Unambiguous through-bond sugar-to-base correlations for purines in 13C, 15N-labeled nucleic acids: The HsCsNb,HsCs(N)bCb,and HbNbCb experiments

Summary A set of three 3D (¹H, ¹³C, ¹⁵N) triple-resonance correlation experiments has been designed to provide H1-H8 intraresidue sugar-to-base correlations in purines in an unambiguous and efficient manner. Together, the H_sC_sN_b, H_sC_s(N)_bC_b, and H_bN_bC_b experiments correlate the H1 sugar proton to the H8 proton of the attached base by means of the {H1, C1, N9, C8, H8} heteronuclear scalar coupling network. The assignment strategy presented here allows for unambiguous H1-H8 intraresidue correlations, provided that no two purines have both the same H1 and C1 chemical shifts and the same C8 and N9 chemical shifts. These experiments have yielded H1-H8 intraresidue sugar-to-base correlations for all five guanosines in the [¹³C, ¹⁵N] isotopically labeled RNA duplex r(GGCGCUUGCGUC)₂.     

Crystal structure of the ternary FimC-FimF(t)-FimD(N) complex indicates conserved pilus chaperone-subunit complex recognition by the usher FimD

Type 1 pili, anchored to the outer membrane protein FimD, enable uropathogenic Escherichia coli to attach to host cells. During pilus biogenesis, the N-terminal periplasmic domain of FimD (FimD(N)) binds complexes between the chaperone FimC and pilus subunits via its partly disordered N-terminal segment, as recently shown for the FimC-FimH(P)-FimD(N) ternary complex. We report the structure of a new ternary complex (FimC-FimF(t)-FimD(N)) with the subunit FimF(t) instead of FimH(p). FimD(N) recognizes FimC-FimF(t) and FimC-FimH(P) very similarly, predominantly through hydrophobic interactions. The conserved binding mode at a "hot spot" on the chaperone surface could guide the design of pilus assembly inhibitors.     

μ- and μ4-η coordination of A2H2 (A = C, Si, Ge, Sn and Pb) ligands with transition metals

The heavier analogs of C₂H₂ have been studied at the B3LYP level for their μ and μ₄-η² coordination properties with the transition metals. Based on known alkyne compounds, transition metal fragments [W₂(μ-NH)(Cp)₂(Cl)₂] and [Fe₄(CO)₁₂] have been chosen. The SBKJC relativistic effective core potentials and their associated basis sets were used on W, Fe, Sn and Pb, and the 6-31G(d) basis set was used on all other elements. All the complexes of Si₂H₂, Ge₂H₂, Sn₂H₂ and Pb₂H₂ are found to be local minima. The trans-twist nature of the ligand A₂H₂ (A = Si-Pb) is large in μ-coordinated complexes of W, and it is very small in μ₄-η² coordinated complexes of Fe. The electronic structure of these complexes was investigated using fragment molecular orbital method (FMO).     

Acetylcholinesterase/Butyrylcholinesterase inhibition activity of some new carbacylamidophosphate deriviatives

Eight newly synthesized carbacylamidophosphates with the general formula RC(O)NHP(O)Cl₂ with R = pCl–C₆H₄ 1a, pBr–C₆H₄ 2a, C₆H₅ 3a, and pMe–C₆H₄ 4a and RC(O)NHP(O)(NC₄H₈O)₂ R = pCl–C₆H₄ 1b, pBr–C₆H₄ 2b, C₆H₅ 3b, pMe–C₆H₄ 4b, were selected to compare the inhibition kinetic parameters, IC₅₀, K_i, k_p and K_D, on human erythrocyte acetylcholinesterase (hAChE) and bovine serum butyrylcholinesterase (BuChE), Also, the in vivo inhibition potency of compound 2a, 2b and 3a, were studied. The data demonstrates that compound 2a and compound 2b are the potent sensitive as AChE and BuChE inhibitors respectively, and the inhibition of hAChE is about 10-fold greater than that of BuChE.     

Antibacterial properties of recombinant human non-pancreatic secretory phospholipase A2

Human non-pancreatic secretory phospholipase A₂ (hnpsPLA₂) is a group IIA phospholipase A₂ which plays an important role in the innate immune response. This enzyme was found to exhibit bactericidal activity toward Gram-positive bacteria, but not Gram-negative ones. Though native hnpsPLA₂ is active over a broad pH range, it is only highly active at alkaline conditions with the optimum activity pH of about 8.5. In order to make it highly active at neutral pH, we have obtained two hnpsPLA₂ mutants, Glu89Lys and Arg100Glu that work better at neutral pH in a previous study. In the present study, we tested the bactericidal effects of the native hnpsPLA₂ and the two mutants. Both native hnpsPLA₂ and the two mutants exhibit bactericidal activity toward Gram-positive bacteria. Furthermore, they can also kill Escherichia coli, a Gram-negative bacterium. The two mutants showed better bactericidal activity for E. coli at neutral pH than the native enzyme, which is consistent with the enzyme activities. As hnpsPLA₂ is highly stable and biocompatible, it may provide a promising therapy for bacteria infection treatment or other bactericidal applications.     

Introduction: A Close Look at the Vacuolar ATPase

The vacuolar ATPases (V-type ATPases) are a family of ATP-dependent ion pumps and found in two principal locations, in endomembranes and in plasma membranes. This family of ATPases is responsible for acidification of intracellulare compartments and, in certain cases, ion transport across the plasma membrane of eucaryotic cells. V-ATPases are composed of two distinct domains: a catalytic V₁ sector, in which ATP hydrolysis takes place, and the membrane-embedded sector, V₀, which functions in ion conduction. In the past decade impressive progress has been made in elucidating the properties structure, function and moleculare biology. These knowledge sheds light also on the evolution of V-ATPases and their related families of A-(A₁A₀-ATPase) and F-type (F₁F₀-ATPases)ATPases.     

Earthworm effects on gaseous emissions during vermifiltration of pig fresh slurry

Treatment of liquid manure can result in the production of ammonia, nitrous oxide and methane. Earthworms mix and transform nitrogen and carbon without consuming additional energy. The objective of this paper is to analyse whether earthworms modify the emissions of NH₃, N₂O, CH₄ and CO₂ during vermifiltration of pig slurry.The experiment used mesocosms of around 50 L, made from a vermifilter treating the diluted manure of a swine house. Three levels of slurry were added to the mesocosms, with or without earthworms, during one month, in triplicate. Earthworm abundance and gas emissions were measured three and five times, respectively.There was a decrease in emissions of ammonia and nitrous oxide and a sink of methane in treatments with earthworms. We suggest that earthworm abundance can be used as a bioindicator of low energy input, and low greenhouse gas and ammonia output in systems using fresh slurry with water recycling.     

Assessing the Impact of Advected African Dust on Air Quality and Health in the Eastern United States

Large quantities of African dust are carried into the southeastern United States each summer with concentrations typically in the range of 10 to 100?µg m^?3. Because approximately one-third to one-half of the dust mass is in the size range under 2.5?µm diameter, the advection of African dust has implications for the EPA's newly implemented standard for PM_2.5 particulate matter and for the assessment of human health effects. It will be difficult to assess the impact of African dust events on air quality because they occur during the summer (maximum in July) when photochemical pollution events are frequent and intense in the eastern United States. Indeed, the presence of dust could affect the evolution of photochemical dust events. In order to assess the role of African dust in air quality in the United States, it will be necessary to develop a set of diagnostic indicators; it appears that dust mineralogy and elemental composition might be useful for this purpose. Various satellite products can be used to characterize the spatial coverage of dust events and, when coupled with meteorological tools, to predict impact regions.     

Crystal structure of the archaeal A1Ao ATP synthase subunit B from Methanosarcina mazei Gö1: Implications of nucleotide-binding differences in the major A1Ao subunits A and B

The A1Ao ATP synthase from archaea represents a class of chimeric ATPases/synthases, whose function and general structural design share characteristics both with vacuolar V1Vo ATPases and with F1Fo ATP synthases. The primary sequences of the two large polypeptides A and B, from the catalytic part, are closely related to the eukaryotic V1Vo ATPases. The chimeric nature of the A1Ao ATP synthase from the archaeon Methanosarcina mazei G?1 was investigated in terms of nucleotide interaction. Here, we demonstrate the ability of the overexpressed A and B subunits to bind ADP and ATP by photoaffinity labeling. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to map the peptide of subunit B involved in nucleotide interaction. Nucleotide affinities in both subunits were determined by fluorescence correlation spectroscopy, indicating a weaker binding of nucleotide analogues to subunit B than to A. In addition, the nucleotide-free crystal structure of subunit B is presented at 1.5 A resolution, providing the first view of the so-called non-catalytic subunit of the A1Ao ATP synthase. Superposition of the A-ATP synthase non-catalytic B subunit and the F-ATP synthase non-catalytic alpha subunit provides new insights into the similarities and differences of these nucleotide-binding ATPase subunits in particular, and into nucleotide binding in general. The arrangement of subunit B within the intact A1Ao ATP synthase is presented.     

Microbial 2-Cys Peroxiredoxins: Insights into Their Complex Physiological Roles

The peroxiredoxins (Prxs) constitute a very large and highly conserved family of thiol-based peroxidases that has been discovered only very recently. We consider here these enzymes through the angle of their discovery, and of some features of their molecular and physiological functions, focusing on complex phenotypes of the gene mutations of the 2-Cys Prxs subtype in yeast. As scavengers of the low levels of H₂O₂ and as H₂O₂ receptors and transducers, 2-Cys Prxs have been highly instrumental to understand the biological impact of H₂O₂, and in particular its signaling function. 2-Cys Prxs can also become potent chaperone holdases, and unveiling the in vivo relevance of this function, which is still not established, should further increase our knowledge of the biological impact and toxicity of H₂O₂. The diverse molecular functions of 2-Cys Prx explain the often-hard task of relating them to peroxiredoxin genes phenotypes, which underscores the pleiotropic physiological role of these enzymes and complex biologic impact of H₂O₂.     

Leaf carbon isotope ratios of plants from a subtropical monsoon forest

Summary Carbon isotope ratios were used to survey the distribution of photosynthetic pathways among taxa, the relationship between photosynthetic pathway and habitat light levels, and the relationship between intercellular CO₂ levels of C₃ plants and habitat light levels within a subtropical monsoon forest in southern China. Of 128 species, most (94) possessed the C₃ photosynthetic pathway; 33 species possessed the C₄ pathway and all of these were restricted to high light locations. There was one epiphytic CAM species. The C₃ species were classified as occurring in open, intermediate, and closed canopy sites. Among C₃ species, carbon isotope ratios tended to become more negative with decreasing light availability in the habitat.C.I.W.D.P.B. Pub no 931     

Mitochondrial and cell-surface F<Subscript>0</Subscript>F<Subscript>1</Subscript>ATPsynthase in innate and acquired cardioprotection

Mitochondria are central to heart function and dysfunction, and the pathways activated by different cardioprotective interventions mostly converge on mitochondria. In a context of perspectives in innate and acquired cardioprotection, we review some recent advances in F₀F₁ATPsynthase structure/function and regulation in cardiac cells. We focus on three topics regarding the mitochondrial F₀F₁ATPsynthase and the plasma membrane enzyme, i.e.: i) the crucial role of cardiac mitochondrial F₀F₁ATPsynthase regulation by the inhibitory protein IF₁ in heart preconditioning strategies; ii) the structure and function of mitochondrial F₀F₁ATPsynthase oligomers in mammalian myocardium as possible endogenous factors of mitochondria resistance to ischemic insult; iii) the external location and characterization of plasma membrane F₀F₁ ATP synthase in search for possible actors of its regulation, such as IF₁ and calmodulin, at cell surface.     

Oriented solids as a colloid suspension in nematic liquid crystal – New tool for IR-spectroscopic and structural elucidation of inorganic compounds and glasses

Possibilities of the linear-polarized infrared (IR-LD) spectroscopy of oriented colloid suspensions in nematic liquid crystals, for structural and local structural elucidation for first time are demonstrated of inorganic compounds and glasses. The advantages of the method for tellurite and borate glasses are shown. The IR-band assignment of the typical local structural units in the glasses are proposed by a comparison with the IR-characteristics of appropriate crystalline analogues as α-TeO₂, V₂O₅, MoO₃ · H₂O and its high temperature form. The IR-spectroscopic characteristics of BO₃, BO₄ and boroxol ring are elucidated, using crystalline β-BaB₂O₄, SrB₄O₇, H₃BO₃ and B₂O₃ as model systems, where the structural moieties have been refined by single crystal X-ray diffraction.     

Transesterification of sunflower oil to biodiesel on ZrO2 supported La2O3 catalyst

ZrO₂ supported La₂O₃ catalyst prepared by impregnation method was examined in the transesterification reaction of sunflower oil with methanol to produce biodiesel. It was found that the catalyst with 21 wt% loaded La₂O₃ and calcined at 600 °C showed the optimum activity. The basic property of the catalyst was studied by CO₂-TPD, and the results showed that the fatty acid methyl ester (FAME) yield was related to their basicity. The catalyst was also characterized by TG–DTA, XRD, FTIR, SEM and TEM, and the mechanism for the formation of basic sites was discussed. It was also found that the crystallite size of support ZrO₂ decreased by loading of La₂O₃, and the model of the solid-state reaction on the surface of La₂O₃/ZrO₂ catalyst was proposed. Besides, the influence of various reaction variables on the conversion was investigated.     

Vanadyl as a Probe of the Function of the F1-ATPase-Mg2+ Cofactor

The Mg²⁺ dependent asymmetry of the F₁-ATPase catalytic sites leads to the differences in affinity for nucleotides and is an essential component of the binding-change mechanism. Changes in metal ligands during the catalytic cycle responsible for this asymmetry were characterized by vanadyl (V ^IV + O)²⁺, a functional surrogate for Mg²⁺. The ⁵¹V-hyperfine parameters derived from EPR spectra of VO²⁺ bound to specific sites on F₁ provide a direct probe of the metal ligands. Site-directed mutations of metal ligand residues cause measurable changes in the ⁵¹V-hyperfine parameters of the bound VO²⁺, thereby providing a means to identification. Initial binding of the metal–nucleotide to the low-affinity catalytic site conformation results in metal coordination by hydroxyl groups from the P-loop threonine and catch-loop threonine. Upon conversion to the high-affinity conformation, carboxyl groups from the Walker homology B aspartate and MF₁E197 become ligands in lieu of the hydroxyl groups.     

无机磷影响叠氮钠对ATP合成酶合成活性的抑制

利用ADP和放射性磷直接合成ATP的方法,研究了无机磷(P_i)和叠氮钠对猪心线粒体ATP合成酶（F₁F_O-ATPase）ATP合成活性的影响.结果发现无机磷除作为合成ATP的底物参与F₁F_O-ATPase的合成反应外,还对F₁F_O-ATPase的合成活性呈现抑制作用,在1 mmol/L ADP存在时,随着P_i浓度由0.01～10 mmol/L增加,抑制合成作用越来越强.与叠氮钠在低浓度时(小于1 mmol/L)只抑制ATP水解,不影响ATP合成的观点不同.实验结果显示0.1 mmol/L叠氮钠表观激活F₁F_O-ATPase的ATP合成活性,且激活程度与反应体系中所加P_i的浓度呈负相关.当固定P_i浓度（0.1 mmol/L）后,随着叠氮钠浓度的增加表观激活程度也在变化,叠氮钠与磷浓度相等时表观激活程度最大,直至叠氮钠浓度接近0.5 mmol/L时,开始呈现表观抑制现象,叠氮钠浓度高于1 mmol/L之后,就出现解偶联现象.     

Mutagenic Analysis of the F 0 Stator Subunits

The a and b subunits constitute the stator elements in the F₀ sector of F₁F₀-ATP synthase.Both subunits have been difficult to study by physical means, so most of the information onstructure and function relationships in the a and b subunits has been obtained using mutagenesisin combination with biochemical methods. These approaches were used to demonstrate thatthe a subunit in association with the ring of c subunits houses the proton channel throughF₁F₀-ATP synthase. The map of the amino acids contributing to the proton channel is probablycomplete. The two b subunits dimerize, forming an extended flexible unit in the peripheralstalk linking the F₁ and F₀ sectors. The unique characteristics of specific amino acid substitutionsaffecting the a and b subunits suggested differential effects on rotation during F₁F₀-ATPaseactivity.     

Co-function of C3-and C4-photosynthetic pathways in C3, C4 and C3-C4 intermediate Flaveria species

The potential for C₄ photosynthesis was investigated in five C₃-C₄ intermediate species, one C₃ species, and one C₄ species in the genus Flaveria, using ¹⁴CO₂ pulse-¹²CO₂ chase techniques and quantum-yield measurements. All five intermediate species were capable of incorporating ¹⁴CO₂ into the C₄ acids malate and aspartate, following an 8-s pulse. The proportion of ¹⁴C label in these C₄ products ranged from 50–55% to 20–26% in the C₃-C₄ intermediates F. floridana Johnston and F. linearis Lag. respectively. All of the intermediate species incorporated as much, or more, ¹⁴CO₂ into aspartate as into malate. Generally, about 5–15% of the initial label in these species appeared as other organic acids. There was variation in the capacity for C₄ photosynthesis among the intermediate species based on the apparent rate of conversion of ¹⁴C label from the C₄ cycle to the C₃ cycle. In intermediate species such as F. pubescens Rydb., F. ramosissima Klatt., and F. floridana we observed a substantial decrease in label of C₄-cycle products and an increase in percentage label in C₃-cycle products during chase periods with ¹²CO₂, although the rate of change was slower than in the C₄ species, F. palmeri. In these C₃-C₄ intermediates both sucrose and fumarate were predominant products after a 20-min chase period. In the C₃-C₄ intermediates, F. anomala Robinson and f. linearis we observed no significant decrease in the label of C₄-cycle products during a 3-min chase period and a slow turnover during a 20-min chase, indicating a lower level of functional integration between the C₄ and C₃ cycles in these species, relative to the other intermediates. Although F. cronquistii Powell was previously identified as a C₃ species, 7–18% of the initial label was in malate+aspartate. However, only 40–50% of this label was in the C-4 position, indicating C₄-acid formation as secondary products of photosynthesis in F. cronquistii. In 21% O₂, the absorbed quantum yields for CO₂ uptake (in mol CO₂·[mol quanta]^-1) averaged 0.053 in F. cronquistii (C₃), 0.051 in F. trinervia (Spreng.) Mohr (C₄), 0.052 in F. ramosissima (C₃-C₄), 0.051 in F. anomala (C₃-C₄), 0.050 in F. linearis (C₃-C₄), 0.046 in F. floridana (C₃-C₄), and 0.044 in F. pubescens (C₃-C₄). In 2% O₂ an enhancement of the quantum yield was observed in all of the C₃-C₄ intermediate species, ranging from 21% in F. ramosissima to 43% in F. pubescens. In all intermediates the quantum yields in 2% O₂ were intermediate in value to the C₃ and C₄ species, indicating a co-function of the C₃ and C₄ cycles in CO₂ assimilation. The low quantum-yield values for F. pubescens and F. floridana in 21% O₂ presumably reflect an ineffcient transfer of carbon from the C₄ to the C₃ cycle. The response of the quantum yield to four increasing O₂ concentrations (2–35%) showed lower levels of O₂ inhibition in the C₃-C₄ intermediate F. ramosissima, relative to the C₃ species. This indicates that the co-function of the C₃ and C₄ cycles in this intermediate species leads to an increased CO₂ concentration at the site of ribulose-1,5-bisphosphate carboxylase/oxygenase and a concomitant decrease in the competitive inhibition by O₂.Abbreviations PEP phosphoenolpyruvate - PGA 3-phosphoglycerate - RuBP ribulose-1,5-bisphosphate