The application of STEM and in situ controlled dehydration to bacterial systems using ESEM.

Transmission imaging with an environmental scanning electron microscope (ESEM) (Wet STEM) is a recent development in the field of electron microscopy, combining the simple preparation inherent to ESEM work with an alternate form of contrast available through a STEM detector. Because the technique is relatively new, there is little information available on how best to apply this technique and which samples it is best suited for. This work is a description of the sample preparation and microscopy employed by the authors for imaging bacteria with Wet STEM (scanning transmission electron microscopy). Three different bacterial samples will be presented in this study: first, used as a model system, is Escherichia coli for which the contrast mechanisms of STEM are demonstrated along with the visual effects of a dehydration-induced collapse. This collapse, although clearly in some sense artifactual, is thought to lead to structurally meaningful morphological information. Second, Wet STEM is applied to two distinct bacterial systems to demonstrate the novel types of information accessible by this approach: the plastic-producing Cupriavidus necator along with wild-type and ΔmreC knockout mutants of Salmonella enterica serovar Typhimurium. Cupriavidus necator is shown to exhibit clear internal differences between bacteria with and without plastic granules, while the ΔmreC mutant of S. Typhimurium has an internal morphology distinct from that of the wild type.

The application of STEM and in situ controlled dehydration to bacterial systems using ESEM

Transmission imaging with an environmental scanning electron microscope (ESEM) (Wet STEM) is a recent development in the field of electron microscopy, combining the simple preparation inherent to ESEM work with an alternate form of contrast available through a STEM detector. Because the technique is relatively new, there is little information available on how best to apply this technique and which samples it is best suited for. This work is a description of the sample preparation and microscopy employed by the authors for imaging bacteria with Wet STEM (scanning transmission electron microscopy). Three different bacterial samples will be presented in this study: first, used as a model system, is Escherichia coli for which the contrast mechanisms of STEM are demonstrated along with the visual effects of a dehydration-induced collapse. This collapse, although clearly in some sense artifactual, is thought to lead to structurally meaningful morphological information. Second, Wet STEM is applied to two distinct bacterial systems to demonstrate the novel types of information accessible by this approach: the plastic-producing Cupriavidus necator along with wild-type and δmreC knockout mutants of Salmonella enterica serovar Typhimurium. Cupriavidus necator is shown to exhibit clear internal differences between bacteria with and without plastic granules, while the δmreC mutant of S. Typhimurium has an internal morphology distinct from that of the wild type. © 2012 Wiley Periodicals, Inc.

ApcD is necessary for efficient energy transfer from phycobilisomes to photosystem I and helps to prevent photoinhibition in the cyanobacterium Synechococcus sp PCC 7002

Phyrobilisomes (PBS) are the major light-harvesting, protein-pigment complexes in cyanobacteria and red algae. PBS absorb and transfer light energy to photosystem (PS) II as well as PS I, and the distribution of light energy from PBS to the two photosystems is regulated by light conditions through a mechanism known as state transitions. In this study the quantum efficiency of excitation energy transfer from PBS to PS I in the cyanobacterium Synechococcus sp. PCC 7002 was determined, and the results showed that energy transfer from PBS to PS I is extremely efficient. The results further demonstrated that energy transfer from PBS to PS I occurred directly and that efficient energy transfer was dependent upon the allophycocyanin-B alpha subunit, ApcD. In the absence of ApcD, cells were unable to perform state transitions and were trapped in state 1. Action spectra showed that light energy transfer from PBS to PS I was severely impaired in the absence of ApcD. An apcD mutant grew more slowly than the wild type in light preferentially absorbed by phyrobiliproteins and was more sensitive to high light intensity. On the other hand, a mutant lacking ApcF, which is required for efficient energy transfer from PBS to PS II, showed greater resistance to high light treatment. Therefore, state transitions in cyanobacteria have two roles: (1) they regulate light energy distribution between the two photosystems; and (2) they help to protect cells from the effects of light energy excess at high light intensities. (C) 2009 Elsevier B.V. All rights reserved.

The effects of sediment transport on grain-size distributions

Changes in statistics (mean, sorting, and skewness) describing grain-size distributions have long been used to speculate on the direction of sediment transport. We present a simple model whereby the distributions of sediment in transport are related to their source by a sediment transfer function which defines the relative probability that a grain within each particular class interval will be eroded and transported. A variety of empirically derived transfer functions exhibit negatively skewed distributions (on a phi scale). Thus, when a sediment is being eroded, the probability of any grain going into transport increases with diminishing grain size throughout more than half of its size range. This causes the sediment in transport to be finer and more negatively skewed than its source, whereas the remaining sediment (a lag) must become relatively coarser and more positively skewed. Flume experiments show that the distributions of transfer functions change from having a highly negative skewness to being nearly symmetrical (although still negatively skewed) as the energy of the transporting process increases. We call the two extremes low-energy and high-energy transfer functions , respectively. In an expanded sediment-transport model, successive deposits in the direction of transport are related by a combination of two transfer functions. If energy is decreasing and the transfer functions have low-energy distributions, successive deposits will become finer and more negatively skewed. If, however, energy is decreasing, but the initial transfer function has a high-energy distribution, successive deposits will become coarser and more positively skewed. The variance of the distributions of lags, sediment in transport, and successive deposits in the down-current direction must eventually decrease (i.e., the sediments will become better sorted). We demonstrate that it is possible for variance first to increase, but suggest that, in reality, an increasing variance in the direction of transport will seldom be observed, particularly when grain-size distributions are described in phi units. This model describing changes in sediment distributions was tested in a variety of environments where the transport direction was known. The results indicate that the model has real-world validity and can provide a method to predict the directions of sediment transport

The Early Diagenetic Formation of Organic Sulfur in the Sediments of Mangrove Lake, Bermuda

Due to a low mineral content, the sapropelic sediments depositing in Mangrove Lake, Bermuda, provide an excellent opportunity to explore for possible additions of sulfur to organic matter during the early stages of diagenesis. We evaluated early diagenetic organic sulfur transformations by monitoring the concentrations and stable isotopic compositions of a number of inorganic and organic sulfur pools, thereby accounting for all of the sulfur in the sediments. We have identified and quantified the following sulfur pools: porewater sulfate, porewater sulfide, elemental sulfur, pyrite sulfur, hydrolyzable organic sulfur (HYOS), chromium-reducible organic sulfur (CROS), and nonchromium-reducible organic sulfur (Non-CROS). Of the organic sulfur pools, the Non-CROS pool is by far the largest, followed by CROS, and finally HYOS. By 60 cm depth these pools contribute, respectively, to 85, 7.9, and 3.6% of the total solid phase sulfur. The HYOS pool is probably of biological origin and shows no interaction with the sulfur compounds produced during diagenesis. By contrast, CROS is produced, most likely, from the diagenetic addition of polysulfides to functionalized lipids in the upper, H2S-poor, elemental sulfur-rich, region of the sediment. A portion of this sulfur pool is unstable and decomposes on contact with the H2S-rich porewaters. The portion of CROS that remains in the sulfidic waters appears to readily exchange sulfur isotopes with H2S. While some of the Non-CROS pool is of biological origin, some is also formed by the diagenetic addition of sulfur to organic compounds in the upper H2S-poor region of the sediment. By contrast with CROS, Non-CROS is not diagenetically active in the H2S-rich porewaters. Overall, somewhere between 27 and 53 % of the organic sulfur buried in Mangrove Lake sediments is of diagenetic origin, with the remaining organic sulfur derived from biosynthesis. We extrapolate our Mangrove Lake results and calculate that in typical coastal marine sediments between 11 and 29 μmol g−1 of organic sulfur will form during early diagenesis, of which 2–5 μmol g−1 will be chromium reducible.

Novel polyoxometalate-templated, 3-D supramolecular networks based on lanthanide dimers: Synthesis, structure, and fluorescent properties of [Ln(2)(DNBA)(4)(DMF)(8)][Mo6O19] (DNBA=3,5-dinitrobenzoate)

The spherical Lindquist type polyoxometalate, Mo6O192-, has been used as a noncoordinating anionic template for the construction of novel three-dimensional lanthanide-aromatic monocarboxylate dimer supramolecular networks [Ln(2)(DNBA)(4)(DMF)(8)][Mo6O19] (Ln = La 1, Ce 2, and Eu 3, DNBA = 3,5-dinitrobenzoate, DMF = dimethylformamide). The title compounds are characterized by elemental analyses, IR, and single-crystal X-ray diffractions. X-ray diffraction experiments reveal that two Ln(III) ions are bridged by four 3,5-dinitrobenzoate anions as asymmetrically bridging ligands, leading to dimeric cores, [Ln(2)(DNBA)(4)(DMF)(8)](2+); [Ln(2)(DNBA)(4)(DMF)(8)](2+) groups are joined together by pi-pi stacking interactions between the aromatic groups to form a two-dimensional grid-like network; the 2-D supramolecular layers are further extended into 3-D supramolecular networks with 1-D box-like channels by hydrogen-bonding interactions, in which hexamolybdate polyanions reside. The compounds represent the first examples of 3-D carboxylate-bridged lanthanide dimer supramolecular "host" networks formed by pi-pi stacking and hydrogen-bonding interactions encapsulating noncoordinating "guest" polyoxoanion species. The fluorescent activity of compound 3 is reported.

Ocean urea fertilization for carbon credits poses high ecological risks

The proposed plan for enrichment of the Sulu Sea, Philippines, a region of rich marine biodiversity, with thousands of tonnes of urea in order to stimulate algal blooms and sequester carbon is flawed for multiple reasons. Urea is preferentially used as a nitrogen source by some cyanobacteria and dinoflagellates, many of which are neutrally or positively buoyant. Biological pumps to the deep sea are classically leaky, and the inefficient burial of new biomass makes the estimation of a net loss of carbon from the atmosphere questionable at best. The potential for growth of toxic dinoflagellates is also high, as many grow well on urea and some even increase their toxicity when grown on urea. Many toxic dinoflagellates form cysts which can settle to the sediment and germinate in subsequent years, forming new blooms even without further fertilization. If large-scale blooms do occur, it is likely that they will contribute to hypoxia in the bottom waters upon decomposition. Lastly, urea production requires fossil fuel usage, further limiting the potential for net carbon sequestration. The environmental and economic impacts are potentially great and need to be rigorously assessed. (C) 2008 Elsevier Ltd. All rights reserved.

Rede de adaptação de cultivares de aipim e mandioca para o nordeste brasileiro: safra 2006/2007.

2008

Cultivares de milho, feijão, girassol e mandioca para o agreste sergipano com foco na agricultura familiar e no agronegócio.

2008

Error Detection and Recovery for Robot Motion Planning with Uncertainty

Robots must plan and execute tasks in the presence of uncertainty. Uncertainty arises from sensing errors, control errors, and uncertainty in the geometry of the environment. The last, which is called model error, has received little previous attention. We present a framework for computing motion strategies that are guaranteed to succeed in the presence of all three kinds of uncertainty. The motion strategies comprise sensor-based gross motions, compliant motions, and simple pushing motions.

Motion Planning with Six Degrees of Freedom

The motion planning problem is of central importance to the fields of robotics, spatial planning, and automated design. In robotics we are interested in the automatic synthesis of robot motions, given high-level specifications of tasks and geometric models of the robot and obstacles. The Mover's problem is to find a continuous, collision-free path for a moving object through an environment containing obstacles. We present an implemented algorithm for the classical formulation of the three-dimensional Mover's problem: given an arbitrary rigid polyhedral moving object P with three translational and three rotational degrees of freedom, find a continuous, collision-free path taking P from some initial configuration to a desired goal configuration. This thesis describes the first known implementation of a complete algorithm (at a given resolution) for the full six degree of freedom Movers' problem. The algorithm transforms the six degree of freedom planning problem into a point navigation problem in a six-dimensional configuration space (called C-Space). The C-Space obstacles, which characterize the physically unachievable configurations, are directly represented by six-dimensional manifolds whose boundaries are five dimensional C-surfaces. By characterizing these surfaces and their intersections, collision-free paths may be found by the closure of three operators which (i) slide along 5-dimensional intersections of level C-Space obstacles; (ii) slide along 1- to 4-dimensional intersections of level C-surfaces; and (iii) jump between 6 dimensional obstacles. Implementing the point navigation operators requires solving fundamental representational and algorithmic questions: we will derive new structural properties of the C-Space constraints and shoe how to construct and represent C-Surfaces and their intersection manifolds. A definition and new theoretical results are presented for a six-dimensional C-Space extension of the generalized Voronoi diagram, called the C-Voronoi diagram, whose structure we relate to the C-surface intersection manifolds. The representations and algorithms we develop impact many geometric planning problems, and extend to Cartesian manipulators with six degrees of freedom.

Cultivares de milho, feijão, girassol e mandioca para o agreste sergipano com foco na agricultura familiar e no agronegócio.

2008