987 resultados para high resolution
Resumo:
Stable isotope analyses of discrete seasonal layers from a 108-yr annually laminated freeze-core from Baldeg-gersee, a small, eutrophic lake in central Switzerland, provide information on the climatological and environmental factors, including lake eutrophication, that control oxygen and carbon isotopic composition of epilimnic biologically induced calcite precipitate. During the last 100 yr, Baldeggersee has undergone major increases in productivity and eutrophication in response to nutrient loading from agriculture and industrialization in the lake's watershed. Calibration of the isotopic signal in Baldeggersee to historical limnological data quantitatively links evidence of isotopic depletion in the sedimented calcite to trophic state of the lake. δ18O values from the spring/summer “light” sediment layers steadily diverged to more depleted values in response to historical eutrophication: measured δ18O values were up to 21.5‰ more negative than calculated equilibrium δ18O values. Evidence for 13C depletion in the calcite, relative to equilibrium values, is more difficult to ascertain because of an overall dominance of isotopic enrichment in the dissolved inorganic pool as productivity in Baldeggersee increases. A positive association exists between the degree of oxygen-18 depletion and the calcite crystal size. Thus, large amorphous calcite grains can be used as a proxy for recognizing apparent isotopic nonequilibrium in sediment sequences from highly productive lacustrine environments from all geologic time scales. In contrast to the light layers, the oxygen isotopic composition of the calcite in the late summer/fall “dark” sediment layers is unaffected by the apparent isotope nonequilibrium. Oxygen and carbon isotope values from the dark laminae in the Baldeggersee sediment therefore provide environmental and climatological proxies that can be calibrated with known environmental and regional climate data for the last century.
Resumo:
A three-level satellite to ground monitoring scheme for conservation easement monitoring has been implemented in which high-resolution imagery serves as an intermediate step for inspecting high priority sites. A digital vertical aerial camera system was developed to fulfill the need for an economical source of imagery for this intermediate step. A method for attaching the camera system to small aircraft was designed, and the camera system was calibrated and tested. To ensure that the images obtained were of suitable quality for use in Level 2 inspections, rectified imagery was required to provide positional accuracy of 5 meters or less to be comparable to current commercially available high-resolution satellite imagery. Focal length calibration was performed to discover the infinity focal length at two lens settings (24mm and 35mm) with a precision of O.1mm. Known focal length is required for creation of navigation points representing locations to be photographed (waypoints). Photographing an object of known size at distances on a test range allowed estimates of focal lengths of 25.lmm and 35.4mm for the 24mm and 35mm lens settings, respectively. Constants required for distortion removal procedures were obtained using analytical plumb-line calibration procedures for both lens settings, with mild distortion at the 24mm setting and virtually no distortion found at the 35mm setting. The system was designed to operate in a series of stages: mission planning, mission execution, and post-mission processing. During mission planning, waypoints were created using custom tools in geographic information system (GIs) software. During mission execution, the camera is connected to a laptop computer with a global positioning system (GPS) receiver attached. Customized mobile GIs software accepts position information from the GPS receiver, provides information for navigation, and automatically triggers the camera upon reaching the desired location. Post-mission processing (rectification) of imagery for removal of lens distortion effects, correction of imagery for horizontal displacement due to terrain variations (relief displacement), and relating the images to ground coordinates were performed with no more than a second-order polynomial warping function. Accuracy testing was performed to verify the positional accuracy capabilities of the system in an ideal-case scenario as well as a real-world case. Using many welldistributed and highly accurate control points on flat terrain, the rectified images yielded median positional accuracy of 0.3 meters. Imagery captured over commercial forestland with varying terrain in eastern Maine, rectified to digital orthophoto quadrangles, yielded median positional accuracies of 2.3 meters with accuracies of 3.1 meters or better in 75 percent of measurements made. These accuracies were well within performance requirements. The images from the digital camera system are of high quality, displaying significant detail at common flying heights. At common flying heights the ground resolution of the camera system ranges between 0.07 meters and 0.67 meters per pixel, satisfying the requirement that imagery be of comparable resolution to current highresolution satellite imagery. Due to the high resolution of the imagery, the positional accuracy attainable, and the convenience with which it is operated, the digital aerial camera system developed is a potentially cost-effective solution for use in the intermediate step of a satellite to ground conservation easement monitoring scheme.
High-resolution microarray analysis of chromosome 20q in human colon cancer metastasis model systems
Resumo:
Amplification of human chromosome 20q DNA is the most frequently occurring chromosomal abnormality detected in sporadic colorectal carcinomas and shows significant correlation with liver metastases. Through comprehensive high-resolution microarray comparative genomic hybridization and microarray gene expression profiling, we have characterized chromosome 20q amplicon genes associated with human colorectal cancer metastasis in two in vitro metastasis model systems. The results revealed increasing complexity of the 20q genomic profile from the primary tumor-derived cell lines to the lymph node and liver metastasis derived cell lines. Expression analysis of chromosome 20q revealed a subset of over expressed genes residing within the regions of genomic copy number gain in all the tumor cell lines, suggesting these are Chromosome 20q copy number responsive genes. Bases on their preferential expression levels in the model system cell lines and known biological function, four of the over expressed genes mapping to the common intervals of genomic copy gain were considered the most promising candidate colorectal metastasis-associated genes. Validation of genomic copy number and expression array data was carried out on these genes, with one gene, DNMT3B, standing out as expressed at a relatively higher levels in the metastasis-derived cell lines compared with their primary-derived counterparts in both the models systems analyzed. The data provide evidence for the role of chromosome 20q genes with low copy gain and elevated expression in the clonal evolution of metastatic cells and suggests that such genes may serve as early biomarkers of metastatic potential. The data also support the utility of the combined microarray comparative genomic hybridization and expression array analysis for identifying copy number responsive genes in areas of low DNA copy gain in cancer cells. ^
Resumo:
Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.
Resumo:
Changes of glaciers and snow cover in polar regions affect a wide range of physical and ecosystem processes on land and in the adjacent marine environment. In this study, we investigate the potential of 11-day repeat high-resolution satellite image time series from the TerraSAR-X mission to derive glaciological and hydrological parameters on King George Island, Antarctica during the period Oct/25/2010 to Apr/19/2011. The spatial pattern and temporal evolution of snow cover extent on ice-free areas can be monitored using multi-temporal coherence images. SAR coherence is used to map glacier extent of land terminating glaciers with an average accuracy of 25 m. Multi-temporal SAR color composites identify the position of the late summer snow line at about 220 m above sea level. Glacier surface velocities are obtained from intensity feature-tracking. Surface velocities near the calving front of Fourcade Glacier were up to 1.8 ± 0.01 m/d. Using an intercept theorem based on fundamental geometric principles together with differential GPS field measurements, the ice discharge of Fourcade Glacier was estimated to 20700 ± 5500 m**3/d (corresponding to ~19 ± 5 kt/d). The rapidly changing surface conditions on King George Island and the lack of high-resolution digital elevation models for the region remain restrictions for the applicability of SAR data and the precision of derived products.
Resumo:
A high-resolution stratigraphic framework is presented for sapropel S5, which represents the low-mid latitude climate optimum of the previous interglacial period (Eemian). The framework is based on three sites along a transect from west to east through the eastern Mediterranean, and is further validated using a fourth site. This method allows expression of S5-based proxy records of Eemian climate variability along a standardised depth scale that offers unprecedented possibilities for assessment of spatial gradients and signal leads and lags in an interval where highresolution (radiocarbon-style) dating cannot be performed. Our lateral comparison of S5 sapropels suggests that the onset of S5 in ODP site 967C (Eratosthenes seamount) was 1-6 centuries delayed relative to the onsets in more westerly sites.
Resumo:
Changes in past atmospheric carbon dioxide concentrations can be determined by measuring the composition of air trapped in ice cores from Antarctica. So far, the Antarctic Vostok and EPICA Dome C ice cores have provided a composite record of atmospheric carbon dioxide levels over the past 650,000 years. Here we present results of the lowest 200 m of the Dome C ice core, extending the record of atmospheric carbon dioxide concentration by two complete glacial cycles to 800,000 yr before present. From previously published data and the present work, we find that atmospheric carbon dioxide is strongly correlated with Antarctic temperature throughout eight glacial cycles but with significantly lower concentrations between 650,000 and 750,000 yr before present. Carbon dioxide levels are below 180 parts per million by volume (p.p.m.v.) for a period of 3,000 yr during Marine Isotope Stage 16, possibly reflecting more pronounced oceanic carbon storage. We report the lowest carbon dioxide concentration measured in an ice core, which extends the pre-industrial range of carbon dioxide concentrations during the late Quaternary by about 10 p.p.m.v. to 172-300 p.p.m.v.