Scientific Reports 6: Article number: 23934; published online: 31 March 2016; updated: 7 December 2016; updated: 10 November 2017; updated: 20 March 2018 This Article reports an application of ...methodology originally reported in Reference 33 to recombination spot identification. Reference 33 (Ghandi,M.
Coevolution between transposable elements and recombination Kent, Tyler V.; Uzunović, Jasmina; Wright, Stephen I.
Philosophical transactions of the Royal Society of London. Series B. Biological sciences,
12/2017, Volume:
372, Issue:
1736
Journal Article
Peer reviewed
Open access
One of the most striking patterns of genome structure is the tight, typically negative, association between transposable elements (TEs) and meiotic recombination rates. While this is a highly ...recurring feature of eukaryotic genomes, the mechanisms driving correlations between TEs and recombination remain poorly understood, and distinguishing cause versus effect is challenging. Here, we review the evidence for a relation between TEs and recombination, and discuss the underlying evolutionary forces. Evidence to date suggests that overall TE densities correlate negatively with recombination, but the strength of this correlation varies across element types, and the pattern can be reversed. Results suggest that heterogeneity in the strength of selection against ectopic recombination and gene disruption can drive TE accumulation in regions of low recombination, but there is also strong evidence that the regulation of TEs can influence local recombination rates. We hypothesize that TE insertion polymorphism may be important in driving within-species variation in recombination rates in surrounding genomic regions. Furthermore, the interaction between TEs and recombination may create positive feedback, whereby TE accumulation in non-recombining regions contributes to the spread of recombination suppression. Further investigation of the coevolution between recombination and TEs has important implications for our understanding of the evolution of recombination rates and genome structure.
This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.
Characterisation and optimization of next-generation silicon solar cell concepts rely on an accurate knowledge of intrinsic charge carrier recombination in crystalline silicon. Reports of measured ...lifetimes exceeding the previous accepted parameterisation of intrinsic recombination indicate an overestimation of this recombination in certain injection regimes and hence the need for revision. In this work, twelve high-quality silicon sample sets covering a wide doping range are fabricated using state-of-the-art processing routes in order to permit an accurate assessment of intrinsic recombination based on wafer thickness variation. Special care is taken to mitigate extrinsic recombination due to bulk contamination or at the wafer surfaces. The combination of the high-quality samples with refined sample characterisation and lifetime measurements enables a much higher level of accuracy to be achieved compared to previous studies. We observe that reabsorption of luminescence photons inside the sample must be accounted for to achieve a precise description of radiative recombination. With this effect taken into account, we extract the lifetime limitation due to Auger recombination. We find that the extracted Auger recombination rate can accurately be parameterized using a physically motivated equation based on Coulomb-enhanced Auger recombination for all doping and injection conditions relevant for silicon-based photovoltaics. The improved accuracy of data description obtained with the model suggests that our new parameterisation is more consistent with the actual recombination process than previous models. Due to notable changes in Auger recombination predicted for moderate injection, we further revise the fundamental limiting power conversion efficiency for a single-junction crystalline silicon solar cell to 29.4%, which is within 0.1%abs compared to other recent assessments.
•Previous models for intrinsic recombination in silicon are not sufficient for current needs.•Reabsorption of luminescence photons inside the sample can significantly impact experimentally assessable carrier lifetimes.•The presented experiment features twelve sample sets with state-of-the-art surface passivation and wafer thickness variation.•A new model for Auger recombination is derived and presented.•The new model is used to reassess the theoretical efficiency limit of single junction silicon solar cells to 29.4%.
Owing to their sessile nature, plants are constantly exposed to a multitude of environmental stresses to which they react with a battery of responses. The result is plant tolerance to conditions such ...as excessive or inadequate light, water, salt and temperature, and resistance to pathogens. Not only is plant physiology known to change under abiotic or biotic stress, but changes in the genome have also been identified. However, it was not determined whether plants from successive generations of the original, stressed plants inherited the capacity for genomic change. Here we show that in Arabidopsis thaliana plants treated with short-wavelength radiation (ultraviolet-C) or flagellin (an elicitor of plant defences), somatic homologous recombination of a transgenic reporter is increased in the treated population and these increased levels of homologous recombination persist in the subsequent, untreated generations. The epigenetic trait of enhanced homologous recombination could be transmitted through both the maternal and the paternal crossing partner, and proved to be dominant. The increase of the hyper-recombination state in generations subsequent to the treated generation was independent of the presence of the transgenic allele (the recombination substrate under consideration) in the treated plant. We conclude that environmental factors lead to increased genomic flexibility even in successive, untreated generations, and may increase the potential for adaptation.
The presence of non‐radiative recombination at the perovskite surface/interface limits the overall efficiency of perovskite solar cells (PSCs). Surface passivation has been demonstrated as an ...efficient strategy to suppress such recombination in Si cells. Here, 1‐naphthylmethylamine iodide (NMAI) is judiciously selected to passivate the surface of the perovskite film. In contrast to the popular phenylethylammonium iodide, NMAI post‐treatment primarily leaves NMAI salt on the surface of the perovskite film. The formed NMAI layer not only efficiently decreases the defect‐assisted recombination for chemical passivation, but also retards the charge accumulation of energy level mis‐alignment for vacuum level bending and prevents minority carrier recombination due to the charge‐blocking effect. Consequently, planar PSCs with high efficiency of 21.04% and improved long‐term stability (98.9% of the initial efficiency after 3240 h) are obtained. Moreover, open‐circuit voltage as high as 1.20 V is achieved at the absorption threshold of 1.61 eV, which is among the highest reported values in planar PSCs. This work provides new insights into the passivation mechanisms of organic ammonium salts and suggests future guidelines for developing improved passivation layers.
A unique ammonium salt, 1‐naphthylmethylamine iodide (NMAI) is shown to passivate the surface defects of perovskite, induce upward energy level bending and block electrons at the interface between the perovskite and hole transport layer in perovskite solar cells. These combined effects result in reduced non‐radiative recombination. Hence, more intensified electroluminescence and a champion open‐circuit voltage of 1.20 V are achieved in NMAI‐based devices.
•Detailed balance limit of performances of solar cell is estimated.•Auger recombination is considered for practical detailed balance limit.•VOC of perovskite cells is mainly reduced with increasing ...Auger coefficient (Cp).•Cp of perovskites is lower than 1 × 10−31 cm6.s−1 to avoid Auger recombination.•Effect of Shockley-Read-Hall recombination is discussed.
Theoretical limit (or detailed balance limit) of photovoltaic performances of single-junction solar cell was estimated under consideration of radiative recombination, where the solar cell was assumed as blackbody with temperature (T) of 298.15 K. The detailed balance limit of the perovskite solar cell is furthermore calculated under considerations of not only radiative recombination but also Auger recombination. It is revealed that open-circuit voltage (VOC) is primarily reduced with increasing the intrinsic density (ni) and Auger recombination coefficient (Cp), thus decreasing the conversion efficiency (η). Under the Eg of 1.55 eV and ni of 1 × 107 cm−3, the η of perovskite solar cell is reduced from 31.41% (without Auger recombination consideration) to 28.92% with the increased Cp to 1 × 10−29 cm6.s−1. According to the result, the Cp should be lower than 1 × 10−31 cm6.s−1 to avoid the impact of Auger recombination for the improved performances of perovskite solar cells, where it is suggested that the Cp can be reduced through band-structure engineering and alloying with other halide perovskites, thereby providing the avenues for material design. Furthermore, the effect of Shockley-Read-Hall recombination in the perovskite solar cell on its efficiency limit is discussed.
Meiotic recombination is an essential feature of sexual reproduction that ensures faithful segregation of chromosomes and redistributes genetic variants in populations. Multiparent populations such ...as the Diversity Outbred (DO) mouse stock accumulate large numbers of crossover (CO) events between founder haplotypes, and thus present a unique opportunity to study the role of genetic variation in shaping the recombination landscape. We obtained high-density genotype data from Formula: see text DO mice, and localized 2.2 million CO events to intervals with a median size of 28 kb. The resulting sex-averaged genetic map of the DO population is highly concordant with large-scale (order 10 Mb) features of previously reported genetic maps for mouse. To examine fine-scale (order 10 kb) patterns of recombination in the DO, we overlaid putative recombination hotspots onto our CO intervals. We found that CO intervals are enriched in hotspots compared to the genomic background. However, as many as Formula: see text of CO intervals do not overlap any putative hotspots, suggesting that our understanding of hotspots is incomplete. We also identified coldspots encompassing 329 Mb, or Formula: see text of observable genome, in which there is little or no recombination. In contrast to hotspots, which are a few kilobases in size, and widely scattered throughout the genome, coldspots have a median size of 2.1 Mb and are spatially clustered. Coldspots are strongly associated with copy-number variant (CNV) regions, especially multi-allelic clusters, identified from whole-genome sequencing of 228 DO mice. Genes in these regions have reduced expression, and epigenetic features of closed chromatin in male germ cells, which suggests that CNVs may repress recombination by altering chromatin structure in meiosis. Our findings demonstrate how multiparent populations, by bridging the gap between large-scale and fine-scale genetic mapping, can reveal new features of the recombination landscape.
Synthetic lethality is an approach to study selective cell killing based on genotype. Previous work in our laboratory has shown that loss of RAD52 is synthetically lethal with BRCA2 deficiency, while ...exhibiting no impact on cell growth and viability in BRCA2-proficient cells. We now show that this same synthetically lethal relationship is evident in cells with deficiencies in BRCA1 or PALB2, which implicates BRCA1, PALB2 and BRCA2 in an epistatic relationship with one another. When RAD52 was depleted in BRCA1- or PALB2-deficient cells, a severe reduction in plating efficiency was observed, with many abortive attempts at cell division apparent in the double-depleted background. In contrast, when RAD52 was depleted in a BRCA1- or PALB2-wildtype background, a negligible decrease in colony survival was observed. The frequency of ionizing radiation-induced RAD51 foci formation and double-strand break-induced homologous recombination (HR) was decreased by 3- and 10-fold, respectively, when RAD52 was knocked down in BRCA1- or PALB2-depleted cells, with minimal effect in BRCA1- or PALB2-proficient cells. RAD52 function was independent of BRCA1 status, as evidenced by the lack of any defect in RAD52 foci formation in BRCA1-depleted cells. Collectively, these findings suggest that RAD52 is an alternative repair pathway of RAD51-mediated HR, and a target for therapy in cells deficient in the BRCA1-PALB2-BRCA2 repair pathway.
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