DNA Elasticity from Short DNA to Nucleosomal DNA

Active biological processes like transcription, replication, recombination, DNA repair, and DNA packaging encounter bent DNA. Machineries associated with these processes interact with the DNA at short length (<100 base pair) scale. Thus, the study of elasticity of DNA at such length scale is very important. We use fully atomistic molecular dynamics (MD) simulations along with various theoretical methods to determine elastic properties of dsDNA of different lengths and base sequences. We also study DNA elasticity in nucleosome core particle (NCP) both in the presence and the absence of salt. We determine stretch modulus and persistence length of short dsDNA and nucleosomal DNA from contour length distribution and bend angle distribution, respectively. For short dsDNA, we find that stretch modulus increases with ionic strength while persistence length decreases. Calculated values of stretch modulus and persistence length for DNA are in quantitative agreement with available experimental data. The trend is opposite for NCP DNA. We find that the presence of histone core makes the DNA stiffer and thus making the persistence length 3-4 times higher than the bare DNA. Similarly, we also find an increase in the stretch modulus for the NCP DNA. Our study for the first time reports the elastic properties of DNA when it is wrapped around the histone core in NCP. We further show that the WLC model is inadequate to describe DNA elasticity at short length scale. Our results provide a deeper understanding of DNA mechanics and the methods are applicable to most protein-DNA complexes.

The electronic, chemical and electrocatalytic processes and intermediates on iron oxide surfaces during photoelectrochemical water splitting

We re-assess experimental soft X-ray absorption spectra of the oxygen K-shell which we recorded operando from iron oxide during photoelectrochemical water splitting in KOH electrolyte. In particular, we refer to recently reported transitional electron hole states which originate within the charge carrier depletion layer of the iron oxide and on the iron oxide surface. For the latter we find that an intermediate oxy-peroxo species is formed on the iron oxide with increasing bias potential, which disappears upon further polarization of the electrode, concomitantly with the evolution and disappearance of the aforementioned surface state. The oxygen spectra contain also the spectroscopic signatures of the electrolyte water, the position of which changes with increasing bias potential towards lower X-ray energies, revealing the breaking and formation of hydrogen bonds in the water during the experiment. Combined with potential dependent impedance spectroscopy data we are able to sketch the molecular structure of chemical intermediates and their charge carrier dynamics. (C) 2015 Elsevier B.V. All rights reserved.

Nonparametric Bayesian Density Modeling with Gaussian Processes

We present the Gaussian process density sampler (GPDS), an exchangeable generative model for use in nonparametric Bayesian density estimation. Samples drawn from the GPDS are consistent with exact, independent samples from a distribution defined by a density that is a transformation of a function drawn from a Gaussian process prior. Our formulation allows us to infer an unknown density from data using Markov chain Monte Carlo, which gives samples from the posterior distribution over density functions and from the predictive distribution on data space. We describe two such MCMC methods. Both methods also allow inference of the hyperparameters of the Gaussian process.

Tractable nonparametric bayesian inference in poisson processes with Gaussian process intensities

The inhomogeneous Poisson process is a point process that has varying intensity across its domain (usually time or space). For nonparametric Bayesian modeling, the Gaussian process is a useful way to place a prior distribution on this intensity. The combination of a Poisson process and GP is known as a Gaussian Cox process, or doubly-stochastic Poisson process. Likelihood-based inference in these models requires an intractable integral over an infinite-dimensional random function. In this paper we present the first approach to Gaussian Cox processes in which it is possible to perform inference without introducing approximations or finitedimensional proxy distributions. We call our method the Sigmoidal Gaussian Cox Process, which uses a generative model for Poisson data to enable tractable inference via Markov chain Monte Carlo. We compare our methods to competing methods on synthetic data and apply it to several real-world data sets. Copyright 2009.

Tractable nonparametric Bayesian inference in Poisson processes with Gaussian process intensities

The inhomogeneous Poisson process is a point process that has varying intensity across its domain (usually time or space). For nonparametric Bayesian modeling, the Gaussian process is a useful way to place a prior distribution on this intensity. The combination of a Poisson process and GP is known as a Gaussian Cox process, or doubly-stochastic Poisson process. Likelihood-based inference in these models requires an intractable integral over an infinite-dimensional random function. In this paper we present the first approach to Gaussian Cox processes in which it is possible to perform inference without introducing approximations or finite-dimensional proxy distributions. We call our method the Sigmoidal Gaussian Cox Process, which uses a generative model for Poisson data to enable tractable inference via Markov chain Monte Carlo. We compare our methods to competing methods on synthetic data and apply it to several real-world data sets.

Bayesian learning of noisy Markov decision processes

This work addresses the problem of estimating the optimal value function in a Markov Decision Process from observed state-action pairs. We adopt a Bayesian approach to inference, which allows both the model to be estimated and predictions about actions to be made in a unified framework, providing a principled approach to mimicry of a controller on the basis of observed data. A new Markov chain Monte Carlo (MCMC) sampler is devised for simulation from theposterior distribution over the optimal value function. This step includes a parameter expansion step, which is shown to be essential for good convergence properties of the MCMC sampler. As an illustration, the method is applied to learning a human controller.

A Bayesian approach to tracking in single molecule fluorescence microscopy

Using fluorescence microscopy with single molecule sensitivity it is now possible to follow the movement of individual fluorophore tagged molecules such as proteins and lipids in the cell membrane with nanometer precision. These experiments are important as they allow many key biological processes on the cell membrane and in the cell, such as transcription, translation and DNA replication, to be studied at new levels of detail. Computerized microscopes generate sequences of images (in the order of tens to hundreds) of the molecules diffusing and one of the challenges is to track these molecules to obtain reliable statistics such as speed distributions, diffusion patterns, intracellular positioning, etc. The data set is challenging because the molecules are tagged with a single or small number of fluorophores, which makes it difficult to distinguish them from the background, the fluorophore bleaches irreversibly over time, the number of tagged molecules are unknown and there is occasional loss of signal from the tagged molecules. All these factors make accurate tracking over long trajectories difficult. Also the experiments are technically difficulty to conduct and thus there is a pressing need to develop better algorithms to extract the maximum information from the data. For this purpose we propose a Bayesian approach and apply our technique to synthetic and a real experimental data set.

SEM and EDS Characterisation of Layering TiOx Growth onto the Cutting Tool Surface in Hard Drilling Processes of Ti-Al-V Alloys

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Techniques for spatial analysis and visualization of benthic mapping data: final report

The mapping and geospatial analysis of benthic environments are multidisciplinary tasks that have become more accessible in recent years because of advances in technology and cost reductions in survey systems. The complex relationships that exist among physical, biological, and chemical seafloor components require advanced, integrated analysis techniques to enable scientists and others to visualize patterns and, in so doing, allow inferences to be made about benthic processes. Effective mapping, analysis, and visualization of marine habitats are particularly important because the subtidal seafloor environment is not readily viewed directly by eye. Research in benthic environments relies heavily, therefore, on remote sensing techniques to collect effective data. Because many benthic scientists are not mapping professionals, they may not adequately consider the links between data collection, data analysis, and data visualization. Projects often start with clear goals, but may be hampered by the technical details and skills required for maintaining data quality through the entire process from collection through analysis and presentation. The lack of technical understanding of the entire data handling process can represent a significant impediment to success. While many benthic mapping efforts have detailed their methodology as it relates to the overall scientific goals of a project, only a few published papers and reports focus on the analysis and visualization components (Paton et al. 1997, Weihe et al. 1999, Basu and Saxena 1999, Bruce et al. 1997). In particular, the benthic mapping literature often briefly describes data collection and analysis methods, but fails to provide sufficiently detailed explanation of particular analysis techniques or display methodologies so that others can employ them. In general, such techniques are in large part guided by the data acquisition methods, which can include both aerial and water-based remote sensing methods to map the seafloor without physical disturbance, as well as physical sampling methodologies (e.g., grab or core sampling). The terms benthic mapping and benthic habitat mapping are often used synonymously to describe seafloor mapping conducted for the purpose of benthic habitat identification. There is a subtle yet important difference, however, between general benthic mapping and benthic habitat mapping. The distinction is important because it dictates the sequential analysis and visualization techniques that are employed following data collection. In this paper general seafloor mapping for identification of regional geologic features and morphology is defined as benthic mapping. Benthic habitat mapping incorporates the regional scale geologic information but also includes higher resolution surveys and analysis of biological communities to identify the biological habitats. In addition, this paper adopts the definition of habitats established by Kostylev et al. (2001) as a “spatially defined area where the physical, chemical, and biological environment is distinctly different from the surrounding environment.” (PDF contains 31 pages)

An oceanographic atlas of the Eastern Tropical Pacific Ocean, based on data from EASTROPIC Expedition, October-December 1955.

ENGLISH: EASTROPIC Expedition was a cooperative oceanographic study of the eastern tropical Pacific Ocean conducted during the period 2 October through 16 December 1955. The five participating agencies and the ships they operated were: Scripps Institution of Oceanography (SIO), Spencer F. Baird and Horizon; Pacific Oceanic Fisheries Investigations (POFI) of the U. S. Fish and Wildlife Service, now Honolulu Biological Laboratory (HBL) of the U. S. Bureau of Commercial Fisheries, Hugh M. Smith; California Department of Fish and Game, N. B. Scofield; the Peruvian Navy, Bondu; and the Inter-American Tropical Tuna Commission which operated no vessels but supplied equipment and personnel. In addition to these planned participations in EASTROPIC Expedition, valuable information was provided by CCOFI Cruise 5512 of the California Cooperative Oceanic Fisheries Investigations, conducted during the period 29 November -16 December 1955 with the two vessels Stranger and Black Douglas. While the observational programs of most of the agencies involved, in part, special hydrographic-biological studies of known features and processes in the region (see reports listed under Data Sources) the deployment of ships and therefore of observations was sufficient that EASTROPIC Expedition could be considered a survey of the eastern tropical Pacific. This report is concerned with that aspect of the Expedition and is a presentation in atlas form of most of the hydrographic data collected. For reasons given below, emphasis has been placed on the upper 300 m of the water column. SPANISH: La Expedición EASTROPIC es un estudio oceanográfico cooperativo del Océano Pacífico Oriental Tropical llevado a cabo durante el período del 2 de octubre al 16 de dícíembre de 1955. Las cinco agencias participantes y los barcos operados por ellas son los siguientes: Scrípps Instítutíon of Oceanography (SIO) , Spencer F. Baird y Horizon; Pacific Oceanic Fisheries Investigatíons (PO'FI) del U. S. Fish and Wildlife Service, ahora Honolulu Biological Laboratory (BHL) del U. S. Bureau of Commercial Fisheries, Hugh M. Smith; California Department of Fish and Game, N. B. Scofield; la Marina Peruana, Bondu; y la Comisión Interamericana del Atún Tropical que no dirigió ningún barco pero proporcionó equipo y personal. Además de estas participaciones planeadas en la Expedición EASTROPIC, fué suministrada información de valor por el Crucero CCOFI 5512 del California Cooperative Fisheries Investigatíons, llevado a cabo durante el período del 29 de noviembre al 16 de diciembre de 1955 con los barcos Stranger y Black Douglas. Aunque los programas de observación de la mayoría de las agencias, comprendieron en parte estudios especiales hidrográficos y biológicos de las características y de los procesos conocidos de la región (véase los informes indicados bajo Fuente de Datos), el despliegue de los barcos, y por lo tanto, de las observaciones, fué suficiente para que la Expedición EASTROPIC pudiera ser considerada como una encuesta del Pacífico Oriental Tropical. Este informe se refiere a este aspecto de la Expedición y es una presentación, en forma de un atlas, de la mayoría de los datos hidrográficos recolectados. Por las razones que se dan a continuación, se le dió énfasis a los 300 m., superiores de la columna de agua. (PDF contains 136 pages.)

Towed vehicles: undulating platforms as tools for maping coastal processes and water quality assessment, Seaside, California, February 5-7,2007. Workshop proceedings

The Alliance for Coastal Technologies (ACT) Workshop on Towed Vehicles: Undulating Platforms As Tools for Mapping Coastal Processes and Water Quality Assessment was convened February 5-7,2007 at The Embassy Suites Hotel, Seaside, California and sponsored by the ACT-Pacific Coast partnership at the Moss Landing Marine Laboratories (MLML). The TUV workshop was co-chaired by Richard Burt (Chelsea Technology Group) and Stewart Lamerdin (MLML Marine Operations). Invited participants were selected to provide a uniform representation of the academic researchers, private sector product developers, and existing and potential data product users from the resource management community to enable development of broad consensus opinions on the application of TUV platforms in coastal resource assessment and management. The workshop was organized to address recognized limitations of point-based monitoring programs, which, while providing valuable data, are incapable of describing the spatial heterogeneity and the extent of features distributed in the bulk solution. This is particularly true as surveys approach the coastal zone where tidal and estuarine influences result in spatially and temporally heterogeneous water masses and entrained biological components. Aerial or satellite based remote sensing can provide an assessment of the aerial extent of plumes and blooms, yet provide no information regarding the third dimension of these features. Towed vehicles offer a cost-effective solution to this problem by providing platforms, which can sample in the horizontal, vertical, and time-based domains. Towed undulating vehicles (henceforth TUVs) represent useful platforms for event-response characterization. This workshop reviewed the current status of towed vehicle technology focusing on limitations of depth, data telemetry, instrument power demands, and ship requirements in an attempt to identify means to incorporate such technology more routinely in monitoring and event-response programs. Specifically, the participants were charged to address the following: (1) Summarize the state of the art in TUV technologies; (2) Identify how TUV platforms are used and how they can assist coastal managers in fulfilling their regulatory and management responsibilities; (3) Identify barriers and challenges to the application of TUV technologies in management and research activities, and (4) Recommend a series of community actions to overcome identified barriers and challenges. A series of plenary presentation were provided to enhance subsequent breakout discussions by the participants. Dave Nelson (University of Rhode Island) provided extensive summaries and real-world assessment of the operational features of a variety of TUV platforms available in the UNOLs scientific fleet. Dr. Burke Hales (Oregon State University) described the modification of TUV to provide a novel sampling platform for high resolution mapping of chemical distributions in near real time. Dr. Sonia Batten (Sir Alister Hardy Foundation for Ocean Sciences) provided an overview on the deployment of specialized towed vehicles equipped with rugged continuous plankton recorders on ships of opportunity to obtain long-term, basin wide surveys of zooplankton community structure, enhancing our understanding of trends in secondary production in the upper ocean. [PDF contains 32 pages]

Application of participatory rural appraisal (PRA) techniques in the verification of fisheries data and trend on Lake Kainji

After several years of surveys on the Kainji Lake fisheries activities by the Nigerian German Kainji Lake Fish promotion Project (KLFPP) trends regarding catches, yield and other parameter begin to emerge. However, it became obvious that some of the data were not quite as accurate as they were believed to be. Looking at the different editions of the statistical bulletin of Kainji Lake, concerning one given fisheries parameter, sometimes it is possible to reveal inconsistencies and unexplained trends. As compared to the survey method, PRA is primarily for analysis of differences in local phenomenon and processes. Therefore, PRA was used as a complementary tool to enhance the knowledge on issues like fisher women, entrepreneurs, gear ownership structure, mode of operation by owners of large gear number, preference in the use of twine and nylon gill nets, and reasons for misinformation on the number of fishing equipment owned by entrepreneurs, which cannot be done with frame survey. PRA techniques like timeline, mapping, seasonal calendar, transect walk and key informant interviews were utilized in the study process

Sulfur-Cycling in Methane-Rich Ecosystems: Uncovering Microbial Processes and Novel Niches

Microbial sulfur cycling communities were investigated in two methane-rich ecosystems, terrestrial mud volcanoes (TMVs) and marine methane seeps, in order to investigate niches and processes that would likely be central to the functioning of these crucial ecosystems. Terrestrial mud volcanoes represent geochemically diverse habitats with varying sulfur sources and yet sulfur-cycling in these environments remains largely unexplored. Here we characterized the sulfur-metabolizing microorganisms and activity in 4 TMVs in Azerbaijan, supporting the presence of active sulfur-oxidizing and sulfate-reducing guilds in all 4 TMVs across a range of physiochemical conditions, with diversity of these guilds being unique to each TMV. We also found evidence for the anaerobic oxidation of methane coupled to sulfate reduction, a process which we explored further in the more tractable marine methane seeps. Diverse associations between methanotrophic archaea (ANME) and sulfate-reducing bacterial groups (SRB) often co-occur in marine methane seeps, however the ecophysiology of these different symbiotic associations has not been examined. Using a combination of molecular, geochemical and fluorescence in situ hybridization coupled to nano-scale secondary ion mass spectrometry (FISH-NanoSIMS) analyses of in situ seep sediments and methane-amended sediment incubations from diverse locations, we show that the unexplained diversity in SRB associated with ANME cells can be at least partially explained by preferential nitrate utilization by one particular partner, the seepDBB. This discovery reveals that nitrate is likely an important factor in community structuring and diversity in marine methane seep ecosystems. The thesis concludes with a study of the dynamics between ANME and their associated SRB partners. We inhibited sulfate reduction and followed the metabolic processes of the community as well as the effect of ANME/SRB aggregate composition and growth on a cellular level by tracking 15N substrate incorporation into biomass using FISH-NanoSIMS. We revealed that while sulfate-reducing bacteria gradually disappeared over time in incubations with an SRB inhibitor, the ANME archaea persisted in the form of ANME-only aggregates, which are capable of little to no growth when sulfate reduction is inhibited. These data suggest ANME are not able to synthesize new proteins when sulfate reduction is inhibited.

I. Application of multi-Regge theory to production processes. II. High energy model for proton-proton scattering

This dissertation consists of two parts. The first part presents an explicit procedure for applying multi-Regge theory to production processes. As an illustrative example, the case of three body final states is developed in detail, both with respect to kinematics and multi-Regge dynamics. Next, the experimental consistency of the multi-Regge hypothesis is tested in a specific high energy reaction; the hypothesis is shown to provide a good qualitative fit to the data. In addition, the results demonstrate a severe suppression of double Pomeranchon exchange, and show the coupling of two "Reggeons" to an external particle to be strongly damped as the particle's mass increases. Finally, with the use of two body Regge parameters, order of magnitude estimates of the multi-Regge cross section for various reactions are given.

The second part presents a diffraction model for high energy proton-proton scattering. This model developed by Chou and Yang assumes high energy elastic scattering results from absorption of the incident wave into the many available inelastic channels, with the absorption proportional to the amount of interpenetrating hadronic matter. The assumption that the hadronic matter distribution is proportional to the charge distribution relates the scattering amplitude for pp scattering to the proton form factor. The Chou-Yang model with the empirical proton form factor as input is then applied to calculate a high energy, fixed momentum transfer limit for the scattering cross section, This limiting cross section exhibits the same "dip" or "break" structure indicated in present experiments, but falls significantly below them in magnitude. Finally, possible spin dependence is introduced through a weak spin-orbit type term which gives rather good agreement with pp polarization data.

Characterization of the human SCF ubiquitin ligases - structure, function, and regulation

The SCF ubiquitin ligase complex of budding yeast triggers DNA replication by cata lyzi ng ubiquitination of the S phase CDK inhibitor SIC1. SCF is composed of several evolutionarily conserved proteins, including ySKP1, CDC53 (Cullin), and the F-box protein CDC4. We isolated hSKP1 in a two-hybrid screen with hCUL1, the human homologue of CDC53. We showed that hCUL1 associates with hSKP1 in vivo and directly interacts with hSKP1 and the human F-box protein SKP2 in vitro, forming an SCF-Iike particle. Moreover, hCUL1 complements the growth defect of yeast CDC53^(ts) mutants, associates with ubiquitination-promoting activity in human cell extracts, and can assemble into functional, chimeric ubiquitin ligase complexes with yeast SCF components. These data demonstrated that hCUL1 functions as part of an SCF ubiquitin ligase complex in human cells. However, purified human SCF complexes consisting of CUL1, SKP1, and SKP2 are inactive in vitro, suggesting that additional factors are required.

Subsequently, mammalian SCF ubiquitin ligases were shown to regulate various physiological processes by targeting important cellular regulators, like lĸBα, β-catenin, and p27, for ubiquitin-dependent proteolysis by the 26S proteasome. Little, however, is known about the regulation of various SCF complexes. By using sequential immunoaffinity purification and mass spectrometry, we identified proteins that interact with human SCF components SKP2 and CUL1 in vivo. Among them we identified two additional SCF subunits: HRT1, present in all SCF complexes, and CKS1, that binds to SKP2 and is likely to be a subunit of SCF5^(SKP2) complexes. Subsequent work by others demonstrated that these proteins are essential for SCF activity. We also discovered that COP9 Signalosome (CSN), previously described in plants as a suppressor of photomorphogenesis, associates with CUL1 and other SCF subunits in vivo. This interaction is evolutionarily conserved and is also observed with other Cullins, suggesting that all Cullin based ubiquitin ligases are regulated by CSN. CSN regulates Cullin Neddylation presumably through CSNS/JAB1, a stochiometric Signalosome subunit and a putative deneddylating enzyme. This work sheds light onto an intricate connection that exists between signal transduction pathways and protein degradation machinery inside the cell and sets stage for gaining further insights into regulation of protein degradation.