Molecular modeling on some human interleukins sharing gamma c of interleukin-2 receptor, and structure-function relationships

Five models for human interleukin-7 (HIL-7), HIL-9, HIL-13, HIL-15 and HIL-17 have been generated by SYBYL software package. The primary models were optimized using molecular dynamics and molecular mechanics methods. The final models were optimized using a steepest descent algorithm and a subsequent conjugate gradient method. The complexes with these interleukins and the common gamma chain of interleukin-2 receptor (IL-2R) were constructed and subjected to energy minimization. We found residues, such as Gln127 and Tyr103, of the common gamma chain of IL-2R are very important. Other residues, e.g. Lys70, Asn128 and Glu162, are also significant. Four hydrophobic grooves and two hydrophilic sites converge at the active site triad of the gamma chain. The binding sites of these interleukins interaction with the common gamma chain exist in the first helical and/or the fourth helical domains. Therefore, we conclude that these interleukins binds to the common gamma chain of IL-2R by the first and the fourth helix domain. Especially at the binding sites of some residues (lysine, arginine, asparagine, glutamic acid and aspartic acid), with a discontinuous region of the common gamma chain of IL-2R, termed the interleukins binding sites (103-210). The study of these sites can be important for the development of new drugs. (C) 2000 Elsevier Science B.V. All rights reserved.

The search for the IFN-gamma receptor in fish: Functional and expression analysis of putative binding and signalling chains in rainbow trout Oncorhynchus mykiss

Interferons (IFNs), consisting of three major subfamilies, type I, type II (gamma) and type III (lambda) IFN, activate vertebrate antiviral defences once bound to their receptors. The three IFN subfamilies bind to different receptors, IFNAR1 and IFNAR2 for type I IFNs, IFN gamma R1 and IFN gamma R2 for type II IFN, and IL-28R1 and IL-10R2 for type III IFNs. In fish, although many types I and II IFN genes have been cloned, little is known about their receptors. In this report, two putative IFN-gamma receptor chains were identified and sequenced in rainbow trout (Oncorhynchus mykiss), and found to have many common characteristics with mammalian type II IFN receptor family members. The presented gene synteny analysis, phylogenetic tree analysis and ligand binding analysis all suggest that these molecules are the authentic IFN gamma Rs in fish. They are widely expressed in tissues, with IFN gamma R1 typically more highly expressed than IFN gamma R2. Using the trout RTG-2 cell line it was possible to show that the individual chains could be differentially modulated, with rIFN-gamma and rIL-1 beta down regulating IFN gamma R1 expression but up regulating IFN gamma R2 expression. Overexpression of the two receptor chains in RTG-2 cells revealed that the level of IFN gamma R2 transcript was crucial for responsiveness to rIFN-gamma, in terms of inducing gamma IP expression. Transfection experiments showed that the two putative receptors specifically bound to rIFN-gamma. These findings are discussed in the context of how the IFN gamma R may bind IFN-gamma in fish and the importance of the individual receptor chains to signal transduction. (c) 2009 Elsevier Ltd. All rights reserved.

Comparative study and expression analysis of the interferon gamma gene locus cytokines in Xenopus tropicalis

Using bioinformatics approach, the genome locus containing interleukin (IL)-22, IL-26, and interferon gamma (IFN-gamma) genes has been identified in the amphibian, Xenopus tropicalis. Like that in other vertebrates such as fish, birds, and mammals, the Xenopus IL-22, IL-26, and IFN-gamma are clustered in the same chromosome and the adjacent genes are conserved. The genomic structures of the Xenopus IL-22, IL-26, and IFN-gamma gene were identical to that of their mammalian counterparts. The Xenopus IL-22 and IL-26 genes contained five exons and four introns while the Xenopus IFN-gamma gene consisted of four exons and three introns. The Xenopus IL-22, IL-26, and IFN-gamma share 14.1-41.6%, 14.6-31.2%, and 23.7-36.5% identity to their counterparts in other species, respectively. Reverse-transcription polymerase chain reaction (PCR) and real-time quantitative PCR analyses revealed that the expression of IL-22, IL-26, and IFN-gamma genes was significantly upregulated after simulation with bacterial polyliposaccharide and/or synthetic double-stranded poly(I:C), suggesting these cytokines like those in other vertebrates play an important role in regulating immune response in Xenopus.

Molecular cloning and characterization of common carp (Cyprinus carpio L.) TCR gamma and CD3 gamma/delta chains

Partial cDNA sequences of TCR gamma and CD3 gamma/delta were isolated from the thymus of common carp (Cyprinus carpio L.) by the method of suppression subtractive hybridization (SSH). Subsequently the full length cDNAs of carp TCR gamma and CD3 gamma/delta were obtained by means of 3' RACE and 5' RACE, respectively. The full length of carp TCR gamma chain is 1368 bp and encodes 326 amino acids including a signal peptide region of 19 amino acids and a transmembrane region of 23 amino acids at the C-terminal region from aa 291 to 313. The V region of carp TCR gamma contains 109 amino acids, the core motif FGXG in J segment was also found in carp TCR gamma. The C region of carp TCR gamma contains the characteristic CX6PX6WX45C motif. The CP region of carp TCR C gamma contains 37 amino acids. The full length of carp CD3 gamma/delta is 790 bp and encodes 175 amino acids including a signal peptide region of 17 amino acids and a transmembrane region of 23 amino acids from aa 93 to 115. Similar to other known CD3 gamma/delta s, four cysteine residues in the extracellular domain and an immunoreceptor tyrosine-based activation motif ITAM (YxxL/Ix6-8YxxL/I) in the intracellular domain are also included in carp CD3 gamma/delta. Differing from other known CD3 gamma/delta s, carp CD3 gamma/delta tacks the CXXCXE motif in the extracellular domain. RTPCR analysis demonstrated that the expression of TCR gamma gene was mainly in the thymus and gill of 6-month carp, but in 18-month carp, TCR gamma gene was detected in all the examined tissues. The expression of CD3 gamma/delta gene was detected in all examined tissues of 6 and 18-month carp; among them, the highest expression level was in the thymus of 6-month carp. In situ hybridization showed that CD3 gamma/delta-expressing cells were widely distributed in the head kidney, spleen and kidney of carp, whereas in the thymus, they were densely distributed in the lymphoid outer zone and scattered in the epithelioid inner zone. (c) 2007 Published by Etsevier Ltd.

Preliminary study on the photoproduction of hydroxyl radicals in aqueous solution with Aldrich humic acid, algae and Fe(III) under high-pressure mercury lamp irradiation

Under a high-pressure mercury lamp (HPML) and using an exposure time of 4 h, the photoproduction of hydroxyl radicals ((OH)-O-.) could be induced in an aqueous solution containing humic acid (HA). Hydroxyl radicals were determined by high-performance liquid chromatography using benzene as a probe. The results showed that (OH)-O-. photoproduction increased from 1.80 to 2.74 muM by increasing the HA concentration from 10 to 40 mg L-1 at an exposure time of 4 h (pH 6.5). Hydroxyl radical photoproduction in aqueous solutions of HA containing algae was greater than that in the aqueous solutions of HA without algae. The photoproduction of (OH)-O-. in the HA solution with Fe(111) was greater than that of the solution without Fe(III) at pH ranging from 4.0 to 8.0. The photoproduction of (OH)-O-. in HA solution with algae with or without Fe(111) under a 250 W HPML was greater than that under a 125 W HPML. The photoproduction of (OH)-O-. in irradiated samples was influenced by the pH. The results showed that HPML exposure for 4 h in the 4-8 pH range led to the highest (OH)-O-. photoproduction at pH 4.0.

Influence of electron irradiation on hydrothermally grown zinc oxide single crystals

The resistivity of hydrothermally grown ZnO single crystals increased from similar to 10(3) Omega cm to similar to 10(6) Omega cm after 1.8 MeV electron irradiation with a fluence of similar to 10(16) cm(-2), and to similar to 10(9) Omega cm as the fluence increased to similar to 10(18) cm(-2). Defects in samples were studied by thermally stimulated current (TSC) spectroscopy and positron lifetime spectroscopy (PLS). After the electron irradiation with a fluence of 10(18) cm(-2), the normalized TSC signal increased by a factor of similar to 100. A Zn vacancy was also introduced by the electron irradiation, though with a concentration lower than expected. After annealing in air at 400 degrees C, the resistivity and the deep traps concentrations recovered to the levels of the as-grown sample, and the Zn vacancy was removed.

n-type Ge-SiGe quantum cascade structure utilizing quantum wells for electrons in the L and Gamma valleys

In this letter, we propose an n-type vertical transition bound-to-continuum Ge-SiGe quantum cascade structure utilizing electronic quantum wells in the L and F valleys of the Ge layers. The optical transition levels are located in the quantum wells in the L valley. Under a bias of 80 kV/cm, the carriers in the lower level are extracted by miniband transport and L - Gamma tunneling into the subband in the Gamma well of the next period. And then the electrons are injected into the upper level by ultrafast intervalley scattering, which not only effectively increases the tunneling rate and suppresses the thermal backfilling of electrons, but also enhances the injection efficiency of the upper level. The performance of the laser is discussed.

Neutron irradiation effect in two-dimensional electron gas of AlGaN/GaN heterostructures

AlGaN/GaN heterostructures have been irradiated by neutrons with different influences and characterized by means of temperature-dependent Hall measurements and Micro-Raman scattering techniques. It is found that the carrier mobility of two-dimensional electron gas (2DEG) is very sensitive to neutrons. At a low influence of 6.13 x 10(15) cm(-2), the carrier mobility drops sharply, while the sheet carrier density remains the same as that of an unirradiated sample. Moreover, even for a fluence of up to 3.66 x 10(16) cm(-2), the sheet carrier density shows only a slight drop. We attribute the degradation of the figure-of-merit (product of n(s) x mu) of 2DEG to the defects induced by neutron irradiation. Raman measurements show that neutron irradiation does not yield obvious change to the strain state of AlGaN/GaN heterostructures, which proves that degradation of sheet carrier density has no relation to strain relaxation in the present study. The increase of the product of n(s) x mu of 2DEG during rapid thermal annealing processes at relatively high temperature has been attributed to the activation of Ge-Ga transmuted from Ga and the recovery of displaced defects.

Proton irradiation-induced defects in undoped GaSb studied by positron lifetime spectroscopy and photoluminescence

Undoped GaSb was irradiated by 2.6 MeV protons. The irradiation-induced defects were studied by positron lifetime spectroscopy (PLS) and photoluminescence (PL). Positron lifetime measurements showed that vacancy-type defects were introduced after irradiation, and divacancies were formed at higher irradiation dose. Annealing experiments revealed there were different annealing steps between the as grown and proton-irradiated samples, the reason for which was tentatively attributed to the formation of divacancies in the proton-irradiated samples during annealing. All the vacancy defects could be annealed out at around 500 degrees C. The PL intensity quickly fell down after proton irradiation and decreased with increasing irradiation dose, indicating that irradiation induced non-irradiative recombination centers, whose candidates were assigned to the vacancy defects induced by proton irradiation.

Growth and characterization of GaInNAs by molecular beam epitaxy using a nitrogen irradiation method

We propose an innovative technique, making use of the In segregation effect, referred as the N irradiation method, to enhance In-N bonding and extend the emission wavelength of GaInNAs quantum wells (QWs). After the formation of a complete In floating layer, the growth is interrupted and N irradiation is initiated. The majority of N atoms are forced to bond with In atoms and their incorporation is regulated independently by the N exposure time and the As pressure. The effect of the N exposure time and As pressure on the N incorporation and the optical quality of GaInNAs QWs were investigated. Anomalous photoluminescence (PL) wavelength red shifts after rapid thermal annealing (RTA) were observed in the N-irradiated samples, whereas a normal GaInNAs sample revealed a blue shift. This method provides an alternative way to extend the emission wavelength of GaInNAs QWs with decent optical quality. We demonstrate light emission at 1546 nm from an 11-nm-thick QW, using this method and the PL intensity is similar to that of a 7-nm-thick GaInNAs QW grown at a reduced rate. (C) 2008 Elsevier B.V. All rights reserved.

Enhancement of Exciton-Phonon Interaction in InGaN Quantum Wells Induced by Electron-Beam Irradiation

InGaN/GAN multiple quantum wells grown by metal-organic chemical vapor deposition were irradiated with the electron beam from a low energy accelerator. The electron irradiation induced a redshift by 50 meV in the photoluminescence spectra of the electron-irradiated InGaN/GaN quantum wells, irrespective of the exposure time to the electron beam which ranges from 10 to 1000s. The localization parameter extracted from the temperature-dependent photoluminescence spectra was found to increase in the Irradiated samples. Analysis of the intensity of the longitudinal optical phonon sidebands showed the enhancement of the exciton-phonon coupling, indicating that the excitons are more strongly localized in the irradiated InGaN wells. The change in the pholotuminescence spectra. In the irradiated InGa/GAN quantum wells were explained in terms of the increase of indium concentration in indium rich clusters induced by the electron irradiation (C) 2009 The Japan Society of Applied Physics

Controlling electronic structures by irradiation in single-walled SiC nanotubes: a first-principles molecular dynamics study

Using first-principles molecular dynamics simulations, the displacement threshold energy and defect configurations are determined in SiC nanotubes. The simulation results reveal that a rich variety of defect structures (vacancies, Stone-Wales defects and antisite defects) are formed with threshold energies from 11 to 64 eV. The threshold energy shows an anisotropic behavior and exhibits a dramatic decrease with decreasing tube diameter. The electronic structure can be altered by the defects formed by irradiation, which suggests that the electron irradiation may be a way to use defect engineering to tailor electronic properties of SiC nanotubes.

Effect of beta-irradiation on photoluminescence of MOCVD grown GaN

The effect of beta particles interaction on the optical properties of MOCVD grown GaN is reported. A significant change in luminescence properties of GaN is observed after exposing the material with 0.6 MeV beta particles with low dose of 10(12) cm(-2). The results obtained from photoluminescence measurements of irradiated GaN samples in low dose are found contradictory to those reported in literature for samples irradiated with heavy dose (> 10(15) cm(-2)) of electron. An increase in intensity of yellow luminescence has been observed with increasing dose of beta particles which is in disagreement to the already reported results in literature for heavily irradiated samples. A model has been proposed to sort out this inconsistency. The increase in YL intensity at low dose is attributed to the increase in concentration of VGaON complex whereas production of non-radiative VGaON clusters is assumed to justify the decrease in YL intensity at high dose.

Silicon-on-insulating multi-layers for total-dose irradiation hardness

Silicon-on-insulating multi-layer (SOIM) materials were fabricated by co-implantation of oxygen and nitrogen ions with different energies and doses. The multilayer microstructure was investigated by cross-sectional transmission electron microscopy. P-channel metal-oxide-semiconductor (PMOS) transistors and metal-semiconductor-insulator-semiconductor (MSIS) capacitors were produced by these materials. After the irradiated total dose reaches 3 x 10(5) rad (Si), the threshold voltage of the SOIM-based PMOS transistor only shifts 0.07 V, while thin silicon-on-insulating buried-oxide SIMOX-based PMOS transistors have a shift of 1.2V, where SIMOX represents the separated by implanted oxygen. The difference of capacitance of the SOIM-based MSIS capacitors before and after irradiation is less than that of the thin-box SIMOX-based MSIS capacitor. The results suggest that the SOIM materials have a more remarkable irradiation tolerance of total dose effect, compared to the thin-buried-oxide SIMOX materials.

Effects of crystalline quality on the phase stability of cubic boron nitride thin films under medium-energy ion irradiation

To investigate the effect of radiation damage on the stability and the compressive stress of cubic boron nitride (c-BN) thin films, c-BN films with various crystalline qualities prepared by dual beam ion assisted deposition were irradiated at room temperature with 300 keV Ar+ ions over a large fluence range up to 2 x 10(16) cm(-2). Fourier transform infrared spectroscopy (FTIR) data were taken before and after each irradiation step. The results show that the c-BN films with high crystallinity are significantly more resistant against medium-energy bombardment than those of lower crystalline quality. However, even for pure c-BN films without any sp(2)-bonded BN, there is a mechanism present, which causes the transformation from pure c-BN to h-BN or to an amorphous BN phase. Additional high resolution transmission electron microscopy (HRTEM) results support the conclusion from the FTIR data. For c-BN films with thickness smaller than the projected range of the bombarding Ar ions, complete stress relaxation was found for ion fluences approaching 4 x 10(15) cm(-2). This relaxation is accompanied, however, by a significant increase of the width of c-BN FTIR TO-line. This observation points to a build-up of disorder and/or a decreasing average grain size due to the bombardment. (c) 2005 Elsevier B.V. All rights reserved.