The influence of rivers on marine boron isotopes and implications for reconstructing past ocean pH

Isotopic history of seawater: the stable isotope character of the global ocean at present and in the geological past

After the atmosphere, the ocean is the most well-mixed and homogeneous global geochemical reservoir. Both physical and biological processes generate elemental and isotope variations in seawater. Contrasting geochemical behaviors cause elements to be susceptible to different fractionation mechanisms, with their isotopes providing unique insights into the composition and evolution of the ocean over the course of geological history. Supplementing the traditional stable isotopes (H, C, O, N, S) that provide information about ocean processes and past environmental conditions, radiogenic isotope (Sr, Nd, Os, Pb, U) systems can be used as time markers, indicators of terrestrial weathering, and ocean water mass mixing. Recent instrumentation advances have made possible the measurement of natural stable isotope variations produced by both mass-dependent and mass-independent fractionation for an ever-increasing number of metal elements (e.g. Li, B, Mg, Si, Ca, V, Cr, Fe, Ni, Cu, Zn, Se, Mo, Cd, Tl, U). The major emphasis in this review is on the isotopic composition of the light elements based on a comparatively large literature. Unlike O, H and S, the stable isotopes of C, N and Si do not have a constant isotopic composition in the modern ocean. The major cations Ca, Mg, and Sr fixed in carbonate shells provide the best proxies for reconstruction of the composition of the ocean in the past. Exhibiting large isotope enrichments in ocean water, B and Li are suitable for the investigation of water/rock interactions and can act as monitors of former oceanic pH. The bioessential elements Zn, Cd, and Ni are indicators of paleoproductivity in the ocean. Characteristic isotope enrichments or depletions of the multivalent elements V, Cr, Fe, Se, Mo, and U record the past redox state of the ocean/atmosphere system. Case studies describe how isotopes have been used to define the seawater composition in the geological past.

Carbon allocation of Spirodela polyrhiza under boron toxicity

Pectic polysaccharides containing apiose, xylose, and uronic acids are excellent candidates for boron fixation. Duckweeds are the fastest-growing angiosperms that can absorb diverse metals and contaminants from water and have high pectin content in their cell walls. Therefore, these plants can be considered excellent boron (B) accumulators. This work aimed to investigate the relationship between B assimilation capacity with apiose content in the cell wall of Spirodela polyrhiza subjected to different boric acid concentrations. Plants were grown for 7 and 10 days in ½ Schenck-Hildebrandt media supplemented with 0 to 56 mg B.L^-1, the non-structural and structural carbohydrates, and related genes were evaluated. The results showed that B altered the morphology and carbohydrate composition of this species during plant development. The optimum B concentration (1.8 mg B.L^-1) led to the highest relative growth and biomass accumulation, reduced starch, and high pectin and apiose contents, together with increased expression of UDP-apiose/UDP-xylose synthase (AXS) and 1,4-α-galacturonosyltransferase (GAUT). The toxic state (28 and 56 mg B.L^-1) increased the hexose contents in the cell wall with a concomitant reduction of pectins, apiose, and growth. The pectin content of S. polyrhiza was strongly associated with its growth capacity and regulation of B content within the cells, which have AXS as an important regulator. These findings suggest that duckweeds are suitable for B remediation, and their biomass can be used for bioenergy production.

Hydrogeochemical controls on As and B enrichment in the aqueous environment from the Western Tibetan Plateau: A case study from the Singe Tsangpo River Basin

Although enrichment of As and B has been extensively observed in major rivers within the Tibetan Plateau, the mechanisms regulating natural enrichment of As and B in the river basins remain poorly understood. To evaluate the hydrogeochemical controls on the As and B enrichment in the aqueous environment in the western Tibetan Plateau, samples of river waters, river sediments, and groundwater were collected within the Singe Tsangpo River basin. The results revealed significant enrichment of As and B in river water (up to 104 μg L^-1 for As and 3.2 mg/L for B), river sediment (up to 141 mg/kg for As and 79.4 mg/kg for B), and groundwater (up to 73 μg /L for As and 2.5 mg/L for B). Moreover, the decreases in the molar ratios from the Ca²⁺ /(Na⁺+K⁺) in river water and the chemical index of alteration (CIA) in the sediments accompanied with the enrichment of heavier δ¹⁸O values along the river flow path suggested that, carbonate and silicate weathering were more substantial at the upper reaches, and the dissolution of evaporites was enhanced at the lower reaches. The As and B enrichment in the river waters primarily resulted from the discharge of geothermal springs, while the carbonate weathering has facilitated the B enrichment through providing HCO₃^- for the competitive adsorption with H₃BO₃ or B(OH)₄^- . In addition, the recharge of surface water into groundwater resulted in elevated As and B concentrations in the alluvial aquifers at the lower reaches of the Singe Tsangpo River. The present study highlighted that variations in the weathering processes within the river basin could significantly contribute to the enrichment of As and B, which can improve our understanding of hydrogeochemical controls on the transport and enrichment of trace elements at the catchment scale worldwide.

Hydrochemistry and source apportionment of boron, sulfate, and nitrate in the Fen River, a typical loess covered area in the eastern Chinese Loess Plateau

Fen River Basin (FRB) is water-deficient and strongly influenced by human activities in the eastern Chinese Loess Plateau. The spatio-temporal variation and controlling factors of hyrochemistry and quality, sources of high boron, sulfate, and nitrate of surface waters in FRB were unclear. Major ions, δ¹¹B, δ¹⁵N, and δ¹⁸O in surface waters in dry season and wet season of FRB were analyzed and correlation analysis (CA), principal component analysis (PCA), self-organizing map (SOM), forward model, and Bayesian isotope mixing model (MixSIAR) were used to solve above problems. Results showed that average riverine δ¹¹B, δ¹⁵N, and δ¹⁸O of FRB was 7.8‰, 11.2‰, and 1.3‰ (1SD), respectively. Dissolved solutes ranked midstream > downstream > upstream with water type of Na ⁺-Cl^-, Ca²⁺-Mg²⁺-Cl^-, and Ca²⁺-HCO₃^-, respectively. Low dissolved solutes were in forest areas while high values were in cropland and city areas. SOM analysis indicated that hydrochemistry was both influenced by natural (upstream) and pollutional input (midstream and downstream) and variation between dry season and wet season was minor. The abnormally high boron concentrations were mainly from silicate weathering (43%) and evaporites dissolution of loess (32%), urban and industrial input contributed 15% of riverine boron. High SO₄^2- (207 ± 267 mg/L, 1SD) was mainly from sulfates. δ¹⁵N and δ¹⁸O analysis indicated that nitrification was the primary N cycling process. Further, MixSIAR showed that NO₃^- was mainly from municipal sewage (∼67%) and the total contribution of chemical fertilizer and soil nitrogen was ∼30% with slightly higher values in upstream and wet season. Influenced by land-use types, evaporite dissolution, and anthropogenic input, water quality below midstream was worse and strict sewage reduction policies must be developed. This study highlights the significant influence of evaporite dissolution of loess and anthropogenic input (urban and industrial input for B and sewage for NO₃^-) on hydrochemistry and water quality.

Mechanistic insight on boron-mediated toxicity in plant vis-a-vis its mitigation strategies: a review

Boron (B) is an essential micronutrient, crucial for the growth and development of crop plants. However, the essential to a toxic range of B in the plant is exceptionally narrow, and symptoms develop with a slight change in its concentration in soil. The morphological and anatomical response, such as leaf chlorosis, stunted growth, and impairment in the xylem and phloem development occurs under B-toxicity. The transport of B in the plant occurs via transpiration stream with the involvement of B-channels and transporter in the roots. The higher accumulation of B in source and sink tissue tends to have lower photosynthetic, chlorophyll content, infertility, failure of pollen tube formation and germination, impairment of cell wall formation, and disruption of membrane systems. Excess B in the plant hinders the uptake of other micronutrients, hormone transport, and metabolite partitioning. B-mediated reactive oxygen species production leads to the synthesis of antioxidant enzymes which help to scavenge these molecules and prevent the plant from further oxidative damage. This review highlights morpho-anatomical, physiological, biochemical, and molecular responses of the plant under B toxicity and thereby might help the researchers to understand the related mechanism and design strategies to develop B tolerant cultivars.

B and δ11B biogeochemical cycle in a beech forest developed on a calcareous soil: Pools, fluxes, and forcing parameters

Rock weathering and biological cycling hold the development and sustainability of continental ecosystems, yet the interdependence of macro- and micro-nutrients biogeochemical cycles and their implications for ecosystem functioning remains unclear, despite being of particular importance in the context of global changes. This study focuses on the stocks, fluxes and processes constituting the biogeochemical cycle of boron. Vegetation, soils and solutions were monitored for a full year in a temperate beech forest developed on calcareous soil. Despite an overwhelmingly large B pool in soils, this study points to limited influence of weathering emphasizing the importance of vegetation cycling on this site. The biological imprint on the B cycle is marked by (1) a strong ¹¹B enrichment of solutions compared to the mineral source and (2) systematic correlations observed between B and other strongly recycled elements in all water samples. B isotopes are fractionated within the beech stand with higher values in leaves (23.5‰) and lower in fine roots (-11.7‰), suggesting that the light ¹⁰B isotope is preferentially assimilated during plant growth. B isotopic data are consistent with a Rayleigh-like behaviour during xylem transfer leading to an ¹¹B enrichment in the higher parts of the trees, putting internal B transfer as the main driver of the large range of isotopic compositions between plant tissues. B apparent isotopic fractionations are observed in the annually produced biomass and total beech stand, albeit with different values: α_{xylem-biomass} = 0.980 ± 0.009 and 0.990 ± 0.002, respectively, suggesting ¹¹B transfer from old to new tissue. The developed model also points to an isotopic fractionation factor during B uptake much higher than previously evaluated (0.979 < α_uptake < 0.994). Overall, this study demonstrates that B isotopes appear as a promising tracer of soil-plant interactions with particular emphasis on tree adaptation to B bioavailability in soil.

The seawater carbon inventory at the Paleocene-Eocene Thermal Maximum

The Paleocene-Eocene Thermal Maximum (PETM) (55.6 Mya) was a geologically rapid carbon-release event that is considered the closest natural analog to anthropogenic CO₂ emissions. Recent work has used boron-based proxies in planktic foraminifera to characterize the extent of surface-ocean acidification that occurred during the event. However, seawater acidity alone provides an incomplete constraint on the nature and source of carbon release. Here, we apply previously undescribed culture calibrations for the B/Ca proxy in planktic foraminifera and use them to calculate relative changes in seawater-dissolved inorganic carbon (DIC) concentration, surmising that Pacific surface-ocean DIC increased by [Formula: see text] µmol/kg during the peak-PETM. Making reasonable assumptions for the pre-PETM oceanic DIC inventory, we provide a fully data-driven estimate of the PETM carbon source. Our reconstruction yields a mean source carbon δ¹³C of -10‰ and a mean increase in the oceanic C inventory of +14,900 petagrams of carbon (PgC), pointing to volcanic CO₂ emissions as the main carbon source responsible for PETM warming.

Stabilization of borate by hot isostatic pressing after co-precipitation with hydroxyapatite using MAP

Boric acid is one of the most mobile inorganic contaminant species in nature due to its pK_a of 9.23. Co-precipitation of borate with hydroxyapatite (HAp: Ca₅(PO₄)₃OH) facilitates the simultaneous removal of borate with co-existing oxoanions in natural waters. The cost of phosphate is an impediment to industrialize the co-precipitation of borate with HAp for treatment of geothermal waters. In the present work, an inexpensive industrial by-product of magnesium ammonium phosphate (MAP) derived from sewage sludge, was examined as a phosphate source. MAP includes 89% pure magnesium ammonium phosphate, resulting in better performance than the pure chemical form of NH₄H₂PO₄, because Mg²⁺ and Al³⁺ (trace elements in MAP product) play roles in enhancing the removal rate of borate and lowering the equilibrium borate concentration. These ions have a good affinity with phosphate to nucleate crystal seeds independently of powdery Ca sources. To reduce the bulky volume of solid residues, hot isostatic pressing (HIP) was applied. There is structural water in HAp; therefore, the greatest volume reduction was achieved with 78.3 ± 2.0% (n = 3). Additionally, a synergic effect to suppress the released borate, greater than the sequential combination of calcination and cold isostatic pressing was accomplished in the toxicity contents leaching procedure (TCLP) test. This is not due to larger crystal sizes alone, but it is derived from boron stabilization in HAp at an atomic level by the synergic effect of heating and pressing simultaneously.

Early Pleistocene obliquity-scale pCO2 variability at ~1.5 million years ago

In the early Pleistocene, global temperature cycles predominantly varied with ~41-kyr (obliquity-scale) periodicity. Atmospheric greenhouse gas concentrations likely played a role in these climate cycles; marine sediments provide an indirect geochemical means to estimate early Pleistocene CO2. Here we present a boron isotope-based record of continuous high-resolution surface ocean pH and inferred atmospheric CO2 changes. Our results show that, within a window of time in the early Pleistocene (1.38-1.54 Ma), pCO2 varied with obliquity, confirming that, analogous to late Pleistocene conditions, the carbon cycle and climate covaried at ~1.5 Ma. Pairing the reconstructed early Pleistocene pCO2 amplitude (92 ±13 μatm) with a comparably smaller global surface temperature glacial/interglacial amplitude (3.0 ±0.5 K), yields a surface temperature change to CO2 radiative forcing ratio of S [CO2]~0.75 (± 0.5) °C/Wm-2, as compared to the late Pleistocene S [CO2] value of ~1.75 (± 0.6) °C/Wm-2. This direct comparison of pCO2 and temperature implicitly incorporates the large ice sheet forcing as an internal feedback and is not directly applicable to future warming. We evaluate this result with a simple climate model, and show that the presumably thinner, though extensive, northern hemisphere ice sheets would increase surface temperature sensitivity to radiative forcing. Thus, the mechanism to dampen actual temperature variability in the early Pleistocene more likely lies with Southern Ocean circulation dynamics or antiphase hemispheric forcing. We also compile this new carbon dioxide record with published Plio-Pleistocene δ11B records using consistent boundary conditions and explore potential reasons for the discrepancy between Pliocene pCO2 based on different planktic foraminifera.

Simultaneous immobilization of borate, arsenate, and silicate from geothermal water derived from mining activity by co-precipitation with hydroxyapatite

The treatment of the geothermal water discharged through mining activity is a critical issue because the rate of discharge is 12,000 m³ per day and the discharge contains high concentrations of borate (>20 mg/L) and arsenate (ca. 0.4 mg/L) as well as silicate and carbonate. The simultaneous reduction of borate and arsenate concentrations to acceptable levels was successfully performed by co-precipitation with hydroxyapatite (HAp). Although the coexisting high concentrations of carbonate act as a disturbing element, the co-precipitation equilibrium of borate was shifted to lower values by adjusting the P/Ca molar ratio, and the removal rate of borate was accelerated by using Al³⁺ additives, resulting in the efficient reduction of borate within 1 h. The initially immobilized boron in HAp is in the tetragonal form, which probably occupies the hydroxyl sites in HAp, gradually transforming into the trigonal form in the solid state, as interpreted by ¹H NMR and ¹¹B-NMR. The coexisting silicate was also immobilized in an ellestadite form, as confirmed by ²⁹Si-NMR measurements. Arsenate and silicate were immobilized before borate in geothermal water. A dissolution assay of borate in the solid residues after co-precipitation with HAp verified the acceptable stability of borate, which is independent of the amount of added Al³⁺.

Correlation of Apiose Levels and Growth Rates in Duckweeds

The carbon assimilated by photosynthesis in plants can be partitioned into starch, soluble sugars, and cell wall polymers. Higher levels of starch accumulation in leaves are usually correlated with a lower growth capacity. Duckweeds are fast-growing aquatic monocot plants that can accumulate high levels of starch. They are an unusual group because their cell wall has very low levels of lignin while accumulating apiogalacturonan, a pectic polysaccharide that could be involved with boron assimilation. In this work, five duckweed species from different genera (Spirodela polyrhiza, Landoltia punctata, Lemna gibba, Wolffiella caudata, and Wolffia borealis) were cultivated under two light intensities (20 and 500 μmoles of photons m⁻² s⁻¹) to evaluate the effects of growth rate on carbohydrate metabolism. A comparative analysis was performed by measuring their relative growth rates (RGR), and their content for starch, as well as soluble and cell wall carbohydrates. We found that the faster-growing species (the Lemnoideae) accumulate lower starch and higher soluble sugars than the slower-growing species within the Wolffioideae. Interestingly, analysis of the cell wall monosaccharides revealed that the slower-growing species displayed lower content of apiose in their walls. Our results indicate that higher accumulation of apiose observed in cell walls of the Lemnoideae species, which likely correlates with a higher proportion of apiogalacturonan, may lead to higher efficiency in the assimilation of boron. This is consistent with the increased RGR observed under conditions with higher apiose in the cell wall, such as higher light intensity. Consistent with their lower growth capacity, the Wolffioideae species we studied shows higher starch accumulation in comparison with the Lemnoideae species. We suggest that apiose levels could be good biomarkers for growth capacity of duckweeds and suggest that boron uptake could be an important factor for growth control in this aquatic plant family.

A review on the determination of isotope ratios of boron with mass spectrometry

The present review discusses different mass spectrometric techniques-viz, thermal ionization mass spectrometry (TIMS), inductively coupled plasma mass spectrometry (ICPMS), and secondary ion mass spectrometry (SIMS)-used to determine ¹¹ B/¹⁰ B isotope ratio, and concentration of boron required for various applications in earth sciences, marine geochemistry, nuclear technology, environmental, and agriculture sciences, etc. The details of the techniques-P-TIMS, which uses Cs₂ BO₂⁺ , N-TIMS, which uses BO₂^- , and MC-ICPMS, which uses B⁺ ions for bulk analysis or B^- and B⁺ ions for in situ micro-analysis with SIMS-are highlighted. The capabilities, advantages, limitations, and problems in each mass spectrometric technique are summarized. The results of international interlaboratory comparison experiments conducted at different times are summarized. The certified isotopic reference materials available for boron are also listed. Recent developments in laser ablation (LA) ICPMS and QQQ-ICPMS for solids analysis and MS/MS analysis, respectively, are included. The different aspects of sample preparation and analytical chemistry of boron are summarized. Finally, the future requirements of boron isotope ratios for future applications are also given. Presently, MC-ICPMS provides the best precision and accuracy (0.2-0.4‰) on isotope ratio measurements, whereas N-TIMS holds the potential to analyze smallest amount of boron, but has the issue of bias (+2‰ to 4‰) which needs further investigations. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:499-519, 2017.

Ocean acidification and the Permo-Triassic mass extinction

Ocean acidification triggered by Siberian Trap volcanism was a possible kill mechanism for the Permo-Triassic Boundary mass extinction, but direct evidence for an acidification event is lacking. We present a high-resolution seawater pH record across this interval, using boron isotope data combined with a quantitative modeling approach. In the latest Permian, increased ocean alkalinity primed the Earth system with a low level of atmospheric CO2 and a high ocean buffering capacity. The first phase of extinction was coincident with a slow injection of carbon into the atmosphere, and ocean pH remained stable. During the second extinction pulse, however, a rapid and large injection of carbon caused an abrupt acidification event that drove the preferential loss of heavily calcified marine biota.

A high-throughput system for boron microsublimation and isotope analysis by total evaporation thermal ionization mass spectrometry

RATIONALE

Research on the ocean carbon cycle is vitally important due to the projected impacts of atmospheric CO2 on global temperatures and climate change, but also on ocean chemistry. The direct influence of this CO2 rise on the seawater pH can be evaluated from the boron isotopic composition in biogenic carbonates; however, conscientious laboratory techniques and data treatment are vital in obtaining accurate and precise results. A rapid-throughput boron purification and Total Evaporation Thermal Ionization Mass Spectrometry method was developed for high accuracy and precision boron isotopic analysis for small (ng) sample sizes.

METHODS

An improved microsublimation method, in which up to 20 samples can be processed simultaneously under identical temperature conditions, was developed. Several tests have confirmed the viability of this technique. First, seawater and Porites coral samples were processed with H2 O2 and the results compared with those obtained using microsublimation; second, the impact of various sublimation times was evaluated; and third, quantitative recovery was assessed using standard addition.

RESULTS

Microsublimation provides a valid method for the quantitative recovery and separation of boron from both major elements and organic matter under low-blank conditions. The close agreement of our results with published values validates the accuracy of the measurements. The isotopic ratio for SRM 951a boric acid isotopic standard was 4.0328 ± 0.0054 (2 STD, n = 25). The reproducibility of boron isotopic composition for standards including AE121, IAEA B-1 and an in-house coral standard UM-CP1 was ±0.68‰ (2 STD, n = 15), ±1.12‰ (2 STD, n = 24), and ±1.17‰ (2 STD, n = 14), respectively. The sample sizes were <1 ng for each measurement.

CONCLUSIONS

The developed method for preparing and measuring boron isotopic values in a variety of carbonate materials should facilitate the reconstruction of past ocean pH conditions with decadal-scale resolution.

Geobiological constraints on Earth system sensitivity to CO₂ during the Cretaceous and Cenozoic

Earth system climate sensitivity (ESS) is the long-term (>10³ year) response of global surface temperature to doubled CO₂ that integrates fast and slow climate feedbacks. ESS has energy policy implications because global temperatures are not expected to decline appreciably for at least 10³ year, even if anthropogenic greenhouse gas emissions drop to zero. We report provisional ESS estimates of 3 °C or higher for some of the Cretaceous and Cenozoic based on paleo-reconstructions of CO₂ and temperature. These estimates are generally higher than climate sensitivities simulated from global climate models for the same ancient periods (approximately 3 °C). Climate models probably do not capture the full suite of positive climate feedbacks that amplify global temperatures during some globally warm periods, as well as other characteristic features of warm climates such as low meridional temperature gradients. These absent feedbacks may be related to clouds, trace greenhouse gases (GHGs), seasonal snow cover, and/or vegetation, especially in polar regions. Better characterization and quantification of these feedbacks is a priority given the current accumulation of atmospheric GHGs.

Boron and marine life: a new look at an enigmatic bioelement

On the occasion of the 200th anniversary of the discovery of boron, we review the oceanic biogeochemistry of boron as well as suitable analytical techniques for its determination. This overview includes aspects of biogeochemistry including geochemical stable isotope variations, uptake, transport, storage, nutritional value, toxicity, and distribution within biological materials, providing a framework for discussion of the role of boron in marine organisms, which remains largely enigmatic.

Boron in plants: deficiency and toxicity

Boron (B) is an essential nutrient for normal growth of higher plants, and B availability in soil and irrigation water is an important determinant of agricultural production. To date, a primordial function of B is undoubtedly its structural role in the cell wall; however, there is increasing evidence for a possible role of B in other processes such as the maintenance of plasma membrane function and several metabolic pathways. In recent years, the knowledge of the molecular basis of B deficiency and toxicity responses in plants has advanced greatly. The aim of this review is to provide an update on recent findings related to these topics, which can contribute to a better understanding of the role of B in plants.

Isotope and ion selectivity in reverse osmosis desalination: geochemical tracers for man-made freshwater

A systematic measurement of ions and 2H/1H, 7Li/6Li, 11B/10B, 18O/ 16O, and 87Sr/86Sr isotopes in feed-waters, permeates, and brines from commercial reverse osmosis (RO) desalination plants in Israel (Ashkelon, Eilat, and Nitzana) and Cyprus (Larnaca) reveals distinctive geochemical and isotopic fingerprints of fresh water generated from desalination of seawater (SWRO) and brackish water (BWRO). The degree of isotope fractionation during the passage of water and solutes through the RO membranes depends on the medium (solvent-water vs. solutes), chemical speciation of the solutes, their charge, and their mass difference. O, H, and Sr isotopes are not fractionated during the RO process. 7Li is preferentially rejected in low pH RO, and B isotope fractionation depends on the pH conditions. Under low pH conditions, B isotopes are not significantly fractionated, whereas at high pH, RO permeates are enriched by 20 per thousand in 11B due to selective rejection of borate ion and preferential permeation of 11B-enriched boric acid through the membrane. The specific geochemical and isotopic fingerprints of SWRO provide a unique tool for tracing "man-made" fresh water as an emerging recharge component of natural water resources.

Photoinduced electron and proton transfer in the hydrogen-bonded pyridine-pyrrole system

We present here a detailed analysis of the mechanism of photoinduced electron and proton transfer in the planar pyrrole-pyridine hydrogen-bonded system, a model for the photochemistry of hydrogen bonds in DNA base pairs. Two different crossings, an avoided crossing and a conical intersection, are the key steps for forward and backward electron and proton transfer providing to the system photostability against UV radiation by restoring the system in its initial electronic and geometric structure.

Hydrogen-Abstracted Adenine−Thymine Radicals with Interesting Transferable Properties

The formation of radicals on DNA bases through various pathways can lead to harmful structural alterations. Such processes are of interest for preventing alteration of healthy DNA and, conversely, to develop more refined methods for inhibiting the replication of unwanted mutagenic DNA. In the present work, we explore theoretically the energetic and structural properties of the nine possible neutral radicals formed via hydrogen abstraction from the adenine-thymine base pair. The lowest energy radical is formed by loss of a hydrogen atom from the methyl group of thymine. The next lowest energy radicals, lying 8 and 9 kcal mol-1 higher than the global minimum, are those in which hydrogens are removed from the two nitrogens that would join the base pair to 2-deoxyribose in double-stranded DNA. The other six radicals lie between 16 and 32 kcal mol-1 higher in energy. Unlike the guanine-cytosine base pair, adenine-thymine (A-T) exhibits only minor structural changes upon hydrogen abstraction, with all A-T derived radicals maintaining planarity. Moreover, the energetic ordering for the radicals of the two isolated bases (adenine and thymine) is preserved upon formation of the base pair, though with a wider spread of energies. Even more significantly, the energetic interleaving of the (A-H)*-T and A-(T-H)* radicals is correctly predicted from the X-H bond dissociation energies of the isolated adenine and thymine. This suggests that the addition of the hydrogen-bonded complement base only marginally affects the bond energies.

Coadsorption of guanine and cytosine on graphite: ordered structure based on GC pairing

Nanostructures formed by coadsorption of the complementary DNA bases guanine (G) and cytosine (C) at a graphite surface in 1-octanol solvent were investigated by in situ scanning tunneling microscopy. The high-resolution observations showed for the first time a well-ordered coadsorption structure, attributed to rows formed from Watson-Crick G-C pairs, which was distinctly different from the structures observed for the individual G/C components. The observed coadsorption structure has been modeled by self-consistent charge density-functional-based tight-binding (SCC-DFTB) calculations, providing information on the intermolecular interactions underlying its formation.

Ionization spectroscopy of a DNA base: vacuum-ultraviolet mass-analyzed threshold ionization spectroscopy of jet-cooled thymine

The high-resolution ionization spectroscopy of DNA bases is reported for the first time. Vacuum-UV mass-analyzed threshold ionization (VUV-MATI) spectrum of jet-cooled thymine provides not only the most precise ionization potential but also its vibrational structure in the ground cationic state.

Triplet (pi,pi) reactivity of the guanine-cytosine DNA base pair: benign deactivation versus double tautomerization via intermolecular hydrogen transfer

Ab initio computations (CASSCF/6-31G* supported by CAS-PT2 single-point calculations) are used to study the reactivity of the triplet excited state of the guanine-cytosine DNA base pair. When the triplet excitation is centered on cytosine there is a competition between benign deactivation to the ground state and a hydrogen transfer route that can trigger double tautomerization. The calculated barriers favor the benign deactivation, but this route goes through a singlet/triplet intersystem crossing with small spin-orbit coupling. Therefore, the potentially mutagenic, double tautomerization route cannot be ruled out completely, and the two paths are probably an alternative to the well-known cytidine photodimerization reaction.

Why boron?

It is now more than 80 years since boron was convincingly demonstrated to be essential for normal growth of higher plants. However, its biochemical role is not well understood at the moment. Several recent reviews propose that B is implicated in three main processes: keeping cell wall structure, maintaining membrane function, and supporting metabolic activities. However, in the absence of conclusive evidence, the primary role of boron in plants remains elusive. Besides plants, growth of specific bacteria, such as heterocystous cyanobacteria and the recently reported actinomycetes of the genus Frankia, requires B, particularly for the stability of the envelopes that control the access of the nitrogenase-poisoning oxygen when they grow under N2-fixing conditions. Likewise, a role for B for animal embryogenesis and other developmental processes is being established. Finally, a new feature of the role of boron comes from signaling mechanisms for communication among bacteria and among legumes and rhizobia leading to N2-fixing symbiosis, and it is possible that new roles for B, based on its special chemistry and its interaction with Ca would appear in the world of signal transduction pathways. In conclusion, the diversity of roles played by B might indicate that either the micronutrient is involved in numerous processes or that its deficiency has a pleiotropic effect. The arising question is why such an element? Since all of the roles clearly established for B are related to its capacity to form diester bridges between cis-hydroxyl-containing molecules, we propose that the main reason for B essentiality is the stabilization of molecules with cis-diol groups turning them effective, irrespectively of their function.

Accurate interaction energies of hydrogen-bonded nucleic acid base pairs

Hydrogen-bonded nucleic acids base pairs substantially contribute to the structure and stability of nucleic acids. The study presents reference ab initio structures and interaction energies of selected base pairs with binding energies ranging from -5 to -47 kcal/mol. The molecular structures are obtained using the RI-MP2 (resolution of identity MP2) method with extended cc-pVTZ basis set of atomic orbitals. The RI-MP2 method provides results essentially identical with the standard MP2 method. The interaction energies are calculated using the Complete Basis Set (CBS) extrapolation at the RI-MP2 level. For some base pairs, Coupled-Cluster corrections with inclusion of noniterative triple contributions (CCSD(T)) are given. The calculations are compared with selected medium quality methods. The PW91 DFT functional with the 6-31G basis set matches well the RI-MP2/CBS absolute interaction energies and reproduces the relative values of base pairing energies with a maximum relative error of 2.6 kcal/mol when applied with Becke3LYP-optimized geometries. The Becke3LYP DFT functional underestimates the interaction energies by few kcal/mol with relative error of 2.2 kcal/mol. Very good performance of nonpolarizable Cornell et al. force field is confirmed and this indirectly supports the view that H-bonded base pairs are primarily stabilized by electrostatic interactions.

Carbon dioxide and climate over the past 300 Myr

The link between atmospheric CO(2) levels and global warming is an axiom of current public policy, and is well supported by physicochemical experiments, by comparative planetary climatology and by geochemical modelling. Geological tests of this idea seek to compare proxies of past atmospheric CO(2) with other proxies of palaeotemperature. For at least the past 300 Myr, there is a remarkably high temporal correlation between peaks of atmospheric CO(2), revealed by study of stomatal indices of fossil leaves of Ginkgo, Lepidopteris, Tatarina and Rhachiphyllum, and palaeotemperature maxima, revealed by oxygen isotopic (delta(18)O) composition of marine biogenic carbonate. Large and growing databases on these proxy indicators support the idea that atmospheric CO(2) and temperature are coupled. In contrast, CO(2)-temperature uncoupling has been proposed from geological time-series of carbon isotopic composition of palaeosols and of marine phytoplankton compared with foraminifera, which fail to indicate high CO(2) at known times of high palaeotemperature. Failure of carbon isotopic palaeobarometers may be due to episodic release of CH(4), which has an unusually light isotopic value (down to -110 per thousand, and typically -60 per thousand delta(13)C) and which oxidizes rapidly (within 7-24 yr) to isotopically light CO(2). Past CO(2) highs (above 2000 ppmv) were not only times of catastrophic release of CH(4) from clathrates, but of asteroid and comet impacts, flood basalt eruptions and mass extinctions. The primary reason for iterative return to low CO(2) was carbon consumption by hydrolytic weathering and photosynthesis, perhaps stimulated by mountain uplift and changing patterns of oceanic thermohaline circulation. Sequestration of carbon was promoted in the long term by such evolutionary innovations as the lignin of forests and the sod of grasslands, which accelerated physicochemical weathering and delivery of nutrients to fuel oceanic productivity and carbon burial.

Reading a CO2 signal from fossil stomata

The inverse relationship between atmospheric CO₂ and the stomatal index (proportion of epidermal cells that are stomata) of vascular land plant leaves has led to the use of fossil plant cuticles for determining ancient levels of CO₂ . In contemporary plants the stomatal index repeatedly shows a lower sensitivity atmospheric CO₂ levels above 340 ppm in the short term. These observations demonstrate that the phenotypic response is nonlinear and may place constraints on estimating higher-than-present palaeo-CO₂ levels in this way. We review a range of evidence to investigate the nature of this nonlinearity. Our new data, from fossil Ginkgo cuticles, suggest that the genotypic response of fossil Ginkgo closely tracks the phenotypic response seen in CO₂ enrichment experiments. Reconstructed atmospheric CO₂ values from fossil Ginkgo cuticles compare well with the stomatal ratio method of obtaining a quantitative CO₂ signal from extinct fossil plants, and independent geochemical modelling studies of the long-term carbon cycle. Although there is self-consistency between palaeobiological and geochemical CO₂ estimates, it should be recognized that the nonlinear response is a limitation of the stomatal approach to estimating high palaeo-CO₂ levels.

Paleobotanical evidence for near present-day levels of atmospheric Co2 during part of the tertiary

Understanding the link between the greenhouse gas carbon dioxide (CO(2)) and Earth's temperature underpins much of paleoclimatology and our predictions of future global warming. Here, we use the inverse relationship between leaf stomatal indices and the partial pressure of CO(2) in modern Ginkgo biloba and Metasequoia glyptostroboides to develop a CO(2) reconstruction based on fossil Ginkgo and Metasequoia cuticles for the middle Paleocene to early Eocene and middle Miocene. Our reconstruction indicates that CO(2) remained between 300 and 450 parts per million by volume for these intervals with the exception of a single high estimate near the Paleocene/Eocene boundary. These results suggest that factors in addition to CO(2) are required to explain these past intervals of global warmth.

A 300-million-year record of atmospheric carbon dioxide from fossil plant cuticles

To understand better the link between atmospheric CO2 concentrations and climate over geological time, records of past CO2 are reconstructed from geochemical proxies. Although these records have provided us with a broad picture of CO2 variation throughout the Phanerozoic eon (the past 544 Myr), inconsistencies and gaps remain that still need to be resolved. Here I present a continuous 300-Myr record of stomatal abundance from fossil leaves of four genera of plants that are closely related to the present-day Ginkgo tree. Using the known relationship between leaf stomatal abundance and growing season CO2 concentrations, I reconstruct past atmospheric CO2 concentrations. For the past 300 Myr, only two intervals of low CO2 (<1,000 p.p.m.v.) are inferred, both of which coincide with known ice ages in Neogene (1-8 Myr) and early Permian (275-290 Myr) times. But for most of the Mesozoic era (65-250 Myr), CO2 levels were high (1,000-2,000 p.p.m.v.), with transient excursions to even higher CO2 (>2,000 p.p.m.v.) concentrations. These results are consistent with some reconstructions of past CO2 (refs 1, 2) and palaeotemperature records, but suggest that CO2 reconstructions based on carbon isotope proxies may be compromised by episodic outbursts of isotopically light methane. These results support the role of water vapour, methane and CO2 in greenhouse climate warming over the past 300 Myr.