Beta Region Research Articles

Magnetosheath plasma expansion: Hybrid simulations

We investigate the effect of slow expansion on a magnetosheath plasma and low‐frequency waves using a two‐dimensional hybrid expanding box simulation. We start our simulation with a homogeneous high beta plasma, which is marginally stable to the mirror and proton cyclotron instabilities. The expansion is imposed as an external force: the physical size of the simulation box increases in two dimensions: one parallel and one perpendicular with respect to the ambient magnetic field. This expansion leads to a continuous decrease of proton beta and drives an increase of the proton temperature anisotropy. In the early stages of the simulation, both mirror and proton cyclotron waves appear. The system establishes a marginally stable state with respect to both mirror and proton cyclotron instabilities. Initially, the mirror waves dominate the proton cyclotron waves, even when the system is below the linear mirror threshold, but as time increases the proton cyclotron waves become dominant in the low beta region. We also include an initial comparison of the simulated data with Cluster observations.

Platelet integrin alpha(IIb)beta(3): activation mechanisms.

Integrin alpha(IIb)beta(3) plays a critical role in platelet aggregation, a central response in hemostasis and thrombosis. This function of alpha(IIb)beta(3) depends upon a transition from a resting to an activated state such that it acquires the capacity to bind soluble ligands. Diverse platelet agonists alter the cytoplasmic domain of alpha(IIb)beta(3) and initiate a conformational change that traverses the transmembrane region and ultimately triggers rearrangements in the extracellular domain to permit ligand binding. The membrane-proximal regions of alpha(IIb) and beta(3) cytoplasmic tails, together with the transmembrane segments of the subunits, contact each other to form a complex which restrains the integrin in the resting state. It is unclasping of this complex that induces integrin activation. This clasping/unclasping process is influenced by multiple cytoplasmic tail binding partners. Among them, talin appears to be a critical trigger of alpha(IIb)beta(3) activation, but other binding partners, which function as activators or suppressors, are likely to act as co-regulators of integrin activation.

Structural Basis of the Catalytic Reaction Mechanism of Novel 1,2-α-L-Fucosidase from Bifidobacterium bifidum

1,2-alpha-L-fucosidase (AfcA), which hydrolyzes the glycosidic linkage of Fucalpha1-2Gal via an inverting mechanism, was recently isolated from Bifidobacterium bifidum and classified as the first member of the novel glycoside hydrolase family 95. To better understand the molecular mechanism of this enzyme, we determined the x-ray crystal structures of the AfcA catalytic (Fuc) domain in unliganded and complexed forms with deoxyfuconojirimycin (inhibitor), 2'-fucosyllactose (substrate), and L-fucose and lactose (products) at 1.12-2.10 A resolution. The AfcA Fuc domain is composed of four regions, an N-terminal beta region, a helical linker, an (alpha/alpha)6 helical barrel domain, and a C-terminal beta region, and this arrangement is similar to bacterial phosphorylases. In the complex structures, the ligands were buried in the central cavity of the helical barrel domain. Structural analyses in combination with mutational experiments revealed that the highly conserved Glu566 probably acts as a general acid catalyst. However, no carboxylic acid residue is found at the appropriate position for a general base catalyst. Instead, a water molecule stabilized by Asn423 in the substrate-bound complex is suitably located to perform a nucleophilic attack on the C1 atom of L-fucose moiety in 2'-fucosyllactose, and its location is nearly identical near the O1 atom of beta-L-fucose in the products-bound complex. Based on these data, we propose and discuss a novel catalytic reaction mechanism of AfcA.

Ring current at Saturn: Energetic particle pressure in Saturn's equatorial magnetosphere measured with Cassini/MIMI

The Magnetospheric Imaging Instrument (MIMI) on the Cassini spacecraft provides measurements of the energetic ion population within the magnetosphere of Saturn. Energetic ion directional intensities, energy spectra and ion composition, are measured by the Charge Energy Mass Spectrometer (CHEMS) over the range ∼3 to 236 keV per charge and by the Low Energy Magnetospheric Measurements System (LEMMS) for ions in the range 0.024 < E < 18 MeV. This work reports preliminary results of partial particle pressure distributions throughout the equatorial magnetosphere and comparison with in situ measurements of the magnetic pressure provided by Cassini's magnetometer. The results cover 11 passes from late 2005 to early 2006, when the spacecraft was particularly close to the nominal magnetic equator in the range 5 < R < 20 RS and can be summarized as follows: (1) the plasma β (particle pressure/magnetic pressure) profile increases radially outward to maximum values of ≥ 1 at L >10 RS; (2) most particle pressure is contained in the range of 10 < E < 150 keV; and (3) in the high beta region 10 < L < 19, where the apparent ring current resides, oxygen generally contributes more than 50% of the total particle pressure. The results demonstrate that typical assumptions of MHD models, whereby particle pressure is presumed to reside with the cold plasma, are not supported by the data.

Electrostatic screening and backbone preferences of amino acid residues in urea‐denatured ubiquitin

Local structures in denatured proteins may be important in guiding a polypeptide chain during the folding and misfolding processes. Existence of local structures in chemically denatured proteins is a highly controversial issue. NMR parameters [coupling constants (3) J(H(alpha),H(N)) and chemical shifts] of chemically denatured proteins in general deviate little from their values in small peptides. These peptides were presumed to be completely unstructured; therefore, it was considered that chemically denatured proteins are random coils. But recent experimental studies show that small peptides adopt relatively stable structures in aqueous solutions. Small deviations of the NMR parameters from their values in small peptides may thus actually indicate the existence of local structures in chemically denatured proteins. Using NMR data and theoretical predictions we show here that fluctuating beta-strands exist in urea-denatured ubiquitin (8 M urea at pH 2). Residues in such beta-strands populate more frequently the left side of the broad beta region of -psi space. Urea-denatured ubiquitin contains no detectable beta-sheet secondary structures; nevertheless, the fluctuating beta-strands in urea-denatured ubiquitin coincide to the beta-strands in the native state. Formation of beta-strands is in accord with the electrostatic screening model of unfolded proteins. The free energy of a residue in an unfolded protein is in this model determined by the local backbone electrostatics and its screening by backbone solvation. These energy terms introduce strong electrostatic coupling between neighboring residues, which causes cooperative formation of beta-strands in denatured proteins. We propose that fluctuating beta-strands in denatured proteins may serve as initiation sites to form fibrils.

High‐molecular intestinal alkaline phosphatase in chronic liver diseases

The presence of high-molecular intestinal alkaline phosphatase (HIALP) different from bone ALP detected in the alpha(2)beta region was recently clarified. In this study we used a novel method in which HIALP was detected after conversion to ALP(5) by protease to investigate the clinical significance of the appearance of HIALP in patients with chronic liver disease. The subjects were 241 patients with chronic liver disease. When a decrease in ALP(3) in the alpha(2)beta region and an increase in ALP(5) in the beta region were noted, the patient was judged HIALP-positive. In the patients with chronic liver disease, the total ALP activity (T-ALP) increased with progression of the pathology in the order of chronic hepatitis (CH), liver cirrhosis (LC), and hepatocellular carcinoma (HCC). HIALP appeared in 22.4% and 49.3% of patients with CH and LC, respectively, but the positivity rate decreased to 30.4% in HCC. As autoimmune liver diseases, primary biliary cirrhosis (PBC) and autoimmune hepatitis (AIH) were investigated. T-ALP was lower in PBC+AIH than in LC and HCC, but the HIALP-positive rate was high (44.4%). The HIALP-positive rate was dependent on ABO blood groups, and was high in blood groups B and O. In conclusion, the HIALP-positive rate was particularly high in patients with chronic liver disease, and was related to the pathological progression, which suggests that the method is clinically useful.

High‐molecular intestinal alkaline phosphatase by agarose gel electrophoresis

The presence of high-molecular intestinal ALP (HIALP) overlapping with bone ALP in the alpha(2)beta region has been demonstrated. In this study we evaluated a method of separating HIALP after its conversion into ALP(5) by the action of protease. Serum samples from patients were mixed with protease at a ratio of 5:1 and left at room temperature for more than 30 min. The protease-treated and nontreated samples were both subjected to agarose gel electrophoresis. Patients who showed a decrease in ALP(3) in the alpha2beta region and an increase in ALP(5) in the beta region were regarded as HIALP-positive. HIALP was observed in 26.7-33.1% of patients with liver diseases, collagen diseases, and diabetes mellitus. Renal disease was ABO blood group-dependent and showed high positive rates for blood groups B and O. The HIALP-positive rate was low (7.1-15.5%) in patients with cardiovascular diseases, malignant tumors, and other disorders. ALP(5) was also observed in 98.4% of HIALP-positive patients with liver diseases. In patients with collagen diseases or diabetes mellitus, the positive rate of ALP(5) was 40.4-66.7%. In conclusion, this method, in which HIALP is converted into ALP(5) by protease pretreatment and is separated from bone ALP, allows HIALP to be identified while other fractions remain unaffected.

Cloning and structure analysis of sheep fertilin β coding region

Fertilin beta may play an important role in sperm-egg plasma membrane adhesion and fusion. To explore the effects of fertilin beta, the sperm membrane protein subunit, in the sheep fertilization process, we used RACE technique for cloning the full length cDNA of the coding region (CDS) of fertilin beta. The coding region was 2, 217 bp, which consists of 738 amino acids. The fertilin beta in the sperm membrane of sheep shares 79.4%, 66.7%, and 58.1% sequence identity with that in bovine, pig and human, respectively. The phylogenetic analysis of the fertilin beta gene family indicated the fertilin beta was clustered with bovine, and is closest to the one of bovine. This result is consistent with the result of the traditional classification. The protein structure analysis showed the disintegrin domain of sheep fertilin beta contains a TDE. Besides the above tripeptide sequence, the family member of ADAM (A Disintegrin and A Metalloprotease) follow the conserved sequence of ECD of X-D/E-E, and formed the conserved sequence of X-D/E-ECD. The pentapeptide sequence of the sheep fertilin beta is TDECE.

A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences

Chemical shifts contain substantial information about protein local conformations. We present a method to assign individual protein backbone dihedral angles into specific regions on the Ramachandran map based on the amino acid sequences and the chemical shifts of backbone atoms of tripeptide segments. The method uses a scoring function derived from the Bayesian probability for the central residue of a query tripeptide segment to have a particular conformation. The Ramachandran map is partitioned into representative regions at two levels of resolution. The lower resolution partitioning is equivalent to the conventional definitions of different secondary structure regions on the map. At the higher resolution level, the alpha and beta regions are further divided into subregions. Predictions are attempted at both levels of resolution. We compared our method with TALOS using the original TALOS database, and obtained comparable results. Although TALOS may produce the best results with currently available databases which are much enlarged, the Bayesian-probability-based approach can provide a quantitative measure for the reliability of predictions.

Structure of SAICAR synthase fromThermotoga maritimaat 2.2 Å reveals an unusual covalent dimer

As a part of a structural genomics program, the 2.2 angstroms resolution crystal structure of the PurC gene product from Thermotoga maritima has been solved. This 26.2 kDa protein belongs to the phophoribosylaminoimidazole-succinocarboxamide or SAICAR synthase family of enzymes, the members of which are involved in de novo purine biosynthesis. SAICAR synthase can be divided into three subdomains: two alpha+beta regions exhibiting structural homology with ATP-binding proteins and a carboxy-terminal subdomain of two alpha-helices. The asymmetric unit contains two copies of the protein which are covalently linked by a disulfide bond between Cys126(A) and Cys126(B). This 230-amino-acid protein exhibits high structural homology with SAICAR synthase from baker's yeast. The protein structure is described and compared with that of the ATP-SAICAR synthase complex from yeast.

Substrate Distortion in the Michaelis Complex of Bacillus 1,3–1,4-β-Glucanase: INSIGHT FROM FIRST PRINCIPLES MOLECULAR DYNAMICS SIMULATIONS

The structure and dynamics of the enzyme-substrate complex of Bacillus 1,3-1,4-beta-glucanase, one of the most active glycoside hydrolases, is investigated by means of Car-Parrinello molecular dynamics simulations (CPMD) combined with force field molecular dynamics (QM/MM CPMD). It is found that the substrate sugar ring located at the -1 subsite adopts a distorted 1S3 skew-boat conformation upon binding to the enzyme. With respect to the undistorted 4C1 chair conformation, the 1S3 skew-boat conformation is characterized by: (a) an increase of charge at the anomeric carbon (C1), (b) an increase of the distance between C1 and the leaving group, and (c) a decrease of the intraring O5-C1 distance. Therefore, our results clearly show that the distorted conformation resembles both structurally and electronically the transition state of the reaction in which the substrate acquires oxocarbenium ion character, and the glycosidic bond is partially broken. Together with analysis of the substrate conformational dynamics, it is concluded that the main determinants of substrate distortion have a structural origin. To fit into the binding pocket, it is necessary that the aglycon leaving group is oriented toward the beta region, and the skew-boat conformation naturally fulfills this premise. Only when the aglycon is removed from the calculation the substrate recovers the all-chair conformation, in agreement with the recent determination of the enzyme product structure. The QM/MM protocol developed here is able to predict the conformational distortion of substrate binding in glycoside hydrolases because it accounts for polarization and charge reorganization at the -1 sugar ring. It thus provides a powerful tool to model E.S complexes for which experimental information is not yet available.

Supersymmetric heavy Higgs bosons ate+e−linear collider and dark-matter physics

We consider the capability of the e^+e^- linear collider (which is recently called as the International Linear Collider, or ILC) for studying the properties of the heavy Higgs bosons in the supersymmetric standard model. We pay special attention to the large \tan\beta region which is motivated, in particular, by explaining the dark-matter density of the universe (i.e., so-called ``rapid-annihilation funnels''). We perform a systematic analysis to estimate expected uncertainties in the masses and widths of the heavy Higgs bosons assuming an energy and integrated luminosity of \sqrt{s}=1 TeV and L=1 ab^{-1}. We also discuss its implication to the reconstruction of the dark-matter density of the universe.

Influence of thermomechanical processing on microstructural evolution in near-α alloy IMI834

The effect of processing parameters on the evolution of the microstructural characteristics of IMI834 were examined over the temperature range 950–1125 °C at constant strain rates of 0.001–1 s −1 and true strains up to 1.2. During isothermal deformation, differences in the flow softening behavior were observed for processing in the single-phase beta region, as compared to the two-phase alpha–beta region, which has been related to differences in the structural changes occurring in IMI834. In particular, deformation processing of the alpha–beta structure was observed to work the lamellar alpha structure of the transformed beta grains without recrystallization of either phase, whilst microstructural development in a predominately beta structure resulted in the formation of dynamically recrystallized grains that were necklaced around the deformed and elongated beta phase. For the later case, the variation in the dynamically recrystallized grain size was determined to follow a Zener–Hollomon relationship between a strain rate range 0.001 and 1 s −1.

Interaction between the 90-kDa Heat Shock Protein and Soluble Guanylyl Cyclase: Physiological Significance and Mapping of the Domains Mediating Binding

The 90-kDa heat shock protein (hsp90) regulates the stability and function of many client proteins, including members of the NO-cGMP signaling pathway. Soluble guanylyl cyclase (sGC), an NO receptor, was recently reported to be an hsp90-interacting partner. In the present study, we show that hsp90 binds to both subunits of the most common sGC form (alpha(1)beta(1)) when these are expressed individually but only interacts with beta(1) in the heterodimeric form of the enzyme. Characterization of the region of hsp90 required to bind each subunit in immunoprecipitation experiments revealed that residues 310 to 456 of hsp90 interact with the sGC subunits. The region of beta(1) responsible for binding to hsp90beta was mapped using in vitro binding assays and immunoprecipitation experiments and was found to lie in the regulatory domain. The physiological importance of the hsp90/sGC interaction was investigated by treating rat smooth muscle cells with the hsp90 inhibitors radicicol and geldanamycin (GA) and determining both sGC activity and protein levels. Long-term (24 or 48 h) inhibition of hsp90 resulted in a strong decrease of both alpha(1) and beta(1) protein levels and sGC activity. Moreover, incubation of smooth muscle cells with the proteasome inhibitor N-benzoyloxycarbonyl (Z)-Leu-Leu-leucinal (MG132) blocked the GA-induced down-regulation of sGC. We conclude that the N-terminal region of the beta(1) subunit mediates binding of the heterodimeric form of sGC to hsp90 and that this interaction involves the M domain of hsp90. Hsp90 binding to sGC regulates the pool of active enzymes by affecting the protein levels of the two subunits.

Stimulation of the XPB ATP-dependent helicase by the beta subunit of TFIIE.

TFIIE and TFIIH are essential for the promoter opening and escape that occurs as RNA polymerase II transits into early elongation. XPB, a subunit of TFIIH, contains an ATP-dependent helicase activity that is used in both of these processes. Here, we show that the smaller beta subunit of TFIIE stimulates the XPB helicase and ATPase activities. The larger alpha subunit can use its known inhibitory activity to moderate the stimulation by the beta subunit. Regions of TFIIE beta required for the helicase stimulation were identified. Mutants were constructed that are defective in stimulating the XPB helicase but still allow intact TFIIE to bind and recruit XPB and TFIIH to form the pre-initiation complex. In a test for the functional significance of the stimulatory effect of TFIIE beta, these mutant forms of TFIIE were shown to be defective in a transcription assay on linear DNA. The data suggest that the beta subunit of TFIIE is an ATPase and helicase co-factor that can assist the XPB subunit of TFIIH during transcription initiation and the transition to early elongation, enhancing the potential diversity of regulatory targets.

Sintering kinetics of micrometric titanium powder

Attempts have been made to ascertain the mechanism of mass transport through the evaluation of the activation energies for different temperature ranges and through the sintering diagram approach of Ashby during sintering of microcrystalline titanium powders (average particle size of ∼3 μm). Present studies reveal that the sintering in the alpha range is controlled by lattice diffusion with source of matter at grain boundaries and the sintering in beta region appears to be controlled by lattice diffusion along with some kind of grain boundary rotation mechanism.

Contribution from neutrino Yukawa couplings to lepton electric dipole moments

To explain the observed neutrino masses through the seesaw mechanism, a supersymmetric generalization of the Standard Model should include heavy right-handed neutrino supermultiplets. Then the neutrino Yukawa couplings can induce CP violation in the lepton sector. In this paper, we compute the contribution of these CP violating terms to lepton electric dipole moments. We introduce a new formalism that makes use of supersymmetry to expose the GIM cancellations. In the region of small tan beta, we find a different result from that given previously by Ellis, Hisano, Raidal, and Shimizu. We confirm the structure found by this group, but with a much smaller overall coefficient. In the region of large tan beta, we recompute the leading term that has been identified by Masina and confirm her result.We discuss the implications of these results for constraints on the neutrino Yukawa couplings.

ALLVAC Ti-17

Abstract Allvac Ti-17 is a high-strength deep-hardening alloy. The alloy is alpha-beta, but beta-rich, and can be worked in both the beta and alpha-beta region. The alloy is commonly referred to as grade 17 in specifications. This datasheet provides information on composition, physical properties, hardness, and tensile properties. It also includes information on high temperature performance and corrosion resistance as well as joining. Filing Code: TI-135. Producer or source: Allvac, An Allegheny Technologies Company.

Near‐Infrared Spectroscopy of High‐Redshift Active Galactic Nuclei. I. A Metallicity–Accretion Rate Relationship

We present new near infrared spectroscopic measurements of the H_beta region for a sample of 29 luminous high redshift quasars. We have measured the width of H_beta in those sources, and added archival H_beta width measurements, to create a sample of 92 active galactic nuclei (AGNs) for which H_beta width and rest-frame UV measurements of N V \lambda 1240 and C IV \lambda 1549 emission-lines are available. Our sample spans six orders of magnitude in luminosity and includes 31 radio-loud AGNs. It also includes 10 narrow-line Seyfert 1 galaxies and one broad absorption-line quasar. We find that metallicity, indicated by the N V/C IV line ratio, is primarily correlated with accretion rate, which is a function of luminosity and H_beta line-width. This may imply an intimate relation between starburst, responsible for the metal enrichment of the nuclear gas, and AGN fueling, represented by the accretion rate. The correlation of metallicity with luminosity, or black hole (BH) mass, is weaker in contrast with recent results which were based on measurements of the width of C IV. We argue that using C IV as a proxy to H_beta in estimating M_BH might be problematic and lead to spurious BH mass and accretion rate estimates in individual sources. We discuss the potential implications of our new result in the framework of the starburst-AGN connection and theories of BH growth.

Functional and molecular characterization of the frataxin homolog from Arabidopsis thaliana

Frataxin is a highly conserved protein from bacteria to mammals that has been proposed to participate in iron–sulfur cluster assembly and mitochondrial iron homeostasis. In higher organisms, the frataxin gene is nuclear-encoded and the protein is required for maintenance of normal mitochondrial iron levels and respiration. We describe here AtFH, a plant gene with significant homology to other members of the frataxin family. Plant frataxin has five segments of beta regions and two alpha helices, which are characteristics of human frataxin, as well as a potential N-terminal targeting peptide for the mitochondrial localization. Transcription analysis showed that AtFH is ubiquitously expressed with high levels in flowers. Complementation of a Saccharomyces cerevisiae mutant (Δ yfh) lacking the frataxin gene proved that AtFH is a functional protein, because it restored normal rates of respiration, growth and sensitivity to H 2O 2 of the null mutant. Our results support the involvement of AtFH in mitochondrial respiration and survival during oxidative stress in plants. This is the first report of a functional frataxin gene in plants.