PHYLOGENETIC ANALYSES, GENE DOSAGE EFFECT AND SELECTION IN MEMBERS OF THE LATERAL BOUNDARY DOMAIN (LBD) GENES TRANSCRIPTION FACTOR FAMILY

Wood formation is an economically and environmentally important process and has played a significant role in the evolution of terrestrial plants. Despite its significance, the molecular underpinnings of the process are still poorly understood. We have previously shown that four Lateral Boundary Domain (LBD) transcription factors have important roles in the regulation of wood formation with two (LBD1 and LBD4) involved in secondary phloem and ray cell development and two (LBD15 and LBD18) in secondary xylem formation. Here, we used comparative phylogenetic analyses to test potential roles of the four LBD genes in the evolution of woodiness. We studied the copy number and variation in DNA and amino acid sequences of the four LBDs in a wide range of woody and herbaceous plant taxa with fully sequenced and annotated genomes. LBD1 showed the highest gene copy number across the studied species, and LBD1 gene copy number was strongly and significantly correlated with the level of ray seriation. The lianas, cucumber and grape, with multiseriate ray cells showed the highest gene copy number (12 and 11, respectively). Because lianas’ growth habit requires significant twisting and bending, the less lignified ray parenchyma cells likely facilitate stem flexibility and maintenance of xylem conductivity. We further demonstrate conservation of amino acids in the LBD18 protein sequences that are specific to woody taxa. Neutrality tests showed evidence for strong purifying selection on these gene regions across various orders, indicating adaptive convergent evolution of LBD18. Structural modeling demonstrates that the conserved amino acids have a significant impact on the tertiary protein structure and thus are likely of significant functional importance.

Influence of Mechanical and Thermal Boundary Conditions on Stabilizing/Destabilizing Mechanisms in Evaporating Liquid Films

Liquid films, evaporating or non-evaporating, are ubiquitous in nature and technology. The dynamics of evaporating liquid films is a study applicable in several industries such as water recovery, heat exchangers, crystal growth, drug design etc. The theory describing the dynamics of liquid films crosses several fields such as engineering, mathematics, material science, biophysics and volcanology to name a few. Interfacial instabilities typically manifest by the undulation of an interface from a presumed flat state or by the onset of a secondary flow state from a primary quiescent state or both. To study the instabilities affecting liquid films, an evaporating/non-evaporating Newtonian liquid film is subject to a perturbation. Numerical analysis is conducted on configurations of such liquid films being heated on solid surfaces in order to examine the various stabilizing and destabilizing mechanisms that can cause the formation of different convective structures. These convective structures have implications towards heat transfer that occurs via this process. Certain aspects of this research topic have not received attention, as will be obvious from the literature review. Static, horizontal liquid films on solid surfaces are examined for their resistance to long wave type instabilities via linear stability analysis, method of normal modes and finite difference methods. The spatiotemporal evolution equation, available in literature, describing the time evolution of a liquid film heated on a solid surface, is utilized to analyze various stabilizing/destabilizing mechanisms affecting evaporating and non-evaporating liquid films. The impact of these mechanisms on the film stability and structure for both buoyant and non-buoyant films will be examined by the variation of mechanical and thermal boundary conditions. Films evaporating in zero gravity are studied using the evolution equation. It is found that films that are stable to long wave type instabilities in terrestrial gravity are prone to destabilization via long wave instabilities in zero gravity.

Diagenesis of a light, tight-oil chert reservoir at the Ediacaran/Cambrian boundary, Sultanate of Oman

The Al Shomou Silicilyte Member (Athel Formation) in the South Oman Salt Basin shares many of the characteristics of a light, tight-oil (LTO) reservoir: it is a prolifi c source rock mature for light oil, it produces light oil from a very tight matrix and reservoir, and hydraulic fracking technology is required to produce the oil. What is intriguing about the Al Shomou Silicilyte, and different from other LTO reservoirs, is its position related to the Precambrian/Cambrian Boundary (PCB) and the fact that it is a ‘laminated chert‘ rather than a shale. In an integrated diagenetic study we applied microstructural analyses (SEM, BSE) combined with state-of-the-art stable isotope and trace element analysis of the silicilyte matrix and fractures. Fluid inclusion microthermometry was applied to record the salinity and minimum trapping temperatures. The microstructural investigations reveal a fi ne lamination of the silicilyte matrix with a mean lamina thickness of ca. 20 μm consisting of predominantly organic matter-rich and fi nely crystalline quartz-rich layers, respectively. Authigenic, micron-sized idiomorphic quartz crystals are the main matrix components of the silicilyte. Other diagenetic phases are pyrite, apatite, dolomite, magnesite and barite cements. Porosity values based on neutron density logs and core plug data indicate porosity in the silicilyte ranges from less than 2% to almost to 40%. The majority of the pore space in the silicilyte is related to (primary) inter-crystalline pores, with locally important oversized secondary pores. Pore casts of the silica matrix show that pores are extremely irregular in three dimensions, and are generally interconnected by a complex web or meshwork of fi ne elongate pore throats. Mercury injection capillary data are in line with the microstructural observations suggesting two populations of pore throats, with an effective average modal diameter of 0.4 μm. The acquired geochemical data support the interpretation that the primary source of the silica is the ambient seawater rather than hydrothermal or biogenic. A maximum temperature of ca. 45°C for the formation of microcrystalline quartz in the silicilyte is good evidence that the lithifi cation and crystallization of quartz occurred in the fi rst 5 Ma after deposition. Several phases of brittle fracturing and mineralization occurred in response to salt tectonics during burial. The sequences of fracture-fi lling mineral phases (dolomite - layered chalcedony – quartz – apatite - magnesite I+II - barite – halite) indicates a complex fl uid evolution after silicilyte lithifi cation. Primary, all-liquid fl uid inclusions in the fracturefi lling quartz are good evidence of growth beginning at low temperatures, i.e. ≤ 50ºC. Continuous precipitation during increasing temperature and burial is documented by primary two-phase fl uid inclusions in quartz cements that show brines at 50°C and fi rst hydrocarbons at ca. 70°C. The absolute timing of each mineral phase can be constrained based on U-Pb geochronometry, and basin modelling. Secondary fl uid inclusions in quartz, magnesite and barite indicate reactivation of the fracture system after peak burial temperature during the major cooling event, i.e. uplift, between 450 and 310 Ma. A number of fi rst-order trends in porosity and reservoir-quality distribution are observed which are strongly related to the diagenetic and fl uid history of the reservoir: the early in-situ generation of hydrocarbons and overpressure development arrests diagenesis and preserves matrix porosity. Chemical compaction by pressure dissolution in the fl ank areas could be a valid hypothesis to explain the porosity variations in the silicilitye slabs resulting in lower porosity and poorer connectivity on the fl anks of the reservoir. Most of the hydrocarbon storage and production comes from intervals characterized by Amthor et al. 114488 preserved micropores, not hydrocarbon storage in a fracture system. The absence of oil expulsion results in present-day high oil saturations. The main diagenetic modifi cations of the silicilyte occurred and were completed relatively early in its history, i.e. before 300 Ma. An instrumental factor for preserving matrix porosity is the diffi culty for a given slab to evacuate all the fl uids (water and hydrocarbons), or in other words, the very good sealing capacity of the salt embedding the slab.

Stabilization of subcritical bypass transition in the leading-edge boundary layer by suction

This work investigates the subcritical spatial transition in the swept Hiemenz boundary layer by means of direct numerical simulations (DNS). A pair of steady co-rotating vortices located at the attachment line is enforced as a primary disturbance leading to streaks which are stable. A small secondary, time-dependent disturbance interacts with these streaks such that instability and breakdown to turbulence may occur. The instability only occurs for a certain band of secondary disturbance frequencies. Positive secondary instability growth rates could be observed for Reynolds numbers as low as , whereas the linear critical Reynolds number is. Uniform wall suction is shown to stabilise this transition mechanism, analogously to results from linear stability theory. The effects of suction on the formation of primary streaks and on the secondary growth rate are decoupled. For streaks of different suction whose amplitude is held constant by adjusting the Reynolds number, the suction is shown to increase the growth rate of the secondary instability. The stabilising influence of wall suction consists in decreasing the streak amplitude only. Depending on the Reynolds number and the suction strength, breakdown may either occur locally and may be convected along the far-field streamlines, or occur globally and cover broad regions in the downstream direction.

Mineralogical and isotopic record of diagenesis from the Opalinus Clay formation at Benken, Switzerland: Implications for the modeling of pore-water chemistry in a clay formation

Argillaceous rocks are considered to be a suitable geological barrier for the long-term containment of wastes. Their efficiency at retarding contaminant migration is assessed using reactive-transport experiments and modeling, the latter requiring a sound understanding of pore-water chemistry. The building of a pore-water model, which is mandatory for laboratory experiments mimicking in situ conditions, requires a detailed knowledge of the rock mineralogy and of minerals at equilibrium with present-day pore waters. Using a combination of petrological, mineralogical, and isotopic studies, the present study focused on the reduced Opalinus Clay formation (Fm) of the Benken borehole (30 km north of Zurich) which is intended for nuclear-waste disposal in Switzerland. A diagenetic sequence is proposed, which serves as a basis for determining the minerals stable in the formation and their textural relationships. Early cementation of dominant calcite, rare dolomite, and pyrite formed by bacterial sulfate reduction, was followed by formation of iron-rich calcite, ankerite, siderite, glauconite, (Ba, Sr) sulfates, and traces of sphalerite and galena. The distribution and abundance of siderite depends heavily on the depositional environment (and consequently on the water column). Benken sediment deposition during Aalenian times corresponds to an offshore environment with the early formation of siderite concretions at the water/sediment interface at the fluctuating boundary between the suboxic iron reduction and the sulfate reduction zones. Diagenetic minerals (carbonates except dolomite, sulfates, silicates) remained stable from their formation to the present. Based on these mineralogical and geochemical data, the mineral assemblage previously used for the geochemical model of the pore waters at Mont Terri may be applied to Benken without significant changes. These further investigations demonstrate the need for detailed mineralogical and geochemical study to refine the model of pore-water chemistry in a clay formation.

Topology of the ambient boundary and the convergence of causal curves

We discuss the topological nature of the boundary spacetime, the conformal infinity of the ambient cosmological metric. Due to the existence of a homothetic group, the bounding spacetime must be equipped not with the usual Euclidean metric topology but with the Zeeman fine topology. This then places severe constraints to the convergence of a sequence of causal curves and the extraction of a limit curve, and also to our ability to formulate conditions for singularity formation.

Kelvin-Helmholtz instabilities at the magnetic cavity boundary of comet 67P/Churyumov-Gerasimenko

We investigate the plasma environment of comet 67P/Churyumov-Gerasimenko, the target of the European Space Agency's Rosetta mission. Rosetta will rendezvous with the comet in 2014 at almost 3.5 AU and follow it all the way to and past perihelion at 1.3 AU. During its journey towards the inner solar system the comet's environment will significantly change. The interaction of the solar wind with a well developed neutral coma leads to the formation of an upstream bow shock and, closer to the comet, the inner shock separating the solar wind, with cometary pick-up ions mass-loaded, from the inner cometary ions which are dragged outward through abundant collisions and charge exchange with the expanding neutral gas. As a consequence the interplanetary magnetic field is prevented from penetrating the innermost region of the comet, the so-called magnetic cavity. We use our magnetohydrodynamics model BATSRUS (Block-Adaptive-Tree-Solarwind-Roe-Upwind-Scheme) to simulate the solar wind - comet interaction. The model includes photoionization, ion-electron recombination, and charge exchange. Under certain conditions our model predicts an unstable plasma flow at the inner shock. We show that the plasma shear flow around the magnetic cavity can lead to Kelvin-Helmholtz instabilities. We investigate the onset of this phenomenon with change of heliocentric distance and furthermore show that a previously stable magnetic cavity boundary can become unstable when the neutral gas is predominately released from the dayside of the comet.

Volcanic terrain and the possible periglacial formation of "excess ice" at the mid-latitudes of Utopia Planitia, Mars

At the mid-latitudes of Utopia Planitia (UP), Mars, a suite of spatially-associated landforms exhibit geomorphological traits that, on Earth, would be consistent with periglacial processes and the possible freeze-thaw cycling of water. The suite comprises small-sized polygonally-patterned ground, polygon-junction and -margin pits, and scalloped, rimless depressions. Typically, the landforms incise a dark-toned terrain that is thought to be ice-rich. Here, we investigate the dark-toned terrain by using high resolution images from the HiRISE as well as near-infrared spectral-data from the OMEGA and CRISM. The terrain displays erosional characteristics consistent with a sedimentary nature and near-infrared spectra characterised by a blue slope similar to that of weathered basaltic-tephra. We also describe volcanic terrain that is dark-toned and periglacially-modified in the Kamchatka mountain-range of eastern Russia. The terrain is characterised by weathered tephra inter-bedded with snow, ice-wedge polygons and near-surface excess ice. The excess ice forms in the pore space of the tephra as the result of snow-melt infiltration and, subsequently, in-situ freezing. Based on this possible analogue, we construct a three-stage mechanism that explains the possible ice-enrichment of a broad expanse of dark-toned terrain at the mid-latitudes of UP: (1) the dark-toned terrain accumulates and forms via the regional deposition of sediments sourced from explosive volcanism; (2) the volcanic sediments are blanketed by atmospherically-precipitated (H2O) snow, ice or an admixture of the two, either concurrent with the volcanic-events or between discrete events; and, (3) under the influence of high obliquity or explosive volcanism, boundary conditions tolerant of thaw evolve and this, in turn, permits the migration, cycling and eventual formation of excess ice in the volcanic sediments. Over time, and through episodic iterations of this scenario, excess ice forms to decametres of depth. (C) 2015 Elsevier B.V. All rights reserved.

Comparative studies of Hox genes in mammalian limb and vertebral pattern formation

Divergence of anterior-posterior (AP) limb pattern and differences in vertebral column morphology are the two main examples of mammalian evolution. The Hox genes (homeobox containing gene) have been implicated in driving evolution of these structures. However, regarding Hox genes, how they contribute to the generation of mammalian morphological diversities, is still unclear. Implementing comparative gene expression and phenotypic rescue studies for different mammalian Hox genes could aid in unraveling this mystery. In the first part of this thesis, the expression pattern of Hoxd13 gene, a key Hox gene in the establishment of the limb AP pattern, was examined in developing limbs of bats and mice. Bat forelimbs exhibit a pronounced asymmetric AP pattern and offer a good model to study the molecular mechanisms that contribute to the variety of mammalian limbs. The data showed that the expression domain of bat Hoxd13 was shifted prior to the asymmetric limb plate expansion, whereas its domain in mice was much more symmetric. This finding reveals a correlation between the divergence of Hoxd13 expression and the AP patterning difference in limb development. The second part of this thesis details a phenotypic rescue approach by human HOXB1-9 transgenes in mice with Hoxb1-9 deletion, The mouse mutants displayed homeosis in cervical and anterior thoracic vertebrae. The human transgenes entirely rescued the mouse mutants, suggesting that these human HOX genes have similar functions to their mouse orthologues in anterior axial skeletal patterning. The anterior expressing human HOXB transgenes such as HOXB1-3 were expressed in the mouse embryonic trunk in a similar manner as their murine orthologues. However, the anterior boundary of human HOXB9 expression domain was more posterior than that of the mouse Hoxb9 by 2-3 somites. These data provide the molecular support for the hypothesis that Hox genes are responsible for maintaining similar anterior axial skeletal architectures cervical and anterior thoracic regions, but different architectures in lumbar and posterior thoracic regions between humans and mice. ^

Mineralogy and stable oxygen isotope ratios of the Cretaceous-Tertiary boundary

Results of detailed mineralogical, chemical, and oxygen isotope analyses of the clay minerals and zeolites from two Cretaceous-Tertiary (K/T) boundary regions, Stevns Klint, Denmark, and Deep Sea Drilling Project (DSDP) Hole 465A in the north central Pacific Ocean, are presented. In the central part of the Stevns Klint K/T boundary layer, the only clay mineral detected by x-ray diffraction is a pure smectite with > 95 percent expandable layers. No detrital clay minerals or quartz were observed in the clay size fraction in these beds, whereas the clay minerals above and below the boundary layer are illite and mixed-layer smectite-illite of detrital origin as well as quartz. The mineralogical purity of the clay fraction, the presence of smectite only at the boundary, and the d18O value of the smectite (27.2 ± 0.2 per mil) suggest that it formed in situ by alteration of glass. Formation from impact rather than from volcanic glass is supported by its major element chemistry. The high content of iridium and other siderophile elements is not due to the cessation of calcium carbonate deposition and resulting slow sedimentation rates. At DSDP Hole 465A, the principal clay mineral in the boundary zone (80 to 143 centimeters) is a mixed-layer smectite-illite with >=90 percent expandable layers, accompanied by some detrital quartz and small amounts of a euhedral authigenic zeolite (clinoptilolite). The mixed-layer smectite-illite from the interval 118 to 120 centimeters in the zone of high iridium abundance has a very low rare earth element content; the negative cerium anomaly indicates formation in the marine environment. This conclusion is corroborated by the d18O value of this clay mineral (27.1 ± 0.2 per mil). Thus, this mixed-layer smectite-illite formed possibly from the same glass as the K/T boundary smectite at Stevns Klint, Denmark.

Tab. 1 Analyses of major phases in Vestgötabreen formation schists

The glaucophane schists of Oscar II Land, it has been suggested, originated in a compressive plate boundary subduction zone environment. An alternative hypothesis is presented here linking the metamorphism of these schists with that of the surrounding pre-Carboniferous rocks. It has been estimated from mineralogical and textural relationships that at the time of metamorphism these rocks exceeded 30 km in thickness. Similarly, an ambient geothermal gradient of 15° C/km has been calculated for the now exposed succession. Pressures of sufficient magnitude would be realised near the base of this geosynclinal pile to produce eclogite from rocks of basic composition. Subsequent synmetamorphic penetrative deformation would give rise to glaucophane and greenschist facies assemblages.

Oxygen isotope values from biogenic apatie (conodont elements and fish teeth) from the Lower Triassic Mianwali Formation (Salt Range, Pakistan)

Recovery from the end-Permian mass extinction is frequently described as delayed, with complex ecological communities typically not found in the fossil record until the Middle Triassic epoch. However, the taxonomic diversity of a number of marine groups, ranging from ammonoids to benthic foraminifera, peaked rapidly in the Early Triassic. These variations in biodiversity occur amidst pronounced excursions in the carbon isotope record, which are compatible with episodes of massive CO2 outgassing from the Siberian Large Igneous Province. Here we present a high-resolution Early Triassic temperature record based on the oxygen isotope composition of pristine apatite from fossil conodonts. Our reconstruction shows that the beginning of the Smithian substage of the Early Triassic was marked by a cooler climate, followed by an interval of warmth lasting until the Spathian substage boundary. Cooler conditions resumed in the Spathian. We find the greatest increases in taxonomic diversity during the cooler phases of the early Smithian and early Spathian. In contrast, a period of extreme warmth in the middle and late Smithian was associated with floral ecological change and high faunal taxonomic turnover in the ocean. We suggest that climate upheaval and carbon-cycle perturbations due to volcanic outgassing were important drivers of Early Triassic biotic recovery.

Larcform 1 - single column model intercomparison of Arctic air formation, link to model results in NetCDF format

Weather and climate models struggle to represent lower tropospheric temperature and moisture profiles and surface fluxes in Arctic winter, not least because they lack or misrepresent physical processes that are specific to high latitudes. The Arctic boundary layer in winter has been observed to be in either a radiatively clear or cloudy state: The radiatively clear state is characterized by strong surface radiative cooling leading to the build-up of surface-based temperature inversions, whereas the cloudy state occurs when cloud liquid water is present in the atmospheric column, allowing little or no surface radiative cooling and leading to weaker and typically elevated temperature inversions. Many large-scale models have been shown to lack the cloudy state, and some do substantially underestimate stability in the clear state. We here present results from the first Lagrangian ARCtic air FORMation experiment (Larcform 1), a GASS (Global atmospheric system studies) single-column model intercomparison which reproduces these biases of large-scale models in an idealised setup.

Atmospheric nitrate concentrations and isotope composition for samples collected in the marine boundary layer in 2006 and 2007

The comprehensive isotopic composition of atmospheric nitrate (i.e., the simultaneous measurement of all its stable isotope ratios: 15N/14N, 17O/16O and 18O/16O) has been determined for aerosol samples collected in the marine boundary layer (MBL) over the Atlantic Ocean from 65°S (Weddell Sea) to 79°N (Svalbard), along a ship-borne latitudinal transect. In nonpolar areas, the d15N of nitrate mostly deriving from anthropogenically emitted NOx is found to be significantly different (from 0 to 6 per mil) from nitrate sampled in locations influenced by natural NOx sources (-4 ± 2) per mil. The effects on d15N(NO3-) of different NOx sources and nitrate removal processes associated with its atmospheric transport are discussed. Measurements of the oxygen isotope anomaly (D17O = d17O - 0.52 × d18O) of nitrate suggest that nocturnal processes involving the nitrate radical play a major role in terms of NOx sinks. Different D17O between aerosol size fractions indicate different proportions between nitrate formation pathways as a function of the size and composition of the particles. Extremely low d15N values (down to -40 per mil) are found in air masses exposed to snow-covered areas, showing that snowpack emissions of NOx from upwind regions can have a significant impact on the local surface budget of reactive nitrogen, in conjunction with interactions with active halogen chemistry. The implications of the results are discussed in light of the potential use of the stable isotopic composition of nitrate to infer atmospherically relevant information from nitrate preserved in ice cores.