Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data.

Genome sequences from evolving infectious pathogens allow quantification of case introductions and local transmission dynamics. We sequenced 11,357 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Switzerland in 2020-the sixth largest effort globally. Using a representative subset of these data, we estimated viral introductions to Switzerland and their persistence over the course of 2020. We contrasted these estimates with simple null models representing the absence of certain public health measures. We show that Switzerland's border closures decoupled case introductions from incidence in neighboring countries. Under a simple model, we estimate an 86 to 98% reduction in introductions during Switzerland's strictest border closures. Furthermore, the Swiss 2020 partial lockdown roughly halved the time for sampled introductions to die out. Last, we quantified local transmission dynamics once introductions into Switzerland occurred using a phylodynamic model. We found that transmission slowed 35 to 63% upon outbreak detection in summer 2020 but not in fall. This finding may indicate successful contact tracing over summer before overburdening in fall. The study highlights the added value of genome sequencing data for understanding transmission dynamics.

Planarizing cytosine: The S1 state structure, vibrations, and nonradiative dynamics of jet-cooled 5,6-trimethylenecytosine.

We measure the S0 → S1 spectrum and time-resolved S1 state nonradiative dynamics of the "clamped" cytosine derivative 5,6-trimethylenecytosine (TMCyt) in a supersonic jet, using two-color resonant two-photon ionization (R2PI), UV/UV holeburning, and ns time-resolved pump/delayed ionization. The experiments are complemented with spin-component scaled second-order approximate coupled cluster (SCS-CC2), time-dependent density functional theory, and multi-state second-order perturbation-theory (MS-CASPT2) ab initio calculations. While the R2PI spectrum of cytosine breaks off ∼500 cm-1 above its 000 band, that of TMCyt extends up to +4400 cm-1 higher, with over a hundred resolved vibronic bands. Thus, clamping the cytosine C5-C6 bond allows us to explore the S1 state vibrations and S0 → S1 geometry changes in detail. The TMCyt S1 state out-of-plane vibrations ν1', ν3', and ν5' lie below 420 cm-1, and the in-plane ν11', ν12', and ν23' vibrational fundamentals appear at 450, 470, and 944 cm-1. S0 → S1 vibronic simulations based on SCS-CC2 calculations agree well with experiment if the calculated ν1', ν3', and ν5' frequencies are reduced by a factor of 2-3. MS-CASPT2 calculations predict that the ethylene-type S1 ⇝ S0 conical intersection (CI) increases from +366 cm-1 in cytosine to >6000 cm-1 in TMCyt, explaining the long lifetime and extended S0 → S1 spectrum. The lowest-energy S1 ⇝ S0 CI of TMCyt is the "amino out-of-plane" (OPX) intersection, calculated at +4190 cm-1. The experimental S1 ⇝ S0 internal conversion rate constant at the S1(v'=0) level is kIC=0.98-2.2⋅108 s-1, which is ∼10 times smaller than in 1-methylcytosine and cytosine. The S1(v'=0) level relaxes into the T1(3ππ*) state by intersystem crossing with kISC=0.41-1.6⋅108 s-1. The T1 state energy is measured to lie 24 580±560 cm-1 above the S0 state. The S1(v'=0) lifetime is τ=2.9 ns, resulting in an estimated fluorescence quantum yield of Φfl=24%. Intense two-color R2PI spectra of the TMCyt amino-enol tautomers appear above 36 000 cm-1. A sharp S1 ionization threshold is observed for amino-keto TMCyt, yielding an adiabatic ionization energy of 8.114±0.002 eV.

Temperature-dependent benefits of bacterial exposure in embryonic development of Daphnia magna resting eggs.

The environments in which animals develop and evolve are profoundly shaped by bacteria, which affect animals both indirectly through their role in biogeochemical processes and directly through antagonistic or beneficial interactions. The outcomes of these activities can differ according to environmental context. In a series of laboratory experiments with diapausing eggs of the water flea Daphnia magna, we manipulated two environmental parameters, temperature and presence of bacteria, and examined their effect on development. At elevated temperatures (≥ 26 °C), resting eggs developing without live bacteria had reduced hatching success and correspondingly higher rates of severe morphological abnormalities compared with eggs with bacteria in their environment. The beneficial effect of bacteria was strongly reduced at 20 °C. Neither temperature nor the presence of bacteria affected directly developing parthenogenetic eggs. The mechanistic basis of this effect of bacteria on development is unclear, but these results highlight the complex interplay of biotic and abiotic factors influencing animal development after diapause.

Low-lying excited states and nonradiative processes of 9-methyl-2-aminopurine.

The UV spectrum of the adenine analogue 9-methyl-2-aminopurine (9M-2AP) is investigated with one- and two-color resonant two-photon ionization spectroscopy at 0.3 and 0.05 cm(-1) resolution in a supersonic jet. The electronic origin at 32,252 cm(-1) exhibits methyl torsional subbands that originate from the 0A1'' (l = 0) and 1E(″) (l = ±1) torsional levels. These and further torsional bands that appear up to 00 (0)+230 cm(-1) allow to fit the threefold (V3) barriers of the torsional potentials as |V3''|=50 cm(-1) in the S0 and |V3'|=126 cm(-1) in the S1 state. Using the B3LYP density functional and correlated approximate second-order coupled cluster CC2 methods, the methyl orientation is calculated to be symmetric relative to the 2AP plane in both states, with barriers of V3''=20 cm(-1) and V3'=115 cm(-1). The 00 (0) rotational band contour is 75% in-plane (a/b) polarized, characteristic for a dominantly long-axis (1)ππ(*) excitation. The residual 25% c-axis polarization may indicate coupling of the (1)ππ(*) to the close-lying (1)nπ(*) state, calculated at 4.00 and 4.01 eV with the CC2 method. However, the CC2 calculated (1)nπ oscillator strength is only 6% of that of the (1)ππ(*) transition. The (1)ππ(*) vibronic spectrum is very complex, showing about 40 bands within the lowest 500 cm(-1). The methyl torsion and the low-frequency out-of-plane ν1' and ν2' vibrations are strongly coupled in the (1)ππ(*) state. This gives rise to many torsion-vibration combination bands built on out-of-plane fundamentals, which are without precedence in the (1)ππ(*) spectrum of 9H-2-aminopurine [S. Lobsiger, R. K. Sinha, M. Trachsel, and S. Leutwyler, J. Chem. Phys. 134, 114307 (2011)]. From the Lorentzian broadening needed to fit the 00 (0) contour of 9M-2AP, the (1)ππ(*) lifetime is τ ⩾ 120 ps, reflecting a rapid nonradiative transition.