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  1. Real-time detection of intermediate species and final products at the surface and near-surface in interfacial solid–gas reactions is critical for an accurate understanding of heterogeneous reaction mechanisms. In this article, an experimental method that can simultaneously monitor the ultrafast dynamics at the surface and above the surface in photoinduced heterogeneous reactions is presented. This method relies on a combination of mass spectrometry and femtosecond pump–probe spectroscopy. As a model system, the photoinduced reaction of methyl iodide on and above a cerium oxide surface is investigated. The species that are simultaneously detected from the surface and gas-phase present distinct features in the mass spectra, such as a sharp peak followed by an adjacent broad shoulder. The sharp peak is attributed to the species detected from the surface, while the broad shoulder is due to the detection of gas-phase species above the surface, as confirmed by multiple experiments. By monitoring the evolution of the sharp peak and broad shoulder as a function of the pump–probe time delay, transient signals are obtained that describe the ultrafast photoinduced reaction dynamics of methyl iodide on the surface and in the gas-phase. Finally, SimION simulations are performed to confirm the origin of the ions produced on the surface and in the gas-phase.

     
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    Free, publicly-accessible full text available August 1, 2025
  2. Real-time detection of intermediate species and final products at the surface and near-surface in interfacial solid-gas reactions is critical for an accurate understanding of heterogeneous reaction mechanisms. In this contribution, an experimental method that can simultaneously monitor the ultrafast dynamics at the surface and above the surface in photoinduced heterogeneous reactions is presented. The method relies on a combination of mass spectrometry and femtosecond pump-probe spectroscopy. As a model system, the photoinduced reaction of methyl iodide on and above a cerium oxide surface is investigated. The species that are simultaneously detected from the surface and gas-phase present distinct features in the mass spectra, such as a sharp peak followed by an adjacent broad shoulder. The sharp peak is attributed to the species detected from the surface while the broad shoulder is due to the detection of gas-phase species above the surface, as confirmed by multiple experiments. By monitoring the evolution of the sharp peak and broad shoulder as a function of the pump-probe time delay, transient signals are obtained that describe the ultrafast photoinduced reaction dynamics of methyl iodide on the surface and in gas-phase. Finally, SimION simulations are performed to confirm the origin of the ions produced on the surface and gas-phase.

     
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    Free, publicly-accessible full text available May 9, 2025
  3. Identifying genetic loci underlying trait variation provides insights into the mechanisms of diversification, but demonstrating causality and characterizing the role of genetic loci requires testing candidate gene function, often in non-model species. Here we establish CRISPR/Cas9 editing in Astatotilapia calliptera , a generalist cichlid of the remarkably diverse Lake Malawi radiation. By targeting the gene oca2 required for melanin synthesis in other vertebrate species, we show efficient editing and germline transmission. Gene edits include indels in the coding region, probably a result of non-homologous end joining, and a large deletion in the 3′ untranslated region due to homology-directed repair. We find that oca2 knock-out A. calliptera lack melanin, which may be useful for developmental imaging in embryos and studying colour pattern formation in adults. As A. calliptera resembles the presumed generalist ancestor of the Lake Malawi cichlid radiation, establishing genome editing in this species will facilitate investigating speciation, adaptation and trait diversification in this textbook radiation. 
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  4. null (Ed.)
    Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species 1–4 . To address this issue, the international Genome 10K (G10K) consortium 5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences. 
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