Applications of Thermodynamic Modelling Techniques in Earth and Environmental Sciences

In nature, kinetic laws control how fast one reaction is, but thermodynamic laws determine whether one reaction can happen or not. In this talk, Dr. Hao will introduce some basic thermodynamic theories and explain how to determine affinity of reaction in natural environments. In addition, Dr. Hao will present several examples of using thermodynamics to understand cycles of elements on our Earth based on his own research outputs. Furthermore, this talk will cover some discussions on how to apply thermodynamic simulations to figure out potential ways to maintain sustainability in nature

GEOCHEMICAL SIGNATURES OF WEATHERING AND SURFACE WATER CHEMISTRY IN THE LATE ARCHEAN

Earth’s Archean surface environment was important for the origin and evolution of life. Here, it is proposed that the pH2,g controlled the redox state of the Archean atmosphere, consistent with the stabilities of detrital minerals, such as pyrite, siderite, and uraninite. In the marine environment, greenalite, siderite, and hematite, or amorphous precursors, were primary minerals. Magnetite was formed during diagenesis and metamorphism. Fluctuations of pH2,g or pH could oxidize elements such as Mo and Re. Organic acids were metastable in the surface waters at high pH2,g values, possibly stimulating biologic activity and the formation of organic hazes in the atmosphere. Reaction path models were used to simulate rainwater, weathering, and river water chemistry under present-day and late Archean conditions. The thermodynamic properties of ferrous iron and other end-member minerals important on the early Earth were estimated using an extended Linear Free Energy Relationship. Modeling of the present-day weathering of basalt + calcite produced hematite, kaolinite, Na-Mg-saponite, and chalcedony, and world average river water (WARW) after destruction of 10-4 moles kg-1 H2O. Late Archean weathering of olivine basalt + calcite produced kaolinite, chalcedony, and Fe(II)-rich clays, and WARW with low pH, and high HCO3- and Fe. The behavior of P, Mn, Cr, and Cu during late Archean weathering was investigated during weathering of olivine basalt. Apatite and Mn-olivine dissolved, producing high phosphate and Mn(II) in Archean WARW. Insoluble MnO2,cr and hematite formed during whiff of oxidants. Chromite hardly dissolved but Cr(OH)3,am dissolved completely, forming high Cr(III) waters. Weathering of chalcopyrite produced chalcocite and bornite, but whiffs of oxidants produced native copper, chalcocite, bornite, and hematite, and high dissolved Cu. Aqueous Cr2+ could be stable in hydrothermal solutions and a dominant species even with Cr(III)-Cl complexation whereas higher pressure favors Cr(III). For example, at 5 GPa and 1000 °C, Cr2+ is the dominant species at geologically reasonable pH and log fO2 values. However, at 5 GPa and 600 °C, Cr3+ and Cr2+ might coexist. It appears likely that Cr(II) could play a significant role in low pressure hydrothermal fluids and in subduction zone fluids

Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel Biomarker for Cancers

Cysteine-rich intestinal protein 1 (CRIP1) has been identified as a novel marker for early detection of cancers. Here we report on the use of phage display in combination with molecular modeling to identify a high-affinity ligand for CRIP1. Panning experiments using a circularized C7C phage library yielded several consensus sequences with modest binding affinities to purified CRIP1. Two sequence motifs, A1 and B5, having the highest affinities for CRIP1, were chosen for further study. With peptide structure information and the NMR structure of CRIP1, the higher-affinity A1 peptide was computationally redesigned, yielding a novel peptide, A1M, whose affinity was predicted to be much improved. Synthesis of the peptide and saturation and competitive binding studies demonstrated approximately a 10–28-fold improvement in the affinity of A1M compared to that of either A1 or B5 peptide. These techniques have broad application to the design of novel ligand peptides

Abundant phosphorus expected for possible life in Enceladus’s ocean

Saturn’s moon Enceladus has a potentially habitable subsurface water ocean that contains canonical building blocks of life (organic and inorganic carbon, ammonia, possibly hydrogen sulfide) and chemical energy (disequilibria for methanogenesis). However, its habitability could be strongly affected by the unknown availability of phosphorus (P). Here, we perform thermodynamic and kinetic modeling that simulates P geochemistry based on recent insights into the geochemistry of the ocean–seafloor system on Enceladus. We find that aqueous P should predominantly exist as orthophosphate (e.g., HPO42−), and total dissolved inorganic P could reach 10−7 to 10−2 mol/kg H2O, generally increasing with lower pH and higher dissolved CO2, but also depending upon dissolved ammonia and silica. Levels are much higher than <10−10 mol/kg H2O from previous estimates and close to or higher than ∼10−6 mol/kg H2O in modern Earth seawater. The high P concentration is primarily ascribed to a high (bi)carbonate concentration, which decreases the concentrations of multivalent cations via carbonate mineral formation, allowing phosphate to accumulate. Kinetic modeling of phosphate mineral dissolution suggests that geologically rapid release of P from seafloor weathering of a chondritic rocky core could supply millimoles of total dissolved P per kilogram of H2O within 105 y, much less than the likely age of Enceladus’s ocean (108 to 109 y). These results provide further evidence of habitable ocean conditions and show that any oceanic life would not be inhibited by low P availability

Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel Biomarker for Cancers

Cysteine-rich intestinal protein 1 (CRIP1) has been identified as a novel marker for early detection of cancers. Here we report on the use of phage display in combination with molecular modeling to identify a high-affinity ligand for CRIP1. Panning experiments using a circularized C7C phage library yielded several consensus sequences with modest binding affinities to purified CRIP1. Two sequence motifs, A1 and B5, having the highest affinities for CRIP1, were chosen for further study. With peptide structure information and the NMR structure of CRIP1, the higher-affinity A1 peptide was computationally redesigned, yielding a novel peptide, A1M, whose affinity was predicted to be much improved. Synthesis of the peptide and saturation and competitive binding studies demonstrated approximately a 10–28-fold improvement in the affinity of A1M compared to that of either A1 or B5 peptide. These techniques have broad application to the design of novel ligand peptides

Single-cell analysis reveals dysregulated inflammatory response in peripheral blood immunity in patients with acute respiratory distress syndrome

Introduction: Acute respiratory distress syndrome (ARDS) remains a major clinical challenge for patients in intensive care units. Determining the differential mechanisms underlying ARDS with different etiologies is a key goal to improve the effectiveness of ARDS therapy. Despite growing evidence that different immune cell types are involved in ARDS, the role of altered immune cell subpopulations in disease progression is unelucidated.Methods: In this study, we combined scRNA-seq and bulk-level sequencing to analyze the transcriptomes of peripheral blood mononuclear cells from healthy volunteers and patients with septic ARDS (sep-ARDS) and pneumonic ARDS (PNE-ARDS).Results: Our data revealed differential alterations at the cellular and molecular levels and within biological signaling pathways in ARDS with different etiologies. The dynamics of neutrophils, macrophages (Macs), classical dendritic cells (cDCs), myeloid-derived suppressive cells (MDSCs), and CD8+ T cells varied significantly among groups of different samples, with neutrophils and cDCs at higher, and Macs at significantly lower, amounts in the patients with sep-ARDS. Furthermore, MDSCs were highly enriched only in the sep-ARDS patients, whereas a higher abundance of CD8+ T cells was observed in patients with PNE-ARDS. In addition, these cell subpopulations were found to be significantly involved in apoptosis, inflammatory, and immune-related pathways. In particular, a significant enhancement of the oxidative stress response was observed in the neutrophil subpopulation.Conclusion: Our study shows that the composition of cells involved in the main peripheral circulation differs in patients with ARDS with different etiologies. Studying the role and mechanism of action of these cells during ARDS will provide new opportunities for the treatment of this condition

Evolution of the crustal phosphorus reservoir

The release of phosphorus (P) from crustal rocks during weathering plays a key role in determining the size of Earth's biosphere, yet the concentration of P in crustal rocks over time remains controversial. Here, we combine spatial, temporal, and chemical measurements of preserved rocks to reconstruct the lithological and chemical evolution of Earth's continental crust. We identify a threefold increase in average crustal P concentrations across the Neoproterozoic-Phanerozoic boundary (600 to 400 million years), showing that preferential biomass burial on shelves acted to progressively concentrate P within continental crust. Rapid compositional change was made possible by massive removal of ancient P-poor rock and deposition of young P-rich sediment during an episode of enhanced global erosion. Subsequent weathering of newly P-rich crust led to increased riverine P fluxes to the ocean. Our results suggest that global erosion coupled to sedimentary P-enrichment forged a markedly nutrient-rich crust at the dawn of the Phanerozoic

Novel variation and <i>de novo </i>mutation rates in population-wide <i>de novo</i> assembled Danish trios

Building a population-specific catalogue of single nucleotide variants (SNVs), indels and structural variants (SVs) with frequencies, termed a national pan-genome, is critical for further advancing clinical and public health genetics in large cohorts. Here we report a Danish pan-genome obtained from sequencing 10 trios to high depth (50 × ). We report 536k novel SNVs and 283k novel short indels from mapping approaches and develop a population-wide de novo assembly approach to identify 132k novel indels larger than 10 nucleotides with low false discovery rates. We identify a higher proportion of indels and SVs than previous efforts showing the merits of high coverage and de novo assembly approaches. In addition, we use trio information to identify de novo mutations and use a probabilistic method to provide direct estimates of 1.27e−8 and 1.5e−9 per nucleotide per generation for SNVs and indels, respectively