SEARCH · PubMed Health

Results for “Transition Elements”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 487 records · Page 27Linked to original sources

PubMed2006

A systems view of haloarchaeal strategies to withstand stress from transition metals.

Given that transition metals are essential cofactors in central biological processes, misallocation of the wrong metal ion to a metalloprotein can have resounding and often detrimental effects on diverse aspects of cellular physiology. Therefore, in an attempt to characterize unique and shared responses to chemically similar metals, we have reconstructed physiological behaviors of Halobacterium NRC-1, an archaeal halophile, in sublethal levels of Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II). Over 20% of all genes responded transiently within minutes of exposure to Fe(II), perhaps reflecting immediate large-scale physiological adjustments to maintain homeostasis. At steady state, each transition metal induced growth arrest, attempts to minimize oxidative stress, toxic ion scavenging, increased protein turnover and DNA repair, and modulation of active ion transport. While several of these constitute generalized stress responses, up-regulation of active efflux of Co(II), Ni(II), Cu(II), and Zn(II), down-regulation of Mn(II) uptake and up-regulation of Fe(II) chelation, confer resistance to the respective metals. We have synthesized all of these discoveries into a unified systems-level model to provide an integrated perspective of responses to six transition metals with emphasis on experimentally verified regulatory mechanisms. Finally, through comparisons across global transcriptional responses to different metals, we provide insights into putative in vivo metal selectivity of metalloregulatory proteins and demonstrate that a systems approach can help rapidly unravel novel metabolic potential and regulatory programs of poorly studied organisms.

Adenosine Triphosphatases↗

PubMed2000

Driven electron transfer in an environment with slow and fast degrees of freedom.

Driven electron transfer in a polar medium with slow and fast degrees of freedom is studied in the framework of a spin-boson Hamiltonian. Evolution dynamics is rigorously found when omega(s)(c)/(Gamma(a))sqrt[E(rs)/kT]<<1, where omega(s)(c) is the Debye cutoff frequency in the spectral function for the slow modes, E(rs) is the reorganization energy of slow degrees of freedom, and Gamma(-1)(a) is the reaction time dependent on the laser intensity parameter a=muE(0)/Planck's over 2piomega. Here omega and E0 are the frequency and the amplitude of a cw electric field, and mu is the electron dipole moment difference between the initial and final states. The master equation is derived for an arbitrary driving force affecting both the transition matrix element and the potential energy. For a cw electric field, the time dependent probability of staying at the product state, P1(t), is shown to be strongly dependent on the field intensity parameter a: P1(a,t) approximately (Gamma(m(1),m(2))t)(-E(rf)/E(rs)) or P1(a,t) approximately (Gamma(m(0))t)(-E(rf)/E(rs)), double or single resonances, respectively. Here E(rf) is the reorganization energy of fast degrees of freedom, Gamma(m(1),m(2)) approximately J(2)(m(1))(a)+J(2)(m(2))(a), and Gamma(m(0)) approximately J(2)(m(0))(a), where J(a) is a Bessel function. By changing the parameter a, one is able to manipulate the rate and direction of the reaction. When J(2)(m(0))(a) is close to zero the reaction is slow. Hence, slow modes turn out to be fast. This changes the character of the evolution dynamics from non- to mono- exponential decay, respectively. For the double resonance, the equilibrium constant is studied with the field intensity. It is shown that the reaction is almost insensitive to temperature. However, it strongly depends on the reaction heat, which provides a condition for the resonance.

Journal Article↗

PubMed2002

Observation of optical Smith-Purcell radiation at an electron beam energy of 855 MeV.

Smith-Purcell radiation, generated when a beam of charged particles passes close to the surface of a diffraction grating, has been studied in the visible spectral range at wavelengths of 360 and 546 nm with the low emittance 855 MeV electron beam of the Mainz Microtron MAMI. The beam focused to a spot size of 4 microm (full width at half maximum) passed over optical diffraction gratings of echelle profiles with blaze angles of 0.8 degrees, 17.27 degrees, and 41.12 degrees and grating periods of 0.833 and 9.09 microm. Taking advantage of the specific emission characteristics of Smith-Purcell radiation a clear separation from background components, such as diffracted synchrotron radiation from upstream beam optical elements and transition radiation, was possible. The intensity scales with a modified Bessel function of the first kind as a function of the distance between electron beam and grating surface. Experimental radiation factors have been determined and compared with calculations on the basis of Van den Berg's theory [P.M. Van den Berg, J. Opt. Soc. Am. 63, 689 (1973)]. Fair agreement has been found for gratings with large blaze angles while the measurement with the shallow grating (blaze angle 0.8 degrees ) is at variance with this theory. Finally, the optimal operational parameters of a Smith-Purcell radiation source in view of already existing powerful undulator sources are discussed.

Journal Article↗

PubMed2005

Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithm.

We examine an application of the Gillespie algorithm to simulating spatially inhomogeneous reaction-diffusion systems in mesoscopic volumes such as cells and microchambers. The method involves discretizing the chamber into elements and modeling the diffusion of chemical species by the movement of molecules between neighboring elements. These transitions are expressed in the form of a set of reactions which are added to the chemical system. The derivation of the rates of these diffusion reactions is by comparison with a finite volume discretization of the heat equation on an unevenly spaced grid. The diffusion coefficient of each species is allowed to be inhomogeneous in space, including discontinuities. The resulting system is solved by the Gillespie algorithm using the fast direct method. We show that in an appropriate limit the method reproduces exact solutions of the heat equation for a purely diffusive system and the nonlinear reaction-rate equation describing the cubic autocatalytic reaction.

Journal Article↗

PubMed2002

rf Spectroscopy with a single Ba+ ion.

We have employed the method of shelving to measure Zeeman resonances of a single trapped Ba+ ion. We use optical pumping to place the ion in a selected magnetic sublevel of either the 6S(1/2) ground state or the 5D(3/2) metastable state. The ion is exposed to an rf field, and a probing/shelving mechanism detects whether spin-flip transitions have taken place. We have observed rf transitions with linewidths of 15 Hz, limited by magnetic-field noise. We have also observed the shift in the Zeeman frequency when the ion is illuminated by off-resonant light. A simultaneous measurement of such light shifts in two atomic states of Ba+ will permit a precise determination of the ratio of transition matrix elements.

Journal Article↗

PubMed2004

Role of the lattice in the gamma-->alpha phase transition of Ce: a high-pressure neutron and x-ray diffraction study.

The temperature and pressure dependence of the thermal displacements and lattice parameters were obtained across the gamma-->alpha phase transition of Ce using high-pressure, high-resolution neutron and synchrotron x-ray powder diffraction. The estimated vibrational entropy change per atom in the gamma-->alpha phase transition, DeltaS(gamma-alpha)(vib) approximately (0.75+/-0.15)k(B), is about half of the total entropy change. The bulk modulus follows a power-law pressure dependence that is well described using the framework of electron-phonon coupling. These results clearly demonstrate the importance of lattice vibrations, in addition to the spin and charge degrees of freedom, for a complete description of the gamma-->alpha phase transition in elemental Ce.

Journal Article↗

PubMed2006

Vanishing N = 20 shell gap: study of excited states in (27,28)Ne.

This Letter reports on the (1)H((28)Ne, (28)Ne) and (1)H((28)Ne, (27)Ne) reactions studied at intermediate energy using a liquid hydrogen target. From the cross section populating the first 2(+) excited state of (28)Ne, and using the previously determined BE(2) value, the neutron quadrupole transition matrix element has been calculated to be M(n)=13.8 +/- 3.7 fm(2). In the neutron knockout reaction, two low-lying excited states were populated in (27)Ne. Only one of them can be interpreted by the sd shell model while the additional state may intrude from the fp shell. These experimental observations are consistent with the presence of fp shell configurations at low excitation energy in (27,28)Ne nuclei caused by a vanishing N=20 shell gap at Z=10.

Journal Article↗

PubMed2001

Orientation effects in elastic scattering of polarized X-rays by linear molecules.

Strong orientation effect is discovered theoretically upon the change of the scheme of suggested experiment on anomalous elastic x-ray scattering of linearly polarized x-ray radiation by linear diatomics near the ionization thresholds of inner molecular orbitals. Studied are the effects on the shape of theoretical scattering spectra of additional excitations/ionizations of outer-shell electrons. Within the one-centre approximation for the molecular orbitals wavefunctions the analytical structure of the linear molecule's formfactor is obtained. The dipole transition matrix elements and photoabsorption cross sections are calculated by the methods of the theory of non-orthogonal orbitals.

Journal Article↗

PubMed2005

Resonant soft X-ray diffraction - in extremis.

The use of softer-energy X-rays produced by synchrotron radiation for diffraction is an area of current interest. In this paper, experiments exploiting resonant scattering at the L absorption edges of 3d transition metal elements are reported. Such energies, typically 500-1000 eV, are at the extreme limit of soft X-ray diffraction where absorption effects are so severe that the sample and diffractometer must be placed in a windowless high-vacuum vessel. In addition, the Ewald sphere is so small as to likely contain, at most, only a single Bragg reflection. Advantages of using such radiation for the study of weak diffraction effects such as anomalous scattering, charge ordering, magnetic diffraction and orbital ordering are reported.

Computer Simulation↗

PubMed2004

FoldMiner: structural motif discovery using an improved superposition algorithm.

We report an unsupervised structural motif discovery algorithm, FoldMiner, which is able to detect global and local motifs in a database of proteins without the need for multiple structure or sequence alignments and without relying on prior classification of proteins into families. Motifs, which are discovered from pairwise superpositions of a query structure to a database of targets, are described probabilistically in terms of the conservation of each secondary structure element's position and are used to improve detection of distant structural relationships. During each iteration of the algorithm, the motif is defined from the current set of homologs and is used both to recruit additional homologous structures and to discard false positives. FoldMiner thus achieves high specificity and sensitivity by distinguishing between homologous and nonhomologous structures by the regions of the query to which they align. We find that when two proteins of the same fold are aligned, highly conserved secondary structure elements in one protein tend to align to highly conserved elements in the second protein, suggesting that FoldMiner consistently identifies the same motif in members of a fold. Structural alignments are performed by an improved superposition algorithm, LOCK 2, which detects distant structural relationships by placing increased emphasis on the alignment of secondary structure elements. LOCK 2 obeys several properties essential in automated analysis of protein structure: It is symmetric, its alignments of secondary structure elements are transitive, its alignments of residues display a high degree of transitivity, and its scoring system is empirically found to behave as a metric.

Algorithms↗

PubMed2006

Selection of allosteric beta-lactamase mutants featuring an activity regulation by transition metal ions.

Libraries of phage-displayed beta-lactamase mutants in which up to three loops have been engineered by genetic introduction of random peptide sequences or by randomization of the wild-type sequence have been submitted to selection protocols designed to find mutants in which binding of transition metal ions to the engineered secondary binding site leads to significant effects on the enzymatic activity. A double-selection protocol was applied: The phage-displayed libraries were first selected for transition metal ions affinity by panning on IMAC support, then a second selection step was applied to isolate mutants that have retained significant catalytic activity. The analysis of the kinetic properties of mutants in the presence of nickel, copper, or zinc ions allowed isolation of a few mutants whose activity was either enhanced or inhibited by factors up to three and >10, respectively, in a metal-specific manner. A remarkable mutant exhibiting differential allosteric regulation depending on the metal was found. Its activity was activated by nickel ion binding, inhibited by cupric ion binding, and nearly unaffected by zinc ions. These observations point to an interesting potential for up- or down-regulation of activity within a monomeric enzyme by binding to an "allosteric site" relatively remote from the active site.

Allosteric Regulation↗

PubMed1990

Bladder carcinosarcomas: three cases with diverse histogenesis.

Carcinosarcomas of the bladder are rare. We describe three such tumours, including an apparently unique case in which the components comprised liposarcoma and poorly-differentiated transitional cell elements. A second example included chondrosarcomatous elements. These two tumours showed architectural and immunocytochemical features which suggested that they had originated as carcinomas but had subsequently differentiated along both epithelial and mesenchymal pathways. The third tumour contained both carcinoma and osteosarcoma and may represent a collision tumour.

Aged↗

PubMed1993

Endothelin-converting enzyme: the binding of metal ions.

The metal ion of endothelin-converting enzyme (ECE) was investigated by inhibiting the enzyme with ethylenediaminetetraacetic acid (EDTA) and restoring activity by adding divalent metal salts in quantities less than the concentration of EDTA. Under these conditions, only metal ions that bind to ECE with high affinity can affect the enzyme. The ferrous enzyme had an activity of 76% relative to the native enzyme, the manganous enzyme 76%, the nickelous enzyme 77%, the cupric enzyme 17%, the zinc enzyme 98% and the cobaltous enzyme 122%. Of these first transition series elements only zinc can be the metal of the native enzyme. The zinc enzyme has the same Km and turnover number as the native enzyme.

Amino Acid Sequence↗

PubMed1989

Identification of the 16 degrees C compartment of the endoplasmic reticulum in rat liver and cultured hamster kidney cells.

In many systems transfer between the endoplasmic reticulum and the Golgi apparatus is blocked at temperatures below 16 degrees C. In virus-infected cells in culture, a special membrane compartment is seen to accumulate. Our studies with rat liver show a similar response to temperature both in situ with slices and in vitro with isolated transitional endoplasmic reticulum fractions. With isolated transitional endoplasmic reticulum fractions, when incubated in the presence of nucleoside triphosphate and a cytosol fraction, temperature dependent formation of vesicles occurred with a Q10 of approximately 2 but was apparent only at temperatures greater than 12 degrees C. A similar response was seen in situ at 12 degrees C and 16 degrees C where fusion of transition vesicles with cis Golgi apparatus, but not their formation, was blocked and transition vesicles accumulated in large numbers. At 18 degrees C and below and especially at 8 degrees C and 12 degrees C, the cells responded by accumulating smooth tubular transitional membranes near the cis Golgi apparatus face. With cells and tissue slices at 20 degrees C neither transition vesicles nor the smooth tubular elements accumulated. Those transition vesicles which formed at 37 degrees C were of a greater diameter than those formed at 4 degrees C both in situ and in vitro. The findings show parallel responses between the temperature dependency of transition vesicle formation in vitro and in situ and suggest that a subpopulation of the transitional endoplasmic reticulum may be morphologically and functionally homologous to the 16 degrees C compartment observed in virally-infected cell lines grown at low temperatures.

Adenosine Triphosphate↗

PubMed1991

A two-compartment dispersion model describes the hepatic outflow profile of diclofenac in the presence of its binding protein.

The residence-time distribution (RTD) of diclofenac in the rat single-pass isolated perfused in-situ liver (n = 4) was determined after bolus input into the hepatic portal vein. Addition of human serum albumin (5 g L-1) ensured extensive (greater than 98%) binding of diclofenac within the perfusate. The one-compartment form of the axial dispersion model of hepatic elimination, which assumes instantaneous radial distribution of substrate within the accessible spaces of the liver, failed to describe adequately the RTD of diclofenac. In contrast, the two-compartment form of this model, which assumes that the radial transfer of unbound substrate between the vascular and cellular space is non-instantaneous, provided an excellent description of the diclofenac data. Moreover, the mean (+/- s.d.) value for the hepatic dispersion number (DN) for diclofenac (0.354 +/- 0.076) compared well with that determined for simultaneously injected [125I]human serum albumin (0.456 +/- 0.078) using the one-compartment dispersion model. These estimates of DN, a stochastic parameter which characterizes the axial spreading of individual elements during transit through the liver, were similar in magnitude to those reported for other tracers in the rat perfused liver. The findings suggest that common factors influenced the RTD of diclofenac and its binding protein, and indicate that the two-compartment dispersion model may be a valuable tool for interpreting hepatic impulse-response data for solutes whose hepatic distribution and elimination is influenced by membrane permeability.

Algorithms↗

PubMed2005

Carnosine: a versatile antioxidant and antiglycating agent.

Carnosine (beta-alanyl-L-histidine) has recently attracted much attention as a naturally occurring antioxidant and transition-metal ion sequestering agent. It has also been shown to act as an anti-glycating agent, inhibiting the formation of advanced glycation end products (AGEs). Through its distinctive combination of antioxidant and antiglycating properties, carnosine is able to attenuate cellular oxidative stress and can inhibit the intracellular formation of reactive oxygen species and reactive nitrogen species. By controlling oxidative stress, suppressing glycation, and chelating metal ions, carnosine is able to reduce harmful sequelae such as DNA damage. AGEs are known contributors to the pathology of Alzheimer's disease, and carnosine therefore merits serious attention as a possible therapeutic agent.

Aging↗

PubMed2003

Transition metal speciation in the cell: insights from the chemistry of metal ion receptors.

The essential transition metal ions are avidly accumulated by cells, yet they have two faces: They are put to use as required cofactors, but they also can catalyze cytotoxic reactions. Several families of proteins are emerging that control the activity of intracellular metal ions and help confine them to vital roles. These include integral transmembrane transporters, metalloregulatory sensors, and diffusible cytoplasmic metallochaperone proteins that protect and guide metal ions to targets. It is becoming clear that many of these proteins use atypical coordination chemistry to accomplish their unique goals. The different coordination numbers, types of coordinating residues, and solvent accessibilities of these sites are providing insight into the inorganic chemistry of the cytoplasm.

Bacteria↗

PubMed2004

RETRACTED: A late-transition metal oxo complex: K7Na9[O=PtIV(H2O)L2], L = [PW9O34]9-.

Terminal mono-oxo complexes of the late transition metal elements have long been considered too unstable to synthesize because of repulsion between the oxygen electrons and the mostly filled metal d orbitals. A platinum(IV)-oxo compound flanked by two polytungstate ligands, K7Na9[O=Pt(H2O)L2], L = [PW9O34(9-)], has now been prepared and isolated at room temperature as air-stable brown crystals. X-ray and neutron diffraction at 30 kelvin revealed a very short [1.720(18) angstrom] Pt-O bond and no evidence of a hydrogen atom at the terminal oxygen, ruling out a better precedented Pt-OH complex. Density functional theory and spectroscopic data account for the stability of the Pt(IV)-oxo unit by electron withdrawal into delocalized orbitals of the polytungstates.

Chemical Phenomena↗