpf domain. Then specifities and relative affinities of mAbs were identified by ELISA. The fusion protein was purified by metal chelate affinity chromatography under denaturing condition. Three cloned mAbs were prepared from the mice immunized by Rpf domain. All of them could recognize Rpf domain. specifically. The prepared mAbs against Rpf domain have strong specificity with high titers, which provides useful tools for further study of the function of Rpf domain in TB prevention.

Identification of novel key amino acids at the interface of the transmembrane domains of human BST-2 and HIV-1 Vpu.

PubMed

Pang, Xiaojing; Hu, Siqi; Li, Jian; Xu, Fengwen; Mei, Shan; Zhou, Jinming; Cen, Shan; Jin, Qi; Guo, Fei

2013-08-06

BST-2 (bone marrow stromal cell antigen 2) is an interferon-inducible protein that inhibits virus release by tethering viral particles to the cell surface. This antiviral activity of BST-2 is antagonized by HIV-1 accessory protein Vpu. Vpu physically interacts with BST-2 through their mutual transmembrane (TM) domains. In this study, we utilized the BRET assay and molecular dynamics (MD) simulation method to further characterize the interaction of BST-2 and Vpu. Amino acids I34, L37, P40 and L41 in the TM domain of BST-2, and L11, A18 and W22 in the TM domain of Vpu were identified to be critical for the interaction between BST-2 and Vpu. The residues P40 in the TM domain of BST-2 and L11 in the TM domain of Vpu were shown, for the first time, to be important for their interaction. Furthermore, triple-amino-acid substitutions, 14-16 (AII to VAA) and 26-28 (IIE to AAA) in Vpu TM, not the single-residue mutation, profoundly disrupted BST-2/Vpu interaction. The results of MD simulation revealed significant conformational changes of the BST-2/Vpu complex as a result of mutating P40 of BST-2 and L11, 14-16 (AII to VAA) and 26-28 (IIE to AAA) of Vpu. In addition, disrupting the interaction between BST-2 and Vpu rendered BST-2 resistant to Vpu antagonization. Through use of the BRET assay, we identified novel key residues P40 in the TM domain of BST-2 and L11 in the TM domain of Vpu that are important for their interaction. These results add new insights into the molecular mechanism behind BST-2 antagonization by HIV-1 Vpu.

Identification of novel key amino acids at the interface of the transmembrane domains of human BST-2 and HIV-1 Vpu

PubMed Central

2013-01-01

Background BST-2 (bone marrow stromal cell antigen 2) is an interferon-inducible protein that inhibits virus release by tethering viral particles to the cell surface. This antiviral activity of BST-2 is antagonized by HIV-1 accessory protein Vpu. Vpu physically interacts with BST-2 through their mutual transmembrane (TM) domains. In this study, we utilized the BRET assay and molecular dynamics (MD) simulation method to further characterize the interaction of BST-2 and Vpu. Results Amino acids I34, L37, P40 and L41 in the TM domain of BST-2, and L11, A18 and W22 in the TM domain of Vpu were identified to be critical for the interaction between BST-2 and Vpu. The residues P40 in the TM domain of BST-2 and L11 in the TM domain of Vpu were shown, for the first time, to be important for their interaction. Furthermore, triple-amino-acid substitutions, 14–16 (AII to VAA) and 26–28 (IIE to AAA) in Vpu TM, not the single-residue mutation, profoundly disrupted BST-2/Vpu interaction. The results of MD simulation revealed significant conformational changes of the BST-2/Vpu complex as a result of mutating P40 of BST-2 and L11, 14–16 (AII to VAA) and 26–28 (IIE to AAA) of Vpu. In addition, disrupting the interaction between BST-2 and Vpu rendered BST-2 resistant to Vpu antagonization. Conclusions Through use of the BRET assay, we identified novel key residues P40 in the TM domain of BST-2 and L11 in the TM domain of Vpu that are important for their interaction. These results add new insights into the molecular mechanism behind BST-2 antagonization by HIV-1 Vpu. PMID:23919512

Synthesis of nano-TiO2 photocatalysts with tunable Fe doping concentration from Ti-bearing tailings

NASA Astrophysics Data System (ADS)

Sui, Yulei; Liu, Qingxia; Jiang, Tao; Guo, Yufeng

2018-01-01

In this work, highly pure nano-TiO2 photocatalysts with varying Fe doping concentration were successfully synthesized from low-cost Ti-bearing tailings by an acidolysis-hydrothermal route. The effects of H2SO4 concentration, leaching temperature, acid/tailings ratio and leaching time on the recovery of TiO2 from the tailings were investigated. Synthesized samples were characterized by XRD, TEM, EDS, XPS, and UV-vis spectroscopy. The results showed that the material prepared is characteristic anatase with the average size of 20 nm and the Fe doping concentration in the synthesized nano-TiO2 is tunable. The photocatalytic activity of synthesized nano-TiO2 photocatalyst was also evaluated by the photodegradation of Rhodamine B under visible light and UV light irradiation. Our study demonstrates a low-cost approach to synthesize highly efficient and visible light responsive catalysts.

The flotation tailings of the former Pb-Zn mine of Touiref (NW Tunisia): mineralogy, mine drainage prediction, base-metal speciation assessment and geochemical modeling.

PubMed

Othmani, Mohamed Ali; Souissi, Fouad; Bouzahzah, Hassan; Bussière, Bruno; da Silva, Eduardo Ferreira; Benzaazoua, Mostafa

2015-02-01

The underground extraction of Pb-Zn mineralization in the Touiref area stopped in 1958. A large volume of flotation tailings (more than 500 Mt) containing sulfides were deposited in a tailings impoundment. The goals of this study are to evaluate the neutralization capacity of the unoxidized and oxidized tailings, to assess the speciation of metals between the different components of the tailings material, and to assess the mobility of metals and the secondary minerals' precipitation in pore waters using geochemical modeling. To accomplish these objectives, representative samples from both fresh and oxidized zones were collected along a vertical profile through the tailings pile. Physical, chemical (ICP-MS), and mineralogical characterization (X-ray diffraction (XRD), reflected light microscopy, scanning electron microscope (SEM)) of these samples was performed. Grain size analysis shows that the tailings are dominated by silt- to sand-sized fractions. The microscopic observation highlights the presence of pyrite, marcasite, galena, and sphalerite as primary minerals in a carbonated matrix. The study reveals also the presence of secondary minerals represented by cerussite, smithsonite, anglesite, and Fe oxi-hydroxides as important scavengers for trace elements. The static tests show that the presence of calcite in the tailing samples ensures acid-neutralizing capacity (ANC), which is significantly greater than the acidity potential (PA). The geochemical characterization of the unoxidized samples shows higher Cd, Pb, and Zn concentrations than the oxidized samples containing the highest values for Fe and SO4. Sequential extraction tests show that significant percentages of metals are distributed between the acid-soluble fractions (Cd, Pb, and Zn) and the reducible one (Zn). Pore water analysis indicates that Ca is the dominant cation (8,170 and 6,200 mg L(-1), respectively), whereas sulfate is the principal anion (6,900 and 5,100 mg L(-1), respectively). Saturation

NMR assignments of SPOC domain of the human transcriptional corepressor SHARP in complex with a C-terminal SMRT peptide.

PubMed

Mikami, Suzuka; Kanaba, Teppei; Ito, Yutaka; Mishima, Masaki

2013-10-01

The transcriptional corepressor SMRT/HDAC1-associated repressor protein (SHARP) recruits histone deacetylases. Human SHARP protein is thought to function in processes involving steroid hormone responses and the Notch signaling pathway. SHARP consists of RNA recognition motifs (RRMs) in the N-terminal region and the spen paralog and ortholog C-terminal (SPOC) domain in the C-terminal region. It is known that the SPOC domain binds the LSD motif in the C-terminal tail of corepressors silencing mediator for retinoid and thyroid receptor (SMRT)/nuclear receptor corepressor (NcoR). We are interested in delineating the mechanism by which the SPOC domain recognizes the LSD motif of the C-terminal tail of SMRT/NcoR. To this end, we are investigating the tertiary structure of the SPOC/SMRT peptide using NMR. Herein, we report on the (1)H, (13)C and (15)N resonance assignments of the SPOC domain in complex with a SMRT peptide, which contributes towards a structural understanding of the SPOC/SMRT peptide and its molecular recognition.

MDC9, a widely expressed cellular disintegrin containing cytoplasmic SH3 ligand domains

PubMed Central

1996-01-01

Cellular disintegrins are a family of proteins that are related to snake venom integrin ligands and metalloproteases. We have cloned and sequenced the mouse and human homologue of a widely expressed cellular disintegrin, which we have termed MDC9 (for metalloprotease/disintegrin/cysteine-rich protein 9). The deduced mouse and human protein sequences are 82% identical. MDC9 contains several distinct protein domains: a signal sequence is followed by a prodomain and a domain with sequence similarity to snake venom metalloproteases, a disintegrin domain, a cysteine-rich region, an EGF repeat, a membrane anchor, and a cytoplasmic tail. The cytoplasmic tail of MDC9 has two proline-rich sequences which can bind the SH3 domain of Src, and may therefore function as SH3 ligand domains. Western blot analysis shows that MDC9 is an approximately 84-kD glycoprotein in all mouse tissues examined, and in NIH 3T3 fibroblast and C2C12 myoblast mouse cell lines. MDC9 can be both cell surface biotinylated and 125I-labeled in NIH 3T3 mouse fibroblasts, indicating that the protein is present on the plasma membrane. Expression of MDC9 in COS-7 cells yields an 84-kD protein, and immunofluorescence analysis of COS-7 cells expressing MDC9 shows a staining pattern that is consistent with a plasma membrane localization. The apparent molecular mass of 84 kD suggests that MDC9 contains a membrane-anchored metalloprotease and disintegrin domain. We propose that MDC9 might function as a membrane-anchored integrin ligand or metalloprotease, or that MDC9 may combine both activities in one protein. PMID:8647900

Ecological aspects of microorganisms inhabiting uranium mill tailings

USGS Publications Warehouse

Miller, C.L.; Landa, E.R.; Updegraff, D.M.

1987-01-01

Numbers and types of microorganisms in uranium mill tailings were determined using culturing techniques. Arthrobacter were found to be the predominant microorganism inhabiting the sandy tailings, whereas Bacillus and fungi predominated in the slime tailings. Sulfate-reducing bacteria, capable of leaching radium, were isolated in low numbers from tailings samples but were isolated in significantly high numbers from topsoil in contact with the tailings. The results are placed in the context of the magnitude of uranium mill tailings in the United States, the hazards posed by the tailings, and how such hazards could be enhanced or diminished by microbial activities. Patterns in the composition of the microbial population are evaluated with respect to the ecological variables that influence microbial growth. ?? 1987 Springer-Verlag New York Inc.

Evolution of soil properties and metals in acid and alkaline mine tailing ponds after amendments and microorganisms application

NASA Astrophysics Data System (ADS)

Acosta, Jose A.; Faz, Ángel; Zornoza, Raúl; Martínez-Martínez, Silvia; Bech, Jaume

2015-04-01

Intense mining activities in the past were carried out in Cartagena-La Unión mining district, SE Spain, and caused excessive accumulation of toxic metals in tailing ponds which poses a high environmental and ecological risk. One of the remediation options gaining considerable interest in recent years is the in situ immobilization of metals. A corresponding reduction in the plant-available metal fraction allows re-vegetation and ecosystem restoration of the heavily contaminated sites. In addition, the use of microorganisms to improve the soil condition is a new tool used to increase spontaneous plant colonization. The aim of this research was to assess the effect of amendments (pig manure, sewage sludge, and lime) and microorganisms on the evolution of soil properties and metals in acid and alkaline tailing ponds and to evaluate the content of metals in Zygophylum fabago one year after amendments application. The study was carried out in two mine ponds (acid and alkaline). Twenty seven square field plots, each one consisting of 4 m2, were located in each pond. Four different doses of microorganism (EM) (0 ml, 20 ml, 100 ml and 200 ml of microorganism solution in each plot) and one dose of pig manure (5 kg per plot), sewage sludge (4 kg per plot) and lime (22 kg per plot) were used. Organic amendment doses were calculated according to European nitrogen legislations, and lime dose was calculated according with the potential acid production through total sulphur oxidation. Three replicates of each treatment (organic amendment + lime + microorganism dose 0, 1, 2, or 3) and control soil (with no amendments) were carried out. Plots were left to the semi-arid climate conditions after the addition of amendments to simulate real potential applications of the results. Soil samples was collected every 4 month from each plot during one year, after this time Zygophylum fabago plants were sampled from each plots. Soil properties including: pH, salinity, total, inorganic and

All-trans retinol, vitamin D and other hydrophobic compounds bind in the axial pore of the five-stranded coiled-coil domain of cartilage oligomeric matrix protein.

PubMed Central

Guo, Y; Bozic, D; Malashkevich, V N; Kammerer, R A; Schulthess, T; Engel, J

1998-01-01

The potential storage and delivery function of cartilage oligomeric matrix protein (COMP) for cell signaling molecules was explored by binding hydrophobic compounds to the recombinant five-stranded coiled-coil domain of COMP. Complex formation with benzene, cyclohexane, vitamin D3 and elaidic acid was demonstrated through increases in denaturation temperatures of 2-10 degreesC. For all-trans retinol and all-trans retinoic acid, an equilibrium dissociation constant KD = 0.6 microM was evaluated by fluorescence titration. Binding of benzene and all-trans retinol into the hydrophobic axial pore of the COMP coiled-coil domain was proven by the X-ray crystal structures of the corresponding complexes at 0.25 and 0.27 nm resolution, respectively. Benzene binds with its plane perpendicular to the pore axis. The binding site is between the two internal rings formed by Leu37 and Thr40 pointing into the pore of the COMP coiled-coil domain. The retinol beta-ionone ring is positioned in a hydrophobic environment near Thr40, and the 1.1 nm long isoprene tail follows a completely hydrophobic region of the pore. Its terminal hydroxyl group complexes with a ring of the five side chains of Gln54. A mutant in which Gln54 is replaced by Ile binds all-trans retinol with affinity similar to the wild-type, demonstrating that hydrophobic interactions are predominant. PMID:9736606

CCL19 with CCL21-tail displays enhanced glycosaminoglycan binding with retained chemotactic potency in dendritic cells.

PubMed

Jørgensen, Astrid S; Adogamhe, Pontian E; Laufer, Julia M; Legler, Daniel F; Veldkamp, Christopher T; Rosenkilde, Mette M; Hjortø, Gertrud M

2018-05-16

CCL19 is more potent than CCL21 in inducing chemotaxis of human dendritic cells (DC). This difference is attributed to 1) a stronger interaction of the basic C-terminal tail of CCL21 with acidic glycosaminoglycans (GAGs) in the environment and 2) an autoinhibitory function of this C-terminal tail. Moreover, different receptor docking modes and tissue expression patterns of CCL19 and CCL21 contribute to fine-tuned control of CCR7 signaling. Here, we investigate the effect of the tail of CCL21 on chemokine binding to GAGs and on CCR7 activation. We show that transfer of CCL21-tail to CCL19 (CCL19 CCL21-tail ) markedly increases binding of CCL19 to human dendritic cell surfaces, without impairing CCL19-induced intracellular calcium release or DC chemotaxis, although it causes reduced CCR7 internalization. The more potent chemotaxis induced by CCL19 and CCL19 CCL21-tail compared to CCL21 is not transferred to CCL21 by replacing its N-terminus with that of CCL19 (CCL21 CCL19-N-term ). Measurements of cAMP production in CHO cells uncover that CCL21-tail transfer (CCL19 CCL21-tail ) negatively affects CCL19 potency, whereas removal of CCL21-tail (CCL21 tailless ) increases signaling compared to full-length CCL21, indicating that the tail negatively affects signaling via cAMP. Similar to chemokine-driven calcium mobilization and chemotaxis, the potency of CCL21 in cAMP is not improved by transfer of the CCL19 N-terminus to CCL21 (CCL21 CCL19-N-term ). Together these results indicate that ligands containing CCL21 core and C-terminal tail (CCL21 and CCL21 CCL19-N-term ) are most restricted in their cAMP signaling; a phenotype attributed to a stronger GAG binding of CCL21 and defined structural differences between CCL19 and CCL21. ©2018 Society for Leukocyte Biology.

Med5(Nut1) and Med17(Srb4) Are Direct Targets of Mediator Histone H4 Tail Interactions

PubMed Central

Liu, Zhongle; Myers, Lawrence C.

2012-01-01

The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. In addition to its canonical role in transcriptional activation, recent studies have demonstrated that S. cerevisiae Mediator can interact directly with nucleosomes, and their histone tails. Mutations in Mediator subunits have shown that Mediator and certain chromatin structures mutually impact each other structurally and functionally in vivo. We have taken a UV photo cross-linking approach to further delineate the molecular basis of Mediator chromatin interactions and help determine whether the impact of certain Mediator mutants on chromatin is direct. Specifically, by using histone tail peptides substituted with an amino acid analog that is a UV activatible crosslinker, we have identified specific subunits within Mediator that participate in histone tail interactions. Using Mediator purified from mutant yeast strains we have evaluated the impact of these subunits on histone tail binding. This analysis has identified the Med5 subunit of Mediator as a target for histone tail interactions and suggests that the previously observed effect of med5 mutations on telomeric heterochromatin and silencing is direct. PMID:22693636

Regulation of the Electric Charge in Phosphatidic Acid Domains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Wenjie; Anderson, Nathaniel A.; Travesset, Alex

Although a minor component of the lipidome, phosphatidic acid (PA) plays a crucial role in nearly all signaling pathways involving cell membranes, in part because of its variable electrical charge in response to environmental conditions. To investigate how charge is regulated in domains of PA, we applied surface-sensitive X-ray reflectivity and fluorescence near-totalreflection techniques to determine the binding of divalent ions (Ca2+ at various pH values) to 1,2-dimyristoyl-sn-glycero-3-phosphate (DMPA) and to the simpler lipid dihexadecyl phosphate (DHDP) spread as monolayers at the air/water interface. We found that the protonation state of PA is controlled not only by the pKa andmore » local pH but also by the strong affinity to PA driven by electrostatic correlations from divalent ions and the cooperative effect of the two dissociable protons, which dramatically enhance the surface charge. A precise theoretical model is presented providing a general framework to predict the protonation state of PA. Implications for recent experiments on charge regulation by hydrogen bonding and the role of pH in PA signaling are discussed in detail.« less

The X-ray Crystal Structure of the Phage Tail Terminator Protein Reveals the Biologically Relevant Hexameric Rang Structure and Demonstrates a Conserved mechanism of Tail Termination among Divrse Long Tailed Phages

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pell, L.; Liu, A; Edmonds, L

The tail terminator protein (TrP) plays an essential role in phage tail assembly by capping the rapidly polymerizing tail once it has reached its requisite length and serving as the interaction surface for phage heads. Here, we present the 2.7-A crystal structure of a hexameric ring of gpU, the TrP of phage ?. Using sequence alignment analysis and site-directed mutagenesis, we have shown that this multimeric structure is biologically relevant and we have delineated its functional surfaces. Comparison of the hexameric crystal structure with the solution structure of gpU that we previously solved using NMR spectroscopy shows large structural changesmore » occurring upon multimerization and suggests a mechanism that allows gpU to remain monomeric at high concentrations on its own, yet polymerize readily upon contact with an assembled tail tube. The gpU hexamer displays several flexible loops that play key roles in head and tail binding, implying a role for disorder-to-order transitions in controlling assembly as has been observed with other ? morphogenetic proteins. Finally, we have found that the hexameric structure of gpU is very similar to the structure of a putative TrP from a contractile phage tail even though it displays no detectable sequence similarity. This finding coupled with further bioinformatic investigations has led us to conclude that the TrPs of non-contractile-tailed phages, such as ?, are evolutionarily related to those of contractile-tailed phages, such as P2 and Mu, and that all long-tailed phages may utilize a conserved mechanism for tail termination.« less

Total sialic acid profile in regressing and remodelling organs during the metamorphosis of marsh frog (Pelophylax ridibundus Pallas 1771).

PubMed

Kaptan, Engin; Bas, Serap Sancar; Inceli, Meliha Sengezer

2013-03-01

This study aimed to investigate the functional relationship of sialic acid in regressing and remodelling organs such as the tail, small intestine and liver during the metamorphosis of Pelophylax ridibundus. For this purpose, four groups were composed according to developmental periods by considering Gosner's criteria (1964). Our findings showed that the sialic acid content of the larval tail has an opposite profile to cell death process. Although the sialic acid content of the small intestine and liver did not change evidently during metamorphosis, it increased after the completion of metamorphosis. Frog tail extensively exhibited cell death process and decreased proliferative activity and underwent complete degeneration during metamorphic climax. In spite of increased apoptotic index, a decreased sialic acid level in the tail tissues during climax can be the indication of a death cell removal process. However, the intestine and the liver included both cell death and proliferative process and remodelling in their adult forms. Thus, their sialic acid profiles during metamorphosis were different from the tail's profile. These data show that sialic acid may be an indicator of the presence of some cellular events during metamorphosis and that it can have different roles in the developmental process depending on the organ's fate throughout metamorphosis. Copyright © 2012 John Wiley & Sons, Ltd.

Cyclopiazonic acid biosynthesis in Aspergillus sp.: characterization of a reductase-like R* domain in cyclopiazonate synthetase that forms and releases cyclo-acetoacetyl-L-tryptophan.

PubMed

Liu, Xinyu; Walsh, Christopher T

2009-09-15

The fungal neurotoxin alpha-cyclopiazonic acid (CPA), a nanomolar inhibitor of Ca2+-ATPase, has a pentacyclic indole tetramic acid scaffold that arises from one molecule of tryptophan, acetyl-CoA, malonyl-CoA, and dimethylallyl pyrophosphate by consecutive action of three enzymes, CpaS, CpaD, and CpaO. CpaS is a hybrid, two module polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) that makes and releases cyclo-acetoacetyl-L-tryptophan (cAATrp), the tetramic acid that serves as substrate for subsequent prenylation and oxidative cyclization to the five ring CPA scaffold. The NRPS module in CpaS has a predicted four-domain organization of condensation, adenylation, thiolation, and reductase* (C-A-T-R*), where R* lacks the critical Ser-Tyr-Lys catalytic triad of the short chain dehydrogenase/reductase (SDR) superfamily. By heterologous overproduction in Escherichia coli of the 56 kDa Aspergillus flavus CpaS TR* didomain and the single T and R* domains, we demonstrate that CpaS catalyzes a Dieckmann-type cyclization on the N-acetoacetyl-Trp intermediate bound in thioester linkage to the phosphopantetheinyl arm of the T domain to form and release cAATrp. This occurs without any participation of NAD(P)H, so R* does not function as a canonical SDR family member. Use of the T and R* domains in in trans assays enabled multiple turnovers and evaluation of specific mutants. Mutation of the D3803 residue in the R* domain, conserved in other fungal tetramate synthetases, abolished activity both in in trans and in cis (TR*) activity assays. It is likely that cyclization of beta-ketoacylaminoacyl-S-pantetheinyl intermediates to released tetramates represents a default cyclization/release route for redox-incompetent R* domains embedded in NRPS assembly lines.

Assessing Natural Radionuclide Migration in the Legacy Tailings of Uranium Production

NASA Astrophysics Data System (ADS)

Bondarenko, G.; Koliabina, I.; Marinich, O.

2011-12-01

The former Prydniprovsky Chemical Plant in Dniprodzerzhynsk, Ukraine, processed uranium ore from 1949 until 1991. Multiple tailing ponds containing solid residual waste products from the uranium leaching and processing of uranium were accumulated along the Dnieper River, including the largest, adjacent to the Dnieper Reservoir, containing over 12 million tons of tailings. Samples for this study were selected from a core recovered from the Dnieper tailing pit in 2009, and used to assess radionuclide migration from tailing ponds. Samples were selected from different depths of the tailing pit core, analyzed for total radionuclide concentrations [Marinich et al., 2009], and successively leached using distilled water, followed by 1N ammonium acetate solution, and finally by 1N HCl solution. Leaching times were ~24 h at 15.17 °C. 238U, 230Th and 226Ra leachate activities were measured by γ-spectrometry with a Ge(Li) detector. 210Pb activity was measured using a SEB-01 scintillation β-spectrometer. Errors depended on measuring method, radionuclide, activity and exposure time: 238U, 11.9%; 230Th, 10.9%; 226Ra, 9.3%; 210Pb ~30%. The average total 238U activity in the tailing profile was 4 Bq/g. The concentration of 238U in the water leachates increased with depth from 14.5% (7-7.5 m), to 43% (11-11.5 m). The concentration of 238U in the acid leachates behaved similarly, increasing from 5.5 % to 15.5% with depth. While the total 230Th activity in increased from 30 Bq/g (7-7.5 m) to 540 Bq/g (11-11.5 m), the 230Th concentration in ammonium acetate leachates decreased from ˜15% to ˜1%. The concentration of 226Ra in all leachates was <1%, indicating that, under conditions of the Dnieper tailing pit, 226Ra is essentially immobile. The concentration of 210Pb in the leachates was as high as 10%. In general, the magnitude of mobile activity from the Dnieper tailing pit core samples decreases in the order 238U>230Th≥210Pb> 226Ra. Secular radioactive equilibrium in the 238U

Comparison of structure, function and regulation of plant cold shock domain proteins to bacterial and animal cold shock domain proteins.

PubMed

Chaikam, Vijay; Karlson, Dale T

2010-01-01

The cold shock domain (CSD) is among the most ancient and well conserved nucleic acid binding domains from bacteria to higher animals and plants. The CSD facilitates binding to RNA, ssDNA and dsDNA and most functions attributed to cold shock domain proteins are mediated by this nucleic acid binding activity. In prokaryotes, cold shock domain proteins only contain a single CSD and are termed cold shock proteins (Csps). In animal model systems, various auxiliary domains are present in addition to the CSD and are commonly named Y-box proteins. Similar to animal CSPs, plant CSPs contain auxiliary C-terminal domains in addition to their N-terminal CSD. Cold shock domain proteins have been shown to play important roles in development and stress adaptation in wide variety of organisms. In this review, the structure, function and regulation of plant CSPs are compared and contrasted to the characteristics of bacterial and animal CSPs. [BMB reports 2010; 43(1): 1-8].

EAR AND TAIL LESIONS ON CAPTIVE WHITE-TAILED DEER FAWNS (ODOCOILEUS VIRGINIANUS): A CASE STUDY.

PubMed

Ferguson, Treena L; Demarais, Stephen; Cooley, Jim; Fleming, Sherrill; Michel, Eric S; Flinn, Emily

2016-06-01

During the 2008-2011 time period, undiagnosed lesions were observed in 21 of 150 white-tailed deer fawns (Odocoileus virginianus) that were part of a captive deer herd at Mississippi State University. Clinical findings in healthy and diseased fawns from 0 to 90 days of age included bite and scratch marks followed by moderate to severe ear and tail necrosis. Gross necropsy findings of necrotizing ulcerative dermatitis correlated with histopathologic findings that included focally severe multifocal vasculitis, vascular necrosis, and thrombosis. This article is a clinical description of these previously unreported lesions associated with tissue necrosis in young captive white-tailed deer.

On the average configuration of the geomagnetic tail

NASA Technical Reports Server (NTRS)

Fairfield, D. H.

1978-01-01

Over 3000 hours of IMP-6 magnetic field data obtained between 20 and 33 R sub E in the geomagnetic tail have been used in a statistical study of the tail configuration. A distribution of 2.5 minute averages of B sub Z as a function of position across the tail reveals that more flux crosses the equatorial plane near the dawn and dusk flanks than near midnight. The tail field projected in the solar magnetospheric equatorial plane deviates from the X axis due to flaring and solar wind aberration by an angle alpha = -0.9 y sub SM - 1.7 where Y sub SM is in earth radii and alpha is in degrees. After removing these effects the Y component of the tail field is found to depend on interplanetary sector structure. During an away sector the B sub Y component of the tail field is on average 0.5 gamma greater than that during a toward sector, a result that is true in both tail lobes and is independent of location across the tail.

Identification, characterization and leucocyte expression of Siglec-10, a novel human sialic acid-binding receptor.

PubMed Central

Munday, J; Kerr, S; Ni, J; Cornish, A L; Zhang, J Q; Nicoll, G; Floyd, H; Mattei, M G; Moore, P; Liu, D; Crocker, P R

2001-01-01

Here we characterize Siglec-10 as a new member of the Siglec family of sialic acid-binding Ig-like lectins. A full-length cDNA was isolated from a human spleen library and the corresponding gene identified. Siglec-10 is predicted to contain five extracellular Ig-like domains and a cytoplasmic tail containing three putative tyrosine-based signalling motifs. Siglec-10 exhibited a high degree of sequence similarity to CD33-related Siglecs and mapped to the same region, on chromosome 19q13.3. The expressed protein was able to mediate sialic acid-dependent binding to human erythrocytes and soluble sialoglycoconjugates. Using specific antibodies, Siglec-10 was detected on subsets of human leucocytes including eosinophils, monocytes and a minor population of natural killer-like cells. The molecular properties and expression pattern suggest that Siglec-10 may function as an inhibitory receptor within the innate immune system. PMID:11284738

Mineralogy and geochemistry of efflorescent minerals on mine tailings and their potential impact on water chemistry.

PubMed

Grover, B P C; Johnson, R H; Billing, D G; Weiersbye, I M G; Tutu, H

2016-04-01

In the gold mining Witwatersrand Basin of South Africa, efflorescent mineral crusts are a common occurrence on and nearby tailings dumps during the dry season. The crusts are readily soluble and generate acidic, metal- and sulphate-rich solutions on dissolution. In this study, the metal content of efflorescent crusts at an abandoned gold mine tailings dump was used to characterise surface and groundwater discharges from the site. Geochemical modelling of the pH of the solution resulting from the dissolution of the crusts was used to better understand the crusts' potential impact on water chemistry. The study involved two approaches: (i) conducting leaching experiments on oxidised and unoxidised tailings using artificial rainwater and dilute sulphuric acid and correlating the composition of crusts to these leachates and (ii) modelling the dissolution of the crusts in order to gain insight into their mineralogy and their potential impact on receiving waters. The findings suggested that there were two chemically distinct discharges from the site, namely an aluminium- and magnesium-rich surface water plume and an iron-rich groundwater plume. The first plume was observed to originate from the oxidised tailings following leaching with rainwater while the second plume originated from the underlying unoxidised tailings with leaching by sulphuric acid. Both groups of minerals forming from the respective plumes were found to significantly lower the pH of the receiving water with simulations of their dissolution found to be within 0.2 pH units of experimental values. It was observed that metals in a low abundance within the crust (for example, iron) had a stronger influence on the pH of the resulting solutions than metals in a greater abundance (aluminium or magnesium). Techniques such as powder X-ray diffraction (PXRD) and in situ mineral determination techniques such as remote sensing can effectively determine the dominant mineralogy. However, the minerals or metals

Gain-of-function mutations identify amino acids within transmembrane domains of the yeast vacuolar transporter Zrc1 that determine metal specificity

PubMed Central

Lin, Huilan; Burton, Damali; Li, Liangtao; Warner, David E.; Phillips, John D.; Ward, Diane McVEY; Kaplan, Jerry

2015-01-01

Cation diffusion facilitator transporters are found in all three Kingdoms of life and are involved in transporting transition metals out of the cytosol. The metals they transport include Zn2+, Co2+, Fe2+, Cd2+, Ni2+ and Mn2+; however, no single transporter transports all metals. Previously we showed that a single amino acid mutation in the yeast vacuolar zinc transporter Zrc1 changed its substrate specificity from Zn2+ to Fe2+ and Mn2+ [Lin, Kumanovics, Nelson, Warner, Ward and Kaplan (2008) J. Biol. Chem. 283, 33865–33873]. Mutant Zrc1 that gained iron transport activity could protect cells with a deletion in the vacuolar iron transporter (CCC1) from high iron toxicity. Utilizing suppression of high iron toxicity and PCR mutagenesis of ZRC1, we identified other amino acid substitutions within ZRC1 that changed its metal specificity. All Zrc1 mutants that transported Fe2+ could also transport Mn2+. Some Zrc1 mutants lost the ability to transport Zn2+, but others retained the ability to transport Zn2+. All of the amino acid substitutions that resulted in a gain in Fe2+ transport activity were found in transmembrane domains. In addition to alteration of residues adjacent to the putative metal-binding site in two transmembrane domains, alteration of residues distant from the binding site affected substrate specificity. These results suggest that substrate selection involves co-operativity between transmembrane domains. PMID:19538181

Impact of fresh tailing deposition on the evolution of groundwater hydrogeochemistry at the abandoned Manitou mine site, Quebec, Canada.

PubMed

Maqsoud, Abdelkabir; Neculita, Carmen Mihaela; Bussière, Bruno; Benzaazoua, Mostafa; Dionne, Jean

2016-05-01

The abandoned Manitou mine site has produced acid mine drainage (AMD) for several decades. In order to limit the detrimental environmental impacts of AMD, different rehabilitation scenarios were proposed and analyzed. The selected rehabilitation scenario was to use fresh tailings from the neighboring Goldex gold mine as monolayer cover and to maintain an elevated water table. In order to assess the impact of the Goldex tailing deposition on the hydrogeochemistry of the Manitou mine site, a network of 30 piezometers was installed. These piezometers were used for continuous measurement of the groundwater level, as well as for water sampling campaigns for chemical quality monitoring, over a 3-year period. Hydrochemical data were analyzed using principal component analysis. Results clearly showed the benefic impact of fresh tailing deposition on the groundwater quality around the contaminated area. These findings were also confirmed by the evolution of electrical conductivity. In addition to the improvement of the physicochemical quality of water on the Manitou mine site, new tailing deposition induced an increase of water table level. However, at this time, the Manitou reactive tailings are not completely submerged and possible oxidation might still occur, especially after ceasing of the fresh tailing deposition. Therefore, complementary rehabilitation scenarios should still be considered.

Critical study of current situation of Vrănicioara tailing pond on Cavnicului Valley, risks and consequences

NASA Astrophysics Data System (ADS)

Bud, I.; Duma, S.; Gusat, D.; Pasca, I.; Bud, A.

2017-05-01

In northern Romania, there are numerous tailing ponds, resulting from mining activities that present significant environmental risks. Some of them, including Vrănicioara tailing pond, were the subject of technical projects for ecological rehabilitation. Vrănicioara pond is located on the right side of Cavnic Valley, downstream Cavnic town, about 4 kilometers far. It has about 500 m length and is located parallel to the road linking Baia Sprie and Cavnic localities. Chemical and physical stability of the tailing pond before rehabilitation interest the research, analysis and conclusions were published in several scientific meetings. In addition, close to the pond at less than 100 m, an open pit has developed, exploiting andesite by mining blast, increasing the risk of physical stability by continuous exposure to vibration. This activity currently continues, advancing towards the tailing pond body. The critical study addresses the current state of Vrănicioara Tailing Pond, analysis of some rehabilitation works done incorrectly, analysis of chemical stability that was not a priority during rehabilitation. Research intention is heading to water analysis confirming the existence of acid drainage that was not stopped or at least reduced. The scientific approach is based on the Technical Standards for Waste Deposits, in force in Romania, providing the rules to ensure physical and chemical stability.

Tail Shape Design of Boat Wind Turbines

NASA Astrophysics Data System (ADS)

Singamsitty, Venkatesh

Wind energy is a standout among the most generally utilized sustainable power source assets. A great deal of research and improvements have been happening in the wind energy field. Wind turbines are mechanical devices that convert kinetic energy into electrical power. Boat wind turbines are for the small-scale generation of electric power. In order to catch wind energy effectively, boat wind turbines need to face wind direction. Tails are used in boat wind turbines to alter the wind turbine direction and receive the variation of the incoming direction of wind. Tails are used to change the performance of boat wind turbines in an effective way. They are required to generate a quick and steady response as per change in wind direction. Tails can have various shapes, and their effects on boat wind turbines are different. However, the effects of tail shapes on the performance of boat wind turbines are not thoroughly studied yet. In this thesis, five tail shapes were studied. Their effects on boat wind turbines were investigated. The power extracted by the turbines from the air and the force acting on the boat wind turbine tail were analyzed. The results of this thesis provide a guideline of tail shape design for boat wind turbines.

Quasi-steady state aerodynamics of the cheetah tail

PubMed Central

Boje, Edward; Fisher, Callen; Louis, Leeann; Lane, Emily

2016-01-01

ABSTRACT During high-speed pursuit of prey, the cheetah (Acinonyx jubatus) has been observed to swing its tail while manoeuvring (e.g. turning or braking) but the effect of these complex motions is not well understood. This study demonstrates the potential of the cheetah's long, furry tail to impart torques and forces on the body as a result of aerodynamic effects, in addition to the well-known inertial effects. The first-order aerodynamic forces on the tail are quantified through wind tunnel testing and it is observed that the fur nearly doubles the effective frontal area of the tail without much mass penalty. Simple dynamic models provide insight into manoeuvrability via simulation of pitch, roll and yaw tail motion primitives. The inertial and quasi-steady state aerodynamic effects of tail actuation are quantified and compared by calculating the angular impulse imparted onto the cheetah's body and its shown aerodynamic effects contribute to the tail's angular impulse, especially at the highest forward velocities. PMID:27412267

Wing-Fuselage Interference, Tail Buffeting, and Air Flow About the Tail of a Low-Wing Monoplane

NASA Technical Reports Server (NTRS)

White, James A; Hood, Manley J

1935-01-01

This report presents the results of wind tunnel tests on a Mcdonnell Douglas airplane to determine the wing-fuselage interference of a low-wing monoplane. The tests included a study of tail buffeting and the air flow in the region of the tail. The airplane was tested with and without the propeller slipstream, both in the original condition and with several devices designed to reduce or eliminate tail buffeting. The devices used were wing-fuselage fillets, a NACA cowling, reflexed trailing edge of the wing, and stub auxiliary airfoils.

Using terahertz time-domain spectroscopical technique to monitor cocrystal formation between piracetam and 2,5-dihydroxybenzoic acid

NASA Astrophysics Data System (ADS)

Du, Yong; Xia, Yi; Zhang, Huili; Hong, Zhi

2013-07-01

Far-infrared vibrational absorption of cocrystal formation between 2,5-dihydroxybenzoic acid (2,5-DHBA) and piracetam compounds under solvent evaporation and grinding methods have been investigated using terahertz time-domain spectroscopy (THz-TDS) at room temperature. The experimental results show large difference among absorption spectra of the formed cocrystals and the involved individual parent molecules in 0.20-1.50 THz region, which probably originated from the intra-molecular and inter-molecular hydrogen bonds due to the presence of two hydroxyl groups in 2,5-DHBA and amide moieties in piracetam compound. The THz absorption spectra of two formed cocrystals with different methods are almost identical. With grinding method, the reaction process can be monitored directly from both time-domain and frequency-domain spectra using THz-TDS technique. The results indicate that THz-TDS technology can absolutely offer us a high potential method to identify and characterize the formed cocrystals, and also provide the rich information about their reaction dynamic process involving two or more molecular crystals in situ to better know the corresponding reaction mechanism in pharmaceutical fields.

SH3-like motif-containing C-terminal domain of staphylococcal teichoic acid transporter suggests possible function.

PubMed

Ko, Tzu-Ping; Tseng, Shih-Ting; Lai, Shu-Jung; Chen, Sheng-Chia; Guan, Hong-Hsiang; Shin Yang, Chia; Jung Chen, Chun; Chen, Yeh

2016-09-01

The negatively charged bacterial polysaccharides-wall teichoic acids (WTAs) are synthesized intracellularly and exported by a two-component transporter, TagGH, comprising a transmembrane subunit TagG and an ATPase subunit TagH. We determined the crystal structure of the C-terminal domain of TagH (TagH-C) to investigate its function. The structure shows an N-terminal SH3-like subdomain wrapped by a C-terminal subdomain with an anti-parallel β-sheet and an outer shell of α-helices. A stretch of positively charged surface across the subdomain interface is flanked by two negatively charged regions, suggesting a potential binding site for negatively charged polymers, such as WTAs or acidic peptide chains. Proteins 2016; 84:1328-1332. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Four tails problems for dynamical collapse theories

NASA Astrophysics Data System (ADS)

McQueen, Kelvin J.

2015-02-01

The primary quantum mechanical equation of motion entails that measurements typically do not have determinate outcomes, but result in superpositions of all possible outcomes. Dynamical collapse theories (e.g. GRW) supplement this equation with a stochastic Gaussian collapse function, intended to collapse the superposition of outcomes into one outcome. But the Gaussian collapses are imperfect in a way that leaves the superpositions intact. This is the tails problem. There are several ways of making this problem more precise. But many authors dismiss the problem without considering the more severe formulations. Here I distinguish four distinct tails problems. The first (bare tails problem) and second (structured tails problem) exist in the literature. I argue that while the first is a pseudo-problem, the second has not been adequately addressed. The third (multiverse tails problem) reformulates the second to account for recently discovered dynamical consequences of collapse. Finally the fourth (tails problem dilemma) shows that solving the third by replacing the Gaussian with a non-Gaussian collapse function introduces new conflict with relativity theory.

Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

PubMed Central

Liu, Jun; Hua, Zheng-Shuang; Chen, Lin-Xing; Kuang, Jia-Liang; Li, Sheng-Jin; Shu, Wen-Sheng

2014-01-01

Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions

Some Effects of Horizontal-Tail Position on the Vertical-Tail Pressure Distributions of a Complete Model in Sideslip at High Subsonic Speeds

NASA Technical Reports Server (NTRS)

Alford, William J., Jr.

1958-01-01

An investigation has been made in the Langley high-speed 7- by 10-foot tunnel of some effects of horizontal-tail position on the vertical-tail pressure distributions of a complete model in sideslip at high subsonic speeds. The wing of the model was swept back 28.82 deg at the quarter-chord line and had an aspect ratio of 3.50, a taper ratio of 0.067, and NACA 65A004 airfoil sections parallel to the model plane of symmetry. Tests were made with the horizontal tail off, on the wing-chord plane extended, and in T-tail arrangements in forward and rearward locations. The test Mach numbers ranged from 0.60 to 0.92, which corresponds to a Reynolds number range from approximately 2.93 x 10(exp 6) to 3.69 x 10(exp 6), based on the wing mean aerodynamic chord. The sideslip angles varied from -3.9 deg to 12.7 deg at several selected angles of attack. The results indicated that, for a given angle of sideslip, increases in angle of attack caused reductions in the vertical-tail loads in the vicinity of the root chord and increases at the midspan and tip locations, with rearward movements in the local chordwise centers of pressure for the midspan locations and forward movements near the tip of the vertical tail. At the higher angles of attack all configurations investigated experienced outboard and rearward shifts in the center of pressure of the total vertical-tail load. Location of the horizontal tail on the wing- chord plane extended produced only small effects on the vertical-tail loads and centers of pressure. Locating the horizontal tail at the tip of the vertical tail in the forward position caused increases in the vertical-tail loads; this configuration, however, experienced considerable reduction in loads with increasing Mach number. Location of the horizontal tail at the tip of the vertical tail in the rearward position produced the largest increases in vertical-tail loads per degree sideslip angle; this configuration experienced the smallest variations of loads with

Activating glutamate decarboxylase activity by removing the autoinhibitory domain leads to hyper γ-aminobutyric acid (GABA) accumulation in tomato fruit.

PubMed

Takayama, Mariko; Matsukura, Chiaki; Ariizumi, Tohru; Ezura, Hiroshi

2017-01-01

The C-terminal extension region of SlGAD3 is likely involved in autoinhibition, and removing this domain increases GABA levels in tomato fruits. γ-Aminobutyric acid (GABA) is a ubiquitous non-protein amino acid with several health-promoting benefits. In many plants including tomato, GABA is synthesized via decarboxylation of glutamate in a reaction catalyzed by glutamate decarboxylase (GAD), which generally contains a C-terminal autoinhibitory domain. We previously generated transgenic tomato plants in which tomato GAD3 (SlGAD3) was expressed using the 35S promoter/NOS terminator expression cassette (35S-SlGAD3-NOS), yielding a four- to fivefold increase in GABA levels in red-ripe fruits compared to the control. In this study, to further increase GABA accumulation in tomato fruits, we expressed SlGAD3 with (SlGAD3 OX ) or without (SlGAD3ΔC OX ) a putative autoinhibitory domain in tomato using the fruit ripening-specific E8 promoter and the Arabidopsis heat shock protein 18.2 (HSP) terminator. Although the GABA levels in SlGAD3 OX fruits were equivalent to those in 35S-SlGAD3-NOS fruits, GABA levels in SlGAD3ΔC OX fruits increased by 11- to 18-fold compared to control plants, indicating that removing the autoinhibitory domain increases GABA biosynthesis activity. Furthermore, the increased GABA levels were accompanied by a drastic reduction in glutamate and aspartate levels, indicating that enhanced GABA biosynthesis affects amino acid metabolism in ripe-fruits. Moreover, SlGAD3ΔC OX fruits exhibited an orange-ripe phenotype, which was associated with reduced levels of both carotenoid and mRNA transcripts of ethylene-responsive carotenogenic genes, suggesting that over activation of GAD influences ethylene sensitivity. Our strategy utilizing the E8 promoter and HSP terminator expression cassette, together with SlGAD3 C-terminal deletion, would facilitate the production of tomato fruits with increased GABA levels.

Microbial Diversity and Metal Speciation Changes in Mine Tailings Following Compost-Assisted Direct Planting: A Four-Year Superfund Site Field Study

NASA Astrophysics Data System (ADS)

Maier, R. M.; Gil-Loaiza, J.; Honeker, L. K.; Hottenstein, J. D.; Valentin-Vargas, A.; Jennings, L. L.; Hammond, C.; Neilson, J. W.; Root, R. A.; Chorover, J.

2014-12-01

EPA estimates that future mine tailings remediation costs will exceed US $50 billion using present technologies based on constructing an inert or biological cap on the tailings. Both approaches require large amounts of capping materials that can be difficult and expensive to obtain especially for sites several thousand hectares in size. An alternative technology is direct planting into tailings. However, direct planting alone is not feasible for many legacy sites due to extreme acidity and high metal content which prevent plant germination and growth. Therefore the process must be "assisted" through the addition of amendments such as compost. Here we present results from the first four years of a field study at the Iron King Mine and Humboldt Smelter Superfund site demonstrating the feasibility of compost-assisted direct planting. Parameters measured during the field study included: canopy cover, pH, nutrient content, plant metal uptake, metal(loid) speciation, mineral analysis, microbiome analysis, and plant root-metal-microbe interactions. Integrated analysis of these parameters suggests that even in this "worst-case scenario" mine tailings site (pH 2.5; As and Pb each exceeding 2 g kg-1), we have created a sustainable system. In this system, phyto-catalyzed stabilization of inorganic contaminants in the root zone is driven by plant root exudates and the associated rhizosphere microbial community. The results of this research will be put into context of a larger topic- that of ecological engineering of mine tailings sites - a technique being proposed to prevent creation of acidic conditions and metal(loid) mobilization in the first place.

Microbial Diversity and Metal Speciation Changes in Mine Tailings Following Compost-Assisted Direct Planting: A Four-Year Superfund Site Field Study

NASA Astrophysics Data System (ADS)

Maier, R. M.; Gil-Loaiza, J.; Honeker, L. K.; Hottenstein, J. D.; Valentin-Vargas, A.; Jennings, L. L.; Hammond, C.; Neilson, J. W.; Root, R. A.; Chorover, J.

2015-12-01

EPA estimates that future mine tailings remediation costs will exceed US $50 billion using present technologies based on constructing an inert or biological cap on the tailings. Both approaches require large amounts of capping materials that can be difficult and expensive to obtain especially for sites several thousand hectares in size. An alternative technology is direct planting into tailings. However, direct planting alone is not feasible for many legacy sites due to extreme acidity and high metal content which prevent plant germination and growth. Therefore the process must be "assisted" through the addition of amendments such as compost. Here we present results from the first four years of a field study at the Iron King Mine and Humboldt Smelter Superfund site demonstrating the feasibility of compost-assisted direct planting. Parameters measured during the field study included: canopy cover, pH, nutrient content, plant metal uptake, metal(loid) speciation, mineral analysis, microbiome analysis, and plant root-metal-microbe interactions. Integrated analysis of these parameters suggests that even in this "worst-case scenario" mine tailings site (pH 2.5; As and Pb each exceeding 2 g kg-1), we have created a sustainable system. In this system, phyto-catalyzed stabilization of inorganic contaminants in the root zone is driven by plant root exudates and the associated rhizosphere microbial community. The results of this research will be put into context of a larger topic- that of ecological engineering of mine tailings sites - a technique being proposed to prevent creation of acidic conditions and metal(loid) mobilization in the first place.

Distinct functional domains within the acidic cluster of tegument protein pp28 required for trafficking and cytoplasmic envelopment of human cytomegalovirus.

PubMed

Seo, Jun-Young; Jeon, Hyejin; Hong, Sookyung; Britt, William J

2016-10-01

Human cytomegalovirus UL99-encoded tegument protein pp28 contains a 16 aa acidic cluster that is required for pp28 trafficking to the assembly compartment (AC) and the virus assembly. However, functional signals within the acidic cluster of pp28 remain undefined. Here, we demonstrated that an acidic cluster rather than specific sorting signals was required for trafficking to the AC. Recombinant viruses with chimeric pp28 proteins expressing non-native acidic clusters exhibited delayed viral growth kinetics and decreased production of infectious virus, indicating that the native acidic cluster of pp28 was essential for wild-type virus assembly. These results suggested that the acidic cluster of pp28 has distinct functional domains required for trafficking and for efficient virus assembly. The first half (aa 44-50) of the acidic cluster was sufficient for pp28 trafficking, whereas the native acidic cluster consisting of aa 51-59 was required for the assembly of wild-type levels of infectious virus.

The Distant Sodium Tail of Mercury

NASA Technical Reports Server (NTRS)

Potter, A. E.; Killen, R. M.; Morgan, T. H.

2001-01-01

Models of the sodium atmosphere of Mercury predict the possible existence of a cornet-like sodium tail. Detection and mapping of the predicted sodium tail would provide quantitative data on the energy of the process that produces sodium atoms from the planetary surface. Previous efforts to detect the sodium tail by means of observations done during daylight hours have been only partially successful because scattered sunlight obscured the weak sodium emissions in the tail. However, at greatest eastern elongation around the March equinox in the northern hemisphere, Mercury can be seen as an evening star in astronomical twilight. At this time, the intensity of scattered sunlight is low enough that sodium emissions as low as 500 Rayleighs can be detected. Additional information is contained in the original extended abstract.

Detection of Mercury's Potassium Tail

NASA Astrophysics Data System (ADS)

Schmidt, Carl; Leblanc, Francois; Moore, Luke; Bida, Thomas A.

2017-10-01

Ground-based observations of Mercury's exosphere bridge the gap between the MESSENGER and BepiColombo missions and provide a broad counterpart to their in situ measurements. Here we report the first detection of Mercury's potassium tail in both emission lines of the D doublet. The sodium to potassium abundance ratio at 5 planetary radii down-tail is approximately 95, near the mid-point of a wide range of values that have been quoted over the planet's disk. This is several times the Na/K present in atmospheres of the Galilean satellites and more than an order of magnitude above Mercury's usual analogue, the Moon. The observations confirm that Mercury's anomalously high Na/K ratios cannot be explained by differences in neutral loss rates. The width and structure of the Na and K tails is comparable and both exhibit a persistent enhancement in their northern lobe. We interpret this as a signature of Mercury's offset magnetosphere; the exosphere's source rates are locally enhanced at the southern surface, and sloshing from radiation pressure and gravity guides this population into the northern region of the tail.

Effectiveness of various cover scenarios on the rate of sulfide oxidation of mine tailings

NASA Astrophysics Data System (ADS)

Romano, Connie G.; Ulrich Mayer, K.; Jones, David R.; Ellerbroek, David A.; Blowes, David W.

2003-02-01

Long term environmentally sound disposal of the millions of tons of mining residue is a serious challenge to the international mining industry. This paper evaluates, through a numerical investigation, the potential performance of desulfurized tailings as a cover material for the reduction of acidic drainage from sulfidic tailings. This evaluation is facilitated through a comparison of various cover types as decommissioning options. The cover types considered consist of a desulfurized tailings material cover exposed to ambient climate conditions, a water cover (flooded tailings), and a combination cover type. As part of the evaluation of cover performances, the effect of climatic variability on the potential rate of sulfide oxidation in tailings with an open ground surface, was also assessed. The numerical analysis was conducted using the model PYROX, which was modified to allow for variably-saturated conditions, time varying moisture contents, and to account for the temperature dependence of Henry's law and gas diffusion. In the case study presented here, the benign cover material consists of a low sulfide waste stream (cassiterite float tails, CFT), a by-product of the production of tin concentrate (cassiterite, SnO 2). Modelling results after a simulation period of 100 years indicate that a water cover alone or an exposed CFT cover alone are both less effective options than the combined cover type. A water cover alone leads to a reduction of approximately 99.1%, in the oxidation rate relative to uncovered tailings while the combined cover type results in the lowest potential extent of sulfide oxidation after mine closure-an approximately 99.8% reduction. Importantly, a CFT cover exposed to ambient environmental conditions can still substantially reduce the sulfide oxidation rate, by approximately 75-82% over a 100-year time period, relative to uncovered tailings. Variability in precipitation (and hence percent saturation of the surface layer) had less of an

Determining Phthalic Acid Esters Using Terahertz Time Domain Spectroscopy

NASA Astrophysics Data System (ADS)

Liu, L.; Shen, L.; Yang, F.; Han, F.; Hu, P.; Song, M.

2016-09-01

In this report terahertz time domain spectroscopy (THz-TDS) is applied for determining phthalic acid esters (PAEs) in standard materials. We reported the THz transmission spectrum in the frequency range of 0.2 to 2.0 THz for three PAEs: di-n-butyl phthalate (DBP), di-isononyl phthalate (DINP), and di-2-ethylhexyl phthalate ester (DEHP). The study provided the refractive indices and absorption features of these materials. The absorption spectra of three PAEs were simulated by using Gaussian software with Density Functional Theory (DFT) methods. For pure standard PAEs, the values of the refractive indices changed between 1.50 and 1.60. At 1.0 THz, the refractive indices were 1.524, 1.535, and 1.563 for DINP, DEHP, and DBP, respectively. In this experiment different concentrations of DBP were investigated using THz-TDS. Changes were measured in the low THz frequency range for refractive indices and characteristic absorption. The results indicated that THz-TDS is promising as a new method in determining PAEs in many materials. The results of this study could be used to support the practical application of THz-TDS in quality detection and food monitoring. In particular, this new technique could be used in detecting hazardous materials and other substances present in wine or foods.

DEFECTS IN CERVICAL VERTEBRAE IN BORIC ACID-EXPOSED RAT EMBRYOS ARE ASSOCIATED WITH ANTERIOR SHIFTS OF HOX GENE EXPRESSION DOMAINS

EPA Science Inventory

Defects in cervical vertebrae in boric acid-exposed rat embryos are associated with anterior shifts of hox gene expression domains

Nathalie Wery,1 Michael G. Narotsky,2 Nathalie Pacico,1 Robert J. Kavlock,2 Jacques J. Picard,1 AND Francoise Gofflot,1*
1Unit of Developme...

Black-tailed and white-tailed jackrabbits in the American West: History, ecology, ecological significance, and survey methods

USGS Publications Warehouse

Simes, Matthew; Longshore, Kathleen M.; Nussear, Kenneth E.; Beatty, Greg L.; Brown, David E.; Esque, Todd C.

2015-01-01

Across the western United States, Leporidae are the most important prey item in the diet of Golden Eagles (Aquila chrysaetos). Leporids inhabiting the western United States include black-tailed (Lepus californicus) and white-tailed jackrabbits (Lepus townsendii) and various species of cottontail rabbit (Sylvilagus spp.). Jackrabbits (Lepus spp.) are particularly important components of the ecological and economic landscape of western North America because their abundance influences the reproductive success and population trends of predators such as coyotes (Canis latrans), bobcats (Lynx rufus), and a number of raptor species. Here, we review literature pertaining to black-tailed and white-tailed jackrabbits comprising over 170 published journal articles, notes, technical reports, conference proceedings, academic theses and dissertations, and other sources dating from the late 19th century to the present. Our goal is to present information to assist those in research and management, particularly with regard to protected raptor species (e.g., Golden Eagles), mammalian predators, and ecological monitoring. We classified literature sources as (1) general information on jackrabbit species, (2) black-tailed or (3) white-tailed jackrabbit ecology and natural history, or (4) survey methods. These categories, especially 2, 3, and 4, were further subdivided as appropriate. The review also produced several tables on population trends, food habits, densities within various habitats, and jackrabbit growth and development. Black-tailed and white-tailed jackrabbits are ecologically similar in general behaviors, use of forms, parasites, and food habits, and they are prey to similar predators; but they differ in their preferred habitats. While the black-tailed jackrabbit inhabits agricultural land, deserts, and shrublands, the white-tailed jackrabbit is associated with prairies, alpine tundra, and sagebrush-steppe. Frequently considered abundant, jackrabbit numbers in western North

Speciation of mercury and mode of transport from placer gold mine tailings

USGS Publications Warehouse

Slowey, A.J.; Rytuba, J.J.; Brown, Gordon E.

2005-01-01

Historic placer gold mining in the Clear Creek tributary to the Sacramento River (Redding, CA) has highly impacted the hydrology and ecology of an important salmonid spawning stream. Restoration of the watershed utilized dredge tailings contaminated with mercury (Hg) introduced during gold mining, posing the possibility of persistent Hg release to the surrounding environment, including the San Francisco Bay Delta. Column experiments have been performed to evaluate the extent of Hg transport under chemical conditions potentially similar to those in river restoration projects utilizing dredge tailings such as at Clear Creek. Physicochemical perturbations, in the form of shifts in column influent ionic strength and the presence of a low molecular weight organic acid, were applied to coarse and fine sand placer tailings containing 109-194 and 69-90 ng of Hg/g, respectively. Significant concentrations of mercury, up to 16 ??g/L, leach from these sediments in dissolved and particle-associated forms. Sequential chemical extractions (SCE) of these tailings indicate that elemental Hg initially introduced during gold mining has been transformed to readily soluble species, such as mercury oxides and chlorides (3-4%), intermediately extractable phases that likely include (in)organic sorption complexes and amalgams (75-87%), and fractions of highly insoluble forms such as mercury sulfides (6-20%; e.g., cinnabar and metacinnabar). Extended X-ray absorption fine structure (EXAFS) spectroscopic analysis of colloids obtained from column effluent identified cinnabar particles as the dominant mobile mercury-bearing phase. The fraction of intermediately extractable Hg phases also likely includes mobile colloids to which Hg is adsorbed. ?? 2005 American Chemical Society.

An Evolutionarily Conserved Family of Virion Tail Needles Related to Bacteriophage P22 gp26: Correlation between Structural Stability and Length of the -Helical Trimeric Coiled Coil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhardwaj, A.; Walker-Kopp, N; Casjens, S

2009-01-01

Bacteriophages of the Podoviridae family use short noncontractile tails to inject their genetic material into Gram-negative bacteria. In phage P22, the tail contains a thin needle, encoded by the phage gene 26, which is essential both for stabilization and for ejection of the packaged viral genome. Bioinformatic analysis of the N-terminal domain of gp26 (residues 1-60) led us to identify a family of genes encoding putative homologues of the tail needle gp26. To validate this idea experimentally and to explore their diversity, we cloned the gp26-like gene from phages HK620, Sf6 and HS1, and characterized these gene products in solution.more » All gp26-like factors contain an elongated {alpha}-helical coiled-coil core consisting of repeating, adjacent trimerization heptads and form trimeric fibers with length ranging between about 240 to 300 {angstrom}. gp26 tail needles display a high level of structural stability in solution, with Tm (temperature of melting) between 85 and 95 C. To determine how the structural stability of these phage fibers correlates with the length of the {alpha}-helical core, we investigated the effect of insertions and deletions in the helical core. In the P22 tail needle, we identified an 85-residue-long helical domain, termed MiCRU (minimal coiled-coil repeat unit), that can be inserted in-frame inside the gp26 helical core, preserving the straight morphology of the fiber. Likewise, we were able to remove three quarters of the helical core of the HS1 tail needle, minimally decreasing the stability of the fiber. We conclude that in the gp26 family of tail needles, structural stability increases nonlinearly with the length of the {alpha}-helical core. Thus, the overall stability of these bacteriophage fibers is not solely dependent on the number of trimerization repeats in the {alpha}-helical core.« less

Uranium association with iron-bearing phases in mill tailings from Gunnar, Canada.

PubMed

Othmane, Guillaume; Allard, Thierry; Morin, Guillaume; Sélo, Madeleine; Brest, Jessica; Llorens, Isabelle; Chen, Ning; Bargar, John R; Fayek, Mostafa; Calas, Georges

2013-11-19

The speciation of uranium was studied in the mill tailings of the Gunnar uranium mine (Saskatchewan, Canada), which operated in the 1950s and 1960s. The nature, quantification, and spatial distribution of uranium-bearing phases were investigated by chemical and mineralogical analyses, fission track mapping, electron microscopy, and X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectroscopies at the U LIII-edge and Fe K-edge. In addition to uranium-containing phases from the ore, uranium is mostly associated with iron-bearing minerals in all tailing sites. XANES and EXAFS data and transmission electron microscopy analyses of the samples with the highest uranium concentrations (∼400-700 mg kg(-1) of U) demonstrate that uranium primarily occurs as monomeric uranyl ions (UO2(2+)), forming inner-sphere surface complexes bound to ferrihydrite (50-70% of the total U) and to a lesser extent to chlorite (30-40% of the total U). Thus, the stability and mobility of uranium at the Gunnar site are mainly influenced by sorption/desorption processes. In this context, acidic pH or alkaline pH with the presence of UO2(2+)- and/or Fe(3+)-complexing agents (e.g., carbonate) could potentially solubilize U in the tailings pore waters.

Heavy Tail Behavior of Rainfall Extremes across Germany

NASA Astrophysics Data System (ADS)

Castellarin, A.; Kreibich, H.; Vorogushyn, S.; Merz, B.

2017-12-01

Distributions are termed heavy-tailed if extreme values are more likely than would be predicted by probability distributions that have exponential asymptotic behavior. Heavy-tail behavior often leads to surprise, because historical observations can be a poor guide for the future. Heavy-tail behavior seems to be widespread for hydro-meteorological extremes, such as extreme rainfall and flood events. To date there have been only vague hints to explain under which conditions these extremes show heavy-tail behavior. We use an observational data set consisting of 11 climate variables at 1440 stations across Germany. This homogenized, gap-free data set covers 110 years (1901-2010) at daily resolution. We estimate the upper tail behavior, including its uncertainty interval, of daily precipitation extremes for the 1,440 stations at the annual and seasonal time scales. Different tail indicators are tested, including the shape parameter of the Generalized Extreme Value distribution, the upper tail ratio and the obesity index. In a further step, we explore to which extent the tail behavior can be explained by geographical and climate factors. A large number of characteristics is derived, such as station elevation, degree of continentality, aridity, measures for quantifying the variability of humidity and wind velocity, or event-triggering large-scale atmospheric situation. The link between the upper tail behavior and these characteristics is investigated via data mining methods capable of detecting non-linear relationships in large data sets. This exceptionally rich observational data set, in terms of number of stations, length of time series and number of explaining variables, allows insights into the upper tail behavior which is rarely possible given the typical observational data sets available.

Structure of the extracellular domains of the human interleukin-6 receptor α-chain

PubMed Central

Varghese, J. N.; Moritz, R. L.; Lou, M.-Z.; van Donkelaar, A.; Ji, H.; Ivancic, N.; Branson, K. M.; Hall, N. E.; Simpson, R. J.

2002-01-01

Dysregulated production of IL-6 and its receptor (IL-6R) are implicated in the pathogenesis of multiple myeloma, autoimmune diseases and prostate cancer. The IL-6R complex comprises two molecules each of IL-6, IL-6R, and the signaling molecule, gp130. Here, we report the x-ray structure (2.4 Å) of the IL-6R ectodomains. The N-terminal strand of the Ig-like domain (D1) is disulfide-bonded to domain D2, and domains D2 and D3, the cytokine-binding domain, are structurally similar to known cytokine-binding domains. The head-to-tail packing of two closely associated IL-6R molecules observed in the crystal may be representative of the configuration of the physiological dimer of IL-6R and provides new insight into the architecture of the IL-6R complex. PMID:12461182

Quasi-steady state aerodynamics of the cheetah tail.

PubMed

Patel, Amir; Boje, Edward; Fisher, Callen; Louis, Leeann; Lane, Emily

2016-08-15

During high-speed pursuit of prey, the cheetah (Acinonyx jubatus) has been observed to swing its tail while manoeuvring (e.g. turning or braking) but the effect of these complex motions is not well understood. This study demonstrates the potential of the cheetah's long, furry tail to impart torques and forces on the body as a result of aerodynamic effects, in addition to the well-known inertial effects. The first-order aerodynamic forces on the tail are quantified through wind tunnel testing and it is observed that the fur nearly doubles the effective frontal area of the tail without much mass penalty. Simple dynamic models provide insight into manoeuvrability via simulation of pitch, roll and yaw tail motion primitives. The inertial and quasi-steady state aerodynamic effects of tail actuation are quantified and compared by calculating the angular impulse imparted onto the cheetah's body and its shown aerodynamic effects contribute to the tail's angular impulse, especially at the highest forward velocities. © 2016. Published by The Company of Biologists Ltd.

Numeral series hidden in the distribution of atomic mass of amino acids to codon domains in the genetic code.

PubMed

Wohlin, Åsa

2015-03-21

The distribution of codons in the nearly universal genetic code is a long discussed issue. At the atomic level, the numeral series 2x(2) (x=5-0) lies behind electron shells and orbitals. Numeral series appear in formulas for spectral lines of hydrogen. The question here was if some similar scheme could be found in the genetic code. A table of 24 codons was constructed (synonyms counted as one) for 20 amino acids, four of which have two different codons. An atomic mass analysis was performed, built on common isotopes. It was found that a numeral series 5 to 0 with exponent 2/3 times 10(2) revealed detailed congruency with codon-grouped amino acid side-chains, simultaneously with the division on atom kinds, further with main 3rd base groups, backbone chains and with codon-grouped amino acids in relation to their origin from glycolysis or the citrate cycle. Hence, it is proposed that this series in a dynamic way may have guided the selection of amino acids into codon domains. Series with simpler exponents also showed noteworthy correlations with the atomic mass distribution on main codon domains; especially the 2x(2)-series times a factor 16 appeared as a conceivable underlying level, both for the atomic mass and charge distribution. Furthermore, it was found that atomic mass transformations between numeral systems, possibly interpretable as dimension degree steps, connected the atomic mass of codon bases with codon-grouped amino acids and with the exponent 2/3-series in several astonishing ways. Thus, it is suggested that they may be part of a deeper reference system. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

Identification of amino acids in the transmembrane and juxtamembrane domains of the platelet-derived growth factor receptor required for productive interaction with the bovine papillomavirus E5 protein.

PubMed

Petti, L M; Reddy, V; Smith, S O; DiMaio, D

1997-10-01

The bovine papillomavirus E5 protein forms a stable complex with the cellular platelet-derived growth factor (PDGF) beta receptor, resulting in receptor activation and cell transformation. Amino acids in both the putative transmembrane domain and extracytoplasmic carboxyl-terminal domain of the E5 protein appear important for PDGF receptor binding and activation. Previous analysis indicated that the transmembrane domain of the receptor was also required for complex formation and receptor activation. Here we analyzed receptor chimeras and point mutants to identify specific amino acids in the PDGF beta receptor required for productive interaction with the E5 protein. These receptor mutants were analyzed in murine Ba/F3 cells, which do not express endogenous receptor. Our results confirmed the importance of the transmembrane domain of the receptor for complex formation, receptor tyrosine phosphorylation, and mitogenic signaling in response to the E5 protein and established that the threonine residue in this domain is required for these activities. In addition, a positive charge in the extracellular juxtamembrane domain of the receptor was required for E5 interaction and signaling, whereas replacement of the wild-type lysine with either a neutral or acidic amino acid inhibited E5-induced receptor activation and transformation. All of the receptor mutants defective for activation by the E5 protein responded to acute treatment with PDGF and to stable expression of v-Sis, a form of PDGF. The required juxtamembrane lysine and transmembrane threonine are predicted to align precisely on the same face of an alpha helix packed in a left-handed coiled-coil geometry. These results establish that the E5 protein and v-Sis recognize distinct binding sites on the PDGF beta receptor and further clarify the nature of the interaction between the viral transforming protein and its cellular target.

Structured Post-IQ Domain Governs Selectivity of Myosin X for Fascin-Actin Bundles*

PubMed Central

Nagy, Stanislav; Rock, Ronald S.

2010-01-01

Without guidance cues, cytoskeletal motors would traffic components to the wrong destination with disastrous consequences for the cell. Recently, we identified a motor protein, myosin X, that identifies bundled actin filaments for transport. These bundles direct myosin X to a unique destination, the tips of cellular filopodia. Because the structural and kinetic features that drive bundle selection are unknown, we employed a domain-swapping approach with the nonselective myosin V to identify the selectivity module of myosin X. We found a surprising role of the myosin X tail region (post-IQ) in supporting long runs on bundles. Moreover, the myosin X head is adapted for initiating processive runs on bundles. We found that the tail is structured and biases the orientation of the two myosin X heads because a targeted insertion that introduces flexibility in the tail abolishes selectivity. Together, these results suggest how myosin motors may manage to read cellular addresses. PMID:20538587

Physicochemical and mineralogical characterization of Musina mine copper and New Union gold mine tailings: Implications for fabrication of beneficial geopolymeric construction materials

NASA Astrophysics Data System (ADS)

Gitari, M. W.; Akinyemi, S. A.; Thobakgale, R.; Ngoejana, P. C.; Ramugondo, L.; Matidza, M.; Mhlongo, S. E.; Dacosta, F. A.; Nemapate, N.

2018-01-01

The mining industries in South Africa generates huge amounts of mine waste that includes tailings; waste rocks and spoils. The tailings materials are dumped in surface impoundments that turn to be sources of hazards to the environment and the surrounding communities. The main environmental hazards posed by these tailings facilities are associated with their chemical constituents. Exposure to chemical constituents can occur through windblown dust, erosion to surface water bodies, inhalation by human beings and animals and through bioaccumulation and bio magnification by plants. Numerous un-rehabilitated tailings dumps exist in Limpopo province of South Africa. The communities found around these mines are constantly exposed to the environmental hazards posed by these tailing facilities. Development of a cost-effective technology that can beneficially utilize these tailings can reduce the environmental hazards and benefit the communities. This paper presents the initial evaluation of the copper and gold mine tailings in Limpopo, South Africa with a view to assessing the suitability of conversion into beneficial geopolymeric materials. Copper tailings leachates had alkaline pH (7.34-8.49) while the gold tailings had acidic pH. XRD confirmed presence of aluminosilicate minerals. Geochemical fractionation indicates that majority of the major and trace species are present in residual fraction. A significant amount of Ca, Cu and K was available in the mobile fraction and is expected to be released on tailings contacting aqueous solutions. Results from XRF indicates the tailings are rich in SiO2, Al2O3 and CaO which are the main ingredients in geopolymerization process. The SiO2/Al2O3 ratios indicates the tailings would require blending with Al2O3 rich feedstock for them to develop maximum strength. Moreover, the tailings have particle size in the range of fine sand which indicates potential application as aggregates in conventional brick manufacture.

The Sodium Tail of the Moon

NASA Technical Reports Server (NTRS)

Matta, M.; Smith, S.; Baumgardner, J.; Wilson, J.; Martinis, C.; Mendillo, M.

2009-01-01

During the few days centered about new Moon, the lunar surface is optically hidden from Earth-based observers. However, the Moon still offers an observable: an extended sodium tail. The lunar sodium tail is the escaping "hot" component of a coma-like exosphere of sodium generated by photon-stimulated desorption, solar wind sputtering and meteoroid impact. Neutral sodium atoms escaping lunar gravity experience solar radiation pressure that drives them into the anti-solar direction forming a comet-like tail. During new Moon time, the geometry of the Sun, Moon and Earth is such that the anti-sunward sodium flux is perturbed by the terrestrial gravitational field resulting in its focusing into a dense core that extends beyond the Earth. An all-sky camera situated at the El Leoncito Observatory (CASLEO) in Argentina has been successfully imaging this tail through a sodium filter at each lunation since April 2006. This paper reports on the results of the brightness of the lunar sodium tail spanning 31 lunations between April 2006 and September 2008. Brightness variability trends are compared with both sporadic and shower meteor activity, solar wind proton energy flux and solar near ultra violet (NUV) patterns for possible correlations. Results suggest minimal variability in the brightness of the observed lunar sodium tail, generally uncorrelated with any single source, yet consistent with a multi-year period of minimal solar activity and non-intense meteoric fluxes.

Identification and functional characterization of the Arabidopsis Snf1-related protein kinase SnRK2.4 phosphatidic acid-binding domain.

PubMed

Julkowska, Magdalena M; McLoughlin, Fionn; Galvan-Ampudia, Carlos S; Rankenberg, Johanna M; Kawa, Dorota; Klimecka, Maria; Haring, Michel A; Munnik, Teun; Kooijman, Edgar E; Testerink, Christa

2015-03-01

Phosphatidic acid (PA) is an important signalling lipid involved in various stress-induced signalling cascades. Two SnRK2 protein kinases (SnRK2.4 and SnRK2.10), previously identified as PA-binding proteins, are shown here to prefer binding to PA over other anionic phospholipids and to associate with cellular membranes in response to salt stress in Arabidopsis roots. A 42 amino acid sequence was identified as the primary PA-binding domain (PABD) of SnRK2.4. Unlike the full-length SnRK2.4, neither the PABD-YFP fusion protein nor the SnRK2.10 re-localized into punctate structures upon salt stress treatment, showing that additional domains of the SnRK2.4 protein are required for its re-localization during salt stress. Within the PABD, five basic amino acids, conserved in class 1 SnRK2s, were found to be necessary for PA binding. Remarkably, plants overexpressing the PABD, but not a non-PA-binding mutant version, showed a severe reduction in root growth. Together, this study biochemically characterizes the PA-SnRK2.4 interaction and shows that functionality of the SnRK2.4 PABD affects root development. © 2014 The Authors. Plant, Cell & Environment published by John Wiley & Sons Ltd.

Physical space and long-tail markets

NASA Astrophysics Data System (ADS)

Bentley, R. Alexander; Madsen, Mark E.; Ormerod, Paul

2009-03-01

The Internet is known to have had a powerful impact on on-line retailer strategies in markets characterised by long-tail distribution of sales [C. Anderson, Long Tail: Why the Future of Business is Selling Less of More, Hyperion, New York, 2006]. Such retailers can exploit the long tail of the market, since they are effectively without physical limit on the number of choices on offer. Here we examine two extensions of this phenomenon. First, we introduce turnover into the long-tail distribution of sales. Although over any given period such as a week or a month, the distribution is right-skewed and often power law distributed, over time there is considerable turnover in the rankings of sales of individual products. Second, we establish some initial results on the implications for shelf-space and physical retailers in such markets.

Cellular abundance of Mps1 and the role of its carboxyl terminal tail in substrate recruitment.

PubMed

Sun, Tingting; Yang, Xiaomei; Wang, Wei; Zhang, Xiaojuan; Xu, Quanbin; Zhu, Songcheng; Kuchta, Robert; Chen, Guanjun; Liu, Xuedong

2010-12-03

Mps1 is a protein kinase that regulates normal mitotic progression and the spindle checkpoint in response to spindle damage. The levels of Mps1 are relatively low in cells during interphase but elevated in mitosis or upon activation of the spindle checkpoint, although the dynamic range of Mps1 expression and the Mps1 catalytic mechanism have not been carefully characterized. Our recent structural studies of the Mps1 kinase domain revealed that the carboxyl-terminal tail region of Mps1 is unstructured, raising the question of whether this region has any functional role in Mps1 catalysis. Here we first determined the cellular abundance of Mps1 during cell cycle progression and found that Mps1 levels vary between 60,000 per cell in early G(1) and 110,000 per cell during mitosis. We studied phosphorylation of a number of Mps1 substrates in vitro and in culture cells. Unexpectedly, we found that the unstructured carboxyl-terminal region of Mps1 plays an essential role in substrate recruitment. Kinetics studies using the purified recombinant wild type and mutant kinases indicate that the carboxyl-terminal tail is largely dispensable for autophosphorylation of Mps1 but critical for trans-phosphorylation of substrates in vitro and in cultured cells. Mps1 mutant without the unstructured tail region is defective in mediating spindle assembly checkpoint activation. Our results underscore the importance of the unstructured tail region of Mps1 in kinase activation.

Interkinase domain of kit contains the binding site for phosphatidylinositol 3' kinase.

PubMed Central

Lev, S; Givol, D; Yarden, Y

1992-01-01

Our previous analysis of the signal transduction pathway used by the c-kit-encoded receptor for the stem cell factor (SCF) indicated efficient coupling to the type I phosphatidylinositol 3' kinase (PI3K). In an attempt to localize the receptor's site of interaction with PI3K, we separately deleted either the noncatalytic 68-amino-acid-long interkinase domain or the carboxyl-terminal portion distal to the catalytic sequences. Loss of ligand-induced association of PI3K with the former deletion mutant and retention of the PI3K association by the carboxyl-terminally deleted receptor implied interactions of PI3K with the kinase insert. This was further supported by partial inhibition of the association by an anti-peptide antibody directed against the kinase insert and lack of effect of an antibody directed to the carboxyl tail of the SCF receptor. A bacterially expressed kinase insert domain was used as a fusion protein to directly test its presumed function as a PI3K association site. This protein bound PI3K from cell lysate as demonstrated by PI3K activity and by an associated phosphoprotein of 85 kDa. The association was dependent on phosphorylation of the tyrosine residues on the expressed kinase insert. On the basis of these observations, we conclude that the kinase insert domain of the SCF receptor selectively interacts with the p85 regulatory subunit of PI3K and that this association requires phosphorylation of tyrosine residues in the kinase insert region, with apparently no involvement of the bulk cytoplasmic structure or tyrosine kinase function of the receptor. Images PMID:1370584

Functional and structural analysis of the sialic acid-binding domain of rotaviruses.

PubMed Central

Isa, P; López, S; Segovia, L; Arias, C F

1997-01-01

The infectivity of most animal rotaviruses is dependent on the interaction of the virus spike protein VP4 with a sialic acid (SA)-containing cell receptor, and the SA-binding domain of this protein has been mapped between amino acids 93 and 208 of its trypsin cleavage fragment VP8. To identify which residues in this region are essential for the SA-binding activity, we performed alanine mutagenesis of the rotavirus RRV VP8 expressed in bacteria as a fusion polypeptide with glutathione S-transferase. Tyrosines were primarily targeted since tyrosine has been involved in the interaction of other viral hemagglutinins with SA. Of the 15 substitutions carried out, 10 abolished the SA-dependent hemagglutination activity of the protein, as well as its ability to bind to glycophorin A in a solid-phase assay. However, only alanine substitutions for tyrosines 155 and 188 and for serine 190 did not affect the overall conformation of the protein, as judged by their interaction with a panel of conformationally sensitive neutralizing VP8 monoclonal antibodies (MAbs). These findings suggest that these three amino acids play an essential role in the SA-binding activity of the protein, presumably by interacting directly with the SA molecule. The predicted secondary structure of VP8 suggests that it is organized as 11 beta-strands separated by loops; in this model, Tyr-155 maps to loop 7 while Tyr-188 and Ser-190 map to loop 9. The close proximity of these two loops is also supported by previous results from competition experiments with neutralizing MAbs directed at RRV VP8. PMID:9261399

The closed MTIP-MyosinA-tail complex from the malaria parasite invasion machinery

PubMed Central

Bosch, Jürgen; Turley, Stewart; Roach, Claudia M.; Daly, Thomas M.; Bergman, Lawrence W.; Hol, Wim G. J.

2009-01-01

The Myosin A-tail Interacting Protein (MTIP) of the malaria parasite links the actomyosin motor of the host cell invasion machinery to its inner membrane complex. We report here that at neutral pH Plasmodium falciparum MTIP in complex with Myosin A adopts a compact conformation, with its two domains completely surrounding the Myosin A-tail helix, dramatically different from previously observed extended MTIP structures. Crystallographic and mutagenesis studies show that H810 and K813 of Myosin A are key players in the formation of the compact MTIP:Myosin A complex. Only the unprotonated state of Myosin A-H810 is compatible with the compact complex. Most surprisingly, every side chain atom of Myosin A-K813 is engaged in contacts with MTIP. While this side chain was previously considered to prevent a compact conformation of MTIP with Myosin A, it actually appears to be essential for the formation of the compact complex. The hydrophobic pockets and adaptability seen in the available series of MTIP structures bodes well for the discovery of inhibitors of cell invasion by malaria parasites. PMID:17628590

Domain wall structure and interactions in 50 nm wide Cobalt nanowires

NASA Astrophysics Data System (ADS)

Tu, Kun-Hua; Ojha, Shuchi; Ross, Caroline A.

2018-05-01

Arrays of cobalt nanowires with widths of 50 nm, thickness of 5 and 20 nm and periodicity of 70 nm were fabricated by pattern transfer from a self-assembled block copolymer film. Transverse domain walls (DWs) were imaged by magnetic force microscopy, indicating repulsive interactions between DWs of the same sign in the 20 nm thick wires. Micromagnetic simulations were used to identify the interactions in the six distinct cases of a pair of transverse DWs in adjacent wires, considering all the possible combinations of head-to-head and tail-to-tail DWs and the orientation of the core magnetization. The boundary between repulsive and attractive DW interactions is mapped out for wires as a function of thickness, width and interwire spacing.

Metal mobilization under alkaline conditions in ash-covered tailings.

PubMed

Lu, Jinmei; Alakangas, Lena; Wanhainen, Christina

2014-06-15

The aim of this study was to determine element mobilization and accumulation in mill tailings under alkaline conditions. The tailings were covered with 50 cm of fly ash, and above a sludge layer. The tailings were geochemically and mineralogically investigated. Sulfides, such as pyrrhotite, sphalerite and galena along with gangue minerals such as dolomite, calcite, micas, chlorite, epidote, Mn-pyroxene and rhodonite were identified in the unoxidized tailings. The dissolution of the fly ash layer resulted in a high pH (close to 12) in the underlying tailings. This, together with the presence of organic matter, increased the weathering of the tailings and mobilization of elements in the uppermost 47 cm of the tailings. All primary minerals were depleted, except quartz and feldspar which were covered by blurry secondary carbonates. Sulfide-associated elements such as Cd, Fe, Pb, S and Zn and silicate-associated elements such as Fe, Mg and Mn were released from the depletion zone and accumulated deeper down in the tailings where the pH decreased to circum-neutral. Sequential extraction suggests that Cd, Cu, Fe, Pb, S and Zn were retained deeper down in the tailings and were mainly associated with the sulfide phase. Calcium, Cr, K and Ni released from the ash layer were accumulated in the uppermost depletion zone of the tailings. Copyright © 2014 Elsevier Ltd. All rights reserved.

Potential of Cassia alata L. Coupled with Biochar for Heavy Metal Stabilization in Multi-Metal Mine Tailings.

PubMed

Huang, Lige; Li, Yuanyuan; Zhao, Man; Chao, Yuanqing; Qiu, Rongliang; Yang, Yanhua; Wang, Shizhong

2018-03-12

To explore the effect of different biochars on Cassia alata L. growth and heavy metal immobilization in multi-metal mine tailings, a 100-day pot experiment was conducted. Three biochars derived from Hibiscus cannabinus core (HB), sewage sludge (SB) and chicken manure (MB), were added to mine tailings at rates of 0.4%, 1% and 3% ( w / w ). The results showed that the root biomass, shoot biomass, plant height and root length were 1.2-2.8, 1.7-3.2, 1-1.5 and 1.6-3.3 times of those in the control group, respectively. Pb, Zn, Cu, Cd and As contents in the shoot decreased by 63.9-89.5%, 46.9-66.0%, 32.7-62.4%, 40.4-76.4% and 54.9-77.5%, respectively. The biochar significantly increased the pH and decreased the mild acid-soluble Pb and Cu concentrations in the mine tailings. Specifically, SB immobilized Pb and Cu better than MB and HB did, although it did not immobilize As, Zn or Cd. Meanwhile, more attention should be paid to the potential As release as the biochar application rate increases. In conclusion, Cassia alata L. coupled with 3% of SB could be an effective measure for restoring multi-metal mine tailings. This study herein provided a promising ecological restoration technique for future practice of heavy metal stabilization in mine tailings.

The central domain of bovine submaxillary mucin consists of over 50 tandem repeats of 329 amino acids. Chromosomal localization of the BSM1 gene and relations to ovine and porcine counterparts.

PubMed

Jiang, W; Gupta, D; Gallagher, D; Davis, S; Bhavanandan, V P

2000-04-01

We previously elucidated five distinct protein domains (I-V) for bovine submaxillary mucin, which is encoded by two genes, BSM1 and BSM2. Using Southern blot analysis, genomic cloning and sequencing of the BSM1 gene, we now show that the central domain (V) consists of approximately 55 tandem repeats of 329 amino acids and that domains III-V are encoded by a 58.4-kb exon, the largest exon known for all genes to date. The BSM1 gene was mapped by fluorescence in situ hybridization to the proximal half of chromosome 5 at bands q2. 2-q2.3. The amino-acid sequence of six tandem repeats (two full and four partial) were found to have only 92-94% identities. We propose that the variability in the amino-acid sequences of the mucin tandem repeat is important for generating the combinatorial library of saccharides that are necessary for the protective function of mucins. The deduced peptide sequences of the central domain match those determined from the purified bovine submaxillary mucin and also show 68-94% identity to published peptide sequences of ovine submaxillary mucin. This indicates that the core protein of ovine submaxillary mucin is closely related to that of bovine submaxillary mucin and contains similar tandem repeats in the central domain. In contrast, the central domain of porcine submaxillary mucin is reported to consist of 81-amino-acid tandem repeats. However, both bovine submaxillary mucin and porcine submaxillary mucin contain similar N-terminal and C-terminal domains and the corresponding genes are in the conserved linkage regions of the respective genomes.

Characterization of the interactions between the nucleoprotein and the phosphoprotein of Henipavirus.

PubMed

Habchi, Johnny; Blangy, Stéphanie; Mamelli, Laurent; Jensen, Malene Ringkjøbing; Blackledge, Martin; Darbon, Hervé; Oglesbee, Michael; Shu, Yaoling; Longhi, Sonia

2011-04-15

The Henipavirus genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that recruits the polymerase complex via the phosphoprotein (P). In a previous study, we reported that in henipaviruses, the N-terminal domain of the phosphoprotein and the C-terminal domain of the nucleoprotein (N(TAIL)) are both intrinsically disordered. Here we show that Henipavirus N(TAIL) domains are also disordered in the context of full-length nucleoproteins. We also report the cloning, purification, and characterization of the C-terminal X domains (P(XD)) of Henipavirus phosphoproteins. Using isothermal titration calorimetry, we show that N(TAIL) and P(XD) form a 1:1 stoichiometric complex that is stable under NaCl concentrations as high as 1 M and has a K(D) in the μM range. Using far-UV circular dichroism and nuclear magnetic resonance, we show that P(XD) triggers an increase in the α-helical content of N(TAIL). Using fluorescence spectroscopy, we show that P(XD) has no impact on the chemical environment of a Trp residue introduced at position 527 of the Henipavirus N(TAIL) domain, thus arguing for the lack of stable contacts between the C termini of N(TAIL) and P(XD). Finally, we present a tentative structural model of the N(TAIL)-P(XD) interaction in which a short, order-prone region of N(TAIL) (α-MoRE; amino acids 473-493) adopts an α-helical conformation and is embedded between helices α2 and α3 of P(XD), leading to a relatively small interface dominated by hydrophobic contacts. The present results provide the first detailed experimental characterization of the N-P interaction in henipaviruses and designate the N(TAIL)-P(XD) interaction as a valuable target for rational antiviral approaches.

Vertical Tail Buffeting Alleviation Using Piezoelectric Actuators-Some Results of the Actively Controlled Response of Buffet-Affected Tails (ACROBAT) Program

NASA Technical Reports Server (NTRS)

Moses, Robert W.

1997-01-01

Buffet is an aeroelastic phenomenon associated with high performance aircraft especially those with twin vertical tails. In particular, for the F/A-18 aircraft at high angles of attack, vortices emanating from wing/fuselage leading edge extensions burst, immersing the vertical tails in their wake. The resulting buffet loads on the vertical tails are a concern from fatigue and inspection points of view. Recently, a 1/6-scale F-18 wind-tunnel model was tested in the Transonic Dynamics Tunnel at the NASA Langley Research Center as part of the Actively Controlled Response Of Buffet Affected Tails (ACROBAT) Program to assess the use of active controls in reducing vertical tail buffeting. The starboard vertical tail was equipped with an active rudder and the port vertical tail was equipped with piezoelectric actuators. The tunnel conditions were atmospheric air at Mach 0.10. By using single-input-single-output control laws at gains well below the physical limits of the actuators, the power spectral density of the root strains at the frequency of the first bending mode of the vertical tail was reduced by as much as 60 percent up to angles of attack of 37 degrees. Root mean square (RMS) values of root strain were reduced by as much as 19 percent. The results herein illustrate that buffet alleviation of vertical tails can be accomplished using simple active control of the rudder or piezoelectric actuators. In fact, as demonstrated herein, a fixed gain single input single output control law that commands piezoelectric actuators may be active throughout the high angle-of-attack maneuver without requiring any changes during the maneuver. Future tests are mentioned for accentuating the international interest in this area of research.

Mutations in the Transmembrane Domain and Cytoplasmic Tail of Hendra Virus Fusion Protein Disrupt Virus-Like-Particle Assembly.

PubMed

Cifuentes-Muñoz, Nicolás; Sun, Weina; Ray, Greeshma; Schmitt, Phuong Tieu; Webb, Stacy; Gibson, Kathleen; Dutch, Rebecca Ellis; Schmitt, Anthony P

2017-07-15

Hendra virus (HeV) is a zoonotic paramyxovirus that causes deadly illness in horses and humans. An intriguing feature of HeV is the utilization of endosomal protease for activation of the viral fusion protein (F). Here we investigated how endosomal F trafficking affects HeV assembly. We found that the HeV matrix (M) and F proteins each induced particle release when they were expressed alone but that their coexpression led to coordinated assembly of virus-like particles (VLPs) that were morphologically and physically distinct from M-only or F-only VLPs. Mutations to the F protein transmembrane domain or cytoplasmic tail that disrupted endocytic trafficking led to failure of F to function with M for VLP assembly. Wild-type F functioned normally for VLP assembly even when its cleavage was prevented with a cathepsin inhibitor, indicating that it is endocytic F trafficking that is important for VLP assembly, not proteolytic F cleavage. Under specific conditions of reduced M expression, we found that M could no longer induce significant VLP release but retained the ability to be incorporated as a passenger into F-driven VLPs, provided that the F protein was competent for endocytic trafficking. The F and M proteins were both found to traffic through Rab11-positive recycling endosomes (REs), suggesting a model in which F and M trafficking pathways converge at REs, enabling these proteins to preassemble before arriving at plasma membrane budding sites. IMPORTANCE Hendra virus and Nipah virus are zoonotic paramyxoviruses that cause lethal infections in humans. Unlike that for most paramyxoviruses, activation of the henipavirus fusion protein occurs in recycling endosomal compartments. In this study, we demonstrate that the unique endocytic trafficking pathway of Hendra virus F protein is required for proper viral assembly and particle release. These results advance our basic understanding of the henipavirus assembly process and provide a novel model for the interplay between

Clinical and histologic description of ocular anatomy in captive black-tailed prairie dogs (Cynomys ludovicianus).

PubMed