X-ray structure determination of a metastable state of carbonmonoxy myoglobin after photodissociation.

The x-ray structure of carbon monoxide (CO)-ligated myoglobin illuminated during data collection by a laser diode at the wavelength lambda = 690 nm has been determined to a resolution of 1.7 A at T = 36 K. For comparison, we also measured data sets of deoxymyoglobin and CO-ligated myoglobin. In the photon-induced structure the electron density associated with the CO ligand can be described by a tube extending from the iron into the heme pocket over more than 4 A. This density can be interpreted by two discrete positions of the CO molecule. One is close to the heme iron and can be identified to be bound CO. In the second, the CO is dissociated from the heme iron and lies on top of pyrrole ring C. At our experimental conditions the overall structure of myoglobin in the metastable state is close to the structure of a CO-ligated molecule. However, the iron has essentially relaxed into the position of deoxymyoglobin. We compare our results with those of Schlichting el al. [Schlichting, I., Berendzen, J., Phillips, G. N., Jr., & Sweet, R. M. (1994) Nature 317, 808-812], who worked with the myoglobin mutant (D122N) that crystallizes in the space group P6 and Teng et al. [Teng, T. Y., Srajer, V. & Moffat, K. (1994) Nat. Struct. Biol. 1, 701-705], who used native myoglobin crystals of the space group P2(1). Possible reasons for the structural differences are discussed.

Independent determination of symmetry and polarity in the Drosophila eye.

In each facet of the Drosophila compound eye, a cluster of photoreceptor cells assumes an asymmetric trapezoidal pattern. These clusters have opposite orientations above and below an equator, showing global dorsoventral mirror symmetry. However, in the mutant spiny legs, the polarization of each cluster appears to be random, so that no equator is evident. The apparent lack of an equator suggests that spiny legs+ may be involved in the establishment of global dorsoventral identity that might be essential for proper polarization of the photoreceptor clusters. Alternatively, a global dorsoventral pattern could be present, but spiny legs+ may be required for local polarization of individual clusters. Using an enhancer trap strain in which white+ gene expression is restricted to the dorsal field, we show that white+ expression in spiny legs correctly respects dorsoventral position even in facets with inappropriate polarizations; the dorsoventral boundary is indeed present, whereas the mechanism for polarization is perturbed. It is suggested that the boundary is established before the action of spiny legs+ by an independent mechanism.

A method for distance determination in proteins using a designed metal ion binding site and site-directed spin labeling: evaluation with T4 lysozyme.

The use of molecular genetics to introduce both a metal ion binding site and a nitroxide spin label into the same protein opens the use of paramagnetic metalnitroxyl interactions to estimate intramolecular distances in a wide variety of proteins. In this report, a His-Xaa3-His metal ion binding motif was introduced at the N terminus of the long interdomain helix of T4 lysozyme (Lys-65 --> His/Gln-69 --> His) of three mutants, each containing a single nitroxide-labeled cysteine residue at position 71, 76, or 80. The results show that Cu(II)-induced relaxation effects on the nitroxide can be quantitatively analyzed in terms of interspin distance in the range of 10-25 A using Redfield theory, as first suggested by Leigh [Leigh, J.S. (1970) J. Chem. Phys. 52, 2608-2612]. Of particular interest is the observation that distances can be determined both under rigid lattice conditions in frozen solution and in the presence of motion of the spins at room temperature under physiological conditions. The method should be particularly attractive for investigating structure in membrane proteins that are difficult to crystallize. In the accompanying paper, the technique is applied to a polytopic membrane protein, lactose permease.

Age determination of sediments of Site LO09-14 (Table 1)

A composite record (LO09-14) of three sediment cores from the subpolar North Atlantic (Reykjanes Ridge) was investigated in order to assess surface ocean variability during the last 11 kyr. The core site is today partly under the influence of the Irminger Current (IC), a branch of the North Atlantic Drift continuing northwestward around Iceland. However, it is also proximal to the Sub-Arctic Front (SAF) that may cause extra dynamic hydrographic conditions. We used statistical methods applied to the fossil assemblages of diatoms to reconstruct quantitative sea surface temperatures (SSTs). Our investigations give evidence for different regional signatures of Holocene surface oceanographic changes in the North Atlantic. Core LO09-14 reveal relatively low and highly variable SSTs during the early Holocene, indicating a weak IC and increased advection of subpolar water over the site. A mid-Holocene thermal optimum with a strong IC occurs from 7.5 to 5 kyr and is followed by cooler and more stable late Holocene surface conditions. Several intervals throughout the Holocene are dominated by the diatom species Rhizosolenia borealis, which we suggest indicates proximity to a strongly defined convergence front, most likely the SAF. Several coolings, reflecting southeastward advection of cold and ice-bearing waters, occur at 10.4, 9.8, 8.3, 7.9, 6.4, 4.7, 4.3 and 2.8 kyr. The cooling events recorded in the LO09-14 SSTs correlate well with both other surface records from the area and the NADW reductions observed at ODP Site 980 indicating a surface-deepwater linkage through the Holocene.

(Table 1) Age determination of sediment core PS51/092-12

Diatom assemblages were employed to study temporal changes of Siberian river runoff on the Laptev Sea shelf. Using a correlation between freshwater diatoms (%) in core-top sediments and summer surface water salinities from the inner Kara Sea, salinity conditions were reconstructed for a site northeast of the Lena River Delta (present water depth 32 m) since 9 calendar years (cal) ka. The reconstruction indicate a strong, near-coastal, and river-influenced environment at the site until about 8.6 cal ka. Corroborated by comparison with other proxy records from further to the east, surface salinities increased from 9 to 14 until about 7.4 cal ka, owing to ongoing global sea level rise and synchronous southward shift of the coastline. Although riverine water became less influential at the site since then, salinities still varied between 12.5 and 15, particularly during the last 3.5 kyr. These more recent salinity fluctuations agree well with reconstructions from just north of the Lena Delta, emphasizing the strong linkage between shelf hydrography and riverine discharge patterns in Arctic Siberia.

Age determination and stable isotope records of sediment core M78/1_235-1

Paleoenvironmental studies and climate models demonstrate that fluvial runoff and moisture availability in the Caribbean hinterland react very sensitively to climatic variations. Late Pleistocene and Holocene climate records document pronounced dry and wet periods over tropical South America mainly caused by shifts of the Intertropical Convergence Zone (ITCZ). However, forcing mechanisms for changes in the ITCZ position remain controversial. Here we present high-resolution foraminiferal Ba/Ca and d18Oseawater records from a core located within the Orinoco River outflow documenting abrupt hydrological changes in the Orinoco catchment area during the deglacial and Holocene. Our data, obtained from the surface-dwelling foraminifera Globigerinoides ruber (pink), show an abrupt increase in Ba/Ca ratios in the early Holocene, starting ~600 yr after the end of the Younger Dryas (YD) cold interval at ca. 10.8 ka and suggesting a massive reorganization of moisture sources in northern South America. In contrast, the salinity dependent d18Oseawater from the same samples shows a gradual decrease starting at the end of the YD. The offset of our Ba/Ca peak excludes meltwater release in conjunction with the northern Andean glacier retreat well before the end of the YD as a forcing mechanism. We suggest that the Ba/Ca record documents an abrupt increase in Ba-rich waters of a northern Andean source caused by the insolation-driven shift of the ITCZ and/or enhanced monsoon activity.

(Table 1) Age determination of sediment cores south of the Faeroe Islands

A study was made of three cores from the Faeroe-Shetland gateway, based on planktonic foraminifera, oxygen isotopes, accelerator mass spectrometry 14C dates, magnetic susceptibility, and counts of ice rafted debris (IRD). The data, covering the period 30-10 ka, show that during the Last Glacial Maximum the Arctic Front occupied a position close to the Faeroes, allowing a persisting inflow of Atlantic surface water into the Faeroe-Shetland Channel. The oceanographic environment during deposition of two IRD layers is influenced by Atlantic surface water masses during the lower IRD layer, with transport of icebergs from N-NW. Polar surface water conditions prevailed only during deposition of the upper IRD layer. There is no indication of surface meltwater influence in the region during the deglaciation, but there is a persistent influence of Atlantic surface water masses in the region. Thus we conclude that during almost the entire period (30-10 ka) the Faeroe-Shetland Channel was a gateway for transport of Atlantic surface water toward the Norwegian Sea.

High throughput determination of sequence-function relationships in protein and RNA

Thesis (Ph.D.)--University of Washington, 2016-06

Robust bucket position tracking for a large hydraulic excavator

The device we study is the excavation arm of a large hydraulic mining shovel having a multi-loop kinematic form. We describe an iterative algorithm that allows the position of the bucket to be tracked from measurements of the linear actuator extensions. The important characteristic of this algorithm is that it is numerically well-behaved when the linkage is close to singular configurations. While we focus on a specific device, the algorithm is easy to adapt to other multi-loop linkages. (C) 2004 Elsevier Ltd. All rights reserved.

Numerical method for determination of the NMR frequency of the single-qubit operation in a silicon-based solid-state quantum computer

A numerical method is introduced to determine the nuclear magnetic resonance frequency of a donor (P-31) doped inside a silicon substrate under the influence of an applied electric field. This phosphorus donor has been suggested for operation as a qubit for the realization of a solid-state scalable quantum computer. The operation of the qubit is achieved by a combination of the rotation of the phosphorus nuclear spin through a globally applied magnetic field and the selection of the phosphorus nucleus through a locally applied electric field. To realize the selection function, it is required to know the relationship between the applied electric field and the change of the nuclear magnetic resonance frequency of phosphorus. In this study, based on the wave functions obtained by the effective-mass theory, we introduce an empirical correction factor to the wave functions at the donor nucleus. Using the corrected wave functions, we formulate a first-order perturbation theory for the perturbed system under the influence of an electric field. In order to calculate the potential distributions inside the silicon and the silicon dioxide layers due to the applied electric field, we use the multilayered Green's functions and solve an integral equation by the moment method. This enables us to consider more realistic, arbitrary shape, and three-dimensional qubit structures. With the calculation of the potential distributions, we have investigated the effects of the thicknesses of silicon and silicon dioxide layers, the relative position of the donor, and the applied electric field on the nuclear magnetic resonance frequency of the donor.

Precise orbit determination and analysis from satellite altimetry and laser ranging

For optimum utilization of satellite-borne instrumentation, it is necessary to know precisely the orbital position of the spacecraft. The aim of this thesis is therefore two-fold - firstly to derive precise orbits with particular emphasis placed on the altimetric satellite SEASAT and secondly, to utilize the precise orbits, to improve upon atmospheric density determinations for satellite drag modelling purposes. Part one of the thesis, on precise orbit determinations, is particularly concerned with the tracking data - satellite laser ranging, altimetry and crossover height differences - and how this data can be used to analyse errors in the orbit, the geoid and sea-surface topography. The outcome of this analysis is the determination of a low degree and order model for sea surface topography. Part two, on the other hand, mainly concentrates on using the laser data to analyse and improve upon current atmospheric density models. In particular, the modelling of density changes associated with geomagnetic disturbances comes under scrutiny in this section. By introducing persistence modelling of a geomagnetic event and solving for certain geomagnetic parameters, a new density model is derived which performs significantly better than the state-of-the-art models over periods of severe geomagnetic storms at SEASAT heights. This is independently verified by application of the derived model to STARLETTE orbit determinations.

Voluntary Termination In Restaurants: An Exploratory Determination of Causes

Each year high numbers of employees voluntarily terminate their employment with restaurant organizations. The author reports the results of an exploratory determination of the reasons why a group of employees who left during a three-month period did terminate with the organizations. The subjects were examined as a total group and as subgroups identified by position. It was found that 47.8 percent of the time the manager is able to influence the factors which may lead to voluntary separation from the organization.

Age determination and paleotemperatures of western Mediterranean Sea sediments

Sea surface temperature (SST) profiles over the last 25 kyr derived from alkenone measurements are studied in four cores from a W-E latitudinal transect encompassing the Gulf of Cadiz (Atlantic Ocean), the Alboran Sea, and the southern Tyrrhenian Sea (western Mediterranean). The results document the sensitivity of the Mediterranean region to the short climatic changes of the North Atlantic Ocean, particularly those involving the latitudinal position of the polar front. The amplitude of the SST oscillations increases toward the Tyrrhenian Sea, indicating an amplification effect of the Atlantic signal by the climatic regime of the Mediterranean region. All studied cores show a shorter cooling phase (700 years) for the Younger Dryas (YD) than that observed in the North Atlantic region (1200 years). This time diachroneity is related to an intra-YD climatic change documented in the European continent. Minor oscillations in the southward displacement of the North Atlantic polar front may also have driven this early warming in the studied area. During the Holocene a regional diachroneity propagating west to east is observed for the SST maxima, 11.5-10.2 kyr B.P. in the Gulf of Cadiz, 10-9 kyr B.P. in the Alboran Sea, and 8.9-8.4 kyr B.P. in the Thyrrenian Sea. A general cooling trend from these SST maxima to present day is observed during this stage, which is marked by short cooling oscillations with a periodicity of 730±40 years and its harmonics.

(Table 1) Age determination of sediments from the Campbell Plateau

Campbell Plateau occupies a key position in the southwest Pacific sector of the Southern Ocean. The plateau confines and steers the Antarctic Circumpolar Current (ACC) along its flanks, isolating the Subantarctic plateau from cold polar waters. Oxygen and carbon isotope records from Campbell Plateau cores provide new records of water mass stratification for the past 130 kyr. During glacial climes, strengthening of the Subantarctic Front (SAF) caused waters over the plateau flanks to be deeply mixed and ~3°C cooler. Waters of the plateau interior remained stratified and isolated from the cold southern waters. In the west, waters cooled markedly (~4°C) owing to reduced entrainment of Tasman Sea water. Marked cooling also occurred north of Campbell Plateau under increased entrainment of polar water by a branch of the SAF. The ACC remained along the flanks of Campbell Plateau during the last interglacial, when interior waters were stratified and warmer by ~1°C than now.