Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.

Temperature driven transformations of glycine molecules embedded in interstellar ice

The formation of glycine amino acid on ice grains in space raises fundamental questions about glycine chemistry in interstellar media. In this work, we studied glycine conformational space and the related tautomerization mechanisms in water media by means of QM/MM molecular dynamics simulations of four glycine conformational isomers (cc, ct, tc, and tt). Interstellar low density amorphous (LDA) ice and T = 20 K were considered as representative for a cold interstellar ice environment, while temperatures of 250 and 450 K were included to model rapid local heating in the ice. In addition to the LDA environment, water clusters with 4, 17, and 27 H2O molecules were subjected to QM/MM dynamics simulations that allowed glycine tautomerization behaviour to be evaluated in water surface-like environments. The tautomerization processes were found to be strongly dependent on the number of water molecules and specific isomer structure. All the glycine isomers mostly preserve their canonical "neutral" conformations under interstellar conditions.

Spiers Memorial Lecture: Astrochemistry at high resolution

Astrochemistry is the science that studies the chemistry in the Universe, namely the combination of two fields: astronomy and chemistry. It started about fifty years ago and it has progressed in leaps and bounds, often triggered by the advent of new telescopes. From the collection of new interstellar molecule detections, astrochemistry has evolved more and more in the quest to understand how they are formed and thrive in the harsh conditions of the interstellar medium. Collaboration between astronomers and chemists has never been more necessary than today, when new powerful astronomical facilities provide us with ever sharper images of the regions where interstellar molecules are present. This review focuses on the special case of interstellar complex organic molecules (iCOMs), one the most debated astrochemical fields and where the astronomers-chemists collaboration and synergy is indispensable. The review will go through the various phases of the formation of planetary system similar to the solar system, providing the most recent observational picture at each step. The current scenarios of the iCOMs formation will be laid down and the critical chemical processes and quantities involved in each of them will be discussed. The major goal of this review is not only to present the progress but, more importantly, to highlight the many areas of uncertainty. A few specific cases will be discussed to give practical examples of why the huge challenge that represents the formation of iCOMs can only be won if chemists and astronomers work together.

Molecular simulation of enhanced separation of humid air components using GO-PVA nanocomposite membranes under differential pressures

Hydrophilic nanocomposite membranes have significant advantages in the separation of water vapor which is the core process in air dehumidification. This paper focuses on exploring the micro-mechanism of enhanced separation using graphene oxide-polyvinyl alcohol (GO-PVA) nanocomposite membranes. The sorption and diffusion behaviors of water vapor and nitrogen in GO-PVA membranes were investigated using molecular dynamics (MD) and Monte Carlo (MC) methods. The study showed that embedding GO into a PVA matrix results in a higher glass transition temperature and fractional free volume. The latter is believed to enhance the diffusivity of gas molecules in polymeric membranes. The interaction between the polymer chains and GO nanoparticles notably promotes the adsorption capacity of water vapor and inhibits nitrogen adsorption in the membrane. A water vapor permeance of 8844.07 Barrer and a separation factor of 3.53 could be achieved with the GO-PVA-0.5 membrane. The analysis confirmed that GO has the same effect on single gas and binary gas mixtures, i.e., increasing the water vapor permeability and selectivity. The calculated water vapor permeance of binary gas is 83% lower than that of single gas permeation. It is expected that this research could provide fundamentals for the optimization and synthesis of gas separation membranes.

Possible Ribose Synthesis in Carbonaceous Planetesimals

The origin of life might be sparked by the polymerization of the first RNA molecules in Darwinian ponds during wet-dry cycles. The key life-building block ribose was found in carbonaceous chondrites. Its exogenous delivery onto the Hadean Earth could be a crucial step toward the emergence of the RNA world. Here, we investigate the formation of ribose through a simplified version of the formose reaction inside carbonaceous chondrite parent bodies. Following up on our previous studies regarding nucleobases with the same coupled physico-chemical model, we calculate the abundance of ribose within planetesimals of different sizes and heating histories. We perform laboratory experiments using catalysts present in carbonaceous chondrites to infer the yield of ribose among all pentoses (5Cs) forming during the formose reaction. These laboratory yields are used to tune our theoretical model that can only predict the total abundance of 5Cs. We found that the calculated abundances of ribose were similar to the ones measured in carbonaceous chondrites. We discuss the possibilities of chemical decomposition and preservation of ribose and derived constraints on time and location in planetesimals. In conclusion, the aqueous formose reaction might produce most of the ribose in carbonaceous chondrites. Together with our previous studies on nucleobases, we found that life-building blocks of the RNA world could be synthesized inside parent bodies and later delivered onto the early Earth.

Energy Redistribution Following CO2 Formation on Cold Amorphous Solid Water

The formation of molecules in and on amorphous solid water (ASW) as it occurs in interstellar space releases appreciable amounts of energy that need to be dissipated to the environment. Here, energy transfer between CO₂ formed within and on the surface of amorphous solid water (ASW) and the surrounding water is studied. Following CO(¹Σ⁺) + O(¹D) recombination the average translational and internal energy of the water molecules increases on the ∼10 ps time scale by 15–25% depending on whether the reaction takes place on the surface or in an internal cavity of ASW. Due to tight coupling between CO₂ and the surrounding water molecules the internal energy exhibits a peak at early times which is present for recombination on the surface but absent for the process inside ASW. Energy transfer to the water molecules is characterized by a rapid ∼10 ps and a considerably slower ∼1 ns component. Within 50 ps a mostly uniform temperature increase of the ASW across the entire surface is found. The results suggest that energy transfer between a molecule formed on and within ASW is efficient and helps to stabilize the reaction products generated.

Where in the cell is my protein?

The application of cryo-correlative light and cryo-electron microscopy (cryo-CLEM) gives us a way to locate structures of interest in the electron microscope. In brief, the structures of interest are fluorescently tagged, and images from the cryo-fluorescent microscope (cryo-FM) maps are superimposed on those from the cryo-electron microscope (cryo-EM). By enhancing cryo-FM to include single-molecule localization microscopy (SMLM), we can achieve much better localization. The introduction of cryo-SMLM increased the yield of photons from fluorophores, which can benefit localization efforts. Dahlberg and Moerner (2021, Annual Review of Physical Chemistry, 72, 253-278) have a recent broad and elegant review of super-resolution cryo-CLEM. This paper focuses on cryo(F)PALM/STORM for the cryo-electron tomography community. I explore the current challenges to increase the accuracy of localization by SMLM and the mapping of those positions onto cryo-EM images and maps. There is much to consider: we need to know if the excitation of fluorophores damages the structures we seek to visualize. We need to determine if higher numerical aperture (NA) objectives, which add complexity to image analysis but increase resolution and the efficiency of photon collection, are better than lower NA objectives, which pose fewer problems. We need to figure out the best way to determine the axial position of fluorophores. We need to have better ways of aligning maps determined by FM with those determined by EM. We need to improve the instrumentation to be easier to use, more accurate, and ice-contamination free. The bottom line is that we have more work to do.

Hydrogen and Deuterium Molecular Escape from Clathrate Hydrates: "Leaky" Microsecond-Molecular-Dynamics Predictions

It is predicted herewith that the leakage of both hydrogen (H2) and deuterium (D2) from sII clathrate hydrates, borne of guest chemical-potential equalization driving enhanced nonequilibrium intercage hopping, should be observable experimentally. To this end, we have designed simulations to realize and study this process by microsecond molecular dynamics within the temperature range of 150-180 K-for which the hydrate lattice was found to be stable. In this pursuit, we considered initial large-cage (51264) guest occupancies of 1-4, with single occupation of 512 cavities. Examining transient, nonequilibrium intercage hopping, we present a lattice-escape activation energy for the four nominal large-cage occupancies (1-4), by fitting to the hydrate-leakage rate. The intercage hopping of H2 and D2 was studied using Markov-chain models and expressed at different temperatures and large-cage occupancies. The free energy of guest "binding" in the large and small cages was also computed for all of the occupancies. Toward equilibrium, following the majority of H2/D2 escape via leakage, the percentage of occupancies was calculated for both H2 and D2 for all of the systems for all initial nominal large-cage occupancies; here, not unexpectedly, double occupancies occurred more favorably in large cages and single occupancies dominated in small cages.

Hydrogen Inter-Cage Hopping and Cage Occupancies inside Hydrogen Hydrate: Molecular-Dynamics Analysis

The inter-cage hopping in a type II clathrate hydrate with different numbers of H2 and D2 molecules, from 1 to 4 molecules per large cage, was studied using a classical molecular dynamics simulation at temperatures of 80 to 240 K. We present the results for the diffusion of these guest molecules (H2 or D2) at all of the different occupations and temperatures, and we also calculated the activation energy as the energy barrier for the diffusion using the Arrhenius equation. The average occupancy number over the simulation time showed that the structures with double and triple large-cage H2 occupancy appeared to be the most stable, while the small cages remained with only one guest molecule. A Markov model was also calculated based on the number of transitions between the different cage types.

X-ray processing of a realistic ice mantle can explain the gas abundances in protoplanetary disks

The Atacama Large Millimeter Array has allowed a detailed observation of molecules in protoplanetary disks, which can evolve toward solar systems like our own. While CO, [Formula: see text], HCO, and [Formula: see text] are often abundant species in the cold zones of the disk, [Formula: see text] or [Formula: see text] are only found in a few regions, and more-complex organic molecules are not observed. We simulate, experimentally, ice processing in disks under realistic conditions, that is, layered ices irradiated by soft X-rays. X-ray emission from young solar-type stars is thousands of times brighter than that of today's sun. The ice mantle is composed of a [Formula: see text]:[Formula: see text]:[Formula: see text] mixture, covered by a layer made of [Formula: see text] and CO. The photoproducts found desorbing from both ice layers to the gas phase during the irradiation converge with those detected in higher abundances in the gas phase of protoplanetary disks, providing important insights on the nonthermal processes that drive the chemistry in these objects.

Persistence times of refractory materials in landfills: A review of rate limiting conditions by mass transfer and reaction kinetics

Monitoring programs at closed landfills show that transformation of plastics, wood, and metals continue long after the active decomposition of the waste fractions are considered as complete. Studies conducted in natural anaerobic environments (e.g., marine sediments and rocks) provide insight for slow degradation mechanisms involving coupling of thermodynamically favorable and unfavorable reactions and biochemical transformations by microbial consortia. These transformations occur at much slower rates through more complex and less obvious mechanisms and are not evident until after the primary decomposition mechanisms become less significant. This study presents a review of the conditions that limit the mass transfer and reaction kinetics for anaerobic transformations in landfills and provides new insights for reaction mechanisms (e.g., anaerobic oxidation and anaerobic corrosion) that occur at relatively slow rates in mature landfills. Conditions and mechanisms of slow transformations by microbial and chemical activities with relatively small energy yields and availability of electron acceptors (e.g., inorganics, plastics) and/or diffusion of gas and moisture into the previously isolated areas in waste deposits were discussed. Time scales for mass transfer and reaction kinetics were compared under anaerobic conditions for different waste components deposited at municipal solid waste landfills. Half-lives of different materials under anaerobic conditions were estimated and compared. Emergence of syntrophic methanogenic communities and conditions for triboelectric effects were evaluated as possible electron transfer mechanisms between waste layers for occurrence of extremely slow transformations of wastes deposited in landfills.

Prediction of the near-IR spectra of ices by ab initio molecular dynamics

Use of ab initio molecular dynamics to predict the near-IR spectra of ices and application to astronomical models.

Observation of nuclear quantum effects and hydrogen bond symmetrisation in high pressure ice

Hydrogen bond symmetrisations in H-bonded systems triggered by pressure-induced nuclear quantum effects (NQEs) is a long-known concept but experimental evidence in high-pressure ices has remained elusive with conventional methods. Theoretical works predicted quantum-mechanical tunneling of protons within water ices to occur at pressures above 30 GPa, and the H-bond symmetrisation transition to occur above 60 GPa. Here we used 1H-NMR on high-pressure ice up to 97 GPa, and demonstrate that NQEs govern the behavior of the hydrogen bonded protons in ice VII already at significantly lower pressures than previously expected. A pronounced tunneling mode was found to be present up to the highest pressures of 97 GPa, well into the stability field of ice X, where NQEs are not anticipated in a fully symmetrised H-bond network. We found two distinct transitions in the NMR shift data at about 20 GPa and 75 GPa attributed to the step-wise symmetrisation of the H-bond.

Diffusive dynamics during the high-to-low density transition in amorphous ice

Water exists in high- and low-density amorphous ice forms (HDA and LDA), which could correspond to the glassy states of high- (HDL) and low-density liquid (LDL) in the metastable part of the phase diagram. However, the nature of both the glass transition and the high-to-low-density transition are debated and new experimental evidence is needed. Here we combine wide-angle X-ray scattering (WAXS) with X-ray photon-correlation spectroscopy (XPCS) in the small-angle X-ray scattering (SAXS) geometry to probe both the structural and dynamical properties during the high-to-low-density transition in amorphous ice at 1 bar. By analyzing the structure factor and the radial distribution function, the coexistence of two structurally distinct domains is observed at T = 125 K. XPCS probes the dynamics in momentum space, which in the SAXS geometry reflects structural relaxation on the nanometer length scale. The dynamics of HDA are characterized by a slow component with a large time constant, arising from viscoelastic relaxation and stress release from nanometer-sized heterogeneities. Above 110 K a faster, strongly temperature-dependent component appears, with momentum transfer dependence pointing toward nanoscale diffusion. This dynamical component slows down after transition into the low-density form at 130 K, but remains diffusive. The diffusive character of both the high- and low-density forms is discussed among different interpretations and the results are most consistent with the hypothesis of a liquid-liquid transition in the ultraviscous regime.

Neutron Scattering Analysis of Water's Glass Transition and Micropore Collapse in Amorphous Solid Water

The question of the nature of water's glass transition has continued to be disputed over many years. Here we use slow heating scans (0.4  K min^{-1}) of compact amorphous solid water deposited at 77 K and an analysis of the accompanying changes in the small-angle neutron scattering signal, to study mesoscale changes in the ice network topology. From the data we infer the onset of rotational diffusion at 115 K, a sudden switchover from nondiffusive motion and enthalpy relaxation of the network at <121  K to diffusive motion across sample grains and sudden pore collapse at >121  K, in excellent agreement with the glass transition onset deduced from heat capacity and dielectric measurements. This indicates that water's glass transition is linked with long-range transport of water molecules on the time scale of minutes and, thus, clarifies its nature. Furthermore, the slow heating rates combined with the high crystallization resistance of the amorphous sample allow us to identify the glass transition end point at 136 K, which is well separated from the crystallization onset at 144 K-in contrast to all earlier experiments in the field.