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In the present work the erosion behavior on the surface of GaN epi-layer by the impact of various slow highly charged heavy ions (SHCIs, including Arq+. Xeq+ and Pbq+, in two incidence geometries) was investigated. Atomic force microscopy reveals a well-defined threshold of potential energy carried by the incident heavy ions accounting for the surface erosion. This threshold also depends on the projected range of the SHCIs, the longer the projected range, the higher the potential energy required for the onset of surface erosion. And the etched depth is close to a linear function of potential energy deposited, increasing with the potential energy increases. Moreover, the etching rate for 60 degrees off normal incidence is by more than a factor of 2 larger than etching rate for normal incidence, and the etch rate by Xeq+ is larger than by Pbq+ under the same potential energy and incident direction. And a mechanism is discussed. (C) 2010 Elsevier B.V. All rights reserved.

Chitinases are a group of enzymes capable of hydrolysing theβ-(1,4)-glycosidic bonds of chitin, an essential component of the fungal cell wall, the shells of nematode eggs, and arthropod exoskeletons. Chitinases from pathogenic fungi have been shown to be putative virulence factors, and can play important roles in infecting hosts. However, very limited information is available on the structure of chitinases from nematophagous fungi. Here, we present the 1.8 Å resolution of the first structure of a Family 18 chitinase from this group of fungi, that ofClonostachys roseaCrChi1, and the 1.6 Å resolution of CrChi1 in complex with a potent inhibitor, caffeine. Like other Family 18 chitinases, CrChi1 has the DXDXE motif at the end of strandβ5, with Glu174 as the catalytic residue in the middle of the open end of the (β/α)8barrel. Two caffeine molecules were shown to bind to CrChi1 in subsites −1 to +1 in the substrate-binding domain. Moreover, site-directed mutagenesis of the amino acid residues forming hydrogen bonds with caffeine molecules suggests that these residues are important for substrate binding and the hydrolytic process. Our results provide a foundation for elucidating the catalytic mechanism of chitinases from nematophagous fungi and for improving the pathogenicity of nematophagous fungi against agricultural pest hosts.

InAs 0.05 Sb 0.95 film with thickness of 100 μm has been grown by a modified LPE technique, and optical properties of the material have been investigated using spectroscopic-ellipsometry at room temperature within 1.5–4.5 eV. The dielectric function e ( E ) spectra that show high-lying interband structure associated with E 1 , E 1 + Δ 1 , and E 2 transition have been observed and analyzed on the basis of a simplified model of the interband transitions. Results agree satisfactorily with the experimental data over the entire range of photon energies. The transition energies E 1 and E 2 , the spin–orbit splitting energy Δ 1 , and the broadening parameters are given, respectively.

Cuticle-degrading proteases are involved in the breakdown of cuticle/eggshells of nematodes or insects, a hard physical barrier against fungal infections. Understanding the 3-dimensional structures of these proteins can provide crucial information for improving the effectiveness of these fungi in biocontrol applications, e.g., by targeted protein engineering. However, the structures of these proteases remain unknown. Here, we report the structures of two cuticle-degrading proteases from two species of nematophagous fungi. The two structures were solved with X-ray crystallography to resolutions of 1.65 A (Ver112) and 2.1 A (PL646), respectively. Crystal structures of PL646 and Ver112 were found to be very similar to each other, and similar to that of proteinase K from another fungus Tritirachium album. Differences between the structures were found among residues of the substrate binding sites (S1 and S4). Experimental studies showed that the enzymes differed in hydrolytic activity to synthetic peptide substrates. Our analyses of the hydrophobic/hydrophilic and electrostatic features of these two proteins suggest that their surfaces likely play important roles during fungal infection against nematodes. The two crystal structures provide a solid basis for investigating the relationship between structure and function of cuticle-degrading proteases.

Cobalt nanowires with diameter 75 nm were synthesized in ion track-etched membranes by electrochemical deposition. Scanning electron microscopy displays cylindrical wires with smooth and homogeneous contours. X-ray diffraction studies indicate that the wires possess a face centered cubic structure and a preferred growth orientation along the [1 1 0] direction. The wires exhibit magnetic anisotropy, which is observed and is ascribed to shape anisotropy. The optical extinction spectrum shows a band which probably originates from a surface plasmon resonance.

The InAsSb epilayers with a cutoff wavelength of 11.5 μm were successfully grown on highly lattice-mismatched semi-insulating (1 0 0) GaAs substrate by the modified liquid phase epitaxy (LPE) technique. Fourier transform infrared (FTIR) transmission spectrum revealed a strong band gap narrowing for this alloy. The electrical properties were investigated by the Van der Pauw measurements at 300 and 77 K. InAsSb epilayers showed high Hall mobilities being 11,800 cm 2 /V s at room temperature (RT). After an annealing treament for 10 h, the electron mobility at 77 K were improved from 1730 cm 2 /V s (prior to annealing) to 13,470 cm 2 /V s. Wet etching was used to display the surface etch pits prior to and after annealing treatment, showing that the mobility improvement was due to the reduction of the etch pits density.

Cuticle-degrading proteases are extracellular subtilisin-like serine proteases that are secreted by entomopathogenic and nematophagous fungi. These proteases can digest the host cuticle during invasion of an insect or nematode and serve as a group of important virulence factors during the infection of nematodes by nematophagous fungi. To elucidate the mechanism of interaction between the proteases and the nematode cuticle, two cuticle-degrading proteases, Ver112 from Lecanicillium psalliotae (syn. Verticillium psalliotae) and PL646 from Paecilomyces lilacinus, were studied. The Ver112 protein and the complex between PL646 and the substrate-like tetrapeptide inhibitor methoxysuccinyl-Ala-Ala-Pro-Val-chloromethyl ketone (MSU-AAPV) were crystallized using the hanging-drop vapour-diffusion method at 289 K. The crystals were analyzed by X-ray diffraction to resolutions of 1.65 and 2.2 A, respectively. These analyses identified that crystals of Ver112 belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 43.7, b = 67.8, c = 76.3 A, alpha = beta = gamma = 90 degrees . In contrast, crystals of the PL646-MSU-AAPV complex belonged to space group P2(1), with unit-cell parameters a = 65.1, b = 62.5, c = 67.6 A, beta = 92.8 degrees .

InAs0.05Sb0.95 thick film with thickness of about 120 μm was grown by modified LPE technique on InAs substrate. The Fourier transform infrared (FTIR) transmission measurement revealed that the cutoff wavelength (defined at the mid-transmittance) is 12.5 μm for InAs0.05Sb0.95 thick film. An electron mobility of 23,900 cm2/V s with a carrier density of 2.37 × 1016 cm−3 at 300 K has been achieved. The investigation of the lattice dynamics of InAs0.05Sb0.95 has been made by using Raman scattering. These results indicate its potential applications for infrared detectors in long wavelength range and high-speed electron devices.

CdS nanotubes and nanowires have been synthesized with controlled dimensions by means of template-electrodeposition method in etched ion-track membranes. The diameters of nanotubes and nanowires are between 20 and 110 nm, and the lengths are up to tens of micrometers. X-ray diffraction (XRD) and selected area electron diffraction (SAED) pattern investigations demonstrate that CdS nanotubes and nanowires are polycrystalline in nature. The UV–vis absorption spectra of CdS nanotubes and nanowires embedded in polycarbonate (PC) membranes show that the absorption edges of PC films shift towards the shorter wavelength, with decreasing diameters of the deposited nanostructures. The results indicate that nanowires are formed from nanotubes by nanotube-stuffing-growth mechanism.

ZnO nanorods with 30 nm-diameter ultra-thin pinheads and ultra-thin nanobelts were successfully synthesized using a thiourea solution to etch nanorods and nancombs, which were obtained by a conventional thermal evaporation method. The materials obtained were investigated by field emission scanning electron microscopy and energy-dispersive X-ray fluorescence. The data shows that hydrogen ions play an important role in synthesizing ZnO nanorods with ultra-thin pinheads and ultra-thin nanobelts. Field emission plots indicated that the turn-on field was reduced from 2.10 V/μm to 1.55 V/μm after thiourea solution treatment at a current density of 0.1 μA/cm2. Room-temperature photoluminescence spectra from ZnO nanostructures showed the PL spectrum peaks shifted towards short wavelengths with a large enhancement of UV bands compared with those of ZnO nanorods and nanocombs.

In the present work specimens of mono-crystalline silicon carbide (4H polytype) were irradiated to three successively increasing ion fluences ranging from 7.2 × 10 14 to 6.0 × 10 16 ions/cm 2 (corresponding to the peak displacement damage of 1, 4 and 13 dpa) with Ne and Xe ions respectively with the energy of 2.3 MeV/amu. The irradiated specimens were subsequently annealed at temperatures of 1173 and 1273 K. Defect structure was investigated with transmission electron microscopy (TEM) using a cross-sectional specimen preparation technique. The typical microstructures of the annealed specimens irradiated with Ne or Xe ions to high fluences are characterized by small gas bubbles in high concentration in the peak damage region and black dots and dislocation loops (located in the basal plane) in a shallower and broader depth region. Larger dislocation loops were observed in the Xe-ion irradiated specimen than in the Ne-ion irradiated specimen at the same peak damage level. The enhanced formation of dislocation loops in the case of Xe-ion irradiation is understandable by assuming stronger inclination of heavier inert-gas atoms to occupy substitute site in the peak damage region.

Thermally grown amorphous SiO2 samples were implanted at room temperature (RT) with 120 keV C-ions to a dose ranging from 1.0 × 1016 to 8.6 × 1017C ions/cm2, then irradiated at RT with 950 MeV Pb, 345 or 1754 MeV Xe ions to a fluence in the region from 1.0 × 1011 to 3.8 × 1012 ions/cm2, respectively. The irradiated samples were investigated using micro-FTIR and micro-Raman spectroscopes. It was found that new chemical bonds such as Si–C, C C(O), C C and Si(C)–O–C bonds formed significantly in the C-doped SiO2 films after heavy ion irradiations. The evolution of Si–O–C bonds and possible mechanism of structural modification in C-doped SiO2 induced by swift heavy ion irradiations were discussed.

In this work a study of damage production in gallium nitride via elastic collision process (nuclear energy deposition) and inelastic collision process (electronic energy deposition) using various heavy ions is presented. Ordinary low-energy heavy ions (Fe+ and Mo+ ions of 110 keV), swift heavy ions (Pb-208(27+) ions of 1.1 MeV/u) and slow highly-charged heavy ions (Xen+ ions of 180 keV) were employed in the irradiation. Damage accumulation in the GaN crystal films as a function of ion fluence and temperature was studied with RBS-channeling technique, Raman scattering technique, scanning electron microscopy (SEM) and transmission electron microscopy (TEM). For ordinary low-energy heavy ion irradiation, the temperature dependence of damage production is moderate up to about 413 K resulting in amorphization of the damaged layer. Enhanced dynamic annealing of defects dominates at higher temperatures. Correlation of amorphization with material decomposition and nitrogen bubble formation was found. In the irradiation of swift heavy ions, rapid damage accumulation and efficient erosion of the irradiated layer occur at a rather low value of electronic energy deposition (about 1.3 keV/nm(3)),. which also varies with irradiation temperature. In the irradiation of slow highly-charged heavy ions (SHCI), enhanced amorphization and surface erosion due to potential energy deposition of SHCI was found. It is indicated that damage production in GaN is remarkably more sensitive to electronic energy loss via excitation and ionization than to nuclear energy loss via elastic collisions. (c) 2006 Elsevier B.V. All rights reserved.

The rare-earth manganites R 1−x A x MnO 3 have stimulated considerable scientific and technological interest in recent years due to their exotic electronic and magnetic properties [1]The fascinating physics of these materials is driven by a close coupling between charge, spin, lattice and orbital degree of freedom, which has commonly resulted in phase separation between charge/orbital order (COO) and ferromagnetic (FM) metallic phase. One family of these manganites is Pr 1−x Ca x MnO 3 with 0.3≤ × ≤0.75 which has a narrow one-electron bandwidth of e band (W) and exhibits an insulator-metal transition (IMT) [2]. With the doping level unchanged, the substitution of Sr2+ for Ca2+ would modify the local structural parameters such as Mn-O-Mn bond angel and bond length, hence widens the W. As a result, an intense competition between the COO phase and FM metallic phase upon Sr doping is expected. Strain or pressure would provide a very efficient means of modulating the magnetic and electric properties of these materials. Here we investigate the strain effect on phase separation in Pr 0.7 (Ca 0.6 Sr 0.4 ) 0.3 MnO 3 (PCSMO) system with electron spin resonance (ESR). ESR is an efficacious method for the study of magnetic interaction and phase separation in these manganites due to its extreme sensitivity to spin correlation and local environment [3].

Highly oriented pyrolytic graphite (HOPG) samples were irradiated by Xe ions of initial kinetic energy of 3 MeV/u. The irradiations were performed at temperatures of 500 and 800 K. Scanning tunneling microscopy (STM) images show that the tracks occasionally have elongated structures under high-temperature irradiation. The track creation yield at 800 K is by three orders of magnitude smaller compared to that obtained during room-temperature irradiation. STM and Raman spectra show that amorphization occurs in graphite samples irradiated at 500 K to higher fluences, but not at 800 K. The obtained experimental results clearly reveal that the irradiation under high temperature causes track annealing.

In the present work the photoluminescence (PL) character of sapphire implanted with 110-keV He, Ar or Ne ions and subsequently irradiated with 230-MeV Pb was studied. The implantation was performed at 320 and 600 K using fluences from 5.0 × 10 16 to 2.0 × 10 17 ions/cm 2 . The Pb ion irradiation was carried out at 320 K. The obtained PL spectra showed peaks at 375, 413 and 450 nm with maximum intensity at an implantation fluence of 5.0 × 10 16 ions/cm 2 and a new peak at 390 nm appeared in the He-implanted and subsequently Pb-irradiated samples. Infrared spectra showed a broadening of the absorption band between 460 and 510 nm indicating strongly damaged regions formed in the Al 2 O 3 samples. A possible PL mechanism is discussed.

This paper presents the vulnerabilities of single event effects (SEEs) simulated by heavy ions on ground and observed on SJ-5 research satellite in space for static random access memories (SRAMs). A single event upset (SEU) prediction code has been used to estimate the proton-induced upset rates based on the ground test curve of SEU cross-section versus heavy ion linear energy transfer (LET). The result agrees with that of the flight data.

In the present work, 120 keV N-ion doped and 30 MeV C60 ion irradiated graphite-like-carbon samples were characterized by RBS, micro-FTIR, micro-Raman, XPS spectroscopy and the variation of the properties of the samples with the N-dopant and/or C60 irradiation fluence have been studied. The RBS spectra showed that C60 irradiation can induce a partial diffusion of N atoms to the surface and the amount of the diffused N atoms increases slightly with increasing C60 irradiation fluence. The FTIR and Raman spectra exhibit characteristic bands of carbon nitrogen bonds showing that the C and N atoms are chemically bonded. The amount of chemically bonded C and N atoms increases with increasing N-dopant. By deconvolution of the XPS spectra, the atomic concentration of N and C atoms were obtained and it was identified that the samples mainly consist of three phases, namely, C3N4, CNx and tetrahedral amorphous carbon. The effect of N-dopant and C60 irradiation fluence on the modification of the properties of the samples is also discussed.

In this work, the annealing behavior of microstructures in 4H-SiC helium-implanted at about 500 K to moderate doses (2.5–5) × 1016 ions cm−2 is studied by combining transmission electron microscopy (TEM) and Rutherford backscattering spectrometry (RBS). It is found that a low concentration of planar clusters of helium bubbles in ring structures was formed in a narrow range of dose in a well-defined depth region of the specimens on annealing above 973 K. The formation of the bubble layer is associated with remarkable distortion and deformation in the matrix. A simple model based on the frozen matrix assumption was developed to study the production of defects in SiC below the temperature of vacancy mobility. We found that the main features of the depth distribution of the bubble layer can be understood using this model if assuming the planar clusters of bubbles evolve from vacancy clusters larger than a critical size through an intermediate stage of helium platelets.

In this paper, the formation of the new phase and chemical bonds in N-doped diamond films after swift heavy ion irradiations was studied. The original samples were diamond films grown on (1 1 1) oriented p-Si by CVD deposition. These samples were implanted with 100 keV N-ions at room temperature to 5 × 10 17 , 1 × 10 18 and 5 × 10 18 N/cm 2 , irradiated with 345 MeV Xe or 2.64 GeV U ions, and then analyzed by means of RBS, micro-FTIR, micro-Raman and XRD spectroscopy. The obtained results suggested that N-sp 2 C and N-sp 3 C bonds formed in all N-doped diamond films, CN bond exists in all 5 × 10 18 N/cm 2 doped samples but could not form in the 5 × 10 17 N/cm 2 doped samples. In the 1 × 10 18 N/cm 2 doped sample, CN bond could form only after swift heavy ion irradiation. Intense energy deposition from the incident swift heavy ions induces the increase of sp 3 /sp 2 bonding ratio and thus enhances the formation of N-sp 3 C bonds in the samples. Furthermore, the X-ray diffraction analysis indicated that there existed new phases, α- and β-C 3 N 4 in the N-doped diamond samples after irradiation by swift heavy ions.

Highly oriented pyrolytic graphite was irradiated with swift heavy ions (Ne, Cr, Fe, Ni, Zn, Xe and U) of fluences between 10 11 and 10 14 ions/cm 2 in energy range MeV–GeV. The combination of scanning tunneling microscopy (STM) and Raman spectroscopy studies shows that large numbers of tracks protrude from the surface. The disordered crystal lattice is leading to a Raman-active D mode. Quantitative analysis of the peak intensity indicates that the size of the crystallite domain is larger than the mean distance between in-plane tracks observed by STM. � 2003 Elsevier B.V. All rights reserved.

One hundred and twenty keV C-ion doped SiO2 films were irradiated at RT with swift Ar, Kr, Xe or U ions and their photoluminescence (PL) properties were examined. From the obtained results, we found that an intense blue–violet PL band centred at ∼435±10 nm was formed in all ion irradiated samples and a weak ultraviolet PL band centred at ∼380 nm was formed only in the samples after Kr, Xe or U ion irradiations. The PL peak intensity of the blue–violet band (i) increases with the increase of the swift heavy ion irradiation fluence, (ii) decreases with the increase of electronic energy loss Se when Se 4.85 keV/nm. Furthermore, the peak central position of the blue–violet PL is shifted slightly to violet with increasing Se and some substructures appeared in the PL spectra of the samples irradiated with Xe or U ions. The appearance of these substructures is due to the high electronic energy loss. For the violet PL band, the intensity increases with Se. Possible origins and formation mechanism of light-emitters corresponding to the observed PL bands are discussed.

The effect of ion incident angle on multiple-bit upset (MBU) has been investigated for static random access memory IDT71256. The test pattern dependent MBU ratio can be as high as 70% when tested by either normal incident 136Xe ions or 36Ar ions incident at large angles. The increase of single event upset cross-section at large angles for light ions are mainly due to occurrence of high-ratio MBU. Charges collected through funnel effect play an important role in inducing MBU in NMOS IDT71256. The MBU ratio is in proportional to energy deposited in whole sensitive layer, but the ratios of more than 2-bit upset is decided by lateral distribution of charges.

BRI1-associated kinase 1 (BAK1) is a member of the plant receptor-like kinase (RLK) superfamily. BAK1 has been shown to initiate brassinosteroid (BR) signalling and innate immune responses in plants by forming receptor complexes with both brassinosteroid-insensitive 1 (BRI1) and flagellin-sensing 2 (FLS2). To gain a better understanding of the structural details and the mechanism of action of the BAK1 kinase domain, recombinant BAK1 cytoplasmic domain has been expressed, purified and crystallized at 291 K using PEG 3350 as a precipitant. A 2.6 Å resolution data set was collected from a single flash-cooled crystal at 100 K. This crystal belonged to space group C2, with unit-cell parameters a = 70.3, b = 75.6, c = 71.9 Å, β = 93.1°. Assuming the presence of one molecule in the asymmetric unit, the Matthews coefficient was 2.6 Å(3) Da(-1).

In the present work, a novel technique, “low energy ion implantation+high-energy heavy ion irradiation”, was used to synthesis light-emitting material. Experimentally, thermal-grown SiO 2 films were firstly implanted with 120 keV C + ions at room temperature (RT) to total doses in the range of (5.0×10 16 –1.0×10 18 ) ions/cm 2 . These C-doped SiO 2 films were then irradiated at RT with 335 and 855 MeV 40 Ar or 1.98 GeV 84 Kr ions to a fluence of 1.0×10 12 ions/cm 2 , or with 1.75 GeV 136 Xe ions to 1×10 11 , 5×10 11 or 1×10 12 ions/cm 2 , respectively. By measuring photoluminescence (PL) spectra of these samples excited by 320 nm light, the PL bands were investigated as functions of implantation ion dose, irradiation ion fluence and electronic energy loss S e . It was found that this technique is a useful tool to produce high quality light-emission structures, and that high-energy heavy ion irradiated C-doped SiO 2 films should be an efficient blue–violet emitting material. Furthermore, S e plays a dominant role in the formation of the PL bands, and proper C-dopant and suitable irradiation fluence will enhance the PL efficiency. Possible origins of the blue-violet PL bands formed in the ion irradiated C-doped SiO 2 films were discussed.

In this paper we present experimental results on irradiation effects of C 60 films induced by 2.0 GeV Xe 136 ions, delivered by HIRFL at Lanzhou of China. The irradiated C 60 films were analyzed by means of Fourier transform infrared, Raman scattering and X-ray diffraction spectroscopies. The analysis results indicated that electronic energy transfer dominates the damage process of C 60 films. The partial recovery of the damage in irradiated C 60 films at certain electronic energy loss is attributed to an annealing effect of strong electronic excitation. The ion velocity also plays a role in the process of the damage creation.

A novel technique,‘‘low energy ion implantation þ swift heavy ion irradiation’’,was used to synthesize lightemitting materials. In the present work,SiO 2 films were implanted with 120 keV C þ ions at room temperature (RT) to total doses from 5:0 � 10 16 to 1:0 � 10 18 ions/cm 2 ,and then irradiated at RT with swift Xe or U ions to different irradiation fluences. Photoluminescence (PL) spectra of these samples were measured at RT and intense blue–violet PL bands were observed. The properties of the PL bands were analyzed as a function of implantation ion dose,swift heavy ion irradiation fluence and electronic energy loss of the irradiation ion in the sample. The possible origins of the observed blue and violet emissions were also discussed. 2002 Elsevier Science B.V. All rights reserved.

Enterovirus 71 (EV71), a primary pathogen of hand, foot, and mouth disease (HFMD), affects primarily infants and children. Currently, there are no effective drugs against HFMD. EV71 3C protease performs multiple tasks in the viral replication, which makes it an ideal antiviral target. We synthesized a small set of fluorogenic model peptides derived from cleavage sites of EV71 polyprotein and examined their efficiencies of cleavage by EV71 3C protease. The novel peptide P08 [(2-( N -methylamino)benzoyl) (NMA)-IEALFQGPPK(DNP)FR] was determined to be the most efficiently cleaved by EV71 3C protease, with a kinetic constant k cat / K m of 11.8 ± 0.82 mM −1 min −1 . Compared with literature reports, P08 gave significant improvement in the signal/background ratio, which makes it an attractive substrate for assay development. A Molecular dynamics simulation study elaborated the interactions between substrate P08 and EV71 3C protease. Arg39, which is located at the bottom of the S2 pocket of EV71 3C protease, may participate in the proteolysis process of substrates. With an aim to evaluate EV71 3C protease inhibitors, a reliable and robust biochemical assay with a Z ′ factor of 0.87 ± 0.05 was developed. A novel compound (compound 3) (50% inhibitory concentration [IC 50 ] = 1.89 ± 0.25 μM) was discovered using this assay, which effectively suppressed the proliferation of EV 71 (strain Fuyang) in rhabdomyosarcoma (RD) cells with a highly selective index (50% effective concentration [EC 50 ] = 4.54 ± 0.51 μM; 50% cytotoxic concentration [CC 50 ] > 100 μM). This fast and efficient assay for lead discovery and optimization provides an ideal platform for anti-EV71 drug development targeting 3C protease.

The prevalence of chronic viral infectious diseases, the emergence and re-emergence of new viral infections, and in particular, resistance to currently used antiviral drugs have led to increased demand for new antiviral strategies and reagents. Increased understanding of the molecular mechanisms of viral infection has provided great potential for the discovery of new antiviral agents that target viral proteins or host factors. In this work, we introduce a comprehensive system using enteroviruses 71 (EV71) as an example for leading compound discovery to develop new antiviral.

The initiation of picornavirus replication is featured by the uridylylation of viral protein genome-linked (VPg). In this process, viral RNA-dependent RNA polymerase (RdRp) catalyzes two uridine monophosphate (UMP) molecules to the hydroxyl group of the third tyrosine residue of VPg. Subsequently, the uridylylated VPg (VPg-pUpU) functions as the protein primer to initiate the replication of the viral genome. Although a large body of functional and structural works has been performed to define individual snapshots for particular stages of the VPg uridylylation process, the formation, dynamics and mechanism of the whole VPg uridylylation complex still requires further elucidation. We would like to provide an overview of the current knowledge of the picornaviral VPg uridylylation complex in this paper.

SiO2 thin films were implanted at room temperature (RT) with 120 keV carbon ions to a dose of 1.0×10 17 ions / cm 2 and then irradiated at RT with high-energy 84Kr or 40Ar ions to a fluence of 1.0×10 12 ions / cm 2 . Using 320 nm monochromatic ultra-violet light for excitation, photoluminescence (PL) properties of these samples were examined and intense blue PL bands were observed. It was found that the blue PL peak intensity changes with electronic energy loss of the irradiation ion in the sample. With increasing the electronic energy loss level, the PL peak intensity decreases and the peak position shifts towards to the short-wavelength direction. Furthermore, the existence of C-dopants enhances the luminescence property of the irradiated samples.

This paper presents the results of ground-based heavy ion test of single-event effect (SEE) vulnerability on microcircuits used in space. We observed the dependence of upset cross-sections on the incident angle of ions in Intel 8086 CPU. SEU cross-sections of various SRAMs did not depend on the stored pattern, but 0→1 and 1→0 transitions were completely different for different manufacturer products. Some SEE protection methods were verified in conditions of ground simulation experiments.

PaaX is a global regulator of the phenylacetyl-coenzyme A catabolon that adjusts the expression of different operons to that of the paa-encoded central pathway. In this study, the PaaX-like protein from the hyperthermophilic archaeon Sulfolobus solfataricus P2 was successfully crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as a precipitant. Diffraction data were obtained to a resolution of 3.0 A using synchrotron radiation at the Photon Factory. The crystal belonged to space group P321, with unit-cell parameters a = 86.4, b = 86.4, c = 105.5 A.

Negative-sense single-stranded RNA viruses (NSRVs) possess a ribonucleoprotein (RNP) complex composed of viral polymerase and genomic RNA surrounded by viral nucleoprotein. The RNP facilitates virus replication, transcription, and assembly. To date, a large body of structural work, through crystallography and electron microscopy (EM) analysis, has been performed to aid understanding the molecular mechanism of RNP formation in NSRVs, and provides great potential for the discovery of antiviral agents targeting viral RNP formation.

Picornavirus RNA replication is initiated by VPg uridylylation, during which the hydroxyl group of the third tyrosine residue of the virally encoded protein VPg is covalently linked to two UMP molecules by RNA-dependent RNA polymerase (RdRp; also known as 3D pol ). We previously identified site 311, located at the base of the palm domain of the enterovirus 71 (EV71) RdRp, to be the site for EV71 VPg binding and uridylylation. Here we report the crystal structure of EV71 3D pol complexed with VPg. VPg was anchored at the bottom of the palm domain of the 3D pol molecule and exhibited an extended V-shape conformation. The corresponding interface on 3D pol was mainly formed by residues within site 311 and other residues in the palm and finger domains. Mutations of the amino acids of 3D pol involved in the VPg interaction ( 3D L319A, 3D D320A, and 3D Y335A) significantly disrupted VPg binding to 3D pol , resulting in defective VPg uridylylation. In contrast, these mutations did not affect the RNA elongation activity of 3D pol . In the context of viral genomic RNA, mutations that abolished VPg uridylylation activity were lethal for EV71 replication. Further in vitro analysis showed that the uridylylation activity was restored by mixing VPg-binding-defective and catalysis-defective mutants, indicating a trans mechanism for EV71 VPg uridylylation. Our results, together with previous results of other studies, demonstrate that different picornaviruses use distinct binding sites for VPg uridylylation.

Bunyamwera virus (BUNV), which belongs to the genus Orthobunyavirus , is the prototypical virus of the Bunyaviridae family. Similar to other negative-sense single-stranded RNA viruses, bunyaviruses possess a nucleocapsid protein (NP) to facilitate genomic RNA encapsidation and virus replication. The structures of two NPs of members of different genera within the Bunyaviridae family have been reported. However, their structures, RNA-binding features, and functions beyond RNA binding significantly differ from one another. Here, we report the crystal structure of the BUNV NP–RNA complex. The polypeptide of the BUNV NP was found to possess a distinct fold among viral NPs. An N-terminal arm and a C-terminal tail were found to interact with neighboring NP protomers to form a tetrameric ring-shaped organization. Each protomer bound a 10-nt RNA molecule, which was acquired from the expression host, in the positively charged crevice between the N and C lobes. Inhomogeneous oligomerization was observed for the recombinant BUNV NP–RNA complex, which was similar to the Rift Valley fever virus NP–RNA complex. This result suggested that the flexibility of one NP protomer with adjacent protomers underlies the BUNV ribonucleoprotein complex (RNP) formation. Electron microscopy revealed that the monomer-sized NP–RNA complex was the building block of the natural BUNV RNP. Combined with previous results indicating that mutagenesis of the interprotomer or protein–RNA interface affects BUNV replication, our structure provides a great potential for understanding the mechanism underlying negative-sense single-stranded RNA RNP formation and enables the development of antiviral therapies targeting BUNV RNP formation.

VPg uridylylation is essential for picornavirus RNA replication. The VPg uridylylation reaction consists of the binding of VPg to 3D polymerase (3D pol ) and the transfer of UMP by 3D pol to the hydroxyl group of the third amino acid Tyr of VPg. Previous studies suggested that different picornaviruses employ distinct mechanisms during VPg binding and uridylylation. Here, we report a novel site (Site-311, located at the base of the palm domain of EV71 3D pol ) that is essential for EV71 VPg uridylylation as well as viral replication. Ala substitution of amino acids (T313, F314, and I317) at Site-311 reduced the VPg uridylylation activity of 3D pol by >90%. None of the Site-311 mutations affected the RNA elongation activity of 3D pol , which indicates that Site-311 does not directly participate in RNA polymerization. However, mutations that abrogated VPg uridylylation significantly reduced the VPg binding ability of 3D pol , which suggests that Site-311 is a potential VPg binding site on enterovirus 71 (EV71) 3D pol . Mutation of a polymerase active site in 3D pol and Site-311 in 3D pol remarkably enables trans complementation to restore VPg uridylylation. In contrast, two distinct Site-311 mutants do not cause trans complementation in vitro . These results indicate that Site-311 is a VPg binding site that stabilizes the VPg molecule during the VPg uridylylation process and suggest a two-molecule model for 3D pol during EV71 VPg uridylylation, such that one 3D pol presents the hydroxyl group of Tyr3 of VPg to the polymerase active site of another 3D pol , which in turn catalyzes VPg→VPg-pU conversion. For genome-length RNA, the Site-311 mutations that reduced VPg uridylylation were lethal for EV71 replication, which indicates that Site-311 is a potential antiviral target.

Nucleocapsid protein (NPs) of negative-sense single-stranded RNA (-ssRNA) viruses function in different stages of viral replication, transcription, and maturation. Structural investigations show that -ssRNA viruses that encode NPs preliminarily serve as structural building blocks that encapsidate and protect the viral genomic RNA and mediate the interaction between genomic RNA and RNA-dependent RNA polymerase. However, recent structural results have revealed other biological functions of -ssRNA viruses that extend our understanding of the versatile roles of virally encoded NPs.

Gram-negative Enterobacteriaceae with resistance to carbapenem conferred by New Delhi metallo-β-lactamase 1 (NDM-1) are a type of newly discovered antibioticresistant bacteria. The rapid pandemic spread of NDM-1 bacteria worldwide (spreading to India, Pakistan, Europe, America, and Chinese Taiwan) in less than 2 months characterizes these microbes as a potentially major global health problem. The drug resistance of NDM-1 bacteria is largely due to plasmids containing the blaNDM-1 gene shuttling through bacterial populations. The NDM-1 enzyme encoded by the blaNDM-1 gene hydrolyzes β-lactam antibiotics, allowing the bacteria to escape the action of antibiotics. Although the biological functions and structural features of NDM-1 have been proposed according to results from functional and structural investigation of its homologues, the precise molecular characteristics and mechanism of action of NDM-1 have not been clarified. Here, we report the three-dimensional structure of NDM-1 with two catalytic zinc ions in its active site. Biological and mass spectroscopy results revealed that D-captopril can effectively inhibit the enzymatic activity of NDM-1 by binding to its active site with high binding affinity. The unique features concerning the primary sequence and structural conformation of the active site distinguish NDM-1 from other reported metallo-β-lactamases (MBLs) and implicate its role in wide spectrum drug resistance. We also discuss the molecular mechanism of NDM-1 action and its essential role in the pandemic of drug-resistant NDM-1 bacteria. Our results will provide helpful information for future drug discovery targeting drug resistance caused by NDM-1 and related metallo-β-lactamases.

Microbial ferulic acid decarboxylase (FADase) catalyzes the transformation of ferulic acid to 4-hydroxy-3-methoxystyrene (4-vinylguaiacol) via non-oxidative decarboxylation. Here we report the crystal structures of the Enterobacter sp. Px6-4 FADase and the enzyme in complex with substrate analogues. Our analyses revealed that FADase possessed a half-opened bottom β-barrel with the catalytic pocket located between the middle of the core β-barrel and the helical bottom. Its structure shared a high degree of similarity with members of the phenolic acid decarboxylase (PAD) superfamily. Structural analysis revealed that FADase catalyzed reactions by an "open-closed" mechanism involving a pocket of 8 × 8 × 15 Å dimension on the surface of the enzyme. The active pocket could directly contact the solvent and allow the substrate to enter when induced by substrate analogues. Site-directed mutagenesis showed that the E134A mutation decreased the enzyme activity by more than 60%, and Y21A and Y27A mutations abolished the enzyme activity completely. The combined structural and mutagenesis results suggest that during decarboxylation of ferulic acid by FADase, Trp25 and Tyr27 are required for the entering and proper orientation of the substrate while Glu134 and Asn23 participate in proton transfer.

Fusarium graminearum (sexual stage: Gibberella zeae) is the causative agent of Fusarium Head Blight (FHB), which is one of the most destructive plant disease of cereals, accounting for high grain yield losses, especially for wheat and maize. Like other fungal pathogens, several extracellular enzymes secreted by G. zeae are known to be involved in host infection. Among these secreted lipases, G. zeae lipase (GZEL), which is encoded by the FGL1 gene, was demonstrated to be crucial to G. zeae pathogenicity. However, the precise mechanism of GZEL remains unclear due to a lack of detailed structural information. In this study, we report the crystal structure of GZEL at the atomic level. The structure of GZEL displays distinct structural differences compared to reported homologues and indicates a unique “double lock” enzymatic mechanism. To gain insight into substrate/inhibitor recognition, we proposed a model of GZEL in complex with substrate and the lipase inhibitor ebelactone B (based on the reported structures of GZEL homologues), which defines possible substrate binding sites within the catalytic cleft and suggests an “anti sn-l” binding mode. These results pave the way to elucidating the mechanism of GZEL and thus provide clues for the design of anti-FHB inhibitors.

Porcine reproductive and respiratory syndrome virus (PRRSV), a member of the Arteriviridae family of Nidovirales , is the causative agent of porcine reproductive and respiratory syndrome, which results in enormous economic losses in the swine industry. As the second protein encoded by the PRRSV genome, nsp1β cleaves itself from the downstream nsp2 protein via a C-terminal papain-like cysteine protease (PCP) domain. Although nsp1β is known to be involved in virulence, its precise role in the process of viral infection remains unclear. In this work, we describe the homodimeric crystal structure of PRRSV nsp1β in its natural, self-processed form. We show that the architecture of its N-terminal domain (NTD) adopts a fold closely resembling that of several known nucleases and has intrinsic nuclease activity that is strongly activated by manganese ions in vitro . Key features, however, distinguish nsp1β from characterized nucleases, including the C-terminal PCP domain (which is responsible for the self-release of nsp1β from nsp2), a linker domain (LKD) that connects the NTD and the PCP domain, and a C-terminal extension (CTE) that binds to and is stabilized by the putative substrate binding site of the PCPβ domain. Combined with the reported nuclear localization of this protein, these results shed light on the self-processing mode and precise biological function of nsp1β and thus offer a multitarget template for future drug discovery.

Current in vitro assays for the activity of HIV-RT (reverse transcriptase) require radio-labeled or chemically modified nucleotides to detect reaction products. However, these assays are inherently end-point measurements and labor intensive. Here we describe a novel non-radioactive assay based on the principle of pyrosequencing coupled-enzyme system to monitor the activity of HIV-RT by indirectly measuring the release of pyrophosphate (PP(i)), which is generated during nascent strand synthesis. The results show that our assay could monitor HIV-RT activity with high sensitivity and is suitable for rapid high-throughput drug screening targeting anti-HIV therapies due to its high speed and convenience. Moreover, this assay can be used to measure primase activity in an easy and sensitive manner, which suggests that this novel approach could be wildly used to analyze the activity of PP(i)-generated and ATP-free enzyme reactions.

Porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV), a positive-strand RNA virus that belongs to the Arteriviridae family of Nidovirales , has been identified as the causative agent of PRRS. Nsp1α is the amino (N)-terminal protein in a polyprotein encoded by the PRRSV genome and is reported to be crucial for subgenomic mRNA synthesis, presumably by serving as a transcription factor. Before functioning in transcription, nsp1α proteolytically releases itself from nsp1β. However, the structural basis for the self-releasing and biological functions of nsp1α remains elusive. Here we report the crystal structure of nsp1α of PRRSV (strain XH-GD) in its naturally self-processed form. Nsp1α contains a ZF domain (which may be required for its biological function), a papain-like cysteine protease (PCP) domain with a zinc ion unexpectedly bound at the active site (which is essential for proteolytic self-release of nsp1α), and a carboxyl-terminal extension (which occupies the substrate binding site of the PCP domain). Furthermore, we determined the exact location of the nsp1α self-processing site at Cys-Ala-Met180↓Ala-Asp-Val by use of crystallographic data and N-terminal amino acid sequencing. The crystal structure also suggested an in cis self-processing mechanism for nsp1α. Furthermore, nsp1α appears to have a dimeric architecture both in solution and as a crystal, with a hydrophilic groove on the molecular surface that may be related to nsp1α's biological function. Compared with existing structure and function data, our results suggest that PRRSV nsp1α functions differently from other reported viral leader proteases, such as that of foot-and-mouth disease.

A monolithic integrated amplified feedback semiconductor laser is demonstrated as an optical microwave source. The optical microwave frequency is continuously tunable in the range of 19.87-26.3 GHz with extinction ratio above 6 dB, 3-dB linewidth about 3 MHz.

In this paper, an evanescently coupled uni-traveling carrier photodiodes (EC-UTC-PDs) have been fabricated and investigated, which can benefit from the incorporation of a multimode diluted waveguide of appropriate length with experiment-simulation comparison. A high responsivity of 0.68 A/W at 1.55-mum without an anti-reflection coating, -1 dB compression current of more than 19 mA, and a large -1 dB vertical alignment tolerance of 2.2 mum were achieved.