Developments on Perovskite Solar Cells (PSCs): A Critical Review

This review provides detailed information on perovskite solar cell device background and monitors stepwise scientific efforts applied to improve device performance with time. The work reviews previous studies and the latest developments in the perovskite crystal structure, electronic structure, device architecture, fabrication methods, and challenges. Advantages, such as easy bandgap tunability, low charge recombination rates, and low fabrication cost, are among the topics discussed. Some of the most important elements highlighted in this review are concerns regarding commercialization and prototyping. Perovskite solar cells are generally still lab-based devices suffering from drawbacks such as device intrinsic and extrinsic instabilities and rising environmental concerns due to the use of the toxic inorganic lead (Pb) element in the perovskite (ABX3) light-active material. Some interesting recommendations and possible future perspectives are well articulated.

High homozygosity of inversions in sunflower species largely averts accumulation of deleterious mutations

Recombination is critical both for accelerating adaptation and for the purging of deleterious mutations. Chromosomal inversions can act as recombination modifiers that suppress local recombination and, thus, are predicted to accumulate such mutations. In this study, we investigated patterns of recombination, transposable element abundance and coding sequence evolution across the genomes of 1,445 individuals from three sunflower species, as well as within nine inversions segregating within species. We also analyzed the effects of inversion genotypes on 87 phenotypic traits to test for overdominance. We found significant negative correlations of long terminal repeat retrotransposon abundance and deleterious mutations with recombination rates across the genome in all three species. However, we failed to detect an increase in these features in the inversions, except for a modest increase in the proportion of stop codon mutations in several very large or rare inversions. Moreover, there was little evidence of phenotypic overdominance in inversion heterozygotes, consistent with observations of minimal deleterious load. On the other hand, significantly greater load was observed for inversions in populations polymorphic for a given inversion compared to populations monomorphic for one of the arrangements, suggesting that the local state of inversion polymorphism affects deleterious load. These seemingly contradictory results can be explained by the geographic structuring and consequent excess homozygosity of inversions in wild sunflowers. Inversions contributing to local adaptation often exhibit geographic structure; such inversions represent ideal recombination modifiers, acting to facilitate adaptive divergence with gene flow, while largely averting the accumulation of deleterious mutations due to recombination suppression.

A comparative study of different emitter diffusion profiles on the performance of Si solar cells

We have investigated the effect of emitter design key parameters such as depth factor and the peak concentration for different types of emitter diffusion profiles (uniform, exponential, Gaussian, and Erfc) on the performance of silicon (Si) solar cells. The value of the depth factor is optimized as 0.1 µm for all these emitter diffusion profiles. Afterward, the peak concentration value is optimized for all the diffusion profiles. A close examination of relative diffusion lengths, conductivities, recombination rates, internal and external quantum efficiencies for these diffusion profiles revealed that among all the considered emitter diffusion profiles, the Erfc profile exhibits the maximum efficiency of 23.53% with an optimized peak concentration of 2×1020 cm-3 for emitter and 1×1019 cm-3 for the back surface filed doping. PC1D was used for all the simulations.

Tree House Explorer: A Novel Genome Browser for Phylogenomics

Tree House Explorer (THEx) is a genome browser that integrates phylogenomic data and genomic annotations into a single interactive platform for combined analysis. THEx allows users to visualize genome-wide variation in evolutionary histories and genetic divergence on a chromosome-by-chromosome basis, with continuous sliding window comparisons to gene annotations, recombination rates, and other user-specified, highly customizable feature annotations. THEx provides a new platform for interactive phylogenomic data visualization to analyze and interpret the diverse evolutionary histories woven throughout genomes. Hosted on Conda, THEx integrates seamlessly into new or pre-existing workflows.

A Consensus Genetic Map and Linkage Panel for Fresh-market Tomato

The first consensus genetic map in fresh-market tomato (Solanum lycopersicum) was constructed, combining genetic recombination data from two biparental F2 segregating populations derived from four different fresh-market tomatoes. Each F2 population was nominated by different academic tomato breeding programs located in major fresh-market tomato-producing areas of the United States, and chromosome-wide variation in recombination rates was observed between tomato populations based on the origin of their breeding programs. A consensus map constructed using 335 common single nucleotide polymorphism (SNP) sites found in both populations spanned 737.3 cM across 12 tomato chromosomes, with chromosome 2 containing more than 40% of the total SNPs and chromosomes 4, 5, 7, and 10 together representing less than 10% of the SNPs. There was a high degree of collinearity between the genetic and physical positions of those 335 SNP markers. The integration of 6553 SNP sites that were detected in either of the two populations with 335 common sites resulted in an extended consensus genetic map. The total length of the extended map was estimated to be 1997.9 cM, which was compatible with a previous estimate for large-fruited fresh-market tomato. A linkage panel for fresh-market tomato was also established using the combined dataset of the consensus map of 335 SNP loci and 73 SNP-genotyped core fresh-market tomatoes. An empirical genetic mapping study of the tomato brachytic trait using the linkage panel demonstrated the value of the consensus map and linkage panel for tomato research. The allelic information in the linkage panel will serve as a basis for SNP marker implementation, such as genotyping platforms and genomic association map, in tomato.

The relative strength of selection on modifiers of genetic architecture under migration load

Gene flow between populations adapting to differing local environmental conditions creates a "migration load" because individuals might disperse to habitats where their survival is low or because they might reproduce with locally maladapted individuals. The amount by which the mean relative population fitness is kept below one creates an opportunity for modifiers of the genetic architecture to spread due to selection. Prior work that separately considered modifiers changing dispersal or recombination rates, or altering dominance or epistasis, has typically focused on the direction of selection rather than its absolute magnitude. We here develop methods to determine the strength of selection on modifiers of the genetic architecture, including modifiers of the dispersal rate, after populations evolved local adaptation. We consider scenarios with up to five loci contributing to local adaptation and derive a matrix model for the deterministic spread of modifiers. We find that selection for modifiers of epistasis and dominance is stronger than selection for decreased recombination, and that selection for partial reductions in recombination are extremely weak, regardless of the number of loci contributing to local adaptation. The spread of modifiers for a reduction in dispersal depends on the number of loci, pre-existing epistasis and extent of migration load. We identify a novel effect, that modifiers of dominance are more strongly selected when they are unlinked to the locus that they modify. Overall, these results help explain population differentiation and reproductive isolation and provide a benchmark to compare selection on genetic architecture modifiers in finite population sizes and under demographic stochasticity.

High Recombination Rate of Hepatitis C Virus Revealed by a Green Fluorescent Protein Reconstitution Cell System

Genetic recombination is an important evolutionary mechanism for RNA viruses and can facilitate escape from immune and drug pressure. Recombinant hepatitis C virus (HCV) variants have rarely been detected in patients, suggesting that HCV has intrinsic low recombination rate. Recombination of HCV has been demonstrated in vitro between non-functional genomes, but its frequency and relevance for viral evolution and life cycle has not been clarified. We developed a cell-based assay to detect and quantify recombination between fully viable HCV genomes, using the reconstitution of green fluorescent protein (GFP) as a surrogate marker for recombination. Here, two GFP-expressing HCV genomes carrying different inactivating GFP mutations can produce a virus carrying a functional GFP by recombining within the GFP region. Generated constructs allowed quantification of recombination rates between markers spaced 603 and 553 nucleotides apart by flow cytometry and next-generation sequencing (NGS). Viral constructs showed comparable spread kinetics and reached similar infectivity titers in Huh7.5 cells, allowing their use in co-transfections and co-infections. Single cycle co-transfection experiments, performed in CD81-deficient S29 cells, showed GFP expression in double-infected cells, demonstrating genome mixing and occurrence of recombination. Quantification of recombinant genomes by NGS revealed an average rate of 6.1%, corresponding to 49% of maximum detectable recombination (MDR). Experiments examining recombination during the full replication cycle of HCV, performed in Huh7.5 cells, demonstrated average recombination rates of 5.0 % (40.0% MDR) and 3.6% (28.8% MDR) for markers spaced by 603 and 553 nucleotides, respectively, supporting a linear relationship between marker distance and recombination rates. First passage infections using recombinant virus supernatant resulted in comparable recombination rates of 5.9% (47.2% MDR) and 3.5% (28.0% MDR), respectively, for markers spaced by 603 and 553 nucleotides. We developed a functional cell-based assay that, to our knowledge, allows for the first-time detailed quantification of recombination rates using fully viable HCV constructs. Our data indicate that HCV recombines at high frequency between highly similar genomes, and that the frequency of recombination increases with the distance between marker sites. These results have implication for our understanding of HCV evolution and emphasize the importance of recombination in the reassortment of mutations in the HCV genome.

Background selection under evolving recombination rates

Background selection (BGS), the effect that purifying selection exerts on sites linked to deleterious alleles, is expected to be ubiquitous across eukaryotic genomes. The effects of BGS reflect the interplay of the rates and fitness effects of deleterious mutations with recombination. A fundamental assumption of BGS models is that recombination rates are invariant over time. However, in some lineages recombination rates evolve rapidly, violating this central assumption. Here, we investigate how recombination rate evolution affects genetic variation under BGS. We show that recombination rate evolution modifies the effects of BGS in a manner similar to a localised change in the effective population size, potentially leading to an underestimation of the genome-wide effects of selection. Furthermore, we find evidence that recombination rate evolution in the ancestors of modern house mice may have impacted inferences of the genome-wide effects of selection in that species.

No support for a meiosis suppressor in Daphnia pulex: Comparison of linkage maps reveals normal recombination in males of obligate parthenogenetic lineages.

It is often assumed that obligate parthenogenesis (OP) evolves by a disruption of meiosis and recombination. One emblematic example that appears to support this view is the crustacean Daphnia pulex. Here, by constructing high-density linkage maps, we estimate genome-wide recombination rates in males that are occasionally produced by OP lineages, as well as in males and females of cyclical parthenogenetic (CP) lineages. The results show no significant differences in recombination rates and patterns between CP and OP males nor between CP males and CP females. The observation that recombination is not suppressed in OP males invalidates the hypothesis of a general meiosis suppressor responsible for OP. Rather, our findings suggest that in D. pulex, as in other species where OP evolves from CP ancestors, the CP to OP transition evolves through a re-use of the parthenogenesis pathways already present in CP and through their extension to the entire life cycle, at least in females. In addition to the implications for the evolution of OP, the genetic maps produced by this study constitute an important genomic resource for the model species Daphnia.