Interannual Variability in Timing of Bloom Initiation in the California Current System

In the California Current System the spring transition from poleward to equatorward alongshore wind stress heralds the beginning of upwelling-favorable conditions. The phytoplankton response to this transition is investigated using 8 years ( 1998-2005) of daily, 4-km resolution, Sea-viewing Wide Field of view Sensor ( SeaWiFS) chlorophyll a concentration data. Cluster analysis of the chlorophyll a time series at each location is used to separate the inshore upwelling region from offshore and oligotrophic areas. An objective method for estimating the timing of bloom initiation is used to construct a map of the mean bloom start date. Interannual variability in bloom timing and magnitude is investigated in four regions: 45 degrees N - 50 degrees N, 40 degrees N - 45 degrees N, 35 degrees N - 40 degrees N and 20 degrees N - 35 degrees N. Daily satellite derived wind data ( QuikSCAT) allow the timing of the first episode of persistently upwelling favorable winds to be estimated. Bloom initiation generally coincides with the onset of upwelling winds ( +/- 15 days). South of similar to 35 degrees N, where winds are southward year-round, the timing of increased chlorophyll concentration corresponds closely to timing of the seasonal increase in upwelling intensity. A 1-D model and satellite derived photosynthetically available radiation data are used to estimate time series of depth- averaged irradiance. In the far north of the region (> 46 degrees N) light is shown to limit phytoplankton growth in early spring. In 2005 the spring bloom in the northern regions (> 35 degrees N) had a "false start''. A sharp increase in chl a in February quickly receded, and a sustained increase in biomass was delayed until July. We hypothesize that this resulted in a mismatch in timing of food availability to higher trophic levels.

CHARACTERIZATION OF THE COLONIZATION FACTOR ANTIGEN II PLASMID (CFA/II) FROM ENTEROTOXIGENIC ESCHERICHIA COLI

The etiological role of enterotoxigenic E. coli (ETEC) in diarrheal diseases of man and domestic animals is firmly established. Besides the production of enterotoxins (ST and LT), ETEC produces other important virulence factors; the colonization factor antigens (CFAs). CFAs mediate the attachment of ETEC to the epithelial cells of the small intestine, and this favors colonization by the bacteria and facilitates delivery of the enterotoxins to the intestinal cells.^ The production of enterotoxin and CFA is determined by plasmids and has been found to be restricted to a select number of E. coli serotypes.^ In this work, plasmid DNA analysis was performed in twenty-three CFA/II-producing enterotoxigenic Escherichia coli strains and their spontaneous CFA/II-negative derivatives. In some cases, strains lost the high molecular weight plasmid and also the ability to produce CFA/II, ST and LT. In other cases there was a deletion of the plasmid, which produced strains that were CFA/II('-), ST('-), LT('-) or CFA/II('-), ST('+), LT('+).^ The CFA/II plasmid from strain PB-176 (06:H16:CFA/II('+), ST('+), LT('+)) was transferred by transformation into E. coli K12 with concomitant transfer of the three characteristics: CFA/II, ST and LT.^ A physical map of the prototype CFA/II:ST:LT (pMEP60) plasmid was constructed by restriction endonuclease analysis and compared to plasmids from three other CFA/II-producing strains. A CFA/II-negative (but ST and LT positive) deletion derivative of pMEP60 (pMEP30) was also included in the map. The four CFA/II plasmids analyzed had a common region of approximately 30 kilobase pairs. The toxin genes were approximately 5 kbp apart and about 20 kbp from the common region. The information given by this physical map could be of great value when constructing a clone that will express the CFA/II genes but not the toxin genes. ^

GENETIC ORGANIZATION OF THE STRUCTURAL GENES FOR NITRATE REDUCTASE (TN5)

Nitrate reductase in Escherichia coli is a membrane-bound anaerobic enzyme that is repressed by oxygen and induced by nitrate. The genetic organization of the structural genes for the two larger subunits of nitrate reductase ((alpha) and (beta)) was determined by immunoprecipitation analysis of the formation of these proteins in nitrate reductase-deficient mutants resulting from transposon Tn5 mutagenesis. The results suggested that the genes encoding the (alpha) and (beta) subunits (narG and H) were arranged in an operon with transcription in the direction promoter(--->)(alpha)(--->)(beta). Segments of the chromosome containing the Tn5 inserts from several of the mutants were cloned into plasmid pBR322 and the positions of the transposons determined by restriction mapping. The Tn5 insertion sites were localized on two contiguous EcoRI fragments spanning about 6.6 kilobases of DNA. The narI gene (proposed to encode the (gamma) subunit) was positioned immediately downstream from the (beta)-gene (narH) by Southern analysis of Tn10 insertions into the narI locus. A Tn10 insertion into the narK locus, proposed to encode a nitrate-sensitive repressor of other anaerobic enzymes, was located about 1.5 kilobases upstream from the narGHI operon promoter. The narL locus, proposed to encode a nitrate-sensitive positive regulator of the narGHI operon and known to be genetically linked to the other nar genes, was demonstrated to lie outside a 19.3-kilobase region of the chromosome which encompasses the other nar genes. The physical limit of the narGHI promoter was defined by studying the effect of Tn5 insertions into a hybrid plasmid containing the functional operon. The points of origin of the coding regions for the (alpha) and (beta) genes were deduced by alignment of the chromosomal map of Tn5 insertion sites with the sizes of (alpha) and (beta) subunit fragments produced by plasmids carrying these Tn5 inserts in the nar operon. The coding region for the (alpha) subunit (143,000 daltons) begins about 250 nucleotides downstream from the deduced limit of the promoter region and includes about 4.0 kilobases of DNA; the region encoding (beta) (60,000 daltons) lies immediately downstream from the (alpha)-gene and is approximately 1.6 kilobases in length. The adjacent region encoding the (gamma) subunit (19,000 daltons) is approximately 0.5 kilobase in length. ^

Theoretical and experimental studies of linkage disequilibrium in human populations

Linkage disequilibrium (LD) is defined as the nonrandom association of alleles at two or more loci in a population and may be a useful tool in a diverse array of applications including disease gene mapping, elucidating the demographic history of populations, and testing hypotheses of human evolution. However, the successful application of LD-based approaches to pertinent genetic questions is hampered by a lack of understanding about the forces that mediate the genome-wide distribution of LD within and between human populations. Delineating the genomic patterns of LD is a complex task that will require interdisciplinary research that transcends traditional scientific boundaries. The research presented in this dissertation is predicated upon the need for interdisciplinary studies and both theoretical and experimental projects were pursued. In the theoretical studies, I have investigated the effect of genotyping errors and SNP identification strategies on estimates of LD. The primary importance of these two chapters is that they provide important insights and guidance for the design of future empirical LD studies. Furthermore, I analyzed the allele frequency distribution of 26,530 single nucleotide polymorphisms (SNPs) in three populations and generated the first-generation natural selection map of the human genome, which will be an important resource for explaining and understanding genomic patterns of LD. Finally, in the experimental study, I describe a novel and simple, low-cost, and high-throughput SNP genotyping method. The theoretical analyses and experimental tools developed in this dissertation will facilitate a more complete understanding of patterns of LD in human populations. ^

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

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.

Learning -dependent plasticity of movement representations in the primate primary motor cortex

Primary motor cortex (M1) is involved in the production of voluntary movement and contains a complete functional representation, or map, of the skeletal musculature. This functional map can be altered by pathological experiences, such as peripheral nerve injury or stroke, by pharmacological manipulation, and by behavioral experience. The process by which experience-dependent alterations of cortical function occur is termed plasticity. In this thesis, plasticity of M1 functional organization as a consequence of behavioral experience was examined in adult primates (squirrel monkeys). Maps of movement representations were derived under anesthesia using intracortical microstimulation, whereby a microelectrode was inserted into the cortex to electrically stimulate corticospinal neurons at low current levels and evoke movements of the forelimb, principally of the hand. Movement representations were examined before and at several times after training on behavioral tasks that emphasized use of the fingers. Two behavioral tasks were utilized that dissociated the repetition of motor activity from the acquisition of motor skills. One task was easy to perform, and as such promoted repetitive motor activity without learning. The other task was more difficult, requiring the acquisition of motor skills for successful performance. Kinematic analysis indicated that monkeys used a consistent set of forelimb movements during pellet extractions. Functional mapping revealed that repetitive motor activity during the easier task did not produce plastic changes in movement representations. Instead, map plasticity, in the form of selective expansions of task-related movement representations, was only produced following skill acquisition on the difficult task. Additional studies revealed that, in general, map plasticity persisted without further training for up to three months, in parallel with the retention of task-related motor skills. Also, extensive additional training on the small well task produced further improvements in performance, and further changes in movement maps. In sum, these experiments support the following three conclusions regarding the role of M1 in motor learning. First, behaviorally-driven plasticity is learning-dependent, not activity-dependent. Second, plastic changes in M1 functional representations represent a neural correlate of acquired motor skills. Third, the persistence of map plasticity suggests that M1 is part of the neural substrate for the memory of motor skills. ^

(Table 1) Frequency of wind direction reportings and duration of wave action in Mittelgrund, Eckernfoerder Bay, Germany

A detailed survey of the Mittelgrund in Eckernförde Bay shows slope breaks at 10-12 m and 15-16 m water depth. They are thought to be mainly the result of marine abrasion. Utilizing records from the Edgerton mud-penetrator, a map of holocene sediment thickness has been drawn. From the pattern of bottom echos 4 types of stratification can be recognized. An interpretation of them is attempted, as they are supposed to serve as models for other transgression contacts.

IR spectra from mapping of diamond sample JH7b

This data set contains 1851 infrared (IR) spectra, forming a single IR map of diamond sample JH7b. This data set is used to show the application of DiaMap, a computer routine written using PERL, to automatically process diamond IR spectra to obtain quantitative impurity data from them. Full abstract will be added after acceptance of publication.

Shape-invariant multibeam backscatter data of the eastern slope of the Porcupine Seabight (50 m grid size)

In this study multibeam angular backscatter data acquired in the eastern slope of the Porcupine Seabight are analysed. Processing of the angular backscatter data using the 'NRGCOR' software was made for 29 locations comprising different geological provinces like: carbonate mounds, buried mounds, seafloor channels, and inter-channel areas. A detailed methodology is developed to produce a map of angle-invariant (normalized) backscatter data by correcting the local angular backscatter values. The present paper involves detailed processing steps and related technical aspects of the normalization approach. The presented angle-invariant backscatter map possesses 12 dB dynamic range in terms of grey scale. A clear distinction is seen between the mound dominated northern area (Belgica province) and the Gollum channel seafloor at the southern end of the site. Qualitative analyses of the calculated mean backscatter values i.e., grey scale levels, utilizing angle-invariant backscatter data generally indicate backscatter values are highest (lighter grey scale) in the mound areas followed by buried mounds. The backscatter values are lowest in the inter-channel areas (lowest grey scale level). Moderate backscatter values (medium grey level) are observed from the Gollum and Kings channel data, and significant variability within the channel seafloor provinces. The segmentation of the channel seafloor provinces are made based on the computed grey scale levels for further analyses based on the angular backscatter strength. Three major parameters are utilized to classify four different seafloor provinces of the Porcupine Seabight by employing a semi-empirical method to analyse multibeam angular backscatter data. The predicted backscatter response which has been computed at 20° is the highest for the mound areas. The coefficient of variation (CV) of the mean backscatter response is also the highest for the mound areas. Interestingly, the slope value of the buried mound areas are found to be the highest. However, the channel seafloor of moderate backscatter response presents the lowest slope and CV values. A critical examination of the inter-channel areas indicates less variability within the estimated three parameters.

Methane concentration profiles and isotopic composition of sediment cores from the Black Sea

We present high resolution profiles for the methane concentration and the carbon isotope composition of methane from surface sediments and from the sediment-water transition in the Black Sea. At shallow water sites methane migrates from the sediment into the water column, and the magnitude of this upward migrating flux depends on the depth of the sulfate-methane transition (SMT) in the sediment. The isotope data reveal that the sediments at shallow water sites are a source for methane depleted in 13C relative to the isotope composition of methane in the water column. At deep water sites the methane concentration first decreases with depth in the sediment to reach lowest values at the Unit I to Unit II transition. Below this transition the concentration increases again. Numerical modeling of methane concentration and isotope data shows that high methane oxidation rates occur in the surface sediment layer, indicating that the removal of methane in the surface sediments is not related to the anaerobic oxidation of methane coupled to sulfate reduction that occurs a few meters deep in the sediment, at the SMT. Instead, near-surface methane consumption in the euxinic Black Sea sediments appears to be related to lithological stratification. Furthermore, a map of the diffusive methane fluxes in the Black Sea surface sediments indicates that approximately half of the Black Sea seafloor acts as a sink for methane and thus limits the flux of methane to the atmosphere.

Mapped distribution of tidal flats across China, Manchuria and Korea (1952-1964)

A map of the tidal flats of China, Manchuria and Korea depicted in US Army Map Service Series L500, L542 and L552 topographic maps (compiled between 1950 and 1964). The topographic maps were georeferenced against prominent topographical features in L1T processed Landsat imagery and the foreshore flat class was manually delineated. For further information refer to Murray et. al. (2014).

Maps and acoustic profiles of free gas distribution, Western Baltic Sea and Kattgat-Skagerrak area

A shallow gas depth-contour map covering the Skagerrak-western Baltic Sea region has been constructed using a relatively dense grid of existing shallow seismic lines. The digital map is stored as an ESRI shape file in order to facilitate comparison with other data from the region. Free gas usually occurs in mud and sandy mud but is observed only when sediment thickness exceeds a certain threshold value, depending on the water depth of the area in question. Gassy sediments exist at all water depths from approx. 20 m in the coastal waters of the Kattegat to 360 m in the Skagerrak. In spite of the large difference in water depths, the depth of free gas below seabed varies only little within the region, indicating a relatively fast movement of methane in the gas phase towards the seabed compared to the rate of diffusion of dissolved methane. Seeps of old microbial methane occur in the northern Kattegat where a relatively thin cover of sandy sediments exists over shallow, glacially deformed Pleistocene marine sediments. Previous estimates of total methane escape from the area may be correct but the extrapolation of local methane seepage rate data to much larger areas on the continental shelf is probably not justified. Preliminary data on porewater chemistry were compared with the free gas depth contours in the Aarhus Bay area, which occasionally suffers from oxygen deficiency, in order to examine if acoustic gas mapping may be used for monitoring the condition of the bay.