RecA-mediated, targeted mutagenesis in zebrafish

We have evaluated the efficacy of RecA, a prokaryotic protein involved with homologous recombination, to direct site-specific mutagenesis in zebrafish embryos. For this we coinjected a vector containing a mutated enhanced green fluorescent protein (EGFP) gene plus 236-nucleotide corrective single-stranded DNAs coated with RecA into I-cell zebrafish embryos. Twenty-hours after fertilization, about 5% to 20% of injected embryos showed EGFP expression in I or more cells when RecA-coated corrective DNAs were used, but not when RecA was omitted. Mutated EGFP genes with 1-bp insertions or deletions were inefficiently activated, whereas those with 7-bp insertions were activated about 4-fold more efficiently. RecA-coated template strand had a higher efficiency than its complementary strand in activation of EGFP expression. Prior irradiation of the embryos with UV light enhanced RecA-mediated restoration of gene activity, suggesting that the effects we observed were augmented by one or more factors of zebrafish DNA repair systems.

Development of a positive-negative selection procedure for gene targeting in fish cells

The gene targeting technique is a powerful tool for analyzing functions of cloned genes and for generating transgenic animals with site-directed integration of foreign genes. In order to develop this technique in fish, positive-negative selection (PNS) and homologous recombination vectors were constructed, and their expression was examined in fish cells. A vector (pNK) for PNS consists of the neomycin resistance gene (neo) as a positive selectable marker gene and the herpes simplex virus (HSV) thymidine kinase (tk) gene as a negative selectable marker gene. Positive selection with geneticin (G418) of epithelioma papulosum of carp (EPC) cells transfected with linearized pNK vector yielded 350 colonies, while double selection of transfected EPC cells with G418 and gancyclovir (Gc) resulted in nearly complete cell death, demonstrating that the PNS procedure is effective in fish cells. Homologous recombination vectors consist of the Xiphophorus melanoma receptor kinase (X mrk(Y)) gene as homologous sequence in addition to the neo and tk genes. Conditions for homologous recombination vector transfection and drug selection were established. After verification of the feasibility of expression of homologous recombination vectors in EPC cells, the first gene targeting experiments were attempted in the Xiphophorus melanoma cell line, PSM. Positive-negative selection of the targeting vector-transfectants led to a low enrichment in this particular cell line. The reasons for the low enrichment in PSM cells were discussed. (C) 2002 Elsevier Science B.V. All rights reserved.

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.

Optical analysis of dislocation-related physical processes in GaN-based epilayers

In this paper, recent progresses in optical analysis of dislocation-related physical properties in GaN-based epilayers are surveyed with a brief review. The influence of dislocations on both near-band edge emission and yellow luminescence (YL) is examined either in a statistical way as a function of dislocation density or focused on individual dislocation lines with a high spatial resolution. Threading dislocations may introduce non-radiative recombination centers and enhance YL, but their effects are affected by the structural and chemical environment. The minority carrier diffusion length may be dependent on either dislocation density or impurity doping as confirmed by the result of photovoltaic spectra. The in situ optical monitoring of the strain evolution process is employed during GaN heteroepitaxy using an AIN interlayer. A typical transition of strain from compression to tension is observed and its correlation with the reduction and inclination of threading dislocation lines is revealed. (c) 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Correlation between optical and structural properties of (Al,Ga)N layers grown by MOCVD

For both, (Al,Ga)N with low Al content grown on a GaN nucleation layer and (AI,Ga)N with high Al content gown on an AlN nucleation layer, the inhomogeneous distribution of the luminescence is linked to the distribution of defects, which may be due to inversion domains. In the former system, defect regions exhibit a much lower Al content than the nominal one leading to a splitting of the respective luminescence spectra. In the latter system, a domain-like growth is observed with a pyramidal surface morphology and non-radiative recombination within the domain boundaries. (c) 2007 WILEYNCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid photoluminescence quenching in GaInNAs quantum wells at low temperature

Temperature dependence of optical properties of GaInNAs/GaAs quantum wells (QWs) has been studied by photoluminescence (PL) and time-resolved PL. A rapid PL quenching is observed even at very low temperature and is of the excitation power dependence. These results strongly suggest that the non-radiative recombination process plays a very important role at low temperature. In the TRPL measurement the shape of the PL decay curve shows significant difference under different excitation powers. It is attributed to the different involvement of non-radiative recombination in the overall recombination process. The TRPL data are well fitted with the rate equation involving both the radiative and non-radiative recombination. (c) 2006 Elsevier B.V. All rights reserved.

Time-resolved photoluminescence spectra of self-assembled InAs/GaAs quantum dots

Two types of InAs self-assembled Quantum dots (QDs) were prepared by Molecular beam epitaxy. Atomic force microscopy (AFM) measurements showed that, compared to QDs grown on GaAs substrate, QDs grown on InGaAs layer has a significantly enhanced density. The short spacing (several nanometer) among QDs stimulates strong coupling and leads to a large red-shift of the 1.3 mu m photoluminescence (PL) peak. We study systematically the dependence of PL lifetime on the QDs size, density and temperature (1). We found that, below 50 K, the PL lifetime is insensitive to temperature, which is interpreted from the localization effects. As T increases, the PL lifetime increases, which can be explained from the competition between the carrier redistribution and thermal emission at higher temperature. The increase of carriers in QDs migrated from barriers and wetting layer (WL), and the redistribution of carriers among QDs enhance the PL lifetime as T increases. The thermal emission and non-radiative recombination have effects to reduce the PL lifetime at higher T. As a result, the radiative recombination lifetime is determined by the wave function overlapping of electrons and holes in QDs, and QDs with different densities have different PL lifetime dependence on the QDs size. (c) 2005 Elsevier B.V. All rights reserved.

Anomalous temperature dependence of photoluminescence from a-C : H film deposited by energetic hydrocarbon ion beam

The temperature dependence of photoluminescence (PL) from a-C:H film deposited by CH3+ ion beam has been performed and an anomalous behavior has been reported. A transition temperature at which the PL intensity, peak position and full width at the half maximum change sharply was observed. It is proposed that different structure units. at least three, are responsible for such behavior. Above the transition point. increasing temperature will lead to the dominance of non-radiative recombination process, which quenches the PL overall and preferentially the red part, Possible emission mechanisms have been discussed. (C) 2002 Elsevier Science Ltd. All rights reserved.

Time-resolved photoluminescence spectra of self-assembled InAs/GaAs quantum dots

Two types of InAs self-assembled Quantum dots (QDs) were prepared by Molecular beam epitaxy. Atomic force microscopy (AFM) measurements showed that, compared to QDs grown on GaAs substrate, QDs grown on InGaAs layer has a significantly enhanced density. The short spacing (several nanometer) among QDs stimulates strong coupling and leads to a large red-shift of the 1.3 mu m photoluminescence (PL) peak. We study systematically the dependence of PL lifetime on the QDs size, density and temperature (1). We found that, below 50 K, the PL lifetime is insensitive to temperature, which is interpreted from the localization effects. As T increases, the PL lifetime increases, which can be explained from the competition between the carrier redistribution and thermal emission at higher temperature. The increase of carriers in QDs migrated from barriers and wetting layer (WL), and the redistribution of carriers among QDs enhance the PL lifetime as T increases. The thermal emission and non-radiative recombination have effects to reduce the PL lifetime at higher T. As a result, the radiative recombination lifetime is determined by the wave function overlapping of electrons and holes in QDs, and QDs with different densities have different PL lifetime dependence on the QDs size. (c) 2005 Elsevier B.V. All rights reserved.

Atomic force microscopic study of low temperature induced disassembly of RecA-dsDNA filaments

The assembly and disassembly of RecA-DNA nucleoprotein filaments on double-stranded DNA (dsDNA) or single-stranded DNA (ssDNA) are important steps for homologous recombination and DNA repair. The assembly and disassembly of the nucleoprotein filaments are sensitive to the reaction conditions. In this work, we investigated different morphologies of the formed nucleoprotein filaments at low temperature under different solution conditions by atomic force microscopy (AFM). We found that low temperature and long keeping time could induce the incomplete disassembly of the formed nucleoprotein filaments.

Synaptonemal complex analysis in spermatocytes of diploid and triploid Chinese shrimp Fenneropenaeus chinensis

A modified surface spreading technique for synaptonemal complex (SC) analysis was tested to assess the process of chromosome synapsis in spermatocytes of diploid and induced triploid Fenneropenaeus chinensis. Spermatocytes of diploid shrimp showed typical morphological characteristics of eukaryote SC, with complete synapsis of bivalents. No recognizable bivalent associated with sex chromosomes was observed in spermatocytes of diploid shrimp. However, differences in morphology of SC, including unsynapsed univalents, bivalents, totally paired trivalents with non-homologous synapsis, partnerswitches and triple synapsis were identified at early pachytene stage of triploid spermatocytes. Triple synapsis was especially common at late pachytene stage in spermatocytes of triploid shrimp. The observed abnormal synapsis behavior of chromosomes in spermatocytes indicated that triploid male shrimp may find it difficult to develop normal haploid sperm. (C) 2008 Elsevier Ltd. All rights reserved.

Essential role of beta-adrenergic receptor kinase 1 in cardiac development and function.

The beta-adrenergic receptor kinase 1 (beta ARK1) is a member of the G protein-coupled receptor kinase (GRK) family that mediates the agonist-dependent phosphorylation and desensitization of G protein-coupled receptors. We have cloned and disrupted the beta ARK1 gene in mice by homologous recombination. No homozygote beta ARK1-/- embryos survive beyond gestational day 15.5. Prior to gestational day 15.5, beta ARK1-/- embryos display pronounced hypoplasia of the ventricular myocardium essentially identical to the "thin myocardium syndrome" observed upon gene inactivation of several transcription factors (RXR alpha, N-myc, TEF-1, WT-1). Lethality in beta ARK1-/- embryos is likely due to heart failure as they exhibit a > 70% decrease in cardiac ejection fraction determined by direct in utero intravital microscopy. These results along with the virtual absence of endogenous GRK activity in beta ARK1-/- embryos demonstrate that beta ARK1 appears to be the predominant GRK in early embryogenesis and that it plays a fundamental role in cardiac development.

Examination of Endogenous Rotund Expression and Function in Developing Drosophila Olfactory System Using CRISPR-Cas9-Mediated Protein Tagging.

The zinc-finger protein Rotund (Rn) plays a critical role in controlling the development of the fly olfactory system. However, little is known about its molecular function in vivo. Here, we added protein tags to the rn locus using CRISPR-Cas9 technology in Drosophila to investigate its subcellular localization and the genes that it regulates . We previously used a reporter construct to show that rn is expressed in a subset of olfactory receptor neuron (ORN) precursors and it is required for the diversification of ORN fates. Here, we show that tagged endogenous Rn protein is functional based on the analysis of ORN phenotypes. Using this method, we also mapped the expression pattern of the endogenous isoform-specific tags in vivo with increased precision. Comparison of the Rn expression pattern from this study with previously published results using GAL4 reporters showed that Rn is mainly present in early steps in antennal disc patterning, but not in pupal stages when ORNs are born. Finally, using chromatin immunoprecipitation, we showed a direct binding of Rotund to a previously identified regulatory element upstream of the bric-a-brac gene locus in the developing antennal disc.

Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.

Although cell cycle control is an ancient, conserved, and essential process, some core animal and fungal cell cycle regulators share no more sequence identity than non-homologous proteins. Here, we show that evolution along the fungal lineage was punctuated by the early acquisition and entrainment of the SBF transcription factor through horizontal gene transfer. Cell cycle evolution in the fungal ancestor then proceeded through a hybrid network containing both SBF and its ancestral animal counterpart E2F, which is still maintained in many basal fungi. We hypothesize that a virally-derived SBF may have initially hijacked cell cycle control by activating transcription via the cis-regulatory elements targeted by the ancestral cell cycle regulator E2F, much like extant viral oncogenes. Consistent with this hypothesis, we show that SBF can regulate promoters with E2F binding sites in budding yeast.

Deletion of complement factor H-related genes CFHR1 and CFHR3 is associated with atypical hemolytic uremic syndrome.

Atypical hemolytic uremic syndrome (aHUS) is associated with defective complement regulation. Disease-associated mutations have been described in the genes encoding the complement regulators complement factor H, membrane cofactor protein, factor B, and factor I. In this study, we show in two independent cohorts of aHUS patients that deletion of two closely related genes, complement factor H-related 1 (CFHR1) and complement factor H-related 3 (CFHR3), increases the risk of aHUS. Amplification analysis and sequencing of genomic DNA of three affected individuals revealed a chromosomal deletion of approximately 84 kb in the RCA gene cluster, resulting in loss of the genes coding for CFHR1 and CFHR3, but leaving the genomic structure of factor H intact. The CFHR1 and CFHR3 genes are flanked by long homologous repeats with long interspersed nuclear elements (retrotransposons) and we suggest that nonallelic homologous recombination between these repeats results in the loss of the two genes. Impaired protection of erythrocytes from complement activation is observed in the serum of aHUS patients deficient in CFHR1 and CFHR3, thus suggesting a regulatory role for CFHR1 and CFHR3 in complement activation. The identification of CFHR1/CFHR3 deficiency in aHUS patients may lead to the design of new diagnostic approaches, such as enhanced testing for these genes.