Collectively enhanced Ramsey readout by cavity sub- to superradiant transition.

When an inverted ensemble of atoms is tightly packed on the scale of its emission wavelength or when the atoms are collectively strongly coupled to a single cavity mode, their dipoles will align and decay rapidly via a superradiant burst. However, a spread-out dipole phase distribution theory predicts a required minimum threshold of atomic excitation for superradiance to occur. Here we experimentally confirm this predicted threshold for superradiant emission on a narrow optical transition when exciting the atoms transversely and show how to take advantage of the resulting sub- to superradiant transition. A π/2-pulse places the atoms in a subradiant state, protected from collective cavity decay, which we exploit during the free evolution period in a corresponding Ramsey pulse sequence. The final excited state population is read out via superradiant emission from the inverted atomic ensemble after a second π/2-pulse, and with minimal heating this allows for multiple Ramsey sequences within one experimental cycle. Our scheme is an innovative approach to atomic state readout characterized by its speed, simplicity, and highly directional emission of signal photons. It demonstrates the potential of sensors using collective effects in cavity-coupled quantum emitters.

On the phenology of protists: recurrent patterns reveal seasonal variation of protistan (Rhizaria: Cercozoa and Endomyxa) communities in tree canopies.

Tree canopies are colonized by billions of highly specialized microorganisms that are well adapted to the highly variable microclimatic conditions, caused by diurnal fluctuations and seasonal changes. In this study, we investigated seasonality patterns of protists in the tree canopies of a temperate floodplain forest via high-throughput sequencing with group-specific primers for the phyla Cercozoa and Endomyxa. We observed consistent seasonality, and identified divergent spring and autumn taxa. Tree crowns were characterized by a dominance of bacterivores and omnivores, while eukaryvores gained a distinctly larger share in litter and soil communities on the ground. In the canopy seasonality was largest among communities detected on the foliar surface: In spring, higher variance within alpha diversity of foliar samples indicated greater heterogeneity during initial colonization. However, communities underwent compositional changes during the aging of leaves in autumn, highly reflecting recurring phenological changes during protistan colonization. Surprisingly, endomyxan root pathogens appeared to be exceptionally abundant across tree canopies during autumn, demonstrating a potential role of the canopy surface as a physical filter for air-dispersed propagules. Overall, about 80% of detected OTUs could not be assigned to known species-representing dozens of microeukaryotic taxa whose canopy inhabitants are waiting to be discovered.

To the canopy and beyond: Air dispersal as a mechanism of ubiquitous protistan pathogen assembly in tree canopies.

Cercozoa and Oomycota contain a huge biodiversity and important pathogens of forest trees and other vegetation. We analyzed air dispersal of these protistan phyla with an air sampler near-ground (~2 m) and in tree crowns (~25 m) of three tree species (oak, linden and ash) in a temperate floodplain forest in March (before leafing) and May (after leaf unfolding) 2019 with a cultivation-independent high-throughput metabarcoding approach. We found a high diversity of Cercozoa and Oomycota in air samples with 122 and 81 OTUs, respectively. Especially oomycetes showed a significant difference in community composition between both sampling dates. Differences in community composition between air samples in tree canopies and close to the ground were however negligible, and also tree species identity did not affect communities in air samples, indicating that the distribution of protistan propagules through the air was not spatially restricted in the forest ecosystem. OTUs of plant pathogens, whose host species did not occur in the forest, demonstrate dispersal of propagules from outside the forest biome. Overall, our results lead to a better understanding of the stochastic processes of air dispersal of protists and protistan pathogens, a prerequisite to understand the mechanisms of their community assembly in forest ecosystems.

Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards.

The European green lizards of the Lacerta viridis complex consist of two closely related species, L. viridis and Lacerta bilineata that split less than 7 million years ago in the presence of gene flow. Recently, a third lineage, referred to as the "Adriatic" was described within the L. viridis complex distributed from Slovenia to Greece. However, whether gene flow between the Adriatic lineage and L. viridis or L. bilineata has occurred and the evolutionary processes involved in their diversification are currently unknown. We hypothesized that divergence occurred in the presence of gene flow between multiple lineages and involved tissue-specific gene evolution. In this study, we sequenced the whole genome of an individual of the Adriatic lineage and tested for the presence of gene flow amongst L. viridis, L. bilineata, and Adriatic. Additionally, we sequenced transcriptomes from multiple tissues to understand tissue-specific effects. The species tree supports that the Adriatic lineage is a sister taxon to L. bilineata. We detected gene flow between the Adriatic lineage and L. viridis suggesting that the evolutionary history of the L. viridis complex is likely shaped by gene flow. Interestingly, we observed topological differences between the autosomal and Z-chromosome phylogenies with a few fast evolving genes on the Z-chromosome. Genes highly expressed in the ovaries and strongly co-expressed in the brain experienced accelerated evolution presumably contributing to establishing reproductive isolation in the L. viridis complex.

From Forest Soil to the Canopy: Increased Habitat Diversity Does Not Increase Species Richness of Cercozoa and Oomycota in Tree Canopies.

Tree canopies provide habitats for diverse and until now, still poorly characterized communities of microbial eukaryotes. One of the most general patterns in community ecology is the increase in species richness with increasing habitat diversity. Thus, environmental heterogeneity of tree canopies should be an important factor governing community structure and diversity in this subsystem of forest ecosystems. Nevertheless, it is unknown if similar patterns are reflected at the microbial scale within unicellular eukaryotes (protists). In this study, high-throughput sequencing of two prominent protistan taxa, Cercozoa (Rhizaria) and Oomycota (Stramenopiles), was performed. Group specific primers were used to comprehensively analyze their diversity in various microhabitats of a floodplain forest from the forest floor to the canopy region. Beta diversity indicated highly dissimilar protistan communities in the investigated microhabitats. However, the majority of operational taxonomic units (OTUs) was present in all samples, and therefore differences in beta diversity were mainly related to species performance (i.e., relative abundance). Accordingly, habitat diversity strongly favored distinct protistan taxa in terms of abundance, but due to their almost ubiquitous distribution the effect of species richness on community composition was negligible.

Optical-Clock-Based Time Scale.

A time scale is a procedure for accurately and continuously marking the passage of time. It is exemplified by Coordinated Universal Time (UTC) and provides the backbone for critical navigation tools such as the Global Positioning System. Present time scales employ microwave atomic clocks, whose attributes can be combined and averaged in a manner such that the composite is more stable, accurate, and reliable than the output of any individual clock. Over the past decade, clocks operating at optical frequencies have been introduced that are orders of magnitude more stable than any microwave clock. However, in spite of their great potential, these optical clocks cannot be operated continuously, which makes their use in a time scale problematic. We report the development of a hybrid microwave-optical time scale, which only requires the optical clock to run intermittently while relying upon the ensemble of microwave clocks to serve as the flywheel oscillator. The benefit of using a clock ensemble as the flywheel oscillator instead of a single clock can be understood by the Dick-effect limit. This time scale demonstrates for the first time subnanosecond accuracy over a few months, attaining a fractional frequency stability of 1.45 × 10-16 at 30 days and reaching the 10-17 decade at 50 days, with respect to UTC. This time scale significantly improves the accuracy in timekeeping and could change the existing time-scale architectures.

The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. Viridis.

We sequenced the mitochondrial genome of the Western green lizard (Lacerta bilineata) using Illumina technology and additional Sanger sequencing. The assembled 17 086 bp mitogenome had a GC content of 40.32% and consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region (CR), with a gene order identical to the chordate consensus. In addition, we re-sequenced the mitogenome of the closely related Eastern green lizard L. viridis using the same techniques as for L. bilineata. The mitogenomes of L. bilineata and L. viridis showed a sequence identity of 94.4% and 99.9%, respectively, relative to the previously published L. viridis mitogenome. The phylogenetic reconstruction based on 17 Lacertinae mitogenomes using Anolis carolinensis as the outgroup supported L. bilineata and its sister species L. viridis as distinct lineages.

Unexplored character diversity in onychophora (velvet worms): A comparative study of three peripatid species.

Low character variation among onychophoran species has been an obstacle for taxonomic and phylogenetic studies in the past, however we have identified a number of new and informative characters using morphological, molecular, and chromosomal techniques. Our analyses involved a detailed examination of Epiperipatus biolleyi from Costa Rica, Eoperipatus sp. from Thailand, and a new onychophoran species and genus from Costa Rica, Principapillatus hitoyensisgen. et sp. nov.. Scanning electron microscopy on embryos and specimens of varying age revealed novel morphological characters and character states, including the distribution of different receptor types along the antennae, the arrangement and form of papillae on the head, body and legs, the presence and shape of interpedal structures and fields of modified scales on the ventral body surface, the arrangement of lips around the mouth, the number, position and structure of crural tubercles and anal gland openings, and the presence and shape of embryonic foot projections. Karyotypic analyses revealed differences in the number and size of chromosomes among the species studied. The results of our phylogenetic analyses using mitochondrial COI and 12S rRNA gene sequences are in line with morphological and karyotype data. However, our data show a large number of unexplored, albeit informative, characters in the Peripatidae. We suggest that analysing these characters in additional species would help unravel species diversity and phylogeny in the Onychophora, and that inconsistencies among most diagnostic features used for the peripatid genera in the literature could be addressed by identifying a suite of characters common to all peripatids.

Selective release of multiple DNA oligonucleotides from gold nanorods.

Combination therapy, or the use of multiple drugs, has been proven to be effective for complex diseases, but the differences in chemical properties and pharmacokinetics can be challenging in terms of the loading, delivering, and releasing multiple drugs. Here we demonstrate that we can load and selectively release two different DNA oligonucleotides from two different gold nanorods. DNA was loaded on the nanorods via thiol conjugation. Selective releases were induced by selective melting of gold nanorods via ultrafast laser irradiation at the nanorods' longitudinal surface plasmon resonance peaks. Excitation at one wavelength could selectively melt one type of gold nanorods and selectively release one type of DNA strand. Releases were efficient (50-80%) and externally tunable by laser fluence. Released oligonucleotides were still functional. This proof of concept is potentially a powerful method for multiple-drug delivery strategies.