Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses

Symbiomonas scintillans Guillou et Chrétiennot-Dinet, 1999 is a tiny (1.4 μm) heterotrophic microbial eukaryote. The genus was named based on the presence of endosymbiotic bacteria in its endoplasmic reticulum, however, like most such endosymbionts neither the identity nor functional association with its host were known. We generated both amplification-free shotgun metagenomics and whole genome amplification sequencing data from S. scintillans strains RCC257 and RCC24, but were unable to detect any sequences from known lineages of endosymbiotic bacteria. The absence of endobacteria was further verified with FISH analyses. Instead, numerous contigs in assemblies from both RCC24 and RCC257 were closely related to prasinoviruses infecting the green algae Ostreococcus lucimarinus, Bathycoccus prasinos, and Micromonas pusilla (OlV, BpV, and MpV, respectively). Using the BpV genome as a reference, we assembled a near-complete 190 kbp draft genome encoding all hallmark prasinovirus genes, as well as two additional incomplete assemblies of closely related but distinct viruses from RCC257, and three similar draft viral genomes from RCC24, which we collectively call SsVs. A multi-gene tree showed the three SsV genome types branched within highly supported clades with each of BpV2, OlVs, and MpVs, respectively. Interestingly, transmission electron microscopy also revealed a 190 nm virus-like particle similar the morphology and size of the endosymbiont originally reported in S. scintillans. Overall, we conclude that S. scintillans currently does not harbour an endosymbiotic bacterium, but is associated with giant viruses.journal articl

Extinct and extant termites reveal the fidelity of behavior fossilization in amber

Fossils encompassing multiple individuals provide rare direct evidence of behavioral interactions among extinct organisms. However, the fossilization process can alter the spatial relationship between individuals and hinder behavioral reconstruction. Here, we report a Baltic amber inclusion preserving a female–male pair of the extinct termite species Electrotermes affinis. The head-to-abdomen contact in the fossilized pair resembles the tandem courtship behavior of extant termites, although their parallel body alignment differs from the linear alignment typical of tandem runs. To solve this inconsistency, we simulated the first stage of amber formation, the immobilization of captured organisms, by exposing living termite tandems to sticky surfaces. We found that the posture of the fossilized pair matches trapped tandems and differs from untrapped tandems. Thus, the fossilized pair likely is a tandem running pair, representing the direct evidence of the mating behavior of extinct termites. Furthermore, by comparing the postures of partners on a sticky surface and in the amber inclusion, we estimated that the male likely performed the leader role in the fossilized tandem. Our results demonstrate that past behavioral interactions can be reconstructed despite the spatial distortion of body poses during fossilization. Our taphonomic approach demonstrates how certain behaviors can be inferred from fossil occurrences.journal articl

Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells

Constitutional heterozygous pathogenic variants in the exonuclease domain of POLE and POLD1, which affect the proofreading activity of the corresponding polymerases, cause a cancer predisposition syndrome characterized by increased risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and other tumor types. The generally accepted explanation for the connection between the disruption of the proofreading activity of polymerases epsilon and delta and cancer development is through an increase in the somatic mutation rate. Here we studied an extended family with multiple members heterozygous for the pathogenic POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and cancer phenotypes. Through the analysis of mutational patterns of patient-derived fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons, we concluded that heterozygous POLD1 L474P just subtly increases the somatic and germline mutation burden. In contrast, tumors developed in individuals with a heterozygous mutation in the exonuclease domain of POLD1, including L474P, have an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d. We solved this contradiction through the observation that tumorigenesis involves somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease deficiency of polymerase delta has a recessive effect on mutation rate.journal articl

Atom-light interactions using optical nanofibres—a perspective

Complete control of light-matter interactions at a single quantum level is critical for quantum science applications such as precision measurement and information processing. Nanophotonic devices, developed with recent advancements in nanofabrication techniques, can be used to tailor the interactions between single photons and atoms. One example of such a nanophotonic device is the optical nanofibre, which provides an excellent platform due to the strongly confined transverse light fields, long interaction length, low loss, and diverse optical modes. This facilitates a strong interaction between atoms and guided light, revealing chiral atom-light processes and the prospect of waveguide quantum electrodynamics. This paper highlights recent advances, experimental techniques, and future perspectives of the optical nanofibre-atom hybrid quantum platform.journal articl

Assessing non-Markovian dynamics through moments of the Choi state

Non-Markovian effects in open quantum system dynamics usually manifest the backflow of information from the environment to the system, indicating complete-positive divisibility breaking of the dynamics. We provide a criterion for witnessing such non-Markovian dynamics exhibiting information backflow, based on partial moments of Choi matrices. The moment condition determined by the positive semi-definiteness of a matrix does not hold for a Choi state describing non-Markovian dynamics. We then present some explicit examples in support of our proposed non-Markovianity detection scheme. Finally, a moment-based measure of non-Markovianity for unital dynamics is formulated.journal articl

Circadian control of sleep-related neuronal activity in lizards

Although diurnal animals displaying monophasic sleep patterns exhibit periodic cycles of alternating slow-wave sleep (SWS) and rapid eye movement sleep (REMS), the regulatory mechanisms underlying these regular sleep cycles remain unclear. Here, we report that in the Australian dragon Pogona vitticeps exposed to constant darkness (DD), sleep behavior and sleep-related neuronal activity emerged over a 24-h cycle. However, the regularity of the REMS/SWS alternation was disrupted under these conditions. Notably, when the lizards were then exposed to 12 h of light after DD, the regularity of the sleep stages was restored. These results suggest that sleep-related neuronal activity in lizards is regulated by circadian rhythms and that the regularity of REMS and SWS cycling is influenced by daytime light exposure.journal articl

Self‐Assembled Monolayer Hole‐Selective Contact for Up‐Scalable and Cost‐Effective Inverted Perovskite Solar Cells

Inverted positive-intrinsic-negative (p-i-n) perovskite solar cells (IPSCs) have attracted widespread attention due to their low fabrication temperature, good stability in ambient air, and the potential for use in flexible and tandem devices. In recent years, self-assembled monolayers (SAMs) have been investigated as a promising hole-selective contact for IPSCs, leading to an impressive record efficiency of about 26%, which is comparable to that of the regular n-i-p counterparts. This review focuses on the progress of SAM-based IPSCs from the perspective of energy level matching, defect passivation, interface carrier extraction, and SAMs’ stability improvement, as well as the advances in up-scalable fabrication of SAMs and perovskite layers for efficient solar modules and tandem devices. A cost analysis of the SAMs and other commonly used hole-selective materials is conducted to evaluate their cost-effectiveness for photovoltaic applications. Finally, the future challenges are pointed out and the perspectives on how to up-scale SAM-based IPSCs and improve their long-term operational stability are provided.journal articl

Dually Weighted Multi-matrix Models as a Path to Causal Gravity-Matter Systems

We introduce a dually-weighted multi-matrix model that for a suitable choice of weights reproduce two-dimensional Causal Dynamical Triangulations (CDT) coupled to the Ising model. When Ising degrees of freedom are removed, this model corresponds to the CDT-matrix model introduced by Benedetti and Henson (Phys Lett B 678:222, 2009). We present exact as well as approximate results for the Gaussian averages of characters of a Hermitian matrix A and for a given representation and establish the present limitations that prevent us to solve the model analytically. This sets the stage for the formulation of more sophisticated matter models coupled to two-dimensional CDT as dually weighted multi-matrix models providing a complementary view to the standard simplicial formulation of CDT-matter models.journal articl

Collective excitations of a Bose-condensed gas: Fate of second sound in the crossover regime between hydrodynamic and collisionless regimes

We develop the moment method for Bose-Einstein condensates at finite temperatures that enable us to study collective sound modes from the hydrodynamic to the collisionless regime. In particular, we investigate collective excitations in a weakly interacting dilute Bose gas by applying the moment method to the Zaremba-Nikuni-Griffin equation, which is the coupled equation of the Boltzmann equation with the generalized Gross-Pitaevskii equation. Utilizing the moment method, collective excitations in the crossover regime between the hydrodynamic and collisionless regimes are investigated in detail. In the crossover regime, the second sound mode loses the weight of the density response function because of the significant coupling with incoherent modes, whereas the first sound shows a distinct but broad peak structure. We compare the result obtained by the moment method with that of the Landau two-fluid equations and show that the collective mode predicted by the Landau two-fluid equations well coincides with the result from the moment method even far from the hydrodynamic regime, whereas clear distinction also emerges in the relatively higher momentum regime.journal articl

Exocytic plasma membrane flows remodel endoplasmic reticulum–plasma membrane tethering for septin collar assembly

Endoplasmic reticulum (ER)–plasma membrane (PM) tethering is crucial for the non-vesicular lipid transport between the ER membrane and the PM. However, the PM-associated ER can impede the PM binding of cytoskeletons and other organelles. It is poorly understood how the competition between the ER and cytoskeletons/organelles on the PM is resolved. Here, we show that, upon septin collar assembly, ER-PM tethering proteins are excluded from the yeast bud sites, and the PM-associated ER is locally detached from the PM. Our results suggest that PM flows by polarized exocytosis extrude PM proteins, including ER-PM tethering proteins, from the bud sites. When the reorganization of the ER-PM tethering was inhibited by exocytosis repression, septin localization was restricted to the PM sites poor in ER-PM tethering proteins. This study proposes machinery reconciling ER-septin competition on the PM, providing mechanistic insights into the spatial organization of PM-associated organelles and cytoskeletons.journal articl