Exciton-dominant electroluminescence from a diode of monolayer MoS{sub 2}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ye, Yu; Ye, Ziliang; Gharghi, Majid

2014-05-12

In two-dimensional monolayer MoS{sub 2}, excitons dominate the absorption and emission properties. However, the low electroluminescent efficiency and signal-to-noise ratio limit our understanding of the excitonic behavior of electroluminescence. Here, we study the microscopic origin of the electroluminescence from a diode of monolayer MoS{sub 2} fabricated on a heavily p-type doped silicon substrate. Direct and bound-exciton related recombination processes are identified from the electroluminescence. At a high electron-hole pair injection rate, Auger recombination of the exciton-exciton annihilation of the bound exciton emission is observed at room temperature. Moreover, the efficient electrical injection demonstrated here allows for the observation of amore » higher energy exciton peak of 2.255 eV in the monolayer MoS{sub 2} diode, attributed to the excited exciton state of a direct-exciton transition.« less

RTEL1: an essential helicase for telomere maintenance and the regulation of homologous recombination.

PubMed

Uringa, Evert-Jan; Youds, Jillian L; Lisaingo, Kathleen; Lansdorp, Peter M; Boulton, Simon J

2011-03-01

Telomere maintenance and DNA repair are crucial processes that protect the genome against instability. RTEL1, an essential iron-sulfur cluster-containing helicase, is a dominant factor that controls telomere length in mice and is required for telomere integrity. In addition, RTEL1 promotes synthesis-dependent strand annealing to direct DNA double-strand breaks into non-crossover outcomes during mitotic repair and in meiosis. Here, we review the role of RTEL1 in telomere maintenance and homologous recombination and discuss models linking RTEL1's enzymatic activity to its function in telomere maintenance and DNA repair.

Recombinant Mip-PilE-FlaA dominant epitopes vaccine candidate against Legionella pneumophila.

PubMed

He, Jinlei; Huang, Fan; Chen, Han; Chen, Qiwei; Zhang, Junrong; Li, Jiao; Chen, Dali; Chen, Jianping

2017-06-01

Legionella pneumophila is the main causative agent of Legionnaires' disease, which is a severe multi-system disease with pneumonia as the primary manifestation. We designed a recombinant Mip-PilE-FlaA dominant epitopes vaccine against Legionella pneumophila to prevent the disease and evaluated its immunogenicity and protective immunity. The protein structures of Mip, PilE and FlaA were analyzed using a computer, and the gene sequences of the dominant epitopes of the three proteins were selected to construct and optimize the vaccine. The optimized mip, pilE, flaA and recombinant mip-pilE-flaA gene sequences were cloned, expressed and purified. The purified proteins were used as dominant epitopes vaccines to immunize BALB/c mice and determine the protective immunity and immunogenicity of these purified proteins. The identification confirmed that the recombinant mip-pilE-flaA was successfully cloned and expressed. ELISA revealed that the Mip-PilE-FlaA group produced the highest IgG response, and this protein may considerably improve the production of some cytokines in BALB/c mice. Histopathology analyses of lungs from mice immunized with Mip-PilE-FlaA revealed a certain protective effect. Our work demonstrated that the recombinant dominant epitopes of Mip-PilE-FlaA exhibited strong immunogenicity and immune protection, and this protein may be an efficient epitopes vaccine candidate against Legionella pneumophila. Copyright © 2017 European Federation of Immunological Societies. Published by Elsevier B.V. All rights reserved.

Effective electron recombination coefficient in ionospheric D-region during the relaxation regime after solar flare from February 18, 2011

NASA Astrophysics Data System (ADS)

Nina, A.; Čadež, V.; Šulić, D.; Srećković, V.; Žigman, V.

2012-05-01

In this paper, we present a model for determination of a weakly time dependent effective recombination coefficient for the perturbed terrestrial ionospheric D-region plasma. We study consequences of a class M1.0 X-ray solar flare, recorded by GOES-15 satellite on February 18, 2011 between 14:00 and 14:15 UT, by analyzing the amplitude and phase real time variations of very low frequency (VLF) radio waves emitted by transmitter DHO (located in Germany) at frequency 23.4 kHz and recorded by the AWESOME receiver in Belgrade (Serbia). Our analysis is limited to ionospheric perturbations localized at altitudes around 70 km where the dominant electron gain and electron loss processes are the photo-ionization and recombination, respectively.

Reduced genetic distance and high replication levels increase the RNA recombination rate of hepatitis delta virus.

PubMed

Lin, Chia-Chi; Yang, Zhi-Wei; Iang, Shan-Bei; Chao, Mei

2015-01-02

Hepatitis delta virus (HDV) replication is carried out by host RNA polymerases. Since homologous inter-genotypic RNA recombination is known to occur in HDV, possibly via a replication-dependent process, we hypothesized that the degree of sequence homology and the replication level should be related to the recombination frequency in cells co-expressing two HDV sequences. To confirm this, we separately co-transfected cells with three different pairs of HDV genomic RNAs and analyzed the obtained recombinants by RT-PCR followed by restriction fragment length polymorphism and sequencing analyses. The sequence divergence between the clones ranged from 24% to less than 0.1%, and the difference in replication levels was as high as 100-fold. As expected, significant differences were observed in the recombination frequencies, which ranged from 0.5% to 47.5%. Furthermore, varying the relative amounts of parental RNA altered the dominant recombinant species produced, suggesting that template switching occurs frequently during the synthesis of genomic HDV RNA. Taken together, these data suggest that during the host RNA polymerase-driven RNA recombination of HDV, both inter- and intra-genotypic recombination events are important in shaping the genetic diversity of HDV. Copyright © 2014 Elsevier B.V. All rights reserved.

Diffusion controlled initial recombination

NASA Astrophysics Data System (ADS)

Christen, T.; Büttiker, M.

1998-08-01

This work addresses nucleation rates in systems with strong initial recombination. Initial (or ``geminate'') recombination is a process where a dissociated structure (anion, vortex, kink, etc.) recombines with its twin brother (cation, antivortex, antikink) generated in the same nucleation event. Initial recombination is important if there is an asymptotically vanishing interaction force instead of a generic saddle-type activation barrier. At low temperatures, initial recombination strongly dominates homogeneous recombination. In a first part, we discuss the effect in one-, two-, and three-dimensional diffusion controlled systems with spherical symmetry. Since there is no well-defined saddle, we introduce a threshold which is to some extent arbitrary but which is restricted by physically reasonable conditions. We show that the dependence of the nucleation rate on the specific choice of this threshold is strongest for one-dimensional systems and decreases in higher dimensions. We also discuss the influence of a weak driving force, and show that the transport current is directly determined by the imbalance of the activation rate in the direction of the field and the rate against this direction. In a second part, we apply the results to the overdamped sine-Gordon system at equilibrium. It turns out that diffusive initial recombination is the essential mechanism which governs the equilibrium kink nucleation rate. We emphasize analogies between the single particle problem with initial recombination and the multidimensional kink-antikink nucleation problem.

Prisoner's dilemma posed by fitness-associated recombination strategies.

PubMed

Wexler, Ydo; Rokhlenko, Oleg

2007-07-07

Genetic recombination is a central and repeated topic of study in the evolution of life. However, along with the influence of recombination on evolution, we understand surprisingly little of how selection shapes the nature of recombination. One explanation for recombination is that it allows organisms to escape from perilous situations where they experience very low fitness. As a corollary, it has been suggested that selection should favor recombination at low fitness and not at high fitness (fitness-associated recombination, FAR), and theory suggests that such strategies can indeed be selected. Here we develop models to further investigate the evolution of FAR. Consistent with previous works, we find that FAR can invade and dominate over a strategy of uniform recombination that is independent of fitness. However, our simulation results suggest that extreme FAR strategies, known as group-elitism, are not necessarily superior to other FAR strategies. Moreover, we argue that FAR domination will often occur with a net loss of mean population fitness. Interestingly, this suggests that the strategy of not recombining at high fitness will sometimes be analogous to a defector strategy from the famous "prisoner's dilemma" game: a selfish strategy that is selected but leads to a loss of mean fitness for all players.

Different annealing temperature suitable for different Mg doped P-GaN

NASA Astrophysics Data System (ADS)

Liu, S. T.; Yang, J.; Zhao, D. G.; Jiang, D. S.; Liang, F.; Chen, P.; Zhu, J. J.; Liu, Z. S.; Li, X.; Liu, W.; Zhang, L. Q.; Long, H.; Li, M.

2017-04-01

In this work, epitaxial GaN with different Mg doping concentration annealed at different temperature is investigated. Through Hall and PL spectra measurement we found that when Mg doping concentration is different, different annealing temperature is needed for obtaining the best p-type conduction of GaN, and this difference comes from the different influence of annealing on compensated donors. For ultra-heavily Mg doped sample, the process of Mg related donors transferring to non-radiative recombination centers is dominated, so the performance of P-GaN deteriorates with temperature increase. But for low Mg doped sample, the process of Mg related donors transfer to non-raditive recombination is weak compare to the Mg acceptor activation, so along the annealing temperature increase the performance GaN gets better.

Communication: Classical threshold law for ion-neutral-neutral three-body recombination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pérez-Ríos, Jesús; Greene, Chris H.

2015-07-28

A very recently method for classical trajectory calculations for three-body collision [Pérez-Ríos et al., J. Chem. Phys. 140, 044307 (2014)] has been applied to describe ion-neutral-neutral ternary processes for low energy collisions: 0.1 mK–10 mK. As a result, a threshold law for the three-body recombination cross section is obtained and corroborated numerically. The derived threshold law predicts the formation of weakly bound dimers, with binding energies comparable to the collision energy of the collisional partners. In this low energy range, this analysis predicts that molecular ions should dominate over molecular neutrals as the most products formed.

Time-resolved photoluminescence investigation of (Mg, Zn) O alloy growth on a non-polar plane

NASA Astrophysics Data System (ADS)

Mohammed Ali, Mohammed Jassim; Chauveau, J. M.; Bretagnon, T.

2018-04-01

Excitons recombination dynamics in ZnMgO alloy have been studied by time-resolved photoluminescence according to temperature. At low temperature, localisation effects of the exciton are found to play a significant role. The photoluminescence (PL) decays are bi-exponential. The short lifetime has a constant value, whereas the long lifetime shows a dependency with temperature. For temperature higher than 100 K the declines show a mono-exponential decay. The PL declines are dominated by non-radiative process at temperatures above 150 K. The PL lifetime dependancy with temperature is analysed using a model including localisation effects and non-radiative recombinations.

RTEL1: an essential helicase for telomere maintenance and the regulation of homologous recombination

PubMed Central

Uringa, Evert-Jan; Youds, Jillian L.; Lisaingo, Kathleen; Lansdorp, Peter M.; Boulton, Simon J.

2011-01-01

Telomere maintenance and DNA repair are crucial processes that protect the genome against instability. RTEL1, an essential iron–sulfur cluster-containing helicase, is a dominant factor that controls telomere length in mice and is required for telomere integrity. In addition, RTEL1 promotes synthesis-dependent strand annealing to direct DNA double-strand breaks into non-crossover outcomes during mitotic repair and in meiosis. Here, we review the role of RTEL1 in telomere maintenance and homologous recombination and discuss models linking RTEL1’s enzymatic activity to its function in telomere maintenance and DNA repair. PMID:21097466

Extreme Recombination Frequencies Shape Genome Variation and Evolution in the Honeybee, Apis mellifera

PubMed Central

Wallberg, Andreas; Glémin, Sylvain; Webster, Matthew T.

2015-01-01

Meiotic recombination is a fundamental cellular process, with important consequences for evolution and genome integrity. However, we know little about how recombination rates vary across the genomes of most species and the molecular and evolutionary determinants of this variation. The honeybee, Apis mellifera, has extremely high rates of meiotic recombination, although the evolutionary causes and consequences of this are unclear. Here we use patterns of linkage disequilibrium in whole genome resequencing data from 30 diploid honeybees to construct a fine-scale map of rates of crossing over in the genome. We find that, in contrast to vertebrate genomes, the recombination landscape is not strongly punctate. Crossover rates strongly correlate with levels of genetic variation, but not divergence, which indicates a pervasive impact of selection on the genome. Germ-line methylated genes have reduced crossover rate, which could indicate a role of methylation in suppressing recombination. Controlling for the effects of methylation, we do not infer a strong association between gene expression patterns and recombination. The site frequency spectrum is strongly skewed from neutral expectations in honeybees: rare variants are dominated by AT-biased mutations, whereas GC-biased mutations are found at higher frequencies, indicative of a major influence of GC-biased gene conversion (gBGC), which we infer to generate an allele fixation bias 5 – 50 times the genomic average estimated in humans. We uncover further evidence that this repair bias specifically affects transitions and favours fixation of CpG sites. Recombination, via gBGC, therefore appears to have profound consequences on genome evolution in honeybees and interferes with the process of natural selection. These findings have important implications for our understanding of the forces driving molecular evolution. PMID:25902173

Distribution of recombination hotspots in the human genome--a comparison of computer simulations with real data.

PubMed

Mackiewicz, Dorota; de Oliveira, Paulo Murilo Castro; Moss de Oliveira, Suzana; Cebrat, Stanisław

2013-01-01

Recombination is the main cause of genetic diversity. Thus, errors in this process can lead to chromosomal abnormalities. Recombination events are confined to narrow chromosome regions called hotspots in which characteristic DNA motifs are found. Genomic analyses have shown that both recombination hotspots and DNA motifs are distributed unevenly along human chromosomes and are much more frequent in the subtelomeric regions of chromosomes than in their central parts. Clusters of motifs roughly follow the distribution of recombination hotspots whereas single motifs show a negative correlation with the hotspot distribution. To model the phenomena related to recombination, we carried out computer Monte Carlo simulations of genome evolution. Computer simulations generated uneven distribution of hotspots with their domination in the subtelomeric regions of chromosomes. They also revealed that purifying selection eliminating defective alleles is strong enough to cause such hotspot distribution. After sufficiently long time of simulations, the structure of chromosomes reached a dynamic equilibrium, in which number and global distribution of both hotspots and defective alleles remained statistically unchanged, while their precise positions were shifted. This resembles the dynamic structure of human and chimpanzee genomes, where hotspots change their exact locations but the global distributions of recombination events are very similar.

Distribution of Recombination Hotspots in the Human Genome – A Comparison of Computer Simulations with Real Data

PubMed Central

Mackiewicz, Dorota; de Oliveira, Paulo Murilo Castro; Moss de Oliveira, Suzana; Cebrat, Stanisław

2013-01-01

Recombination is the main cause of genetic diversity. Thus, errors in this process can lead to chromosomal abnormalities. Recombination events are confined to narrow chromosome regions called hotspots in which characteristic DNA motifs are found. Genomic analyses have shown that both recombination hotspots and DNA motifs are distributed unevenly along human chromosomes and are much more frequent in the subtelomeric regions of chromosomes than in their central parts. Clusters of motifs roughly follow the distribution of recombination hotspots whereas single motifs show a negative correlation with the hotspot distribution. To model the phenomena related to recombination, we carried out computer Monte Carlo simulations of genome evolution. Computer simulations generated uneven distribution of hotspots with their domination in the subtelomeric regions of chromosomes. They also revealed that purifying selection eliminating defective alleles is strong enough to cause such hotspot distribution. After sufficiently long time of simulations, the structure of chromosomes reached a dynamic equilibrium, in which number and global distribution of both hotspots and defective alleles remained statistically unchanged, while their precise positions were shifted. This resembles the dynamic structure of human and chimpanzee genomes, where hotspots change their exact locations but the global distributions of recombination events are very similar. PMID:23776462

Recombination and Population Mosaic of a Multifunctional Viral Gene, Adeno-Associated Virus cap

PubMed Central

Takeuchi, Yasuhiro; Myers, Richard; Danos, Olivier

2008-01-01

Homologous recombination is a dominant force in evolution and results in genetic mosaics. To detect evidence of recombination events and assess the biological significance of genetic mosaics, genome sequences for various viral populations of reasonably large size are now available in the GenBank. We studied a multi-functional viral gene, the adeno-associated virus (AAV) cap gene, which codes for three capsid proteins, VP1, VP2 and VP3. VP1-3 share a common C-terminal domain corresponding to VP3, which forms the viral core structure, while the VP1 unique N-terminal part contains an enzymatic domain with phospholipase A2 activity. Our recombinant detection program (RecI) revealed five novel recombination events, four of which have their cross-over points in the N-terminal, VP1 and VP2 unique region. Comparison of phylogenetic trees for different cap gene regions confirmed discordant phylogenies for the recombinant sequences. Furthermore, differences in the phylogenetic tree structures for the VP1 unique (VP1u) region and the rest of cap highlighted the mosaic nature of cap gene in the AAV population: two dominant forms of VP1u sequences were identified and these forms are linked to diverse sequences in the rest of cap gene. This observation together with the finding of frequent recombination in the VP1 and 2 unique regions suggests that this region is a recombination hot spot. Recombination events in this region preserve protein blocks of distinctive functions and contribute to convergence in VP1u and divergence of the rest of cap. Additionally the possible biological significance of two dominant VP1u forms is inferred. PMID:18286191

A low-frequency noise model with carrier generation-recombination process for pentacene organic thin-film transistor

NASA Astrophysics Data System (ADS)

Han, C. Y.; Qian, L. X.; Leung, C. H.; Che, C. M.; Lai, P. T.

2013-07-01

By including the generation-recombination process of charge carriers in conduction channel, a model for low-frequency noise in pentacene organic thin-film transistors (OTFTs) is proposed. In this model, the slope and magnitude of power spectral density for low-frequency noise are related to the traps in the gate dielectric and accumulation layer of the OTFT for the first time. The model can well fit the measured low-frequency noise data of pentacene OTFTs with HfO2 or HfLaO gate dielectric, which validates this model, thus providing an estimate on the densities of traps in the gate dielectric and accumulation layer. It is revealed that the traps in the accumulation layer are much more than those in the gate dielectric, and so dominate the low-frequency noise of pentacene OTFTs.

Identification of the limiting factors for high-temperature GaAs, GaInP, and AlGaInP solar cells from device and carrier lifetime analysis

NASA Astrophysics Data System (ADS)

Perl, E. E.; Kuciauskas, D.; Simon, J.; Friedman, D. J.; Steiner, M. A.

2017-12-01

We analyze the temperature-dependent dark saturation current density and open-circuit voltage (VOC) for GaAs, GaInP, and AlGaInP solar cells from 25 to 400 °C. As expected, the intrinsic carrier concentration, ni, dominates the temperature dependence of the dark currents. However, at 400 °C, we measure VOC that is ˜50 mV higher for the GaAs solar cell and ˜60-110 mV lower for the GaInP and AlGaInP solar cells compared to what would be expected from commonly used solar cell models that consider only the ni2 temperature dependence. To better understand these deviations, we measure the carrier lifetimes of p-type GaAs, GaInP, and AlGaInP double heterostructures (DHs) from 25 to 400 °C using time-resolved photoluminescence. Temperature-dependent minority carrier lifetimes are analyzed to determine the relative contributions of the radiative recombination, interface recombination, Shockley-Read-Hall recombination, and thermionic emission processes. We find that radiative recombination dominates for the GaAs DHs with the effective lifetime approximately doubling as the temperature is increased from 25 °C to 400 °C. In contrast, we find that thermionic emission dominates for the GaInP and AlGaInP DHs at elevated temperatures, leading to a 3-4× reduction in the effective lifetime and ˜40× increase in the surface recombination velocity as the temperature is increased from 25 °C to 400 °C. These observations suggest that optimization of the minority carrier confinement layers for the GaInP and AlGaInP solar cells could help to improve VOC and solar cell efficiency at elevated temperatures. We demonstrate VOC improvement at 200-400 °C in GaInP solar cells fabricated with modified AlGaInP window and back surface field layers.

Identification of the limiting factors for high-temperature GaAs, GaInP, and AlGaInP solar cells from device and carrier lifetime analysis

DOE PAGES

Perl, E. E.; Kuciauskas, D.; Simon, J.; ...

2017-12-21

We analyze the temperature-dependent dark saturation current density and open-circuit voltage (VOC) for GaAs, GaInP, and AlGaInP solar cells from 25 to 400 degrees C. As expected, the intrinsic carrier concentration, ni, dominates the temperature dependence of the dark currents. However, at 400 degrees C, we measure VOC that is ~50 mV higher for the GaAs solar cell and ~60-110 mV lower for the GaInP and AlGaInP solar cells compared to what would be expected from commonly used solar cell models that consider only the ni2 temperature dependence. To better understand these deviations, we measure the carrier lifetimes of p-typemore » GaAs, GaInP, and AlGaInP double heterostructures (DHs) from 25 to 400 degrees C using time-resolved photoluminescence. Temperature-dependent minority carrier lifetimes are analyzed to determine the relative contributions of the radiative recombination, interface recombination, Shockley-Read-Hall recombination, and thermionic emission processes. We find that radiative recombination dominates for the GaAs DHs with the effective lifetime approximately doubling as the temperature is increased from 25 degrees C to 400 degrees C. In contrast, we find that thermionic emission dominates for the GaInP and AlGaInP DHs at elevated temperatures, leading to a 3-4x reduction in the effective lifetime and ~40x increase in the surface recombination velocity as the temperature is increased from 25 degrees C to 400 degrees C. These observations suggest that optimization of the minority carrier confinement layers for the GaInP and AlGaInP solar cells could help to improve VOC and solar cell efficiency at elevated temperatures. We demonstrate VOC improvement at 200-400 degrees C in GaInP solar cells fabricated with modified AlGaInP window and back surface field layers.« less

Identification of the limiting factors for high-temperature GaAs, GaInP, and AlGaInP solar cells from device and carrier lifetime analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perl, E. E.; Kuciauskas, D.; Simon, J.

We analyze the temperature-dependent dark saturation current density and open-circuit voltage (VOC) for GaAs, GaInP, and AlGaInP solar cells from 25 to 400 degrees C. As expected, the intrinsic carrier concentration, ni, dominates the temperature dependence of the dark currents. However, at 400 degrees C, we measure VOC that is ~50 mV higher for the GaAs solar cell and ~60-110 mV lower for the GaInP and AlGaInP solar cells compared to what would be expected from commonly used solar cell models that consider only the ni2 temperature dependence. To better understand these deviations, we measure the carrier lifetimes of p-typemore » GaAs, GaInP, and AlGaInP double heterostructures (DHs) from 25 to 400 degrees C using time-resolved photoluminescence. Temperature-dependent minority carrier lifetimes are analyzed to determine the relative contributions of the radiative recombination, interface recombination, Shockley-Read-Hall recombination, and thermionic emission processes. We find that radiative recombination dominates for the GaAs DHs with the effective lifetime approximately doubling as the temperature is increased from 25 degrees C to 400 degrees C. In contrast, we find that thermionic emission dominates for the GaInP and AlGaInP DHs at elevated temperatures, leading to a 3-4x reduction in the effective lifetime and ~40x increase in the surface recombination velocity as the temperature is increased from 25 degrees C to 400 degrees C. These observations suggest that optimization of the minority carrier confinement layers for the GaInP and AlGaInP solar cells could help to improve VOC and solar cell efficiency at elevated temperatures. We demonstrate VOC improvement at 200-400 degrees C in GaInP solar cells fabricated with modified AlGaInP window and back surface field layers.« less

Magnetic resonance studies of atomic hydrogen at zero field and low temperature: Recombination and binding on liquid helium

NASA Astrophysics Data System (ADS)

Jochemsen, R.; Morrow, M.; Berlinsky, A. J.; Hardy, W. N.

1982-07-01

Magnetic resonance studies at zero field are reported for atomic hydrogen gas confined in a closed glass bulb with helium-coated walls for T < 1 K in a dilution refrigerator. Low-energy r.f. discharge pulses have been used to produce H atoms at temperatures as low as T = 0.06 K. The atom density nH (10 9 < nH < 10 13) measured by the strength of the free induction decay signal, follows a second-order rate equation {dn H}/{dt} = -Kn H2. At the lowest temperatures recombination is dominated by the process H + H+ wall → H 2 + wall. From the temperature dependence of the rate constant K we have determined the binding energy of H on liquid 4He and 3He, and also the cross section for recombination on the surface.

Investigation of Exciton Recombination Zone in Quantum Dot Light-Emitting Diodes Using a Fluorescent Probe.

PubMed

Huang, Xiaoyu; Zhang, Heng; Xu, Dingxin; Wen, Feng; Chen, Shuming

2017-08-23

Exciton recombination zone, where the photons are generated, can greatly affect the performance, such as the efficiency and color purity, of the quantum dot (QD) light-emitting diodes (QLEDs). To probe the exciton recombination zone, 4-(dicyanomethylene)-2-t-butyl-6(1,1,7,7-tetramethyljulolidyl-9-enyl)-4H-pyran (DCJTB) is doped into the charge transport layer as a fluorescent sensor; by monitoring the Förster resonant energy transfer (FRET) between QD and DCJTB, the location of the recombination zone can be determined. It is found that the electron transport layer (ETL) has a great impact on the recombination zone. For example, in QLEDs with ZnMgO ETL, the recombination zone is near the interface of the QD/hole transport layer (HTL) and is shifted to the interface of the QD/ETL as the driving voltage is increased, whereas in devices with 1,3,5-tris(2-N-phenylbenzimidazolyl) benzene (TPBi) ETL, the recombination zone is close to the interface of the QD/ETL and moved to the interface of the QD/HTL with the increase in the driving voltage. Our results can also clarify the light emission mechanism in QLEDs. In devices with ZnMgO ETL, the emission is dominated by the direct charge recombination, whereas in devices with TPBi ETL, the emission is contributed by both FRET and direct charge recombination. Our studies suggest that fluorescent probe can be a powerful tool for investigating the exciton recombination zone, light emission mechanism, and other fundamental processes in QLEDs.

Dark current of organic heterostructure devices with insulating spacer layers

NASA Astrophysics Data System (ADS)

Yin, Sun; Nie, Wanyi; Mohite, Aditya D.; Saxena, Avadh; Smith, Darryl L.; Ruden, P. Paul

2015-03-01

The dark current density at fixed voltage bias in donor/acceptor organic planar heterostructure devices can either increase or decrease when an insulating spacer layer is added between the donor and acceptor layers. The dominant current flow process in these systems involves the formation and subsequent recombination of an interfacial exciplex state. If the exciplex formation rate limits current flow, the insulating interface layer can increase dark current whereas, if the exciplex recombination rate limits current flow, the insulating interface layer decreases dark current. We present a device model to describe this behavior and illustrate it experimentally for various donor/acceptor systems, e.g. P3HT/LiF/C60.

Current–voltage characteristics of organic heterostructure devices with insulating spacer layers

DOE PAGES

Yin, Sun; Nie, Wanyi; Mohite, Aditya D.; ...

2015-05-14

The dark current density in donor/acceptor organic planar heterostructure devices at a given forward voltage bias can either increase or decrease when an insulating spacer layer is added between the donor and acceptor layers. The dominant current flow process in these systems involves the formation and subsequent recombination of interfacial exciplex states. If the exciplex recombination rate limits current flow, an insulating interface layer decreases the dark current. However, if the exciplex formation rate limits the current, an insulating interface layer may increase the dark current. As a result, we present a device model to describe this behavior, and wemore » discuss relevant experimental data.« less

Atomic Data for Nebular Abundance Determinations: Photoionization and Recombination Properties of Xenon Ions

NASA Astrophysics Data System (ADS)

Sterling, Nicholas C.; Kerlin, Austin B.

2016-01-01

We present preliminary results of a study of the photoionization (PI) and recombination properties of low-charge Xe ions. The abundances of neutron(n)-capture elements (atomic number Z > 30) are of interest in planetary nebulae (PNe) since they can be enriched by slow n-capture nucleosynthesis (the ``s-process'') in the progenitor asymptotic giant branch (AGB) stars. Xe is particularly valuable, because it is the most widely-observed ``heavy-s'' species (Z > 40) in PNe. Its abundance relative to lighter n-capture elements can be used to determine s-process neutron exposures, and constrain s-process enrichment patterns as a function of progenitor metallicity. Using the atomic structure code AUTOSTRUCTURE (Badnell 2011, Comp. Phys. Comm., 182, 1528), we have computed multi-configuration Breit-Pauli distorted-wave PI cross sections and radiative recombination (RR) and dielectronic recombination (DR) rate coefficients for neutral through six-times ionized Xe, data which are critically needed for accurate Xe abundance determinations in ionized nebulae. We find good agreement between our computed direct PI cross sections and experimental measurements. Internal uncertainties are estimated for our calculations by using three different configuration interaction expansions for each ion, and by testing the sensitivity of our results to the radial orbital scaling parameters. As found for other n-capture elements (Sterling & Witthoeft 2011, A&A, 529, A147; Sterling 2011, A&A, 533, A62), DR is the dominant recombination mechanism for Xe ions at nebular temperatures (~104 K). Following Sterling et al. (2015, ApJS, 218, 25), these data will be added to nebular modeling codes to compute ionization correction factors for unobserved Xe ions in PNe, which will enable elemental Xe abundances to be determined with much higher accuracy than is currently possible. This work is supported by NSF award AST-1412928.

Transient dominant host-range selection using Chinese hamster ovary cells to generate marker-free recombinant viral vectors from vaccinia virus.

PubMed

Liu, Liang; Cooper, Tamara; Eldi, Preethi; Garcia-Valtanen, Pablo; Diener, Kerrilyn R; Howley, Paul M; Hayball, John D

2017-04-01

Recombinant vaccinia viruses (rVACVs) are promising antigen-delivery systems for vaccine development that are also useful as research tools. Two common methods for selection during construction of rVACV clones are (i) co-insertion of drug resistance or reporter protein genes, which requires the use of additional selection drugs or detection methods, and (ii) dominant host-range selection. The latter uses VACV variants rendered replication-incompetent in host cell lines by the deletion of host-range genes. Replicative ability is restored by co-insertion of the host-range genes, providing for dominant selection of the recombinant viruses. Here, we describe a new method for the construction of rVACVs using the cowpox CP77 protein and unmodified VACV as the starting material. Our selection system will expand the range of tools available for positive selection of rVACV during vector construction, and it is substantially more high-fidelity than approaches based on selection for drug resistance.

Selections that isolate recombinant mitochondrial genomes in animals

PubMed Central

Ma, Hansong; O'Farrell, Patrick H

2015-01-01

Homologous recombination is widespread and catalyzes evolution. Nonetheless, its existence in animal mitochondrial DNA is questioned. We designed selections for recombination between co-resident mitochondrial genomes in various heteroplasmic Drosophila lines. In four experimental settings, recombinant genomes became the sole or dominant genome in the progeny. Thus, selection uncovers occurrence of homologous recombination in Drosophila mtDNA and documents its functional benefit. Double-strand breaks enhanced recombination in the germline and revealed somatic recombination. When the recombination partner was a diverged Drosophila melanogaster genome or a genome from a different species such as Drosophila yakuba, sequencing revealed long continuous stretches of exchange. In addition, the distribution of sequence polymorphisms in recombinants allowed us to map a selected trait to a particular region in the Drosophila mitochondrial genome. Thus, recombination can be harnessed to dissect function and evolution of mitochondrial genome. DOI: http://dx.doi.org/10.7554/eLife.07247.001 PMID:26237110

Structural dynamics of a noncovalent charge transfer complex from femtosecond stimulated Raman spectroscopy.

PubMed

Fujisawa, Tomotsumi; Creelman, Mark; Mathies, Richard A

2012-09-06

Femtosecond stimulated Raman spectroscopy is used to examine the structural dynamics of photoinduced charge transfer within a noncovalent electron acceptor/donor complex of pyromellitic dianhydride (PMDA, electron acceptor) and hexamethylbenzene (HMB, electron donor) in ethylacetate and acetonitrile. The evolution of the vibrational spectrum reveals the ultrafast structural changes that occur during the charge separation (Franck-Condon excited state complex → contact ion pair) and the subsequent charge recombination (contact ion pair → ground state complex). The Franck-Condon excited state is shown to have significant charge-separated character because its vibrational spectrum is similar to that of the ion pair. The charge separation rate (2.5 ps in ethylacetate and ∼0.5 ps in acetonitrile) is comparable to solvation dynamics and is unaffected by the perdeuteration of HMB, supporting the dominant role of solvent rearrangement in charge separation. On the other hand, the charge recombination slows by a factor of ∼1.4 when using perdeuterated HMB, indicating that methyl hydrogen motions of HMB mediate the charge recombination process. Resonance Raman enhancement of the HMB vibrations in the complex reveals that the ring stretches of HMB, and especially the C-CH(3) deformations are the primary acceptor modes promoting charge recombination.

Exciton recombination dynamics in CdSe nanowires: bimolecular to three-carrier Auger kinetics.

PubMed

Robel, István; Bunker, Bruce A; Kamat, Prashant V; Kuno, Masaru

2006-07-01

Ultrafast relaxation dynamics of charge carriers in CdSe quantum wires with diameters between 6 and 8 nm are studied as a function of carrier density. At high electron-hole pair densities above 10(19) cm(-3) the dominant process for carrier cooling is the "bimolecular" Auger recombination of one-dimensional (1D) excitons. However, below this excitation level an unexpected transition from a bimolecular (exciton-exciton) to a three-carrier Auger relaxation mechanism occurs. Thus, depending on excitation intensity, electron-hole pair relaxation dynamics in the nanowires exhibit either 1D or 0D (quantum dot) character. This dual nature of the recovery kinetics defines an optimal intensity for achieving optical gain in solution-grown nanowires given the different carrier-density-dependent scaling of relaxation rates in either regime.

Efficient long wavelength interband photoluminescence from HgCdTe epitaxial films at wavelengths up to 26 μm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morozov, S. V.; Rumyantsev, V. V., E-mail: rumyantsev@ipmras.ru; Antonov, A. V.

2014-02-17

Photoluminescence (PL) and photoconductivity (PC) studies of Hg{sub 1−x}Cd{sub x}Te (0.19 ≤ x ≤ 0.23) epitaxial films are presented. Interband PL is observed at wavelengths from 26 to 6 μm and in the temperature range 18 K–200 K. The PL line full width at half maximum is about 6 meV (4kT) at 18 K and approaches its theoretical limit of 1.8kT at higher temperatures. Carrier recombination process is also investigated by time resolved studies of PL and PC at pulsed excitation. Radiative transitions are shown to be the dominating mechanism of carrier recombination at high excitation levels.

Minority carrier lifetime in mid-wavelength infrared InAs/InAsSb superlattices: Photon recycling and the role of radiative and Shockley-Read-Hall recombination mechanisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Höglund, L.; Ting, D. Z.; Soibel, A.

The influence of radiative recombination on the minority carrier lifetime in mid-wavelength InAs/InAsSb superlattices was investigated. From the lifetime's dependence on temperature, photon recycling, and carrier concentration, it was demonstrated that radiative lifetime dominates for carrier concentrations >5 × 10{sup 14} cm{sup −3}, and Shockley-Read-Hall recombination starts to dominate the minority carrier lifetime for carrier concentrations <5 × 10{sup 14} cm{sup −3}. An observed increase of the minority carrier lifetime with increasing superlattice thickness was attributed to photon recycling, and good agreement between measured and theoretical values of the photon recycling factor was obtained.

Hydrogen loss and its improved retention in hydrogen plasma treated a-SiNx:H films: ERDA study with 100 MeV Ag7+ ions

NASA Astrophysics Data System (ADS)

Bommali, R. K.; Ghosh, S.; Khan, S. A.; Srivastava, P.

2018-05-01

Hydrogen loss from a-SiNx:H films under irradiation with 100 MeV Ag7+ ions using elastic recoil detection analysis (ERDA) experiment is reported. The results are explained under the basic assumptions of the molecular recombination model. The ERDA hydrogen concentration profiles are composed of two distinct hydrogen desorption processes, limited by rapid molecular diffusion in the initial stages of irradiation, and as the fluence progresses a slow process limited by diffusion of atomic hydrogen takes over. Which of the aforesaid processes dominates, is determined by the continuously evolving Hydrogen concentration within the films. The first process dominates when the H content is high, and as the H concentration falls below a certain threshold (Hcritical) the irradiation generated H radicals have to diffuse through larger distances before recombining to form H2, thereby significantly bringing down the hydrogen evolution rate. The ERDA measurements were also carried out for films treated with low temperature (300 °C) hydrogen plasma annealing (HPA). The HPA treated films show a clear increase in Hcritical value, thus indicating an improved diffusion of atomic hydrogen, resulting from healing of weak bonds and passivation of dangling bonds. Further, upon HPA films show a significantly higher H concentration relative to the as-deposited films, at advanced fluences. These results indicate the potential of HPA towards improved H retention in a-SiNx:H films. The study distinguishes clearly the presence of two diffusion processes in a-SiNx:H whose diffusion rates differ by an order of magnitude, with atomic hydrogen not being able to diffuse further beyond ∼ 1 nm from the point of its creation.

Dissociative Recombination without a Curve Crossing

NASA Technical Reports Server (NTRS)

Guberman, Steven L.

1994-01-01

Ab initio calculations show that a curve crossing is not always needed for a high dissociative- recombination cross section. For HeH(+), in which no neutral states cross the ion potential curve, dissociative recombination is driven by the nuclear kinetic-energy operator on adiabatic potential curves. The kinetic-energy derivative operator allows for capture into repulsive curves that are outside of the classical turning points for the nuclear motion. The dominant dissociative route is the C (2)Sigma(+) state leading to H(n = 2) atoms. An analogous mechanism is proposed for the dissociative recombination of H3(+).

Process Research On Polycrystalline Silicon Material (PROPSM)

NASA Technical Reports Server (NTRS)

Culik, J. S.; Wohlgemuth, J. H.

1982-01-01

Performance limiting mechanisms in polycrystalline silicon are investigated by fabricating a matrix of solar cells of various thicknesses from polycrystalline silicon wafers of several bulk resistivities. The analysis of the results for the entire matrix indicates that bulk recombination is the dominant factor limiting the short circuit current in large grain (greater than 1 to 2 mm diameter) polycrystalline silicon, the same mechanism that limits the short circuit current in single crystal silicon. An experiment to investigate the limiting mechanisms of open circuit voltage and fill factor for large grain polycrystalline silicon is designed. Two process sequences to fabricate small cells are investigated.

Time-resolved, nonequilibrium carrier dynamics in Si-on-glass thin films for photovoltaic cells

DOE PAGES

Serafini, John; Akbas, Yunus; Crandall, Lucas; ...

2016-03-02

Here, a femtosecond pump–probe spectroscopy method was used to characterize the growth process and transport properties of amorphous silicon-on-glass, thin films, intended as absorbers for photovoltaic cells. We collected normalized transmissivity change (ΔT/T) waveforms and interpreted them using a comprehensive three-rate equation electron trapping and recombination model. Optically excited ~300–500 nm thick Si films exhibited a bi-exponential carrier relaxation with the characteristic times varying from picoseconds to nanoseconds depending on the film growth process. From our comprehensive trapping model, we could determine that for doped and intrinsic films with very low hydrogen dilution the dominant relaxation mode was carrier trapping;more » while for intrinsic films with large hydrogen content and some texture, it was the standard electron–phonon cooling. In both cases, the initial nonequilibrium relaxation was followed by Shockley–Read–Hall recombination. An excellent fit between the model and the ΔT/T experimental transients was obtained and a correlation between the Si film growth process, its hydrogen content, and the associated trap concentration was demonstrated.« less

Transient photocurrent responses in amorphous Zn-Sn-O thin films

NASA Astrophysics Data System (ADS)

Kim, Ju-Yeon; Oh, Sang-A.; Yu, Kyeong Min; Bae, Byung Seong; Yun, Eui-Jung

2015-04-01

In this study we characterized the transient photocurrent responses in solution-processed amorphous zinc-tin-oxide (a-ZTO) thin films measured under light illumination with a wavelength of 400 nm at different temperatures. By using the temperature-dependent photoconductivities of a-ZTO thin films, we extracted the activation energies (E ac ) of photo-excitation and dark relaxation through an extended stretched exponential analysis (SEA). The SEA was found to describe well the dark relaxation characteristics as well as the photo-excitation processes. The SEA also indicates that the dark relaxation process reveals a dispersive transient photoconductivity with a broader distribution of the E ac while the photo-excitation process shows non-dispersive characteristics. Samples exposed by light at temperatures less than 373 K possess the fast processes of photo-excitation and dark relaxation. This suggests that a fast process, for example, a generation/recombination of charged carriers related to a band-to-band transition and/or shallow/deep oxygen-vacancy (V o ) sub-gap donor states, is dominant in the case of light illumination at low temperatures of less than 373 K. The SEA indicates, however, that a much slower process due mainly to the delay of the onset of ionization/neutralization of the deep V o states by multiple-trapping is dominant for samples under light illumination at a high temperature of 373 K. Based on the experimental results, for the dark relaxation process, we conclude that the process transitions from a fast recombination of electrons through band-to-band transitions and/or shallow/deep V o donor states to a slow neutralization of the ionized V o states occurs due to enhanced carrier multiple-trapping by relatively deep V o trap states when the temperature becomes greater than 363 K. An energy band diagram of a-ZTO thin films was proposed in terms of the temperature and the E ac distribution to explain these observed results.

Analysis of different forward current-voltage behaviours of Al implanted 4H-SiC vertical p-i-n diodes

NASA Astrophysics Data System (ADS)

Megherbi, M. L.; Pezzimenti, F.; Dehimi, L.; Rao, S.; Della Corte, F. G.

2015-07-01

In this work different experimental current-voltage behaviours of several Al implanted 4H-SiC p-i-n diodes are investigated by means of numerical simulations in a wide range of currents and temperatures. Some devices for which recombination and tunneling are the dominant current processes at all biases are classified as "leaky" diodes. The well behaved diodes, instead, show good rectifying characteristics with a current conduction due to tunneling below 1.7 V, recombination between 1.7 V and 2.5 V, and diffusion processes above 2.5 V. At higher current regimes, a series resistance in excess of 1 mΩ cm2 becomes the main current limiting factor. Depending on the relative weight between the contact resistances and the internal diode resistance, different temperature dependencies of the current are obtained. A good agreement between numerical and measured data is achieved employing temperature-dependent carrier lifetime and mobility as fitting parameters.

Probing Photoexcited Carriers in a Few-Layer MoS2 Laminate by Time-Resolved Optical Pump-Terahertz Probe Spectroscopy.

PubMed

Kar, Srabani; Su, Y; Nair, R R; Sood, A K

2015-12-22

We report the dynamics of photoinduced carriers in a free-standing MoS2 laminate consisting of a few layers (1-6 layers) using time-resolved optical pump-terahertz probe spectroscopy. Upon photoexcitation with the 800 nm pump pulse, the terahertz conductivity increases due to absorption by the photoinduced charge carriers. The relaxation of the non-equilibrium carriers shows fast as well as slow decay channels, analyzed using a rate equation model incorporating defect-assisted Auger scattering of photoexcited electrons, holes, and excitons. The fast relaxation time occurs due to the capture of electrons and holes by defects via Auger processes, resulting in nonradiative recombination. The slower relaxation arises since the excitons are bound to the defects, preventing the defect-assisted Auger recombination of the electrons and the holes. Our results provide a comprehensive understanding of the non-equilibrium carrier kinetics in a system of unscreened Coulomb interactions, where defect-assisted Auger processes dominate and should be applicable to other 2D systems.

Insights into H2 formation in space from ab initio molecular dynamics

PubMed Central

Casolo, Simone; Tantardini, Gian Franco; Martinazzo, Rocco

2013-01-01

Hydrogen formation is a key process for the physics and the chemistry of interstellar clouds. Molecular hydrogen is believed to form on the carbonaceous surface of dust grains, and several mechanisms have been invoked to explain its abundance in different regions of space, from cold interstellar clouds to warm photon-dominated regions. Here, we investigate direct (Eley–Rideal) recombination including lattice dynamics, surface corrugation, and competing H-dimers formation by means of ab initio molecular dynamics. We find that Eley–Rideal reaction dominates at energies relevant for the interstellar medium and alone may explain observations if the possibility of facile sticking at special sites (edges, point defects, etc.) on the surface of the dust grains is taken into account. PMID:23572584

Meiotic Crossover Control by Concerted Action of Rad51-Dmc1 in Homolog Template Bias and Robust Homeostatic Regulation

PubMed Central

Huang, Chu-Chun; Grubb, Jennifer; Thacker, Drew; Lee, Chih-Ying; Dresser, Michael E.; Hunter, Neil; Bishop, Douglas K.

2013-01-01

During meiosis, repair of programmed DNA double-strand breaks (DSBs) by recombination promotes pairing of homologous chromosomes and their connection by crossovers. Two DNA strand-exchange proteins, Rad51 and Dmc1, are required for meiotic recombination in many organisms. Studies in budding yeast imply that Rad51 acts to regulate Dmc1's strand exchange activity, while its own exchange activity is inhibited. However, in a dmc1 mutant, elimination of inhibitory factor, Hed1, activates Rad51's strand exchange activity and results in high levels of recombination without participation of Dmc1. Here we show that Rad51-mediated meiotic recombination is not subject to regulatory processes associated with high-fidelity chromosome segregation. These include homolog bias, a process that directs strand exchange between homologs rather than sister chromatids. Furthermore, activation of Rad51 does not effectively substitute for Dmc1's chromosome pairing activity, nor does it ensure formation of the obligate crossovers required for accurate homolog segregation. We further show that Dmc1's dominance in promoting strand exchange between homologs involves repression of Rad51's strand-exchange activity. This function of Dmc1 is independent of Hed1, but requires the meiotic kinase, Mek1. Hed1 makes a relatively minor contribution to homolog bias, but nonetheless this is important for normal morphogenesis of synaptonemal complexes and efficient crossing-over especially when DSB numbers are decreased. Super-resolution microscopy shows that Dmc1 also acts to organize discrete complexes of a Mek1 partner protein, Red1, into clusters along lateral elements of synaptonemal complexes; this activity may also contribute to homolog bias. Finally, we show that when interhomolog bias is defective, recombination is buffered by two feedback processes, one that increases the fraction of events that yields crossovers, and a second that we propose involves additional DSB formation in response to defective homolog interactions. Thus, robust crossover homeostasis is conferred by integrated regulation at initiation, strand-exchange and maturation steps of meiotic recombination. PMID:24367271

Wave propagation in a quasi-chemical equilibrium plasma

NASA Technical Reports Server (NTRS)

Fang, T.-M.; Baum, H. R.

1975-01-01

Wave propagation in a quasi-chemical equilibrium plasma is studied. The plasma is infinite and without external fields. The chemical reactions are assumed to result from the ionization and recombination processes. When the gas is near equilibrium, the dominant role describing the evolution of a reacting plasma is played by the global conservation equations. These equations are first derived and then used to study the small amplitude wave motion for a near-equilibrium situation. Nontrivial damping effects have been obtained by including the conduction current terms.

Evaluation of algorithms used to order markers on genetic maps.

PubMed

Mollinari, M; Margarido, G R A; Vencovsky, R; Garcia, A A F

2009-12-01

When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F(2) populations were randomly simulated with 100 and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results.

CAST constraints on the axion-electron coupling

DOE PAGES

None, None

2013-05-09

In non-hadronic axion models, which have a tree-level axion-electron interaction, the Sun produces a strong axion flux by bremsstrahlung, Compton scattering, and axio- recombination, the “BCA processes.” Based on a new calculation of this flux, including for the first time axio-recombination, we derive limits on the axion-electron Yukawa coupling g ae and axion-photon interaction strength g aγ using the CAST phase-I data (vacuum phase). For m a ≲ 10 meV/c 2 we find g aγ gae < 8.1 × 10–23 GeV–1 at 95% CL. We stress that a next-generation axion helioscope such as the proposed IAXO could push this sensitivitymore » into a range beyond stellar energy-loss limits and test the hypothesis that white-dwarf cooling is dominated by axion emission.« less

Genome-wide variation in recombination rate in Eucalyptus.

PubMed

Gion, Jean-Marc; Hudson, Corey J; Lesur, Isabelle; Vaillancourt, René E; Potts, Brad M; Freeman, Jules S

2016-08-09

Meiotic recombination is a fundamental evolutionary process. It not only generates diversity, but influences the efficacy of natural selection and genome evolution. There can be significant heterogeneity in recombination rates within and between species, however this variation is not well understood outside of a few model taxa, particularly in forest trees. Eucalypts are forest trees of global economic importance, and dominate many Australian ecosystems. We studied recombination rate in Eucalyptus globulus using genetic linkage maps constructed in 10 unrelated individuals, and markers anchored to the Eucalyptus reference genome. This experimental design provided the replication to study whether recombination rate varied between individuals and chromosomes, and allowed us to study the genomic attributes and population genetic parameters correlated with this variation. Recombination rate varied significantly between individuals (range = 2.71 to 3.51 centimorgans/megabase [cM/Mb]), but was not significantly influenced by sex or cross type (F1 vs. F2). Significant differences in recombination rate between chromosomes were also evident (range = 1.98 to 3.81 cM/Mb), beyond those which were due to variation in chromosome size. Variation in chromosomal recombination rate was significantly correlated with gene density (r = 0.94), GC content (r = 0.90), and the number of tandem duplicated genes (r = -0.72) per chromosome. Notably, chromosome level recombination rate was also negatively correlated with the average genetic diversity across six species from an independent set of samples (r = -0.75). The correlations with genomic attributes are consistent with findings in other taxa, however, the direction of the correlation between diversity and recombination rate is opposite to that commonly observed. We argue this is likely to reflect the interaction of selection and specific genome architecture of Eucalyptus. Interestingly, the differences amongst chromosomes in recombination rates appear stable across Eucalyptus species. Together with the strong correlations between recombination rate and features of the Eucalyptus reference genome, we maintain these findings provide further evidence for a broad conservation of genome architecture across the globally significant lineages of Eucalyptus.

The first does the work, but the third time's the charm: the effects of massed repetition on episodic encoding of multimodal face-name associations.

PubMed

Mangels, Jennifer A; Manzi, Alberto; Summerfield, Christopher

2010-03-01

In social interactions, it is often necessary to rapidly encode the association between visually presented faces and auditorily presented names. The present study used event-related potentials to examine the neural correlates of associative encoding for multimodal face-name pairs. We assessed study-phase processes leading to high-confidence recognition of correct pairs (and consistent rejection of recombined foils) as compared to lower-confidence recognition of correct pairs (with inconsistent rejection of recombined foils) and recognition failures (misses). Both high- and low-confidence retrieval of face-name pairs were associated with study-phase activity suggestive of item-specific processing of the face (posterior inferior temporal negativity) and name (fronto-central negativity). However, only those pairs later retrieved with high confidence recruited a sustained centro-parietal positivity that an ancillary localizer task suggested may index an association-unique process. Additionally, we examined how these processes were influenced by massed repetition, a mnemonic strategy commonly employed in everyday situations to improve face-name memory. Differences in subsequent memory effects across repetitions suggested that associative encoding was strongest at the initial presentation, and thus, that the initial presentation has the greatest impact on memory formation. Yet, exploratory analyses suggested that the third presentation may have benefited later memory by providing an opportunity for extended processing of the name. Thus, although encoding of the initial presentation was critical for establishing a strong association, the extent to which processing was sustained across subsequent immediate (massed) presentations may provide additional encoding support that serves to differentiate face-name pairs from similar (recombined) pairs by providing additional encoding opportunities for the less dominant stimulus dimension (i.e., name).

Selection of recombinant MVA by rescue of the essential D4R gene.

PubMed

Ricci, Patricia S; Schäfer, Birgit; Kreil, Thomas R; Falkner, Falko G; Holzer, Georg W

2011-12-12

Modified vaccinia virus Ankara (MVA) has become a promising vaccine vector due to its immunogenicity and its proven safety in humans. As a general approach for stringent and rapid selection of recombinant MVA, we assessed marker rescue of the essential viral D4R gene in an engineered deletion mutant that is fully replication defective in wild-type cells. Recombinant, replicating virus was obtained by re-introduction of the deleted viral gene as a dominant selection marker into the deletion mutant.

Construction of recombinant Mip-FlaA dominant epitope vaccine against Legionella pneumophila and evaluation of the immunogenicity and protective immunity.

PubMed

He, Jinlei; Zhang, Junrong; He, Yanxia; Huang, Fan; Li, Jiao; Chen, Qiwei; Chen, Dali; Chen, Jianping

2016-02-01

Legionnaires' disease, a kind of systemic disease with pneumonia as the main manifestation, is caused by Legionella pneumophila (L. pneumophila). In order to prevent the disease, we optimized Mip and FlaA, the virulence factors of L. pneumophila, to design recombinant Mip-FlaA dominant epitope vaccine against the pathogen. Firstly, the coding sequences of mip and flaA were optimized by DNAStar software and Expasy protein analysis system, and then, the tertiary structure and function of recombinant Mip-FlaA were predicted by PHYRE2 Protein Fold Recognition Server. After that, the optimized mip, flaA and mip-flaA were cloned, expressed and purified, and the proteins were used as dominant epitope vaccines to immunize BABL/c mice. Moreover, the IgG titers, histological changes in lung and the level of TNF-α, IFN-γ, IL-6 and IL-1β were detected to reflect the immunogenicity and protective immunity of the vaccines. The results of SDS-PAGE and Western blot proved the recombinant Mip-FlaA was successfully expressed. ELISA results of IgG titers and these cytokines showed Mip-FlaA group was capable to induce the strongest immune response, compared to PBS, Mip and FlaA groups. In addition, histopathology analysis demonstrated the mice immunized with Mip-FlaA showed better immune protection. Therefore, the work indicated that the above-described biological tools were useful in optimization of epitope vaccine. Antigenic characterization and immune protection of recombinant Mip-FlaA would be of great value in understanding the immunopathogenesis of the disease and in developing possible vaccine against the pathogen.

Poly(4-Vinylpyridine)-Based Interfacial Passivation to Enhance Voltage and Moisture Stability of Lead Halide Perovskite Solar Cells.

PubMed

Chaudhary, Bhumika; Kulkarni, Ashish; Jena, Ajay Kumar; Ikegami, Masashi; Udagawa, Yosuke; Kunugita, Hideyuki; Ema, Kazuhiro; Miyasaka, Tsutomu

2017-06-09

It is well known that the surface trap states and electronic disorders in the solution-processed CH 3 NH 3 PbI 3 perovskite film affect the solar cell performance significantly and moisture sensitivity of photoactive perovskite material limits its practical applications. Herein, we show the surface modification of a perovskite film with a solution-processable hydrophobic polymer (poly(4-vinylpyridine), PVP), which passivates the undercoordinated lead (Pb) atoms (on the surface of perovskite) by its pyridine Lewis base side chains and thereby eliminates surface-trap states and non-radiative recombination. Moreover, it acts as an electron barrier between the perovskite and hole-transport layer (HTL) to reduce interfacial charge recombination, which led to improvement in open-circuit voltage (V oc ) by 120 to 160 mV whereas the standard cell fabricated in same conditions showed V oc as low as 0.9 V owing to dominating interfacial recombination processes. Consequently, the power conversion efficiency (PCE) increased by 3 to 5 % in the polymer-modified devices (PCE=15 %) with V oc more than 1.05 V and hysteresis-less J-V curves. Advantageously, hydrophobicity of the polymer chain was found to protect the perovskite surface from moisture and improved stability of the non-encapsulated cells, which retained their device performance up to 30 days of exposure to open atmosphere (50 % humidity). © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of a recombinant insect-derived amylase performance in simultaneous saccharification and fermentation process with industrial yeasts.

PubMed

Celińska, Ewelina; Borkowska, Monika; Białas, Wojciech

2016-03-01

Starch is the dominant feedstock consumed for the bioethanol production, accounting for 60 % of its global production. Considering the significant contribution of bioethanol to the global fuel market, any improvement in its major operating technologies is economically very attractive. It was estimated that up to 40 % of the final ethanol unit price is derived from the energy input required for the substrate pre-treatment. Application of raw starch hydrolyzing enzymes (RSHE), combined with operation of the process according to a simultaneous saccharification and fermentation (SSF) strategy, constitutes the most promising solutions to the current technologies limitations. In this study, we expressed the novel RSHE derived from an insect in Saccharomyces cerevisiae strain dedicated for the protein overexpression. Afterwards, the enzyme performance was assessed in SSF process conducted by industrial ethanologenic or thermotolerant yeast species. Comparison of the insect-derived RSHE preparation with commercially available amylolytic RSH preparation was conducted. Our results demonstrate that the recombinant alpha-amylase from rice weevil can be efficiently expressed and secreted with its native signal peptide in S. cerevisiae INVSc-pYES2-Amy1 expression system (accounting for nearly 72 % of the strain's secretome). Application of the recombinant enzyme-based preparation in SSF process secured sufficient amylolytic activity for the yeast cell propagation and ethanol formation from raw starch. (Oligo)saccharide profiles generated by the compared preparations differed with respect to homogeneity of the sugar mixtures. Concomitantly, as demonstrated by a kinetic model developed in this study, the kinetic parameters describing activity of the compared preparations were different.

Multi-Orbital contributions in High Harmonic Generation

NASA Astrophysics Data System (ADS)

Guehr, Markus

2009-05-01

The high harmonic spectrum generated from atoms or molecules in a strong laser field contains information about the electronic structure of the generation medium. In the high harmonic generation (HHG) process, a free electron wave packet tunnel-ionizes from the molecular orbital in a strong laser field. After being accelerated by the laser electric field, the free electron wave packet coherently recombines to the orbital from which is was initially ionized, thereby emitting the harmonic spectrum. Interferences between the free electron wave packet and the molecular orbital will shape the spectrum in a characteristic way. These interferences have been used to tomographically image the highest occupied molecular orbital (HOMO) of N2 [1]. Molecular electronic states energetically below the HOMO should contribute to laser-driven high harmonic generation (HHG), but this behavior has not been observed previously. We have observed evidence of HHG from multiple orbitals in aligned N2 [2]. The tunneling ionization (and therefore the harmonic generation) is most efficient if the orbital has a large extension in the direction of the harmonic generation polarization. The HOMO with its σg symmetry therefore dominates the harmonic spectrum if the molecular axis is parallel to the harmonic generation polarization, the lower bound πu HOMO-1 dominates in the perpendicular case. The HOMO contributions appear as a regular plateau with a cutoff in the HHG spectrum. In contrast, the HOMO-1 signal is strongly peaked in the cutoff region. We explain this by semi-classical simulations of the recombination process that show constructive interferences between the HOMO-1 and the recombining wave packet in the cutoff region. The ability to monitor several orbitals opens the route to imaging coherent superpositions of electronic orbitals. [1] J. Itatani et al., Nature 432, 867 (2004)[2] B. K. McFarland, J. P. Farrell, P. H. Bucksbaum and M. Gühr, Science 322, 1232 (2008)

Development of a Glycoprotein D-Expressing Dominant-Negative and Replication-Defective Herpes Simplex Virus 2 (HSV-2) Recombinant Viral Vaccine against HSV-2 Infection in Mice ▿

PubMed Central

Akhrameyeva, Natalie V.; Zhang, Pengwei; Sugiyama, Nao; Behar, Samuel M.; Yao, Feng

2011-01-01

Using the T-REx (Invitrogen, California) gene switch technology and a dominant-negative mutant polypeptide of herpes simplex virus 1 (HSV-1)-origin binding protein UL9, we previously constructed a glycoprotein D-expressing replication-defective and dominant-negative HSV-1 recombinant viral vaccine, CJ9-gD, for protection against HSV infection and disease. It was demonstrated that CJ9-gD is avirulent following intracerebral inoculation in mice, cannot establish detectable latent infection following different routes of infection, and offers highly effective protective immunity against primary HSV-1 and HSV-2 infection and disease in mouse and guinea pig models of HSV infections. Given these favorable safety and immunological profiles of CJ9-gD, aiming to maximize levels of HSV-2 glycoprotein D (gD2) expression, we have constructed an ICP0 null mutant-based dominant-negative and replication-defective HSV-2 recombinant, CJ2-gD2, that contains 2 copies of the gD2 gene driven by the tetracycline operator (tetO)-bearing HSV-1 major immediate-early ICP4 promoter. CJ2-gD2 expresses gD2 as efficiently as wild-type HSV-2 infection and can lead to a 150-fold reduction in wild-type HSV-2 viral replication in cells coinfected with CJ2-gD2 and wild-type HSV-2 at the same multiplicity of infection. CJ2-gD2 is avirulent following intracerebral injection and cannot establish a detectable latent infection following subcutaneous (s.c.) immunization. CJ2-gD2 is a more effective vaccine than HSV-1 CJ9-gD and a non-gD2-expressing dominant-negative and replication-defective HSV-2 recombinant in protection against wild-type HSV-2 genital disease. Using recall response, we showed that immunization with CJ2-gD2 elicited strong HSV-2-specific memory CD4+ and CD8+ T-cell responses. Collectively, given the demonstrated preclinical immunogenicity and its unique safety profiles, CJ2-gD2 represents a new class of HSV-2 replication-defective recombinant viral vaccines in protection against HSV-2 genital infection and disease. PMID:21389121

The evolution of dominance in sporophytic self-incompatibility systems. II. Mate availability and recombination.

PubMed

Schoen, Daniel J; Busch, Jeremiah W

2009-08-01

Sporophytic self-incompatibility (SSI) is a self-pollen recognition system that enforces outcrossing in plants. Recognition in SSI systems is typically controlled by a complex locus (S-locus) with separate genes that determine pollen and stigma specificity. Experimental studies show that S-alleles can be dominant, recessive, or codominant, and that the dominance level of a given S-allele can depend upon whether pollen or stigma specificity is examined. Here and in the companion paper by Llaurens and colleagues, the evolution of dominance in single-locus SSI is explored using numerical models and simulation. Particular attention is directed at factors that can cause S-allele dominance to differ in pollen versus stigma. The effect of recombination between the S-locus and modifier locus is also examined. The models predict that limitation in the number of compatible mates is required for the evolution of S-allele dominance in the stigma but not in the pollen. Tight linkage between the S-locus and modifier promotes the evolution of S-allele dominance hierarchies. Model results are interpreted with respect to published information on the molecular basis of dominance in SSI systems, and reported S-allele dominance relationships in a variety of species. These studies show that dominant S-alleles are more common in the pollen than in the stigma, a pattern that when interpreted in light of model predictions, suggests that mate limitation may be relatively infrequent in natural populations with SSI.

An open circuit voltage decay system for performing injection dependent lifetime spectroscopy

NASA Astrophysics Data System (ADS)

Lacouture, Shelby; Schrock, James; Hirsch, Emily; Bayne, Stephen; O'Brien, Heather; Ogunniyi, Aderinto A.

2017-09-01

Of all of the material parameters associated with a semiconductor, the carrier lifetime is by far the most complex and dynamic, being a function of the dominant recombination mechanism, the equilibrium number of carriers, the perturbations in carriers (e.g., carrier injection), and the temperature, to name the most prominent variables. The carrier lifetime is one of the most important parameters in bipolar devices, greatly affecting conductivity modulation, on-state voltage, and reverse recovery. Carrier lifetime is also a useful metric for device fabrication process control and material quality. As it is such a dynamic quantity, carrier lifetime cannot be quoted in a general range such as mobility; it must be measured. The following describes a stand-alone, wide-injection range open circuit voltage decay system with unique lifetime extraction algorithms. The system is initially used along with various lifetime spectroscopy techniques to extract fundamental recombination parameters from a commercial high-voltage PIN diode.

Derivation of the open-circuit voltage of organic solar cells

NASA Astrophysics Data System (ADS)

Staple, Douglas B.; Oliver, Patricia A. K.; Hill, Ian G.

2014-05-01

Organic photovoltaic cells have improved in efficiency from 1% two decades ago to over 10% today. Continued improvement necessitates a theoretical understanding of the factors determining efficiency. Organic photovoltaic efficiency can be parameterized in terms of open-circuit voltage, short-circuit current, and fill factor. Here we present a theory that explains the dependencies of open-circuit voltage on semiconductor energy levels, light intensity, solar cell and light-source temperatures, charge-carrier recombination, and external fluorescence efficiency. The present theory also explains why recombination at the donor-acceptor heterointerface is a dominant process in heterojunction-based cells. Furthermore, the Carnot efficiency appears, highlighting the connection to basic thermodynamics. The theory presented here is consistent with and builds on the experimental and theoretical observations already in the literature. Crucially, the present theory can be straightforwardly derived in a line-by-line fashion using standard tools from statistical physics.

RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia

PubMed Central

Papaemmanuil, Elli; Rapado, Inmaculada; Li, Yilong; Potter, Nicola E; Wedge, David C; Tubio, Jose; Alexandrov, Ludmil B; Van Loo, Peter; Cooke, Susanna L; Marshall, John; Martincorena, Inigo; Hinton, Jonathan; Gundem, Gunes; van Delft, Frederik W; Nik-Zainal, Serena; Jones, David R; Ramakrishna, Manasa; Titley, Ian; Stebbings, Lucy; Leroy, Catherine; Menzies, Andrew; Gamble, John; Robinson, Ben; Mudie, Laura; Raine, Keiran; O’Meara, Sarah; Teague, Jon W; Butler, Adam P; Cazzaniga, Giovanni; Biondi, Andrea; Zuna, Jan; Kempski, Helena; Muschen, Markus; Ford, Anthony M; Stratton, Michael R; Greaves, Mel; Campbell, Peter J

2014-01-01

The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL), is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, characterized by recombination signal sequence motifs near the breakpoints; incorporation of non-templated sequence at the junction; ~30-fold enrichment at promoters and enhancers of genes actively transcribed in B-cell development and an unexpectedly high ratio of recurrent to non-recurrent structural variants. Single cell tracking shows that this mechanism is active throughout leukemic evolution with evidence of localized clustering and re-iterated deletions. Integration of point mutation and rearrangement data identifies ATF7IP and MGA as two new tumor suppressor genes in ALL. Thus, a remarkably parsimonious mutational process transforms ETV6-RUNX1 lymphoblasts, targeting the promoters, enhancers and first exons of genes that normally regulate B-cell differentiation. PMID:24413735

Evaluation of physics-based numerical modelling for diverse design architecture of perovskite solar cells

NASA Astrophysics Data System (ADS)

Mishra, A. K.; Catalan, Jorge; Camacho, Diana; Martinez, Miguel; Hodges, D.

2017-08-01

Solution processed organic-inorganic metal halide perovskite based solar cells are emerging as a new cost effective photovoltaic technology. In the context of increasing the power conversion efficiency (PCE) and sustainability of perovskite solar cells (PSC) devices, we comprehensively analyzed a physics-based numerical modelling for doped and un-doped PSC devices. Our analytics emphasized the role of different charge carrier layers from the view point of interfacial adhesion and its influence on charge extraction rate and charge recombination mechanism. Morphological and charge transport properties of perovskite thin film as a function of device architecture are also considered to investigate the photovoltaic properties of PSC. We observed that photocurrent is dominantly influenced by interfacial recombination process and photovoltage has functional relationship with defect density of perovskite absorption layer. A novel contour mapping method to understand the characteristics of current density-voltage (J-V) curves for each device as a function of perovskite layer thickness provide an important insight about the distribution spectrum of photovoltaic properties. Functional relationship of device efficiency and fill factor with absorption layer thickness are also discussed.

The Evolution of the Large-Scale ISM: Bubbles, Superbubbles and Non-Equilibrium Ionization

NASA Astrophysics Data System (ADS)

de Avillez, M. A.; Breitschwerdt, D.

2010-12-01

The ISM, powered by SNe, is turbulent and permeated by a magnetic field (with a mean and a turbulent component). It constitutes a frothy medium that is mostly out of equilibrium and is ram pressure dominated on most of the temperature ranges, except for T < 200 K and T > 106K, where magnetic and thermal pressures dominate, respectively. Such lack of equilibrium is also imposed by the feedback of the radiative processes into the ISM flow. Many models of the ISM or isolated phenomena, such as bubbles, superbubbles, clouds evolution, etc., take for granted that the flow is in the so-called collisional ionization equilibrium (CIE). However, recombination time scales of most of the ions below 106 K are longer than the cooling time scale. This implies that the recombination lags behind and the plasma is overionized while it cools. As a consequence cooling deviates from CIE. This has severe implications on the evolution of the ISM flow and its ionization structure. Here, besides reviewing several models of the ISM, including bubbles and superbubbles, the validity of the CIE approximation is discussed, and a presentation of recent developments in modeling the ISM by taking into account the time-dependent ionization structure of the flow in a full-blown numerical 3D high resolution simulation is presented.

The physics of background discrimination in liquid xenon, and first results from Xenon10 in the hunt for WIMP dark matter

NASA Astrophysics Data System (ADS)

Dahl, Carl Eric

2009-06-01

The WIMP limit set by the Xenon10 experiment in 2007 signals a new era in direct detection of dark matter, with several large-scale liquid target detectors now under construction. A major challenge in these detectors will be to understand backgrounds at the level necessary to claim a positive WIMP signal. In liquid xenon, these backgrounds are dominated by electron recoils, which may be distinguished from the WIMP signal (nuclear recoils) by their higher charge-to-light ratio. During the construction and operation of Xenon10, the prototype detector Xed probed the physics of this discrimination. Particle interactions in liquid xenon both ionize and excite xenon atoms, giving charge and scintillation signals, respectively. Some fraction of ions recombine, reducing the charge signal and creating additional scintillation. The charge-to-light ratio, determined by the initial exciton-ion ratio and the ion recombination fraction, provides the basis for discrimination between electron and nuclear recoils. Intrinsic fluctuations in the recombination fraction limit discrimination. Changes in recombination induce an exact anti-correlation between charge and light, and when calibrated this anti-correlation distinguishes recombination fluctuations from uncorrelated fluctuations in the measured signals. We determine the mean recombination and recombination fluctuations as a function of energy and applied field for electron and nuclear recoils, finding that recombination fluctuations are already the limiting factor for discrimination above ~12 keVr (nuclear recoil energy). Below 12 keVr statistical fluctuations in the number of scintillation photons counted dominate, and we project a x6 improvement in background rejection with a x2 increase in light collection efficiency. We also build a simple recombination model that successfully reproduces the mean recombination in electron and nuclear recoils, including the surprising reversal of the expected trend for recombination with ionization density in low energy electron recoils. The model also reproduces the measured recombination fluctuations to within a factor of two at high energies. Surprisingly, the model suggests that recombination at low energies is independent of ionization density, and our observed discrimination is due not to the different stopping powers of electrons and nuclei as was thought, but rather to a different initial exciton-ion ratio. We suggest two possible physical models for this new result.

Photoluminescence study of carbon dots from ginger and galangal herbs using microwave technique

NASA Astrophysics Data System (ADS)

Isnaeni; Rahmawati, I.; Intan, R.; Zakaria, M.

2018-03-01

Carbon dots are new type of fluorescent nanoparticle that can be synthesis easily from natural sources. We have synthesized carbon dots from ginger and galangal herbs using microwave technique and studied their optical properties. We synthesized colloidal carbon dots in water solvent by varying microwave processing time. UV-Vis absorbance, photoluminescence, time-resolved photoluminescence, and transmission electron microscope were utilized to study properties of carbon dots. We found that microwave processing time significantly affect optical properties of synthesized carbon dots. UV-Vis absorbance spectra and time-resolved photoluminescence results show that luminescent of carbon dots is dominated by recombination process from n-π* surface energy level. With further development, these carbon dots are potential for several applications.

On the density and field sensitivities of dielectronic recombination. [rates in coronal plasmas of late stars and sun

NASA Technical Reports Server (NTRS)

Reisenfeld, Daniel B.; Raymond, John C.; Young, Albert R.; Kohl, John L.

1992-01-01

Dielectronic recombination dominates the recombination rates of most ions in coronal plasmas at their temperatures of peak concentration. Because dielectronic recombination goes by way of high nl doubly excited levels, it is susceptible to collisional excitation and ionization, leading to a decreased rate. On the other hand, theoretical studies show that Stark mixing of the nl levels by a modest electric field enhances the dielectronic recombination rate severalfold. The ionization balance is computed here as as function of density, and it is found that the new results require increased emission measures to match the C IV emission line intensities observed in the sun and in late-type stars. They also make it more difficult to interpret the overall EUV emission line spectrum of the sun.

Recombination emissions and spectral blueshift of pump radiation from ultrafast laser induced plasma in a planar water microjet

NASA Astrophysics Data System (ADS)

Anija, M.; Philip, Reji

2009-09-01

We report spectroscopic investigations of an ultrafast laser induced plasma generated in a planar water microjet. Plasma recombination emissions along with the spectral blueshift and broadening of the pump laser pulse contribute to the total emission. The laser pulses are of 100 fs duration, and the incident intensity is around 10 15 W/cm 2. The dominant mechanisms leading to plasma formation are optical tunnel ionization and collisional ionization. Spectrally resolved polarization measurements show that the high frequency region of the emission is unpolarized whereas the low frequency region is polarized. Results indicate that at lower input intensities the emission arises mainly from plasma recombinations, which is accompanied by a weak blueshift of the incident laser pulse. At higher input intensities strong recombination emissions are seen, along with a broadening and asymmetric spectral blueshift of the pump laser pulse. From the nature of the blueshifted laser pulse it is possible to deduce whether the rate of change of free electron density is a constant or variable within the pulse lifetime. Two input laser intensity regimes, in which collisional and tunnel ionizations are dominant respectively, have been thus identified.

Impact of extended defects on recombination in CdTe heterostructures grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Zaunbrecher, Katherine N.; Kuciauskas, Darius; Swartz, Craig H.; Dippo, Pat; Edirisooriya, Madhavie; Ogedengbe, Olanrewaju S.; Sohal, Sandeep; Hancock, Bobby L.; LeBlanc, Elizabeth G.; Jayathilaka, Pathiraja A. R. D.; Barnes, Teresa M.; Myers, Thomas H.

2016-08-01

Heterostructures with CdTe and CdTe1-xSex (x ˜ 0.01) absorbers between two wider-band-gap Cd1-xMgxTe barriers (x ˜ 0.25-0.3) were grown by molecular beam epitaxy to study carrier generation and recombination in bulk materials with passivated interfaces. Using a combination of confocal photoluminescence (PL), time-resolved PL, and low-temperature PL emission spectroscopy, two extended defect types were identified and the impact of these defects on charge-carrier recombination was analyzed. The dominant defects identified by confocal PL were dislocations in samples grown on (211)B CdTe substrates and crystallographic twinning-related defects in samples on (100)-oriented InSb substrates. Low-temperature PL shows that twin-related defects have a zero-phonon energy of 1.460 eV and a Huang-Rhys factor of 1.50, while dislocation-dominated samples have a 1.473-eV zero-phonon energy and a Huang-Rhys factor of 1.22. The charge carrier diffusion length near both types of defects is ˜6 μm, suggesting that recombination is limited by diffusion dynamics. For heterostructures with a low concentration of extended defects, the bulk lifetime was determined to be 2.2 μs with an interface recombination velocity of 160 cm/s and an estimated radiative lifetime of 91 μs.

Impact of extended defects on recombination in CdTe heterostructures grown by molecular beam epitaxy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zaunbrecher, Katherine N.; Kuciauskas, Darius; Swartz, Craig H.

Heterostructures with CdTe and CdTe 1-xSex (x ~ 0.01) absorbers between two wider-band-gap Cd1-xMgxTe barriers (x ~ 0.25-0.3) were grown by molecular beam epitaxy to study carrier generation and recombination in bulk materials with passivated interfaces. Using a combination of confocal photoluminescence (PL), time-resolved PL, and low-temperature PL emission spectroscopy, two extended defect types were identified and the impact of these defects on charge-carrier recombination was analyzed. The dominant defects identified by confocal PL were dislocations in samples grown on (211)B CdTe substrates and crystallographic twinning-related defects in samples on (100)-oriented InSb substrates. Low-temperature PL shows that twin-related defects havemore » a zero-phonon energy of 1.460 eV and a Huang-Rhys factor of 1.50, while dislocation-dominated samples have a 1.473-eV zero-phonon energy and a Huang-Rhys factor of 1.22. The charge carrier diffusion length near both types of defects is ~6 um, suggesting that recombination is limited by diffusion dynamics. For heterostructures with a low concentration of extended defects, the bulk lifetime was determined to be 2.2 us with an interface recombination velocity of 160 cm/s and an estimated radiative lifetime of 91 us.« less

Emergence of recombinant forms in geographic regions with co-circulating HIV subtypes in the dynamic HIV-1 epidemic

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Ming; Letiner, Thomas K; Korber, Bette T

2009-01-01

We have reexamined the subtype designations of {approx}10,000 subtype A, B, C, G, and AG, BC, BF recombinant sequences, and compared the results of the new analysis with their published designations. Intersubtype recombinants dominate HIV epidemics in three different geographical regions. The circulating recombinant from (CRF) CRF02-AG, common in West Central Africa, appears to result from a recombination event that occurred early in the divergence between subtypes A and G, although additional more recent recombination events may have contributed to the breakpoint pattern in this recombinant lineage as well. The Chinese recombinant epidemic strains CRF07 and CRF08, in contrast, resultmore » from recent recombinations between more contemporary strains. Nevertheless, CRF07 and CRF08 contributed to many subsequent recombination events. The BF recombinant epidemics in two HIV-1 epicenters in South America are not independent and BF epidemics in South America have an unusually high fraction of unique recombinant forms (URFs) that have each been found only once and carry distinctive breakpoints. Taken together, these analyses reveal a complex and dynamic picture of the current HIV-1 epidemic, and suggest a means of grouping and tracking relationships between viruses through preservation of shared breakpints.« less

Exciton Recombination, Energy-, and Charge Transfer in Single- and Multilayer Quantum-Dot Films on Silver Plasmonic Resonators.

PubMed

Shin, Taeho; Cho, Kyung-Sang; Yun, Dong-Jin; Kim, Jinwoo; Li, Xiang-Shu; Moon, Eui-Seong; Baik, Chan-Wook; Il Kim, Sun; Kim, Miyoung; Choi, Jun Hee; Park, Gyeong-Su; Shin, Jai-Kwang; Hwang, Sungwoo; Jung, Tae-Sung

2016-05-17

We examine exciton recombination, energy-, and charge transfer in multilayer CdS/ZnS quantum dots (QDs) on silver plasmonic resonators using photoluminescence (PL) and excitation spectroscopy along with kinetic modeling and simulations. The exciton dynamics including all the processes are strongly affected by the separation distance between QDs and silver resonators, excitation wavelength, and QD film thickness. For a direct contact or very small distance, interfacial charge transfer and tunneling dominate over intrinsic radiative recombination and exciton energy transfer to surface plasmons (SPs), resulting in PL suppression. With increasing distance, however, tunneling diminishes dramatically, while long-range exciton-SP coupling takes place much faster (>6.5 ns) than intrinsic recombination (~200 ns) causing considerable PL enhancement. The exciton-SP coupling strength shows a strong dependence on excitation wavelengths, suggesting the state-specific dynamics of excitons and the down-conversion of surface plasmons involved. The overlayers as well as the bottom monolayer of QD multilayers exhibit significant PL enhancement mainly through long-range exciton-SP coupling. The overall emission behaviors from single- and multilayer QD films on silver resonators are described quantitatively by a photophysical kinetic model and simulations. The present experimental and simulation results provide important and useful design rules for QD-based light harvesting applications using the exciton-surface plasmon coupling.

Exciton Recombination, Energy-, and Charge Transfer in Single- and Multilayer Quantum-Dot Films on Silver Plasmonic Resonators

PubMed Central

Shin, Taeho; Cho, Kyung-Sang; Yun, Dong-Jin; Kim, Jinwoo; Li, Xiang-Shu; Moon, Eui-Seong; Baik, Chan-Wook; Il Kim, Sun; Kim, Miyoung; Choi, Jun Hee; Park, Gyeong-Su; Shin, Jai-Kwang; Hwang, Sungwoo; Jung, Tae-Sung

2016-01-01

We examine exciton recombination, energy-, and charge transfer in multilayer CdS/ZnS quantum dots (QDs) on silver plasmonic resonators using photoluminescence (PL) and excitation spectroscopy along with kinetic modeling and simulations. The exciton dynamics including all the processes are strongly affected by the separation distance between QDs and silver resonators, excitation wavelength, and QD film thickness. For a direct contact or very small distance, interfacial charge transfer and tunneling dominate over intrinsic radiative recombination and exciton energy transfer to surface plasmons (SPs), resulting in PL suppression. With increasing distance, however, tunneling diminishes dramatically, while long-range exciton-SP coupling takes place much faster (>6.5 ns) than intrinsic recombination (~200 ns) causing considerable PL enhancement. The exciton-SP coupling strength shows a strong dependence on excitation wavelengths, suggesting the state-specific dynamics of excitons and the down-conversion of surface plasmons involved. The overlayers as well as the bottom monolayer of QD multilayers exhibit significant PL enhancement mainly through long-range exciton-SP coupling. The overall emission behaviors from single- and multilayer QD films on silver resonators are described quantitatively by a photophysical kinetic model and simulations. The present experimental and simulation results provide important and useful design rules for QD-based light harvesting applications using the exciton-surface plasmon coupling. PMID:27184469

Structural, optical, and LED characteristics of ZnO and Al doped ZnO thin films

NASA Astrophysics Data System (ADS)

Sandeep, K. M.; Bhat, Shreesha; Dharmaprakash, S. M.

2017-05-01

ZnO (pristine) and Al doped ZnO (AZO) films were prepared using sol-gel spin coating method. The XRD analysis showed the enhanced compressive stress in AZO film. The presence of extended states below the conduction band edge in AZO accounts for the redshift in optical bandgap. The PL spectra of AZO showed significant blue emission due to the carrier recombination from defect states. The TRPL curves showed the dominant DAP recombination in ZnO film, whereas defect related recombination in Al doped ZnO film. Color parameters viz: the dominant wavelength, color coordinates (x,y), color purity, luminous efficiency and correlated color temperature (CCT) of ZnO and AZO films are calculated using 1931 (CIE) diagram. Further, a strong blue emission with color purity more than 96% is observed in both the films. The enhanced blue emission in AZO significantly increased the luminous efficiency (22.8%) compared to ZnO film (10.8%). The prepared films may be used as blue phosphors in white light generation.

Magnetic field enhancement of generation-recombination and shot noise in organic light emitting diodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Djidjou, T. K.; Basel, Tek; Rogachev, A.

We have studied the effect of magnetic field on noise in series of 2-methoxy-5-(2′-ethylhexyloxy)-1,4-phenylenevinylene-based organic light emitting diodes with dominant hole injection, dominant electron injection, and balanced electron and hole injection. The noise spectra of the balanced devices revealed the generation-recombination (g-r) noise term, which we associated with bimolecular electron-hole recombination. The presence of the g-r noise term is correlated with the strong organic magnetoresistance (up to 25%) observed in the balanced devices. The noise spectra also have the shot noise contribution with the Fano factor 0.25–0.4. We found that time constant of the g-r term decreases and the magnitudemore » of shot noise increases when magnetic field is applied. This behavior can be consistently explained within the polaron-polaron model of organic magnetoresistance. We have not found any evidence that the magnetoresistance in studied devices is affected by traps.« less

IONIZATION AND DUST CHARGING IN PROTOPLANETARY DISKS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ivlev, A. V.; Caselli, P.; Akimkin, V. V., E-mail: ivlev@mpe.mpg.de

2016-12-10

Ionization–recombination balance in dense interstellar and circumstellar environments is a key factor for a variety of important physical processes, such as chemical reactions, dust charging and coagulation, coupling of the gas with magnetic field, and development of instabilities in protoplanetary disks. We determine a critical gas density above which the recombination of electrons and ions on the grain surface dominates over the gas-phase recombination. For this regime, we present a self-consistent analytical model, which allows us to calculate exactly the abundances of charged species in dusty gas, without making assumptions on the grain charge distribution. To demonstrate the importance ofmore » the proposed approach, we check whether the conventional approximation of low grain charges is valid for typical protoplanetary disks, and discuss the implications for dust coagulation and development of the “dead zone” in the disk. The presented model is applicable for arbitrary grain-size distributions and, for given dust properties and conditions of the disk, has only one free parameter—the effective mass of the ions, shown to have a small effect on the results. The model can be easily included in numerical simulations following the dust evolution in dense molecular clouds and protoplanetary disks.« less

RTEL1 contributes to DNA replication and repair and telomere maintenance.

PubMed

Uringa, Evert-Jan; Lisaingo, Kathleen; Pickett, Hilda A; Brind'Amour, Julie; Rohde, Jan-Hendrik; Zelensky, Alex; Essers, Jeroen; Lansdorp, Peter M

2012-07-01

Telomere maintenance and DNA repair are important processes that protect the genome against instability. mRtel1, an essential helicase, is a dominant factor setting telomere length in mice. In addition, mRtel1 is involved in DNA double-strand break repair. The role of mRtel1 in telomere maintenance and genome stability is poorly understood. Therefore we used mRtel1-deficient mouse embryonic stem cells to examine the function of mRtel1 in replication, DNA repair, recombination, and telomere maintenance. mRtel1-deficient mouse embryonic stem cells showed sensitivity to a range of DNA-damaging agents, highlighting its role in replication and genome maintenance. Deletion of mRtel1 increased the frequency of sister chromatid exchange events and suppressed gene replacement, demonstrating the involvement of the protein in homologous recombination. mRtel1 localized transiently at telomeres and is needed for efficient telomere replication. Of interest, in the absence of mRtel1, telomeres in embryonic stem cells appeared relatively stable in length, suggesting that mRtel1 is required to allow extension by telomerase. We propose that mRtel1 is a key protein for DNA replication, recombination, and repair and efficient elongation of telomeres by telomerase.

Similar Replicative Fitness Is Shared by the Subtype B and Unique BF Recombinant HIV-1 Isolates that Dominate the Epidemic in Argentina

PubMed Central

Rubio, Andrea E.; Abraha, Awet; Carpenter, Crystal A.; Troyer, Ryan M.; Reyes-Rodríguez, Ángel L.; Salomon, Horacio; Arts, Eric J.; Tebit, Denis M.

2014-01-01

The HIV-1 epidemic in South America is dominated by pure subtypes (mostly B and C) and more than 7 BF and BC recombinant forms. In Argentina, circulating recombinant forms (CRFs) comprised of subtypes B and F make up more than 50% of HIV infections. For this study, 28 HIV-1 primary isolates were obtained from patients in Buenos Aires, Argentina and initially classified into subtype B (n = 9, 32.1%), C (n = 1, 3.6%), and CRFs (n = 18, 64.3%) using partial pol and vpu-env sequences, which proved to be inconsistent and inaccurate for these phylogenetic analyses. Near full length genome sequences of these primary HIV-1 isolates revealed that nearly all intersubtype BF recombination sites were unique and countered previous “CRF” B/F classifications. The majority of these Argentinean HIV-1 isolates were CCR5-using but 4 had a dual/mixed tropism as predicted by both phenotypic and genotypic assays. Comparison of the replicative fitness of these BF primary HIV-1 isolates to circulating B, F, and C HIV-1 using pairwise competitions in peripheral blood mononuclear cells (PBMCs) indicated a similarity in fitness of these BF recombinants to subtypes B and F HIV-1 (of the same co-receptor usage) whereas subtype C HIV-1 was significantly less fit than all as previously reported. These results suggest that the multitude of BF HIV-1 strains present within the Argentinean population do not appear to have gained replicative fitness following recent B and F recombination events. PMID:24727861

Time-resolved optical studies of wide-gap II-VI semiconductor heterostructures

NASA Astrophysics Data System (ADS)

Wang, Hong

ZnSe and ZnSe-based quantum well and superlattice structures are potential candidates for light emitting devices and other optical devices such as switches and modulators working in the blue-green wavelength range. Carrier dynamics studies of these structures are important in evaluating device performance as well as understanding the underlying physical processes. In this thesis, a carrier dynamics investigation is conducted for temperature from 77K to 295K on CdZnSSe/ZnSSe single quantum well structure (SQW) and ZnSe/ZnSTe superlattice fabricated by molecular beam epitaxy (MBE). Two experimental techniques with femtosecond time resolution are used in this work: up-conversion technique for time- resolved photoluminescence (PL) and pump-probe technique for time-resolved differential absorption studies. For both heterostructures, the radiative recombination is dominated by exciton transition due to the large exciton binding energy as a result of quantum confinement effect. The measured decay time of free exciton PL in CdZnSSe/ZnSSe SQW increases linearly with increasing temperature which agrees with the theoretical prediction by considering the conservation of momentum requirement for radiative recombination. However, the recombination of free carriers is also observed in CdZnSSe/ZnSSe SQW for the whole temperature range studied. On the other hand, in ZnSe/ZnSTe superlattice structures, the non- radiative recombination processes are non-negligible even at 77K and become more important in higher temperature range. The relaxation processes such as spectral hole burning, carrier thermalization and hot-carrier cooling are observed in ZnSe/ZnSTe superlattices at room temperature (295K) by the femtosecond pump-probe measurements. A rapid cooling of the thermalized hot- carrier from 763K to 450K within 4ps is deduced. A large optical nonlinearity (i.e., the induced absorption change) around the heavy-hole exciton energy is also obtained.

Quantifying Impact of Chromosome Copy Number on Recombination in Escherichia coli.

PubMed

Reynolds, T Steele; Gill, Ryan T

2015-07-17

The ability to precisely and efficiently recombineer synthetic DNA into organisms of interest in a quantitative manner is a key requirement in genome engineering. Even though considerable effort has gone into the characterization of recombination in Escherichia coli, there is still substantial variability in reported recombination efficiencies. We hypothesized that this observed variability could, in part, be explained by the variability in chromosome copy number as well as the location of the replication forks relative to the recombination site. During rapid growth, E. coli cells may contain several pairs of open replication forks. While recombineered forks are resolving and segregating within the population, changes in apparent recombineering efficiency should be observed. In the case of dominant phenotypes, we predicted and then experimentally confirmed that the apparent recombination efficiency declined during recovery until complete segregation of recombineered and wild-type genomes had occurred. We observed the reverse trend for recessive phenotypes. The observed changes in apparent recombination efficiency were found to be in agreement with mathematical calculations based on our proposed mechanism. We also provide a model that can be used to estimate the total segregated recombination efficiency based on an initial efficiency and growth rate. These results emphasize the importance of employing quantitative strategies in the design of genome-scale engineering efforts.

Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots

PubMed Central

Stukenbrock, Eva H.; Dutheil, Julien Y.

2018-01-01

Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae. We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species. PMID:29263029

Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots.

PubMed

Stukenbrock, Eva H; Dutheil, Julien Y

2018-03-01

Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species. Copyright © 2018 Stukenbrock and Dutheil.

Report of recombinant norovirus GII.g/GII.12 in Beijing, China.

PubMed

Sang, Shaowei; Zhao, Zhongtang; Suo, Jijiang; Xing, Yubin; Jia, Ning; Gao, Yan; Xie, Lijun; Du, Mingmei; Liu, Bowei; Ren, Shiwang; Liu, Yunxi

2014-01-01

Norovirus (NoV) has been recognized as the most important cause of nonbacterial acute gastroenteritis affecting all age group people in the world. Genetic recombination is a common occurance in RNA viruses and many recombinant NoV strains have been described since it was first reported in 1997. However, the knowledge of recombinant NoV in China is extremely limited. A total of 685 stool specimens were tested for NoV infection from the acute gastroenteritis patients who visited one general hospital in Beijing from April 2009 to November 2011. The virus recombination was identified by constructing phylogenetic trees of two genes, further SimPlot and the maximum chi-square analysis. The overall positive rate was 9.6% (66/685). GII.4 New Orleans 2009 and GII.4 2006b variants were the dominant genotype. Four GII.g/GII.12 and one GII.12/GII.3 recombinant strains were confirmed, and all derived from adult outpatients. The predictive recombination point occurred at the open reading frame (ORF)1/ORF2 overlap. The GII.g ORF1/GII.12ORF2 recombinant has been reported in several countries and it was the first report of this recombinant in China.

Impact of extended defects on recombination in CdTe heterostructures grown by molecular beam epitaxy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zaunbrecher, Katherine N.; National Renewable Energy Laboratory, Golden, Colorado 80401; Kuciauskas, Darius

Heterostructures with CdTe and CdTe{sub 1-x}Se{sub x} (x ∼ 0.01) absorbers between two wider-band-gap Cd{sub 1-x}Mg{sub x}Te barriers (x ∼ 0.25–0.3) were grown by molecular beam epitaxy to study carrier generation and recombination in bulk materials with passivated interfaces. Using a combination of confocal photoluminescence (PL), time-resolved PL, and low-temperature PL emission spectroscopy, two extended defect types were identified and the impact of these defects on charge-carrier recombination was analyzed. The dominant defects identified by confocal PL were dislocations in samples grown on (211)B CdTe substrates and crystallographic twinning-related defects in samples on (100)-oriented InSb substrates. Low-temperature PL shows that twin-related defects have amore » zero-phonon energy of 1.460 eV and a Huang-Rhys factor of 1.50, while dislocation-dominated samples have a 1.473-eV zero-phonon energy and a Huang-Rhys factor of 1.22. The charge carrier diffusion length near both types of defects is ∼6 μm, suggesting that recombination is limited by diffusion dynamics. For heterostructures with a low concentration of extended defects, the bulk lifetime was determined to be 2.2 μs with an interface recombination velocity of 160 cm/s and an estimated radiative lifetime of 91 μs.« less

Recombination in Enteroviruses Is a Biphasic Replicative Process Involving the Generation of Greater-than Genome Length ‘Imprecise’ Intermediates

PubMed Central

Lowry, Kym; Woodman, Andrew; Cook, Jonathan; Evans, David J.

2014-01-01

Recombination in enteroviruses provides an evolutionary mechanism for acquiring extensive regions of novel sequence, is suggested to have a role in genotype diversity and is known to have been key to the emergence of novel neuropathogenic variants of poliovirus. Despite the importance of this evolutionary mechanism, the recombination process remains relatively poorly understood. We investigated heterologous recombination using a novel reverse genetic approach that resulted in the isolation of intermediate chimeric intertypic polioviruses bearing genomes with extensive duplicated sequences at the recombination junction. Serial passage of viruses exhibiting such imprecise junctions yielded progeny with increased fitness which had lost the duplicated sequences. Mutations or inhibitors that changed polymerase fidelity or the coalescence of replication complexes markedly altered the yield of recombinants (but did not influence non-replicative recombination) indicating both that the process is replicative and that it may be possible to enhance or reduce recombination-mediated viral evolution if required. We propose that extant recombinants result from a biphasic process in which an initial recombination event is followed by a process of resolution, deleting extraneous sequences and optimizing viral fitness. This process has implications for our wider understanding of ‘evolution by duplication’ in the positive-strand RNA viruses. PMID:24945141

Shared Subgenome Dominance Following Polyploidization Explains Grass Genome Evolutionary Plasticity from a Seven Protochromosome Ancestor with 16K Protogenes

PubMed Central

Murat, Florent; Zhang, Rongzhi; Guizard, Sébastien; Flores, Raphael; Armero, Alix; Pont, Caroline; Steinbach, Delphine; Quesneville, Hadi; Cooke, Richard; Salse, Jerome

2013-01-01

Modern plant genomes are diploidized paleopolyploids. We revisited grass genome paleohistory in response to the diploidization process through a detailed investigation of the evolutionary fate of duplicated blocks. Ancestrally duplicated genes can be conserved, deleted, and shuffled, defining dominant (bias toward duplicate retention) and sensitive (bias toward duplicate erosion) chromosomal fragments. We propose a new grass genome paleohistory deriving from an ancestral karyotype structured in seven protochromosomes containing 16,464 protogenes and following evolutionary rules where 1) ancestral shared polyploidizations shaped conserved dominant (D) and sensitive (S) subgenomes, 2) subgenome dominance is revealed by both gene deletion and shuffling from the S blocks, 3) duplicate deletion/movement may have been mediated by single-/double-stranded illegitimate recombination mechanisms, 4) modern genomes arose through centromeric fusion of protochromosomes, leading to functional monocentric neochromosomes, 5) the fusion of two dominant blocks leads to supradominant neochromosomes (D + D = D) with higher ancestral gene retention compared with D + S = D (i.e., fusion of blocks with opposite sensitivity) or even S + S = S (i.e., fusion of two sensitive ancestral blocks). A new user-friendly online tool named “PlantSyntenyViewer,” available at http://urgi.versailles.inra.fr/synteny-cereal, presents the refined comparative genomics data. PMID:24317974

Two-level quenching of photoluminescence in hexagonal boron nitride micropowder

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henaish, A. M. A.; Tanta University, Physics Department, Tanta, Egypt, 31527; Vokhmintsev, A. S.

2016-03-29

The processes of photoluminescence thermal quenching in the range RT – 800 K of h-BN micropowder in the 3.56 eV band were studied. It was found that two non-radiative channels of excitations relaxation with activation energies of 0.27 and 0.81 eV control the quenching for emission observed. It was assumed that emptying the shallow traps based on O{sub N}-centers characterized external quenching in RT – 530 K range and non-radiative mechanism of donor-acceptor recombination began to dominate at T > 530 K.

Ras Family GTPases Control Growth of Astrocyte Processes

PubMed Central

Kalman, Daniel; Gomperts, Stephen N.; Hardy, Stephen; Kitamura, Marina; Bishop, J. Michael

1999-01-01

Astrocytes in neuron-free cultures typically lack processes, although they are highly process-bearing in vivo. We show that basic fibroblast growth factor (bFGF) induces cultured astrocytes to grow processes and that Ras family GTPases mediate these morphological changes. Activated alleles of rac1 and rhoA blocked and reversed bFGF effects when introduced into astrocytes in dissociated culture and in brain slices using recombinant adenoviruses. By contrast, dominant negative (DN) alleles of both GTPases mimicked bFGF effects. A DN allele of Ha-ras blocked bFGF effects but not those of Rac1-DN or RhoA-DN. Our results show that bFGF acting through c-Ha-Ras inhibits endogenous Rac1 and RhoA GTPases thereby triggering astrocyte process growth, and they provide evidence for the regulation of this cascade in vivo by a yet undetermined neuron-derived factor. PMID:10233170

Biparental inheritance of organelles in Pelargonium: evidence for intergenomic recombination of mitochondrial DNA.

PubMed

Apitz, Janina; Weihe, Andreas; Pohlheim, Frank; Börner, Thomas

2013-02-01

While uniparental transmission of mtDNA is widespread and dominating in eukaryotes leaving mutation as the major source of genotypic diversity, recently, biparental inheritance of mitochondrial genes has been demonstrated in reciprocal crosses of Pelargonium zonale and P. inquinans. The thereby arising heteroplasmy carries the potential for recombination between mtDNAs of different descent, i.e. between the parental mitochondrial genomes. We have analyzed these Pelargonium hybrids for mitochondrial intergenomic recombination events by examining differences in DNA blot hybridization patterns of the mitochondrial genes atp1 and cob. Further investigation of these genes and their flanking regions using nucleotide sequence polymorphisms and PCR revealed DNA segments in the progeny, which contained both P. zonale and P. inquinans sequences suggesting an intergenomic recombination in hybrids of Pelargonium. This turns Pelargonium into an interesting subject for studies of recombination and evolutionary dynamics of mitochondrial genomes.

Hybrid Perovskites for Photovoltaics: Charge-Carrier Recombination, Diffusion, and Radiative Efficiencies.

PubMed

Johnston, Michael B; Herz, Laura M

2016-01-19

Photovoltaic (PV) devices that harvest the energy provided by the sun have great potential as renewable energy sources, yet uptake has been hampered by the increased cost of solar electricity compared with fossil fuels. Hybrid metal halide perovskites have recently emerged as low-cost active materials in PV cells with power conversion efficiencies now exceeding 20%. Rapid progress has been achieved over only a few years through improvements in materials processing and device design. In addition, hybrid perovskites appear to be good light emitters under certain conditions, raising the prospect of applications in low-cost light-emitting diodes and lasers. Further optimization of such hybrid perovskite devices now needs to be supported by a better understanding of how light is converted into electrical currents and vice versa. This Account provides an overview of charge-carrier recombination and mobility mechanisms encountered in such materials. Optical-pump-terahertz-probe (OPTP) photoconductivity spectroscopy is an ideal tool here, because it allows the dynamics of mobile charge carriers inside the perovskite to be monitored following excitation with a short laser pulse whose photon energy falls into the range of the solar spectrum. We first review our insights gained from transient OPTP and photoluminescence spectroscopy on the mechanisms dominating charge-carrier recombination in these materials. We discuss that mono-molecular charge-recombination predominantly originates from trapping of charges, with trap depths being relatively shallow (tens of millielectronvolts) for hybrid lead iodide perovskites. Bimolecular recombination arises from direct band-to-band electron-hole recombination and is found to be in significant violation of the simple Langevin model. Auger recombination exhibits links with electronic band structure, in accordance with its requirement for energy and momentum conservation for all charges involved. We further discuss charge-carrier mobility values extracted from OPTP measurements and their dependence on perovskite composition and morphology. The significance of the reviewed charge-carrier recombination and mobility parameters is subsequently evaluated in terms of the charge-carrier diffusion lengths and radiative efficiencies that may be obtained for such hybrid perovskites. We particularly focus on calculating such quantities in the limit of ultra-low trap-related recombination, which has not yet been demonstrated but could be reached through further advances in material processing. We find that for thin films of hybrid lead iodide perovskites with typical charge-carrier mobilities of ∼30cm(2)/(V s), charge-carrier diffusion lengths at solar (AM1.5) irradiation are unlikely to exceed ∼10 μm even if all trap-related recombination is eliminated. We further examine the radiative efficiency for hybrid lead halide perovskite films and show that if high efficiencies are to be obtained for intermediate charge-carrier densities (n ≈ 10(14) cm(-3)) trap-related recombination lifetimes will have to be enhanced well into the microsecond range.

Veritable electronic characteristics in ZnO nanowire circuits uncovered by the four-terminal method at a low temperature

NASA Astrophysics Data System (ADS)

Li, Xin; Zhang, Qi

2017-04-01

Understanding the natural electrical properties in semiconductor channels and the carrier transport across the metal-semiconductor contact is essential to improve the performance of nanowire devices. This work presents the true electronic characteristics of ZnO nanowire devices measured by a four-electrode method at a low-temperature environment. The temperature rise leads to the decrease in near-band-gap emission, which is attributed to two non-radiative recombination processes. For ZnO circuits, thermionic emission carrier transport mechanism plays a dominant role at Ti-Au/ZnO interface and the transport mechanism in ZnO nanowires is governed by two competitive thermal activation conduction processes: optical or acoustic phonons assisting hopping.

Non-Radiative Carrier Recombination Enhanced by Two-Level Process: A First-Principles Study

NASA Astrophysics Data System (ADS)

Yang, Ji-Hui; Shi, Lin; Wang, Lin-Wang; Wei, Su-Huai

2016-02-01

Non-radiative recombination plays an important role in the performance of optoelectronic semiconductor devices such as solar cells and light-emitting diodes. Most textbook examples assume that the recombination process occurs through a single defect level, where one electron and one hole are captured and recombined. Based on this simple picture, conventional wisdom is that only defect levels near the center of the bandgap can be effective recombination centers. Here, we present a new two-level recombination mechanism: first, one type of carrier is captured through a defect level forming a metastable state; then the local defect configuration rapidly changes to a stable state, where the other type of carrier is captured and recombined through another defect level. This novel mechanism is applied to the recombination center in CdTe. We show that this two-level process can significantly increase the recombination rate (by three orders of magnitude) in agreement with experiments. We expect that this two-level recombination process can exist in a wide range of semiconductors, so its effect should be carefully examined in characterizing optoelectronic materials.

Threshold kinetics of a solar-simulator-pumped iodine laser

NASA Technical Reports Server (NTRS)

Wilson, J. W.; Lee, Y.; Weaver, W. R.; Humes, D. H.; Lee, J. H.

1984-01-01

A model of the chemical kinetics of the n-C3F7I solar-simulator-pumped iodine laser is utilized to study the major kinetic processes associated with the threshold behavior of this experimental system. Excited-state diffusion to the cell wall is the dominant limiting factor below 5 torr. Excited-state diffusion to the cell wall is the dominant limiting factor below 5 torr. Excited-state recombination with the alkyl radical and quenching by the parent gas control threshold at higher pressures. Treatment of the hyperfine splitting and uncertainty in the pressure broadening are important factors in fixing the threshold level. In spite of scatter in the experimental data caused by instabilities in the simulator high-pressure high-pressure arc, reasonable agreement is achieved between the model and experiment. Model parameters arrived at are within the uncertainty range of values found in the literature.

Spectroscopic measurements of hydrogen ion temperature during divertor recombination

NASA Astrophysics Data System (ADS)

Stotler, D. P.; Skinner, C. H.; Karney, C. F. F.

1999-01-01

We explore the possibility of using the neutral Hα spectral line profile to measure the ion temperature, Ti, in a recombining plasma. Since the Hα emissions due to recombination are larger than those due to other mechanisms, interference from nonrecombining regions contributing to the chord integrated data is insignificant. A Doppler and Stark broadened Hα spectrum is simulated by the DEGAS 2 neutral transport code using assumed plasma conditions. The application of a simple fitting procedure to this spectrum yields an electron density, ne, and Ti consistent with the assumed plasma parameters if the spectrum is dominated by recombination from a region of modest ne variation. General measurements of the ion temperature by Hα spectroscopy appear feasible within the context of a model for the entire divertor plasma.

Identification of quantitative trait loci controlling root and shoot traits associated to drought tolerance in a lentil (Lens culinaris Medik.) recombinant inbred line population

USDA-ARS?s Scientific Manuscript database

Drought is one of the major abiotic stresses limiting lentil productivity in rainfed production systems. Specific rooting patterns can be associated with drought avoidance mechanisms that can be used in lentil breeding. In all, 252 co-dominant and dominant markers were used for genetic linkage map c...

Variation in recombination frequency and distribution across eukaryotes: patterns and processes

PubMed Central

Feulner, Philine G. D.; Johnston, Susan E.; Santure, Anna W.; Smadja, Carole M.

2017-01-01

Recombination, the exchange of DNA between maternal and paternal chromosomes during meiosis, is an essential feature of sexual reproduction in nearly all multicellular organisms. While the role of recombination in the evolution of sex has received theoretical and empirical attention, less is known about how recombination rate itself evolves and what influence this has on evolutionary processes within sexually reproducing organisms. Here, we explore the patterns of, and processes governing recombination in eukaryotes. We summarize patterns of variation, integrating current knowledge with an analysis of linkage map data in 353 organisms. We then discuss proximate and ultimate processes governing recombination rate variation and consider how these influence evolutionary processes. Genome-wide recombination rates (cM/Mb) can vary more than tenfold across eukaryotes, and there is large variation in the distribution of recombination events across closely related taxa, populations and individuals. We discuss how variation in rate and distribution relates to genome architecture, genetic and epigenetic mechanisms, sex, environmental perturbations and variable selective pressures. There has been great progress in determining the molecular mechanisms governing recombination, and with the continued development of new modelling and empirical approaches, there is now also great opportunity to further our understanding of how and why recombination rate varies. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’. PMID:29109219

Transposon-like properties of the major, long repetitive sequence family in the genome of Physarum polycephalum

PubMed Central

Pearston, Douglas H.; Gordon, Mairi; Hardman, Norman

1985-01-01

A family of long, highly-repetitive sequences, referred to previously as `HpaII-repeats', dominates the genome of the eukaryotic slime mould Physarum polycephalum. These sequences are found exclusively in scrambled clusters. They account for about one-half of the total complement of repetitive DNA in Physarum, and represent the major sequence component found in hypermethylated, 20-50 kb segments of Physarum genomic DNA that fail to be cleaved using the restriction endonuclease HpaII. The structure of this abundant repetitive element was investigated by analysing cloned segments derived from the hypermethylated genomic DNA compartment. We show that the `HpaII-repeat' forms part of a larger repetitive DNA structure, ∼8.6 kb in length, with several structural features in common with recognised eukaryotic transposable genetic elements. Scrambled clusters of the sequence probably arise as a result of transposition-like events, during which the element preferentially recombines in either orientation with target sites located in other copies of the same repeated sequence. The target sites for transposition/recombination are not related in sequence but in all cases studied they are potentially capable of promoting the formation of small `cruciforms' or `Z-DNA' structures which might be recognised during the recombination process. ImagesFig. 3.Fig. 4. PMID:16453652

Highly Efficient Visible Colloidal Lead-Halide Perovskite Nanocrystal Light-Emitting Diodes

NASA Astrophysics Data System (ADS)

Yan, Fei; Xing, Jun; Xing, Guichuan; Quan, Lina; Tan, Swee Tiam; Zhao, Jiaxin; Su, Rui; Zhang, Lulu; Chen, Shi; Zhao, Yawen; Huan, Alfred; Sargent, Edward H.; Xiong, Qihua; Demir, Hilmi Volkan

2018-05-01

Lead-halide perovskites have been attracting attention for potential use in solid-state lighting. Following the footsteps of solar cells, the field of perovskite light-emitting diodes (PeLEDs) has been growing rapidly. Their application prospects in lighting, however, remain still uncertain due to a variety of shortcomings in device performance including their limited levels of luminous efficiency achievable thus far. Here we show high-efficiency PeLEDs based on colloidal perovskite nanocrystals (PeNCs) synthesized at room temperature possessing dominant first-order excitonic radiation (enabling a photoluminescence quantum yield of 71% in solid film), unlike in the case of bulk perovskites with slow electron-hole bimolecular radiative recombination (a second-order process). In these PeLEDs, by reaching charge balance in the recombination zone, we find that the Auger nonradiative recombination, with its significant role in emission quenching, is effectively suppressed in low driving current density range. In consequence, these devices reach a record high maximum external quantum efficiency of 12.9% reported to date and an unprecedentedly high power efficiency of 30.3 lm W-1 at luminance levels above 1000 cd m-2 as required for various applications. These findings suggest that, with feasible levels of device performance, the PeNCs hold great promise for their use in LED lighting and displays.

Non-radiative carrier recombination enhanced by two-level process: A first-principles study

DOE PAGES

Yang, Ji -Hui; Shi, Lin; Wang, Lin -Wang; ...

2016-02-16

In this study, non-radiative recombination plays an important role in the performance of optoelectronic semiconductor devices such as solar cells and light-emitting diodes. Most textbook examples assume that the recombination process occurs through a single defect level, where one electron and one hole are captured and recombined. Based on this simple picture, conventional wisdom is that only defect levels near the center of the bandgap can be effective recombination centers. Here, we present a new two-level recombination mechanism: first, one type of carrier is captured through a defect level forming a metastable state; then the local defect configuration rapidly changesmore » to a stable state, where the other type of carrier is captured and recombined through another defect level. This novel mechanism is applied to the recombination center Te 2+ cd in CdTe. We show that this two-level process can significantly increase the recombination rate (by three orders of magnitude) in agreement with experiments. We expect that this two-level recombination process can exist in a wide range of semiconductors, so its effect should be carefully examined in characterizing optoelectronic materials.« less

Nonhomologous Pairing in Mice Heterozygous for a t Haplotype Can Produce Recombinant Chromosomes with Duplications and Deletions

PubMed Central

Sarvetnick, Nora; Fox, Howard S.; Mann, Elizabeth; Mains, Paul E.; Elliott, Rosemary W.; Silver, Lee M.

1986-01-01

We have investigated the structure and properties of a chromosomal product recovered from a rare recombination event between a t haplotype and a wild-type form of mouse chromosome 17. Our embryological and molecular studies indicate that this chromosome (twLub2 ) is characterized by both a deletion and duplication of adjacent genetic material. The deletion appears to be responsible for a dominant lethal maternal effect and a recessive embryonic lethality. The duplication provides an explanation for the twLub2 suppression of the dominant T locus phenotype. A reanalysis of previously described results with another chromosome 17 variant called TtOrl indicates a structure for this chromosome that is reciprocal to that observed for twLub2. We have postulated the existence of an inversion over the proximal portion of all complete t haplotypes in order to explain the generation of the partial t haplotypes t wLub2 and TtOrl. This proximal inversion and the previously described distal inversion are sufficient to account for all of the recombination properties that are characteristic of complete t haplotypes. The structures determined for twLub2 and TtOrl indicate that rare recombination can occur between nonequivalent genomic sequences within the inverted proximal t region when wild-type and t chromosomes are paired in a linear, nonhomologous configuration. PMID:3732789

Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution.

PubMed

Mostowy, Rafal; Croucher, Nicholas J; Hanage, William P; Harris, Simon R; Bentley, Stephen; Fraser, Christophe

2014-05-01

The bacterium Streptococcus pneumoniae (pneumococcus) is one of the most important human bacterial pathogens, and a leading cause of morbidity and mortality worldwide. The pneumococcus is also known for undergoing extensive homologous recombination via transformation with exogenous DNA. It has been shown that recombination has a major impact on the evolution of the pathogen, including acquisition of antibiotic resistance and serotype-switching. Nevertheless, the mechanism and the rates of recombination in an epidemiological context remain poorly understood. Here, we proposed several mathematical models to describe the rate and size of recombination in the evolutionary history of two very distinct pneumococcal lineages, PMEN1 and CC180. We found that, in both lineages, the process of homologous recombination was best described by a heterogeneous model of recombination with single, short, frequent replacements, which we call micro-recombinations, and rarer, multi-fragment, saltational replacements, which we call macro-recombinations. Macro-recombination was associated with major phenotypic changes, including serotype-switching events, and thus was a major driver of the diversification of the pathogen. We critically evaluate biological and epidemiological processes that could give rise to the micro-recombination and macro-recombination processes.

Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution

PubMed Central

Hanage, William P.; Harris, Simon R.; Bentley, Stephen; Fraser, Christophe

2014-01-01

The bacterium Streptococcus pneumoniae (pneumococcus) is one of the most important human bacterial pathogens, and a leading cause of morbidity and mortality worldwide. The pneumococcus is also known for undergoing extensive homologous recombination via transformation with exogenous DNA. It has been shown that recombination has a major impact on the evolution of the pathogen, including acquisition of antibiotic resistance and serotype-switching. Nevertheless, the mechanism and the rates of recombination in an epidemiological context remain poorly understood. Here, we proposed several mathematical models to describe the rate and size of recombination in the evolutionary history of two very distinct pneumococcal lineages, PMEN1 and CC180. We found that, in both lineages, the process of homologous recombination was best described by a heterogeneous model of recombination with single, short, frequent replacements, which we call micro-recombinations, and rarer, multi-fragment, saltational replacements, which we call macro-recombinations. Macro-recombination was associated with major phenotypic changes, including serotype-switching events, and thus was a major driver of the diversification of the pathogen. We critically evaluate biological and epidemiological processes that could give rise to the micro-recombination and macro-recombination processes. PMID:24786281

Linkage and clinical characterization of families with the RP10 (chromosome 7q) form of autosomal dominant retinitis pigmentosa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jordan, S.A.; Humphries, P.; McGuire, R.E.

1994-09-01

Retinitis pigmentosa is a set of degenerative retinal diseases characterized by night blindness and loss of peripheral vision, often followed by loss of central vision. Genetically heterogeneous, retinitis pigmentosa has been found in autosomal dominant, autosomal recessive and X-linked forms. For autosomal dominant retinitis pigmentosa (adRP), 6 loci have been mapped: rhodopsin on chromosome 3q, peripherin/RDS on 6p, RP9 on 7p, RP10 on 7q, RP1 on 8q, and RP11 on 19q. Jordan et al. first reported linkage to 7q in a Spanish family with early onset disease. Recently, McGuire et al. reported the existence of a second, unrelated family ofmore » American descent with adRP that maps to the same region of 7q. The second family also has classical, diffuse retinitis pigmentosa though with later onset. The finding of two unrelated families that map to this region suggests that RP10 may account for a significant fraction of retinitis pigmentosa cases. Combining data from both families localizes the disease gene to 7q31.1-q35. In the Spanish family a Z{sub max} of 7.2 at 0% recombination was found with the marker D7S480 and affected individuals recombinant for D7S486 and D7S650 flank the disease. The American family showed a Z{sub max} of 5.3 at 0% recombination wtih the marker D7S514 and there are affected individuals recombinant for the markers D7S522, D7S677 and D7S486, and one affected individual recombinant for D7S530. Together, these data place the disease locus between D7S522 and D7S650. In addition, blue cone pigment, which maps to 7q31.3-q32, was excluded as a candidate gene in both families by linkage testing using intragenic polymorphisms and mutation screening.« less

Fast Dissemination of New HIV-1 CRF02/A1 Recombinants in Pakistan

PubMed Central

Chen, Yue; Hora, Bhavna; DeMarco, Todd; Shah, Sharaf Ali; Ahmed, Manzoor; Sanchez, Ana M.; Su, Chang; Carter, Meredith; Stone, Mars; Hasan, Rumina; Hasan, Zahra; Busch, Michael P.; Denny, Thomas N.; Gao, Feng

2016-01-01

A number of HIV-1 subtypes are identified in Pakistan by characterization of partial viral gene sequences. Little is known whether new recombinants are generated and how they disseminate since whole genome sequences for these viruses have not been characterized. Near full-length genome (NFLG) sequences were obtained by amplifying two overlapping half genomes or next generation sequencing from 34 HIV-1-infected individuals in Pakistan. Phylogenetic tree analysis showed that the newly characterized sequences were 16 subtype As, one subtype C, and 17 A/G recombinants. Further analysis showed that all 16 subtype A1 sequences (47%), together with the vast majority of sequences from Pakistan from other studies, formed a tight subcluster (A1a) within the subtype A1 clade, suggesting that they were derived from a single introduction. More in-depth analysis of 17 A/G NFLG sequences showed that five shared similar recombination breakpoints as in CRF02 (15%) but were phylogenetically distinct from the prototype CRF02 by forming a tight subcluster (CRF02a) while 12 (38%) were new recombinants between CRF02a and A1a or a divergent A1b viruses. Unique recombination patterns among the majority of the newly characterized recombinants indicated ongoing recombination. Interestingly, recombination breakpoints in these CRF02/A1 recombinants were similar to those in prototype CRF02 viruses, indicating that recombination at these sites more likely generate variable recombinant viruses. The dominance and fast dissemination of new CRF02a/A1 recombinants over prototype CRF02 suggest that these recombinant have more adapted and may become major epidemic strains in Pakistan. PMID:27973597

Products of Dissociative Recombination in the Ionosphere

NASA Technical Reports Server (NTRS)

Cosby, Philip

1996-01-01

SRI International undertook a novel experimental measurement of the product states formed by dissociative ro-combination (DR) of C2(+), NO(+), and N2(+) as a function of both electron energy and reactant ion vibrational level. For these measurements we used a recently developed experimental technique for measuring dissociation product distributions that allows both the branching ratios to be accurately determined and the electronic and ro-vibrational state composition of the reactant ions to be specified. DR is the dominant electron loss mechanism in all regions of the ionosphere. In this process, electron attachment to the molecular ion produces an unstable neutral molecule that rapidly dissociates.

Ultrafast carrier capture and Auger recombination in single GaN/InGaN multiple quantum well nanowires

DOE PAGES

Boubanga-Tombet, Stephane; Wright, Jeremy B.; Lu, Ping; ...

2016-11-04

Ultrafast optical microscopy is an important tool for examining fundamental phenomena in semiconductor nanowires with high temporal and spatial resolution. In this paper, we used this technique to study carrier dynamics in single GaN/InGaN core–shell nonpolar multiple quantum well nanowires. We find that intraband carrier–carrier scattering is the main channel governing carrier capture, while subsequent carrier relaxation is dominated by three-carrier Auger recombination at higher densities and bimolecular recombination at lower densities. Finally, the Auger constants in these nanowires are approximately 2 orders of magnitude lower than in planar InGaN multiple quantum wells, highlighting their potential for future light-emitting devices.

The energetics of hydrogen atom recombination - Analysis, experiments, and modeling. [in electrothermal propulsion system

NASA Technical Reports Server (NTRS)

Filpus, J. W.; Hawley, M. C.

1984-01-01

A theoretical investigation of the effect of the microscopic energetics of the recombination reaction on the performance of a microwave-plasma electrothermal propulsion system is described, and the results of the analysis are presented. A series of experiments to test the concept is described and analyzed by comparison with a computer model of the recombination reaction. It is concluded that internal energy considerations are not likely to significantly affect the design of a microwave-plasma electrothermal rocket. The experimental results indicate that the microwave power is far higher than the capacity of the gas to absorb it; the cooling needed to control the energy dominates the experimental results.

Measurement and analysis of solar cell current-voltage characteristics

NASA Technical Reports Server (NTRS)

Olsen, Larry C.; Addis, F. William; Doyle, Dan H.; Miller, Wesley A.

1985-01-01

Approaches to measurement and analysis of solar cell current-voltage characteristics under dark and illuminated conditions are discussed. Measurements are taken with a computer based data acquisition system for temperatures in the range of -100 to +100 C. In the fitting procedure, the various I(oi) and C(i) as well as R(S) and R(SH) are determined. Application to current-voltage analyses of high efficiency silicon cells and Boeing CdS/CuInSe2 are discussed. In silicon MINP cells, it is found that at low voltages a tunneling mechanism is dominant, while at larger voltages the I-V characteristics are usually dominated by emitter recombination. In the case of Boeing cells, a current transport model based on a tunneling mechanism and interface recombination acting in series has been developed as a result of I-V analyses.

Recombination suppression at the dominant Rhg1/Rfs2 locus underlying soybean resistance to the cyst nematode.

PubMed

Afzal, Ahmed J; Srour, Ali; Saini, Navinder; Hemmati, Naghmeh; El Shemy, Hany A; Lightfoot, David A

2012-04-01

Host resistance to "yellow dwarf" or "moonlight" disease cause by any population (Hg type) of Heterodera glycines I., the soybean cyst nematode (SCN), requires a functional allele at rhg1. The host resistance encoded appears to mimic an apoptotic response in the giant cells formed at the nematode feeding site about 24-48 h after nematode feeding commences. Little is known about how the host response to infection is mediated but a linked set of 3 genes has been identified within the rhg1 locus. This study aimed to identify the role of the genes within the locus that includes a receptor-like kinase (RLK), a laccase and an ion antiporter. Used were near isogeneic lines (NILs) that contrasted at their rhg1 alleles, gene-based markers, and a new Hg type 0 and new recombination events. A syntenic gene cluster on Lg B1 was found. The effectiveness of SNP probes from the RLK for distinguishing homolog sequence variants on LgB1 from alleles at the rhg1 locus on LgG was shown. The resistant allele of the rhg1 locus was shown to be dominant in NILs. None of the recombination events were within the cluster of the three candidate genes. Finally, rhg1 was shown to reduce the plant root development. A model for rhg1 as a dominant multi-gene resistance locus based on the developmental control was inferred.

Deleterious mutations and selection for sex in finite diploid populations.

PubMed

Roze, Denis; Michod, Richard E

2010-04-01

In diploid populations, indirect benefits of sex may stem from segregation and recombination. Although it has been recognized that finite population size is an important component of selection for recombination, its effects on selection for segregation have been somewhat less studied. In this article, we develop analytical two- and three-locus models to study the effect of recurrent deleterious mutations on a modifier gene increasing sex, in a finite diploid population. The model also incorporates effects of mitotic recombination, causing loss of heterozygosity (LOH). Predictions are tested using multilocus simulations representing deleterious mutations occurring at a large number of loci. The model and simulations show that excess of heterozygosity generated by finite population size is an important component of selection for sex, favoring segregation when deleterious alleles are nearly additive to dominant. Furthermore, sex tends to break correlations in homozygosity among selected loci, which disfavors sex when deleterious alleles are either recessive or dominant. As a result, we find that it is difficult to maintain costly sex when deleterious alleles are recessive. LOH tends to favor sex when deleterious mutations are recessive, but the effect is relatively weak for rates of LOH corresponding to current estimates (of the order 10(-4)-10(-5)).

Non-thermal recombination - a neglected source of flare hard X-rays and fast electron diagnostics (Corrigendum)

NASA Astrophysics Data System (ADS)

Brown, J. C.; Mallik, P. C. V.; Badnell, N. R.

2010-06-01

Brown and Mallik (BM) recently claimed that non-thermal recombination (NTR) can be a dominant source of flare hard X-rays (HXRs) from hot coronal and chromospheric sources. However, major discrepancies between the thermal continua predicted by BM and by the Chianti database as well as RHESSI flare data, led us to discover substantial errors in the heuristic expression used by BM to extend the Kramers expressions beyond the hydrogenic case. Here we present the relevant corrected expressions and show the key modified results. We conclude that, in most cases, NTR emission was overestimated by a factor of 1-8 by BM but is typically still large enough (as much as 20-30% of the total emission) to be very important for electron spectral inference and detection of electron spectral features such as low energy cut-offs since the recombination spectra contain sharp edges. For extreme temperature regimes and/or if the Fe abundance were as high as some values claimed, NTR could even be the dominant source of flare HXRs, reducing the electron number and energy budget, problems such as in the extreme coronal HXR source cases reported by e.g. Krucker et al.

Intra-genomic variation in symbiotic dinoflagellates: recent divergence or recombination between lineages?

PubMed

Wilkinson, Shaun P; Fisher, Paul L; van Oppen, Madeleine J H; Davy, Simon K

2015-03-14

The symbiosis between corals and the dinoflagellate alga Symbiodinium is essential for the development and survival of coral reefs. Yet this fragile association is highly vulnerable to environmental disturbance. A coral's ability to tolerate temperature stress depends on the fitness of its resident symbionts, whose thermal optima vary extensively between lineages. However, the in hospite population genetic structure of Symbiodinium is poorly understood and mostly based on analysis of bulk DNA extracted from thousands to millions of cells. Using quantitative single-cell PCR, we enumerated DNA polymorphisms in the symbionts of the reef-building coral Pocillopora damicornis, and applied a model selection approach to explore the potential for recombination between coexisting Symbiodinium populations. Two distinct Symbiodinium ITS2 sequences (denoted C100 and C109) were retrieved from all P. damicornis colonies analysed. However, the symbiont assemblage consisted of three distinct Symbiodinium populations: cells featuring pure arrays of ITS2 type C109, near-homogeneous cells of type C100 (with trace ITS2 copies of type C109), and those with co-dominant C100 and C109 ITS2 repeats. The symbiont consortia of some colonies consisted almost entirely of these putative C100 × C109 recombinants. Our results are consistent with the occurrence of sexual recombination between Symbiodinium types C100 and C109. While the multiple-copy nature of the ITS2 dictates that the observed pattern of intra-genomic co-dominance may be a result of incomplete concerted evolution of intra-genomic polymorphisms, this is a less likely explanation given the occurrence of homogeneous cells of the C109 type. Conclusive evidence for inter-lineage recombination and introgression in this genus will require either direct observational evidence or a single-cell genotyping approach targeting multiple, single-copy loci.

Recombination in Perovskite Solar Cells: Significance of Grain Boundaries, Interface Traps, and Defect Ions.

PubMed

Sherkar, Tejas S; Momblona, Cristina; Gil-Escrig, Lidón; Ávila, Jorge; Sessolo, Michele; Bolink, Henk J; Koster, L Jan Anton

2017-05-12

Trap-assisted recombination, despite being lower as compared with traditional inorganic solar cells, is still the dominant recombination mechanism in perovskite solar cells (PSCs) and limits their efficiency. We investigate the attributes of the primary trap-assisted recombination channels (grain boundaries and interfaces) and their correlation to defect ions in PSCs. We achieve this by using a validated device model to fit the simulations to the experimental data of efficient vacuum-deposited p-i-n and n-i-p CH 3 NH 3 PbI 3 solar cells, including the light intensity dependence of the open-circuit voltage and fill factor. We find that, despite the presence of traps at interfaces and grain boundaries (GBs), their neutral (when filled with photogenerated charges) disposition along with the long-lived nature of holes leads to the high performance of PSCs. The sign of the traps (when filled) is of little importance in efficient solar cells with compact morphologies (fused GBs, low trap density). On the other hand, solar cells with noncompact morphologies (open GBs, high trap density) are sensitive to the sign of the traps and hence to the cell preparation methods. Even in the presence of traps at GBs, trap-assisted recombination at interfaces (between the transport layers and the perovskite) is the dominant loss mechanism. We find a direct correlation between the density of traps, the density of mobile ionic defects, and the degree of hysteresis observed in the current-voltage ( J - V ) characteristics. The presence of defect states or mobile ions not only limits the device performance but also plays a role in the J - V hysteresis.

[From theory to clinical practice: recombinant FSH in daily practice].

PubMed

Kably Ambe, A; Barrón Vallejo, J; Góngora Rodríguez, A; Carballo Mondragón, E; Anta Jaén, E

1999-08-01

The purpose of the present study is to determine the efficacy of induction ovulation with recombinant FSH in patients treated with in vitro fertilization and embryo transfer (IVF-ET) and basic assisted reproductive techniques (ART). One hundred seven cycles were analyzed. The patients were divided in two groups: Group 1, treated with IVF (n = 12) and group 2, treated with basic ART (n = 95). Only recombinant FSH was utilized for ovulation induction; human corionic gonadotropin (hCG), 10,000 IU, were administered when one or more dominant follicles with diameter > or = 18 mm were presents; oocyte retrieval was performed 34 hour, while intrauterine insemination was practiced at 36 hours after the hCG injection. The pregnancy rate per IVF cycle was 25.0%, and 16.4% for basic ART. It is concluded that ovulation induction with recombinant FSH is a good and efficient alternative for both variations of ART.

The Accuracy of Molecular Processes

NASA Astrophysics Data System (ADS)

Stavans, Joel

Recombination is arguably one of the most fundamental mechanisms driving genetic diversity during evolution. Recombination takes place in one way or another from viruses such as HIV and polio, to bacteria, and finally to man. In both prokaryotes and eukaryotes, homologous recombination is assisted by enzymes, recombinases, that promote the exchange of strands between two segments of DNA, thereby creating new genetic combinations. In bacteria, homologous recombination takes place as a pathway for the repair of DNA lesions and also during horizontal or lateral gene transfer processes, in which cells take in exogenous pieces of DNA. This allows bacteria to evolve rapidly by acquiring large sequences of DNA, a process which would take too long by gene duplications and single mutations. I will survey recent results on the fidelity of homologous recombination as catalyzed by the bacterial recombinase RecA. These results show discrimination up to the level of single base mismatches, during the initial stages of the recombination process. A cascaded kinetic proofreading process is proposed to explain this high discrimination. Kinetic proofreading ideas are also reviewed.

Recombination, Pairing, and Synapsis of Homologs during Meiosis

PubMed Central

Zickler, Denise; Kleckner, Nancy

2015-01-01

Recombination is a prominent feature of meiosis in which it plays an important role in increasing genetic diversity during inheritance. Additionally, in most organisms, recombination also plays mechanical roles in chromosomal processes, most notably to mediate pairing of homologous chromosomes during prophase and, ultimately, to ensure regular segregation of homologous chromosomes when they separate at the first meiotic division. Recombinational interactions are also subject to important spatial patterning at both early and late stages. Recombination-mediated processes occur in physical and functional linkage with meiotic axial chromosome structure, with interplay in both directions, before, during, and after formation and dissolution of the synaptonemal complex (SC), a highly conserved meiosis-specific structure that links homolog axes along their lengths. These diverse processes also are integrated with recombination-independent interactions between homologous chromosomes, nonhomology-based chromosome couplings/clusterings, and diverse types of chromosome movement. This review provides an overview of these diverse processes and their interrelationships. PMID:25986558

Managing the SOS Response for Enhanced CRISPR-Cas-Based Recombineering in E. coli through Transient Inhibition of Host RecA Activity.

PubMed

Moreb, Eirik Adim; Hoover, Benjamin; Yaseen, Adam; Valyasevi, Nisakorn; Roecker, Zoe; Menacho-Melgar, Romel; Lynch, Michael D

2017-12-15

Phage-derived "recombineering" methods are utilized for bacterial genome editing. Recombineering results in a heterogeneous population of modified and unmodified chromosomes, and therefore selection methods, such as CRISPR-Cas9, are required to select for edited clones. Cells can evade CRISPR-Cas-induced cell death through recA-mediated induction of the SOS response. The SOS response increases RecA dependent repair as well as mutation rates through induction of the umuDC error prone polymerase. As a result, CRISPR-Cas selection is more efficient in recA mutants. We report an approach to inhibiting the SOS response and RecA activity through the expression of a mutant dominant negative form of RecA, which incorporates into wild type RecA filaments and inhibits activity. Using a plasmid-based system in which Cas9 and recA mutants are coexpressed, we can achieve increased efficiency and consistency of CRISPR-Cas9-mediated selection and recombineering in E. coli, while reducing the induction of the SOS response. To date, this approach has been shown to be independent of recA genotype and host strain lineage. Using this system, we demonstrate increased CRISPR-Cas selection efficacy with over 10 000 guides covering the E. coli chromosome. The use of dominant negative RecA or homologues may be of broad use in bacterial CRISPR-Cas-based genome editing where the SOS pathways are present.

The ABC model of recombination reinterpreted: Impact on understanding carrier transport and efficiency droop in InGaN/GaN light emitting diodes

NASA Astrophysics Data System (ADS)

Hopkins, M. A.; Allsopp, D. W. E.; Kappers, M. J.; Oliver, R. A.; Humphreys, C. J.

2017-12-01

The efficiency of light emitting diodes (LEDs) remains a topic of great contemporary interest due to their potential to reduce the amount of energy consumed in lighting. The current consensus is that electrons and holes distribute themselves through the emissive region by a drift-diffusion process which results in a highly non-uniform distribution of the light emission and can reduce efficiency. In this paper, the measured variations in the external quantum efficiency of a range of InGaN/GaN LEDs with different numbers of quantum wells (QWs) are shown to compare closely with the predictions of a revised ABC model, in which it is assumed that the electrically injected electrons and holes are uniformly distributed through the multi-quantum well (MQW) region, or nearly so, and hence carrier recombination occurs equally in all the quantum wells. The implications of the reported results are that drift-diffusion plays a far lesser role in cross-well carrier transport than previously thought; that the dominant cause of efficiency droop is intrinsic to the quantum wells and that reductions in the density of non-radiative recombination centers in the MQW would enable the use of more QWs and thereby reduce Auger losses by spreading carriers more evenly across a wider emissive region.

Excitation correlation photoluminescence in the presence of Shockley-Read-Hall recombination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borgwardt, M., E-mail: mario.borgwardt@helmholtz-berlin.de; Sippel, P.; Eichberger, R.

Excitation correlation photoluminescence (ECPL) measurements are often analyzed in the approximation of a cross correlation of charge carrier populations generated by the two delayed pulses. In semiconductors, this approach is valid for a linear non-radiative recombination path, but not for a non-linear recombination rate as in the general Shockley-Read-Hall recombination scenario. Here, the evolution of the ECPL signal was studied for deep trap recombination following Shockley-Read-Hall statistics. Analytic solutions can be obtained for a fast minority trapping regime and steady state recombination. For the steady state case, our results show that the quadratic radiative term plays only a minor role,more » and that the shape of the measured signal is mostly determined by the non-linearity of the recombination itself. We find that measurements with unbalanced intense pump and probe pulses can directly provide information about the dominant non-radiative recombination mechanism. The signal traces follow the charge carrier concentrations, despite the complex origins of the signal, thus showing that ECPL can be applied to study charge carrier dynamics in semiconductors without requiring elaborate calculations. The model is compared with measurements on a reference sample with alternating layers of InGaAs/InAlAs that were additionally cross-checked with time resolved optical pump terahertz probe measurements and found to be in excellent agreement.« less

Temperature- and Intensity-Dependent Photovoltaic Measurements to Identify Dominant Recombination Pathways

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brandt, Riley E.; Mangan, Niall M.; Li, Jian V.

2016-11-21

In novel photovoltaic absorbers, it is often difficult to assess the root causes of low open-circuit voltages, which may be due to bulk recombination or sub-optimal contacts. In the present work, we discuss the role of temperature- and illumination-dependent device electrical measurements in quantifying and distinguishing these performance losses - in particular, for determining bounds on interface recombination velocities, band alignment, and minority carrier lifetime. We assess the accuracy of this approach by direct comparison to photoelectron spectroscopy. Then, we demonstrate how more computationally intensive model parameter fitting approaches can draw more insights from this broad measurement space. We applymore » this measurement and modeling approach to high-performance III-V and thin-film chalcogenide devices.« less

Copper interstitial recombination centers in Cu3N

NASA Astrophysics Data System (ADS)

Yee, Ye Sheng; Inoue, Hisashi; Hultqvist, Adam; Hanifi, David; Salleo, Alberto; Magyari-Köpe, Blanka; Nishi, Yoshio; Bent, Stacey F.; Clemens, Bruce M.

2018-06-01

We present a comprehensive study of the earth-abundant semiconductor Cu3N as a potential solar energy conversion material, using density functional theory and experimental methods. Density functional theory indicates that among the dominant intrinsic point defects, copper vacancies VCu have shallow defect levels while copper interstitials Cui behave as deep potential wells in the conduction band, which mediate Shockley-Read-Hall recombination. The existence of Cui defects has been experimentally verified using photothermal deflection spectroscopy. A Cu3N /ZnS heterojunction diode with good current-voltage rectification behavior has been demonstrated experimentally, but no photocurrent is generated under illumination. The absence of photocurrent can be explained by a large concentration of Cui recombination centers capturing electrons in p -type Cu3N .

Ultraviolet/blue light-emitting diodes based on single horizontal ZnO microrod/GaN heterojunction.

PubMed

Du, Chia-Fong; Lee, Chen-Hui; Cheng, Chao-Tsung; Lin, Kai-Hsiang; Sheu, Jin-Kong; Hsu, Hsu-Cheng

2014-01-01

We report electroluminescence (EL) from single horizontal ZnO microrod (MR) and p-GaN heterojunction light-emitting diodes under forward and reverse bias. EL spectra were composed of two blue emissions centered at 431 and 490 nm under forward biases, but were dominated by a ultraviolet (UV) emission located at 380 nm from n-ZnO MR under high reverse biases. Light-output-current characteristic of the UV emission reveals that the rate of radiative recombination is faster than that of the nonradiative recombination. Highly efficient ZnO excitonic recombination at reverse bias is caused by electrons tunneling from deep-level states near the n-ZnO/p-GaN interface to the conduction band in n-ZnO.

Architecture of a Species: Phylogenomics of Staphylococcus aureus.

PubMed

Planet, Paul J; Narechania, Apurva; Chen, Liang; Mathema, Barun; Boundy, Sam; Archer, Gordon; Kreiswirth, Barry

2017-02-01

A deluge of whole-genome sequencing has begun to give insights into the patterns and processes of microbial evolution, but genome sequences have accrued in a haphazard manner, with biased sampling of natural variation that is driven largely by medical and epidemiological priorities. For instance, there is a strong bias for sequencing epidemic lineages of methicillin-resistant Staphylococcus aureus (MRSA) over sensitive isolates (methicillin-sensitive S. aureus: MSSA). As more diverse genomes are sequenced the emerging picture is of a highly subdivided species with a handful of relatively clonal groups (complexes) that, at any given moment, dominate in particular geographical regions. The establishment of hegemony of particular clones appears to be a dynamic process of successive waves of replacement of the previously dominant clone. Here we review the phylogenomic structure of a diverse range of S. aureus, including both MRSA and MSSA. We consider the utility of the concept of the 'core' genome and the impact of recombination and horizontal transfer. We argue that whole-genome surveillance of S. aureus populations could lead to better forecasting of antibiotic resistance and virulence of emerging clones, and a better understanding of the elusive biological factors that determine repeated strain replacement. Copyright © 2016. Published by Elsevier Ltd.

A novel variant of the infectious bronchitis virus resulting from recombination events in Italy and Spain.

PubMed

Moreno, Ana; Franzo, G; Massi, P; Tosi, G; Blanco, A; Antilles, N; Biarnes, M; Majó, N; Nofrarías, M; Dolz, R; Lelli, D; Sozzi, E; Lavazza, A; Cecchinato, M

2017-02-01

Infectious bronchitis is considered to be one of the most devastating diseases in poultry. Control of its spread is typically attempted through biosecurity measures and extensive vaccination. However, the remarkable genetic and antigenic variability of the virus, which originate from both mutations and recombination events, represents an unsolved challenge for this disease. The present study reports on the emergence and spread of recombinant clusters detected in Italy and Spain between 2012 and 2014. A total of 36 Spanish and Italian infectious bronchitis virus (IBV) field strains were investigated and genetically characterized using phylogenetic, molecular, recombination and selection pressure analyses of the complete S1 gene. Based on the partial S1 sequencing, 27 IBV strains originating from Spain and nine from Italy were initially classified as being closely related to the Guandong/Xindadi (XDN) genotype. Phylogenetic analysis of the complete S1 gene revealed that the XDN strains formed a homogeneous clade with the Spanish IBV isolates within the QX genotype, whereas there was higher variability within the Italian strains. Recombination analysis determined that these strains belonged to four groups, which originated from independent recombination events between the QX and 793B IBV genotypes. Our data support the hypothesis of two different scenarios: firstly, in Spain, the large and homogeneous clade probably originated from a single offspring of the recombinant founder, which became dominant and spread throughout the country. Secondly, the nine Italian recombinants, which are characterized by three different recombination patterns, probably represent less fitted strains, because they were less viable with respect to their recombinant parents.

Fabrication of CuInS2-sensitized solar cells via an improved SILAR process and its interface electron recombination.

PubMed

Xu, Xueqing; Wan, Qingcui; Luan, Chunyan; Mei, Fengjiao; Zhao, Qian; An, Ping; Liang, Zhurong; Xu, Gang; Zapien, Juan Antonio

2013-11-13

Tetragonal CuInS2 (CIS) has been successfully deposited onto mesoporous TiO2 films by in-sequence growth of InxS and CuyS via a successive ionic layer absorption and reaction (SILAR) process and postdeposition annealing in sulfur ambiance. X-ray diffraction and Raman measurements showed that the obtained tetragonal CIS consisted of a chalcopyrite phase and Cu-Au ordering, which related with the antisite defect states. For a fixed Cu-S deposition cycle, an interface layer of β-In2S3 formed at the TiO2/CIS interface with suitable excess deposition of In-S. In the meantime, the content of the Cu-Au ordering phase decreased to a reasonable level. These facts resulted in the retardance of electron recombination in the cells, which is proposed to be dominated by electron transfer from the conduction band of TiO2 to the unoccupied defect states in CIS via exponentially distributed surface states. As a result, a relatively high efficiency of ~0.92% (V(oc) = 0.35 V, J(sc) = 8.49 mA cm(-2), and FF = 0.31) has been obtained. Last, but not least, with an overloading of the sensitizers, a decrease in the interface area between the sensitized TiO2 and electrolytes resulted in deceleration of hole extraction from CIS to the electrolytes, leading to a decrease in the fill factor of the solar cells. It is indicated that the unoccupied states in CIS with energy levels below EF0 of the TiO2 films play an important role in the interface electron recombination at low potentials and has a great influence on the fill factor of the solar cells.

Memory effects in the afterglow: open questions on long-lived species and the role of surface processes

NASA Astrophysics Data System (ADS)

Petrovic, Z. Lj; Markovic, V. Lj; Pejovic, M. M.; Gocic, S. R.

2001-06-01

The memory effect, the phenomenon that some active species survive very long afterglow periods and affect subsequent breakdown, was observed more than 40 years ago. The effects have been observed even over periods of several hours. Attempts to explain the memory effect in nitrogen were mostly based on hypothetical metastables and on the A3Σ state. However, such explanations had to neglect some quenching processes which are known to be very effective under the conditions of the experiments. The explanation based on atoms remaining from the previous discharge and recombining on the cathode to produce initial electrons was shown to be fully consistent with all the experimental data for nitrogen including a wide range of pressures and the addition of oxygen impurities. The memory effect was also shown to be sensitive to the work function of the cathode material. Thus, an attempt was made to use the memory effect as a diagnostic tool to establish the data on the dominant loss of nitrogen atoms from the discharge which is recombination on the walls of the tube. However, a possible role of higher vibrational levels has not been fully addressed, mainly due to the shortage of data. On the other hand, the memory effect which was observed for rare gases cannot be explained on the basis of the standard data unless the presence of molecular impurities is invoked. Another open issue would be the role of charges accumulated on the glass surfaces and whether those may be released to the gas phase. The aim of this paper is to summarize the achievements of the model based on atom recombination and to point out how the breakdown model associated with the memory effect may be completed and how it may be applied in practical discharges.

Production of the entire range of r-process nuclides by black hole accretion disc outflows from neutron star mergers

NASA Astrophysics Data System (ADS)

Wu, Meng-Ru; Fernández, Rodrigo; Martínez-Pinedo, Gabriel; Metzger, Brian D.

2016-12-01

We consider r-process nucleosynthesis in outflows from black hole accretion discs formed in double neutron star and neutron star-black hole mergers. These outflows, powered by angular momentum transport processes and nuclear recombination, represent an important - and in some cases dominant - contribution to the total mass ejected by the merger. Here we calculate the nucleosynthesis yields from disc outflows using thermodynamic trajectories from hydrodynamic simulations, coupled to a nuclear reaction network. We find that outflows produce a robust abundance pattern around the second r-process peak (mass number A ˜ 130), independent of model parameters, with significant production of A < 130 nuclei. This implies that dynamical ejecta with high electron fraction may not be required to explain the observed abundances of r-process elements in metal poor stars. Disc outflows reach the third peak (A ˜ 195) in most of our simulations, although the amounts produced depend sensitively on the disc viscosity, initial mass or entropy of the torus, and nuclear physics inputs. Some of our models produce an abundance spike at A = 132 that is absent in the Solar system r-process distribution. The spike arises from convection in the disc and depends on the treatment of nuclear heating in the simulations. We conclude that disc outflows provide an important - and perhaps dominant - contribution to the r-process yields of compact binary mergers, and hence must be included when assessing the contribution of these systems to the inventory of r-process elements in the Galaxy.

Spectroscopic Measurements of Hydrogen Ion Temperature During Divertor Recombination

NASA Astrophysics Data System (ADS)

Stotler, D. P.; Skinner, C. H.; Karney, C. F. F.

1998-11-01

We explore the possibility of using the neutral H_α spectral line profile to measure the ion temperature Ti in a recombining plasma. Since the H_α emissions due to recombination are larger than those due to other mechanisms, interference from non-recombining regions contributing to the chord integrated data is insignificant. A chord integrated, Doppler and Stark broadened H_α spectrum is simulated by the DEGAS 2 Monte Carlo neutral transport code(D. Stotler and C. Karney, Contrib. Plasma Phys.) 34, 392 (1994). using assumed plasma conditions. The application of a simple fitting procedure to this spectrum yields an average electron density ne and Ti consistent with the assumed plasma parameters if the spectrum is dominated by recombination from a region of modest ne variation. The interpretation of experimental data is complicated by Zeeman splitting and light reflection off surfaces. Ion temperature measurements by H_α spectroscopy appear feasible within the context of a model for the entire divertor plasma that takes these effects into account.

Altitude distribution of electron concentration in ionospheric D-region in presence of time-varying solar radiation flux

NASA Astrophysics Data System (ADS)

Nina, A.; Čadež, V.; Srećković, V.; Šulić, D.

2012-05-01

In this paper, we study the influence of solar flares on electron concentration in the terrestrial ionospheric D-region by analyzing the amplitude and phase time variations of very low frequency (VLF) radio waves emitted by DHO transmitter (Germany) and recorded by the AWESOME receiver in Belgrade (Serbia) in real time. The rise of photo-ionization rate in the ionospheric D-region is a typical consequence of solar flare activity as recorded by GOES-15 satellite for the event on March 24, 2011 between 12:01 UT and 12:11 UT. At altitudes around 70 km, the photo-ionization and recombination are the dominant electron gain and electron loss processes, respectively. We analyze the relative contribution of each of these two processes in the resulting electron concentration variation in perturbed ionosphere.

An analysis of polygenes affecting wing shape on chromosome 2 in Drosophila melanogaster.

PubMed Central

Weber, K; Eisman, R; Higgins, S; Morey, L; Patty, A; Tausek, M; Zeng, Z B

2001-01-01

Genetic effects on an index of wing shape on chromosome 2 of Drosophila melanogaster were mapped using isogenic recombinants with transposable element markers. At least 10 genes with small additive effects are dispersed evenly along the chromosome. Many interactions exist, with only small net effects in homozygous recombinants and little effect on phenotypic variance. Heterozygous chromosome segments show almost no dominance. Pleiotropic effects on leg shape are only minor. At first view, wing shape genes form a rather homogeneous class, but certain complexities remain unresolved. PMID:11729152

Rectifying properties of p-GaN nanowires and an n-silicon heterojunction vertical diode.

PubMed

Manna, Sujit; Ashok, Vishal D; De, S K

2010-12-01

The heterojunction of a Pd-doped p-GaN nanowire and n-Si (100) is fabricated vertically by the vapor-liquid-solid method. The average diameter of the nanowire is 40 nm. The vertical junction reveals a significantly high rectification ratio of 10(3) at 5 V, a moderate ideality factor of ∼2, and a high breakdown voltage of ∼40 V. The charge transport across the p-n junction is dominated by the electron-hole recombination process. The voltage dependence of capacitance indicates a graded-type junction. The resistance of the junction decreases with an increase in the bias voltage confirmed by impedance measurements.

Atomic-scale luminescence measurement and theoretical analysis unveiling electron energy dissipation at a p-type GaAs(110) surface.

PubMed

Imada, Hiroshi; Miwa, Kuniyuki; Jung, Jaehoon; Shimizu, Tomoko K; Yamamoto, Naoki; Kim, Yousoo

2015-09-11

Luminescence of p-type GaAs was induced by electron injection from the tip of a scanning tunnelling microscope into a GaAs(110) surface. Atomically-resolved photon maps revealed a significant reduction in luminescence intensity at surface electronic states localized near Ga atoms. Theoretical analysis based on first principles calculations and a rate equation approach was performed to describe the perspective of electron energy dissipation at the surface. Our study reveals that non-radiative recombination through the surface states (SS) is a dominant process for the electron energy dissipation at the surface, which is suggestive of the fast scattering of injected electrons into the SS.

Atomic Data for Neutron-capture Elements I. Photoionization and Recombination Properties of Low-charge Selenium Ions

NASA Technical Reports Server (NTRS)

Sterling, N. C.; Witthoeft, Michael

2011-01-01

We present multi-configuration Breit-Pauli AUTOSTRUCTURE calculations of distorted-wave photoionization (PI) cross sections. and total and partial final-state resolved radiative recombination (RR) and dielectronic recombination (DR) rate coefficients for the first six ions of the trans-iron element Se. These calculations were motivated by the recent detection of Se emission lines in a large number of planetary nebulae. Se is a potentially useful tracer of neutron-capture nucleosynthesis. but accurate determinations of its abundance in photoionized nebulae have been hindered by the lack of atomic data governing its ionization balance. Our calculations were carried out in intermediate coupling with semi re1ativistic radial wavefunctions. PI and recombination data were determined for levels within the ground configuration of each ion, and experimental PI cross-section measurements were used to benchmark our results. For DR, we allowed (Delta)n = 0 core excitations, which are important at photoionized plasma temperatures. We find that DR is the dominant recombination process for each of these Se ions at temperatures representative of photoionized nebulae (approx.10(exp 4) K). In order to estimate the uncertainties of these data, we compared results from three different configuration-interaction expansions for each ion, and also tested the sensitivity of the results to the radial scaling factors in the structure calculations. We find that the internal uncertainties are typically 30-50% for the direct PI cross sections and approx.10% for the computed RR rate coefficients, while those for low-temperature DR can be considerably larger (from 15-30% up to two orders of magnitude) due to the unknown energies of near-threshold autoionization resonances. These data are available at the CDS, and fitting coefficients to the total RR and DR rate coefficients are presented. The results are suitable for incorporation into photoionization codes used to numerically simulate astrophysical nebulae, and will enable robust determinations of nebular Se abundances.

The nature of trapping sites and recombination centres in PVK and PVK-PBD electroluminescent matrices seen by spectrally resolved thermoluminescence

NASA Astrophysics Data System (ADS)

Glowacki, Ireneusz; Szamel, Zbigniew

2010-07-01

Two electroluminescent polymer matrices poly(N-vinylcarbazole) (PVK) and PVK with 40 wt% of 2-tert-butylphenyl-5-biphenyl-1,3,4-oxadiazole (PBD) were studied using spectrally resolved thermoluminescence (SRTL) in the temperature range 15-325 K. The comparison of the SRTL results with the electroluminescence (EL) spectra has allowed identification of the localized (trapping) sites and the radiative recombination centres present in the investigated matrices. In the neat PVK films deep traps with a depth about 200 meV, related to triplet excimers dominate, while in the PVK-PBD (40 wt%) blend films the traps that are related to triplet exciplexes formed by the carbazole groups and the PBD molecules dominate. Depth of the traps in the PVK-PBD blend is somewhat lower than that in the neat PVK. An analysis of the EL spectra shows that in the PVK and in the PVK-PBD blend the dominant radiative centres are singlet excimers and singlet exciplexes, respectively. However, in the neat PVK some contributions of the triplet monomer and the triplet excimer states in the EL were also detected.

Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation.

PubMed

Simmons, Sheri L; Dibartolo, Genevieve; Denef, Vincent J; Goltsman, Daniela S Aliaga; Thelen, Michael P; Banfield, Jillian F

2008-07-22

Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth approximately 20x). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types ( approximately 94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination.

Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation

PubMed Central

Denef, Vincent J; Goltsman, Daniela S. Aliaga; Thelen, Michael P; Banfield, Jillian F

2008-01-01

Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth ∼20×). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types (∼94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination. PMID:18651792

Strain-balanced Indium Arsenide-Indium Arsenic Antimonide Type-II Superlattices on Gallium Antimonide Substrates for Infrared Photodetector Applications

NASA Astrophysics Data System (ADS)

Steenbergen, Elizabeth H.

Infrared photodetectors, used in applications for sensing and imaging, such as military target recognition, chemical/gas detection, and night vision enhancement, are predominantly comprised of an expensive II-VI material, HgCdTe. III-V type-II superlattices (SLs) have been studied as viable alternatives for HgCdTe due to the SL advantages over HgCdTe: greater control of the alloy composition, resulting in more uniform materials and cutoff wavelengths across the wafer; stronger bonds and structural stability; less expensive substrates, i.e., GaSb; mature III-V growth and processing technologies; lower band-to-band tunneling due to larger electron effective masses; and reduced Auger recombination enabling operation at higher temperatures and longer wavelengths. However, the dark current of InAs/Ga1-xInxSb SL detectors is higher than that of HgCdTe detectors and limited by Shockley-Read-Hall (SRH) recombination rather than Auger recombination. This dissertation work focuses on InAs/InAs1-xSbx SLs, another promising alternative for infrared laser and detector applications due to possible lower SRH recombination and the absence of gallium, which simplifies the SL interfaces and growth processes. InAs/InAs1-xSbx SLs strain-balanced to GaSb substrates were designed for the mid- and long-wavelength infrared (MWIR and LWIR) spectral ranges and were grown using MOCVD and MBE by various groups. Detailed characterization using high-resolution x-ray diffraction, atomic force microscopy, photoluminescence (PL), and photoconductance revealed the excellent structural and optical properties of the MBE materials. Two key material parameters were studied in detail: the valence band offset (VBO) and minority carrier lifetime. The VBO between InAs and InAs 1-xSbx strained on GaSb with x = 0.28--0.41 was best described by Qv = DeltaEv/DeltaE g = 1.75 +/- 0.03. Time-resolved PL experiments on a LWIR SL revealed a lifetime of 412 ns at 77 K, one order of magnitude greater than that of InAs/Ga1-xInxSb LWIR SLs due to less SRH recombination. MWIR SLs also had 100's of ns lifetimes that were dominated by radiative recombination due to shorter periods and larger wave function overlaps. These results allow InAs/InAs1-xSbx SLs to be designed for LWIR photodetectors with minority carrier lifetimes approaching those of HgCdTe, lower dark currents, and higher operating temperatures.

Structural dependences of localization and recombination of photogenerated carriers in the top GaInP Subcells of GaInP/GaAs double-junction tandem solar cells.

PubMed

Deng, Zhuo; Ning, Jiqiang; Su, Zhicheng; Xu, Shijie; Xing, Zheng; Wang, Rongxin; Lu, Shulong; Dong, Jianrong; Zhang, Baoshun; Yang, Hui

2015-01-14

In high-efficiency GaInP/GaAs double-junction tandem solar cells, GaInP layers play a central role in determining the performance of the solar cells. Therefore, gaining a deeper understanding of the optoelectronic processes in GaInP layers is crucial for improving the energy conversion efficiency of GaInP-based photovoltaic devices. In this work, we firmly show strong dependences of localization and recombination of photogenerated carriers in the top GaInP subcells in the GaInP/GaAs double-junction tandem solar cells on the substrate misorientation angle with excitation intensity- and temperature-dependent photoluminescence (PL). The entire solar cell structures including GaInP layers were grown with metalorganic chemical vapor deposition on GaAs substrates with misorientation angles of 2° (denoted as Sample 2°) and 7° (Sample 7°) off (100) toward (111)B. The PL spectral features of the two top GaInP subcells, as well as their excitation-power and temperature dependences exhibit remarkable variation on the misorientation angle. In Sample 2°, the dominant localization mechanism and luminescence channels are due to the energy potential minima caused by highly ordered atomic domains; In Sample 7°, the main localization and radiative recombination of photogenerated carriers occur in the atomically disordered regions. Our results reveal a more precise picture on the localization and recombination mechanisms of photogenerated carriers in the top GaInP subcells, which could be the crucial factors in controlling the optoelectronic efficiency of the GaInP-based multijunction photovoltaic devices.

Light illumination intensity dependence of photovoltaic parameter in polymer solar cells with ammonium heptamolybdate as hole extraction layer.

PubMed

Liu, Zhiyong; Niu, Shengli; Wang, Ning

2018-01-01

A low-temperature, solution-processed molybdenum oxide (MoO X ) layer and a facile method for polymer solar cells (PSCs) is developed. The PSCs based on a MoO X layer as the hole extraction layer (HEL) is a significant advance for achieving higher photovoltaic performance, especially under weaker light illumination intensity. Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) measurements show that the (NH 4 ) 6 Mo 7 O 24 molecule decomposes and forms the molybdenum oxide (MoO X ) molecule when undergoing thermal annealing treatment. In this study, PSCs with the MoO X layer as the HEL exhibited better photovoltaic performance, especially under weak light illumination intensity (from 100 to 10mWcm -2 ) compared to poly(3,4-ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS)-based PSCs. Analysis of the current density-voltage (J-V) characteristics at various light intensities provides information on the different recombination mechanisms in the PSCs with a MoO X and PEDOT:PSS layer as the HEL. That the slopes of the open-circuit voltage (V OC ) versus light illumination intensity plots are close to 1 unity (kT/q) reveals that bimolecular recombination is the dominant and weaker monomolecular recombination mechanism in open-circuit conditions. That the slopes of the short-circuit current density (J SC ) versus light illumination intensity plots are close to 1 reveals that the effective charge carrier transport and collection mechanism of the MoO X /indium tin oxide (ITO) anode is the weaker bimolecular recombination in short-circuit conditions. Our results indicate that MoO X is an alternative candidate for high-performance PSCs, especially under weak light illumination intensity. Copyright © 2017 Elsevier Inc. All rights reserved.

Active region dimensionality and quantum efficiencies of InGaN LEDs from temperature dependent photoluminescence transients

NASA Astrophysics Data System (ADS)

Can, Nuri; Okur, Serdal; Monavarian, Morteza; Zhang, Fan; Avrutin, Vitaliy; Morkoç, Hadis; Teke, Ali; Özgür, Ümit

2015-03-01

Temperature dependent recombination dynamics in c-plane InGaN light emitting diodes (LEDs) with different well thicknesses, 1.5, 2, and 3 nm, were investigated to determine the active region dimensionality and its effect on the internal quantum efficiencies. It was confirmed for all LEDs that the photoluminescence (PL) transients are governed by radiative recombination at low temperatures while nonradiative recombination dominates at room temperature. At photoexcited carrier densities of 3 - 4.5 x 1016 cm-3 , the room-temperature Shockley-Read-Hall (A) and the bimolecular (B) recombination coefficients (A, B) were deduced to be (9.2x107 s-1, 8.8x10-10 cm3s-1), (8.5x107 s-1, 6.6x10-10 cm3s-1), and (6.5x107 s-1, 1.4x10-10 cm3s-1) for the six period 1.5, 2, and 3 nm well-width LEDs, respectively. From the temperature dependence of the radiative lifetimes, τrad α Tn/2, the dimensionality n of the active region was found to decrease consistently with decreasing well width. The 3 nm wide wells exhibited ~T1.5 dependence, suggesting a three-dimensional nature, whereas the 1.5 nm wells were confirmed to be two-dimensional (~T1) and the 2 nm wells close to being two-dimensional. We demonstrate that a combination of temperature dependent PL and time-resolved PL techniques can be used to evaluate the dimensionality as well as the quantum efficiencies of the LED active regions for a better understanding of the relationship between active-region design and the efficiency limiting processes in InGaN LEDs.

Activation induced deaminase C-terminal domain links DNA breaks to end protection and repair during class switch recombination

PubMed Central

Zahn, Astrid; Eranki, Anil K.; Patenaude, Anne-Marie; Methot, Stephen P.; Fifield, Heather; Cortizas, Elena M.; Foster, Paul; Imai, Kohsuke; Durandy, Anne; Larijani, Mani; Verdun, Ramiro E.; Di Noia, Javier M.

2014-01-01

Activation-induced deaminase (AID) triggers antibody class switch recombination (CSR) in B cells by initiating DNA double strand breaks that are repaired by nonhomologous end-joining pathways. A role for AID at the repair step is unclear. We show that specific inactivation of the C-terminal AID domain encoded by exon 5 (E5) allows very efficient deamination of the AID target regions but greatly impacts the efficiency and quality of subsequent DNA repair. Specifically eliminating E5 not only precludes CSR but also, causes an atypical, enzymatic activity-dependent dominant-negative effect on CSR. Moreover, the E5 domain is required for the formation of AID-dependent Igh-cMyc chromosomal translocations. DNA breaks at the Igh switch regions induced by AID lacking E5 display defective end joining, failing to recruit DNA damage response factors and undergoing extensive end resection. These defects lead to nonproductive resolutions, such as rearrangements and homologous recombination that can antagonize CSR. Our results can explain the autosomal dominant inheritance of AID variants with truncated E5 in patients with hyper-IgM syndrome 2 and establish that AID, through the E5 domain, provides a link between DNA damage and repair during CSR. PMID:24591601

The autosomal dominant familial exudative vitreoretinopathy locus maps on 11q and is closely linked to D11S533

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yuen; Schwinger, D.; Gal, A.

1992-10-01

Autosomal dominant familial exudative vitreoretinopathy (adFEVR) is a hereditary disorder characterized by the incomplete vascularization of the peripheral retina. The primary biochemical defect in adFEVR is unknown. The adFEVR locus has tentatively been assigned to 11q by linkage studies. The authors report the results of an extended multipoint linkage analysis of two families with adFEVR by using five markers (INT2, D11S533, D11S527, D11S35, and CD3D) from 11q13-q23. Pairwise linkage data obtained in the two families were rather similar and hence have not provided evidence for genetic heterogeneity. The highest compiled two-point lod score (3.67, at a recombination fraction of .07)more » was obtained for the disease locus versus D11S533. Multipoint analyses showed that the adFEVR locus maps most likely, with a maximum location score of over 20, between D11S533/D11S526 and D11S35, at recombination rates of .147 and .104, respectively. Close linkage without recombination (maximum lod score 11.26) has been found between D11S533 and D11S526. 15 refs., 3 figs., 4 tabs.« less

Interfacial Passivation of the p-Doped Hole-Transporting Layer Using General Insulating Polymers for High-Performance Inverted Perovskite Solar Cells.

PubMed

Zhang, Fan; Song, Jun; Hu, Rui; Xiang, Yuren; He, Junjie; Hao, Yuying; Lian, Jiarong; Zhang, Bin; Zeng, Pengju; Qu, Junle

2018-05-01

Organic-inorganic lead halide perovskite solar cells (PVSCs), as a competing technology with traditional inorganic solar cells, have now realized a high power conversion efficiency (PCE) of 22.1%. In PVSCs, interfacial carrier recombination is one of the dominant energy-loss mechanisms, which also results in the simultaneous loss of potential efficiency. In this work, for planar inverted PVSCs, the carrier recombination is dominated by the dopant concentration in the p-doped hole transport layers (HTLs), since the F4-TCNQ dopant induces more charge traps and electronic transmission channels, thus leading to a decrease in open-circuit voltages (V OC ). This issue is efficiently overcome by inserting a thin insulating polymer layer (poly(methyl methacrylate) or polystyrene) as a passivation layer with an appropriate thickness, which allows for increases in the V OC without significantly sacrificing the fill factor. It is believed that the passivation layer attributes to the passivation of interfacial recombination and the suppression of current leakage at the perovskite/HTL interface. By manipulating this interfacial passivation technique, a high PCE of 20.3% is achieved without hysteresis. Consequently, this versatile interfacial passivation methodology is highly useful for further improving the performance of planar inverted PVSCs. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Within-Host Dynamics of the Emergence of Tomato Yellow Leaf Curl Virus Recombinants

PubMed Central

Urbino, Cica; Gutiérrez, Serafin; Antolik, Anna; Bouazza, Nabila; Doumayrou, Juliette; Granier, Martine; Martin, Darren P.; Peterschmitt, Michel

2013-01-01

Tomato yellow leaf curl virus (TYLCV) is a highly damaging begomovirus native to the Middle East. TYLCV has recently spread worldwide, recombining with other begomoviruses. Recent analysis of mixed infections between TYLCV and Tomato leaf curl Comoros begomovirus (ToLCKMV) has shown that, although natural selection preserves certain co-evolved intra-genomic interactions, numerous and diverse recombinants are produced at 120 days post-inoculation (dpi), and recombinant populations from different tomato plants are very divergent. Here, we investigate the population dynamics that lead to such patterns in tomato plants co-infected with TYLCV and ToLCKMV either by agro-inoculation or using the natural whitefly vector Bemisia tabaci. We monitored the frequency of parental and recombinant genotypes independently in 35 plants between 18 and 330 dpi and identified 177 recombinants isolated at different times. Recombinants were detected from 18 dpi and their frequency increased over time to reach about 50% at 150 dpi regardless of the inoculation method. The distribution of breakpoints detected on 96 fully sequenced recombinants was consistent with a continuous generation of new recombinants as well as random and deterministic effects in their maintenance. A severe population bottleneck of around 10 genomes was estimated during early systemic infection–a phenomenon that could account partially for the heterogeneity in recombinant patterns observed among plants. The detection of the same recombinant genome in six of the thirteen plants analysed beyond 30 dpi supported the influence of selection on observed recombination patterns. Moreover, a highly virulent recombinant genotype dominating virus populations within one plant has, apparently, the potential to be maintained in the natural population according to its infectivity, within-host accumulation, and transmission efficiency - all of which were similar or intermediate to those of the parent genotypes. Our results anticipate the outcomes of natural encounters between TYLCV and ToLCKMV. PMID:23472190

Solar X-Ray Processes

NASA Astrophysics Data System (ADS)

Mallik, P. C. V.; Brown, J. C.; MacKinnon, A. L.

Past analyses of solar flares have ignored nonthermal recombination (NTR) emission as a means of producing Hard X-rays (HXRs) in the corona and chromosphere. However, Brown and Mallik (2008, A&A, 481, 507) have shown that NTR can be significant and even exceed nonthermal bremsstrahlung (NTB) emission for certain flare conditions that are quite common. For hot enough plasma (T > 10 MK), HXR emission of a few deka-keV has a large contribution from NTR onto highly ionized heavy elements, especially Fe. Consequently, including NTR has implications for the magnitude and the form of the inferred electron spectrum, F(E), and hence for fast-electron density and energy budgets and for the acceleration mechanisms. We show under what circumstances NTR dominates in deka-keV HXR emission. It is important to note that at high temperatures, HXR emission from thermal electrons (recombination and bremsstrahlung) becomes important. However, NTR dominates over NTB without being swamped by thermal emission in the photon energy (ɛ) regime of 20-30 keV and temperature range of 10-25MK (Fig. 1, left). By integrating the flux for all ɛ > 20keV, i.e., looking at the source luminosity function above 20 keV, we were able to show that by including NTR, the acceleration requirements are less demanding for every event, but to varying degrees based on temperature (T), spectral index (δ) and electron low-energy cut-off (Ec). Our key result is that, for T > 10MK and δ ≈ 5, including NTR reduces the demand for nonthermal electrons by up to 85%. Our paper with these results will be submitted to ApJ Letters.

Copper interstitial recombination centers in Cu 3 N

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yee, Ye Sheng; Inoue, Hisashi; Hultqvist, Adam

We present a comprehensive study of the earth-abundant semiconductor Cu 3N as a potential solar energy conversion material, using density functional theory and experimental methods. Density functional theory indicates that among the dominant intrinsic point defects, copper vacancies V Cu have shallow defect levels while copper interstitials Cu i behave as deep potential wells in the conduction band which mediate Shockley-Read-Hall recombination. The existence of Cu i defects has been experimentally verified using photothermal deflection spectroscopy. A Cu 3N/ZnS heterojunction diode with good current-voltage rectification behavior has been demonstrated experimentally, but no photocurrent is generated under illumination. Finally, the absencemore » of photocurrent can be explained by a large concentration of Cu i recombination centers capturing electrons in p-type Cu 3N.« less

Efficiency droop in GaN LEDs at high injection levels: Role of hydrogen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bochkareva, N. I.; Sheremet, I. A.; Shreter, Yu. G., E-mail: y.shreter@mail.ioffe.ru

2016-10-15

Point defects in GaN and, in particular, their manifestation in the photoluminescence, optical absorption, and recombination current in light-emitting diodes with InGaN/GaN quantum wells are analyzed. The results of this analysis demonstrate that the wide tail of defect states in the band gap of GaN facilitates the trap-assisted tunneling of thermally activated carriers into the quantum well, but simultaneously leads to a decrease in the nonradiative-recombination lifetime and to an efficiency droop as the quasi-Fermi levels intersect the defect states with increasing forward bias. The results reveal the dominant role of hydrogen in the recombination activity of defects with danglingmore » bonds and in the efficiency of GaN-based devices.« less

Copper interstitial recombination centers in Cu 3 N

DOE PAGES

Yee, Ye Sheng; Inoue, Hisashi; Hultqvist, Adam; ...

2018-06-04

We present a comprehensive study of the earth-abundant semiconductor Cu 3N as a potential solar energy conversion material, using density functional theory and experimental methods. Density functional theory indicates that among the dominant intrinsic point defects, copper vacancies V Cu have shallow defect levels while copper interstitials Cu i behave as deep potential wells in the conduction band which mediate Shockley-Read-Hall recombination. The existence of Cu i defects has been experimentally verified using photothermal deflection spectroscopy. A Cu 3N/ZnS heterojunction diode with good current-voltage rectification behavior has been demonstrated experimentally, but no photocurrent is generated under illumination. Finally, the absencemore » of photocurrent can be explained by a large concentration of Cu i recombination centers capturing electrons in p-type Cu 3N.« less

Ultraviolet/blue light-emitting diodes based on single horizontal ZnO microrod/GaN heterojunction

PubMed Central

2014-01-01

We report electroluminescence (EL) from single horizontal ZnO microrod (MR) and p-GaN heterojunction light-emitting diodes under forward and reverse bias. EL spectra were composed of two blue emissions centered at 431 and 490 nm under forward biases, but were dominated by a ultraviolet (UV) emission located at 380 nm from n-ZnO MR under high reverse biases. Light-output-current characteristic of the UV emission reveals that the rate of radiative recombination is faster than that of the nonradiative recombination. Highly efficient ZnO excitonic recombination at reverse bias is caused by electrons tunneling from deep-level states near the n-ZnO/p-GaN interface to the conduction band in n-ZnO. PMID:25232299

Photoionization and Recombination

NASA Technical Reports Server (NTRS)

Nahar, Sultana N.

2000-01-01

Theoretically self-consistent calculations for photoionization and (e + ion) recombination are described. The same eigenfunction expansion for the ion is employed in coupled channel calculations for both processes, thus ensuring consistency between cross sections and rates. The theoretical treatment of (e + ion) recombination subsumes both the non-resonant recombination ("radiative recombination"), and the resonant recombination ("di-electronic recombination") processes in a unified scheme. In addition to the total, unified recombination rates, level-specific recombination rates and photoionization cross sections are obtained for a large number of atomic levels. Both relativistic Breit-Pauli, and non-relativistic LS coupling, calculations are carried out in the close coupling approximation using the R-matrix method. Although the calculations are computationally intensive, they yield nearly all photoionization and recombination parameters needed for astrophysical photoionization models with higher precision than hitherto possible, estimated at about 10-20% from comparison with experimentally available data (including experimentally derived DR rates). Results are electronically available for over 40 atoms and ions. Photoionization and recombination of He-, and Li-like C and Fe are described for X-ray modeling. The unified method yields total and complete (e+ion) recombination rate coefficients, that can not otherwise be obtained theoretically or experimentally.

Production of recombinant allergens in plants.

PubMed

Schmidt, Georg; Gadermaier, Gabriele; Pertl, Heidi; Siegert, Marc; Oksman-Caldentey, Kirsi-Marja; Ritala, Anneli; Himly, Martin; Obermeyer, Gerhard; Ferreira, Fatima

2008-10-01

A large percentage of allergenic proteins are of plant origin. Hence, plant-based expression systems are considered ideal for the recombinant production of certain allergens. First attempts to establish production of plant-derived allergens in plants focused on transient expression in Nicotiana benthamiana infected with recombinant viral vectors. Accordingly, allergens from birch and mugwort pollen, as well as from apple have been expressed in plants. Production of house dust mite allergens has been achieved by Agrobacterium-mediated transformation of tobacco plants. Beside the use of plants as production systems, other approaches have focused on the development of edible vaccines expressing allergens or epitopes thereof, which bypasses the need of allergen purification. The potential of this approach has been convincingly demonstrated for transgenic rice seeds expressing seven dominant human T cell epitopes derived from Japanese cedar pollen allergens. Parallel to efforts in developing recombinant-based diagnostic and therapeutic reagents, different gene-silencing approaches have been used to decrease the expression of allergenic proteins in allergen sources. In this way hypoallergenic ryegrass, soybean, rice, apple, and tomato were developed.

Inner Magnetospheric Superthermal Electron Transport: Photoelectron and Plasma Sheet Electron Sources

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Liemohn, M. W.; Kozyra, J. U.; Moore, T. E.

1998-01-01

Two time-dependent kinetic models of superthermal electron transport are combined to conduct global calculations of the nonthermal electron distribution function throughout the inner magnetosphere. It is shown that the energy range of validity for this combined model extends down to the superthermal-thermal intersection at a few eV, allowing for the calculation of the en- tire distribution function and thus an accurate heating rate to the thermal plasma. Because of the linearity of the formulas, the source terms are separated to calculate the distributions from the various populations, namely photoelectrons (PEs) and plasma sheet electrons (PSEs). These distributions are discussed in detail, examining the processes responsible for their formation in the various regions of the inner magnetosphere. It is shown that convection, corotation, and Coulomb collisions are the dominant processes in the formation of the PE distribution function and that PSEs are dominated by the interplay between the drift terms. Of note is that the PEs propagate around the nightside in a narrow channel at the edge of the plasmasphere as Coulomb collisions reduce the fluxes inside of this and convection compresses the flux tubes inward. These distributions are then recombined to show the development of the total superthermal electron distribution function in the inner magnetosphere and their influence on the thermal plasma. PEs usually dominate the dayside heating, with integral energy fluxes to the ionosphere reaching 10(exp 10) eV/sq cm/s in the plasmasphere, while heating from the PSEs typically does not exceed 10(exp 8) eV/sq cm/s. On the nightside, the inner plasmasphere is usually unheated by superthermal electrons. A feature of these combined spectra is that the distribution often has upward slopes with energy, particularly at the crossover from PE to PSE dominance, indicating that instabilities are possible.

Dominant Sequences of Human Major Histocompatibility Complex Conserved Extended Haplotypes from HLA-DQA2 to DAXX

PubMed Central

Larsen, Charles E.; Alford, Dennis R.; Trautwein, Michael R.; Jalloh, Yanoh K.; Tarnacki, Jennifer L.; Kunnenkeri, Sushruta K.; Fici, Dolores A.; Yunis, Edmond J.; Awdeh, Zuheir L.; Alper, Chester A.

2014-01-01

We resequenced and phased 27 kb of DNA within 580 kb of the MHC class II region in 158 population chromosomes, most of which were conserved extended haplotypes (CEHs) of European descent or contained their centromeric fragments. We determined the single nucleotide polymorphism and deletion-insertion polymorphism alleles of the dominant sequences from HLA-DQA2 to DAXX for these CEHs. Nine of 13 CEHs remained sufficiently intact to possess a dominant sequence extending at least to DAXX, 230 kb centromeric to HLA-DPB1. We identified the regions centromeric to HLA-DQB1 within which single instances of eight “common” European MHC haplotypes previously sequenced by the MHC Haplotype Project (MHP) were representative of those dominant CEH sequences. Only two MHP haplotypes had a dominant CEH sequence throughout the centromeric and extended class II region and one MHP haplotype did not represent a known European CEH anywhere in the region. We identified the centromeric recombination transition points of other MHP sequences from CEH representation to non-representation. Several CEH pairs or groups shared sequence identity in small blocks but had significantly different (although still conserved for each separate CEH) sequences in surrounding regions. These patterns partly explain strong calculated linkage disequilibrium over only short (tens to hundreds of kilobases) distances in the context of a finite number of observed megabase-length CEHs comprising half a population's haplotypes. Our results provide a clearer picture of European CEH class II allelic structure and population haplotype architecture, improved regional CEH markers, and raise questions concerning regional recombination hotspots. PMID:25299700

Identification of Two New HIV-1 Circulating Recombinant Forms (CRF87_cpx and CRF88_BC) from Reported Unique Recombinant Forms in Asia.

PubMed

Hu, Yihong; Wan, Zhenzhou; Zhou, Yan-Heng; Smith, Davey; Zheng, Yong-Tang; Zhang, Chiyu

2017-04-01

The on-going generation of HIV-1 intersubtype recombination has led to new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) in Asia. In this study, we evaluated whether previously reported URFs were actually CRFs. All available complete or near full-length HIV-1 URF sequences from Asia were retrieved from the HIV Los Alamos National Laboratory Sequence database, and phylogenetic, transmission cluster, and bootscan analyses were performed using MEGA 6.0, Cluster Picker 1.2.1, and SimPlot3.5.1. According to the criterion of new CRFs, two new HIV-1 CRFs (CRF87_cpx and CRF88_BC) were identified from these available URFs. CRF87_cpx comprised HIV-1 subtypes B, C, and CRF01_AE, and CRF88_BC comprised subtypes B and C. HIV Blast and bootscan analysis revealed that besides the three representative strains, there were two additional CRF87_cpx strains. Furthermore, we defined seven dominant URFs (dURF01-dURF07), each of which contained two strains sharing same recombination map and can be used as sequence references to facilitate the finding of new potential CRFs in future. These results will benefit the molecular epidemiological investigation of HIV-1 in Asia.

Immune-driven recombination and loss of control after HIV superinfection.

PubMed

Streeck, Hendrik; Li, Bin; Poon, Art F Y; Schneidewind, Arne; Gladden, Adrianne D; Power, Karen A; Daskalakis, Demetre; Bazner, Suzane; Zuniga, Rosario; Brander, Christian; Rosenberg, Eric S; Frost, Simon D W; Altfeld, Marcus; Allen, Todd M

2008-08-04

After acute HIV infection, CD8(+) T cells are able to control viral replication to a set point. This control is often lost after superinfection, although the mechanism behind this remains unclear. In this study, we illustrate in an HLA-B27(+) subject that loss of viral control after HIV superinfection coincides with rapid recombination events within two narrow regions of Gag and Env. Screening for CD8(+) T cell responses revealed that each of these recombination sites (approximately 50 aa) encompassed distinct regions containing two immunodominant CD8 epitopes (B27-KK10 in Gag and Cw1-CL9 in Env). Viral escape and the subsequent development of variant-specific de novo CD8(+) T cell responses against both epitopes were illustrative of the significant immune selection pressures exerted by both responses. Comprehensive analysis of the kinetics of CD8 responses and viral evolution indicated that the recombination events quickly facilitated viral escape from both dominant WT- and variant-specific responses. These data suggest that the ability of a superinfecting strain of HIV to overcome preexisting immune control may be related to its ability to rapidly recombine in critical regions under immune selection pressure. These data also support a role for cellular immune pressures in driving the selection of new recombinant forms of HIV.

Computational Study of Nonequilibrium Chemistry in High Temperature Flows

NASA Astrophysics Data System (ADS)

Doraiswamy, Sriram

Recent experimental measurements in the reflected shock tunnel CUBRC LENS-I facility raise questions about our ability to correctly model the recombination processes in high enthalpy flows. In the carbon dioxide flow, the computed shock standoff distance over the Mars Science Laboratory (MSL) shape was less than half of the experimental result. For the oxygen flows, both pressure and heat transfer data on the double cone geometry were not correctly predicted. The objective of this work is to investigate possible reasons for these discrepancies. This process involves systematically addressing different factors that could possibly explain the differences. These factors include vibrational modeling, role of electronic states and chemistry-vibrational coupling in high enthalpy flows. A state-specific vibrational model for CO2, CO, O2 and O system is devised by taking into account the first few vibrational states of each species. All vibrational states with energies at or below 1 eV are included in the present work. Of the three modes of vibration in CO2 , the antisymmetric mode is considered separately from the symmetric stretching mode and the doubly degenerate bending modes. The symmetric and the bending modes are grouped together since the energy transfer rates between the two modes are very large due to Fermi resonance. The symmetric and bending modes are assumed to be in equilibrium with the translational and rotational modes. The kinetic rates for the vibrational-translation energy exchange reactions, and the intermolecular and intramolecular vibrational-vibrational energy exchange reactions are based on experimental data to the maximum extent possible. Extrapolation methods are employed when necessary. This vibrational model is then coupled with an axisymmetric computational fluid dynamics code to study the expansion of CO2 in a nozzle. The potential role of low lying electronic states is also investigated. Carbon dioxide has a single excited state just below the dissociation limit. CO and O recombine exclusively to this excited state and then relaxes to the ground electronic state. A simple model is proposed to represent the effect of this intermediate state in the recombination process. Preliminary results show that this excited electronic state is a potential reason for increased shock standoff distance observed in LENS facility. The general role of chemistry-vibrational coupling in modeling recombination dominated flows is also investigated. A state-specific model is developed to analyze the complex chemistry-vibration coupling present in high enthalpy nozzle flows. A basic model is formulated assuming molecules are formed at a specific vibrational level and then allowed to relax through a series of vibration-vibration and vibration-translation processes. This is carried out assuming that the molecules behave as either harmonic or anharmonic oscillators. The results are compared with the standard vibration-chemistry model for high enthalpy nozzle flows. Next, a prior recombination model that accounts for the rotational-vibrational coupling is used to obtain prior recombination distribution. A distribution of recombining states is obtained as a function of the total energy available to the system. The results of this model are compared with recent experiments. Additionally, a reduced model is formulated using the concepts of the state-specific model. The results of this reduced model is compared with the state specific model.

Genetic fine-mapping of DIPLOSPOROUS in Taraxacum (dandelion; Asteraceae) indicates a duplicated DIP-gene

PubMed Central

2010-01-01

Background DIPLOSPOROUS (DIP) is the locus for diplospory in Taraxacum, associated to unreduced female gamete formation in apomicts. Apomicts reproduce clonally through seeds, including apomeiosis, parthenogenesis, and autonomous or pseudogamous endosperm formation. In Taraxacum, diplospory results in first division restitution (FDR) nuclei, and inherits as a dominant, monogenic trait, independent from the other apomixis elements. A preliminary genetic linkage map indicated that the DIP-locus lacks suppression of recombination, which is unique among all other map-based cloning efforts of apomeiosis to date. FDR as well as apomixis as a whole are of interest in plant breeding, allowing for polyploidization and fixation of hybrid vigor, respectively. No dominant FDR or apomixis genes have yet been isolated. Here, we zoom-in to the DIP-locus by largely extending our initial mapping population, and by analyzing (local) suppression of recombination and allele sequence divergence (ASD). Results We identified 24 recombinants between two most closely linked molecular markers to DIP in an F1-population of 2227 plants that segregates for diplospory and lacks parthenogenesis. Both markers segregated c. 1:1 in the entire population, indicating a 1:1 segregation rate of diplospory. Fine-mapping showed three amplified fragment length polymorphisms (AFLPs) closest to DIP at 0.2 cM at one flank and a single AFLP at 0.4 cM at the other flank. Our data lacked strong evidence for ASD at marker regions close to DIP. An unexpected bias towards diplosporous plants among the recombinants (20 out of 24) was found. One third of these diplosporous recombinants showed incomplete penetrance of 50-85% diplospory. Conclusions Our data give interesting new insights into the structure of the diplospory locus in Taraxacum. We postulate a locus with a minimum of two DIP-genes and possibly including one or two enhancers or cis-regulatory elements on the basis of the bias towards diplosporous recombinants and incomplete penetrance of diplospory in some of them. We define the DIP-locus to 0.6 cM, which is estimated to cover ~200-300 Kb, with the closest marker at 0.2 cM. Our results confirm the minor role of suppression of recombination and ASD around DIP, making it an excellent candidate to isolate via a chromosome-walking approach. PMID:20659311

Genetic fine-mapping of DIPLOSPOROUS in Taraxacum (dandelion; Asteraceae) indicates a duplicated DIP-gene.

PubMed

Vijverberg, Kitty; Milanovic-Ivanovic, Slavica; Bakx-Schotman, Tanja; van Dijk, Peter J

2010-07-26

DIPLOSPOROUS (DIP) is the locus for diplospory in Taraxacum, associated to unreduced female gamete formation in apomicts. Apomicts reproduce clonally through seeds, including apomeiosis, parthenogenesis, and autonomous or pseudogamous endosperm formation. In Taraxacum, diplospory results in first division restitution (FDR) nuclei, and inherits as a dominant, monogenic trait, independent from the other apomixis elements. A preliminary genetic linkage map indicated that the DIP-locus lacks suppression of recombination, which is unique among all other map-based cloning efforts of apomeiosis to date. FDR as well as apomixis as a whole are of interest in plant breeding, allowing for polyploidization and fixation of hybrid vigor, respectively. No dominant FDR or apomixis genes have yet been isolated. Here, we zoom-in to the DIP-locus by largely extending our initial mapping population, and by analyzing (local) suppression of recombination and allele sequence divergence (ASD). We identified 24 recombinants between two most closely linked molecular markers to DIP in an F1-population of 2227 plants that segregates for diplospory and lacks parthenogenesis. Both markers segregated c. 1:1 in the entire population, indicating a 1:1 segregation rate of diplospory. Fine-mapping showed three amplified fragment length polymorphisms (AFLPs) closest to DIP at 0.2 cM at one flank and a single AFLP at 0.4 cM at the other flank. Our data lacked strong evidence for ASD at marker regions close to DIP. An unexpected bias towards diplosporous plants among the recombinants (20 out of 24) was found. One third of these diplosporous recombinants showed incomplete penetrance of 50-85% diplospory. Our data give interesting new insights into the structure of the diplospory locus in Taraxacum. We postulate a locus with a minimum of two DIP-genes and possibly including one or two enhancers or cis-regulatory elements on the basis of the bias towards diplosporous recombinants and incomplete penetrance of diplospory in some of them. We define the DIP-locus to 0.6 cM, which is estimated to cover approximately 200-300 Kb, with the closest marker at 0.2 cM. Our results confirm the minor role of suppression of recombination and ASD around DIP, making it an excellent candidate to isolate via a chromosome-walking approach.

The near-infrared structure and spectra of the bipolar nebulae M2-9 and AFGL 2688: The role of ultraviolet pumping and shocks in molecular hydrogen excitation

NASA Technical Reports Server (NTRS)

Hora, Joseph L.; Latter, William B.

1994-01-01

High-resolution near-infrared images and moderate resolution spectra were obtained of the bipolar nebulae M2-9 and AFGL 2688. The ability to spatially and spectrally resolve the various components of the nebulae has proved to be important in determining their physical structure and characteristics. In M2-9, the lobes are found to have a double-shell structure. The inner shell is dominated by emission from hydrogen recombination lines, and the outer shell is primarily emission from H2 lines in teh 2-2.5 micron region. Analysis of H2 line ratios indicates that the H2 emission is radiatively excited. A well-resolved photodissociation region is observed in the lobes. The spectrum of the central source is dominated by H recombination lines and a strong continuum rising toward longer wavelengths consistent with a T = 795 K blackbody. Also present are lines of He I and Fe II. In contrast, the N knot and E lobe of M2-9 show little continuum emission. The N knot spectrum consists of lines of (Fe II) and hydrogen recombination lines. In AGFL 2688, the emission from the bright lobes is mainly continuum reflected from the central star. Several molecular features from C2 and CN are present. In the extreme end of the N lobe and in the E equatorial region, the emission is dominated by lines of H2 in the 2-2.5 region. The observed H2 line ratios indicate that the emission is collisionally excited, with an excitation temperature T(sub ex) approixmately = 1600 +/- 100 K.

25th anniversary article: charge transport and recombination in polymer light-emitting diodes.

PubMed

Kuik, Martijn; Wetzelaer, Gert-Jan A H; Nicolai, Herman T; Craciun, N Irina; De Leeuw, Dago M; Blom, Paul W M

2014-01-01

This article reviews the basic physical processes of charge transport and recombination in organic semiconductors. As a workhorse, LEDs based on a single layer of poly(p-phenylene vinylene) (PPV) derivatives are used. The hole transport in these PPV derivatives is governed by trap-free space-charge-limited conduction, with the mobility depending on the electric field and charge-carrier density. These dependencies are generally described in the framework of hopping transport in a Gaussian density of states distribution. The electron transport on the other hand is orders of magnitude lower than the hole transport. The reason is that electron transport is hindered by the presence of a universal electron trap, located at 3.6 eV below vacuum with a typical density of ca. 3 × 10¹⁷ cm⁻³. The trapped electrons recombine with free holes via a non-radiative trap-assisted recombination process, which is a competing loss process with respect to the emissive bimolecular Langevin recombination. The trap-assisted recombination in disordered organic semiconductors is governed by the diffusion of the free carrier (hole) towards the trapped carrier (electron), similar to the Langevin recombination of free carriers where both carriers are mobile. As a result, with the charge-carrier mobilities and amount of trapping centers known from charge-transport measurements, the radiative recombination as well as loss processes in disordered organic semiconductors can be fully predicted. Evidently, future work should focus on the identification and removing of electron traps. This will not only eliminate the non-radiative trap-assisted recombination, but, in addition, will shift the recombination zone towards the center of the device, leading to an efficiency improvement of more than a factor of two in single-layer polymer LEDs. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Selective resolution of photocurrent generating pathways in transition metal dichalcogenides by ultrafast microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Graham, Matthew W.

2017-02-01

Presently, there exists no reliable in-situ time-resolved method that selectively isolates both the recombination and escape times relevant to photocurrent generation in the ultrafast regime. Transport based measurements lack the required time resolution, while purely optical measurement give a convoluted weighted-average of all electronic dynamics, offering no selectivity for photocurrent generating pathways. Recently, the ultrafast photocurrent (U-PC) autocorrelation method has successfully measured the rate limiting electronic relaxation processes in materials such as graphene, carbon nanotubes, and transition metal dichalcogenide (TMD) materials. Here, we unambiguously derive and experimentally confirm a generic U-PC response function by simultaneously resolving the transient absorption (TA) and U-PC response for highly-efficient (48% IQE at 0 bias) WSe2 devices and twisted bilayer graphene. Surprisingly, both optical TA and electrical U-PC responses give the same E-field-dependent electronic escape and recombination rates. These rates further accurately quantify a material's intrinsic PC generation efficiency. We demonstrate that the chirality of the incident light impacts the U-PC kinetics, suggesting such measurements directly access the ultrafast dynamics need to complex electronic physics such as the valley-Hall effect. By combining E-field dependent ultrafast photocurrent with transient absorption microscopy, we have selectively imaged the dominant kinetic bottlenecks that inhibit photocurrent production in devices made from stacked few-layer TMD materials. This provides a new methodology to intelligently select materials that intrinsically avoid recombination bottlenecks and maximize photocurrent yield.

The importance of band tail recombination on current collection and open-circuit voltage in CZTSSe solar cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moore, James E.; Purdue University, West Lafayette, Indiana 47907; Hages, Charles J.

2016-07-11

Cu{sub 2}ZnSn(S,Se){sub 4} (CZTSSe) solar cells typically exhibit high short-circuit current density (J{sub sc}), but have reduced cell efficiencies relative to other thin film technologies due to a deficit in the open-circuit voltage (V{sub oc}), which prevent these devices from becoming commercially competitive. Recent research has attributed the low V{sub oc} in CZTSSe devices to small scale disorder that creates band tail states within the absorber band gap, but the physical processes responsible for this V{sub oc} reduction have not been elucidated. In this paper, we show that carrier recombination through non-mobile band tail states has a strong voltage dependencemore » and is a significant performance-limiting factor, and including these effects in simulation allows us to simultaneously explain the V{sub oc} deficit, reduced fill factor, and voltage-dependent quantum efficiency with a self-consistent set of material parameters. Comparisons of numerical simulations to measured data show that reasonable values for the band tail parameters (characteristic energy, capture rate) can account for the observed low V{sub oc}, high J{sub sc}, and voltage dependent collection efficiency. These results provide additional evidence that the presence of band tail states accounts for the low efficiencies of CZTSSe solar cells and further demonstrates that recombination through non-mobile band tail states is the dominant efficiency limiting mechanism.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meusel, O., E-mail: o.meusel@iap.uni-frankfurt.de; Droba, M.; Noll, D.

The transport of intense ion beams is affected by the collective behavior of this kind of multi-particle and multi-species system. The space charge expressed by the generalized perveance dominates the dynamical process of thermalisation, which leads to emittance growth. To prevent changes of intrinsic beam properties and to reduce the intensity dependent focusing forces, space charge compensation seems to be an adequate solution. In the case of positively charged ion beams, electrons produced by residual gas ionization and secondary electrons provide the space charge compensation. The influence of the compensation particles on the beam transport and the local degree ofmore » space charge compensation is given by different beam properties as well as the ion beam optics. Especially for highly charged ion beams, space charge compensation in combination with poor vacuum conditions leads to recombination processes and therefore increased beam losses. Strategies for providing a compensation-electron reservoir at very low residual gas pressures will be discussed.« less

Ultrafast carrier dynamics of titanic acid nanotubes investigated by transient absorption spectroscopy.

PubMed

Wang, Li; Zhao, Hui; Pan, Lin Yun; Weng, Yu Xiang; Nakato, Yoshihiro; Tamai, Naoto

2010-12-01

Carrier dynamics of titanic acid nanotubes (phase of H2Ti2O5.H2O) deposited on a quartz plate was examined by visible/near-IR transient absorption spectroscopy with an ultraviolet excitation. The carrier dynamics of titanic acid nanotubes follows the fast trapping process which attributed to the intrinsic tubular structure, the relaxation of shallow trapped carriers and the recombination as a second-order kinetic process. Transient absorption of titanic acid nanotubes was dominated by the absorption of surface-trapped holes in visible region around 500 nm, which was proved by the faster decay dynamics in the presence of polyvinyl alcohol as a hole-scavenger. However, the slow relaxation of free carriers was much more pronounced in the TiO2 single crystals, as compared with the transient absorption spectra of titanic acid nanotubes under the similar excitation.

RPA homologs and ssDNA processing during meiotic recombination.

PubMed

Ribeiro, Jonathan; Abby, Emilie; Livera, Gabriel; Martini, Emmanuelle

2016-06-01

Meiotic homologous recombination is a specialized process that involves homologous chromosome pairing and strand exchange to guarantee proper chromosome segregation and genetic diversity. The formation and repair of DNA double-strand breaks (DSBs) during meiotic recombination differs from those during mitotic recombination in that the homologous chromosome rather than the sister chromatid is the preferred repair template. The processing of single-stranded DNA (ssDNA) formed on intermediate recombination structures is central to driving the specific outcomes of DSB repair during meiosis. Replication protein A (RPA) is the main ssDNA-binding protein complex involved in DNA metabolism. However, the existence of RPA orthologs in plants and the recent discovery of meiosis specific with OB domains (MEIOB), a widely conserved meiosis-specific RPA1 paralog, strongly suggest that multiple RPA complexes evolved and specialized to subdivide their roles during DNA metabolism. Here we review ssDNA formation and maturation during mitotic and meiotic recombination underlying the meiotic specific features. We describe and discuss the existence and properties of MEIOB and multiple RPA subunits in plants and highlight how they can provide meiosis-specific fates to ssDNA processing during homologous recombination. Understanding the functions of these RPA homologs and how they interact with the canonical RPA subunits is of major interest in the fields of meiosis and DNA repair.

Effect of sex, age, and breed on genetic recombination features in cattle

USDA-ARS?s Scientific Manuscript database

Meiotic recombination is a fundamental biological process which generates genetic diversity, affects fertility, and influences evolvability. Here we investigate the roles of sex, age, and breed in cattle recombination features, including recombination rate, location and crossover interference. Usin...

Comparative genomic analysis reveals occurrence of genetic recombination in virulent Cryptosporidium hominis subtypes and telomeric gene duplications in Cryptosporidium parvum.

PubMed

Guo, Yaqiong; Tang, Kevin; Rowe, Lori A; Li, Na; Roellig, Dawn M; Knipe, Kristine; Frace, Michael; Yang, Chunfu; Feng, Yaoyu; Xiao, Lihua

2015-04-18

Cryptosporidium hominis is a dominant species for human cryptosporidiosis. Within the species, IbA10G2 is the most virulent subtype responsible for all C. hominis-associated outbreaks in Europe and Australia, and is a dominant outbreak subtype in the United States. In recent yearsIaA28R4 is becoming a major new subtype in the United States. In this study, we sequenced the genomes of two field specimens from each of the two subtypes and conducted a comparative genomic analysis of the obtained sequences with those from the only fully sequenced Cryptosporidium parvum genome. Altogether, 8.59-9.05 Mb of Cryptosporidium sequences in 45-767 assembled contigs were obtained from the four specimens, representing 94.36-99.47% coverage of the expected genome. These genomes had complete synteny in gene organization and 96.86-97.0% and 99.72-99.83% nucleotide sequence similarities to the published genomes of C. parvum and C. hominis, respectively. Several major insertions and deletions were seen between C. hominis and C. parvum genomes, involving mostly members of multicopy gene families near telomeres. The four C. hominis genomes were highly similar to each other and divergent from the reference IaA25R3 genome in some highly polymorphic regions. Major sequence differences among the four specimens sequenced in this study were in the 5' and 3' ends of chromosome 6 and the gp60 region, largely the result of genetic recombination. The sequence similarity among specimens of the two dominant outbreak subtypes and genetic recombination in chromosome 6, especially around the putative virulence determinant gp60 region, suggest that genetic recombination plays a potential role in the emergence of hyper-transmissible C. hominis subtypes. The high sequence conservation between C. parvum and C. hominis genomes and significant differences in copy numbers of MEDLE family secreted proteins and insulinase-like proteases indicate that telomeric gene duplications could potentially contribute to host expansion in C. parvum.

Mapping of a gene for autosomal dominant juvenile-onset open-angle glaucoma to chromosome 1 q

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richards, J.E.; Lichter, P.R.; Torrez, D.

1994-01-01

A large Caucasian family is presented, in which a juvenile-onset form of open-angle glaucoma is transmitted in an autosomal dominant fashion. Sixteen affected family members were identified from 31 at-risk individuals descended from the affected founder. Affected patients developed high intraocular pressures (sometimes >40 mm Hg) within the first 2 decades of life. Linkage analysis between the disease phenotype and 12 microsatellite repeat markers located on chromosome 1 q gave a maximum lod score of 8.38 at a recombination fraction of zero for marker D1S210. Analysis of recombinant haplotypes suggests a total inclusion region of about 14 cM between markersmore » D1S194 and D1S218 at 1q21-q31. This represents the second juvenile-glaucoma family, in which the disease has been mapped to the long arm of chromosome 1. 57 refs., 2 figs., 3 tabs.« less

Determining the linkage of disease-resistance genes to molecular markers: the LOD-SCORE method revisited with regard to necessary sample sizes.

PubMed

Hühn, M

1995-05-01

Some approaches to molecular marker-assisted linkage detection for a dominant disease-resistance trait based on a segregating F2 population are discussed. Analysis of two-point linkage is carried out by the traditional measure of maximum lod score. It depends on (1) the maximum-likelihood estimate of the recombination fraction between the marker and the disease-resistance gene locus, (2) the observed absolute frequencies, and (3) the unknown number of tested individuals. If one replaces the absolute frequencies by expressions depending on the unknown sample size and the maximum-likelihood estimate of recombination value, the conventional rule for significant linkage (maximum lod score exceeds a given linkage threshold) can be resolved for the sample size. For each sub-population used for linkage analysis [susceptible (= recessive) individuals, resistant (= dominant) individuals, complete F2] this approach gives a lower bound for the necessary number of individuals required for the detection of significant two-point linkage by the lod-score method.

Biophysical characterization and immunization studies of dominant negative inhibitor (DNI), a candidate anthrax toxin subunit vaccine.

PubMed

Iyer, Vidyashankara; Hu, Lei; Schanté, Carole E; Vance, David; Chadwick, Chrystal; Jain, Nishant Kumar; Brey, Robert N; Joshi, Sangeeta B; Volkin, David B; Andra, Kiran K; Bann, James G; Mantis, Nicholas J; Middaugh, C Russell

2013-11-01

Dominant Negative Inhibitor (DNI) is a translocation-deficient homolog of recombinant protective antigen of Bacillus anthracis that is a candidate for a next generation anthrax vaccine. This study demonstrates that the biophysical characteristics of the DNI protein stored in lyophilized form at 4°C for 8 y were similar to recombinant Protective Antigen (rPA). To provide information on the accelerated stability of DNI, samples in the lyophilized form were subjected to thermal stress (40°C and 70°C for up to 4 weeks) and thoroughly evaluated using various biophysical and chemical characterization techniques. Results demonstrate preserved structural stability of the DNI protein under extreme conditions, suggesting long-term stability can be achieved for a vaccine that employs DNI, as desired for a biodefense countermeasure. Furthermore, the biological activity of the stressed DNI bound to the adjuvant Alhydrogel (®) was evaluated in mice and it was found that the immunogenicity DNI was not affected by thermal stress.

Mutation mechanisms that underlie turnover of a human telomere-adjacent segmental duplication containing an unstable minisatellite.

PubMed

Hills, Mark; Jeyapalan, Jennie N; Foxon, Jennifer L; Royle, Nicola J

2007-04-01

Subterminal regions, juxtaposed to telomeres on human chromosomes, contain a high density of segmental duplications, but relatively little is known about the evolutionary processes that underlie sequence turnover in these regions. We have characterized a segmental duplication adjacent to the Xp/Yp telomere, each copy containing a hypervariable array of the DXYS14 minisatellite. Both DXYS14 repeat arrays mutate at a high rate (0.3 and 0.2% per gamete) but linkage disequilibrium analysis across 27 SNPs and a direct crossover assay show that recombination during meiosis is suppressed. Therefore instability at DXYS14a and b is dominated by intra-allelic processes or possibly conversion limited to the repeat arrays. Furthermore some chromosomes (14%) carry only one copy of the duplicon, including one DXYS14 repeat array that is also highly mutable (1.2% per gamete). To explain these and other observations, we propose there is another low-rate mutation process that causes copy number change in part or all of the duplicon.

On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity.

PubMed

Renzette, Nicholas; Kowalik, Timothy F; Jensen, Jeffrey D

2016-01-01

A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, although these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analysing the relationship among intraspecies diversity, interspecies divergence and rates of recombination. We show that there is a strong correlation between diversity and divergence, consistent with expectations of neutral evolution. However, after correcting for divergence, there remains a significant correlation between intraspecies diversity and recombination rates, with additional analyses suggesting that this correlation is largely due to the effects of background selection. In addition, a small number of loci, centred on long noncoding RNAs, also show evidence of selective sweeps. These data suggest that HCMV evolution is dominated by neutral mechanisms as well as background selection, expanding our understanding of linked selection to a novel class of organisms. © 2015 John Wiley & Sons Ltd.

Quantum tunneling recombination in a system of randomly distributed trapped electrons and positive ions.

PubMed

Pagonis, Vasilis; Kulp, Christopher; Chaney, Charity-Grace; Tachiya, M

2017-09-13

During the past 10 years, quantum tunneling has been established as one of the dominant mechanisms for recombination in random distributions of electrons and positive ions, and in many dosimetric materials. Specifically quantum tunneling has been shown to be closely associated with two important effects in luminescence materials, namely long term afterglow luminescence and anomalous fading. Two of the common assumptions of quantum tunneling models based on random distributions of electrons and positive ions are: (a) An electron tunnels from a donor to the nearest acceptor, and (b) the concentration of electrons is much lower than that of positive ions at all times during the tunneling process. This paper presents theoretical studies for arbitrary relative concentrations of electrons and positive ions in the solid. Two new differential equations are derived which describe the loss of charge in the solid by tunneling, and they are solved analytically. The analytical solution compares well with the results of Monte Carlo simulations carried out in a random distribution of electrons and positive ions. Possible experimental implications of the model are discussed for tunneling phenomena in long term afterglow signals, and also for anomalous fading studies in feldspars and apatite samples.

Factors influencing photoluminescence and photocarrier lifetime in CdSeTe/CdMgTe double heterostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swartz, Craig H.; Zaunbrecher, K. N.; Sohal, S.

2016-10-28

CdSeTe/CdMgTe double heterostructures were produced with both n-type and unintentionally doped absorber layers. Measurements of the dependence of photoluminescence intensity on excitation intensity were carried out, as well as measurements of time-resolved photoluminescence decay after an excitation pulse. It was found that decay times under very low photon injection conditions are dominated by a non-radiative Shockley-Read-Hall process described using a recombination center with an asymmetric capture cross section, where the cross section for holes is larger than that for electrons. As a result of the asymmetry, the center effectively extends photoluminescence decay by a hole trapping phenomenon. A reduction inmore » electron capture cross section appeared at doping densities over 10 16cm -3. An analysis of the excitation intensity dependence of room temperature photoluminescence revealed a strong relationship with doping concentration. Here, this allows estimates of the carrier concentration to be made through a non-destructive optical method. Iodine was found to be an effective n-type dopant for CdTe, allowing controllable carrier concentrations without an increased rate of non-radiative recombination.« less

Overexpression of dominant negative PARP interferes with tumor formation of HeLa cells in nude mice: evidence for increased tumor cell apoptosis in vivo.

PubMed

Hans, M A; Müller, M; Meyer-Ficca, M; Bürkle, A; Küpper, J H

1999-11-25

Poly(ADP-ribose) polymerase (PARP4) catalyzes the formation of ADP-ribose polymers covalently attached to proteins by using NAD+ as substrate. PARP is strongly activated by DNA single- or double-strand breaks and is thought to be involved in cellular responses to DNA damage. We characterized a dominant negative PARP mutant, i.e. the DNA-binding domain of this enzyme, whose overexpression in cells leads to increased genetic instability following DNA damage. In order to study whether PARP activity is also implicated in the process of tumorigenesis, we generated stably transfected HeLa cell clones with constitutive overexpression of dominant negative PARP and investigated tumor formation of these clones in nude mice. We found that inhibition of PARP activity dramatically reduces tumor forming ability of HeLa cells. Moreover, we provide strong evidence that the observed reduction in tumor forming ability is due to increased tumor cell apoptosis in vivo. Viewed together, our data and those from other groups show that inhibition of PARP enzyme activity interferes with DNA base excision repair and leads to increased genetic instability and recombination but, on the other hand, can sensitize cells to apoptotic stimuli and by this mechanism may prevent tumor formation.

SUPPRESSOR OF APICAL DOMINANCE1 of Sporisorium reilianum Modulates Inflorescence Branching Architecture in Maize and Arabidopsis1[OPEN

PubMed Central

Ghareeb, Hassan; Löfke, Christian; Teichmann, Thomas; Schirawski, Jan

2015-01-01

The biotrophic fungus Sporisorium reilianum causes head smut of maize (Zea mays) after systemic plant colonization. Symptoms include the formation of multiple female inflorescences at subapical nodes of the stalk because of loss of apical dominance. By deletion analysis of cluster 19-1, the largest genomic divergence cluster in S. reilianum, we identified a secreted fungal effector responsible for S. reilianum-induced loss of apical dominance, which we named SUPPRESSOR OF APICAL DOMINANCE1 (SAD1). SAD1 transcript levels were highly up-regulated during biotrophic fungal growth in all infected plant tissues. SAD1-green fluorescent protein fusion proteins expressed by recombinant S. reilianum localized to the extracellular hyphal space. Transgenic Arabidopsis (Arabidopsis thaliana)-expressing green fluorescent protein-SAD1 displayed an increased number of secondary rosette-leaf branches. This suggests that SAD1 manipulates inflorescence branching architecture in maize and Arabidopsis through a conserved pathway. Using a yeast (Saccharomyces cerevisiae) two-hybrid library of S. reilianum-infected maize tissues, we identified potential plant interaction partners that had a predicted function in ubiquitination, signaling, and nuclear processes. Presence of SAD1 led to an increase of the transcript levels of the auxin transporter PIN-FORMED1 in the root and a reduction of the branching regulator TEOSINTE BRANCHED1 in the stalk. This indicates a role of SAD1 in regulation of apical dominance by modulation of branching through increasing transcript levels of the auxin transporter PIN1 and derepression of bud outgrowth. PMID:26511912

Anomalous charge storage exponents of organic bulk heterojunction solar cells.

NASA Astrophysics Data System (ADS)

Nair, Pradeep; Dwivedi, Raaz; Kumar, Goutam; Dept of Electrical Engineering, IIT Bombay Team

2013-03-01

Organic bulk heterojunction (BHJ) devices are increasingly being researched for low cost solar energy conversion. The efficiency of such solar cells is dictated by various recombination processes involved. While it is well known that the ideality factor and hence the charge storage exponents of conventional PN junction diodes are influenced by the recombination processes, the same aspects are not so well understood for organic solar cells. While dark currents of such devices typically show an ideality factor of 1 (after correcting for shunt resistance effects, if any), surprisingly, a wide range of charge storage exponents for such devices are reported in literature alluding to apparent concentration dependence for bi-molecular recombination rates. In this manuscript we critically analyze the role of bi-molecular recombination processes on charge storage exponents of organic solar cells. Our results indicate that the charge storage exponents are fundamentally influenced by the electrostatics and recombination processes and can be correlated to the dark current ideality factors. We believe that our findings are novel, and advance the state-of the art understanding on various recombination processes that dictate the performance limits of organic solar cells. The authors would like to thank the Centre of Excellence in Nanoelectronics (CEN) and the National Centre for Photovoltaic Research and Education (NCPRE), IIT Bombay for computational and financial support

Collisional-radiative model including recombination processes for W27+ ion★

NASA Astrophysics Data System (ADS)

Murakami, Izumi; Sasaki, Akira; Kato, Daiji; Koike, Fumihiro

2017-10-01

We have constructed a collisional-radiative (CR) model for W27+ ions including 226 configurations with n ≤ 9 and ł ≤ 5 for spectroscopic diagnostics. We newly include recombination processes in the model and this is the first result of extreme ultraviolet spectrum calculated for recombining plasma component. Calculated spectra in 40-70 Å range in ionizing and recombining plasma components show similar 3 strong lines and 1 line weak in recombining plasma component at 45-50 Å and many weak lines at 50-65 Å for both components. Recombination processes do not contribute much to the spectrum at around 60 Å for W27+ ion. Dielectronic satellite lines are also minor contribution to the spectrum of recombining plasma component. Dielectronic recombination (DR) rate coefficient from W28+ to W27+ ions is also calculated with the same atomic data in the CR model. We found that larger set of energy levels including many autoionizing states gave larger DR rate coefficients but our rate agree within factor 6 with other works at electron temperature around 1 keV in which W27+ and W28+ ions are usually observed in plasmas. Contribution to the Topical Issue "Atomic and Molecular Data and their Applications", edited by Gordon W.F. Drake, Jung-Sik Yoon, Daiji Kato, and Grzegorz Karwasz.

Identification of Novel Recombinant Forms of Hepatitis B Virus Generated from Genotypes Ae and G in HIV-1-Positive Japanese Men Who Have Sex with Men.

PubMed

Kojima, Yoko; Kawahata, Takuya; Mori, Haruyo; Furubayashi, Keiichi; Taniguchi, Yasushi; Itoda, Ichiro; Komano, Jun

2015-07-01

The rare hepatitis B virus (HBV) genotype G (HBV/G) coinfects HIV-1-positive individuals along with HBV/A and generates recombinants. However, the circulation of HBV A/G recombinants remains poorly understood. This molecular epidemiologic study examined HBV A/G recombinants in Japanese HIV-1-positive men who have sex with men (MSM). Initially, blood specimens submitted for confirmatory tests of HIV infection in Osaka and Tokyo, Japan, from 2006 to 2013 were examined for HIV-1, and HIV-1-positive specimens were screened for HBV. Among 817 specimens from HIV-1-positive individuals, HBsAg was detected in 59 specimens; of these, HBV/Ae (alternatively A2), a subgenotype of HBV/A prevalent in Europe and North America, was identified in 70.2%, HBV/C in 17.5%, and HBV/G in 10.5%, and HBV/E in 1.8% according to the core gene sequence. The full-length genome analysis of HBV was performed on HBV/G-positive specimens because some HBV A/G recombinants were historically overlooked by genotyping based on a partial genome analysis. It revealed that five of the specimens contained novel Ae/G recombinants, the core gene of which had a high sequence similarity to HBV/G. Detailed analyses showed that novel recombinants were coinfected with HBV/Ae in a recombinant-dominant fashion. No major drug-resistant mutations were found in the newly identified HBV Ae/G recombinants. Some of the individuals asymptomatically coinfected with HIV/HBV suffered mild liver injury. This study demonstrated that novel Ae/G HBV recombinants were identified in Japanese HIV-1-positive MSM. The pathogenicity of novel HBV Ae/G recombinants should be examined in a future longitudinal study. Surveillance of such viruses in HIV-1-positive individuals should be emphasized.

Luminescence in Conjugated Molecular Materials under Sub-bandgap Excitation

DOE Office of Scientific and Technical Information (OSTI.GOV)

So, Franky

2014-05-08

Light emission in semiconductors occurs when they are under optical and electrical excitation with energy larger than the bandgap energy. In some low-dimensional semiconductor heterostructure systems, this thermodynamic limit can be violated due to radiative Auger recombination (AR), a process in which the sub-bandgap energy released from a recombined electron-hole pair is transferred to a third particle leading to radiative band-to-band recombination.1 Thus far, photoluminescence up-conversion phenomenon has been observed in some low dimensional semiconductor systems, and the effect is very weak and it can only be observed at low temperatures. Recently, we discovered that efficient electroluminescence in poly[2-methoxy-5-(2’-ethylhexyloxy)-1, phenylenevinylene]more » (MEH-PPV) polymer light-emitting devices (PLEDs) at drive voltages below its bandgap voltage could be observed when a ZnO nanoparticles (NPs) electron injection layer was inserted between the polymer and the aluminum electrode. Specifically, emitted photons with energy of 2.13 eV can be detected at operating voltages as low as 1.2 V at room temperature. Based on these data, we propose that the sub-bandgap turn-on in the MEH-PPV device is due to an Auger-assisted energy up-conversion process. The significance of this discovery is three-fold. First, radiative recombination occurs at operating voltages below the thermodynamic bandgap voltage. This process can significantly reduce the device operating voltage. For example, the current density of the device with the ZnO NC layer is almost two orders of magnitude higher than that of the device without the NC layer. Second, a reactive metal is no longer needed for the cathode. Third, this electroluminescence up-conversion process can be applied to inorganic semiconductors systems as well and their operation voltages of inorganic LEDs can be reduced to about half of the bandgap energy. Based on our initial data, we propose that the sub-bandgap turn-on in MEH-PPV devices is due to Auger-assisted energy up-conversion process. Specifically, we propose that the up-conversion process is due to charge accumulation at the polymer/NPs interface. This model requires that holes should be the dominant carriers in the polymer and the polymer/ZnO NCs heterojunction should be a type II alignment. In order to determine the mechanism of the up-conversion process, we will characterize devices fabricated using polymers with different carrier transporting properties to determine whether hole accumulation at the polymer/nanocrystals is required. Likewise, we will also use NPs with different electronic structures to fabricate devices to determine how electron accumulation affects the up-conversion process. Finally, we will measure quantitatively the interface charge accumulation by electroabsorption and correlate the results with the up-conversion photoluminescence efficiency measurements under an applied electric field.« less

A set of recombinant antigens from Echinococcus granulosus with potential for use in the immunodiagnosis of human cystic hydatid disease

PubMed Central

VIRGINIO, V G; HERNÁNDEZ, A; ROTT, M B; MONTEIRO, K M; ZANDONAI, A F; NIETO, A; ZAHA, A; FERREIRA, H B

2003-01-01

Several recombinant clones expressing antigens from Echinococcus granulosus were isolated previously from a parasite cDNA library using cystic hydatid disease (CHD) patients’ sera or rabbit hyperimmune antiserum against a lipoproteic fraction from bovine cyst fluid. Six of these antigens were expressed in Escherichia coli and the purified recombinant proteins were tested in enzyme-linked immunosorbent assay (ELISA) for specific IgG with a panel of sera from patients with surgically confirmed (n = 58) or immunologically diagnosed (n = 71) CHD. Sera from clinically normal individuals (n = 203) and sera from individuals with other helminthic infections (n = 65) were assayed for the assessment of specificity. A cut-off value was determined by receiver-operating-characteristic plots for each antigen. A recombinant antigen B subunit (AgB8/2) presented the highest sensitivity (93·1%), considering the group of sera from patients with CHD surgically confirmed, and specificity (99·5%) and is proposed as the basis for an immunodiagnostic test. The other recombinant antigens tested presented sensitivities between 58·6% and 89·7%, and three of them were considered of complementary value. In subclass-specific ELISA, different IgG isotypes showed dominance in the response for each of the recombinant antigens. There was a clear predominance of IgG4 response for all antigens tested, indicating that this would be the subclass of choice to be assessed for these recombinant proteins. PMID:12699422

Diversification of Orientia tsutsugamushi genotypes by intragenic recombination and their potential expansion in endemic areas

PubMed Central

Kim, Gwanghun; Ha, Na-Young; Min, Chan-Ki; Kim, Hong-Il; Yen, Nguyen Thi Hai; Lee, Keun-Hwa; Oh, Inbo; Kang, Jae-Seung; Choi, Myung-Sik; Kim, Ik-Sang

2017-01-01

Background Scrub typhus is a mite-borne febrile disease caused by O. tsutsugamushi infection. Recently, emergence of scrub typhus has attracted considerable attention in several endemic countries in Asia and the western Pacific. In addition, the antigenic diversity of the intracellular pathogen has been a serious obstacle for developing effective diagnostics and vaccine. Methodology/Principal findings To understand the evolutionary pathway of genotypic diversification of O. tsutsugamushi and the environmental factors associated with the epidemiological features of scrub typhus, we analyzed sequence data, including spatiotemporal information, of the tsa56 gene encoding a major outer membrane protein responsible for antigenic variation. A total of 324 tsa56 sequences covering more than 85% of its open reading frame were analyzed and classified into 17 genotypes based on phylogenetic relationship. Extensive sequence analysis of tsa56 genes using diverse informatics tools revealed multiple intragenic recombination events, as well as a substantially higher mutation rate than other house-keeping genes. This suggests that genetic diversification occurred via frequent point mutations and subsequent genetic recombination. Interestingly, more diverse bacterial genotypes and dominant vector species prevail in Taiwan compared to other endemic regions. Furthermore, the co-presence of identical and sub-identical clones of tsa56 gene in geographically distant areas implies potential spread of O. tsutsugamushi genotypes. Conclusions/Significance Fluctuation and diversification of vector species harboring O. tsutsugamushi in local endemic areas may facilitate genetic recombination among diverse genotypes. Therefore, careful monitoring of dominant vector species, as well as the prevalence of O. tsutsugamushi genotypes may be advisable to enable proper anticipation of epidemiological changes of scrub typhus. PMID:28248956

Recombinant protein production and insect cell culture and process

NASA Technical Reports Server (NTRS)

Spaulding, Glenn (Inventor); Prewett, Tacey (Inventor); Goodwin, Thomas (Inventor); Francis, Karen (Inventor); Andrews, Angela (Inventor); Oconnor, Kim (Inventor)

1993-01-01

A process has been developed for recombinant production of selected polypeptides using transformed insect cells cultured in a horizontally rotating culture vessel modulated to create low shear conditions. A metabolically transformed insect cell line is produced using the culture procedure regardless of genetic transformation. The recombinant polypeptide can be produced by an alternative process using the cultured insect cells as host for a virus encoding the described polypeptide such as baculovirus. The insect cells can also be a host for viral production.

Recombinant Protein Production and Insect Cell Culture and Process

NASA Technical Reports Server (NTRS)

Spaulding, Glenn F. (Inventor); Goodwin, Thomas J. (Inventor); OConnor, Kim C. (Inventor); Francis, Karen M. (Inventor); Andrews, Angela D. (Inventor); Prewett, Tracey L. (Inventor)

1997-01-01

A process has been developed for recombinant production of selected polypeptides using transformed insect cells cultured in a horizontally rotating culture vessel modulated to create low shear conditions. A metabolically transformed insect cell line is produced using the culture procedure regardless of genetic transformation. The recombinant polypeptide can be produced by an alternative process using virtually infected or stably transformed insect cells containing a gene encoding the described polypeptide. The insect cells can also be a host for viral production.

Recombinant microorganisms for increased production of organic acids

DOEpatents

Yi, Jian [East Lansing, MI; Kleff, Susanne [East Lansing, MI; Guettler, Michael V [Holt, MI

2012-02-21

Disclosed are recombinant microorganisms for producing organic acids. The recombinant microorganisms express a polypeptide that has the enzymatic activity of an enzyme that is utilized in the pentose phosphate cycle. The recombinant microorganism may include recombinant Actinobacillus succinogenes that has been transformed to express a Zwischenferment (Zwf) gene. The recombinant microorganisms may be useful in fermentation processes for producing organic acids such as succinic acid and lactic acid. Also disclosed are novel plasmids that are useful for transforming microorganisms to produce recombinant microorganisms that express enzymes such as Zwf.

Recombinant microorganisms for increased production of organic acids

DOEpatents

Yi, Jian; Kleff, Susanne; Guettler, Michael V

2013-04-30

Disclosed are recombinant microorganisms for producing organic acids. The recombinant microorganisms express a polypeptide that has the enzymatic activity of an enzyme that is utilized in the pentose phosphate cycle. The recombinant microorganism may include recombinant Actinobacillus succinogenes that has been transformed to express a Zwischenferment (Zwf) gene. The recombinant microorganisms may be useful in fermentation processes for producing organic acids such as succinic acid and lactic acid. Also disclosed are novel plasmids that are useful for transforming microorganisms to produce recombinant microorganisms that express enzymes such as Zwf.

Break-induced replication and recombinational telomere elongation in yeast.

PubMed

McEachern, Michael J; Haber, James E

2006-01-01

When a telomere becomes unprotected or if only one end of a chromosomal double-strand break succeeds in recombining with a template sequence, DNA can be repaired by a recombination-dependent DNA replication process termed break-induced replication (BIR). In budding yeasts, there are two BIR pathways, one dependent on the Rad51 recombinase protein and one Rad51 independent; these two repair processes lead to different types of survivors in cells lacking the telomerase enzyme that is required for normal telomere maintenance. Recombination at telomeres is triggered by either excessive telomere shortening or disruptions in the function of telomere-binding proteins. Telomere elongation by BIR appears to often occur through a "roll and spread" mechanism. In this process, a telomeric circle produced by recombination at a dysfunctional telomere acts as a template for a rolling circle BIR event to form an elongated telomere. Additional BIR events can then copy the elongated sequence to all other telomeres.

Substrate nitridation induced modulations in transport properties of wurtzite GaN/p-Si (100) heterojunctions grown by molecular beam epitaxy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhat, Thirumaleshwara N.; Rajpalke, Mohana K.; Krupanidhi, S. B.

Phase pure wurtzite GaN films were grown on Si (100) substrates by introducing a silicon nitride layer followed by low temperature GaN growth as buffer layers. GaN films grown directly on Si (100) were found to be phase mixtured, containing both cubic ({beta}) and hexagonal ({alpha}) modifications. The x-ray diffraction (XRD), scanning electron microscopy (SEM), photoluminescence (PL) spectroscopy studies reveal that the significant enhancement in the structural as well as in the optical properties of GaN films grown with silicon nitride buffer layer grown at 800 deg. C when compared to the samples grown in the absence of silicon nitridemore » buffer layer and with silicon nitride buffer layer grown at 600 deg. C. Core-level photoelectron spectroscopy of Si{sub x}N{sub y} layers reveals the sources for superior qualities of GaN epilayers grown with the high temperature substrate nitridation process. The discussion has been carried out on the typical inverted rectification behavior exhibited by n-GaN/p-Si heterojunctions. Considerable modulation in the transport mechanism was observed with the nitridation conditions. The heterojunction fabricated with the sample of substrate nitridation at high temperature exhibited superior rectifying nature with reduced trap concentrations. Lowest ideality factors ({approx}1.5) were observed in the heterojunctions grown with high temperature substrate nitridation which is attributed to the recombination tunneling at the space charge region transport mechanism at lower voltages and at higher voltages space charge limited current conduction is the dominating transport mechanism. Whereas, thermally generated carrier tunneling and recombination tunneling are the dominating transport mechanisms in the heterojunctions grown without substrate nitridation and low temperature substrate nitridation, respectively.« less

X-linked dominant retinitis pigmentosa in an American family

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGuire, R.E.; Daiger, S.P.; Blanton, S.H.

1994-09-01

Retinitis pigmentosa is a genetically heterogeneous disease with autosomal dominant (adRP), autosomal recessive and X-linked forms. At least 3 forms of X-linked retinitis pigmentosa have been reported: RP2 which maps to Xp11.4-p 11.23, RP3 which maps to Xp21.1 and RP6, which maps to Xp21.3-p21.1. The X-linked forms of retinitis pigmentosa are generally considered to be recessive as female carriers are not affected or are much less affected than males. Here we report a five generation American family with X-linked retinitis pigmentosa in which both males and females are significantly affected. The disease locus in this family appears to be distinctmore » from RP2 and RP3. The American family (UTAD054) presents with early-onset retinitis pigmentosa. The family appeared to fit an autosomal dominant pattern; however, linkage testing excluded all known adRP loci. Absence of male-to-male transmission in the pedigree suggested the possibility of X-linked dominant inheritance. Thus we tested six microsatellite markers that map to Xp (DXS987, DXS989, DXS993, DXS999, DXS1003 and DXS1110). Of these, DXS989 showed tight linkage with one allele (199) showing a 100% concordance with disease status. The odds favoring an X-linked dominant mode of inheritance in this family, versus autosomal dominant, are 10{sup 5}:1. In addition, recombinations for DXS999, and dXS1110, the two markers flanking DXS989, were observed in affected individuals. These data map the disease locus in this family to a 9 mb region on the X chromosome between Xp22.11 and Xp21.41. In addition, the recombinant individuals exclude close linkage to RP2 and RP3. The observance of high penetrance in females indicates that this family has X-linked dominant retinitis pigmentosa. We suggest that this mode of inheritance should be considered in other families with dominant retinitis pigmentosa but an absence of male-to-male transmission.« less

Progressive Recombination Suppression and Differentiation in Recently Evolved Neo-sex Chromosomes

PubMed Central

Natri, Heini M.; Shikano, Takahito; Merilä, Juha

2013-01-01

Recombination suppression leads to the structural and functional differentiation of sex chromosomes and is thus a crucial step in the process of sex chromosome evolution. Despite extensive theoretical work, the exact processes and mechanisms of recombination suppression and differentiation are not well understood. In threespine sticklebacks (Gasterosteus aculeatus), a different sex chromosome system has recently evolved by a fusion between the Y chromosome and an autosome in the Japan Sea lineage, which diverged from the ancestor of other lineages approximately 2 Ma. We investigated the evolutionary dynamics and differentiation processes of sex chromosomes based on comparative analyses of these divergent lineages using 63 microsatellite loci. Both chromosome-wide differentiation patterns and phylogenetic inferences with X and Y alleles indicated that the ancestral sex chromosomes were extensively differentiated before the divergence of these lineages. In contrast, genetic differentiation appeared to have proceeded only in a small region of the neo-sex chromosomes. The recombination maps constructed for the Japan Sea lineage indicated that recombination has been suppressed or reduced over a large region spanning the ancestral and neo-sex chromosomes. Chromosomal regions exhibiting genetic differentiation and suppressed or reduced recombination were detected continuously and sequentially in the neo-sex chromosomes, suggesting that differentiation has gradually spread from the fusion point following the extension of recombination suppression. Our study illustrates an ongoing process of sex chromosome differentiation, providing empirical support for the theoretical model postulating that recombination suppression and differentiation proceed in a gradual manner in the very early stage of sex chromosome evolution. PMID:23436913

Production of recombinant allergens in plants

PubMed Central

2010-01-01

A large percentage of allergenic proteins are of plant origin. Hence, plant-based expression systems are considered ideal for the recombinant production of certain allergens. First attempts to establish production of plant-derived allergens in plants focused on transient expression in Nicotiana benthamiana infected with recombinant viral vectors. Accordingly, allergens from birch and mugwort pollen, as well as from apple have been expressed in plants. Production of house dust mite allergens has been achieved by Agrobacterium-mediated transformation of tobacco plants. Beside the use of plants as production systems, other approaches have focused on the development of edible vaccines expressing allergens or epitopes thereof, which bypasses the need of allergen purification. The potential of this approach has been convincingly demonstrated for transgenic rice seeds expressing seven dominant human T cell epitopes derived from Japanese cedar pollen allergens. Parallel to efforts in developing recombinant-based diagnostic and therapeutic reagents, different gene-silencing approaches have been used to decrease the expression of allergenic proteins in allergen sources. In this way hypoallergenic ryegrass, soybean, rice, apple, and tomato were developed. PMID:21258627

C III spectra in WC Wolf-Rayet stars - Does collisional excitation dominate?

NASA Technical Reports Server (NTRS)

Kastner, S. O.; Bhatia, A. K.

1993-01-01

A direct comparison of the spectra emitted by an improved collisionally excited C III atomic model, with observations of C III spectra in Wolf-Rayet WC stars, shows agreement for UV, visible, and near-infrared lines including lines usually considered to be recombination lines. The agreement implies high-density and temperature source conditions corresponding to log (Ne Te) is greater than 16 as a lower limit, whereas most current modeling assumes log (Ne Te) is less than 15.5. This raises questions concerning the photoionization/recombination assumptions on which most WR modeling is based. Recent models are discussed from this point of view.

Origin of genetic variation: regulation of genetic recombination in the higher organisms - a theory.

PubMed

Pandey, K K

1972-01-01

Recent studies in the fungi, particularly Neurospora and Schizophyllum, have revealed a number of genetic features which, viewed in conjunction with earlier observations on other organisms, form a pattern, or model, which appears to be basic to the control of recombination in all eukaryotes, including higher organisms. It is assumed that the control is exercised on mechanisms that produce new alleles through recombination, as understood in broad terms and including such a likely phenomenon as gene conversion, which may or may not involve crossing-over, as well as equal and unequal crossing-over. The recombination may thus occur between alleles in either the homozygous or heterozygous condition. In the model, regulatory genes and breeding behaviour are integrated into one self-regulatory system controlling the production of new genetic variation.The model is based on the following five general features, largely substantiated by the results in Neurospora and Schizophyllum: 1) The frequency of recombination in a particular chromosomal region is controlled by specific regulatory genes (rec). 2) There may be a number of such specific, regulatory genes responsible for recombination in a given region. 3) A rec. locus may influence recombination in more than one region. 4) The regulatory genes have no specific physical relationship with the region(s) they control, and are usually located at random in the genome. 5) Of the allelic forms of the regulatory genes it is always the dominant gene which suppresses recombination and the recessive gene which increases recombination. The rec system is epistatic to other genetic elements jointly involved in the overall control of recombination in a specific region. It is suggested that usually the control of recombination in a given region is exercised, cumulatively, by the balance of the dominant and recessive genes of the specific rec loci in the organism. Outbreeding, with the associated high heterozygosity of the regulatory rec loci, virtually "switches off" recombination, producing few new variations. Inbreeding produces homozygosity of these loci, resulting in certain individuals which will have a considerable number of their regulatory loci in the homozygous recessive condition and in which recombination will be "switched on", producing new variation at a high frequency. Inbreeding is thus an integrated, evolutionary system of considerable importance, and is not a degenerate "dead end", as many investigators have previously thought.The model has another compensatory function in evolution. In major loci, or in an operon, where there are structural genes and closely linked operator genes, as exemplified by the S locus, there are indications that the present model is concerned with the regulation of both structural and operator genes. The consequences of the model in the two classes of genes, however, are in direct contrast to each other: High heterozygosity which is instrumental in switching "off" recombination, and which is therefore helpful in maintaining stability in the structural gene, is conducive to functional variation of the operator gene; and high homozygosity, which is instrumental in switching "on" recombination, and which is therefore helpful in producing variation in the structural gene, is conducive to the stability of the operator gene.This model of the control of genetic variation in a specific chromosomal region is significant in development as well as in evolution, and throws light on a number of hitherto "intractable" problems peculiar to the higher organisms. For example, the model is helpful in explaining: 1) the origin of new self-incompatibility alleles in the flowering plants; 2) the impressive speciation in the waif flora (and fauna) of the oceanic islands; 3) the presence of high genetic variability in inbreeding species of plants; 4) environmentally-induced heritable variation in certain plants; and 5) the genetic mechanism of antibody diversity in animals.

Better understanding of homologous recombination through a 12-week laboratory course for undergraduates majoring in biotechnology.

PubMed

Li, Ming; Shen, Xiaodong; Zhao, Yan; Hu, Xiaomei; Hu, Fuquan; Rao, Xiancai

2017-07-08

Homologous recombination, a central concept in biology, is defined as the exchange of DNA strands between two similar or identical nucleotide sequences. Unfortunately, undergraduate students majoring in biotechnology often experience difficulties in understanding the molecular basis of homologous recombination. In this study, we developed and implemented a 12-week laboratory course for biotechnology undergraduates in which gene targeting in Streptococcus suis was used to facilitate their understanding of the basic concept and process of homologous recombination. Students worked in teams of two to select a gene of interest to create a knockout mutant using methods that relied on homologous recombination. By integrating abstract knowledge and practice in the process of scientific research, students gained hands-on experience in molecular biology techniques while learning about the principle and process of homologous recombination. The learning outcomes and survey-based assessment demonstrated that students substantially enhanced their understanding of how homologous recombination could be used to study gene function. Overall, the course was very effective for helping biotechnology undergraduates learn the theory and application of homologous recombination, while also yielding positive effects in developing confidence and scientific skills for future work in research. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):329-335, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

Homologous Recombination—Experimental Systems, Analysis and Significance

PubMed Central

Kuzminov, Andrei

2014-01-01

Homologous recombination is the most complex of all recombination events that shape genomes and produce material for evolution. Homologous recombination events are exchanges between DNA molecules in the lengthy regions of shared identity, catalyzed by a group of dedicated enzymes. There is a variety of experimental systems in E. coli and Salmonella to detect homologous recombination events of several different kinds. Genetic analysis of homologous recombination reveals three separate phases of this process: pre-synapsis (the early phase), synapsis (homologous strand exchange) and post-synapsis (the late phase). In E. coli, there are at least two independent pathway of the early phase and at least two independent pathways of the late phase. All this complexity is incongruent with the originally ascribed role of homologous recombination as accelerator of genome evolution: there is simply not enough duplication and repetition in enterobacterial genomes for homologous recombination to have a detectable evolutionary role, and therefore not enough selection to maintain such a complexity. At the same time, the mechanisms of homologous recombination are uniquely suited for repair of complex DNA lesions called chromosomal lesions. In fact, the two major classes of chromosomal lesions are recognized and processed by the two individual pathways at the early phase of homologous recombination. It follows, therefore, that homologous recombination events are occasional reflections of the continual recombinational repair, made possible in cases of natural or artificial genome redundancy. PMID:26442506

Numerical study of the intrinsic recombination carriers lifetime in extended short-wavelength infrared detector materials: A comparison between InGaAs and HgCdTe

NASA Astrophysics Data System (ADS)

Wen, Hanqing; Bellotti, Enrico

2016-05-01

Intrinsic carrier lifetime due to radiative and Auger recombination in HgCdTe and strained InGaAs has been computed in the extended short-wavelength infrared (ESWIR) spectrum from 1.7 μm to 2.7 μm. Using the Green's function theory, both direct and phonon-assisted indirect Auger recombination rates as well as the radiative recombination rates are calculated for different cutoff wavelengths at 300 K with full band structures of the materials. In order to properly model the full band structures of strained InGaAs, an empirical pseudo-potential model for the alloy is fitted using the virtual crystal approximation with spin-orbit coupling included. The results showed that for InxGa1-xAs grown on InP substrate, the compressive strain, which presents in the film when the cutoff wavelength is longer than 1.7 μm, leads to decrease of Auger recombination rate and increase of radiative recombination rate. Since the dominant intrinsic recombination mechanism in this spectral range is radiative recombination, the overall intrinsic carrier lifetime in the strained InGaAs alloys is shorter than that in the relaxed material. When compared to the relaxed HgCdTe, both relaxed and compressively strained InGaAs alloys show shorter intrinsic carrier lifetime at the same cutoff wavelength in room temperature which confirms the potential advantage of HgCdTe as wide-band infrared detector material. While HgCdTe offers superior performance, ultimately the material of choice for ESWIR application will also depend on material quality and cost.

Numerical study of the intrinsic recombination carriers lifetime in extended short-wavelength infrared detector materials: A comparison between InGaAs and HgCdTe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wen, Hanqing; Bellotti, Enrico, E-mail: bellotti@bu.edu

2016-05-28

Intrinsic carrier lifetime due to radiative and Auger recombination in HgCdTe and strained InGaAs has been computed in the extended short-wavelength infrared (ESWIR) spectrum from 1.7 μm to 2.7 μm. Using the Green's function theory, both direct and phonon-assisted indirect Auger recombination rates as well as the radiative recombination rates are calculated for different cutoff wavelengths at 300 K with full band structures of the materials. In order to properly model the full band structures of strained InGaAs, an empirical pseudo-potential model for the alloy is fitted using the virtual crystal approximation with spin-orbit coupling included. The results showed that for In{sub x}Ga{submore » 1−x}As grown on InP substrate, the compressive strain, which presents in the film when the cutoff wavelength is longer than 1.7 μm, leads to decrease of Auger recombination rate and increase of radiative recombination rate. Since the dominant intrinsic recombination mechanism in this spectral range is radiative recombination, the overall intrinsic carrier lifetime in the strained InGaAs alloys is shorter than that in the relaxed material. When compared to the relaxed HgCdTe, both relaxed and compressively strained InGaAs alloys show shorter intrinsic carrier lifetime at the same cutoff wavelength in room temperature which confirms the potential advantage of HgCdTe as wide-band infrared detector material. While HgCdTe offers superior performance, ultimately the material of choice for ESWIR application will also depend on material quality and cost.« less

Recombination Processes on Low Bandgap Antimonides for Thermophotovoltaic Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saroop, Sudesh

1999-09-01

Recombination processes in antimonide-based (TPV) devices have been investigated using a technique, in which a Nd-YAG pulsed laser is materials for thermophotovoltaic radio-frequency (RF) photoreflectance used to excite excess carriers and the short-pulse response and photoconductivity decay are monitored with an inductively-coupled non-contacting RF probe. The system has been used to characterize surface and bulk recombination mechanisms in Sb-based materials.

Update on thrombopoietin in preclinical and clinical trials.

PubMed

Miyazaki, H

1998-05-01

Thrombopoietin, also termed the c-Mpl ligand, is a lineage-dominant hematopoietic factor that primarily regulates megakaryopoiesis and thrombopoiesis. Treatment of normal animals with recombinant human megakaryocyte growth and development factor, a truncated molecule of the c-Mpl ligand, which is modified with polyethylene glycol (PEG-rHuMGDF), and glycosylated recombinant thrombopoietin stimulates the expansion of bone marrow megakaryocytes and their progenitors, and greatly enhances the production of morphologically and functionally normal platelets. In contrast, this cytokine has only minimal effects on peripheral leukocyte and erythrocyte counts. In myelosuppressed animals, PEG-rHuMGDF or glycosylated thrombopoietin accelerates multilineage hematopoietic recovery effectively improving thrombocytopenia and, in most models, leukopenia (or neutropenia) and anemia. In addition to daily multiple injections, even a single injection of PEG-rHuMGDF after myelosuppressive treatment is fully effective for hematopoietic recovery. In clinical trials, PEG-rHuMGDF or glycosylated recombinant human thrombopoietin potently stimulates thrombopoiesis in cancer patients before chemotherapy. The administration of PEG-rHuMGDF alone or in combination with recombinant human granulocyte colony-stimulating factor (rhG-CSF) reduces the duration of severe thrombocytopenia and in some cases platelet nadirs in patients with advanced cancers after dose-intensive chemotherapy. The recombinant hormone is well-tolerated with little drug-related toxicity.

Recent Theoretical Studies On Excitation and Recombination

NASA Technical Reports Server (NTRS)

Pradhan, Anil K.

2000-01-01

New advances in the theoretical treatment of atomic processes in plasmas are described. These enable not only an integrated, unified, and self-consistent treatment of important radiative and collisional processes, but also large-scale computation of atomic data with high accuracy. An extension of the R-matrix work, from excitation and photoionization to electron-ion recombination, includes a unified method that subsumes both the radiative and the di-electronic recombination processes in an ab initio manner. The extensive collisional calculations for iron and iron-peak elements under the Iron Project are also discussed.

Telomerase Activity Impacts on Epstein-Barr Virus Infection of AGS Cells

PubMed Central

Rac, Jürgen; Haas, Florian; Schumacher, Andrina; Middeldorp, Jaap M.; Delecluse, Henri-Jacques; Speck, Roberto F.

2015-01-01

The Epstein-Barr virus (EBV) is transmitted from host-to-host via saliva and is associated with epithelial malignancies including nasopharyngeal carcinoma (NPC) and some forms of gastric carcinoma (GC). Nevertheless, EBV does not transform epithelial cells in vitro where it is rapidly lost from infected primary epithelial cells or epithelial tumor cells. Long-term infection by EBV, however, can be established in hTERT-immortalized nasopharyngeal epithelial cells. Here, we hypothesized that increased telomerase activity in epithelial cells enhances their susceptibility to infection by EBV. Using HONE-1, AGS and HEK293 cells we generated epithelial model cell lines with increased or suppressed telomerase activity by stable ectopic expression of hTERT or of a catalytically inactive, dominant negative hTERT mutant. Infection experiments with recombinant prototypic EBV (rB95.8), recombinant NPC EBV (rM81) with increased epithelial cell tropism compared to B95.8, or recombinant B95.8 EBV with BZLF1-knockout that is not able to undergo lytic replication, revealed that infection frequencies positively correlate with telomerase activity in AGS cells but also partly depend on the cellular background. AGS cells with increased telomerase activity showed increased expression mainly of latent EBV genes, suggesting that increased telomerase activity directly acts on the EBV infection of epithelial cells by facilitating latent EBV gene expression early upon virus inoculation. Thus, our results indicate that infection of epithelial cells by EBV is a very selective process involving, among others, telomerase activity and cellular background to allow for optimized host-to-host transmission via saliva. PMID:25856387

Developmental plasticity and the origin of species differences

PubMed Central

West-Eberhard, Mary Jane

2005-01-01

Speciation is the origin of reproductive isolation and divergence between populations, according to the “biological species concept” of Mayr. Studies of reproductive isolation have dominated research on speciation, leaving the origin of species differences relatively poorly understood. Here, I argue that the origin of species differences, and of novel phenotypes in general, involves the reorganization of ancestral phenotypes (developmental recombination) followed by the genetic accommodation of change. Because selection acts on phenotypes, not directly on genotypes or genes, novel traits can originate by environmental induction as well as mutation, then undergo selection and genetic accommodation fueled by standing genetic variation or by subsequent mutation and genetic recombination. Insofar as phenotypic novelties arise from adaptive developmental plasticity, they are not “random” variants, because their initial form reflects adaptive responses with an evolutionary history, even though they are initiated by mutations or novel environmental factors that are random with respect to (future) adaptation. Change in trait frequency involves genetic accommodation of the threshold or liability for expression of a novel trait, a process that follows rather than directs phenotypic change. Contrary to common belief, environmentally initiated novelties may have greater evolutionary potential than mutationally induced ones. Thus, genes are probably more often followers than leaders in evolutionary change. Species differences can originate before reproductive isolation and contribute to the process of speciation itself. Therefore, the genetics of speciation can profit from studies of changes in gene expression as well as changes in gene frequency and genetic isolation. PMID:15851679

The SMC-5/6 Complex and the HIM-6 (BLM) Helicase Synergistically Promote Meiotic Recombination Intermediate Processing and Chromosome Maturation during Caenorhabditis elegans Meiosis

PubMed Central

Hong, Ye; Sonneville, Remi; Agostinho, Ana; Meier, Bettina; Wang, Bin; Blow, J. Julian; Gartner, Anton

2016-01-01

Meiotic recombination is essential for the repair of programmed double strand breaks (DSBs) to generate crossovers (COs) during meiosis. The efficient processing of meiotic recombination intermediates not only needs various resolvases but also requires proper meiotic chromosome structure. The Smc5/6 complex belongs to the structural maintenance of chromosome (SMC) family and is closely related to cohesin and condensin. Although the Smc5/6 complex has been implicated in the processing of recombination intermediates during meiosis, it is not known how Smc5/6 controls meiotic DSB repair. Here, using Caenorhabditis elegans we show that the SMC-5/6 complex acts synergistically with HIM-6, an ortholog of the human Bloom syndrome helicase (BLM) during meiotic recombination. The concerted action of the SMC-5/6 complex and HIM-6 is important for processing recombination intermediates, CO regulation and bivalent maturation. Careful examination of meiotic chromosomal morphology reveals an accumulation of inter-chromosomal bridges in smc-5; him-6 double mutants, leading to compromised chromosome segregation during meiotic cell divisions. Interestingly, we found that the lethality of smc-5; him-6 can be rescued by loss of the conserved BRCA1 ortholog BRC-1. Furthermore, the combined deletion of smc-5 and him-6 leads to an irregular distribution of condensin and to chromosome decondensation defects reminiscent of condensin depletion. Lethality conferred by condensin depletion can also be rescued by BRC-1 depletion. Our results suggest that SMC-5/6 and HIM-6 can synergistically regulate recombination intermediate metabolism and suppress ectopic recombination by controlling chromosome architecture during meiosis. PMID:27010650

The SMC-5/6 Complex and the HIM-6 (BLM) Helicase Synergistically Promote Meiotic Recombination Intermediate Processing and Chromosome Maturation during Caenorhabditis elegans Meiosis.

PubMed

Hong, Ye; Sonneville, Remi; Agostinho, Ana; Meier, Bettina; Wang, Bin; Blow, J Julian; Gartner, Anton

2016-03-01

Meiotic recombination is essential for the repair of programmed double strand breaks (DSBs) to generate crossovers (COs) during meiosis. The efficient processing of meiotic recombination intermediates not only needs various resolvases but also requires proper meiotic chromosome structure. The Smc5/6 complex belongs to the structural maintenance of chromosome (SMC) family and is closely related to cohesin and condensin. Although the Smc5/6 complex has been implicated in the processing of recombination intermediates during meiosis, it is not known how Smc5/6 controls meiotic DSB repair. Here, using Caenorhabditis elegans we show that the SMC-5/6 complex acts synergistically with HIM-6, an ortholog of the human Bloom syndrome helicase (BLM) during meiotic recombination. The concerted action of the SMC-5/6 complex and HIM-6 is important for processing recombination intermediates, CO regulation and bivalent maturation. Careful examination of meiotic chromosomal morphology reveals an accumulation of inter-chromosomal bridges in smc-5; him-6 double mutants, leading to compromised chromosome segregation during meiotic cell divisions. Interestingly, we found that the lethality of smc-5; him-6 can be rescued by loss of the conserved BRCA1 ortholog BRC-1. Furthermore, the combined deletion of smc-5 and him-6 leads to an irregular distribution of condensin and to chromosome decondensation defects reminiscent of condensin depletion. Lethality conferred by condensin depletion can also be rescued by BRC-1 depletion. Our results suggest that SMC-5/6 and HIM-6 can synergistically regulate recombination intermediate metabolism and suppress ectopic recombination by controlling chromosome architecture during meiosis.

Clonality, recombination, and hybridization in the plumbing-inhabiting human pathogen Fusarium keratoplasticum inferred from multilocus sequence typing

USDA-ARS?s Scientific Manuscript database

Recent work has shown that Fusarium species and genotypes most commonly associated with human infections, particularly of the cornea (mycotic keratitis), are the same as those most commonly isolated from plumbing systems. The species most dominant in plumbing biofilms is Fusarium keratoplasticum, a ...

A novel Fanconi anaemia subtype associated with a dominant-negative mutation in RAD51

PubMed Central

Ameziane, Najim; May, Patrick; Haitjema, Anneke; van de Vrugt, Henri J.; van Rossum-Fikkert, Sari E.; Ristic, Dejan; Williams, Gareth J.; Balk, Jesper; Rockx, Davy; Li, Hong; Rooimans, Martin A.; Oostra, Anneke B.; Velleuer, Eunike; Dietrich, Ralf; Bleijerveld, Onno B.; Maarten Altelaar, A. F.; Meijers-Heijboer, Hanne; Joenje, Hans; Glusman, Gustavo; Roach, Jared; Hood, Leroy; Galas, David; Wyman, Claire; Balling, Rudi; den Dunnen, Johan; de Winter, Johan P.; Kanaar, Roland; Gelinas, Richard; Dorsman, Josephine C.

2015-01-01

Fanconi anaemia (FA) is a hereditary disease featuring hypersensitivity to DNA cross-linker-induced chromosomal instability in association with developmental abnormalities, bone marrow failure and a strong predisposition to cancer. A total of 17 FA disease genes have been reported, all of which act in a recessive mode of inheritance. Here we report on a de novo g.41022153G>A; p.Ala293Thr (NM_002875) missense mutation in one allele of the homologous recombination DNA repair gene RAD51 in an FA-like patient. This heterozygous mutation causes a novel FA subtype, ‘FA-R', which appears to be the first subtype of FA caused by a dominant-negative mutation. The patient, who features microcephaly and mental retardation, has reached adulthood without the typical bone marrow failure and paediatric cancers. Together with the recent reports on RAD51-associated congenital mirror movement disorders, our results point to an important role for RAD51-mediated homologous recombination in neurodevelopment, in addition to DNA repair and cancer susceptibility. PMID:26681308

Marker-assisted pyramiding of brown planthopper (Nilaparvata lugens Stål) resistance genes Bph1 and Bph2 on rice chromosome 12.

PubMed

Sharma, Prem N; Torii, Akihide; Takumi, Shigeo; Mori, Naoki; Nakamura, Chiharu

2004-01-01

Brown planthopper (BPH) (Nilaparvata lugens Stål) is a significant insect pest of rice (Oryza sativa L.). We constructed a gene-pyramided japonica line, in which two BPH resistance genes Bph1 and Bph2 on the long arm of chromosome 12 independently derived from two indica resistance lines were combined through the recombinant selection. The gene-pyramiding was achieved based on the previously constructed high-resolution linkage maps of the two genes. Two co-dominant and four dominant PCR-based markers flanking the loci were used to select for a homozygous recombinant line in a segregating population that was derived from a cross between the parental homozygous single-gene introgression lines. BPH bioassay showed that the resistance level of the pyramided line was equivalent to that of the Bph1-single introgression line, which showed a higher level of resistance than the Bph2-single introgression line. The pyramid line should provide a useful experimental means for studying the fine structure of the chromosomal region covering these two major BPH resistance genes.

Evaluation of the effectiveness and safety of the thermo-treatment process to dispose of recombinant DNA waste from biological research laboratories.

PubMed

Li, Meng-Nan; Zheng, Guang-Hong; Wang, Lei; Xiao, Wei; Fu, Xiao-Hua; Le, Yi-Quan; Ren, Da-Ming

2009-01-01

The discharge of recombinant DNA waste from biological laboratories into the eco-system may be one of the pathways resulting in horizontal gene transfer or "gene pollution". Heating at 100 degrees C for 5-10 min is a common method for treating recombinant DNA waste in biological research laboratories in China. In this study, we evaluated the effectiveness and the safety of the thermo-treatment method in the disposal of recombinant DNA waste. Quantitative PCR, plasmid transformation and electrophoresis technology were used to evaluate the decay/denaturation efficiency during the thermo-treatment process of recombinant plasmid, pET-28b. Results showed that prolonging thermo-treatment time could improve decay efficiency of the plasmid, and its decay half-life was 2.7-4.0 min during the thermo-treatment at 100 degrees C. However, after 30 min of thermo-treatment some transforming activity remained. Higher ionic strength could protect recombinant plasmid from decay during the treatment process. These results indicate that thermo-treatment at 100 degrees C cannot decay and inactivate pET-28b completely. In addition, preliminary results showed that thermo-treated recombinant plasmids were not degraded completely in a short period when they were discharged into an aquatic environment. This implies that when thermo-treated recombinant DNAs are discharged into the eco-system, they may have enough time to re-nature and transform, thus resulting in gene diffusion.

Biochemical and genetic analysis of the role of the viral polymerase in enterovirus recombination.

PubMed

Woodman, Andrew; Arnold, Jamie J; Cameron, Craig E; Evans, David J

2016-08-19

Genetic recombination in single-strand, positive-sense RNA viruses is a poorly understand mechanism responsible for generating extensive genetic change and novel phenotypes. By moving a critical cis-acting replication element (CRE) from the polyprotein coding region to the 3' non-coding region we have further developed a cell-based assay (the 3'CRE-REP assay) to yield recombinants throughout the non-structural coding region of poliovirus from dually transfected cells. We have additionally developed a defined biochemical assay in which the only protein present is the poliovirus RNA dependent RNA polymerase (RdRp), which recapitulates the strand transfer events of the recombination process. We have used both assays to investigate the role of the polymerase fidelity and nucleotide turnover rates in recombination. Our results, of both poliovirus intertypic and intratypic recombination in the CRE-REP assay and using a range of polymerase variants in the biochemical assay, demonstrate that RdRp fidelity is a fundamental determinant of recombination frequency. High fidelity polymerases exhibit reduced recombination and low fidelity polymerases exhibit increased recombination in both assays. These studies provide the basis for the analysis of poliovirus recombination throughout the non-structural region of the virus genome and provide a defined biochemical assay to further dissect this important evolutionary process. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genetic recombination of the hepatitis C virus: clinical implications.

PubMed

Morel, V; Fournier, C; François, C; Brochot, E; Helle, F; Duverlie, G; Castelain, S

2011-02-01

Genetic recombination is a well-known feature of RNA viruses that plays a significant role in their evolution. Although recombination is well documented for Flaviviridae family viruses, the first natural recombinant strain of hepatitis C virus (HCV) was identified as recently as 2002. Since then, a few other natural inter-genotypic, intra-genotypic and intra-subtype recombinant HCV strains have been described. However, the frequency of recombination may have been underestimated because not all known HCV recombinants are screened for in routine practice. Furthermore, the choice of treatment regimen and its predictive outcome remain problematic as the therapeutic strategy for HCV infection is genotype dependent. HCV recombination also raises many questions concerning its mechanisms and effects on the epidemiological and physiopathological features of the virus. This review provides an update on recombinant HCV strains, the process that gives rise to recombinants and clinical implications of recombination. © 2010 Blackwell Publishing Ltd.

The Development of Novel Recombinant Human Gelatins as Replacements for Animal-Derived Gelatin in Pharmaceutical Applications

NASA Astrophysics Data System (ADS)

Olsen, David; Chang, Robert; Williams, Kim E.; Polarek, James W.

We have developed a recombinant expression system to produce a series of novel recombinant human gelatins that can substitute for animal sourced gelatin preparations currently used in pharmaceutical and nutraceutical applications. This system allows the production of human sequence gelatins, or, if desired, gelatins from any other species depending on the availability of the cloned gene. The gelatins produced with this recombinant system are of defined molecular weight, unlike the animal-sourced gelatins, which consist of numerous polypeptides of varying size. The fermentation and purification process used to prepare these recombinant gelatins does not use any human- or animal-derived components and thus this recombinant material should be free from viruses and agents that cause transmissible spongiform encephalopathies. The recombinant gelatins exhibit lot-to-lot reproducibility and we have performed extensive analytical testing on them. We have demonstrated the utility of these novel gelatins as biological stabilizers and plasma expanders, and we have shown they possess qualities that are important in applications where gel formation is critical. Finally, we provide examples of how our system allows the engineering of these recombinant gelatins to optimize the production process.

DNA polymorphism in recombining and non-recombing mating-type-specific loci of the smut fungus Microbotryum

PubMed Central

Votintseva, A A; Filatov, D A

2011-01-01

The population-genetic processes leading to the genetic degeneration of non-recombining regions have mainly been studied in animal and plant sex chromosomes. Here, we report population genetic analysis of the processes in the non-recombining mating-type-specific regions of the smut fungus Microbotryum violaceum. M. violaceum has A1 and A2 mating types, determined by mating-type-specific ‘sex chromosomes' that contain 1–2 Mb long non-recombining regions. If genetic degeneration were occurring, then one would expect reduced DNA polymorphism in the non-recombining regions of this fungus. The analysis of DNA diversity among 19 M. violaceum strains, collected across Europe from Silene latifolia flowers, revealed that (i) DNA polymorphism is relatively low in all 20 studied loci (π∼0.15%), (ii) it is not significantly different between the two mating-type-specific chromosomes nor between the non-recombining and recombining regions, (iii) there is substantial population structure in M. violaceum populations, which resembles that of its host species, S. latifolia, and (iv) there is significant linkage disequilibrium, suggesting that widespread selfing in this species results in a reduction of the effective recombination rate across the genome. We hypothesise that selfing-related reduction of recombination across the M. violaceum genome negates the difference in the level of DNA polymorphism between the recombining and non-recombining regions, and may possibly lead to similar levels of genetic degeneration in the mating-type-specific regions of the non-recombining ‘sex chromosomes' and elsewhere in the genome. PMID:21081967

A Genome-Wide Map of Mitochondrial DNA Recombination in Yeast

PubMed Central

Fritsch, Emilie S.; Chabbert, Christophe D.; Klaus, Bernd; Steinmetz, Lars M.

2014-01-01

In eukaryotic cells, the production of cellular energy requires close interplay between nuclear and mitochondrial genomes. The mitochondrial genome is essential in that it encodes several genes involved in oxidative phosphorylation. Each cell contains several mitochondrial genome copies and mitochondrial DNA recombination is a widespread process occurring in plants, fungi, protists, and invertebrates. Saccharomyces cerevisiae has proved to be an excellent model to dissect mitochondrial biology. Several studies have focused on DNA recombination in this organelle, yet mostly relied on reporter genes or artificial systems. However, no complete mitochondrial recombination map has been released for any eukaryote so far. In the present work, we sequenced pools of diploids originating from a cross between two different S. cerevisiae strains to detect recombination events. This strategy allowed us to generate the first genome-wide map of recombination for yeast mitochondrial DNA. We demonstrated that recombination events are enriched in specific hotspots preferentially localized in non-protein-coding regions. Additionally, comparison of the recombination profiles of two different crosses showed that the genetic background affects hotspot localization and recombination rates. Finally, to gain insights into the mechanisms involved in mitochondrial recombination, we assessed the impact of individual depletion of four genes previously associated with this process. Deletion of NTG1 and MGT1 did not substantially influence the recombination landscape, alluding to the potential presence of additional regulatory factors. Our findings also revealed the loss of large mitochondrial DNA regions in the absence of MHR1, suggesting a pivotal role for Mhr1 in mitochondrial genome maintenance during mating. This study provides a comprehensive overview of mitochondrial DNA recombination in yeast and thus paves the way for future mechanistic studies of mitochondrial recombination and genome maintenance. PMID:25081569

A genome-wide map of mitochondrial DNA recombination in yeast.

PubMed

Fritsch, Emilie S; Chabbert, Christophe D; Klaus, Bernd; Steinmetz, Lars M

2014-10-01

In eukaryotic cells, the production of cellular energy requires close interplay between nuclear and mitochondrial genomes. The mitochondrial genome is essential in that it encodes several genes involved in oxidative phosphorylation. Each cell contains several mitochondrial genome copies and mitochondrial DNA recombination is a widespread process occurring in plants, fungi, protists, and invertebrates. Saccharomyces cerevisiae has proved to be an excellent model to dissect mitochondrial biology. Several studies have focused on DNA recombination in this organelle, yet mostly relied on reporter genes or artificial systems. However, no complete mitochondrial recombination map has been released for any eukaryote so far. In the present work, we sequenced pools of diploids originating from a cross between two different S. cerevisiae strains to detect recombination events. This strategy allowed us to generate the first genome-wide map of recombination for yeast mitochondrial DNA. We demonstrated that recombination events are enriched in specific hotspots preferentially localized in non-protein-coding regions. Additionally, comparison of the recombination profiles of two different crosses showed that the genetic background affects hotspot localization and recombination rates. Finally, to gain insights into the mechanisms involved in mitochondrial recombination, we assessed the impact of individual depletion of four genes previously associated with this process. Deletion of NTG1 and MGT1 did not substantially influence the recombination landscape, alluding to the potential presence of additional regulatory factors. Our findings also revealed the loss of large mitochondrial DNA regions in the absence of MHR1, suggesting a pivotal role for Mhr1 in mitochondrial genome maintenance during mating. This study provides a comprehensive overview of mitochondrial DNA recombination in yeast and thus paves the way for future mechanistic studies of mitochondrial recombination and genome maintenance. Copyright © 2014 by the Genetics Society of America.

Novel strategy for phenyllactic acid biosynthesis from phenylalanine by whole cell recombinant Escherichia coli coexpressing L-phenylalanine oxidase and L-lactate dehydrogenase.

PubMed

Zhang, Jianzhi; Li, Xi

2018-01-01

To enhance the efficiency of phenyllactic acid (PLA) production from L-phenylalanine (L-Phe) by introducing a novel artificial pathway into Escherichia coli RESULTS: The production of PLA from L-Phe by recombinant E. coli (ldh-lpox) coexpressing L-phenylalanine oxidase and L-lactate dehydrogenase was studied. The new PLA synthesis pathway was confirmed to be efficient in recombinant E. coli. Subsequently, two different biocatalyst processes were carried out and optimized for PLA production. In the whole cell biosynthesis process at high cell density using collected recombinant cells as catalyst, at optimal conditions (L-Phe 6 g/l, pH 7.5, 35 °C, CDW 24.5 g/l and 200 rpm), the recombinant E. coli (ldh-lpox) produced 1.62 g PLA/l with a conversion of 28% from L-Phe. Similarly, during the two-temperature-stage fermentation process in flasks using IPTG-induced cells, the temperature in the second stage was increased to 35 °C to benefit the biocatalyst process, and comparable phenyllactic acid production of 1.47 g/l was obtained from 12 g L-Phe/l. Recombinant E. coli (ldh-lpox) was efficient in PLA production realizing a high titer of several folds compared with studies using L-Phe as substrate.

Mitochondrial genetics in Bakers' yeast: a molecular mechanism for recombinational polarity and suppressiveness.

PubMed

Perlman, P S; Birky, C W

1974-11-01

Recombinational polarity and suppressiveness are two well-known but puzzling cytoplasmic genetic phenomena in bakers' yeast, Saccharomyces cerevisiae. Little progress has been made in characterizing the underlying molecular mechanisms of these phenomena. In this paper we describe a molecular model for recombinational polarity that is compatible with the available genetic evidence. The model stresses the role of small deletions and excision/repair processes in otherwise canonical recombinational events. According to the model, both phenomena require recombination and may share mechanistic elements.

An active recombinant cocoonase from the silkworm Bombyx mori: bleaching, degumming and sericin degrading activities.

PubMed

Unajak, Sasimanas; Aroonluke, Suradet; Promboon, Amornrat

2015-04-01

Cocoonase is a serine protease produced by silk moths and used for softening the cocoons so that they can escape. Degumming is one of the important steps in silk processing. This research aimed to produce an active recombinant Bombyx mori cocoonase (BmCoc) for the silk degumming process. A recombinant BmCoc was successfully expressed in a Pichia pastoris system. The purified enzyme showed specific activity of 227 U mg(-1) protein, 2.4-fold purification, 95% yield and a molecular weight of 26 kDa. The enzyme exhibited optimal temperature at 40 °C and optimal pH at 8, and showed thermal stability at 25-45 °C and pH stability at 5-9. The recombinant enzyme exhibited sericin degumming ability and color bleaching characteristics, and did not affect the fibroin fiber. The enzyme also degraded sericin substrate with a product size about 30-70 kDa. In this study, we successfully produced the active recombinant BmCoc in P. pastoris with promising functions for the Thai silk degumming process, which includes degumming, sericin degrading and color bleaching activities. Our data clearly indicated that the recombinant enzyme had proteolytic activity on sericin but not on fibroin proteins. The recombinant BmCoc has proven to be suitable for numerous applications in the silk industry. © 2014 Society of Chemical Industry.

Biochemistry of homologous recombination in Escherichia coli.

PubMed Central

Kowalczykowski, S C; Dixon, D A; Eggleston, A K; Lauder, S D; Rehrauer, W M

1994-01-01

Homologous recombination is a fundamental biological process. Biochemical understanding of this process is most advanced for Escherichia coli. At least 25 gene products are involved in promoting genetic exchange. At present, this includes the RecA, RecBCD (exonuclease V), RecE (exonuclease VIII), RecF, RecG, RecJ, RecN, RecOR, RecQ, RecT, RuvAB, RuvC, SbcCD, and SSB proteins, as well as DNA polymerase I, DNA gyrase, DNA topoisomerase I, DNA ligase, and DNA helicases. The activities displayed by these enzymes include homologous DNA pairing and strand exchange, helicase, branch migration, Holliday junction binding and cleavage, nuclease, ATPase, topoisomerase, DNA binding, ATP binding, polymerase, and ligase, and, collectively, they define biochemical events that are essential for efficient recombination. In addition to these needed proteins, a cis-acting recombination hot spot known as Chi (chi: 5'-GCTGGTGG-3') plays a crucial regulatory function. The biochemical steps that comprise homologous recombination can be formally divided into four parts: (i) processing of DNA molecules into suitable recombination substrates, (ii) homologous pairing of the DNA partners and the exchange of DNA strands, (iii) extension of the nascent DNA heteroduplex; and (iv) resolution of the resulting crossover structure. This review focuses on the biochemical mechanisms underlying these steps, with particular emphases on the activities of the proteins involved and on the integration of these activities into likely biochemical pathways for recombination. Images PMID:7968921

Optical and ultraviolet spectroscopic analysis of SN 2011fe at late times

NASA Astrophysics Data System (ADS)

Friesen, Brian; Baron, E.; Parrent, Jerod T.; Thomas, R. C.; Branch, David; Nugent, Peter E.; Hauschildt, Peter H.; Foley, Ryan J.; Wright, Darryl E.; Pan, Yen-Chen; Filippenko, Alexei V.; Clubb, Kelsey I.; Silverman, Jeffrey M.; Maeda, Keiichi; Shivvers, Isaac; Kelly, Patrick L.; Cohen, Daniel P.; Rest, Armin; Kasen, Daniel

2017-05-01

We present optical spectra of the nearby Type Ia supernova SN 2011fe at 100, 205, 311, 349 and 578 d post-maximum light, as well as an ultraviolet (UV) spectrum obtained with the Hubble Space Telescope at 360 d post-maximum light. We compare these observations with synthetic spectra produced with the radiative transfer code phoenix. The day +100 spectrum can be well fitted with models that neglect collisional and radiative data for forbidden lines. Curiously, including these data and recomputing the fit yields a quite similar spectrum, but with different combinations of lines forming some of the stronger features. At day +205 and later epochs, forbidden lines dominate much of the optical spectrum formation; however, our results indicate that recombination, not collisional excitation, is the most influential physical process driving spectrum formation at these late times. Consequently, our synthetic optical and UV spectra at all epochs presented here are formed almost exclusively through recombination-driven fluorescence. Furthermore, our models suggest that the UV spectrum even as late as day +360 is optically thick and consists of permitted lines from several iron-peak species. These results indicate that the transition to the 'nebular' phase in Type Ia supernovae is complex and highly wavelength dependent.

Roles of conformational stability and colloidal stability in the aggregation of recombinant human granulocyte colony-stimulating factor

PubMed Central

Chi, Eva Y.; Krishnan, Sampathkumar; Kendrick, Brent S.; Chang, Byeong S.; Carpenter, John F.; Randolph, Theodore W.

2003-01-01

We studied the non-native aggregation of recombinant human granulocyte stimulating factor (rhGCSF) in solution conditions where native rhGCSF is both conformationally stable compared to its unfolded state and at concentrations well below its solubility limit. Aggregation of rhGCSF first involves the perturbation of its native structure to form a structurally expanded transition state, followed by assembly process to form an irreversible aggregate. The energy barriers of the two steps are reflected in the experimentally measured values of free energy of unfolding (ΔGunf) and osmotic second virial coefficient (B22), respectively. Under solution conditions where rhGCSF conformational stability dominates (i.e., large ΔGunf and negative B22), the first step is rate-limiting, and increasing ΔGunf (e.g., by the addition of sucrose) decreases aggregation. In solutions where colloidal stability is high (i.e., large and positive B22 values) the second step is rate-limiting, and solution conditions (e.g., low pH and low ionic strength) that increase repulsive interactions between protein molecules are effective at reducing aggregation. rhGCSF aggregation is thus controlled by both conformational stability and colloidal stability, and depending on the solution conditions, either could be rate-limiting. PMID:12717013

Gene and process level modulation to overcome the bottlenecks of recombinant proteins expression in Pichia pastoris.

PubMed

Prabhu, Ashish A; Boro, Bibari; Bharali, Biju; Chakraborty, Shuchishloka; Dasu, Veeranki V

2017-01-01

Process development involving system metabolic engineering and bioprocess engineering has become one of the major thrust for the development of therapeutic proteins or enzymes. Pichia pastoris has emerged as a prominent host for the production of therapeutic protein or enzymes. Regardless of producing high protein titers, various cellular and process level bottlenecks restrict the expression of recombinant proteins in P. pastoris. In the present review, we have summarized the recent developments in the expression of foreign proteins in P. pastoris. Further, we have discussed various cellular engineering strategies which include codon optimization, pathway engineering, signal peptide processing, development of protease deficient strain and glyco-engineered strains for the high yield protein secretion of recombinant protein. Bioprocess development of recombinant proteins in large-scale bioreactor including medium optimization, optimum feeding strategy and co-substrate feeding in fed-batch as well as continuous cultivation have been described. The recent advances in system and synthetic biology studies including metabolic flux analysis in understanding the phenotypic characteristics of recombinant Pichia and genome editing with CRISPR-CAS system have also been summarized. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

LABORATORY STUDIES ON THE FORMATION OF FORMIC ACID (HCOOH) IN INTERSTELLAR AND COMETARY ICES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bennett, Chris J.; Kim, Yong Seol; Kaiser, Ralf I.

2011-01-20

Mixtures of water (H{sub 2}O) and carbon monoxide (CO) ices were irradiated at 10 K with energetic electrons to simulate the energy transfer processes that occur in the track of galactic cosmic-ray particles penetrating interstellar ices. We identified formic acid (HCOOH) through new absorption bands in the infrared spectra at 1690 and 1224 cm{sup -1} (5.92 and 8.17 {mu}m, respectively). During the subsequent warm-up of the irradiated samples, formic acid is evident from the mass spectrometer signal at the mass-to-charge ratio, m/z = 46 (HCOOH{sup +}) as the ice sublimates. The detection of formic acid was confirmed using isotopically labeledmore » water-d2 with carbon monoxide, leading to formic acid-d2 (DCOOD). The temporal fits of the reactants, reaction intermediates, and products elucidate two reaction pathways to formic acid in carbon monoxide-water ices. The reaction is induced by unimolecular decomposition of water forming atomic hydrogen (H) and the hydroxyl radical (OH). The dominating pathway to formic acid (HCOOH) was found to involve addition of suprathermal hydrogen atoms to carbon monoxide forming the formyl radical (HCO); the latter recombined with neighboring hydroxyl radicals to yield formic acid (HCOOH). To a lesser extent, hydroxyl radicals react with carbon monoxide to yield the hydroxyformyl radical (HOCO), which recombined with atomic hydrogen to produce formic acid. Similar processes are expected to produce formic acid within interstellar ices, cometary ices, and icy satellites, thus providing alternative processes for the generation of formic acid whose abundance in hot cores such as Sgr-B2 cannot be accounted for solely by gas-phase chemistry.« less

Expression and Purification of the Main Component Contained in Camel Milk and Its Antimicrobial Activities Against Bacterial Plant Pathogens.

PubMed

Tanhaeian, Abbas; Shahriari Ahmadi, Farajollah; Sekhavati, Mohammad Hadi; Mamarabadi, Mojtaba

2018-04-04

Lactoferrin is the most dominant protein in milk after casein. This protein plays a crucial role in many biological processes including the regulation of iron metabolism, induction and modulation of the immune system, the primary defense against microorganisms, inhibiting lipid peroxidation and presenting antimicrobial activity against various pathogens such as parasites, fungi, bacteria, and viruses. The major antimicrobial effect of lactoferrin is related to its N-terminal tail where different peptides for instance lactoferricin and lactoferrampin which are important for their antimicrobial abilities are present. The growth rate of bacterial cells in camel milk is lower than that of the cow milk due to having more antimicrobial compounds. In this study, we have fused a codon-optimized partial camel lactoferrcin and lactoferrampin DNA sequences in order to construct a fused peptide via a lysine. This chimeric 42-mer peptide consists of complete and partial amino acid sequence of camel lactoferrampin and lactoferricin, respectively. Human embryonic kidney 293 (HEK-293) cells were used for synthesizing this recombinant peptide. Finally, the antibacterial activities of this constructed peptide were investigated under in vitro condition. The result showed that, all construction, cloning and expression processes were successfully performed in HEK-293. One His-tag tail was added to the chimera in order to optimize the isolation and purification processes and also reduce the cost of production. Additionally, His-tag retained the antimicrobial activity of the chimera. The antimicrobial tests showed that the growth rate in the majority of bacterial plant pathogens, including gram negative and positive bacteria, was inhibited by recombinant chimera as the level of MIC values were evaluated between 0.39 and 25.07 μg/ml for different bacterial isolates.

Large-scale chromatin remodeling at the immunoglobulin heavy chain locus: a paradigm for multigene regulation.

PubMed

Bolland, Daniel J; Wood, Andrew L; Corcoran, Anne E

2009-01-01

V(D)J recombination in lymphocytes is the cutting and pasting together of antigen receptor genes in cis to generate the enormous variety of coding sequences required to produce diverse antigen receptor proteins. It is the key role of the adaptive immune response, which must potentially combat millions of different foreign antigens. Most antigen receptor loci have evolved to be extremely large and contain multiple individual V, D and J genes. The immunoglobulin heavy chain (Igh) and immunoglobulin kappa light chain (Igk) loci are the largest multigene loci in the mammalian genome and V(D)J recombination is one of the most complicated genetic processes in the nucleus. The challenge for the appropriate lymphocyte is one of macro-management-to make all of the antigen receptor genes in a particular locus available for recombination at the appropriate developmental time-point. Conversely, these large loci must be kept closed in lymphocytes in which they do not normally recombine, to guard against genomic instability generated by the DNA double strand breaks inherent to the V(D)J recombination process. To manage all of these demanding criteria, V(D)J recombination is regulated at numerous levels. It is restricted to lymphocytes since the Rag genes which control the DNA double-strand break step of recombination are only expressed in these cells. Within the lymphocyte lineage, immunoglobulin recombination is restricted to B-lymphocytes and TCR recombination to T-lymphocytes by regulation of locus accessibility, which occurs at multiple levels. Accessibility of recombination signal sequences (RSSs) flanking individual V, D and J genes at the nucleosomal level is the key micro-management mechanism, which is discussed in greater detail in other chapters. This chapter will explore how the antigen receptor loci are regulated as a whole, focussing on the Igh locus as a paradigm for the mechanisms involved. Numerous recent studies have begun to unravel the complex and complementary processes involved in this large-scale locus organisation. We will examine the structure of the Igh locus and the large-scale and higher-order chromatin remodelling processes associated with V(D)J recombination, at the level of the locus itself, its conformational changes and its dynamic localisation within the nucleus.

Experimental evidence for glycolaldehyde and ethylene glycol formation by surface hydrogenation of CO molecules under dense molecular cloud conditions

NASA Astrophysics Data System (ADS)

Fedoseev, G.; Cuppen, H. M.; Ioppolo, S.; Lamberts, T.; Linnartz, H.

2015-04-01

This study focuses on the formation of two molecules of astrobiological importance - glycolaldehyde (HC(O)CH2OH) and ethylene glycol (H2C(OH)CH2OH) - by surface hydrogenation of CO molecules. Our experiments aim at simulating the CO freeze-out stage in interstellar dark cloud regions, well before thermal and energetic processing become dominant. It is shown that along with the formation of H2CO and CH3OH - two well-established products of CO hydrogenation - also molecules with more than one carbon atom form. The key step in this process is believed to be the recombination of two HCO radicals followed by the formation of a C-C bond. The experimentally established reaction pathways are implemented into a continuous-time random-walk Monte Carlo model, previously used to model the formation of CH3OH on astrochemical time-scales, to study their impact on the solid-state abundances in dense interstellar clouds of glycolaldehyde and ethylene glycol.

Process Research On Polycrystalline Silicon Material (PROPSM). [flat plate solar array project

NASA Technical Reports Server (NTRS)

Culik, J. S.

1983-01-01

The performance-limiting mechanisms in large-grain (greater than 1 to 2 mm in diameter) polycrystalline silicon solar cells were investigated by fabricating a matrix of 4 sq cm solar cells of various thickness from 10 cm x 10 cm polycrystalline silicon wafers of several bulk resistivities. Analysis of the illuminated I-V characteristics of these cells suggests that bulk recombination is the dominant factor limiting the short-circuit current. The average open-circuit voltage of the polycrystalline solar cells is 30 to 70 mV lower than that of co-processed single-crystal cells; the fill-factor is comparable. Both open-circuit voltage and fill-factor of the polycrystalline cells have substantial scatter that is not related to either thickness or resistivity. This implies that these characteristics are sensitive to an additional mechanism that is probably spatial in nature. A damage-gettering heat-treatment improved the minority-carrier diffusion length in low lifetime polycrystalline silicon, however, extended high temperature heat-treatment degraded the lifetime.

Structural constraints determine the glycosylation of HIV-1 envelope trimers

PubMed Central

Pritchard, Laura K.; Vasiljevic, Snezana; Ozorowski, Gabriel; Seabright, Gemma E.; Cupo, Albert; Ringe, Rajesh; Kim, Helen J.; Sanders, Rogier W.; Doores, Katie J.; Burton, Dennis R.; Wilson, Ian A.; Ward, Andrew B.; Moore, John P.; Crispin, Max

2015-01-01

A highly glycosylated, trimeric envelope glycoprotein (Env) mediates HIV-1 cell entry. The high density and heterogeneity of the glycans shield Env from recognition by the immune system but, paradoxically, many potent broadly neutralizing antibodies (bNAbs) recognize epitopes involving this glycan shield. To better understand Env glycosylation and its role in bNAb recognition, we characterized a soluble, cleaved recombinant trimer (BG505 SOSIP.664) that is a close structural and antigenic mimic of native Env. Large, unprocessed oligomannose-type structures (Man8-9GlcNAc2) are notably prevalent on the gp120 components of the trimer, irrespective of the mammalian cell expression system or the bNAb used for affinity-purification. In contrast, gp41 subunits carry more highly processed glycans. The glycans on uncleaved, non-native oligomeric gp140 proteins are also highly processed. A homogeneous, oligomannose-dominated glycan profile is therefore a hallmark of a native Env conformation and a potential Achilles’ heel that can be exploited for bNAb recognition and vaccine design. PMID:26051934

Cloning of a Recombinant Plasmid Encoding Thiol-Specific Antioxidant Antigen (TSA) Gene of Leishmania majorand Expression in the Chinese Hamster Ovary Cell Line.

PubMed

Fatemeh, Ghaffarifar; Fatemeh, Tabatabaie; Zohreh, Sharifi; Abdolhosein, Dalimiasl; Mohammad Zahir, Hassan; Mehdi, Mahdavi

2012-01-01

TSA (thiol-specific antioxidant antigen) is the immune-dominant antigen of Leishmania major and is considered to be the most promising candidate molecule for a recombinant or DNA vaccine against leishmaniasis. The aim of the present work was to express a plasmid containing the TSA gene in eukaryotic cells. Genomic DNA was extracted, and the TSA gene was amplified by polymerase chain reaction (PCR). The PCR product was cloned into the pTZ57R/T vector, followed by subcloning into the eukaryotic expression vector pcDNA3 (EcoRI and HindIII sites). The recombinant plasmid was characterised by restriction digest and PCR. Eukaryotic Chinese hamster ovary cells were transfected with the plasmid containing the TSA gene. Expression of the L. major TSA gene was confirmed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and Western blotting. The plasmid containing the TSA gene was successfully expressed, as demonstrated by a band of 22.1 kDa on Western blots. The plasmid containing the TSA gene can be expressed in a eukaryotic cell line. Thus, the recombinant plasmid may potentially be used as a DNA vaccine in animal models.

Comparison of Yeasts as Hosts for Recombinant Protein Production.

PubMed

Vieira Gomes, Antonio Milton; Souza Carmo, Talita; Silva Carvalho, Lucas; Mendonça Bahia, Frederico; Parachin, Nádia Skorupa

2018-04-29

Recombinant protein production emerged in the early 1980s with the development of genetic engineering tools, which represented a compelling alternative to protein extraction from natural sources. Over the years, a high level of heterologous protein was made possible in a variety of hosts ranging from the bacteria Escherichia coli to mammalian cells. Recombinant protein importance is represented by its market size, which reached $1654 million in 2016 and is expected to reach $2850.5 million by 2022. Among the available hosts, yeasts have been used for producing a great variety of proteins applied to chemicals, fuels, food, and pharmaceuticals, being one of the most used hosts for recombinant production nowadays. Historically, Saccharomyces cerevisiae was the dominant yeast host for heterologous protein production. Lately, other yeasts such as Komagataella sp., Kluyveromyces lactis , and Yarrowia lipolytica have emerged as advantageous hosts. In this review, a comparative analysis is done listing the advantages and disadvantages of using each host regarding the availability of genetic tools, strategies for cultivation in bioreactors, and the main techniques utilized for protein purification. Finally, examples of each host will be discussed regarding the total amount of protein recovered and its bioactivity due to correct folding and glycosylation patterns.

Recombination Promoted by DNA Viruses: Phage λ to Herpes Simplex Virus

PubMed Central

Weller, Sandra K.; Sawitzke, James A.

2015-01-01

The purpose of this review is to explore recombination strategies in DNA viruses. Homologous recombination is a universal genetic process that plays multiple roles in the biology of all organisms, including viruses. Recombination and DNA replication are interconnected, with recombination being essential for repairing DNA damage and supporting replication of the viral genome. Recombination also creates genetic diversity, and viral recombination mechanisms have important implications for understanding viral origins as well as the dynamic nature of viral-host interactions. Both bacteriophage λ and herpes simplex virus (HSV) display high rates of recombination, both utilizing their own proteins and commandeering cellular proteins to promote recombination reactions. We focus primarily on λ and HSV, as they have proven amenable to both genetic and biochemical analysis and have recently been shown to exhibit some surprising similarities that will guide future studies. PMID:25002096

Detecting and Analyzing Genetic Recombination Using RDP4.

PubMed

Martin, Darren P; Murrell, Ben; Khoosal, Arjun; Muhire, Brejnev

2017-01-01

Recombination between nucleotide sequences is a major process influencing the evolution of most species on Earth. The evolutionary value of recombination has been widely debated and so too has its influence on evolutionary analysis methods that assume nucleotide sequences replicate without recombining. When nucleic acids recombine, the evolution of the daughter or recombinant molecule cannot be accurately described by a single phylogeny. This simple fact can seriously undermine the accuracy of any phylogenetics-based analytical approach which assumes that the evolutionary history of a set of recombining sequences can be adequately described by a single phylogenetic tree. There are presently a large number of available methods and associated computer programs for analyzing and characterizing recombination in various classes of nucleotide sequence datasets. Here we examine the use of some of these methods to derive and test recombination hypotheses using multiple sequence alignments.

Population analysis of clinical and environmental Vibrio parahaemolyticus isolated from eastern provinces in China by removing the recombinant SNPs in the MLST loci.

PubMed

Lu, Xin; Zhou, Haijian; Du, Xiaoli; Liu, Sha; Xu, Jialiang; Cui, Zhigang; Pang, Bo; Kan, Biao

2016-11-01

Vibrio parahaemolyticus is a common seafood-borne pathogenic bacterium which causes gastroenteritis in humans. Continuous surveillance on the molecular characters of the clinical and environmental V. parahaemolyticus strains needs to be conducted for the epidemiological and genetic purposes. To generate a picture of the population distribution of V. parahaemolyticus in eastern China isolated from clinical cases of gastroenteritis and environmental samples, we investigated the genetic and evolutionary relationships of the strains using the commonly used multi-locus sequence typing (MLST, in which seven house-keeping genes are used in the protocol). A highly genetic diversity within the V. parahaemolyticus population was observed but ST3 was still dominant in the clinical strains, and 103 new sequence types (ST) were found in the clinical strains by searching in the global V. parahaemolyticus MLST database. With these genetically diverse strains, we estimated the recombination rates of the loci in MLST analysis. The locus recA was found to be subject to exceptionally high rate of recombination, and the recombinant single nucleotide polymorphisms (SNPs) were also identified within the seven loci. The phylogenetic tree of the strains was re-constructed using the maximum likelihood method by removing the recombination SNPs of the seven loci, and the minimum spanning tree was re-constructed with the six loci without recA. Some changes were observed in comparison with the previously used methods, suggesting that the homologous recombination has roles in shaping the clonal structure of V. parahaemolyticus. We propose the recombination-free SNPs strategy in the clonality analysis of V. parahaemolyticus, especially when using the maximum likelihood method. Copyright © 2016. Published by Elsevier B.V.

Recombinant mouse periostin ameliorates coronal sutures fusion in Twist1+/- mice.

PubMed

Bai, Shanshan; Li, Dong; Xu, Liang; Duan, Huichuan; Yuan, Jie; Wei, Min

2018-04-17

Saethre-Chotzen syndrome is an autosomal dominantly inherited disorder caused by mutations in the twist family basic helix-loop-helix transcription factor 1 (TWIST1) gene. Surgical procedures are frequently required to reduce morphological and functional defects in patients with Saethre-Chotzen syndrome. Therefore, the development of noninvasive procedures to treat Saethre-Chotzen syndrome is critical. We identified that periostin, which is an extracellular matrix protein that plays an important role in both bone and connective tissues, is downregulated in craniosynostosis patients. We aimed to verify the effects of different concentrations (0, 50, 100, and 200 μg/l) of recombinant mouse periostin in Twist1 +/- mice (a mouse model of Saethre-Chotzen syndrome) coronal suture cells in vitro and in vivo. Cell proliferation, migration, and osteogenic differentiation were observed and detected. Twist1 +/- mice were also injected with recombinant mouse periostin to verify the treatment effects. Cell Counting Kit-8 results showed that recombinant mouse periostin inhibited the proliferation of suture-derived cells in a time- and concentration-dependent manner. Cell migration was also suppressed when treated with recombinant mouse periostin. Real-time quantitative PCR and Western blotting results suggested that messenger ribonucleic acid and protein expression of alkaline phosphatase, bone sialoprotein, collagen type I, and osteocalcin were all downregulated after treatment with recombinant mouse periostin. However, the expression of Wnt-3a, Wnt-1, and β-catenin were upregulated. The in vivo results demonstrated that periostin-treated Twist1 +/- mice showed patent coronal sutures in comparison with non-treated Twist1 +/- mice which have coronal craniosynostosis. Our results suggest that recombinant mouse periostin can inhibit coronal suture cell proliferation and migration and suppress osteogenic differentiation of suture-derived cells via Wnt canonical signaling, as well as ameliorate coronal suture fusion in Twist1 +/- mice.

Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots.

PubMed

Baker, Christopher L; Petkova, Pavlina; Walker, Michael; Flachs, Petr; Mihola, Ondrej; Trachtulec, Zdenek; Petkov, Petko M; Paigen, Kenneth

2015-09-01

Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9+/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape.

Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots

PubMed Central

Baker, Christopher L.; Petkova, Pavlina; Walker, Michael; Flachs, Petr; Mihola, Ondrej; Trachtulec, Zdenek; Petkov, Petko M.; Paigen, Kenneth

2015-01-01

Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9 +/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape. PMID:26368021

Recombination radius of a Frenkel pair and capture radius of a self-interstitial atom by vacancy clusters in bcc Fe

NASA Astrophysics Data System (ADS)

Nakashima, Kenichi; Stoller, Roger E.; Xu, Haixuan

2015-08-01

The recombination radius of a Frenkel pair is a fundamental parameter for the object kinetic Monte Carlo (OKMC) and mean field rate theory (RT) methods that are used to investigate irradiation damage accumulation in irradiated materials. The recombination radius in bcc Fe has been studied both experimentally and numerically, however there is no general consensus about its value. The detailed atomistic processes of recombination also remain uncertain. Values from 1.0a0 to 3.3a0 have been employed as a recombination radius in previous studies using OKMC and RT. The recombination process of a Frenkel pair is investigated at the atomic level using the self-evolved atomistic kinetic Monte Carlo (SEAKMC) method in this paper. SEAKMC calculations reveal that a self-interstitial atom recombines with a vacancy in a spontaneous reaction from several nearby sites following characteristic pathways. The recombination radius of a Frenkel pair is estimated to be 2.26a0 by taking the average of the recombination distances from 80 simulation cases. In addition, we apply these procedures to the capture radius of a self-interstitial atom by a vacancy cluster. The capture radius is found to gradually increase with the size of the vacancy cluster. The fitting curve for the capture radius is obtained as a function of the number of vacancies in the cluster.

Recombination Processes and Nonlinear Markov Chains.

PubMed

Pirogov, Sergey; Rybko, Alexander; Kalinina, Anastasia; Gelfand, Mikhail

2016-09-01

Bacteria are known to exchange genetic information by horizontal gene transfer. Since the frequency of homologous recombination depends on the similarity between the recombining segments, several studies examined whether this could lead to the emergence of subspecies. Most of them simulated fixed-size Wright-Fisher populations, in which the genetic drift should be taken into account. Here, we use nonlinear Markov processes to describe a bacterial population evolving under mutation and recombination. We consider a population structure as a probability measure on the space of genomes. This approach implies the infinite population size limit, and thus, the genetic drift is not assumed. We prove that under these conditions, the emergence of subspecies is impossible.

Data Base for CFD Validation

NASA Technical Reports Server (NTRS)

Deiwert, George S.

1997-01-01

The flow behind the shock wave formed around objects which fly at hypervelocity behaves differently from that of a perfect gas. Molecules become vibrationally excited, dissociated, and ionized. The hot gas may emit or absorb radiation. When the atoms produced by dissociation reach the wall surface, chemical reactions, including recombination, may occur. The thermochemical phenomena of vibration, dissociation, ionization, surface chemical reaction, and radiation are referred to commonly as high-temperature real-gas phenomena. The phenomena cause changes in the dynamic behavior of the flow and the surface pressure and heat transfer distribution around the object. The character of a real gas is described by the internal degrees of freedom and state of constituent molecules; nitrogen and oxygen for air. The internal energy states, rotation, vibration and electronic, of the molecules are excited and, in the limit, the molecular bonds are exceeded and the gas dissociated into atomic and, possibly, ionic constituents. The process of energy transfer causing excitation, dissociation and recombination is a rate process controlled by particle collisions. Binary, two-body, collisions are sufficient to cause internal excitation, dissociation and ionization while three-body collisions are required to recombine the particles into molecular constituents. If the rates of energy transfer are fast with respect to the local fluid dynamic time scale the gas is in, or nearly in, equilibrium. If the energy transfer rates are very slow the gas can be described as frozen. In all other instances, wherein any of the energy exchange rates are comparable to the local fluid time scale, the gas will be thermally or chemically reacting and out of equilibrium. Real gas thermochemical nonequilibrium processes are important in the determination of aerodynamic heating; both convective (including wall catalytic effects) and radiative heating. To illustrate this we consider the hypervelocity flow over a bluff body typical of an atmospheric entry vehicle or an aerospace transfer vehicle (ASTV). The qualitative aspects of a hypersonic flow field over a bluff body are discussed in two parts, forebody and afterbody, with attention to which particular physical effects must be included in an analysis. This will indicate what type of numerical modeling will be adequate in each region of the flow. A bluff forebody flow field is dominated by the presence of the strong bow shock wave and the consequent heating, and chemical reaction of the gas. At high altitude hypersonic flight conditions the thermal excitation and chemical reaction of the gas occur slowly enough that a significant portion of the flow field is in a state of thermochemical nonequilibrium. A second important effect is the presence of the thick boundary layer along the forebody surface. In this region there are large thermal and chemical species gradients due to the interaction of the gas with the wall. Also at high altitudes the shock wave and the boundary layer may become so thick that they merge; in this case the entire shock layer is dominated by viscous effects.

Mechanisms and Factors that Influence High Frequency Retroviral Recombination

PubMed Central

Delviks-Frankenberry, Krista; Galli, Andrea; Nikolaitchik, Olga; Mens, Helene; Pathak, Vinay K.; Hu, Wei-Shau

2011-01-01

With constantly changing environmental selection pressures, retroviruses rely upon recombination to reassort polymorphisms in their genomes and increase genetic diversity, which improves the chances for the survival of their population. Recombination occurs during DNA synthesis, whereby reverse transcriptase undergoes template switching events between the two copackaged RNAs, resulting in a viral recombinant with portions of the genetic information from each parental RNA. This review summarizes our current understanding of the factors and mechanisms influencing retroviral recombination, fidelity of the recombination process, and evaluates the subsequent viral diversity and fitness of the progeny recombinant. Specifically, the high mutation rates and high recombination frequencies of HIV-1 will be analyzed for their roles in influencing HIV-1 global diversity, as well as HIV-1 diagnosis, drug treatment, and vaccine development. PMID:21994801

Ion recombination correction in carbon ion beams.

PubMed

Rossomme, S; Hopfgartner, J; Lee, N D; Delor, A; Thomas, R A S; Romano, F; Fukumura, A; Vynckier, S; Palmans, H

2016-07-01

In this work, ion recombination is studied as a function of energy and depth in carbon ion beams. Measurements were performed in three different passively scattered carbon ion beams with energies of 62 MeV/n, 135 MeV/n, and 290 MeV/n using various types of plane-parallel ionization chambers. Experimental results were compared with two analytical models for initial recombination. One model is generally used for photon beams and the other model, developed by Jaffé, takes into account the ionization density along the ion track. An investigation was carried out to ascertain the effect on the ion recombination correction with varying ionization chamber orientation with respect to the direction of the ion tracks. The variation of the ion recombination correction factors as a function of depth was studied for a Markus ionization chamber in the 62 MeV/n nonmodulated carbon ion beam. This variation can be related to the depth distribution of linear energy transfer. Results show that the theory for photon beams is not applicable to carbon ion beams. On the other hand, by optimizing the value of the ionization density and the initial mean-square radius, good agreement is found between Jaffé's theory and the experimental results. As predicted by Jaffé's theory, the results confirm that ion recombination corrections strongly decrease with an increasing angle between the ion tracks and the electric field lines. For the Markus ionization chamber, the variation of the ion recombination correction factor with depth was modeled adequately by a sigmoid function, which is approximately constant in the plateau and strongly increasing in the Bragg peak region to values of up to 1.06. Except in the distal edge region, all experimental results are accurately described by Jaffé's theory. Experimental results confirm that ion recombination in the investigated carbon ion beams is dominated by initial recombination. Ion recombination corrections are found to be significant and cannot be neglected for reference dosimetry and for the determination of depth dose curves in carbon ion beams.

Heparin-binding peptide as a novel affinity tag for purification of recombinant proteins.

PubMed

Morris, Jacqueline; Jayanthi, Srinivas; Langston, Rebekah; Daily, Anna; Kight, Alicia; McNabb, David S; Henry, Ralph; Kumar, Thallapuranam Krishnaswamy Suresh

2016-10-01

Purification of recombinant proteins constitutes a significant part of the downstream processing in biopharmaceutical industries. Major costs involved in the production of bio-therapeutics mainly depend on the number of purification steps used during the downstream process. Affinity chromatography is a widely used method for the purification of recombinant proteins expressed in different expression host platforms. Recombinant protein purification is achieved by fusing appropriate affinity tags to either N- or C- terminus of the target recombinant proteins. Currently available protein/peptide affinity tags have proved quite useful in the purification of recombinant proteins. However, these affinity tags suffer from specific limitations in their use under different conditions of purification. In this study, we have designed a novel 34-amino acid heparin-binding affinity tag (HB-tag) for the purification of recombinant proteins expressed in Escherichia coli (E. coli) cells. HB-tag fused recombinant proteins were overexpressed in E. coli in high yields. A one-step heparin-Sepharose-based affinity chromatography protocol was developed to purify HB-fused recombinant proteins to homogeneity using a simple sodium chloride step gradient elution. The HB-tag has also been shown to facilitate the purification of target recombinant proteins from their 8 M urea denatured state(s). The HB-tag has been demonstrated to be successfully released from the fusion protein by an appropriate protease treatment to obtain the recombinant target protein(s) in high yields. Results of the two-dimensional NMR spectroscopy experiments indicate that the purified recombinant target protein(s) exist in the native conformation. Polyclonal antibodies raised against the HB-peptide sequence, exhibited high binding specificity and sensitivity to the HB-fused recombinant proteins (∼10 ng) in different crude cell extracts obtained from diverse expression hosts. In our opinion, the HB-tag provides a cost-effective, rapid, and reliable avenue for the purification of recombinant proteins in heterologous hosts. Copyright © 2016 Elsevier Inc. All rights reserved.

Three-Dimensional Spin Texture in Hybrid Perovskites and Its Impact on Optical Transitions

DOE PAGES

Zhang, Xie; Shen, Jimmy -Xuan; Van de Walle, Chris G.

2018-05-15

Hybrid perovskites such as MAPbI 3 (MA = CH 3NH 3) exhibit a unique spin texture. The spin texture (as calculated within the Rashba model) has been suggested to be responsible for a suppression of radiative recombination due to a mismatch of spins at the band edges. Here we compute the spin texture from first principles and demonstrate that it does not suppress recombination. The exact spin texture is dominated by the inversion asymmetry of the local electrostatic potential, which is determined by the structural distortion induced by the MA molecule. In addition, the rotation of the MA molecule atmore » room temperature leads to a dynamic spin texture in MAPbI 3. Furthermore these insights call for a reconsideration of the scenario that radiative recombination is suppressed and provide an in-depth understanding of the origin of the spin texture in hybrid perovskites, which is crucial for designing spintronic devices.« less

Twilight airglow. I - Photoelectrons and forbidden O I 5577-angstrom radiation.

NASA Technical Reports Server (NTRS)

Hays, P. B.; Sharp, W. E.

1973-01-01

A payload consisting of a number of experiments to study the earth's atmosphere was launched from White Sands on Feb. 8, 1971. The differential photoelectron flux spectrum was measured as a function of altitude. The energy distribution revealed the N2 vibrational structure appearing at 2.8 V, rising to a maximum at 4 eV, decreasing to an 8-volt-wide plateau at 20 V, and then further decreasing. The ion and electron density distributions were measured simultaneously. An optical measurement of forbidden O I 5577-A radiation was made. Both electron impact on atomic oxygen and dissociative recombination of O2(+) were found to produce this emission above 150 km. The recombination rate for the O(1 S) found from a reported nightglow profile is 2.5 plus or minus 1.5 x 10 to the minus 9th cu cm/sec. Between 140 and 120 km, photodissociation is a source of 5577 radiation. Chapman three-body recombination is dominant below 120 km.

Three-Dimensional Spin Texture in Hybrid Perovskites and Its Impact on Optical Transitions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xie; Shen, Jimmy -Xuan; Van de Walle, Chris G.

Hybrid perovskites such as MAPbI 3 (MA = CH 3NH 3) exhibit a unique spin texture. The spin texture (as calculated within the Rashba model) has been suggested to be responsible for a suppression of radiative recombination due to a mismatch of spins at the band edges. Here we compute the spin texture from first principles and demonstrate that it does not suppress recombination. The exact spin texture is dominated by the inversion asymmetry of the local electrostatic potential, which is determined by the structural distortion induced by the MA molecule. In addition, the rotation of the MA molecule atmore » room temperature leads to a dynamic spin texture in MAPbI 3. Furthermore these insights call for a reconsideration of the scenario that radiative recombination is suppressed and provide an in-depth understanding of the origin of the spin texture in hybrid perovskites, which is crucial for designing spintronic devices.« less

Photoluminescence and lasing properties of MAPbBr3 single crystals grown from solution

NASA Astrophysics Data System (ADS)

Aryal, Sandip; Lafalce, Evan; Zhang, Chuang; Zhai, Yaxin; Vardeny, Z. Valy

Recent studies of solution-grown single crystals of inorganic-organic hybrid lead-trihalide perovskites have suggested that surface traps may play a significant role in their photophysics. We study electron-hole recombination in single crystal MAPbBr3 through such trap states using cw photoluminescence (PL) and ps transient photoinduced absorption (PA) spectroscopies. By varying the depth of the collecting optics we examined the contributions from surface and bulk radiative recombination. We found a surface dominated PL band at the band-edge that is similar to that observed from polycrystalline thin films, as well as a weaker red-shifted emission band that originates from the bulk crystal. The two PL bands are distinguished in their temperature, excitation intensity and polarization dependencies, as well as their ps dynamics. Additionally, amplified spontaneous emission and crystal-related cavity lasing modes were observed in the same spectral range as the PL band assigned to the surface recombination. This work was funded by AFOSR through MURI Grant RA 9550-14-1-0037.

Strain variation, based on the hemagglutinin gene, in Norwegian ISA virus isolates collected from 1987 to 2001: indications of recombination.

PubMed

Devold, M; Falk, K; Dale, B; Krossøy, B; Biering, E; Aspehaug, V; Nilsen, F; Nylund, A

2001-11-08

Infectious salmon anemia (ISA) is caused by a virus that probably belongs to the Orthomyxoviridae and was first recorded in Norway in 1984. The disease has since spread along the Norwegian coast and has later been found in Canada, Scotland, the Faroe Islands, Chile, and the USA. This study presents sequence variation of the hemagglutinin gene from 37 ISA virus isolates, viz. one isolate from Scotland, one from Canada and 35 from Norway. The hemagglutinin gene contains a highly polymorphic region (HPR), which together with the rest of the gene sequence provides a good tool for studies of epizootics. The gene shows temporal and geographical sequence variation, where certain areas are dominated by distinct groups of isolates. Evidence of transmission of ISA virus isolates within and between regions is given. It is suggested that the hemagglutinin gene from different isolates may recombine. Possible recombination sites are found within the HPR and in the 5'-end flanking region close to the HPR.

Recombinant protein expression for structural biology in HEK 293F suspension cells: a novel and accessible approach.

PubMed

Portolano, Nicola; Watson, Peter J; Fairall, Louise; Millard, Christopher J; Milano, Charles P; Song, Yun; Cowley, Shaun M; Schwabe, John W R

2014-10-16

The expression and purification of large amounts of recombinant protein complexes is an essential requirement for structural biology studies. For over two decades, prokaryotic expression systems such as E. coli have dominated the scientific literature over costly and less efficient eukaryotic cell lines. Despite the clear advantage in terms of yields and costs of expressing recombinant proteins in bacteria, the absence of specific co-factors, chaperones and post-translational modifications may cause loss of function, mis-folding and can disrupt protein-protein interactions of certain eukaryotic multi-subunit complexes, surface receptors and secreted proteins. The use of mammalian cell expression systems can address these drawbacks since they provide a eukaryotic expression environment. However, low protein yields and high costs of such methods have until recently limited their use for structural biology. Here we describe a simple and accessible method for expressing and purifying milligram quantities of protein by performing transient transfections of suspension grown HEK (Human Embryonic Kidney) 293 F cells.

Structural and optical characterization of ZnO nanowires grown on alumina by thermal evaporation method.

PubMed

Mute, A; Peres, M; Peiris, T C; Lourenço, A C; Jensen, Lars R; Monteiro, T

2010-04-01

Zinc oxide nanowires have been grown on alumina substrate by thermal evaporation of zinc nanopowder in the presence of oxygen flow. The growth was performed under ambient pressure and without the use of foreign catalyst. Scanning electron microscopy (SEM) observation showed that the as-grown sample consists of bulk ZnO crystal on the substrate surface with nanowires growing from this base. Growth mechanism of the observed morphology is suggested to be governed by the change of zinc vapour supersaturation during the growth process. X-ray diffraction (XRD) measurement was used to identify the crystalline phase of the nanowires. Optical properties of the nanowires were investigated using Raman scattering and photoluminescence (PL). The appearance of dominant, Raman active E2 (high) phonon mode in the Raman spectrum has confirmed the wurtzite hexagonal phase of the nanowires. With above bandgap excitation the low temperature PL recombination is dominated by donor bound exciton luminescence at -3.37 eV with a narrow full width at half maximum. Free exciton emission is also seen at low temperature and can be observed up to room temperature. The optical data indicates that the grown nanowires have high optical quality.

A DN-mda5 transgenic zebrafish model demonstrates that Mda5 plays an important role in snakehead rhabdovirus resistance.

PubMed

Gabor, K A; Charette, J R; Pietraszewski, M J; Wingfield, D J; Shim, J S; Millard, P J; Kim, C H

2015-08-01

Melanoma Differentiation-Associated protein 5 (MDA5) is a member of the retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) family, which is a cytosolic pattern recognition receptor that detects viral nucleic acids. Here we show an Mda5-dependent response to rhabdovirus infection in vivo using a dominant-negative mda5 transgenic zebrafish. Dominant-negative mda5 zebrafish embryos displayed an impaired antiviral immune response compared to wild-type counterparts that can be rescued by recombinant full-length Mda5. To our knowledge, we have generated the first dominant-negative mda5 transgenic zebrafish and demonstrated a critical role for Mda5 in the antiviral response to rhabdovirus. Copyright © 2015 Elsevier Ltd. All rights reserved.

Flexible Retrieval: When True Inferences Produce False Memories

ERIC Educational Resources Information Center

Carpenter, Alexis C.; Schacter, Daniel L.

2017-01-01

Episodic memory involves flexible retrieval processes that allow us to link together distinct episodes, make novel inferences across overlapping events, and recombine elements of past experiences when imagining future events. However, the same flexible retrieval and recombination processes that underpin these adaptive functions may also leave…

Quantitative X-ray - UV Line and Continuum Spectroscopy with Application to AGN: State-Specific Hydrogenic Recombination Cooling Coefficients for a Wide Range of Conditions

NASA Technical Reports Server (NTRS)

LaMothe, J.; Ferland, Gary J.

2002-01-01

Recombination cooling, in which a free electron emits light while being captured to an ion, is an important cooling process in photoionized clouds that are optically thick or have low metallicity. State specific rather than total recombination cooling rates are needed since the hydrogen atom tends to become optically thick in high-density regimes such as Active Galactic Nuclei. This paper builds upon previous work to derive the cooling rate over the full temperature range where the process can be a significant contributor in a photoionized plasma. We exploit the fact that the recombination and cooling rates are given by intrinsically similar formulae to express the cooling rate in terms of the closely related radiative recombination rate. We give an especially simple but accurate approximation that works for any high hydrogenic level and can be conveniently employed in large-scale numerical simulations.

Effect of interface roughness on Auger recombination in semiconductor quantum wells

NASA Astrophysics Data System (ADS)

Tan, Chee-Keong; Sun, Wei; Wierer, Jonathan J.; Tansu, Nelson

2017-03-01

Auger recombination in a semiconductor is a three-carrier process, wherein the energy from the recombination of an electron and hole pair promotes a third carrier to a higher energy state. In semiconductor quantum wells with increased carrier densities, the Auger recombination becomes an appreciable fraction of the total recombination rate and degrades luminescence efficiency. Gaining insight into the variables that influence Auger recombination in semiconductor quantum wells could lead to further advances in optoelectronic and electronic devices. Here we demonstrate the important role that interface roughness has on Auger recombination within quantum wells. Our computational studies find that as the ratio of interface roughness to quantum well thickness is increased, Auger recombination is significantly enhanced. Specifically, when considering a realistic interface roughness for an InGaN quantum well, the enhancement in Auger recombination rate over a quantum well with perfect heterointerfaces can be approximately four orders of magnitude.

Bound exciton and free exciton states in GaSe thin slab.

PubMed

Wei, Chengrong; Chen, Xi; Li, Dian; Su, Huimin; He, Hongtao; Dai, Jun-Feng

2016-09-22

The photoluminescence (PL) and absorption experiments have been performed in GaSe slab with incident light polarized perpendicular to c-axis of sample at 10 K. An obvious energy difference of about 34 meV between exciton absorption peak and PL peak (the highest energy peak) is observed. By studying the temperature dependence of PL and absorption spectra, we attribute it to energy difference between free exciton and bound exciton states, where main exciton absorption peak comes from free exciton absorption, and PL peak is attributed to recombination of bound exciton at 10 K. This strong bound exciton effect is stable up to 50 K. Moreover, the temperature dependence of integrated PL intensity and PL lifetime reveals that a non-radiative process, with activation energy extracted as 0.5 meV, dominates PL emission.

Sordaria, a model system to uncover links between meiotic pairing and recombination

PubMed Central

Zickler, Denise; Espagne, Eric

2017-01-01

The mycelial fungus Sordaria macrospora was first used as experimental system for meiotic recombination. This review shows that it provides also a powerful cytological system for dissecting chromosome dynamics in wild-type and mutant meioses. Fundamental cytogenetic findings include: (1) The identification of presynaptic alignment as a key step in pairing of homologous chromosomes. (2) The discovery that biochemical complexes that mediate recombination at the DNA level concomitantly mediate pairing of homologs. (3) This pairing process involves not only resolution but also avoidance of chromosomal entanglements and the resolution system includes dissolution of constraining DNA recombination interactions, achieved by a unique role of Mlh1. (4) Discovery that the central components of the synaptonemal complex directly mediate the re-localization of the recombination proteins from on-axis to in-between homologue axis positions. (5) Identification of putative STUbL protein Hei10 as a structure-based signal transduction molecule that coordinates progression and differentiation of recombinational interactions at multiple stages. (6) Discovery that a single interference process mediates both nucleation of the SC and designation of crossover sites, thereby ensuring even spacing of both features. (7) Discovery of local modulation of sister-chromatid cohesion at sites of crossover recombination. PMID:26877138

Empirically based device modeling of bulk heterojunction organic photovoltaics

NASA Astrophysics Data System (ADS)

Pierre, Adrien; Lu, Shaofeng; Howard, Ian A.; Facchetti, Antonio; Arias, Ana Claudia

2013-04-01

We develop an empirically based optoelectronic model to accurately simulate the photocurrent in organic photovoltaic (OPV) devices with novel materials including bulk heterojunction OPV devices based on a new low band gap dithienothiophene-DPP donor polymer, P(TBT-DPP), blended with PC70BM at various donor-acceptor weight ratios and solvent compositions. Our devices exhibit power conversion efficiencies ranging from 1.8% to 4.7% at AM 1.5G. Electron and hole mobilities are determined using space-charge limited current measurements. Bimolecular recombination coefficients are both analytically calculated using slowest-carrier limited Langevin recombination and measured using an electro-optical pump-probe technique. Exciton quenching efficiencies in the donor and acceptor domains are determined from photoluminescence spectroscopy. In addition, dielectric and optical constants are experimentally determined. The photocurrent and its bias-dependence that we simulate using the optoelectronic model we develop, which takes into account these physically measured parameters, shows less than 7% error with respect to the experimental photocurrent (when both experimentally and semi-analytically determined recombination coefficient is used). Free carrier generation and recombination rates of the photocurrent are modeled as a function of the position in the active layer at various applied biases. These results show that while free carrier generation is maximized in the center of the device, free carrier recombination is most dominant near the electrodes even in high performance devices. Such knowledge of carrier activity is essential for the optimization of the active layer by enhancing light trapping and minimizing recombination. Our simulation program is intended to be freely distributed for use in laboratories fabricating OPV devices.

Dual Thermosensitive Hydrogels Assembled from the Conserved C-Terminal Domain of Spider Dragline Silk.

PubMed

Qian, Zhi-Gang; Zhou, Ming-Liang; Song, Wen-Wen; Xia, Xiao-Xia

2015-11-09

Stimuli-responsive hydrogels have great potentials in biomedical and biotechnological applications. Due to the advantages of precise control over molecular weight and being biodegradable, protein-based hydrogels and their applications have been extensively studied. However, protein hydrogels with dual thermosensitive properties are rarely reported. Here we present the first report of dual thermosensitive hydrogels assembled from the conserved C-terminal domain of spider dragline silk. First, we found that recombinant C-terminal domain of major ampullate spidroin 1 (MaSp1) of the spider Nephila clavipes formed hydrogels when cooled to approximately 2 °C or heated to 65 °C. The conformational changes and self-assembly of the recombinant protein were studied to understand the mechanism of the gelation processes using multiple methods. It was proposed that the gelation in the low-temperature regime was dominated by hydrogen bonding and hydrophobic interaction between folded protein molecules, whereas the gelation in the high-temperature regime was due to cross-linking of the exposed hydrophobic patches resulting from partial unfolding of the protein upon heating. More interestingly, genetic fusion of the C-terminal domain to a short repetitive region of N. clavipes MaSp1 resulted in a chimeric protein that formed a hydrogel with significantly improved mechanical properties at low temperatures between 2 and 10 °C. Furthermore, the formation of similar hydrogels was observed for the recombinant C-terminal domains of dragline silk of different spider species, thus demonstrating the conserved ability to form dual thermosensitive hydrogels. These findings may be useful in the design and construction of novel protein hydrogels with tunable multiple thermosensitivity for applications in the future.

Fusion tags for protein solubility, purification and immunogenicity in Escherichia coli: the novel Fh8 system

PubMed Central

Costa, Sofia; Almeida, André; Castro, António; Domingues, Lucília

2014-01-01

Proteins are now widely produced in diverse microbial cell factories. The Escherichia coli is still the dominant host for recombinant protein production but, as a bacterial cell, it also has its issues: the aggregation of foreign proteins into insoluble inclusion bodies is perhaps the main limiting factor of the E. coli expression system. Conversely, E. coli benefits of cost, ease of use and scale make it essential to design new approaches directed for improved recombinant protein production in this host cell. With the aid of genetic and protein engineering novel tailored-made strategies can be designed to suit user or process requirements. Gene fusion technology has been widely used for the improvement of soluble protein production and/or purification in E. coli, and for increasing peptide’s immunogenicity as well. New fusion partners are constantly emerging and complementing the traditional solutions, as for instance, the Fh8 fusion tag that has been recently studied and ranked among the best solubility enhancer partners. In this review, we provide an overview of current strategies to improve recombinant protein production in E. coli, including the key factors for successful protein production, highlighting soluble protein production, and a comprehensive summary of the latest available and traditionally used gene fusion technologies. A special emphasis is given to the recently discovered Fh8 fusion system that can be used for soluble protein production, purification, and immunogenicity in E. coli. The number of existing fusion tags will probably increase in the next few years, and efforts should be taken to better understand how fusion tags act in E. coli. This knowledge will undoubtedly drive the development of new tailored-made tools for protein production in this bacterial system. PMID:24600443

Accumulation and processing of a recombinant protein designed as a cleavable fusion to the endogenous Rubisco LSU protein in Chlamydomonas chloroplast

PubMed Central

Muto, Machiko; Henry, Ryan E; Mayfield, Stephen P

2009-01-01

Background Expression of recombinant proteins in green algal chloroplast holds substantial promise as a platform for the production of human therapeutic proteins. A number of proteins have been expressed in the chloroplast of Chlamydomonas reinhardtii, including complex mammalian proteins, but many of these proteins accumulate to significantly lower levels than do endogenous chloroplast proteins. We examined if recombinant protein accumulation could be enhanced by genetically fusing the recombinant reporter protein, luciferase, to the carboxy-terminal end of an abundant endogenous protein, the large subunit of ribulose bisphosphate carboxylase (Rubisco LSU). Additionally, as recombinant proteins fused to endogenous proteins are of little clinical or commercial value, we explored the possibility of engineering our recombinant protein to be cleavable from the endogenous protein in vivo. This strategy would obviate the need for further in vitro processing steps in order to produce the desired recombinant protein. To achieve this, a native protein-processing site from preferredoxin (preFd) was placed between the Rubisco LSU and luciferase coding regions in the fusion protein construct. Results The luciferase from the fusion protein accumulated to significantly higher levels than luciferase expressed alone. By eliminating the endogenous Rubisco large subunit gene (rbcL), we achieved a further increase in luciferase accumulation with respect to luciferase expression in the WT background. Importantly, near-wild type levels of functional Rubisco holoenzyme were generated following the proteolytic removal of the fused luciferase, while luciferase activity for the fusion protein was almost ~33 times greater than luciferase expressed alone. These data demonstrate the utility of using fusion proteins to enhance recombinant protein accumulation in algal chloroplasts, and also show that engineered proteolytic processing sites can be used to liberate the exogenous protein from the endogenous fusion partner, allowing for the purification of the intended mature protein. Conclusion These results demonstrate the utility of fusion proteins in algal chloroplast as a method to increase accumulation of recombinant proteins that are difficult to express. Since Rubisco is ubiquitous to land plants and green algae, this strategy may also be applied to higher plant transgenic expression systems. PMID:19323825

The remarkable frequency of human immunodeficiency virus type 1 genetic recombination.

PubMed

Onafuwa-Nuga, Adewunmi; Telesnitsky, Alice

2009-09-01

The genetic diversity of human immunodeficiency virus type 1 (HIV-1) results from a combination of point mutations and genetic recombination, and rates of both processes are unusually high. This review focuses on the mechanisms and outcomes of HIV-1 genetic recombination and on the parameters that make recombination so remarkably frequent. Experimental work has demonstrated that the process that leads to recombination--a copy choice mechanism involving the migration of reverse transcriptase between viral RNA templates--occurs several times on average during every round of HIV-1 DNA synthesis. Key biological factors that lead to high recombination rates for all retroviruses are the recombination-prone nature of their reverse transcription machinery and their pseudodiploid RNA genomes. However, HIV-1 genes recombine even more frequently than do those of many other retroviruses. This reflects the way in which HIV-1 selects genomic RNAs for coencapsidation as well as cell-to-cell transmission properties that lead to unusually frequent associations between distinct viral genotypes. HIV-1 faces strong and changeable selective conditions during replication within patients. The mode of HIV-1 persistence as integrated proviruses and strong selection for defective proviruses in vivo provide conditions for archiving alleles, which can be resuscitated years after initial provirus establishment. Recombination can facilitate drug resistance and may allow superinfecting HIV-1 strains to evade preexisting immune responses, thus adding to challenges in vaccine development. These properties converge to provide HIV-1 with the means, motive, and opportunity to recombine its genetic material at an unprecedented high rate and to allow genetic recombination to serve as one of the highest barriers to HIV-1 eradication.

The evolution of HIV-1 group M genetic variability in Southern Cameroon is characterized by several emerging recombinant forms of CRF02_AG and viruses with drug resistance mutations.

PubMed

Agyingi, Lucy; Mayr, Luzia M; Kinge, Thompson; Orock, George Enow; Ngai, Johnson; Asaah, Bladine; Mpoame, Mbida; Hewlett, Indira; Nyambi, Phillipe

2014-03-01

The HIV epidemic in Cameroon is marked by a broad genetic diversity dominated by circulating recombinant forms (CRFs). Studies performed more than a decade ago in urban settings of Southern Cameroon revealed a dominance of the CRF02_AG and clade A variants in >90% of the infected subjects; however, little is known about the evolving viral variants circulating in this region. To document circulating HIV viral diversity, four regions of the viral genome (gag, PR, reverse transcriptase, env) in 116 HIV-1 positive individuals in Limbe, Southern Cameroon, were PCR-amplified. Sequences obtained at the RT and protease regions were analyzed for mutations that conferred drug resistance using the Stanford Drug Resistance Database. The present study reveals a broad genetic diversity characterized by several unique recombinant forms (URF) accounting for 36% of infections, 48.6% of patients infected with CRF02_AG, and the emergence of CRF22_01A1 in 7.2% of patients. Three out of 15 (20%) treated patients and 13 out of 93 (13.9%) drug naïve patients harbor drug resistance mutations to RT inhibitors, while 3.2% of drug naïve patients harbor drug resistance mutations associated with protease inhibitors. The high proportion (13.9%) of drug resistance mutations among the drug naïve patients reveals the ongoing transmission of these viruses in this region of Cameroon and highlights the need for drug resistance testing before starting treatment for patients infected with HIV-1. © 2013 Wiley Periodicals, Inc.

Pangenome Analysis of Burkholderia pseudomallei: Genome Evolution Preserves Gene Order despite High Recombination Rates.

PubMed

Spring-Pearson, Senanu M; Stone, Joshua K; Doyle, Adina; Allender, Christopher J; Okinaka, Richard T; Mayo, Mark; Broomall, Stacey M; Hill, Jessica M; Karavis, Mark A; Hubbard, Kyle S; Insalaco, Joseph M; McNew, Lauren A; Rosenzweig, C Nicole; Gibbons, Henry S; Currie, Bart J; Wagner, David M; Keim, Paul; Tuanyok, Apichai

2015-01-01

The pangenomic diversity in Burkholderia pseudomallei is high, with approximately 5.8% of the genome consisting of genomic islands. Genomic islands are known hotspots for recombination driven primarily by site-specific recombination associated with tRNAs. However, recombination rates in other portions of the genome are also high, a feature we expected to disrupt gene order. We analyzed the pangenome of 37 isolates of B. pseudomallei and demonstrate that the pangenome is 'open', with approximately 136 new genes identified with each new genome sequenced, and that the global core genome consists of 4568±16 homologs. Genes associated with metabolism were statistically overrepresented in the core genome, and genes associated with mobile elements, disease, and motility were primarily associated with accessory portions of the pangenome. The frequency distribution of genes present in between 1 and 37 of the genomes analyzed matches well with a model of genome evolution in which 96% of the genome has very low recombination rates but 4% of the genome recombines readily. Using homologous genes among pairs of genomes, we found that gene order was highly conserved among strains, despite the high recombination rates previously observed. High rates of gene transfer and recombination are incompatible with retaining gene order unless these processes are either highly localized to specific sites within the genome, or are characterized by symmetrical gene gain and loss. Our results demonstrate that both processes occur: localized recombination introduces many new genes at relatively few sites, and recombination throughout the genome generates the novel multi-locus sequence types previously observed while preserving gene order.

Spatial variation in carrier dynamics along a single CdSSe nanowire

NASA Astrophysics Data System (ADS)

Blake, Jolie C.; Eldridge, Peter S.; Gundlach, Lars

2014-10-01

Ultrafast charge carrier dynamics along individual CdSxSe1-x nanowires has been measured. The use of an improved ultrafast Kerr-gated microscope allows for spatially resolved luminescence measurements along a single nanowire. Amplified spontaneous emission (ASE) was observed at high excitation fluences. Position dependent variations of ultrafast ASE dynamics were observed. SEM and colorimetric measurements showed that the difference in dynamics can be attributed to variations in non-radiative recombination rates along the wire. The dominant Shockley-Read recombination rate can be extracted from ASE dynamics and can be directly related to charge carrier mobility and defect density. Employing ASE as a probe for defect densities provides a new sub-micron spatially resolved, contactless method for measurements of charge carrier mobility.

Properties of p-n-junctions formed by a laser irradiation of a surface of n-Cd1-xZnxTe single crystal

NASA Astrophysics Data System (ADS)

Khomyak, V. V.; Ilashchuk, M. I.; Shtepliuk, I. I.

2015-03-01

Photosensitive barrier structures were fabricated by high-power pulsed laser irradiation of a freshly-cleaved surface of п-type bulk Cd1-xZnxTe substrates. Their electrical properties were investigated and discussed. Dominant carrier mechanisms at a forward and a reverse bias in terms of a recombination and tunnel-recombination model were analyzed. At the illumination reaching 100 mW · cm-2, these surface-barrier р-Cd1-хZnхTe/п-Cd1-хZnхTe structures were possessed by the following photoelectric parameters: open-circuit voltage Voc = 0.61 V, short-circuit current Isc = 0.21 mА and fill factor FF = 0.49, respectively.

Proton enhancement at large pT at the CERN large hadron collider without structure in associated-particle distribution.

PubMed

Hwa, Rudolph C; Yang, C B

2006-07-28

The production of pions and protons in the pT range between 10 and 20 GeV/c for Pb+Pb collisions at CERN LHC is studied in the recombination model. It is shown that the dominant mechanism for hadronization is the recombination of shower partons from neighboring jets when the jet density is high. Protons are more copiously produced than pions in that pT range because the coalescing partons can have lower momentum fractions, but no thermal partons are involved. The proton-to-pion ratio can be as high as 20. When such high pT hadrons are used as trigger particles, there will not be any associated particles that are not in the background.

A novel truncation mutation in CRYBB1 associated with autosomal dominant congenital cataract with nystagmus.

PubMed

Rao, Yan; Dong, Sufang; Li, Zuhua; Yang, Guohua; Peng, Chunyan; Yan, Ming; Zheng, Fang

2017-01-01

To identify the potential candidate genes for a large Chinese family with autosomal dominant congenital cataract (ADCC) and nystagmus, and investigate the possible molecular mechanism underlying the role of the candidate genes in cataractogenesis. We combined the linkage analysis and direct sequencing for the candidate genes in the linkage regions to identify the causative mutation. The molecular and bio-functional properties of the proteins encoded by the candidate genes was further explored with biophysical and biochemical studies of the recombinant wild-type and mutant proteins. We identified a c. C749T (p.Q227X) transversion in exon 6 of CRYBB1 , a cataract-causative gene. This nonsense mutation changes a phylogenetically conserved glutamine to a stop codon and is predicted to truncate the C-terminus of the wild-type protein by 26 amino acids. Comparison of the biophysical and biochemical properties of the recombinant full-length and truncated βB1-crystallins revealed that the mutation led to the insolubility and the phase separation phenomenon of the truncated protein with a changed conformation. Meanwhile, the thermal stability of the truncated βB1-crystallin was significantly decreased, and the mutation diminished the chaperoning ability of αA-crystallin with the mutant under heating stress. Our findings highlight the importance of the C-terminus in βB1-crystallin in maintaining the crystalline function and stability, and provide a novel insight into the molecular mechanism underlying the pathogenesis of human autosomal dominant congenital cataract.

Recombination radius of a Frenkel pair and capture radius of a self-interstitial atom by vacancy clusters in bcc Fe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakashima, Kenichi; Stoller, Roger E.; Xu, Haixuan

The recombination radius of a Frenkel pair is a fundamental parameter for the object kinetic Monte Carlo (OKMC) and mean field rate theory (RT) methods that are used to investigate irradiation damage accumulation in neutron irradiated nuclear materials. The recombination radius in bcc Fe has been studied both experimentally and numerically, however there is no general consensus about its value. The detailed atomistic processes of recombination also remain uncertain. Values from 1:0a₀ to 3:3a₀ have been employed as a recombination radius in previous studies using OKMC and RT. The recombination process of a Frenkel pair is investigated at the atomicmore » level using the self-evolved atomistic kinetic Monte Carlo (SEAKMC) method in this paper. SEAKMC calculations reveal that a self-interstitial atom recombines with a vacancy in a spontaneous reaction from several nearby sites following characteristic pathways. The recombination radius of a Frenkel pair is estimated to be 2.26a₀ by taking the average of the recombination distances from 80 simulation cases. This value agrees well with the experimental estimate. In addition, we apply these procedures to the capture radius of a self-interstitial atom by a vacancy cluster. The capture radius is found to gradually increase with the size of the vacancy cluster. The fitting curve for the capture radius is obtained as a function of the number of vacancies in the cluster.« less

Recombination radius of a Frenkel pair and capture radius of a self-interstitial atom by vacancy clusters in bcc Fe

DOE PAGES

Nakashima, Kenichi; Stoller, Roger E.; Xu, Haixuan

2015-08-04

The recombination radius of a Frenkel pair is a fundamental parameter for the object kinetic Monte Carlo (OKMC) and mean field rate theory (RT) methods that are used to investigate irradiation damage accumulation in neutron irradiated nuclear materials. The recombination radius in bcc Fe has been studied both experimentally and numerically, however there is no general consensus about its value. The detailed atomistic processes of recombination also remain uncertain. Values from 1:0a₀ to 3:3a₀ have been employed as a recombination radius in previous studies using OKMC and RT. The recombination process of a Frenkel pair is investigated at the atomicmore » level using the self-evolved atomistic kinetic Monte Carlo (SEAKMC) method in this paper. SEAKMC calculations reveal that a self-interstitial atom recombines with a vacancy in a spontaneous reaction from several nearby sites following characteristic pathways. The recombination radius of a Frenkel pair is estimated to be 2.26a₀ by taking the average of the recombination distances from 80 simulation cases. This value agrees well with the experimental estimate. In addition, we apply these procedures to the capture radius of a self-interstitial atom by a vacancy cluster. The capture radius is found to gradually increase with the size of the vacancy cluster. The fitting curve for the capture radius is obtained as a function of the number of vacancies in the cluster.« less

Epstein-Barr virus (EBV) recombinants: use of positive selection markers to rescue mutants in EBV-negative B-lymphoma cells.

PubMed Central

Wang, F; Marchini, A; Kieff, E

1991-01-01

The objective of these experiments was to develop strategies for creation and identification of recombinant mutant Epstein-Barr viruses (EBV). EBV recombinant molecular genetics has been limited to mutations within a short DNA segment deleted from a nontransforming EBV and an underlying strategy which relies on growth transformation of primary B lymphocytes for identification of recombinants. Thus, mutations outside the deletion or mutations which affect transformation cannot be easily recovered. In these experiments we investigated whether a toxic drug resistance gene, guanine phosphoribosyltransferase or hygromycin phosphotransferase, driven by the simian virus 40 promoter can be recombined into the EBV genome and can function to identify B-lymphoma cells infected with recombinant virus. Two different strategies were used to recombine the drug resistance marker into the EBV genome. Both utilized transfection of partially permissive, EBV-infected B95-8 cells and positive selection for cells which had incorporated a functional drug resistance gene. In the first series of experiments, B95-8 clones were screened for transfected DNA that had recombined into the EBV genome. In the second series of experiments, the transfected drug resistance marker was linked to the plasmid and lytic EBV origins so that it was maintained as an episome and could recombine with the B95-8 EBV genome during virus replication. The recombinant EBV from either experiment could be recovered by infection and toxic drug selection of EBV-negative B-lymphoma cells. The EBV genome in these B-lymphoma cells is frequently an episome. Virus genes associated with latent infection of primary B lymphocytes are expressed. Expression of Epstein-Barr virus nuclear antigen 2 (EBNA-2) and the EBNA-3 genes is variable relative to that of EBNA-1, as is characteristic of some naturally infected Burkitt tumor cells. Moreover, the EBV-infected B-lymphoma cells are often partially permissive for early replicative cycle gene expression and virus replication can be induced, in contrast to previously reported in vitro infected B-lymphoma cells. These studies demonstrate that dominant selectable markers can be inserted into the EBV genome, are active in the context of the EBV genome, and can be used to recover recombinant EBV in B-lymphoma cells. This system should be particularly useful for recovering EBV genomes with mutations in essential transforming genes. Images PMID:1848303

Epstein-Barr virus (EBV) recombinants: use of positive selection markers to rescue mutants in EBV-negative B-lymphoma cells.

PubMed

Wang, F; Marchini, A; Kieff, E

1991-04-01

The objective of these experiments was to develop strategies for creation and identification of recombinant mutant Epstein-Barr viruses (EBV). EBV recombinant molecular genetics has been limited to mutations within a short DNA segment deleted from a nontransforming EBV and an underlying strategy which relies on growth transformation of primary B lymphocytes for identification of recombinants. Thus, mutations outside the deletion or mutations which affect transformation cannot be easily recovered. In these experiments we investigated whether a toxic drug resistance gene, guanine phosphoribosyltransferase or hygromycin phosphotransferase, driven by the simian virus 40 promoter can be recombined into the EBV genome and can function to identify B-lymphoma cells infected with recombinant virus. Two different strategies were used to recombine the drug resistance marker into the EBV genome. Both utilized transfection of partially permissive, EBV-infected B95-8 cells and positive selection for cells which had incorporated a functional drug resistance gene. In the first series of experiments, B95-8 clones were screened for transfected DNA that had recombined into the EBV genome. In the second series of experiments, the transfected drug resistance marker was linked to the plasmid and lytic EBV origins so that it was maintained as an episome and could recombine with the B95-8 EBV genome during virus replication. The recombinant EBV from either experiment could be recovered by infection and toxic drug selection of EBV-negative B-lymphoma cells. The EBV genome in these B-lymphoma cells is frequently an episome. Virus genes associated with latent infection of primary B lymphocytes are expressed. Expression of Epstein-Barr virus nuclear antigen 2 (EBNA-2) and the EBNA-3 genes is variable relative to that of EBNA-1, as is characteristic of some naturally infected Burkitt tumor cells. Moreover, the EBV-infected B-lymphoma cells are often partially permissive for early replicative cycle gene expression and virus replication can be induced, in contrast to previously reported in vitro infected B-lymphoma cells. These studies demonstrate that dominant selectable markers can be inserted into the EBV genome, are active in the context of the EBV genome, and can be used to recover recombinant EBV in B-lymphoma cells. This system should be particularly useful for recovering EBV genomes with mutations in essential transforming genes.

Signals from the epoch of cosmological recombination (Karl Schwarzschild Award Lecture 2008)

NASA Astrophysics Data System (ADS)

Sunyaev, R. A.; Chluba, J.

2009-07-01

The physical ingredients to describe the epoch of cosmological recombination are amazingly simple and well-understood. This fact allows us to take into account a very large variety of physical processes, still finding potentially measurable consequences for the energy spectrum and temperature anisotropies of the Cosmic Microwave Background (CMB). In this contribution we provide a short historical overview in connection with the cosmological recombination epoch and its connection to the CMB. Also we highlight some of the detailed physics that were studied over the past few years in the context of the cosmological recombination of hydrogen and helium. The impact of these considerations is two-fold: The associated release of photons during this epoch leads to interesting and unique deviations of the Cosmic Microwave Background (CMB) energy spectrum from a perfect blackbody, which, in particular at decimeter wavelength and the Wien part of the CMB spectrum, may become observable in the near future. Despite the fact that the abundance of helium is rather small, it still contributes a sizeable amount of photons to the full recombination spectrum, leading to additional distinct spectral features. Observing the spectral distortions from the epochs of hydrogen and helium recombination, in principle would provide an additional way to determine some of the key parameters of the Universe (e.g. the specific entropy, the CMB monopole temperature and the pre-stellar abundance of helium). Also it permits us to confront our detailed understanding of the recombination process with direct observational evidence. In this contribution we illustrate how the theoretical spectral template of the cosmological recombination spectrum may be utilized for this purpose. We also show that because hydrogen and helium recombine at very different epochs it is possible to address questions related to the thermal history of our Universe. In particular the cosmological recombination radiation may allow us to distinguish between Compton y-distortions that were created by energy release before or after the recombination of the Universe finished. With the advent of high precision CMB data, e.g. as will be available using the PLANCK Surveyor or CMBPOL, a very accurate theoretical understanding of the ionization history of the Universe becomes necessary for the interpretation of the CMB temperature and polarization anisotropies. Here we show that the uncertainty in the ionization history due to several processes, which until now were not taken in to account in the standard recombination code RECFAST, reaches the percent level. In particular He II->He I recombination occurs significantly faster because of the presence of a tiny fraction of neutral hydrogen at {z⪉ 2400}. Also recently it was demonstrated that in the case of H I Lyman α photons the time-dependence of the emission process and the asymmetry between the emission and absorption profile cannot be ignored. However, it is indeed surprising how inert the cosmological recombination history is even at percent-level accuracy. Observing the cosmological recombination spectrum should in principle allow us to directly check this conclusion, which until now is purely theoretical. Also it may allow to reconstruct the ionization history using observational data.

Requirements for high-efficiency solar cells

NASA Technical Reports Server (NTRS)

Sah, C. T.

1986-01-01

Minimum recombination and low injection level are essential for high efficiency. Twenty percent AM1 efficiency requires a dark recombination current density of 2 x 10 to the minus 13th power A/sq cm and a recombination center density of less than 10 to the 10th power /cu cm. Recombination mechanisms at thirteen locations in a conventional single crystalline silicon cell design are reviewed. Three additional recombination locations are described at grain boundaries in polycrystalline cells. Material perfection and fabrication process optimization requirements for high efficiency are outlined. Innovative device designs to reduce recombination in the bulk and interfaces of single crystalline cells and in the grain boundary of polycrystalline cells are reviewed.

Self-consistent ab initio Calculations for Photoionization and Electron-Ion Recombination Using the R-Matrix Method

NASA Astrophysics Data System (ADS)

Nahar, S. N.

2003-01-01

Most astrophysical plasmas entail a balance between ionization and recombination. We present new results from a unified method for self-consistent and ab initio calculations for the inverse processes of photoionization and (e + ion) recombination. The treatment for (e + ion) recombination subsumes the non-resonant radiative recombination and the resonant dielectronic recombination processes in a unified scheme (S.N. Nahar and A.K. Pradhan, Phys. Rev. A 49, 1816 (1994);H.L. Zhang, S.N. Nahar, and A.K. Pradhan, J.Phys.B, 32,1459 (1999)). Calculations are carried out using the R-matrix method in the close coupling approximation using an identical wavefunction expansion for both processes to ensure self-consistency. The results for photoionization and recombination cross sections may also be compared with state-of-the-art experiments on synchrotron radiation sources for photoionization, and on heavy ion storage rings for recombination. The new experiments display heretofore unprecedented detail in terms of resonances and background cross sections and thereby calibrate the theoretical data precisely. We find a level of agreement between theory and experiment at about 10% for not only the ground state but also the metastable states. The recent experiments therefore verify the estimated accuracy of the vast amount of photoionization data computed under the OP, IP and related works. features. Present work also reports photoionization cross sections including relativistic effects in the Breit-Pauli R-matrix (BPRM) approximation. Detailed features in the calculated cross sections exhibit the missing resonances due to fine structure. Self-consistent datasets for photoionization and recombination have so far been computed for approximately 45 atoms and ions. These are being reported in a continuing series of publications in Astrophysical J. Supplements (e.g. references below). These data will also be available from the electronic database TIPTOPBASE (http://heasarc.gsfc.nasa.gov)

SELECTIVE ADVANTAGE OF RECOMBINATION IN EVOLVING PROTEIN POPULATIONS: A LATTICE MODEL STUDY

PubMed Central

WILLIAMS, PAUL D.; POLLOCK, DAVID D.

2010-01-01

Recent research has attempted to clarify the contributions of several mutational processes, such as substitutions or homologous recombination. Simplistic, tractable protein models, which determine the compact native structure phenotype from the sequence genotype, are well-suited to such studies. In this paper, we use a lattice-protein model to examine the effects of point mutation and homologous recombination on evolving populations of proteins. We find that while the majority of mutation and recombination events are neutral or deleterious, recombination is far more likely to be beneficial. This results in a faster increase in fitness during evolution, although the final fitness level is not significantly changed. This transient advantage provides an evolutionary advantage to subpopulations that undergo recombination, allowing fixation of recombination to occur in the population. PMID:25473139

Selective Advantage of Recombination in Evolving Protein Populations:. a Lattice Model Study

NASA Astrophysics Data System (ADS)

Williams, Paul D.; Pollock, David D.; Goldstein, Richard A.

Recent research has attempted to clarify the contributions of several mutational processes, such as substitutions or homologous recombination. Simplistic, tractable protein models, which determine the compact native structure phenotype from the sequence genotype, are well-suited to such studies. In this paper, we use a lattice-protein model to examine the effects of point mutation and homologous recombination on evolving populations of proteins. We find that while the majority of mutation and recombination events are neutral or deleterious, recombination is far more likely to be beneficial. This results in a faster increase in fitness during evolution, although the final fitness level is not significantly changed. This transient advantage provides an evolutionary advantage to subpopulations that undergo recombination, allowing fixation of recombination to occur in the population.

Extraction and purification methods in downstream processing of plant-based recombinant proteins.

PubMed

Łojewska, Ewelina; Kowalczyk, Tomasz; Olejniczak, Szymon; Sakowicz, Tomasz

2016-04-01

During the last two decades, the production of recombinant proteins in plant systems has been receiving increased attention. Currently, proteins are considered as the most important biopharmaceuticals. However, high costs and problems with scaling up the purification and isolation processes make the production of plant-based recombinant proteins a challenging task. This paper presents a summary of the information regarding the downstream processing in plant systems and provides a comprehensible overview of its key steps, such as extraction and purification. To highlight the recent progress, mainly new developments in the downstream technology have been chosen. Furthermore, besides most popular techniques, alternative methods have been described. Copyright © 2015 Elsevier Inc. All rights reserved.

New Tool Quantitatively Maps Minority-Carrier Lifetime of Multicrystalline Silicon Bricks (Fact Sheet)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

2011-11-01

NREL's new imaging tool could provide manufacturers with insight on their processes. Scientists at the National Renewable Energy Laboratory (NREL) have used capabilities within the Process Development and Integration Laboratory (PDIL) to generate quantitative minority-carrier lifetime maps of multicrystalline silicon (mc-Si) bricks. This feat has been accomplished by using the PDIL's photoluminescence (PL) imaging system in conjunction with transient lifetime measurements obtained using a custom NREL-designed resonance-coupled photoconductive decay (RCPCD) system. PL imaging can obtain rapid high-resolution images that provide a qualitative assessment of the material lifetime-with the lifetime proportional to the pixel intensity. In contrast, the RCPCD technique providesmore » a fast quantitative measure of the lifetime with a lower resolution and penetrates millimeters into the mc-Si brick, providing information on bulk lifetimes and material quality. This technique contrasts with commercially available minority-carrier lifetime mapping systems that use microwave conductivity measurements. Such measurements are dominated by surface recombination and lack information on the material quality within the bulk of the brick. By combining these two complementary techniques, we obtain high-resolution lifetime maps at very fast data acquisition times-attributes necessary for a production-based diagnostic tool. These bulk lifetime measurements provide manufacturers with invaluable feedback on their silicon ingot casting processes. NREL has been applying the PL images of lifetime in mc-Si bricks in collaboration with a U.S. photovoltaic industry partner through Recovery Act Funded Project ARRA T24. NREL developed a new tool to quantitatively map minority-carrier lifetime of multicrystalline silicon bricks by using photoluminescence imaging in conjunction with resonance-coupled photoconductive decay measurements. Researchers are not hindered by surface recombination and can look deeper into the material to map bulk lifetimes. The tool is being applied to silicon bricks in a project collaborating with a U.S. photovoltaic industry partner. Photovoltaic manufacturers can use the NREL tool to obtain valuable feedback on their silicon ingot casting processes.« less

Tritium waste package

DOEpatents

Rossmassler, Rich; Ciebiera, Lloyd; Tulipano, Francis J.; Vinson, Sylvester; Walters, R. Thomas

1995-01-01

A containment and waste package system for processing and shipping tritium xide waste received from a process gas includes an outer drum and an inner drum containing a disposable molecular sieve bed (DMSB) seated within outer drum. The DMSB includes an inlet diffuser assembly, an outlet diffuser assembly, and a hydrogen catalytic recombiner. The DMSB absorbs tritium oxide from the process gas and converts it to a solid form so that the tritium is contained during shipment to a disposal site. The DMSB is filled with type 4A molecular sieve pellets capable of adsorbing up to 1000 curies of tritium. The recombiner contains a sufficient amount of catalyst to cause any hydrogen add oxygen present in the process gas to recombine to form water vapor, which is then adsorbed onto the DMSB.

Tritium waste package

DOEpatents

Rossmassler, R.; Ciebiera, L.; Tulipano, F.J.; Vinson, S.; Walters, R.T.

1995-11-07

A containment and waste package system for processing and shipping tritium oxide waste received from a process gas includes an outer drum and an inner drum containing a disposable molecular sieve bed (DMSB) seated within the outer drum. The DMSB includes an inlet diffuser assembly, an outlet diffuser assembly, and a hydrogen catalytic recombiner. The DMSB absorbs tritium oxide from the process gas and converts it to a solid form so that the tritium is contained during shipment to a disposal site. The DMSB is filled with type 4A molecular sieve pellets capable of adsorbing up to 1000 curies of tritium. The recombiner contains a sufficient amount of catalyst to cause any hydrogen and oxygen present in the process gas to recombine to form water vapor, which is then adsorbed onto the DMSB. 1 fig.

Biotechnological advances towards an enhanced peroxidase production in Pichia pastoris.

PubMed

Krainer, Florian W; Gerstmann, Michaela A; Darnhofer, Barbara; Birner-Gruenberger, Ruth; Glieder, Anton

2016-09-10

Horseradish peroxidase (HRP) is a high-demand enzyme for applications in diagnostics, bioremediation, biocatalysis and medicine. Current HRP preparations are isolated from horseradish roots as mixtures of biochemically diverse isoenzymes. Thus, there is a strong need for a recombinant production process enabling a steady supply with enzyme preparations of consistent high quality. However, most current recombinant production systems are limited at titers in the low mg/L range. In this study, we used the well-known yeast Pichia pastoris as host for recombinant HRP production. To enhance recombinant enzyme titers we systematically evaluated engineering approaches on the secretion process, coproduction of helper proteins, and compared expression from the strong methanol-inducible PAOX1 promoter, the strong constitutive PGAP promoter, and a novel bidirectional promoter PHTX1. Ultimately, coproduction of HRP and active Hac1 under PHTX1 control yielded a recombinant HRP titer of 132mg/L after 56h of cultivation in a methanol-independent and easy-to-do bioreactor cultivation process. With regard to the many versatile applications for HRP, the establishment of a microbial host system suitable for efficient recombinant HRP production was highly overdue. The novel HRP production platform in P. pastoris presented in this study sets a new benchmark for this medically relevant enzyme. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

A Multi-Site Study of Norovirus Molecular Epidemiology in Australia and New Zealand, 2013-2014

PubMed Central

Lim, Kun Lee; Hewitt, Joanne; Sitabkhan, Alefiya; Eden, John-Sebastian; Lun, Jennifer; Levy, Avram; Merif, Juan; Smith, David; Rawlinson, William D.; White, Peter A.

2016-01-01

Background Norovirus (NoV) is the major cause of acute gastroenteritis across all age groups. In particular, variants of genogroup II, genotype 4 (GII.4) have been associated with epidemics globally, occurring approximately every three years. The pandemic GII.4 variant, Sydney 2012, was first reported in early 2012 and soon became the predominant circulating NoV strain globally. Despite its broad impact, both clinically and economically, our understanding of the fundamental diversity and mechanisms by which new NoV strains emerge remains limited. In this study, we describe the molecular epidemiological trends of NoV-associated acute gastroenteritis in Australia and New Zealand between January 2013 and June 2014. Methodology Overall, 647 NoV-positive clinical faecal samples from 409 outbreaks and 238 unlinked cases of acute gastroenteritis were examined by RT-PCR and sequencing. Phylogenetic analysis was then performed to identify NoV capsid genotypes and to establish the temporal dominance of circulating pandemic GII.4 variants. Recombinant viruses were also identified based on analysis of the ORF1/2 overlapping region. Findings Peaks in NoV activity were observed, however the timing of these epidemics varied between different regions. Overall, GII.4 NoVs were the dominant cause of both outbreaks and cases of NoV-associated acute gastroenteritis (63.1%, n = 408/647), with Sydney 2012 being the most common GII.4 variant identified (98.8%, n = 403/408). Of the 409 reported NoV outbreaks, aged-care facilities were the most common setting in both Western Australia (87%, n = 20/23) and New Zealand (58.1%, n = 200/344) while most of the NoV outbreaks were reported from hospitals (38%, n = 16/42) in New South Wales, Australia. An analysis of a subset of non-GII.4 viruses from all locations (125/239) showed the majority (56.8%, n = 71/125) were inter-genotype recombinants. These recombinants were surprisingly diverse and could be classified into 18 distinct recombinant types, with GII.P16/GII.13 (24% of recombinants) the most common. Conclusion This study revealed that following its emergence in 2012, GII.4 Sydney 2012 variant continued to be the predominant cause of NoV-associated acute gastroenteritis in Australia and New Zealand between 2013 and 2014. PMID:27116221

Sordaria, a model system to uncover links between meiotic pairing and recombination.

PubMed

Zickler, Denise; Espagne, Eric

2016-06-01

The mycelial fungus Sordaria macrospora was first used as experimental system for meiotic recombination. This review shows that it provides also a powerful cytological system for dissecting chromosome dynamics in wild-type and mutant meioses. Fundamental cytogenetic findings include: (1) the identification of presynaptic alignment as a key step in pairing of homologous chromosomes. (2) The discovery that biochemical complexes that mediate recombination at the DNA level concomitantly mediate pairing of homologs. (3) This pairing process involves not only resolution but also avoidance of chromosomal entanglements and the resolution system includes dissolution of constraining DNA recombination interactions, achieved by a unique role of Mlh1. (4) Discovery that the central components of the synaptonemal complex directly mediate the re-localization of the recombination proteins from on-axis to in-between homologue axis positions. (5) Identification of putative STUbL protein Hei10 as a structure-based signal transduction molecule that coordinates progression and differentiation of recombinational interactions at multiple stages. (6) Discovery that a single interference process mediates both nucleation of the SC and designation of crossover sites, thereby ensuring even spacing of both features. (7) Discovery of local modulation of sister-chromatid cohesion at sites of crossover recombination. Copyright © 2016 Elsevier Ltd. All rights reserved.

RNA Recombination Enhances Adaptability and Is Required for Virus Spread and Virulence.

PubMed

Xiao, Yinghong; Rouzine, Igor M; Bianco, Simone; Acevedo, Ashley; Goldstein, Elizabeth Faul; Farkov, Mikhail; Brodsky, Leonid; Andino, Raul

2016-04-13

Mutation and recombination are central processes driving microbial evolution. A high mutation rate fuels adaptation but also generates deleterious mutations. Recombination between two different genomes may resolve this paradox, alleviating effects of clonal interference and purging deleterious mutations. Here we demonstrate that recombination significantly accelerates adaptation and evolution during acute virus infection. We identified a poliovirus recombination determinant within the virus polymerase, mutation of which reduces recombination rates without altering replication fidelity. By generating a panel of variants with distinct mutation rates and recombination ability, we demonstrate that recombination is essential to enrich the population in beneficial mutations and purge it from deleterious mutations. The concerted activities of mutation and recombination are key to virus spread and virulence in infected animals. These findings inform a mathematical model to demonstrate that poliovirus adapts most rapidly at an optimal mutation rate determined by the trade-off between selection and accumulation of detrimental mutations. Copyright © 2016 Elsevier Inc. All rights reserved.

A comparative study on charge carrier recombination across the junction region of Cu{sub 2}ZnSn(S,Se){sub 4} and Cu(In,Ga)Se{sub 2} thin film solar cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halim, Mohammad Abdul, E-mail: halimtsukuba2012@gmail.com; Islam, Muhammad Monirul; Luo, Xianjia

A comparative study with focusing on carrier recombination properties in Cu{sub 2}ZnSn(S,Se){sub 4} (CZTSSe) and the CuInGaSe{sub 2} (CIGS) solar cells has been carried out. For this purpose, electroluminescence (EL) and also bias-dependent time resolved photoluminescence (TRPL) using femtosecond (fs) laser source were performed. For the similar forward current density, the EL-intensity of the CZTSSe sample was obtained significantly lower than that of the CIGS sample. Primarily, it can be attributed to the existence of excess amount of non-radiative recombination center in the CZTSSe, and/or CZTSSe/CdS interface comparing to that of CIGS sample. In case of CIGS sample, TRPL decaymore » time was found to increase with the application of forward-bias. This can be attributed to the reduced charge separation rate resulting from the reduced electric-field at the junction. However, in CZTSSe sample, TRPL decay time has been found almost independent under the forward and reverse-bias conditions. This phenomenon indicates that the charge recombination rate strongly dominates over the charge separation rate across the junction of the CZTSSe sample. Finally, temperature dependent V{sub OC} suggests that interface related recombination in the CZTSSe solar cell structure might be one of the major factors that affect EL-intensity and also, TRPL decay curves.« less

Recombination within the apospory specific genomic region leads to the uncoupling of apomixis components in Cenchrus ciliaris.

PubMed

Conner, Joann A; Gunawan, Gunawati; Ozias-Akins, Peggy

2013-07-01

Apomixis enables the clonal propagation of maternal genotypes through seed. If apomixis could be harnessed via genetic engineering or introgression, it would have a major economic impact for agricultural crops. In the grass species Pennisetum squamulatum and Cenchrus ciliaris (syn. P. ciliare), apomixis is controlled by a single dominant "locus", the apospory-specific genomic region (ASGR). For P. squamulatum, 18 published sequenced characterized amplified region (SCAR) markers have been identified which always co-segregate with apospory. Six of these markers are conserved SCARs in the closely related species, C. ciliaris and co-segregate with the trait. A screen of progeny from a cross of sexual × apomictic C. ciliaris genotypes identified a plant, A8, retaining two of the six ASGR-linked SCAR markers. Additional and newly identified ASGR-linked markers were generated to help identify the extent of recombination within the ASGR. Based on analysis of missing markers, the A8 recombinant plant has lost a significant portion of the ASGR but continues to form aposporous embryo sacs. Seedlings produced from aposporous embryo sacs are 6× in ploidy level and hence the A8 recombinant does not express parthenogenesis. The recombinant A8 plant represents a step forward in reducing the complexity of the ASGR locus to determine the factor(s) required for aposporous embryo sac formation and documents the separation of expression of the two components of apomixis in C. ciliaris.

Construction and application of MCBL plate for facilitation of chromosome recombination in fungi.

PubMed

Ai, Y; Meng, F

1998-01-01

A medium with camphor and benomyl MCBL plate was designed and constructed based on the proposed mechanism that d-camphor could induce the fusion of nuclear membrane while benomyl could induce the nondisjunctional recombination of chromosome in fungi. This so-called co-induction plate consisted of 0.1% d-camphor (W/V) and 0.5 microgram/L benomyl contained in Czapek's minimal medium. The precautions to be taken in the construction procedure of this plate was described in detail. One typical example of intergeneric fusion-cross, Aspergillus niger x Trichoderma reesei, was investigated, comparing the ratios of genotypes and phenotypes of fusant progenies produced by the co-induction of MCBL plate and by the step-by-step induction with camphor and benomyl separately. The results showed that the heterodiploid state was extremely transient and the recombinant haploid was hardly obtained when induced by the routine step-by-step method, whereas the ratios of apparent diplodization and nondisjunctional recombinant haplodization among all types of varied segregates on MCBL plate were greatly improved, compared with those on the routine plates containing single reagents, which indicated that the transient heterodiploid could be grasped and transformed further into nondisjunctional recombinant haploid when co-induced on the MCBL plate. The age of regenerated mycelium to be induced was found to have a dominant influence on the co-induction effects of MCBL plate. The mechanism of co-induction by MCBL plate and its promising applications were discussed.

Electronic properties of light-induced recombination centers in boron-doped Czochralski silicon

NASA Astrophysics Data System (ADS)

Schmidt, Jan; Cuevas, Andrés

1999-09-01

In order to study the electronic properties of the recombination centers responsible for the light-induced carrier lifetime degradation commonly observed in high-purity boron-doped Czochralski (Cz) silicon, injection-level dependent carrier lifetime measurements are performed on a large number of boron-doped p-type Cz silicon wafers of various resistivities (1-31 Ω cm) prior to and after light degradation. The measurement technique used is the contactless quasi-steady-state photoconductance method, allowing carrier lifetime measurements over a very broad injection range between 1012 and 1017cm-3. To eliminate all recombination channels not related to the degradation effect, the difference of the inverse lifetimes measured after and before light degradation is evaluated. A detailed analysis of the injection level dependence of the carrier lifetime change using the Shockley-Read-Hall theory shows that the fundamental recombination center created during illumination has an energy level between Ev+0.35 and Ec-0.45 eV and an electron/hole capture time constant ratio between 0.1 and 0.2. This deep-level center is observed in all samples and is attributed to a new type of boron-oxygen complex. Besides this fundamental defect, in some samples an additional shallow-level recombination center at 0.15 eV below Ec or above Ev is found to be activated during light exposure. This second center dominates the light-degraded carrier lifetime only under high-injection conditions and is hence only of minor importance for low-injection operated devices.

Study of extending carrier lifetime in ZnTe quantum dots coupled with ZnCdSe quantum well

NASA Astrophysics Data System (ADS)

Fan, W. C.; Chou, W. C.; Lee, J. D.; Lee, Ling; Phu, Nguyen Dang; Hoang, Luc Huy

2018-03-01

We demonstrated the growth of a self-assembled type-II ZnTe/ZnSe quantum dot (QD) structure coupled with a type-I Zn0.88Cd0.12Se/ZnSe quantum well (QW) on the (001) GaAs substrate by molecular beam epitaxy (MBE). As the spacer thickness is less than 2 nm, the carrier lifetime increasing from 20 ns to nearly 200 ns was successfully achieved. By utilizing the time-resolved photoluminescence (TRPL) and PL with different excitation power, we identify the PL emission from the coupled QDs consisting of two recombination mechanisms. One is the recombination between electrons in ZnSe barrier and holes confined within ZnTe QDs, and the other is between electrons confined in Zn0.88Cd0.12Se QW and holes confined within ZnTe QDs. According to the band diagram and power-dependent PL, both of the two recombinations reveal the type-II transition. In addition, the second recombination mechanism dominates the whole carrier recombination as the spacer thickness is less than 2 nm. A significant extension of carrier lifetime by increasing the electron and hole separation is illustrated in a type-II ZnTe/ZnSe QD structure coupling with a type-I ZnCdSe/ZnSe QW. Current sample structure could be used to increase the quantum efficient of solar cell based on the II-VI compound semiconductors.

Meiotic Parthenogenesis in a Root-Knot Nematode Results in Rapid Genomic Homozygosity

PubMed Central

Liu, Qingli L.; Thomas, Varghese P.; Williamson, Valerie M.

2007-01-01

Many isolates of the plant-parasitic nematode Meloidogyne hapla reproduce by facultative meiotic parthenogenesis. Sexual crosses can occur, but, in the absence of males, the diploid state appears to be restored by reuniting sister chromosomes of a single meiosis. We have crossed inbred strains of M. hapla that differ in DNA markers and produced hybrids and F2 lines. Here we show that heterozygous M. hapla females, upon parthenogenetic reproduction, produce progeny that segregate 1:1 for the presence or absence of dominant DNA markers, as would be expected if sister chromosomes are rejoined, rather than the 3:1 ratio typical of a Mendelian cross. Codominant markers also segregate 1:1 and heterozygotes are present at low frequency (<3%). Segregation patterns and recombinant analysis indicate that a homozygous condition is prevalent for markers flanking recombination events, suggesting that recombination occurs preferentially as four-strand exchanges at similar locations between both pairs of non-sister chromatids. With this mechanism, meiotic parthenogenesis would be expected to result in rapid genomic homozygosity. This type of high negative crossover interference coupled with positive chromatid interference has not been observed in fungal or other animal systems in which it is possible to examine the sister products of a single meiosis and may indicate that meiotic recombination in this nematode has novel features. PMID:17483427

Sticking and recombination of the SiH 3 radical on hydrogenated amorphous silicon: The catalytic effect of diborane

NASA Astrophysics Data System (ADS)

Perrin, Jérôme; Takeda, Yoshihiko; Hirano, Naoto; Takeuchi, Yoshiaki; Matsuda, Akihisa

1989-03-01

The deposition rate of hydrogenated amorphous silicon films in SiH 4 glow-discharge is drastically enhanced upon addition of B 2H 6 when the gas-phase concentration exceeds 10 -4. This cannot be attributed to gas-phase reactions and must be interpreted as an increase of the sticking probability of the dominant SiH 3 radical. However, the total surface loss probability ( β) of SiH 3 which includes both sticking ( s) and recombination ( γ) increases only above 10 -2 B 2H 6 concentration, which reveals that between 10 -4 and 10 -2 the ratio {s}/{β} increases. A precursor-state model is proposed in which SiH 3 first physisorbs on the H-covered surface and migrates until it recombines, or chemisorbs on a free dangling bond site. At a typical deposition temperature of 200° C, the only mechanism of creation of dangling bonds in the absence of B 2H 6 is precisely the recombination of SiH 3 as SiH 4 by H abstraction, which limits the sticking probability to a fraction of β. This restriction is overcome with the help of hydroboron radicals, presumably BH 3, which catalyze H 2 desorption.

Ionization equilibrium and radiative energy loss rates for C, N, and O ions in low-density plasmas

NASA Technical Reports Server (NTRS)

Jacobs, V. L.; Davis, J.; Rogerson, J. E.; Blaha, M.

1978-01-01

The results of calculations of the ionization equilibrium and radiative energy loss rates for C, N and O ions in low-density plasmas are presented for electron temperatures in the range 10,000-10,000,000 K. The ionization structure is determined by using the steady-state corona model, in which electron impact ionization from the ground states is balanced by direct radiative and dielectronic recombination. With an improved theory, detailed calculations are carried out for the dielectronic recombination rates in which account is taken of all radiative and autoionization processes involving a single-electron electric-dipole transition of the recombining ion. The radiative energy loss processes considered are electron-impact excitation of resonance line emission, direct radiative recombination, dielectronic recombination, and electron-ion bremsstrahlung. For all three elements, resonance line emission resulting from 2s-2p transitions produces a broad maximum in the energy loss rate near 100,000 K.

Optical determination of Shockley-Read-Hall and interface recombination currents in hybrid perovskites

PubMed Central

Sarritzu, Valerio; Sestu, Nicola; Marongiu, Daniela; Chang, Xueqing; Masi, Sofia; Rizzo, Aurora; Colella, Silvia; Quochi, Francesco; Saba, Michele; Mura, Andrea; Bongiovanni, Giovanni

2017-01-01

Metal-halide perovskite solar cells rival the best inorganic solar cells in power conversion efficiency, providing the outlook for efficient, cheap devices. In order for the technology to mature and approach the ideal Shockley-Queissier efficiency, experimental tools are needed to diagnose what processes limit performances, beyond simply measuring electrical characteristics often affected by parasitic effects and difficult to interpret. Here we study the microscopic origin of recombination currents causing photoconversion losses with an all-optical technique, measuring the electron-hole free energy as a function of the exciting light intensity. Our method allows assessing the ideality factor and breaks down the electron-hole recombination current into bulk defect and interface contributions, providing an estimate of the limit photoconversion efficiency, without any real charge current flowing through the device. We identify Shockley-Read-Hall recombination as the main decay process in insulated perovskite layers and quantify the additional performance degradation due to interface recombination in heterojunctions. PMID:28317883

Solvation suppression of ion recombination in gas discharge afterglow

NASA Astrophysics Data System (ADS)

Amirov, R. Kh.; Lankin, A. V.; Norman, G. E.

2018-03-01

An effect which suppresses recombination in ion plasmas is considered both theoretically and experimentally. Experimental results are presented for the ion recombination rate in fluorine plasma, which are obtained from data for the gas discharge afterglow. To interpret them, a suppression factor is considered: ion solvation in weakly ionized plasma. It is shown that the recombination process has a two-stage character with the formation of intermediate metastable ion pairs. The pairs consist of negative and positive ion-molecular clusters. A theoretical explanation is given for the slowing down of the ion recombination with the increase of the Coulomb coupling compared to the ion recombination rate calculated in the ideal plasma approximation. The approximate similarity of the recombination rate of the ion temperature and concentration and reasons for the slight deviation from the similarity are elucidated.

Recombinant human leptin in women with hypothalamic amenorrhea.

PubMed

Welt, Corrine K; Chan, Jean L; Bullen, John; Murphy, Robyn; Smith, Patricia; DePaoli, Alex M; Karalis, Aspasia; Mantzoros, Christos S

2004-09-02

Disruptions in hypothalamic-gonadal and other endocrine axes due to energy deficits are associated with low levels of the adipocyte-secreted hormone leptin and may result in hypothalamic amenorrhea. We hypothesized that exogenous recombinant leptin replacement would improve reproductive and neuroendocrine function in women with hypothalamic amenorrhea. Eight women with hypothalamic amenorrhea due to strenuous exercise or low weight were studied for one month before receiving recombinant human leptin and then while receiving treatment for up to three months. Six control subjects with hypothalamic amenorrhea received no treatment and were studied for a mean (+/-SD) of 8.5+/-8.1 months. Luteinizing hormone (LH) pulsatility, body weight, ovarian variables, and hormone levels did not change significantly over time in the controls and during a one-month control period before recombinant leptin therapy in the treated subjects. In contrast, recombinant leptin treatment increased mean LH levels and LH pulse frequency after two weeks and increased maximal follicular diameter, the number of dominant follicles, ovarian volume, and estradiol levels over a period of three months. Three patients had an ovulatory menstrual cycle (P<0.05 for the comparison with an expected rate of spontaneous ovulation of 10 percent); two others had preovulatory follicular development and withdrawal bleeding during treatment (P<0.05). Recombinant leptin significantly increased levels of free triiodothyronine, free thyroxine, insulin-like growth factor 1, insulin-like growth factor-binding protein 3, bone alkaline phosphatase, and osteocalcin but not cortisol, corticotropin, or urinary N-telopeptide. Leptin administration for the relative leptin deficiency in women with hypothalamic amenorrhea appears to improve reproductive, thyroid, and growth hormone axes and markers of bone formation, suggesting that leptin, a peripheral signal reflecting the adequacy of energy stores, is required for normal reproductive and neuroendocrine function. Copyright 2004 Massachusetts Medical Society

The Recombinant Inhibitor of DNA Binding Id2 Forms Multimeric Structures via the Helix-Loop-Helix Domain and the Nuclear Export Signal.

PubMed

Roschger, Cornelia; Schubert, Mario; Regl, Christof; Andosch, Ancuela; Marquez, Augusto; Berger, Thomas; Huber, Christian G; Lütz-Meindl, Ursula; Cabrele, Chiara

2018-04-07

The inhibitor of DNA binding and cell differentiation 2 (Id2) is a helix-loop-helix (HLH) protein that acts as negative dominant regulator of basic-HLH transcription factors during development and in cancer. The structural properties of Id2 have been investigated so far by using synthetic or recombinant fragments reproducing single domains (N-terminus, HLH, C-terminus): the HLH domain tends to dimerize into a four-helix bundle, whereas the flanking regions are flexible. In this work, the intact protein was expressed in E. coli , solubilized from inclusion bodies with urea, purified and dissolved in water at pH~4. Under these conditions, Id2 was obtained with both cysteine residues disulfide-bonded to β-mercaptoethanol that was present during the solubilization process. Moreover, it existed in a self-assembled state, in which the N-terminus remained highly flexible, while the HLH domain and, surprisingly, part of the C-terminus, which corresponds to the nuclear export signal (NES), both were involved in slowly tumbling, rigid structures. The protein oligomers also formed twisted fibrils that were several micrometers long and up to 80 nm thick. These results show that self-assembly decreases the backbone flexibility of those two protein regions (HLH and NES) that are important for interaction with basic-HLH transcription factors or for nucleocytoplasmic shuttling.

Dissociative recombination and electron-impact de-excitation in CH photon emission under ITER divertor-relevant plasma conditions

NASA Astrophysics Data System (ADS)

van Swaaij, G. A.; Bystrov, K.; Borodin, D.; Kirschner, A.; van der Vegt, L. B.; van Rooij, G. J.; De Temmerman, G.; Goedheer, W. J.

2012-09-01

For understanding carbon erosion and redeposition in nuclear fusion devices, it is important to understand the transport and chemical break-up of hydrocarbon molecules in edge plasmas, often diagnosed by emission of the CH A 2Δ-X 2Π Gerö band around 430 nm. The CH A-level can be excited either by electron-impact (EI) or by dissociative recombination (DR) of hydrocarbon ions. These processes were included in the 3D Monte Carlo impurity transport code ERO. A series of methane injection experiments was performed in the high-density, low-temperature linear plasma generator Pilot-PSI, and simulated emission intensity profiles were benchmarked against these experiments. It was confirmed that excitation by DR dominates at Te < 1.5 eV. The results indicate that the fraction of DR events that lead to a CH radical in the A-level and consequent photon emission is at least 10%. Additionally, quenching of the excited CH radicals by EI de-excitation was included in the modeling. This quenching is shown to be significant: depending on the electron density, it reduces the effective CH emission by a factor of 1.4 at ne = 1.3 × 1020 m-3, to 2.8 at ne = 9.3 × 1020 m-3. Its inclusion significantly improved agreement between experiment and modeling.

The effect of crystal size on tunneling phenomena in luminescent nanodosimetric materials

NASA Astrophysics Data System (ADS)

Pagonis, Vasilis; Bernier, Shannon; Vieira, Francisco Marques dos Santos; Steele, Shane

2017-12-01

The study of luminescence signals from nanodosimetric materials is an active research area, due to the many possible practical applications of such materials. In several of these materials it has been shown that quantum tunneling is a dominant mechanism for recombination processes associated with luminescence phenomena. This paper examines the effect of crystal size on quantum tunneling phenomena in nanocrystals, based on the assumption of a random distribution of electrons and positive ions. The behavior of such random distributions is determined by three characteristic lengths: the radius of the crystal R, the tunneling length a, and the initial average distance 〈d〉 between electrons and positive ions (which is directly related to the density of charges in the material). Two different cases are examined, depending on the relative concentrations of electrons and ions. In the first case the concentration of electrons is assumed to be much smaller than the concentration of positive ions. Examination of a previously derived analytical equation demonstrates two different types of crystal size effects. When the tunneling length a is much smaller than both R and 〈d〉, the analytical equations show that smaller crystals exhibit a faster tunneling recombination rate. However, when the tunneling length a is of the same order of magnitude as both R and 〈d〉, the opposite effect is observed, with smaller crystals exhibiting a slower tunneling recombination rate. As the crystal size increases, the rate of tunneling in both cases reaches the limit expected for bulk materials. In the second case we examine the situation where the concentrations of electrons and positive ions are equal at all times. In this situation there is no analytical equation available to describe the process, and the crystal size effects are simulated by using Monte Carlo (MC) techniques. The two opposite behaviors as a function of the crystal size are also observed in these MC simulations. The effect of sample temperature is also studied by extending the MC simulations to include thermal characteristics of the defects. The relevance of the simulated results for luminescence dosimetry is discussed.

PCR-mediated recombination in amplification products derived from polyploid cotton.

Treesearch

Richard C. Cronn; M. Cedroni; T. Haselkorn; C. Grover; Jonathan F. Wendel

2002-01-01

PCR recombination describes a process of in vitro chimera formation from non-identical templates. The key requirements of this process is the inclusion of two partially homologous templates in one reaction, a condition met when amplifying any locus from polyploid organisms and members of multigene families from diploid organisms. Because polyploids possess two or more...

Recombinant organisms for production of industrial products

PubMed Central

Adrio, Jose-Luis

2010-01-01

A revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of DNA and the development of recombinant DNA technology. Traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. Novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding techniques and their modifications are contributing greatly to the development of improved industrial processes. In addition, functional genomics, proteomics and metabolomics are being exploited for the discovery of novel valuable small molecules for medicine as well as enzymes for catalysis. The sequencing of industrial microbal genomes is being carried out which bodes well for future process improvement and discovery of new industrial products. PMID:21326937

A study of trap and recombination centers in MAPbI3 perovskites.

PubMed

Gordillo, G; Otálora, C A; Ramirez, A A

2016-12-07

Trapping and recombination processes in thin films of CH 3 NH 3 PbI 3 (MAPbI 3 ) were studied by means of transient photoconductivity measurements and theoretical simulations of the relaxation curves resulting from the photocurrent measurements; in particular, the influence of temperature as well as of the sample temperature and intensity of illumination and pressure inside the measurement system on the photoconductivity response, were studied. The experimental curves of photocurrent were analyzed using the real part of the Fourier transform. The study revealed that the photocurrent of the MAPbI 3 films, measured at atmospheric pressure, is mainly governed by surface related processes induced by chemisorption and desorption of oxygen, whereas the photocurrent resulting from measurements performed in a vacuum is mainly governed by bulk related processes. It was found that, in general, the photocurrent response is affected by both trap assisted fast recombination processes and traps whose activation process is delayed, with the contribution in the intensity of the photocurrent of the first process being greater that of the second one. Evidence that the MAPbI 3 film exhibits a deep trap state at around 459 meV attributed to trap assisted recombination was found; furthermore, the MAPbI 3 films present shallow trap states at 129 and 24 meV that correspond to trap states whose activation process is delayed.

Current status and recent topics of rare-earth permanent magnets

NASA Astrophysics Data System (ADS)

Sugimoto, S.

2011-02-01

After the development of Nd-Fe-B magnets, rare-earth magnets are now essential components in many fields of technology, because of their ability to provide a strong magnetic flux. There are two, well-established techniques for the manufacture of rare earth magnets: powder metallurgy is used to obtain high-performance, anisotropic, fully dense magnet bodies; and the melt-spinning or HDDR (hydrogenation, disproportionation, desorption and recombination) process is widely used to produce magnet powders for bonded magnets. In the industry of sintered Nd-Fe-B magnets, the total amount of production has increased and their dominant application has been changed to motors. In particular, their use for motors in hybrid cars is one of the most attractive applications. Bonded magnets have also been used for small motors, and the studies of nanocomposite and Sm-Fe-N magnets have become widespread. This paper reviews the current status and future trend in the research of permanent magnets.

Fabrication and properties of gallium phosphide variable colour displays

NASA Technical Reports Server (NTRS)

Effer, D.; Macdonald, R. A.; Macgregor, G. M.; Webb, W. A.; Kennedy, D. I.

1973-01-01

The unique properties of single-junction gallium phosphide devices incorporating both red and green radiative recombination centers were investigated in application to the fabrication of monolithic 5 x 7 displays capable of displaying symbolic and alphanumeric information in a multicolor format. A number of potentially suitable material preparation techniques were evaluated in terms of both material properties and device performance. Optimum results were obtained for double liquid-phase-epitaxial process in which an open-tube dipping technique was used for n-layer growth and a sealed tipping procedure for subsequent p-layer growth. It was demonstrated that to prepare devices exhibiting a satisfactory range of dominant wavelengths which can be perceived as distinct emission colors extending from the red through green region of the visible spectrum involves a compromise between the material properties necessary for efficient red emission and those considered optimum for efficient green emission.

Experimental Evolution as a High-Throughput Screen for Genetic Adaptations.

PubMed

Cooper, Vaughn S

2018-06-27

Experimental evolution is a method in which populations of organisms, often microbes, are founded by one or more ancestors of known genotype and then propagated under controlled conditions to study the evolutionary process. These evolving populations are influenced by all population genetic forces, including selection, mutation, drift, and recombination, and the relative contributions of these forces may be seen as mysterious. Here, I describe why the outcomes of experimental evolution should be viewed with greater certainty because the force of selection typically dominates. Importantly, any mutant rising rapidly to high frequency in large populations must have acquired adaptive traits in the selective environment. Sequencing the genomes of these mutants can identify genes or pathways that contribute to an adaptation. I review the logic and simple mathematics why this evolve-and-resequence approach is a powerful way to find the mutations or mutation combinations that best increase fitness in any new environment. Copyright © 2018 Cooper.

The Physics of Semiconductors

NASA Astrophysics Data System (ADS)

Brennan, Kevin F.

1999-02-01

Modern fabrication techniques have made it possible to produce semiconductor devices whose dimensions are so small that quantum mechanical effects dominate their behavior. This book describes the key elements of quantum mechanics, statistical mechanics, and solid-state physics that are necessary in understanding these modern semiconductor devices. The author begins with a review of elementary quantum mechanics, and then describes more advanced topics, such as multiple quantum wells. He then disusses equilibrium and nonequilibrium statistical mechanics. Following this introduction, he provides a thorough treatment of solid-state physics, covering electron motion in periodic potentials, electron-phonon interaction, and recombination processes. The final four chapters deal exclusively with real devices, such as semiconductor lasers, photodiodes, flat panel displays, and MOSFETs. The book contains many homework exercises and is suitable as a textbook for electrical engineering, materials science, or physics students taking courses in solid-state device physics. It will also be a valuable reference for practicing engineers in optoelectronics and related areas.

Spinning of Fibers from Aqueous Solutions

DTIC Science & Technology

2003-08-01

recombinant silk product BioSteel . Publications, patents and presentations 1. Arcidiacono, S., et al., Purification and characterization of recombinant...ABSTRACT Previous funding supporting this research focused primarily on development of the aqueous-based method for processing silk into spin solutions. Much...of this effort consisted of production of recombinant silk protein in bacterial and yeast expression systems. In spite of the small quantities

The Role of Trap-assisted Recombination in Luminescent Properties of Organometal Halide CH3NH3PbBr3 Perovskite Films and Quantum Dots

NASA Astrophysics Data System (ADS)

Zhang, Zhen-Yu; Wang, Hai-Yu; Zhang, Yan-Xia; Hao, Ya-Wei; Sun, Chun; Zhang, Yu; Gao, Bing-Rong; Chen, Qi-Dai; Sun, Hong-Bo

2016-06-01

Hybrid metal halide perovskites have been paid enormous attentions in photophysics research, whose excellent performances were attributed to their intriguing charge carriers proprieties. However, it still remains far from satisfaction in the comprehensive understanding of perovskite charge-transport properities, especially about trap-assisted recombination process. In this Letter, through time-resolved transient absorption (TA) and photoluminescence (PL) measurements, we provided a relative comprehensive investigation on the charge carriers recombination dynamics of CH3NH3PbBr3 (MAPbBr3) perovskite films and quantum dots (QDs), especially about trap-assisted recombination. It was found that the integral recombination mode of MAPbBr3 films was highly sensitive to the density distribution of generated charge carriers and trap states. Additional, Trap effects would be gradually weakened with elevated carrier densities. Furthermore, the trap-assisted recombination can be removed from MAPbBr3 QDs through its own surface passivation mechanism and this specialty may render the QDs as a new material in illuminating research. This work provides deeper physical insights into the dynamics processes of MAPbBr3 materials and paves a way toward more light-harvesting applications in future.

Multiple exciton generation and recombination in carbon nanotubes and nanocrystals.

PubMed

Kanemitsu, Yoshihiko

2013-06-18

Semiconducting nanomaterials such as single-walled carbon nanotubes (SWCNTs) and nanocrystals (NCs) exhibit unique size-dependent quantum properties. They have therefore attracted considerable attention from the viewpoints of fundamental physics and functional device applications. SWCNTs and NCs also provide an excellent new stage for experimental studies of many-body effects of electrons and excitons on optical processes in nanomaterials. In this Account, we discuss multiple exciton generation and recombination in SWCNTs and NCs for next-generation photovoltaics. Strongly correlated ensembles of conduction-band electrons and valence-band holes in semiconductors are complex quantum systems that exhibit unique optical phenomena. In bulk crystals, the carrier recombination dynamics can be described by a simple model, which includes the nonradiative single-carrier trapping rate, the radiative two-carrier recombination rate, and the nonradiative three-carrier Auger recombination rate. The nonradiative Auger recombination rate determines the carrier recombination dynamics at high carrier density and depends on the spatial localization of carriers in two-dimensional quantum wells. The Auger recombination and multiple exciton generation rates can be advantageously manipulated by nanomaterials with designated energy structures. In addition, SWCNTs and NCs show quantized recombination dynamics of multiple excitons and carriers. In one-dimensional SWCNTs, excitons have large binding energies and are very stable at room temperature. The extremely rapid Auger recombination between excitons determines the photoluminescence (PL) intensity, the PL linewidth, and the PL lifetime. SWCNTs can undergo multiple exciton generation, while strong exciton-exciton interactions and complicated exciton structures affect the quantized Auger rate and the multiple exciton generation efficiency. Interestingly, in zero-dimensional NC quantum dots, quantized Auger recombination causes unique optical phenomena. The breakdown of the k-conversion rule and strong Coulomb interactions between carriers in NCs enhance Auger recombination rate and decrease the energy threshold for multiple exciton generation. We discuss this impact of the k-conservation rule on two-carrier radiative recombination and the three-carrier Auger recombination processes in indirect-gap semiconductor Si NCs. In NCs and SWCNTs, multiple exciton generation competes with Auger recombination, surface trapping of excitons, and cooling of hot electrons or excitons. In addition, we explore heterostructured NCs and impurity-doped NCs in the context of the optimization of charge carrier extraction from excitons in NCs.

Direct evidence of recombination between electrons in InGaN quantum discs and holes in p-type GaN.

PubMed

Sun, Xiaoxiao; Wang, Xinqiang; Wang, Ping; Wang, Tao; Sheng, Bowen; Zheng, Xiantong; Li, Mo; Zhang, Jian; Yang, Xuelin; Xu, Fujun; Ge, Weikun; Shen, Bo

2017-11-27

Intense emission from an InGaN quantum disc (QDisc) embedded in a GaN nanowire p-n junction is directly resolved by performing cathodoluminescence spectroscopy. The luminescence observed from the p-type GaN region is exclusively dominated by the emission at 380 nm, which has been usually reported as the emission from Mg induced impurity bands. Here, we confirm that the robust emission from 380 nm is actually not due to the Mg induced impurity bands, but rather due to being the recombination between electrons in the QDisc and holes in the p-type GaN. This identification helps to get a better understanding of the confused luminescence from nanowires with thin QDiscs embedded for fabricating electrically driven single photon emitters.

Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses.

PubMed

Su, Shuo; Wong, Gary; Shi, Weifeng; Liu, Jun; Lai, Alexander C K; Zhou, Jiyong; Liu, Wenjun; Bi, Yuhai; Gao, George F

2016-06-01

Human coronaviruses (HCoVs) were first described in the 1960s for patients with the common cold. Since then, more HCoVs have been discovered, including those that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), two pathogens that, upon infection, can cause fatal respiratory disease in humans. It was recently discovered that dromedary camels in Saudi Arabia harbor three different HCoV species, including a dominant MERS HCoV lineage that was responsible for the outbreaks in the Middle East and South Korea during 2015. In this review we aim to compare and contrast the different HCoVs with regard to epidemiology and pathogenesis, in addition to the virus evolution and recombination events which have, on occasion, resulted in outbreaks amongst humans. Copyright © 2016 Elsevier Ltd. All rights reserved.

Enhanced production of recombinant proteins with Corynebacterium glutamicum by deletion of insertion sequences (IS elements).

PubMed

Choi, Jae Woong; Yim, Sung Sun; Kim, Min Jeong; Jeong, Ki Jun

2015-12-29

In most bacteria, various jumping genetic elements including insertion sequences elements (IS elements) cause a variety of genetic rearrangements resulting in harmful effects such as genome and recombinant plasmid instability. The genetic stability of a plasmid in a host is critical for high-level production of recombinant proteins, and in this regard, the development of an IS element-free strain could be a useful strategy for the enhanced production of recombinant proteins. Corynebacterium glutamicum, which is a workhorse in the industrial-scale production of various biomolecules including recombinant proteins, also has several IS elements, and it is necessary to identify the critical IS elements and to develop IS element deleted strain. From the cultivation of C. glutamicum harboring a plasmid for green fluorescent protein (GFP) gene expression, non-fluorescent clones were isolated by FACS (fluorescent activated cell sorting). All the isolated clones had insertions of IS elements in the GFP coding region, and two major IS elements (ISCg1 and ISCg2 families) were identified. By co-cultivating cells harboring either the isolated IS element-inserted plasmid or intact plasmid, it was clearly confirmed that cells harboring the IS element-inserted plasmids became dominant during the cultivation due to their growth advantage over cells containing intact plasmids, which can cause a significant reduction in recombinant protein production during cultivation. To minimize the harmful effects of IS elements on the expression of heterologous genes in C. glutamicum, two IS element free C. glutamicum strains were developed in which each major IS element was deleted, and enhanced productivity in the engineered C. glutamicum strain was successfully demonstrated with three models: GFP, poly(3-hydroxybutyrate) [P(3HB)] and γ-aminobutyrate (GABA). Our findings clearly indicate that the hopping of IS elements could be detrimental to the production of recombinant proteins in C. glutamicum, emphasizing the importance of developing IS element free host strains.

Temporal Trends in the Swedish HIV-1 Epidemic: Increase in Non-B Subtypes and Recombinant Forms over Three Decades

PubMed Central

Santacatterina, Michele; Bratt, Göran; Gisslén, Magnus; Albert, Jan; Sonnerborg, Anders

2014-01-01

Background HIV-1 subtype B (HIV-1B) still dominates in resource-rich countries but increased migration contributes to changes in the global subtype distribution. Also, spread of non-B subtypes within such countries occurs. The trend of the subtype distribution from the beginning of the epidemic in the country has earlier not been reported in detail. Thus the primary objective of this study is to describe the temporal trend of the subtype distribution from the beginning of the HIV-1 epidemic in Sweden over three decades. Methods HIV-1 pol sequences from patients (n = 3967) diagnosed in Sweden 1983– 2012, corresponding to >40% of patients ever diagnosed, were re-subtyped using several automated bioinformatics tools. The temporal trends of subtypes and recombinants during three decades were described by a multinomial logistic regression model. Results All eleven group M HIV-1 subtypes and sub-subtypes (78%), 17 circulating recombinant forms (CRFs) (19%) and 32 unique recombinants forms (URF) (3%) were identified. When all patients were analysed, there was an increase of newly diagnosed HIV-1C (RR, 95%CI: 1.10, 1.06–1.14), recombinants (1.20, 1.17–1.24) and other pure subtypes (1.11, 1.07–1.16) over time compared to HIV-1B. The same pattern was found when all patients infected in Sweden (n = 1165) were analysed. Also, for MSM patients infected in Sweden (n = 921), recombinant forms and other pure subtypes increased. Significance Sweden exhibits one of the most diverse subtype epidemics outside Africa. The increase of non-B subtypes is due to migration and to a spread among heterosexually infected patients and MSM within the country. This viral heterogeneity may become a hotspot for development of more diverse and complex recombinant forms if the epidemics converge. PMID:24922326

Temporal trends in the Swedish HIV-1 epidemic: increase in non-B subtypes and recombinant forms over three decades.

PubMed

Neogi, Ujjwal; Häggblom, Amanda; Santacatterina, Michele; Bratt, Göran; Gisslén, Magnus; Albert, Jan; Sonnerborg, Anders

2014-01-01

HIV-1 subtype B (HIV-1B) still dominates in resource-rich countries but increased migration contributes to changes in the global subtype distribution. Also, spread of non-B subtypes within such countries occurs. The trend of the subtype distribution from the beginning of the epidemic in the country has earlier not been reported in detail. Thus the primary objective of this study is to describe the temporal trend of the subtype distribution from the beginning of the HIV-1 epidemic in Sweden over three decades. HIV-1 pol sequences from patients (n = 3967) diagnosed in Sweden 1983-2012, corresponding to >40% of patients ever diagnosed, were re-subtyped using several automated bioinformatics tools. The temporal trends of subtypes and recombinants during three decades were described by a multinomial logistic regression model. All eleven group M HIV-1 subtypes and sub-subtypes (78%), 17 circulating recombinant forms (CRFs) (19%) and 32 unique recombinants forms (URF) (3%) were identified. When all patients were analysed, there was an increase of newly diagnosed HIV-1C (RR, 95%CI: 1.10, 1.06-1.14), recombinants (1.20, 1.17-1.24) and other pure subtypes (1.11, 1.07-1.16) over time compared to HIV-1B. The same pattern was found when all patients infected in Sweden (n = 1165) were analysed. Also, for MSM patients infected in Sweden (n = 921), recombinant forms and other pure subtypes increased. Sweden exhibits one of the most diverse subtype epidemics outside Africa. The increase of non-B subtypes is due to migration and to a spread among heterosexually infected patients and MSM within the country. This viral heterogeneity may become a hotspot for development of more diverse and complex recombinant forms if the epidemics converge.

Anomalous Abundances in Gaseous Nebulae From Recombination and Collisional Lines: Improved Photoionization and Recombination Studies

NASA Astrophysics Data System (ADS)

Pradhan, Anil Kumar; Nahar, S. N.; Eissner, W. B.; Montenegro, M.

2011-01-01

A perplexing anomaly arises in the determination of abundances of common elements in gaseous nebulae, as derived from collisionally excited lines (CEL) as opposed to those from Recombination Lines (RCL). The "abundance discrepancy factors" can range from a factor of 2 to an order of magnitude or more. That has led to quite different interpretation of the physical structure and processes in gaseous nebulae, such as temperature fluctuations across the object, or metal-rich concentrations leading to a dual-abundnace scenario. We show that the problem may lie in inaccuracies in photoionization and recombination models neglecting low-energy resonance phenomena due to fine structure. Whereas the atomic physics of electron impact excitation of forbidden lines is well understood, and accurate collision strengths have long been available, that is not generally the case for electron-ion recombination cross sections. A major problem is the inclusion of relativisitic effects as it pertains to the existence of very low-energy fine structure resonances in photoionization cross sections. We carry out new relativistic calculations for photoionization and recombination cross sections using a recently extended version of the Breit-Pauli R-matrix codes, and the unified electron-ion recombination method that subsumes both the radiative and the dielectronic recombination (RR and DR) processes in an ab initio and self-consistent manner. We find that near-thresold resonances manifest themselves within fine structure levels of the ground state of ions, enhancing low-temperature recombination rate coefficients at 1000-10,000 K. The resulting enahncement in level-specific and total recombination rate coefficients should therefore lead to reduced abundances derived from RCL, and in accordance with those from CEL. We present results for photoionization of O II into, and recombination from, O III. Theoretical cross sections are benchmarked against high-resolution measurements from synchrotron based light sources. Work on other atomic species is in progress.

The chromatography-free release, isolation and purification of recombinant peptide for fibril self-assembly.

PubMed

Hartmann, B M; Kaar, W; Yoo, I K; Lua, L H L; Falconer, R J; Middelberg, A P J

2009-12-01

One of the major expenses associated with recombinant peptide production is the use of chromatography in the isolation and purification stages of a bioprocess. Here we report a chromatography-free isolation and purification process for recombinant peptide expressed in Escherichia coli (E. coli). Initial peptide release is by homogenization and then by enzymatic cleavage of the peptide-containing fusion protein, directly in the E. coli homogenate. Release is followed by selective solvent precipitation (SSP) to isolate and purify the peptide away from larger cell contaminants. Specifically, we expressed in E. coli the self-assembling beta-sheet forming peptide P(11)-2 in fusion to thioredoxin. Homogenate was heat treated (55 degrees C, 15 min) and then incubated with tobacco etch virus protease (TEVp) to release P(11)-2 having a native N-terminus. SSP with ethanol at room temperature then removed contaminating proteins in an integrated isolation-purification step; it proved necessary to add 250 mM NaCl to homogenate to prevent P(11)-2 from partitioning to the precipitate. This process structure gave recombinant P(11)-2 peptide at 97% polypeptide purity and 40% overall yield, without a single chromatography step. Following buffer-exchange of the 97% pure product by bind-elute chromatography into defined chemical conditions, the resulting peptide was shown to be functionally active and able to form self-assembled fibrils. To the best of our knowledge, this manuscript reports the first published process for chromatography-free recombinant peptide release, isolation and purification. The process proved able to deliver functional recombinant peptide at high purity and potentially low cost, opening cost-sensitive materials applications for peptide-based materials.

The Great Wall in the CfA survey - Its origin and imprint on the microwave background radiation

NASA Technical Reports Server (NTRS)

Atrio-Barandela, F.; Kashlinsky, A.

1992-01-01

The paper models the evolution of the Great Wall (GW) after recombination and the influence of its time-dependent gravitational potential on the MBR. It is shown that within the framework of the Zel'dovich approximation the (pre)GW region can be treated as an ellipsoid. The GW is approximated as an oblate ellipsoid that started at recombination with an almost spherical shape, but with initial density contrast, delta-i, much smaller than it had to be in the spherical model in order to reach the observed density contrast of beta-f of 5. The resultant delta-i is compatible with the rms value of delta-rho/rho on the GW scale at recombination for models with the n less than 0 power spectrum of the primordial density field. It is shown that the time-dependent potential of the GW will induce a detectable fluctuation in MBR. The possibility of similar structures located at higher redshifts producing measurable and perhaps dominant statistical MBR anisotropies by this effect is also discussed.

Recombinant Influenza Virus Carrying the Conserved Domain of Respiratory Syncytial Virus (RSV) G Protein Confers Protection against RSV without inflammatory disease

PubMed Central

Lee, Yu-Na; Hwang, Hye Suk; Kim, Min-Chul; Lee, Young-Tae; Cho, Min-Kyoung; Kwon, Young-Man; Lee, Jong Seok; Plemper, Richard K.; Kang, Sang-Moo

2014-01-01

Respiratory syncytial virus (RSV) is one of the most important causes for viral lower respiratory tract disease in humans. There is no licensed RSV vaccine. Here, we generated recombinant influenza viruses (PR8/RSV.HA-G) carrying the chimeric constructs of hemagglutinin (HA) and central conserved-domains of the RSV G protein. PR8/RSV.HA-G virus showed lower pathogenicity without compromising immunogenicity in mice. Single intranasal inoculation of mice with PR8/RSV.HA-G induced IgG2a isotype dominant antibodies and RSV neutralizing activity. Mice with single intranasal inoculation of PR8/RSV.HA-G were protected against RSV infection as evidenced by significant reduction of lung viral loads to a detection limit upon RSV challenge. PR8/RSV.HA-G inoculation of mice did not induce pulmonary eosinophilia and inflammation upon RSV infection. These findings support a concept that recombinant influenza viruses carrying the RSV G conserved-domain can be developed as a promising RSV vaccine candidate without pulmonary disease. PMID:25553517

Ion Storage Ring Measurements of Low Temperature Dielectronic Recombination Rate Coefficients for Modeling X-Ray Photoionized Cosmic Plasmas

NASA Technical Reports Server (NTRS)

Savin, D. W.; Gwinner, G.; Schwalm, D.; Wolf, A.; Mueller, A.; Schippers, S.

2002-01-01

Low temperature dielectronic recombination (DR) is the dominant recombination mechanism for most ions in X-ray photoionized cosmic plasmas. Reliably modeling and interpreting spectra from these plasmas requires accurate low temperature DR rate Coefficients. Of particular importance are the DR rate coefficients for the iron L-shell ions (Fe XVII-Fe XXIV). These ions are predicted to play an important role in determining the thermal structure and line emission of X-ray photoionized plasmas, which form in the media surrounding accretion powered sources such as X-ray binaries (XRBs), active galactic nuclei (AGN), and cataclysmic variables (Savin et al., 2000). The need for reliable DR data of iron L-shell ions has become particularly urgent after the launches of Chandra and XMM-Newton. These satellites are now providing high-resolution X-ray spectra from a wide range of X-ray photoionized sources. Interpreting the spectra from these sources requires reliable DR rate coefficients. However, at the temperatures relevant, for X-ray photoionized plasmas, existing theoretical DR rate coefficients can differ from one another by factors of two to orders of magnitudes.

The effects of electronic impurities and electron-hole recombination dynamics on large-grain organic-inorganic perovskite photovoltaic efficiencies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blancon, Jean-Christophe Robert; Nie, Wanyi; Neukirch, Amanda J.

2016-04-27

Hybrid organic-inorganic perovskites have attracted considerable attention after promising developments in energy harvesting and other optoelectronic applications. However, further optimization will require a deeper understanding of the intrinsic photophysics of materials with relevant structural characteristics. Here, the dynamics of photoexcited charge carriers in large-area grain organic-inorganic perovskite thin films is investigated via confocal time-resolved photoluminescence spectroscopy. It is found that the bimolecular recombination of free charges is the dominant decay mechanism at excitation densities relevant for photovoltaic applications. Bimolecular coefficients are found to be on the order of 10 –9 cm 3 s –1, comparable to typical direct-gap semiconductors, yetmore » significantly smaller than theoretically expected. It is also demonstrated that there is no degradation in carrier transport in these thin films due to electronic impurities. Here, suppressed electron–hole recombination and transport that is not limited by deep level defects provide a microscopic model for the superior performance of large-area grain hybrid perovskites for photovoltaic applications.« less

High-Efficiency InGaN/GaN Quantum Well-Based Vertical Light-Emitting Diodes Fabricated on β-Ga2O3 Substrate.

PubMed

Muhammed, Mufasila M; Alwadai, Norah; Lopatin, Sergei; Kuramata, Akito; Roqan, Iman S

2017-10-04

We demonstrate a state-of-the-art high-efficiency GaN-based vertical light-emitting diode (VLED) grown on a transparent and conductive (-201)-oriented (β-Ga 2 O 3 ) substrate, obtained using a straightforward growth process that does not require a high-cost lift-off technique or complex fabrication process. The high-resolution scanning transmission electron microscopy (STEM) images confirm that we produced high quality upper layers, including a multiquantum well (MQW) grown on the masked β-Ga 2 O 3 substrate. STEM imaging also shows a well-defined MQW without InN diffusion into the barrier. Electroluminescence (EL) measurements at room temperature indicate that we achieved a very high internal quantum efficiency (IQE) of 78%; at lower temperatures, IQE reaches ∼86%. The photoluminescence (PL) and time-resolved PL analysis indicate that, at a high carrier injection density, the emission is dominated by radiative recombination with a negligible Auger effect; no quantum-confined Stark effect is observed. At low temperatures, no efficiency droop is observed at a high carrier injection density, indicating the superior VLED structure obtained without lift-off processing, which is cost-effective for large-scale devices.

Recombination activity of grain boundaries in high-performance multicrystalline Si during solar cell processing

NASA Astrophysics Data System (ADS)

Adamczyk, Krzysztof; Søndenâ, Rune; Stokkan, Gaute; Looney, Erin; Jensen, Mallory; Lai, Barry; Rinio, Markus; Di Sabatino, Marisa

2018-02-01

In this work, we applied internal quantum efficiency mapping to study the recombination activity of grain boundaries in High Performance Multicrystalline Silicon under different processing conditions. Wafers were divided into groups and underwent different thermal processing, consisting of phosphorus diffusion gettering and surface passivation with hydrogen rich layers. After these thermal treatments, wafers were processed into heterojunction with intrinsic thin layer solar cells. Light Beam Induced Current and Electron Backscatter Diffraction were applied to analyse the influence of thermal treatment during standard solar cell processing on different types of grain boundaries. The results show that after cell processing, most random-angle grain boundaries in the material are well passivated, but small-angle grain boundaries are not well passivated. Special cases of coincidence site lattice grain boundaries with high recombination activity are also found. Based on micro-X-ray fluorescence measurements, a change in the contamination level is suggested as the reason behind their increased activity.

Dmc1 Functions in a Saccharomyces Cerevisiae Meiotic Pathway That Is Largely Independent of the Rad51 Pathway

PubMed Central

Dresser, M. E.; Ewing, D. J.; Conrad, M. N.; Dominguez, A. M.; Barstead, R.; Jiang, H.; Kodadek, T.

1997-01-01

Meiotic recombination in the yeast Saccharomyces cerevisiae requires two similar recA-like proteins, Dmc1p and Rad51p. A screen for dominant meiotic mutants provided DMC1-G126D, a dominant allele mutated in the conserved ATP-binding site (specifically, the A-loop motif) that confers a null phenotype. A recessive null allele, dmc1-K69E, was isolated as an intragenic suppressor of DMC1-G126D. Dmc1-K69Ep, unlike Dmc1p, does not interact homotypically in a two-hybrid assay, although it does interact with other fusion proteins identified by two-hybrid screen with Dmc1p. Dmc1p, unlike Rad51p, does not interact in the two-hybrid assay with Rad52p or Rad54p. However, Dmc1p does interact with Tid1p, a Rad54p homologue, with Tid4p, a Rad16p homologue, and with other fusion proteins that do not interact with Rad51p, suggesting that Dmc1p and Rad51p function in separate, though possibly overlapping, recombinational repair complexes. Epistasis analysis suggests that DMC1 and RAD51 function in separate pathways responsible for meiotic recombination. Taken together, our results are consistent with a requirement for DMC1 for meiosis-specific entry of DNA double-strand break ends into chromatin. Interestingly, the pattern on CHEF gels of chromosome fragments that result from meiotic DNA double-strand break formation is different in DMC1 mutant strains from that seen in rad50S strains. PMID:9335591

Displacement cascades and defect annealing in tungsten, Part III: The sensitivity of cascade annealing in tungsten to the values of kinetic parameters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.

2015-07-01

Object kinetic Monte Carlo (OKMC) simulations have been performed to investigate various aspects of cascade aging in bulk tungsten and to determine the sensitivity of the results to the kinetic parameters. The primary focus is on how the kinetic parameters affect the initial recombination of defects in the first few ns of a simulation. The simulations were carried out using the object kinetic Monte Carlo (OKMC) code KSOME (kinetic simulations of microstructure evolution), using a database of cascades obtained from results of molecular dynamics (MD) simulations at various primary knock-on atom (PKA) energies and directions at temperatures of 300, 1025more » and 2050 K. The OKMC model was parameterized using defect migration barriers and binding energies from ab initio calculations. Results indicate that, due to the disparate mobilities of SIA and vacancy clusters in tungsten, annealing is dominated by SIA migration even at temperatures as high as 2050 K. For 100 keV cascades initiated at 300 K recombination is dominated by annihilation of large defect clusters. But for all other PKA energies and temperatures most of the recombination is due to the migration and rotation of small SIA clusters, while all the large SIA clusters escape the cubic simulation cell. The inverse U-shape behavior exhibited by the annealing efficiency as a function of temperature curve, especially for cascades of large PKA energies, is due to asymmetry in SIA and vacancy clustering assisted by the large difference in mobilities of SIAs and vacancies. This annealing behavior is unaffected by the dimensionality of SIA migration persists over a broad range of relative mobilities of SIAs and vacancies.« less

Immunization with a dominant-negative recombinant Herpes Simplex Virus (HSV) type 1 protects against HSV-2 genital disease in guinea pigs

PubMed Central

2010-01-01

Background CJ9-gD is a novel dominant-negative recombinant herpes simplex virus type 1 (HSV-1) that is completely replication-defective, cannot establish detectable latent infection in vivo, and expresses high levels of the major HSV-1 antigen glycoprotein D immediately following infection. In the present study, CJ9-gD was evaluated as a vaccine against HSV-2 genital infection in guinea pigs. Results Animals immunized with CJ9-gD developed at least 700-fold higher titers of HSV-2-specific neutralization antibodies than mock-immunized controls. After challenge with wild-type HSV-2, all 10 control guinea pigs developed multiple genital lesions with an average of 21 lesions per animal. In contrast, only 2 minor lesions were found in 2 of 8 CJ9-gD-immunized animals, representing a 40-fold reduction on the incidence of primary genital lesions in immunized animals (p < 0.0001). Immunization significantly reduced the amount and duration of viral shedding and provided complete protection against neurological symptoms, while 90% of mock-immunized animals succumbed due to the severity of disease. Importantly, immunized animals showed no signs of recurrent disease or viral shedding during a 60-days observation period after recovery from primary infection, and carried 50-fold less latent viral DNA load in their dorsal root ganglia than the surviving mock-vaccinated controls (p < 0.0001). Conclusions Collectively, we demonstrate that vaccination with the HSV-1 recombinant CJ9-gD elicits strong and protective immune responses against primary and recurrent HSV-2 genital disease and significantly reduces the extent of latent infection. PMID:20525279

Development of a fed-batch process for a recombinant Pichia pastoris Δoch1 strain expressing a plant peroxidase.

PubMed

Gmeiner, Christoph; Saadati, Amirhossein; Maresch, Daniel; Krasteva, Stanimira; Frank, Manuela; Altmann, Friedrich; Herwig, Christoph; Spadiut, Oliver

2015-01-08

Pichia pastoris is a prominent host for recombinant protein production, amongst other things due to its capability of glycosylation. However, N-linked glycans on recombinant proteins get hypermannosylated, causing problems in subsequent unit operations and medical applications. Hypermannosylation is triggered by an α-1,6-mannosyltransferase called OCH1. In a recent study, we knocked out OCH1 in a recombinant P. pastoris CBS7435 Mut(S) strain (Δoch1) expressing the biopharmaceutically relevant enzyme horseradish peroxidase. We characterized the strain in the controlled environment of a bioreactor in dynamic batch cultivations and identified the strain to be physiologically impaired. We faced cell cluster formation, cell lysis and uncontrollable foam formation.In the present study, we investigated the effects of the 3 process parameters temperature, pH and dissolved oxygen concentration on 1) cell physiology, 2) cell morphology, 3) cell lysis, 4) productivity and 5) product purity of the recombinant Δoch1 strain in a multivariate manner. Cultivation at 30°C resulted in low specific methanol uptake during adaptation and the risk of methanol accumulation during cultivation. Cell cluster formation was a function of the C-source rather than process parameters and went along with cell lysis. In terms of productivity and product purity a temperature of 20°C was highly beneficial. In summary, we determined cultivation conditions for a recombinant P. pastoris Δoch1 strain allowing high productivity and product purity.

A novel inherited mutation of the transcription factor RUNX1 causes thrombocytopenia and may predispose to acute myeloid leukaemia.

PubMed

Walker, Logan C; Stevens, Jane; Campbell, Hamish; Corbett, Rob; Spearing, Ruth; Heaton, David; Macdonald, Donald H; Morris, Christine M; Ganly, Peter

2002-06-01

The RUNX1 (AML1, CBFA2) gene is a member of the runt transcription factor family, responsible for DNA binding and heterodimerization of other non-DNA binding transcription factors. RUNX1 plays an important part in regulating haematopoiesis and it is frequently disrupted by illegitimate somatic recombination in both acute myeloid and lymphoblastic leukaemia. Germline mutations of RUNX1 have also recently been described and are dominantly associated with inherited leukaemic conditions. We have identified a unique point mutation of the RUNX1 gene (A107P) in members of a family with autosomal dominant inheritance of thrombocytopenia. One member has developed acute myeloid leukaemia (AML).

Heterologously expressed Aspergillus aculeatus β-glucosidase in Saccharomyces cerevisiae is a cost-effective alternative to commercial supplementation of β-glucosidase in industrial ethanol production using Trichoderma reesei cellulases.

PubMed

Treebupachatsakul, Treesukon; Nakazawa, Hikaru; Shinbo, Hideaki; Fujikawa, Hiroki; Nagaiwa, Asami; Ochiai, Nobuhiro; Kawaguchi, Takashi; Nikaido, Mitsuru; Totani, Kazuhide; Shioya, Koki; Shida, Yosuke; Morikawa, Yasushi; Ogasawara, Wataru; Okada, Hirofumi

2016-01-01

Trichoderma reesei is a filamentous organism that secretes enzymes capable of degrading cellulose to cellobiose. The culture supernatant of T. reesei, however, lacks sufficient activity to convert cellobiose to glucose using β-glucosidase (BGL1). In this study, we identified a BGL (Cel3B) from T. reesei (TrCel3B) and compared it with the active β-glucosidases from Aspergillus aculeatus (AaBGL1). AaBGL1 showed higher stability and conversion of sugars to ethanol compared to TrCel3B, and therefore we chose to express this recombinant protein for use in fermentation processes. We expressed the recombinant protein in the yeast Saccharomyces cerevisiae, combined it with the superb T. reesei cellulase machinery and used the combination in a simultaneous saccharification and fermentation (SSF) process, with the hope that the recombinant would supplement the BGL activity. As the sugars were processed, the yeast immediately converted them to ethanol, thereby eliminating the problem posed by end product inhibition. Recombinant AaBGL1 activity was compared with Novozyme 188, a commercially available supplement for BGL activity. Our results show that the recombinant protein is as effective as the commercial supplement and can process sugars with equal efficiency. Expression of AaBGL1 in S. cerevisiae increased ethanol production effectively. Thus, heterologous expression of AaBGL1 in S. cerevisiae is a cost-effective and efficient process for the bioconversion of ethanol from lignocellulosic biomass. Copyright © 2015. Published by Elsevier B.V.

Auger recombination in sodium iodide

NASA Astrophysics Data System (ADS)

McAllister, Andrew; Kioupakis, Emmanouil; Åberg, Daniel; Schleife, André

2014-03-01

Scintillators are an important tool used to detect high energy radiation - both in the interest of national security and in medicine. However, scintillator detectors currently suffer from lower energy resolutions than expected from basic counting statistics. This has been attributed to non-proportional light yield compared to incoming radiation, but the specific mechanism for this non-proportionality has not been identified. Auger recombination is a non-radiative process that could be contributing to the non-proportionality of scintillating materials. Auger recombination comes in two types - direct and phonon-assisted. We have used first-principles calculations to study Auger recombination in sodium iodide, a well characterized scintillating material. Our findings indicate that phonon-assisted Auger recombination is stronger in sodium iodide than direct Auger recombination. Computational resources provided by LLNL and NERSC. Funding provided by NA-22.

Reversing Bacterial Resistance to Antibiotics by Phage-Mediated Delivery of Dominant Sensitive Genes

PubMed Central

Edgar, Rotem; Friedman, Nir; Molshanski-Mor, Shahar

2012-01-01

Pathogen resistance to antibiotics is a rapidly growing problem, leading to an urgent need for novel antimicrobial agents. Unfortunately, development of new antibiotics faces numerous obstacles, and a method that resensitizes pathogens to approved antibiotics therefore holds key advantages. We present a proof of principle for a system that restores antibiotic efficiency by reversing pathogen resistance. This system uses temperate phages to introduce, by lysogenization, the genes rpsL and gyrA conferring sensitivity in a dominant fashion to two antibiotics, streptomycin and nalidixic acid, respectively. Unique selective pressure is generated to enrich for bacteria that harbor the phages carrying the sensitizing constructs. This selection pressure is based on a toxic compound, tellurite, and therefore does not forfeit any antibiotic for the sensitization procedure. We further demonstrate a possible way of reducing undesirable recombination events by synthesizing dominant sensitive genes with major barriers to homologous recombination. Such synthesis does not significantly reduce the gene's sensitization ability. Unlike conventional bacteriophage therapy, the system does not rely on the phage's ability to kill pathogens in the infected host, but instead, on its ability to deliver genetic constructs into the bacteria and thus render them sensitive to antibiotics prior to host infection. We believe that transfer of the sensitizing cassette by the constructed phage will significantly enrich for antibiotic-treatable pathogens on hospital surfaces. Broad usage of the proposed system, in contrast to antibiotics and phage therapy, will potentially change the nature of nosocomial infections toward being more susceptible to antibiotics rather than more resistant. PMID:22113912

Reversing bacterial resistance to antibiotics by phage-mediated delivery of dominant sensitive genes.

PubMed

Edgar, Rotem; Friedman, Nir; Molshanski-Mor, Shahar; Qimron, Udi

2012-02-01

Pathogen resistance to antibiotics is a rapidly growing problem, leading to an urgent need for novel antimicrobial agents. Unfortunately, development of new antibiotics faces numerous obstacles, and a method that resensitizes pathogens to approved antibiotics therefore holds key advantages. We present a proof of principle for a system that restores antibiotic efficiency by reversing pathogen resistance. This system uses temperate phages to introduce, by lysogenization, the genes rpsL and gyrA conferring sensitivity in a dominant fashion to two antibiotics, streptomycin and nalidixic acid, respectively. Unique selective pressure is generated to enrich for bacteria that harbor the phages carrying the sensitizing constructs. This selection pressure is based on a toxic compound, tellurite, and therefore does not forfeit any antibiotic for the sensitization procedure. We further demonstrate a possible way of reducing undesirable recombination events by synthesizing dominant sensitive genes with major barriers to homologous recombination. Such synthesis does not significantly reduce the gene's sensitization ability. Unlike conventional bacteriophage therapy, the system does not rely on the phage's ability to kill pathogens in the infected host, but instead, on its ability to deliver genetic constructs into the bacteria and thus render them sensitive to antibiotics prior to host infection. We believe that transfer of the sensitizing cassette by the constructed phage will significantly enrich for antibiotic-treatable pathogens on hospital surfaces. Broad usage of the proposed system, in contrast to antibiotics and phage therapy, will potentially change the nature of nosocomial infections toward being more susceptible to antibiotics rather than more resistant.

Effect of heterogeneity and assumed mode of inheritance on lod scores.

PubMed

Durner, M; Greenberg, D A

1992-02-01

Heterogeneity is a major factor in many common, complex diseases and can confound linkage analysis. Using computer-simulated heterogeneous data we tested what effect unlinked families have on a linkage analysis when heterogeneity is not taken into account. We created 60 data sets of 40 nuclear families each with different proportions of linked and unlinked families and with different modes of inheritance. The ascertainment probability was 0.05, the disease had a penetrance of 0.6, and the recombination fraction for the linked families was zero. For the analysis we used a variety of assumed modes of inheritance and penetrances. Under these conditions we looked at the effect of the unlinked families on the lod score, the evaluation of the mode of inheritance, and the estimate of penetrance and of the recombination fraction in the linked families. 1. When the analysis was done under the correct mode of inheritance for the linked families, we found that the mode of inheritance of the unlinked families had minimal influence on the highest maximum lod score (MMLS) (i.e., we maximized the maximum lod score with respect to penetrance). Adding sporadic families decreased the MMLS less than adding recessive or dominant unlinked families. 2. The mixtures of dominant linked families with unlinked families always led to a higher MMLS when analyzed under the correct (dominant) mode of inheritance than when analyzed under the incorrect mode of inheritance. In the mixtures with recessive linked families, assuming the correct mode of inheritance generally led to a higher MMLS, but we observed broad variation.(ABSTRACT TRUNCATED AT 250 WORDS)

Variation block-based genomics method for crop plants.

PubMed

Kim, Yul Ho; Park, Hyang Mi; Hwang, Tae-Young; Lee, Seuk Ki; Choi, Man Soo; Jho, Sungwoong; Hwang, Seungwoo; Kim, Hak-Min; Lee, Dongwoo; Kim, Byoung-Chul; Hong, Chang Pyo; Cho, Yun Sung; Kim, Hyunmin; Jeong, Kwang Ho; Seo, Min Jung; Yun, Hong Tai; Kim, Sun Lim; Kwon, Young-Up; Kim, Wook Han; Chun, Hye Kyung; Lim, Sang Jong; Shin, Young-Ah; Choi, Ik-Young; Kim, Young Sun; Yoon, Ho-Sung; Lee, Suk-Ha; Lee, Sunghoon

2014-06-15

In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for the screening of target loci for agricultural traits. We propose the variation block method, which is a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing the short-read DNA sequences of the cultivar to the reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are termed variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybean and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. We suggest that the variation block method is an efficient genomics method for the recombination block-level comparison of crop genomes. We expect that this method will facilitate the development of crop genomics by bringing genomics technologies to the field of crop breeding.

The core structure and recombination energy of a copper screw dislocation: a Peierls study

NASA Astrophysics Data System (ADS)

Szajewski, B. A.; Hunter, A.; Beyerlein, I. J.

2017-09-01

The recombination process of dislocations is central to cross-slip, and transmission through ?3 grain boundaries among other fundamental plastic deformation processes. Despite its importance, a detailed mechanistic understanding remains lacking. We apply a continuous dislocation model, inspired by Peierls and Nabarro, complete with an ab-initio computed ?-surface and continuous units of infinitesimal dislocation slip, towards computing the stress-dependent recombination path of both an isotropic and anisotropic Cu screw dislocation. Under no applied stress, our model reproduces the stacking fault width between Shockley partial dislocations as predicted by discrete linear elasticity. Upon application of a compressive Escaig stress, the two partial dislocations coalesce to a separation of ??. Upon increased loading the edge components of each partial dislocation recede, leaving behind a spread Peierls screw dislocation, indicating the recombined state. We demonstrate that the critical stress required to achieve the recombined state is independent of the shear modulus. Rather the critical recombination stress depends on an energy difference between an unstable fault energy (?) and the intrinsic stacking fault energy (?-?). We report recombination energies of ?W = 0.168 eV/Å and ?W = 0.084 eV/Å, respectively, for the Cu screw dislocation within isotropic and anisotropic media. We develop an analytic model which provides insight into our simulation results which compare favourably with other (similar) models.

Trends in recombinant protein use in animal production.

PubMed

Gifre, Laia; Arís, Anna; Bach, Àlex; Garcia-Fruitós, Elena

2017-03-04

Recombinant technologies have made possible the production of a broad catalogue of proteins of interest, including those used for animal production. The most widely studied proteins for the animal sector are those with an important role in reproduction, feed efficiency, and health. Nowadays, mammalian cells and fungi are the preferred choice for recombinant production of hormones for reproductive purposes and fibrolytic enzymes to enhance animal performance, respectively. However, the development of low-cost products is a priority, particularly in livestock. The study of cell factories such as yeast and bacteria has notably increased in the last decades to make the new developed reproductive hormones and fibrolytic enzymes a real alternative to the marketed ones. Important efforts have also been invested to developing new recombinant strategies for prevention and therapy, including passive immunization and modulation of the immune system. This offers the possibility to reduce the use of antibiotics by controlling physiological processes and improve the efficacy of preventing infections. Thus, nowadays different recombinant fibrolytic enzymes, hormones, and therapeutic molecules with optimized properties have been successfully produced through cost-effective processes using microbial cell factories. However, despite the important achievements for reducing protein production expenses, alternative strategies to further reduce these costs are still required. In this context, it is necessary to make a giant leap towards the use of novel strategies, such as nanotechnology, that combined with recombinant technology would make recombinant molecules affordable for animal industry.

Dissociative recombination in aeronomy

NASA Technical Reports Server (NTRS)

Fox, J. L.

1989-01-01

The importance of dissociative recombination in planetary aeronomy is summarized, and two examples are discussed. The first is the role of dissociative recombination of N2(+) in the escape of nitrogen from Mars. A previous model is updated to reflect new experimental data on the electronic states of N produced in this process. Second, the intensity of the atomic oxygen green line on the nightside of Venus is modeled. Use is made of theoretical rate coefficients for production of O (1S) in dissociative recombination from different vibrational levels of O2(+).

Structures of the G85R Variant of SOD1 in Familial Amyotrophic Lateral Sclerosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Xiaohang; Antonyuk, Svetlana V.; Seetharaman, Sai V.

2008-07-21

Mutations in the gene encoding human copper-zinc superoxide dismutase (SOD1) cause a dominant form of the progressive neurodegenerative disease amyotrophic lateral sclerosis. Transgenic mice expressing the human G85R SOD1 variant develop paralytic symptoms concomitant with the appearance of SOD1-enriched proteinaceous inclusions in their neural tissues. The process(es) through which misfolding or aggregation of G85R SOD1 induces motor neuron toxicity is not understood. Here we present structures of the human G85R SOD1 variant determined by single crystal x-ray diffraction. Alterations in structure of the metal-binding loop elements relative to the wild type enzyme suggest a molecular basis for the metal ionmore » deficiency of the G85R SOD1 protein observed in the central nervous system of transgenic mice and in purified recombinant G85R SOD1. These findings support the notion that metal-deficient and/or disulfide-reduced mutant SOD1 species contribute to toxicity in SOD1-linked amyotrophic lateral sclerosis.« less

Feline immunodeficiency virus (FIV) env recombinants are common in natural infections.

PubMed

Bęczkowski, Paweł M; Hughes, Joseph; Biek, Roman; Litster, Annette; Willett, Brian J; Hosie, Margaret J

2014-09-17

Recombination is a common feature of retroviral biology and one of the most important factors responsible for generating viral diversity at both the intra-host and the population levels. However, relatively little is known about rates and molecular processes of recombination for retroviruses other than HIV, including important model viruses such as feline immunodeficiency virus (FIV). We investigated recombination in complete FIV env gene sequences (n = 355) isolated from 43 naturally infected cats. We demonstrated that recombination is abundant in natural FIV infection, with over 41% of the cats being infected with viruses containing recombinant env genes. In addition, we identified shared recombination breakpoints; the most significant hotspot occurred between the leader/signal fragment and the remainder of env. Our results have identified the leader/signal fragment of env as an important site for recombination and highlight potential limitations of the current phylogenetic classification of FIV based on partial env sequences. Furthermore, the presence of abundant recombinant FIV in the USA poses a significant challenge for commercial diagnostic tests and should inform the development of the next generation of FIV vaccines.

Display of phytase on the cell surface of Saccharomyces cerevisiae to degrade phytate phosphorus and improve bioethanol production.

PubMed

Chen, Xianzhong; Xiao, Yan; Shen, Wei; Govender, Algasan; Zhang, Liang; Fan, You; Wang, Zhengxiang

2016-03-01

Currently, development of biofuels as an alternative fuel has gained much attention due to resource and environmental challenges. Bioethanol is one of most important and dominant biofuels, and production using corn or cassava as raw materials has become a prominent technology. However, phytate contained in the raw material not only decreases the efficiency of ethanol production, but also leads to an increase in the discharge of phosphorus, thus impacting on the environment. In this study, to decrease phytate and its phosphorus content in an ethanol fermentation process, Saccharomyces cerevisiae was engineered through a surface-displaying system utilizing the C-terminal half of the yeast α-agglutinin protein. The recombinant yeast strain, PHY, was constructed by successfully displaying phytase on the surface of cells, and enzyme activity reached 6.4 U/g wet biomass weight. Ethanol productions using various strains were compared, and the results demonstrated that the specific growth rate and average fermentation rate of the PHY strain were higher 20 and 18 %, respectively, compared to the control strain S. cerevisiae CICIMY0086, in a 5-L bioreactor process by simultaneous saccharification and fermentation. More importantly, the phytate phosphorus concentration decreased by 89.8 % and free phosphorus concentration increased by 142.9 % in dry vinasse compared to the control in a 5-L bioreactor. In summary, we constructed a recombinant S. cerevisiae strain displaying phytase on the cell surface, which could improve ethanol production performance and effectively reduce the discharge of phosphorus. The strain reported here represents a useful novel engineering platform for developing an environment-friendly system for bioethanol production from a corn substrate.

Molecular Diversity of HIV-1 among People Who Inject Drugs in Kuala Lumpur, Malaysia: Massive Expansion of Circulating Recombinant Form (CRF) 33_01B and Emergence of Multiple Unique Recombinant Clusters

PubMed Central

Chow, Wei Zhen; Ng, Kim Tien; Yong, Yean Kong; Azmel, Azureen; Takebe, Yutaka; Al-Darraji, Haider Abdulrazzaq Abed; Kamarulzaman, Adeeba; Tee, Kok Keng

2013-01-01

Since the discovery of HIV-1 circulating recombinant form (CRF) 33_01B in Malaysia in the early 2000 s, continuous genetic diversification and active recombination involving CRF33_01B and other circulating genotypes in the region including CRF01_AE and subtype B′ of Thai origin, have led to the emergence of novel CRFs and unique recombinant forms. The history and magnitude of CRF33_01B transmission among various risk groups including people who inject drugs (PWID) however have not been investigated despite the high epidemiological impact of CRF33_01B in the region. We update the most recent molecular epidemiology of HIV-1 among PWIDs recruited in Malaysia between 2010 and 2011 by population sequencing and phylogenetic analysis of 128 gag-pol sequences. HIV-1 CRF33_01B was circulating among 71% of PWIDs whilst a lower prevalence of other previously dominant HIV-1 genotypes [subtype B′ (11%) and CRF01_AE (5%)] and CRF01_AE/B′ unique recombinants (13%) were detected, indicating a significant shift in genotype replacement in this population. Three clusters of CRF01_AE/B′ recombinants displaying divergent yet phylogenetically-related mosaic genomes to CRF33_01B were identified and characterized, suggestive of an abrupt emergence of multiple novel CRF clades. Using rigorous maximum likelihood approach and the Bayesian Markov chain Monte Carlo (MCMC) sampling of CRF33_01Bpol sequences to elucidate the past population dynamics, we found that the founder lineages of CRF33_01B were likely to have first emerged among PWIDs in the early 1990 s before spreading exponentially to various high and low-risk populations (including children who acquired infections from their mothers) and later on became endemic around the early 2000 s. Taken together, our findings provide notable genetic evidence indicating the widespread expansion of CRF33_01B among PWIDs and into the general population. The emergence of numerous previously unknown recombinant clades highlights the escalating genetic complexity of HIV-1 in the Southeast Asian region. PMID:23667490

Molecular diversity of HIV-1 among people who inject drugs in Kuala Lumpur, Malaysia: massive expansion of circulating recombinant form (CRF) 33_01B and emergence of multiple unique recombinant clusters.

PubMed

Chow, Wei Zhen; Ong, Lai Yee; Razak, Siti Humaira; Lee, Yeat Mei; Ng, Kim Tien; Yong, Yean Kong; Azmel, Azureen; Takebe, Yutaka; Al-Darraji, Haider Abdulrazzaq Abed; Kamarulzaman, Adeeba; Tee, Kok Keng

2013-01-01

Since the discovery of HIV-1 circulating recombinant form (CRF) 33_01B in Malaysia in the early 2000 s, continuous genetic diversification and active recombination involving CRF33_01B and other circulating genotypes in the region including CRF01_AE and subtype B' of Thai origin, have led to the emergence of novel CRFs and unique recombinant forms. The history and magnitude of CRF33_01B transmission among various risk groups including people who inject drugs (PWID) however have not been investigated despite the high epidemiological impact of CRF33_01B in the region. We update the most recent molecular epidemiology of HIV-1 among PWIDs recruited in Malaysia between 2010 and 2011 by population sequencing and phylogenetic analysis of 128 gag-pol sequences. HIV-1 CRF33_01B was circulating among 71% of PWIDs whilst a lower prevalence of other previously dominant HIV-1 genotypes [subtype B' (11%) and CRF01_AE (5%)] and CRF01_AE/B' unique recombinants (13%) were detected, indicating a significant shift in genotype replacement in this population. Three clusters of CRF01_AE/B' recombinants displaying divergent yet phylogenetically-related mosaic genomes to CRF33_01B were identified and characterized, suggestive of an abrupt emergence of multiple novel CRF clades. Using rigorous maximum likelihood approach and the Bayesian Markov chain Monte Carlo (MCMC) sampling of CRF33_01Bpol sequences to elucidate the past population dynamics, we found that the founder lineages of CRF33_01B were likely to have first emerged among PWIDs in the early 1990 s before spreading exponentially to various high and low-risk populations (including children who acquired infections from their mothers) and later on became endemic around the early 2000 s. Taken together, our findings provide notable genetic evidence indicating the widespread expansion of CRF33_01B among PWIDs and into the general population. The emergence of numerous previously unknown recombinant clades highlights the escalating genetic complexity of HIV-1 in the Southeast Asian region.

Spectroscopic Non-LTE Modeling of Highly Charged Gold Plasma

NASA Astrophysics Data System (ADS)

Dasgupta, A.; Ouart, N. D.; Giuliani, J. L.; Obenschain, S. P.; Clark, R. W.; Aglitskiy, Y.

2013-10-01

An X-ray spectrometer is under development at the Naval Research Laboratory (NRL) to investigate emissions from gold targets irradiated by the NIKE KrF facility. This effort is in support of the indirect drive campaign on the National Ignition Facility (NIF). To analyze and interpret the NIKE experimental spectra, we are theoretically exploring line emissions from a gold plasma in the M-band, i.e., 1.5 to 3.5 keV. We employ a detailed Non-LTE atomic model for ions near Ni-like gold by including an adequate number of configurations to obtain spectroscopic details in this range. The atomic states are coupled both collisionally and radiatively, including all dominant atomic processes that have significant contributions to the ionization and emitted synthetic spectra. In particular, we will investigate the effect of dielectronic recombination, which can have a dominant effect on level populations for highly ionized high Z plasmas. Since the radiation field can affect level populations through photoionization and photoexcitation, our collisional-radiative model will include non-local radiation transport. The line shapes of the strong overlapping lines will be resolved by a multifrequency radiation transport method. Synthetic spectra with radiation transport, including resonant photo-pumping, will be generated for realistic densities and temperatures to compare with the NIKE data. Work supported by DOE/NNSA.

Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast.

PubMed

Wu, Min; Kwoh, Chee-Keong; Li, Xiaoli; Zheng, Jie

2014-09-11

The regulatory mechanism of recombination is one of the most fundamental problems in genomics, with wide applications in genome wide association studies (GWAS), birth-defect diseases, molecular evolution, cancer research, etc. Recombination events cluster into short genomic regions called "recombination hotspots". Recently, a zinc finger protein PRDM9 was reported to regulate recombination hotspots in human and mouse genomes. In addition, a 13-mer motif contained in the binding sites of PRDM9 is found to be enriched in human hotspots. However, this 13-mer motif only covers a fraction of hotspots, indicating that PRDM9 is not the only regulator of recombination hotspots. Therefore, the challenge of discovering other regulators of recombination hotspots becomes significant. Furthermore, recombination is a complex process. Hence, multiple proteins acting as machinery, rather than individual proteins, are more likely to carry out this process in a precise and stable manner. Therefore, the extension of the prediction of individual trans-regulators to protein complexes is also highly desired. In this paper, we introduce a pipeline to identify genes and protein complexes associated with recombination hotspots. First, we prioritize proteins associated with hotspots based on their preference of binding to hotspots and coldspots. Second, using the above identified genes as seeds, we apply the Random Walk with Restart algorithm (RWR) to propagate their influences to other proteins in protein-protein interaction (PPI) networks. Hence, many proteins without DNA-binding information will also be assigned a score to implicate their roles in recombination hotspots. Third, we construct sub-PPI networks induced by top genes ranked by RWR for various species (e.g., yeast, human and mouse) and detect protein complexes in those sub-PPI networks. The GO term analysis show that our prioritizing methods and the RWR algorithm are capable of identifying novel genes associated with recombination hotspots. The trans-regulators predicted by our pipeline are enriched with epigenetic functions (e.g., histone modifications), demonstrating the epigenetic regulatory mechanisms of recombination hotspots. The identified protein complexes also provide us with candidates to further investigate the molecular machineries for recombination hotspots. Moreover, the experimental data and results are available on our web site http://www.ntu.edu.sg/home/zhengjie/data/RecombinationHotspot/NetPipe/.

Recombinant organisms for production of industrial products.

PubMed

Adrio, Jose-Luis; Demain, Arnold L

2010-01-01

A revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of DNA and the development of recombinant DNA technology. Traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. Novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding techniques and their modifications are contributing greatly to the development of improved industrial processes. In addition, functional genomics, proteomics and metabolomics are being exploited for the discovery of novel valuable small molecules for medicine as well as enzymes for catalysis. The sequencing of industrial microbal genomes is being carried out which bodes well for future process improvement and discovery of new industrial products. © 2010 Landes Bioscience

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Yuqian; Hellinga, Homme W.; Beese, Lorena S.

Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5'-nuclease superfamily. Its dominant, processive 5'–3' exonuclease and secondary 5'-flap endonuclease activities participate in various DNA repair, recombination, and replication processes. A single active site processes both recessed ends and 5'-flap substrates. By initiating enzyme reactions in crystals, we have trapped hExo1 reaction intermediates that reveal structures of these substrates before and after their exo- and endonucleolytic cleavage, as well as structures of uncleaved, unthreaded, and partially threaded 5' flaps. Their distinctive 5' ends are accommodated by a small, mobile arch in the active site that binds recessed endsmore » at its base and threads 5' flaps through a narrow aperture within its interior. A sequence of successive, interlocking conformational changes guides the two substrate types into a shared reaction mechanism that catalyzes their cleavage by an elaborated variant of the two-metal, in-line hydrolysis mechanism. Coupling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate or premature cleavage, enhancing processing fidelity. The striking reduction in flap conformational entropy is catalyzed, in part, by arch motions and transient binding interactions between the flap and unprocessed DNA strand. At the end of the observed reaction sequence, hExo1 resets without relinquishing DNA binding, suggesting a structural basis for its processivity.« less

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.

PubMed

Shi, Yuqian; Hellinga, Homme W; Beese, Lorena S

2017-06-06

Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5'-nuclease superfamily. Its dominant, processive 5'-3' exonuclease and secondary 5'-flap endonuclease activities participate in various DNA repair, recombination, and replication processes. A single active site processes both recessed ends and 5'-flap substrates. By initiating enzyme reactions in crystals, we have trapped hExo1 reaction intermediates that reveal structures of these substrates before and after their exo- and endonucleolytic cleavage, as well as structures of uncleaved, unthreaded, and partially threaded 5' flaps. Their distinctive 5' ends are accommodated by a small, mobile arch in the active site that binds recessed ends at its base and threads 5' flaps through a narrow aperture within its interior. A sequence of successive, interlocking conformational changes guides the two substrate types into a shared reaction mechanism that catalyzes their cleavage by an elaborated variant of the two-metal, in-line hydrolysis mechanism. Coupling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate or premature cleavage, enhancing processing fidelity. The striking reduction in flap conformational entropy is catalyzed, in part, by arch motions and transient binding interactions between the flap and unprocessed DNA strand. At the end of the observed reaction sequence, hExo1 resets without relinquishing DNA binding, suggesting a structural basis for its processivity.

Sex in a test tube: testing the benefits of in vitro recombination.

PubMed

Pesce, Diego; Lehman, Niles; de Visser, J Arjan G M

2016-10-19

The origin and evolution of sex, and the associated role of recombination, present a major problem in biology. Sex typically involves recombination of closely related DNA or RNA sequences, which is fundamentally a random process that creates but also breaks up beneficial allele combinations. Directed evolution experiments, which combine in vitro mutation and recombination protocols with in vitro or in vivo selection, have proved to be an effective approach for improving functionality of nucleic acids and enzymes. As this approach allows extreme control over evolutionary conditions and parameters, it also facilitates the detection of small or position-specific recombination benefits and benefits associated with recombination between highly divergent genotypes. Yet, in vitro approaches have been largely exploratory and motivated by obtaining improved end products rather than testing hypotheses of recombination benefits. Here, we review the various experimental systems and approaches used by in vitro studies of recombination, discuss what they say about the evolutionary role of recombination, and sketch their potential for addressing extant questions about the evolutionary role of sex and recombination, in particular on complex fitness landscapes. We also review recent insights into the role of 'extracellular recombination' during the origin of life.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'. © 2016 The Author(s).

Transformative Colloidal Nanomaterials for Mid- Infrared Devices

DTIC Science & Technology

2015-06-11

like. Luminescence has been detected up to the detection limit of our MCT detector (11 microns). Inorganic ligand exchange using ammonium sulfide...biexciton lifetime is not changing significantly, being about 30-50 ps. One issue with CQDs films for mid-IR detection will be to achieve noise ...limited by generation/recombination. Our first studies showed that at 1kHz, 1/f noise dominated starting at temperatures of 100K and increased

Direct observation of lifetime killing defects in 4H SiC epitaxial layers through spin dependent recombination in bipolar junction transistors

NASA Astrophysics Data System (ADS)

Cochrane, C. J.; Lenahan, P. M.; Lelis, A. J.

2009-03-01

We have identified a magnetic resonance spectrum associated with minority carrier lifetime killing defects in device quality 4H SiC through magnetic resonance measurements in bipolar junction transistors using spin dependent recombination (SDR). The SDR spectrum has nine distinguishable lines; it is, within experimental error, essentially isotropic with four distinguishable pairs of side peaks symmetric about the strong center line. The line shape is, within experimental error, independent of bias voltage and recombination current. The large amplitude and spacing of the inner pair of side peaks and three more widely separated pairs of side peaks are not consistent with either a simple silicon or carbon vacancy or a carbon or silicon antisite. This indicates that the lifetime killing defect is not a simple defect but a defect aggregate. The spectrum is consistent with a multidefect cluster with an electron spin S =1/2. (The observed spectrum has not been reported previously in the magnetic resonance literature on SiC.) A fairly strong argument can be made in terms of a first order model linking the SDR spectrum to a divacancy or possibly a vacancy/antisite pair. The SDR amplitude versus gate voltage is semiquantitatively consistent with a very simple model in which the defect is uniformly distributed within the depletion region of the base/collector junction and is also the dominating recombination center. The large relative amplitude of the SDR response is more nearly consistent with a Kaplan-Solomon-Mott-like model for spin dependent recombination than the Lepine model.

[Exogenous luteinizing hormone for assisted reproduction techniques in poor response patients].

PubMed

Spremović-Radjenović, Svetlana; Gudović, Aleksandra; Lazović, Gordana

2010-07-01

Two gonadotrophins, two cell theory refers to necessity of both gonadotrophin activities for theca and granulose cells steroidogenesis of dominant follicle. The aim of this study was to determine the influence of recombinant LH in women qualified as poor responders in the first assisted reproduction procedure (IVF), on fertility results, expressed as percentage of clinical pregnancies. The study included 12 women, 35 years and older who were their own controls. The next trial of IVF was with the same dose of recombinant FSH and GnRH agonist, and with the same, long protocol. Recombinant LH was added in the dose of 75 IU from the 2nd to 7th day of the cycle, and 150 IU from the 8th day of the cycle to the aspiration of oocytes. Within the two different protocols: there was no significant difference between LH concentration in 8th and 12th day of cycle; there was no significant difference between E2 concentration on day 2nd and day 8th; there was a significant difference between E2 concentrations on day 12th; endometrial thickness was not significantly different on the day of aspiration, neither was the number of follicles and embryos. In the two patients, clinical pregnancy was detected (pregnancy rate 17%), and they delivered in term. So, a statistically significant difference between the two protocols was in the rate of clinical pregnancies. The patients with low response to a long protocol in IVF procedures had significantly better results according to the clinical pregnancy rate when the recombinant LH was added to recombinant FSH in the stimulation protocol.

[Molecular epidemiological analysis of HIV-1 variants circulating in Russia in 1987-2015].

PubMed

Lapovok, I A; Lopatukhin, A E; Kireev, D E; Kazennova, E V; Lebedev, A V; Bobkova, M R; Kolomeets, A N; Turbina, G I; Shipulin, G A; Ladnaya, N N; Pokrovsky, V V

To simultaneously analyze HIV-1 samples from all Russian regions to characterize the epidemiology of HIV infection in the country as a whole. The most extensive study was conducted to examine nucleotide sequences of the pol gene of HIV-1 samples isolated from HIV-positive persons in different regions of Russia, with the diagnosis date being fixed during 1987-2015. The nucleotide sequences of the HIV-1 genome were analyzed using computer programs and on-line applications to identify a virus subtype and new recombinant forms. The nucleotide sequences of the pol gene were analyzed in 1697 HIV-1 samples and the findings were that the genetic variant subtype A1 (IDU-A) was dominant throughout the entire territory of Russia (in more than 80% of all infection cases). Other virus variants circulating in Russia were analyzed; the phenomenon of the higher distribution of the recombinant form CRF63/02A in Siberia, which had been previously described in the literature, was also confirmed. Four new recombinant forms generated by the virus subtype A1 (IDU-A) and B and two AG recombinant forms were found. There was a larger genetic distance between the viruses of IDU-A variant circulating among the injecting drug users and those infected through heterosexual contact, as well as a change in the viruses of subtype G that caused the outbreak in the south of the country over time in 1988-1989. The findings demonstrate continuous HIV-1 genetic variability and recombination over time in Russia, as well as increased genetic diversity with higher HIV infection rates in the population.

A Critical Review of the Concept of Transgenic Plants: Insights into Pharmaceutical Biotechnology and Molecular Farming.

PubMed

Abiri, Rambod; Valdiani, Alireza; Maziah, Mahmood; Shaharuddin, Noor Azmi; Sahebi, Mahbod; Yusof, Zetty Norhana Balia; Atabaki, Narges; Talei, Daryush

2016-01-01

Using transgenic plants for the production of high-value recombinant proteins for industrial and clinical applications has become a promising alternative to using conventional bioproduction systems, such as bacteria, yeast, and cultured insect and animal cells. This novel system offers several advantages over conventional systems in terms of safety, scale, cost-effectiveness, and the ease of distribution and storage. Currently, plant systems are being utilised as recombinant bio-factories for the expression of various proteins, including potential vaccines and pharmaceuticals, through employing several adaptations of recombinant processes and utilizing the most suitable tools and strategies. The level of protein expression is a critical factor in plant molecular farming, and this level fluctuates according to the plant species and the organs involved. The production of recombinant native and engineered proteins is a complicated procedure that requires an inter- and multi-disciplinary effort involving a wide variety of scientific and technological disciplines, ranging from basic biotechnology, biochemistry, and cell biology to advanced production systems. This review considers important plant resources, affecting factors, and the recombinant-protein expression techniques relevant to the plant molecular farming process.

Evolution of meiotic recombination genes in maize and teosinte.

PubMed

Sidhu, Gaganpreet K; Warzecha, Tomasz; Pawlowski, Wojciech P

2017-01-25

Meiotic recombination is a major source of genetic variation in eukaryotes. The role of recombination in evolution is recognized but little is known about how evolutionary forces affect the recombination pathway itself. Although the recombination pathway is fundamentally conserved across different species, genetic variation in recombination components and outcomes has been observed. Theoretical predictions and empirical studies suggest that changes in the recombination pathway are likely to provide adaptive abilities to populations experiencing directional or strong selection pressures, such as those occurring during species domestication. We hypothesized that adaptive changes in recombination may be associated with adaptive evolution patterns of genes involved in meiotic recombination. To examine how maize evolution and domestication affected meiotic recombination genes, we studied patterns of sequence polymorphism and divergence in eleven genes controlling key steps in the meiotic recombination pathway in a diverse set of maize inbred lines and several accessions of teosinte, the wild ancestor of maize. We discovered that, even though the recombination genes generally exhibited high sequence conservation expected in a pathway controlling a key cellular process, they showed substantial levels and diverse patterns of sequence polymorphism. Among others, we found differences in sequence polymorphism patterns between tropical and temperate maize germplasms. Several recombination genes displayed patterns of polymorphism indicative of adaptive evolution. Despite their ancient origin and overall sequence conservation, meiotic recombination genes can exhibit extensive and complex patterns of molecular evolution. Changes in these genes could affect the functioning of the recombination pathway, and may have contributed to the successful domestication of maize and its expansion to new cultivation areas.

Parallel steady state studies on a milliliter scale accelerate fed-batch bioprocess design for recombinant protein production with Escherichia coli.

PubMed

Schmideder, Andreas; Cremer, Johannes H; Weuster-Botz, Dirk

2016-11-01

In general, fed-batch processes are applied for recombinant protein production with Escherichia coli (E. coli). However, state of the art methods for identifying suitable reaction conditions suffer from severe drawbacks, i.e. direct transfer of process information from parallel batch studies is often defective and sequential fed-batch studies are time-consuming and cost-intensive. In this study, continuously operated stirred-tank reactors on a milliliter scale were applied to identify suitable reaction conditions for fed-batch processes. Isopropyl β-d-1-thiogalactopyranoside (IPTG) induction strategies were varied in parallel-operated stirred-tank bioreactors to study the effects on the continuous production of the recombinant protein photoactivatable mCherry (PAmCherry) with E. coli. Best-performing induction strategies were transferred from the continuous processes on a milliliter scale to liter scale fed-batch processes. Inducing recombinant protein expression by dynamically increasing the IPTG concentration to 100 µM led to an increase in the product concentration of 21% (8.4 g L -1 ) compared to an implemented high-performance production process with the most frequently applied induction strategy by a single addition of 1000 µM IPGT. Thus, identifying feasible reaction conditions for fed-batch processes in parallel continuous studies on a milliliter scale was shown to be a powerful, novel method to accelerate bioprocess design in a cost-reducing manner. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1426-1435, 2016. © 2016 American Institute of Chemical Engineers.

Microfluidic chips with multi-junctions: an advanced tool in recovering proteins from inclusion bodies

PubMed Central

Yamaguchi, Hiroshi; Miyazaki, Masaya

2015-01-01

Active recombinant proteins are used for studying the biological functions of genes and for the development of therapeutic drugs. Overexpression of recombinant proteins in bacteria often results in the formation of inclusion bodies, which are protein aggregates with non-native conformations. Protein refolding is an important process for obtaining active recombinant proteins from inclusion bodies. However, the conventional refolding method of dialysis or dilution is time-consuming and recovered active protein yields are often low, and a cumbersome trial-and-error process is required to achieve success. To circumvent these difficulties, we used controllable diffusion through laminar flow in microchannels to regulate the denaturant concentration. This method largely aims at reducing protein aggregation during the refolding procedure. This Commentary introduces the principles of the protein refolding method using microfluidic chips and the advantage of our results as a tool for rapid and efficient recovery of active recombinant proteins from inclusion bodies. PMID:25531187

Microfluidic chips with multi-junctions: an advanced tool in recovering proteins from inclusion bodies.

PubMed

Yamaguchi, Hiroshi; Miyazaki, Masaya

2015-01-01

Active recombinant proteins are used for studying the biological functions of genes and for the development of therapeutic drugs. Overexpression of recombinant proteins in bacteria often results in the formation of inclusion bodies, which are protein aggregates with non-native conformations. Protein refolding is an important process for obtaining active recombinant proteins from inclusion bodies. However, the conventional refolding method of dialysis or dilution is time-consuming and recovered active protein yields are often low, and a cumbersome trial-and-error process is required to achieve success. To circumvent these difficulties, we used controllable diffusion through laminar flow in microchannels to regulate the denaturant concentration. This method largely aims at reducing protein aggregation during the refolding procedure. This Commentary introduces the principles of the protein refolding method using microfluidic chips and the advantage of our results as a tool for rapid and efficient recovery of active recombinant proteins from inclusion bodies.

Exciton-dissociation and charge-recombination processes in pentacene/C60 solar cells: theoretical insight into the impact of interface geometry.

PubMed

Yi, Yuanping; Coropceanu, Veaceslav; Brédas, Jean-Luc

2009-11-04

The exciton-dissociation and charge-recombination processes in organic solar cells based on pentacene/C(60) heterojunctions are investigated by means of quantum-mechanical calculations. The electronic couplings and the rates of exciton dissociation and charge recombination have been evaluated for several geometrical configurations of the pentacene/C(60) complex, which are relevant to bilayer and bulk heterojunctions. The results suggest that, irrespective of the actual pentacene-fullerene orientation, both pentacene-based and C(60)-based excitons are able to dissociate efficiently. Also, in the case of parallel configurations of the molecules at the pentacene/C(60) interface, the decay of the lowest charge-transfer state to the ground state is calculated to be very fast; as a result, it can compete with the dissociation process into mobile charge carriers. Since parallel configurations are expected to be found more frequently in bulk heterojunctions than in bilayer heterojunctions, the performance of pentacene/C(60) bulk-heterojunction solar cells is likely to be more affected by charge recombination than that of bilayer devices.

Recombinant spider silk from aqueous solutions via a bio-inspired microfluidic chip

NASA Astrophysics Data System (ADS)

Peng, Qingfa; Zhang, Yaopeng; Lu, Li; Shao, Huili; Qin, Kankan; Hu, Xuechao; Xia, Xiaoxia

2016-11-01

Spiders achieve superior silk fibres by controlling the molecular assembly of silk proteins and the hierarchical structure of fibres. However, current wet-spinning process for recombinant spidroins oversimplifies the natural spinning process. Here, water-soluble recombinant spider dragline silk protein (with a low molecular weight of 47 kDa) was adopted to prepare aqueous spinning dope. Artificial spider silks were spun via microfluidic wet-spinning, using a continuous post-spin drawing process (WS-PSD). By mimicking the natural spinning apparatus, shearing and elongational sections were integrated in the microfluidic spinning chip to induce assembly, orientation of spidroins, and fibril structure formation. The additional post-spin drawing process following the wet-spinning section partially mimics the spinning process of natural spider silk and substantially contributes to the compact aggregation of microfibrils. Subsequent post-stretching further improves the hierarchical structure of the fibres, including the crystalline structure, orientation, and fibril melting. The tensile strength and elongation of post-treated fibres reached up to 510 MPa and 15%, respectively.

The effect of recombination under short-circuit conditions on the determination of charge transport properties in nanostructured photoelectrodes.

PubMed

Villanueva-Cab, J; Anta, J A; Oskam, G

2016-01-28

We report on the commonly unaccounted for process of recombination under short-circuit conditions in nanostructured photoelectrodes with special attention to the charge collection efficiency. It is observed that when recombination under short circuit conditions is significant, small perturbation methods overestimate the charge-collection efficiency, which is related to the inaccurate determination of the electron diffusion coefficient and diffusion length.

Methods and materials for the production of L-lactic acid in yeast

DOEpatents

Hause, Ben [Jordan, MN; Rajgarhia, Vineet [Minnetonka, MN; Suominen, Pirkko [Maple Grove, MN

2009-05-19

Recombinant yeast are provided having, in one aspect, multiple exogenous LDH genes integrated into the genome, while leaving native PDC genes intact. In a second aspect, recombinant yeast are provided having an exogenous LDH gene integrated into its genome at the locus of a native PDC gene, with deletion of the native PDC gene. The recombinant yeast are useful in fermentation process for producing lactic acid.

Production of Prebiotic Molecule Precursors from Hypervelocity Impact Simulation Experiments on Carbonate Sediments

NASA Astrophysics Data System (ADS)

Farcy, B. J.; Grubisic, A.; Li, X.; Pinnick, V. T.; Sutton, M.; Pavlov, A.; Brinckerhoff, W. B.

2017-12-01

Organic molecules, including amino acids and other biotic precursors, have been shown to form in the cooling and expanding plasma plume generated from hypervelocity impacts through the processes of atomization, ionization, and molecular recombination of impactor and impact surface. Various sources of carbon, such as atmospheric methane and carbonaceous material from meteorites, are known to yield cyano-bearing molecules and simple amino acids from impact plasmas. However, the role of mineralogical carbon has not yet been investigated in this process. We have performed experiments using laser ablation mass spectrometry (LA-MS) to study the negative ion yield of plasma-produced prebiotic molecules. A mixture of 10% NH4Cl and 90% CaCO3 was pressed into a pellet and ablated with a 1064 nm Nd:YAG laser, and the resultant negative ions were measured by a plasma analyzer quadrupole MS. Mass spectra show characteristic peaks at m/z = 26 and m/z = 42, indicating the presence of CN- and CNO- ions. When isotopically labeled 15NH4Cl and Ca13CO3 were used in the sample ablation pellet, the purported CN- and CNO- peaks shifted according to their added isotopic mass. Indeed, comparison of resulting ion formation from momentum-based techniques, such as massive cluster secondary ion mass spectrometry, show comparable fragmentation and recombination of CN- and CNO- ions. These findings show that CN- ions, as well as CN radicals and thus HCN, can be formed during meteoritic bombardment of carbonate minerals. During the late heavy bombardment of the earth from 4.1-3.8 Ga, impact-driven chemistry could have played a dominant role in shaping the earth's early prebiotic inventory and sources of chemical energy. As carbonate sediments are common in the Archean, carbonate deposits are most likely an important contributor of carbon for this process, along with atmospheric and meteoritic carbon sources.

Minority-carrier lifetime in InP as a function of light bias

NASA Technical Reports Server (NTRS)

Yater, Jane A.; Weinberg, I.; Jenkins, Phillip P.; Landis, Geoffrey A.

1995-01-01

Minority-carrier lifetime in InP is studied as a function of doping level and laser intensity using time-resolved photoluminescence. A continuous wave diode laser illuminates bulk InP and acts as a light bias, injecting a steady-state concentration of carriers. A 200 ps laser pulse produces a small transient signal on top of the steady-state luminescence, allowing lifetime to be measured directly as a function of incident intensity. For p-InP, lifetime increases with light bias up to a maximum value. Bulk recombination centers are presumably filled to saturation, allowing minority carriers to live longer. The saturation bias scales with dopant concentration for a particular dopant species. As light bias is increased for n-InP, minority-carrier lifetime increases slightly but then decreases, suggesting radiative recombination as a dominant decay mechanism.

Two Mechanisms Determine Quantum Dot Blinking.

PubMed

Yuan, Gangcheng; Gómez, Daniel E; Kirkwood, Nicholas; Boldt, Klaus; Mulvaney, Paul

2018-04-24

Many potential applications of quantum dots (QDs) can only be realized once the luminescence from single nanocrystals (NCs) is understood. These applications include the development of quantum logic devices, single-photon sources, long-life LEDs, and single-molecule biolabels. At the single-nanocrystal level, random fluctuations in the QD photoluminescence occur, a phenomenon termed blinking. There are two competing models to explain this blinking: Auger recombination and surface trap induced recombination. Here we use lifetime scaling on core-shell chalcogenide NCs to demonstrate that both types of blinking occur in the same QDs. We prove that Auger-blinking can yield single-exponential on/off times in contrast to earlier work. The surface passivation strategy determines which blinking mechanism dominates. This study summarizes earlier studies on blinking mechanisms and provides some clues that stable single QDs can be engineered for optoelectronic applications.

Nitrogen vacancies as a common element of the green luminescence and nonradiative recombination centers in Mg-implanted GaN layers formed on a GaN substrate

NASA Astrophysics Data System (ADS)

Kojima, Kazunobu; Takashima, Shinya; Edo, Masaharu; Ueno, Katsunori; Shimizu, Mitsuaki; Takahashi, Tokio; Ishibashi, Shoji; Uedono, Akira; Chichibu, Shigefusa F.

2017-06-01

The photoluminescences of ion-implanted (I/I) and epitaxial Mg-doped GaN (GaN:Mg) are compared. The intensities and lifetimes of the near-band-edge and ultraviolet luminescences associated with a MgGa acceptor of I/I GaN:Mg were significantly lower and shorter than those of the epilayers, respectively. Simultaneously, the green luminescence (GL) became dominant. These emissions were quenched far below room temperature. The results indicate the generation of point defects common to GL and nonradiative recombination centers (NRCs) by I/I. Taking the results of positron annihilation measurement into account, N vacancies are the prime candidate to emit GL and create NRCs with Ga vacancies, (VGa) m (VN) n , as well as to inhibit p-type conductivity.

Validation of chemistry models employed in a particle simulation method

NASA Technical Reports Server (NTRS)

Haas, Brian L.; Mcdonald, Jeffrey D.

1991-01-01

The chemistry models employed in a statistical particle simulation method, as implemented in the Intel iPSC/860 multiprocessor computer, are validated and applied. Chemical relaxation of five-species air in these reservoirs involves 34 simultaneous dissociation, recombination, and atomic-exchange reactions. The reaction rates employed in the analytic solutions are obtained from Arrhenius experimental correlations as functions of temperature for adiabatic gas reservoirs in thermal equilibrium. Favorable agreement with the analytic solutions validates the simulation when applied to relaxation of O2 toward equilibrium in reservoirs dominated by dissociation and recombination, respectively, and when applied to relaxation of air in the temperature range 5000 to 30,000 K. A flow of O2 over a circular cylinder at high Mach number is simulated to demonstrate application of the method to multidimensional reactive flows.

The core structure and recombination energy of a copper screw dislocation: a Peierls study

DOE PAGES

Szajewski, B. A.; Hunter, A.; Beyerlein, I. J.

2017-05-19

The recombination process of dislocations is central to cross-slip, and transmission through Σ3 grain boundaries among other fundamental plastic deformation processes. Despite its importance, a detailed mechanistic understanding remains lacking. In this paper, we apply a continuous dislocation model, inspired by Peierls and Nabarro, complete with an ab-initio computed -surface and continuous units of infinitesimal dislocation slip, towards computing the stress-dependent recombination path of both an isotropic and anisotropic Cu screw dislocation. Under no applied stress, our model reproduces the stacking fault width between Shockley partial dislocations as predicted by discrete linear elasticity. Upon application of a compressive Escaig stress,more » the two partial dislocations coalesce to a separation of ~|b|. Upon increased loading the edge components of each partial dislocation recede, leaving behind a spread Peierls screw dislocation, indicating the recombined state. We demonstrate that the critical stress required to achieve the recombined state is independent of the shear modulus. Rather the critical recombination stress depends on an energy difference between an unstable fault energy (γτ) and the intrinsic stacking fault energy (γτ-γisf). We report recombination energies of ΔW = 0.168 eV/Å and ΔW = 0.084 eV/Å, respectively, for the Cu screw dislocation within isotropic and anisotropic media. Finally, we develop an analytic model which provides insight into our simulation results which compare favourably with other (similar) models.« less

The core structure and recombination energy of a copper screw dislocation: a Peierls study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Szajewski, B. A.; Hunter, A.; Beyerlein, I. J.

The recombination process of dislocations is central to cross-slip, and transmission through Σ3 grain boundaries among other fundamental plastic deformation processes. Despite its importance, a detailed mechanistic understanding remains lacking. In this paper, we apply a continuous dislocation model, inspired by Peierls and Nabarro, complete with an ab-initio computed -surface and continuous units of infinitesimal dislocation slip, towards computing the stress-dependent recombination path of both an isotropic and anisotropic Cu screw dislocation. Under no applied stress, our model reproduces the stacking fault width between Shockley partial dislocations as predicted by discrete linear elasticity. Upon application of a compressive Escaig stress,more » the two partial dislocations coalesce to a separation of ~|b|. Upon increased loading the edge components of each partial dislocation recede, leaving behind a spread Peierls screw dislocation, indicating the recombined state. We demonstrate that the critical stress required to achieve the recombined state is independent of the shear modulus. Rather the critical recombination stress depends on an energy difference between an unstable fault energy (γτ) and the intrinsic stacking fault energy (γτ-γisf). We report recombination energies of ΔW = 0.168 eV/Å and ΔW = 0.084 eV/Å, respectively, for the Cu screw dislocation within isotropic and anisotropic media. Finally, we develop an analytic model which provides insight into our simulation results which compare favourably with other (similar) models.« less

Horizontal transmissible protection against myxomatosis and rabbit hemorrhagic disease by using a recombinant myxoma virus.

PubMed

Bárcena, J; Morales, M; Vázquez, B; Boga, J A; Parra, F; Lucientes, J; Pagès-Manté, A; Sánchez-Vizcaíno, J M; Blasco, R; Torres, J M

2000-02-01

We have developed a new strategy for immunization of wild rabbit populations against myxomatosis and rabbit hemorrhagic disease (RHD) that uses recombinant viruses based on a naturally attenuated field strain of myxoma virus (MV). The recombinant viruses expressed the RHDV major capsid protein (VP60) including a linear epitope tag from the transmissible gastroenteritis virus (TGEV) nucleoprotein. Following inoculation, the recombinant viruses induced specific antibody responses against MV, RHDV, and the TGEV tag. Immunization of wild rabbits by the subcutaneous and oral routes conferred protection against virulent RHDV and MV challenges. The recombinant viruses showed a limited horizontal transmission capacity, either by direct contact or in a flea-mediated process, promoting immunization of contact uninoculated animals.

Horizontal Transmissible Protection against Myxomatosis and Rabbit Hemorrhagic Disease by Using a Recombinant Myxoma Virus

PubMed Central

Bárcena, Juan; Morales, Mónica; Vázquez, Belén; Boga, José A.; Parra, Francisco; Lucientes, Javier; Pagès-Manté, Albert; Sánchez-Vizcaíno, José M.; Blasco, Rafael; Torres, Juan M.

2000-01-01

We have developed a new strategy for immunization of wild rabbit populations against myxomatosis and rabbit hemorrhagic disease (RHD) that uses recombinant viruses based on a naturally attenuated field strain of myxoma virus (MV). The recombinant viruses expressed the RHDV major capsid protein (VP60) including a linear epitope tag from the transmissible gastroenteritis virus (TGEV) nucleoprotein. Following inoculation, the recombinant viruses induced specific antibody responses against MV, RHDV, and the TGEV tag. Immunization of wild rabbits by the subcutaneous and oral routes conferred protection against virulent RHDV and MV challenges. The recombinant viruses showed a limited horizontal transmission capacity, either by direct contact or in a flea-mediated process, promoting immunization of contact uninoculated animals. PMID:10627521

Compartmentalization of the yeast meiotic nucleus revealed by analysis of ectopic recombination.

PubMed

Schlecht, Hélène B; Lichten, Michael; Goldman, Alastair S H

2004-11-01

As yeast cells enter meiosis, chromosomes move from a centromere-clustered (Rabl) to a telomere-clustered (bouquet) configuration and then to states of progressive homolog pairing where telomeres are more dispersed. It is uncertain at which stage of this process sequences commit to recombine with each other. Previous analyses using recombination between dispersed homologous sequences (ectopic recombination) support the view that, on average, homologs are aligned end to end by the time of commitment to recombination. We have undertaken further analyses incorporating new inserts, chromosome rearrangements, an alternate mode of recombination initiation, and mutants that disrupt nuclear structure or telomere metabolism. Our findings support previous conclusions and reveal that distance from the nearest telomere is an important parameter influencing recombination between dispersed sequences. In general, the farther dispersed sequences are from their nearest telomere, the less likely they are to engage in ectopic recombination. Neither the mode of initiating recombination nor the formation of the bouquet appears to affect this relationship. We suggest that aspects of telomere localization and behavior influence the organization and mobility of chromosomes along their entire length, during a critical period of meiosis I prophase that encompasses the homology search.

Development of a scaled-down aerobic fermentation model for scale-up in recombinant protein vaccine manufacturing.

PubMed

Farrell, Patrick; Sun, Jacob; Gao, Meg; Sun, Hong; Pattara, Ben; Zeiser, Arno; D'Amore, Tony

2012-08-17

A simple approach to the development of an aerobic scaled-down fermentation model is presented to obtain more consistent process performance during the scale-up of recombinant protein manufacture. Using a constant volumetric oxygen mass transfer coefficient (k(L)a) for the criterion of a scale-down process, the scaled-down model can be "tuned" to match the k(L)a of any larger-scale target by varying the impeller rotational speed. This approach is demonstrated for a protein vaccine candidate expressed in recombinant Escherichia coli, where process performance is shown to be consistent among 2-L, 20-L, and 200-L scales. An empirical correlation for k(L)a has also been employed to extrapolate to larger manufacturing scales. Copyright © 2012 Elsevier Ltd. All rights reserved.

Analysis of Recombinant Proteins in Transgenic Rice Seeds: Identity, Localization, Tolerance to Digestion, and Plant Stress Response.

PubMed

Wakasa, Yuhya; Takaiwa, Fumio

2016-01-01

Rice seeds are an ideal production platform for high-value recombinant proteins in terms of economy, scalability, safety, and stability. Strategies for the expression of large amounts of recombinant proteins in rice seeds have been established in the past decade and transgenic rice seeds that accumulate recombinant products such as bioactive peptides and proteins, which promote the health and quality of life of humans, have been generated in many laboratories worldwide. One of the most important advantages is the potential for direct oral delivery of transgenic rice seeds without the need for recombinant protein purification (downstream processing), which has been attributed to the high expression levels of recombinant products. Transgenic rice will be beneficial as a delivery system for pharmaceuticals and nutraceuticals in the future. This chapter introduces the strategy for producing recombinant protein in the edible part (endosperm) of the rice grain and describes methods for the analysis of transgenic rice seeds in detail.

Ethanol production by recombinant hosts

DOEpatents

Fowler, David E.; Horton, Philip G.; Ben-Bassat, Arie

1996-01-01

Novel plasmids comprising genes which code for the alcohol dehydrogenase and pyruvate decarboxylase are described. Also described are recombinant hosts which have been transformed with genes coding for alcohol dehydrogenase and pyruvate. By virtue of their transformation with these genes, the recombinant hosts are capable of producing significant amounts of ethanol as a fermentation product. Also disclosed are methods for increasing the growth of recombinant hosts and methods for reducing the accumulation of undesirable metabolic products in the growth medium of these hosts. Also disclosed are recombinant host capable of producing significant amounts of ethanol as a fermentation product of oligosaccharides and plasmids comprising genes encoding polysaccharases, in addition to the genes described above which code for the alcohol dehydrogenase and pyruvate decarboxylase. Further, methods are described for producing ethanol from oligomeric feedstock using the recombinant hosts described above. Also provided is a method for enhancing the production of functional proteins in a recombinant host comprising overexpressing an adhB gene in the host. Further provided are process designs for fermenting oligosaccharide-containing biomass to ethanol.

Ethanol production by recombinant hosts

DOEpatents

Ingram, Lonnie O.; Beall, David S.; Burchhardt, Gerhard F. H.; Guimaraes, Walter V.; Ohta, Kazuyoshi; Wood, Brent E.; Shanmugam, Keelnatham T.

1995-01-01

Novel plasmids comprising genes which code for the alcohol dehydrogenase and pyruvate decarboxylase are described. Also described are recombinant hosts which have been transformed with genes coding for alcohol dehydrogenase and pyruvate. By virtue of their transformation with these genes, the recombinant hosts are capable of producing significant amounts of ethanol as a fermentation product. Also disclosed are methods for increasing the growth of recombinant hosts and methods for reducing the accumulation of undesirable metabolic products in the growth medium of these hosts. Also disclosed are recombinant host capable of producing significant amounts of ethanol as a fermentation product of oligosaccharides and plasmids comprising genes encoding polysaccharases, in addition to the genes described above which code for the alcohol dehydrogenase and pyruvate decarboxylase. Further, methods are described for producing ethanol from oligomeric feedstock using the recombinant hosts described above. Also provided is a method for enhancing the production of functional proteins in a recombinant host comprising overexpressing an adhB gene in the host. Further provided are process designs for fermenting oligosaccharide-containing biomass to ethanol.

Ethanol precipitation for purification of recombinant antibodies.

PubMed

Tscheliessnig, Anne; Satzer, Peter; Hammerschmidt, Nikolaus; Schulz, Henk; Helk, Bernhard; Jungbauer, Alois

2014-10-20

Currently, the golden standard for the purification of recombinant humanized antibodies (rhAbs) from CHO cell culture is protein A chromatography. However, due to increasing rhAbs titers alternative methods have come into focus. A new strategy for purification of recombinant human antibodies from CHO cell culture supernatant based on cold ethanol precipitation (CEP) and CaCl2 precipitation has been developed. This method is based on the cold ethanol precipitation, the process used for purification of antibodies and other components from blood plasma. We proof the applicability of the developed process for four different antibodies resulting in similar yield and purity as a protein A chromatography based process. This process can be further improved using an anion-exchange chromatography in flowthrough mode e.g. a monolith as last step so that residual host cell protein is reduced to a minimum. Beside the ethanol based process, our data also suggest that ethanol could be replaced with methanol or isopropanol. The process is suited for continuous operation. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Investigation of chromatography and polymer/salt aqueous two-phase processes for downstream processing development of recombinant phenylalanine dehydrogenase.

PubMed

Omidinia, Eskandar; Shahbaz Mohamadi, Hamid; Dinarvand, Rassoul; Taherkhani, Heshmat-Allah

2010-03-01

This work presents a comprehensive study between the polymer/salt aqueous two-phase systems (ATPS) and chromatography process for downstream processing of recombinant Bacillus badius phenylalanine dehydrogenase (PheDH). First, the partitioning behavior of recombinant PheDH in polyethylene glycol (PEG)/K2HPO4 ATPS was examined. For comparative purpose, a classical chromatographic protocol was performed as well. Investigation of chromatography and ATPS procedures revealed that the ATPS comprising of 9% (w/w) PEG-6000, 16% (w/w) K2HPO4 and 16% (w/w) KCl with pH of 8.0, volume ratio (V ( R )) of 0.25, temperature of 25 degrees C and 40% (w/w) cell lysate ensured the most favorable approach for PheDH downstream process. A specific activity of 4,231.4 U/mg, a yield of 96.7% and a recovery of 162.0% were obtained. Furthermore, the shorter process time (4 vs. 48 h) and the lower total cost (4 vs. 20 euro) were additionally features that confirmed the suitability of proposed technique.

Requirement of mismatch repair genes MSH2 and MSH3 in the RAD1-RAD10 pathway of mitotic recombination in Saccharomyces cerevisiae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saparbaev, M.; Prakash, L.; Prakash, S.

1996-03-01

The RAD1 and RAD10 genes of Saccharomyces cerevisiae are required for nucleotide excision repair and they also act in mitotic recombination. The Rad1-Rad10 complex has a single-stranded DNA endonuclease activity. Here, we show that the mismatch repair genes MSH2 and MSH3 function in mitotic recombination. For both his3 and his4 duplications, and for homologous integration of a linear DNA fragment into the genome, the msh3-A mutation has an effect on recombination similar to that of the rad1{Delta} and rad10{Delta} mutations. The msh2{Delta} mutation also reduces the rate of recombination of the his3 duplication and lowers the incidence of homologous integrationmore » of a linear DNA fragment. Epistasis analyses indicate that MSH2 and MSH3 function in the RAD1-RAD10 recombination pathway, and studies presented here suggest an involvement of the RAM-RAD10 pathway in reciprocal recombination. The possible roles of Msh2, Msh3, Rad1, and Rad10 proteins in genetic recombination are discussed. Coupling of mismatch binding proteins with the recombinational machinery could be important for ensuring genetic fidelity in the recombination process. 59 refs., 2 figs., 7 tabs.« less

Requirement of mismatch repair genes MSH2 and MSH3 in the RAD1-RAD10 pathway of mitotic recombination in Saccharomyces cerevisiae.

PubMed

Saparbaev, M; Prakash, L; Prakash, S

1996-03-01

The RAD1 and RAD10 genes of Saccharomyces cerevisiae are required for nucleotide excision repair and they also act in mitotic recombination. The Rad1-Rad10 complex has a single-stranded DNA endonuclease activity. Here, we show that the mismatch repair genes MSH2 and MSH3 function in mitotic recombination. For both his3 and his4 duplications, and for homologous integration of a linear DNA fragment into the genome, the msh3 delta mutation has an effect on recombination similar to that of the rad1 delta and rad10 delta mutations. The msh2 delta mutation also reduces the rate of recombination of the his3 duplication and lowers the incidence of homologous integration of a linear DNA fragment. Epistasis analyses indicate that MSH2 and MSH3 function in the RAD1-RAD10 recombination pathway, and studies presented here suggest an involvement of the RAD1-RAD10 pathway in reciprocal recombination. The possible roles of Msh2, Msh3, Rad1, and Rad10 proteins in genetic recombination are discussed. Coupling of mismatch binding proteins with the recombinational machinery could be important for ensuring genetic fidelity in the recombination process.

The Recombination Landscape in Wild House Mice Inferred Using Population Genomic Data.

PubMed

Booker, Tom R; Ness, Rob W; Keightley, Peter D

2017-09-01

Characterizing variation in the rate of recombination across the genome is important for understanding several evolutionary processes. Previous analysis of the recombination landscape in laboratory mice has revealed that the different subspecies have different suites of recombination hotspots. It is unknown, however, whether hotspots identified in laboratory strains reflect the hotspot diversity of natural populations or whether broad-scale variation in the rate of recombination is conserved between subspecies. In this study, we constructed fine-scale recombination rate maps for a natural population of the Eastern house mouse, Mus musculus castaneus We performed simulations to assess the accuracy of recombination rate inference in the presence of phase errors, and we used a novel approach to quantify phase error. The spatial distribution of recombination events is strongly positively correlated between our castaneus map, and a map constructed using inbred lines derived predominantly from M. m. domesticus Recombination hotspots in wild castaneus show little overlap, however, with the locations of double-strand breaks in wild-derived house mouse strains. Finally, we also find that genetic diversity in M. m. castaneus is positively correlated with the rate of recombination, consistent with pervasive natural selection operating in the genome. Our study suggests that recombination rate variation is conserved at broad scales between house mouse subspecies, but it is not strongly conserved at fine scales. Copyright © 2017 by the Genetics Society of America.

RECOMBINATION PROCESSES AND NATURE OF THE TAIL AND GAP STATES IN a-Si:H and a-Si:H/a-SiNx:H MULTILAYERS

NASA Astrophysics Data System (ADS)

Morigaki, K.

We discuss recombination processes and nature of the tail and gap states in a-Si:H and a-Si:H/a-SiNx:H multilayers on the basis of our ODMR, luminescence, photoinduced absorption and ENDOR measurements. We present other results relevant to this subject and attempt to interpret them in terms of our model.

[Recombinant granulocyte-colony stimulating factor (filgrastim): optimization of conditions of isolation and purification from inclusion body].

PubMed

Kononova, N V; Iakovlev, A V; Zhuravko, A M; Pankeev, N N; Minaev, S V; Bobruskin, A I; Mart'ianov, V A

2014-01-01

We developed a unified process platform for two recombinant human GCSF medicines--one with the non-prolonged and the other with prolonged action. This unified technology led to a simpler and cheaper production while introduction of the additional pegylation stage to the technological line eased obtaining of the medicines with different action and allowed to standardize technological process documenting according to GMP requirements.

Theoretical prediction of the impact of Auger recombination on charge collection from an ion track

NASA Technical Reports Server (NTRS)

Edmonds, Larry D.

1991-01-01

A recombination mechanism that significantly reduces charge collection from very dense ion tracks in silicon devices was postulated by Zoutendyk et al. The theoretical analysis presented here concludes that Auger recombination is such a mechanism and is of marginal importance for higher density tracks produced by 270-MeV krypton, but of major importance for higher density tracks. The analysis shows that recombination loss is profoundly affected by track diffusion. As the track diffuses, the density and recombination rate decrease so fast that the linear density (number of electron-hole pairs per unit length) approaches a non-zero limiting value as t yields infinity. Furthermore, the linear density is very nearly equal to this limiting value in a few picoseconds or less. When Auger recombination accompanies charge transport processes that have much longer time scales, it can be simulated by assigning a reduced linear energy transfer to the ion.

Putative recombination events and evolutionary history of five economically important viruses of fruit trees based on coat protein-encoding gene sequence analysis.

PubMed

Boulila, Moncef

2010-06-01

To enhance the knowledge of recombination as an evolutionary process, 267 accessions retrieved from GenBank were investigated, all belonging to five economically important viruses infecting fruit crops (Plum pox, Apple chlorotic leaf spot, Apple mosaic, Prune dwarf, and Prunus necrotic ringspot viruses). Putative recombinational events were detected in the coat protein (CP)-encoding gene using RECCO and RDP version 3.31beta algorithms. Based on RECCO results, all five viruses were shown to contain potential recombination signals in the CP gene. Reconstructed trees with modified topologies were proposed. Furthermore, RECCO performed better than the RDP package in detecting recombination events and exhibiting their evolution rate along the sequences of the five viruses. RDP, however, provided the possible major and minor parents of the recombinants. Thus, the two methods should be considered complementary.

Heterojunction photodiode on cleaved SiC

NASA Astrophysics Data System (ADS)

Solovan, Mykhailo M.; Farah, John; Kovaliuk, Taras T.; Brus, Viktor V.; Mostovyi, Andrii I.; Maistruk, Eduard V.; Maryanchuk, Pavlo D.

2018-01-01

Graphite/n-SiC Shottky diodes were prepared by means of the recently proposed technique based on the transferring of drawn graphite films onto the n-SiC single crystal substrate. Current-voltage characteristics were measured and analyzed. High quality ohmic contancts were prepared by the DC magnetron sputtering of Ni thin films onto cleaved n-type SiC single crystal substrates. The height of the potential barrier and the series resistance of the graphite/n-SiC junctions were measured and analysed. The dominant current transport mechanisms through the diodes were determined. There was shown that the dominant current transport mechanisms through the graphite/n-SiC Shottky diodes were the multi-step tunnel-recombination at forward bias and the tunnelling mechanisms at reverse bias.

Radio Recombination Lines at Decametre Wavelengths. Prospects for the Future

DTIC Science & Technology

2010-09-15

dark matter decay) can produce either an absorption or emission H  signal relative to the cosmic microwave background (CMB). At least three distinct...and 2). Most observations have focussed on sightlines towards known bright background sources or pass- ing through gas-rich regions along the inner...combina- tion of the Galactic synchrotron emission and the extragalactic background but is likely to be dominated by the former (Bridle, 1967). The

Processing of human cytomegalovirus glycoprotein B in recombinant adenovirus-infected cells.

PubMed

Marshall, G S; Fenger, D P; Stout, G G; Knights, M E; Hunt, L A

1996-07-01

Intracellular processing of human cytomegalovirus (HCMV) glycoprotein B (gB; gpUL55) expressed by a recombinant adenovirus (Ad-gB) was studied in human A549 cells as processing events could affect immunogenicity when such viruses are used as live-recombinant vaccines. Cleavage of [35S]methionine-labelled gp13O into gp93 and gp55 reached a maximum after a 3 h chase. Cleavage was completely inhibited by brefeldin A, suggesting that processing normally occurs as a late Golgi or post-Golgi event. Uncleaved gp 130 remained completely sensitive to endo-beta-N-acetylglucosaminidase H (Endo-H) in untreated cells following long chase periods, indicating high-mannose oligosaccharides at all of the 18 N-linked glycosylation sites (Asn-X-Ser/Thr) and retention in the endoplasmic reticulum. Endo-H analysis of gp55 from swainsonine-treated and untreated cells was consistent with glycosylation at all three potential sites, with two oligosaccharides remaining sensitive to Endo-H and one being processed to Endo-H resistance. The heavily glycosylated N-terminal gp93 subunit was not detected by [35S]methionine-labelling but was easily detected along with gp55 after labelling with [3H]mannose. No cleavage of gp 130 was observed in analogous pulse-chase radiolabelling of Ad-gB-infected human fibroblasts, even though these cells are permissive for HCMV replication and can process the native gB molecule. Processing of gB in recombinant adenovirus-infected A549 cells was generally similar to that previously reported for native gB in HCMV-infected fibroblasts.

Evidence for Radiative Recombination of O+ Ions as a Significant Source of O 844.6 nm Emission Excitation

NASA Astrophysics Data System (ADS)

Waldrop, L.; Kerr, R. B.; Huang, Y.

2018-04-01

Photoelectron (PE) impact on ground-state O(3P) atoms is well known as a major source of twilight 844.6 nm emission in the midlatitude thermosphere. Knowledge of the PE flux can be used to infer thermospheric oxygen density, [O], from photometric measurements of 844.6 nm airglow, provided that PE impact is the dominant process generating the observed emission. During several spring observational campaigns at Arecibo Observatory, however, we have observed significant 844.6 nm emission throughout the night, which is unlikely to arise from PE impact excitation which requires solar illumination of either the local or geomagnetically conjugate thermosphere. Here we show that radiative recombination (RR) of O+ ions is likely responsible for the observed nighttime emission, based on model predictions of electron and O+ ion density and temperature by the Incoherent Scatter Radar Ionosphere Model. The calculated emission brightness produced by O + RR exhibits good agreement with the airglow data, in that both decay approximately monotonically throughout the night at similar rates. We conclude that the conventional assumption of a pure PE impact source is most likely to be invalid during dusk twilight, when RR-generated emission is most significant. Estimation of [O] from measurements of 844.6 nm emission demands isolation of the PE impact source via coincident estimation of the RR source, and the effective cross section for RR-generated emission is found here to be consistent with optically thin conditions.

High redshift quasars and high metallicities

NASA Technical Reports Server (NTRS)

Ferland, Gary J.

1997-01-01

A large-scale code called Cloudy was designed to simulate non-equilibrium plasmas and predict their spectra. The goal was to apply it to studies of galactic and extragalactic emission line objects in order to reliably deduce abundances and luminosities. Quasars are of particular interest because they are the most luminous objects in the universe and the highest redshift objects that can be observed spectroscopically, and their emission lines can reveal the composition of the interstellar medium (ISM) of the universe when it was well under a billion years old. The lines are produced by warm (approximately 10(sup 4)K) gas with moderate to low density (n less than or equal to 10(sup 12) cm(sup -3)). Cloudy has been extended to include approximately 10(sup 4) resonance lines from the 495 possible stages of ionization of the lightest 30 elements, an extension that required several steps. The charge transfer database was expanded to complete the needed reactions between hydrogen and the first four ions and fit all reactions with a common approximation. Radiative recombination rate coefficients were derived for recombination from all closed shells, where this process should dominate. Analytical fits to Opacity Project (OP) and other recent photoionization cross sections were produced. Finally, rescaled OP oscillator strengths were used to compile a complete set of data for 5971 resonance lines. The major discovery has been that high redshift quasars have very high metallicities and there is strong evidence that the quasar phenomenon is associated with the birth of massive elliptical galaxies.

Influence of sulfur oxidation state and steric bulk upon trifluoromethyl ketone (TFK) binding kinetics to carboxylesterases and fatty acid amide hydrolase (FAAH)

PubMed Central

Wheelock, Craig E.; Nishi, Kosuke; Ying, Andy; Jones, Paul D.; Colvin, Michael E.; Olmstead, Marilyn M.; Hammock, Bruce D.

2009-01-01

Carboxylesterases metabolize numerous exogenous and endogenous ester-containing compounds including the chemotherapeutic agent CPT-11, anti-influenza viral agent oseltamivir and many agrochemicals. Trifluoromethyl ketone (TFK)-containing compounds with a sulfur atom beta to the ketone moiety are some of the most potent carboxylesterase and amidase inhibitors identified to date. This study examined the effects of alkyl chain length (i.e., steric effects) and sulfur oxidation state upon TFK inhibitor potency (IC50) and binding kinetics (ki). The selective carboxylesterase inhibitor benzil was used as a non-TFK containing control. These effects were examined using two commercial esterases (porcine and rabbit liver esterase) and two human recombinant esterases (hCE-1 and hCE-2) as well as human recombinant fatty acid amide hydrolase (FAAH). In addition, the inhibition mechanism was examined using a combination of 1H NMR, X-ray crystallography and ab initio calculations. Overall, the data show that while sulfur oxidation state profoundly affects both inhibitor potency and binding kinetics, the steric effects dominate and override the contributions of sulfur oxidation. In addition, the data suggest that inclusion of a sulfur atom beta to the ketone contributes an increase (~5-fold) in inhibitor potency due to effects upon ketone hydration and/or intramolecular hydrogen bond formation. These results provide further information on the nature of the TFK binding interaction and will be useful in increasing our understanding of this basic biochemical process. PMID:18023188

Use of a protein engineering strategy to overcome limitations in the production of "Difficult to Express" recombinant proteins.

PubMed

Hussain, Hirra; Fisher, David I; Abbott, W Mark; Roth, Robert G; Dickson, Alan J

2017-10-01

Certain recombinant proteins are deemed "difficult to express" in mammalian expression systems requiring significant cell and/or process engineering to abrogate expression bottlenecks. With increasing demand for the production of recombinant proteins in mammalian cells, low protein yields can have significant consequences for industrial processes. To investigate the molecular mechanisms that restrict expression of recombinant proteins, naturally secreted model proteins were analyzed from the tissue inhibitors of metalloproteinase (TIMP) protein family. In particular, TIMP-2 and TIMP-3 were subjected to detailed study. TIMP proteins share significant sequence homology (∼50% identity and ∼70% similarity in amino acid sequence). However, they show marked differences in secretion in mammalian expression systems despite this extensive sequence homology. Using these two proteins as models, this study characterized the molecular mechanisms responsible for poor recombinant protein production. Our results reveal that both TIMP-2 and TIMP-3 are detectable at mRNA and protein level within the cell but only TIMP-2 is secreted effectively into the extracellular medium. Analysis of protein localization and the nature of intracellular protein suggest TIMP-3 is severely limited in its post-translational processing. To overcome this challenge, modification of the TIMP-3 sequence to include a furin protease-cleavable pro-sequence resulted in secretion of the modified TIMP-3 protein, however, incomplete processing was observed. Based on the TIMP-3 data, the protein engineering approach was optimized and successfully applied in combination with cell engineering, the overexpression of furin, to another member of the TIMP protein family (the poorly expressed TIMP-4). Use of the described protein engineering strategy resulted in successful secretion of poorly (TIMP-4) and non-secreted (TIMP-3) targets, and presents a novel strategy to enhance the production of "difficult" recombinant targets. Biotechnol. Bioeng. 2017;114: 2348-2359. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Identification of Quantitative Trait Loci Controlling Root and Shoot Traits Associated with Drought Tolerance in a Lentil (Lens culinaris Medik.) Recombinant Inbred Line Population

PubMed Central

Idrissi, Omar; Udupa, Sripada M.; De Keyser, Ellen; McGee, Rebecca J.; Coyne, Clarice J.; Saha, Gopesh C.; Muehlbauer, Fred J.; Van Damme, Patrick; De Riek, Jan

2016-01-01

Drought is one of the major abiotic stresses limiting lentil productivity in rainfed production systems. Specific rooting patterns can be associated with drought avoidance mechanisms that can be used in lentil breeding programs. In all, 252 co-dominant and dominant markers were used for Quantitative Trait Loci (QTL) analysis on 132 lentil recombinant inbred lines based on greenhouse experiments for root and shoot traits during two seasons under progressive drought-stressed conditions. Eighteen QTLs controlling a total of 14 root and shoot traits were identified. A QTL-hotspot genomic region related to a number of root and shoot characteristics associated with drought tolerance such as dry root biomass, root surface area, lateral root number, dry shoot biomass and shoot length was identified. Interestingly, a QTL (QRSratioIX-2.30) related to root-shoot ratio, an important trait for drought avoidance, explaining the highest phenotypic variance of 27.6 and 28.9% for the two consecutive seasons, respectively, was detected. This QTL was closed to the co-dominant SNP marker TP6337 and also flanked by the two SNP TP518 and TP1280. An important QTL (QLRNIII-98.64) related to lateral root number was found close to TP3371 and flanked by TP5093 and TP6072 SNP markers. Also, a QTL (QSRLIV-61.63) associated with specific root length was identified close to TP1873 and flanked by F7XEM6b SRAP marker and TP1035 SNP marker. These two QTLs were detected in both seasons. Our results could be used for marker-assisted selection in lentil breeding programs targeting root and shoot characteristics conferring drought avoidance as an efficient alternative to slow and labor-intensive conventional breeding methods. PMID:27602034

Highly sensitive detection of mutations in CHO cell recombinant DNA using multi-parallel single molecule real-time DNA sequencing.

PubMed

Cartwright, Joseph F; Anderson, Karin; Longworth, Joseph; Lobb, Philip; James, David C

2018-06-01

High-fidelity replication of biologic-encoding recombinant DNA sequences by engineered mammalian cell cultures is an essential pre-requisite for the development of stable cell lines for the production of biotherapeutics. However, immortalized mammalian cells characteristically exhibit an increased point mutation frequency compared to mammalian cells in vivo, both across their genomes and at specific loci (hotspots). Thus unforeseen mutations in recombinant DNA sequences can arise and be maintained within producer cell populations. These may affect both the stability of recombinant gene expression and give rise to protein sequence variants with variable bioactivity and immunogenicity. Rigorous quantitative assessment of recombinant DNA integrity should therefore form part of the cell line development process and be an essential quality assurance metric for instances where synthetic/multi-component assemblies are utilized to engineer mammalian cells, such as the assessment of recombinant DNA fidelity or the mutability of single-site integration target loci. Based on Pacific Biosciences (Menlo Park, CA) single molecule real-time (SMRT™) circular consensus sequencing (CCS) technology we developed a rDNA sequence analysis tool to process the multi-parallel sequencing of ∼40,000 single recombinant DNA molecules. After statistical filtering of raw sequencing data, we show that this analytical method is capable of detecting single point mutations in rDNA to a minimum single mutation frequency of 0.0042% (<1/24,000 bases). Using a stable CHO transfectant pool harboring a randomly integrated 5 kB plasmid construct encoding GFP we found that 28% of recombinant plasmid copies contained at least one low frequency (<0.3%) point mutation. These mutations were predominantly found in GC base pairs (85%) and that there was no positional bias in mutation across the plasmid sequence. There was no discernable difference between the mutation frequencies of coding and non-coding DNA. The putative ratio of non-synonymous and synonymous changes within the open reading frames (ORFs) in the plasmid sequence indicates that natural selection does not impact upon the prevalence of these mutations. Here we have demonstrated the abundance of mutations that fall outside of the reported range of detection of next generation sequencing (NGS) and second generation sequencing (SGS) platforms, providing a methodology capable of being utilized in cell line development platforms to identify the fidelity of recombinant genes throughout the production process. © 2018 Wiley Periodicals, Inc.

Vibroacoustic processes and structural variations in muscular tissue

NASA Astrophysics Data System (ADS)

Antonets, V. A.; Klochkov, B. N.; Kovaleva, E. P.

1995-03-01

This paper reviews the problems and results obtained in the course of experimental and theoretical investigations of the vibroacoustic activity of contracting muscles. Two types of such processes are examined: (1) acoustic vibrations due to the macromolecular recombinations of muscle proteins, which are responsible for the muscle contraction, and (2) acoustic vibrations associated with the finite accuracy and speed of the receptor-effector system that controls the muscle contraction. By investigating the acoustic vibrations, we examine structural recombinations (conformation variations) in macromolecules during mechanochemical reactions. Since chemical reactions of macromolecules are always accompanied by conformational recombinations, the generation mechanism, which is responsible for the contraction processes in a muscular tissue, can also be extended to other macromolecular media. Investigation of infrasound vibrations makes it possible to explore the quality and error of control for the processes in the muscle under different types of loading. Since a living body is controlled via perceptions, the latter can be quantitatively estimated by the parametess of infrasound vibrations.

Solid methane in neutron radiation: Cryogenic moderators and cometary cryo volcanism

NASA Astrophysics Data System (ADS)

Kirichek, O.; Lawson, C. R.; Jenkins, D. M.; Ridley, C. J. T.; Haynes, D. J.

2017-12-01

The effect of ionizing radiation on solid methane has previously been an area of interest in the astrophysics community. In the late 1980s this interest was further boosted by the possibility of using solid methane as a moderating medium in spallation neutron sources. Here we present test results of solid methane moderators commissioned at the ISIS neutron source, and compare them with a model based on the theory of thermal explosion. Good agreement between the moderator test data and our model suggests that the process of radiolysis defect recombination happens at two different temperature ranges: the ;lower temperature; recombination process occurs at around 20 K, with the ;higher temperature; process taking place between 50 and 60 K. We discuss consequences of this mechanism for the designing and operation of solid methane moderators used in advanced neutron sources. We also discuss the possible role of radiolysis defect recombination processes in cryo-volcanism on comets, and suggest an application based on this phenomenon.

Evidence for Protection against Chronic Hepatitis C Virus Infection in Chimpanzees by Immunization with Replicating Recombinant Vaccinia Virus▿

PubMed Central

Youn, Jin-Won; Hu, Yu-Wen; Tricoche, Nancy; Pfahler, Wolfram; Shata, Mohamed Tarek; Dreux, Marlene; Cosset, François-Loic; Folgori, Antonella; Lee, Dong-Hun; Brotman, Betsy; Prince, Alfred M.

2008-01-01

Given the failures of nonreplicating vaccines against chronic hepatitis C virus (HCV) infection, we hypothesized that a replicating viral vector may provide protective immunity. Four chimpanzees were immunized transdermally twice with recombinant vaccinia viruses (rVV) expressing HCV genes. After challenge with 24 50% chimpanzee infective doses of homologous HCV, the two control animals that had received only the parental VV developed chronic HCV infection. All four immunized animals resolved HCV infection. The difference in the rate of chronicity between the immunized and the control animals was close to statistical significance (P = 0.067). Immunized animals developed vigorous gamma interferon enzyme-linked immunospot responses and moderate proliferative responses. To investigate cross-genotype protection, the immunized recovered chimpanzees were challenged with a pool of six major HCV genotypes. During the acute phase after the multigenotype challenge, all animals had high-titer viremia in which genotype 4 dominated (87%), followed by genotype 5 (13%). However, after fluctuating low-level viremia, the viremia finally turned negative or persisted at very low levels. This study suggests the potential efficacy of replicating recombinant vaccinia virus-based immunization against chronic HCV infection. PMID:18753204

Minority carrier lifetimes in very long-wave infrared InAs/GaInSb superlattices

DOE PAGES

Olson, Benjamin Varberg; Haugan, Heather J.; Brown, Gail J.; ...

2016-01-01

Here, significantly improved carrier lifetimes in very-long wave infrared InAs/GaInSb superlattice(SL) absorbers are demonstrated by using time-resolved microwave reflectance (TMR) measurements. A nominal 47.0 Å InAs/21.5 Å Ga 0.75In 0.25Sb SLstructure that produces an approximately 25 μm response at 10 K has a minority carrier lifetime of 140 ± 20 ns at 18 K, which is markedly long for SL absorber with such a narrow bandgap. This improvement is attributed to the strain-engineered ternary design. Such SL employs a shorter period with reduced gallium in order to achieve good optical absorption and epitaxial advantages, which ultimately leads to the improvementsmore » in the minority carrier lifetime by reducing Shockley–Read–Hall (SRH) defects. By analyzing the temperature-dependence of TMR decay data, the recombination mechanisms and trap states that currently limit the performance of this SL absorber have been identified. The results show a general decrease in the long-decay lifetime component, which is dominated by the SRH recombination at temperature below ~30 K, and by Auger recombination at temperatures above ~45 K.« less

Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum

PubMed Central

Miles, Alistair; Iqbal, Zamin; Vauterin, Paul; Pearson, Richard; Campino, Susana; Theron, Michel; Gould, Kelda; Mead, Daniel; Drury, Eleanor; O'Brien, John; Ruano Rubio, Valentin; MacInnis, Bronwyn; Mwangi, Jonathan; Samarakoon, Upeka; Ranford-Cartwright, Lisa; Ferdig, Michael; Hayton, Karen; Su, Xin-zhuan; Wellems, Thomas; Rayner, Julian; McVean, Gil; Kwiatkowski, Dominic

2016-01-01

The malaria parasite Plasmodium falciparum has a great capacity for evolutionary adaptation to evade host immunity and develop drug resistance. Current understanding of parasite evolution is impeded by the fact that a large fraction of the genome is either highly repetitive or highly variable and thus difficult to analyze using short-read sequencing technologies. Here, we describe a resource of deep sequencing data on parents and progeny from genetic crosses, which has enabled us to perform the first genome-wide, integrated analysis of SNP, indel and complex polymorphisms, using Mendelian error rates as an indicator of genotypic accuracy. These data reveal that indels are exceptionally abundant, being more common than SNPs and thus the dominant mode of polymorphism within the core genome. We use the high density of SNP and indel markers to analyze patterns of meiotic recombination, confirming a high rate of crossover events and providing the first estimates for the rate of non-crossover events and the length of conversion tracts. We observe several instances of meiotic recombination within copy number variants associated with drug resistance, demonstrating a mechanism whereby fitness costs associated with resistance mutations could be compensated and greater phenotypic plasticity could be acquired. PMID:27531718

Combination of a recombinant bacterium with organonitrile-degrading and biofilm-forming capability and a positively charged carrier for organonitriles removal.

PubMed

Li, Chunyan; Sun, Yueling; Yue, Zhenlei; Huang, Mingyan; Wang, Jinming; Chen, Xi; An, Xuejiao; Zang, Hailian; Li, Dapeng; Hou, Ning

2018-04-10

The immobilization of organonitrile-degrading bacteria via the addition of biofilm-forming bacteria represents a promising technology for the treatment of organonitrile-containing wastewater, but biofilm-forming bacteria simply mixed with degrading bacteria may reduce the biodegradation efficiency. Nitrile hydratase and amidase genes, which play critical roles in organonitriles degradation, were cloned and transformed into the biofilm-forming bacterium Bacillus subtilis N4 to construct a recombinant bacterium B. subtilis N4/pHTnha-ami. Modified polyethylene carriers with positive charge was applied to promote bacterial adherence and biofilm formation. The immobilized B. subtilis N4/pHTnha-ami was resistant to organonitriles loading shocks and could remove organic cyanide ion with a initial concentration of 392.6 mg/L for 24 h in a moving bed biofilm reactor. The imputed quorum-sensing signal and the high-throughput sequencing analysis of the biofilm indicated that B. subtilis N4/pHTnha-ami was successfully immobilized and became dominant. The successful application of the immobilized recombinant bacterium offers a novel strategy for the biodegradation of recalcitrant compounds. Copyright © 2018 Elsevier B.V. All rights reserved.

Rhizomucor miehei triglyceride lipase is processed and secreted from transformed Aspergillus oryzae.

PubMed

Huge-Jensen, B; Andreasen, F; Christensen, T; Christensen, M; Thim, L; Boel, E

1989-09-01

The cDNA encoding the precursor of the Rhizomucor miehei triglyceride lipase was inserted in an Aspergillus oryzae expression vector. In this vector the expression of the lipase cDNA is under control of the Aspergillus oryzae alpha-amylase gene promoter and the Aspergillus niger glucoamylase gene terminator. The recombinant plasmid was introduced into Aspergillus oryzae, and transformed colonies were selected and screened for lipase expression. Lipase-positive transformants were grown in a small fermentor, and recombinant triglyceride lipase was purified from the culture broth. The purified enzymatically active recombinant lipase (rRML) secreted from A. oryzae was shown to have the same characteristics with respect to mobility on reducing SDS-gels and amino acid composition as the native enzyme. N-terminal amino acid sequencing indicated that approximately 70% of the secreted rRML had the same N-terminal sequence as the native Rhizomucor miehei enzyme, whereas 30% of the secreted rRML was one amino acid residue shorter in the N-terminal. The recombinant lipase precursor, which has a 70 amino acid propeptide, is thus processed in and secreted from Aspergillus oryzae. We have hereby demonstrated the utility of this organism as a host for the production of recombinant triglyceride lipases.

Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections

PubMed Central

Stenglein, Mark D.; Jacobson, Elliott R.; Chang, Li-Wen; Sanders, Chris; Hawkins, Michelle G.; Guzman, David S-M.; Drazenovich, Tracy; Dunker, Freeland; Kamaka, Elizabeth K.; Fisher, Debbie; Reavill, Drury R.; Meola, Linda F.; Levens, Gregory; DeRisi, Joseph L.

2015-01-01

Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes. Arenaviruses package a large (L) and small (S) genome segment in their virions. For segmented RNA viruses like these, novel genotypes can be generated through mutation, recombination, and reassortment. Although it is believed that an ancient recombination event led to the emergence of a new lineage of mammalian arenaviruses, neither recombination nor reassortment has been definitively documented in natural arenavirus infections. Here, we used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected animals, we determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected, with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes, and a particular S segment genotype dominated in individual animals and at a population level. We corroborated sequencing results by qRT-PCR and virus isolation, and isolates replicated as ensembles in culture. Numerous instances of recombination and reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication and transmission despite their atypical structures. Overall, this represents intrahost diversity of an extent and form that goes well beyond what has been observed for arenaviruses or for viruses in general. This diversity can be plausibly attributed to the captive intermingling of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique opportunity to study arenavirus evolution and adaptation, these findings allow the investigation of unintended anthropogenic impacts on viral ecology, diversity, and disease potential. PMID:25993603

Quantifying and resolving multiple vector transformants in S. cerevisiae plasmid libraries.

PubMed

Scanlon, Thomas C; Gray, Elizabeth C; Griswold, Karl E

2009-11-20

In addition to providing the molecular machinery for transcription and translation, recombinant microbial expression hosts maintain the critical genotype-phenotype link that is essential for high throughput screening and recovery of proteins encoded by plasmid libraries. It is known that Escherichia coli cells can be simultaneously transformed with multiple unique plasmids and thusly complicate recombinant library screening experiments. As a result of their potential to yield misleading results, bacterial multiple vector transformants have been thoroughly characterized in previous model studies. In contrast to bacterial systems, there is little quantitative information available regarding multiple vector transformants in yeast. Saccharomyces cerevisiae is the most widely used eukaryotic platform for cell surface display, combinatorial protein engineering, and other recombinant library screens. In order to characterize the extent and nature of multiple vector transformants in this important host, plasmid-born gene libraries constructed by yeast homologous recombination were analyzed by DNA sequencing. It was found that up to 90% of clones in yeast homologous recombination libraries may be multiple vector transformants, that on average these clones bear four or more unique mutant genes, and that these multiple vector cells persist as a significant proportion of library populations for greater than 24 hours during liquid outgrowth. Both vector concentration and vector to insert ratio influenced the library proportion of multiple vector transformants, but their population frequency was independent of transformation efficiency. Interestingly, the average number of plasmids born by multiple vector transformants did not vary with their library population proportion. These results highlight the potential for multiple vector transformants to dominate yeast libraries constructed by homologous recombination. The previously unrecognized prevalence and persistence of multiply transformed yeast cells have important implications for yeast library screens. The quantitative information described herein should increase awareness of this issue, and the rapid sequencing approach developed for these studies should be widely useful for identifying multiple vector transformants and avoiding complications associated with cells that have acquired more than one unique plasmid.

A Sabin 3-Derived Poliovirus Recombinant Contained a Sequence Homologous with Indigenous Human Enterovirus Species C in the Viral Polymerase Coding Region†

PubMed Central

Arita, Minetaro; Zhu, Shuang-Li; Yoshida, Hiromu; Yoneyama, Tetsuo; Miyamura, Tatsuo; Shimizu, Hiroyuki

2005-01-01

Outbreaks of poliomyelitis caused by circulating vaccine-derived polioviruses (cVDPVs) have been reported in areas where indigenous wild polioviruses (PVs) were eliminated by vaccination. Most of these cVDPVs contained unidentified sequences in the nonstructural protein coding region which were considered to be derived from human enterovirus species C (HEV-C) by recombination. In this study, we report isolation of a Sabin 3-derived PV recombinant (Cambodia-02) from an acute flaccid paralysis (AFP) case in Cambodia in 2002. We attempted to identify the putative recombination counterpart of Cambodia-02 by sequence analysis of nonpolio enterovirus isolates from AFP cases in Cambodia from 1999 to 2003. Based on the previously estimated evolution rates of PVs, the recombination event resulting in Cambodia-02 was estimated to have occurred within 6 months after the administration of oral PV vaccine (99.3% nucleotide identity in VP1 region). The 2BC and the 3Dpol coding regions of Cambodia-02 were grouped into the genetic cluster of indigenous coxsackie A virus type 17 (CAV17) (the highest [87.1%] nucleotide identity) and the cluster of indigenous CAV13-CAV18 (the highest [94.9%] nucleotide identity) by the phylogenic analysis of the HEV-C isolates in 2002, respectively. CAV13-CAV18 and CAV17 were the dominant HEV-C serotypes in 2002 but not in 2001 and in 2003. We found a putative recombination between CAV13-CAV18 and CAV17 in the 3CDpro coding region of a CAV17 isolate. These results suggested that a part of the 3Dpol coding region of PV3(Cambodia-02) was derived from a HEV-C strain genetically related to indigenous CAV13-CAV18 strains in 2002 in Cambodia. PMID:16188967

Carbon recombination lines as a diagnostic of photodissociation regions

NASA Technical Reports Server (NTRS)

Natta, A.; Walmsley, C. M.; Tielens, A. G. G. M.

1994-01-01

We have observed the C91 alpha radio recombination line toward the Orion H II region. This narrow (approximately 3-5 km per sec full width at half maximum (FWHM)) line is spatially very extended (approximately 8 arcmin or 1 pc). These charateristics compare well with the observed characteristics of the C II fine structure line at 158 microns. Thus, the C91 alpha line originates in the predominantly neutral photodissociation regions separating the H II region from the molecular cloud. We have developed theoretical models for the C II radio recombination lines from photodissociation regions. The results show that the I(C91 alpha)/I(C158) intensity ratio is a sensitive function of the temperature and density of the emitting gas. We have also extended theoretical models for photodissociation regions to include the C II recombination lines. Comparison with these models show that, in the central portion of the Orion region, the C91 alpha line originates in dense (10(exp 6) per cu cm), warm (500-1000 K) gas. Even at large projected distances (approximately 1 pc), the inferred density is still high (10(exp 5) per cu cm) and implies extremely high thermal pressures. As in the case of the (C II) 158 microns line, the large extent of the C91 alpha line shows that (FUV) photons can penetrate to large distances from the illuminating source. The decline of the intensity of the incident radiation field with distance from Theta(sup 1) C seems to be dominated by geometrical dilution, rather than dust extinction. Finally, we have used our models to calculate the intensity of the 9850 A recombination line of C II. The physical conditions inferred from this line are in good agreement with those determined from the radio recombination and the far-infrared fine-structure lines. We show that the ratio of the 9850 A to the C91 alpha lines is a very good probe of very high density clumps.

Joint Molecule Resolution Requires the Redundant Activities of MUS-81 and XPF-1 during Caenorhabditis elegans Meiosis

PubMed Central

O'Neil, Nigel J.; Martin, Julie S.; Youds, Jillian L.; Ward, Jordan D.; Petalcorin, Mark I. R.; Rose, Anne M.; Boulton, Simon J.

2013-01-01

The generation and resolution of joint molecule recombination intermediates is required to ensure bipolar chromosome segregation during meiosis. During wild type meiosis in Caenorhabditis elegans, SPO-11-generated double stranded breaks are resolved to generate a single crossover per bivalent and the remaining recombination intermediates are resolved as noncrossovers. We discovered that early recombination intermediates are limited by the C. elegans BLM ortholog, HIM-6, and in the absence of HIM-6 by the structure specific endonuclease MUS-81. In the absence of both MUS-81 and HIM-6, recombination intermediates persist, leading to chromosome breakage at diakinesis and inviable embryos. MUS-81 has an additional role in resolving late recombination intermediates in C. elegans. mus-81 mutants exhibited reduced crossover recombination frequencies suggesting that MUS-81 is required to generate a subset of meiotic crossovers. Similarly, the Mus81-related endonuclease XPF-1 is also required for a subset of meiotic crossovers. Although C. elegans gen-1 mutants have no detectable meiotic defect either alone or in combination with him-6, mus-81 or xpf-1 mutations, mus-81;xpf-1 double mutants are synthetic lethal. While mus-81;xpf-1 double mutants are proficient for the processing of early recombination intermediates, they exhibit defects in the post-pachytene chromosome reorganization and the asymmetric disassembly of the synaptonemal complex, presumably triggered by crossovers or crossover precursors. Consistent with a defect in resolving late recombination intermediates, mus-81; xpf-1 diakinetic bivalents are aberrant with fine DNA bridges visible between two distinct DAPI staining bodies. We were able to suppress the aberrant bivalent phenotype by microinjection of activated human GEN1 protein, which can cleave Holliday junctions, suggesting that the DNA bridges in mus-81; xpf-1 diakinetic oocytes are unresolved Holliday junctions. We propose that the MUS-81 and XPF-1 endonucleases act redundantly to process late recombination intermediates to form crossovers during C. elegans meiosis. PMID:23874209

Development of a silicon limitation inducible expression system for recombinant protein production in the centric diatoms Thalassiosira pseudonana and Cyclotella cryptica

DOE PAGES

Shrestha, Roshan P.; Hildebrand, Mark

2017-08-17

An inducible promoter for recombinant protein expression provides substantial benefits because under induction conditions cellular energy and metabolic capability can be directed into protein synthesis. The most widely used inducible promoter for diatoms is for nitrate reductase, however, nitrogen metabolism is tied into diverse aspects of cellular function, and the induction response is not necessarily robust. Silicon limitation offers a means to eliminate energy and metabolic flux into cell division processes, with little other detrimental effect on cellular function, and a protein expression system that works under those conditions could be advantageous. In this study, we evaluate a number ofmore » promoters for recombinant protein expression induced by silicon limitation and repressed by the presence of silicon in the diatoms Thalassiosira pseudonana and Cyclotella cryptica. In addition to silicon limitation, we describe additional strategies to elevate recombinant protein expression level, including inclusion of the 5' fragment of the coding region of the native gene and reducing carbon flow into ancillary processes of pigment synthesis and formation of photosynthetic storage products. We achieved yields of eGFP to 1.8% of total soluble protein in C. cryptica, which is about 3.6-fold higher than that obtained with chloroplast expression and ninefold higher than nuclear expression in another well-established algal system. Our studies demonstrate that the combination of inducible promoter and other strategies can result in robust expression of recombinant protein in a nuclear-based expression system in diatoms under silicon limited conditions, separating the protein expression regime from growth processes and improving overall recombinant protein yields.« less

Development of a silicon limitation inducible expression system for recombinant protein production in the centric diatoms Thalassiosira pseudonana and Cyclotella cryptica

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shrestha, Roshan P.; Hildebrand, Mark

An inducible promoter for recombinant protein expression provides substantial benefits because under induction conditions cellular energy and metabolic capability can be directed into protein synthesis. The most widely used inducible promoter for diatoms is for nitrate reductase, however, nitrogen metabolism is tied into diverse aspects of cellular function, and the induction response is not necessarily robust. Silicon limitation offers a means to eliminate energy and metabolic flux into cell division processes, with little other detrimental effect on cellular function, and a protein expression system that works under those conditions could be advantageous. In this study, we evaluate a number ofmore » promoters for recombinant protein expression induced by silicon limitation and repressed by the presence of silicon in the diatoms Thalassiosira pseudonana and Cyclotella cryptica. In addition to silicon limitation, we describe additional strategies to elevate recombinant protein expression level, including inclusion of the 5' fragment of the coding region of the native gene and reducing carbon flow into ancillary processes of pigment synthesis and formation of photosynthetic storage products. We achieved yields of eGFP to 1.8% of total soluble protein in C. cryptica, which is about 3.6-fold higher than that obtained with chloroplast expression and ninefold higher than nuclear expression in another well-established algal system. Our studies demonstrate that the combination of inducible promoter and other strategies can result in robust expression of recombinant protein in a nuclear-based expression system in diatoms under silicon limited conditions, separating the protein expression regime from growth processes and improving overall recombinant protein yields.« less

Optimization of Ammonium Sulfate Concentration for Purification of Colorectal Cancer Vaccine Candidate Recombinant Protein GA733-FcK Isolated from Plants.

PubMed

Park, Se-Ra; Lim, Chae-Yeon; Kim, Deuk-Su; Ko, Kisung

2015-01-01

A protein purification procedure is required to obtain high-value recombinant injectable vaccine proteins produced in plants as a bioreactor. However, existing purification procedures for plant-derived recombinant proteins are often not optimized and are inefficient, with low recovery rates. In our previous study, we used 25-30% ammonium sulfate to precipitate total soluble proteins (TSPs) in purification process for recombinant proteins from plant leaf biomass which has not been optimized. Thus, the objective in this study is to optimize the conditions for plant-derived protein purification procedures. Various ammonium sulfate concentrations (15-80%) were compared to determine their effects on TSPs yield. With 50% ammonium sulfate, the yield of precipitated TSP was the highest, and that of the plant-derived colorectal cancer-specific surface glycoprotein GA733 fused to the Fc fragment of human IgG tagged with endoplasmic reticulum retention signal KDEL (GA733(P)-FcK) protein significantly increased 1.8-fold. SDS-PAGE analysis showed that the purity of GA733(P)-FcK protein band appeared to be similar to that of an equal dose of mammalian-derived GA733-Fc (GA733(M)-Fc). The binding activity of purified GA733(P)-FcK to anti-GA733 mAb was as efficient as the native GA733(M)-Fc. Thus, the purification process was effectively optimized for obtaining a high yield of plant-derived antigenic protein with good quality. In conclusion, the purification recovery rate of large quantities of recombinant protein from plant expression systems can be enhanced via optimization of ammonium sulfate concentration during downstream processes, thereby offering a promising solution for production of recombinant GA733-Fc protein in plants.

Simplified model to describe the dissociative recombination of linear polyatomic ions of astrophysical interest

NASA Astrophysics Data System (ADS)

Douguet, N.; Fonseca dos Santos, S.; Kokoouline, V.; Orel, A. E.

2015-01-01

We present results of a theoretical study on dissociative recombination of the HCNH+, HCO+ and N2H+ linear polyatomic ions at low energies using a simple theoretical model. In the present study, the indirect mechanism for recombination proceeds through the capture of the incoming electron in excited vibrational Rydberg states attached to the degenerate transverse modes of the linear ions. The strength of the non-adiabatic coupling responsible for dissociative recombination is determined directly from the near-threshold scattering matrix obtained numerically using the complex Kohn variational method. The final cross sections for the process are compared with available experimental data. It is demonstrated that at low collision energies, the major contribution to the dissociative recombination cross section is due to the indirect mechanism.

Effects of high optical injection levels in polycrystalline Si wafers on carrier transport

NASA Astrophysics Data System (ADS)

Steele, Doneisha; Semichaevsky, Andrey

High levels of carrier injection in polycrystalline Si may arise, for example, in solar cells under concentrated sunlight. Mechanisms for non-radiative carrier recombination include trap-mediated SRH and higher-order processes, e.g., Auger recombination. In this paper we present our experimental results for intensity-dependent carrier lifetimes and conduction currents in polycrystalline Si wafers illuminated with pulses of up to 50 Sun intensity. We also use a computational model for carrier transport that includes both SRH and Auger recombination mechanisms, in order to explain our experiments. The model allows quantifying recombination rate dependence on carrier concentration. Our goal is to relate the recombination rates to Si microstructure and defect densities that are revealed by IR PL images. We acknowledge the NSF support through Grant 1505377.

Mechanism of homologous recombination and implications for aging-related deletions in mitochondrial DNA.

PubMed

Chen, Xin Jie

2013-09-01

Homologous recombination is a universal process, conserved from bacteriophage to human, which is important for the repair of double-strand DNA breaks. Recombination in mitochondrial DNA (mtDNA) was documented more than 4 decades ago, but the underlying molecular mechanism has remained elusive. Recent studies have revealed the presence of a Rad52-type recombination system of bacteriophage origin in mitochondria, which operates by a single-strand annealing mechanism independent of the canonical RecA/Rad51-type recombinases. Increasing evidence supports the notion that, like in bacteriophages, mtDNA inheritance is a coordinated interplay between recombination, repair, and replication. These findings could have profound implications for understanding the mechanism of mtDNA inheritance and the generation of mtDNA deletions in aging cells.

Mechanism of Homologous Recombination and Implications for Aging-Related Deletions in Mitochondrial DNA

PubMed Central

2013-01-01

SUMMARY Homologous recombination is a universal process, conserved from bacteriophage to human, which is important for the repair of double-strand DNA breaks. Recombination in mitochondrial DNA (mtDNA) was documented more than 4 decades ago, but the underlying molecular mechanism has remained elusive. Recent studies have revealed the presence of a Rad52-type recombination system of bacteriophage origin in mitochondria, which operates by a single-strand annealing mechanism independent of the canonical RecA/Rad51-type recombinases. Increasing evidence supports the notion that, like in bacteriophages, mtDNA inheritance is a coordinated interplay between recombination, repair, and replication. These findings could have profound implications for understanding the mechanism of mtDNA inheritance and the generation of mtDNA deletions in aging cells. PMID:24006472

Two mechanisms of constructive recollection: Perceptual recombination and conceptual fluency.

PubMed

Doss, Manoj K; Bluestone, Maximilian R; Gallo, David A

2016-11-01

Recollection is constructive and prone to distortion, but the mechanisms through which recollections can become embellished with rich yet illusory details are still debated. According to the conceptual fluency hypothesis, abstract semantic or conceptual activation increases the familiarity of a nonstudied event, causing one to falsely attribute imagined features to actual perception. In contrast, according to the perceptual recombination hypothesis, details from actually perceived events are partially recollected and become erroneously bound to a nonstudied event, again causing a detailed yet false recollection. Here, we report the first experiments aimed at disentangling these 2 mechanisms. Participants imagined pictures of common objects, and then they saw an actual picture of some of the imagined objects. We next presented misinformation associated with these studied items, designed to increase conceptual fluency (i.e., semantically related words) or perceptual recombination (i.e., perceptually similar picture fragments). Finally, we tested recollection for the originally seen pictures using verbal labels as retrieval cues. Consistent with conceptual fluency, processing-related words increased false recollection of pictures that were never seen, and consistent with perceptual recombination, processing picture fragments further increased false recollection. We also found that conceptual fluency was more short-lived than perceptual recombination, further dissociating these 2 mechanisms. These experiments provide strong evidence that conceptual fluency and perceptual recombination independently contribute to the constructive aspects of recollection. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

The Kinetics of Oxygen Atom Recombination in the Presence of Carbon Dioxide

NASA Astrophysics Data System (ADS)

Jamieson, C. S.; Garcia, R. M.; Pejakovic, D.; Kalogerakis, K.

2009-12-01

Understanding processes involving atomic oxygen is crucial for the study and modeling of composition, energy transfer, airglow, and transport dynamics in planetary atmospheres. Significant gaps and uncertainties exist in the understanding of these processes and often the relevant input from laboratory measurements is missing or outdated. We are conducting laboratory experiments to measure the rate coefficient for O + O + CO2 recombination and investigating the O2 excited states produced following the recombination. These measurements will provide key input for a quantitative understanding and reliable modeling of the atmospheres of the CO2 planets and their airglow. An excimer laser providing pulsed output at either 193 nm or 248 nm is employed to produce O atoms by dissociating carbon dioxide, nitrous oxide, or ozone. In an ambient-pressure background of CO2, O atoms recombine in a time scale of a few milliseconds. Detection of laser-induced fluorescence at 845 nm following two-photon excitation near 226 nm monitors the decay of the oxygen atom population. From the temporal evolution of the signal the recombination rate coefficient is extracted. Fluorescence spectroscopy is used to detect the products of O-atom recombination and subsequent relaxation in CO2. This work is supported by the US National Science Foundation’s (NSF) Planetary Astronomy Program. Rosanne Garcia’s participation was funded by the NSF Research Experiences for Undergraduates (REU) Program.

Dissociative recombination in interstellar clouds

NASA Technical Reports Server (NTRS)

Black, John H.; Van Dishoeck, Ewine F.

1989-01-01

Molecular ions play a significant role in the chemistry and evolution of interstellar molecular clouds, even though these regions are overwhelmingly neutral. The dissociative recombination (DR) process governs the abundances of many of these ions and of related neutral species. The gas-phase ion-molecule chemistry of the simplest species is summarized, with emphasis on those problems which are most sensitive to uncertain rates or product branching ratios of DR processes. Examples of the kinds of information needed about DR processes are presented. The importance of the H3(+) ion and prospects for its direct observation are discussed.

Focusing homologous recombination: pilin antigenic variation in the pathogenic Neisseria

PubMed Central

Cahoon, Laty A.; Seifert, H. Steven

2011-01-01

Summary Some pathogenic microbes utilize homologous recombination to generate antigenic variability in targets of immune surveillance. These specialized systems rely on the cellular recombination machinery to catalyze dedicated, high-frequency reactions that provide extensive diversity in the genes encoding surface antigens. A description of the specific mechanisms that allow unusually high rates of recombination without deleterious effects on the genome in the well characterized pilin antigenic variation systems of Neisseria gonorrhoeae and Neisseria meningitidis is presented. We will also draw parallels to selected bacterial and eukaryotic antigenic variation systems, and suggest the most pressing unanswered questions related to understanding these important processes. PMID:21812841

DNA recombination protein-dependent mechanism of homoplasmy and its proposed functions.

PubMed

Shibata, Takehiko; Ling, Feng

2007-01-01

Homoplasmy is a basic genetic state of mitochondria, in which all of the hundreds to thousands of mitochondrial (mt)DNA copies within a cell or an individual have the same nucleotide-sequence. It was recently found that "vegetative segregation" to generate homoplasmic cells is an active process under genetic control. In the yeast Saccharomyces cerevisiae, the Mhr1 protein which catalyzes a key reaction in mtDNA homologous recombination, plays a pivotal role in vegetative segregation. Conversely, within the nuclear genome, homologous DNA recombination causes genetic diversity. Considering these contradictory roles of this key reaction in DNA recombination, possible functions of homoplasmy are discussed.

Detecting Genetic Introgression: High Levels of Intersubspecific Recombination Found in Xylella fastidiosa in Brazil

PubMed Central

Yuan, Xiaoli; Bromley, Robin E.; Stouthamer, Richard

2012-01-01

Documenting the role of novel mutation versus homologous recombination in bacterial evolution, and especially in the invasion of new hosts, is central to understanding the long-term dynamics of pathogenic bacteria. We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS). All 55 citrus isolates typed (plus one coffee isolate) defined three similar sequence types (STs) dominated by ST11 (85%), while the remaining 22 coffee isolates defined two STs, mainly ST16 (74%). This low level of variation masked unusually large allelic differences (>1% divergence with no intermediates) at five loci (leuA, petC, malF, cysG, and holC). We developed an introgression test to detect whether these large differences were due to introgression via homologous recombination from another X. fastidiosa subspecies. Using additional sequencing around these loci, we established that the seven randomly chosen MLST targets contained seven regions of introgression totaling 2,172 bp of 4,161 bp (52%), only 409 bp (10%) of which were detected by other recombination tests. This high level of introgression suggests the hypothesis that X. fastidiosa subsp. pauca became pathogenic on citrus and coffee (crops cultivated in Brazil for several hundred years) only recently after it gained genetic variation via intersubspecific recombination, facilitating a switch from native hosts. A candidate donor is the subspecies infecting plum in the region since 1935 (possibly X. fastidiosa subsp. multiplex). This hypothesis predicts that nonrecombinant native X. fastidiosa subsp. pauca (not yet isolated) does not cause disease in citrus or coffee. PMID:22544234

Detecting genetic introgression: high levels of intersubspecific recombination found in Xylella fastidiosa in Brazil.

PubMed

Nunney, Leonard; Yuan, Xiaoli; Bromley, Robin E; Stouthamer, Richard

2012-07-01

Documenting the role of novel mutation versus homologous recombination in bacterial evolution, and especially in the invasion of new hosts, is central to understanding the long-term dynamics of pathogenic bacteria. We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS). All 55 citrus isolates typed (plus one coffee isolate) defined three similar sequence types (STs) dominated by ST11 (85%), while the remaining 22 coffee isolates defined two STs, mainly ST16 (74%). This low level of variation masked unusually large allelic differences (>1% divergence with no intermediates) at five loci (leuA, petC, malF, cysG, and holC). We developed an introgression test to detect whether these large differences were due to introgression via homologous recombination from another X. fastidiosa subspecies. Using additional sequencing around these loci, we established that the seven randomly chosen MLST targets contained seven regions of introgression totaling 2,172 bp of 4,161 bp (52%), only 409 bp (10%) of which were detected by other recombination tests. This high level of introgression suggests the hypothesis that X. fastidiosa subsp. pauca became pathogenic on citrus and coffee (crops cultivated in Brazil for several hundred years) only recently after it gained genetic variation via intersubspecific recombination, facilitating a switch from native hosts. A candidate donor is the subspecies infecting plum in the region since 1935 (possibly X. fastidiosa subsp. multiplex). This hypothesis predicts that nonrecombinant native X. fastidiosa subsp. pauca (not yet isolated) does not cause disease in citrus or coffee.

Advanced control of dissolved oxygen concentration in fed batch cultures during recombinant protein production.

PubMed

Kuprijanov, A; Gnoth, S; Simutis, R; Lübbert, A

2009-02-01

Design and experimental validation of advanced pO(2) controllers for fermentation processes operated in the fed-batch mode are described. In most situations, the presented controllers are able to keep the pO(2) in fermentations for recombinant protein productions exactly on the desired value. The controllers are based on the gain-scheduling approach to parameter-adaptive proportional-integral controllers. In order to cope with the most often appearing distortions, the basic gain-scheduling feedback controller was complemented with a feedforward control component. This feedforward/feedback controller significantly improved pO(2) control. By means of numerical simulations, the controller behavior was tested and its parameters were determined. Validation runs were performed with three Escherichia coli strains producing different recombinant proteins. It is finally shown that the new controller leads to significant improvements in the signal-to-noise ratio of other key process variables and, thus, to a higher process quality.

The HIV-1 epidemic in Bolivia is dominated by subtype B and CRF12_BF "family" strains.

PubMed

Guimarães, Monick L; Velarde-Dunois, Ketty G; Segurondo, David; Morgado, Mariza G

2012-01-16

Molecular epidemiological studies of HIV-1 in South America have revealed the occurrence of subtypes B, F1 and BF1 recombinants. Even so, little information concerning the HIV-1 molecular epidemiology in Bolivia is available. In this study we performed phylogenetic analyses from samples collected in Bolivia at two different points in time over a 10 year span. We analyzed these samples to estimate the trends in the HIV subtype and recombinant forms over time. Fifty one HIV-1 positive samples were collected in Bolivia over two distinct periods (1996 and 2005). These samples were genetically characterized based on partial pol protease/reverse transcriptase (pr/rt) and env regions. Alignment and neighbor-joining (NJ) phylogenetic analyses were established from partial env (n = 37) and all pol sequences using Mega 4. The remaining 14 env sequences from 1996 were previously characterized based on HMA-env (Heteroduplex mobility assay). The Simplot v.3.5.1 program was used to verify intragenic recombination, and SplitsTree 4.0 was employed to confirm the phylogenetic relationship of the BF1 recombinant samples. Phylogenetic analysis of both env and pol regions confirmed the predominance of "pure" subtype B (72.5%) samples circulating in Bolivia and revealed a high prevalence of BF1 genotypes (27.5%). Eleven out of 14 BF1 recombinants displayed a mosaic structure identical or similar to that described for the CRF12_BF variant, one sample was classified as CRF17_BF, and two others were F1pol/Benv. No "pure" HIV-1 subtype F1 or B" variant of subtype B was detected in the present study. Of note, samples characterized as CRF12_BF-related were depicted only in 2005. HIV-1 genetic diversity in Bolivia is mostly driven by subtype B followed by BF1 recombinant strains from the CRF12_BF "family". No significant temporal changes were detected between the mid-1990s and the mid-2000s for subtype B (76.2% vs 70.0%) or BF1 recombinant (23.8% vs 30.0%) samples from Bolivia.

The HIV-1 epidemic in Bolivia is dominated by subtype B and CRF12_BF "family" strains

PubMed Central

2012-01-01

Background Molecular epidemiological studies of HIV-1 in South America have revealed the occurrence of subtypes B, F1 and BF1 recombinants. Even so, little information concerning the HIV-1 molecular epidemiology in Bolivia is available. In this study we performed phylogenetic analyses from samples collected in Bolivia at two different points in time over a 10 year span. We analyzed these samples to estimate the trends in the HIV subtype and recombinant forms over time. Materials and methods Fifty one HIV-1 positive samples were collected in Bolivia over two distinct periods (1996 and 2005). These samples were genetically characterized based on partial pol protease/reverse transcriptase (pr/rt) and env regions. Alignment and neighbor-joining (NJ) phylogenetic analyses were established from partial env (n = 37) and all pol sequences using Mega 4. The remaining 14 env sequences from 1996 were previously characterized based on HMA-env (Heteroduplex mobility assay). The Simplot v.3.5.1 program was used to verify intragenic recombination, and SplitsTree 4.0 was employed to confirm the phylogenetic relationship of the BF1 recombinant samples. Results Phylogenetic analysis of both env and pol regions confirmed the predominance of "pure" subtype B (72.5%) samples circulating in Bolivia and revealed a high prevalence of BF1 genotypes (27.5%). Eleven out of 14 BF1 recombinants displayed a mosaic structure identical or similar to that described for the CRF12_BF variant, one sample was classified as CRF17_BF, and two others were F1pol/Benv. No "pure" HIV-1 subtype F1 or B" variant of subtype B was detected in the present study. Of note, samples characterized as CRF12_BF-related were depicted only in 2005. Conclusion HIV-1 genetic diversity in Bolivia is mostly driven by subtype B followed by BF1 recombinant strains from the CRF12_BF "family". No significant temporal changes were detected between the mid-1990s and the mid-2000s for subtype B (76.2% vs 70.0%) or BF1 recombinant (23.8% vs 30.0%) samples from Bolivia. PMID:22248191

DNA Strand Exchange and RecA Homologs in Meiosis

PubMed Central

Brown, M. Scott; Bishop, Douglas K.

2015-01-01

Homology search and DNA strand–exchange reactions are central to homologous recombination in meiosis. During meiosis, these processes are regulated such that the probability of choosing a homolog chromatid as recombination partner is enhanced relative to that of choosing a sister chromatid. This regulatory process occurs as homologous chromosomes pair in preparation for assembly of the synaptonemal complex. Two strand–exchange proteins, Rad51 and Dmc1, cooperate in regulated homology search and strand exchange in most organisms. Here, we summarize studies on the properties of these two proteins and their accessory factors. In addition, we review current models for the assembly of meiotic strand–exchange complexes and the possible mechanisms through which the interhomolog bias of recombination partner choice is achieved. PMID:25475089

Impact of the HIV-1 genetic background and HIV-1 population size on the evolution of raltegravir resistance.

PubMed

Fun, Axel; Leitner, Thomas; Vandekerckhove, Linos; Däumer, Martin; Thielen, Alexander; Buchholz, Bernd; Hoepelman, Andy I M; Gisolf, Elizabeth H; Schipper, Pauline J; Wensing, Annemarie M J; Nijhuis, Monique

2018-01-05

Emergence of resistance against integrase inhibitor raltegravir in human immunodeficiency virus type 1 (HIV-1) patients is generally associated with selection of one of three signature mutations: Y143C/R, Q148K/H/R or N155H, representing three distinct resistance pathways. The mechanisms that drive selection of a specific pathway are still poorly understood. We investigated the impact of the HIV-1 genetic background and population dynamics on the emergence of raltegravir resistance. Using deep sequencing we analyzed the integrase coding sequence (CDS) in longitudinal samples from five patients who initiated raltegravir plus optimized background therapy at viral loads > 5000 copies/ml. To investigate the role of the HIV-1 genetic background we created recombinant viruses containing the viral integrase coding region from pre-raltegravir samples from two patients in whom raltegravir resistance developed through different pathways. The in vitro selections performed with these recombinant viruses were designed to mimic natural population bottlenecks. Deep sequencing analysis of the viral integrase CDS revealed that the virological response to raltegravir containing therapy inversely correlated with the relative amount of unique sequence variants that emerged suggesting diversifying selection during drug pressure. In 4/5 patients multiple signature mutations representing different resistance pathways were observed. Interestingly, the resistant population can consist of a single resistant variant that completely dominates the population but also of multiple variants from different resistance pathways that coexist in the viral population. We also found evidence for increased diversification after stronger bottlenecks. In vitro selections with low viral titers, mimicking population bottlenecks, revealed that both recombinant viruses and HXB2 reference virus were able to select mutations from different resistance pathways, although typically only one resistance pathway emerged in each individual culture. The generation of a specific raltegravir resistant variant is not predisposed in the genetic background of the viral integrase CDS. Typically, in the early phases of therapy failure the sequence space is explored and multiple resistance pathways emerge and then compete for dominance which frequently results in a switch of the dominant population over time towards the fittest variant or even multiple variants of similar fitness that can coexist in the viral population.

Evolution of hierarchical cytoplasmic inheritance in the plasmodial slime mold Physarum polycephalum.

PubMed

Iwanaga, Akiko; Sasaki, Akira

2004-04-01

A striking linear dominance relationship for uniparental mitochondrial transmission is known between many mating types of plasmodial slime mold Physarum polycephalum. We herein examine how such hierarchical cytoplasmic inheritance evolves in isogamous organisms with many self-incompatible mating types. We assume that a nuclear locus determines the mating type of gametes and that another nuclear locus controls the digestion of mitochondria DNAs (mtDNAs) of the recipient gamete after fusion. We then examine the coupled genetic dynamics for the evolution of self-incompatible mating types and biased mitochondrial transmission between them. In Physarum, a multiallelic nuclear locus matA controls both the mating type of the gametes and the selective elimination of the mtDNA in the zygotes. We theoretically examine two potential mechanisms that might be responsible for the preferential digestion of mitochondria in the zygote. In the first model, the preferential digestion of mitochondria is assumed to be the outcome of differential expression levels of a suppressor gene carried by each gamete (suppression-power model). In the second model (site-specific nuclease model), the digestion of mtDNAs is assumed to be due to their cleavage by a site-specific nuclease that cuts the mtDNA at unmethylated recognition sites. Also assumed is that the mtDNAs are methylated at the same recognition site prior to the fusion, thereby being protected against the nuclease of the same gamete, and that the suppressor alleles convey information for the recognition sequences of nuclease and methylase. In both models, we found that a linear dominance hierarchy evolves as a consequence of the buildup of a strong linkage disequilibrium between the mating-type locus and the suppressor locus, though it fails to evolve if the recombination rate between the two loci is larger than a threshold. This threshold recombination rate depends on the number of mating types and the degree of fitness reduction in the heteroplasmic zygotes. If the recombination rate is above the threshold, suppressor alleles are equally distributed in each mating type at evolutionary equilibrium. Based on the theoretical results of the site-specific nuclease model, we propose that a nested subsequence structure in the recognition sequence should underlie the linear dominance hierarchy of mitochondrial transmission.

Monitoring Recombination During Meiosis in Budding Yeast.

PubMed

Owens, Shannon; Tang, Shangming; Hunter, Neil

2018-01-01

Homologous recombination is fundamental to sexual reproduction, facilitating accurate segregation of homologous chromosomes at the first division of meiosis, and creating novel allele combinations that fuel evolution. Following initiation of meiotic recombination by programmed DNA double-strand breaks (DSBs), homologous pairing and DNA strand exchange form joint molecule (JM) intermediates that are ultimately resolved into crossover and noncrossover repair products. Physical monitoring of the DNA steps of meiotic recombination in Saccharomyces cerevisiae (budding yeast) cultures undergoing synchronous meiosis has provided seminal insights into the molecular basis of meiotic recombination and affords a powerful tool for dissecting the molecular roles of recombination factors. This chapter describes a suit of electrophoretic and Southern hybridization techniques used to detect and quantify the DNA intermediates of meiotic recombination at recombination hotspots in budding yeast. DSBs and recombination products (crossovers and noncrossovers) are resolved using one-dimensional electrophoresis and distinguished by restriction site polymorphisms between the parental chromosomes. Psoralen cross-linking is used to stabilize branched JMs, which are resolved from linear species by native/native two-dimensional electrophoresis. Native/denaturing two-dimensional electrophoresis is employed to determine the component DNA strands of JMs and to measure the processing of DSBs. These techniques are generally applicable to any locus where the frequency of recombination is high enough to detect intermediates by Southern hybridization. © 2018 Elsevier Inc. All rights reserved.

Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations

PubMed Central

Petit, Morgane; Astruc, Jean-Michel; Sarry, Julien; Drouilhet, Laurence; Fabre, Stéphane; Moreno, Carole R.; Servin, Bertrand

2017-01-01

Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and data sets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified ∼50,000 crossover hotspots on the genome, and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting interindividual variation in recombination rate in Lacaune, including the RNF212 and HEI10 genes and possibly two other loci of smaller effects including the KCNJ15 and FSHR genes. The comparison of these new results to those obtained previously in a distantly related population of domestic sheep (the Soay) revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome. The two data sets were thus combined to create more precise male meiotic recombination maps in Sheep. However, despite their similar recombination maps, Soay and Lacaune males were found to exhibit different heritabilities and QTL effects for interindividual variation in genome-wide recombination rates. This highlights the robustness of recombination patterns to underlying variation in their genetic determinism. PMID:28978774

Variation in Recombination Rate and Its Genetic Determinism in Sheep Populations.

PubMed

Petit, Morgane; Astruc, Jean-Michel; Sarry, Julien; Drouilhet, Laurence; Fabre, Stéphane; Moreno, Carole R; Servin, Bertrand

2017-10-01

Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and data sets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified ∼50,000 crossover hotspots on the genome, and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting interindividual variation in recombination rate in Lacaune, including the RNF212 and HEI10 genes and possibly two other loci of smaller effects including the KCNJ15 and FSHR genes. The comparison of these new results to those obtained previously in a distantly related population of domestic sheep (the Soay) revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome. The two data sets were thus combined to create more precise male meiotic recombination maps in Sheep. However, despite their similar recombination maps, Soay and Lacaune males were found to exhibit different heritabilities and QTL effects for interindividual variation in genome-wide recombination rates. This highlights the robustness of recombination patterns to underlying variation in their genetic determinism. Copyright © 2017 by the Genetics Society of America.

Increasing the efficiency of organic solar cells by photonic and electrostatic-field enhancements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nalwa, Kanwar

2011-01-01

Organic photovoltaic (OPV) technology is an attractive solar-electric conversion paradigm due to the promise of low cost roll-to-roll production and amenability to flexible substrates. Power conversion efficiency (PCE) exceeding 7% has recently been achieved. OPV cells suffer from low charge carrier mobilities of polymers, leading to recombination losses, higher series resistances and lower fill-factors. Thus, it is imperative to develop fabrication methodologies that can enable efficient optical absorption in films thinner than optical absorption length. Active layers conformally deposited on light-trapping, microscale textured, grating-type surfaces is one possible approach to achieve this objective. In this study, 40% theoretical increase inmore » photonic absorption over flat OPVs is shown for devices with textured geometry by the simulation results. For verifying this theoretical result and improving the efficiency of OPVs by light trapping, OPVs were fabricated on grating-type textured substrates possessing t pitch and -coat PV active-layer on these textured substrates led to over filling of the valleys and shunts at the crest, which severely affected the performance of the resultant PV devices. Thus, it is established that although the optical design is important for OPV performance but the potential of light trapping can only be effectively tapped if the textures are amenable for realizing a conformal active layer. It is discovered that if the height of the underlying topographical features is reduced to sub-micron regime (e.g. 300 nm) and the pitch is increased to more than a micron (e.g. 2 μm), the textured surface becomes amenable to coating a conformal PV active-layer. The resultant PV cells showed 100% increase in average light absorption near the band edge due to trapping of higher wavelength photons, and 20% improvement in power conversion efficiency as compared with the flat PV cell. Another factor that severely limits the performance of OPVs is recombination of charge carriers. Thus it becomes imperative to understand the effect of processing conditions such as spin coating speed and drying rate on defect density and hence induced carrier recombination mechanism. In this study, It is shown that slow growth (longer drying time) of the active-layer leads to reduction of sub-bandgap traps by an order of magnitude as compared to fast grown active-layer. By coupling the experimental results with simulations, it is demonstrated that at one sun condition, slow grown device has bimolecular recombination as the major loss mechanism while in the fast grown device with high trap density, the trap assisted recombination dominates. It has been estimated that non-radiative recombination accounts nearly 50% of efficiency loss in modern OPVs. Generally, an external bias (electric field) is required to collect all the photogenerated charges and thus prevent their recombination. The motivation is to induce additional electric field in otherwise low mobility conjugated polymer based active layer by incorporating ferroelectric dipoles. This is expected to facilitate singlet exciton dissociation in polymer matrix and impede charge transfer exciton (CTE) recombination at polymer:fullerene interface. For the first time, it is shown that the addition of ferroelectric dipoles to modern bulk heterojunction (BHJ) can significantly improve exciton dissociation, resulting in a ~50% enhancement of overall solar cell efficiency. The devices also exhibit the unique ferroelectric-photovoltaic effect with polarization-controlled power conversion efficiency.« less

Frequency and genetic characterization of V(DD)J recombinants in the human peripheral blood antibody repertoire.

PubMed

Briney, Bryan S; Willis, Jordan R; Hicar, Mark D; Thomas, James W; Crowe, James E

2012-09-01

Antibody heavy-chain recombination that results in the incorporation of multiple diversity (D) genes, although uncommon, contributes substantially to the diversity of the human antibody repertoire. Such recombination allows the generation of heavy chain complementarity determining region 3 (HCDR3) regions of extreme length and enables junctional regions that, because of the nucleotide bias of N-addition regions, are difficult to produce through normal V(D)J recombination. Although this non-classical recombination process has been observed infrequently, comprehensive analysis of the frequency and genetic characteristics of such events in the human peripheral blood antibody repertoire has not been possible because of the rarity of such recombinants and the limitations of traditional sequencing technologies. Here, through the use of high-throughput sequencing of the normal human peripheral blood antibody repertoire, we analysed the frequency and genetic characteristics of V(DD)J recombinants. We found that these recombinations were present in approximately 1 in 800 circulating B cells, and that the frequency was severely reduced in memory cell subsets. We also found that V(DD)J recombination can occur across the spectrum of diversity genes, indicating that virtually all recombination signal sequences that flank diversity genes are amenable to V(DD)J recombination. Finally, we observed a repertoire bias in the diversity gene repertoire at the upstream (5') position, and discovered that this bias was primarily attributable to the order of diversity genes in the genomic locus. © 2012 The Authors. Immunology © 2012 Blackwell Publishing Ltd.

Strong Artificial Selection in Domestic Mammals Did Not Result in an Increased Recombination Rate

PubMed Central

Muñoz-Fuentes, Violeta; Marcet-Ortega, Marina; Alkorta-Aranburu, Gorka; Linde Forsberg, Catharina; Morrell, Jane M.; Manzano-Piedras, Esperanza; Söderberg, Arne; Daniel, Katrin; Villalba, Adrian; Toth, Attila; Di Rienzo, Anna; Roig, Ignasi; Vilà, Carles

2015-01-01

Recombination rates vary in intensity and location at the species, individual, sex and chromosome levels. Despite the fundamental biological importance of this process, the selective forces that operate to shape recombination rate and patterns are unclear. Domestication offers a unique opportunity to study the interplay between recombination and selection. In domesticates, intense selection for particular traits is imposed on small populations over many generations, resulting in organisms that differ, sometimes dramatically, in morphology and physiology from their wild ancestor. Although earlier studies suggested increased recombination rate in domesticates, a formal comparison of recombination rates between domestic mammals and their wild congeners was missing. In order to determine broad-scale recombination rate, we used immunolabeling detection of MLH1 foci as crossover markers in spermatocytes in three pairs of closely related wild and domestic species (dog and wolf, goat and ibex, and sheep and mouflon). In the three pairs, and contrary to previous suggestions, our data show that contemporary recombination rate is higher in the wild species. Subsequently, we inferred recombination breakpoints in sequence data for 16 genomic regions in dogs and wolves, each containing a locus associated with a dog phenotype potentially under selection during domestication. No difference in the number and distribution of recombination breakpoints was found between dogs and wolves. We conclude that our data indicate that strong directional selection did not result in changes in recombination in domestic mammals, and that both upper and lower bounds for crossover rates may be tightly regulated. PMID:25414125

Morphology effects on spin-dependent transport and recombination in polyfluorene thin films

NASA Astrophysics Data System (ADS)

Miller, Richards; van Schooten, K. J.; Malissa, H.; Joshi, G.; Jamali, S.; Lupton, J. M.; Boehme, C.

2016-12-01

We have studied the role of spin-dependent processes on conductivity in polyfluorene (PFO) thin films by preforming continuous wave (cw) electrically detected magnetic resonance (EDMR) spectroscopy at temperatures between 10 K and room temperature using microwave frequencies between about 1 GHz and 20 GHz, as well as pulsed EDMR at the X band (10 GHz). Variable frequency EDMR allows us to establish the role of spin-orbit coupling in spin-dependent processes whereas pulsed EDMR allows for the observation of coherent spin motion effects. We used PFO for this study in order to allow for the investigation of the effects of microscopic morphological ordering since this material can adopt two distinct intrachain morphologies: an amorphous (glassy) phase, in which monomer units are twisted with respect to each other, and an ordered (β) phase, where all monomers lie within one plane. In thin films of organic light-emitting diodes, the appearance of a particular phase can be controlled by deposition parameters and solvent vapor annealing, and is verified by electroluminescence spectroscopy. Under bipolar charge-carrier injection conditions, we conducted multifrequency cw EDMR, electrically detected Rabi spin-beat experiments, and Hahn echo and inversion-recovery measurements. Coherent echo spectroscopy reveals electrically detected electron-spin-echo envelope modulation due to the coupling of the carrier spins to nearby nuclear spins. Our results demonstrate that, while conformational disorder can influence the observed EDMR signals, including the sign of the current changes on resonance as well as the magnitudes of local hyperfine fields and charge-carrier spin-orbit interactions, it does not qualitatively affect the nature of spin-dependent transitions in this material. In both morphologies, we observe the presence of at least two different spin-dependent recombination processes. At room temperature and 10 K, polaron-pair recombination through weakly spin-spin coupled intermediate charge-carrier pair states is dominant, while at low temperatures, additional signatures of spin-dependent charge transport through the interaction of polarons with triplet excitons are seen in the half-field resonance of a triplet spin-1 species. This additional contribution arises since triplet lifetimes are increased at lower temperatures. We tentatively conclude that spectral broadening induced by hyperfine coupling is slightly weaker in the more ordered β-phase than in the glassy phase since protons are more evenly spaced, whereas broadening effects due to spin-orbit coupling, which impacts the distribution of g -factors, appear to be somewhat more significant in the β-phase.

Effect of dopants on annealing performance of silicon solar cells

NASA Technical Reports Server (NTRS)

Scott-Monck, J. A.; Anspaugh, B. E.

1979-01-01

The optimum annealing parameters of time and temperature for producing cell output recovery were established. Devices made from gallium doped and boron doped silicon were investigated. The cells ranged in resistivity from 0.1 to 20 ohm-cm and in thickness from 50 to 250 micrometers. The observations can be explained in a qualitative manner by postulating a pair of competing mechanisms to account for the low temperature reverse annealing seen in most boron and gallium doped silicon solar cells. Still another mechanism dominates at higher temperatures (350 C and greater) to complete this model. One of the mechanisms, defined as B, allows migrators to couple with radiation induced recombination sites thus increasing or enhancing their capture cross sections. This would tend to reduce minority carrier diffusion length. The new recombination complex is postulated to be thermally stable up to temperatures of approximately 350 C.

The recombination mechanisms leading to amplified spontaneous emission at the true-green wavelength in CH3NH3PbBr3 perovskites

NASA Astrophysics Data System (ADS)

Priante, D.; Dursun, I.; Alias, M. S.; Shi, D.; Melnikov, V. A.; Ng, T. K.; Mohammed, O. F.; Bakr, O. M.; Ooi, B. S.

2015-02-01

We investigated the mechanisms of radiative recombination in a CH3NH3PbBr3 hybrid perovskite material using low-temperature, power-dependent (77 K), and temperature-dependent photoluminescence (PL) measurements. Two bound-excitonic radiative transitions related to grain size inhomogeneity were identified. Both transitions led to PL spectra broadening as a result of concurrent blue and red shifts of these excitonic peaks. The red-shifted bound-excitonic peak dominated at high PL excitation led to a true-green wavelength of 553 nm for CH3NH3PbBr3 powders that are encapsulated in polydimethylsiloxane. Amplified spontaneous emission was eventually achieved for an excitation threshold energy of approximately 350 μJ/cm2. Our results provide a platform for potential extension towards a true-green light-emitting device for solid-state lighting and display applications.

Population structuring of multi-copy, antigen-encoding genes in Plasmodium falciparum

PubMed Central

Artzy-Randrup, Yael; Rorick, Mary M; Day, Karen; Chen, Donald; Dobson, Andrew P; Pascual, Mercedes

2012-01-01

The coexistence of multiple independently circulating strains in pathogen populations that undergo sexual recombination is a central question of epidemiology with profound implications for control. An agent-based model is developed that extends earlier ‘strain theory’ by addressing the var gene family of Plasmodium falciparum. The model explicitly considers the extensive diversity of multi-copy genes that undergo antigenic variation via sequential, mutually exclusive expression. It tracks the dynamics of all unique var repertoires in a population of hosts, and shows that even under high levels of sexual recombination, strain competition mediated through cross-immunity structures the parasite population into a subset of coexisting dominant repertoires of var genes whose degree of antigenic overlap depends on transmission intensity. Empirical comparison of patterns of genetic variation at antigenic and neutral sites supports this role for immune selection in structuring parasite diversity. DOI: http://dx.doi.org/10.7554/eLife.00093.001 PMID:23251784

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beard, Matthew C; Chen, Xihan; Lu, Haipeng

The exciton binding energy in methylammonium lead iodide (MAPbI3) is about 10 meV, around 1/3 of the available thermal energy (kBT ~ 26 meV) at room temperature. Thus, exciton populations are not stable at room temperature at moderate photoexcited carrier densities. However, excitonic resonances dominate the absorption onset. Furthermore, these resonances determine the transient absorbance and transient reflectance spectra. The exciton binding energy is a reflection of the Coulomb interaction energy between photoexcited electrons and holes. As such, it serves as a marker for the strength of electron/hole interactions and impacts a variety of phenomena, such as, absorption, radiative recombination,more » and Auger recombination. In this Perspective, we discuss the role of excitons and excitonic resonances in the optical properties of lead-halide perovskite semiconductors. Finally, we discuss how the strong light-matter interactions induce an optical stark effect splitting the doubly spin degenerate ground exciton states and are easily observed at room temperature.« less

Dominant hemimelia and En-1 on mouse chromosome 1 are not allelic.

PubMed

Higgins, M; Hill, R E; West, J D

1992-08-01

Previous studies have shown that En-1, a homeobox-containing gene, maps close to or at the Dh locus in the mouse. Since homeobox-containing genes are key genes in the control of development the close proximity of En-1 to the developmentally significant gene Dh raised the possibility that the Dh mutation represented a mutant allele of En-1. A genetic analysis involving En-1, Dh, and other chromosome 1 markers (Emv-17, ln and Pep-3) shows that although Dh and En-1 are closely linked they are separable by recombination (4/563). The likely gene order and recombination frequencies of these loci are: ln (5.2 +/- 0.9) Emv-17 (1.1 +/- 0.4) Dh (0.7 +/- 0.4) En-1 (3.0 +/- 0.7) Pep-3. This shows that Dh is not a mutant allele of En-1.

Process for Assembly and Transformation into Saccharomyces cerevisiae of a Synthetic Yeast Artificial Chromosome Containing a Multigene Cassette to Express Enzymes That Enhance Xylose Utilization Designed for an Automated Platform.

PubMed

Hughes, Stephen R; Cox, Elby J; Bang, Sookie S; Pinkelman, Rebecca J; López-Núñez, Juan Carlos; Saha, Badal C; Qureshi, Nasib; Gibbons, William R; Fry, Michelle R; Moser, Bryan R; Bischoff, Kenneth M; Liu, Siqing; Sterner, David E; Butt, Tauseef R; Riedmuller, Steven B; Jones, Marjorie A; Riaño-Herrera, Néstor M

2015-12-01

A yeast artificial chromosome (YAC) containing a multigene cassette for expression of enzymes that enhance xylose utilization (xylose isomerase [XI] and xylulokinase [XKS]) was constructed and transformed into Saccharomyces cerevisiae to demonstrate feasibility as a stable protein expression system in yeast and to design an assembly process suitable for an automated platform. Expression of XI and XKS from the YAC was confirmed by Western blot and PCR analyses. The recombinant and wild-type strains showed similar growth on plates containing hexose sugars, but only recombinant grew on D-xylose and L-arabinose plates. In glucose fermentation, doubling time (4.6 h) and ethanol yield (0.44 g ethanol/g glucose) of recombinant were comparable to wild type (4.9 h and 0.44 g/g). In whole-corn hydrolysate, ethanol yield (0.55 g ethanol/g [glucose + xylose]) and xylose utilization (38%) for recombinant were higher than for wild type (0.47 g/g and 12%). In hydrolysate from spent coffee grounds, yield was 0.46 g ethanol/g (glucose + xylose), and xylose utilization was 93% for recombinant. These results indicate introducing a YAC expressing XI and XKS enhanced xylose utilization without affecting integrity of the host strain, and the process provides a potential platform for automated synthesis of a YAC for expression of multiple optimized genes to improve yeast strains. © 2015 Society for Laboratory Automation and Screening.

Modulating Excitonic Recombination Effects through One-Step Synthesis of Perovskite Nanoparticles for Light-Emitting Diodes.

PubMed

Kulkarni, Sneha A; Muduli, Subas; Xing, Guichuan; Yantara, Natalia; Li, Mingjie; Chen, Shi; Sum, Tze Chien; Mathews, Nripan; White, Tim J; Mhaisalkar, Subodh G

2017-10-09

The primary advantages of halide perovskites for light-emitting diodes (LEDs) are solution processability, direct band gap, good charge-carrier diffusion lengths, low trap density, and reasonable carrier mobility. The luminescence in 3 D halide perovskite thin films originates from free electron-hole bimolecular recombination. However, the slow bimolecular recombination rate is a fundamental performance limitation. Perovskite nanoparticles could result in improved performance but processability and cumbersome synthetic procedures remain challenges. Herein, these constraints are overcome by tailoring the 3 D perovskite as a near monodisperse nanoparticle film prepared through a one-step in situ deposition method. Replacing methyl ammonium bromide (CH 3 NH 3 Br, MABr) partially by octyl ammonium bromide [CH 3 (CH 2 ) 7 NH 3 Br, OABr] in defined mole ratios in the perovskite precursor proved crucial for the nanoparticle formation. Films consisting of the in situ formed nanoparticles displayed signatures associated with excitonic recombination, rather than that of bimolecular recombination associated with 3 D perovskites. This transition was accompanied by enhanced photoluminescence quantum yield (PLQY≈20.5 % vs. 3.40 %). Perovskite LEDs fabricated from the nanoparticle films exhibit a one order of magnitude improvement in current efficiency and doubling in luminance efficiency. The material processing systematics derived from this study provides the means to control perovskite morphologies through the selection and mixing of appropriate additives. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Recombinant levels of Escherichia coli K-12 mutants deficient in various replication, recombination, or repair genes.

PubMed Central

Zieg, J; Maples, V F; Kushner, S R

1978-01-01

Escherichia coli strains containing mutations in lexA, rep, uvrA, uvrD, uvrE, lig, polA, dam, or xthA were constructed and tested for conjugation and transduction proficiencies and ability to form Lac+ recombinants in an assay system utilizing a nontandem duplication of two partially deleted lactose operons (lacMS286phi80dIIlacBK1). lexA and rep mutants were as deficient (20% of wild type) as recB and recC strains in their ability to produce Lac+ progeny. All the other strains exhibited increased frequencies of Lac+ recombinant formation, compared with wild type, ranging from 2- to 13-fold. Some strains showed markedly increased conjugation proficiency (dam uvrD) compared to wild type, while others appeared deficient (polA107). Some differences in transduction proficiency were also observed. Analysis of the Lac+ recombinants formed by the various mutants indicated that they were identical to the recombinants formed by a wild-type strain. The results indicate that genetic recombination in E. coli is a highly regulated process involving multiple gene products. PMID:350859

Marker-Dependent Recombination in T4 Bacteriophage. IV. Recombinational Effects of Antimutator T4 DNA Polymerase

PubMed Central

Shcherbakov, V. P.; Plugina, L. A.; Kudryashova, E. A.

1995-01-01

Recombinational effects of the antimutator allele tsL42 of gene 43 of phage T4, encoding DNA polymerase, were studied in crosses between rIIB mutants. Recombination under tsL42-restricted conditions differed from the normal one in several respects: (1) basic recombination was enhanced, especially within very short distances; (2) mismatch repair tracts were shortened, while the contribution of mismatch repair to recombination was not changed; (3) marker interference at very short distances was augmented. We infer that the T4 DNA polymerase is directly involved in mismatch repair, performing both excision of a nonmatched single strand (by its 3' -> 5' exonuclease) and filling the resulting gap. A pathway for the mismatch repair was substantiated; it includes sequential action of endo VII (gp49) -> 3'->5' exonuclease (gp43) -> DNA polymerase (gp43) -> DNA ligase (gp30). It is argued that the marker interference at very short distances may result from the same sequence of events during the final processing of recombinational intermediates. PMID:7635281

An overview on the strategies to exploit rice endosperm as production platform for biopharmaceuticals.

PubMed

Takaiwa, Fumio; Wakasa, Yuhya; Hayashi, Shimpei; Kawakatsu, Taiji

2017-10-01

Cereal seed has been utilized as production platform for high-value biopharmaceutical proteins. Especially, protein bodies (PBs) in seeds are not only natural specialized storage organs of seed storage proteins (SSPs), but also suitable intracellular deposition compartment for recombinant proteins. When various recombinant proteins were produced as secretory proteins by attaching N terminal ER signal peptide and C terminal KDEL endoplasmic reticulum (ER) retention signal or as fusion proteins with SSPs, high amounts of recombinant proteins can be predominantly accumulated in the PBs. Recombinant proteins bioencapsulated in PBs exhibit high resistance to digestive enzymes in gastrointestinal tract than other intracellular compartments and are highly stable at ambient temperature, thus allowing oral administration of PBs containing recombinant proteins as oral drugs or functional nutrients in cost-effective minimum processed formulation. In this review, we would like to address key factors determining accumulation levels of recombinant proteins in PBs. Understanding of bottle neck parts and improvement of specific deposition to PBs result in much higher levels of production of high quality recombinant proteins. Copyright © 2017. Published by Elsevier B.V.

LDSplitDB: a database for studies of meiotic recombination hotspots in MHC using human genomic data.

PubMed

Guo, Jing; Chen, Hao; Yang, Peng; Lee, Yew Ti; Wu, Min; Przytycka, Teresa M; Kwoh, Chee Keong; Zheng, Jie

2018-04-20

Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serious human diseases such as birth defects. Although the regulatory mechanism of recombination events is still unclear, DNA sequence polymorphisms have been found to play crucial roles in the regulation of recombination hotspots. To facilitate the studies of the underlying mechanism, we developed a database named LDSplitDB which provides an integrative and interactive data mining and visualization platform for the genome-wide association studies of recombination hotspots. It contains the pre-computed association maps of the major histocompatibility complex (MHC) region in the 1000 Genomes Project and the HapMap Phase III datasets, and a genome-scale study of the European population from the HapMap Phase II dataset. Besides the recombination profiles, related data of genes, SNPs and different types of epigenetic modifications, which could be associated with meiotic recombination, are provided for comprehensive analysis. To meet the computational requirement of the rapidly increasing population genomics data, we prepared a lookup table of 400 haplotypes for recombination rate estimation using the well-known LDhat algorithm which includes all possible two-locus haplotype configurations. To the best of our knowledge, LDSplitDB is the first large-scale database for the association analysis of human recombination hotspots with DNA sequence polymorphisms. It provides valuable resources for the discovery of the mechanism of meiotic recombination hotspots. The information about MHC in this database could help understand the roles of recombination in human immune system. DATABASE URL: http://histone.scse.ntu.edu.sg/LDSplitDB.

Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.

PubMed

Ma, Li; O'Connell, Jeffrey R; VanRaden, Paul M; Shen, Botong; Padhi, Abinash; Sun, Chuanyu; Bickhart, Derek M; Cole, John B; Null, Daniel J; Liu, George E; Da, Yang; Wiggans, George R

2015-11-01

Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half a million genotyped animals, we extracted 186,927 three-generation families, identified over 8.5 million maternal and paternal recombination events, and constructed sex-specific recombination maps for 59,309 autosomal SNPs. The recombination map spans for 25.5 Morgans in males and 23.2 Morgans in females, for a total studied region of 2,516 Mb (986 kb/cM in males and 1,085 kb/cM in females). The male map is 10% longer than the female map and the sex difference is most pronounced in the subtelomeric regions. We identified 1,792 male and 1,885 female putative recombination hotspots, with 720 hotspots shared between sexes. These hotspots encompass 3% of the genome but account for 25% of the genome-wide recombination events in both sexes. During the past forty years, males showed a decreasing trend in recombination rate that coincided with the artificial selection for milk production. Sex-specific GWAS analyses identified PRDM9 and CPLX1 to have significant effects on genome-wide recombination rate in both sexes. Two novel loci, NEK9 and REC114, were associated with recombination rate in both sexes, whereas three loci, MSH4, SMC3 and CEP55, affected recombination rate in females only. Among the multiple PRDM9 paralogues on the bovine genome, our GWAS of recombination hotspot usage together with linkage analysis identified the PRDM9 paralogue on chromosome 1 to be associated in the U.S. Holstein data. Given the largest sample size ever reported for such studies, our results reveal new insights into the understanding of cattle and mammalian recombination.

Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis

PubMed Central

Ma, Li; O'Connell, Jeffrey R.; VanRaden, Paul M.; Shen, Botong; Padhi, Abinash; Sun, Chuanyu; Bickhart, Derek M.; Cole, John B.; Null, Daniel J.; Liu, George E.; Da, Yang; Wiggans, George R.

2015-01-01

Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half a million genotyped animals, we extracted 186,927 three-generation families, identified over 8.5 million maternal and paternal recombination events, and constructed sex-specific recombination maps for 59,309 autosomal SNPs. The recombination map spans for 25.5 Morgans in males and 23.2 Morgans in females, for a total studied region of 2,516 Mb (986 kb/cM in males and 1,085 kb/cM in females). The male map is 10% longer than the female map and the sex difference is most pronounced in the subtelomeric regions. We identified 1,792 male and 1,885 female putative recombination hotspots, with 720 hotspots shared between sexes. These hotspots encompass 3% of the genome but account for 25% of the genome-wide recombination events in both sexes. During the past forty years, males showed a decreasing trend in recombination rate that coincided with the artificial selection for milk production. Sex-specific GWAS analyses identified PRDM9 and CPLX1 to have significant effects on genome-wide recombination rate in both sexes. Two novel loci, NEK9 and REC114, were associated with recombination rate in both sexes, whereas three loci, MSH4, SMC3 and CEP55, affected recombination rate in females only. Among the multiple PRDM9 paralogues on the bovine genome, our GWAS of recombination hotspot usage together with linkage analysis identified the PRDM9 paralogue on chromosome 1 to be associated in the U.S. Holstein data. Given the largest sample size ever reported for such studies, our results reveal new insights into the understanding of cattle and mammalian recombination. PMID:26540184

1.55 um aluminum gallium indium arsenide strained MQW laser diodes

NASA Astrophysics Data System (ADS)

Yang, Chi

At the 1.55 mum eye-safe, telecommunications operating wavelength, semiconductor diode lasers must have low threshold currents and operate at high temperatures without thermoelectric coolers. Existing diode lasers in this wavelength range based on the GaInAsP/InP materials system are very sensitive to operating temperature. To obtain high temperature, high power 1.55 mum semiconductor diode lasers, the AlGaInAs/InP materials system with strained quantum well (QW) active regions was investigated with the goal of improving temperature performance. A set of lasers with active regions consisting of different numbers of QWs (2 to 4) and different QW strains (1.2% and 1.6%) were designed taking into account the quaternary alloy bandgap of AlGaInAs, the effect of strain on the bandgap, and the quantum size effects within the QW. The active region growth temperature was optimized using photoluminescence intensity. The wafers were first processed into broad-area lasers and measured under pulsed injection. The characteristic threshold current temperature, T0, for all AlGaInAs lasers was higher (60-70 K) than for GaInAsP lasers. No strong dependence of temperature parameters on strain was observed, while properties varied significantly with the number of QWs. With more QWs, both internal efficiency and T0 increases, but internal loss increases, reducing the characteristic temperature of the differential efficiency T1. The results show that uncooled laser operation at 1.55 mum is very promising with strained AlGaInAs QWs. Ridge waveguide devices demonstrated low threshold and high output power as well as good temperature performance under continuous wave operation. Devices with different ridge heights were fabricated from one wafer and their performance was compared. It was found that current spreading was significant in these devices and a simple current density-versus-applied voltage analysis was developed to determine the spreading factor. The analysis shows that the current spreading was not effectively limited until etching went below the doped cladding layer. A recombination coefficient analysis was performed to investigate the effect of strain on Auger recombination predicted by theory. An indirect method to infer both the nonradiative recombination coefficient and the Auger recombination coefficient was initially used. The measured values of the recombination coefficients were consistent with theoretical predictions and measurements based on other material systems. The Auger recombination was lower than expected, indicating that Auger recombination is reduced in these strained QWs. To understand the carrier dynamics, impedance measurements were carried out for the first time in AlGaInAs strained QW lasers. A small-signal, sub-threshold equivalent circuit model was derived from the laser rate equations to model the measured laser impedance. Several characteristic carrier lifetimes were obtained directly from these electrical impedance measurements. From the temperature dependence of the QW escape time, it was found that hole rather than electron leakage is dominant in the AlGaInAs system due to the relatively low valence band offset. This may explain why the improvement of T0 in AlGaInAs QW 1.55 mum active regions is limited.

Development and Evaluation of Recombinant Nucleocapsid Protein Based Diagnostic ELISA for Detection of Nipah Virus Infection in Pigs.

PubMed

Kulkarni, Diwakar D; Venkatesh, Govindarajalu; Tosh, Chakradhar; Patel, Priyanka; Mashoria, Anita; Gupta, Vandana; Gupta, Sourabh; D, Senthilkumar

2016-01-01

The recombinant viral protein-based indirect enzyme-linked immunosorbent assay (ELISA) is a cost-effective, safe, specific, and rapid tool to diagnose the viral infection. Nipah virus nucleocapsid (NiV-N) protein was expressed in Escherichia coli and purified by histidine tag-based affinity chromatography. The N protein was selected based on its immuno dominance and conservation among different NiV strains. An indirect immunoglobulin G (IgG) enzyme-linked immunosorbent assay (ELISA) for swine sera was optimized using the recombinant NiV-N protein as an antigen along with negative and positive controls. The background reading was blocked using skim milk powder and chicken serum. A total number of 1709 swine serum samples from various states of India were tested with indirect ELISA and Western blot. The test was considered positive only when its total reactivity reading was higher than 0.2 cut-off value and the ratio of the total reactivity to the background reading was more than 2.0. Since specificity is high for Western blotting it was used as standard test for comparison of results of indirect ELISA. Sensitivity and specificity of indirect ELISA was 100% and 98.7%, respectively, in comparison with Western blotting. Recombinant N protein-based ELISA can be used in screening large number of serum samples for epidemiological investigations in developing countries where high containment laboratories are not available to handle this zoonotic virus.

Synthesis and characterization of recombinant abductin-based proteins.

PubMed

Su, Renay S-C; Renner, Julie N; Liu, Julie C

2013-12-09

Recombinant proteins are promising tools for tissue engineering and drug delivery applications. Protein-based biomaterials have several advantages over natural and synthetic polymers, including precise control over amino acid composition and molecular weight, modular swapping of functional domains, and tunable mechanical and physical properties. In this work, we describe recombinant proteins based on abductin, an elastomeric protein that is found in the inner hinge of bivalves and functions as a coil spring to keep shells open. We illustrate, for the first time, the design, cloning, expression, and purification of a recombinant protein based on consensus abductin sequences derived from Argopecten irradians . The molecular weight of the protein was confirmed by mass spectrometry, and the protein was 94% pure. Circular dichroism studies showed that the dominant structures of abductin-based proteins were polyproline II helix structures in aqueous solution and type II β-turns in trifluoroethanol. Dynamic light scattering studies illustrated that the abductin-based proteins exhibit reversible upper critical solution temperature behavior and irreversible aggregation behavior at high temperatures. A LIVE/DEAD assay revealed that human umbilical vein endothelial cells had a viability of 98 ± 4% after being cultured for two days on the abductin-based protein. Initial cell spreading on the abductin-based protein was similar to that on bovine serum albumin. These studies thus demonstrate the potential of abductin-based proteins in tissue engineering and drug delivery applications due to the cytocompatibility and its response to temperature.

Growth and Optimization of 2 Micrometers InGaSb/AlGaSb Quantum-Well-Based VECSELs on GaAs/AlGaAs DBRs

DTIC Science & Technology

2013-08-01

overwhelming nonradiative recombination losses in the antimonide active region. Furthermore, if the growth of the antimonide active region is done on a GaAs...This is important as threading dislocations would introduce a strong nonradiative recombination process in the QWs and relaxation that is not 100...These defects can act as nonradiative recombination centers. Thus, the source of the threading dislocations and their density in the active region

Screw dislocation-induced growth spirals as emissive exciton localization centers in Al-rich AlGaN/AlN quantum wells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Funato, Mitsuru, E-mail: funato@kuee.kyoto-u.ac.jp; Banal, Ryan G.; Kawakami, Yoichi

2015-11-15

Screw dislocations in Al-rich AlGaN/AlN quantum wells cause growth spirals with an enhanced Ga incorporation, which create potential minima. Although screw dislocations and their surrounding potential minima suggest non-radiative recombination processes within growth spirals, in reality, screw dislocations are not major non-radiative sinks for carriers. Consequently, carriers localized within growth spirals recombine radiatively without being captured by non-radiative recombination centers, resulting in intense emissions from growth spirals.

Graph Model of Coalescence with Recombinations

NASA Astrophysics Data System (ADS)

Parida, Laxmi

One of the primary genetic events shaping an autosomal chromosome is recombination. This is a process that occurs during meiosis, in eukaryotes, that results in the offsprings having different combinations of (homologous) genes, or chromosomal segments, of the two parents. The presence of these recombination events in the evolutionary history of each chromosome complicates the genetic landscape of a population, and understanding the manifestations of these genetic exchanges in the chromosome sequences has been a subject of intense curiosity (see [Hud83, Gri99, HSW05] and citations therein).

Vaccinia-based influenza vaccine overcomes previously induced immunodominance hierarchy for heterosubtypic protection.

PubMed

Kwon, Ji-Sun; Yoon, Jungsoon; Kim, Yeon-Jung; Kang, Kyuho; Woo, Sunje; Jung, Dea-Im; Song, Man Ki; Kim, Eun-Ha; Kwon, Hyeok-Il; Choi, Young Ki; Kim, Jihye; Lee, Jeewon; Yoon, Yeup; Shin, Eui-Cheol; Youn, Jin-Won

2014-08-01

Growing concerns about unpredictable influenza pandemics require a broadly protective vaccine against diverse influenza strains. One of the promising approaches was a T cell-based vaccine, but the narrow breadth of T-cell immunity due to the immunodominance hierarchy established by previous influenza infection and efficacy against only mild challenge condition are important hurdles to overcome. To model T-cell immunodominance hierarchy in humans in an experimental setting, influenza-primed C57BL/6 mice were chosen and boosted with a mixture of vaccinia recombinants, individually expressing consensus sequences from avian, swine, and human isolates of influenza internal proteins. As determined by IFN-γ ELISPOT and polyfunctional cytokine secretion, the vaccinia recombinants of influenza expanded the breadth of T-cell responses to include subdominant and even minor epitopes. Vaccine groups were successfully protected against 100 LD50 challenges with PR/8/34 and highly pathogenic avian influenza H5N1, which contained the identical dominant NP366 epitope. Interestingly, in challenge with pandemic A/Cal/04/2009 containing mutations in the dominant epitope, only the group vaccinated with rVV-NP + PA showed improved protection. Taken together, a vaccinia-based influenza vaccine expressing conserved internal proteins improved the breadth of influenza-specific T-cell immunity and provided heterosubtypic protection against immunologically close as well as distant influenza strains. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Free-Free Radiation Cannot Make the UV/Soft-X-Ray Excess in AGN

NASA Astrophysics Data System (ADS)

Kriss, G. A.

1994-05-01

Thermal gas always has associated atomic spectral features either in absorption or in emission. In optically thin gas the emission spectrum is dominated by line radiation and recombination continua. An example of radiation from optically thin material in accreting systems is the emission-line-dominated spectrum of a cataclysmic variable in its low state. Barvainis (1993, ApJ, 412, 513) and others have proposed that the UV/soft-X-ray excess prominent in the spectra of many AGN is due to free-free emission from gas at temperatures of 10(5) - 10(6) K. Simple arguments using only atomic data show that the recombination radiation from emission lines would produce UV, optical, and soft X-ray spectral features orders of magnitude stronger than observed. Collisional excitation produces even more line radiation under most physical conditions. As a particular example I take the Astro-1 observations of the Seyfert 1 galaxy Mrk 335 by HUT and BBXRT. Depending on the ionization state of the gas (which may be photoionized by the central source), the emission measure of the free-free radiation necessary to produce the UV continuum (3 times 10(68) cm(-3) at 8.2 times 10(5) K for H_o = 75 km s(-1) Mpc(-1) ) implies line emission from O VI, O VII, or O VIII more than a factor of 10 stronger than any features observed by HUT or BBXRT.

Cattle sex-specific recombination and genetic control from a very large pedigree

USDA-ARS?s Scientific Manuscript database

Meiotic recombination is an essential biological process that generates novel genetic variants and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half million genotyped animals, we extracted 186,927 three-generation families, identified ov...

A Locus for Autosomal Dominant Hereditary Spastic Ataxia, SAX1, Maps to Chromosome 12p13

PubMed Central

Meijer, I. A.; Hand, C. K.; Grewal, K. K.; Stefanelli, M. G.; Ives, E. J.; Rouleau, G. A.

2002-01-01

The hereditary spastic ataxias (HSA) are a group of clinically heterogeneous neurodegenerative disorders characterized by lower-limb spasticity and generalized ataxia. HSA was diagnosed in three unrelated autosomal dominant families from Newfoundland, who presented mainly with severe leg spasticity, dysarthria, dysphagia, and ocular-movement abnormalities. A genomewide scan was performed on one family, and linkage to a novel locus for HSA on chromosome 12p13, which contains the as-yet-unidentified gene locus SAX1, was identified. Fine mapping confirmed linkage in the two large families, and the third, smaller family showed LOD scores suggestive of linkage. Haplotype construction by use of 13 polymorphic markers revealed that all three families share a disease haplotype, which key recombinants and overlapping haplotypes refine to ∼5 cM, flanked by markers D12S93 and GATA151H05. SAX1 is the first locus mapped for autosomal dominant HSA. PMID:11774073

X-linked dominant cone-rod degeneration: Linkage mapping of a new locus for retinitis pigmentosa (RP15) to Xp22.13-p22.11

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGuire, R.E.; Sullivan, L.S.; Daiger, S.P.

1995-07-01

Retinitis pigmentosa is the name given to a heterogeneous group of hereditary retinal degenerations characterized by progressive visual field loss, pigmentary changes of the retina, abnormal electroretinograms, and, frequently, night blindness. In this study, we investigated a family with dominant cone-rod degeneration, a variant form of retinitis pigmentosa. We used microsatellite markers to test for linkage to the disease locus and exluded all mapped autosomal loci. However, a marker from the short arm of the X chromosome, DXS989, showed 0% recombination to the disease locus, with a maximum lod (log-odds) score of 3.3. On the basis of this marker, themore » odds favoring X-linked dominant versus autosomal dominant inheritance are > 10{sup 5}:1. Haplotype analysis using an additional nine microsatellite markers places the disease locus in the Xp22.13-p22.11 region and excludes other X-linked disease loci causing retinal degeneration. The clinical expression of the retinal degeneration is consistent with X-linked dominant inheritance with milder, variable effects of Lyonization affecting expression in females. On the basis of these data we propose that this family has a novel form of dominant, X-linked cone-rod degeneration with the gene symbol {open_quotes}RP15{close_quotes}. 17 refs., 2 figs., 4 tabs.« less

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I

PubMed Central

Shi, Yuqian; Hellinga, Homme W.; Beese, Lorena S.

2017-01-01

Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5′-nuclease superfamily. Its dominant, processive 5′–3′ exonuclease and secondary 5′-flap endonuclease activities participate in various DNA repair, recombination, and replication processes. A single active site processes both recessed ends and 5′-flap substrates. By initiating enzyme reactions in crystals, we have trapped hExo1 reaction intermediates that reveal structures of these substrates before and after their exo- and endonucleolytic cleavage, as well as structures of uncleaved, unthreaded, and partially threaded 5′ flaps. Their distinctive 5′ ends are accommodated by a small, mobile arch in the active site that binds recessed ends at its base and threads 5′ flaps through a narrow aperture within its interior. A sequence of successive, interlocking conformational changes guides the two substrate types into a shared reaction mechanism that catalyzes their cleavage by an elaborated variant of the two-metal, in-line hydrolysis mechanism. Coupling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate or premature cleavage, enhancing processing fidelity. The striking reduction in flap conformational entropy is catalyzed, in part, by arch motions and transient binding interactions between the flap and unprocessed DNA strand. At the end of the observed reaction sequence, hExo1 resets without relinquishing DNA binding, suggesting a structural basis for its processivity. PMID:28533382

Efficiency enhancement of ZnO nanostructure assisted Si solar cell based on fill factor enlargement and UV-blue spectral down-shifting

NASA Astrophysics Data System (ADS)

Gholizadeh, A.; Reyhani, A.; Parvin, P.; Mortazavi, S. Z.

2017-05-01

ZnO nanostructures (including nano-plates and nano-rods (NRs)) are grown in various temperatures and Ar/O2 flow rates using thermal chemical vapor deposition, which affect the structure, nano-plate/NR population, and the quality of ZnO nanostructures. X-ray diffraction (XRD) attests that the peak intensity of the crystallographic plane (1 0 0) is correlated to nano-plate abundance. Moreover, optical properties elucidate that the population of nano-plates in samples strongly affect the band gap, binding energy of the exciton, and UV-visible (UV-vis) absorption and spectral luminescence emissions. In fact, the exciton binding energy reduces from ~100 to 80 meV when the population of nano-plates increases in samples. Photovoltaic characteristics based on the drop-casting on Si solar cells reveals three dominant factors, namely, the equivalent series resistance, decreasing reflectance, and down-shifting, in order to scale up the absolute efficiency by 3%. As a consequence, the oxygen vacancies in ZnO nanostructures give rise to the down-shifting and increase of free-carriers, leading to a reduction in the equivalent series resistance and an enlargement of fill factor. To obtain a larger I sc, reduction of spectral reflectance is essential; however, the down-shifting process is shown to be dominant by lessening the surface electron-hole recombination rate over the UV-blue spectral range.

Genetic Diversity and Evolution of Bradyrhizobium Populations Nodulating Erythrophleum fordii, an Evergreen Tree Indigenous to the Southern Subtropical Region of China

PubMed Central

Yao, Yao; Wang, Rui; Lu, Jun Kun; Wang, En Tao; Chen, Wen Xin

2014-01-01

The nodulation of Erythrophleum fordii has been recorded recently, but its microsymbionts have never been studied. To investigate the diversity and biogeography of rhizobia associated with this leguminous evergreen tree, root nodules were collected from the southern subtropical region of China. A total of 166 bacterial isolates were obtained from the nodules and characterized. In a PCR-based restriction fragment length polymorphism (RFLP) analysis of ribosomal intergenic sequences, the isolates were classified into 22 types within the genus Bradyrhizobium. Sequence analysis of 16S rRNA, ribosomal intergenic spacer (IGS), and the housekeeping genes recA and glnII classified the isolates into four groups: the Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi groups, comprising the dominant symbionts, Bradyrhizobium yuanmingense, and an unclassified group comprising the minor symbionts. The nodC and nifH phylogenetic trees defined five or six lineages among the isolates, which was largely consistent with the definition of genomic species. The phylogenetic results and evolutionary analysis demonstrated that mutation and vertical transmission of genes were the principal processes for the divergent evolution of Bradyrhizobium species associated with E. fordii, while lateral transfer and recombination of housekeeping and symbiotic genes were rare. The distribution of the dominant rhizobial populations was affected by soil pH and effective phosphorus. This is the first report to characterize E. fordii rhizobia. PMID:25085491

Miscibility as a factor for component crystallization in multisolute frozen solutions.

PubMed

Izutsu, Ken-Ichi; Shibata, Hiroko; Yoshida, Hiroyuki; Goda, Yukihiro

2014-07-01

The relationship between the miscibility of formulation ingredients and their crystallization during the freezing segment of the lyophilization process was studied. The thermal properties of frozen solutions containing myo-inositol and cosolutes were obtained by performing heating scans from -70 °C before and after heat treatment at -20 °C to -5 °C. Addition of dextran 40,000 reduced and prevented crystallization of myo-inositol. In the first scan, some frozen solutions containing an inositol-rich mixture with dextran showed single broad transitions (Tg's: transition temperatures of maximally freeze-concentrated solutes) that indicated incomplete mixing of the concentrated amorphous solutes. Heat treatment of these frozen solutions induced separation of the solutes into inositol-dominant and solute mixture phases (Tg' splitting) following crystallization of myo-inositol (Tg' shifting). The crystal growth involved myo-inositol molecules in the solute mixture phase. The amorphous-amorphous phase separation and resulting loss of the heteromolecular interaction in the freeze-concentrated inositol-dominant phase should allow ordered assembly of the solute molecules required for nucleation. Some dextran-rich and intermediate concentration ratio frozen solutions retained single Tg's of the amorphous solute mixture, both before and after heat treatments. The relevance of solute miscibility on the crystallization of myo-inositol was also indicated in the systems containing glucose or recombinant human albumin. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Low-pressure hydrogen plasmas explored using a global model

NASA Astrophysics Data System (ADS)

Samuell, Cameron M.; Corr, Cormac S.

2016-02-01

Low-pressure hydrogen plasmas have found applications in a variety of technology areas including fusion, neutral beam injection and material processing applications. To better understand these discharges, a global model is developed to predict the behaviour of electrons, ground-state atomic and molecular hydrogen, three positive ion species (H+, \\text{H}2+ , and \\text{H}3+ ), a single negative ion species (H-), and fourteen vibrationally excited states of molecular hydrogen ({{\\text{H}}2}≤ft(\\upsilon =1\\right. -14)). The model is validated by comparison with experimental results from a planar inductively coupled GEC reference cell and subsequently applied to the MAGPIE linear helicon reactor. The MAGPIE reactor is investigated for a range of pressures from 1 to 100 mTorr and powers up to 5 kW. With increasing power between 50 W and 5 kW at 10 mTorr the density of all charged species increases as well as the dissociative fraction while the electron temperature remains almost constant at around 3 eV. For gas pressures from 1-100 mTorr at an input power of 1 kW, the electron density remains almost constant, the electron temperature and dissociative fraction decreases, while \\text{H}3+ density increases in density and also dominates amongst ion species. Across these power and pressure scans, electronegativity remains approximately constant at around 2.5%. The power and pressure determines the dominant ion species in the plasma with \\text{H}3+ observed to dominate at high pressures and low powers whereas H+ tends to be dominant at low pressures and high powers. A sensitivity analysis is used to demonstrate how experimental parameters (power, pressure, reactor wall material, geometry etc) influence individual species’ density as well as the electron temperature. Physical reactor changes including the length, radius and wall recombination coefficient are found to have the largest influence on outputs obtained from the model.

Progress in Studying Scintillator Proportionality: Phenomenological Model

NASA Astrophysics Data System (ADS)

Bizarri, G.; Cherepy, N. J.; Choong, W. S.; Hull, G.; Moses, W. W.; Payne, S. A.; Singh, J.; Valentine, J. D.; Vasilev, A. N.; Williams, R. T.

2009-08-01

We present a model to describe the origin of non-proportional dependence of scintillator light yield on the energy of an ionizing particle. The non-proportionality is discussed in terms of energy relaxation channels and their linear and non-linear dependences on the deposited energy. In this approach, the scintillation response is described as a function of the deposited energy deposition and the kinetic rates of each relaxation channel. This mathematical framework allows both a qualitative interpretation and a quantitative fitting representation of scintillation non-proportionality response as function of kinetic rates. This method was successfully applied to thallium doped sodium iodide measured with SLYNCI, a new facility using the Compton coincidence technique. Finally, attention is given to the physical meaning of the dominant relaxation channels, and to the potential causes responsible for the scintillation non-proportionality. We find that thallium doped sodium iodide behaves as if non-proportionality is due to competition between radiative recombinations and non-radiative Auger processes.

SEMICONDUCTOR TECHNOLOGY: Influence of hydrogenation on the dark current mechanism of HgCdTe photovoltaic detectors

NASA Astrophysics Data System (ADS)

Hui, Qiao; Weida, Hu; Zhenhua, Ye; Xiangyang, Li; Haimei, Gong

2010-03-01

The influence of hydrogenation on the dark current mechanism of HgCdTe photovoltaic detectors is studied. The hydrogenation is achieved by exposing samples to a H2/Ar plasma atmosphere that was produced during a reactive ion etching process. A set of variable-area photomask was specially designed to evaluate the hydrogenation effect. It was found that the current-voltage characteristics were gradually improved when detectors were hydrogenated by different areas. The fitting results of experimental results at reverse bias conditions sustained that the improvement of current-voltage curves was due to the suppression of trap assisted tunneling current and the enhancement of minority lifetime in the depletion region. It was also found that the dominative forward current was gradually converted from a generation-recombination current to a diffusion current with the enlargement of the hydrogenation area, which was infered from the ideality factors by abstraction of forward resistance-voltage curves of different detectors.

Induction of potential protective immunity against enterotoxemia in calves by single or multiple recombinant Clostridium perfringens toxoids.

PubMed

Jiang, Zhigang; De, Yanyan; Chang, Jitao; Wang, Fang; Yu, Li

2014-11-01

Cattle enterotoxemia caused by Clostridium perfringens toxins is a noncontagious, sporadic, and fatal disease characterized by sudden death. Strategies for controlling and preventing cattle enterotoxemia are based on systematic vaccination of herds with toxoids. Because the process of producing conventional clostridial vaccines is dangerous, expensive, and time-consuming, the prospect of recombinant toxoid vaccines against diseases caused by C. perfringens toxins is promising. In this study, nontoxic recombinant toxoids derived from α-, β- and ε-toxins of C. perfringens, namely, rCPA247-370 , rCPB and rEtxHP, respectively, were expressed in Escherichia coli. High levels of specific IgG antibodies and neutralizing antibodies against the toxins were detected in sera from calves vaccinated with either a single recombinant toxoid or a mixed cocktail of all three recombinant toxoids, indicating the potential of these recombinant toxoids to provide calves with protective immunity against enterotoxemia caused by C. perfringens. © 2014 The Societies and Wiley Publishing Asia Pty Ltd.

The BCL11A Transcription Factor Directly Activates RAG Gene Expression and V(D)J Recombination

PubMed Central

Lee, Baeck-seung; Dekker, Joseph D.; Lee, Bum-kyu; Iyer, Vishwanath R.; Sleckman, Barry P.; Shaffer, Arthur L.; Ippolito, Gregory C.

2013-01-01

Recombination-activating gene 1 protein (RAG1) and RAG2 are critical enzymes for initiating variable-diversity-joining (VDJ) segment recombination, an essential process for antigen receptor expression and lymphocyte development. The transcription factor BCL11A is required for B cell development, but its molecular function(s) in B cell fate specification and commitment is unknown. We show here that the major B cell isoform, BCL11A-XL, binds the RAG1 promoter and Erag enhancer to activate RAG1 and RAG2 transcription in pre-B cells. We employed BCL11A overexpression with recombination substrates in a cultured pre-B cell line as well as Cre recombinase-mediated Bcl11alox/lox deletion in explanted murine pre-B cells to demonstrate direct consequences of BCL11A/RAG modulation on V(D)J recombination. We conclude that BCL11A is a critical component of a transcriptional network that regulates B cell fate by controlling V(D)J recombination. PMID:23438597

Electron-temperature dependence of dissociative recombination of electrons with N2/+/.N2 dimer ions

NASA Technical Reports Server (NTRS)

Whitaker, M.; Biondi, M. A.; Johnsen, R.

1981-01-01

The variation with electron temperature of the dissociative recombination of electrons with N2(+).N2 dimer ions is investigated in light of the importance of such ions in the lower ionosphere and in laser plasmas. Dissociative recombination coefficients were determined by means of a microwave afterglow mass spectrometer technique for electron temperatures from 300-5600 K and an ion and neutral temperature of 300 K. The recombination coefficient is found to be proportional to the -0.41 power of the electron temperature in this range, similar to that observed for the CO(+).CO dimer ion and consistent with the expected energy dependence for a fast dissociative process.

The Biological Big Bang model for the major transitions in evolution.

PubMed

Koonin, Eugene V

2007-08-20

Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal. I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. This biphasic model of evolution incorporates the previously developed concepts of the emergence of protein folds by recombination of small structural units and origin of viruses and cells from a pre-cellular compartmentalized pool of recombining genetic elements. The model is extended to encompass other major transitions. It is proposed that bacterial and archaeal phyla emerged independently from two distinct populations of primordial cells that, originally, possessed leaky membranes, which made the cells prone to rampant gene exchange; and that the eukaryotic supergroups emerged through distinct, secondary endosymbiotic events (as opposed to the primary, mitochondrial endosymbiosis). This biphasic model of evolution is substantially analogous to the scenario of the origin of universes in the eternal inflation version of modern cosmology. Under this model, universes like ours emerge in the infinite multiverse when the eternal process of exponential expansion, known as inflation, ceases in a particular region as a result of false vacuum decay, a first order phase transition process. The result is the nucleation of a new universe, which is traditionally denoted Big Bang, although this scenario is radically different from the Big Bang of the traditional model of an expanding universe. Hence I denote the phase transitions at the end of each inflationary epoch in the history of life Biological Big Bangs (BBB). A Biological Big Bang (BBB) model is proposed for the major transitions in life's evolution. According to this model, each transition is a BBB such that new classes of biological entities emerge at the end of a rapid phase of evolution (inflation) that is characterized by extensive exchange of genetic information which takes distinct forms for different BBBs. The major types of new forms emerge independently, via a sampling process, from the pool of recombining entities of the preceding generation. This process is envisaged as being qualitatively different from tree-pattern cladogenesis.

The Biological Big Bang model for the major transitions in evolution

PubMed Central

Koonin, Eugene V

2007-01-01

Background Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal. Hypothesis I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. This biphasic model of evolution incorporates the previously developed concepts of the emergence of protein folds by recombination of small structural units and origin of viruses and cells from a pre-cellular compartmentalized pool of recombining genetic elements. The model is extended to encompass other major transitions. It is proposed that bacterial and archaeal phyla emerged independently from two distinct populations of primordial cells that, originally, possessed leaky membranes, which made the cells prone to rampant gene exchange; and that the eukaryotic supergroups emerged through distinct, secondary endosymbiotic events (as opposed to the primary, mitochondrial endosymbiosis). This biphasic model of evolution is substantially analogous to the scenario of the origin of universes in the eternal inflation version of modern cosmology. Under this model, universes like ours emerge in the infinite multiverse when the eternal process of exponential expansion, known as inflation, ceases in a particular region as a result of false vacuum decay, a first order phase transition process. The result is the nucleation of a new universe, which is traditionally denoted Big Bang, although this scenario is radically different from the Big Bang of the traditional model of an expanding universe. Hence I denote the phase transitions at the end of each inflationary epoch in the history of life Biological Big Bangs (BBB). Conclusion A Biological Big Bang (BBB) model is proposed for the major transitions in life's evolution. According to this model, each transition is a BBB such that new classes of biological entities emerge at the end of a rapid phase of evolution (inflation) that is characterized by extensive exchange of genetic information which takes distinct forms for different BBBs. The major types of new forms emerge independently, via a sampling process, from the pool of recombining entities of the preceding generation. This process is envisaged as being qualitatively different from tree-pattern cladogenesis. Reviewers This article was reviewed by William Martin, Sergei Maslov, and Leonid Mirny. PMID:17708768

Thickness-dependent carrier and phonon dynamics of topological insulator Bi2Te3 thin films.

PubMed

Zhao, Jie; Xu, Zhongjie; Zang, Yunyi; Gong, Yan; Zheng, Xin; He, Ke; Cheng, Xiang'ai; Jiang, Tian

2017-06-26

As a new quantum state of matter, topological insulators offer a new platform for exploring new physics, giving rise to fascinating new phenomena and new devices. Lots of novel physical properties of topological insulators have been studied extensively and are attributed to the unique electron-phonon interactions at the surface. Although electron behavior in topological insulators has been studied in detail, electron-phonon interactions at the surface of topological insulators are less understood. In this work, using optical pump-optical probe technology, we performed transient absorbance measurement on Bi 2 Te 3 thin films to study the dynamics of its hot carrier relaxation process and coherent phonon behavior. The excitation and dynamics of phonon modes are observed with a response dependent on the thickness of the samples. The thickness-dependent characteristic time, amplitude and frequency of the damped oscillating signals are acquired by fitting the signal profiles. The results clearly indicate that the electron-hole recombination process gradually become dominant with the increasing thickness which is consistent with our theoretical calculation. In addition, a frequency modulation phenomenon on the high-frequency oscillation signals induced by coherent optical phonons is observed.

Modeling of helicon wave propagation and the physical process of helicon plasma production

NASA Astrophysics Data System (ADS)

Isayama, Shogo; Hada, Tohru; Shinohara, Shunjiro; Tanikawa, Takao

2014-10-01

Helicon plasma is a high-density and low-temperature plasma generated by the helicon wave, and is expected to be useful for various applications. On the other hand, there still remain a number of unsolved physical issues regarding how the plasma is generated using the helicon wave. The generation involves such physical processes as wave propagation, mode conversion, and collisionless as well as collisional wave damping that leads to ionization/recombination of neutral particles. In this study, we attempt to construct a model for the helicon plasma production using numerical simulations. In particular, we will make a quantitative argument on the roles of the mode conversion from the helicon to the electrostatic Trivelpiece-Gould (TG) wave, as first proposed by Shamrai. According to his scenario, the long wavelength helicon wave linearly mode converts to the TG wave, which then dissipates rapidly due to its large wave number. On the other hand, the efficiency of the mode conversion depends strongly on the magnitudes of dissipation parameters. Particularly when the dissipation is dominant, the TG wave is no longer excited and the input helicon wave directly dissipates. In the presentation, we will discuss the mode conversion and the plasma heating using numerical simulations.

A comparison of protein A chromatographic stationary phases: performance characteristics for monoclonal antibody purification.

PubMed

Liu, Zhuo; Mostafa, Sigma S; Shukla, Abhinav A

2015-01-01

Protein A chromatography remains the dominant capture step used during the downstream purification of monoclonal antibodies (mAbs). With the recent expiry of the Repligen patent on recombinant Protein A, a variety of new Protein A resins have been introduced in the market. Given productivity limitations during downstream processing that have come into sharper focus with the recent increase in cell culture titers for mAbs, the selection of an appropriate Protein A resin has direct implications on the overall process economics of mAb production. The performance of seven different Protein A chromatographic resins was compared with respect to static binding capacity and dynamic binding capacity as a function of flow rate. This data was translated into a comparison of productivity (g mAb purified per unit resin volume per unit time) for the seven stationary phases. In addition, elution pH and host cell protein impurity levels after product capture on each of these resins were determined. The current article provides an effective methodology and dataset for the selection of the optimal Protein A chromatographic resin. © 2014 International Union of Biochemistry and Molecular Biology, Inc.

Crystal growth and characterization of Ce:Gd3(Ga,Al)5O12 single crystal using floating zone method in different O2 partial pressure

NASA Astrophysics Data System (ADS)

Yoshikawa, Akira; Fujimoto, Yutaka; Yamaji, Akihiro; Kurosawa, Shunsuke; Pejchal, Jan; Sugiyama, Makoto; Wakahara, Shingo; Futami, Yoshisuke; Yokota, Yuui; Kamada, Kei; Yubuta, Kunio; Shishido, Toetsu; Nikl, Martin

2013-09-01

Multicomponent garnet Ce:Gd3(Ga,Al)5O12 (Ce:GAGG) single crystals show very high light yield with reasonably fast scintillation response. Therefore, they can be promising scintillators for gamma-ray detection. However, in the decay curve a very slow component does exist. Therefore, it is necessary to optimize further the crystal growth technology of Ce:GAGG. In this study, Ce:GAGG single crystals were grown by the floating zone (FZ) method under atmospheres of various compositions such as Ar 100%, Ar 80% + O2 20%, Ar 60% + O2 40% and O2 100%. Radioluminescence spectra are dominated by the band at about 540 nm due to Ce3+ 5d1-4f transition. The Ce:GAGG single crystal grown under Ar atmosphere shows an intense slower decay component. It can be related to the processes of the delayed radiative recombination and thermally induced ionization of 5d1 level of Ce3+ center possibly further affected by oxygen vacancies. This slower decay process is significantly suppressed in the samples grown under the O2 containing atmosphere.

Linkage analysis with chromosome 9 markers in hereditary essential tremor.

PubMed

Conway, D; Bain, P G; Warner, T T; Davis, M B; Findley, L J; Thompson, P D; Marsden, C D; Harding, A E

1993-07-01

Hereditary essential tremor (ET) is an autosomal dominant disorder with variable expression and reduced penetrance. A tremor indistinguishable from ET may be observed in patients with autosomal dominant idiopathic torsion dystonia (ITD), in which the disease locus has been mapped to 9q32-34 in some kindreds, tightly linked to the argininosuccinate synthetase (ASS) locus. We performed linkage analysis in 15 families with ET containing 60 definitely affected individuals, using dinucleotide repeat polymorphisms at the ASS locus and the Abelson locus (ABL). Cumulative lod scores were -19.5 for ASS and -10.8 for ABL at a recombination fraction of 0.01, and tight linkage to ASS was excluded individually in 11 of the families. These data indicate that the ET gene is not allelic to that causing ITD.

Selection of specific inhibitor peptides in enzyme-linked immunosorbent assay (ELISA) of cardiac troponin I using immuno-dominant epitopes as competitor.

PubMed

Rezaee, Majid Asiabanha; Rasaee, Mohammad Javad; Mohammadnejad, Javad

2017-01-01

Human cardiac troponin I (cTni) is the gold marker for early diagnosis of myocardial infarction. In this regard, four immune-dominant epitopes of cTni were predicted and their 3D structures were determined. Thereafter, the competitive performance of the peptides was monitored with the developed polyclonal antibody-based indirect competitive ELISA; a half-maximal inhibitory concentration (IC50) of 0.49 (µg/mL) and detection limit of 0.037 (µg/mL) were achieved for recombinant cTni. The competitive ELISA determined sensitivity levels of 0.306, 0.141, 0.960, and 0.155 (µg/mL), respectively, for each peptide as competitor. We indicated that two of the selected epitopes have significant sensitivity scales and inhibition ability.

21 CFR 514.8 - Supplements and other changes to an approved application.

Code of Federal Regulations, 2013 CFR

2013-04-01

... method(s) or an addition, deletion, or substitution of steps in an aseptic processing operation; (D... solely affecting a natural product, a recombinant DNA-derived protein/polypeptide, or a complex or...) or references to previously approved documentation; (H) For a natural product, a recombinant DNA...

21 CFR 514.8 - Supplements and other changes to an approved application.

Code of Federal Regulations, 2014 CFR

2014-04-01

... method(s) or an addition, deletion, or substitution of steps in an aseptic processing operation; (D... solely affecting a natural product, a recombinant DNA-derived protein/polypeptide, or a complex or...) or references to previously approved documentation; (H) For a natural product, a recombinant DNA...

21 CFR 514.8 - Supplements and other changes to an approved application.

Code of Federal Regulations, 2012 CFR

2012-04-01

... method(s) or an addition, deletion, or substitution of steps in an aseptic processing operation; (D... solely affecting a natural product, a recombinant DNA-derived protein/polypeptide, or a complex or...) or references to previously approved documentation; (H) For a natural product, a recombinant DNA...

Recombinant DNA for Teachers.

ERIC Educational Resources Information Center

Duvall, James G., III

1992-01-01

A science teacher describes his experience at a workshop to learn to teach the Cold Spring Harbor DNA Science Laboratory Protocols. These protocols lead students through processes for taking E. coli cells and transforming them into a new antibiotic resistant strain. The workshop featured discussions of the role of DNA recombinant technology in…

Airbreathing Pulse Detonation Engine Performance

NASA Technical Reports Server (NTRS)

Povinelli, Louis A.; Yungster, Shaye

2002-01-01

This paper presents performance results for pulse detonation engines taking into account the effects of dissociation and recombination. The amount of sensible heat recovered through recombination in the PDE chamber and exhaust process was found to be significant. These results have an impact on the specific thrust, impulse and fuel consumption of the PDE.

Sexuality Generates Diversity in the Aflatoxin Gene Cluster: Evidence on a Global Scale

PubMed Central

Moore, Geromy G.; Elliott, Jacalyn L.; Singh, Rakhi; Horn, Bruce W.; Dorner, Joe W.; Stone, Eric A.; Chulze, Sofia N.; Barros, German G.; Naik, Manjunath K.; Wright, Graeme C.; Hell, Kerstin; Carbone, Ignazio

2013-01-01

Aflatoxins are produced by Aspergillus flavus and A. parasiticus in oil-rich seed and grain crops and are a serious problem in agriculture, with aflatoxin B1 being the most carcinogenic natural compound known. Sexual reproduction in these species occurs between individuals belonging to different vegetative compatibility groups (VCGs). We examined natural genetic variation in 758 isolates of A. flavus, A. parasiticus and A. minisclerotigenes sampled from single peanut fields in the United States (Georgia), Africa (Benin), Argentina (Córdoba), Australia (Queensland) and India (Karnataka). Analysis of DNA sequence variation across multiple intergenic regions in the aflatoxin gene clusters of A. flavus, A. parasiticus and A. minisclerotigenes revealed significant linkage disequilibrium (LD) organized into distinct blocks that are conserved across different localities, suggesting that genetic recombination is nonrandom and a global occurrence. To assess the contributions of asexual and sexual reproduction to fixation and maintenance of toxin chemotype diversity in populations from each locality/species, we tested the null hypothesis of an equal number of MAT1-1 and MAT1-2 mating-type individuals, which is indicative of a sexually recombining population. All samples were clone-corrected using multi-locus sequence typing which associates closely with VCG. For both A. flavus and A. parasiticus, when the proportions of MAT1-1 and MAT1-2 were significantly different, there was more extensive LD in the aflatoxin cluster and populations were fixed for specific toxin chemotype classes, either the non-aflatoxigenic class in A. flavus or the B1-dominant and G1-dominant classes in A. parasiticus. A mating type ratio close to 1∶1 in A. flavus, A. parasiticus and A. minisclerotigenes was associated with higher recombination rates in the aflatoxin cluster and less pronounced chemotype differences in populations. This work shows that the reproductive nature of the population (more sexual versus more asexual) is predictive of aflatoxin chemotype diversity in these agriculturally important fungi. PMID:24009506

Expression of three Trichoderma reesei cellulase genes in Saccharomyces pastorianus for the development of a two-step process of hydrolysis and fermentation of cellulose.

PubMed

Fitzpatrick, J; Kricka, W; James, T C; Bond, U

2014-07-01

To compare the production of recombinant cellulase enzymes in two Saccharomyces species so as to ascertain the most suitable heterologous host for the degradation of cellulose-based biomass and its conversion into bioethanol. cDNA copies of genes representing the three major classes of cellulases (Endoglucanases, Cellobiohydrolases and β-glucosidases) from Trichoderma reesei were expressed in Saccharomyces pastorianus and Saccharomyces cerevisiae. The recombinant enzymes were secreted by the yeast hosts into the medium and were shown to act in synergy to hydrolyse cellulose. The conditions required to achieve maximum release of glucose from cellulose by the recombinant enzymes were defined and the activity of the recombinant enzymes was compared to a commercial cocktail of T. reesei cellulases. We demonstrate that significantly higher levels of cellulase activity were achieved by expression of the genes in S. pastorianus compared to S. cerevisiae. Hydrolysis of cellulose by the combined activity of the recombinant enzymes was significantly better at 50°C than at 30°C, the temperature used for mesophilic yeast fermentations, reflecting the known temperature profiles of the native enzymes. The results demonstrate that host choice is important for the heterologous production of cellulases. On the basis of the low activity of the T. reesei recombinant enzymes at fermentation temperatures, we propose a two-step process for the hydrolysis of cellulose and its fermentation into alcohol using cellulases produced in situ. © 2014 The Society for Applied Microbiology.

Size and Temperature Dependence of Electron Transfer between CdSe Quantum Dots and a TiO 2 Nanobelt

DOE PAGES

Tafen, De Nyago; Prezhdo, Oleg V.

2015-02-24

Understanding charge transfer reactions between quantum dots (QD) and metal oxides is fundamental for improving photocatalytic, photovoltaic and electronic devices. The complexity of these processes makes it difficult to find an optimum QD size with rapid charge injection and low recombination. We combine time-domain density functional theory with nonadiabatic molecular dynamics to investigate the size and temperature dependence of the experimentally studied electron transfer and charge recombination at CdSe QD-TiO 2 nanobelt (NB) interfaces. The electron injection rate shows strong dependence on the QD size, increasing for small QDs. The rate exhibits Arrhenius temperature dependence, with the activation energy ofmore » the order of millielectronvolts. The charge recombination process occurs due to coupling of the electronic subsystem to vibrational modes of the TiO 2 NB. Inelastic electron-phonon scattering happens on a picosecond time scale, with strong dependence on the QD size. Our simulations demonstrate that the electron-hole recombination rate decreases significantly as the QD size increases, in excellent agreement with experiments. The temperature dependence of the charge recombination rates can be successfully modeled within the framework of the Marcus theory through optimization of the electronic coupling and the reorganization energy. Our simulations indicate that by varying the QD size, one can modulate the photoinduced charge separation and charge recombination, fundamental aspects of the design principles for high efficiency devices.« less

Charge Separation and Recombination at Polymer-Fullerene Heterojunctions: Delocalization and Hybridization Effects.

PubMed

D'Avino, Gabriele; Muccioli, Luca; Olivier, Yoann; Beljonne, David

2016-02-04

We address charge separation and recombination in polymer/fullerene solar cells with a multiscale modeling built from accurate atomistic inputs and accounting for disorder, interface electrostatics and genuine quantum effects on equal footings. Our results show that bound localized charge transfer states at the interface coexist with a large majority of thermally accessible delocalized space-separated states that can be also reached by direct photoexcitation, thanks to their strong hybridization with singlet polymer excitons. These findings reconcile the recent experimental reports of ultrafast exciton separation ("hot" process) with the evidence that high quantum yields do not require excess electronic or vibrational energy ("cold" process), and show that delocalization, by shifting the density of charge transfer states toward larger effective electron-hole radii, may reduce energy losses through charge recombination.

Engineer Medium and Feed for Modulating N-Glycosylation of Recombinant Protein Production in CHO Cell Culture.

PubMed

Fan, Yuzhou; Kildegaard, Helene Faustrup; Andersen, Mikael Rørdam

2017-01-01

Chinese hamster ovary (CHO) cells have become the primary expression system for the production of complex recombinant proteins due to their long-term success in industrial scale production and generating appropriate protein N-glycans similar to that of humans. Control and optimization of protein N-glycosylation is crucial, as the structure of N-glycans can largely influence both biological and physicochemical properties of recombinant proteins. Protein N-glycosylation in CHO cell culture can be controlled and tuned by engineering medium, feed, culture process, as well as genetic elements of the cell. In this chapter, we will focus on how to carry out experiments for N-glycosylation modulation through medium and feed optimization. The workflow and typical methods involved in the experiment process will be presented.

Dissociative recombination of N2/+/ in the ionosphere

NASA Technical Reports Server (NTRS)

Torr, M. R.; Torr, D. G.

1979-01-01

N2(+) ion measurements are examined which were made with the Atmospheric Explorer-C satellite during a phase of solar activity in 1978 that was significantly higher than near the earlier minimum. It is found that the major source of N2(+) is photoionization, rather than charge exchange with O(+) (2D), and that the major loss process above 300 km is dissociative recombination with electrons. A data sample for which the electron temperature (T sub e) covered the range from 1000 to 3400 K is used to evaluate the rate constant, alpha, for the dissociative-recombination process. The results show good agreement with laboratory measurements given by the expression: alpha = 1.8 x 10 to the -7th (T sub e/300) to the -0.39th cu cm/sec.

Recombinatorial biases and convergent recombination determine interindividual TCRβ sharing in murine thymocytes.

PubMed

Li, Hanjie; Ye, Congting; Ji, Guoli; Wu, Xiaohui; Xiang, Zhe; Li, Yuanyue; Cao, Yonghao; Liu, Xiaolong; Douek, Daniel C; Price, David A; Han, Jiahuai

2012-09-01

Overlap of TCR repertoires among individuals provides the molecular basis for public T cell responses. By deep-sequencing the TCRβ repertoires of CD4+CD8+ thymocytes from three individual mice, we observed that a substantial degree of TCRβ overlap, comprising ∼10-15% of all unique amino acid sequences and ∼5-10% of all unique nucleotide sequences across any two individuals, is already present at this early stage of T cell development. The majority of TCRβ sharing between individual thymocyte repertoires could be attributed to the process of convergent recombination, with additional contributions likely arising from recombinatorial biases; the role of selection during intrathymic development was negligible. These results indicate that the process of TCR gene recombination is the major determinant of clonotype sharing between individuals.

Dissecting repulsion linkage in the dwarfing gene Dw3 region for sorghum plant height provides insights into heterosis.

PubMed

Li, Xin; Li, Xianran; Fridman, Eyal; Tesso, Tesfaye T; Yu, Jianming

2015-09-22

Heterosis is a main contributor to yield increase in many crop species. Different mechanisms have been proposed for heterosis: dominance, overdominance, epistasis, epigenetics, and protein metabolite changes. However, only limited examples of molecular dissection and validation of these mechanisms are available. Here, we present an example of discovery and validation of heterosis generated by a combination of repulsion linkage and dominance. Using a recombinant inbred line population, a separate quantitative trait locus (QTL) for plant height (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 gene. With two loci having repulsion linkage between two inbreds, heterosis in the hybrid can appear as a single locus with an overdominance mode of inheritance (i.e., pseudo-overdominance). Individually, alleles conferring taller plant height exhibited complete dominance over alleles conferring shorter height. Detailed analyses of different height components demonstrated that qHT7.1 affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. Computer simulations show that repulsion linkage could influence QTL detection and estimation of effect in segregating populations. Guided by findings in linkage mapping, a genome-wide association study of plant height with a sorghum diversity panel pinpointed genomic regions underlying the trait variation, including Dw1, Dw2, Dw3, Dw4, and qHT7.1. Multilocus mixed model analysis confirmed the advantage of complex trait dissection using an integrated approach. Besides identifying a specific genetic example of heterosis, our research indicated that integrated molecular dissection of complex traits in different population types can enable plant breeders to fine tune the breeding process for crop production.

Improved photovoltaic performance and stability of quantum dot sensitized solar cells using Mn-ZnSe shell structure with enhanced light absorption and recombination control.

PubMed

Gopi, Chandu V V M; Venkata-Haritha, M; Kim, Soo-Kyoung; Kim, Hee-Je

2015-08-07

To make quantum-dot-sensitized solar cells (QDSSCs) competitive, photovoltaic parameters comparable to those of other emerging solar cell technologies are necessary. In the present study, ZnSe was used as an alternative to ZnS, one of the most widely used passivation materials in QDSSCs. ZnSe was deposited on a TiO2-CdS-CdSe photoanode to form a core-shell structure, which was more efficient in terms of reducing the electron recombination in QDSSCs. The development of an efficient passivation layer is a requirement for preventing recombination processes in order to attain high-performance and stable QDSSCs. A layer of inorganic Mn-ZnSe was applied to a QD-sensitized photoanode to enhance the adsorption and strongly inhibit interfacial recombination processes in QDSSCs, which greatly improved the power conversion efficiency. Impedance spectroscopy revealed that the combined Mn doping with ZnSe treatment reduces interfacial recombination and increases charge collection efficiency compared with Mn-ZnS, ZnS, and ZnSe. A solar cell based on the CdS-CdSe-Mn-ZnSe photoanode yielded excellent performance with a solar power conversion efficiency of 5.67%, Voc of 0.584 V, and Jsc of 17.59 mA cm(-2). Enhanced electron transport and reduced electron recombination are responsible for the improved Jsc and Voc of the QDSSCs. The effective electron lifetime of the device with Mn-ZnSe was higher than those with Mn-ZnS, ZnSe, and ZnS, leading to more efficient electron-hole separation and slower electron recombination.

Selective binding of meiosis-specific yeast Hop1 protein to the holliday junctions distorts the DNA structure and its implications for junction migration and resolution.

PubMed

Tripathi, Pankaj; Anuradha, S; Ghosal, Gargi; Muniyappa, K

2006-12-08

Saccharomyces cerevisiae HOP1, which encodes a component of synaptonemal complex (SC), plays an important role in both gene conversion and crossing over between homologs, as well as enforces meiotic recombination checkpoint control over the progression of recombination intermediates. In hop1Delta mutants, meiosis-specific double-strand breaks (DSBs) are reduced to 10% of the wild-type level, and at aberrantly late times, these DSBs are processed into inter-sister recombination intermediates. However, the underlying mechanism by which Hop1 protein regulates these nuclear events remains obscure. Here we show that Hop1 protein interacts selectively with the Holliday junction, changes its global conformation and blocks the dissolution of the junction by a RecQ helicase. The Holliday junction-Hop1 protein complexes are significantly more stable at higher ionic strengths and molar excess of unlabeled competitor DNA than complexes containing other recombination intermediates. Structural analysis of the Holliday junction using 2-aminopurine fluorescence emission, DNase I footprinting and KMnO4 probing provide compelling evidence that Hop1 protein binding induces significant distortion at the center of the Holliday junction. We propose that Hop1 protein might coordinate the physical monitoring of meiotic recombination intermediates with the process of branch migration of Holliday junction.

Hybridization-based antibody cDNA recovery for the production of recombinant antibodies identified by repertoire sequencing.

PubMed

Valdés-Alemán, Javier; Téllez-Sosa, Juan; Ovilla-Muñoz, Marbella; Godoy-Lozano, Elizabeth; Velázquez-Ramírez, Daniel; Valdovinos-Torres, Humberto; Gómez-Barreto, Rosa E; Martinez-Barnetche, Jesús

2014-01-01

High-throughput sequencing of the antibody repertoire is enabling a thorough analysis of B cell diversity and clonal selection, which may improve the novel antibody discovery process. Theoretically, an adequate bioinformatic analysis could allow identification of candidate antigen-specific antibodies, requiring their recombinant production for experimental validation of their specificity. Gene synthesis is commonly used for the generation of recombinant antibodies identified in silico. Novel strategies that bypass gene synthesis could offer more accessible antibody identification and validation alternatives. We developed a hybridization-based recovery strategy that targets the complementarity-determining region 3 (CDRH3) for the enrichment of cDNA of candidate antigen-specific antibody sequences. Ten clonal groups of interest were identified through bioinformatic analysis of the heavy chain antibody repertoire of mice immunized with hen egg white lysozyme (HEL). cDNA from eight of the targeted clonal groups was recovered efficiently, leading to the generation of recombinant antibodies. One representative heavy chain sequence from each clonal group recovered was paired with previously reported anti-HEL light chains to generate full antibodies, later tested for HEL-binding capacity. The recovery process proposed represents a simple and scalable molecular strategy that could enhance antibody identification and specificity assessment, enabling a more cost-efficient generation of recombinant antibodies.

Nanobodies and recombinant binders in cell biology

PubMed Central

Helma, Jonas; Cardoso, M. Cristina; Muyldermans, Serge

2015-01-01

Antibodies are key reagents to investigate cellular processes. The development of recombinant antibodies and binders derived from natural protein scaffolds has expanded traditional applications, such as immunofluorescence, binding arrays, and immunoprecipitation. In addition, their small size and high stability in ectopic environments have enabled their use in all areas of cell research, including structural biology, advanced microscopy, and intracellular expression. Understanding these novel reagents as genetic modules that can be integrated into cellular pathways opens up a broad experimental spectrum to monitor and manipulate cellular processes. PMID:26056137

The Genetics of Hybrid Male Sterility Between the Allopatric Species Pair Drosophila persimilis and D. pseudoobscura bogotana: Dominant Sterility Alleles in Collinear Autosomal Regions

PubMed Central

Chang, Audrey S.; Noor, Mohamed A. F.

2007-01-01

F1 hybrid male sterility is thought to result from interactions between loci on the X chromosome and dominant-acting loci on the autosomes. While X-linked loci that contribute to hybrid male sterility have been precisely localized in many animal taxa, their dominant autosomal interactors have been more difficult to localize precisely and/or have been shown to be of relatively smaller effect. Here, we identified and mapped at least four dominant autosomal factors contributing to hybrid male sterility in the allopatric species pair Drosophila persimilis and D. pseudoobscura bogotana. Using these results, we tested predictions of reduced recombination models of speciation. Consistent with these models, three of the four QTL associated with hybrid male sterility occur in collinear (uninverted) regions of these genomes. Furthermore, these QTL do not contribute significantly to hybrid male sterility in crosses between the sympatric species D. persimilis and D. pseudoobscura pseudoobscura. The autosomal loci identified in this study provide the basis for introgression mapping and, ultimately, for molecular cloning of interacting genes that contribute to F1 hybrid sterility. PMID:17277364