相关论文
2007 - Journal of Applied Physics
Recombination activity of interstitial chromium and chromium-boron pairs in silicon

The recombination activity of interstitial chromium (Cri) and pairs of interstitial chromium and substitutional boron (CriBs) in crystalline silicon is studied by combining temperature- and injection-dependent lifetime and deep-level transient spectroscopy measurements on intentionally chromium-contaminated n- and p-type silicon wafers. Cri as well as CriBs pairs are found to be one order of magnitude less recombination active than widely assumed. In the case of Cri, a defect energy level of EC−Et=0.24 eV, an electron capture cross section of σn=2×10−14 cm2, and a hole capture cross section of σp=4×10−15 cm2 are determined. For CriBs pairs, measurements on boron-doped p-type silicon result in Et−EV=0.28 eV, σn=5×10−15 cm2, and σp=1×10−14 cm2. Theoretical calculations using the Shockley–Read–Hall theory show that it depends crucially on the doping concentration whether Cri or CriBs is the more active recombination center. Using a calibration function calculated from the defect parameters determined in this...

1998 - Physics in medicine and biology
Ion recombination corrections for the NACP parallel-plate chamber in a pulsed electron beam.

The NACP electron chamber is one of three parallel-plate chambers recommended for use in the UK. Measurements with this chamber type have indicated a problem in determining the recombination correction. This is due to a variation of the ionization current I with polarizing voltage V which deviates from the accepted Boag theory. It is shown that there is a chamber-dependent threshold voltage below which the NACP chamber follows the Boag theory. Above this voltage the chamber should be used with caution, although it is still possible to correct for the dependence of the chamber response on the dose per pulse. The existence of such deviations from theory demonstrates the usefulness of the 1/I against 1/V plot and the limitations of the Boag two-voltage analysis. Values for the initial recombination and the coefficient of general recombination are measured for several NACP chambers. It is shown that from these one can derive a value for the effective plate separation and the collector radius of each chamber. Differences in the behaviour of NACP chambers manufactured by Scanditronix and Dosetek are discussed and the implications of free-electron collection are considered.

2002 - Genome Biology
Identification and utilization of arbitrary correlations in models of recombination signal sequences

BackgroundA significant challenge in bioinformatics is to develop methods for detecting and modeling patterns in variable DNA sequence sites, such as protein-binding sites in regulatory DNA. Current approaches sometimes perform poorly when positions in the site do not independently affect protein binding. We developed a statistical technique for modeling the correlation structure in variable DNA sequence sites. The method places no restrictions on the number of correlated positions or on their spatial relationship within the site. No prior empirical evidence for the correlation structure is necessary.ResultsWe applied our method to the recombination signal sequences (RSS) that direct assembly of B-cell and T-cell antigen-receptor genes via V(D)J recombination. The technique is based on model selection by cross-validation and produces models that allow computation of an information score for any signal-length sequence. We also modeled RSS using order zero and order one Markov chains. The scores from all models are highly correlated with measured recombination efficiencies, but the models arising from our technique are better than the Markov models at discriminating RSS from non-RSS.ConclusionsOur model-development procedure produces models that estimate well the recombinogenic potential of RSS and are better at RSS recognition than the order zero and order one Markov models. Our models are, therefore, valuable for studying the regulation of both physiologic and aberrant V(D)J recombination. The approach could be equally powerful for the study of promoter and enhancer elements, splice sites, and other DNA regulatory sites that are highly variable at the level of individual nucleotide positions.

1999 - Molecular and Cellular Biology
Detection of RAG Protein-V(D)J Recombination Signal Interactions Near the Site of DNA Cleavage by UV Cross-Linking

ABSTRACT V(D)J recombination is initiated by double-strand cleavage at recombination signal sequences (RSSs). DNA cleavage is mediated by the RAG1 and RAG2 proteins. Recent experiments describing RAG protein-RSS complexes, while defining the interaction of RAG1 with the nonamer, have not assigned contacts immediately adjacent to the site of DNA cleavage to either RAG polypeptide. Here we use UV cross-linking to define sequence- and site-specific interactions between RAG1 protein and both the heptamer element of the RSS and the coding flank DNA. Hence, RAG1-DNA contacts span the site of cleavage. We also detect cross-linking of RAG2 protein to some of the same nucleotides that cross-link to RAG1, indicating that, in the binding complex, both RAG proteins are in close proximity to the site of cleavage. These results suggest how the heptamer element, the recognition surface essential for DNA cleavage, is recognized by the RAG proteins and have implications for the stoichiometry and active site organization of the RAG1-RAG2-RSS complex.

1970 - Solid-state Electronics
The equivalent circuit model in solid-state electronics—III: Conduction and displacement currents

Abstract The equilibrium and nonequilibrium equivalent circuits of a single and a multiple energy level recombination centers were developed in parts I and II. This paper extends the analysis to include the nonequilibrium case arising from a d.c. steady state conduction current in the semiconductor structure. Application is made to minority carrier small signal transport in both homogeneous and heterogeneous semiconductors at low steady state levels ( P « N in n- type sample ) . Samples containing p-n junctions are not included but the effect of static, built-in electric field on the signal propagation is considered. In an extrinsic sample, it is shown that the nonequilibrium equivalent circuit is identical to the equilibrium case for considering carrier trapping, recombination and generation at the defect or impurity centers if the recombination conductances and capacitances are defined in terms of the steady-state carrier concentrations. The conditions on the properties of the imperfection centers and the frequency range in which trapping, recombination or generation event dominates at the centers are discussed in detail. It is shown that the effective small-signal minority carrier lifetime, τp in n-type semiconductor, is a complex variable due to the charge storage or trapping effect at the centers. In addition, τp is positional dependent due to the spatial variation of the steady state carrier concentrations. The small-signal lifetime, τp, is substantially different from the steady state lifetime τpSS which is commonly used in high-frequency, lumped-model device analysis. For strongly extrinsic samples with low concentration of recombination centers, the usual approximation, τ p ⋍ τ pSS ⋍ τ p 0 = 1/c p N TT , is valid. The lump model approximation to a specimen of length W is rigorously derived for minority carrier transport. It is shown that the commonly used stored-charge lump model is valid only at low frequency and zero recombination when the sample is geometrically divided into two or more lumps. For finite recombination, the effective length of each lump is shorter than at zero recombination and the sum of the length of each lump is less than the physical length of the sample.

1996 - Proceedings of the National Academy of Sciences of the United States of America
RecA protein stimulates homologous recombination in plants.

A number of RecA-like proteins have been found in eukaryotic organisms. We demonstrate that the prokaryotic recombination protein RecA itself is capable of interacting with genomic homologous DNA in somatic plant cells. Resistance to the DNA crosslinking agent mitomycin C requires homologous recombination as well as excision repair activity. Tobacco protoplasts expressing a nucleus-targeted RecA protein were at least three times as efficient as wild-type cells in repairing mitomycin C-induced damage. Moreover, homologous recombination at a defined locus carrying an endogenous nuclear marker gene was stimulated at least 10-fold in transgenic plant cells expressing nucleus-targeted RecA. The increase in resistance to mitomycin C and the stimulation of intrachromosomal recombination demonstrate that Escherichia coli RecA protein is functional in genomic homologous recombination in plants, especially when targeted to the plant nucleus.

2017 - Cell reports
BRCA1 Directs the Repair Pathway to Homologous Recombination by Promoting 53BP1 Dephosphorylation.

BRCA1 promotes homologous recombination (HR) by activating DNA-end resection. By contrast, 53BP1 forms a barrier that inhibits DNA-end resection. Here, we show that BRCA1 promotes DNA-end resection by relieving the 53BP1-dependent barrier. We show that 53BP1 is phosphorylated by ATM in S/G2 phase, promoting RIF1 recruitment, which inhibits resection. 53BP1 is promptly dephosphorylated and RIF1 released, despite remaining unrepaired DNA double-strand breaks (DSBs). When resection is impaired by CtIP/MRE11 endonuclease inhibition, 53BP1 phosphorylation and RIF1 are sustained due to ongoing ATM signaling. BRCA1 depletion also sustains 53BP1 phosphorylation and RIF1 recruitment. We identify the phosphatase PP4C as having a major role in 53BP1 dephosphorylation and RIF1 release. BRCA1 or PP4C depletion impairs 53BP1 repositioning, EXO1 recruitment, and HR progression. 53BP1 or RIF1 depletion restores resection, RAD51 loading, and HR in PP4C-depleted cells. Our findings suggest that BRCA1 promotes PP4C-dependent 53BP1 dephosphorylation and RIF1 release, directing repair toward HR.

2008 - The Plant Cell Online
Maize Genome Structure Variation: Interplay between Retrotransposon Polymorphisms and Genic Recombination[W]

Although maize (Zea mays) retrotransposons are recombinationally inert, the highly polymorphic structure of maize haplotypes raises questions regarding the local effect of intergenic retrotransposons on recombination. To examine this effect, we compared recombination in the same genetic interval with and without a large retrotransposon cluster. We used three different bz1 locus haplotypes, McC, B73, and W22, in the same genetic background. We analyzed recombination between the bz1 and stc1 markers in heterozygotes that differ by the presence and absence of a 26-kb intergenic retrotransposon cluster. To facilitate the genetic screen, we used Ds and Ac markers that allowed us to identify recombinants by their seed pigmentation. We sequenced 239 recombination junctions and assigned them to a single nucleotide polymorphism–delimited interval in the region. The genetic distance between the markers was twofold smaller in the presence of the retrotransposon cluster. The reduction was seen in bz1 and stc1, but no recombination occurred in the highly polymorphic intergenic region of either heterozygote. Recombination within genes shuffled flanking retrotransposon clusters, creating new chimeric haplotypes and either contracting or expanding the physical distance between markers. Our findings imply that haplotype structure will profoundly affect the correlation between genetic and physical distance for the same interval in maize.

1997 - Applied Physics Letters
Auger recombination in 4H-SiC: Unusual temperature behavior

The band-to-band Auger recombination in 4H-SiC material is studied using a time-resolved photoinduced absorption technique. The Auger recombination coefficient is derived from the kinetics of electron-hole plasma in heavily doped n-type 4H-SiC and in low-doped 4H-SiC epitaxial layers in the temperature interval 300–565 K. Within this range, its value decreases from γ3=(7±1)×10−31 cm6 s−1 to γ3=(4±1)×10−32 cm6 s−1. The observed pronounced reduction of Auger recombination rate with temperature is correlated to temperature dependent threshold energy of Auger process.

1997 - Plasmid
Minimum length of sequence homology required for in vivo cloning by homologous recombination in yeast.

With efficient homologous recombination in Saccharomyces cerevisiae, a rapid in vivo cloning technique has been available. Here we demonstrated that 30 bp of a homologous sequence at each end of a DNA fragment is sufficient to integrate the fragment into a linearized plasmid in yeast. To obtain a high yield of recombination transformants, however, more than 60 bp are desirable. Interestingly, we observed that 20 bp of homology at one end of a DNA fragment is sufficient for efficient recombination provided that the other end contains 80 bp of homologous sequence. Some applications, including high-throughput transferring of EST inserts to the yeast expression systems for the Human Genome Project, are discussed.

1996 - The EMBO journal
SMC proteins constitute two subunits of the mammalian recombination complex RC‐1.

Recombination protein complex RC‐1, purified from calf thymus nuclear extracts, catalyzes cell‐free DNA strand transfer and repair of gaps and deletions through DNA recombination. DNA polymerase E, DNA ligase III and a DNA structure‐specific endonuclease co‐purify with the five polypeptide complex. Here we describe the identification of two hitherto unknown subunits of RC‐1. N‐terminal amino acid sequences of the 160 and 130 kDa polypeptides display up to 100% identity to proteins of the structural maintenance of chromosomes (SMC) subfamilies 1 and 2. SMC proteins are involved in mitotic chromosome segregation and condensation, as well as in certain DNA repair pathways in fission (rad18 gene) and budding (RHC18 gene) yeast. The assignment was substantiated by immuno‐cross‐reactivity of the RC‐1 subunits with polyclonal antibodies specific for Xenopus laevis SMC proteins. These antibodies, and polyclonal antibodies directed against the bovine 160 and 130 kDa polypeptides, named BSMC1 and BSMC2 (bovine SMC), inhibited RC‐1‐mediated DNA transfer, indicating that the SMC proteins are necessary components of the reaction. Two independent assays revealed DNA reannealing activity of RC‐1, which resides in its BSMC subunits, thereby demonstrating a novel function of these proteins. To our knowledge, this is the first evidence for the association of mammalian SMC proteins with a multiprotein complex harboring, among others, DNA recombination, DNA ligase and DNA polymerase activities.

1997 - American journal of human genetics
Characterization of recombination in the HLA class II region.

Studies of linkage disequilibrium across the HLA class II region have been useful in predicting where recombination is most likely to occur. The strong associations between genes within the 85-kb region from DQB1 to DRB1 are consistent with low frequency of recombination in this segment of DNA. Conversely, a lack of association between alleles of TAP1 and TAP2 (approximately 15 kb) has been observed, suggesting that recombination occurs here with relatively high frequency. Much of the HLA class II region has now been sequenced, providing the tools to undertake detailed analysis of recombination. Twenty-seven families containing one or two recombinant chromosomes within the 500-kb interval between the DPB1 and DRB1 genes were used to determine patterns of recombination across this region. SSCP analysis and microsatellite typing yielded identification of 127 novel polymorphic markers distributed throughout the class II region, allowing refinement of the site of crossover in 30 class II recombinant chromosomes. The three regions where recombination was observed most frequently are as follows: the 45-kb interval between HLA-DNA and RING3 (11 cases), the 50-kb interval between DQB3 and DQB1 (6 cases), and an 8.8-kb segment of the TAP2 gene (3 cases). Six of the 10 remaining recombinants await further characterization, pending identification of additional informative markers, while four recombinants were localized to other intervals (outliers). Analysis of association between markers flanking HLA-DNA to RING3 (45 kb), as well as TAP1 to TAP2 (15 kb), by use of independent CEPH haplotypes indicated little or no linkage disequilibrium, supporting the familial recombination data. A notable sequence motif located within a region associated with increased rates of recombination consisted of a (TGGA)12 tandem repeat within the TAP2 gene.

2014
Minority carrier lifetime in silicon photovoltaics: The effect of oxygen precipitation

Single-crystal Czochralski silicon used for photovoltaics is typically supersaturated with interstitial oxygen at temperatures just below the melting point. Oxide precipitates therefore can form during ingot cooling and cell processing, and nucleation sites are typically vacancy-rich regions. Oxygen precipitation gives rise to recombination centres, which can reduce cell efficiencies by as much as 4% (absolute). We have studied the recombination behaviour in p-type and n-type monocrystalline silicon with a range of doping levels intentionally processed to contain oxide precipitates with a range of densities, sizes and morphologies. We analyse injection-dependent minority carrier lifetime measurements to give a full parameterisation of the recombination activity in terms of Shockley–Read–Hall statistics. We intentionally contaminate specimens with iron, and show recombination activity arises from iron segregated to oxide precipitates and surrounding defects. We find that phosphorus diffusion gettering reduces the recombination activity of the precipitates to some extent. We also find that bulk iron is preferentially gettered to the phosphorus diffused layer rather than to oxide precipitates. & 2013 The Authors. Published by Elsevier B.V.Open access under CC BY license.

2010 - Applied Physics Letters
Carrier recombination mechanisms and efficiency droop in GaInN/GaN light-emitting diodes

We model the carrier recombination mechanisms in GaInN/GaN light-emitting diodes as R=An+Bn2+Cn3+f(n), where f(n) represents carrier leakage out of the active region. The term f(n) is expanded into a power series and shown to have higher-than-third-order contributions to the recombination. The total third-order nonradiative coefficient (which may include an f(n) leakage contribution and an Auger contribution) is found to be 8×10−29 cm6 s−1. Comparison of the theoretical ABC+f(n) model with experimental data shows that a good fit requires the inclusion of the f(n) term.

1962 - Advances in Genetics
Linkage and Recombination in Evolution

Publisher Summary This chapter discusses the linkage and recombination in evolution. The discovery of large amounts of naturally occurring genetic variability is one of the most striking features of modern evolutionary studies. The immediate fitness of a species depends on a certain uniformity of the genotype whereas long-term survival depends on the production of adequate genetic variability. The diverse environmental agencies alter recombination and interference. Maternal age and sex also affect recombination. Artificia1 alteration of the genetic background by selection or inbreeding frequently changes recombination. In micro-organisms, diverse alternatives to the sexual system exist for the promotion of genetic recombination, such as transduction, transformation, and the quasi-sexual mating system of Escherichia coli and the parasexual cycle of the filamentous fungi. These systems provide ample opportunity for recombination. In some microorganisms, cases of linked blocks of genes controlling closely related biochemical reactions occur. Classical linkage experiments were done under diverse environmental conditions and differing genetic backgrounds provide abundant evidence for the variability of recombination. The effect of temperature on recombination is the best studied variable. Recombination frequencies and chiasma frequencies are affected by differences of temperature, age, genetic background, and other variables.

2000 - Genetics
The correlation between intron length and recombination in drosophila. Dynamic equilibrium between mutational and selective forces.

Intron length is negatively correlated with recombination in both Drosophila melanogaster and humans. This correlation is not likely to be the result of mutational processes alone: evolutionary analysis of intron length polymorphism in D. melanogaster reveals equivalent ratios of deletion to insertion in regions of high and low recombination. The polymorphism data do reveal, however, an excess of deletions relative to insertions (i.e., a deletion bias), with an overall deletion-to-insertion events ratio of 1.35. We propose two types of selection favoring longer intron lengths. First, the natural mutational bias toward deletion must be opposed by strong selection in very short introns to maintain the minimum intron length needed for the intron splicing reaction. Second, selection will favor insertions in introns that increase recombination between mutations under the influence of selection in adjacent exons. Mutations that increase recombination, even slightly, will be selectively favored because they reduce interference among selected mutations. Interference selection acting on intron length mutations must be very weak, as indicated by frequency spectrum analysis of Drosophila intron length polymorphism, making the equilibrium for intron length sensitive to changes in the recombinational environment and population size. One consequence of this sensitivity is that the advantage of longer introns is expected to decrease inversely with the rate of recombination, thus leading to a negative correlation between intron length and recombination rate. Also in accord with this model, intron length differs between closely related Drosophila species, with the longest variant present more often in D. melanogaster than in D. simulans. We suggest that the study of the proposed dynamic model, taking into account interference among selected sites, might shed light on many aspects of the comparative biology of genome sizes including the C value paradox.

1998 - Molecular and Cellular Biology
Homologous Recombination, but Not DNA Repair, Is Reduced in Vertebrate Cells Deficient in RAD52

ABSTRACT Rad52 plays a pivotal role in double-strand break (DSB) repair and genetic recombination in Saccharomyces cerevisiae, where mutation of this gene leads to extreme X-ray sensitivity and defective recombination. Yeast Rad51 and Rad52 interact, as do their human homologues, which stimulates Rad51-mediated DNA strand exchange in vitro, suggesting that Rad51 and Rad52 act cooperatively. To define the role of Rad52 in vertebrates, we generatedRAD52−/− mutants of the chicken B-cell line DT40. Surprisingly, RAD52 −/− cells were not hypersensitive to DNA damages induced by γ-irradiation, methyl methanesulfonate, or cis-platinum(II)diammine dichloride (cisplatin). Intrachromosomal recombination, measured by immunoglobulin gene conversion, and radiation-induced Rad51 nuclear focus formation, which is a putative intermediate step during recombinational repair, occurred as frequently inRAD52 −/− cells as in wild-type cells. Targeted integration frequencies, however, were consistently reduced inRAD52 −/− cells, showing a clear role for Rad52 in genetic recombination. These findings reveal striking differences between S. cerevisiae and vertebrates in the functions of RAD51 and RAD52.

2007 - The Journal of Immunology
TLR9 Signaling in B Cells Determines Class Switch Recombination to IgG2a

Although IgG2a is the most potent Ab isotype in the host response to viral and bacterial infections, the regulation of class switch recombination to IgG2a in vivo is not yet well understood. Recognition of pathogen-associated molecular patterns by dendritic cells expressing TLRs, like TLR7, recognizing ssRNA, or TLR9, recognizing DNA rich in nonmethylated CG motifs (CpG), favors induction of Th1 responses. It is generally assumed that these Th1 responses are responsible for the TLR-mediated induction of IgG2a. Using virus-like particles loaded with CpGs, we show here that TLR9 ligands can directly stimulate B cells to undergo isotype switching to IgG2a. Unexpectedly, TLR9 expression in non-B cells did not affect isotype switching in the Ab response against virus-like particles. Thus, TLR9 can regulate isotype switching to IgG2a directly by interacting with B cells rather than indirectly by inducing Th1 responses.

2008 - PLoS Genetics
The Impact of Recombination on Nucleotide Substitutions in the Human Genome

Unraveling the evolutionary forces responsible for variations of neutral substitution patterns among taxa or along genomes is a major issue for detecting selection within sequences. Mammalian genomes show large-scale regional variations of GC-content (the isochores), but the substitution processes at the origin of this structure are poorly understood. We analyzed the pattern of neutral substitutions in 1 Gb of primate non-coding regions. We show that the GC-content toward which sequences are evolving is strongly negatively correlated to the distance to telomeres and positively correlated to the rate of crossovers (R2 = 47%). This demonstrates that recombination has a major impact on substitution patterns in human, driving the evolution of GC-content. The evolution of GC-content correlates much more strongly with male than with female crossover rate, which rules out selectionist models for the evolution of isochores. This effect of recombination is most probably a consequence of the neutral process of biased gene conversion (BGC) occurring within recombination hotspots. We show that the predictions of this model fit very well with the observed substitution patterns in the human genome. This model notably explains the positive correlation between substitution rate and recombination rate. Theoretical calculations indicate that variations in population size or density in recombination hotspots can have a very strong impact on the evolution of base composition. Furthermore, recombination hotspots can create strong substitution hotspots. This molecular drive affects both coding and non-coding regions. We therefore conclude that along with mutation, selection and drift, BGC is one of the major factors driving genome evolution. Our results also shed light on variations in the rate of crossover relative to non-crossover events, along chromosomes and according to sex, and also on the conservation of hotspot density between human and chimp.

1998
Resource recombinations in the firm: knowledge structures and the potential for schumpeterian innovation

Building on the resource-based view of the firm, this paper explores the notion of ‘resource recombinations’ within the firm. We suggest such recombinations can occur when competencies within the firm (which are interpreted as organized clusters of firm resources) either combine to synthesize novel competencies (synthesis-based recombinations) or experience a reconfiguration or relinking with other competencies (reconfiguration-based recombinations). Central to this paper is an examination of the antecedents necessary for such innovation to occur, and in particular the nature of knowledge in the firm. We argue that several characteristics of knowledge (tacitness, context specificity, dispersion) and its social organization (the way competencies come to be formed and institutionalized) will have important consequences on the likelihoods of resource recombinations. Our paper develops a model of resource recombination likelihoods and propositions. © 1998 John Wiley & Sons, Ltd.

RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination.

D. Schatz
|
D. Baltimore
|
M. Oettinger
|
D Baltimore
|
C. Gorka
|
D G Schatz
|
M A Oettinger
|
C Gorka

Abstract:The vast repertoire of immunoglobulins and T cell receptors is generated, in part, by V(D)J recombination, a series of genomic rearrangements that occur specifically in developing lymphocytes. The recombination activating gene, RAG-1, which is a gene expressed exclusively in maturing lymphoid cells, was previously isolated. RAG-1 inefficiently induced V(D)J recombinase activity when transfected into fibroblasts, but cotransfection with an adjacent gene, RAG-2, has resulted in at least a 1000-fold increase in the frequency of recombination. The 2.1-kilobase RAG-2 complementary DNA encodes a putative protein of 527 amino acids whose sequence is unrelated to that of RAG-1. Like RAG-1, RAG-2 is conserved between species that carry out V(D)J recombination, and its expression pattern correlates precisely with that of V(D)J recombinase activity. In addition to being located just 8 kilobases apart, these convergently transcribed genes are unusual in that most, if not all, of their coding and 3' untranslated sequences are contained in single exons. RAG-1 and RAG-2 might activate the expression of the V(D)J recombinase but, more likely, they directly participate in the recombination reaction.

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Modern Prometheus: Editing the Human Genome with Crispr-Cas9
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1999
RAG-1 and RAG-2-dependent assembly of functional complexes with V(D)J recombination substrates in solution
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