Nutritional strategy for the preferential uptake of $${{\text{NO}}_{3}}^{ - } {\text{{-}N}}$$ NO 3 - -N by Phaeocystis globosa

Hydrobiologia - Phytoplankton productivity standardized to chlorophyll a and photon flux (mg C mg chl. a−1 mol photons−1) of natural communities from northern Bothnian Sea under dynamic...     

Analysis of {}^{13}{\text{C}}^{{{\upalpha}}} and {}^{13}{\text{C}}^{{{\upbeta}}} chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach

Cysteines possess a unique property among the 20 naturally occurring amino acids: it can be present in proteins in either the reduced or oxidized form, and can regulate the activity of some proteins. Consequently, to augment our previous treatment of the other types of residues, the $ {}^{13}{\text{C}}^{{{\upalpha}}} $ and $ {}^{13}{\text{C}}^{{{\upbeta}}} $ chemical shifts of 837 cysteines in disulfide-bonded cystine from a set of seven non-redundant proteins, determined by X-ray crystallography and NMR spectroscopy, were computed at the DFT level of theory. Our results indicate that the errors between observed and computed $ {}^{13}{\text{C}}^{{{\upalpha}}} $ chemical shifts of such oxidized cysteines can be attributed to several effects such as: (a) the quality of the NMR-determined models, as evaluated by the conformational-average (ca) rmsd value; (b) the existence of high B-factor or crystal-packing effects for the X-ray-determined structures; (c) the dynamics of the disulfide bonds in solution; and (d) the differences in the experimental conditions under which the observed $ {}^{13}{\text{C}}^{{{\upalpha}}} $ chemical shifts and the protein models were determined by either X-ray crystallography or NMR-spectroscopy. These quantum-chemical-based calculations indicate the existence of two, almost non-overlapped, basins for the oxidized and reduced ?SH $ {}^{13}{\text{C}}^{{{\upbeta}}} $ , but not for the $ {}^{13}{\text{C}}^{{{\upalpha}}} $ , chemical shifts, in good agreement with the observation of 375 $ {}^{13}{\text{C}}^{{{\upalpha}}} $ and 337 $ {}^{13}{\text{C}}^{{{\upbeta}}} $ resonances from 132 proteins by Sharma and Rajarathnam (2000). Overall, our results indicate that explicit consideration of the disulfide bonds is a necessary condition for an accurate prediction of $ {}^{13}{\text{C}}^{{{\upalpha}}} $ and $ {}^{13}{\text{C}}^{{{\upbeta}}} $ chemical shifts of cysteines in cystines.     

ROS Scavenging and $${\text{NH}}_{4}^{ + }$$ Nitrogen Fertilizer Roles in Alleviation of Cd-Induced Oxidative Stress in Arabidopsis thaliana

Russian Journal of Plant Physiology - Arabidopsis thaliana (L.) Heynh. receiving ammonium, were transferred on modified Hoagland nutrient solution containing Cd (25 µM) alone or supplemented...     

Influence of {\text{NH - }}{{\text{S}}^\gamma } bonding interactions on the structure and dynamics of metallothioneins

Mammalian metallothioneins ( \textM₇^\textIIMTs {\text{M}}_7^{\text{IIMTs}} ) show a clustered arrangement of the metal ions and a nonregular protein structure. The solution structures of Cd₃-thiolate cluster containing β-domain of mouse β-MT-1 and rat β-MT-2 show high structural similarities, but widely differing structure dynamics. Molecular dynamics simulations revealed a substantially increased number of \textNH - \textS^g {\text{NH - }}{{\text{S}}^\gamma } hydrogen bonds in β-MT-2, features likely responsible for the increased stability of the Cd₃-thiolate cluster and the enfolding protein domain. Alterations in the \textNH - \textS^g {\text{NH - }}{{\text{S}}^\gamma } hydrogen-bonding network may provide a rationale for the differences in dynamic properties encountered in the β-domains of MT-1, -2, and -3 isoforms, believed to be essential for their different biological function.     

Release of non-exchangeable {}^{{{\text{15}}}}{\text{NH}}^{{\text{ + }}}_{{\text{4}}} from subgrade, decomposed granite substrates and uptake by non-mycorrhizal and mycorrhizal California native annual grass, Vulpia microstachys

Release rates of recently fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ from non-exchangeable interlayer sites in 2:1 silicate minerals were determined for decomposed granite (DG) saprolites from three locations in California, USA. Recently-fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release from the DG substrate was quantified by extracting diffused $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ with H-resin, as well as a native, annual grass Vulpia microstachys. The $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release data varied with via the method of extraction, which included H-resin pre-treatments (Na⁺ or H⁺) and V. microstachys uptake (mycorrhizal inoculated or uninoculated). After 6 weeks (1008 h), more $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ was recovered from fixed interlayer positions by the H-resins as compared to uptake by V. microstachys. The H⁺ treated H-resins recovered more released $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ (≈94 mg ${\text{NH}}^{{\text{ + }}}_{{\text{4}}} - {\text{N}}\;{\text{kg}}^{1} $ or (12%) of total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ ) in two of the three DG samples as compared to the Na⁺ treated resins, (which recovered ≈70–78 mg ${\text{NH}}^{{\text{ + }}}_{{\text{4}}} - {\text{N}}\;{\text{kg}}^{{{\text{ - 1}}}} $ (or 9–10%) of the total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ ). The V. microstachys assimilated 8–9% of the total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ with mycorrhizal inoculum as compared to only 2% without a mycorrhizal inoculum, over the same time period. The fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release kinetics from the H-resin experiments were most accurately described by first order and power function models, and can be characterized as biphasic using a heterogeneous diffusion model. Uptake of both the ¹⁵N and ambient, unlabelled N from the soils was closely related to plant biomass. There was no significant difference in percent of N per unit of biomass between the control and mycorrhizal treatments. The findings presented here indicate that observed, long-term $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release rates from DG in studies utilizing resins, may overestimate the levels of fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ made available to plants and microorganisms. Additionally, the study suggested that mycorrhizae facilitate the acquisition and plant uptake of fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ , resulting in markedly increased plant biomass production.     

The human V pre B gene is located on chromosome 22 near a cluster of {\text{V}}_{\lambda _1 } gene segments

The chromosomal location of the human V _pre B gene was determined by Southern blotting analysis of restriction enzyme-digested DNAs from a panel of 17 mouse-human somatic cell hybrids. The pattern of hybridization of a V_preB-specific probe in conjunction with earlier analysis of several marker genes allowed the following conclusions: 1) V _pre B is on human chromosome 22 within band 22q11.2 distal to the bcr-like gene, bcr-2 and proximal to the bcr-like gene, bcr-4. 2) V_preB has been localized relative to several constitutional and tumor-specific breakpoints within 22q 11.2, segregates in hybrids retaining 22q^–chromosomes with some but not with all members of the subgroup of the V genes, and is amplified with these genes in K562 cells. 3) The order of the loci on chromosome 22 is centromerebcr-2, V _preB, .     

H2O2 but not $${\hbox{O}_{2}^{-}}$$ elevated by oxidized LDL enhances human aortic smooth muscle cell proliferation

The oxidation of low density lipoprotein (LDL) as a key event in atherosclerosis suggests that antioxidant interventions may reduce the risk of atherosclerosis. However, the better strategies among antioxidant remedies for atherosclerosis remains difficult to be determined. Here, we show that oxidized LDL increases the steady-state level of intracellular hydrogen peroxide through stimulating the protein expressions of Nox1 and Cu/Zn superoxide dismutase (SOD) in human aortic smooth muscle cells (SMCs). The intracellular content of hydrogen peroxide rather than superoxide is a key modulator for vascular SMC (VSMC) proliferation, implying that without co-expression of catalase, increased Cu/Zn-SOD activity alone may not be beneficial to reduce the growth of VSMC in an atherosclerotic plaque.     

Control of struvite precipitation by selective removal of $${\text{NH}}^{{\text{ + }}}_{{\text{4}}} $$ with dialyzer/zeolite in an anaerobic membrane bioreactor

This study focused on the mitigation of membrane fouling caused by struvite precipitation using a dialyzer/zeolite (D/Z) unit in an anaerobic membrane bioreactor. The D/Z unit was designed to selectively remove NH(4)+ ions, one of the main components of the inorganic foulant, struvite. The maximum mass transfer coefficient for NH(4)+ through the dialyzer was estimated to be 0.92 l m(-2)h(-1), whereas the Na-substituted zeolite had the highest ion exchange capacity with respect to ammonium among intact or differently pretreated zeolites. During a single passage of dialysate through the zeolite column, substantial NH(4)+ removal (in excess of 90%) was achieved, leading to the reduction in struvite precipitation in the digester. The D/Z unit played a significant role in controlling struvite precipitation, thereby enhancing permeate flux for the case of the ceramic membrane, in which struvite fouling would be more pronounced compared to the polymeric membrane. For the polymeric membrane, however, no significant improvement in flux was observed even with the D/Z unit because the fouling of the polymeric membrane was mainly due to the deposition of biomass rather than the struvite precipitation.     

Study on the Interaction Between {\mathrm{Cu}}{\left( {{\mathrm{phen}}} \right)}^{{2 + }}_{3} and Bovine Serum Albumin by Spectroscopic Methods

In this work, the interaction between ${\text{Cu}}\left( {{\text{phen}}} \right)_3^{\,\,2 + } In this work, the interaction between Cu(phen)(2+)(3) and bovine serum albumin (BSA) was investigated by fluorescence spectroscopy combined with UV-vis absorption and circular dichroism (CD) spectroscopic techniques under physiological conditions. The fluorescence data proved that the fluorescence quenching of BSA by Cu(phen)(2+)(3) was the result of the Cu(phen)(2+)(3) -BSA complex formation. The binding constants (K (a)) between Cu(phen)(2+)(3) and BSA at four different temperatures were calculated according to the modified Stern-Volmer equation. The enthalpy change (DeltaH) and entropy change (DeltaS) were calculated to be 10.74 kJ mol(-1) and 54.35 J mol(-1) K(-1), respectively, which indicated that electrostatic interactions played a major role in the formation of Cu(phen)(2+)(3) -BSA complex. The distance r between the donor (BSA) and acceptor[Cu(phen)(2+)(3)] was obtained to be 3.55 nm based on F?rster's energy transfer theory. The synchronous fluorescence and CD spectroscopy results showed that the polarity of the residues increased and the lost of the alpha-helix content of BSA (from 59.84 to 53.70%). These indicated that the microenvironment and conformation of BSA were changed in the presence of Cu(phen)(2+)(3).     

Three phases of energy-dependent induction of $${\text{P}}_{{700}}^{+}$$ P 700 + and Chl a fluorescence in Tradescantia fluminensis leaves

Photosynthesis Research - In plants, the short-term regulation (STR, seconds to minute time scale) of photosynthetic apparatus is associated with the energy-dependent control in the chloroplast...     

Estimation of ^{3}J_{HN\hbox{-}H\alpha} and ^{3}J_{H\alpha\hbox{-}H\beta} coupling constants from heteronuclear TOCSY spectra

(3)J proton-proton coupling constants bear information on the intervening dihedral angles. Methods have been developed to derive this information from NMR spectra of proteins. Using series expansion of the time dependent density matrix, and exploiting the simple topology of amino acid spin-systems, formulae for estimation of (3)J(HN-Halpha) and (3)J(Halpha-Hbeta) from HSQC-TOCSY spectra are derived. The results obtained on a protein entailing both alpha-helix and beta-sheet secondary structure elements agree very well with J-coupling constants computed from the X-ray structure. The method compares well with existing methods and requires only 2D spectra which would be typically otherwise recorded for structural studies.     

Delay decomposition approach to $$\mathcal {H}_{\infty }$$ filtering analysis of genetic oscillator networks with time-varying delays

In this paper, the \(\mathcal {H}_{\infty }\) filtering problem is treated for N coupled genetic oscillator networks with time-varying delays and extrinsic molecular noises. Each individual genetic oscillator is a complex dynamical network that represents the genetic oscillations in terms of complicated biological functions with inner or outer couplings denote the biochemical interactions of mRNAs, proteins and other small molecules. Throughout the paper, first, by constructing appropriate delay decomposition dependent Lyapunov–Krasovskii functional combined with reciprocal convex approach, improved delay-dependent sufficient conditions are obtained to ensure the asymptotic stability of the filtering error system with a prescribed \(\mathcal {H}_{\infty }\) performance. Second, based on the above analysis, the existence of the designed \(\mathcal {H}_{\infty }\) filters are established in terms of linear matrix inequalities with Kronecker product. Finally, numerical examples including a coupled Goodwin oscillator model are inferred to illustrate the effectiveness and less conservatism of the proposed techniques.     

Lanthanide complexes of a cross-bridged cyclam ligand: Isolation and structural characterization of unusual trinuclear μ3-imido Yb(III) cluster cations and a mixed valence Yb(II/III) salt containing an Yb(II) anion

The reaction of the cross-bridged cyclam ligand H₂CBC with divalent ytterbium precursors, Yb[N(SiMe₃)₂]₂[L]₂ (L = THF or Et₂O) or Yb(C₅Me₅)₂(OEt₂) afforded polymeric [Yb(CBC)]_n (1), as the primary product. In addition, the Yb[N(SiMe₃)₂]₂[L]₂ reactions also afforded a small amount of an unusual mixed valence salt containing a trinuclear Yb(III) cluster cation featuring a triply bridging NH group and a mononuclear Yb(II) anion, {[Yb(CBC)]₃[μ³-NH]}⁺ {Yb[N(SiMe₃)₂]₃}⁻ (2). A related cluster containing an iodide counterion, {[Yb(CBC)]₃[μ³-NH]}⁺ I⁻ (3), was also isolated in one case. The structures of salts 2 and 3 were determined by X-ray crystallography. Reaction of [Yb(CBC)]_n with p-tolyldisulfide, (C₆H₄MeS)₂, produced burgundy crystals of [Yb(CBC)(S-p-C₆H₄Me)]_n (4). The ¹H NMR spectra of 2 suggests that the trinuclear cation remains intact in THF-d₈ solution.     

Ab initio molecular dynamics of the reactivity of vitamin C toward hydroxyl and $$ {HO}_2/{O}_2^{-} $$ radicals

Vitamin C is one of the most abundant exogenous antioxidants in the cell, and it is of the utmost importance to elucidate its mechanism of action against radicals. In this study, the reactivity of vitamin C toward OH and \( {HO}_2/{O}_2^{-} \) radicals in aqueous medium was analyzed by ab initio molecular dynamics using CPMD code. The simulations led to results similar to those of static studies or experiments for the pair of \( {HO}_2/{O}_2^{-} \) radicals but bring new insights for the reactivity with hydroxyl radical: the reaction takes place before the formation of an adduct and consists of two steps: first an electron is transferred to hydroxyl radical and then the ascorbyl radical loses a proton.

Open image in new window

Graphical Abstract Reactivity of vitamin C toward hydroxyl and \( {HO}_2/{O}_2^{-} \) radicals

     

Crystal structures, antioxidation and DNA binding properties of Yb(III) complexes with Schiff-base ligands derived from 8-hydroxyquinoline-2-carbaldehyde and four aroylhydrazines

X-ray crystal and other structural analyses indicate that Yb(III) and all four newly synthesized ligands can form a binuclear Yb(III) complex with a 1:1 metal to ligand stoichiometry by octacoordination at the Yb(III) center. Investigations of DNA binding properties show that all the ligands and Yb(III) complexes can bind to Calf thymus DNA through intercalations with the binding constants at the order of magnitude 10⁵–10⁷ M⁻¹, but Yb(III) complexes present stronger affinities to DNA than ligands. All the ligands and Yb(III) complexes may be used as potential anticancer drugs. Investigations of antioxidation properties show that all the ligands and Yb(III) complexes have strong scavenging effects for hydroxyl radicals and superoxide radicals but Yb(III) complexes show stronger scavenging effects for hydroxyl radicals than ligands. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

N$_{3}^{-}$ azide anion confined inside finite-size carbon nanotubes

In this work, the confinement of an N\(_{3}^{-}\) azide anion inside finite-size single-wall zigzag and armchair carbon nanotubes of different diameters has been studied by wave function and density functional theory. Unrelaxed and relaxed interaction energies have been computed, resulting in a favorable interaction between the guest and host system. In particular, the largest interaction has been observed for the confinement in an armchair (5,5) carbon nanotube, for which a natural population analysis as well as an investigation based on the molecular electrostatic potential has been carried out. The nature of the interaction between the two fragments appears to be mainly electrostatic, favored by the enhanced polarizability of the nanotube wall treated as a finite system and passivated by hydrogen atoms. The results obtained are promising for possible applications of this complex as a starting point for the stabilization of larger polynitrogen compounds, suitable as a high-energy density material.     

Endor characterization and D2O exchange in the \begin{array}{*{20}c} {\mathop Z\nolimits^{\begin{array}{*{20}c} + \\ . \\ \end{array} } } \\ \end{array} /{\kern 1pt} \begin{array}{*{20}c} {\mathop D\nolimits^{\begin{array}{*{20}c} + \\ . \\ \end{array} } } \\ \end{array} radical in photosystem II

The early suggestion by Lozier and Butler (Photochem. Photobiol. 17, 133–137 (1973)) that EPR Signal II arises from radicals associated with the water-splitting process in PSII has been confirmed and extended over the intervening years. Recent work has identified the Signal II radicals, \(\begin{array}{*{20}c} {\mathop D\nolimits^{\begin{array}{*{20}c} + \\ . \\ \end{array} } } \\ \end{array}\) and \(\begin{array}{*{20}c} {\mathop Z\nolimits^{\begin{array}{*{20}c} + \\ . \\ \end{array} } } \\ \end{array}\) , with plastosemiquinone cation species. In the experiments presented here we have used ENDOR spectroscopy and D₂O/H₂O exchange to characterize these paramagnets in more detail. The ENDOR matrix region, which arises from protons which interact weakly with the unpaired electron spin, is well-resolved at 4 K and at least seven resonances are apparent. A number of hyperfine couplings in the 3–8 MHz range are observed and are suggested to arise from methyl or hydroxyl protons which occur as substituents on the plastosemiquinone cation ring or from amino acid protons hydrogen-bonded to the 1,4-hydroxyl groups. Orientation selection experiments are consistent with these possibilities. D₂O/H₂O exchange shows that the D⁺/Z⁺ site is accessible to solvent. However, the exchange occurs slowly and is not complete even after 72 hours which suggests that the free radicals are functionally isolated from solvent water.