Hybridization, polyploidy, and evolutionary transitions between monoecy and dioecy in Bryonia (Cucurbitaceae)

Correns’s 1903 (Berichte der Deutschen Botanischen Gesellschaft 21: 133 – 147) crosses between a monoecious and a dioecious species of Bryonia revealed the simple Mendelian inheritance of dioecy and provided the first instance of an XY sex determination system in any organism. Bryonia ranges from the Canary Islands to Central Asia and comprises seven dioecious and three monoecious species; its closest relative, Ecballium elaterium, has dioecious and monoecious populations. We used chloroplast (cp) and nuclear (nr) gene phylogenies to infer sexual system evolution in Bryonia. We also tested for associations between sexual system and ploidy level, based on published and original chromosome counts. Conflicts between cp and nr topologies imply that the dioecious hexaploid B. cretica arose from hybridization(s), probably involving the dioecious diploids B. dioica, B. syriaca, and/or B. multiflora. A tetraploid dioecious endemic on Corsica and Sardinia probably originated from B. dioica via autopolyploidy. While the cp phylogeny resolves few species relationships, the nr tree implies at least two evolutionary changes in sexual system. There is no correlation between sexual system and ploidy level. Molecular clocks suggest that the deepest divergence, between a species on the Canary Islands and the ancestor of all remaining species, occurred ca. 10 million years ago

Nonequilibrium phonon mean free paths in anharmonic chains

Harnessing the power of low-dimensional materials in thermal applications calls for a solid understanding of the anomalous thermal properties of such systems. We analyze thermal conduction in one-dimensional systems by determining the frequency-dependent phonon mean free paths (MFPs) for an anharmonic chain, delivering insight into the diverging thermal conductivity observed in computer simulations. In our approach, the MFPs are extracted from the length-dependence of the spectral heat current obtained from nonequilibrium molecular dynamics simulations. At low frequencies, the results reveal a power-law dependence of the MFPs on frequency, in agreement with the diverging conductivity and the recently determined equilibrium MFPs. At higher frequencies, however, the nonequilibrium MFPs consistently exceed the equilibrium MFPs, highlighting the differences between the two quantities. Exerting pressure on the chain is shown to suppress the mean free paths and to generate a weaker divergence of MFPs at low frequencies. The results deliver important insight into anomalous thermal conduction in low-dimensional systems and also reveal differences between the MFPs obtained from equilibrium and nonequilibrium simulations.Comment: 8 pages, 7 figures, minor changes to v

Collisional decay of 87Rb Feshbach molecules at 1005.8 G

We present measurements of the loss-rate coefficients K_am and K_mm caused by inelastic atom-molecule and molecule-molecule collisions. A thermal cloud of atomic 87Rb is prepared in an optical dipole trap. A magnetic field is ramped across the Feshbach resonance at 1007.4 G. This associates atom pairs to molecules. A measurement of the molecule loss at 1005.8 G yields K_am=2 10^-10 cm^3/s. Additionally, the atoms can be removed with blast light. In this case, the measured molecule loss yields K_mm=3 10^-10 cm^3/s

Role of anharmonic phonon scattering in the spectrally decomposed thermal conductance at planar interfaces

Detailed understanding of vibrational heat transfer mechanisms between solids is essential for the efficient thermal engineering and control of nanomaterials. We investigate the frequency dependence of anharmonic scattering and interfacial thermal conduction between two acoustically mismatched solids in planar contact by calculating the spectral decomposition of the heat current flowing through an interface between two materials. The calculations are based on analyzing the correlations of atomic vibrations using the data extracted from non-equilibrium molecular dynamics simulations. Inelastic effects arising from anharmonic interactions are shown to significantly facilitate heat transfer between two mass-mismatched face-centered cubic lattices even at frequencies exceeding the cut-off frequency of the heavier material due to (i) enhanced dissipation of evanescent vibrational modes and (ii) frequency-doubling and frequency-halving three-phonon energy transfer processes at the interface. The results provide substantial insight into interfacial energy transfer mechanisms especially at high temperatures, where inelastic effects become important and other computational methods are ineffective.Comment: minor changes to v

Phylodynamic analysis of ebola virus in the 2014 sierra leone epidemic.

BACKGROUND: The Ebola virus (EBOV) epidemic in Western Africa is the largest in recorded history and control efforts have so far failed to stem the rapid growth in the number of infections. Mathematical models serve a key role in estimating epidemic growth rates and the reproduction number (R0) from surveillance data and, recently, molecular sequence data. Phylodynamic analysis of existing EBOV time-stamped sequence data may provide independent estimates of the unobserved number of infections, reveal recent epidemiological history, and provide insight into selective pressures acting upon viral genes. METHODS: We fit a series mathematical models of infectious disease dynamics to phylogenies estimated from 78 whole EBOV genomes collected from distinct patients in May and June of 2014 in Sierra Leone, and perform evolutionary analysis on these genomes combined with closely related EBOV genomes from previous outbreaks. Two analyses are conducted with values of the latent period that have been used in recent modelling efforts. We also examined the EBOV sequences for evidence of possible episodic adaptive molecular evolution during the 2014 outbreak. RESULTS: We find evidence for adaptive evolution affecting L and GP protein coding regions of the EBOV genome, which is unlikely to bias molecular clock and phylodynamic analyses. We estimate R0=2.40 (95% HPD:1.54-3.87 ) if the mean latent period is 5.3 days, and R0=3.81, (95% HPD:2.47-6.3) if the mean latent period is 12.7 days. The estimated coefficient of variation (CV) of the number of transmissions per infected host is very high, and a large proportion of infections yield no transmissions. CONCLUSIONS: Estimates of R0 are sensitive to the unknown latent infectious period which can not be reliably estimated from genetic data alone. EBOV phylogenies show significant evidence for superspreading and extreme variance in the number of transmissions per infected individual during the early epidemic in Sierra Leone

A Mott-like State of Molecules

We prepare a quantum state where each site of an optical lattice is occupied by exactly one molecule. This is the same quantum state as in a Mott insulator of molecules in the limit of negligible tunneling. Unlike previous Mott insulators, our system consists of molecules which can collide inelastically. In the absence of the optical lattice these collisions would lead to fast loss of the molecules from the sample. To prepare the state, we start from a Mott insulator of atomic 87Rb with a central region, where each lattice site is occupied by exactly two atoms. We then associate molecules using a Feshbach resonance. Remaining atoms can be removed using blast light. Our method does not rely on the molecule-molecule interaction properties and is therefore applicable to many systems.Comment: Proceedings of the 20th International Conference on Atomic Physics (ICAP 2006), edited by C. Roos, H. Haffner, and R. Blatt, AIP Conference Proceedings, Melville, 2006, Vol. 869, pp. 278-28

Non-Fourier heat transport in metal-dielectric core-shell nanoparticles under ultrafast laser pulse excitation

Relaxation dynamics of embedded metal nanoparticles after ultrafast laser pulse excitation is driven by thermal phenomena of different origins the accurate description of which is crucial for interpreting experimental results: hot electron gas generation, electron-phonon coupling, heat transfer to the particle environment and heat propagation in the latter. Regardingthis last mechanism, it is well known that heat transport in nanoscale structures and/or at ultrashort timescales may deviate from the predictions of the Fourier law. In these cases heat transport may rather be described by the Boltzmann transport equation. We present a numerical model allowing us to determine the electron and lattice temperature dynamics in a spherical gold nanoparticle core under subpicosecond pulsed excitation, as well as that of the surrounding shell dielectric medium. For this, we have used the electron-phonon coupling equation in the particle with a source term linked with the laser pulse absorption, and the ballistic-diffusive equations for heat conduction in the host medium. Either thermalizing or adiabatic boundary conditions have been considered at the shell external surface. Our results show that the heat transfer rate from the particle to the matrix can be significantly smaller than the prediction of Fourier's law. Consequently, the particle temperature rise is larger and its cooling dynamics might be slower than that obtained by using Fourier's law. This difference is attributed to the nonlocal and nonequilibrium heat conduction in the vicinity of the core nanoparticle. These results are expected to be of great importance for analyzing pump-probe experiments performed on single nanoparticles or nanocomposite media

Experimental Acute Exposure to Thirdhand Smoke and Changes in the Human Nasal Epithelial Transcriptome: A Randomized Clinical Trial.

Importance:No previous studies have shown that acute inhalation of thirdhand smoke (THS) activates stress and survival pathways in the human nasal epithelium. Objective:To evaluate gene expression in the nasal epithelium of nonsmoking women following acute inhalation of clean air and THS. Design, Setting, and Participants:Nasal epithelium samples were obtained from participants in a randomized clinical trial (2011-2015) on the health effects of inhaled THS. In a crossover design, participants were exposed, head only, to THS and to conditioned, filtered air in a laboratory setting. The order of exposures was randomized and exposures were separated by at least 21 days. Ribonucleic acid was obtained from a subset of 4 healthy, nonsmoking women. Exposures:By chance, women in the subset were randomized to receive clean air exposure first and THS exposure second. Exposures lasted 3 hours. Main Outcomes and Measures:Differentially expressed genes were identified using RNA sequencing with a false-discovery rate less than 0.1. Results:Participants were 4 healthy, nonsmoking women aged 27 to 49 years (mean [SD] age, 42 [10.2] years) with no chronic diseases. A total of 389 differentially expressed genes were identified in nasal epithelium exposed to THS, while only 2 genes, which were not studied further, were affected by clean air. Enriched gene ontology terms associated with stress-induced mitochondrial hyperfusion were identified, such as respiratory electron transport chain (q = 2.84 × 10-3) and mitochondrial inner membrane (q = 7.21 × 10-6). Reactome pathway analysis identified terms associated with upregulation of DNA repair mechanisms, such as nucleotide excision repair (q = 1.05 × 10-2). Enrichment analyses using ingenuity pathway analysis identified canonical pathways related to stress-induced mitochondrial hyperfusion (eg, increased oxidative phosphorylation) (P = .001), oxidative stress (eg, glutathione depletion phase II reactions) (P = .04), and cell survival (z score = 5.026). Conclusions and Relevance:This study found that acute inhalation of THS caused cell stress that led to the activation of survival pathways. Some responses were consistent with stress-induced mitochondrial hyperfusion and similar to those demonstrated previously in vitro. These data may be valuable to physicians treating patients exposed to THS and may aid in formulating regulations for the remediation of THS-contaminated environments

Atom-molecule Rabi oscillations in a Mott insulator

We observe large-amplitude Rabi oscillations between an atomic and a molecular state near a Feshbach resonance. The experiment uses 87Rb in an optical lattice and a Feshbach resonance near 414 G. The frequency and amplitude of the oscillations depend on magnetic field in a way that is well described by a two-level model. The observed density dependence of the oscillation frequency agrees with the theoretical expectation. We confirmed that the state produced after a half-cycle contains exactly one molecule at each lattice site. In addition, we show that for energies in a gap of the lattice band structure, the molecules cannot dissociate