Next-generation in vivo optical imaging with short-wave infrared quantum dots

The short-wavelength infrared region (SWIR; 1000—2000 nm) provides several advantages over the visible and near-infrared regions for in vivo imaging. The general lack of autofluorescence, low light absorption by blood and tissue, and reduced scattering can render a mouse translucent when imaged in the SWIR region. Despite these advantages, the lack of a versatile emitter platform has prevented its general adoption by the biomedical research community. Here we introduce high-quality SWIR-emitting core/shell quantum dots (QDs) for the next generation of in vivo SWIR imaging. Our QDs exhibit a dramatically higher emission quantum yield (QY) than previously described SWIR probes, as well as a narrow and size-tunable emission that allows for multiplexing in the SWIR region. To demonstrate some of its capabilities, we used this imaging platform to measure the heartbeat and breathing rates in awake and unrestrained mice, as well as to quantify the metabolic turnover rates of lipoproteins in several organs simultaneously in real time in mice. Finally, we generate detailed three-dimensional quantitative flow maps of brain vasculature by intravital microscopy and visualize the differences between healthy tissue and a tumor in the brain. In conclusion, SWIR QDs enable biological optical imaging with an unprecedented combination of deep penetration, high spatial resolution, and fast acquisition speed

One thousand plant transcriptomes and the phylogenomics of green plants

Abstract: Green plants (Viridiplantae) include around 450,000–500,000 species1, 2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects

Phylogenomics Resolves The Timing And Pattern Of Insect Evolution: Supplementary File Archives.

Phylogenomics Resolves The Timing And Pattern Of Insect Evolution: Supplementary File Archives. This file includes 14 supplementary archives which are in detail described in the README