Updated single cell reference atlas for the starlet anemone Nematostella vectensis

BACKGROUND

The recent combination of genomics and single cell transcriptomics has allowed to assess a variety of non-conventional model organisms in much more depth. Single cell transcriptomes can uncover hidden cellular complexity and cell lineage relationships within organisms. The recent developmental cell atlases of the sea anemone Nematostella vectensis, a representative of the basally branching Cnidaria, has provided new insights into the development of all cell types (Steger et al Cell Rep 40(12):111370, 2022; Sebé-Pedrós et al. Cell 173(6):1520-1534.e20). However, the mapping of the single cell reads still suffers from relatively poor gene annotations and a draft genome consisting of many scaffolds.

RESULTS

Here we present a new wildtype resource of the developmental single cell atlas, by re-mapping of sequence data first published in Steger et al. (2022) and Cole et al. (Nat Commun 14(1):1747, 2023), to the new chromosome-level genome assembly and corresponding gene models in Zimmermann et al. (Nat Commun 14, 8270 (2023). https://doi.org/10.1038/s41467-023-44080-7 ). We expand the pre-existing dataset through the incorporation of additional sequence data derived from the capture and sequencing of cell suspensions from four additional samples: 24 h gastrula, 2d planula, an inter-parietal region of the bodywall from a young unsexed animal, and another adult mesentery from a mature male animal.

CONCLUSION

Our analyses of the full cell-state inventory provide transcriptomic signatures for 127 distinct cell states, of which 47 correspond to neuroglandular subtypes. We also identify two distinct putatively immune-related transcriptomic profiles that segregate between the inner and outer cell layers. Furthermore, the new gene annotation Nv2 has markedly improved the mapping on the single cell transcriptome data and will therefore be of great value for the community and anyone using the dataset.

Muscle cell-type diversification is driven by bHLH transcription factor expansion and extensive effector gene duplications

Animals are typically composed of hundreds of different cell types, yet mechanisms underlying the emergence of new cell types remain unclear. Here we address the origin and diversification of muscle cells in the non-bilaterian, diploblastic sea anemone Nematostella vectensis. We discern two fast and two slow-contracting muscle cell populations, which differ by extensive sets of paralogous structural protein genes. We find that the regulatory gene set of the slow cnidarian muscles is remarkably similar to the bilaterian cardiac muscle, while the two fast muscles differ substantially from each other in terms of transcription factor profiles, though driving the same set of structural protein genes and having similar physiological characteristics. We show that anthozoan-specific paralogs of Paraxis/Twist/Hand-related bHLH transcription factors are involved in the formation of fast and slow muscles. Our data suggest that the subsequent recruitment of an entire effector gene set from the inner cell layer into the neural ectoderm contributes to the evolution of a novel muscle cell type. Thus, we conclude that extensive transcription factor gene duplications and co-option of effector modules act as an evolutionary mechanism underlying cell type diversification during metazoan evolution.

Precise predictions for V + jets dark matter backgrounds

High-energy jets recoiling against missing transverse energy (MET) are powerful probes of dark matter at the LHC. Searches based on large MET signatures require a precise control of the Z ( ν ν ¯ ) +  jet background in the signal region. This can be achieved by taking accurate data in control regions dominated by Z ( ℓ + ℓ - ) +  jet, W ( ℓ ν ) +  jet and γ +  jet production, and extrapolating to the Z ( ν ν ¯ ) +  jet background by means of precise theoretical predictions. In this context, recent advances in perturbative calculations open the door to significant sensitivity improvements in dark matter searches. In this spirit, we present a combination of state-of-the-art calculations for all relevant V +  jets processes, including throughout NNLO QCD corrections and NLO electroweak corrections supplemented by Sudakov logarithms at two loops. Predictions at parton level are provided together with detailed recommendations for their usage in experimental analyses based on the reweighting of Monte Carlo samples. Particular attention is devoted to the estimate of theoretical uncertainties in the framework of dark matter searches, where subtle aspects such as correlations across different V +  jet processes play a key role. The anticipated theoretical uncertainty in the Z ( ν ν ¯ ) +  jet background is at the few percent level up to the TeV range.

Electroweak Corrections to pp→μ^{+}μ^{-}e^{+}e^{-}+X at the LHC: A Higgs Boson Background Study

The first complete calculation of the next-to-leading-order electroweak corrections to four-lepton production at the LHC is presented, where all off-shell effects of intermediate Z bosons and photons are taken into account. Focusing on the mixed final state μ^{+}μ^{-}e^{+}e^{-}, we study differential cross sections that are particularly interesting for Higgs boson analyses. The electroweak corrections are divided into photonic and purely weak corrections. The former exhibit patterns familiar from similar W- or Z-boson production processes with very large radiative tails near resonances and kinematical shoulders. The weak corrections are of the generic size of 5% and show interesting variations, in particular, a sign change between the regions of resonant Z-pair production and the Higgs signal.

Physics at the [Formula: see text] linear collider

A comprehensive review of physics at an [Formula: see text] linear collider in the energy range of [Formula: see text] GeV-3 TeV is presented in view of recent and expected LHC results, experiments from low-energy as well as astroparticle physics. The report focusses in particular on Higgs-boson, top-quark and electroweak precision physics, but also discusses several models of beyond the standard model physics such as supersymmetry, little Higgs models and extra gauge bosons. The connection to cosmology has been analysed as well.

Diversity of honey stores and their impact on pathogenic bacteria of the honeybee, Apis mellifera

Honeybee colonies offer an excellent environment for microbial pathogen development. The highest virulent, colony killing, bacterial agents are Paenibacillus larvae causing American foulbrood (AFB), and European foulbrood (EFB) associated bacteria. Besides the innate immune defense, honeybees evolved behavioral defenses to combat infections. Foraging of antimicrobial plant compounds plays a key role for this "social immunity" behavior. Secondary plant metabolites in floral nectar are known for their antimicrobial effects. Yet, these compounds are highly plant specific, and the effects on bee health will depend on the floral origin of the honey produced. As worker bees not only feed themselves, but also the larvae and other colony members, honey is a prime candidate acting as self-medication agent in honeybee colonies to prevent or decrease infections. Here, we test eight AFB and EFB bacterial strains and the growth inhibitory activity of three honey types. Using a high-throughput cell growth assay, we show that all honeys have high growth inhibitory activity and the two monofloral honeys appeared to be strain specific. The specificity of the monofloral honeys and the strong antimicrobial potential of the polyfloral honey suggest that the diversity of honeys in the honey stores of a colony may be highly adaptive for its "social immunity" against the highly diverse suite of pathogens encountered in nature. This ecological diversity may therefore operate similar to the well-known effects of host genetic variance in the arms race between host and parasite.

Human hamstring tenocytes survive when seeded into a decellularized porcine Achilles tendon extracellular matrix

Tendon ruptures and defects remain major orthopaedic challenges. Tendon healing is a time-consuming process, which results in scar tissue with an altered biomechanical competence. Using a xenogeneic tendon extracellular matrix (ECM) as a natural scaffold, which can be reseeded with autologous human tenocytes, might be a promising approach to reconstruct damaged tendons. For this purpose, the porcine Achilles (AS) tendons serving as a scaffold were histologically characterized in comparison to human cell donor tendons. AS tendons were decellularized and then reseeded with primary human hamstring tenocytes using cell centrifuging, rotating culture and cell injection techniques. Vitality testing, histology and glycosaminoglycan/DNA quantifications were performed to document the success of tendon reseeding. Porcine AS tendons were characterized by a higher cell and sulfated glycosaminoglycan content than human cell donor tendons. Complete decellularization could be achieved, but led to a wash out of sulfated glycosaminoglycans. Nevertheless, porcine tendon could be recellularized with vital human tenocytes. The recellularization led to a slight increase in cell number compared to the native tendon and some glycosaminoglycan recovery. This study indicates that porcine tendon can be de- and recellularized using adult human tenocytes. Future work should optimize cell distribution within the recellularized tendon ECM and consider tendon- and donor species-dependent differences.

Next-to-leading-order QCD corrections to W+W-bb production at hadron colliders

Top-antitop quark pairs belong to the most abundantly produced and precisely measurable heavy-particle signatures at hadron colliders and allow for crucial tests of the standard model and new physics searches. Here we report on the calculation of the next-to-leading order (NLO) QCD corrections to hadronic W(+)W(-)bb production, which provides a complete NLO description of the production of top-antitop pairs and their subsequent decay into W bosons and bottom quarks, including interferences, off-shell effects, and nonresonant backgrounds. Numerical predictions for the Tevatron and the LHC are presented.

Next-to-leading order QCD corrections to pp-->ttbb+X at the LHC

We report on the calculation of the full next-to-leading-order QCD corrections to the production of ttbb final states at the LHC, which deliver a serious background contribution to the production of a Higgs boson (decaying into a bb pair) in association with a tt pair. While the corrections significantly reduce the unphysical scale dependence of the leading-order cross section, our results predict an enhancement of the ttbb production cross section by a K factor of about 1.8.

Strong and electroweak corrections to the production of a Higgs boson+2 jets via weak interactions at the Large Hadron Collider

Radiative corrections of strong and electroweak interactions are presented at next-to-leading order for the production of a Higgs boson plus two hard jets via weak interactions at the CERN Large Hadron Collider. The calculation includes all weak-boson fusion and quark-antiquark annihilation diagrams as well as the corresponding interferences. The electroweak corrections, which are discussed here for the first time, reduce the cross sections by 5% and thus are of the same order of magnitude as the QCD corrections.