Project description:A system of edge cracks was applied to polished (010) surfaces of K-rich gem-quality alkali feldspar by diffusion-mediated cation exchange between oriented feldspar plates and a Na-rich NaCl-KCl salt melt. The cation exchange produced a Na-rich layer at and beneath the specimen surface, and the associated strongly anisotropic lattice contraction lead to a tensile stress state at the specimen surface, which induced fracturing. Cation exchange along the newly formed crack flanks produced Na-enriched diffusion halos around the cracks, and the associated lattice contraction and tensile stress state caused continuous crack growth. The cracks nucleated with non-uniform spacing on the sample surface and quickly attained nearly uniform spacing below the surface by systematic turning along their early propagation paths. In places, conspicuous wavy cracks oscillating several times before attaining their final position between the neighboring cracks were produced. It is shown that the evolution of irregularly spaced towards regularly spaced cracks including the systematic turning and wavyness along the early propagation paths maximizes the rate of free energy dissipation in every evolutionary stage of the system. Maximization of the dissipation rate is suggested as a criterion for selection of the most probable evolution path for a system undergoing chemically induced diffusion mediated fracturing in an anisotropic homogeneous brittle material.Supplementary informationThe online version contains supplementary material available at 10.1007/s00269-022-01183-9.
Project description:Proteins from thermophiles are generally more thermostable than their mesophilic homologs, but little is known about the evolutionary process driving these differences. Here we attempt to understand how the diverse thermostabilities of bacterial ribonuclease H1 (RNH) proteins evolved. RNH proteins from Thermus thermophilus (ttRNH) and Escherichia coli (ecRNH) share similar structures but differ in melting temperature (T(m)) by 20 °C. ttRNH's greater stability is caused in part by the presence of residual structure in the unfolded state, which results in a low heat capacity of unfolding (ΔCp) relative to ecRNH. We first characterized RNH proteins from a variety of extant bacteria and found that Tm correlates with the species' growth temperatures, consistent with environmental selection for stability. We then used ancestral sequence reconstruction to statistically infer evolutionary intermediates along lineages leading to ecRNH and ttRNH from their common ancestor, which existed approximately 3 billion years ago. Finally, we synthesized and experimentally characterized these intermediates. The shared ancestor has a melting temperature between those of ttRNH and ecRNH; the T(m)s of intermediate ancestors along the ttRNH lineage increased gradually over time, while the ecRNH lineage exhibited an abrupt drop in Tm followed by relatively little change. To determine whether the underlying mechanisms for thermostability correlate with the changes in T(m), we measured the thermodynamic basis for stabilization--ΔCp and other thermodynamic parameters--for each of the ancestors. We observed that, while the T(m) changes smoothly, the mechanistic basis for stability fluctuates over evolutionary time. Thus, even while overall stability appears to be strongly driven by selection, the proteins explored a wide variety of mechanisms of stabilization, a phenomenon we call "thermodynamic system drift." This suggests that even on lineages with strong selection to increase stability, proteins have wide latitude to explore sequence space, generating biophysical diversity and potentially opening new evolutionary pathways.
Project description:The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, yet its origin and evolutionary history are still unclear and controversial. Here, we report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany. We reconstructed two Neolithic and one medieval HBV genome by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results demonstrated that HBV has circulated in the European population for at least 7000 years. The Neolithic HBV genomes show a high genomic similarity to each other. In a phylogenetic network, they do not group with any human-associated HBV genome and are most closely related to those infecting African non-human primates. The ancient viruses appear to represent distinct lineages that have no close relatives today and possibly went extinct. Our results reveal the great potential of ancient DNA from human skeletons in order to study the long-time evolution of blood borne viruses.
Project description:The superadiabatic combustion for non-stationary filtration combustion is analytically studied. The non-dimensional excess enthalpy function (H) equation is theoretically derived based on a one-dimensional, two-temperature model. In contrast to the H equation for the stationary filtration combustion, a new term, which takes into account the effect of non-dimensional combustion wave speed, is included in the H equation for transient filtration combustion. The governing equations with boundary conditions are solved by commercial software Fluent. The predictions show that the maximum non-dimensional gas and solid temperatures in the flame zone are greater than 3 for equivalence ratio of 0.15. An examination of the four source terms in the H equation indicates that the thermal conductivity ratio ( Γ s ) between the solid and gas phases is the dominant one among the four terms and basically determines H distribution. For lean premixed combustion in porous media, the superadiabatic combustion effect is more pronounced for the lower Γ s .
Project description:Combustion ion chromatography (CIC) has found a role in environmental analytical chemistry for fluorine content analysis. It is used for extractable organofluorine (EOF) analysis to evaluate perfluoroalkyl and polyfluoroalkyl substances (PFASs) and other organofluorine burden. The prevailing assumption has been that all PFASs are incinerated in CIC and matrix components have no impact on this process, but this has not been experimentally evaluated. In this work, the combustion efficiencies of 13 different PFASs were determined (66-110%). A notable difference was observed between calibrating the CIC with inorganic fluorine or organofluorine. Potential interferences from cations and coextracted matrix components from whole blood and surface water samples were evaluated. These observations should be acknowledged when performing EOF analysis using CIC, overlooking either non-100% combustion efficiencies or the differences in calibrating the CIC with inorganic fluorine or organofluorine could lead to underestimating EOF content and through that to misguide policy decisions.
Project description:AIM:To perform a genetic characterization of 7 skeletons from medieval age found in a burial site in the Aragonese Pyrenees. METHODS:Allele frequencies of autosomal short tandem repeats (STR) loci were determined by 3 different STR systems. Mitochondrial DNA (mtDNA) and Y-chromosome haplogroups were determined by sequencing of the hypervariable segment 1 of mtDNA and typing of phylogenetic Y chromosome single nucleotide polymorphisms (Y-SNP) markers, respectively. Possible familial relationships were also investigated. RESULTS:Complete or partial STR profiles were obtained in 3 of the 7 samples. Mitochondrial DNA haplogroup was determined in 6 samples, with 5 of them corresponding to the haplogroup H and 1 to the haplogroup U5a. Y-chromosome haplogroup was determined in 2 samples, corresponding to the haplogroup R. In one of them, the sub-branch R1b1b2 was determined. mtDNA sequences indicated that some of the individuals could be maternally related, while STR profiles indicated no direct family relationships. CONCLUSIONS:Despite the antiquity of the samples and great difficulty that genetic analyses entail, the combined use of autosomal STR markers, Y-chromosome informative SNPs, and mtDNA sequences allowed us to genotype a group of skeletons from the medieval age.
Project description:In order to explore the influence of different chemical demineralizations on coal combustion characteristics and combustion kinetics, five coals subjected to different chemical demineralization processes were investigated via thermogravimetric analysis. The ash contents of clean coal was reduced to 0.1-1.55% after different chemical demineralizations. The ignition temperature of coal decreased by 12-69 °C, and the peak temperature decreased by 7-62 °C. The burnout temperature of clean coal increased by 63 °C after demineralization by NaOH. The adsorption of noncombustible NaOH into the porous structure of TaiXi-3 caused an increase in burnout temperature. Alkali-soluble minerals were proven to have a negative effect on the combustion performance of coal, while acid-soluble minerals had the opposite effect. The combustion kinetics of five kinds of coals at a heating rate of 10 °C/min was investigated. The activation energy of coal obviously changes before and after demineralization (58.39-91.39 kJ mol-1). The activation energy of clean coal is obviously lower than that of raw coal.
Project description:Microorganisms provide a wealth of biodegradative potential in the reduction and elimination of xenobiotic compounds in the environment. One useful metric to evaluate potential biodegradation pathways is thermodynamic feasibility. However, experimental data for the thermodynamic properties of xenobiotics is scarce. The present work uses a group contribution method to study the thermodynamic properties of the University of Minnesota Biocatalysis/Biodegradation Database. The Gibbs free energies of formation and reaction are estimated for 914 compounds (81%) and 902 reactions (75%), respectively, in the database. The reactions are classified based on the minimum and maximum Gibbs free energy values, which accounts for uncertainty in the free energy estimates and a feasible concentration range relevant to biodegradation. Using the free energy estimates, the cumulative free energy change of 89 biodegradation pathways (51%) in the database could be estimated. A comparison of the likelihood of the biotransformation rules in the Pathway Prediction System and their thermodynamic feasibility was then carried out. This analysis revealed that when evaluating the feasibility of biodegradation pathways, it is important to consider the thermodynamic topology of the reactions in the context of the complete pathway. Group contribution is shown to be a viable tool for estimating, a priori, the thermodynamic feasibility and the relative likelihood of alternative biodegradation reactions. This work offers a useful tool to a broad range of researchers interested in estimating the feasibility of the reactions in existing or novel biodegradation pathways.
Project description:Protein stability arises from a combination of factors which are often difficult to rationalise. Therefore its improvement is better addressed through directed evolution than by rational design approaches. In this study, five rounds of mutagenesis/recombination followed by high-throughput screening (≈10,000 clones) yielded the hit 1B6 showing a 300-fold higher half life at 50°C than that exhibited by the homodimeric wild type PpAzoR azoreductase from Pseudomonas putida MET94. The characterization using fluorescence, calorimetry and light scattering shows that 1B6 has a folded state slightly less stable than the wild type (with lower melting and optimal temperatures) but in contrast is more resistant to irreversible denaturation. The superior kinetic stability of 1B6 variant was therefore related to an increased resistance of the unfolded monomers to aggregation through the introduction of mutations that disturbed hydrophobic patches and increased the surface net charge of the protein. Variants 2A1 and 2A1-Y179H with increased thermodynamic stability (10 to 20°C higher melting temperature than wild type) were also examined showing the distinctive nature of mutations that lead to improved structural robustness: these occur in residues that are mostly involved in strengthening the solvent-exposed loops or the inter-dimer interactions of the folded state.