Dense attosecond electron sheets from laser wakefields using an up-ramp density transition

Controlled electron injection into a laser-driven wakefield at a well defined space and time is reported based on particle-in-cell simulations. Key novel ingredients are an underdense plasma target with an up-ramp density profile followed by a plateau and a fairly large laser focus diameter that leads to an essentially one-dimensional (1D) regime of laser wakefield, which is different from the bubble (complete blowout) regime occurring for tightly focused drive beams. The up-ramp profile causes 1D wave breaking to occur sharply at the up-ramp-plateau transition. As a result, it generates an ultrathin (few nanometer, corresponding to attosecond duration), strongly overdense relativistic electron sheet that is injected and accelerated in the wakefield. A peaked electron energy spectrum and high charge (∼nC) distinguish the final sheet.

Site specificity on OH α-H abstraction reaction for a zwitterionic β-hairpin peptide in aqueous solution: a theoretical investigation

Protein backbone oxidation was investigated by studying the α-H abstraction reaction in a ß-hairpin peptide, called Chignolin (PDB ID 1UAO), with density functional theory calculation at B3LYP/6-31G(d,p) without any constraint. In order to stabilize the zwitterionic form of Chignolin with the salt bridges, the effects of aqueous solution were implemented by using microsolvation combined with a conductor-like polarizable continuum model (CPCM). Comparison between three glycine residues located at three different sites in Chignolin was used to examine the possible site specificity of this backbone oxidation. To construct the reaction profile of these α-H abstraction reactions, the pre- and postreactive complexes along with their associated transition states were located and verified with the intrinsic reaction coordinate (IRC) method. The bond dissociation energy and reaction rates of these OH α-H abstraction reactions were calculated with transition state theory. The differences in this abstraction reaction between the neutral and zwitterionic forms of Chignolin were also compared. A molecular dynamics simulation was implemented to study the explicit solvation effect on the abstracted Chignolin structure. The range of the simulation time scale covers from femtoseconds to microseconds, i.e., from onset of the abstraction to the abstracted products reaching thermal equilibrium. Our results show that there are three kinds of site-specificity in this abstraction reaction. The reactivity and stability of the abstraction products and their abstraction modes are all dependent on the location where OH attacks. Furthermore, the free energy landscapes of these abstraction products are distinctively different. This may imply that the pathological disorders or diseases caused by this type of radicals are also dependent on the abstraction location.

Inhibition of Na+/K+-ATPase by Antcins, Unique Steroid-Like Compounds in Antrodia camphorate

The inhibition of Na+/K+ -ATPase by versatile steroid-like compounds contributes to the putative therapeutic effects of many Chinese medicinal cardiac products via the same molecular mechanism triggered by cardiac glycosides. Five major steroid-like compounds, antcin A, B, C, H, and K were isolated from Niuchangchih (Antrodia camphorata), a unique Taiwan mushroom, and all inhibited Na+/K+ -ATPase. Antcin A exhibited significantly higher inhibitory potency than the other four antcins, though weaker than ginsenoside Rh2 . In contrast, cortisone (an analogous steroid with anti-inflammatory effects stronger than antcin A) showed no detectable inhibitory potency. Molecular modeling has shown that antcins bind to Na+/K+ -ATPase with the steroidal skeleton structurally upside-down in comparison with ginsenoside Rh2 . The inhibitory potency of antcin A is attributed to steroidal hydrophobic interaction within the binding pocket and the formation of three hydrogen bonds between its carboxyl group and two cationic residues around the cavity entrance of Na+/K+ -ATPase. The presence of an additional carbonyl or hydroxyl group at C7 of the other four antcins leads to severe repulsion in the hydrophobic pocket, and thus significantly reduces inhibitory potency. It is proposed that antcin A is a bi-functional compound that exerts anti-inflammatory effects and that enhances blood circulation via two different molecular mechanisms.

Binding orientation and specificity of calmodulin to rat olfactory cyclic nucleotide-gated ion channel

Calmodulin (CaM), the primary intracellular Ca(2+) receptor, regulates a large number of key enzymes and controls a wide spectrum of important biological responses. Recognition between CaM and its target sequence in rat olfactory cyclic nucleotide-gated ion channel (OLFp) was investigated by circular dichroism (CD), fluorescence, and NMR spectroscopy. Fluorescence data showed the OLFp tightly bound to CaM with a dissociation constant of 12 nM in a 1:1 stoichiometry. Far-UV CD data showed that approximately 60% of OLFp residues formed α-helical structures when associated with CaM. NMR data showed that most of the (15)N-(1)H HSQC cross-peaks of the (15)N-labeled CaM not only shifted but also split into two sets of peaks upon association with the OLFp. Our data indicated that the two distinct CaM/OLFp complexes existed simultaneously with stable structures that were not interexchangeable within the NMR time scale. In light of the palindromic sequence of OLFp (FQRIVRLVGVIRDW) for CaM targeting, we proposed that the helical OLFp with C2 symmetry may bind to CaM in two orientations. This hypothesis is supported by the observation that only one set of (15)N-(1)H HSQC cross-peaks of the (15)N-labeled CaM was detected upon association with OLFp-M13 chimeric peptide (OLFMp), a mutated OLFp lacking the palindromic feature. The binding specificity of OLFMp to CaM was restored when the palindromic feature was destroyed. Binding modes of CaM/OLFp and CaM/OLFMp simulated by molecular docking were in accord with their distinct patterns observed in HSQC spectra. Our studies suggest that the palindromic residues in OLFp are crucial for the orientation-specific recognition by CaM.

Oxygen radical-mediated oxidation reactions of an alanine peptide motif - density functional theory and transition state theory study

Background

Oxygen-base (O-base) oxidation in protein backbone is important in the protein backbone fragmentation due to the attack from reactive oxygen species (ROS). In this study, an alanine peptide was used model system to investigate this O-base oxidation by employing density functional theory (DFT) calculations combining with continuum solvent model. Detailed reaction steps were analyzed along with their reaction rate constants.

Results

Most of the O-base oxidation reactions for this alanine peptide are exothermic except for the bond-breakage of the C_α-N bond to form hydroperoxy alanine radical. Among the reactions investigated in this study, the activated energy of OH α-H abstraction is the lowest one, while the generation of alkylperoxy peptide radical must overcome the highest energy barrier. The aqueous situation facilitates the oxidation reactions to generate hydroxyl alanine peptide derivatives except for the fragmentations of alkoxyl alanine peptide radical. The C_α-C_β bond of the alkoxyl alanine peptide radical is more labile than the peptide bond.

Conclusion

the rate-determining step of oxidation in protein backbone is the generation of hydroperoxy peptide radical via the reaction of alkylperoxy peptide radical with HO₂. The stabilities of alkylperoxy peptide radical and complex of alkylperoxy peptide radical with HO₂ are crucial in this O-base oxidation reaction.

Superconductivity above 33 K in (Ca(₁ - x)Na(x))Fe₂As₂

We report the synthesis of (Ca₀.₃₃Na₀.₆₆)Fe₂As₂ showing a superconducting transition with T(c) above 33 K. Both dc magnetic susceptibility or specific heat measurements indicated the bulk superconductivity nature of the sample. We also have successfully grown single crystals of the (Ca₀.₃₃Na₀.₆₆)Fe₂As₂ superconductors. The single crystals exhibit sharp superconducting transitions with T(c) above 33 K. The effects of magnetic field on the superconducting transitions are studied, giving rise to high upper critical fields with H(c₂)(c)≈85 T and H(c₂)(ab)≈172 T, respectively. The anisotropy parameter was calculated to be around 2.

Oocyte and ovary morphological observation of gray wolf (Canis lupus)

Abstract

The present study was carried out to describe the reproductive system of a single adult female wolf, including the uterine horns, cervix, ovaries and follicles. The cumulus oocytes complexes (COCs) and oocytes were also examined. The results showed that the size of each ovary was about 9 × 6 mm with an average of weight of 461.3 mg. The uterus was Y-shaped, and the length of each uterine horn was 14 cm. The distance from the cervix to the bifurcation of the uterine horns was also 14 cm. The left ovary had two large follicles on the surface with a diameter more than 4 mm, while the right ovary had no protuberant follicles. The ovaries were covered with a lot of fat, and were well developed. The COCs derived from the antral follicles were dark, and the nuded oocytes had a dark cytoplasm. The diameter of the oocytes removed from the antral follicles was 116.8 μm on average. The ovaries had a smooth surface and all the follicles were under the surface except for two big follicles on the left ovary. Histological examination of the ovaries by haematoxylin and eosin staining demonstrated that the primordial, primary, preantral and antral follicles were scattered in the cortex, the medulla was abundant with blood vessels. This study preliminarily reveals the features of the wolf reproductive system and the structure of its oocytes and ovaries, which might be indicative for further study and the protection of the species.

Preparation of xanthated bentonite and its removal behavior for Pb(II) ions

Xanthate was successfully grafted onto bentonite by a relatively simple solution reaction. The obtained xanthated bentonite (XBent) was characterized by FT-IR spectrophotometer, thermogravimetric analysis (TG), particle size analysis, x-ray diffraction (XRD) and scanning electron microscopy (SEM). XBent acting as a type of environmentally friendly adsorbent was applied to remove lead ions from aqueous solutions. The optimum conditions were as follows: [Pb(2+)] = 500 mg L(-1), [XBent] = 2 g L(-1), pH = 5.0; oscillating 60 min under 200 rpm at 25 degrees C. The removal rate of lead was up to 99.9%. It was found that the lead(II) ions-XBent adsorption isotherm model fitted well to the Freundlich isotherm. The adsorption mechanism was also investigated by SEM and XRD, which concluded that lead ions were complexed or chelated with XBent. XBent appears to have potential to be used later in water treatment as a type of inorganic polymer reagent.

Preparation of solid composite polyferric sulfate and its flocculation behavior for wastewater containing high concentration organic compounds

A new kind of inorganic polymer flocculant, the solid composite polyferric sulfate (SPFS) was prepared using ferrous sulfate and Na-Bentonite. The obtained SPFS was characterized by FT-IR spectra, thermogravimetric analysis (TG), scanning electron microscope (SEM) and X-ray Diffraction (XRD). It showed that SPFS was a kind of composite inorganic polymer, which was the complex of PFS and Na-Bent, not only a simple mixture of raw materials. The synthetic mechanism and surface structure of SPFS were also discussed. Acting as a kind of environment-friendly flocculating agent, the solid composite polyferric sulfate (SPFS) was applied in pretreatment of potato starch industry wastewater, a typical wastewater containing high concentration organic compounds, which COD was above 6,000 mg/L. The results showed that the COD removal value reached 4,070 mg/L with COD removal rates being 46.6%. Based on these results, it is suggested that the SPFS can be attractive pretreatment agent for the starch industry wastewater.

Construction and comparison of fluorescence and bioluminescence bacterial biosensors for the detection of bioavailable toluene and related compounds

Environmental pollution with petroleum products such as benzene, toluene, ethylbenzene, and xylenes (BTEX) has garnered increasing awareness because of its serious consequences for human health and the environment. We have constructed toluene bacterial biosensors comprised of two reporter genes, gfp and luxCDABE, characterized by green fluorescence and luminescence, respectively, and compared their abilities to detect bioavailable toluene and related compounds. The bacterial luminescence biosensor allowed faster and more-sensitive detection of toluene; the fluorescence biosensor strain was much more stable and thus more applicable for long-term exposure. Both luminescence and fluorescence biosensors were field-tested to measure the relative bioavailability of BTEX in contaminated groundwater and soil samples. The estimated BTEX concentrations determined by the luminescence and fluorescence bacterial biosensors were closely comparable to each other. Our results demonstrate that both bacterial luminescence and fluorescence biosensors are useful in determining the presence and the bioavailable fractions of BTEX in the environment.

Deposition Rate Effect of Alq3 Thin Film Growth: A Kinetic Monte Carlo Study

This paper is the winner of the Young Scientist Award at the Asian Chemical Congress in Kuala Lumpur, 2007. Applying the Kinetic Monte Carlo (KMC) technique, we successfully investigated the effect of deposition rate on the growth pattern of an Alq3 thin film. In good agreement with experimental results, our simulation results indicate that there exists a transition growth in terms of the deposition rate that corresponds to the transition between the island growth and random deposition growth. In the regions of island growth (where the deposition rate is lower than 1.1 Å s–1) and random deposition growth (where the deposition rate is higher than 3 Å s–1), the surface morphology is not suitable for luminant devices because of a high roughness, a larger inner vacancy ratio at higher deposition rate, and low homogeneity at lower deposition rate conditions. Within the transition growth region (deposition rate is between 1.1 and 3.0 Å s–1), the homogeneity of the film surface improves as the deposition rate increases. Not only does the pattern of the island structures become blurred, but the inner vacancy ratio and surface roughness also remain low as the deposition rate increases. From our results, there may exist a deposition rate to optimize the Alq3 film with a suitable surface morphology for luminant devices.

Magnesium lithospermate B possesses inhibitory activity on Na+,K+-ATPase and neuroprotective effects against ischemic stroke

AIM

To examine if magnesium lithospermate B (MLB) extracted from Danshen, the dried roots of Salvia miltiorrhiza, may act as an active component responsible for the cardiac therapeutic effect of this traditional Chinese herb via the same molecular mechanism triggered by cardiac glycosides, such as ouabain and digoxin. Moreover, we wanted to test if MLB may provide neuroprotection against ischemic stroke as observed for cardiac glycosides.

METHODS

Similarity in the chemical structure and molecular configuration between MLB and ouabain was analyzed. The inhibition potency of MLB and ouabain on Na( +),K( +) -ATPase activity of a commercial product, as well as in purified membrane fractions from rat brain and heart tissues, was examined and compared. Neuroprotective effect of MLB against ischemic stroke was also evaluated using a cortical brain slice-based assay model.

RESULTS

Dose-dependent inhibition on the commercial Na( +),K( +)-ATPase equivalent to that for ouabain was observed for MLB of approximately half dosage by weight. This relative potency of ouabain and MLB was also observed for their inhibition on Na( +),K( +)-ATPase activity of plasma membrane purified from rat tissues, although these 2 inhibitors exhibited somewhat lower competence in these crude extracts. In ischemic gerbil brains, post-treatment with MLB significantly reduced the infarct size, visualized by 2,3,5-triphenyltetrazolium chloride staining, by approximately 55% when compared with the control group.

CONCLUSION

These results evidently suggest that the cardiac therapeutic effect of Danshen should be at least partly attributed to the effective inhibition of Na( +),K( +)-ATPase by MLB, and that MLB provides anti-ischemic neuroprotection in gerbils subjected to focal ischemia and reperfusion.

Site specificity of α-H abstraction reaction among secondary structure motif—Anab initio study

The initial step of protein oxidation is studied through alpha-H abstraction by an OH radical with various secondary structure motifs of proteins. It is found that there exist preferential alpha-Hs in this kind of abstractions. The typical abstraction mechanism involves three steps: forming a pre-reactive complex before abstraction, the abstraction reaction, and the H(2)O detachment from a post-reactive complex to form the product, C(alpha)-center radical. Using the stability of the pre-reactive complex and the reaction barrier, we provide some explanation for this site preference. The feasibility of alpha-H abstraction by OH radical depends not only on the types of secondary structure, but also on the reaction condition, such as in aqueous or in gas phase. Moreover, the reactivity of the abstraction also depends on the location of alpha-H in the secondary structure motifs. The preferential alpha-Hs to be abstracted in beta-sheet are those immediate to the amide or carbonyl group, and without involving hydrogen bonding, whereas in reverse turns, the preferential alpha-Hs are near the C-terminal of type I and near the N-terminal of type II. In general, the alpha-Hs in alpha-helix are more difficult to be abstracted than those in beta-sheet and polypeptide in linear form. It is consistent with the trend of their bond dissociation energies. Our theoretical rate constant of N-acetyldiglycin-methylamide (Ac(Gly)(2)NHCH(3)) in aqueous solution (6.75 x 10(8) M(-1) s(-1)) is close to the experimental observation of N-acetyldiglycinamide (Ac(Gly)(2)NH(2)) (8.6 x 10(8) M(-1) s(-1)).

Gene families encoding isoforms of two major sesame seed storage proteins, 11S globulin and 2S albumin

Sesame (Sesamum indicum L.) seed has been recognized as a nutritional protein source owing to its richness in methionine. Storage proteins have been implicated in allergenic responses to sesame consumption. Two abundant storage proteins, 11S globulin and 2S albumin, constitute 60-70 and 15-25% of total sesame proteins, respectively. Two gene families separately encoding four 11S globulin and three 2S albumin isoforms were identified in a database search of 3328 expressed sequence tag (EST) sequences from maturing sesame seeds. Full-length cDNA sequences derived from these two gene families were completed by PCR using a maturing sesame cDNA library as the template. The amino acid compositions of these deduced storage proteins revealed that the richness in methionine is attributed mainly to two 2S albumin isoforms and partly to one 11S globulin isoform. The presence of four 11S globulin and three 2S albumin isoforms resolved in SDS-PAGE was confirmed by MALDI-MS analyses. The abundance of these isoforms was in accord with the occurrence frequency of their EST sequences in the database. A comprehensive understanding of these storage proteins at the molecular level may also facilitate the identification of allergens in crude sesame products that have caused severe allergic reactions increasingly reported in the past decade.

Even-Numbered Metal Chain Complexes: Synthesis, Characterization, and DFT Analysis of [Ni4(μ4-Tsdpda)4(H2O)2] (Tsdpda2- = N-(p-toluenesulfonyl)dipyridyldiamido), [Ni4(μ4-Tsdpda)4]+, and Related Ni4 String Complexes

The synthesis and the X-ray structure of two complexes exhibiting a linear chain of four nickel atoms is reported, following Ni4(mu4-phdpda)4 (1), which had been characterized previously. [Ni4(mu4-Tsdpda)4(H2O)2], where H2Tsdpda is N-(p-toluenesulfonyl)dipyridyldiamine (2), is axially coordinated to two water molecules, at variance with 1. One-electron oxidation of 2 resulted in the loss of the axial ligands, yielding [Ni4(mu4-Tsdpda)4]+, [3]+, which was also structurally characterized. Finally, we report the structure of Ni4(mu4-DAniDANy)4 (4), a complex synthesized starting from the new ligand N,N'-bis-p-anisyl-2,7-diamino-1,8-naphthyridine. Magnetic measurements concluded that 4 is diamagnetic, like 1, whereas 2 is antiferromagnetic (-2J(14) = 80 cm(-)(1), using the Heisenberg Hamiltonian H = -2J(14) S(1).S(4)), as are other axially coordinated chains with an odd number of nickel atoms. DFT calculations are reported on these complexes in order to rationalize their electronic structure and their magnetic behavior. The magnetic properties of the [Ni4]8+ complexes are governed by the electronic state of the Ni(II) atoms, which may be either low-spin (S = 0), or high-spin (S = 1). DFT calculations show that the promotion to high spin of two Ni atoms in the chain, either external or internal, depends on the interplay between axial and equatorial coordination. The synergy between axial coordination and the presence of electron-withdrawing toluenesulfonyl substituents in 2 favors the promotion to the high-spin state of the terminal Ni atoms, thus yielding an antiferromagnetic ground state for the complex. This is at variance with complexes 1 and 4, for which the lowest quintet state results from the promotion to high spin of the internal nickel atoms, together with an important ligand participation, and is destabilized by 9 to 16 kcal mol(-1) with respect to the diamagnetic ground state.

Theoretical investigation of the photoinitiated folding of HP-36

A computational model was developed to examine the phototriggered folding of a caged protein, a protein modified with an organic photolabile cross-linker. Molecular dynamics simulations of the modified 36-residue fragment of subdomain B of chicken villin head piece with a photolabile linker were performed, starting from both the caged and the uncaged structures. Construction of a free-energy landscape, based on principal components as well as on radius of gyration versus root-mean-square deviation, and circular dichroism calculations were employed to characterize folding behavior and structures. The folded structures observed in the molecular dynamics trajectories were found to be similar to that of the wild-type protein, in agreement with the published experimental results. The free-energy landscapes of the modified and wild-type proteins have similar topology, suggesting common thermodynamic/kinetic behavior. The existence of small differences in the free-energy surface of the modified protein from that of the native protein, however, indicates subtle differences in the folding behavior.

Partition functions and finite-size scalings of Ising model on helical tori

The exact closed forms of the partition functions of a two-dimensional Ising model on square lattices with twisted boundary conditions are given. The constructions of helical tori are unambiguously related to the twisted boundary conditions by virtue of the SL(2, Z) transforms. The numerical analyses on the deviations of the specific-heat peaks away from the bulk critical temperature reveal that the finite-size effect of herical tori is independent of the chirality.