Physical basis of coastal productivity: The SEEP and MASAR experiments

Science.gov (United States)

Csanady, G. T.

Two major cooperative experiments, code-named Shelf Edge Exchange Processes (SEEP) I and II, were carried out on the northeast U.S. continental shelf and slope by an interdisciplinary group of scientists in the past decade. The work, supported by the Department of Energy, Office of Health and Environmental Research, had the broad aim of determining whether or to what extent energy-related human activities interfere with the high biological productivity of coastal waters. Much of SEEP I work was reported in a dedicated issue of Continental Shelf Research, including a summary article on the experiment as a whole [Walsh et al., 1988[. A parallel experiment, supported by the Minerals Management Service and code-named Mid Atlantic Slope and Rise (MASAR), had the objective of exploring physical processes over the continental slope and rise, including especially currents in the upper part of the water column. A good deal of MASAR work was also reported in the SEEP issue just mentioned, mainly in an article by Csanady and Hamilton (1988). There have been other papers and publications on these experiments, and more are forthcoming. While many questions remain, our horizons have broadened considerably after a decade of work on this problem, as if our aeroplane had just emerged from clouds to expose an interesting landscape. In this article I shall try to describe the physical (-oceanographic) features of that landscape, not in the chronological order in which we have espied them, but as the logic of the subject dictates.

Signatures of geochemical changes at methane-seeps as recorded by seep carbonates

OpenAIRE

Himmler, Tobias

2011-01-01

This thesis compiles three manuscripts: (1) The first manuscript (chapter 2.1) contains petrographic and geochemical data of aragonitic seep carbonates from the Makran accretionary prism. High-resolution rare earth element (REE) analysis yield distinct total REE[aragonite] concentrations and shale-normalised REE[aragonite] patterns. The REE variations are ascribed to different pore fluid compositions and accompanied redox changes during aragonite precipitation. (2) The second manuscript (chap...

Assessment of seeps in the vicinity of the Mexican Hat tailings disposal cell

International Nuclear Information System (INIS)

1990-10-01

The Phase II remedial action at the Mexican Hat site began in September 1988, and involved the excavation, transportation, and placement of contaminated materials onto the lower tailings pile. These materials were from the upper tailings pile, portions of the lower tailings pile, off-pile contaminated areas, and demolition material stockpiled at the former-mill site. By December 1989, all of the contaminated soils on the upper tailings pile area and most of the off-pile windblown and waterborne contamination had been removed and placed on the lower pile. Since that time, several seeps have been observed near the site. These seeps and some previously identified seeps may be related to remedial action construction activities or the past disposal of mill tailings at the Mexican Hat site. The objectives of this report are to: summarize the geology and hydrostratigraphy of the site; discuss field investigation of the locations, chronology, and flow rates of the seeps; discuss background groundwater quality, tailings pore fluid characterization, and water quality of the seeps; identify possible sources of the seeps; interpret the data; make recommendations for continued site characterization and assessment

Assessment of soil-gas, seep, and soil contamination at the North Range Road Landfill, Fort Gordon, Georgia, 2008-2009

Science.gov (United States)

Landmeyer, James E.; Falls, W. Fred; Ratliff, W. Hagan; Wellborn, John B.

2011-01-01

Soil gas, seeps, and soil were assessed for contaminants at the North Range Road Landfill at Fort Gordon, Georgia, from October 2008 to September 2009. The assessment included delineating organic contaminants present in soil-gas samples beneath the area estimated to be the landfill and in water samples collected from three seeps at the base of the landfill. Inorganic contaminants were determined in three seep samples and in soil samples. This assessment was conducted to provide environmental contamination data to Fort Gordon pursuant to requirements for the Resource Conservation and Recovery Act Part B Hazardous Waste Permit process.

Study of old ecological hazards, oil seeps and contaminations using earth observation methods – spectral library for oil seep

Directory of Open Access Journals (Sweden)

Smejkalová Eva

2017-03-01

Full Text Available The possibilities of remote sensing techniques in the field of the Earth surface monitoring and protection specifically for the problems caused by petroleum contaminations, for the mapping of insufficiently plugged and abandoned old oil wells and for the analysis of onshore oil seeps are described. Explained is the methodology for analyzing and detection of potential hydrocarbon contaminations using the Earth observation in the area of interest in Slovakia (Korňa and in Czech Republic (Nesyt, mainly building and calibrating the spectral library for oil seeps. The acquisition of the in-situ field data (ASD, Cropscan spectroradiometers for this purpose, the successful building and verification of hydrocarbon spectral library, the application of hydrocarbon indexes and use of shift in red-edge part of electromagnetic spectra, the spectral analysis of input data are clarified in the paper. Described is approach which could innovate the routine methods for investigating the occurrence of hydrocarbons and can assist during the mapping and locating the potential oil seep sites. Important outcome is the successful establishment of a spectral library (database with calibration data suitable for further application in data classification for identifying the occurrence of hydrocarbons.

Biogeography and potential exchanges among the atlantic Equatorial belt cold-seep faunas.

Directory of Open Access Journals (Sweden)

Karine Olu

2010-08-01

Full Text Available Like hydrothermal vents along oceanic ridges, cold seeps are patchy and isolated ecosystems along continental margins, extending from bathyal to abyssal depths. The Atlantic Equatorial Belt (AEB, from the Gulf of Mexico to the Gulf of Guinea, was one focus of the Census of Marine Life ChEss (Chemosynthetic Ecosystems program to study biogeography of seep and vent fauna. We present a review and analysis of collections from five seep regions along the AEB: the Gulf of Mexico where extensive faunal sampling has been conducted from 400 to 3300 m, the Barbados accretionary prism, the Blake ridge diapir, and in the Eastern Atlantic from the Congo and Gabon margins and the recently explored Nigeria margin. Of the 72 taxa identified at the species level, a total of 9 species or species complexes are identified as amphi-Atlantic. Similarity analyses based on both Bray Curtis and Hellinger distances among 9 faunal collections, and principal component analysis based on presence/absence of megafauna species at these sites, suggest that within the AEB seep megafauna community structure is influenced primarily by depth rather than by geographic distance. Depth segregation is observed between 1000 and 2000 m, with the middle slope sites either grouped with those deeper than 2000 m or with the shallower sites. The highest level of community similarity was found between the seeps of the Florida escarpment and Congo margin. In the western Atlantic, the highest degree of similarity is observed between the shallowest sites of the Barbados prism and of the Louisiana slope. The high number of amphi-atlantic cold-seep species that do not cluster according to biogeographic regions, and the importance of depth in structuring AEB cold-seep communities are the major conclusions of this study. The hydrothermal vent sites along the Mid Atlantic Ridge (MAR did not appear as "stepping stones" for dispersal of the AEB seep fauna, however, the south MAR and off axis regions

Cold seeps and splay faults on Nankai margin

Science.gov (United States)

Henry, P.; Ashi, J.; Tsunogai, U.; Toki, T.; Kuramoto, S.; Kinoshita, M.; Lallemant, S. J.

2003-04-01

Cold seeps (bacterial mats, specific fauna, authigenic carbonates) are common on the Nankai margin and considered as evidence for seepage of methane bearing fluids. Camera and submersible surveys performed over the years have shown that cold seeps are generally associated with active faults. One question is whether part of the fluids expelled originate from the seismogenic zone and migrate along splay faults to the seafloor. The localisation of most cold seeps on the hanging wall of major thrusts may, however, be interpreted in various ways: (a) footwall compaction and diffuse flow (b) fluid channelling along the fault zone at depths and diffuse flow near the seafloor (c) erosion and channelling along permeable strata. In 2002, new observations and sampling were performed with submersible and ROV (1) on major thrusts along the boundary between the Kumano forearc basin domain and the accretionary wedge domain, (2) on a fault affecting the forearc (Kodaiba fault), (3) on mud volcanoes in the Kumano basin. In area (1) tsunami and seismic inversions indicate that the targeted thrusts are in the slip zone of the To-Nankai 1944 earthquakes. In this area, the largest seep zone, continuous over at least 2 km, coincides with the termination of a thrust trace, indicating local fluid channelling along the edge of the fault zone. Kodaiba fault is part of another splay fault system, which has both thrusting and strike-slip components and terminates westward into an en-echelon fold system. Strong seepage activity with abundant carbonates was found on a fold at the fault termination. One mud volcano, rooted in one of the en-echelon fold, has exceptionally high seepage activity compared with the others and thick carbonate crusts. These observations suggest that fluid expulsion along fault zones is most active at fault terminations and may be enhanced during fault initiation. Preliminary geochemical results indicate signatures differ between seep sites and suggests that the two

Inspection and monitoring plan, contaminated groundwater seeps 317/319/ENE Area, Argonne National Laboratory

International Nuclear Information System (INIS)

1996-01-01

During the course of completing the Resource Conservation and Recovery Act (RCRA) Facility Investigation (RFI) in the 317/319/East-Northeast (ENE) Area of Argonne National Laboratory-East (ANL-E), groundwater was discovered moving to the surface through a series of groundwater seeps. The seeps are located in a ravine approximately 600 ft south of the ANL-E fence line in Waterfall Glen Forest Preserve. Samples of the seep water were collected and analyzed for selected parameters. Two of the five seeps sampled were found to contain detectable levels of organic contaminants. Three chemical species were identified: chloroform (14--25 microg/L), carbon tetrachloride (56--340 microg/L), and tetrachloroethylene (3--6 microg/L). The other seeps did not contain detectable levels of volatile organics. The nature of the contaminants in the seeps will also be monitored on a regular basis. Samples of surface water flowing through the bottom of the ravine and groundwater emanating from the seeps will be collected and analyzed for chemical and radioactive constituents. The results of the routine sampling will be compared with the concentrations used in the risk assessment. If the concentrations exceed those used in the risk assessment, the risk calculations will be revised by using the higher numbers. This revised analysis will determine if additional actions are warranted

Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy

Science.gov (United States)

Ruff, S. Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam

2016-01-01

The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic carbon depleted permeable sands off the Island of Elba (Italy). We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g-1 day-1 indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20–50 cm below seafloor) as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3, and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise distinct

Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy.

Science.gov (United States)

Ruff, S Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam

2016-01-01

The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic carbon depleted permeable sands off the Island of Elba (Italy). We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g(-1) day(-1) indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20-50 cm below seafloor) as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3, and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise distinct

First discovery of a cold seep on the continental margin of the central Red Sea

KAUST Repository

Batang, Zenon B.

2012-06-01

A new cold brine seep system with microbial mats and metazoan assemblages was discovered by a remotely operated vehicle (ROV) on the Saudi continental margin of central Red Sea. Now named as Thuwal Seeps, it has a shallow brine pool between 840 and 850. m water depths that is formed by focused brine expulsions from two sites (Seep I: 22°17.3\\'N, 38°53.8\\'E; Seep II: 22°16.9\\'N, 38°53.9\\'E). The seep is located at the base of a steep wall rock closer to the shore (20. km) than to the axial trough (120. km). The brine pool does not exhibit a significant thermal anomaly (<. 0.3°C) and is so far the coldest (21.7°C) and least saline (74‰) among brine pools in the Red Sea. This discovery provides the first direct evidence of a cold seep with associated biota on the continental margin of the Red Sea. © 2011 Elsevier B.V.

Using Multi-Disciplinary Data to Compile a Hydrocarbon Budget for GC600, a Natural Seep in the Gulf of Mexico

Science.gov (United States)

MacDonald, I. R.; Johansen, C.; Marty, E.; Natter, M.; Silva, M.; Hill, J. C.; Viso, R. F.; Lobodin, V.; Diercks, A. R.; Woolsey, M.; Macelloni, L.; Shedd, W. W.; Joye, S. B.; Abrams, M.

2016-12-01

Fluid exchange between the deep subsurface and the overlying ocean and atmosphere occurs at hydrocarbon seeps along continental margins. Seeps are key features that alter the seafloor morphology and geochemically affect the sediments that support chemosynthetic communities. However, the dynamics and discharge rates of hydrocarbons at cold seeps remain largely unconstrained. Here we merge complementary geochemical (oil fingerprinting), geophysical (seismic, subbottom, backscatter, multibeam) and video/imaging (Video Time Lapse Camera, DSV ALVIN video) data sets to constrain pathways and magnitudes of hydrocarbon fluxes from the source rock to the seafloor at a well-studied, prolific seep site in the Northern Gulf of Mexico (GC600). Oil fingerprinting showed compositional similarities for samples from the following collections: the reservoir, an active vent, and the sea-surface. This was consistent with reservoir structures and pathways identified in seismic data. Video data, which showed the spatial distribution of seep indicators such as bacteria mats, or hydrate outcrops at the sediment interface, were combined with known hydrocarbon fluxes from the literature and used to quantify the total hydrocarbon fluxes in the seep domain. Using a systems approach, we combined data sets and published values at various scales and resolutions to compile a preliminary hydrocarbon budget for the GC600 seep site. Total estimated in-flow of hydrocarbons was 2.07 x 109 mol/yr. The combined total of out-flow and sequestration amounted to 7.56 x 106 mol/yr leaving a potential excess (in-flow - out-flow) of 2.06 x 109 mol/yr. Thus quantification of the potential out-flow from the seep domains based on observable processes does not equilibrate with the theoretical inputs from the reservoir. Processes that might balance this budget include accumulation of gas hydrate and sediment free-gas, as well as greater efficiency of biological sinks.

Hydrothermal Vents and Methane Seeps: Rethinking the Sphere of Influence

Directory of Open Access Journals (Sweden)

Lisa Ann Levin

2016-05-01

Full Text Available Although initially viewed as oases within a barren deep ocean, hydrothermal vent and methane seep communities are now recognized to interact with surrounding ecosystems on the sea floor and in the water column, and to affect global geochemical cycles. The importance of understanding these interactions is growing as the potential rises for disturbance from oil and gas extraction, seabed mining and bottom trawling. Here we synthesize current knowledge of the nature, extent and time and space scales of vent and seep interactions with background systems. We document an expanded footprint beyond the site of local venting or seepage with respect to elemental cycling and energy flux, habitat use, trophic interactions, and connectivity. Heat and energy are released, global biogeochemical and elemental cycles are modified, and particulates are transported widely in plumes. Hard and biotic substrates produced at vents and seeps are used by benthic background fauna for attachment substrata, shelter, and access to food via grazing or through position in the current, while particulates and fluid fluxes modify planktonic microbial communities. Chemosynthetic production provides nutrition to a host of benthic and planktonic heterotrophic background species through multiple horizontal and vertical transfer pathways assisted by flow, gamete release, animal movements, and succession, but these pathways remain poorly known. Shared species, genera and families indicate that ecological and evolutionary connectivity exists among vents, seeps, organic falls and background communities in the deep sea; the genetic linkages with inactive vents and seeps and background assemblages however, are practically unstudied. The waning of venting or seepage activity generates major transitions in space and time that create links to surrounding ecosystems, often with identifiable ecotones or successional stages. The nature of all these interactions is dependent on water depth, as

Hydrothermal vents and methane seeps: Rethinking the sphere of influence

Science.gov (United States)

Levin, Lisa A.; Baco, Amy; Bowden, David; Colaco, Ana; Cordes, Erik E.; Cunha, Marina; Demopoulos, Amanda W.J.; Gobin, Judith; Grupe, Ben; Le, Jennifer; Metaxas, Anna; Netburn, Amanda; Rouse, Greg; Thurber, Andrew; Tunnicliffe, Verena; Van Dover, Cindy L.; Vanreusel, Ann; Watling, Les

2016-01-01

Although initially viewed as oases within a barren deep ocean, hydrothermal vent and methane seep communities are now recognized to interact with surrounding ecosystems on the sea floor and in the water column, and to affect global geochemical cycles. The importance of understanding these interactions is growing as the potential rises for disturbance from oil and gas extraction, seabed mining and bottom trawling. Here we synthesize current knowledge of the nature, extent and time and space scales of vent and seep interactions with background systems. We document an expanded footprint beyond the site of local venting or seepage with respect to elemental cycling and energy flux, habitat use, trophic interactions, and connectivity. Heat and energy are released, global biogeochemical and elemental cycles are modified, and particulates are transported widely in plumes. Hard and biotic substrates produced at vents and seeps are used by “benthic background” fauna for attachment substrata, shelter, and access to food via grazing or through position in the current, while particulates and fluid fluxes modify planktonic microbial communities. Chemosynthetic production provides nutrition to a host of benthic and planktonic heterotrophic background species through multiple horizontal and vertical transfer pathways assisted by flow, gamete release, animal movements, and succession, but these pathways remain poorly known. Shared species, genera and families indicate that ecological and evolutionary connectivity exists among vents, seeps, organic falls and background communities in the deep sea; the genetic linkages with inactive vents and seeps and background assemblages however, are practically unstudied. The waning of venting or seepage activity generates major transitions in space and time that create links to surrounding ecosystems, often with identifiable ecotones or successional stages. The nature of all these interactions is dependent on water depth, as well as

Methane seep in shallow-water permeable sediment harbors high diversity of anaerobic methanotrophic communities, Elba, Italy

Directory of Open Access Journals (Sweden)

S Emil Ruff

2016-03-01

Full Text Available The anaerobic oxidation of methane (AOM is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME and sulfate-reducing bacteria (SRB, and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic-carbon depleted permeable sands off the Island of Elba (Italy. We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g-1 day-1 indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20–50 cm below seafloor as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3 and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise

Faunal and stable isotopic analyses of benthic foraminifera from the Southeast Seep on Kimki Ridge offshore southern California, USA

Science.gov (United States)

McGann, Mary; Conrad, James E.

2018-01-01

We investigated the benthic foraminiferal faunal and stable carbon and oxygen isotopic composition of a 15-cm push core (NA075-092b) obtained on a Telepresence-Enabled cruise to the Southeast Seep on Kimki Ridge offshore southern California. The seep core was taken at a depth of 973 m in the vicinity of a Beggiatoa bacterial mat and vesicomyid clams (Calyptogena) and compared to previously published data of living assemblages from ~ 714 m, four reference cores obtained at ~ 1030 m, and another one at 739 m. All of the reference sites are also from the Inner Continental Borderland but with no evidence of methane seepage.No endemic species were found at the seep site and most of the taxa recovered there have been reported previously from other seep or low oxygen environments. Q- and R-mode cluster analyses clearly illustrated differences in the faunal assemblages of the seep and non-seep sites. The living assemblage at Southeast Seep was characterized by abundant Takayanagia delicata, Cassidulina translucens, and Spiroplectammina biformis, whereas the non-seep San Pedro Basin reference assemblage was comprised primarily of Chilostomella oolina and Globobulimina pacifica. Density and species richness were lower at the seep site compared to the non-seep site, reflecting the harsher living conditions there. The dead assemblage at the seep site was dominated by Gyroidina turgida compared to Cassidulina translucens at the ~ 1030 m non-seep site and Cassidulina translucens, Pseudoparrella pacifica, and Takayanagia delicata at the 739 m non-seep site. Density was three times lower at Southeast Seep than at the non-seep sites of comparable water depth but species richness was ~ 30% higher. Stable carbon isotopic values were considerably depleted in the seep samples compared to the non-seep samples, with a progression from lightest to heaviest average δ13C values evident at the seep site reflecting microhabitat preference and vital effect: the

The origin of gas seeps and shallow gas in northern part of South China Sea

Science.gov (United States)

Li, M.; Jin, X.

2003-04-01

The northern part of South China Sea is of passive continental margin, which geologic units include shelf, slope and deep sea basin. There are rifting basins forming during Paleogene (or Cretaceous ?) to Quaternary developed on shelf and slope, which sediments are dominated by fluvial and lake clastic rock of Paleogene, and marine clastic rock and carbonate of Neogene - Quaternary. The main basins include the Pearl River Mouth Basin, Beibu Gulf basin, Qiongdongnan Basin and Yinggehai basin. They contain rich oil and gas resources, and have become important industrial oil and gas producing region in South China Sea. With the increasing of petroleum exploration actives and marine petroleum engineering, it has been paid more attention to the investigation and research of gas seeps and shallow gas, for they become a potential threaten to the marine engineering while they are regarded as the indicators of industrial oil and gas. By study the distribution and geochemical characteristics of gas seeps in northeast part of Yinggehai basin and shallow gas in sediments on slope, combined with their regional geologic background, this paper deals with the origin, migration pathway and emission mechanism of gas seeps and shallow gas in northern part of South China Sea, for providing a base knowledge for the evaluation of marine engineering geology. In northeast part of Yinggehai basin gas seeps have been found and recorded for near 100 years. During 1990s, as a part of petroleum exploration, the gas seeps in the basin have been investigated and research by oil companies (Baojia Huang et al., 1992; Jiaqiong He et al., 2000). Gas seeps were found in shallow water area along southwest coast of Hainan Island, water depth usually less than 50 m. The occurrence of gas seeps can be divided into two types: (1) gas continuously emission, continuous gas bubbles groups can be detected by sonar underwater and observed on water surface. (2) gas intermittently emission, the time intervals

Fatty Acid and Carbon Isotopic Evidence for type I Methanotrophs in Microbial Mats from a Shallow Marine Gas Seep, Coal Oil Point, CA.

Science.gov (United States)

Ding, H.; Valentine, D.

2005-12-01

To study the microbial community in a Southern California seep field, sediment and bacterial mat samples were collected from natural gas-bearing and gas-free surfaces at two distinct seeps in the Coal Oil Point seep field, offshore Santa Barbara. Fatty acids in these samples were extracted, analyzed and identified. Using gas chromatography (GC), more than 30 different fatty acids were separated. Generally, fatty acid concentrations in natural gas-bearing samples were about 5-fold higher compared to gas-free samples. Using gas chromatography mass sepctrometry (GC-MS), all separated fatty acids were identified in each sample. The major constituents included saturated 14:0, 16:0, 18:0, branched i-15, a-15 and unsaturated 16:1 and 18:1 series fatty acids. GC-IRMS (isotope ratio mass spectrometry) analysis provided the 13C of all major fatty acids and some 16:1 series fatty acids were found to be more depleted than -40% in samples associated with gas seepage. After treatment with dimethyl disufide (DMDS), the 16:1 series fatty acids were resolved into five distinct components, including common composition 16:1(7), bacterial specific i-16:1(7) and typical biomarkers of type I methnotrophs 16:1(8), 16(6) and 16:1(5), suggesting an important role for methnotrophs in seep sediments and microbial mats. These results provide evidence for the activity of type I methanotrophic bacteria in microbial mats and surficial sediments at the Coal Oil Point seep field, and have implications for methane cycling in this and other seep

High pH microbial ecosystems in a newly discovered, ephemeral, serpentinizing fluid seep at Yanartaş (Chimera), Turkey.

Science.gov (United States)

Meyer-Dombard, D'Arcy R; Woycheese, Kristin M; Yargıçoğlu, Erin N; Cardace, Dawn; Shock, Everett L; Güleçal-Pektas, Yasemin; Temel, Mustafa

2014-01-01

Gas seeps emanating from Yanartaş (Chimera), Turkey, have been documented for thousands of years. Active serpentinization produces hydrogen and a range of carbon gases that may provide fuel for life. Here we report a newly discovered, ephemeral fluid seep emanating from a small gas vent at Yanartaş. Fluids and biofilms were sampled at the source and points downstream. We describe site conditions, and provide microbiological data in the form of enrichment cultures, Scanning electron microscopy (SEM), carbon and nitrogen isotopic composition of solids, and PCR screens of nitrogen cycle genes. Source fluids are pH 11.95, with a Ca:Mg of ~200, and sediments under the ignited gas seep measure 60°C. Collectively, these data suggest the fluid is the product of active serpentinization at depth. Source sediments are primarily calcite and alteration products (chlorite and montmorillonite). Downstream, biofilms are mixed with montmorillonite. SEM shows biofilms distributed homogeneously with carbonates. Organic carbon accounts for 60% of the total carbon at the source, decreasing downstream to <15% as inorganic carbon precipitates. δ(13)C ratios of the organic carbon fraction of solids are depleted (-25 to -28‰) relative to the carbonates (-11 to -20‰). We conclude that heterotrophic processes are dominant throughout the surface ecosystem, and carbon fixation may be key down channel. δ(15)N ratios ~3‰, and absence of nifH in extracted DNA suggest that nitrogen fixation is not occurring in sediments. However, the presence of narG and nirS at most locations and in enrichments indicates genomic potential for nitrate and nitrite reduction. This small seep with shallow run-off is likely ephemeral, but abundant preserved microterracettes in the outflow and the surrounding area suggest it has been present for some time. This site and others like it present an opportunity for investigations of preserved deep biosphere signatures, and subsurface-surface interactions.

High pH microbial ecosystems in a newly discovered, ephemeral, serpentinizing fluid seep at Yanartaş (Chimaera, Turkey

Directory of Open Access Journals (Sweden)

D'Arcy Renee Meyer-Dombard

2015-01-01

Full Text Available Gas seeps emanating from ophiolites at Yanartaş (Chimaera, Turkey, have been documented for thousands of years. Active serpentinization produces hydrogen and a range of carbon gases that may provide fuel for life. Here we report a newly discovered, ephemeral fluid seep emanating from a small gas vent at Yanartaş. Fluids and biofilms were sampled at the source and points downstream. We describe site conditions, and provide microbiological data in the form of enrichment cultures, scanning electron microscopy (SEM, carbon and nitrogen isotopic composition of solids, and PCR screens of nitrogen cycle genes. Source fluids are pH 11.95, with a Ca:Mg of ~200, and sediments under the ignited gas seep measure 60°C. Collectively, these data suggest the fluid is the product of active serpentinization at depth. Source sediments are primarily calcite and alteration products (chlorite and montmorillonite. Downstream, biofilms are mixed with montmorillonite. SEM shows biofilms distributed homogeneously with carbonates. Organic carbon accounts for 60% of the total carbon at the source, decreasing downstream to <15% as inorganic carbon precipitates. δ13C ratios of the organic carbon fraction of solids are depleted (−25 to −28 ‰ relative to the carbonates (−11 to −20‰. We conclude that heterotrophic processes are dominant throughout the surface ecosystem, and carbon fixation may be key down channel. δ15N ratios ~ 3‰, and absence of nifH in extracted DNA suggest that nitrogen fixation is not occurring in sediments. However, the presence of narG and nirS at most locations and in enrichments indicates genomic potential for nitrate and nitrite reduction. This small seep with shallow run-off is likely ephemeral, but abundant preserved microterracettes in the outflow and the surrounding area suggest it has been present for some time. This site and others like it present an opportunity for investigations of preserved deep biosphere signatures, and

Facultative methanotrophs are abundant at terrestrial natural gas seeps.

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Farhan Ul Haque, Muhammad; Crombie, Andrew T; Ensminger, Scott A; Baciu, Calin; Murrell, J Colin

2018-06-28

Natural gas contains methane and the gaseous alkanes ethane, propane and butane, which collectively influence atmospheric chemistry and cause global warming. Methane-oxidising bacteria, methanotrophs, are crucial in mitigating emissions of methane as they oxidise most of the methane produced in soils and the subsurface before it reaches the atmosphere. Methanotrophs are usually obligate, i.e. grow only on methane and not on longer chain alkanes. Bacteria that grow on the other gaseous alkanes in natural gas such as propane have also been characterised, but they do not grow on methane. Recently, it was shown that the facultative methanotroph Methylocella silvestris grew on ethane and propane, other components of natural gas, in addition to methane. Therefore, we hypothesised that Methylocella may be prevalent at natural gas seeps and might play a major role in consuming all components of this potent greenhouse gas mixture before it is released to the atmosphere. Environments known to be exposed to biogenic methane emissions or thermogenic natural gas seeps were surveyed for methanotrophs. 16S rRNA gene amplicon sequencing revealed that Methylocella were the most abundant methanotrophs in natural gas seep environments. New Methylocella-specific molecular tools targeting mmoX (encoding the soluble methane monooxygenase) by PCR and Illumina amplicon sequencing were designed and used to investigate various sites. Functional gene-based assays confirmed that Methylocella were present in all of the natural gas seep sites tested here. This might be due to its ability to use methane and other short chain alkane components of natural gas. We also observed the abundance of Methylocella in other environments exposed to biogenic methane, suggesting that Methylocella has been overlooked in the past as previous ecological studies of methanotrophs often used pmoA (encoding the alpha subunit of particulate methane monooxygenase) as a marker gene. New biomolecular tools designed in

Population genetic structure in Sabatieria (Nematoda) reveals intermediary gene flow and admixture between distant cold seeps from the Mediterranean Sea.

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De Groote, Annelies; Hauquier, Freija; Vanreusel, Ann; Derycke, Sofie

2017-07-01

There is a general lack of information on the dispersal and genetic structuring for populations of small-sized deep-water taxa, including free-living nematodes which inhabit and dominate the seafloor sediments. This is also true for unique and scattered deep-sea habitats such as cold seeps. Given the limited dispersal capacity of marine nematodes, genetic differentiation between such geographically isolated habitat patches is expected to be high. Against this background, we examined genetic variation in both mitochondrial (COI) and nuclear (18S and 28S ribosomal) DNA markers of 333 individuals of the genus Sabatieria, abundantly present in reduced cold-seep sediments. Samples originated from four Eastern Mediterranean cold seeps, separated by hundreds of kilometers, and one seep in the Southeast Atlantic. Individuals from the Mediterranean and Atlantic were divided into two separate but closely-related species clades. Within the Eastern Mediterranean, all specimens belonged to a single species, but with a strong population genetic structure (Φ ST  = 0.149). The haplotype network of COI contained 19 haplotypes with the most abundant haplotype (52% of the specimens) shared between all four seeps. The number of private haplotypes was high (15), but the number of mutations between haplotypes was low (1-8). These results indicate intermediary gene flow among the Mediterranean Sabatieria populations with no evidence of long-term barriers to gene flow. The presence of shared haplotypes and multiple admixture events indicate that Sabatieria populations from disjunct cold seeps are not completely isolated, with gene flow most likely facilitated through water current transportation of individuals and/or eggs. Genetic structure and molecular diversity indices are comparable to those of epiphytic shallow-water marine nematodes, while no evidence of sympatric cryptic species was found for the cold-seep Sabatieria.

Hydrocarbon-degrading sulfate-reducing bacteria in marine hydrocarbon seep sediments

OpenAIRE

Kleindienst, Sara

2012-01-01

Microorganisms are key players in our biosphere because of their ability to degrade various organic compounds including a wide range of hydrocarbons. At marine hydrocarbon seeps, more than 90% of sulfate reduction (SR) is potentially coupled to non-methane hydrocarbon oxidation. Several hydrocarbon-degrading sulfate-reducing bacteria (SRB) were enriched or isolated from marine sediments. However, in situ active SRB remained largely unknown. In the present thesis, the global distribution and a...

Food-Web Complexity in Guaymas Basin Hydrothermal Vents and Cold Seeps.

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Marie Portail

Full Text Available In the Guaymas Basin, the presence of cold seeps and hydrothermal vents in close proximity, similar sedimentary settings and comparable depths offers a unique opportunity to assess and compare the functioning of these deep-sea chemosynthetic ecosystems. The food webs of five seep and four vent assemblages were studied using stable carbon and nitrogen isotope analyses. Although the two ecosystems shared similar potential basal sources, their food webs differed: seeps relied predominantly on methanotrophy and thiotrophy via the Calvin-Benson-Bassham (CBB cycle and vents on petroleum-derived organic matter and thiotrophy via the CBB and reductive tricarboxylic acid (rTCA cycles. In contrast to symbiotic species, the heterotrophic fauna exhibited high trophic flexibility among assemblages, suggesting weak trophic links to the metabolic diversity of chemosynthetic primary producers. At both ecosystems, food webs did not appear to be organised through predator-prey links but rather through weak trophic relationships among co-occurring species. Examples of trophic or spatial niche differentiation highlighted the importance of species-sorting processes within chemosynthetic ecosystems. Variability in food web structure, addressed through Bayesian metrics, revealed consistent trends across ecosystems. Food-web complexity significantly decreased with increasing methane concentrations, a common proxy for the intensity of seep and vent fluid fluxes. Although high fluid-fluxes have the potential to enhance primary productivity, they generate environmental constraints that may limit microbial diversity, colonisation of consumers and the structuring role of competitive interactions, leading to an overall reduction of food-web complexity and an increase in trophic redundancy. Heterogeneity provided by foundation species was identified as an additional structuring factor. According to their biological activities, foundation species may have the potential to

Metagenomes from two microbial consortia associated with Santa Barbara seep oil.

Science.gov (United States)

Hawley, Erik R; Malfatti, Stephanie A; Pagani, Ioanna; Huntemann, Marcel; Chen, Amy; Foster, Brian; Copeland, Alexander; del Rio, Tijana Glavina; Pati, Amrita; Jansson, Janet R; Gilbert, Jack A; Tringe, Susannah Green; Lorenson, Thomas D; Hess, Matthias

2014-12-01

The metagenomes from two microbial consortia associated with natural oils seeping into the Pacific Ocean offshore the coast of Santa Barbara (California, USA) were determined to complement already existing metagenomes generated from microbial communities associated with hydrocarbons that pollute the marine ecosystem. This genomics resource article is the first of two publications reporting a total of four new metagenomes from oils that seep into the Santa Barbara Channel. Copyright © 2014 Elsevier B.V. All rights reserved.

The hydraulic connectivity, perennial warming and relationship to seismicity of the Davis-Schrimpf Seep Field, Salton Trough, California from new and recent temperature time-series

Science.gov (United States)

Rao, Amar P.

The Davis-Schrimpf Seep Field is a cluster of about 50 transtension-related geothermal seeps in the Imperial Valley, southeastern California. Five temperature time-series were collected from four features and compared to one another, against prior time-series, and to local seismicity. Loggers placed in separate vents within one seep returned moderate anti-correlation. Vents may selectively clog and unclog. Clogging frequencies explaining the observed level of negative correlation were given. Loggers placed in the same vent produced 87-92% positive correlation. It is therefore likely that the vast majority of temperature data measured with loggers possesses meaningful accuracy. Loggers placed in separate seeps exhibited correlation close to or greater than the statistically significant 60% threshold. I propose two lineaments provide a hydraulic connection between these seeps. Two Mw>3.0 earthquake swarms, including one Mw>4.0 event, within 24 kilometers showed possible linkage with >5 degree Celsius temperature perturbations. Seepage warmed 14.5-36.8 degrees Celsius over 5-7 years.

Application of parasound data for sediment study on methane seep site at Simeulue basin

International Nuclear Information System (INIS)

Wiguna, Taufan; Ardhyastuti, Sri

2015-01-01

The Parasound data presents sea depth and sub-bottom profiler. In terms of geological terminology, parasound data represents significant recent surface sedimentary structures that valuable for the selection of subsequent sampling site such as sampling at methane seep site. Therefore, Parasound is used to detailing methane seep at surface sediment following seismic data interpretation. In this study, parasound is used to focus observe area especially for sediment study on methane seep site. The Parasound systems works both as narrow beam sounder use high frequency and as sediment echosounder use low frequency. Parasound acquisition applies parametric effect. It produces additional frequency by nonlinear acoustic interaction of finite amplitude waves. Parasound transducers have 128 elements on 1 m2 and need transmission power up to 70 kW. The results of this study are discovered large seep carbonate with porous surface which means there are gas expulsions passing through that rock

Stable carbon, nitrogen and sulfur isotopes in non-carbonate fractions of cold-seep carbonates

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Feng, Dong; Peng, Yongbo; Peckmann, Jörn; Roberts, Harry; Chen, Duofu

2017-04-01

Sulfate-driven anaerobic oxidation of methane (AOM) supports chemosynthesis-based communities and limits the release of methane from marine sediments. This process promotes the formation of carbonates close to the seafloor along continental margins. The geochemical characteristics of the carbonate minerals of these rocks are increasingly understood, questions remain about the geochemical characteristics of the non-carbonate fractions. Here, we report stable carbon, nitrogen and sulfur isotope patterns in non-carbonate fractions of seep carbonates. The authigenic carbonates were collected from three modern seep provinces (Black Sea, Gulf of Mexico, and South China Sea) and three ancient seep deposits (Marmorito, northern Italy, Miocene; SR4 deposit of the Lincoln Creek Formation and Whiskey Creek, western Washington, USA, Eocene to Oligocene). The δ13C values of non-carbonate fractions range from ˜-25‰ to -80‰ VPDB. These values indicate that fossil methane mixed with varying amounts of pelagic organic matter is the dominant source of carbon in these fractions. The relatively small offset between the δ34S signatures of the non-carbonate fractions and the respective sulfide minerals suggests that locally produced hydrogen sulfide is the main source of sulfur in seep environments. The δ15N values of the non-carbonate fractions are generally lower than the corresponding values of deep-sea sediments, suggesting that organic nitrogen is mostly of a local origin. This study reveals the potential of using δ13C, δ15N, δ34S values to discern seep and non-seep deposits. In cases where δ13Ccarbonate values are only moderately low due to mixing processes and lipid biomarkers have been erased in the course of burial, it is difficult to trace back AOM owing to the lack of other records. This problem is even more pronounced when authigenic carbonate is not available in ancient seep environments. Acknowledgments: The authors thank BOEM and NOAA for their years' support

Chemosynthetic trophic support for the benthic community at an intertidal cold seep site at Mocha Island off central Chile

Science.gov (United States)

Sellanes, Javier; Zapata-Hernández, Germán; Pantoja, Silvio; Jessen, Gerdhard L.

2011-12-01

We analyzed C and N stable isotope ratios of benthic fauna and their potential food sources at an intertidal methane seep site and a control site without emanation at Mocha Island (central Chile). The objective was to trace the origin of the main food sources used by the local heterotrophic fauna, based on the hypothesis that chemosynthetic production could be partially fueling the local food web at the seep site. Food sources sampled at both sites included macroalgae, particulate organic matter and bacteria-like filaments found growing over the red algae Gelidium lingulatum within the areas of active methane release. At the control site, located 11 km away from the gas emanation, fauna exhibited moderate δ 13C values ranging from -16.2‰ (in a nereid polychaete) to -14.8‰ (in a cirolanid isopod), which were consistent with those of the potential photosynthetic food sources sampled at this site (-20.2 to -16.5‰). δ 13C values of the photosynthetic food sources at the seep site similarly ranged between -25.4 and -17.9‰. However, a portion of the animals at this site were consistently more 13C-depleted, with δ 13C values close to that of the seeping methane (-43.8‰) and the bacteria-like filaments (-39.2 ± 2.5‰) also collected at this site. Specific examples were the Marphysa sp. polychaetes (δ 13C = -44.7 ± 0.6‰), the Schistomeringos sp. dorvilleid polychaetes (δ 13C = -42.9‰), and the tanaid crustacean Zeuxo marmoratus (δ 13C = -37.3 ± 0.2‰). The significantly higher δ 13C values of the herbivorous gastropod Tegula atra at the seep site (-29.3 ± 3.1‰) than at the control site (-12.6 ± 0.3‰) also indicated differences among sites of the preferred carbon sources of this species. Mixing model estimates indicate that at the seep site bacteria-like filaments could be contributing up to ˜60% of the assimilated diet of selected invertebrates. Furthermore, several indicators of trophic structure, based in isotopic niche metrics, indicate a

Methane from shallow seep areas of the NW Svalbard Arctic margin does not reach the sea surface

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Silyakova, Anna; Greinert, Jens; Jansson, Pär; Ferré, Bénédicte

2015-04-01

Methane, an important greenhouse gas, leaks from large areas of the Arctic Ocean floor. One overall question is how much methane passes from the seabed through the water column, potentially reaching the atmosphere. Transport of methane from the ocean floor into and through the water column depends on many factors such as distribution of gas seeps, microbial methane oxidation, and ambient oceanographic conditions, which may trigger a change in seep activity. From June-July 2014 we investigated dissolved methane in the water column emanating from the "Prins Karls Forland seeps" area offshore the NW Svalbard Arctic margin. Measurements of the spatial variability of dissolved methane in the water column included 65 CTD stations located in a grid covering an area of 30 by 15 km. We repeated an oceanographic transect twice in a week for time lapse studies, thus documenting significant temporal variability in dissolved methane above one shallow seep site (~100 m water depth). Analysis of both nutrient concentrations and dissolved methane in water samples from the same transect, reveal striking similarities in spatial patterns of both dissolved methane and nutrients indicating that microbial community is involved in methane cycling above the gas seepage. Our preliminary results suggest that although methane release can increase in a week's time, providing twice as much dissolved gas to the water column, no methane from a seep reaches the sea surface. Instead it spreads horizontally under the pycnocline. Yet microbial communities react rapidly to the methane supply above gas seepage areas and may also have an important role as an effective filter, hindering methane release from the ocean to the atmosphere during rapid methane ebullition. This study is funded by CAGE (Centre for Arctic Gas Hydrate, Environment and Climate), Norwegian Research Council grant no. 223259.

The ground support computer and in-orbit survey data analysis program for the SEEP experiment

International Nuclear Information System (INIS)

Voss, H.D.; Datlowe, D.W.; Mobilia, J.; Roselle, S.N.

1985-01-01

The ground support computer equipment (GSE) and production survey plot and analysis software are described for the Stimulated Emissions of Energetic Particles (SEEP) experiment on the S81-1 satellite. A general purpose satellite data acquisition circuit was developed based on a Z-80 portable microcomputer. By simply changing instrument control software and electrical connectors, automatic testing and control of the various SEEP instruments was accomplished. A new feature incorporated into the SEEP data analysis phase was the development of a correlative data base for all of the SEEP instruments. A CPU efficient survey plot program (with ephemeris) was developed to display the approximate 3100 hours of data, with a time resolution of 0.5 sec, from the ten instrument sensors. The details of the general purpose multigraph algorithms and plot formats are presented. For the first time new associations are being investigated of simultaneous particle, X-ray, optical and plasma density satellite measurements

Food-web structure of seep sediment macrobenthos from the Gulf of Mexico

Science.gov (United States)

Demopoulos, Amanda W.J.; Gualtieri, Daniel; Kovacs, Kaitlin

2010-01-01

The slope environment of the Gulf of Mexico (GOM) supports dense communities of seep megafaunal invertebrates that rely on endosymbiotic bacteria for nutrition. Seep sediments also contain smaller macrofaunal invertebrates whose nutritional pathways are not well understood. Using stable-isotope analysis, we investigate the utilization of chemosynthetically fixed and methane-derived organic matter by macrofauna. Biological sampling was conducted in three lower-slope GOM seep environs: Green Canyon (GC852, 1428 m), Atwater Valley (AT340, 2230 m), and Alaminos Canyon (AC601, 2384 m). Infaunal delta13C and delta15N exhibited a broad range of values; most infauna appeared to be heterotrophic, although several taxa had very light delta15N and delta13C values, indicating possible reliance on chemoautotrophic symbioses. The lightest delta13C and delta15N values were observed in nematodes (delta13C=-54.6 + or - 0.1 per mil, delta15N=-6.1 + or - 0.2 per mil) and one gastropod (delta13C=-54.1 per mil, delta15N=-1.1 per mil) from Green Canyon. Mixing-model results indicated that sulfur-oxidizing Beggiatoa may be an important food source for seep infauna; the rate of utilization ranged from 60% to 100% at Green Canyon and Atwater Valley. The overall range in isotope values was similar across the three sites, suggesting that biogeochemical processes may be very similar in these geographically distinct areas.

Mercury concentrations, speciation, and isotopic composition in sediment from a cold seep in the northern Gulf of Mexico

International Nuclear Information System (INIS)

Brown, Garry; Sleeper, Kenneth; Johnson, Marcus W.; Blum, Joel D.; Cizdziel, James V.

2013-01-01

Highlights: • T-Hg, MMHg, and Hg isotopes were determined in Gulf of Mexico deep marine sediments. • Levels of mass independent fractionation of Hg isotopes varied from coastal sediments. • Levels of the MMHg were only slightly elevated at the cold seep site. • Cold seeps do not appear to be significant sources of MMHg to Gulf of Mexico waters. -- Abstract: Total-Hg, monomethylmercury (MMHg), and mercury isotopic composition was determined in sediment from a cold seep and background sites in the northern Gulf of Mexico (nGoM). Total-Hg averaged 50 ng/g (n = 28), ranged from 31 to 67 ng/g, and decreased with depth (0–15 cm). MMHg averaged 0.91 ng/g (n = 18), and ranged from 0.2 to 1.9 ng/g. There was no significant difference for total-Hg or MMHg between cold seep and background sites. δ 202 Hg ranged from −0.5 to −0.8‰ and becomes more negative with depth (r = 0.989). Mass independent fractionation (Δ 199 Hg) was small but consistently positive (0.04–0.12‰); there was no difference between cold seeps (Δ 199 Hg = +0.09 ± 0.03; n = 7, 1SD) and background sites (Δ 199 Hg = +0.07 ± 0.02; n = 5, 1SD). This suggests that releases of hydrocarbons at the cold seep do not significantly alter Hg levels, and that cold seeps are likely not major sources of MMHg to nGoM waters

Laser fluorosensor overflights of the Santa Barbara oil seeps

Energy Technology Data Exchange (ETDEWEB)

Brown, C. E.; Nelson, R. D.; Fingas, M. [Environment Canada, Ottawa, ON (Canada). Emergencies Science Div.; Mullin, J. V. [Minerals Management Service, Herndon, VA (United States)

1997-10-01

Environment Canada`s Laser Environmental Airborne Fluorosensor (LEAF) system was tested in a series of overflights over naturally occurring oil seeps off Santa Barbara, California. The objective was to test the system`s ability to detect oil in actual marine environments and to distinguish petroleum oil from biogenic oils released by kelp beds in and around these naturally occurring oil seep areas. High resolution colour reconnaissance camera images and down-looking video images were collected concurrently with the fluorescence data for documentation purposes. Results of the experiment were analyzed in detail. They confirmed the system`s ability to produce geo-referenced oil contamination location maps in real-time. The fluorescence data obtained during overflights was most similar to typical crude oil, i. e. the system successfully distinguished between biogenic oil and typical petroleum oil. 9 refs., 1 tab., 3 figs.

Laser fluorosensor overflights of the Santa Barbara oil seeps

International Nuclear Information System (INIS)

Brown, C. E.; Nelson, R. D.; Fingas, M.

1997-01-01

Environment Canada's Laser Environmental Airborne Fluorosensor (LEAF) system was tested in a series of overflights over naturally occurring oil seeps off Santa Barbara, California. The objective was to test the system's ability to detect oil in actual marine environments and to distinguish petroleum oil from biogenic oils released by kelp beds in and around these naturally occurring oil seep areas. High resolution colour reconnaissance camera images and down-looking video images were collected concurrently with the fluorescence data for documentation purposes. Results of the experiment were analyzed in detail. They confirmed the system's ability to produce geo-referenced oil contamination location maps in real-time. The fluorescence data obtained during overflights was most similar to typical crude oil, i. e. the system successfully distinguished between biogenic oil and typical petroleum oil. 9 refs., 1 tab., 3 figs

Characterisation of the nematode community of a low-activity cold seep in the recently ice-shelf free Larsen B area, Eastern Antarctic Peninsula.

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Freija Hauquier

Full Text Available BACKGROUND: Recent climate-induced ice-shelf disintegration in the Larsen A (1995 and B (2002 areas along the Eastern Antarctic Peninsula formed a unique opportunity to assess sub-ice-shelf benthic community structure and led to the discovery of unexplored habitats, including a low-activity methane seep beneath the former Larsen B ice shelf. Since both limited particle sedimentation under previously permanent ice coverage and reduced cold-seep activity are likely to influence benthic meiofauna communities, we characterised the nematode assemblage of this low-activity cold seep and compared it with other, now seasonally ice-free, Larsen A and B stations and other Antarctic shelf areas (Weddell Sea and Drake Passage, as well as cold-seep ecosystems world-wide. PRINCIPAL FINDINGS: The nematode community at the Larsen B seep site differed significantly from other Antarctic sites in terms of dominant genera, diversity and abundance. Densities in the seep samples were high (>2000 individuals per 10 cm(2 and showed below-surface maxima at a sediment depth of 2-3 cm in three out of four replicates. All samples were dominated by one species of the family Monhysteridae, which was identified as a Halomonhystera species that comprised between 80 and 86% of the total community. The combination of high densities, deeper density maxima and dominance of one species is shared by many cold-seep ecosystems world-wide and suggested a possible dependence upon a chemosynthetic food source. Yet stable (13C isotopic signals (ranging between -21.97±0.86‰ and -24.85±1.89‰ were indicative of a phytoplankton-derived food source. CONCLUSION: The recent ice-shelf collapse and enhanced food input from surface phytoplankton blooms were responsible for the shift from oligotrophic pre-collapse conditions to a phytodetritus-based community with high densities and low diversity. The parthenogenetic reproduction of the highly dominant Halomonhystera species is rather unusual

Waste Area Grouping 2 Remedial Investigation Phase 1 Seep Task data report: Contaminant source area assessment

International Nuclear Information System (INIS)

Hicks, D.S.

1996-03-01

This report presents the findings of the Waste Area Grouping (WAG) 2, Phase 1 Remedial Investigation (RI) Seep Task efforts during 1993 and 1994 at Oak Ridge National Laboratory (ORNL). The results presented here follow results form the first year of sampling, 1992, which are contained in the Phase 1 RI report for WAG 2 (DOE 1995a). The WAG 2 Seep Task efforts focused on contaminants in seeps, tributaries, and main streams within the White Oak Creek (WOC) watershed. This report is designed primarily as a reference for contaminants and a resource for guiding remedial decisions. Additional in-depth assessments of the Seep Task data may provide clearer understandings of contaminant transport from the different source areas in the WOC watershed. WAG 2 consists of WOC and its tributaries downstream of the ORNL main plant area, White Oak Lake, the White Oak Creek Embayment of the Clinch River, and the associated flood plains and subsurface environment. The WOC watershed encompasses ORNL and associated WAGs. WAG 2 acts as an integrator for contaminant releases from the contaminated sites at ORNL and as the conduit transporting contaminants to the Clinch River. The main objectives of the Seep Task were to identify and characterize seeps, tributaries and source areas that are responsible for the contaminant releases to the main streams in WAG 2 and to quantify their input to the total contaminant release from the watershed at White Oak Dam (WOD). Efforts focused on 90 Sr, 3 H, and 137 Cs because these contaminants pose the greatest potential human health risk from water ingestion at WOD. Bimonthly sampling was conducted throughout the WOC watershed beginning in March 1993 and ending in August 1994. Samples were also collected for metals, anions, alkalinity, organics, and other radionuclides

Shell growth and environmental control of methanophyllic Thyasirid bivalves from Svalbard cold seeps

Science.gov (United States)

Carroll, Michael; Åström, Emmelie; Ambrose, William; Locke, William; Oliver, Graham; Hong, Wei-Li; Carroll, JoLynn

2016-04-01

The analysis of molluscan shell material (sclerochronology) can provide information about an organism's age, growth history, and environmental conditions during its lifetime. Bivalve molluscs are common members of hydrothermal vents and methane cold seeps communities where, supported by chemosynthetic symbionts, they can reach high density and biomass. But little is known about methane-associated bivalve populations inhabiting high-Arctic cold seeps, and sclerochronological analysis of methane-influenced bivalves is rare. We measured growth rates and elemental and isotopic shell signatures in a newly discovered species of bivalve (Thyasiridae) from cold seeps at 350-390m depth southwest of Svalbard. First discovered in 2014, recently described shells of Thyasira capitanea sp.nov. were found at 2 independent seep systems in Storfjordrenna. Mean shell carbon isotopic ratios from inorganic δ13C (mean = -4.8‰) and organic δ13C (mean = -26.9‰) fractions clearly indicate a methane influenced habitat and food source for these organisms. Shell mineral ratios (Li/Ca, Mg/Ca, Mn/Ca, Fe/Ca, Sr/Ca, Ba/Ca, Pb/Ca) sampled along the axis of growth with laser-ablated ICP-MS exhibit variability through time and between sites, suggesting that concentrations of these elements that may be affected by methane emissions. The mineralogical data also elucidates the internal pattern of shell deposition and growth checks, and combined with the isotopic and growth rate data, enables us to interpret the temporal history of methane release from these locations.

Cold-seep carbonates of the middle and lower continental slope, northern Gulf of Mexico

Science.gov (United States)

Roberts, Harry H.; Feng, Dong; Joye, Samantha B.

2010-11-01

Authigenic carbonates from cold seeps on the middle and lower continental slope of the northern Gulf of Mexico (GOM) exhibit a wide range of mineralogical and stable isotopic compositions. These carbonates consist of concretions and nodules in surface sediments, hardgrounds of crusts and isolated slabs, and mounded buildups of blocks and slabs of up to over 10 meters in relief above the surrounding seafloor. Mineralogically, the carbonates are dominated by high-Mg calcite (HMC) and aragonite. However, low levels (oil, seawater CO2, and 13C-enriched residual CO2 from methanogenesis. A similarly large variability in δ18O values (2.5 to 6.7‰ PDB) demonstrates the geochemical complexity of the slope, with some samples pointing toward an 18O-enriched oxygen source that is possibly related to advection of 18O-enriched formation water and/or to the decomposition of gas hydrate. A considerable range of mineralogical and isotopic variations in cold-seep carbonate composition was noted even within individual study sites. However, common trends occur across multiple geographic areas. This situation suggests that local controls on fluid and gas flux, types of seep hydrocarbons, the presence or absence of gas hydrate in the near-surface sediment, and chemosynthetic communities, as well as the temporal evolution of the local hydrocarbon reservoir, all may play a part in determining carbonate mineralogy and isotope geochemistry. The carbon isotope data clearly indicate that between-site variation is greater than within-site variation. Seep carbonates formed on the middle and lower continental slope of the GOM do not appear to be substantially different from those found on the upper slope (<1000-m water depth). The highly variable fluids and gases that leave their geochemical imprints on seep carbonate of the middle and lower continental slope are similar to their outer shelf and upper slope counterparts.

Short-chain alkane cycling in deep Gulf of Mexico cold-seep sediments

Science.gov (United States)

Sibert, R.; Joye, S. B.; Hunter, K.

2015-12-01

Mixtures of light hydrocarbon gases are common in deep Gulf of Mexico cold-seep sediments, and are typically dissolved in pore fluids, adsorbed to sediment particles, trapped in methane ice, or as free gas. The dominant component in these natural gas mixtures is usually methane (>80% C1), but ethane (C2) and propane (C3) are nearly always present in trace amounts (95% of the methane produced at depth never reaches the water column. Production of C1 and C2 in deep-sea sediments has been historically attributed only to thermocatalytic processes, though limited data suggests production of C2/C3 compounds through the activity of archaea at depth. Furthermore, carbon isotopic data on ethane and propane from deep cores of Gulf of Mexico sediments suggest alkanogenesis at >3 m depth in the sediment column and alkane oxidation in uppermost oxidant-rich sediments. Additional studies have also isolated microorganisms capable of oxidizing ethane and propane in the laboratory, but field studies of microbial-driven dynamics of C2/C3 gases in cold-seep sediments are rare. Here, we present the results of a series of incubation experiments using sediment slurries culled from surface sediments from one of the most prolific natural oil and gas seeps in the Gulf of Mexico. Rates of alkane oxidation were measured under a variety of conditions to assess the surface-driven microbial controls on C2/C3 cycling in cold-seep environments. Such microbial processes are important in terms of the possible 'oxidative overprinting' of alkane isotopic signatures produced at depth, possibly obscuring typical microbial isotopic signals.

Dynamics of rainwater lenses on upward seeping saline groundwater

NARCIS (Netherlands)

Eeman, Sara

2017-01-01

Fresh water is generally a limited resource in coastal areas which are often densely populated. In low-lying areas, groundwater is mostly saline and both agriculture and freshwater nature depend on a thin lens of rainwater that is formed by precipitation surplus on top of saline, upward seeping

Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps.

Directory of Open Access Journals (Sweden)

Lisa A Levin

Full Text Available Carbonate communities: The activity of anaerobic methane oxidizing microbes facilitates precipitation of vast quantities of authigenic carbonate at methane seeps. Here we demonstrate the significant role of carbonate rocks in promoting diversity by providing unique habitat and food resources for macrofaunal assemblages at seeps on the Costa Rica margin (400-1850 m. The attendant fauna is surprisingly similar to that in rocky intertidal shores, with numerous grazing gastropods (limpets and snails as dominant taxa. However, the community feeds upon seep-associated microbes. Macrofaunal density, composition, and diversity on carbonates vary as a function of seepage activity, biogenic habitat and location. The macrofaunal community of carbonates at non-seeping (inactive sites is strongly related to the hydrography (depth, temperature, O2 of overlying water, whereas the fauna at sites of active seepage is not. Densities are highest on active rocks from tubeworm bushes and mussel beds, particularly at the Mound 12 location (1000 m. Species diversity is higher on rocks exposed to active seepage, with multiple species of gastropods and polychaetes dominant, while crustaceans, cnidarians, and ophiuroids were better represented on rocks at inactive sites. Macro-infauna (larger than 0.3 mm from tube cores taken in nearby seep sediments at comparable depths exhibited densities similar to those on carbonate rocks, but had lower diversity and different taxonomic composition. Seep sediments had higher densities of ampharetid, dorvilleid, hesionid, cirratulid and lacydoniid polychaetes, whereas carbonates had more gastropods, as well as syllid, chrysopetalid and polynoid polychaetes. Stable isotope signatures and metrics: The stable isotope signatures of carbonates were heterogeneous, as were the food sources and nutrition used by the animals. Carbonate δ13Cinorg values (mean = -26.98‰ ranged from -53.3‰ to +10.0‰, and were significantly heavier than

Parallels between playbacks and Pleistocene tar seeps suggest sociality in an extinct sabretooth cat, Smilodon

OpenAIRE

Carbone, Chris; Maddox, Tom; Funston, Paul J.; Mills, Michael G.L.; Grether, Gregory F.; Van Valkenburgh, Blaire

2008-01-01

Inferences concerning the lives of extinct animals are difficult to obtain from the fossil record. Here we present a novel approach to the study of extinct carnivores, using a comparison between fossil records (n=3324) found in Late Pleistocene tar seeps at Rancho La Brea in North America and counts (n=4491) from playback experiments used to estimate carnivore abundance in Africa. Playbacks and tar seep deposits represent competitive, potentially dangerous encounters where multiple predators ...

Benthic Community Structure and Sediment Geochemical Properties at Hydrocarbon Seeps Along the Continental Slope of the Western North Atlantic

Science.gov (United States)

Demopoulos, A. W.; Bourque, J. R.; Brooke, S.

2015-12-01

Hydrocarbon seeps support distinct benthic communities capable of utilizing reduced chemical compounds for nutrition. In recent years, methane seepage has been increasingly documented along the continental slope of the U.S. Atlantic margin. In 2012 and 2013, two seeps were investigated in this region: a shallow site near Baltimore Canyon (410-450 m) and a deep site near Norfolk Canyon (1600 m). Both sites contain extensive mussel beds and microbial mats. Sediment cores and grab samples were collected to quantify the abundance, diversity, and community structure of benthic macrofauna (>300 mm) in relationship to the associated sediment environment (organic carbon and nitrogen, stable isotopes 13C and 15N, grain size, and depth) of mussel beds, mats, and slope habitats. Macrofaunal densities in microbial mats were four times greater than those present in mussel beds and slope sediments. Macrofaunal communities were distinctly different both between depths and among habitat types. Specifically, microbial mat sediments were dominated by the annelid families Dorvilleidae, Capitellidae, and Tubificidae, while mussel habitats had higher proportions of crustaceans. Diversity was lower in Baltimore microbial mat habitats, but higher in mussel and slope sediments compared to Norfolk seep habitats found at deeper depths. Multivariate statistical analysis identified sediment carbon:nitrogen (C:N) ratios and 13C values as important variables for structuring the macrofaunal communities. Higher C:N ratios were present within microbial mat habitats and depleted 13C values occurred in sediments adjacent to mussel beds found in Norfolk Canyon seeps. Differences in the quality and source of organic matter present in the seep habitats are known to be important drivers in macrofaunal community structure and associated food webs. The multivariate analysis provides new insight into the relative importance of the seep sediment quality in supporting dense macrofaunal communities compared

Transport and transfer rates in the waters of the continental shelf and slope: SEEP

International Nuclear Information System (INIS)

Biscaye, P.E.; Anderson, R.F.

1993-01-01

The overall Shelf Edge Exchange Processes (SEEP) Program, which began in 1980 or 1981, had as its goal the testing of a hypothesis with respect to the fate of particulate matter formed in and introduced into the waters of the continental shelf adjacent to the northern east coast of the US, i.e., the MAB. The original hypothesis was that a large proportion of the particles in general, and of the particulate organic carbon (POC) in particular, was exported from the shelf, across the shelf/slope break and front, into the waters of, and, to some degree, deposited in the sediments of the continental slope. This hypothesis was based on budgets of organic carbon and lead-210 that did not account for a large proportion of those species in the waters or sediments of the shelf, and on a carbon-rich band of sediments centered on the slope at ∼1,000 m water depth. The results of the first SEEP experiment, south of New England and Long Island (SEEP-1) suggested, but did not prove, that there was only a relatively small proportion of the carbon which was exported from the shelf to the slope. The objective of the second experiment -- SEEP-2 -- done under the subject grant, was to tighten the experiment in terms of the kinds of data collected, and to focus it more on the shelf and only the upper slope, where shelf-derived particles were thought to be deposited

Anaerobic oxidation of methane at a marine methane seep in a forearc sediment basin off Sumatra, Indian Ocean

Directory of Open Access Journals (Sweden)

Michael eSiegert

2011-12-01

Full Text Available A cold methane-seep was discovered in a forearc sediment basin off the island Sumatra, exhibiting a methane-seep adapted microbial community. A defined seep centre of activity, like in mud volcanoes, was not discovered. The seep area was rather characterized by a patchy distribution of active spots. The relevance of AOM was reflected by 13C depleted isotopic signatures of dissolved inorganic carbon (DIC. The anaerobic conversion of methane to CO2 was confirmed in a 13C-labelling experiment. Methane fuelled a vital microbial and invertebrate community which was reflected in cell numbers of up to 4 x 109 cells cm 3 sediment and 13C depleted guts of crabs populating the seep area. The microbial community was analysed by total cell counting, catalyzed reporter deposition – fluorescence in situ hybridisation (CARD-FISH, quantitative real-time PCR (qPCR and denaturing gradient gel electrophoresis (DGGE. CARD-FISH cell counts and qPCR measurements showed the presence of Bacteria and Archaea, but only small numbers of Eukarya. The archaeal community comprised largely members of ANME-1 and ANME-2. Furthermore, members of the Crenarchaeota were frequently detected in the DGGE analysis. Three major bacterial phylogenetic groups (δ-Proteobacteria, candidate division OP9 and Anaerolineaceae were abundant across the study area. Several of these sequences were closely related to the genus Desulfococcus of the family Desulfobacteraceae, which is in good agreement with previously described AOM sites. In conclusion, the majority of the microbial community at the seep consisted of AOM related microorganisms, while the relevance of higher hydrocarbons as microbial substrates was negligible.

Fungal diversity in deep-sea sediments associated with asphalt seeps at the Sao Paulo Plateau

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Nagano, Yuriko; Miura, Toshiko; Nishi, Shinro; Lima, Andre O.; Nakayama, Cristina; Pellizari, Vivian H.; Fujikura, Katsunori

2017-12-01

We investigated the fungal diversity in a total of 20 deep-sea sediment samples (of which 14 samples were associated with natural asphalt seeps and 6 samples were not associated) collected from two different sites at the Sao Paulo Plateau off Brazil by Ion Torrent PGM targeting ITS region of ribosomal RNA. Our results suggest that diverse fungi (113 operational taxonomic units (OTUs) based on clustering at 97% sequence similarity assigned into 9 classes and 31 genus) are present in deep-sea sediment samples collected at the Sao Paulo Plateau, dominated by Ascomycota (74.3%), followed by Basidiomycota (11.5%), unidentified fungi (7.1%), and sequences with no affiliation to any organisms in the public database (7.1%). However, it was revealed that only three species, namely Penicillium sp., Cadophora malorum and Rhodosporidium diobovatum, were dominant, with the majority of OTUs remaining a minor community. Unexpectedly, there was no significant difference in major fungal community structure between the asphalt seep and non-asphalt seep sites, despite the presence of mass hydrocarbon deposits and the high amount of macro organisms surrounding the asphalt seeps. However, there were some differences in the minor fungal communities, with possible asphalt degrading fungi present specifically in the asphalt seep sites. In contrast, some differences were found between the two different sampling sites. Classification of OTUs revealed that only 47 (41.6%) fungal OTUs exhibited >97% sequence similarity, in comparison with pre-existing ITS sequences in public databases, indicating that a majority of deep-sea inhabiting fungal taxa still remain undescribed. Although our knowledge on fungi and their role in deep-sea environments is still limited and scarce, this study increases our understanding of fungal diversity and community structure in deep-sea environments.

Microbial community changes along the active seepage site of one cold seep in the Red Sea.

KAUST Repository

Cao, Huiluo

2015-07-21

The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

Microbial community changes along the active seepage site of one cold seep in the Red Sea.

KAUST Repository

Cao, Huiluo; Zhang, Weipeng; Wang, Yong; Qian, Pei-Yuan

2015-01-01

The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

Satellite SAR inventory of Gulf of Mexico oil seeps and shallow gas hydrates

Science.gov (United States)

Garcia, O.; MacDonald, I. R.; Zimmer, B.; Shedd, W.; Frye, M.

2009-04-01

Satellite synthetic aperture radar (SAR) images from the RADARSAT platform were used to detect and inventory persistent layers of oil released from natural seeps in the Gulf of Mexico. Previously published inventories of natural oil seeps in the Gulf have been limited in scope and have relied on manual interpretation of satellite images (Mitchell et al. 1999; De Beukelaer et al. 2003). We developed a texture classifying neural network algorithm (TCNNA) to rapidly identify floating oil-layers in a semi-supervised operation. Oil layers, known as slicks, were recognized as long (10 km), narrow (100 m), often curvilinear streaks with distinct points of origin where oil reaches the ocean surface. After training the TCNNA over known seep areas and under a range of environmental and viewing conditions, the procedure was applied to 426 separate images that covered ocean areas of 100x100 km (Standard Beam Mode), 102 images that covered ocean areas of 450x450 km(ScanSAR Wide Beam Mode), and 84 images that covered ocean areas of 300x300 km (ScanSAR Narrow Beam Mode). This image data-set was collected between 1994 and 2007. It covered the entire Gulf of Mexico with a repeat rate of 4 to109, with the highest concentration over the continental slope. This effort identified a total of 4957 slicks among all the images. Of these, 287 appeared a single time in isolated locations and may therefore be false targets. The remaining slicks appeared in groups of up to 9 separate features, clustered in areas of 1 to 6.5 km across. When slicks appear within the same area in repeated images, they are judged to have a persistent source—a bubbling vent on the seafloor (MacDonald et al. 2002). Persistent sources represent geologic formations defined by migrating hydrocarbons that may include multiple separate vents. A total of 559 formations were defined by repeated imaging; these comprised a maximum of 1995 and a minimum of 1263 individual vents. This total was distributed between U

The vertical distribution of prokaryotes in the surface sediment of Jiaolong cold seep at the northern South China Sea.

Science.gov (United States)

Wu, Yuzhi; Qiu, Jian-Wen; Qian, Pei-Yuan; Wang, Yong

2018-05-01

In deep-sea cold seeps, microbial communities are shaped by geochemical components in seepage solutions. In the present study, we report the composition of microbial communities and potential metabolic activities in the surface sediment of Jiaolong cold seep at the northern South China Sea. Pyrosequencing of 16S rRNA gene amplicons revealed that a majority of the microbial inhabitants of the surface layers (0-6 cm) were sulfur oxidizer bacteria Sulfurimonas and archaeal methane consumer ANME-1, while sulfate reducer bacteria SEEP-SRB1, ANME-1 and ANME-2 dominated the bottom layers (8-14 cm). The potential ecological roles of the microorganisms were further supported by the presence of functional genes for methane oxidation, sulfur oxidation, sulfur reduction and nitrate reduction in the metagenomes. Metagenomic analysis revealed a significant correlation between coverage of 16S rRNA gene of sulfur oxidizer bacteria, functional genes involved in sulfur oxidation and nitrate reduction in different layers, indicating that sulfur oxidizing may be coupled to nitrate reducing at the surface layers of Jiaolong seeping site. This is probably related to the sulfur oxidizers of Sulfurimonas and Sulfurovum, which may be the capacity of nitrate reduction or associated with unidentified syntrophic nitrate-reducing microbes in the surface of the cold seep.

Out of the dark: transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines).

Science.gov (United States)

Woycheese, Kristin M; Meyer-Dombard, D'Arcy R; Cardace, Dawn; Argayosa, Anacleto M; Arcilla, Carlo A

2015-01-01

In the Zambales ophiolite range, terrestrial serpentinizing fluid seeps host diverse microbial assemblages. The fluids fall within the profile of Ca(2+)-OH(-)-type waters, indicative of active serpentinization, and are low in dissolved inorganic carbon (DIC) (serpentinizing seep ecosystem studies, particularly with regards to tropical biomes.

HYFLUX: Satellite Exploration of Natural Hydrocarbon Seeps and Discovery of a Methane Hydrate Mound at GC600

Science.gov (United States)

Garcia-Pineda, O. G.; MacDonald, I. R.; Shedd, W.; Zimmer, B.

2009-12-01

Analysis of natural hydrocarbon seeps is important to improve our understanding of methane flux from deeper sediments to the water column. In order to quantify natural hydrocarbon seep formations in the Northern Gulf of Mexico, a set of 686 Synthetic Aperture Radar (SAR) images was analyzed using the Texture Classifying Neural Network Algorithm (TCNNA), which processes SAR data to delineate oil slicks. This analysis resulted in a characterization of 396 natural seep sites distributed in the northern GOM. Within these sites, a maximum of 1248 individual vents where identified. Oil reaching the sea-surface is deflected from its source during transit through the water column. This presentation describes a method for estimating locations of active oil vents based on repeated slick detection in SAR. One of the most active seep formations was detected in MMS lease block GC600. A total of 82 SAR scenes (collected by RADARSAT-1 from 1995 to 2007) was processed covering this region. Using TCNNA the area covered by each slick was computed and Oil Slicks Origins (OSO) were selected as single points within detected oil slicks. At this site, oil slick signatures had lengths up to 74 km and up to 27 km^2 of area. Using SAR and TCNNA, four active vents were identified in this seep formation. The geostatistical mean centroid among all detections indicated a location along a ridge-line at ~1200m. Sea truth observations with an ROV, confirmed that the estimated location of vents had a maximum offset of ~30 m from their actual locations on the seafloor. At the largest vent, a 3-m high, 12-m long mound of oil-saturated gas hydrate was observed. The outcrop contained thousands of ice worms and numerous semi-rigid chimneys from where oily bubbles were escaping in a continuous stream. Three additional vents were found along the ridge; these had lower apparent flow, but were also plugged with gas hydrate mounds. These results support use of SAR data for precise delineation of active seep

Management of Herbaceous Seeps and Wet Savannas for Threatened and Endangered Species

National Research Council Canada - National Science Library

Harper, Mary

1998-01-01

Wetland communities such as herbaceous seeps and wet savannas occur on military installations throughout the southeastern United States, usually as pockets of wet habitat within a matrix of drier longleaf pine woodlands...

Spatial structure and activity of sedimentary microbial communities underlying a Beggiatoa spp. mat in a Gulf of Mexico hydrocarbon seep.

Directory of Open Access Journals (Sweden)

Karen G Lloyd

Full Text Available BACKGROUND: Subsurface fluids from deep-sea hydrocarbon seeps undergo methane- and sulfur-cycling microbial transformations near the sediment surface. Hydrocarbon seep habitats are naturally patchy, with a mosaic of active seep sediments and non-seep sediments. Microbial community shifts and changing activity patterns on small spatial scales from seep to non-seep sediment remain to be examined in a comprehensive habitat study. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a transect of biogeochemical measurements and gene expression related to methane- and sulfur-cycling at different sediment depths across a broad Beggiatoa spp. mat at Mississippi Canyon 118 (MC118 in the Gulf of Mexico. High process rates within the mat ( approximately 400 cm and approximately 10 cm from the mat's edge contrasted with sharply diminished activity at approximately 50 cm outside the mat, as shown by sulfate and methane concentration profiles, radiotracer rates of sulfate reduction and methane oxidation, and stable carbon isotopes. Likewise, 16S ribosomal rRNA, dsrAB (dissimilatory sulfite reductase and mcrA (methyl coenzyme M reductase mRNA transcripts of sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae and methane-cycling archaea (ANME-1 and ANME-2 were prevalent at the sediment surface under the mat and at its edge. Outside the mat at the surface, 16S rRNA sequences indicated mostly aerobes commonly found in seawater. The seep-related communities persisted at 12-20 cm depth inside and outside the mat. 16S rRNA transcripts and V6-tags reveal that bacterial and archaeal diversity underneath the mat are similar to each other, in contrast to oxic or microoxic habitats that have higher bacterial diversity. CONCLUSIONS/SIGNIFICANCE: The visual patchiness of microbial mats reflects sharp discontinuities in microbial community structure and activity over sub-meter spatial scales; these discontinuities have to be taken into account in geochemical and

Application of Satellite SAR for Discovery and Quantification of Natural Marine Oil Seeps

Science.gov (United States)

Amos, J.; Lai, R.; Zimmer, B.; Leiva, A.; MacDonald, I.

2006-12-01

Natural marine oil seeps discharge gassy drops from the seafloor. Oil drops and gas bubbles reach the surface from water depths as great as 3000m. The oil spreads rapidly, forming an invisible layer that drifts down-wind and down-current in long, linear streaks called slicks. Oil slicks are visible in SAR data because the surfactant dampens capillary waves and reduces backscatter. Application of SAR as an exploration tool in energy prospecting is well-established. We have applied this technique for discovering the chemosynthetic communities that colonize the seafloor in the vicinity of deep-water seeps on the continental margin of the Gulf of Mexico. The management goal for this effort is to prevent harmful impact to these communities resulting from exploration or production activities. The scientific goals are to delineate the zoogeography of the chemosynthetic fauna, which is widespread on continental margins, and to establish study sites where their life history can be investigated. In the course of an ongoing, multidisciplinary study in the spring and summer of 2006, we explored 20 possible sites where SAR and geophysical data indicated seeps might occur. SAR was only partly diagnostic: all sites with SAR-detected slicks were found to have biologic communities, but communities were also found at geophysical anomalies that did not produce slicks. We acquired over 60 RADARSAT SAR images from the northern Gulf of Mexico in cooperation with the Alaska Satellite Facility. The ship RV ATLANTIS was at sea during the acquisition and collected synoptic weather and oceanographic data. To automate interpretation of large image dataset we have employed texture recognition with use of a library of textons applied iteratively to the images. This treatment shows promise in distinguishing floating oil from false targets generated by rain fronts and other phenomena. One goal of the analysis is to delineate bounding boxes to quantify the ocean area covered by the thin oil layer

Changing composition of microbial communities indicates seepage fluid difference of the Thuwal Seeps in the Red Sea

KAUST Repository

Yang, Bo

2015-06-10

© Springer International Publishing Switzerland 2015. Cold seeps are unique ecosystems that are generally characterized by high salinity and reducing solutions. Seepage fluid, the major water influx of this system, contains hypersaline water, sediment pore water, and other components. The Thuwal cold seeps were recently discovered on the continental margin of the Red Sea. Using 16S rRNA gene pyro-sequencing technology, microbial communities were investigated by comparing samples collected in 2011 and 2013. The results revealed differences in the microbial communities between the two sampling times. In particular, a significantly higher abundance of Marine Group I (MGI) Thaumarchaeota was coupled with lower salinity in 2013. In the brine pool, the dominance of Desulfobacterales in 2011 was supplanted byMGI Thaumarchaeota in 2013, perhaps due to a reduced supply of hydrogen sulfide from the seepage fluid. Collectively, this study revealed a difference in water components in this ecosystem between two sampling times. The results indicated that the seawater in this cold seep displayed a greater number of characteristics of normal seawater in 2013 than in 2011, which might represent the dominant driving force for changes in microbial community structures. This is the first study to provide a temporal comparison of the microbial biodiversity of a cold seep ecosystem in the Red Sea.

Changing composition of microbial communities indicates seepage fluid difference of the Thuwal Seeps in the Red Sea

KAUST Repository

Yang, Bo; Zhang, Weipeng; Tian, Renmao; Wang, Yong; Qian, Pei-Yuan

2015-01-01

© Springer International Publishing Switzerland 2015. Cold seeps are unique ecosystems that are generally characterized by high salinity and reducing solutions. Seepage fluid, the major water influx of this system, contains hypersaline water, sediment pore water, and other components. The Thuwal cold seeps were recently discovered on the continental margin of the Red Sea. Using 16S rRNA gene pyro-sequencing technology, microbial communities were investigated by comparing samples collected in 2011 and 2013. The results revealed differences in the microbial communities between the two sampling times. In particular, a significantly higher abundance of Marine Group I (MGI) Thaumarchaeota was coupled with lower salinity in 2013. In the brine pool, the dominance of Desulfobacterales in 2011 was supplanted byMGI Thaumarchaeota in 2013, perhaps due to a reduced supply of hydrogen sulfide from the seepage fluid. Collectively, this study revealed a difference in water components in this ecosystem between two sampling times. The results indicated that the seawater in this cold seep displayed a greater number of characteristics of normal seawater in 2013 than in 2011, which might represent the dominant driving force for changes in microbial community structures. This is the first study to provide a temporal comparison of the microbial biodiversity of a cold seep ecosystem in the Red Sea.

Anaerobic Oxidation of Methane at a Marine Methane Seep in a Forearc Sediment Basin off Sumatra, Indian Ocean.

Science.gov (United States)

Siegert, Michael; Krüger, Martin; Teichert, Barbara; Wiedicke, Michael; Schippers, Axel

2011-01-01

A cold methane seep was discovered in a forearc sediment basin off the island Sumatra, exhibiting a methane-seep adapted microbial community. A defined seep center of activity, like in mud volcanoes, was not discovered. The seep area was rather characterized by a patchy distribution of active spots. The relevance of anaerobic oxidation of methane (AOM) was reflected by (13)C-depleted isotopic signatures of dissolved inorganic carbon. The anaerobic conversion of methane to CO(2) was confirmed in a (13)C-labeling experiment. Methane fueled a vital microbial community with cell numbers of up to 4 × 10(9) cells cm(-3) sediment. The microbial community was analyzed by total cell counting, catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH), quantitative real-time PCR (qPCR), and denaturing gradient gel electrophoresis (DGGE). CARD-FISH cell counts and qPCR measurements showed the presence of Bacteria and Archaea, but only small numbers of Eukarya. The archaeal community comprised largely members of ANME-1 and ANME-2. Furthermore, members of the Crenarchaeota were frequently detected in the DGGE analysis. Three major bacterial phylogenetic groups (δ-Proteobacteria, candidate division OP9, and Anaerolineaceae) were abundant across the study area. Several of these sequences were closely related to the genus Desulfococcus of the family Desulfobacteraceae, which is in good agreement with previously described AOM sites. In conclusion, the majority of the microbial community at the seep consisted of AOM-related microorganisms, while the relevance of higher hydrocarbons as microbial substrates was negligible.

Quantification of seep-related methane gas emissions at Tommeliten, North Sea

NARCIS (Netherlands)

Schneider von Deimling, J.S.; Rehder, G.; Greinert, J.; McGinnnis, D.F.; Boetius, A.; Linke, P.

2011-01-01

Tommeliten is a prominent methane seep area in the Central North Sea. Previous surveys revealed shallow gas-bearing sediments and methane gas ebullition into the water column. In this study, the in situ methane flux at Tommeliten is re-assessed and the potential methane transport to the atmosphere

High-Resolution Seafloor Mapping at A Deep-Sea Methane Seep Field with an Autonomous Underwater Vehicle

Science.gov (United States)

Skarke, A. D.

2017-12-01

A growing body of research indicates that points of seafloor gas emission, known as cold-seeps, are a common feature along many continental margins. Results from recent exploration efforts show that benthic environments at cold-seeps are characterized by extensive authigenic carbonate crusts and complex chemosynthetic communities. The seafloor morphology and geophysical properties of these locations are heterogeneous and relatively complex due to the three-dimensional structure created by carbonate buildups and dense bivalve beds. Seeps are often found clustered and the spatial extent of associated seafloor crusts and beds can reach multiple square kilometers. Here, the results of a 1.25 km2 autonomous underwater vehicle (AUV) survey of a deep-sea methane seep field with 13 vents, at a nominal depth of 1400 m, located near Veatch Canyon on the US Atlantic margin are presented. Multibeam sonar, sidescan sonar, and a sub bottom profiler on the AUV were used to make high-resolution observations of seafloor bathymetry (resolution 1m2) as well as water column, seafloor, and subsurface acoustic backscatter intensity. Additionally, a downward oriented camera was used to collect seafloor imagery coincident with acoustic observations at select locations. Acoustic results indicated the location of discrete gas plumes as well as a continuous area of elevated seafloor roughness and backscatter intensity consistent with the presence of large scale authigenic rock outcrops and extensive mussel beds, which were visually confirmed with camera imagery. Additionally, a linear area of particularly elevated seafloor roughness and acoustic backscatter intensity that lies sub-parallel to an adjacent ridge was interpreted to be controlled by underlying geologic processes such as soft sediment faulting. Automated analysis of camera imagery and coincident acoustic backscatter and bathymetry data as well as derivative metrics (e.g. slope and rugosity) was used to segment and classify bed

Comparative composition, diversity and trophic ecology of sediment macrofauna at vents, seeps and organic falls.

Directory of Open Access Journals (Sweden)

Angelo F Bernardino

Full Text Available Sediments associated with hydrothermal venting, methane seepage and large organic falls such as whale, wood and plant detritus create deep-sea networks of soft-sediment habitats fueled, at least in part, by the oxidation of reduced chemicals. Biological studies at deep-sea vents, seeps and organic falls have looked at macrofaunal taxa, but there has yet to be a systematic comparison of the community-level attributes of sediment macrobenthos in various reducing ecosystems. Here we review key similarities and differences in the sediment-dwelling assemblages of each system with the goals of (1 generating a predictive framework for the exploration and study of newly identified reducing habitats, and (2 identifying taxa and communities that overlap across ecosystems. We show that deep-sea seep, vent and organic-fall sediments are highly heterogeneous. They sustain different geochemical and microbial processes that are reflected in a complex mosaic of habitats inhabited by a mixture of specialist (heterotrophic and symbiont-associated and background fauna. Community-level comparisons reveal that vent, seep and organic-fall macrofauna are very distinct in terms of composition at the family level, although they share many dominant taxa among these highly sulphidic habitats. Stress gradients are good predictors of macrofaunal diversity at some sites, but habitat heterogeneity and facilitation often modify community structure. The biogeochemical differences across ecosystems and within habitats result in wide differences in organic utilization (i.e., food sources and in the prevalence of chemosynthesis-derived nutrition. In the Pacific, vents, seeps and organic-falls exhibit distinct macrofaunal assemblages at broad-scales contributing to ß diversity. This has important implications for the conservation of reducing ecosystems, which face growing threats from human activities.

Contribution of deep sourced carbon from hydrocarbon seeps to sedimentary organic carbon: Evidence from Δ14C and δ13C isotopes

Science.gov (United States)

Feng, D.; Peckmann, J.; Peng, Y.; Liang, Q.; Roberts, H. H.; Chen, D.

2017-12-01

Sulfate-driven anaerobic oxidation of methane (AOM) limits the release of methane from marine sediments and promotes the formation of carbonates close to the seafloor along continental margins. It has been established that hydrocarbon seeps are a source of dissolved inorganic and organic carbon to marine environments. However, questions remain about the contribution of deep sourced carbon from hydrocarbon seeps to the sedimentary organic carbon pool. For a number of hydrocarbon seeps from the South China Sea and the Gulf of Mexico, the portion of modern carbon was determined based on natural radiocarbon abundances (Δ14C) and stable carbon isotope (δ13Corganic carbon) compositions of the non-carbonate fractions extracted from authigenic carbonates. Samples from both areas show a mixing trend between ideal planktonic organic carbon (δ13C = -22‰ VPDB and 90% modern carbon) and the ambient methane. The δ13Corganic carbon values of non-carbonate fractions from three ancient seep deposits (northern Italy, Miocene; western Washington State, USA, Eocene to Oligocene) confirm that the proxy can be used to constrain the record of sulfate-driven AOM through most of Earth history by measuring the δ13C values of organic carbon. This study reveals the potential of using δ13C values of organic carbon to discern seep and non-seep environments. This new approach is particularly promising when authigenic carbonate is not present in ancient sedimentary environments. Acknowledgments: The authors thank BOEM and NOAA for their years' support of the deep-sea dives. Funding was provided by the NSF of China (Grants: 41422602 and 41373085).

A paradox resolved: Sulfide acquisition by roots of seep tubeworms sustains net chemoautotrophy

Science.gov (United States)

Freytag, John K.; Girguis, Peter R.; Bergquist, Derk C.; Andras, Jason P.; Childress, James J.; Fisher, Charles R.

2001-01-01

Vestimentiferan tubeworms, symbiotic with sulfur-oxidizing chemoautotrophic bacteria, dominate many cold-seep sites in the Gulf of Mexico. The most abundant vestimentiferan species at these sites, Lamellibrachia cf. luymesi, grows quite slowly to lengths exceeding 2 meters and lives in excess of 170–250 years. L. cf. luymesi can grow a posterior extension of its tube and tissue, termed a “root,” down into sulfidic sediments below its point of original attachment. This extension can be longer than the anterior portion of the animal. Here we show, using methods optimized for detection of hydrogen sulfide down to 0.1 μM in seawater, that hydrogen sulfide was never detected around the plumes of large cold-seep vestimentiferans and rarely detectable only around the bases of mature aggregations. Respiration experiments, which exposed the root portions of L. cf. luymesi to sulfide concentrations between 51–561 μM, demonstrate that L. cf. luymesi use their roots as a respiratory surface to acquire sulfide at an average rate of 4.1 μmol⋅g−1⋅h−1. Net dissolved inorganic carbon uptake across the plume of the tubeworms was shown to occur in response to exposure of the posterior (root) portion of the worms to sulfide, demonstrating that sulfide acquisition by roots of the seep vestimentiferan L. cf. luymesi can be sufficient to fuel net autotrophic total dissolved inorganic carbon uptake. PMID:11687647

Anatomy and origin of carbonate structures in a Miocene cold-seep field

Science.gov (United States)

Aiello, Ivano W.; Garrison, Robert E.; Moore, J. Casey; Kastner, Miriam; Stakes, Debra S.

2001-12-01

Miocene calcite concretions resembling modern carbonate structures that form at cold seeps are present in fractured opal- CT porcelanites that are interbedded with mudstones in coastal cliffs at Santa Cruz, California. The morphologies of the carbonate structures differ markedly from conventional concretions and are spatially aligned with orthogonal joints in the porcelanites. The structures contain tubular holes that are identical to fluid and gas conduits in modern carbonate seep structures; the orientations of these tubes suggest that fluid and gas flow was both vertical and horizontal, the latter along extensional joints that formed preferentially in the brittle, silica-rich layers that had enhanced bedding- parallel permeability. Petrographic and isotopic characteristics of the carbonate structures indicate that calcite precipitation occurred in a shallow, subseafloor environment in either the zone of microbial sulfate reduction or of methanogenesis, prior to or possibly simultaneously with the silica phase transformation of opal- A in diatom shells to opal-CT.

A molecular gut content study of Themisto abyssorum (Amphipoda) from Arctic hydrothermal vent and cold seep systems.

Science.gov (United States)

Olsen, Bernt Rydland; Troedsson, Christofer; Hadziavdic, Kenan; Pedersen, Rolf B; Rapp, Hans Tore

2014-08-01

The use of DNA as a marker for prey inside the gut of predators has been instrumental in further understanding of known and unknown interactions. Molecular approaches are in particular useful in unavailable environments like the deep sea. Trophic interactions in the deep sea are difficult to observe in situ, correct deep-sea experimental laboratory conditions are difficult to obtain, animals rarely survive the sampling, or the study organisms feed during the sampling due to long hauls. Preliminary studies of vent and seep systems in the Nordic Seas have identified the temperate-cold-water pelagic amphipod Themisto abyssorum as a potentially important predator in these chemosynthetic habitats. However, the prey of this deep-sea predator is poorly known, and we applied denaturing high performance liquid chromatography (DHPLC) to investigate the predator-prey interactions of T. abyssorum in deep-water vent and seep systems. Two deep-water hydrothermally active localities (The Jan Mayen and Loki's Castle vent fields) and one cold seep locality (The Håkon Mosby mud volcano) in the Nordic Seas were sampled, genomic DNA of the stomachs of T. abyssorum was extracted, and 18S rDNA gene was amplified and used to map the stomach content. We found a wide range of organisms including micro-eukaryotes, metazoans and detritus. Themisto abyssorum specimens from Loki's Castle had the highest diversity of prey. The wide range of prey items found suggests that T. abyssorum might be involved in more than one trophic level and should be regarded as an omnivore and not a strict carnivore as have previously been suggested. © 2013 John Wiley & Sons Ltd.

An Evaluation of Subsurface Plumbing of a Hydrothermal Seep Field and Possible Influence from Local Seismicity from New Time-Series Data Collected at the Davis-Schrimpf Seep Field, Salton Trough, California

Science.gov (United States)

Rao, A.; Onderdonk, N.

2016-12-01

The Davis­-Schrimpf Seep Field (DSSF) is a group of approximately 50 geothermal mud seeps (gryphons) in the Salton Trough of southeastern California. Its location puts it in line with the mapped San Andreas Fault, if extended further south, as well as within the poorly-understood Brawley Seismic Zone. Much of the geomorphology, geochemistry, and other characteristics of the DSSF have been analyzed, but its subsurface structure remains unknown. Here we present data and interpretations from five new temperature time­series from four separate gryphons at the DSSF, and compare them both amongst themselves, and within the context of all previously collected data to identify possible patterns constraining the subsurface dynamics. Simultaneously collected time-series from different seeps were cross-correlated to quantify similarity. All years' time-series were checked against the record of local seismicity to identify any seismic influence on temperature excursions. Time-series captured from the same feature in different years were statistically summarized and the results plotted to examine their evolution over time. We found that adjacent vents often alternate in temperature, suggesting a switching of flow path of the erupted mud at the scale of a few meters or less. Noticeable warming over time was observed in most of the features with time-series covering multiple years. No synchronicity was observed between DSSF features' temperature excursions, and seismic events within a 24 kilometer radius covering most of the width of the surrounding Salton Trough.

Stable isotopes provide new insights into vestimentiferan physiological ecology at Gulf of Mexico cold seeps

Science.gov (United States)

Becker, Erin Leigh; Macko, Stephen A.; Lee, Raymond W.; Fisher, Charles R.

2011-02-01

On the otherwise low-biomass seafloor of the Gulf of Mexico (GoM) continental slope, natural oil and gas seeps are oases of local primary production that support lush animal communities. Hundreds of seep communities have been documented on the continental slope, and nutrition derived from seeps could be an important link in the overall GoM food web. Here, we present a uniquely large and cohesive data set of δ13C, δ15N, and δ34S compositions of the vestimentiferan tubeworms Escarpia laminata and Lamellibrachia sp. 1, which dominate biomass at GoM seeps and provide habitat for hundreds of other species. Our sampling design encompassed an entire region of the GoM lower slope, allowing us for the first time to assess spatial variability in isotope compositions and to robustly address long-standing hypotheses about how vestimentiferans acquire and cycle nutrients over their long lifespan (200+ years). Tissue δ13C values provided strong evidence that larger adult vestimentiferans use their buried roots to take up dissolved inorganic carbon from sediment pore water, while very small individuals use their plume to take up carbon dioxide from the seawater. δ34S values were extremely variable among individuals of the same species within one location (<1 m2 area), indicating high variability in the inorganic sulfur pools on a very small spatial scale. This finding supports the hypothesis that vestimentiferans use their roots to cycle sulfate and sulfide between their symbionts and free-living consortia of sulfate-reducing archaea in the sediment. Finally, consistent differences in δ15N between two cooccurring vestimentiferan species provided the first strong evidence for partitioning of inorganic resources, which has significant implications for the ecology and evolution of this taxonomic group.

In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system

KAUST Repository

Lee, O.O.; Wang, Y.; Tian, R.; Zhang, W.; Shek, C.S.; Bougouffa, Salim; Al-Suwailem, A.; Batang, Z.B.; Xu, W.; Wang, G.C.; Zhang, Xixiang; Lafi, F.F.; Bajic, Vladimir B.; Qian, P.-Y.

2014-01-01

Using microscopic and molecular techniques combined with computational analysis, this study examined the structure and composition of microbial communities in biofilms that formed on different artificial substrates in a brine pool and on a seep vent of a cold seep in the Red Sea to test our hypothesis that initiation of the biofilm formation and spreading mode of microbial structures differs between the cold seep and the other aquatic environments. Biofilms on different substrates at two deployment sites differed morphologically, with the vent biofilms having higher microbial abundance and better structural features than the pool biofilms. Microbes in the pool biofilms were more taxonomically diverse and mainly composed of various sulfate-reducing bacteria whereas the vent biofilms were exclusively dominated by sulfur-oxidizing Thiomicrospira. These results suggest that the redox environments at the deployment sites might have exerted a strong selection on microbes in the biofilms at two sites whereas the types of substrates had limited effects on the biofilm development.

In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system

KAUST Repository

Lee, O.O.

2014-01-08

Using microscopic and molecular techniques combined with computational analysis, this study examined the structure and composition of microbial communities in biofilms that formed on different artificial substrates in a brine pool and on a seep vent of a cold seep in the Red Sea to test our hypothesis that initiation of the biofilm formation and spreading mode of microbial structures differs between the cold seep and the other aquatic environments. Biofilms on different substrates at two deployment sites differed morphologically, with the vent biofilms having higher microbial abundance and better structural features than the pool biofilms. Microbes in the pool biofilms were more taxonomically diverse and mainly composed of various sulfate-reducing bacteria whereas the vent biofilms were exclusively dominated by sulfur-oxidizing Thiomicrospira. These results suggest that the redox environments at the deployment sites might have exerted a strong selection on microbes in the biofilms at two sites whereas the types of substrates had limited effects on the biofilm development.

In situ Raman-based detections of the hydrothermal vent and cold seep fluids

Science.gov (United States)

Zhang, Xin; Du, Zengfeng; Zheng, Ronger; Luan, Zhendong; Qi, Fujun; Cheng, Kai; Wang, Bing; Ye, Wangquan; Liu, Xiaorui; Chen, Changan; Guo, Jinjia; Li, Ying; Yan, Jun

2016-04-01

Hydrothermal vents and cold seeps, and their associated biological communities play an important role in global carbon and sulphur biogeochemical cycles. Most of the studies of fluid composition geochemistry are based on recovered samples, both with gas-tight samplers and as open specimens, but the in situ conditions are difficult to maintain in recovered samples. Determination in situ of the chemical signals of the emerging fluids are challenging due to the high pressure, often strongly acidic and temperature in which few sensors can survive. Most of those sensors used so far are based on electrochemistry, and can typically detect only a few chemical species. Here we show that direct measurement of critical chemical species of hydrothermal vents and cold seeps can be made rapidly and in situ by means of a new hybrid version of earlier deep-sea pore water Raman probe carried on the ROV (Remote Operated Vehicle) Faxian. The fluid was drawn through the probe by actuating a hydraulic pump on the ROV, and measured at the probe optical cell through a sapphire window. We have observed the concentrations of H2S, HS-, SO42-, HSO4-, CO2, and H2 in hydrothermal vent fluids from the Pacmanus and Desmos vent systems in the Manus back-arc basin, Papua New Guinea. Two black smokers (279° C and 186° C) at the Pacmanus site showed the characteristic loss of SO42-, and the increase of CO2 and well resolved H2S and HS- peaks. At the white smoker of Onsen site the strong HSO4-peak observed at high temperature quickly dropped with strong accompanying increase of SO42-and H2 peaks when the sample contained in the Raman sensing cell was removed from the hot fluid due to rapid thermal deprotonation. We report here also the finding of a new lower temperature (88° C) white smoker "Kexue" field at the Desmos site with strong H2S, HS- and CO2 signals. We also have detected the concentrations of CH4,H2S, HS-, SO42-, and S8 in cold seep fluids and the surrounding sediment pore water from

Marine cold seeps and their manifestations: geological control, biogeochemical criteria and environmental conditions

Science.gov (United States)

Suess, Erwin

2014-10-01

Characteristics of cold seeps at different geologic settings are the subject of this review primarily based on results of the Research Consortium SFB 574. Criteria are drawn from examples on the erosive convergent margin off Costa Rica, the accretionary margin off Chile supplemented by examples from the transform margin of the Golf of Cadiz and the convergent Hikurangi margin off New Zealand. Others are from well-studied passive margins of the Black Sea, the Golf of Mexico, the eastern Mediterranean Sea and the South China Sea. Seeps at all settings transport water and dissolved compounds to the ocean through the seafloor by different forcing mechanism and from different depths of the submerged geosphere (10s of meters to 10s of km). The compounds sustain oasis-type ecosystems by providing bioactive reductants sulfide, methane and hydrogen. Hereby, the interaction between fluid composition, flux rates and biota results in a diagnostic hydrocarbon-metazoan-microbe-carbonate association; currently, well over 100 active sites are known. The single most important reaction is microbially mediated anaerobic oxidation of methane with secondary reactions involving S-biogeochemistry and carbonate mineral precipitation. Seep fluids and their seafloor manifestations provide clues as to source depth, fluid-sediment/rock interaction during ascent, lifetime and cyclicity of seepage events but less so on the magnitude of return flow. At erosive margins, Cl-depleted and B-enriched fluids from clay dehydration provide criteria for source depth and temperature. The upward material flow generates mud volcanoes at the seafloor above the projected location of dehydration at depth. At accretionary margins, fluids are derived from more shallow depths by compaction of sediments as they ride on the incoming oceanic plate; they are emitted through thrust faults. At highly sedimented margins, organic-rich and evaporite-containing strata (when present) determine the final fluid composition

Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners revealed by integrated multimodal analytical microscopy.

Science.gov (United States)

McGlynn, Shawn E; Chadwick, Grayson L; O'Neill, Ariel; Mackey, Mason; Thor, Andrea; Deerinck, Thomas J; Ellisman, Mark H; Orphan, Victoria J

2018-04-06

Phylogenetically diverse environmental ANME archaea and sulfate-reducing bacteria cooperatively catalyze the anaerobic oxidation of methane oxidation (AOM) in multi-celled consortia within methane seep environments. To better understand these cells and their symbiotic associations, we applied a suite of electron microscopy approaches including correlative f luorescence i n s itu h ybridization - e lectron m icroscopy (FISH-EM), t ransmission e lectron m icroscopy (TEM), and s erial b lock face scanning e lectron m icroscopy 3D reconstructions (SBEM). FISH-EM of methane seep derived consortia revealed phylogenetic variability in terms of cell morphology, ultrastructure, and storage granules. Representatives of the ANME-2b clade, but not other ANME-2 groups, contained polyphosphate-like granules, while some bacteria associated with ANME-2a/2c contained two distinct phases of iron mineral chains resembling magnetosomes. 3D segmentation of two ANME-2 consortia types revealed cellular volumes of ANME and their symbiotic partners which were larger than previous estimates based on light microscopy. Phosphorous granule containing ANME (tentatively ANME-2b) were larger than both ANME with no granules and partner bacteria. This cell type was observed with up to 4 granules per cell and the volume of the cell was larger in proportion to the number of granules inside it, but the percent of the cell occupied by these granules did not vary with granule number. These results illuminate distinctions between ANME-2 archaeal lineages and partnering bacterial populations that are apparently unified in their capability of performing anaerobic methane oxidation. Importance Methane oxidation in anaerobic environments can be accomplished by a number of archaeal groups, some of which live in syntrophic relationships with bacteria in structured consortia. Little is known as to the distinguishing characteristics of these groups. Here we applied imaging approaches to better understand the

Methane-metabolizing microbial communities in sediments of the Haima cold seep area, northwest slope of the South China Sea.

Science.gov (United States)

Niu, Mingyang; Fan, Xibei; Zhuang, Guangchao; Liang, Qianyong; Wang, Fengping

2017-09-01

Cold seeps are widespread chemosynthetic ecosystems in the deep-sea environment, and cold seep microbial communities of the South China Sea are poorly constrained. Here we report on the archaeal communities, particularly those involved in methane metabolization, in sediments of a newly discovered cold seep (named 'Haima') on the northwest slope of the South China Sea. Archaeal diversity, abundance and distribution were investigated in two piston cores collected from a seep area (QDN-14B) and a non-seep control site (QDN-31B). Geochemical investigation of the QDN-14B core identified an estimated sulfate-methane transition zone (Estimated SMTZ) at 300-400 cm below sea floor (cmbsf), where a high abundance of anaerobic methane-oxidizing archaea (ANME) occurred, as revealed by analysis of the 16S rRNA gene and the gene (mcrA) encoding the α-subunit of the key enzyme methyl-coenzyme M reductase. ANME-2a/b was predominant in the upper and middle layers of the estimated SMTZ, whereas ANME-1b outcompeted ANME-2 in the sulfate-depleted bottom layers of the estimated SMTZ and the methanogenic zone. Fine-scale phylogenetic analysis further divided the ANME-1b group into three subgroups with different distribution patterns: ANME-1bI, ANME-1bII and ANME-1bIII. Multivariate analyses indicated that dissolved inorganic carbon and sulfate may be important factors controlling the composition of the methane-metabolizing community. Our study on ANME niche separation and interactions with other archaeal groups improves our understanding of the metabolic diversity and flexibility of ANME, and the findings further suggest that ANME subgroups may have evolved diversified/specified metabolic capabilities other than syntrophic anaerobic oxidation of methane coupled with sulfate reduction in marine sediments. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool

KAUST Repository

Zhang, Weipeng; Ding, Wei; Yang, Bo; Tian, Renmao; Gu, Shuo; Luo, Haiwei; Qian, Pei-Yuan

2016-01-01

the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota

Anaerobic degradation of propane and butane by sulfate-reducing bacteria enriched from marine hydrocarbon cold seeps.

Science.gov (United States)

Jaekel, Ulrike; Musat, Niculina; Adam, Birgit; Kuypers, Marcel; Grundmann, Olav; Musat, Florin

2013-05-01

The short-chain, non-methane hydrocarbons propane and butane can contribute significantly to the carbon and sulfur cycles in marine environments affected by oil or natural gas seepage. In the present study, we enriched and identified novel propane and butane-degrading sulfate reducers from marine oil and gas cold seeps in the Gulf of Mexico and Hydrate Ridge. The enrichment cultures obtained were able to degrade simultaneously propane and butane, but not other gaseous alkanes. They were cold-adapted, showing highest sulfate-reduction rates between 16 and 20 °C. Analysis of 16S rRNA gene libraries, followed by whole-cell hybridizations with sequence-specific oligonucleotide probes showed that each enrichment culture was dominated by a unique phylotype affiliated with the Desulfosarcina-Desulfococcus cluster within the Deltaproteobacteria. These phylotypes formed a distinct phylogenetic cluster of propane and butane degraders, including sequences from environments associated with hydrocarbon seeps. Incubations with (13)C-labeled substrates, hybridizations with sequence-specific probes and nanoSIMS analyses showed that cells of the dominant phylotypes were the first to become enriched in (13)C, demonstrating that they were directly involved in hydrocarbon degradation. Furthermore, using the nanoSIMS data, carbon assimilation rates were calculated for the dominant cells in each enrichment culture.

Two-Dimensional Heat Transfer Modeling of the Formosa Ridge Offshore SW Taiwan: Implication for Fluid Migrating Paths of a Cold Seep Site

Science.gov (United States)

Tsai, Y.; Chi, W.; Liu, C.; Shyu, C.

2011-12-01

The Formosa Ridge, a small ridge located on the passive China continental slope offshore southwestern Taiwan, is an active cold seep site. Large and dense chemosynthetic communities were found there by the ROV Hyper-Dolphin during the 2007 NT0705 cruise. A vertical blank zone is clearly observed on all the seismic profiles across the cold seep site. This narrow zone is interpreted to be the fluid conduit of the seep site. Previous studies suggest that cold sea water carrying large amount of sulfate could flow into the fluid system from flanks of the ridge, and forms a very effective fluid circulation system that emits both methane and hydrogen sulfide to feed the unusual chemosynthetic communities observed at the Formosa Ridge cold seep site. Here we use thermal signals to study possible fluid flow migration paths. In 2008 and 2010, we have collected vdense thermal probe data at this site. We also study the temperatures at Bottom-Simulating Reflectors (BSRs) based on methane hydrate phase diagram. We perform 2D finite element thermal conductive simulations to study the effects of bathymetry on the temperature field in the ridge, and compare the simulation result with thermal probe and BSR-derived datasets. The boundary conditions include insulated boundaries on both sides, and we assign a fix temperature at the bottom of the model using an average regional geothermal gradient. Sensitivity tests and thermal probe data from a nearby region give a regional background geothermal gradient of 0.04 to 0.05 °C/m. The outputs of the simulation runs include geothermal gradient and temperature at different parts of the model. The model can fit the geothermal gradient at a distance away from the ridge where there is less geophysics evidence of fluid flow. However our model over-predicts the geothermal gradient by 50% at the ridge top. We also compare simulated temperature field and found that under the flanks of the ridge the temperature is cooled by 2 °C compared with the

Hydrocarbon Seeps Formations: a Study Using 3-D Seismic Attributes in Combination with Satellite Data

Science.gov (United States)

Garcia-Pineda, O. G.; MacDonald, I. R.; Shedd, W.

2011-12-01

Analyzing the magnitude of oil discharges from natural hydrocarbon seeps is important in improving our understanding of carbon contribution as oil migrates from deeper sediments to the water column, and then eventually to the atmosphere. Liquid hydrocarbon seepage in the deep water of the Gulf of Mexico (GOM) is associated with deep cutting faults, associated with vertical salt movement, that provide conduits for the upward migration of oil and gas. Seeps transform surface geology and generate prominent geophysical targets that can be identified on 3-D seismic data as seafloor amplitude anomalies maps that correlate with the underlying deep fault systems. Using 3D seismic data, detailed mapping of the northern GOM has identified more than 21,000 geophysical anomalies across the basin. In addition to seismic data, Synthetic Aperture Radar (SAR) images have proven to be a reliable tool for localizing natural seepage of oil. We used a Texture Classifier Neural Network Algorithm (TCNNA) to process more than 1200 SAR images collected over the GOM. We quantified more than 900 individual seep formations distributed along the continental shelf and in deep water. Comparison of the geophysical anomalies with the SAR oil slick targets shows good general agreement between the distributions of the two indicators. However, there are far fewer active oil slicks than geophysical anomalies, most of which are probably associated with gas seepage. By examining several sites where the location of active venting can be determined by submersibles observations, we found that the active oily vents are often spatially offset from the most intense geophysical targets (i.e. GC600, GC767, GC204, etc). In addition to the displacement of the oil by deep sea currents, we propose that during the 100K years of activity, the location of the vents on the seafloor probably migrate as carbonate cementation reduces the permeability of the upper sediment. Many of the geophysical targets may represent

Methane Metabolizing Microbial Communities in the Cold Seep Areas in the Northern Continental Shelf of South China Sea

Science.gov (United States)

Wang, F.; Liang, Q.

2016-12-01

Marine sediment contains large amount of methane, estimated approximately 500-2500 gigatonnes of dissolved and hydrated methane carbon stored therein, mainly in continental margins. In localized specific areas named cold seeps, hydrocarbon (mainly methane) containing fluids rise to the seafloor, and support oases of ecosystem composed of various microorganisms and faunal assemblages. South China Sea (SCS) is surrounded by passive continental margins in the west and north and convergent margins in the south and east. Thick organic-rich sediments have accumulated in the SCS since the late Mesozoic, which are continuing sources to form gas hydrates in the sediments of SCS. Here, Microbial ecosystems, particularly those involved in methane transformations were investigated in the cold seep areas (Qiongdongnan, Shenhu, and Dongsha) in the northern continental shelf of SCS. Multiple interdisciplinary analytic tools such as stable isotope probing, geochemical analysis, and molecular ecology, were applied for a comprehensive understanding of the microbe mediated methane transformation in this project. A variety of sediments cores have been collected, the geochemical profiles and the associated microbial distribution along the sediment cores were recorded. The major microbial groups involved in the methane transformation in these sediment cores were revealed, known methane producing and oxidizing archaea including Methanosarcinales, anaerobic methane oxidizing groups ANME-1, ANME-2 and their niche preference in the SCS sediments were found. In-depth comparative analysis revealed the presence of SCS-specific archaeal subtypes which probably reflected the evolution and adaptation of these methane metabolizing microbes to the SCS environmental conditions. Our work represents the first comprehensive analysis of the methane metabolizing microbial communities in the cold seep areas along the northern continental shelf of South China Sea, would provide new insight into the

Occurrence of faecal pellet-filled simple and composite burrows in cold seep carbonates: A glimpse of a complex benthic ecosystem

Digital Repository Service at National Institute of Oceanography (India)

Mazumdar, A.; Joshi, R.K.; Peketi, A.; Kocherla, M.

of inorganic sulphur in sediments and shales. Chemical Geology 54, 149–155. Cordes, E. E., Carney, S. L., Hourdez, S., Carney, R. S., Brooks, J. M. & Fisher, C. R. 2007. Cold seeps of the deep Gulf of Mexico: Community structure and biogeographic comparisons..., Surficial hydrocarbon seep infauna from the Blake Ridge (Atlantic Ocean, 2150 m) and the Gulf of Mexico (690– 2240 m) PSZN. Marine Ecology 25, 313–336. Sahling, H., Rickert, D., Lee, R.W., Linke, P., Suess, E., 2002, Macrofaunal community structure...

Marine controlled source electromagnetics on the Hikurangi Margin, NZ : coincidence between cold seep sites and electrical resistivity anomalies indicating sub-seafloor gas hydrate deposits

Energy Technology Data Exchange (ETDEWEB)

Schwalenberg, K. [Federal Inst. for Geosciences and Natural Resources, Hannover (Germany); Pecher, I. [Heriot Watt Univ., Edinburgh (United Kingdom). Inst. of Petroleum Engineering; Netzeband, G.; Jegen, M. [IFM-GEOMAR, Kiel (Germany); Port, J. [Ghent Univ., Ghent (Belgium). Renard Centre of Marine Geology

2008-07-01

This study examined the use of marine-controlled source electromagnetic (CSEM) measurements for monitoring the control, release and transformation of methane from gas seep sites and deposits on the Hikurangi Margin near New Zealand. The CSEM experiments were conducted to determine the electrical signature of the gas seeps as a means of identifying the presence of gas hydrate deposits. Data for 4 profiles were obtained and inverted to sub-sea floor resistivities and 1-D layered earth models. An analysis of the data showed a relationship between anomalous resistivities and the location of gas seep sites. Results suggested that concentrated gas hydrates were the cause of the anomalous resistivities. Data obtained from the southeast corner of the North Islands suggested the presence of gas hydrates in the first 100 m of bottom simulating reflector (BSM) data. Seeps were also identified in seismic data that showed faults and high amplitude reflections. A seep site with no resistivity anomalies but with active venting, high heat flow, and seismic fault planes was also identified. The lack of resistive anomalies was attributed to lower concentrations of gas hydrates; strong temporal and spatial variations; and temperature-driven fluid expulsion that hampered gas hydrate formation beneath the vent. The final profile examined in the study demonstrated a single anomaly over a deep, uprising reflective zone cause by both free gas and gas hydrates. 25 refs., 1 tab., 11 figs.

Geochemical Tracers and Rates of Short-Chain Alkane Production in Gulf of Mexico Cold Seep Sediments

Science.gov (United States)

Sibert, R.; Bernard, B. B.; Brooks, J. M.; Hunter, K.; Joye, S. B.

2014-12-01

The organic-rich cold seep sediments in the deep Gulf of Mexico commonly contain mixtures of light hydrocarbon gases either dissolved in pore fluids, adsorbed to sediment particles, trapped in methane ice, or as free gas. The dominant component in these natural gas mixtures is typically methane (C1), but ethane (C2) and propane (C3) are nearly always present in trace or major amounts. The ratio of C1:C2:C3 varies but C2 and C3 are typically present at single digit percent levels, whereas methane usually dominates at >80%. Methane production proceeds by at least two well-studied mechanisms: either 1) by thermocatalytic cracking of fossil organic matter, or 2) as a direct product of microbial metabolism, methanogenesis. In contrast, ethane and propane production in deep-sea sediments has been historically attributed only to thermocatalytic processes. However, limited data suggests production of C2/C3 compounds through the activity of archaea. Such studies of microbial- driven dynamics of C2/C3 gases (i.e. 'alkanogenesis') in cold seep sediments are rare. Furthermore, the identities of potential substrates are poorly constrained and no attempt has been made to quantify production rates of C2/C3 gases. However, carbon isotopic data on ethane and propane from deep cores from the Gulf of Mexico suggest alkanogenesis at depth in the sediment column and alkane oxidation in uppermost oxidant-rich sediments. Here, we present the results of a series of incubation experiments using sediment slurries culled from GC600, one of the most prolific natural oil and gas seeps in the Gulf of Mexico. Rates of both alkane production and oxidation were measured under a variety of conditions to assess the net rates of alkane production and elucidate the driving microbiological mechanisms and controls on the central processes of >C1 alkane cycling in cold seep sediments. Microbial processes are important both in terms of alkane production and oxidation, raising many questions as to the

Methane sources in gas hydrate-bearing cold seeps: Evidence from radiocarbon and stable isotopes

Science.gov (United States)

Pohlman, J.W.; Bauer, J.E.; Canuel, E.A.; Grabowski, K.S.; Knies, D.L.; Mitchell, C.S.; Whiticar, Michael J.; Coffin, R.B.

2009-01-01

Fossil methane from the large and dynamic marine gas hydrate reservoir has the potential to influence oceanic and atmospheric carbon pools. However, natural radiocarbon (14C) measurements of gas hydrate methane have been extremely limited, and their use as a source and process indicator has not yet been systematically established. In this study, gas hydrate-bound and dissolved methane recovered from six geologically and geographically distinct high-gas-flux cold seeps was found to be 98 to 100% fossil based on its 14C content. Given this prevalence of fossil methane and the small contribution of gas hydrate (??? 1%) to the present-day atmospheric methane flux, non-fossil contributions of gas hydrate methane to the atmosphere are not likely to be quantitatively significant. This conclusion is consistent with contemporary atmospheric methane budget calculations. In combination with ??13C- and ??D-methane measurements, we also determine the extent to which the low, but detectable, amounts of 14C (~ 1-2% modern carbon, pMC) in methane from two cold seeps might reflect in situ production from near-seafloor sediment organic carbon (SOC). A 14C mass balance approach using fossil methane and 14C-enriched SOC suggests that as much as 8 to 29% of hydrate-associated methane carbon may originate from SOC contained within the upper 6??m of sediment. These findings validate the assumption of a predominantly fossil carbon source for marine gas hydrate, but also indicate that structural gas hydrate from at least certain cold seeps contains a component of methane produced during decomposition of non-fossil organic matter in near-surface sediment.

Water quality and quantity of selected springs and seeps along the Colorado River corridor, Utah and Arizona: Arches National Park, Canyonlands National Park, Glen Canyon National Recreation Area, and Grand Canyon National Park, 1997-98

Science.gov (United States)

Taylor, Howard E.; Spence, John R.; Antweiler, Ronald C.; Berghoff, Kevin; Plowman, Terry I.; Peart, Dale B.; Roth, David A.

2004-01-01

The U.S. Geological Survey, in cooperation with the National Park Service conducted an intensive assessment of selected springs along the Colorado River Corridor in Arches National Park, Canyonlands National Park, Glen Canyon National Recreation Area, and Grand Canyon National Park in 1997 and 1998, for the purpose of measuring and evaluating the water quality and quantity of the resource. This study was conducted to establish baseline data for the future evaluation of possible effects from recreational use and climate change. Selected springs and seeps were visited over a study period from 1997 to 1998, during which, discharge and on-site chemical measurements were made at selected springs and seeps, and samples were collected for subsequent chemical laboratory analysis. This interdisciplinary study also includes simultaneous studies of flora and fauna, measured and sampled coincidently at the same sites. Samples collected during this study were transported to U.S. Geological Survey laboratories in Boulder, Colorado, where analyses were performed using state-of-the-art laboratory technology. The location of the selected springs and seeps, elevation, geology, aspect, and onsite measurements including temperature, discharge, dissolved oxygen, pH, and specific conductance, were recorded. Laboratory analyses include determinations for alkalinity, aluminum, ammonium (nitrogen), antimony, arsenic, barium, beryllium, bismuth, boron, bromide, cadmium, calcium, cerium, cesium, chloride, chromium, cobalt, copper, dissolved inorganic carbon, dissolved organic carbon, dysprosium, erbium, europium, fluoride, gadolinium, holmium, iodine, iron, lanthanum, lead, lithium, lutetium, magnesium, manganese, mercury, molybdenum, neodymium, nickel, nitrate (nitrogen), nitrite (nitrogen), phosphate, phosphorus, potassium, praseodymium, rhenium, rubidium, samarium, selenium, silica, silver, sodium, strontium, sulfate, tellurium, terbium, thallium, thorium, thulium, tin, titanium, tungsten

Can sediments at hydrocarbon seep sites represent a source for marine bioavailable iron? — A case study from the South China Sea

Science.gov (United States)

Li, N.; Feng, D.; Chen, D.

2017-12-01

Niu Li1, Dong Feng1,2, and Duofu Chen2,31CAS Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China. 2Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China. 3Hadal Science and Technology Research Center, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China. Iron is an essential micronutrient and commonly considered to be one of the key-limiting factors for biological productivity in many ocean regions. Seafloor Fe supply should be most efficient in suboxic conditions. Recent studies shown that widely spread anoxic environments can develop in hydrocarbon seep sediment and local bottom water, owing to the occurrence of aerobic and/or anaerobic methane oxidation. Under this condition, the iron in sediment can be reduced to dissolved Fe2+ in the ocean. However, questions remain about whether the hydrocarbon seep sediment can represent a source for bioavailable iron to the ocean, and the control factor for the transformation of iron in the sediment remains largely unexplored. For a number of hydrocarbon seeps from the northern and southern South China Sea, the iron speciation, pyrite sulfur isotope, and iron isotope, as well as the major and trace elements are used to constrain the intensity of cold seep, and its impact on transformation of iron in sediment. Samples from both areas show sediment iron lost during the high methane flux conditions, owing to the suboxic conditions cause by aerobic methane oxidation. On the other hand, high sediment iron content accompanied by high sulfur content can be seen during the conditions of high methane flux without the occurrence of aerobic methane oxidation, which is possible ascribed to the anaerobic methane oxidation and the release of iron through seep activity. This study reveals the transformation of iron in the sediment is closely related to the

A chemical and biological study of the impact of a suspected oil seep at the coast of Marraat, Nuussuaq, Greenland. With a summary of other environmental studies of hydrocarbons in Greenland

Energy Technology Data Exchange (ETDEWEB)

Mosbech, A.; Hansen, Asger B.; Asmund, G.; Dahlloef, I.; Groth Petersen, D.; Strand, J.

2007-08-15

These studies were conducted on the Nuussuaq Peninsula at Marraat, where GEUS discovered oil in porous volcanics in the early 1990s. This oil was also found in the Marraat-1 core drilled in 1993. At Marraat the presence of oil stained stones scattered along the coast indicates oil bearing strata and the existence of potential oil seeps. The studies reported here had the objective to see, if the suspected seep had a local impact on the chemistry and biological communities in the marine environment at Marraat. The study included sediments, blue mussels and fish that were analyzed for hydrocarbons, a Pollution Induced Community Test (PICT), a sediment toxicity test and a measurement of PAH metabolites in fish gall. The hydrocarbon pattern found in sediment and biota samples indicates input from both immature petrogenic hydrocarbons of possible terrestrial origin and local pollution by fuel oil. But the hydrocarbon levels found were low and do not indicate an input from a natural local oil seep at Marraat. The results of the PICT, the sediment toxicity test and the PAH metabolite study do not either indicate the presence of an oil seep. However, compared to sediments from a larger area of West Greenland the sediments close to Nuussuaq and Disko have higher concentrations of PAH expressed on basis of their content of organic matter. This could be a result of natural seepage of oil in the Nuusuuaq/Disko region. (au)

Chronic oiling of marine birds in California by natural petroleum seeps, shipwrecks, and other sources.

Science.gov (United States)

Henkel, Laird A; Nevins, Hannahrose; Martin, Marida; Sugarman, Susan; Harvey, James T; Ziccardi, Michael H

2014-02-15

We assessed temporal and spatial patterns of chronic oiling of seabirds in California during 2005-2010, using data on: (1) live oiled birds reported to the Oiled Wildlife Care Network (OWCN) from throughout the state, and (2) dead oiled birds found during systematic monthly beached-bird surveys in central California. A mean of 245 (± 141 SD) live miscellaneous oiled birds (not associated with known oil spills) were reported to the OWCN per year, and 0.1 oiled dead birds km(-1) per month were found on beach surveys in central California. Chemical fingerprinting of oiled feathers from a subset of these birds (n=101) indicated that 89% of samples tested were likely from natural petroleum seeps off southern and central California. There was a pronounced peak during late winter in the number of oiled birds reported in southern California, which we theorize may be related to large storm waves disturbing underwater seeps. Copyright © 2014 Elsevier Ltd. All rights reserved.

Extreme Morphologic and Venting Changes in Methane Seeps at Southern Hydrate Ridge, Cascadia Margin

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Bigham, K.; Kelley, D. S.; Solomon, E. A.; Delaney, J. R.

2017-12-01

Two highly active methane hydrate seeps have been visited over a 7-year period as part of the construction and operation of NSF's Ocean Observatory Initiative's Regional Cable Array at Southern Hydrate Ridge. The site is located 90 km west of Newport, Oregon, at a water depth of 800 m. The seeps, Einstein's Grotto (OOI instrument deployment site) and Smokey Tavern (alternate site to the north), have been visited yearly from 2010 to 2017 with ROVs. Additionally, a digital still camera deployed from 2014 to 2017 at Einstein's Grotto, has been documenting the profound morphologic and biological changes at this site. A cabled pressure sensor, Acoustic Doppler Current Profiler, hydrophone, seismometer array, and uncabled fluid samplers have also been operational at the site for the duration of the camera's deployment. During this time, Einstein's Grotto has evolved from a gentle mound with little venting, to a vigorously bubbling pit bounded by a near vertical wall. Early on bubble emissions blew significant amounts of sediment into the water column and thick Beggiatoa mats coverd the mound. Most recently the face of the pit has collapsed, although bubble plumes are still emitted from the site. The Smokey Tavern site has undergone more extreme changes. Similar to Einstein's Grotto it was first characterized by gentle hummocks with dispersed bacterial mats. In subsequent years, it developed an extremely rugged, elongated collapsed area with vertical walls and jets of methane bubbles rising from small pits near the base of the collapse zone. Meter-across nearly sediment-free blocks of methane hydrate were exposed on the surface and in the walls of the collapse zone. In 2016, this area was unrecognizable with a much more subdued topography, and weak venting of bubbles. Exposed methane hydrate was not visible. From these observations new evolutionary models for methane seeps are being developed for Southern Hydrate Ridge.

The Effect of Summer Environmental Education Program (SEEP) on Elementary School Students' Environmental Literacy

Science.gov (United States)

Erdogan, Mehmet

2015-01-01

The purpose of this study was to assess the effects of Summer Environmental Education Program (SEEP) on elementary school students' environmental knowledge, affect, skills and behavior which are the main components of environmental literacy. The sample consisted of 45 students (25 males, 20 females) studying in 4th through 8th grades and living in…

Adaptation to the deep-sea hydrothermal vents and cold seeps: Insights from the transcriptomes of Alvinocaris longirostris in both environments

Science.gov (United States)

Hui, Min; Cheng, Jiao; Sha, Zhongli

2018-05-01

Alvinocaris longirostris Kikuchi and Ohta, 1995 is one of the few species co-distributed in deep-sea hydrothermal vent and cold seep environments. We performed the transcriptome analysis for A. longirostris and identified differentially expressed genes (DEGs) between samples from the Iheya North hydrothermal vent (HV) and a methane seep in the South China Sea (MS). From the 57,801 annotated unigenes, multi-copies of enzyme family members for eliminating toxic xenobiotics were isolated and seven putatively duplicated gene clusters of cytochrome P450s were discovered, which may contribute to adaptation to the harsh conditions. Eight single amino acid substitutions of a Rhodopsin gene with low expression in two deep-sea alvinocaridid species were positively selected when compared with shallow water shrimps, which may be the result of adaptation to the dim-light environment in deep sea. 408 DEGs were identified with 53 and 355 up-regulated in HV and MS, respectively. Various genes associated with sulfur metabolism, detoxification and mitochondria were included, revealing different mechanisms of adaptation to the two types of extreme environments. All results are expected to serve as important basis for the further study.

Biomarker chemistry and flux quantification methods for natural petroleum seeps and produced oils, offshore southern California

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Lorenson, T.D.; Leifer, Ira; Wong, Florence L.; Rosenbauer, Robert J.; Campbell, Pamela L.; Lam, Angela; Hostettler, Frances D.; Greinert, Jens; Finlayson, David P.; Bradley, Eliza S.; Luyendyk, Bruce P.

2011-01-01

Sustained, natural oil seepage from the seafloor is common off southern California, and is of great interest to resource managers, who are tasked with distinguishing natural from anthropogenic oil sources. The major purpose of this study was to build upon the work previously funded by the Bureau of Ocean Energy Management (BOEM) and the U.S. Geological Survey (USGS) that has refined the oil-fingerprinting process to enable differentiation of the highly similar Monterey Formation oils from Outer Continental Shelf (OCS) production and adjacent natural seeps. In these initial studies, biomarker and stable carbon isotope ratios were used to infer the age, lithology, organic-matter input, and depositional environment of the source rocks for 388 samples of produced crude oil, seep oil, and tarballs mainly from coastal California. The analysis resulted in a predictive model of oil source families that could be applied to samples of unknown origin.

Authigenic carbonates from newly discovered active cold seeps on the northwestern slope of the South China Sea: Constraints on fluid sources, formation environments, and seepage dynamics

Science.gov (United States)

Liang, Qianyong; Hu, Yu; Feng, Dong; Peckmann, Jörn; Chen, Linying; Yang, Shengxiong; Liang, Jinqiang; Tao, Jun; Chen, Duofu

2017-06-01

Authigenic carbonates recovered from two newly discovered active cold seeps on the northwestern slope of the South China Sea have been studied using petrography, mineralogy, stable carbon and oxygen isotopic, as well as trace element compositions, together with AMS 14C ages of shells of seep-dwelling bivalves to unravel fluid sources, formation conditions, and seepage dynamics. The two seeps (ROV1 and ROV2), referred to as 'Haima seeps' herein, are approximately 7 kilometers apart, and are typified by abundant carbonate rocks represented bycrusts and nodules. Aragonite and high-Mg calcite are the main carbonate minerals. Based on low δ13Ccarbonate values ranging from -43.0‰ to -27.5‰ (V-PDB) methane is apparently the predominant carbon source of seep carbonates. The corresponding δ18O values, varying from 2.5‰ to 5.8‰ (V-PDB), mostly are higher than calculated values representing precipitation in equilibrium with seawater (2.5‰ to 3.8‰), which probably reflects past destabilization of locally abundant gas hydrates. In addition, we found that carbonates with bivalve shells are generally aragonite-dominated, and bear no barium enrichment but uranium enrichments, reflecting shallow formation depths close to the seafloor. In contrast, carbonate crusts without bivalve shells and nodules contain more calcite, and are characterized by major molybdenum enrichment and different degrees of barium enrichment, agreeing with precipitation at greater depth under strictly anoxic conditions. AMS 14C ages suggest that a major episode of carbonate precipitation occurred between 6.1 ka and 5.1 ka BP at the Haima seeps, followed by a possibly subordinate episode from approximately 3.9 ka to 2.9 ka BP. The common occurrence of dead bivalves at both sites indicates that chemosynthesis-based communities flourished to a greater extent in the past, probably reflecting a decline of seepage activity in recent times. Overall, these results confirm that authigenic carbonates from

Investigating the emission, dissolution, and oxidation of CH4 within and around a seep bubble plume in the Gulf of Mexico.

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Leonte, M.; Kessler, J. D.; Socolofsky, S. A.

2016-02-01

One of the largest carbon reservoirs on the planet is stored as methane (CH4) in and below the seafloor. However, a large discrepancy exists between estimated fluxes of CH4 into the water column and CH4 fluxes from the sea surface to the atmosphere, suggesting that a significant fraction of CH4 released from seafloor seeps is dissolved and potentially removed through microbial oxidation. Here we present data investigating the fate of CH4 released from the Sleeping Dragon seep site in the Gulf of Mexico. The bubble plume was followed from the seafloor until it fully dissolved using a remotely operated vehicle (ROV). Water samples were collected by the ROV at different depths as well as lateral transects through the bubble plume. These samples were analyzed for dissolved concentrations of methane, ethane, propane, and butane as well as the 13C isotopic ratio of methane. Furthermore, seep bubbles from the seafloor were also collected and analyzed for the same properties. Based on these chemical data, the rate of CH4 emission from the seafloor, oxidation in the water column, and dissolution are investigated.

Geological Study of Active Cold Seeps in the Syn-collision Accretionary Prism Kaoping Slope off SW Taiwan

Directory of Open Access Journals (Sweden)

Chi-Yue Huang

2006-01-01

Full Text Available Pogonophoran tube worms, elongated pyrite tubes and authigenic carbonate nodules are used to evaluate the occurrence of potential cold seeps in the syn-collision accretionary prism Kaoping Slope off SW Taiwan. At least two species of pogonophoran tubeworms were found in surface and core sediments. Pyrites occur in three different forms: fillings inside foraminiferal chambers, cements between calcareous microfossils, and elongated tubes. The bottom water off SW Taiwan is aerobic, but authigenic pyrites are found in the surface sediments at several sites, suggesting the existence of local reducing environments enabling the formation of pyrites. These environments are most likely caused by the occurrence of active cold seeps where methane expulses. Authigenic carbonates with highly depleted carbon isotope values (-54 to -43‰ were found at more than 5 locations, in agreement with a methane-derived source for the carbon.

Bedded Barite Deposits from Sonora (nw Mexico): a Paleozoic Analog for Modern Cold Seeps

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Canet, C.; Anadón, P.; González-Partida, E.; Alfonso, P.; Rajabi, A.; Pérez-Segura, E.; Alba-Aldave, L. A.

2013-05-01

The Mazatán barite deposits represent an outstanding example of Paleozoic bedded barite, a poorly understood type of mineral deposit of major economic interest. The largest barite bodies of Mazatán are hosted within an Upper Carboniferous flysch succession, which formed part of an accretionary wedge related to the subduction of the Rheic Ocean beneath Gondwana. As well, a few barite occurrences are hosted in Upper Devonian, pre-orogenic turbidites. A variety of mineralized structures is displayed by barite, including: septaria nodules, enterolitic structures, rosettes and debris-flow conglomerates. Barite is accompanied by chalcedony, pyrite (framboids) and berthierine. Gas-rich fluid inclusions in barite were analyzed by Raman spectroscopy and methane was identified, suggesting the occurrence of light hydrocarbons in the environment within which barite precipitated. 13C-depleted carbonates (δ13C: -24.3 to -18.8‰) were found in the barite deposits; they formed through anaerobic oxidation of methane coupled to sulfate reduction, and yield negative δ18O values (-11.9 to -5.2‰) reflecting the isotopic composition of Devonian-Carboniferous seawater. Methane-derived carbonates occur in modern hydrocarbon seeps and have been reported from Mesozoic and Cenozoic seep sediments, but they have never before been described in Paleozoic bedded barite deposits. δ34S of barite varies from +17.6 to +64.1‰, with the lowest values overlapping the range for coeval seawater sulfate; this distribution indicates a process of sulfate reduction. Barite precipitation can be explained by mixing of methane- and barium-rich fluids with pore-water (seawater) containing sulfate residual from microbial reduction. Two analyses from barite gave an 87Sr/86Sr within and slightly above the range for seawater at the time of deposition, with 0.708130 and 0.708588, which would preclude the involvement of hydrothermal fluids in the mineralization process.

Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea.

Science.gov (United States)

Dang, Hongyue; Luan, Xi-Wu; Chen, Ruipeng; Zhang, Xiaoxia; Guo, Lizhong; Klotz, Martin G

2010-06-01

The ecological characteristics of amoA-encoding archaea (AEA) in deep-sea sediments are largely unsolved. This paper aimed to study the diversity, structure, distribution and abundance of the archaeal community and especially its AEA components in the cold seep surface sediments of the Okhotsk Sea, a marginal sea harboring one of the largest methane hydrate reservoirs in the world. Diverse archaeal 16S rRNA gene sequences were identified, with the majority being related to sequences from other cold seep and methane-rich sediment environments. However, the AEA diversity and abundance were quite low as revealed by amoA gene analyses. Correlation analysis indicates that the abundance of the archaeal amoA genes was correlated with the sediment organic matter content. Thus, it is possible that the amoA-carrying archaea here might utilize organic matter for a living. The affiliation of certain archaeal amoA sequences to the GenBank sequences originally obtained from deep-sea hydrothermal vent environments indicated that the related AEA either have a wide range of temperature adaptation or they have a thermophilic evolutionary history in the modern cold deep-sea sediments of the Okhotsk Sea. The dominance of ammonia-oxidizing bacteria over AEA may indicate that bacteria play a significant role in nitrification in the Okhotsk Sea cold seep sediments.

Reverse transcriptase directs viral evolution in a deep ocean methane seep

Science.gov (United States)

Paul, B. G.; Bagby, S. C.

2013-12-01

Deep ocean methane seeps are sites of intense microbial activity, with complex communities fueled by aerobic and anaerobic methanotrophy. Methane consumption in these communities has a substantial impact on the global carbon cycle, yet little is known about their evolutionary history or their likely evolutionary trajectories in a warming ocean. As in other marine systems, viral predation and virally mediated horizontal gene transfer are expected to be major drivers of evolutionary change in these communities; however, the host cells' resistance to cultivation has impeded direct study of the viral population. We conducted a metagenomic study of viruses in the anoxic sediments of a deep methane seep in the Santa Monica Basin in the Southern California Bight. We retrieved 1660 partial viral genomes, tentatively assigning 1232 to bacterial hosts and 428 to archaea. One abundant viral genome, likely hosted by Clostridia species present in the sediment, was found to encode a diversity-generating retroelement (DGR), a module for reverse transcriptase-mediated directed mutagenesis of a distal tail fiber protein. While DGRs have previously been described in the viruses of human pathogens, where diversification of viral tail fibers permits infection of a range of host cell types, to our knowledge this is the first description of such an element in a marine virus. By providing a mechanism for massively broadening potential host range, the presence of DGRs in these systems may have a major impact on the prevalence of virally mediated horizontal gene transfer, and even on the phylogenetic distances across which genes are moved.

Methane emission and consumption at a North Sea gas seep (Tommeliten area

Directory of Open Access Journals (Sweden)

H. Niemann

2005-01-01

Full Text Available The Tommeliten seepage area is part of the Greater Ekofisk area, which is situated above the Tommeliten Delta salt diapir in the central North Sea (56°29.90' N, 2°59.80' E, Norwegian Block 1/9, 75 m water depth. Here, cracks in a buried marl horizon allow methane to migrate into overlying clay-silt and sandy sediments. Hydroacoustic sediment echosounding showed several venting spots coinciding with the apex of marl domes where methane is released into the water column and potentially to the atmosphere. In the vicinity of the gas seeps, sea floor observations showed small mats of giant sulphide-oxidizing bacteria above patches of black sediments as well as carbonate crusts, which are exposed 10 to 50 cm above seafloor forming small reefs. These Methane-Derived Authigenic Carbonates (MDACs contain 13C-depleted, archaeal lipids indicating previous gas seepage and AOM activity. High amounts of sn2-hydroxyarchaeol relative to archaeol and low abundances of biphytanes in the crusts give evidence that ANaerobic MEthane-oxidising archaea (ANME of the phylogenetic cluster ANME-2 were the potential mediators of Anaerobic Oxidation of Methane (AOM at the time of carbonate formation. Small pieces of MDACs were also found subsurface at about 1.7 m sediment depth, associated with the AOM zone. This zone is characterized by elevated AOM and Sulphate Reduction (SR rates, increased concentrations of 13C-depleted tetraether derived biphytanes, and specific bacterial Fatty Acids (FA. Further biomarker and 16S rDNA based analyses of this horizon give evidence that AOM is mediated by archaea belonging to the ANME-1b group and Sulphate Reducing Bacteria (SRB most likely belonging to the Seep-SRB1 cluster. The zone of active methane consumption was restricted to a distinct horizon of about 20 cm. Concentrations of 13C-depleted lipid biomarkers (e.g. 500 ng g-dw−1 biphythanes, 140 ng g-dw−1 fatty acid ai-C15:0, cell numbers (1.5×108 cells cm−3, AOM and SR

Geochemical Study of Natural Bitumen, Condensate and Gas Seeps from Sousse Area, Central Tunisia

OpenAIRE

A. Belhaj Mohamed; M. Saidi; N. Boucherb; N. Ourtani; A. Soltani; I. Bouazizi; M. Ben Jrad

2015-01-01

Natural hydrocarbon seepage has helped petroleum exploration as a direct indicator of gas and/or oil subsurface accumulations. Surface macro-seeps are generally an indication of a fault in an active Petroleum Seepage System belonging to a Total Petroleum System. This paper describes a case study in which multiple analytical techniques were used to identify and characterize trace petroleum-related hydrocarbons and other volatile organic compounds in groundwater samples col...

Tectono-Stratigraphy of the Seeps on the Guaymas Basin at the Sonora Margin, Gulf of California, Mexico

Science.gov (United States)

Figueroa Albornoz, L. J.; Mortera-Gutierrez, C. A.; Bandy, W. L.; Escobar-Briones, E. G.; Godfroy, A.; Fouquet, Y.

2013-05-01

Recently several hydrothermal and gas seeps systems has been located precisely at the Sonora margin within the Guaymas Basin (GB), Gulf of California. Since late 1970's , several marine studies had reported two main hydrothermal systems in the Guaymas Rift (one at the Northern Rift, and other at the Southern Rift) and a cold seeps system at the Satellite Basin in the Sonora-margin lower edge. During the campaign BIG10, onboard the IFREMER vessel, NO L'Atalante, the EM122 echo-sounder log more than 30,000 water column acoustic images, which allows us to create a data base of the bubble plumes active systems on the northern part of the GB and the Sonora Margin. These plumes are the expression on the water column of an active seeps site during the cruise time. These images document the presence of the cold seep activity around the scarp of the Guaymas Transform Fault (GTF), and within the Satellite Basin. Few active plumes are first located off-axis, on both sides of the Northern Rift. Although it is not observed any plume within NR. Sub-bottom profiles and bathymetric data logged during the campaign GUAYRIV10, onboard the UNAM vessel, BO EL PUMA, are analyzed to determine the shallow tectonic-stratigraphy of GB near the Sonora Margin. We analyze 17 high-resolution seismic profiles (13 with NE-SW strike and 3 with NW-SE strike). From this data set, the continental shelf stratigraphy at the Sonora Margin tilts toward the slope, showing 3 low angle unconformities due to tectonics and slope angle changes. The strata slope changes angle up to 60°. However, the constant trans-tension shear along the GTF causes gravitation instability on the slope, generating a few submarine landslides close to the Northern Rift, and the rotation of blocks, tilting toward the shelf. To the north, the GTF splits in two fault escarpments, forming a narrow pull-apart basin, known as Satellite Basin. The submarine canyon from the Sonora River flows through the Satellite Basin into the GB

Patterns and variability in geochemical signatures and microbial activity within and between diverse cold seep habitats along the lower continental slope, Northern Gulf of Mexico

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Bowles, Marshall; Hunter, Kimberley S.; Samarkin, Vladimir; Joye, Samantha

2016-07-01

We collected 69 sediment cores from distinct ecological and geological settings along the deep slope in the Northern Gulf of Mexico to evaluate whether specific geochemical- or habitat-related factors correlated with rates of microbial processes and geochemical signatures. By collecting replicate cores from distinct habitats across multiple sites, we illustrate and quantify the heterogeneity of cold seep geochemistry and microbial activity. These data also document the factors driving unique aspects of the geochemistry of deep slope gas, oil and brine seeps. Surprisingly little variation was observed between replicate (n=2-5) cores within sites for most analytes (except methane), implying that the common practice of collecting one core for geochemical analysis can capture the signature of a habitat in most cases. Depth-integrated concentrations of methane, dissolved inorganic carbon (DIC), and calcium were the predominant geochemical factors that correlated with a site's ecological or geological settings. Pore fluid methane concentration was related to the phosphate and DIC concentration, as well as to rates of sulfate reduction. While distinctions between seep habitats were identified from geochemical signatures, habitat specific geochemistry varied little across sites. The relative concentration of dissolved inorganic nitrogen versus phosphorus suggests that phosphorus availability limits biomass production at cold seeps. Correlations between calcium, chloride, and phosphate concentrations were indicative of brine-associated phosphate transport, suggesting that in addition to the co-migration of methane, dissolved organic carbon, and ammonium with brine, phosphate delivery is also associated with brine advection.

Characterization of the acidic cold seep emplaced jarositic Golden Deposit, NWT, Canada, as an analogue for jarosite deposition on Mars

Science.gov (United States)

Battler, Melissa M.; Osinski, Gordon R.; Lim, Darlene S. S.; Davila, Alfonso F.; Michel, Frederick A.; Craig, Michael A.; Izawa, Matthew R. M.; Leoni, Lisa; Slater, Gregory F.; Fairén, Alberto G.; Preston, Louisa J.; Banerjee, Neil R.

2013-06-01

Surficial deposits of the OH-bearing iron sulfate mineral jarosite have been observed in several places on Mars, such as Meridiani Planum and Mawrth Vallis. The specific depositional conditions and mechanisms are not known, but by comparing martian sites to analogous locations on Earth, the conditions of formation and, thus, the martian depositional paleoenvironments may be postulated. Located in a cold semi-arid desert ˜100 km east of Norman Wells, Northwest Territories, Canada, the Golden Deposit (GD) is visible from the air as a brilliant golden-yellow patch of unvegetated soil, approximately 140 m × 50 m. The GD is underlain by permafrost and consists of yellow sediment, which is precipitating from seeps of acidic, iron-bearing groundwater. On the surface, the GD appears as a patchwork of raised polygons, with acidic waters flowing from seeps in troughs between polygonal islands. Although UV-Vis-NIR spectral analysis detects only jarosite, mineralogy, as determined by X-ray diffraction and inductively coupled plasma emission spectrometry, is predominantly natrojarosite and jarosite, with hydronium jarosite, goethite, quartz, clays, and small amounts of hematite. Water pH varies significantly over short distances depending on proximity to acid seeps, from 2.3 directly above seeps, to 5.7 several m downstream from seeps within the deposit, and up to 6.5 in ponds proximal to the deposit. Visual observations of microbial filament communities and phospholipid fatty acid analyses confirm that the GD is capable of supporting life for at least part of the year. Jarosite-bearing sediments extend beneath vegetation up to 70 m out from the deposit and are mixed with plant debris and minerals presumably weathered from bedrock and glacial till. This site is of particular interest because mineralogy (natrojarosite, jarosite, hematite, and goethite) and environmental conditions (permafrost and arid conditions) at the time of deposition are conceivably analogous to jarosite

The phase transition of methane caused by pressure change during its seeping up from seepage, revealed by video observation and acoustic reflection data

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Aoyama, C.

2017-12-01

Methane plumes often exist in the vicinity sea area where shallow type methane hydrates are extracted and they are observed as images displayed on monitors of multi-beam sonar and echo sounder onboard, where methane hydrates are expected at sea bottom on ROV observation data. The hydrates are generally considered to be generated in shallow depths below the sea floor. In this study, author examined annual amount of methane dissolving into seawater by measuring the amount of plume in order to make a quantification of dissolving methane from seafloor. Measurement procedure is plume exploration using multi-beam and quantitative echo sounder , submerge ROV to gushing point at seafloor , calculate the rising speed of methane plumes and examine the phases by monitoring seeping plumes from seafloor with high-definition camera. Components of seeping plumes were defined as methane hydrate particles based on the result by measuring water temperature. From this procedure, it can be concluded that the minimum rising speed of methane hydrate particles from gushing point is 1.6×10-1(m/s) and the maximum of 2.0×10-1(m/s) indicating a difference of more than ten times the gaseous theoretical value of 2.74(m/s). This speed is theoretically closer to the solid speed of the material with physical property similar to hydrates, which is 3.05×10-1 (m/s). Therefore, it can be determined that those particles are in the solid state, immediately above seafloor. To measure the amount of plumes seeping from gushing points funnel-shaped instruments with 20cm diameter opening were used to collect methane plumes in this sea area. This was performed in three different gushing points. As a result, 300ml of methane plume was collected in 643 seconds. Assuming that gushing points exist evenly in the sea area, the annual amount of methane gas seeping from these points will be 7.7×105m3 /per m2. Result shows a large quantity of methane seeping from seafloor into the water. This data is an important

Do ampharetids take sedimented steps between vents and seeps? Phylogeny and habitat-use of Ampharetidae (Annelida, Terebelliformia) in chemosynthesis-based ecosystems.

Science.gov (United States)

Eilertsen, Mari H; Kongsrud, Jon A; Alvestad, Tom; Stiller, Josefin; Rouse, Greg W; Rapp, Hans T

2017-10-31

A range of higher animal taxa are shared across various chemosynthesis-based ecosystems (CBEs), which demonstrates the evolutionary link between these habitats, but on a global scale the number of species inhabiting multiple CBEs is low. The factors shaping the distributions and habitat specificity of animals within CBEs are poorly understood, but geographic proximity of habitats, depth and substratum have been suggested as important. Biogeographic studies have indicated that intermediate habitats such as sedimented vents play an important part in the diversification of taxa within CBEs, but this has not been assessed in a phylogenetic framework. Ampharetid annelids are one of the most commonly encountered animal groups in CBEs, making them a good model taxon to study the evolution of habitat use in heterotrophic animals. Here we present a review of the habitat use of ampharetid species in CBEs, and a multi-gene phylogeny of Ampharetidae, with increased taxon sampling compared to previous studies. The review of microhabitats showed that many ampharetid species have a wide niche in terms of temperature and substratum. Depth may be limiting some species to a certain habitat, and trophic ecology and/or competition are identified as other potentially relevant factors. The phylogeny revealed that ampharetids have adapted into CBEs at least four times independently, with subsequent diversification, and shifts between ecosystems have happened in each of these clades. Evolutionary transitions are found to occur both from seep to vent and vent to seep, and the results indicate a role of sedimented vents in the transition between bare-rock vents and seeps. The high number of ampharetid species recently described from CBEs, and the putative new species included in the present phylogeny, indicates that there is considerable diversity still to be discovered. This study provides a molecular framework for future studies to build upon and identifies some ecological and

Estimation of past intermittent methane seep activity using radiocarbon dating of Calyptogena shells in the eastern Nankai subduction zone

Science.gov (United States)

Yagasaki, K.; Ashi, J.; Yokoyama, Y.; Miyairi, Y.; Kuramoto, S.

2013-12-01

Radioisotope carbon dating samples from the deep ocean has always been a difficult phenomenon due to the carbon offset present. This research presents a way of utilizing such method to date shell samples in order to study past fault activities. The research presented will be based on the preliminary data collected thus far. The Nankai and the Tokai regions are common areas for cold seeps, where seepage of hydrogen sulfide and methane rich fluid occurs. These various substances encourage the growth of Calyptogena colonies to flourish at these sites. Cold seeps generally occur at tectonically active continental margins and are mostly ephemeral. This suggests that the cold seep events are possibly influenced by the tectonic activity during the plate divergence. In 1997, a submersible dive by Shinkai 2000 discovered an unusually large Calyptogena colony ranging over 200 m2 off Daini Tenryu Knoll. Majority of the shells were fossilized with few live shells remaining. It is assumed that past tectonic events in the region may have caused a high flux of methane fluid or gas to be released, making it possible to support such a vast scale colony to survive until their eventual death. Previous attempt to reconstruct the cold seep activity history through amino acid racemisation dating revealed two different age grouped shells. Further data using a different method is required to prove its reliability, as acid racemization dating technique can easily be affected by seawater temperature changes and microbial activity. This consequently alters the protein structure of the sample and its overall age. As 14C radioisotope dating is not affected by temperature change, it will provide additional information to the accuracy of the acid racemisation dating of the shell. However, the possibility of contamination is likely due to the shells incorporating older carbon from the sediments during their early stages of growth. The old carbon value can be calculated by subtracting the formerly

Identification of novel methane-, ethane-, and propane-oxidizing bacteria at marine hydrocarbon seeps by stable isotope probing.

Science.gov (United States)

Redmond, Molly C; Valentine, David L; Sessions, Alex L

2010-10-01

Marine hydrocarbon seeps supply oil and gas to microorganisms in sediments and overlying water. We used stable isotope probing (SIP) to identify aerobic bacteria oxidizing gaseous hydrocarbons in surface sediment from the Coal Oil Point seep field located offshore of Santa Barbara, California. After incubating sediment with (13)C-labeled methane, ethane, or propane, we confirmed the incorporation of (13)C into fatty acids and DNA. Terminal restriction fragment length polymorphism (T-RFLP) analysis and sequencing of the 16S rRNA and particulate methane monooxygenase (pmoA) genes in (13)C-DNA revealed groups of microbes not previously thought to contribute to methane, ethane, or propane oxidation. First, (13)C methane was primarily assimilated by Gammaproteobacteria species from the family Methylococcaceae, Gammaproteobacteria related to Methylophaga, and Betaproteobacteria from the family Methylophilaceae. Species of the latter two genera have not been previously shown to oxidize methane and may have been cross-feeding on methanol, but species of both genera were heavily labeled after just 3 days. pmoA sequences were affiliated with species of Methylococcaceae, but most were not closely related to cultured methanotrophs. Second, (13)C ethane was consumed by members of a novel group of Methylococcaceae. Growth with ethane as the major carbon source has not previously been observed in members of the Methylococcaceae; a highly divergent pmoA-like gene detected in the (13)C-labeled DNA may encode an ethane monooxygenase. Third, (13)C propane was consumed by members of a group of unclassified Gammaproteobacteria species not previously linked to propane oxidation. This study identifies several bacterial lineages as participants in the oxidation of gaseous hydrocarbons in marine seeps and supports the idea of an alternate function for some pmoA-like genes.

Families of miocene monterey crude oil, seep, and tarball samples, coastal California

Science.gov (United States)

Peters, K.E.; Hostettler, F.D.; Lorenson, T.D.; Rosenbauer, R.J.

2008-01-01

Biomarker and stable carbon isotope ratios were used to infer the age, lithology, organic matter input, and depositional environment of the source rocks for 388 samples of produced crude oil, seep oil, and tarballs to better assess their origins and distributions in coastal California. These samples were used to construct a chemometric (multivariate statistical) decision tree to classify 288 additional samples. The results identify three tribes of 13C-rich oil samples inferred to originate from thermally mature equivalents of the clayey-siliceous, carbonaceous marl and lower calcareous-siliceous members of the Monterey Formation at Naples Beach near Santa Barbara. An attempt to correlate these families to rock extracts from these members in the nearby COST (continental offshore stratigraphic test) (OCS-Cal 78-164) well failed, at least in part because the rocks are thermally immature. Geochemical similarities among the oil tribes and their widespread distribution support the prograding margin model or the banktop-slope-basin model instead of the ridge-and-basin model for the deposition of the Monterey Formation. Tribe 1 contains four oil families having geochemical traits of clay-rich marine shale source rock deposited under suboxic conditions with substantial higher plant input. Tribe 2 contains four oil families with traits intermediate between tribes 1 and 3, except for abundant 28,30-bisnorhopane, indicating suboxic to anoxic marine marl source rock with hemipelagic input. Tribe 3 contains five oil families with traits of distal marine carbonate source rock deposited under anoxic conditions with pelagic but little or no higher plant input. Tribes 1 and 2 occur mainly south of Point Conception in paleogeographic settings where deep burial of the Monterey source rock favored petroleum generation from all three members or their equivalents. In this area, oil from the clayey-siliceous and carbonaceous marl members (tribes 1 and 2) may overwhelm that from the lower

Seismic imaging of the Formosa Ridge cold seep site offshore of southwestern Taiwan

Science.gov (United States)

Hsu, Ho-Han; Liu, Char-Shine; Morita, Sumito; Tu, Shu-Lin; Lin, Saulwood; Machiyama, Hideaki; Azuma, Wataru; Ku, Chia-Yen; Chen, Song-Chuen

2017-12-01

Multi-scale reflection seismic data, from deep-penetration to high-resolution, have been analyzed and integrated with near-surface geophysical and geochemical data to investigate the structures and gas hydrate system of the Formosa Ridge offshore of southwestern Taiwan. In 2007, dense and large chemosynthetic communities were discovered on top of the Formosa Ridge at water depth of 1125 m by the ROV Hyper-Dolphin. A continuous and strong BSR has been observed on seismic profiles from 300 to 500 ms two-way-travel-time below the seafloor of this ridge. Sedimentary strata of the Formosa Ridge are generally flat lying which suggests that this ridge was formed by submarine erosion processes of down-slope canyon development. In addition, some sediment waves and mass wasting features are present on the ridge. Beneath the cold seep site, a vertical blanking zone, or seismic chimney, is clearly observed on seismic profiles, and it is interpreted to be a fluid conduit. A thick low velocity zone beneath BSR suggests the presence of a gas reservoir there. This "gas reservoir" is shallower than the surrounding canyon floors along the ridge; therefore as warm methane-rich fluids inside the ridge migrate upward, sulfate carried by cold sea water can flow into the fluid system from both flanks of the ridge. This process may drive a fluid circulation system and the active cold seep site which emits both hydrogen sulfide and methane to feed the chemosynthetic communities.

Effects of ocean acidification on the shells of four Mediterranean gastropod species near a CO2 seep.

Science.gov (United States)

Duquette, Ashley; McClintock, James B; Amsler, Charles D; Pérez-Huerta, Alberto; Milazzo, Marco; Hall-Spencer, Jason M

2017-11-30

Marine CO 2 seeps allow the study of the long-term effects of elevated pCO 2 (ocean acidification) on marine invertebrate biomineralization. We investigated the effects of ocean acidification on shell composition and structure in four ecologically important species of Mediterranean gastropods (two limpets, a top-shell snail, and a whelk). Individuals were sampled from three sites near a volcanic CO 2 seep off Vulcano Island, Italy. The three sites represented ambient (8.15pH), moderate (8.03pH) and low (7.73pH) seawater mean pH. Shell mineralogy, microstructure, and mechanical strength were examined in all four species. We found that the calcite/aragonite ratio could vary and increased significantly with reduced pH in shells of one of the two limpet species. Moreover, each of the four gastropods displayed reductions in either inner shell toughness or elasticity at the Low pH site. These results suggest that near-future ocean acidification could alter shell biomineralization and structure in these common gastropods. Copyright © 2017 Elsevier Ltd. All rights reserved.

The microbial ferrous wheel in a neutral pH groundwater seep

Directory of Open Access Journals (Sweden)

Eric eRoden

2012-05-01

Full Text Available Evidence for microbial Fe redox cycling was documented in a circumneutral pH groundwater seep near Bloomington, Indiana. Geochemical and microbiological analyses were conducted at two sites, a semi-consolidated microbial mat and a floating puffball structure. In situ voltammetric microelectrode measurements revealed steep opposing gradients of O2 and Fe(II at both sites, similar to other groundwater seep and sedimentary environments known to support microbial Fe redox cycling. The puffball structure showed an abrupt increase in dissolved Fe(II just at its surface (~ 5 cm depth, suggesting an internal Fe(II source coupled to active Fe(III reduction. MPN enumerations detected microaerophilic Fe(II-oxidizing bacteria (FeOB and dissimilatory Fe(III-reducing bacteria (FeRB at densities of 102-105 cells mL-1 in samples from both sites. In vitro Fe(III reduction experiments revealed the potential for immediate reduction (no lag period of native Fe(III oxides. Conventional full-length 16S rRNA gene clone libraries were compared withhigh throughput barcode sequencing of the V1, V4 or V6 variable regions of 16S rRNA genes in order to evaluate the extent to which new sequencing approaches could provide enhanced insight into the composition of Fe redox cycling microbial community structure. The composition of the clone libraries suggested a lithotroph-dominated microbial community centered around taxa related to known FeOB (e.g. Gallionella, Sideroxydans, Aquabacterium. Sequences related to recognized FeRB (e.g. Rhodoferax, Aeromonas, Geobacter, Desulfovibrio were also well represented. Overall, sequences related to known FeOB and FeRB accounted for 88 and 59% of total clone sequences in the mat and puffball libraries, respectively. Taxa identified in the barcode libraries showed partial overlap with the clone libraries, but were not always consistent across different variable regions and sequencing platforms. However, the barcode libraries provided

Mass transfer between waste canister and water seeping in rock fractures. Revisiting the Q-equivalent model

International Nuclear Information System (INIS)

Neretnieks, Ivars; Liu Longcheng; Moreno, Luis

2010-03-01

Models are presented for solute transport between seeping water in fractured rock and a copper canister embedded in a clay buffer. The migration through an undamaged buffer is by molecular diffusion only as the clay has so low hydraulic conductivity that water flow can be neglected. In the fractures and in any damaged zone seeping water carries the solutes to or from the vicinity of the buffer in the deposition hole. During the time the water passes the deposition hole molecular diffusion aids in the mass transfer of solutes between the water/buffer interface and the water at some distance from the interface. The residence time of the water and the contact area between the water and the buffer determine the rate of mass transfer between water and buffer. Simple analytical solutions are presented for the mass transfer in the seeping water. For complex migration geometries simplifying assumptions are made that allow analytical solutions to be obtained. The influence of variable apertures on the mass transfer is discussed and is shown to be moderate. The impact of damage to the rock around the deposition hole by spalling and by the presence of a cemented and fractured buffer is also explored. These phenomena lead to an increase of mass transfer between water and buffer. The overall rate of mass transfer between the bulk of the water and the canister is proportional to the overall concentration difference and inversely proportional to the sum of the mass transfer resistances. For visualization purposes the concept of equivalent flowrate is introduced. This entity can be thought as of the flowrate of water that will be depleted of its solute during the water passage past the deposition hole. The equivalent flowrate is also used to assess the release rate of radionuclides from a damaged canister. Examples are presented to illustrate how various factors influence the rate of mass transfer

Seasonal monitoring of deep-sea megabenthos in Barkley Canyon cold seep by internet operated vehicle (IOV.

Directory of Open Access Journals (Sweden)

Carolina Doya

Full Text Available Knowledge of the processes shaping deep-sea benthic communities at seasonal scales in cold-seep environments is incomplete. Cold seeps within highly dynamic regions, such as submarine canyons, where variable current regimes may occur, are particularly understudied. Novel Internet Operated Vehicles (IOVs, such as tracked crawlers, provide new techniques for investigating these ecosystems over prolonged periods. In this study a benthic crawler connected to the NEPTUNE cabled infrastructure operated by Ocean Networks Canada was used to monitor community changes across 60 m2 of a cold-seep area of the Barkley Canyon, North East Pacific, at ~890 m depth within an Oxygen Minimum Zone (OMZ. Short video-transects were run at 4-h intervals during the first week of successive calendar months, over a 14 month period (February 14th 2013 to April 14th 2014. Within each recorded transect video megafauna abundances were computed and changes in environmental conditions concurrently measured. The responses of fauna to environmental conditions as a proxy of seasonality were assessed through analysis of abundances in a total of 438 video-transects (over 92 h of total footage. 7698 fauna individuals from 6 phyla (Cnidaria, Ctenophora, Arthropoda, Echinodermata, Mollusca, and Chordata were logged and patterns in abundances of the 7 most abundant taxa (i.e. rockfish Sebastidae, sablefish Anoplopoma fimbria, hagfish Eptatretus stoutii, buccinids (Buccinoidea, undefined small crabs, ctenophores Bolinopsis infundibulum, and Scyphomedusa Poralia rufescens were identified. Patterns in the reproductive behaviour of the grooved tanner crab (Chionnecetes tanneri were also indicated. Temporal variations in biodiversity and abundance in megabenthic fauna was significantly influenced by variabilities in flow velocity flow direction (up or down canyon, dissolved oxygen concentration and month of study. Also reported here for the first time are transient mass aggregations of

Heavy-ion microscopy

International Nuclear Information System (INIS)

Kraft, G.; Yang, T.C.H.; Richards, T.; Tobias, C.A.

1980-01-01

This chapter briefly describes the techniques of optical microscopy, scanning and transmission electron microscopy, soft x-ray microscopy and compares these latter techniques with heavy-ion microscopy. The resolution obtained with these various types of microscopy are compared and the influence of the etching procedure on total resolution is discussed. Several micrographs of mammalian cells are included

Diversity and distribution of eukaryotic microbes in and around a brine pool adjacent to the Thuwal cold seeps in the Red Sea

KAUST Repository

Wang, Yong; Zhang, Wei Peng; Cao, Hui Luo; Shek, Chun Shum; Tian, Ren Mao; Wong, Yue Him; Batang, Zenon B.; Al-Suwailem, Abdulaziz M.; Qian, Pei-Yuan

2014-01-01

abundant species highly similar to invertebrate gregarine parasites identified in different oxygen-depleted sediments. Therefore, the present findings support the uniqueness of some microbial eukaryotic groups in this cold seep brine system. 2014 Wang

Deep Sequencing of Myxilla (Ectyomyxilla) methanophila, an Epibiotic Sponge on Cold-Seep Tubeworms, Reveals Methylotrophic, Thiotrophic, and Putative Hydrocarbon-Degrading Microbial Associations

KAUST Repository

Arellano, Shawn M.; Lee, Onon; Lafi, Feras Fawzi; Yang, Jiangke; Wang, Yong; Young, Craig; Qian, Peiyuan

2012-01-01

The encrusting sponge Myxilla (Ectyomyxilla) methanophila (Poecilosclerida: Myxillidae) is an epibiont on vestimentiferan tubeworms at hydrocarbon seeps on the upper Louisiana slope of the Gulf of Mexico. It has long been suggested that this sponge

A Permian methane seep system as a paleoenvironmental analogue for the pre-metazoan carbonate platforms

Directory of Open Access Journals (Sweden)

Lucas Veríssimo Warren

Full Text Available ABSTRACT: Following the rise of metazoans, the beginning of bioclasticity and substrate competition, the saga of microbial mats was in a fluctuating decline in the end of the Neoproterozoic era. Increases in diversity during the Phanerozoic and punctual upturns in the microbial carbonate production occured after the events of global mass extinctions. Gradually along the Phanerozoic, the microbial colonies occupied isolated niches and grazers-free environments, characterized by physically and/or geochemically stressful conditions, such as those found in saline bays, alkaline lakes and hydrothermal or cold seep vents. Here we report one of the oldest occurrences of a vent camp coupled with cold seepage of methane in the geologic record, associated with well-preserved microbialites and elephant skin structures. During the seep activity, oxygen depletion and high salinity conditions are prohibitive for complex animal life, clearing the way to microbial colonies to flourish. Due to the co-occurrence of high adaptability and low competitiveness of microbial forms, they became highly specialized in stressful conditions. We argue that the sporadic microbial mat upturns in Earth’s history are not restricted to geological periods, following massive death of metazoan species; they also may occur in response to punctual paleoenvironmental conditions that enable microbial colonies to growth. Indeed, the Phanerozoic geological record is punctuated of these examples, in a kind of hide-and-seek game of Precambrian times.

Seeping Deficit Thinking Assumptions Maintain the Neoliberal Education Agenda: Exploring Three Conceptual Frameworks of Deficit Thinking in Inner-City Schools

Science.gov (United States)

Sharma, Manu

2018-01-01

This article draws awareness to the subtle and seeping "common sense" mentality of neoliberalism and deficit thinking assumptions about racially marginalized students in inner-city schools. From a literature review conducted on deficit thinking and deficit practices in schools, I developed three different frameworks for understanding the…

A giant oil seep at a salt-induced escarpment of the São Paulo Plateau, Espírito Santo Basin, off Brazil: Host rock characteristics and geochemistry

Science.gov (United States)

Freire, Antonio Fernando Menezes; Iemini, Juliana Andrade; Viana, Adriano Roessler; Magnavita, Luciano Portugal; Dehler, Nolan Maia; Kowsmann, Renato Oscar; Miller, Dennis James; Bezerra, Sabrina Helena Diniz Gilaberte; Zerfass, Geise de Santana dos Anjos; Shimabukuro, Seirin; Nóbrega, Marcos, II

2017-12-01

An international research cruise named Iatá-Piuna took place on the São Paulo Plateau on May 2013 in the Campos and Espírito Santo basins, off Brazil. The cruise was carried ou on board the research vessel (R/V) Yokosuka that hosts the human operated vehicle (HOV) SHINKAI 6500. It aimed at finding chemosynthetic communities, composed of organisms capable of generating their own vital energy by metabolizing organic and inorganic compounds related to seeps. Identification of these organisms could provide information for understanding the origin of life, since they may resemble primitive organisms that existed in the initial stages of life on Earth. During Leg 2 (May 10-24, 2013), however, dives on the northern part of the São Paulo Plateau at the Espírito Santo Basin led to the discovery of a giant oil seep. The seep, ca. 3 nautical miles (ca. 5.6 km) in length is located along an outcrop of Eocene rocks on a salt-induced escarpment of the plateau and at a water depth of ca. 2700 m. The 200 m relief of the seafloor suggests that the seep takes place along an active fault system driven by salt diapirism. The oil was analyzed and identified as a severely biodegraded marine oil, generated by carbonate rocks within a minibasin located to the east of the escarpment. This represents valuable exploratory information because it proves that an active petroleum system is present in the context of minibasins associated with salt diapirism in the area.

Cold-seep-like macrofaunal communities in organic- and sulfide-rich sediments of the Congo deep-sea fan

Science.gov (United States)

Olu, K.; Decker, C.; Pastor, L.; Caprais, J.-C.; Khripounoff, A.; Morineaux, M.; Ain Baziz, M.; Menot, L.; Rabouille, C.

2017-08-01

Methane-rich fluids arising from organic matter diagenesis in deep sediment layers sustain chemosynthesis-based ecosystems along continental margins. This type of cold seep develops on pockmarks along the Congo margin, where fluids migrate from deep-buried paleo-channels of the Congo River, acting as reservoirs. Similar ecosystems based on shallow methane production occur in the terminal lobes of the present-day Congo deep-sea fan, which is supplied by huge quantities of primarily terrestrial material carried by turbiditic currents along the 800 km channel, and deposited at depths of up to nearly 5000 m. In this paper, we explore the effect of this carbon enrichment of deep-sea sediments on benthic macrofauna, along the prograding lobes fed by the current active channel, and on older lobes receiving less turbiditic inputs. Macrofaunal communities were sampled using either USNEL cores on the channel levees, or ROV blade cores in the chemosynthesis-based habitats patchily distributed in the active lobe complex. The exceptionally high organic content of the surface sediment in the active lobe complex was correlated with unusual densities of macrofauna for this depth, enhanced by a factor 7-8, compared with those of the older, abandoned lobe, whose sediment carbon content is still higher than in Angola Basin at same depth. Macrofaunal communities, dominated by cossurid polychaetes and tanaids were also more closely related to those colonizing low-flow cold seeps than those of typical deep-sea sediment. In reduced sediments, microbial mats and vesicomyid bivalve beds displayed macrofaunal community patterns that were similar to their cold-seep counterparts, with high densities, low diversity and dominance of sulfide-tolerant polychaetes and gastropods in the most sulfidic habitats. In addition, diversity was higher in vesicomyid bivalve beds, which appeared to bio-irrigate the upper sediment layers. High beta-diversity is underscored by the variability of geochemical

Microsensor studies on Padina from a natural CO2 seep: implications of morphology on acclimation to low pH.

Science.gov (United States)

Hofmann, Laurie C; Fink, Artur; Bischof, Kai; de Beer, Dirk

2015-12-01

Low seawater pH can be harmful to many calcifying marine organisms, but the calcifying macroalgae Padina spp. flourish at natural submarine carbon dioxide seeps where seawater pH is low. We show that the microenvironment created by the rolled thallus margin of Padina australis facilitates supersaturation of CaCO3 and calcifi-cation via photosynthesis-induced elevated pH. Using microsensors to investigate oxygen and pH dynamics in the microenvironment of P. australis at a shallow CO2 seep, we found that, under saturating light, the pH inside the microenvironment (pHME ) was higher than the external seawater (pHSW ) at all pHSW levels investigated, and the difference (i.e., pHME - pHSW ) increased with decreasing pHSW (0.9 units at pHSW 7.0). Gross photosynthesis (Pg ) inside the microenvironment increased with decreasing pHSW , but algae from the control site reached a threshold at pH 6.5. Seep algae showed no pH threshold with respect to Pg within the pHSW range investigated. The external carbonic anhydrase (CA) inhibitor, acetazolamide, strongly inhibited Pg of P. australis at pHSW 8.2, but the effect was diminished under low pHSW (6.4-7.5), suggesting a greater dependence on membrane-bound CA for the dehydration of HCO3 (-) ions during dissolved inorganic carbon uptake at the higher pHSW . In comparison, a calcifying green alga, Halimeda cuneata f. digitata, was not inhibited by AZ, suggesting efficient bicarbonate transport. The ability of P. australis to elevate pHME at the site of calcification and its strong dependence on CA may explain why it can thrive at low pHSW . © 2015 Phycological Society of America.

Identification of Novel Methane-, Ethane-, and Propane-Oxidizing Bacteria at Marine Hydrocarbon Seeps by Stable Isotope Probing ▿ †

Science.gov (United States)

Redmond, Molly C.; Valentine, David L.; Sessions, Alex L.

2010-01-01

Marine hydrocarbon seeps supply oil and gas to microorganisms in sediments and overlying water. We used stable isotope probing (SIP) to identify aerobic bacteria oxidizing gaseous hydrocarbons in surface sediment from the Coal Oil Point seep field located offshore of Santa Barbara, California. After incubating sediment with 13C-labeled methane, ethane, or propane, we confirmed the incorporation of 13C into fatty acids and DNA. Terminal restriction fragment length polymorphism (T-RFLP) analysis and sequencing of the 16S rRNA and particulate methane monooxygenase (pmoA) genes in 13C-DNA revealed groups of microbes not previously thought to contribute to methane, ethane, or propane oxidation. First, 13C methane was primarily assimilated by Gammaproteobacteria species from the family Methylococcaceae, Gammaproteobacteria related to Methylophaga, and Betaproteobacteria from the family Methylophilaceae. Species of the latter two genera have not been previously shown to oxidize methane and may have been cross-feeding on methanol, but species of both genera were heavily labeled after just 3 days. pmoA sequences were affiliated with species of Methylococcaceae, but most were not closely related to cultured methanotrophs. Second, 13C ethane was consumed by members of a novel group of Methylococcaceae. Growth with ethane as the major carbon source has not previously been observed in members of the Methylococcaceae; a highly divergent pmoA-like gene detected in the 13C-labeled DNA may encode an ethane monooxygenase. Third, 13C propane was consumed by members of a group of unclassified Gammaproteobacteria species not previously linked to propane oxidation. This study identifies several bacterial lineages as participants in the oxidation of gaseous hydrocarbons in marine seeps and supports the idea of an alternate function for some pmoA-like genes. PMID:20675448

Seeps and springs sampling and analysis plant for the Environmental Monitoring Plan at Waste Area Grouping 6, Oak Ridge National Laboratory, Oak Ridge, Tennessee

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-09-01

This Sampling and Analysis Plan addresses the monitoring, sampling, and analysis activities that will be conducted at seeps and springs and at two french drain outlets in support of the Environmental Monitoring Plan for Waste Area Grouping (WAG) 6. WAG 6 is a shallow-land-burial disposal facility for low-level radioactive waste at Oak Ridge National Laboratory, a research facility owned by the U.S. Department of Energy and operated by Lockheed Martin Energy System, Inc. Initially, sampling will be conducted at as many as 15 locations within WAG 6 (as many as 13 seeps and 2 french drain outlets). After evaluating the results obtained and reviewing the observations made by field personnel during the first round of sampling, several seeps and springs will be chosen as permanent monitoring points, together with the two french drain outlets. Baseline sampling of these points will then be conducted quarterly for 1 year (i.e., four rounds of sampling after the initial round). The samples will be analyzed for various geochemical, organic, inorganic, and radiological parameters. Permanent sampling points having suitable flow rates and conditions may be outfitted with automatic flow-monitoring equipment. The results of the sampling and flow-monitoring efforts will help to quantify flux moving across the ungauged perimeter of the site and will help to identify changes in releases from the contaminant sources.

Seeps and springs sampling and analysis plant for the Environmental Monitoring Plan at Waste Area Grouping 6, Oak Ridge National Laboratory, Oak Ridge, Tennessee

International Nuclear Information System (INIS)

1995-09-01

This Sampling and Analysis Plan addresses the monitoring, sampling, and analysis activities that will be conducted at seeps and springs and at two french drain outlets in support of the Environmental Monitoring Plan for Waste Area Grouping (WAG) 6. WAG 6 is a shallow-land-burial disposal facility for low-level radioactive waste at Oak Ridge National Laboratory, a research facility owned by the U.S. Department of Energy and operated by Lockheed Martin Energy System, Inc. Initially, sampling will be conducted at as many as 15 locations within WAG 6 (as many as 13 seeps and 2 french drain outlets). After evaluating the results obtained and reviewing the observations made by field personnel during the first round of sampling, several seeps and springs will be chosen as permanent monitoring points, together with the two french drain outlets. Baseline sampling of these points will then be conducted quarterly for 1 year (i.e., four rounds of sampling after the initial round). The samples will be analyzed for various geochemical, organic, inorganic, and radiological parameters. Permanent sampling points having suitable flow rates and conditions may be outfitted with automatic flow-monitoring equipment. The results of the sampling and flow-monitoring efforts will help to quantify flux moving across the ungauged perimeter of the site and will help to identify changes in releases from the contaminant sources

Biogeochemistry of a submerged groundwater seep ecosystem in Lake Huron near karst region of Alpena, MI

Science.gov (United States)

Kinsman-Costello, L. E.; Dick, G.; Sheik, C.; Burton, G. A.; Sheldon, N. D.

2015-12-01

Submerged groundwater seeps in Lake Huron establish ecosystems with distinctive geochemical conditions. In the Middle Island Sinkhole (MIS), a 23-m deep seep, groundwater seepage establishes low O2 (< 4 mg L-1), high sulfate (6 mM) conditions, in which a purple cyanobacteria-dominated mat thrives. The mat is capable of anoxygenic photosynthesis, oxygenic photosynthesis, and chemosynthesis. Within the top 3 cm of the mat-water interface, hydrogen sulfide concentrations increase to 1-7 mM. Little is known about the structure and function of microbes within organic-rich, high-sulfide sediments beneath the mat. Using pore water and sediment geochemical characterization along with microbial community analysis, we elucidated relationships between microbial community structure and ecosystem function along vertical gradients. In sediment pore waters, biologically reactive solutes (SO42-, NH4+, PO43-, and CH4) displayed steep vertical gradients, reflecting biological and geochemical functioning. In contrast, more conservative ions (Ca+2, Mg+2, Na+, and Cl-), did not change significantly with depth in MIS sediments, indicating groundwater influence in the sediment profile. MIS sediments contained more organic matter than typical Lake Huron sediments, and were generally higher in nutrients, metals, and sulfur (acid volatile sulfide). Using the Illumina MiSeq platform we detected 14,127 unique operational taxonomic units across sediment and surface mat samples. Microbial community composition in the MIS was distinctly different from non-groundwater affected areas at similar depth nearby in Lake Huron (ANOSIM, R= 0.74, p=0.002). MIS sediment communities were more diverse that MIS surface mat communities and changed with depth into sediments. MIS sediment community composition was related to several geochemical variables, including organic matter and multiple indicators of phosphorus availability. Elucidating the structure and function of microbial consortia in MIS, a highly

E/V Nautilus Detection of Isolated Features in the Eastern Pacific Ocean: Newly Discovered Calderas and Methane Seeps

Science.gov (United States)

Raineault, N.; Irish, O.; Lubetkin, M.

2016-02-01

The E/V Nautilus mapped over 80,000 km2 of the seafloor in the Gulf of Mexico and Eastern Pacific Ocean during its 2015 expedition. The Nautilus used its Kongsberg EM302 multibeam system to map the seafloor prior to remotely operated vehicle (ROV) dives, both for scientific purposes (site selection) and navigational safety. The Nautilus also routinely maps during transits to identify previously un-mapped or unresolved seafloor features. During its transit from the Galapagos Islands to the California Borderland, the Nautilus mapped 44,695 km2 of seafloor. Isolated features on the seafloor and in the water-column, such as calderas and methane seeps, were detected during this data collection effort. Operating at a frequency of 30 kHz in waters ranging from 1000-5500 m, we discovered caldera features off the coast of Central America. Since seamounts are known hotspots of biodiversity, locating new ones may enrich our understanding of seamounts as "stepping stones" for species distribution and ocean current pathways. Satellite altimetry datasets prior to this data either did not discern these calderas or recognized the presence of a bathymetric high without great detail. This new multibeam bathymetry data, gridded at 50 m, gives a precise look at these seamounts that range in elevation from 350 to 1400 m from abyssal depth. The largest of the calderas is circular in shape and is 10,000 m in length and 5,000 m in width, with a distinct circular depression at the center of its highest point, 1,400 m above the surrounding abyssal depth. In the California Borderland region, located between San Diego and Los Angeles, four new seeps were discovered in water depths from 400-1,020 m. ROV exploration of these seeps revealed vent communities. Altogether, these discoveries reinforce how little we know about the global ocean, indicate the presence of isolated deep-sea ecosystems that support biologically diverse communities, and will impact our understanding of seafloor habitat.

Analysis of past recurrent methane seep activity using radiocarbon dating of Calyptogena spp. shells in the eastern Nankai subduction zone, Japan

Science.gov (United States)

Yagasaki, Kazuhiro; Ashi, Juichiro; Yokoyama, Yusuke; Miyairi, Yosuke; Kuramoto, Shin'ichi

2016-04-01

Fault activity around subduction zones have been widely studied and monitored through drilling of oceanic plates, studying piston cores, use of monitoring equipment or through visual analysis using submersible vehicles. Yet the understanding of how small scale faults near shallow regions of the seabed behave in relation to cold seep vent activity is still vague, especially determining when they were active in the past. In tectonically active margins such as the Nankai and Tokai regions off Japan, dense methane hydrate reservoirs have been identified. Cold seeps releasing methane rich hydrocarbon fluids are common here, supporting a wide variety of biological species that hold a symbiotic relationship with the chemosynthetic bacteria. In 1998 a large dead Calyptogena spp. bivalve colony (over 400m2 in size) was discovered off Tokai, Japan. It is unusual for a bivalve colony this size to mostly be dead, raising questions as to what caused their death. In this study we document the radiocarbon 14C age of these bivalve shells to attempt analysing the possible methane seep bahaviour in the past. The measured 14C age ranged in three age groups of 1396±36-1448±34, 1912±31-1938±35 and 5975±34. The 14C age of shells that were alive upon collection and the dissolved inorganic carbon (DIC) in seawater show little difference (˜100 14C age) indicating that shells are not heavily affected by the dead carbon effect from cold seeps that is of biogenic or thermogenic origin, which can make the age to become considerably older than the actual age. Thus the novel calibration model used was based on the seawater DIC collected above the Calyptogena spp. colony site (1133±31), which resulted in the dead shells to be clustered around 1900 Cal AD. This proves to be interesting as the predicted epicenter of the Ansei-Tokai earthquake (M 8.4) in 1854 is extremely close to the bibalve colony site. Using geological data obtained using visual analysis and sub-seafloor structural

Seeps and springs sampling and analysis plan for the environmental monitoring plan for Waste Area Grouping 6 at Oak Ridge National Laboratory, Oak Ridge, Tennessee

Energy Technology Data Exchange (ETDEWEB)

1994-08-01

This Sampling and Analysis Plan addresses the monitoring, sampling, and analysis activities that will be conducted at seeps and springs and at two french drain outlets in support of the Environmental Monitoring Plan for Waste Area Grouping (WAG) 6. WAG 6 is a shallow-land-burial disposal facility for low-level radioactive waste at Oak Ridge National Laboratory, a research facility owned by the US Department of Energy and operated by Martin Marietta Energy Systems, Inc. Initially, sampling will be conducted at as many as 15 locations within WAG 6 (as many as 13 seeps and 2 french drain outlets). After evaluating the results obtained and reviewing the observations made by field personnel during the first round of sampling, several seeps and springs will be chosen as permanent monitoring points, together with the two french drain outlets. Baseline sampling of these points will then be conducted quarterly for 1 year (i.e., four rounds of sampling after the initial round). The samples will be analyzed for various geochemical, organic, inorganic, and radiological parameters. Permanent sampling points having suitable flow rates and conditions may be outfitted with automatic flow-monitoring equipment. The results of the sampling and flow-monitoring efforts will help to quantify flux moving across the ungauged perimeter of the site and will help to identify changes in releases from the contaminant sources.

Seeps and springs sampling and analysis plan for the environmental monitoring plan for Waste Area Grouping 6 at Oak Ridge National Laboratory, Oak Ridge, Tennessee

International Nuclear Information System (INIS)

1994-08-01

This Sampling and Analysis Plan addresses the monitoring, sampling, and analysis activities that will be conducted at seeps and springs and at two french drain outlets in support of the Environmental Monitoring Plan for Waste Area Grouping (WAG) 6. WAG 6 is a shallow-land-burial disposal facility for low-level radioactive waste at Oak Ridge National Laboratory, a research facility owned by the US Department of Energy and operated by Martin Marietta Energy Systems, Inc. Initially, sampling will be conducted at as many as 15 locations within WAG 6 (as many as 13 seeps and 2 french drain outlets). After evaluating the results obtained and reviewing the observations made by field personnel during the first round of sampling, several seeps and springs will be chosen as permanent monitoring points, together with the two french drain outlets. Baseline sampling of these points will then be conducted quarterly for 1 year (i.e., four rounds of sampling after the initial round). The samples will be analyzed for various geochemical, organic, inorganic, and radiological parameters. Permanent sampling points having suitable flow rates and conditions may be outfitted with automatic flow-monitoring equipment. The results of the sampling and flow-monitoring efforts will help to quantify flux moving across the ungauged perimeter of the site and will help to identify changes in releases from the contaminant sources

Lower Carboniferous Siderites: A Product of Bottom Seeps and Bacterial Metanogenesis (Subpolar Urals)

Science.gov (United States)

Antoshkina, A. I.; Ryabinkina, N. N.

2018-02-01

Complex modern micro- and spectroscopic methods for study of siderite concretions in the Lower Carboniferous terrigenous strata on the Kozhym River (Subpolar Urals) have shown that its formation was caused by destruction of clay minerals due to the activity of bacterial communities. The abundance of these bacteria was caused by gas-fluid seeps and bacterial methanogenesis processes in bottom deposits. In basins with normal marine fauna, this led to local desalination, hydrogen sulfide contamination, mass collapse of primary organisms, and the development of element-specific bacteria. The occurrence of these bacteria caused the formation of specific authigenic mineralization in the concretion of sideritic bacteriolites: the framboidal pyrite, sphalerite, galenite, barite, sulfoselenides, and tellurides.

Genomic and Transcriptomic Evidence for Carbohydrate Consumption Among Microorganisms in a Cold Seep Brine Pool

Directory of Open Access Journals (Sweden)

Weipeng Zhang

2016-11-01

Full Text Available The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation. These genes included various glycoside hydrolases, nitrate and sulfate reductases, putative bacterial microcompartment biosynthetic clusters (BMC, and F420H2 dehydrogenases. Phylogenetic analysis suggested that the acquisition of these genes probably occurred through horizontal gene transfer (HGT. Metatranscriptomics illustrated that glycoside hydrolases are among the most highly expressed genes. Our results suggest that the microbial inhabitants are well adapted to this brine environment, and anaerobic carbohydrate consumption mediated by glycoside hydrolases and electron transport systems (ETSs is a dominant process performed by microorganisms from various phyla within this ecosystem.

Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool

KAUST Repository

Zhang, Weipeng

2016-11-15

The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation. These genes included various glycoside hydrolases, nitrate and sulfate reductases, putative bacterial microcompartment biosynthetic clusters (BMC), and F420H2 dehydrogenases. Phylogenetic analysis suggested that the acquisition of these genes probably occurred through horizontal gene transfer (HGT). Metatranscriptomics illustrated that glycoside hydrolases are among the most highly expressed genes. Our results suggest that the microbial inhabitants are well adapted to this brine environment, and anaerobic carbohydrate consumption mediated by glycoside hydrolases and electron transport systems (ETSs) is a dominant process performed by microorganisms from various phyla within this ecosystem.

Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting

KAUST Repository

Zhang, Weipeng; Tian, Renmao; Yang, Bo; Cao, Huiluo; Cai, Lin; Chen, Lianguo; Zhou, Guowei; Sun, Jingya; Zhang, Xixiang; Al-Suwailem, Abdulaziz M.; Qian, Pei-Yuan

2015-01-01

The functional basis for species sorting theory remains elusive, especially for microbial community assembly in deep sea environments. Using artificial surface-based biofilm models, our recent work revealed taxonomic succession during biofilm development in a newly defined cold seep system, the Thuwal cold seeps II, which comprises a brine pool and the adjacent normal bottom water (NBW) to form a metacommunity via the potential immigration of organisms from one patch to another. Here, we designed an experiment to investigate the effects of environmental switching between the brine pool and the NBW on biofilm assembly, which could reflect environmental filtering effects during bacterial immigration to new environments. Analyses of 16S rRNA genes of 71 biofilm samples suggested that the microbial composition of biofilms established in new environments was determined by both the source community and the incubation conditions. Moreover, a comparison of 18 metagenomes provided evidence for biofilm community assembly that was based primarily on functional features rather than taxonomic identities; metal ion resistance and amino acid metabolism were the major species sorting determinants for the succession of biofilm communities. Genome binning and pathway reconstruction of two bacterial species (Marinobacter sp. and Oleispira sp.) further demonstrated metal ion resistance and amino acid metabolism as functional traits conferring the survival of habitat generalists in both the brine pool and NBW. The results of the present study sheds new light on microbial community assembly in special habitats and bridges a gap in species sorting theory.

Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting

KAUST Repository

Zhang, Weipeng

2015-11-28

The functional basis for species sorting theory remains elusive, especially for microbial community assembly in deep sea environments. Using artificial surface-based biofilm models, our recent work revealed taxonomic succession during biofilm development in a newly defined cold seep system, the Thuwal cold seeps II, which comprises a brine pool and the adjacent normal bottom water (NBW) to form a metacommunity via the potential immigration of organisms from one patch to another. Here, we designed an experiment to investigate the effects of environmental switching between the brine pool and the NBW on biofilm assembly, which could reflect environmental filtering effects during bacterial immigration to new environments. Analyses of 16S rRNA genes of 71 biofilm samples suggested that the microbial composition of biofilms established in new environments was determined by both the source community and the incubation conditions. Moreover, a comparison of 18 metagenomes provided evidence for biofilm community assembly that was based primarily on functional features rather than taxonomic identities; metal ion resistance and amino acid metabolism were the major species sorting determinants for the succession of biofilm communities. Genome binning and pathway reconstruction of two bacterial species (Marinobacter sp. and Oleispira sp.) further demonstrated metal ion resistance and amino acid metabolism as functional traits conferring the survival of habitat generalists in both the brine pool and NBW. The results of the present study sheds new light on microbial community assembly in special habitats and bridges a gap in species sorting theory.

Characterization of Methane-Seep Communities in a Deep-Sea Area Designated for Oil and Natural Gas Exploitation Off Trinidad and Tobago

Directory of Open Access Journals (Sweden)

Diva J. Amon

2017-10-01

Full Text Available Exploration of the deep ocean (>200 m is taking on added importance as human development encroaches. Despite increasing oil and natural gas exploration and exploitation, the deep ocean of Trinidad and Tobago is almost entirely unknown. The only scientific team to image the deep seafloor within the Trinidad and Tobago Exclusive Economic Zone was from IFREMER in the 1980s. That exploration led to the discovery of the El Pilar methane seeps and associated chemosynthetic communities on the accretionary prism to the east of Trinidad and Tobago. In 2014, the E/V Nautilus, in collaboration with local scientists, visited two previously sampled as well as two unexplored areas of the El Pilar site between 998 and 1,629 m depth using remotely operated vehicles. Eighty-three megafaunal morphospecies from extensive chemosynthetic communities surrounding active methane seepage were observed at four sites. These communities were dominated by megafaunal invertebrates including mussels (Bathymodiolus childressi, shrimp (Alvinocaris cf. muricola, Lamellibrachia sp. 2 tubeworms, and Pachycara caribbaeum. Adjacent to areas of active seepage was an ecotone of suspension feeders including Haplosclerida sponges, stylasterids and Neovermilia serpulids on authigenic carbonates. Beyond this were large Bathymodiolus shell middens. Finally there was either a zone of sparse octocorals and other non-chemosynthetic species likely benefiting from the carbonate substratum and enriched production within the seep habitat, or sedimented inactive areas. This paper highlights these ecologically significant areas and increases the knowledge of the biodiversity of the Trinidad and Tobago deep ocean. Because methane seepage and chemosynthetic communities are related to the presence of extractable oil and gas resources, development of best practices for the conservation of biodiversity in Trinidad and Tobago waters within the context of energy extraction is critical. Potential impacts

Diversity and composition of the copepod communities associated with megafauna around a cold seep in the Gulf of Mexico with remarks on species biogeography

NARCIS (Netherlands)

Plum, C.; Gollner, S.; Martinez Arbizu, P.; Bright, M.

2015-01-01

In order to characterize the copepod communitiesassociated with tubeworm and mussel aggregations around ahydrocarbon seep in the Green Canyon of the Gulf of Mexico,diversity, abundance, and community composition were analyzed.Also analyzed were species biogeography and the potentialconnectivity to

The oceanic geochemistry of artificial radionuclides: The ''SEEP'' project: [Final] progress report for period 1 August 1986-31 July 1987

International Nuclear Information System (INIS)

Sholkovitz, E.R.; Livingston, H.D.

1986-03-01

The objective of the SEEP project was to quantify the biological and geochemical processes controlling the concentration, distribution, flux, and speciation of natural and artificial radionuclides. The focus is on the shelf/slope region. Research was concentrated on the sediment chemistry of plutonium and on the nature of fallout transuranic transport in, and removal from, waters of the US continental margin

Enhanced CO2 uptake at a shallow Arctic Ocean seep field overwhelms the positive warming potential of emitted methane.

Science.gov (United States)

Pohlman, John W; Greinert, Jens; Ruppel, Carolyn; Silyakova, Anna; Vielstädte, Lisa; Casso, Michael; Mienert, Jürgen; Bünz, Stefan

2017-05-23

Continued warming of the Arctic Ocean in coming decades is projected to trigger the release of teragrams (1 Tg = 10 6 tons) of methane from thawing subsea permafrost on shallow continental shelves and dissociation of methane hydrate on upper continental slopes. On the shallow shelves (shallow ebullitive methane seep field on the Svalbard margin reveal atmospheric CO 2 uptake rates (-33,300 ± 7,900 μmol m -2 ⋅d -1 ) twice that of surrounding waters and ∼1,900 times greater than the diffusive sea-air methane efflux (17.3 ± 4.8 μmol m -2 ⋅d -1 ). The negative radiative forcing expected from this CO 2 uptake is up to 231 times greater than the positive radiative forcing from the methane emissions. Surface water characteristics (e.g., high dissolved oxygen, high pH, and enrichment of 13 C in CO 2 ) indicate that upwelling of cold, nutrient-rich water from near the seafloor accompanies methane emissions and stimulates CO 2 consumption by photosynthesizing phytoplankton. These findings challenge the widely held perception that areas characterized by shallow-water methane seeps and/or strongly elevated sea-air methane flux always increase the global atmospheric greenhouse gas burden.

Electron microscopy of surfaces

International Nuclear Information System (INIS)

Venables, J.A.

1981-01-01

Electron beam techniques used to study clean surfaces and surface processes on a microscopic scale are reviewed. Recent experimental examples and possible future developments are discussed. Special emphasis is given to (i) transmission diffraction and microscopy techniques, including atomic imaging; (ii) Auger microscopy on bulk and thin film samples; (iii) secondary electron microscopy, especially low energy secondaries for work-function imaging and photoelectron imaging; and (iv) reflection electron microscopy and diffraction. (orig.)

Dynamics of cell proliferation and apoptosis reflect different life strategies in hydrothermal vent and cold seep vestimentiferan tubeworms.

Science.gov (United States)

Pflugfelder, Bettina; Cary, S Craig; Bright, Monika

2009-07-01

Deep-sea vestimentiferan tubeworms, which live in symbiosis with bacteria, exhibit different life strategies according to their habitat. At unstable and relatively short-lived hydrothermal vents, they grow extremely fast, whereas their close relatives at stable and long-persisting cold seeps grow slowly and live up to 300 years. Growth and age differences are thought to occur because of ecological and physiological adaptations. However, the underlying mechanisms of cell proliferation and death, which are closely linked to homeostasis, growth, and longevity, are unknown. Here, we show by immunohistochemical and ultrastructural cell cycle analyses that cell proliferation activities of the two species studied are higher than in any other characterized invertebrate, being only comparable with tumor and wound-healing processes. The slow growth in Lamellibrachia luymesi from cold seeps results from balanced activities of proliferation and apoptosis in the epidermis. In contrast, Riftia pachyptila from hydrothermal vents grows fast because apoptosis is down-regulated in this tissue. The symbiont-housing organ, the trophosome, exhibits a complex cell cycle and terminal differentiation pattern in both species, and growth is regulated by proliferation. These mechanisms have similarities to the up- and down-regulation of proliferation or apoptosis in various types of tumor, although they occur in healthy animals in this study, thus providing significant insights into the underlying mechanisms of growth and longevity.

Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting.

Science.gov (United States)

Zhang, Weipeng; Tian, Renmao; Bo, Yang; Cao, Huiluo; Cai, Lin; Chen, Lianguo; Zhou, Guowei; Sun, Jin; Zhang, Xixiang; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

2016-05-01

The functional basis for species sorting theory remains elusive, especially for microbial community assembly in deep-sea environments. Using artificial surface-based biofilm models, our recent work revealed taxonomic succession during biofilm development in a newly defined cold seep system, the Thuwal cold seeps II, which comprises a brine pool and the adjacent normal bottom water (NBW) to form a metacommunity via the potential immigration of organisms from one patch to another. Here, we designed an experiment to investigate the effects of environmental switching between the brine pool and the NBW on biofilm assembly, which could reflect environmental filtering effects during bacterial immigration to new environments. Analyses of 16S rRNA genes of 71 biofilm samples suggested that the microbial composition of biofilms established in new environments was determined by both the source community and the incubation conditions. Moreover, a comparison of 18 metagenomes provided evidence for biofilm community assembly that was based primarily on functional features rather than taxonomic identities; metal ion resistance and amino acid metabolism were the major species sorting determinants for the succession of biofilm communities. Genome binning and pathway reconstruction of two bacterial species (Marinobacter sp. and Oleispira sp.) further demonstrated metal ion resistance and amino acid metabolism as functional traits conferring the survival of habitat generalists in both the brine pool and NBW. The results of this study shed new light on microbial community assembly in special habitats and bridge a gap in species sorting theory. © 2015 John Wiley & Sons Ltd.

Interaction between hydrocarbon seepage, chemosynthetic communities, and bottom water redox at cold seeps of the Makran accretionary prism: insights from habitat-specific pore water sampling and modeling

Directory of Open Access Journals (Sweden)

D. Fischer

2012-06-01

Full Text Available The interaction between fluid seepage, bottom water redox, and chemosynthetic communities was studied at cold seeps across one of the world's largest oxygen minimum zones (OMZ located at the Makran convergent continental margin. Push cores were obtained from seeps within and below the core-OMZ with a remotely operated vehicle. Extracted sediment pore water was analyzed for sulfide and sulfate concentrations. Depending on oxygen availability in the bottom water, seeps were either colonized by microbial mats or by mats and macrofauna. The latter, including ampharetid polychaetes and vesicomyid clams, occurred in distinct benthic habitats, which were arranged in a concentric fashion around gas orifices. At most sites colonized by microbial mats, hydrogen sulfide was exported into the bottom water. Where macrofauna was widely abundant, hydrogen sulfide was retained within the sediment.

Numerical modeling of pore water profiles was performed in order to assess rates of fluid advection and bioirrigation. While the magnitude of upward fluid flow decreased from 11 cm yr⁻¹ to <1 cm yr⁻¹ and the sulfate/methane transition (SMT deepened with increasing distance from the central gas orifice, the fluxes of sulfate into the SMT did not significantly differ (6.6–9.3 mol m⁻² yr⁻¹. Depth-integrated rates of bioirrigation increased from 120 cm yr⁻¹ in the central habitat, characterized by microbial mats and sparse macrofauna, to 297 cm yr⁻¹ in the habitat of large and few small vesicomyid clams. These results reveal that chemosynthetic macrofauna inhabiting the outer seep habitats below the core-OMZ efficiently bioirrigate and thus transport sulfate down into the upper 10 to 15 cm of the sediment. In this way the animals deal with the lower upward flux of methane in outer habitats by stimulating rates of anaerobic oxidation of methane (AOM with sulfate high enough to provide

Assessing submarine gas hydrate at active seeps on the Hikurangi Margin, New Zealand, using controlled source electromagnetic data with constraints from seismic, geochemistry, and heatflow data

Science.gov (United States)

Schwalenberg, K.; Haeckel, M.; Pecher, I. A.; Toulmin, S. J.; Hamdan, L. J.; Netzeband, G.; Wood, W.; Poort, J.; Jegen, M. D.; Coffin, R. B.

2009-12-01

Electrical resistivity is one of the key properties useful for evaluating submarine gas hydrate deposits. Gas hydrates are electrically insulating in contrast to the conductive pore fluid. Where they form in sufficient quantities the bulk resistivity of the sub-seafloor is elevated. CSEM data were collected in 2007 as part of the German - International “New Vents” project on R/V Sonne, cruise SO191, at three target areas on the Hikurangi subduction margin, New Zealand. The margin is characterized by widespread bottom simulating reflectors (BSR), seep structures, and active methane and fluid venting indicating the potential for gas hydrate formation. Opouawe Bank is one of the ridge and basin systems on the accretionary wedge and is located off the Wairarapa coast at water depths of 1000-1100 m. The first observed seep sites (North Tower, South Tower, Pukeko, Takahe, and Tui) were identified from individual gas flares in hydro-acoustic data and video observations during voyages on R/V Tangaroa. Seismic reflection data collected during SO191 subsequently identified more than 25 new seep structures. Two intersecting CSEM profiles have been surveyed across North Tower, South Tower, and Takahe. 1-D inversion of the data reveals anomalously high resistivities at North Tower and South Tower, moderately elevated resistivities at Takahe, and normal background resistivities away from the seeps. The high resistivities are attributed to gas hydrate layers at intermediate depths beneath the seeps. At South Tower the hydrate concentration could be possibly as much as 25% of the total sediment volume within a 50m thick layer. This conforms with geochemical pore water analyses which show a trend of increased methane flux towards South Tower. At Takahe, gas pockets and patchy gas hydrate, as well as sediment heterogeneities and carbonates, or temperature driven upward fluid flow indicated by the observed higher heat flow at this site may explain the resistivity pattern

Coordinated motility of cyanobacteria favor mat formation, photosynthesis and carbon burial in low-oxygen, high-sulfur shallow sinkholes of Lake Huron; whereas deep-water aphotic sinkholes are analogs of deep-sea seep and vent ecosystems

Science.gov (United States)

Biddanda, B. A.; McMillan, A. C.; Long, S. A.; Snider, M. J.; Weinke, A. D.; Dick, G.; Ruberg, S. A.

2016-02-01

Microbial life in submerged sinkhole ecosystems of the Laurentian Great Lakes is relatively understudied in comparison to seeps and vents of the deep-sea. We studied the filamentous benthic mat-forming cyanobacteria consisting primarily of Oscillatoria-like cells growing under low-light, low-oxygen and high-sulfur conditions in Lake Huron's submerged sinkholes using in situ observations, in vitro measurements and time-lapse microscopy. Gliding movement of the cyanobacterial trichomes revealed individual as well as group-coordinated motility. When placed in a petri dish and dispersed in ground water from the sinkhole, filaments re-aggregated into defined colonies within minutes. Measured speed of individual filaments ranged from 50 µm minute-1 or 15 body lengths minute-1 to 215 µm minute-1 or 70 body lengths minute-1 - rates that are rapid relative to non-flagellated/ciliated microbes. Filaments exhibited precise and coordinated positive phototaxis towards pinpoints of light and congregated under the light of foil cutouts. Such light-responsive clusters showed an increase in photosynthetic yield - suggesting phototactic motility aids in light acquisition as well as photosynthesis. Pebbles and pieces of broken shells placed upon the mat in intact sediemnt cores were quickly covered by vertically motile filaments within hours and became fully buried in the anoxic sediments over 3-4 diurnal cycles - likely facilitating the preservation of falling plankton debris. Coordinated horizontal and vertical filament motility optimize mat cohesion and dynamics, photosynthetic efficiency and sedimentary carbon burial in modern-day sinkhole habitats where life operates across sharp redox gradients. Analogous cyanobacterial motility in the shallow seas during Earth's early history, may have played a key role in the oxygenation of the planet by optimizing photosynthesis while favoring carbon burial. We are now eagerly mapping and exploring life in deep-water aphotic sinkholes of

Confocal Raman microscopy

CERN Document Server

Dieing, Thomas; Hollricher, Olaf

2018-01-01

This second edition provides a cutting-edge overview of physical, technical and scientific aspects related to the widely used analytical method of confocal Raman microscopy. The book includes expanded background information and adds insights into how confocal Raman microscopy, especially 3D Raman imaging, can be integrated with other methods to produce a variety of correlative microscopy combinations. The benefits are then demonstrated and supported by numerous examples from the fields of materials science, 2D materials, the life sciences, pharmaceutical research and development, as well as the geosciences.

Cold seeps in Monterey Bay, California: Geochemistry of pore waters and relationship to benthic foraminiferal calcite

International Nuclear Information System (INIS)

Gieskes, Joris; Rathburn, Anthony E.; Martin, Jonathan B.; Perez, M. Elena; Mahn, Chris; Bernhard, Joan M.; Day, Shelley

2011-01-01

Highlights: → We describe the geochemistry of pore waters in the Clam Flats area of Monterey Bay. → The geochemical data are compared with the δ 13 C chemistry of benthic foraminifera. → Living foraminifera indicate little effects of pore water low δ 13 C (DIC) in the clam bed. → This phenomenon and its implications are discussed in detail. → Implications with regards to paleo-methane seepage are discussed. - Abstract: An extensive geochemical and biogeochemical examination of CH 4 seeps in the Clam Flats area of Monterey Bay provides insight into the character of relationships between seep geochemistry and benthic foraminiferal geochemistry. The area is characterized by sulfide-rich fluids. Sulfide increases are associated with large increases in alkalinity, as well as small decreases in dissolved Ca and Mg. In addition, only small increases in NH 4 are observed, but values of δ 13 C of dissolved inorganic C are as low as -60 per mille at shallow depths ( 4 , which is transported upward by slow seepage of pore fluids. The geochemistry of the pore fluids should be relevant to the geochemistry of the carbonate tests of living and dead foraminifera. However, a profound disequilibrium of approximately an order of magnitude occurs between the δ 13 C values of stained (cytoplasm-containing) foraminiferal carbonate and the C isotope values of ambient pore water dissolved inorganic C. Reasons are unclear for this isotopic disequilibrium, but have important implications for interpretations of foraminiferal carbonate as a paleoenvironmental proxy. Much fine scale work is needed to fully understand the relationships between the biogeochemistry of benthic foraminifera and the geochemistry of the pore waters where they live.

Microscopy and Image Analysis.

Science.gov (United States)

McNamara, George; Difilippantonio, Michael; Ried, Thomas; Bieber, Frederick R

2017-07-11

This unit provides an overview of light microscopy, including objectives, light sources, filters, film, and color photography for fluorescence microscopy and fluorescence in situ hybridization (FISH). We believe there are excellent opportunities for cytogeneticists, pathologists, and other biomedical readers, to take advantage of specimen optical clearing techniques and expansion microscopy-we briefly point to these new opportunities. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Electron microscopy for Engineers

International Nuclear Information System (INIS)

Jones, I P

2009-01-01

This paper reviews the application of (mainly) Transmission Electron Microscopy (TEM) in an engineering context. The first two sections are TEM and chemical in nature; the final three sections are more general and include aspects of Scanning Electron Microscopy (SEM).

Exploratory Data Analysis of Synthetic Aperture Radar (SAR Measurements to Distinguish the Sea Surface Expressions of Naturally-Occurring Oil Seeps from Human-Related Oil Spills in Campeche Bay (Gulf of Mexico

Directory of Open Access Journals (Sweden)

Gustavo de Araújo Carvalho

2017-12-01

Full Text Available An Exploratory Data Analysis (EDA aims to use Synthetic Aperture Radar (SAR measurements for discriminating between two oil slick types observed on the sea surface: naturally-occurring oil seeps versus human-related oil spills—the use of satellite sensors for this task is poorly documented in scientific literature. A long-term RADARSAT dataset (2008–2012 is exploited to investigate oil slicks in Campeche Bay (Gulf of Mexico. Simple Classification Algorithms to distinguish the oil slick type are designed based on standard multivariate data analysis techniques. Various attributes of geometry, shape, and dimension that describe the oil slick Size Information are combined with SAR-derived backscatter coefficients—sigma-(σo, beta-(βo, and gamma-(γo naught. The combination of several of these characteristics is capable of distinguishing the oil slick type with ~70% of overall accuracy, however, the sole and simple use of two specific oil slick’s Size Information (i.e., area and perimeter is equally capable of distinguishing seeps from spills. The data mining exercise of our EDA promotes a novel idea bridging petroleum pollution and remote sensing research, thus paving the way to further investigate the satellite synoptic view to express geophysical differences between seeped and spilled oil observed on the sea surface for systematic use.

Geomicrobiological linkages between short-chain alkane consumption and sulfate reduction rates in seep sediments.

Directory of Open Access Journals (Sweden)

Arpita eBose

2013-12-01

Full Text Available Marine hydrocarbon seeps are ecosystems that are rich in methane, and, in some cases, short-chain (C2-C5 and longer alkanes. C2-C4 alkanes such as ethane, propane and butane can be significant components of seeping fluids. Some sulfate-reducing microbes oxidize short-chain alkanes anaerobically, and may play an important role in both the competition for sulfate and the local carbon budget. To better understand the anaerobic oxidation of short-chain n-alkanes coupled with sulfate-reduction, hydrocarbon-rich sediments from the Gulf of Mexico were amended with artificial, sulfate-replete seawater and one of four n-alkanes (C1-C4 then incubated under strict anaerobic conditions. Measured rates of alkane oxidation and sulfate reduction closely follow stoichiometric predictions that assume the complete oxidation of alkanes to CO2 (though other sinks for alkane carbon likely exist. Changes in the δ13C of all the alkanes in the reactors show enrichment over the course of the incubation, with the C3 and C4 incubations showing the greatest enrichment (4.4‰ and 4.5‰ respectively. The concurrent depletion in the δ13C of dissolved inorganic carbon (DIC implies a transfer of carbon from the alkane to the DIC pool (-3.5 and -6.7‰ for C3 and C4 incubations, respectively. Microbial community analyses reveal that certain members of the class Deltaproteobacteria are selectively enriched as the incubations degrade C1-C4 alkanes. Phylogenetic analyses indicate that distinct phylotypes are enriched in the ethane reactors, while phylotypes in the propane and butane reactors align with previously identified C3-C4 alkane-oxidizing sulfate-reducers. These data further constrain the potential influence of alkane oxidation on sulfate reduction rates in cold hydrocarbon-rich sediments, provide insight into their contribution to local carbon cycling, and illustrate the extent to which short-chain alkanes can serve as electron donors and govern microbial community

Medusa-Isosampler: A modular, network-based observatory system for combined physical, chemical and microbiological monitoring, sampling and incubation of hydrothermal and cold seep fluids

Science.gov (United States)

Schultz, A.; Flynn, M.; Taylor, P.

2004-12-01

The study of life in extreme environments provides an important context from which we can undertake the search for extraterrestrial life, and through which we can better understand biogeochemical feedback in terrestrial hydrothermal and cold seep systems. The Medusa-Isosampler project is aimed at fundamental research into understanding the potential for, and limits to, chemolithoautotrophic life, i.e. primary production without photosynthesis. One environment that might foster such life is associated with the high thermal and chemical gradient environment of hydrothermal vent structures. Another is associated with the lower thermal and chemical gradient environment of continental margin cold seeps. Under NERC, NASA and industrial support, we have designed a flexible instrumentation system, operating as networked, autonomous modules on a local area network, that will make possible simultaneous physical and chemical sampling and monitoring of hydrothermal and cold seep fluids, and the in situ and laboratory incubation of chemosynthetic microbes under high pressure, isobaric conditions. The system has been designed with long-term observatory operations in mind, and may be reconfigured dynamically as the requirements of the observatory installation change. The modular design will also accommodate new in situ chemical and biosensor technologies, provided by third parties. The system may be configured for seafloor use, and can be adapted to use in IODP boreholes. Our overall project goals are provide an instrumentation system capable of probing both high and low-gradient water-rock systems for chemolithoautotrophic biospheres, to identify the physical and chemical conditions that define these microhabitats and explore the details of the biogeochemical feedback loops that mediate these microhabitats, and to attempt to culture and identify chemolithoautotrophic microbial communities that might exist there. The Medusa-Isosampler system has been produced and is now

Bacterial diversity and biogeochemistry of different chemosynthetic habitats of the REGAB cold seep (West African margin, 3160 m water depth

Directory of Open Access Journals (Sweden)

P. Pop Ristova

2012-12-01

Full Text Available The giant pockmark REGAB (West African margin, 3160 m water depth is an active methane-emitting cold seep ecosystem, where the energy derived from microbially mediated oxidation of methane supports high biomass and diversity of chemosynthetic communities. Bare sediments interspersed with heterogeneous chemosynthetic assemblages of mytilid mussels, vesicomyid clams and siboglinid tubeworms form a complex seep ecosystem. To better understand if benthic bacterial communities reflect the patchy distribution of chemosynthetic fauna, all major chemosynthetic habitats at REGAB were investigated using an interdisciplinary approach combining pore water geochemistry, in situ quantification of fluxes and consumption of methane, as well as bacterial community fingerprinting. This study revealed that sediments populated by different fauna assemblages show distinct biogeochemical activities and are associated with distinct sediment bacterial communities. The methane consumption rates and methane effluxes ranged over one to two orders of magnitude across habitats, and reached highest values at the mussel habitat, which hosted a different bacterial community compared to the other habitats. Clam assemblages had a profound impact on the sediment geochemistry, but less so on the bacterial community structure. Moreover, all clam assemblages at REGAB were restricted to sediments characterized by complete methane consumption in the seafloor, and intermediate biogeochemical activity. Overall, variations in the sediment geochemistry were reflected in the distribution of both fauna and microbial communities; and were mostly determined by methane flux.

Cold seeps in Monterey Bay, California: Geochemistry of pore waters and relationship to benthic foraminiferal calcite

Energy Technology Data Exchange (ETDEWEB)

Gieskes, Joris, E-mail: jgieskes@ucsd.edu [Scripps Institution of Oceanography, IOD-0208, 9500 Gilman Drive, La Jolla, CA 92093-0208 (United States); Rathburn, Anthony E. [Scripps Institution of Oceanography, IOD-0208, 9500 Gilman Drive, La Jolla, CA 92093-0208 (United States)] [Indiana State University, Department of Earth and Environmental Systems, Terre Haute, IN 47809 (United States); Martin, Jonathan B. [University of Florida, Department of Geological Sciences, Gainesville, FL 32611-2120 (United States); Perez, M. Elena [Indiana State University, Department of Earth and Environmental Systems, Terre Haute, IN 47809 (United States)] [The Natural History Museum, Department of Palaeontology, Cromwell Road, London SW7 5BD (United Kingdom); Mahn, Chris [Scripps Institution of Oceanography, IOD-0208, 9500 Gilman Drive, La Jolla, CA 92093-0208 (United States); Bernhard, Joan M. [Woods Hole Oceanographic Institution, Geology and Geophysics Department, MS52, Woods Hole, MA 02543 (United States); Day, Shelley [University of Florida, Department of Geological Sciences, Gainesville, FL 32611-2120 (United States)

2011-05-15

Highlights: > We describe the geochemistry of pore waters in the Clam Flats area of Monterey Bay. > The geochemical data are compared with the {delta}{sup 13}C chemistry of benthic foraminifera. > Living foraminifera indicate little effects of pore water low {delta}{sup 13}C (DIC) in the clam bed. > This phenomenon and its implications are discussed in detail. > Implications with regards to paleo-methane seepage are discussed. - Abstract: An extensive geochemical and biogeochemical examination of CH{sub 4} seeps in the Clam Flats area of Monterey Bay provides insight into the character of relationships between seep geochemistry and benthic foraminiferal geochemistry. The area is characterized by sulfide-rich fluids. Sulfide increases are associated with large increases in alkalinity, as well as small decreases in dissolved Ca and Mg. In addition, only small increases in NH{sub 4} are observed, but values of {delta}{sup 13}C of dissolved inorganic C are as low as -60 per mille at shallow depths (<3 cm). These observations indicate that all these processes are related to the bacterial oxidation of CH{sub 4}, which is transported upward by slow seepage of pore fluids. The geochemistry of the pore fluids should be relevant to the geochemistry of the carbonate tests of living and dead foraminifera. However, a profound disequilibrium of approximately an order of magnitude occurs between the {delta}{sup 13}C values of stained (cytoplasm-containing) foraminiferal carbonate and the C isotope values of ambient pore water dissolved inorganic C. Reasons are unclear for this isotopic disequilibrium, but have important implications for interpretations of foraminiferal carbonate as a paleoenvironmental proxy. Much fine scale work is needed to fully understand the relationships between the biogeochemistry of benthic foraminifera and the geochemistry of the pore waters where they live.

Exploration and Discovery of Hydrocarbon Seeps, Coral Ecosystems, and Shipwrecks in the Deep Gulf of Mexico

Science.gov (United States)

Shank, T. M.; Hsing, P.; Carney, R. S.; Herrera, S.; Heyl, T.; Munro, C.; Bors, E.; Kiene, W.; Vecchione, M.; Evans, A.; Irion, J.; Warren, D.; Malik, M.; Lobecker, M.; Potter, J.

2012-12-01

Between March 20 and April 6, 2012, the NOAA Ship Okeanos Explorer served as a platform for ship-board and shore-side scientists to explore the deep Gulf of Mexico, targeting the northern West Florida Escarpment, DeSoto Canyon, the vicinity (within 11km) of the Deepwater Horizon (DWH) well, and deepwater shipwrecks. We systematically explored and discovered natural hydrocarbon seeps, diverse coral ecosystems, wooden and iron-hulled shipwrecks more than 100 years old colonized by coral communities, and sperm whale habitat between 600 and 1200m. A total of sixteen dives took advantage of new and recent maps to explore and groundtruth both hard and soft-bottom habitats, from cretaceous carbonates to mounds of coral rubble. The final ROV dive successfully groundtruthed expected methane-release areas imaged by the ship's mapping systems up to 1150m above the seafloor. The source of the mapping imagery was a stream of bubbles issuing from beneath thriving seep mussel communities. We visited five sites in the Mississippi Canyon (MC) area (lease blocks MC294, MC297, MC388, MC255, and MC036; the DWH incident took place in MC252). These sites were 11.3 km SW, 6.8 km SW, 7.6 km SW, 25.7 km E, and 27.4 km to the NE of the DWH, respectively. We used high-definition imaging systems on the Little Hercules ROV and Seirios camera platform to document more than 130 coral colonies and over 400 associated individual animals to continue to assessing the impact of the Deepwater Horizon oil spill. All of these efforts were conducted to provide fundamental knowledge of unknown and poorly known regions, ecosystems, and items of historical significance in the deep Gulf of Mexico.

Formation and migration of Natural Gases: gas composition and isotopes as monitors between source, reservoir and seep

Science.gov (United States)

Schoell, M.; Etiope, G.

2015-12-01

Natural gases form in tight source rocks at temperatures between 120ºC up to 200ºC over a time of 40 to 50my depending on the heating rate of the gas kitchen. Inferring from pyrolysis experiments, gases after primary migration, a pressure driven process, are rich in C2+ hydrocarbons (C2 to C5). This is consistent with gas compositions of oil-associated gases such as in the Bakken Shale which occur in immediate vicinity of the source with little migration distances. However, migration of gases along porous rocks over long distances (up to 200km in the case of the Troll field offshore Norway) changes the gas composition drastically as C2+ hydrocarbons tend to be retained/sequestered during migration of gas as case histories from Virginia and the North Sea will demonstrate. Similar "molecular fractionation" is observed between reservoirs and surface seeps. In contrast to gas composition, stable isotopes in gases are, in general, not affected by the migration process suggesting that gas migration is a steady state process. Changes in isotopic composition, from source to reservoir to surface seeps, is often the result of mixing of gases of different origins. Examples from various gas provinces will support this notion. Natural gas basins provide little opportunity of tracking and identifying gas phase separation. Future research on experimental phase separation and monitoring of gas composition and gas ratio changes e.g. various C2+ compound ratios over C1 or isomer ratios such as iso/n ratios in butane and pentane may be an avenue to develop tracers for phase separation that could possibly be applied to natural systems of retrograde natural condensate fields.

Insights into methane dynamics from analysis of authigenic carbonates and chemosynthetic mussels at newly-discovered Atlantic Margin seeps

Science.gov (United States)

Prouty, Nancy G.; Sahy, Diana; Ruppel, Carolyn D.; Roark, E. Brendan; Condon, Dan; Brooke, Sandra; Ross, Steve W.; Demopoulos, Amanda W.J.

2016-01-01

The recent discovery of active methane venting along the US northern and mid-Atlantic margin represents a new source of global methane not previously accounted for in carbon budgets from this region. However, uncertainty remains as to the origin and history of methane seepage along this tectonically inactive passive margin. Here we present the first isotopic analyses of authigenic carbonates and methanotrophic deep-sea mussels, Bathymodiolus   sp., and the first direct constraints on the timing of past methane emission, based on samples collected at the upper slope Baltimore Canyon (∼385 m water depth) and deepwater Norfolk (∼1600 m) seep fields within the area of newly-discovered venting. The authigenic carbonates at both sites were dominated by aragonite, with an average  signature of −47‰, a value consistent with microbially driven anaerobic oxidation of methane-rich fluids occurring at or near the sediment–water interface. Authigenic carbonate U and Sr isotope data further support the inference of carbonate precipitation from seawater-derived fluids rather than from formation fluids from deep aquifers. Carbonate stable and radiocarbon ( and ) isotope values from living Bathymodiolus   sp. specimens are lighter than those of seawater dissolved inorganic carbon, highlighting the influence of fossil carbon from methane on carbonate precipitation. U–Th dates on authigenic carbonates suggest seepage at Baltimore Canyon between 14.7±0.6 ka to 15.7±1.6 ka, and at the Norfolk seep field between 1.0±0.7 ka to 3.3±1.3 ka, providing constraint on the longevity of methane efflux at these sites. The age of the brecciated authigenic carbonates and the occurrence of pockmarks at the Baltimore Canyon upper slope could suggest a link between sediment delivery during Pleistocene sea-level lowstand, accumulation of pore fluid overpressure from sediment compaction, and release of overpressure through subsequent venting. Calculations show that

International Multidisciplinary Microscopy Congress

CERN Document Server

Oral, Ahmet; Ozer, Mehmet; InterM; INTERM2013

2014-01-01

The International Multidisciplinary Microscopy Congress (INTERM2013) was organized on October 10-13, 2013. The aim of the congress was to bring together scientists from various branches to discuss the latest advances in the field of microscopy. The contents of the congress have been broadened to a more "interdisciplinary" scope, so as to allow all scientists working on related subjects to participate and present their work. These proceedings include 39 peer-reviewed technical papers, submitted by leading academic and research institutions from over 12 countries and representing some of the most cutting-edge research available. The 39 papers are grouped into the following sections: - Applications of Microscopy in the Physical Sciences - Applications of Microscopy in the Biological Sciences

Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool

KAUST Repository

Zhang, Weipeng

2015-07-14

The biology of biofilm in deep-sea environments is barely being explored. Here, biofilms were developed at the brine pool (characterized by limited carbon sources) and the normal bottom water adjacent to Thuwal cold seeps. Comparative metagenomics based on 50 Gb datasets identified polysaccharide degradation, nitrate reduction, and proteolysis as enriched functional categories for brine biofilms. The genomes of two dominant species: a novel deltaproteobacterium and a novel epsilonproteobacterium in the brine biofilms were reconstructed. Despite rather small genome sizes, the deltaproteobacterium possessed enhanced polysaccharide fermentation pathways, whereas the epsilonproteobacterium was a versatile nitrogen reactor possessing nar, nap and nif gene clusters. These metabolic functions, together with specific regulatory and hypersaline-tolerant genes, made the two bacteria unique compared with their close relatives including those from hydrothermal vents. Moreover, these functions were regulated by biofilm development, as both the abundance and the expression level of key functional genes were higher in later-stage biofilms, and co-occurrences between the two dominant bacteria were demonstrated. Collectively, unique mechanisms were revealed: i) polysaccharides fermentation, proteolysis interacted with nitrogen cycling to form a complex chain for energy generation; ii) remarkably, exploiting and organizing niche-specific functions would be an important strategy for biofilm-dependent adaptation to the extreme conditions.

Morphology of First Zoeal Stage of Four Genera of Alvinocaridid Shrimps from Hydrothermal Vents and Cold Seeps: Implications for Ecology, Larval Biology and Phylogeny.

Directory of Open Access Journals (Sweden)

Iván Hernández-Ávila

Full Text Available Alvinocaridid shrimps are endemic species inhabiting hydrothermal vents and/or cold seeps. Although indirect evidences (genetic and lipid markers suggest that their larval stages disperse widely and support large scale connectivity, larval life and mechanisms underlying dispersal are unknown in alvinocaridids. Here we provide for the first time detailed descriptions of the first larval stage (zoea I of four alvinocaridid species: Rimicaris exoculata and Mirocaris fortunata from the Mid-Atlantic Ridge, Alvinocaris muricola from the Congo Basin and Nautilocaris saintlaurentae from the Western Pacific. The larvae were obtained from onboard hatching of brooding females (either at atmospheric pressure or at habitat pressure in hyperbaric chambers and from the water column near adult habitats, sampled with plankton pumps or sediment traps. Major characteristics of the alvinocaridid larvae include undeveloped mandible and almost complete absence of setation in the inner margin of the mouth parts and maxillipeds. Although the larvae are very similar between the four species studied, some morphological features could be used for species identification. In addition, undeveloped mouthparts and the large amount of lipid reserves strongly support the occurrence of primary lecithotrophy in the early stage of alvinocaridids. Although lecithotrophy in decapod crustaceans is usually associated with abbreviated larval development, as a mechanism of larval retention, morphological and physiological evidences suggest the occurrence of an extended and lecithotrophic larval stage in the Alvinocarididae. These traits permit the colonization of widely dispersed and fragmented environments of hydrothermal vents and cold seeps. Distribution of larval traits along the phylogenetic reconstruction of the Alvinocarididae and related families suggest that lecithotrophy/planktotrophy and extended/abbreviated development have evolved independently along related families in all

Microsphere imaging with confocal microscopy and two photon microscopy

International Nuclear Information System (INIS)

Chun, Hyung Su; An, Kyung Won; Lee, Jai Hyung

2002-01-01

We have acquired images of polystyrene and fused-silica microsphere by using conventional optical microscopy, confocal microscopy and two-photon microscopy, and performed comparative analysis of these images. Different from conventional optical microscopy, confocal and two-photon microscopy had good optical sectioning capability. In addition, confocal microscopy and two-photon microscopy had better lateral resolution than conventional optical microscopy. These results are attributed to confocality and nonlinearity of confocal microscopy and two photon microscopy, respectively.

Microscopy image segmentation tool: Robust image data analysis

Energy Technology Data Exchange (ETDEWEB)

Valmianski, Ilya, E-mail: ivalmian@ucsd.edu; Monton, Carlos; Schuller, Ivan K. [Department of Physics and Center for Advanced Nanoscience, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093 (United States)

2014-03-15

We present a software package called Microscopy Image Segmentation Tool (MIST). MIST is designed for analysis of microscopy images which contain large collections of small regions of interest (ROIs). Originally developed for analysis of porous anodic alumina scanning electron images, MIST capabilities have been expanded to allow use in a large variety of problems including analysis of biological tissue, inorganic and organic film grain structure, as well as nano- and meso-scopic structures. MIST provides a robust segmentation algorithm for the ROIs, includes many useful analysis capabilities, and is highly flexible allowing incorporation of specialized user developed analysis. We describe the unique advantages MIST has over existing analysis software. In addition, we present a number of diverse applications to scanning electron microscopy, atomic force microscopy, magnetic force microscopy, scanning tunneling microscopy, and fluorescent confocal laser scanning microscopy.

Microscopy image segmentation tool: Robust image data analysis

Science.gov (United States)

Valmianski, Ilya; Monton, Carlos; Schuller, Ivan K.

2014-03-01

We present a software package called Microscopy Image Segmentation Tool (MIST). MIST is designed for analysis of microscopy images which contain large collections of small regions of interest (ROIs). Originally developed for analysis of porous anodic alumina scanning electron images, MIST capabilities have been expanded to allow use in a large variety of problems including analysis of biological tissue, inorganic and organic film grain structure, as well as nano- and meso-scopic structures. MIST provides a robust segmentation algorithm for the ROIs, includes many useful analysis capabilities, and is highly flexible allowing incorporation of specialized user developed analysis. We describe the unique advantages MIST has over existing analysis software. In addition, we present a number of diverse applications to scanning electron microscopy, atomic force microscopy, magnetic force microscopy, scanning tunneling microscopy, and fluorescent confocal laser scanning microscopy.

Microscopy image segmentation tool: Robust image data analysis

International Nuclear Information System (INIS)

Valmianski, Ilya; Monton, Carlos; Schuller, Ivan K.

2014-01-01

We present a software package called Microscopy Image Segmentation Tool (MIST). MIST is designed for analysis of microscopy images which contain large collections of small regions of interest (ROIs). Originally developed for analysis of porous anodic alumina scanning electron images, MIST capabilities have been expanded to allow use in a large variety of problems including analysis of biological tissue, inorganic and organic film grain structure, as well as nano- and meso-scopic structures. MIST provides a robust segmentation algorithm for the ROIs, includes many useful analysis capabilities, and is highly flexible allowing incorporation of specialized user developed analysis. We describe the unique advantages MIST has over existing analysis software. In addition, we present a number of diverse applications to scanning electron microscopy, atomic force microscopy, magnetic force microscopy, scanning tunneling microscopy, and fluorescent confocal laser scanning microscopy

Characterization of Carbonate Crust from Deep-sea Methane Seeps on the Northern US Atlantic Margin.

Science.gov (United States)

Gabitov, R. I.; Borrelli, C.; Buettner, J.; Testa, M.; Garner, B.; Weremeichik, J.; Thomas, J. B.; Wahidi, M.; Thirumalai, R. V. K. G.; Kirkland, B. L.; Skarke, A. D.

2017-12-01

Authigenic carbonate minerals widely occur at the seafloor as carbonate crusts and are often directly linked to microbial activity, about which promotion of carbonate crystal growth and geochemistry are not entirely understood. To evaluate a potential metabolic contribution, studies were conducted on carbonate crust collected from a methane seep and on precipitation experiments which produced inorganic aragonite crystallized at high pressure. Among the samples collected during a NSF sponsored cruise to the North Atlantic Continental Margin of the United States (off of New England) in July-August 2016, we analyzed one carbonate crust sample (AD4835 BB-4522) collected at 39.805860; -69.592593 and at a depth of 1419.6 m. In this crust sample, two textural types of aragonite were identified: 1) groundmass consisting of fine grey crystals (100 µm, 24.9 wt%), feldspar (5.6 wt%), and dolomite (3.6 wt%), and trace amount of troilite were identified using XRD, SEM, and optical microscopy. The sample was cut into slabs parallel to crust growth assuming the crust grew in a downward direction. Concentrations of Na, Mg, Al, Si, S, K, Ca, Mn, Fe, Sr, Zr, Ba, and U were measured in the direction parallel to growth of the crust using LA-ICP-MS. Proportions of Si, Al, (Na+K), Mg, S, and Fe in the groundmass suggest the occurrence of sub-micron inclusions of alkali feldspar, and potentially pyroxene, Fe oxide, and Fe sulfide, which were impossible to avoid with the instrument's spatial resolution. The occurrence of micro non-carbonate inclusions causes high elemental concentrations compared to the values expected for aragonite crystallized from seawater. White aragonite acicular crystals were free of silicate and sulfide inclusions, and therefore, yielded lower concentrations of all measured elements except Sr compared to the groundmass. Analyzed Mg and Sr are consistent with published data for deep-sea corals. Also, Sr is similar to experimental data on inorganic aragonite. Mg

Mammosomatotroph adenoma of the pituitary associated with gigantism and hyperprolactinemia. A morphological study including immunoelectron microscopy.

Science.gov (United States)

Felix, I A; Horvath, E; Kovacs, K; Smyth, H S; Killinger, D W; Vale, J

1986-01-01

A 29-year old giantess with growth hormone excess and hyperprolactinemia underwent transsphenoidal surgery to remove her pituitary tumor. Electron microscopy revealed a mammosomatotroph adenoma composed of one cell type. Immunoelectron microscopy, using the immunogold technique, demonstrated predominantly growth hormone or prolactin or a varying mixture of both growth hormone and prolactin in the adenoma cells. The presence of growth hormone and prolactin was found not only in the cytoplasm of the same adenoma cells but also in the same secretory granules. In the nontumorous adenohypophysis, somatotrophs and lactotrophs showed ultrastructural signs of hyperactivity. This finding is in contrast with the presence of suppressed somatotrophs and lactotrophs seen in nontumorous portions of adult pituitaries harboring growth hormone or prolactin-secreting adenomas. Our morphological study reinforces the view that growth hormone-producing pituitary tumors, originating in childhood, are different from those of the adult gland.

Deep Sequencing of Myxilla (Ectyomyxilla) methanophila, an Epibiotic Sponge on Cold-Seep Tubeworms, Reveals Methylotrophic, Thiotrophic, and Putative Hydrocarbon-Degrading Microbial Associations

KAUST Repository

Arellano, Shawn M.

2012-10-11

The encrusting sponge Myxilla (Ectyomyxilla) methanophila (Poecilosclerida: Myxillidae) is an epibiont on vestimentiferan tubeworms at hydrocarbon seeps on the upper Louisiana slope of the Gulf of Mexico. It has long been suggested that this sponge harbors methylotrophic bacteria due to its low δ13C value and high methanol dehydrogenase activity, yet the full community of microbial associations in M. methanophila remained uncharacterized. In this study, we sequenced 16S rRNA genes representing the microbial community in M. methanophila collected from two hydrocarbon-seep sites (GC234 and Bush Hill) using both Sanger sequencing and next-generation 454 pyrosequencing technologies. Additionally, we compared the microbial community in M. methanophila to that of the biofilm collected from the associated tubeworm. Our results revealed that the microbial diversity in the sponges from both sites was low but the community structure was largely similar, showing a high proportion of methylotrophic bacteria of the genus Methylohalomonas and polycyclic aromatic hydrocarbon (PAH)-degrading bacteria of the genera Cycloclasticus and Neptunomonas. Furthermore, the sponge microbial clone library revealed the dominance of thioautotrophic gammaproteobacterial symbionts in M. methanophila. In contrast, the biofilm communities on the tubeworms were more diverse and dominated by the chemoorganotrophic Moritella at GC234 and methylotrophic Methylomonas and Methylohalomonas at Bush Hill. Overall, our study provides evidence to support previous suggestion that M. methanophila harbors methylotrophic symbionts and also reveals the association of PAH-degrading and thioautotrophic microbes in the sponge. © 2012 Springer Science+Business Media New York.

Diversity and distribution of eukaryotic microbes in and around a brine pool adjacent to the Thuwal cold seeps in the Red Sea

KAUST Repository

Wang, Yong

2014-02-04

A hypoxic/suboxic brine pool at a depth of about 850 m was discovered near the Thuwal cold seeps in the Red Sea. Filled with high concentrations of hydrogen sulfide and ammonia, such a brine pool might limit the spread of eukaryotic organisms. Here, we compared the communities of the eukaryotic microbes in a microbial mat, sediments and water samples distributed in 7 sites within and adjacent to the brine pool. Taxonomic classification of the pyrosequenced 18S rRNA amplicon reads showed that fungi highly similar to the species identified along the Arabic coast were almost ubiquitous in the water and sediment samples, supporting their wide distribution in various environments. The microbial mat displayed the highest species diversity and contained grazers and a considerable percentage of unclassified species. Phylogeny-based methods revealed novel lineages representing a majority of the reads from the interface between the sea water and brine pool. Phylogenetic relationships with more reference sequences suggest that the lineages were affiliated with novel Alveolata and Euglenozoa inhabiting the interface where chemosynthetic prokaryotes are highly proliferative due to the strong chemocline and halocline. The brine sediments harbored abundant species highly similar to invertebrate gregarine parasites identified in different oxygen-depleted sediments. Therefore, the present findings support the uniqueness of some microbial eukaryotic groups in this cold seep brine system. 2014 Wang, Zhang, Cao, Shek, Tian, Wong, Batang, Al-suwailem and Qian.

Deep sequencing of Myxilla (Ectyomyxilla) methanophila, an epibiotic sponge on cold-seep tubeworms, reveals methylotrophic, thiotrophic, and putative hydrocarbon-degrading microbial associations.

Science.gov (United States)

Arellano, Shawn M; Lee, On On; Lafi, Feras F; Yang, Jiangke; Wang, Yong; Young, Craig M; Qian, Pei-Yuan

2013-02-01

The encrusting sponge Myxilla (Ectyomyxilla) methanophila (Poecilosclerida: Myxillidae) is an epibiont on vestimentiferan tubeworms at hydrocarbon seeps on the upper Louisiana slope of the Gulf of Mexico. It has long been suggested that this sponge harbors methylotrophic bacteria due to its low δ(13)C value and high methanol dehydrogenase activity, yet the full community of microbial associations in M. methanophila remained uncharacterized. In this study, we sequenced 16S rRNA genes representing the microbial community in M. methanophila collected from two hydrocarbon-seep sites (GC234 and Bush Hill) using both Sanger sequencing and next-generation 454 pyrosequencing technologies. Additionally, we compared the microbial community in M. methanophila to that of the biofilm collected from the associated tubeworm. Our results revealed that the microbial diversity in the sponges from both sites was low but the community structure was largely similar, showing a high proportion of methylotrophic bacteria of the genus Methylohalomonas and polycyclic aromatic hydrocarbon (PAH)-degrading bacteria of the genera Cycloclasticus and Neptunomonas. Furthermore, the sponge microbial clone library revealed the dominance of thioautotrophic gammaproteobacterial symbionts in M. methanophila. In contrast, the biofilm communities on the tubeworms were more diverse and dominated by the chemoorganotrophic Moritella at GC234 and methylotrophic Methylomonas and Methylohalomonas at Bush Hill. Overall, our study provides evidence to support previous suggestion that M. methanophila harbors methylotrophic symbionts and also reveals the association of PAH-degrading and thioautotrophic microbes in the sponge.

Electron Microscopy Society of Southern Africa : proceedings

International Nuclear Information System (INIS)

Snyman, H.C.; Coetzee, J.; Coubrough, R.I.

1987-01-01

The proceedings of the 26th annual conference of the Electron Microscopy Society of Southern Africa are presented. Papers were presented on the following topics: techniques and instrumentation used in electron microscopy, and applications of electron microscopy in the life sciences, including applications in medicine, zoology, botany and microbiology. The use of electron microscopy in the physical sciences was also discussed. Separate abstracts were prepared for seven of the papers presented. The remaining papers were considered outside the subject scope of INIS

Correlative Stochastic Optical Reconstruction Microscopy and Electron Microscopy

Science.gov (United States)

Kim, Doory; Deerinck, Thomas J.; Sigal, Yaron M.; Babcock, Hazen P.; Ellisman, Mark H.; Zhuang, Xiaowei

2015-01-01

Correlative fluorescence light microscopy and electron microscopy allows the imaging of spatial distributions of specific biomolecules in the context of cellular ultrastructure. Recent development of super-resolution fluorescence microscopy allows the location of molecules to be determined with nanometer-scale spatial resolution. However, correlative super-resolution fluorescence microscopy and electron microscopy (EM) still remains challenging because the optimal specimen preparation and imaging conditions for super-resolution fluorescence microscopy and EM are often not compatible. Here, we have developed several experiment protocols for correlative stochastic optical reconstruction microscopy (STORM) and EM methods, both for un-embedded samples by applying EM-specific sample preparations after STORM imaging and for embedded and sectioned samples by optimizing the fluorescence under EM fixation, staining and embedding conditions. We demonstrated these methods using a variety of cellular targets. PMID:25874453

Microscopy techniques in flavivirus research.

Science.gov (United States)

Chong, Mun Keat; Chua, Anthony Jin Shun; Tan, Terence Tze Tong; Tan, Suat Hoon; Ng, Mah Lee

2014-04-01

The Flavivirus genus is composed of many medically important viruses that cause high morbidity and mortality, which include Dengue and West Nile viruses. Various molecular and biochemical techniques have been developed in the endeavour to study flaviviruses. However, microscopy techniques still have irreplaceable roles in the identification of novel virus pathogens and characterization of morphological changes in virus-infected cells. Fluorescence microscopy contributes greatly in understanding the fundamental viral protein localizations and virus-host protein interactions during infection. Electron microscopy remains the gold standard for visualizing ultra-structural features of virus particles and infected cells. New imaging techniques and combinatory applications are continuously being developed to push the limit of resolution and extract more quantitative data. Currently, correlative live cell imaging and high resolution three-dimensional imaging have already been achieved through the tandem use of optical and electron microscopy in analyzing biological specimens. Microscopy techniques are also used to measure protein binding affinities and determine the mobility pattern of proteins in cells. This chapter will consolidate on the applications of various well-established microscopy techniques in flavivirus research, and discuss how recently developed microscopy techniques can potentially help advance our understanding in these membrane viruses. Copyright © 2013 Elsevier Ltd. All rights reserved.

Tropical CO2 seeps reveal the impact of ocean acidification on coral reef invertebrate recruitment.

Science.gov (United States)

Allen, Ro; Foggo, Andrew; Fabricius, Katharina; Balistreri, Annalisa; Hall-Spencer, Jason M

2017-11-30

Rising atmospheric CO 2 concentrations are causing ocean acidification by reducing seawater pH and carbonate saturation levels. Laboratory studies have demonstrated that many larval and juvenile marine invertebrates are vulnerable to these changes in surface ocean chemistry, but challenges remain in predicting effects at community and ecosystem levels. We investigated the effect of ocean acidification on invertebrate recruitment at two coral reef CO 2 seeps in Papua New Guinea. Invertebrate communities differed significantly between 'reference' (median pH7.97, 8.00), 'high CO 2 ' (median pH7.77, 7.79), and 'extreme CO 2 ' (median pH7.32, 7.68) conditions at each reef. There were also significant reductions in calcifying taxa, copepods and amphipods as CO 2 levels increased. The observed shifts in recruitment were comparable to those previously described in the Mediterranean, revealing an ecological mechanism by which shallow coastal systems are affected by near-future levels of ocean acidification. Copyright © 2016 Elsevier Ltd. All rights reserved.

A SIMS Study of Sulfur Isotopes of Accessory Pyrites Associated with Barites from Methane Cold Seeps in the Gulf of Mexico

Science.gov (United States)

Morelli, E. C.; Aharon, P.

2017-12-01

Bacteria and archaea associated with seeps can fix methane from sublimating gas hydrates through coupled bacterial sulfate reduction/ anaerobic methane oxidation (BSR/AMO) and prevent outgassing to the atmosphere. The occurrence of such microbial processes has been established on the basis of the sulfur isotope compositions of microbial byproducts (pyrites; FeS2) that reflect the degree of fractionation between SO4 and FeS2 via the production of the H2S intermediate phase. BSR/AMO coupling has been discerned in accessory sulfides associated with carbonates from gas hydrate sites. Whether BSR/AMO coupling is also active in barites, another ubiquitous product of gas hydrate sublimation, has so far been overlooked. Here we present results of a new sulfur isotope study of accessory sulfides in barites associated with gas hydrates at the threshold of stability occurring on the Gulf of Mexico slope. Using a fractionation factor of 1.009 and a seawater δ34SSO4 value of 20.3‰ and assuming a Rayleigh distillation closed system model for marine sulfide precipitation, pyrites from barite gas seeps are predicted to exhibit a range of δ34S values (about -1‰ to 20‰ CDT) as the pool of sulfate is continuously depleted. Actual δ34S values could fall outside of the predicted range because the system in question is likely only partially closed and kinetic fractionations are likely. δ34S of accessory pyrites from three Garden Banks Lease Block 382 (510 - 640m water depth) and one Mississippi Canyon Lease Block 929 (590m) barite samples have been determined using an ims-1290 Secondary Ion Mass Spectrometer (SIMS). Two Garden Banks samples and one Mississippi Canyon sample reveal a spread of values from 5.30 ± 0.04 to 25.90 ± 0.09 (‰ CDT), which follow the predicted trend for gas seeps and indicate the source of fractionation is likely from the coupled BSR/AMO process. One Garden Banks sample yields a wide spread of values from -26.2 ± 0.05 to 20.5 ± 0.4 (‰ CDT). The

Geologic framework, regional aquifer properties (1940s-2009), and spring, creek, and seep properties (2009-10) of the upper San Mateo Creek Basin near Mount Taylor, New Mexico

Science.gov (United States)

Langman, Jeff B.; Sprague, Jesse E.; Durall, Roger A.

2012-01-01

conditions at some time or in some location(s) in most aquifers. Frequent detections of zinc in the alluvium aquifer may represent anthropogenic influences such as mining. Along the mesas in the upper San Mateo Creek Basin, springs that form various creeks, including El Rito and San Mateo Creeks, discharge from the basalt-cap layer and the upper Cretaceous sedimentary layers. Streamflow in El Rito and San Mateo Creeks flows down steep gradients near the mesas sustained by groundwater discharges, and this streamflow transitions to shallow groundwater contained within the valley alluvium through infiltration where the subsequent groundwater is restricted from downward migration by the shaly Menefee Formation. This shallow groundwater reemerges at seeps where the land surface has been eroded below the groundwater level. Spring- and creek-water samples contained small amounts of dissolved solutes, and seep water contained substantially larger amounts of dissolved solutes. The pH of water within the creeks was neutral to alkaline, and all locations exhibited well-oxygenated conditions, although typically at substantially less than saturated levels. Changes in the stable-isotope ratios of water between spring and summer samples indicate differences in source-water inputs that likely pertain to seasonal recharge sources. Results of the water-isotope analysis and geochemical modeling indicate little evaporation and chemical weathering at the spring and creek sites but stronger evaporation and chemical weathering by the time the water reaches the seep locations in the center of the upper San Mateo Creek Basin.

Validation of Digital Microscopy Compared With Light Microscopy for the Diagnosis of Canine Cutaneous Tumors.

Science.gov (United States)

Bertram, Christof A; Gurtner, Corinne; Dettwiler, Martina; Kershaw, Olivia; Dietert, Kristina; Pieper, Laura; Pischon, Hannah; Gruber, Achim D; Klopfleisch, Robert

2018-07-01

Integration of new technologies, such as digital microscopy, into a highly standardized laboratory routine requires the validation of its performance in terms of reliability, specificity, and sensitivity. However, a validation study of digital microscopy is currently lacking in veterinary pathology. The aim of the current study was to validate the usability of digital microscopy in terms of diagnostic accuracy, speed, and confidence for diagnosing and differentiating common canine cutaneous tumor types and to compare it to classical light microscopy. Therefore, 80 histologic sections including 17 different skin tumor types were examined twice as glass slides and twice as digital whole-slide images by 6 pathologists with different levels of experience at 4 time points. Comparison of both methods found digital microscopy to be noninferior for differentiating individual tumor types within the category epithelial and mesenchymal tumors, but diagnostic concordance was slightly lower for differentiating individual round cell tumor types by digital microscopy. In addition, digital microscopy was associated with significantly shorter diagnostic time, but diagnostic confidence was lower and technical quality was considered inferior for whole-slide images compared with glass slides. Of note, diagnostic performance for whole-slide images scanned at 200× magnification was noninferior in diagnostic performance for slides scanned at 400×. In conclusion, digital microscopy differs only minimally from light microscopy in few aspects of diagnostic performance and overall appears adequate for the diagnosis of individual canine cutaneous tumors with minor limitations for differentiating individual round cell tumor types and grading of mast cell tumors.

Fluorescence microscopy.

Science.gov (United States)

Sanderson, Michael J; Smith, Ian; Parker, Ian; Bootman, Martin D

2014-10-01

Fluorescence microscopy is a major tool with which to monitor cell physiology. Although the concepts of fluorescence and its optical separation using filters remain similar, microscope design varies with the aim of increasing image contrast and spatial resolution. The basics of wide-field microscopy are outlined to emphasize the selection, advantages, and correct use of laser scanning confocal microscopy, two-photon microscopy, scanning disk confocal microscopy, total internal reflection, and super-resolution microscopy. In addition, the principles of how these microscopes form images are reviewed to appreciate their capabilities, limitations, and constraints for operation. © 2014 Cold Spring Harbor Laboratory Press.

Internet-Enabled High-Resolution Brain Mapping and Virtual Microscopy

OpenAIRE

Mikula, Shawn; Trotts, Issac; Stone, James M.; Jones, Edward G.

2007-01-01

Virtual microscopy involves the conversion of histological sections mounted on glass microscope slides to high resolution digital images. Virtual microscopy offers several advantages over traditional microscopy, including remote viewing and data-sharing, annotation, and various forms of data-mining.

A correlative optical microscopy and scanning electron microscopy approach to locating nanoparticles in brain tumors.

Science.gov (United States)

Kempen, Paul J; Kircher, Moritz F; de la Zerda, Adam; Zavaleta, Cristina L; Jokerst, Jesse V; Mellinghoff, Ingo K; Gambhir, Sanjiv S; Sinclair, Robert

2015-01-01

The growing use of nanoparticles in biomedical applications, including cancer diagnosis and treatment, demands the capability to exactly locate them within complex biological systems. In this work a correlative optical and scanning electron microscopy technique was developed to locate and observe multi-modal gold core nanoparticle accumulation in brain tumor models. Entire brain sections from mice containing orthotopic brain tumors injected intravenously with nanoparticles were imaged using both optical microscopy to identify the brain tumor, and scanning electron microscopy to identify the individual nanoparticles. Gold-based nanoparticles were readily identified in the scanning electron microscope using backscattered electron imaging as bright spots against a darker background. This information was then correlated to determine the exact location of the nanoparticles within the brain tissue. The nanoparticles were located only in areas that contained tumor cells, and not in the surrounding healthy brain tissue. This correlative technique provides a powerful method to relate the macro- and micro-scale features visible in light microscopy with the nanoscale features resolvable in scanning electron microscopy. Copyright © 2014 Elsevier Ltd. All rights reserved.

A 1.4-Billion Pixel Map of the Seafloor: BOEM's Mission to Visualize Dynamic Geology and Identify Natural Seep Sites in the Gulf of Mexico

Science.gov (United States)

Kramer, K.; Shedd, W. W.

2017-12-01

In May, 2017, the U.S. Department of the Interior's Bureau of Ocean Energy Management (BOEM) published a high-resolution seafloor map of the northern Gulf of Mexico region. The new map, derived from 3-D seismic surveys, provides the scientific community with enhanced resolution and reveals previously undiscovered and poorly resolved geologic features of the continental slope, salt minibasin province, abyssal plain, Mississippi Fan, and the Florida Shelf and Escarpment. It becomes an even more powerful scientific tool when paired with BOEM's public database of 35,000 seafloor features, identifying natural hydrocarbon seeps, hard grounds, mud volcanoes, sediment flows, pockmarks, slumps, and many others. BOEM has mapped the Gulf of Mexico seafloor since 1998 in a regulatory mission to identify natural oil and gas seeps and protect the coral and chemosynthetic communities growing at those sites. The nineteen-year mapping effort, still ongoing, resulted in the creation of the 1.4-billion pixel map and the seafloor features database. With these tools and continual collaboration with academia, professional scientific institutions, and the offshore energy industry, BOEM will continue to incorporate new data to update and expand these two resources on a regular basis. They can be downloaded for free from BOEM's website at https://www.boem.gov/Gulf-of-Mexico-Deepwater-Bathymetry/ and https://www.boem.gov/Seismic-Water-Bottom-Anomalies-Map-Gallery/.

Transmission-type angle deviation microscopy

International Nuclear Information System (INIS)

Chiu, M.-H.; Lai, C.-W.; Tan, C.-T.; Lai, C.-F.

2008-01-01

We present a new microscopy technique that we call transmission angle deviation microscopy (TADM). It is based on common-path heterodyne interferometry and geometrical optics. An ultrahigh sensitivity surface plasmon resonance (SPR) angular sensor is used to expand dynamic measurement ranges and to improve the axial resolution in three-dimensional optical microscopy. When transmitted light is incident upon a specimen, the beam converges or diverges because of refractive and/or surface height variations. Advantages include high axial resolution (∼32 nm), nondestructive and noncontact measurement, and larger measurement ranges (± 80 μm) for a numerical aperture of 0.21in a transparent measurement medium. The technique can be used without conductivity and pretreatment

[Virtual microscopy in pathology teaching and postgraduate training (continuing education)].

Science.gov (United States)

Sinn, H P; Andrulis, M; Mogler, C; Schirmacher, P

2008-11-01

As with conventional microscopy, virtual microscopy permits histological tissue sections to be viewed on a computer screen with a free choice of viewing areas and a wide range of magnifications. This, combined with the possibility of linking virtual microscopy to E-Learning courses, make virtual microscopy an ideal tool for teaching and postgraduate training in pathology. Uses of virtual microscopy in pathology teaching include blended learning with the presentation of digital teaching slides in the internet parallel to presentation in the histology lab, extending student access to histology slides beyond the lab. Other uses are student self-learning in the Internet, as well as the presentation of virtual slides in the classroom with or without replacing real microscopes. Successful integration of virtual microscopy depends on its embedding in the virtual classroom and the creation of interactive E-learning content. Applications derived from this include the use of virtual microscopy in video clips, podcasts, SCORM modules and the presentation of virtual microscopy using interactive whiteboards in the classroom.

Sonar gas flux estimation by bubble insonification: application to methane bubble flux from seep areas in the outer Laptev Sea

Science.gov (United States)

Leifer, Ira; Chernykh, Denis; Shakhova, Natalia; Semiletov, Igor

2017-06-01

Sonar surveys provide an effective mechanism for mapping seabed methane flux emissions, with Arctic submerged permafrost seepage having great potential to significantly affect climate. We created in situ engineered bubble plumes from 40 m depth with fluxes spanning 0.019 to 1.1 L s-1 to derive the in situ calibration curve (Q(σ)). These nonlinear curves related flux (Q) to sonar return (σ) for a multibeam echosounder (MBES) and a single-beam echosounder (SBES) for a range of depths. The analysis demonstrated significant multiple bubble acoustic scattering - precluding the use of a theoretical approach to derive Q(σ) from the product of the bubble σ(r) and the bubble size distribution where r is bubble radius. The bubble plume σ occurrence probability distribution function (Ψ(σ)) with respect to Q found Ψ(σ) for weak σ well described by a power law that likely correlated with small-bubble dispersion and was strongly depth dependent. Ψ(σ) for strong σ was largely depth independent, consistent with bubble plume behavior where large bubbles in a plume remain in a focused core. Ψ(σ) was bimodal for all but the weakest plumes. Q(σ) was applied to sonar observations of natural arctic Laptev Sea seepage after accounting for volumetric change with numerical bubble plume simulations. Simulations addressed different depths and gases between calibration and seep plumes. Total mass fluxes (Qm) were 5.56, 42.73, and 4.88 mmol s-1 for MBES data with good to reasonable agreement (4-37 %) between the SBES and MBES systems. The seepage flux occurrence probability distribution function (Ψ(Q)) was bimodal, with weak Ψ(Q) in each seep area well described by a power law, suggesting primarily minor bubble plumes. The seepage-mapped spatial patterns suggested subsurface geologic control attributing methane fluxes to the current state of subsea permafrost.

Deep Learning Microscopy

KAUST Repository

Rivenson, Yair

2017-05-12

We demonstrate that a deep neural network can significantly improve optical microscopy, enhancing its spatial resolution over a large field-of-view and depth-of-field. After its training, the only input to this network is an image acquired using a regular optical microscope, without any changes to its design. We blindly tested this deep learning approach using various tissue samples that are imaged with low-resolution and wide-field systems, where the network rapidly outputs an image with remarkably better resolution, matching the performance of higher numerical aperture lenses, also significantly surpassing their limited field-of-view and depth-of-field. These results are transformative for various fields that use microscopy tools, including e.g., life sciences, where optical microscopy is considered as one of the most widely used and deployed techniques. Beyond such applications, our presented approach is broadly applicable to other imaging modalities, also spanning different parts of the electromagnetic spectrum, and can be used to design computational imagers that get better and better as they continue to image specimen and establish new transformations among different modes of imaging.

Super-resolution Microscopy in Plant Cell Imaging.

Science.gov (United States)

Komis, George; Šamajová, Olga; Ovečka, Miroslav; Šamaj, Jozef

2015-12-01

Although the development of super-resolution microscopy methods dates back to 1994, relevant applications in plant cell imaging only started to emerge in 2010. Since then, the principal super-resolution methods, including structured-illumination microscopy (SIM), photoactivation localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), and stimulated emission depletion microscopy (STED), have been implemented in plant cell research. However, progress has been limited due to the challenging properties of plant material. Here we summarize the basic principles of existing super-resolution methods and provide examples of applications in plant science. The limitations imposed by the nature of plant material are reviewed and the potential for future applications in plant cell imaging is highlighted. Copyright © 2015 Elsevier Ltd. All rights reserved.

Correlated Light Microscopy and Electron Microscopy

NARCIS (Netherlands)

Sjollema, Klaas A.; Schnell, Ulrike; Kuipers, Jeroen; Kalicharan, Ruby; Giepmans, Ben N. G.; MullerReichert, T; Verkade, P

2012-01-01

Understanding where, when, and how biomolecules (inter)act is crucial to uncover fundamental mechanisms in cell biology. Recent developments in fluorescence light microscopy (FLM) allow protein imaging in living cells and at the near molecular level. However, fluorescence microscopy only reveals

New insight into stratification of anaerobic methanotrophs in cold seep sediments.

Science.gov (United States)

Roalkvam, Irene; Jørgensen, Steffen Leth; Chen, Yifeng; Stokke, Runar; Dahle, Håkon; Hocking, William Peter; Lanzén, Anders; Haflidason, Haflidi; Steen, Ida Helene

2011-11-01

Methane seepages typically harbor communities of anaerobic methane oxidizers (ANME); however, knowledge about fine-scale vertical variation of ANME in response to geochemical gradients is limited. We investigated microbial communities in sediments below a white microbial mat in the G11 pockmark at Nyegga by 16S rRNA gene tag pyrosequencing and real-time quantitative PCR. A vertical stratification of dominating ANME communities was observed at 4 cmbsf (cm below seafloor) and below in the following order: ANME-2a/b, ANME-1 and ANME-2c. The ANME-1 community was most numerous and comprised single or chains of cells with typical rectangular morphology, accounting up to 89.2% of the retrieved 16S rRNA gene sequences. Detection rates for sulfate-reducing Deltaproteobacteria possibly involved in anaerobic oxidation of methane were low throughout the core. However, a correlation in the abundance of Candidate division JS-1 with ANME-2 was observed, indicating involvement in metabolisms occurring in ANME-2-dominated horizons. The white microbial mat and shallow sediments were dominated by organisms affiliated with Sulfurovum (Epsilonproteobacteria) and Methylococcales (Gammaproteobacteria), suggesting that aerobic oxidation of sulfur and methane is taking place. In intermediate horizons, typical microbial groups associated with methane seeps were recovered. The data are discussed with respect to co-occurring microbial assemblages and interspecies interactions. FEMS Microbiology Ecology © 2011 Federation of Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original Norwegian works.

Microscopy of the hair and trichogram

Directory of Open Access Journals (Sweden)

Özlem Dicle

2014-06-01

Full Text Available Hair microscopy is a fast and simple method for the diagnosis of various disorders affecting the hair in daily practice. For the microscopy of the hair, samples are collected by either clipping or plucking. The trichogram technique which the hair sample is collected by a standardized plucking method is used for the diagnosis of hair shedding and of alopecia via hair root pattern. In this review, the examination techniques and details are discussed and the most common indications for the hair microscopy including hair abnormalities as a part of genodermatosis and, infections and infestations affecting the hair are highlighted.

High-resolution electron microscopy

CERN Document Server

Spence, John C H

2013-01-01

This new fourth edition of the standard text on atomic-resolution transmission electron microscopy (TEM) retains previous material on the fundamentals of electron optics and aberration correction, linear imaging theory (including wave aberrations to fifth order) with partial coherence, and multiple-scattering theory. Also preserved are updated earlier sections on practical methods, with detailed step-by-step accounts of the procedures needed to obtain the highest quality images of atoms and molecules using a modern TEM or STEM electron microscope. Applications sections have been updated - these include the semiconductor industry, superconductor research, solid state chemistry and nanoscience, and metallurgy, mineralogy, condensed matter physics, materials science and material on cryo-electron microscopy for structural biology. New or expanded sections have been added on electron holography, aberration correction, field-emission guns, imaging filters, super-resolution methods, Ptychography, Ronchigrams, tomogr...

Atom probe field ion microscopy and related topics: A bibliography 1989

International Nuclear Information System (INIS)

Miller, M.K.; Hawkins, A.R.; Russell, K.F.

1990-12-01

This bibliography includes references related to the following topics: atom probe field ion microscopy (APFIM), field ion spectroscopy (FIM), field emission microscopy (FEM), liquid metal ion sources (LMIS), scanning tunneling microscopy (STM), and theory. Technique-orientated studies and applications are included. This bibliography covers the period 1989. The references contained in this document were compiled from a variety of sources including computer searches and personal lists of publications

Long-term Measurement of Sediment Resuspension and Gas Hydrate Stability at a Gulf of Mexico Seep Site

Science.gov (United States)

Vardaro, M. F.; Bender, L. C.; MacDonald, I. R.

2003-12-01

To study the temporal topographic and hydrologic changes in Gulf of Mexico cold seeps, we deployed a deep-sea time-lapse camera, several temperature probes and an ADCP mooring at the continental shelf seep community surrounding a gas hydrate outcropping. The digital camera recorded one still image every six hours for three months in 2001, every two hours for the month of June 2002 and every six hours for the month of July 2002. A pair of 300 kHz Workhorse acoustic Doppler current profilers (ADCPs) attached to a 540 meter-long mooring were anchored approximately 2 km from the site in 2002. Temperature probes were deployed at the site over the entire experimental period. The data recovered provide a comprehensive record of gas hydrate mound processes. We calculated biological activity by identifying fauna observed in the time-lapse record and recording the number of individuals and species seen in each image. 1,381 individual organisms representing over 20 species were observed. An average of 4.6 (+/-3.0) organisms were seen in each frame during the three-month deployment, while 3.6 (+/-4.2) were seen per frame in the one-month deployment. An extensive amount of sediment suspension and redistribution occurred during the deployment period. By digitally analyzing the luminosity of the water column above the mound and plotting the results over time the turbidity at the site could be quantified. A 24.1-hour diurnal pattern can be seen in the record, indicating a possible tidal or inertial component to deep-sea currents in this area. Contrary to expectations, there was no major change in shape or size of the gas hydrate outcrop being studied. This indicates a higher degree of stability than laboratory studies or prior in situ observations have shown. The stable topography of the gas hydrate mound combines with high organic output and sediment turnover to serve as a focus of benthic predatory activity. The frequency and recurrence of sediment resuspension indicate that

Dictionary of Microscopy

Science.gov (United States)

Heath, Julian

2005-10-01

The past decade has seen huge advances in the application of microscopy in all areas of science. This welcome development in microscopy has been paralleled by an expansion of the vocabulary of technical terms used in microscopy: terms have been coined for new instruments and techniques and, as microscopes reach even higher resolution, the use of terms that relate to the optical and physical principles underpinning microscopy is now commonplace. The Dictionary of Microscopy was compiled to meet this challenge and provides concise definitions of over 2,500 terms used in the fields of light microscopy, electron microscopy, scanning probe microscopy, x-ray microscopy and related techniques. Written by Dr Julian P. Heath, Editor of Microscopy and Analysis, the dictionary is intended to provide easy navigation through the microscopy terminology and to be a first point of reference for definitions of new and established terms. The Dictionary of Microscopy is an essential, accessible resource for: students who are new to the field and are learning about microscopes equipment purchasers who want an explanation of the terms used in manufacturers' literature scientists who are considering using a new microscopical technique experienced microscopists as an aide mémoire or quick source of reference librarians, the press and marketing personnel who require definitions for technical reports.

Electron Microscopy of Ebola Virus-Infected Cells.

Science.gov (United States)

Noda, Takeshi

2017-01-01

Ebola virus (EBOV) replicates in host cells, where both viral and cellular components show morphological changes during the process of viral replication from entry to budding. These steps in the replication cycle can be studied using electron microscopy (EM), including transmission electron microscopy (TEM) and scanning electron microscopy (SEM), which is one of the most useful methods for visualizing EBOV particles and EBOV-infected cells at the ultrastructural level. This chapter describes conventional methods for EM sample preparation of cultured cells infected with EBOV.

Cold-seep-driven carbonate deposits at the Central American forearc: contrasting evolution and timing in escarpment and mound settings

Science.gov (United States)

Liebetrau, V.; Augustin, N.; Kutterolf, S.; Schmidt, M.; Eisenhauer, A.; Garbe-Schönberg, D.; Weinrebe, W.

2014-10-01

Continuous surface cores of cold-seep carbonates were recovered offshore Pacific Nicaragua and Costa Rica from 800 to 1,500-m water depths (Meteor 66/3) in order to decipher their evolution and methane enriched fluid emanation in contrasting geological settings. Cores from the mounds Iguana, Perezoso, Baula V and from the Jaco Scarp escarpment were used for a multi-method approach. For both settings aragonite was revealed as dominant authigenic carbonate phase in vein fillings and matrix cementation, followed by Mg-calcite as second most abundant. This common precipitation process of CaCO3 polymorphs could be ascribed as indirectly driven by chemical changes of the advecting pore water due to anaerobic oxidation of methane. A more direct influence of seep-related microbial activity on the authigenic mineral assemblage in both settings is probably reflected by the observed minor amounts of dolomite and a dolomite-like CaMg carbonate (MgCO3 ~ 42 %). δ13C data of Jaco Scarp samples are significantly lower (-43 to -56 ‰ PDB) than for mound samples (-22 to -36 ‰ PDB), indicating differences in fluid composition and origin. Noteworthy, δ18O values of Scarp samples correlate most closely with the ocean signature at their time of formation. Documenting the archive potential, a high resolution case study of a mound core implies at least 40 changes in fluid supply within a time interval of approximately 14 ky. As most striking difference, the age data indicate a late-stage downward-progressing cementation front for all three mound cap structures (approx. 2-5 cm/ky), but a significantly faster upward carbonate buildup in the bulging sediments on top of the scarp environment (approx. 120 cm/ky). The latter data set leads to the hypothesis of chemoherm carbonate emplacement in accord with reported sedimentation rates until decompression of the advective fluid system, probably caused by the Jaco Scarp landslide and dating this to approximately 13,000 years ago.

Atom probe field ion microscopy and related topics: A bibliography 1992

Energy Technology Data Exchange (ETDEWEB)

Russell, K.F.; Godfrey, R.D.; Miller, M.K.

1993-12-01

This bibliography contains citations of books, conference proceedings, journals, and patents published in 1992 on the following types of microscopy: atom probe field ion microscopy (108 items); field emission microscopy (101 items); and field ion microscopy (48 items). An addendum of 34 items missed in previous bibliographies is included.

Transcription, Signaling Receptor Activity, Oxidative Phosphorylation, and Fatty Acid Metabolism Mediate the Presence of Closely Related Species in Distinct Intertidal and Cold-Seep Habitats.

Science.gov (United States)

Van Campenhout, Jelle; Vanreusel, Ann; Van Belleghem, Steven; Derycke, Sofie

2015-12-03

Bathyal cold seeps are isolated extreme deep-sea environments characterized by low species diversity while biomass can be high. The Håkon Mosby mud volcano (Barents Sea, 1,280 m) is a rather stable chemosynthetic driven habitat characterized by prominent surface bacterial mats with high sulfide concentrations and low oxygen levels. Here, the nematode Halomonhystera hermesi thrives in high abundances (11,000 individuals 10 cm(-2)). Halomonhystera hermesi is a member of the intertidal Halomonhystera disjuncta species complex that includes five cryptic species (GD1-5). GD1-5's common habitat is characterized by strong environmental fluctuations. Here, we compared the transcriptomes of H. hermesi and GD1, H. hermesi's closest relative. Genes encoding proteins involved in oxidative phosphorylation are more strongly expressed in H. hermesi than in GD1, and many genes were only observed in H. hermesi while being completely absent in GD1. Both observations could in part be attributed to high sulfide concentrations and low oxygen levels. Additionally, fatty acid elongation was also prominent in H. hermesi confirming the importance of highly unsaturated fatty acids in this species. Significant higher amounts of transcription factors and genes involved in signaling receptor activity were observed in GD1 (many of which were completely absent in H. hermesi), allowing fast signaling and transcriptional reprogramming which can mediate survival in dynamic intertidal environments. GC content was approximately 8% higher in H. hermesi coding unigenes resulting in differential codon usage between both species and a higher proportion of amino acids with GC-rich codons in H. hermesi. In general our results showed that most pathways were active in both environments and that only three genes are under natural selection. This indicates that also plasticity should be taken in consideration in the evolutionary history of Halomonhystera species. Such plasticity, as well as possible

Application of super-resolution optical microscopy in biology

International Nuclear Information System (INIS)

Mao Xiuhai; Du Jiancong; Huang Qing; Fan Chunhai; Deng Suhui

2013-01-01

Background: A noninvasive, real-time far-field optical microscopy is needed to study the dynamic function inside cells and proteins. However, the resolution limit of traditional optical microscope is about 200 nm due to the diffraction limit of light. So, it's hard to directly observe the subcellular structures. Over the past several years of microscopy development, the diffraction limit of fluorescence microscopy has been overcome and its resolution limit is about tens of nanometers. Methods: To overcome the diffraction limit of light, many super-resolution fluoresce microscopes, including stimulated emission of depletion microscopy (STED), photoactivation localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), have been developed. Conclusions: These methods have been applied in cell biology, microbiology and neurobiology, and the technology of super-resolution provides a new insight into the life science. (authors)

Innovative Strategies for Clinical Microscopy Instruction: Virtual Versus Light Microscopy.

Science.gov (United States)

McDaniel, M Jane; Russell, Gregory B; Crandall, Sonia J

2018-06-01

The purpose of the study was to compare virtual microscopy with light microscopy to determine differences in learning outcomes and learner attitudes in teaching clinical microscopy to physician assistant (PA) students. A prospective, randomized, crossover design study was conducted with a convenience sample of 67 first-year PA students randomized to 2 groups. One group used light microscopes to find microscopic structures, whereas the other group used instructor-directed video streaming of microscopic elements. At the midpoint of the study, the groups switched instructional strategies. Learning outcomes were assessed via posttest after each section of the study, with comparison of final practical examination results to previous cohorts. Attitudes about the 2 educational strategies were assessed through a postcourse questionnaire with a Likert scale. Analysis of the first posttest demonstrated that students in the video-streamed group had significantly better learning outcomes than those in the light microscopy group (P = .004; Cohen's d = 0.74). Analysis of the posttest after crossover showed no differences between the 2 groups (P = .48). Between the 2 posttests, students first assigned to the light microscopy group scored a 6.6 mean point increase (±10.4 SD; p = .0011), whereas students first assigned to the virtual microscopy group scored a 1.3 mean point increase (±7.1 SD; p = .29). The light microscopy group improved more than the virtual microscopy group (P = .019). Analysis of practical examination data revealed higher scores for the study group compared with 5 previous cohorts of first-year students (P virtual microscopy to traditional light microscopy. Virtual microscopy is an effective educational strategy, and students prefer this method when learning to interpret images of clinical specimens.

Optofluidic time-stretch microscopy: recent advances

Science.gov (United States)

Lei, Cheng; Nitta, Nao; Ozeki, Yasuyuki; Goda, Keisuke

2018-04-01

Flow cytometry is an indispensable method for valuable applications in numerous fields such as immunology, pathology, pharmacology, molecular biology, and marine biology. Optofluidic time-stretch microscopy is superior to conventional flow cytometry methods for its capability to acquire high-quality images of single cells at a high-throughput exceeding 10,000 cells per second. This makes it possible to extract copious information from cellular images for accurate cell detection and analysis with the assistance of machine learning. Optofluidic time-stretch microscopy has proven its effectivity in various applications, including microalga-based biofuel production, evaluation of thrombotic disorders, as well as drug screening and discovery. In this review, we discuss the principles and recent advances of optofluidic time-stretch microscopy.

The 2015 super-resolution microscopy roadmap

International Nuclear Information System (INIS)

Hell, Stefan W; Sahl, Steffen J; Bates, Mark; Jakobs, Stefan; Zhuang, Xiaowei; Heintzmann, Rainer; Booth, Martin J; Bewersdorf, Joerg; Shtengel, Gleb; Hess, Harald; Tinnefeld, Philip; Honigmann, Alf; Testa, Ilaria; Cognet, Laurent; Lounis, Brahim; Ewers, Helge; Davis, Simon J; Eggeling, Christian; Klenerman, David; Willig, Katrin I

2015-01-01

Far-field optical microscopy using focused light is an important tool in a number of scientific disciplines including chemical, (bio)physical and biomedical research, particularly with respect to the study of living cells and organisms. Unfortunately, the applicability of the optical microscope is limited, since the diffraction of light imposes limitations on the spatial resolution of the image. Consequently the details of, for example, cellular protein distributions, can be visualized only to a certain extent. Fortunately, recent years have witnessed the development of ‘super-resolution’ far-field optical microscopy (nanoscopy) techniques such as stimulated emission depletion (STED), ground state depletion (GSD), reversible saturated optical (fluorescence) transitions (RESOLFT), photoactivation localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), structured illumination microscopy (SIM) or saturated structured illumination microscopy (SSIM), all in one way or another addressing the problem of the limited spatial resolution of far-field optical microscopy. While SIM achieves a two-fold improvement in spatial resolution compared to conventional optical microscopy, STED, RESOLFT, PALM/STORM, or SSIM have all gone beyond, pushing the limits of optical image resolution to the nanometer scale. Consequently, all super-resolution techniques open new avenues of biomedical research. Because the field is so young, the potential capabilities of different super-resolution microscopy approaches have yet to be fully explored, and uncertainties remain when considering the best choice of methodology. Thus, even for experts, the road to the future is sometimes shrouded in mist. The super-resolution optical microscopy roadmap of Journal of Physics D: Applied Physics addresses this need for clarity. It provides guidance to the outstanding questions through a collection of short review articles from experts in the field, giving a thorough

Pontellid copepods, Labidocera spp., affected by ocean acidification: A field study at natural CO2 seeps.

Science.gov (United States)

Smith, Joy N; Richter, Claudio; Fabricius, Katharina E; Cornils, Astrid

2017-01-01

CO2 seeps in coral reefs were used as natural laboratories to study the impacts of ocean acidification on the pontellid copepod, Labidocera spp. Pontellid abundances were reduced by ∼70% under high-CO2 conditions. Biological parameters and substratum preferences of the copepods were explored to determine the underlying causes of such reduced abundances. Stage- and sex-specific copepod lengths, feeding ability, and egg development were unaffected by ocean acidification, thus changes in these physiological parameters were not the driving factor for reduced abundances under high-CO2 exposure. Labidocera spp. are demersal copepods, hence they live amongst reef substrata during the day and emerge into the water column at night. Deployments of emergence traps showed that their preferred reef substrata at control sites were coral rubble, macro algae, and turf algae. However, under high-CO2 conditions they no longer had an association with any specific substrata. Results from this study indicate that even though the biology of a copepod might be unaffected by high-CO2, Labidocera spp. are highly vulnerable to ocean acidification.

Pontellid copepods, Labidocera spp., affected by ocean acidification: A field study at natural CO2 seeps.

Directory of Open Access Journals (Sweden)

Joy N Smith

Full Text Available CO2 seeps in coral reefs were used as natural laboratories to study the impacts of ocean acidification on the pontellid copepod, Labidocera spp. Pontellid abundances were reduced by ∼70% under high-CO2 conditions. Biological parameters and substratum preferences of the copepods were explored to determine the underlying causes of such reduced abundances. Stage- and sex-specific copepod lengths, feeding ability, and egg development were unaffected by ocean acidification, thus changes in these physiological parameters were not the driving factor for reduced abundances under high-CO2 exposure. Labidocera spp. are demersal copepods, hence they live amongst reef substrata during the day and emerge into the water column at night. Deployments of emergence traps showed that their preferred reef substrata at control sites were coral rubble, macro algae, and turf algae. However, under high-CO2 conditions they no longer had an association with any specific substrata. Results from this study indicate that even though the biology of a copepod might be unaffected by high-CO2, Labidocera spp. are highly vulnerable to ocean acidification.

Investigation of Nematode Diversity using Scanning Electron Microscopy and Fluorescent Microscopy

Science.gov (United States)

Seacor, Taylor; Howell, Carina

2013-03-01

Nematode worms account for the vast majority of the animals in the biosphere. They are colossally important to global public health as parasites, and to agriculture both as pests and as beneficial inhabitants of healthy soil. Amphid neurons are the anterior chemosensory neurons in nematodes, mediating critical behaviors including chemotaxis and mating. We are examining the cellular morphology and external anatomy of amphid neurons, using fluorescence microscopy and scanning electron microscopy, respectively, of a wide range of soil nematodes isolated in the wild. We use both classical systematics (e.g. diagnostic keys) and molecular markers (e.g. ribosomal RNA) to classify these wild isolates. Our ultimate aim is to build a detailed anatomical database in order to dissect genetic pathways of neuronal development and function across phylogeny and ecology. Research supported by NSF grants 092304, 0806660, 1058829 and Lock Haven University FPDC grants

Correlative Super-Resolution Microscopy: New Dimensions and New Opportunities.

Science.gov (United States)

Hauser, Meghan; Wojcik, Michal; Kim, Doory; Mahmoudi, Morteza; Li, Wan; Xu, Ke

2017-06-14

Correlative microscopy, the integration of two or more microscopy techniques performed on the same sample, produces results that emphasize the strengths of each technique while offsetting their individual weaknesses. Light microscopy has historically been a central method in correlative microscopy due to its widespread availability, compatibility with hydrated and live biological samples, and excellent molecular specificity through fluorescence labeling. However, conventional light microscopy can only achieve a resolution of ∼300 nm, undercutting its advantages in correlations with higher-resolution methods. The rise of super-resolution microscopy (SRM) over the past decade has drastically improved the resolution of light microscopy to ∼10 nm, thus creating exciting new opportunities and challenges for correlative microscopy. Here we review how these challenges are addressed to effectively correlate SRM with other microscopy techniques, including light microscopy, electron microscopy, cryomicroscopy, atomic force microscopy, and various forms of spectroscopy. Though we emphasize biological studies, we also discuss the application of correlative SRM to materials characterization and single-molecule reactions. Finally, we point out current limitations and discuss possible future improvements and advances. We thus demonstrate how a correlative approach adds new dimensions of information and provides new opportunities in the fast-growing field of SRM.

3DSEM: A 3D microscopy dataset

Directory of Open Access Journals (Sweden)

Ahmad P. Tafti

2016-03-01

Full Text Available The Scanning Electron Microscope (SEM as a 2D imaging instrument has been widely used in many scientific disciplines including biological, mechanical, and materials sciences to determine the surface attributes of microscopic objects. However the SEM micrographs still remain 2D images. To effectively measure and visualize the surface properties, we need to truly restore the 3D shape model from 2D SEM images. Having 3D surfaces would provide anatomic shape of micro-samples which allows for quantitative measurements and informative visualization of the specimens being investigated. The 3DSEM is a dataset for 3D microscopy vision which is freely available at [1] for any academic, educational, and research purposes. The dataset includes both 2D images and 3D reconstructed surfaces of several real microscopic samples. Keywords: 3D microscopy dataset, 3D microscopy vision, 3D SEM surface reconstruction, Scanning Electron Microscope (SEM

Whole Slide Imaging Versus Microscopy for Primary Diagnosis in Surgical Pathology

Science.gov (United States)

Mukhopadhyay, Sanjay; Feldman, Michael D.; Abels, Esther; Ashfaq, Raheela; Beltaifa, Senda; Cacciabeve, Nicolas G.; Cathro, Helen P.; Cheng, Liang; Cooper, Kumarasen; Dickey, Glenn E.; Gill, Ryan M.; Heaton, Robert P.; Kerstens, René; Lindberg, Guy M.; Malhotra, Reenu K.; Mandell, James W.; Manlucu, Ellen D.; Mills, Anne M.; Mills, Stacey E.; Moskaluk, Christopher A.; Nelis, Mischa; Patil, Deepa T.; Przybycin, Christopher G.; Reynolds, Jordan P.; Rubin, Brian P.; Saboorian, Mohammad H.; Salicru, Mauricio; Samols, Mark A.; Sturgis, Charles D.; Turner, Kevin O.; Wick, Mark R.; Yoon, Ji Y.; Zhao, Po

2018-01-01

Most prior studies of primary diagnosis in surgical pathology using whole slide imaging (WSI) versus microscopy have focused on specific organ systems or included relatively few cases. The objective of this study was to demonstrate that WSI is noninferior to microscopy for primary diagnosis in surgical pathology. A blinded randomized noninferiority study was conducted across the entire range of surgical pathology cases (biopsies and resections, including hematoxylin and eosin, immunohistochemistry, and special stains) from 4 institutions using the original sign-out diagnosis (baseline diagnosis) as the reference standard. Cases were scanned, converted to WSI and randomized. Sixteen pathologists interpreted cases by microscopy or WSI, followed by a wash-out period of ≥4 weeks, after which cases were read by the same observers using the other modality. Major discordances were identified by an adjudication panel, and the differences between major discordance rates for both microscopy (against the reference standard) and WSI (against the reference standard) were calculated. A total of 1992 cases were included, resulting in 15,925 reads. The major discordance rate with the reference standard diagnosis was 4.9% for WSI and 4.6% for microscopy. The difference between major discordance rates for microscopy and WSI was 0.4% (95% confidence interval, −0.30% to 1.01%). The difference in major discordance rates for WSI and microscopy was highest in endocrine pathology (1.8%), neoplastic kidney pathology (1.5%), urinary bladder pathology (1.3%), and gynecologic pathology (1.2%). Detailed analysis of these cases revealed no instances where interpretation by WSI was consistently inaccurate compared with microscopy for multiple observers. We conclude that WSI is noninferior to microscopy for primary diagnosis in surgical pathology, including biopsies and resections stained with hematoxylin and eosin, immunohistochemistry and special stains. This conclusion is valid across a

Removal action report on Waste Area Grouping 4 seeps 4 and 6 at Oak Ridge National Laboratory, Oak Ridge, Tennessee

International Nuclear Information System (INIS)

1996-12-01

This report documents removal action activities for a Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA) non-time-critical removal action as described in the Action Memorandum prepared in 1996. The technical objective of this removal action was to reduce the release of strontium 90 ( 90 Sr) into an ephemeral tributary to White Oak Creek from Waste Area Grouping 4 (WAG 4) seeps, as measured at Monitoring Station (MS) 1 at ORNL, Oak Ridge, TN. Design was initiated in early January 1996 and grouting activities were completed in late October 9996. Portions of four waste disposal trenches were injected using low-temperature permeation grouting technology with multiple formulations of grouts to reduce the in situ hydraulic conductivity of the waste materials and ultimately reduce the off-site transport of 90 Sr

Species sorting during biofilm assembly by artificial substrates deployed in a cold seep system

KAUST Repository

Zhang, Wei Peng

2014-10-17

Studies focusing on biofilm assembly in deep-sea environments are rarely conducted. To examine the effects of substrate type on microbial community assembly, biofilms were developed on different substrates for different durations at two locations in the Red Sea: in a brine pool and in nearby bottom water (NBW) adjacent to the Thuwal cold seep II. The composition of the microbial communities in 51 biofilms and water samples were revealed by classification of pyrosequenced 16S rRNA gene amplicons. Together with the microscopic characteristics of the biofilms, the results indicate a stronger selection effect by the substrates on the microbial assembly in the brine pool compared with the NBW. Moreover, the selection effect by substrate type was stronger in the early stages compared with the later stages of the biofilm development. These results are consistent with the hypotheses proposed in the framework of species sorting theory, which states that the power of species sorting during microbial community assembly is dictated by habitat conditions, duration and the structure of the source community. Therefore, the results of this study shed light on the control strategy underlying biofilm-associated marine fouling and provide supporting evidence for ecological theories important for understanding the formation of deep-sea biofilms.

Species sorting during biofilm assembly by artificial substrates deployed in a cold seep system

KAUST Repository

Zhang, Wei Peng; Wang, Yong; Tian, Ren Mao; Bougouffa, Salim; Yang, Bo; Cao, Hui Luo; Zhang, Gen; Wong, Yue Him; Xu, Wei; Batang, Zenon B.; Al-Suwailem, Abdulaziz M.; Zhang, Xixiang; Qian, Pei-Yuan

2014-01-01

Studies focusing on biofilm assembly in deep-sea environments are rarely conducted. To examine the effects of substrate type on microbial community assembly, biofilms were developed on different substrates for different durations at two locations in the Red Sea: in a brine pool and in nearby bottom water (NBW) adjacent to the Thuwal cold seep II. The composition of the microbial communities in 51 biofilms and water samples were revealed by classification of pyrosequenced 16S rRNA gene amplicons. Together with the microscopic characteristics of the biofilms, the results indicate a stronger selection effect by the substrates on the microbial assembly in the brine pool compared with the NBW. Moreover, the selection effect by substrate type was stronger in the early stages compared with the later stages of the biofilm development. These results are consistent with the hypotheses proposed in the framework of species sorting theory, which states that the power of species sorting during microbial community assembly is dictated by habitat conditions, duration and the structure of the source community. Therefore, the results of this study shed light on the control strategy underlying biofilm-associated marine fouling and provide supporting evidence for ecological theories important for understanding the formation of deep-sea biofilms.

Progress in the Correlative Atomic Force Microscopy and Optical Microscopy

Directory of Open Access Journals (Sweden)

Lulu Zhou

2017-04-01

Full Text Available Atomic force microscopy (AFM has evolved from the originally morphological imaging technique to a powerful and multifunctional technique for manipulating and detecting the interactions between molecules at nanometer resolution. However, AFM cannot provide the precise information of synchronized molecular groups and has many shortcomings in the aspects of determining the mechanism of the interactions and the elaborate structure due to the limitations of the technology, itself, such as non-specificity and low imaging speed. To overcome the technical limitations, it is necessary to combine AFM with other complementary techniques, such as fluorescence microscopy. The combination of several complementary techniques in one instrument has increasingly become a vital approach to investigate the details of the interactions among molecules and molecular dynamics. In this review, we reported the principles of AFM and optical microscopy, such as confocal microscopy and single-molecule localization microscopy, and focused on the development and use of correlative AFM and optical microscopy.

Electron microscopy in metallurgy

International Nuclear Information System (INIS)

Loretto, M.H.

1980-01-01

The aim of this paper is to review briefly the contribution which (TEM) transmission electron microscopy (including high voltage electron microscopy (HVEM)) has made to metallurgy. Since it is straightforward with modern electron microscopes to extract the crystallographic information which provides the basis for any interpretation, the major problem in most metallurgical work lies in assessing how the structure (which TEM has characterised) has arisen and which properties of the specimen can be understood in terms of this structure. Radiation damage, quenching, phase transformations, grain boundaries and plastic deformation have been the main fields in which TEM has contributed significantly. After briefly summarising the role of TEM in each field, examples of recent work will be used to indicate current TEM activity in physical metallurgy. (author)

High-resolution intravital microscopy.

Directory of Open Access Journals (Sweden)

Volker Andresen

Full Text Available Cellular communication constitutes a fundamental mechanism of life, for instance by permitting transfer of information through synapses in the nervous system and by leading to activation of cells during the course of immune responses. Monitoring cell-cell interactions within living adult organisms is crucial in order to draw conclusions on their behavior with respect to the fate of cells, tissues and organs. Until now, there is no technology available that enables dynamic imaging deep within the tissue of living adult organisms at sub-cellular resolution, i.e. detection at the level of few protein molecules. Here we present a novel approach called multi-beam striped-illumination which applies for the first time the principle and advantages of structured-illumination, spatial modulation of the excitation pattern, to laser-scanning-microscopy. We use this approach in two-photon-microscopy--the most adequate optical deep-tissue imaging-technique. As compared to standard two-photon-microscopy, it achieves significant contrast enhancement and up to 3-fold improved axial resolution (optical sectioning while photobleaching, photodamage and acquisition speed are similar. Its imaging depth is comparable to multifocal two-photon-microscopy and only slightly less than in standard single-beam two-photon-microscopy. Precisely, our studies within mouse lymph nodes demonstrated 216% improved axial and 23% improved lateral resolutions at a depth of 80 µm below the surface. Thus, we are for the first time able to visualize the dynamic interactions between B cells and immune complex deposits on follicular dendritic cells within germinal centers (GCs of live mice. These interactions play a decisive role in the process of clonal selection, leading to affinity maturation of the humoral immune response. This novel high-resolution intravital microscopy method has a huge potential for numerous applications in neurosciences, immunology, cancer research and

High-Resolution Intravital Microscopy

Science.gov (United States)

Andresen, Volker; Pollok, Karolin; Rinnenthal, Jan-Leo; Oehme, Laura; Günther, Robert; Spiecker, Heinrich; Radbruch, Helena; Gerhard, Jenny; Sporbert, Anje; Cseresnyes, Zoltan; Hauser, Anja E.; Niesner, Raluca

2012-01-01

Cellular communication constitutes a fundamental mechanism of life, for instance by permitting transfer of information through synapses in the nervous system and by leading to activation of cells during the course of immune responses. Monitoring cell-cell interactions within living adult organisms is crucial in order to draw conclusions on their behavior with respect to the fate of cells, tissues and organs. Until now, there is no technology available that enables dynamic imaging deep within the tissue of living adult organisms at sub-cellular resolution, i.e. detection at the level of few protein molecules. Here we present a novel approach called multi-beam striped-illumination which applies for the first time the principle and advantages of structured-illumination, spatial modulation of the excitation pattern, to laser-scanning-microscopy. We use this approach in two-photon-microscopy - the most adequate optical deep-tissue imaging-technique. As compared to standard two-photon-microscopy, it achieves significant contrast enhancement and up to 3-fold improved axial resolution (optical sectioning) while photobleaching, photodamage and acquisition speed are similar. Its imaging depth is comparable to multifocal two-photon-microscopy and only slightly less than in standard single-beam two-photon-microscopy. Precisely, our studies within mouse lymph nodes demonstrated 216% improved axial and 23% improved lateral resolutions at a depth of 80 µm below the surface. Thus, we are for the first time able to visualize the dynamic interactions between B cells and immune complex deposits on follicular dendritic cells within germinal centers (GCs) of live mice. These interactions play a decisive role in the process of clonal selection, leading to affinity maturation of the humoral immune response. This novel high-resolution intravital microscopy method has a huge potential for numerous applications in neurosciences, immunology, cancer research and developmental biology

Multiphoton Microscopy for Ophthalmic Imaging

Directory of Open Access Journals (Sweden)

Emily A. Gibson

2011-01-01

Full Text Available We review multiphoton microscopy (MPM including two-photon autofluorescence (2PAF, second harmonic generation (SHG, third harmonic generation (THG, fluorescence lifetime (FLIM, and coherent anti-Stokes Raman Scattering (CARS with relevance to clinical applications in ophthalmology. The different imaging modalities are discussed highlighting the particular strength that each has for functional tissue imaging. MPM is compared with current clinical ophthalmological imaging techniques such as reflectance confocal microscopy, optical coherence tomography, and fluorescence imaging. In addition, we discuss the future prospects for MPM in disease detection and clinical monitoring of disease progression, understanding fundamental disease mechanisms, and real-time monitoring of drug delivery.

Use of atomic force microscopy and transmission electron microscopy for correlative studies of bacterial capsules.

Science.gov (United States)

Stukalov, Oleg; Korenevsky, Anton; Beveridge, Terry J; Dutcher, John R

2008-09-01

Bacteria can possess an outermost assembly of polysaccharide molecules, a capsule, which is attached to their cell wall. We have used two complementary, high-resolution microscopy techniques, atomic force microscopy (AFM) and transmission electron microscopy (TEM), to study bacterial capsules of four different gram-negative bacterial strains: Escherichia coli K30, Pseudomonas aeruginosa FRD1, Shewanella oneidensis MR-4, and Geobacter sulfurreducens PCA. TEM analysis of bacterial cells using different preparative techniques (whole-cell mounts, conventional embeddings, and freeze-substitution) revealed capsules for some but not all of the strains. In contrast, the use of AFM allowed the unambiguous identification of the presence of capsules on all strains used in the present study, including those that were shown by TEM to be not encapsulated. In addition, the use of AFM phase imaging allowed the visualization of the bacterial cell within the capsule, with a depth sensitivity that decreased with increasing tapping frequency.

French Society of Microscopy, 10. conference; Societe Francaise des Microscopies, 10. colloque

Energy Technology Data Exchange (ETDEWEB)

Thibault-Penisson, J; Cremer, Ch; Susini, J; Kirklanda, A I; Rigneault, H; Renault, O; Bailly, A; Zagonel, L F; Barrett, N; Bogner, A; Gauthier, C; Jouneau, P H; Thollet, G; Fuchs, G; Basset, D; Deconihout, B; Vurpillot, F; Vella, A; Matthieu, G; Cadel, E; Bostel, A; Blavette, D; Baumeister, W; Usson, Y; Zaefferer, St; Laffont, L; Weyland, M; Thomas, J M; Midgley, P; Benlekbir, S; Epicier, Th; Diop, B N; Roux, St; Ou, M; Perriat, P; Bausach, M; Aouine, M; Berhault, G; Idrissi, H; Cottevieille, M; Jonic, S; Larquet, E; Svergun, D; Vannoni, M A; Boisset, N; Ersena, O; Werckmann, J; Ulhaq, C; Hirlimann, Ch; Tihay, F; Cuong, Pham-Huu; Crucifix, C; Schultz, P; Jornsanoha, P; Thollet, G; Masenelli-Varlot, K; Gauthier, C; Ludwig, W; King, A; Johnson, G; Gonzalves-Hoennicke, M; Reischig, P; Messaoudi, C; Ibrahim, R; Marco, S; Klie, R F; Zhao, Y; Yang, G; Zhu, Y; Hue, F; Hytch, M; Hartmann, J M; Bogumilowicz, Y; Claverie, A; Klein, H; Alloyeau, D; Ricolleau, C; Langlois, C; Le Bouar, Y; Loiseau, A; Colliex, C; Stephan, O; Kociak, M; Tence, M; Gloter, A; Imhoff, D; Walls, M; Nelayah, J; March, K; Couillard, M; Ailliot, C; Bertin, F; Cooper, D; Rivallin, P; Dumelie, N; Benhayoune, H; Balossier, G; Cheynet, M; Pokrant, S; Tichelaar, F; Rouviere, J L; Cooper, D; Truche, R; Chabli, A; Debili, M Y; Houdellier, F; Warot-Fonrose, B; Hytch, M J; Snoeck, E; Calmels, L; Serin, V; Schattschneider, P; Jacob, D; Cordier, P

2007-07-01

This document gathers the resumes of some of the presentations made at this conference whose aim was to present the last developments and achievements of the 3 complementary microscopies: optical microscopy, electron microscopy and X-ray microscopy. The contributions have been organized around the following 12 topics: 1) new technical developments, 2) 3-dimensional imaging, 3) quantitative microscopy, 4) technical progress in photon microscopy, 5) synchrotron radiation, 6) measurements of patterns, deformations and strains, 7) materials for energy and transports, 8) nano-structures, 9) virus: structure and infection mechanisms, 10) 3-dimensional imaging for molecules, cells and cellular tissues, 11) nano-particles and colloids, and 12) liquid crystals.

Coherent light microscopy

CERN Document Server

Ferraro, Pietro; Zalevsky, Zeev

2011-01-01

This book deals with the latest achievements in the field of optical coherent microscopy. While many other books exist on microscopy and imaging, this book provides a unique resource dedicated solely to this subject. Similarly, many books describe applications of holography, interferometry and speckle to metrology but do not focus on their use for microscopy. The coherent light microscopy reference provided here does not focus on the experimental mechanics of such techniques but instead is meant to provide a users manual to illustrate the strengths and capabilities of developing techniques. Th

Lobster eye as a collector for water window microscopy

Science.gov (United States)

Pina, L.; Maršíková, V.; Inneman, A.; Nawaz, M. F.; Jančárek, A.; Havlíková, R.

2017-08-01

Imaging in EUV, SXR and XR spectral bands of radiation is of increasing interest. Material science, biology and hot plasma are examples of relevant fast developing areas. Applications include spectroscopy, astrophysics, Soft X-ray Ray metrology, Water Window microscopy, radiography and tomography. Especially Water Window imaging has still not fully recognized potential in biology and medicine microscopy applications. Theoretical study and design of Lobster Eye (LE) optics as a collector for water window (WW) microscopy and comparison with a similar size ellipsoidal mirror condensor are presented.

Microscopy as a diagnostic tool in pulmonary tuberculosis

Directory of Open Access Journals (Sweden)

Ritu Singhal

2015-01-01

Full Text Available Tuberculosis continues to cast a huge impact on humanity with its high incidence and mortality, especially in developing countries. For tuberculosis case detection, microscopy continues to be indispensible, given its low cost, rapidity, simplicity of procedure and high specificity. Modifications have attempted to improve the sensitivity of microscopy which include: concentration methods such as centrifugation, N-acetyl cysteine–sodium hydroxide, bleach, ammonium sulfate or chitin. Furthermore, classical Ziehl–Neelsen (ZN staining has been subjected to varying carbol fuchsin concentrations or replaced by Kinyoun staining, fluorescent microscopy or immune-fluorescence. Currently, light emitting diode fluorescence is recognizably the most plausible method as an alternative to ZN staining.

Transience and persistence of natural hydrocarbon seepage in Mississippi Canyon, Gulf of Mexico

Science.gov (United States)

Garcia-Pineda, Oscar; MacDonald, Ian; Silva, Mauricio; Shedd, William; Daneshgar Asl, Samira; Schumaker, Bonny

2016-07-01

Analysis of the magnitude of oil discharged from natural hydrocarbon seeps can improve understanding of the carbon cycle and the Gulf of Mexico (GOM) ecosystem. With use of a large archive of remote sensing data, in combination with geophysical and multibeam data, we identified, mapped, and characterized natural hydrocarbon seeps in the Macondo prospect region near the wreck site of the drill-rig Deepwater Horizon (DWH). Satellite image processing and the cluster analysis revealed locations of previously undetected seep zones. Including duplicate detections, a total of 562 individual gas plumes were also observed in multibeam surveys. In total, SAR imagery confirmed 52 oil-producing seep zones in the study area. In almost all cases gas plumes were associated with oil-producing seep zones. The cluster of seeps in the vicinity of lease block MC302 appeared to host the most persistent and prolific oil vents. Oil slicks and gas plumes observed over the DWH site were consistent with discharges of residual oil from the wreckage. In contrast with highly persistent oil seeps observed in the Green Canyon and Garden Banks lease areas, the seeps in the vicinity of Macondo Prospect were intermittent. The difference in the number of seeps and the quantity of surface oil detected in Green Canyon was almost two orders of magnitude greater than in Mississippi Canyon.

Biological applications of phase-contrast electron microscopy.

Science.gov (United States)

Nagayama, Kuniaki

2014-01-01

Here, I review the principles and applications of phase-contrast electron microscopy using phase plates. First, I develop the principle of phase contrast based on a minimal model of microscopy, introducing a double Fourier-transform process to mathematically formulate the image formation. Next, I explain four phase-contrast (PC) schemes, defocus PC, Zernike PC, Hilbert differential contrast, and schlieren optics, as image-filtering processes in the context of the minimal model, with particular emphases on the Zernike PC and corresponding Zernike phase plates. Finally, I review applications of Zernike PC cryo-electron microscopy to biological systems such as protein molecules, virus particles, and cells, including single-particle analysis to delineate three-dimensional (3D) structures of protein and virus particles and cryo-electron tomography to reconstruct 3D images of complex protein systems and cells.

Optofluidic time-stretch quantitative phase microscopy.

Science.gov (United States)

Guo, Baoshan; Lei, Cheng; Wu, Yi; Kobayashi, Hirofumi; Ito, Takuro; Yalikun, Yaxiaer; Lee, Sangwook; Isozaki, Akihiro; Li, Ming; Jiang, Yiyue; Yasumoto, Atsushi; Di Carlo, Dino; Tanaka, Yo; Yatomi, Yutaka; Ozeki, Yasuyuki; Goda, Keisuke

2018-03-01

Innovations in optical microscopy have opened new windows onto scientific research, industrial quality control, and medical practice over the last few decades. One of such innovations is optofluidic time-stretch quantitative phase microscopy - an emerging method for high-throughput quantitative phase imaging that builds on the interference between temporally stretched signal and reference pulses by using dispersive properties of light in both spatial and temporal domains in an interferometric configuration on a microfluidic platform. It achieves the continuous acquisition of both intensity and phase images with a high throughput of more than 10,000 particles or cells per second by overcoming speed limitations that exist in conventional quantitative phase imaging methods. Applications enabled by such capabilities are versatile and include characterization of cancer cells and microalgal cultures. In this paper, we review the principles and applications of optofluidic time-stretch quantitative phase microscopy and discuss its future perspective. Copyright © 2017 Elsevier Inc. All rights reserved.

New microscopy for nanoimaging

CERN Document Server

Kinjo, Y; Watanabe, M

2002-01-01

Two types of new microscopy, namely, X-ray contact microscopy (XRCM) in combination with atomic force microscopy (AFM) and X-ray projection microscopy (XRPM) using synchrotron radiation and zone plate optics were used to image the fine structures of human chromosomes. In the XRCM plus AFM system, location of X-ray images on a photoresist has become far easier than that with our previous method using transmission electron microscopy coupled with the replica method. In addition, the images obtained suggested that the conformation of chromatin fiber differs from the current textbook model regarding the architecture of a eukaryotic chromosome. X-ray images with high contrast of the specimens could be obtained with XRPM. The resolution of each microscopy was about 30 and 200-300 nm for XRCM plus AFM and XRPM, respectively. (author)

2nd International Multidisciplinary Microscopy and Microanalysis Congress

CERN Document Server

Oral, Ahmet; Ozer, Mehmet

2015-01-01

The 2nd International Multidisciplinary Microscopy and Microanalysis Congress & Exhibition (InterM 2014) was held on 16–19 October 2014 in Oludeniz, Fethiye/ Mugla, Turkey. The aim of the congress was to gather scientists from various branches and discuss the latest improvements in the field of microscopy. The focus of the congress has been widened in an "interdisciplinary" manner, so as to allow all scientists working on several related subjects to participate and present their work. These proceedings include 33 peer-reviewed technical papers, submitted by leading academic and research institutions from over 17 countries and representing some of the most cutting-edge research available. The papers were presented at the congress in the following sessions: ·         Applications of Microscopy in the Physical Sciences ·         Applications of Microscopy in the Biological Sciences.

Graphene-enabled electron microscopy and correlated super-resolution microscopy of wet cells.

Science.gov (United States)

Wojcik, Michal; Hauser, Margaret; Li, Wan; Moon, Seonah; Xu, Ke

2015-06-11

The application of electron microscopy to hydrated biological samples has been limited by high-vacuum operating conditions. Traditional methods utilize harsh and laborious sample dehydration procedures, often leading to structural artefacts and creating difficulties for correlating results with high-resolution fluorescence microscopy. Here, we utilize graphene, a single-atom-thick carbon meshwork, as the thinnest possible impermeable and conductive membrane to protect animal cells from vacuum, thus enabling high-resolution electron microscopy of wet and untreated whole cells with exceptional ease. Our approach further allows for facile correlative super-resolution and electron microscopy of wet cells directly on the culturing substrate. In particular, individual cytoskeletal actin filaments are resolved in hydrated samples through electron microscopy and well correlated with super-resolution results.

Reflectance Confocal Microscopy in Lentigo Maligna.

Science.gov (United States)

Gamo, R; Pampín, A; Floristán, U

2016-12-01

Lentigo maligna is the most common type of facial melanoma. Diagnosis is complicated, however, as it shares clinical and dermoscopic characteristics with other cutaneous lesions of the face. Reflectance confocal microscopy is an imaging technique that permits the visualization of characteristic features of lentigo maligna. These include a disrupted honeycomb pattern and pagetoid cells with a tendency to show folliculotropism. These cells typically have a dendritic morphology, although they may also appear as round cells measuring over 20μm with atypical nuclei. Poorly defined dermal papillae and atypical cells may be seen at the dermal-epidermal junction and can form bridges resembling mitochondrial structures. Other characteristic findings include junctional swelling with atypical cells located around the follicles, resembling caput medusae. Reflectance confocal microscopy is a very useful tool for diagnosing lentigo maligna. Copyright © 2016 AEDV. Publicado por Elsevier España, S.L.U. All rights reserved.

Two-Photon Excitation Microscopy for the Study of Living Cells and Tissues

Science.gov (United States)

Benninger, Richard K.P.; Piston, David W.

2013-01-01

Two-photon excitation microscopy is an alternative to confocal microscopy that provides advantages for three-dimensional and deep tissue imaging. This unit will describe the basic physical principles behind two-photon excitation and discuss the advantages and limitations of its use in laser-scanning microscopy. The principal advantages of two-photon microscopy are reduced phototoxicity, increased imaging depth, and the ability to initiate highly localized photochemistry in thick samples. Practical considerations for the application of two-photon microscopy will then be discussed, including recent technological advances. This unit will conclude with some recent applications of two-photon microscopy that highlight the key advantages over confocal microscopy and the types of experiments which would benefit most from its application. PMID:23728746

Atom probe field ion microscopy and related topics: A bibliography 1993

Energy Technology Data Exchange (ETDEWEB)

Godfrey, R.D.; Miller, M.K.; Russell, K.F.

1994-10-01

This bibliography, covering the period 1993, includes references related to the following topics: atom probe field ion microscopy (APFIM), field emission (FE), and field ion microscopy (FIM). Technique-oriented studies and applications are included. The references contained in this document were compiled from a variety of sources including computer searches and personal lists of publications. To reduce the length of this document, the references have been reduced to the minimum necessary to locate the articles. The references are listed alphabetically by authors, an Addendum of references missed in previous bibliographies is included.

Atom probe field ion microscopy and related topics: A bibliography 1993

International Nuclear Information System (INIS)

Godfrey, R.D.; Miller, M.K.; Russell, K.F.

1994-10-01

This bibliography, covering the period 1993, includes references related to the following topics: atom probe field ion microscopy (APFIM), field emission (FE), and field ion microscopy (FIM). Technique-oriented studies and applications are included. The references contained in this document were compiled from a variety of sources including computer searches and personal lists of publications. To reduce the length of this document, the references have been reduced to the minimum necessary to locate the articles. The references are listed alphabetically by authors, an Addendum of references missed in previous bibliographies is included

The OptIPuter microscopy demonstrator: enabling science through a transatlantic lightpath.

Science.gov (United States)

Ellisman, M; Hutton, T; Kirkland, A; Lin, A; Lin, C; Molina, T; Peltier, S; Singh, R; Tang, K; Trefethen, A E; Wallom, D C H; Xiong, X

2009-07-13

The OptIPuter microscopy demonstrator project has been designed to enable concurrent and remote usage of world-class electron microscopes located in Oxford and San Diego. The project has constructed a network consisting of microscopes and computational and data resources that are all connected by a dedicated network infrastructure using the UK Lightpath and US Starlight systems. Key science drivers include examples from both materials and biological science. The resulting system is now a permanent link between the Oxford and San Diego microscopy centres. This will form the basis of further projects between the sites and expansion of the types of systems that can be remotely controlled, including optical, as well as electron, microscopy. Other improvements will include the updating of the Microsoft cluster software to the high performance computing (HPC) server 2008, which includes the HPC basic profile implementation that will enable the development of interoperable clients.

The OptIPuter microscopy demonstrator: enabling science through a transatlantic lightpath

Science.gov (United States)

Ellisman, M.; Hutton, T.; Kirkland, A.; Lin, A.; Lin, C.; Molina, T.; Peltier, S.; Singh, R.; Tang, K.; Trefethen, A.E.; Wallom, D.C.H.; Xiong, X.

2009-01-01

The OptIPuter microscopy demonstrator project has been designed to enable concurrent and remote usage of world-class electron microscopes located in Oxford and San Diego. The project has constructed a network consisting of microscopes and computational and data resources that are all connected by a dedicated network infrastructure using the UK Lightpath and US Starlight systems. Key science drivers include examples from both materials and biological science. The resulting system is now a permanent link between the Oxford and San Diego microscopy centres. This will form the basis of further projects between the sites and expansion of the types of systems that can be remotely controlled, including optical, as well as electron, microscopy. Other improvements will include the updating of the Microsoft cluster software to the high performance computing (HPC) server 2008, which includes the HPC basic profile implementation that will enable the development of interoperable clients. PMID:19487201

The art in science: electron microscopy and paintings conservation

International Nuclear Information System (INIS)

Waters, L.

2003-01-01

Full text: When examining a painting, a conservator uses many different and complementary methods of analysis to build an understanding of the materials and way the painting was constructed. Common methods of examination include x-radiography, infrared reflectography, ultraviolet fluorescence and optical microscopy of the surface of the painting. Minute samples of paint prepared as cross-sections are sometimes taken for optical examination under the microscope, and it is these that can, conveniently, be further analysed with electron microscopy to yield another level of information. Electron microscopy has a valuable role to play within the examination of paintings, be it for pigment identification alone, or at the other end of the spectrum, for informing issues around the attribution of works of art. This paper provides an overview of the use of electron microscopy in the conservation of paintings by discussing examples of work undertaken by the National Gallery of Victoria and the CSIRO. Work described includes the problem of distinguishing between restorers' original paint in a landscape by Arthur Streeton, and the examination of the ground or priming layer in a Rembrandt portrait which clarified its attribution to his studio. Copyright (2003) Australian Microbeam Analysis Society

Transmission Electron Microscopy Physics of Image Formation

CERN Document Server

Kohl, Helmut

2008-01-01

Transmission Electron Microscopy: Physics of Image Formation presents the theory of image and contrast formation, and the analytical modes in transmission electron microscopy. The principles of particle and wave optics of electrons are described. Electron-specimen interactions are discussed for evaluating the theory of scattering and phase contrast. Also discussed are the kinematical and dynamical theories of electron diffraction and their applications for crystal-structure analysis and imaging of lattices and their defects. X-ray microanalysis and electron energy-loss spectroscopy are treated as analytical methods. Specimen damage and contamination by electron irradiation limits the resolution for biological and some inorganic specimens. This fifth edition includes discussion of recent progress, especially in the area of aberration correction and energy filtering; moreover, the topics introduced in the fourth edition have been updated. Transmission Electron Microscopy: Physics of Image Formation is written f...

Short-chain alkanes fuel mussel and sponge Cycloclasticus symbionts from deep-sea gas and oil seeps.

Science.gov (United States)

Rubin-Blum, Maxim; Antony, Chakkiath Paul; Borowski, Christian; Sayavedra, Lizbeth; Pape, Thomas; Sahling, Heiko; Bohrmann, Gerhard; Kleiner, Manuel; Redmond, Molly C; Valentine, David L; Dubilier, Nicole

2017-06-19

Cycloclasticus bacteria are ubiquitous in oil-rich regions of the ocean and are known for their ability to degrade polycyclic aromatic hydrocarbons (PAHs). In this study, we describe Cycloclasticus that have established a symbiosis with Bathymodiolus heckerae mussels and poecilosclerid sponges from asphalt-rich, deep-sea oil seeps at Campeche Knolls in the southern Gulf of Mexico. Genomic and transcriptomic analyses revealed that, in contrast to all previously known Cycloclasticus, the symbiotic Cycloclasticus appears to lack the genes needed for PAH degradation. Instead, these symbionts use propane and other short-chain alkanes such as ethane and butane as carbon and energy sources, thus expanding the limited range of substrates known to power chemosynthetic symbioses. Analyses of short-chain alkanes in the environment of the Campeche Knolls symbioses revealed that these are present at high concentrations (in the μM to mM range). Comparative genomic analyses revealed high similarities between the genes used by the symbiotic Cycloclasticus to degrade short-chain alkanes and those of free-living Cycloclasticus that bloomed during the Deepwater Horizon oil spill. Our results indicate that the metabolic versatility of bacteria within the Cycloclasticus clade is higher than previously assumed, and highlight the expanded role of these keystone species in the degradation of marine hydrocarbons.

X-ray microscopy in Aarhus

International Nuclear Information System (INIS)

Uggerhoej, Erik; Abraham-Peskir, Joanna V.

2000-01-01

The Aarhus imaging soft X-ray microscope is now a busy multi-user facility. The optical set-up will be described and project highlights discussed. a) Metal-induced structural changes in whole cells in solution. The effects of aluminum, copper, nickel and zinc on protozoa investigated by using a combination of light microscopy, confocal scanning laser microscopy and X-ray microscopy. b) Botanical studies by X-ray microscopy used to compliment electron microscopy studies. c) Sludge morphology and iron precipitation in Danish freshwater plants by combining X-ray, scanning electron and transmission electron microscopy

Advanced Microscopy of Microbial Cells

DEFF Research Database (Denmark)

Haagensen, Janus Anders Juul; Regenberg, Birgitte; Sternberg, Claus

2011-01-01

microscopy, super-resolution optical microscopy (STED, SIM, PALM) as well as atomic force microscopy and Raman spectroscopy. Using examples of bistability in microbial populations as well as biofilm development and differentiation in bacterial and yeast consortia, we demonstrate the importance of microscopy...

Networking strategies of the microscopy community for improved utilization of advanced instruments: (1) The Australian Microscopy and Microanalysis Research Facility (AMMRF)

International Nuclear Information System (INIS)

Ringer, S.P.; Apperley, M.H.

2014-01-01

This paper describes the strategy underpinning the formation and operation of the Australian Microscopy and Microanalysis Research Facility (AMMRF). AMMRF is a formal collaboration that links eight Australian Universities together to create a user-focused national capability in microscopy and microanalysis. The AMMRF flagship capabilities include: Cameca IMS-1280 and NanoSIMS-50 ion microprobes (University of Western Australia); High-throughput, high-resolution cryoTEM (University of Queensland); Atom Probe Microscopy (University of Sydney); High-resolution Focussed Ion-Beam and SEM (Universities of Adelaide and NSW); High-resolution SEM microanalysis facility (University of New South Wales); and PHI TRIFT V nanoToF ToF-SIMS (University of South Australia). Secondly, a network of peer support and expert training has been established amongst facility professional support staff. The governance and funding of the organisation are described and the advantages and achievements of a nationally coordinated facility for microscopy and microanalysis are set out. Selected data are presented that benchmark the performance of the facility, describe the economic impact and demonstrate the impact on the quality of research outcomes as a result of operating national collaborative research infrastructure for microscopy and microanalysis

Circumventing photodamage in live-cell microscopy

Science.gov (United States)

Magidson, Valentin; Khodjakov, Alexey

2013-01-01

Fluorescence microscopy has become an essential tool in cell biology. This technique allows researchers to visualize the dynamics of tissue, cells, individual organelles and macromolecular assemblies inside the cell. Unfortunately, fluorescence microscopy is not completely ‘non-invasive’ as the high-intensity excitation light required for excitation of fluorophores is inherently toxic for live cells. Physiological changes induced by excessive illumination can lead to artifacts and abnormal responses. In this chapter we review major factors that contribute to phototoxicity and discuss practical solutions for circumventing photodamage. These solutions include the proper choice of image acquisition parameters, optimization of filter sets, hardware synchronization, and the use of intelligent illumination to avoid unnecessary light exposure. PMID:23931522

Investigation of graphite composite anodes surfaces by atomic force microscopy and related techniques

Energy Technology Data Exchange (ETDEWEB)

Hirasawa, Karen Akemi; Nishioka, Keiko; Sato, Tomohiro; Yamaguchi, Shoji; Mori, Shoichiro [Mitsubishi Chemical Corp., Tsukuba Research Center, Ibaraki (Japan)

1997-11-01

The surface of a synthetic graphite (KS-44) and polyvinylidene difluoride binder (PVDF) anode for lithium-ion secondary batteries is imaged using atomic force microscopy (AFM) and several related scanning probe microscope (SPM) instruments including: dynamic force microscopy (DFM), friction force microscopy (FFM), laterally-modulated friction force microscopy (LM-FFM), visco-elasticity atomic force microscopy (VE-AFM), and AFM/simultaneous current measurement mode (SCM). DFM is found to be an exceptional mode for topographic imaging while FFM results in the clearest contrast distinction between PVDF binder and KS-44 graphite regions. (orig.)

Helium ion microscopy and ultra-high-resolution scanning electron microscopy analysis of membrane-extracted cells reveals novel characteristics of the cytoskeleton of Giardia intestinalis.

Science.gov (United States)

Gadelha, Ana Paula Rocha; Benchimol, Marlene; de Souza, Wanderley

2015-06-01

Giardia intestinalis presents a complex microtubular cytoskeleton formed by specialized structures, such as the adhesive disk, four pairs of flagella, the funis and the median body. The ultrastructural organization of the Giardia cytoskeleton has been analyzed using different microscopic techniques, including high-resolution scanning electron microscopy. Recent advances in scanning microscopy technology have opened a new venue for the characterization of cellular structures and include scanning probe microscopy techniques such as ultra-high-resolution scanning electron microscopy (UHRSEM) and helium ion microscopy (HIM). Here, we studied the organization of the cytoskeleton of G. intestinalis trophozoites using UHRSEM and HIM in membrane-extracted cells. The results revealed a number of new cytoskeletal elements associated with the lateral crest and the dorsal surface of the parasite. The fine structure of the banded collar was also observed. The marginal plates were seen linked to a network of filaments, which were continuous with filaments parallel to the main cell axis. Cytoplasmic filaments that supported the internal structures were seen by the first time. Using anti-actin antibody, we observed a labeling in these filamentous structures. Taken together, these data revealed new surface characteristics of the cytoskeleton of G. intestinalis and may contribute to an improved understanding of the structural organization of trophozoites. Copyright © 2015 Elsevier Inc. All rights reserved.

Toward single cell traction microscopy within 3D collagen matrices

International Nuclear Information System (INIS)

Hall, Matthew S.; Long, Rong; Feng, Xinzeng; Huang, YuLing; Hui, Chung-Yuen; Wu, Mingming

2013-01-01

Mechanical interaction between the cell and its extracellular matrix (ECM) regulates cellular behaviors, including proliferation, differentiation, adhesion, and migration. Cells require the three-dimensional (3D) architectural support of the ECM to perform physiologically realistic functions. However, current understanding of cell–ECM and cell–cell mechanical interactions is largely derived from 2D cell traction force microscopy, in which cells are cultured on a flat substrate. 3D cell traction microscopy is emerging for mapping traction fields of single animal cells embedded in either synthetic or natively derived fibrous gels. We discuss here the development of 3D cell traction microscopy, its current limitations, and perspectives on the future of this technology. Emphasis is placed on strategies for applying 3D cell traction microscopy to individual tumor cell migration within collagen gels. - Highlights: • Review of the current state of the art in 3D cell traction force microscopy. • Bulk and micro-characterization of remodelable fibrous collagen gels. • Strategies for performing 3D cell traction microscopy within collagen gels

Toward single cell traction microscopy within 3D collagen matrices

Energy Technology Data Exchange (ETDEWEB)

Hall, Matthew S. [Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853 (United States); Long, Rong [Department of Mechanical Engineering, University of Alberta, Edmonton, AB, Canada T6G 2G8 (Canada); Feng, Xinzeng [Department of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14853 (United States); Huang, YuLing [Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853 (United States); Hui, Chung-Yuen [Department of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14853 (United States); Wu, Mingming, E-mail: mw272@cornell.edu [Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853 (United States)

2013-10-01

Mechanical interaction between the cell and its extracellular matrix (ECM) regulates cellular behaviors, including proliferation, differentiation, adhesion, and migration. Cells require the three-dimensional (3D) architectural support of the ECM to perform physiologically realistic functions. However, current understanding of cell–ECM and cell–cell mechanical interactions is largely derived from 2D cell traction force microscopy, in which cells are cultured on a flat substrate. 3D cell traction microscopy is emerging for mapping traction fields of single animal cells embedded in either synthetic or natively derived fibrous gels. We discuss here the development of 3D cell traction microscopy, its current limitations, and perspectives on the future of this technology. Emphasis is placed on strategies for applying 3D cell traction microscopy to individual tumor cell migration within collagen gels. - Highlights: • Review of the current state of the art in 3D cell traction force microscopy. • Bulk and micro-characterization of remodelable fibrous collagen gels. • Strategies for performing 3D cell traction microscopy within collagen gels.

Advanced Microscopy of Microbial Cells

DEFF Research Database (Denmark)

Haagensen, Janus Anders Juul; Regenberg, Birgitte; Sternberg, Claus

2011-01-01

Growing awareness of heterogeneity in cells of microbial populations has emphasized the importance of advanced microscopy for visualization and understanding of the molecular mechanisms underlying cell-to-cell variation. In this review, we highlight some of the recent advances in confocal...... microscopy, super-resolution optical microscopy (STED, SIM, PALM) as well as atomic force microscopy and Raman spectroscopy. Using examples of bistability in microbial populations as well as biofilm development and differentiation in bacterial and yeast consortia, we demonstrate the importance of microscopy...

Photoinduced force microscopy: A technique for hyperspectral nanochemical mapping

Science.gov (United States)

Murdick, Ryan A.; Morrison, William; Nowak, Derek; Albrecht, Thomas R.; Jahng, Junghoon; Park, Sung

2017-08-01

Advances in nanotechnology have intensified the need for tools that can characterize newly synthesized nanomaterials. A variety of techniques has recently been shown which combines atomic force microscopy (AFM) with optical illumination including tip-enhanced Raman spectroscopy (TERS), scattering-type scanning near-field optical microscopy (sSNOM), and photothermal induced resonance microscopy (PTIR). To varying degrees, these existing techniques enable optical spectroscopy with the nanoscale spatial resolution inherent to AFM, thereby providing nanochemical interrogation of a specimen. Here we discuss photoinduced force microscopy (PiFM), a recently developed technique for nanoscale optical spectroscopy that exploits image forces acting between an AFM tip and sample to detect wavelength-dependent polarization within the sample to generate absorption spectra. This approach enables ∼10 nm spatial resolution with spectra that show correlation with macroscopic optical absorption spectra. Unlike other techniques, PiFM achieves this high resolution with virtually no constraints on sample or substrate properties. The applicability of PiFM to a variety of archetypal systems is reported here, highlighting the potential of PiFM as a useful tool for a wide variety of industrial and academic investigations, including semiconducting nanoparticles, nanocellulose, block copolymers, and low dimensional systems, as well as chemical and morphological mixing at interfaces.

Kelvin probe force microscopy from single charge detection to device characterization

CERN Document Server

Glatzel, Thilo

2018-01-01

This book provides a comprehensive introduction to the methods and variety of Kelvin probe force microscopy, including technical details. It also offers an overview of the recent developments and numerous applications, ranging from semiconductor materials, nanostructures and devices to sub-molecular and atomic scale electrostatics. In the last 25 years, Kelvin probe force microscopy has developed from a specialized technique applied by a few scanning probe microscopy experts into a tool used by numerous research and development groups around the globe. This sequel to the editors’ previous volume “Kelvin Probe Force Microscopy: Measuring and Compensating Electrostatic Forces,” presents new and complementary topics. It is intended for a broad readership, from undergraduate students to lab technicians and scanning probe microscopy experts who are new to the field.

Simultaneous differential spinning disk fluorescence optical sectioning microscopy and nanomechanical mapping atomic force microscopy

International Nuclear Information System (INIS)

Miranda, Adelaide; De Beule, Pieter A. A.; Martins, Marco

2015-01-01

Combined microscopy techniques offer the life science research community a powerful tool to investigate complex biological systems and their interactions. Here, we present a new combined microscopy platform based on fluorescence optical sectioning microscopy through aperture correlation microscopy with a Differential Spinning Disk (DSD) and nanomechanical mapping with an Atomic Force Microscope (AFM). The illumination scheme of the DSD microscope unit, contrary to standard single or multi-point confocal microscopes, provides a time-independent illumination of the AFM cantilever. This enables a distortion-free simultaneous operation of fluorescence optical sectioning microscopy and atomic force microscopy with standard probes. In this context, we discuss sample heating due to AFM cantilever illumination with fluorescence excitation light. Integration of a DSD fluorescence optical sectioning unit with an AFM platform requires mitigation of mechanical noise transfer of the spinning disk. We identify and present two solutions to almost annul this noise in the AFM measurement process. The new combined microscopy platform is applied to the characterization of a DOPC/DOPS (4:1) lipid structures labelled with a lipophilic cationic indocarbocyanine dye deposited on a mica substrate

Simultaneous differential spinning disk fluorescence optical sectioning microscopy and nanomechanical mapping atomic force microscopy

Energy Technology Data Exchange (ETDEWEB)

Miranda, Adelaide; De Beule, Pieter A. A., E-mail: pieter.de-beule@inl.int [Applied Nano-Optics Laboratory, International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga, s/n, 4715-330 Braga (Portugal); Martins, Marco [Nano-ICs Group, International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga, s/n, 4715-330 Braga (Portugal)

2015-09-15

Combined microscopy techniques offer the life science research community a powerful tool to investigate complex biological systems and their interactions. Here, we present a new combined microscopy platform based on fluorescence optical sectioning microscopy through aperture correlation microscopy with a Differential Spinning Disk (DSD) and nanomechanical mapping with an Atomic Force Microscope (AFM). The illumination scheme of the DSD microscope unit, contrary to standard single or multi-point confocal microscopes, provides a time-independent illumination of the AFM cantilever. This enables a distortion-free simultaneous operation of fluorescence optical sectioning microscopy and atomic force microscopy with standard probes. In this context, we discuss sample heating due to AFM cantilever illumination with fluorescence excitation light. Integration of a DSD fluorescence optical sectioning unit with an AFM platform requires mitigation of mechanical noise transfer of the spinning disk. We identify and present two solutions to almost annul this noise in the AFM measurement process. The new combined microscopy platform is applied to the characterization of a DOPC/DOPS (4:1) lipid structures labelled with a lipophilic cationic indocarbocyanine dye deposited on a mica substrate.

Immobilization of uranium in biofilm microorganisms exposed to groundwater seeps over granitic rock tunnel walls in Olkiluoto, Finland

Science.gov (United States)

Krawczyk-Bärsch, Evelyn; Lünsdorf, Heinrich; Pedersen, Karsten; Arnold, Thuro; Bok, Frank; Steudtner, Robin; Lehtinen, Anne; Brendler, Vinzenz

2012-11-01

In an underground rock characterization facility, the ONKALO tunnel in Finland, massive 5-10-mm thick biofilms were observed attached to tunnel walls where groundwater was seeping from bedrock fractures at a depth of 70 m. In laboratory experiments performed in a flow cell with detached biofilms to study the effect of uranium on the biofilm, uranium was added to the circulating groundwater (CGW) obtained from the fracture feeding the biofilm. The final uranium concentration in the CGW was adjusted to 4.25 × 10-5 M, in the range expected from a leaking spent nuclear fuel (SNF) canister in a future underground repository. The effects were investigated using microelectrodes to measure pH and Eh, time-resolved laser fluorescence spectroscopy (TRLFS), energy-filtered transmission electron microscopy (EF-TEM), and electron energy-loss spectroscopy (EELS) studies and thermodynamic calculations were utilized as well. The results indicated that the studied biofilms constituted their own microenvironments, which differed significantly from that of the CGW. A pH of 5.37 was recorded inside the biofilm, approximately 3.5 units lower than the pH observed in the CGW, due to sulfide oxidation to sulfuric acid in the biofilm. Similarly, the Eh of +73 mV inside the biofilm was approximately 420 mV lower than the Eh measured in the CGW. Adding uranium increased the pH in the biofilm to 7.27 and reduced the Eh to -164 mV. The changes of Eh and pH influenced the bioavailability of uranium, since microbial metabolic processes are sensitive to metals and their speciation. EF-TEM investigations indicated that uranium in the biofilm was immobilized intracellularly in microorganisms by the formation of metabolically mediated uranyl phosphate, similar to needle-shaped autunite (Ca[UO2]2[PO4]2·2-6H2O) or meta-autunite (Ca[UO2]2[PO4]2·10-12H2O). In contrast, TRLFS studies of the contaminated CGW identified aqueous uranium carbonate species, likely (Ca2UO2[CO3]3), formed due to the high

Detection of laser damage by Raman microscopy

International Nuclear Information System (INIS)

Fauchet, P.M.; Campbell, I.H.; Adar, F.

1988-01-01

The authors demonstrate that Raman miroscopy is a sensitive and quantitative tool to detect and characterize laser-induced damage in solids. After damage is induced with single or multiple high power laser pulses, a Raman microprobe maps the surface of the sample with one micron spatial resolution. By performing accurate measurements of the Stokes line, the authors have been able to measure stress, strain and crystallinity in various samples which had been exposed to high intensity pulses. These results are compared to those obtained using conventional tools such as Nomarski microscopy. Major advantages of Raman microscopy include sensitivity to subtle structural modifications and the fact that it gives quantitative measurements

Fluorescence (Multiwave) Confocal Microscopy.

Science.gov (United States)

Welzel, J; Kästle, Raphaela; Sattler, Elke C

2016-10-01

In addition to reflectance confocal microscopy, multiwave confocal microscopes with different laser wavelengths in combination with exogenous fluorophores allow fluorescence mode confocal microscopy in vivo and ex vivo. Fluorescence mode confocal microscopy improves the contrast between the epithelium and the surrounding soft tissue and allows the depiction of certain structures, like epithelial tumors, nerves, and glands. Copyright © 2016 Elsevier Inc. All rights reserved.

Phylogenomic analysis of Candidatus ‘Izimaplasma’ species: free-living representatives from a Tenericutes clade found in methane seeps

KAUST Repository

Skennerton, Connor T.

2016-04-08

Tenericutes are a unique class of bacteria that lack a cell wall and are typically parasites or commensals of eukaryotic hosts. Environmental 16S rDNA surveys have identified a number of tenericute clades in diverse environments, introducing the possibility that these Tenericutes may represent non-host-associated, free-living microorganisms. Metagenomic sequencing of deep-sea methane seep sediments resulted in the assembly of two genomes from a Tenericutes-affiliated clade currently known as \\'NB1-n\\' (SILVA taxonomy) or \\'RF3\\' (Greengenes taxonomy). Metabolic reconstruction revealed that, like cultured members of the Mollicutes, these \\'NB1-n\\' representatives lack a tricarboxylic acid cycle and instead use anaerobic fermentation of simple sugars for substrate level phosphorylation. Notably, the genomes also contained a number of unique metabolic features including hydrogenases and a simplified electron transport chain containing an RNF complex, cytochrome bd oxidase and complex I. On the basis of the metabolic potential predicted from the annotated genomes, we devised an anaerobic enrichment media that stimulated the growth of these Tenericutes at 10 °C, resulting in a mixed culture where these organisms represented ∼60% of the total cells by targeted fluorescence in situ hybridization (FISH). Visual identification by FISH confirmed these organisms were not directly associated with Eukaryotes and electron cryomicroscopy of cells in the enrichment culture confirmed an ultrastructure consistent with the defining phenotypic property of Tenericutes, with a single membrane and no cell wall. On the basis of their unique gene content, phylogenetic placement and ultrastructure, we propose these organisms represent a novel class within the Tenericutes, and suggest the names Candidatus \\'Izimaplasma sp. HR1\\' and Candidatus \\'Izimaplasma sp. HR2\\' for the two genome representatives.

Using comprehensive two-dimensional gas chromatography to explore the geochemistry of the Santa Barbara oil seeps

Energy Technology Data Exchange (ETDEWEB)

Reddy, Christopher; Nelson, Robert

2013-03-27

The development of comprehensive two-dimensional gas chromatography (GC x GC) has expanded the analytical window for studying complex mixtures like oil. Compared to traditional gas chromatography, this technology separates and resolves at least an order of magnitude more compounds, has a much larger signal to noise ratio, and sorts compounds based on their chemical class; hence, providing highly refined inventories of petroleum hydrocarbons in geochemical samples that was previously unattainable. In addition to the increased resolution afforded by GC x GC, the resulting chromatograms have been used to estimate the liquid vapor pressures, aqueous solubilities, octanol-water partition coefficients, and vaporization enthalpies of petroleum hydrocarbons. With these relationships, powerful and incisive analyses of phase-transfer processes affecting petroleum hydrocarbon mixtures in the environment are available. For example, GC x GC retention data has been used to quantitatively deconvolve the effects of phase transfer processes such as water washing and evaporation. In short, the positive attributes of GC x GC-analysis have led to a methodology that has revolutionized the analysis of petroleum hydrocarbons. Overall, this research has opened numerous fields of study on the biogeochemical "genetics" (referred to as petroleomics) of petroleum samples in both subsurface and surface environments. Furthermore, these new findings have already been applied to the behavior of oil at other seeps as well, for petroleum exploration and oil spill studies.

Immunofluorescence Microscopy and mRNA Analysis of Human Embryonic Stem Cells (hESCs) Including Primary Cilia Associated Signaling Pathways

DEFF Research Database (Denmark)

Vestergaard, Maj Linea; Awan, Aashir; Warzecha, Caroline Becker

2016-01-01

onto 16-well glass chambers, and continuing with the general IFM and qPCR anlysis. The techniques are illustrated with results on cellular localization of transcriptional factors and components of the Hedgehog, Wnt, PDGF, and TGFβ signaling pathways to primary cilia in stem cell maintenance......This chapter describes the procedures for immunofluorescence microscopy (IFM) and quantitative PCR (qPCR) analyses of human embryonic stem cells (hESCs) grown specifically under feeder-free conditions. A detailed protocol is provided outlining the steps from initially growing the cells, passaging...

Developments in contact X-ray microscopy in biomedical research

International Nuclear Information System (INIS)

Davies, R.L.; Flores, N.A.; Pye, J.K.

1985-01-01

Contact X-ray microscopy (microradiography) is a method of studying the microstructure of biological tissue. These techniques have been used to study the historadiological details of human breast tissue and sections of human ear ossicles. X-ray microscopy can also be used to demonstrate variations in structural densities seen in histological specimens including the detection of microcalcification. A modification of existing apparatus is described which has resulted in improved image-contrast and detail. The ability of X-rays to penetrate relatively thick sections of tissue makes it an ideal method for studying the morphology of biological structures, particularly in calcified tissue. The tissues may be further examined by conventional histology, elemental analysis, etc. The technique has a complementary role to alternative methods of tissue microscopy. (author)

Data Validation Package October 2015 Groundwater and Surface Water Sampling at the Monticello, Utah, Processing Site January 2016

Energy Technology Data Exchange (ETDEWEB)

Nguyen, Jason [U.S. Dept. of Energy, Washington, DC (United States). Office of Legacy Management; Smith, Fred [Navarro Research and Engineering, Inc., Oak Ridge, TN (United States)

2016-01-21

Sampling Period: October 12–14, 2015. This semiannual event includes sampling groundwater and surface water at the Monticello Mill Tailings Site. Sampling and analyses were conducted as specified in the 2004 Monticello Mill Tailings Site Operable Unit III Post-Record of Decision Monitoring Plan, Draft Final and Sampling and Analysis Plan for U.S. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated). Samples were collected from 52 of 61 planned locations (15 of 17 former mill site wells, 17 of 18 downgradient wells, 9 of 9 downgradient permeable reactive barrier wells, 2 of 7 seeps and wetlands, and 9 of 10 surface water locations). Locations MW00-07, Seep 1, Seep 2, Seep 3, Seep 5, Seep 6, SW00-01, T01-13, and T01-19 were not sampled because of insufficient water availability. All samples were filtered as specified in the monitoring plan. Duplicate samples were collected from surface water location W3-04 and from monitoring wells 82-08, 92-09, and 92-10. Water levels were measured at all but one sampled well and an additional set of wells. The contaminants of concern (COCs) for the Monticello Mill Tailings Site are arsenic, manganese, molybdenum, nitrate + nitrite as nitrogen (nitrate + nitrite as N), selenium, uranium, and vanadium. Time-concentration graphs of the COCs for all groundwater and surface water locations are included in this report. Locations with COCs that exceeded remediation goals are listed.

Polarization contrast in photon scanning tunnelling microscopy combined with atomic force microscopy

NARCIS (Netherlands)

Propstra, K.; Propstra, K.; van Hulst, N.F.

1995-01-01

Photon scanning tunnelling microscopy combined with atomic force microscopy allows simultaneous acquisition and direct comparison of optical and topographical images, both with a lateral resolution of about 30 nm, far beyond the optical diffraction limit. The probe consists of a modified

CARS microscopy for imaging

International Nuclear Information System (INIS)

Arzumanyan Grigory; Voskanyan Karine

2013-01-01

Optical microscopy grows in its importance with the development of modern nanotechnology, biotechnology, methods of diagnostics and treatment of most dangerous diseases for mankind. There are several important goals of optical microscopy for biomedical studies among which the next three may be distinguished: fast imaging with high lateral spatial resolution, 3-D sectioning capability and high contrast for chemical selectivity. To meet these specific requirements, various types of both linear and nonlinear optical microscopy were elaborated. (authors)

Concepts in Light Microscopy of Viruses

Science.gov (United States)

Witte, Robert; Georgi, Fanny

2018-01-01

Viruses threaten humans, livestock, and plants, and are difficult to combat. Imaging of viruses by light microscopy is key to uncover the nature of known and emerging viruses in the quest for finding new ways to treat viral disease and deepening the understanding of virus–host interactions. Here, we provide an overview of recent technology for imaging cells and viruses by light microscopy, in particular fluorescence microscopy in static and live-cell modes. The review lays out guidelines for how novel fluorescent chemical probes and proteins can be used in light microscopy to illuminate cells, and how they can be used to study virus infections. We discuss advantages and opportunities of confocal and multi-photon microscopy, selective plane illumination microscopy, and super-resolution microscopy. We emphasize the prevalent concepts in image processing and data analyses, and provide an outlook into label-free digital holographic microscopy for virus research. PMID:29670029

Exploring neural cell dynamics with digital holographic microscopy

KAUST Repository

Marquet, Pierre; Depeursinge, Christian D.; Magistretti, Pierre J.

2013-01-01

In this review, we summarize how the new concept of digital optics applied to the field of holographic microscopy has allowed the development of a reliable and flexible digital holographic quantitative phase microscopy (DH-QPM) technique at the nanoscale particularly suitable for cell imaging. Particular emphasis is placed on the original biological ormation provided by the quantitative phase signal. We present the most relevant DH-QPM applications in the field of cell biology, including automated cell counts, recognition, classification, three-dimensional tracking, discrimination between physiological and pathophysiological states, and the study of cell membrane fluctuations at the nanoscale. In the last part, original results show how DH-QPM can address two important issues in the field of neurobiology, namely, multiple-site optical recording of neuronal activity and noninvasive visualization of dendritic spine dynamics resulting from a full digital holographic microscopy tomographic approach. Copyright © 2013 by Annual Reviews.

Exploring neural cell dynamics with digital holographic microscopy

KAUST Repository

Marquet, Pierre

2013-07-11

In this review, we summarize how the new concept of digital optics applied to the field of holographic microscopy has allowed the development of a reliable and flexible digital holographic quantitative phase microscopy (DH-QPM) technique at the nanoscale particularly suitable for cell imaging. Particular emphasis is placed on the original biological ormation provided by the quantitative phase signal. We present the most relevant DH-QPM applications in the field of cell biology, including automated cell counts, recognition, classification, three-dimensional tracking, discrimination between physiological and pathophysiological states, and the study of cell membrane fluctuations at the nanoscale. In the last part, original results show how DH-QPM can address two important issues in the field of neurobiology, namely, multiple-site optical recording of neuronal activity and noninvasive visualization of dendritic spine dynamics resulting from a full digital holographic microscopy tomographic approach. Copyright © 2013 by Annual Reviews.

Bridging fluorescence microscopy and electron microscopy

NARCIS (Netherlands)

Giepmans, Ben N. G.

Development of new fluorescent probes and fluorescence microscopes has led to new ways to study cell biology. With the emergence of specialized microscopy units at most universities and research centers, the use of these techniques is well within reach for a broad research community. A major

All-optical optoacoustic microscopy based on probe beam deflection technique

OpenAIRE

Maswadi, Saher M.; Ibey, Bennett L.; Roth, Caleb C.; Tsyboulski, Dmitri A.; Beier, Hope T.; Glickman, Randolph D.; Oraevsky, Alexander A.

2016-01-01

Optoacoustic (OA) microscopy using an all-optical system based on the probe beam deflection technique (PBDT) for detection of laser-induced acoustic signals was investigated as an alternative to conventional piezoelectric transducers. PBDT provides a number of advantages for OA microscopy including (i) efficient coupling of laser excitation energy to the samples being imaged through the probing laser beam, (ii) undistorted coupling of acoustic waves to the detector without the need for separa...

French Society of Microscopy, 10. conference

International Nuclear Information System (INIS)

Thibault-Penisson, J.; Cremer, Ch.; Susini, J.; Kirklanda, A.I.; Rigneault, H.; Renault, O.; Bailly, A.; Zagonel, L.F.; Barrett, N.; Bogner, A.; Gauthier, C.; Jouneau, P.H.; Thollet, G.; Fuchs, G.; Basset, D.; Deconihout, B.; Vurpillot, F.; Vella, A.; Matthieu, G.; Cadel, E.; Bostel, A.; Blavette, D.; Baumeister, W.; Usson, Y.; Zaefferer, St.; Laffont, L.; Weyland, M.; Thomas, J.M.; Midgley, P.; Benlekbir, S.; Epicier, Th.; Diop, B.N.; Roux, St.; Ou, M.; Perriat, P.; Bausach, M.; Aouine, M.; Berhault, G.; Idrissi, H.; Cottevieille, M.; Jonic, S.; Larquet, E.; Svergun, D.; Vannoni, M.A.; Boisset, N.; Ersena, O.; Werckmann, J.; Ulhaq, C.; Hirlimann, Ch.; Tihay, F.; Cuong, Pham-Huu; Crucifix, C.; Schultz, P.; Jornsanoha, P.; Thollet, G.; Masenelli-Varlot, K.; Gauthier, C.; Ludwig, W.; King, A.; Johnson, G.; Gonzalves-Hoennicke, M.; Reischig, P.; Messaoudi, C.; Ibrahim, R.; Marco, S.; Klie, R.F.; Zhao, Y.; Yang, G.; Zhu, Y.; Hue, F.; Hytch, M.; Hartmann, J.M.; Bogumilowicz, Y.; Claverie, A.; Klein, H.; Alloyeau, D.; Ricolleau, C.; Langlois, C.; Le Bouar, Y.; Loiseau, A.; Colliex, C.; Stephan, O.; Kociak, M.; Tence, M.; Gloter, A.; Imhoff, D.; Walls, M.; Nelayah, J.; March, K.; Couillard, M.; Ailliot, C.; Bertin, F.; Cooper, D.; Rivallin, P.; Dumelie, N.; Benhayoune, H.; Balossier, G.; Cheynet, M.; Pokrant, S.; Tichelaar, F.; Rouviere, J.L.; Cooper, D.; Truche, R.; Chabli, A.; Debili, M.Y.; Houdellier, F.; Warot-Fonrose, B.; Hytch, M.J.; Snoeck, E.; Calmels, L.; Serin, V.; Schattschneider, P.; Jacob, D.; Cordier, P.

2007-01-01

This document gathers the resumes of some of the presentations made at this conference whose aim was to present the last developments and achievements of the 3 complementary microscopies: optical microscopy, electron microscopy and X-ray microscopy. The contributions have been organized around the following 12 topics: 1) new technical developments, 2) 3-dimensional imaging, 3) quantitative microscopy, 4) technical progress in photon microscopy, 5) synchrotron radiation, 6) measurements of patterns, deformations and strains, 7) materials for energy and transports, 8) nano-structures, 9) virus: structure and infection mechanisms, 10) 3-dimensional imaging for molecules, cells and cellular tissues, 11) nano-particles and colloids, and 12) liquid crystals

Characterization of duplex stainless steels by TEM [transmission electron microscopy], SANS [small-angle neutron scattering], and APFIM [atom-probe field ion microscopy] techniques

International Nuclear Information System (INIS)

Chung, H.M.; Chopra, O.K.

1987-06-01

Results are presented of complementary characterization of aged duplex stainless steels by advanced metallographic techniques, including transmission and high-voltage electron microscopies; small-angle neutron scattering; and atom-probe field ion microscopy. On the basis of the characterization, the mechanisms of aging embrittlement have been shown to be associated with the precipitation of Ni- and Si-rich G phase and Cr-rich α' in the ferrite, and M 23 C 6 carbides on the austenite-ferrite phase boundaries. 19 refs., 19 figs., 1 tab

Microsphere-aided optical microscopy and its applications for super-resolution imaging

Science.gov (United States)

Upputuri, Paul Kumar; Pramanik, Manojit

2017-12-01

The spatial resolution of a standard optical microscope (SOM) is limited by diffraction. In visible spectrum, SOM can provide ∼ 200 nm resolution. To break the diffraction limit several approaches were developed including scanning near field microscopy, metamaterial super-lenses, nanoscale solid immersion lenses, super-oscillatory lenses, confocal fluorescence microscopy, techniques that exploit non-linear response of fluorophores like stimulated emission depletion microscopy, stochastic optical reconstruction microscopy, etc. Recently, photonic nanojet generated by a dielectric microsphere was used to break the diffraction limit. The microsphere-approach is simple, cost-effective and can be implemented under a standard microscope, hence it has gained enormous attention for super-resolution imaging. In this article, we briefly review the microsphere approach and its applications for super-resolution imaging in various optical imaging modalities.

Confocal Raman Microscopy

CERN Document Server

Dieing, Thomas; Toporski, Jan

2011-01-01

Confocal Raman Microscopy is a relatively new technique that allows chemical imaging without specific sample preparation. By integrating a sensitive Raman spectrometer within a state-of-the-art microscope, Raman microscopy with a spatial resolution down to 200nm laterally and 500nm vertically can be achieved using visible light excitation. Recent developments in detector and computer technology as well as optimized instrument design have reduced integration times of Raman spectra by orders of magnitude, so that complete images consisting of tens of thousands of Raman spectra can be acquired in seconds or minutes rather than hours, which used to be standard just one decade ago. The purpose of this book is to provide the reader a comprehensive overview of the rapidly developing field of Confocal Raman Microscopy and its applications.

Fluorescence confocal microscopy for pathologists.

Science.gov (United States)

Ragazzi, Moira; Piana, Simonetta; Longo, Caterina; Castagnetti, Fabio; Foroni, Monica; Ferrari, Guglielmo; Gardini, Giorgio; Pellacani, Giovanni

2014-03-01

Confocal microscopy is a non-invasive method of optical imaging that may provide microscopic images of untreated tissue that correspond almost perfectly to hematoxylin- and eosin-stained slides. Nowadays, following two confocal imaging systems are available: (1) reflectance confocal microscopy, based on the natural differences in refractive indices of subcellular structures within the tissues; (2) fluorescence confocal microscopy, based on the use of fluorochromes, such as acridine orange, to increase the contrast epithelium-stroma. In clinical practice to date, confocal microscopy has been used with the goal of obviating the need for excision biopsies, thereby reducing the need for pathological examination. The aim of our study was to test fluorescence confocal microscopy on different types of surgical specimens, specifically breast, lymph node, thyroid, and colon. The confocal images were correlated to the corresponding histological sections in order to provide a morphologic parallel and to highlight current limitations and possible applications of this technology for surgical pathology practice. As a result, neoplastic tissues were easily distinguishable from normal structures and reactive processes such as fibrosis; the use of fluorescence enhanced contrast and image quality in confocal microscopy without compromising final histologic evaluation. Finally, the fluorescence confocal microscopy images of the adipose tissue were as accurate as those of conventional histology and were devoid of the frozen-section-related artefacts that can compromise intraoperative evaluation. Despite some limitations mainly related to black/white images, which require training in imaging interpretation, this study confirms that fluorescence confocal microscopy may represent an alternative to frozen sections in the assessment of margin status in selected settings or when the conservation of the specimen is crucial. This is the first study to employ fluorescent confocal microscopy on

A novel fiber laser development for photoacoustic microscopy

Science.gov (United States)

Yavas, Seydi; Aytac-Kipergil, Esra; Arabul, Mustafa U.; Erkol, Hakan; Akcaalan, Onder; Eldeniz, Y. Burak; Ilday, F. Omer; Unlu, Mehmet B.

2013-03-01

Photoacoustic microscopy, as an imaging modality, has shown promising results in imaging angiogenesis and cutaneous malignancies like melanoma, revealing systemic diseases including diabetes, hypertension, tracing drug efficiency and assessment of therapy, monitoring healing processes such as wound cicatrization, brain imaging and mapping. Clinically, photoacoustic microscopy is emerging as a capable diagnostic tool. Parameters of lasers used in photoacoustic microscopy, particularly, pulse duration, energy, pulse repetition frequency, and pulse-to-pulse stability affect signal amplitude and quality, data acquisition speed and indirectly, spatial resolution. Lasers used in photoacoustic microscopy are typically Q-switched lasers, low-power laser diodes, and recently, fiber lasers. Significantly, the key parameters cannot be adjusted independently of each other, whereas microvasculature and cellular imaging, e.g., have different requirements. Here, we report an integrated fiber laser system producing nanosecond pulses, covering the spectrum from 600 nm to 1100 nm, developed specifically for photoacoustic excitation. The system comprises of Yb-doped fiber oscillator and amplifier, an acousto-optic modulator and a photonic-crystal fiber to generate supercontinuum. Complete control over the pulse train, including generation of non-uniform pulse trains, is achieved via the AOM through custom-developed field-programmable gate-array electronics. The system is unique in that all the important parameters are adjustable: pulse duration in the range of 1-3 ns, pulse energy up to 10 μJ, repetition rate from 50 kHz to 3 MHz. Different photocoustic imaging probes can be excited with the ultrabroad spectrum. The entire system is fiber-integrated; guided-beam-propagation rendersit misalignment free and largely immune to mechanical perturbations. The laser is robust, low-cost and built using readily available components.

Superresolution size determination in fluorescence microscopy: A comparison between spatially modulated illumination and confocal laser scanning microscopy

International Nuclear Information System (INIS)

Spoeri, Udo; Failla, Antonio Virgilio; Cremer, Christoph

2004-01-01

Recently developed far field light optical methods are a powerful tool to analyze biological nanostructures and their dynamics, in particular including the interior of three-dimensionally conserved cells. In this article, the recently described method of spatially modulated illumination (SMI) microscopy has been further extended to the online determination of the extension of small, subwavelength sized, fluorescent objects (nanosizing). Using fluorescence excitation with 488 nm, the determination of fluorescent labeled object diameters down to 40 nm corresponding to about 1/12th of the wavelength used for one-photon excitation could be shown. The results of the SMI nanosizing procedure for a detailed, systematic variation of the object diameter are presented together with a fast algorithm for online size evaluation. In addition, we show a direct comparison of the diameter of 'colocalization volumes' between SMI nanosizing and conventional confocal laser scanning microscopy

Solid-immersion fluorescence microscopy with increased emission and super resolution

Energy Technology Data Exchange (ETDEWEB)

Liau, Z. L.; Porter, J. M. [Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, Massachusetts 02420 (United States); Liau, A. A.; Chen, J. J. [Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Salmon, W. C. [Whitehead Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Sheu, S. S. [Department of Medicine, Jefferson Medical College, Philadelphia, Pennsylvania 19107 (United States)

2015-01-07

We investigate solid-immersion fluorescence microscopy suitable for super-resolution nanotechnology and biological imaging, and have observed limit of resolution as small as 15 nm with microspheres, mitochondria, and chromatin fibers. We have further observed that fluorescence efficiency increases with excitation power density, implicating appreciable stimulated emission and increased resolution. We discuss potential advantages of the solid-immersion microscopy, including combined use with previously established super-resolution techniques for reaching deeper beyond the conventional diffraction limit.

Atomic force microscopy and confocal laser scanning microscopy on the cytoskeleton of permeabilised and embedded cells

International Nuclear Information System (INIS)

Meller, Karl; Theiss, Carsten

2006-01-01

We describe a technical method of cell permeabilisation and embedding to study the organisation and distribution of intracellular proteins with aid of atomic force microscopy and confocal laser scanning microscopy in identical areas. While confocal laser scanning microscopy is useful for the identification of certain proteins subsequent labelling with markers or antibodies, atomic force microscopy allows the observation of macromolecular structures in fixed and living cells. To demonstrate the field of application of this preparatory technique, cells were permeabilised, fixed, and the actin cytoskeleton was stained with phalloidin-rhodamine. Confocal laser scanning microscopy was used to show the organisation of these microfilaments, e.g. geodesic dome structures. Thereafter, cells were embedded in Durcupan water-soluble resin, followed by UV-polymerisation of resin at 4 o C. This procedure allowed intracellular visualisation of the cell nucleus or cytoskeletal elements by atomic force microscopy, for instance to analyse the globular organisation of actin filaments. Therefore, this method offers a great potential to combine both microscopy techniques in order to understand and interpret intracellular protein relations, for example, the biochemical and morphological interaction of the cytoskeleton

Low Dimensional Representation of Fisher Vectors for Microscopy Image Classification.

Science.gov (United States)

Song, Yang; Li, Qing; Huang, Heng; Feng, Dagan; Chen, Mei; Cai, Weidong

2017-08-01

Microscopy image classification is important in various biomedical applications, such as cancer subtype identification, and protein localization for high content screening. To achieve automated and effective microscopy image classification, the representative and discriminative capability of image feature descriptors is essential. To this end, in this paper, we propose a new feature representation algorithm to facilitate automated microscopy image classification. In particular, we incorporate Fisher vector (FV) encoding with multiple types of local features that are handcrafted or learned, and we design a separation-guided dimension reduction method to reduce the descriptor dimension while increasing its discriminative capability. Our method is evaluated on four publicly available microscopy image data sets of different imaging types and applications, including the UCSB breast cancer data set, MICCAI 2015 CBTC challenge data set, and IICBU malignant lymphoma, and RNAi data sets. Our experimental results demonstrate the advantage of the proposed low-dimensional FV representation, showing consistent performance improvement over the existing state of the art and the commonly used dimension reduction techniques.

Induction of morphological changes in death-induced cancer cells monitored by holographic microscopy.

Science.gov (United States)

El-Schich, Zahra; Mölder, Anna; Tassidis, Helena; Härkönen, Pirkko; Falck Miniotis, Maria; Gjörloff Wingren, Anette

2015-03-01

We are using the label-free technique of holographic microscopy to analyze cellular parameters including cell number, confluence, cellular volume and area directly in the cell culture environment. We show that death-induced cells can be distinguished from untreated counterparts by the use of holographic microscopy, and we demonstrate its capability for cell death assessment. Morphological analysis of two representative cell lines (L929 and DU145) was performed in the culture flasks without any prior cell detachment. The two cell lines were treated with the anti-tumour agent etoposide for 1-3days. Measurements by holographic microscopy showed significant differences in average cell number, confluence, volume and area when comparing etoposide-treated with untreated cells. The cell volume of the treated cell lines was initially increased at early time-points. By time, cells decreased in volume, especially when treated with high doses of etoposide. In conclusion, we have shown that holographic microscopy allows label-free and completely non-invasive morphological measurements of cell growth, viability and death. Future applications could include real-time monitoring of these holographic microscopy parameters in cells in response to clinically relevant compounds. Copyright © 2015 Elsevier Inc. All rights reserved.

Sample Preparation and Imaging of Exosomes by Transmission Electron Microscopy.

Science.gov (United States)

Jung, Min Kyo; Mun, Ji Young

2018-01-04

Exosomes are nano-sized extracellular vesicles secreted by body fluids and are known to represent the characteristics of cells that secrete them. The contents and morphology of the secreted vesicles reflect cell behavior or physiological status, for example cell growth, migration, cleavage, and death. The exosomes' role may depend highly on size, and the size of exosomes varies from 30 to 300 nm. The most widely used method for exosome imaging is negative staining, while other results are based on Cryo-Transmission Electron Microscopy, Scanning Electron Microscopy, and Atomic Force Microscopy. The typical exosome's morphology assessed through negative staining is a cup-shape, but further details are not yet clear. An exosome well-characterized through structural study is necessary particular in medical and pharmaceutical fields. Therefore, function-dependent morphology should be verified by electron microscopy techniques such as labeling a specific protein in the detailed structure of exosome. To observe detailed structure, ultrathin sectioned images and negative stained images of exosomes were compared. In this protocol, we suggest transmission electron microscopy for the imaging of exosomes including negative staining, whole mount immuno-staining, block preparation, thin section, and immuno-gold labelling.

Head-facial hemangiomas studied with scanning electron microscopy.

Science.gov (United States)

Cavallotti, Carlo; Cavallotti, Chiara; Giovannetti, Filippo; Iannetti, Giorgio

2009-11-01

Hemangiomas of the head or face are a frequent vascular pathology, consisting in an embryonic dysplasia that involves the cranial-facial vascular network. Hemangiomas show clinical, morphological, developmental, and structural changes during their course. Morphological, structural, ultrastructural, and clinical characteristics of head-facial hemangiomas were studied in 28 patients admitted in our hospital. Nineteen of these patients underwent surgery for the removal of the hemangiomas, whereas 9 patients were not operated on. All the removed tissues were transferred in our laboratories for the morphological staining. Light microscopy, transmission electron microscopy, and scanning electron microscopy techniques were used for the observation of all microanatomical details. All patients were studied for a clinical diagnosis, and many were subjected to surgical therapy. The morphological results revealed numerous microanatomical characteristics of the hemangiomatous vessels. The observation by light microscopy shows the afferent and the efferent vessels for every microhemangioma. All the layers of the arterial wall are uneven. The lumen of the arteriole is entirely used by a blood clot. The observation by transmission electron microscopy shows that it was impossible to see the limits of the different layers (endothelium, medial layer, and adventitia) in the whole wall of the vessels. Moreover, both the muscular and elastic components are disarranged and replaced with connective tissue. The observation by scanning electron microscopy shows that the corrosion cast of the hemangioma offers 3 periods of filling: initially with partial filling of the arteriolar and of the whole cast, intermediate with the entire filling of the whole cast (including arteriole and venule), and a last period with a partial emptying of the arteriolar and whole cast while the venule remains totally injected with resin. Our morphological results can be useful to clinicians for a precise

Investigation of autofocus algorithms for brightfield microscopy of unstained cells

Science.gov (United States)

Wu, Shu Yu; Dugan, Nazim; Hennelly, Bryan M.

2014-05-01

In the past decade there has been significant interest in image processing for brightfield cell microscopy. Much of the previous research on image processing for microscopy has focused on fluorescence microscopy, including cell counting, cell tracking, cell segmentation and autofocusing. Fluorescence microscopy provides functional image information that involves the use of labels in the form of chemical stains or dyes. For some applications, where the biochemical integrity of the cell is required to remain unchanged so that sensitive chemical testing can later be applied, it is necessary to avoid staining. For this reason the challenge of processing images of unstained cells has become a topic of increasing attention. These cells are often effectively transparent and appear to have a homogenous intensity profile when they are in focus. Bright field microscopy is the most universally available and most widely used form of optical microscopy and for this reason we are interested in investigating image processing of unstained cells recorded using a standard bright field microscope. In this paper we investigate the application of a range of different autofocus metrics applied to unstained bladder cancer cell lines using a standard inverted bright field microscope with microscope objectives that have high magnification and numerical aperture. We present a number of conclusions on the optimum metrics and the manner in which they should be applied for this application.

Subsurface measurement of nanostructures on GaAs by electrostatic force microscopy

International Nuclear Information System (INIS)

Yamada, Fumihiko; Kamiya, Itaru

2013-01-01

The size of surface buried oxide nanostructures are measured by electrostatic force microscopy (EFM). In contrast to atomic force microscopy that cannot probe subsurface structures and thickness, we show that EFM data include information about the thickness of individual nanostructures, consequently allowing us to determine the thickness of buried nanostructures on semiconductor substrates. We further show that this measurement can be performed simultaneously with AFM using EFM modulation spectroscopy.

Polarized Light Microscopy

Science.gov (United States)

Frandsen, Athela F.

2016-01-01

Polarized light microscopy (PLM) is a technique which employs the use of polarizing filters to obtain substantial optical property information about the material which is being observed. This information can be combined with other microscopy techniques to confirm or elucidate the identity of an unknown material, determine whether a particular contaminant is present (as with asbestos analysis), or to provide important information that can be used to refine a manufacturing or chemical process. PLM was the major microscopy technique in use for identification of materials for nearly a century since its introduction in 1834 by William Fox Talbot, as other techniques such as SEM (Scanning Electron Microscopy), FTIR (Fourier Transform Infrared spectroscopy), XPD (X-ray Powder Diffraction), and TEM (Transmission Electron Microscopy) had not yet been developed. Today, it is still the only technique approved by the Environmental Protection Agency (EPA) for asbestos analysis, and is often the technique first applied for identification of unknown materials. PLM uses different configurations in order to determine different material properties. With each configuration additional clues can be gathered, leading to a conclusion of material identity. With no polarizing filter, the microscope can be used just as a stereo optical microscope, and view qualities such as morphology, size, and number of phases. With a single polarizing filter (single polars), additional properties can be established, such as pleochroism, individual refractive indices, and dispersion staining. With two polarizing filters (crossed polars), even more can be deduced: isotropy vs. anisotropy, extinction angle, birefringence/degree of birefringence, sign of elongation, and anomalous polarization colors, among others. With the use of PLM many of these properties can be determined in a matter of seconds, even for those who are not highly trained. McCrone, a leader in the field of polarized light microscopy, often

Electron microscopy of nanostructured semiconductor materials

International Nuclear Information System (INIS)

Neumann, Wolfgang

2003-01-01

For various material systems of low dimensions, including multilayers, islands, and quantum dots, the potential applicability of transmission electron microscopy (TEM) is demonstrated. Conventional TEM is applied to elucidate size, shape, and arrangement of nanostructures, whereas high-resolution imaging is used for visualizing their atomic structure. In addition, microchemical peculiarities of the nanoscopic objects are investigated by analytical TEM techniques (energy-filtered TEM, energy-dispersive X-ray spectroscopy)

Virtual Microscopy in Histopathology Training: Changing Student Attitudes in 3 Successive Academic Years.

Science.gov (United States)

Bertram, Christof A; Firsching, Theresa; Klopfleisch, Robert

2018-01-01

Several veterinary faculties have integrated virtual microscopy into their curricula in recent years to improve and refine their teaching techniques. The many advantages of this recent technology are described in the literature, including remote access and an equal and constant slide quality for all students. However, no study has analyzed the change of perception toward virtual microscopy at different time points of students' academic educations. In the present study, veterinary students in 3 academic years were asked for their perspectives and attitudes toward virtual microscopy and conventional light microscopy. Third-, fourth-, and fifth-year veterinary students filled out a questionnaire with 12 questions. The answers revealed that virtual microscopy was overall well accepted by students of all academic years. Most students even suggested that virtual microscopy be implemented more extensively as the modality for final histopathology examinations. Nevertheless, training in the use of light microscopy and associated skills was surprisingly well appreciated. Regardless of their academic year, most students considered these skills important and necessary, and they felt that light microscopy should not be completely replaced. The reasons for this view differed depending on academic year, as the perceived main disadvantage of virtual microscopy varied. Third-year students feared that they would not acquire sufficient light microscopy skills. Fifth-year students considered technical difficulties (i.e., insufficient transmission speed) to be the main disadvantage of this newer teaching modality.

Nano-contact microscopy of supracrystals

Directory of Open Access Journals (Sweden)

Adam Sweetman

2015-05-01

Full Text Available Background: Highly ordered three-dimensional colloidal crystals (supracrystals comprised of 7.4 nm diameter Au nanocrystals (with a 5% size dispersion have been imaged and analysed using a combination of scanning tunnelling microscopy and dynamic force microscopy.Results: By exploring the evolution of both the force and tunnel current with respect to tip–sample separation, we arrive at the surprising finding that single nanocrystal resolution is readily obtained in tunnelling microscopy images acquired more than 1 nm into the repulsive (i.e., positive force regime of the probe–nanocrystal interaction potential. Constant height force microscopy has been used to map tip–sample interactions in this regime, revealing inhomogeneities which arise from the convolution of the tip structure with the ligand distribution at the nanocrystal surface.Conclusion: Our combined STM–AFM measurements show that the contrast mechanism underpinning high resolution imaging of nanoparticle supracrystals involves a form of nanoscale contact imaging, rather than the through-vacuum tunnelling which underpins traditional tunnelling microscopy and spectroscopy.

Fast electron microscopy via compressive sensing

Science.gov (United States)

Larson, Kurt W; Anderson, Hyrum S; Wheeler, Jason W

2014-12-09

Various technologies described herein pertain to compressive sensing electron microscopy. A compressive sensing electron microscope includes a multi-beam generator and a detector. The multi-beam generator emits a sequence of electron patterns over time. Each of the electron patterns can include a plurality of electron beams, where the plurality of electron beams is configured to impart a spatially varying electron density on a sample. Further, the spatially varying electron density varies between each of the electron patterns in the sequence. Moreover, the detector collects signals respectively corresponding to interactions between the sample and each of the electron patterns in the sequence.

Transmission electron microscopy physics of image formation and microanalysis

CERN Document Server

Reimer, Ludwig

1993-01-01

"Transmission Electron Microscopy" presents the theory of image and contrastformation, and the analytical modes in transmission electron microscopy Theprinciples of particle and wave optics of electrons are described Electron-specimen interactions are discussed for evaluating the theory of scattering and phase contrast Also analysed are the kinetical and dynamical theories of electron diffraction and their applications for crystal-structure determination and imaging of lattices and their defects X-ray microanalysis and electron energy-loss spectroscopy are treated as analytical methods The third edition includes a brief discussionof Schottky emission guns, some clarification of minor details, and references to the recent literature

Super-resolution binding activated localization microscopy through reversible change of DNA conformation.

Science.gov (United States)

Szczurek, Aleksander; Birk, Udo; Knecht, Hans; Dobrucki, Jurek; Mai, Sabine; Cremer, Christoph

2018-01-01

Methods of super-resolving light microscopy (SRM) have found an exponentially growing range of applications in cell biology, including nuclear structure analyses. Recent developments have proven that Single Molecule Localization Microscopy (SMLM), a type of SRM, is particularly useful for enhanced spatial analysis of the cell nucleus due to its highest resolving capability combined with very specific fluorescent labeling. In this commentary we offer a brief review of the latest methodological development in the field of SMLM of chromatin designated DNA Structure Fluctuation Assisted Binding Activated Localization Microscopy (abbreviated as fBALM) as well as its potential future applications in biology and medicine.

Traditional microscopy instruction versus process-oriented virtual microscopy instruction: a naturalistic experiment with control group.

Science.gov (United States)

Helle, Laura; Nivala, Markus; Kronqvist, Pauliina; Gegenfurtner, Andreas; Björk, Pasi; Säljö, Roger

2011-03-30

Virtual microscopy is being introduced in medical education as an approach for learning how to interpret information in microscopic specimens. It is, however, far from evident how to incorporate its use into existing teaching practice. The aim of the study was to explore the consequences of introducing virtual microscopy tasks into an undergraduate pathology course in an attempt to render the instruction more process-oriented. The research questions were: 1) How is virtual microscopy perceived by students? 2) Does work on virtual microscopy tasks contribute to improvement in performance in microscopic pathology in comparison with attending assistant-led demonstrations only? During a one-week period, an experimental group completed three sets of virtual microscopy homework assignments in addition to attending demonstrations. A control group attended the demonstrations only. Performance in microscopic pathology was measured by a pre-test and a post-test. Student perceptions of regular instruction and virtual microscopy were collected one month later by administering the Inventory of Intrinsic Motivation and open-ended questions. The students voiced an appreciation for virtual microscopy for the purposes of the course and for self-study. As for learning gains, the results indicated that learning was speeded up in a subgroup of students consisting of conscientious high achievers. The enriched instruction model may be suited as such for elective courses following the basic course. However, the instructional model needs further development to be suited for basic courses.

In situ transmission electron microscopy for magnetic nanostructures

DEFF Research Database (Denmark)

Ngo, Duc-The; Kuhn, Luise Theil

2016-01-01

Nanomagnetism is a subject of great interest because of both application and fundamental aspects in which understanding of the physical and electromagnetic structure of magnetic nanostructures is essential to explore the magnetic properties. Transmission electron microscopy (TEM) is a powerful tool...... that allows understanding of both physical structure and micromagnetic structure of the thin samples at nanoscale. Among TEM techniques, in situ TEM is the state-of-the-art approach for imaging such structures in dynamic experiments, reconstructing a real-time nanoscale picture of the properties......-structure correlation. This paper aims at reviewing and discussing in situ TEM magnetic imaging studies, including Lorentz microscopy and electron holography in TEM, applied to the research of magnetic nanostructures....

14th Conference on "Microscopy of Semiconducting Materials"

CERN Document Server

Hutchison, J

2005-01-01

This is a long-established international biennial conference series, organised in conjunction with the Royal Microscopical Society, Oxford, the Institute of Physics, London and the Materials Research Society, USA. The 14th conference in the series focused on the most recent advances in the study of the structural and electronic properties of semiconducting materials by the application of transmission and scanning electron microscopy. The latest developments in the use of other important microcharacterisation techniques were also covered and included the latest work using scanning probe microscopy and also X-ray topography and diffraction. Developments in materials science and technology covering the complete range of elemental and compound semiconductors are described in this volume.

Labeling Human Mesenchymal Stem Cells with Gold Nanocages for in vitro and in vivo Tracking by Two-Photon Microscopy and Photoacoustic Microscopy

Science.gov (United States)

Zhang, Yu Shrike; Wang, Yu; Wang, Lidai; Wang, Yucai; Cai, Xin; Zhang, Chi; Wang, Lihong V.; Xia, Younan

2013-01-01

Stem cell tracking is a highly important subject. Current techniques based on nanoparticle-labeling, such as magnetic resonance imaging, fluorescence microscopy, and micro-computed tomography, are plagued by limitations including relatively low sensitivity or penetration depth, involvement of ionizing irradiation, and potential cytotoxicity of the nanoparticles. Here we introduce a new class of contrast agents based on gold nanocages (AuNCs) with hollow interiors and porous walls to label human mesenchymal stem cells (hMSCs) for both in vitro and in vivo tracking using two-photon microscopy and photoacoustic microscopy. As demonstrated by the viability assay, the AuNCs showed negligible cytotoxicity under a reasonable dose, and did not alter the differentiation potential of the hMSCs into desired lineages. We were able to image the cells labeled with AuNCs in vitro for at least 28 days in culture, as well as to track the cells that homed to the tumor region in nude mice in vivo. PMID:23946820

Super-nonlinear fluorescence microscopy for high-contrast deep tissue imaging

Science.gov (United States)

Wei, Lu; Zhu, Xinxin; Chen, Zhixing; Min, Wei

2014-02-01

Two-photon excited fluorescence microscopy (TPFM) offers the highest penetration depth with subcellular resolution in light microscopy, due to its unique advantage of nonlinear excitation. However, a fundamental imaging-depth limit, accompanied by a vanishing signal-to-background contrast, still exists for TPFM when imaging deep into scattering samples. Formally, the focusing depth, at which the in-focus signal and the out-of-focus background are equal to each other, is defined as the fundamental imaging-depth limit. To go beyond this imaging-depth limit of TPFM, we report a new class of super-nonlinear fluorescence microscopy for high-contrast deep tissue imaging, including multiphoton activation and imaging (MPAI) harnessing novel photo-activatable fluorophores, stimulated emission reduced fluorescence (SERF) microscopy by adding a weak laser beam for stimulated emission, and two-photon induced focal saturation imaging with preferential depletion of ground-state fluorophores at focus. The resulting image contrasts all exhibit a higher-order (third- or fourth- order) nonlinear signal dependence on laser intensity than that in the standard TPFM. Both the physical principles and the imaging demonstrations will be provided for each super-nonlinear microscopy. In all these techniques, the created super-nonlinearity significantly enhances the imaging contrast and concurrently extends the imaging depth-limit of TPFM. Conceptually different from conventional multiphoton processes mediated by virtual states, our strategy constitutes a new class of fluorescence microscopy where high-order nonlinearity is mediated by real population transfer.

A Seeping Commodification: The Long Revolution in the Proliferation of Communication Commodities

Directory of Open Access Journals (Sweden)

Jernej A. Prodnik

2014-02-01

Full Text Available The main goal of this paper is to conceptualize a seeping commodification. The author of the paper claims we are in the midst of a considerable qualitative transformation in the processes of commodification that is, in large part, owed to an overwhelming capitalist enclosure of the wider communicative field. The key reason for what seems to be an important qualitative transformation in the commodification process lies in the fact that communication and information flows today run through most social relations and spheres – which non-critical approaches often explain with the concept of the ‘mediatization of society’. A materialist approach, distinctive of (critical political economy of communication, enables an apt critique of these processes. In an epoch, in which capital has enclosed the wider field of communication, mediatization is in fact nothing else than a continuing commodification of our everyday lives. The author of the paper claims that commodification of communication and informational resources must be seen as a long-term process, which has accompanied the rise of capitalism. A considerable proliferation of the economic importance of communication, information, and culture has – to be precise – been enhanced in a large part by political interventions occurring in the last decades (which were a response to the economic tendencies and crises of the time. While the immediate results are observable especially in the proliferation of the new information and communication technologies and the global role of intellectual property rights, the wider social consequences of these developments have been much broader and more influential. This study proceeds from the perspective of historical materialism and adopts dialectics in an attempt to grasp contradictory social changes. The analysis is done through different methods of historicizing: firstly, by observing long-term changes in communication, information, and culture, as they

High spatial resolution soft-x-ray microscopy

Energy Technology Data Exchange (ETDEWEB)

Meyer-Ilse, W.; Medecki, H.; Brown, J.T. [Ernest Orlando Lawrence Berkeley National Lab., CA (United States)] [and others

1997-04-01

A new soft x-ray microscope (XM-1) with high spatial resolution has been constructed by the Center for X-ray Optics. It uses bending magnet radiation from beamline 6.1 at the Advanced Light Source, and is used in a variety of projects and applications in the life and physical sciences. Most of these projects are ongoing. The instrument uses zone plate lenses and achieves a resolution of 43 nm, measured over 10% to 90% intensity with a knife edge test sample. X-ray microscopy permits the imaging of relatively thick samples, up to 10 {mu}m thick, in water. XM-1 has an easy to use interface, that utilizes visible light microscopy to precisely position and focus the specimen. The authors describe applications of this device in the biological sciences, as well as in studying industrial applications including structured polymer samples.

The Use Of Scanning Probe Microscopy To Investigate Crystal-Fluid Interfaces

International Nuclear Information System (INIS)

Orme, C A; Giocondi, J L

2007-01-01

Over the past decade there has been a natural drive to extend the investigation of dynamic surfaces in fluid environments to higher resolution characterization tools. Various aspects of solution crystal growth have been directly visualized for the first time. These include island nucleation and growth using transmission electron microscopy and scanning tunneling microscopy; elemental step motion using scanning probe microscopy; and the time evolution of interfacial atomic structure using various diffraction techniques. In this lecture we will discuss the use of one such in situ method, scanning probe microscopy, as a means of measuring surface dynamics during crystal growth and dissolution. We will cover both practical aspects of imaging such as environmental control, fluid flow, and electrochemical manipulation, as well as the types of physical measurements that can be made. Measurements such as step motion, critical lengths, nucleation density, and step fluctuations, will be put in context of the information they provide about mechanistic processes at surfaces using examples from metal and mineral crystal growth

Confocal scanning microscopy

DEFF Research Database (Denmark)

Bariani, Paolo

This report is based on a metrological investigation on confocal microscopy technique carried out by Uffe Rolf Arlø Theilade and Paolo Bariani. The purpose of the experimental activity was twofold a metrological instrument characterization and application to assessment of rough PP injection moulded...... replicated topography. Confocal microscopy is seen to be a promising technique in metrology of microstructures. Some limitations with respect to surface metrology were found during the experiments. The experiments were carried out using a Zeiss LSM 5 Pascal microscope owned by the Danish Polymer Centre...

Microfabricated high-bandpass foucault aperture for electron microscopy

Energy Technology Data Exchange (ETDEWEB)

Glaeser, Robert; Cambie, Rossana; Jin, Jian

2014-08-26

A variant of the Foucault (knife-edge) aperture is disclosed that is designed to provide single-sideband (SSB) contrast at low spatial frequencies but retain conventional double-sideband (DSB) contrast at high spatial frequencies in transmission electron microscopy. The aperture includes a plate with an inner open area, a support extending from the plate at an edge of the open area, a half-circle feature mounted on the support and located at the center of the aperture open area. The radius of the half-circle portion of reciprocal space that is blocked by the aperture can be varied to suit the needs of electron microscopy investigation. The aperture is fabricated from conductive material which is preferably non-oxidizing, such as gold, for example.

Correlative cryo-fluorescence light microscopy and cryo-electron tomography of Streptomyces.

Science.gov (United States)

Koning, Roman I; Celler, Katherine; Willemse, Joost; Bos, Erik; van Wezel, Gilles P; Koster, Abraham J

2014-01-01

Light microscopy and electron microscopy are complementary techniques that in a correlative approach enable identification and targeting of fluorescently labeled structures in situ for three-dimensional imaging at nanometer resolution. Correlative imaging allows electron microscopic images to be positioned in a broader temporal and spatial context. We employed cryo-correlative light and electron microscopy (cryo-CLEM), combining cryo-fluorescence light microscopy and cryo-electron tomography, on vitrified Streptomyces bacteria to study cell division. Streptomycetes are mycelial bacteria that grow as long hyphae and reproduce via sporulation. On solid media, Streptomyces subsequently form distinct aerial mycelia where cell division leads to the formation of unigenomic spores which separate and disperse to form new colonies. In liquid media, only vegetative hyphae are present divided by noncell separating crosswalls. Their multicellular life style makes them exciting model systems for the study of bacterial development and cell division. Complex intracellular structures have been visualized with transmission electron microscopy. Here, we describe the methods for cryo-CLEM that we applied for studying Streptomyces. These methods include cell growth, fluorescent labeling, cryo-fixation by vitrification, cryo-light microscopy using a Linkam cryo-stage, image overlay and relocation, cryo-electron tomography using a Titan Krios, and tomographic reconstruction. Additionally, methods for segmentation, volume rendering, and visualization of the correlative data are described. © 2014 Elsevier Inc. All rights reserved.

Evaluation of mobile digital light-emitting diode fluorescence microscopy in Hanoi, Viet Nam.

Science.gov (United States)

Chaisson, L H; Reber, C; Phan, H; Switz, N; Nilsson, L M; Myers, F; Nhung, N V; Luu, L; Pham, T; Vu, C; Nguyen, H; Nguyen, A; Dinh, T; Nahid, P; Fletcher, D A; Cattamanchi, A

2015-09-01

Hanoi Lung Hospital, Hanoi, Viet Nam. To compare the accuracy of CellScopeTB, a manually operated mobile digital fluorescence microscope, with conventional microscopy techniques. Patients referred for sputum smear microscopy to the Hanoi Lung Hospital from May to September 2013 were included. Ziehl-Neelsen (ZN) smear microscopy, conventional light-emitting diode (LED) fluorescence microscopy (FM), CellScopeTB-based LED FM and Xpert(®) MTB/RIF were performed on sputum samples. The sensitivity and specificity of microscopy techniques were determined in reference to Xpert results, and differences were compared using McNemar's paired test of proportions. Of 326 patients enrolled, 93 (28.5%) were Xpert-positive for TB. The sensitivity of ZN microscopy, conventional LED FM, and CellScopeTB-based LED FM was respectively 37.6% (95%CI 27.8-48.3), 41.9% (95%CI 31.8-52.6), and 35.5% (95%CI 25.8-46.1). The sensitivity of CellScopeTB was similar to that of conventional LED FM (difference -6.5%, 95%CI -18.2 to 5.3, P = 0.33) and ZN microscopy (difference -2.2%, 95%CI -9.2 to 4.9, P = 0.73). The specificity was >99% for all three techniques. CellScopeTB performed similarly to conventional microscopy techniques in the hands of experienced TB microscopists. However, the sensitivity of all sputum microscopy techniques was low. Options enabled by digital microscopy, such as automated imaging with real-time computerized analysis, should be explored to increase sensitivity.

Dysprosium disilicide nanostructures on silicon(001) studied by scanning tunneling microscopy and transmission electron microscopy

International Nuclear Information System (INIS)

Ye Gangfeng; Nogami, Jun; Crimp, Martin A.

2006-01-01

The microstructure of self-assembled dysprosium silicide nanostructures on silicon(001) has been studied by scanning tunneling microscopy and transmission electron microscopy. The studies focused on nanostructures that involve multiple atomic layers of the silicide. Cross-sectional high resolution transmission electron microscopy images and fast Fourier transform analysis showed that both hexagonal and orthorhombic/tetragonal silicide phases were present. Both the magnitude and the anisotropy of lattice mismatch between the silicide and the substrate play roles in the morphology and epitaxial growth of the nanostructures formed

Microscopy

Science.gov (United States)

Patricia A. Moss; Les Groom

2001-01-01

Microscopy is the study and interpretation of images produced by a microscope. "Interpretation" is the keyword, because the microscope enables one to see structures that are too small or too close together to be resolved by the unaided eye. (The human eye cannot separate two points or lines that are closer together than 0.1 mm.) it is important to...

Probing cytotoxicity of nanoparticles and organic compounds using scanning proton microscopy, scanning electron microscopy and fluorescence microscopy

Energy Technology Data Exchange (ETDEWEB)

Tong Yongpeng [Institute of Nuclear Techniques, Shenzhen University, Nanhai Avenue 3688, Shenzhen 518060 (China)], E-mail: yongpengt@yahoo.com.cn; Li Changming [School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637457 (Singapore); Liang Feng [Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200025 (China); Chen Jianmin [Shenzhen Municipal Hospital for Chronic Disease Control and Prevention, Guangdong 518020 (China); Zhang Hong; Liu Guoqing; Sun Huibin [Institute of Nuclear Techniques, Shenzhen University, Nanhai Avenue 3688, Shenzhen 518060 (China); Luong, John H.T. [Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, H4P 2R2 (Canada)

2008-12-15

Scanning proton microscopy, scanning electron microscopy (SEM) and fluorescence microscopy have been used to probe the cytotoxicity effect of benzo[a]pyrene (BaP), ethidium bromide (EB) and nanoparticles (ZnO, Al{sub 2}O{sub 3} and TiO{sub 2}) on a T lymphoblastic leukemia Jurkat cell line. The increased calcium ion (from CaCl{sub 2}) in the culture medium stimulated the accumulation of BaP and EB inside the cell, leading to cell death. ZnO, Al{sub 2}O{sub 3} and TiO{sub 2} nanoparticles, however, showed a protective effect against these two organic compounds. Such inorganic nanoparticles complexed with BaP or EB which became less toxic to the cell. Fe{sub 2}O{sub 3} nanoparticles as an insoluble particle model scavenged by macrophage were investigated in rats. They were scavenged out of the lung tissue about 48 h after infection. This result suggest that some insoluble inorganic nanoparticles of PM (particulate matters) showed protective effects on organic toxins induced acute toxic effects as they can be scavenged by macrophage cells. Whereas, some inorganic ions such as calcium ion in PM may help environmental organic toxins to penetrate cell membrane and induce higher toxic effect.

Tip-Enhanced Raman Scattering Microscopy: A Step toward Nanoscale Control of Intrinsic Molecular Properties

Science.gov (United States)

Yano, Taka-aki; Hara, Masahiko

2018-06-01

Tip-enhanced Raman scattering microscopy, a family of scanning probe microscopy techniques, has been recognized as a powerful surface analytical technique with both single-molecule sensitivity and angstrom-scale spatial resolution. This review covers the current status of tip-enhanced Raman scattering microscopy in surface and material nanosciences, including a brief history, the basic principles, and applications for the nanoscale characterization of a variety of nanomaterials. The focus is on the recent trend of combining tip-enhanced Raman scattering microscopy with various external stimuli such as pressure, voltage, light, and temperature, which enables the local control of the molecular properties and functions and also enables chemical reactions to be induced on a nanometer scale.

Correlative microscopy including CLSM and SEM to improve high-speed, high-resolution laser-engraved print and embossing forms

Science.gov (United States)

Bohrer, Markus; Schweitzer, Michael; Nirnberger, Robert; Weinberger, Bernhard

2015-10-01

The industrial market for processing large-scale films has seen dramatic changes since the 1980s and has almost completely been replaced by lasers and digital processes. A commonly used technology for engraving screens, print and embossing forms in the printing industry, well known since then, is the use of RF-excited CO2 lasers with a beam power up to about 1 kW, modulated in accordance to the pattern to be engraved. Future needs for high-security printing (banknotes, security papers, passports, etc.) will require laser engraving of at least half a million or even more structured elements with a depth from some μm up to 500 μm. Industry now wants photorealistic pictures in packaging design, which requires a similar performance. To ensure 'trusted pulses' from the digital process to the print result the use of correlative microscopy (CLSM and SEM) is demonstrated as a complete chain for a correlative print process in this paper.

Atomic force microscopy. A new method for atom identification and manipulation

International Nuclear Information System (INIS)

Abe, Masayuki; Sugimoto, Yoshiaki; Morita, Seizo

2007-01-01

Frequency modulation atomic force microscopy (FM-AFM) is a scanning probe technique that detects the interaction forces between the outermost atom of a sharp tip and the atoms at a surface to image the sample surface. It is expected that the FM-AFM can cover the research field which scanning tunneling microscopy does not provide. In this article, we would introduce FM-AFM experiments applied to site-specific force measurements and atom manipulation, including how to solve the problems to achieve precise FM-AFM measurements. (author)

Bessel light sheet structured illumination microscopy

Science.gov (United States)

Noshirvani Allahabadi, Golchehr

Biomedical study researchers using animals to model disease and treatment need fast, deep, noninvasive, and inexpensive multi-channel imaging methods. Traditional fluorescence microscopy meets those criteria to an extent. Specifically, two-photon and confocal microscopy, the two most commonly used methods, are limited in penetration depth, cost, resolution, and field of view. In addition, two-photon microscopy has limited ability in multi-channel imaging. Light sheet microscopy, a fast developing 3D fluorescence imaging method, offers attractive advantages over traditional two-photon and confocal microscopy. Light sheet microscopy is much more applicable for in vivo 3D time-lapsed imaging, owing to its selective illumination of tissue layer, superior speed, low light exposure, high penetration depth, and low levels of photobleaching. However, standard light sheet microscopy using Gaussian beam excitation has two main disadvantages: 1) the field of view (FOV) of light sheet microscopy is limited by the depth of focus of the Gaussian beam. 2) Light-sheet images can be degraded by scattering, which limits the penetration of the excitation beam and blurs emission images in deep tissue layers. While two-sided sheet illumination, which doubles the field of view by illuminating the sample from opposite sides, offers a potential solution, the technique adds complexity and cost to the imaging system. We investigate a new technique to address these limitations: Bessel light sheet microscopy in combination with incoherent nonlinear Structured Illumination Microscopy (SIM). Results demonstrate that, at visible wavelengths, Bessel excitation penetrates up to 250 microns deep in the scattering media with single-side illumination. Bessel light sheet microscope achieves confocal level resolution at a lateral resolution of 0.3 micron and an axial resolution of 1 micron. Incoherent nonlinear SIM further reduces the diffused background in Bessel light sheet images, resulting in

Hydrocarbon Plume Dynamics in the Worldś Most Spectacular Hydrocarbon Seeps, Santa Barbara Channel, California

Science.gov (United States)

Mau, S.; Reed, J.; Clark, J.; Valentine, D.

2006-12-01

Large quantities of natural gas are emitted from the seafloor into the coastal ocean near Coal Oil Point, Santa Barbara Channel (SBC), California. Methane, ethane, and propane were quantified in the surface water at 79 stations in a 270 km2 area in order to map the surficial hydrocarbon plume and to quantify air-sea exchange of these gases. A time series was initiated for 14 stations to identify the variability of the mapped plume, and biologically-mediated oxidation rates of methane were measured to quantify the loss of methane in surface water. The hydrocarbon plume was found to comprise ~70 km2 and extended beyond study area. The plume width narrowed from 3 km near the source to 0.7 km further from the source, and then expanded to 6.7 km at the edge of the study area. This pattern matches the cyclonic gyre which is the normal current flow in this part of the Santa Barbara Channel - pushing water to the shore near the seep field and then broadening the plume while the water turns offshore further from the source. Concentrations of gaseous hydrocarbons decrease as the plume migrates. Time series sampling shows similar plume width and hydrocarbon concentrations when normal current conditions prevail. In contrast, smaller plume width and low hydrocarbon concentrations were observed when an additional anticyclonic eddy reversed the normal current flow, and a much broader plume with higher hydrocarbon concentrations was observed during a time of diminished speed within the current gyre. These results demonstrate that surface currents control hydrocarbon plume dynamics in the SBC, though hydrocarbon flux to the atmosphere is likely less dependent on currents. Estimates of air- sea hydrocarbon flux and biological oxidation rates will also be presented.

Optically sectioned in vivo imaging with speckle illumination HiLo microscopy

Science.gov (United States)

Lim, Daryl; Ford, Tim N.; Chu, Kengyeh K.; Mertz, Jerome

2011-01-01

We present a simple wide-field imaging technique, called HiLo microscopy, that is capable of producing optically sectioned images in real time, comparable in quality to confocal laser scanning microscopy. The technique is based on the fusion of two raw images, one acquired with speckle illumination and another with standard uniform illumination. The fusion can be numerically adjusted, using a single parameter, to produce optically sectioned images of varying thicknesses with the same raw data. Direct comparison between our HiLo microscope and a commercial confocal laser scanning microscope is made on the basis of sectioning strength and imaging performance. Specifically, we show that HiLo and confocal 3-D imaging of a GFP-labeled mouse brain hippocampus are comparable in quality. Moreover, HiLo microscopy is capable of faster, near video rate imaging over larger fields of view than attainable with standard confocal microscopes. The goal of this paper is to advertise the simplicity, robustness, and versatility of HiLo microscopy, which we highlight with in vivo imaging of common model organisms including planaria, C. elegans, and zebrafish.

Analyzing Lysosome-Related Organelles by Electron Microscopy

KAUST Repository

Hurbain, Ilse

2017-04-29

Intracellular organelles have a particular morphological signature that can only be appreciated by ultrastructural analysis at the electron microscopy level. Optical imaging and associated methodologies allow to explore organelle localization and their dynamics at the cellular level. Deciphering the biogenesis and functions of lysosomes and lysosome-related organelles (LROs) and their dysfunctions requires their visualization and detailed characterization at high resolution by electron microscopy. Here, we provide detailed protocols for studying LROs by transmission electron microscopy. While conventional electron microscopy and its recent improvements is the method of choice to investigate organelle morphology, immunoelectron microscopy allows to localize organelle components and description of their molecular make up qualitatively and quantitatively.

Stochastic Optical Reconstruction Microscopy (STORM).

Science.gov (United States)

Xu, Jianquan; Ma, Hongqiang; Liu, Yang

2017-07-05

Super-resolution (SR) fluorescence microscopy, a class of optical microscopy techniques at a spatial resolution below the diffraction limit, has revolutionized the way we study biology, as recognized by the Nobel Prize in Chemistry in 2014. Stochastic optical reconstruction microscopy (STORM), a widely used SR technique, is based on the principle of single molecule localization. STORM routinely achieves a spatial resolution of 20 to 30 nm, a ten-fold improvement compared to conventional optical microscopy. Among all SR techniques, STORM offers a high spatial resolution with simple optical instrumentation and standard organic fluorescent dyes, but it is also prone to image artifacts and degraded image resolution due to improper sample preparation or imaging conditions. It requires careful optimization of all three aspects-sample preparation, image acquisition, and image reconstruction-to ensure a high-quality STORM image, which will be extensively discussed in this unit. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Physical and geochemical drivers of CDOM variability near a natural seep site in the Gulf of Mexico

Science.gov (United States)

Edwards, C. R.; Powers, L.; Medeiros, P. M.

2016-02-01

Colored dissolved organic matter (CDOM) on the continental shelf and slope can serve as a marker for fresh water influence, indicate the presence of hydrocarbons, and provide important clues about nutrient content and organic matter cycling. Autonomous underwater vehicles such as gliders allow for subsurface measurement of CDOM fluorescence for weeks to months; these time series may be especially valuable in the northern Gulf of Mexico, where CDOM inputs of both terrestrial and oil and gas sources can be significant. Data from a recent glider deployment near a natural seep site (GC600) on the continental slope over 180km from shore suggest simultaneous influence of Mississippi plume water and hydrocarbon inputs in the upper 200m, with variability in fluorescence at a range of vertical and temporal scales. We will explore patterns in spatial and temporal variability of glider-measured hydrography, dissolved oxygen, and bio-optical data (CDOM, chlorophyll-a, backscatter fluorescence), and use their combination to infer a terrigenous and/or fossil fuel source(s). Taking advantage of a combination of satellite sea surface temperature, ocean color, wind, and data from moored and mobile platforms, we will examine physical controls on transport and vertical mixing of CDOM and the potential role of nonlinear mesoscale eddies, which can trap water in their interior and may transport river- or hydrocarbon-derived CDOM over long distances. The combined data set will be used to consider and potentially constrain the effect of photodegradation and other biogeochemical causes for CDOM fluorescence variability in the upper 200m.

NICHD Microscopy and Imaging Core (MIC)

Data.gov (United States)

Federal Laboratory Consortium — The NICHD Microscopy and Imaging Core (MIC) is designed as a multi-user research facility providing training and instrumentation for high resolution microscopy and...

Magnetoelectric force microscopy based on magnetic force microscopy with modulated electric field.

Science.gov (United States)

Geng, Yanan; Wu, Weida

2014-05-01

We present the realization of a mesoscopic imaging technique, namely, the Magnetoelectric Force Microscopy (MeFM), for visualization of local magnetoelectric effect. The basic principle of MeFM is the lock-in detection of local magnetoelectric response, i.e., the electric field-induced magnetization, using magnetic force microscopy. We demonstrate MeFM capability by visualizing magnetoelectric domains on single crystals of multiferroic hexagonal manganites. Results of several control experiments exclude artifacts or extrinsic origins of the MeFM signal. The parameters are tuned to optimize the signal to noise ratio.

Evaluation of Yogurt Microstructure Using Confocal Laser Scanning Microscopy and Image Analysis

DEFF Research Database (Denmark)

Skytte, Jacob Lercke; Ghita, Ovidiu; Whelan, Paul F.

2015-01-01

The microstructure of protein networks in yogurts defines important physical properties of the yogurt and hereby partly its quality. Imaging this protein network using confocal scanning laser microscopy (CSLM) has shown good results, and CSLM has become a standard measuring technique for fermented...... to image texture description. Here, CSLM images from a yogurt fermentation study are investigated, where production factors including fat content, protein content, heat treatment, and incubation temperature are varied. The descriptors are evaluated through nearest neighbor classification, variance analysis...... scanning microscopy images can be used to provide information on the protein microstructure in yogurt products. For large numbers of microscopy images, subjective evaluation becomes a difficult or even impossible approach, if the images should be incorporated in any form of statistical analysis alongside...

Scanning probe microscopy experiments in microgravity

International Nuclear Information System (INIS)

Drobek, Tanja; Reiter, Michael; Heckl, Wolfgang M.

2004-01-01

The scanning probe microscopy setups are small, lightweight and do not require vacuum or high voltage supply. In addition, samples can be investigated directly without further preparation. Therefore, these techniques are well-suited for applications in space, in particular, for operation on the International Space Station (ISS) or for high resolution microscopy on planetary missions. A feasibility study for a scanning tunneling microscopy setup was carried out on a parabolic flight campaign in November 2001 in order to test the technical setup for microgravity applications. With a pocket-size design microscope, a graphite surface was imaged under ambient conditions. Atomic resolution was achieved although the quality of the images was inferior in comparison to laboratory conditions. Improvements for future scanning probe microscopy experiments in microgravity are suggested

Combined time-lapse cinematography and immuno-electron microscopy.

Science.gov (United States)

Balfour, B M; Goscicka, T; MacKenzie, J L; Gautam, A; Tate, M; Clark, J

1990-04-01

A method was developed to record interactions between mobile non-adherent immunocytes by time-lapse cinematography and then to study the same cells by immuno-electron microscopy, using monoclonal antibodies against surface components. For this purpose a modified stage was designed to fit an inverted microscope. The attachment included a device to cool the culture chamber with N2 gas, a micro-injector for monoclonal antibody and immuno-gold treatment, and two pairs of washing needles to change the medium without disturbance. The technique was first employed to study the formation of aggregates around the antigen-presenting cells in cultures containing cells from hyper-immunized animals. Recently peripheral blood cells from normal subjects and patients with immune deficiency syndromes were stimulated with pokeweed mitogen, cluster formation was recorded, and the cells were processed for immuno-electron microscopy.

Electronic Blending in Virtual Microscopy

Science.gov (United States)

Maybury, Terrence S.; Farah, Camile S.

2010-01-01

Virtual microscopy (VM) is a relatively new technology that transforms the computer into a microscope. In essence, VM allows for the scanning and transfer of glass slides from light microscopy technology to the digital environment of the computer. This transition is also a function of the change from print knowledge to electronic knowledge, or as…

Light Microscopy at Maximal Precision

Science.gov (United States)

Bierbaum, Matthew; Leahy, Brian D.; Alemi, Alexander A.; Cohen, Itai; Sethna, James P.

2017-10-01

Microscopy is the workhorse of the physical and life sciences, producing crisp images of everything from atoms to cells well beyond the capabilities of the human eye. However, the analysis of these images is frequently little more accurate than manual marking. Here, we revolutionize the analysis of microscopy images, extracting all the useful information theoretically contained in a complex microscope image. Using a generic, methodological approach, we extract the information by fitting experimental images with a detailed optical model of the microscope, a method we call parameter extraction from reconstructing images (PERI). As a proof of principle, we demonstrate this approach with a confocal image of colloidal spheres, improving measurements of particle positions and radii by 10-100 times over current methods and attaining the maximum possible accuracy. With this unprecedented accuracy, we measure nanometer-scale colloidal interactions in dense suspensions solely with light microscopy, a previously impossible feat. Our approach is generic and applicable to imaging methods from brightfield to electron microscopy, where we expect accuracies of 1 nm and 0.1 pm, respectively.

Light Microscopy at Maximal Precision

Directory of Open Access Journals (Sweden)

Matthew Bierbaum

2017-10-01

Full Text Available Microscopy is the workhorse of the physical and life sciences, producing crisp images of everything from atoms to cells well beyond the capabilities of the human eye. However, the analysis of these images is frequently little more accurate than manual marking. Here, we revolutionize the analysis of microscopy images, extracting all the useful information theoretically contained in a complex microscope image. Using a generic, methodological approach, we extract the information by fitting experimental images with a detailed optical model of the microscope, a method we call parameter extraction from reconstructing images (PERI. As a proof of principle, we demonstrate this approach with a confocal image of colloidal spheres, improving measurements of particle positions and radii by 10–100 times over current methods and attaining the maximum possible accuracy. With this unprecedented accuracy, we measure nanometer-scale colloidal interactions in dense suspensions solely with light microscopy, a previously impossible feat. Our approach is generic and applicable to imaging methods from brightfield to electron microscopy, where we expect accuracies of 1 nm and 0.1 pm, respectively.

Localization of fluorescently labeled structures in frozen-hydrated samples using integrated light electron microscopy.

Science.gov (United States)

Faas, F G A; Bárcena, M; Agronskaia, A V; Gerritsen, H C; Moscicka, K B; Diebolder, C A; van Driel, L F; Limpens, R W A L; Bos, E; Ravelli, R B G; Koning, R I; Koster, A J

2013-03-01

Correlative light and electron microscopy is an increasingly popular technique to study complex biological systems at various levels of resolution. Fluorescence microscopy can be employed to scan large areas to localize regions of interest which are then analyzed by electron microscopy to obtain morphological and structural information from a selected field of view at nm-scale resolution. Previously, an integrated approach to room temperature correlative microscopy was described. Combined use of light and electron microscopy within one instrument greatly simplifies sample handling, avoids cumbersome experimental overheads, simplifies navigation between the two modalities, and improves the success rate of image correlation. Here, an integrated approach for correlative microscopy under cryogenic conditions is presented. Its advantages over the room temperature approach include safeguarding the native hydrated state of the biological specimen, preservation of the fluorescence signal without risk of quenching due to heavy atom stains, and reduced photo bleaching. The potential of cryo integrated light and electron microscopy is demonstrated for the detection of viable bacteria, the study of in vitro polymerized microtubules, the localization of mitochondria in mouse embryonic fibroblasts, and for a search into virus-induced intracellular membrane modifications within mammalian cells. Copyright © 2012 Elsevier Inc. All rights reserved.

Comparative morphology of zebra (Dreissena polymorpha) and quagga (Dreissena bugensis) mussel sperm: Light and electron microscopy

Science.gov (United States)

Walker, G.K.; Black, M.G.; Edwards, C.A.

1996-01-01

Adult zebra (Dreissena polymorpha) and quagga (Dreissena bugensis) mussels were induced to release large quantities of live spermatozoa by the administration of 5-hydroxytryptamine (serotonin). Sperm were photographed alive using phase-contrast microscopy and were fixed subsequently with glutaraldehyde followed by osmium tetroxide for eventual examination by transmission or scanning electron microscopy. The sperm of both genera are of the ect-aquasperm type. Their overall dimensions and shape allow for easy discrimination at the light and scanning electron microscopy level. Transmission electron microscopy of the cells reveals a barrel-shaped nucleus in zebra mussel sperm and an elongated nucleus in quagga mussel sperm. In both species, an acrosome is cradled in a nuclear fossa. The ultrastructure of the acrosome and axial body, however, is distinctive for each species. The structures of the midpiece are shown, including a unique mitochondrial "skirt" that includes densely packed parallel cristae and extends in a narrow sheet from the mitochondria.

Penetration of silver nanoparticles into porcine skin ex vivo using fluorescence lifetime imaging microscopy, Raman microscopy, and surface-enhanced Raman scattering microscopy.

Science.gov (United States)

Zhu, Yongjian; Choe, Chun-Sik; Ahlberg, Sebastian; Meinke, Martina C; Alexiev, Ulrike; Lademann, Juergen; Darvin, Maxim E

2015-05-01

In order to investigate the penetration depth of silver nanoparticles (Ag NPs) inside the skin, porcine ears treated with Ag NPs are measured by two-photon tomography with a fluorescence lifetime imaging microscopy (TPT-FLIM) technique, confocal Raman microscopy (CRM), and surface-enhanced Raman scattering (SERS) microscopy. Ag NPs are coated with poly-N-vinylpyrrolidone and dispersed in pure water solutions. After the application of Ag NPs, porcine ears are stored in the incubator for 24 h at a temperature of 37°C. The TPT-FLIM measurement results show a dramatic decrease of the Ag NPs' signal intensity from the skin surface to a depth of 4 μm. Below 4 μm, the Ag NPs' signal continues to decline, having completely disappeared at 12 to 14 μm depth. CRM shows that the penetration depth of Ag NPs is 11.1 ± 2.1 μm. The penetration depth measured with a highly sensitive SERS microscopy reaches 15.6 ± 8.3 μm. Several results obtained with SERS show that the penetration depth of Ag NPs can exceed the stratum corneum (SC) thickness, which can be explained by both penetration of trace amounts of Ag NPs through the SC barrier and by the measurements inside the hair follicle, which cannot be excluded in the experiment.

Structured illumination microscopy and its new developments

Directory of Open Access Journals (Sweden)

Jianling Chen

2016-05-01

Full Text Available Optical microscopy allows us to observe the biological structures and processes within living cells. However, the spatial resolution of the optical microscopy is limited to about half of the wavelength by the light diffraction. Structured illumination microscopy (SIM, a type of new emerging super-resolution microscopy, doubles the spatial resolution by illuminating the specimen with a patterned light, and the sample and light source requirements of SIM are not as strict as the other super-resolution microscopy. In addition, SIM is easier to combine with the other imaging techniques to improve their imaging resolution, leading to the developments of diverse types of SIM. SIM has great potential to meet the various requirements of living cells imaging. Here, we review the recent developments of SIM and its combination with other imaging techniques.

Super-resolved linear fluorescence localization microscopy using photostable fluorophores: A virtual microscopy study

Science.gov (United States)

Birk, Udo; Szczurek, Aleksander; Cremer, Christoph

2017-12-01

Current approaches to overcome the conventional limit of the resolution potential of light microscopy (of about 200 nm for visible light), often suffer from non-linear effects, which render the quantification of the image intensities in the reconstructions difficult, and also affect the quantification of the biological structure under investigation. As an attempt to face these difficulties, we discuss a particular method of localization microscopy which is based on photostable fluorescent dyes. The proposed method can potentially be implemented as a fast alternative for quantitative localization microscopy, circumventing the need for the acquisition of thousands of image frames and complex, highly dye-specific imaging buffers. Although the need for calibration remains in order to extract quantitative data (such as the number of emitters), multispectral approaches are largely facilitated due to the much less stringent requirements on imaging buffers. Furthermore, multispectral acquisitions can be readily obtained using commercial instrumentation such as e.g. the conventional confocal laser scanning microscope.

Digital stereo-holographic microscopy for studying three-dimensional particle dynamics

Science.gov (United States)

Byeon, Hyeokjun; Go, Taesik; Lee, Sang Joon

2018-06-01

A digital stereo-holographic microscopy (DsHM) with two viewing angles is proposed to measure 3D information of microscale particles. This approach includes two volumetric recordings and numerical reconstruction, and it involves the combination of separately reconstructed holograms. The 3D positional information of a particle was determined by searching the center of the overlapped reconstructed volume. After confirming the proposed technique using static spherical particles, the 3D information of moving particles suspended in a Hagen-Poiseiulle flow was successfully obtained. Moreover, the 3D information of nonspherical particles, including ellipsoidal particles and red blood cells, were measured using the proposed technique. In addition to 3D positional information, the orientation and shape of the test samples were obtained from the plane images by slicing the overlapped volume perpendicular to the directions of the image recordings. This DsHM technique will be useful in analyzing the 3D dynamic behavior of various nonspherical particles, which cannot be measured by conventional digital holographic microscopy.

Progress and new advances in simulating electron microscopy datasets using MULTEM

Energy Technology Data Exchange (ETDEWEB)

Lobato, I., E-mail: Ivan.Lobato@uantwerpen.be; Van Aert, S.; Verbeeck, J.

2016-09-15

A new version of the open source program MULTEM is presented here. It includes a graphical user interface, tapering truncation of the atomic potential, CPU multithreading functionality, single/double precision calculations, scanning transmission electron microscopy (STEM) simulations using experimental detector sensitivities, imaging STEM (ISTEM) simulations, energy filtered transmission electron microscopy (EFTEM) simulations, STEM electron energy loss spectroscopy (EELS) simulations along with other improvements in the algorithms. We also present a mixed channeling approach for the calculation of inelastic excitations, which allows one to considerably speed up time consuming EFTEM/STEM-EELS calculations. - Highlights: • We present a new version of the CPU/GPU open source program MULTEM. • A cross-platform graphical user interface is developed. • We include inelastic excitations for EFTEM/STEM-EELS calculations. • We add CPU multithreading functionality and single/double precision calculations.

Progress and new advances in simulating electron microscopy datasets using MULTEM

International Nuclear Information System (INIS)

Lobato, I.; Van Aert, S.; Verbeeck, J.

2016-01-01

A new version of the open source program MULTEM is presented here. It includes a graphical user interface, tapering truncation of the atomic potential, CPU multithreading functionality, single/double precision calculations, scanning transmission electron microscopy (STEM) simulations using experimental detector sensitivities, imaging STEM (ISTEM) simulations, energy filtered transmission electron microscopy (EFTEM) simulations, STEM electron energy loss spectroscopy (EELS) simulations along with other improvements in the algorithms. We also present a mixed channeling approach for the calculation of inelastic excitations, which allows one to considerably speed up time consuming EFTEM/STEM-EELS calculations. - Highlights: • We present a new version of the CPU/GPU open source program MULTEM. • A cross-platform graphical user interface is developed. • We include inelastic excitations for EFTEM/STEM-EELS calculations. • We add CPU multithreading functionality and single/double precision calculations.

Micromagnetism in (001) magnetite by spin-polarized low-energy electron microscopy

International Nuclear Information System (INIS)

Figuera, Juan de la; Vergara, Lucía; N'Diaye, Alpha T.; Quesada, Adrian; Schmid, Andreas K.

2013-01-01

Spin-polarized low-energy electron microscopy was used to image a magnetite crystal with (001) surface orientation. Sets of spin-dependent images of magnetic domain patterns observed in this surface were used to map the direction of the magnetization vector with high spatial and angular resolution. We find that domains are magnetized along the surface directions, and domain wall structures include 90° and 180° walls. A type of unusually curved domain walls are interpreted as Néel-capped surface terminations of 180° Bloch walls. - Highlights: ► The (001) surface of magnetite is imaged by spin-polarized low-energy electron microscopy. ► The magnetic domain microstructure is resolved. ► Magnetic easy axes in this surface are found to be along directions. ► Magnetic domain wall structures include wide Néel-caps

Micromagnetism in (001) magnetite by spin-polarized low-energy electron microscopy

Energy Technology Data Exchange (ETDEWEB)

Figuera, Juan de la, E-mail: juan.delafiguera@iqfr.csic.es [Instituto de Química-Física “Rocasolano”, CSIC, Madrid 28006 (Spain); Vergara, Lucía [Instituto de Química-Física “Rocasolano”, CSIC, Madrid 28006 (Spain); N' Diaye, Alpha T. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Quesada, Adrian [Instituto de Cerámica y Vidrio, CSIC, Calle Kelsen 5, 28049, Madrid (Spain); Schmid, Andreas K. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)

2013-07-15

Spin-polarized low-energy electron microscopy was used to image a magnetite crystal with (001) surface orientation. Sets of spin-dependent images of magnetic domain patterns observed in this surface were used to map the direction of the magnetization vector with high spatial and angular resolution. We find that domains are magnetized along the surface <110> directions, and domain wall structures include 90° and 180° walls. A type of unusually curved domain walls are interpreted as Néel-capped surface terminations of 180° Bloch walls. - Highlights: ► The (001) surface of magnetite is imaged by spin-polarized low-energy electron microscopy. ► The magnetic domain microstructure is resolved. ► Magnetic easy axes in this surface are found to be along <110> directions. ► Magnetic domain wall structures include wide Néel-caps.

Leakage radiation interference microscopy.

Science.gov (United States)

Descrovi, Emiliano; Barakat, Elsie; Angelini, Angelo; Munzert, Peter; De Leo, Natascia; Boarino, Luca; Giorgis, Fabrizio; Herzig, Hans Peter

2013-09-01

We present a proof of principle for a new imaging technique combining leakage radiation microscopy with high-resolution interference microscopy. By using oil immersion optics it is demonstrated that amplitude and phase can be retrieved from optical fields, which are evanescent in air. This technique is illustratively applied for mapping a surface mode propagating onto a planar dielectric multilayer on a thin glass substrate. The surface mode propagation constant estimated after Fourier transformation of the measured complex field is well matched with an independent measurement based on back focal plane imaging.

Human enamel structure studied by high resolution electron microscopy

International Nuclear Information System (INIS)

Wen, S.L.

1989-01-01

Human enamel structural features are characterized by high resolution electron microscopy. The human enamel consists of polycrystals with a structure similar to Ca10(PO4)6(OH)2. This article describes the structural features of human enamel crystal at atomic and nanometer level. Besides the structural description, a great number of high resolution images are included. Research into the carious process in human enamel is very important for human beings. This article firstly describes the initiation of caries in enamel crystal at atomic and unit-cell level and secondly describes the further steps of caries with structural and chemical demineralization. The demineralization in fact, is the origin of caries in human enamel. The remineralization of carious areas in human enamel has drawn more and more attention as its potential application is realized. This process has been revealed by high resolution electron microscopy in detail in this article. On the other hand, the radiation effects on the structure of human enamel are also characterized by high resolution electron microscopy. In order to reveal this phenomenon clearly, a great number of electron micrographs have been shown, and a physical mechanism is proposed. 26 references

Cell reactions with biomaterials: the microscopies

Directory of Open Access Journals (Sweden)

Curtis A. S.G.

2001-01-01

Full Text Available The methods and results of optical microscopy that can be used to observe cell reactions to biomaterials are Interference Reflection Microscopy (IRM, Total Internal Reflection Fluorescence Microscopy (TIRFM, Surface Plasmon Resonance Microscopy (SPRM and Forster Resonance Energy Transfer Microscopy (FRETM and Standing Wave Fluorescence Microscopy. The last three are new developments, which have not yet been fully perfected. TIRFM and SPRM are evanescent wave methods. The physics of these methods depend upon optical phenomena at interfaces. All these methods give information on the dimensions of the gap between cell and the substratum to which it is adhering and thus are especially suited to work with biomaterials. IRM and FRETM can be used on opaque surfaces though image interpretation is especially difficult for IRM on a reflecting opaque surface. These methods are compared with several electron microscopical methods for studying cell adhesion to substrata. These methods all yield fairly consistent results and show that the cell to substratum distance on many materials is in the range 5 to 30 nm. The area of contact relative to the total projected area of the cell may vary from a few per cent to close to 100% depending on the cell type and substratum. These methods show that those discrete contact areas well known as focal contacts are frequently present. The results of FRETM suggest that the separation from the substratum even in a focal contact is about 5 nm.

Resolution doubling in fluorescence microscopy with confocal spinning-disk image scanning microscopy.

Science.gov (United States)

Schulz, Olaf; Pieper, Christoph; Clever, Michaela; Pfaff, Janine; Ruhlandt, Aike; Kehlenbach, Ralph H; Wouters, Fred S; Großhans, Jörg; Bunt, Gertrude; Enderlein, Jörg

2013-12-24

We demonstrate how a conventional confocal spinning-disk (CSD) microscope can be converted into a doubly resolving image scanning microscopy (ISM) system without changing any part of its optical or mechanical elements. Making use of the intrinsic properties of a CSD microscope, we illuminate stroboscopically, generating an array of excitation foci that are moved across the sample by varying the phase between stroboscopic excitation and rotation of the spinning disk. ISM then generates an image with nearly doubled resolution. Using conventional fluorophores, we have imaged single nuclear pore complexes in the nuclear membrane and aggregates of GFP-conjugated Tau protein in three dimensions. Multicolor ISM was shown on cytoskeletal-associated structural proteins and on 3D four-color images including MitoTracker and Hoechst staining. The simple adaptation of conventional CSD equipment allows superresolution investigations of a broad variety of cell biological questions.

4Pi-confocal microscopy of live cells

Science.gov (United States)

Bahlmann, Karsten; Jakobs, Stefan; Hell, Stefan W.

2002-06-01

By coherently adding the spherical wavefronts of two opposing lenses, two-photon excitation 4Pi-confocal fluorescence microscopy has achieved three-dimensional imaging with an axial resolution 3-7 times better than confocal microscopy. So far this improvement was possible only in glycerol-mounted, fixed cells. Here we report 4Pi-confocal microscopy of watery objects and its application to the imaging of live cells. Water immersion 4Pi-confocal microscopy of membrane stained live Escherichia coli bacteria attains a 4.3 fold better axial resolution as compared to the best water immersion confocal microscope. The resolution enhancement results into a vastly improved three-dimensional representation of the bacteria. The first images of live biological samples with an all-directional resolution in the 190-280 nm range are presented here, thus establishing a new resolution benchmark in live cell microscopy.

Electron microscopy investigations of changes in morphology and conductivity of LiFePO4/C electrodes

DEFF Research Database (Denmark)

Scipioni, Roberto; Jørgensen, Peter S.; Ngo, Duc-The

2016-01-01

In this work we study the structural degradation of a laboratory Li-ion battery LiFePO4/Carbon Black (LFP/CB) cathode by various electron microscopy techniques including low kV Focused Ion Beam (FIB)/Scanning Electron Microscopy (SEM) 3D tomography. Several changes are observed in FIB/SEM images...

The X-ray microscopy project at saga SLS

International Nuclear Information System (INIS)

Yasumoto, M.; Ishiguro, E.; Takemoto, K.; Kihara, H.; Kamijo, N.; Tomimasu, T.; Tsurushima, T.; Takahara, A.; Hara, K.; Chikaura, Y.

2002-01-01

A new high resolution X-ray microscopy project has been proposed at Saga synchrotron light source, which is a third generation synchrotron light facility in Japan. Two microscopy beamlines are planned for this project. One is a scanning microscope in the water window region, and the other is a full-field imaging microscope in the multi-keV X-ray energy region. To demonstrate the feasibility of the project, the optical layout of the scanning microscope was designed. The beamline mainly consists of a 3.5 cm periodical undulator, a varied line-spacing plane grating monochromator (600 lines/mm) and an end-station including a zone plate. Thus, the calculated X-ray properties focused on the sample position are as follows: the spot size is ∼ 70 nm, the monochromaticity is ∼2000, and the photon flux is 10 9 ∼ 10 10 photons/sec. (authors)

Characterization of Preferential Ground-Water Seepage From a Chlorinated Hydrocarbon-Contaminated Aquifer to West Branch Canal Creek, Aberdeen Proving Ground, Maryland, 2002-04

Science.gov (United States)

Majcher, Emily H.; Phelan, Daniel J.; Lorah, Michelle M.; McGinty, Angela L.

2007-01-01

Wetlands act as natural transition zones between ground water and surface water, characterized by the complex interdependency of hydrology, chemical and physical properties, and biotic effects. Although field and laboratory demonstrations have shown efficient natural attenuation processes in the non-seep wetland areas and stream bottom sediments of West Branch Canal Creek, chlorinated volatile organic compounds are present in a freshwater tidal creek at Aberdeen Proving Ground, Maryland. Volatile organic compound concentrations in surface water indicate that in some areas of the wetland, preferential flow paths or seeps allow transport of organic compounds from the contaminated sand aquifer to the overlying surface water without undergoing natural attenuation. From 2002 through 2004, the U.S. Geological Survey, in cooperation with the Environmental Conservation and Restoration Division of the U.S. Army Garrison, Aberdeen Proving Ground, characterized preferential ground-water seepage as part of an ongoing investigation of contaminant distribution and natural attenuation processes in wetlands at this site. Seep areas were discrete and spatially consistent during thermal infrared surveys in 2002, 2003, and 2004 throughout West Branch Canal Creek wetlands. In these seep areas, temperature measurements in shallow pore water and sediment more closely resembled those in ground water than those in nearby surface water. Generally, pore water in seep areas contaminated with chlorinated volatile organic compounds had lower methane and greater volatile organic compound concentrations than pore water in non-seep wetland sediments. The volatile organic compounds detected in shallow pore water in seeps were spatially similar to the dominant volatile organic compounds in the underlying Canal Creek aquifer, with both parent and anaerobic daughter compounds detected. Seep locations characterized as focused seeps contained the highest concentrations of chlorinated parent compounds

High-speed atomic force microscopy combined with inverted optical microscopy for studying cellular events.

OpenAIRE

Suzuki, Yuki; Sakai, Nobuaki; Yoshida, Aiko; Uekusa, Yoshitsugu; Yagi, Akira; Imaoka, Yuka; Ito, Shuichi; Karaki, Koichi; Takeyasu, Kunio

2013-01-01

A hybrid atomic force microscopy (AFM)-optical fluorescence microscopy is a powerful tool for investigating cellular morphologies and events. However, the slow data acquisition rates of the conventional AFM unit of the hybrid system limit the visualization of structural changes during cellular events. Therefore, high-speed AFM units equipped with an optical/fluorescence detection device have been a long-standing wish. Here we describe the implementation of high-speed AFM coupled with an optic...

Assessment of nerve ultrastructure by fibre-optic confocal microscopy.

Science.gov (United States)

Cushway, T R; Lanzetta, M; Cox, G; Trickett, R; Owen, E R

1996-01-01

Fibre-optic technology combined with confocality produces a microscope capable of optical thin sectioning. In this original study, tibial nerves have been stained in a rat model with a vital dye, 4-(4-diethylaminostyryl)-N-methylpyridinium iodide, and analysed by fibre-optic confocal microscopy to produce detailed images of nerve ultrastructure. Schwann cells, nodes of Ranvier and longitudinal myelinated sheaths enclosing axons were clearly visible. Single axons appeared as brightly staining longitudinal structures. This allowed easy tracing of multiple signal axons within the nerve tissue. An accurate measurement of internodal lengths was easily accomplished. This technique is comparable to current histological techniques, but does not require biopsy, thin sectioning or tissue fixing. This study offers a standard for further in vivo microscopy, including the possibility of monitoring the progression of nerve regeneration following microsurgical neurorraphy.

Transmission electron microscopy physics of image formation and microanalysis

CERN Document Server

Reimer, Ludwig

1997-01-01

Transmission Electron Microscopy presents the theory of image and contrast formation, and the analytical modes in transmission electron microscopy. The principles of particle and wave optics of electrons are described. Electron-specimen interactions are discussed for evaluating the theory of scattering and phase contrast. Also discussed are the kinematical and dynamical theories of electron diffraction and their applications for crystal-structure analysis and imaging of lattices and their defects. X-ray micronanalysis and electron energy-loss spectroscopy are treated as analytical methods. Specimen damage and contamination by electron irradiation limits the resolution for biological and some inorganic specimens. This fourth edition includes discussion of recent progress, especially in the area of Schottky emission guns, convergent-beam electron diffraction, electron tomography, holography and the high resolution of crystal lattices.

Investigation of Shallow Structures as The Pathway of Oil Seep in The Alue Punoe Village, Bireuen District, Aceh Province, Indonesia

Directory of Open Access Journals (Sweden)

. Asrillah

2016-08-01

Full Text Available Measurement of magnetic data has been done in the area of oil seeps in the village of the Alue Punoe, with 121 measurement points as a grid within 500 m x 500 m area where each grid is approximately in 250 m2. The total magnetic field measurement has been examined by using Proton Precession Magnetometer (PPM. Upward continuation correction was applied to obtain residual magnetic field anomaly. Residual magnetic field anomaly data are mapped using the Surfer software, while subsurface models are made using the Mag2DC software. Based on the models that have been sliced from the local magnetic anomalies along the cross section of A-B and C-D from which then obtained a shallow structure which is a fault whose an approximate depth from 30 to 100 meters and three stratified media. The stratified media of the study area are interpreted as an alluvial deposit, alternating sandstone and clay and igneous rocks. Interpretation of subsurface models shows that there exists a shallow structure assumed as a fault. Expected fault has an adjacent to the manifestations which are about 50 to 70 m. It strengthens the case that the fault is strongly related to as the pathways of oil seepsfrom possibly existed petroleum system below subsurface of unknown strata

Observation of multicellular spinning behavior of Proteus mirabilis by atomic force microscopy and multifunctional microscopy.

Science.gov (United States)

Liu, Yanxia; Deng, Yuanxin; Luo, Shuxiu; Deng, Yu; Guo, Linming; Xu, Weiwei; Liu, Lei; Liu, Junkang

2014-01-01

This study aimed to observe the multicellular spinning behavior of Proteus mirabilis by atomic force microscopy (AFM) and multifunctional microscopy in order to understand the mechanism underlying this spinning movement and its biological significance. Multifunctional microscopy with charge-coupled device (CCD) and real-time AFM showed changes in cell structure and shape of P. mirabilis during multicellular spinning movement. Specifically, the morphological characteristics of P. mirabilis, multicellular spinning dynamics, and unique movement were observed. Our findings indicate that the multicellular spinning behavior of P. mirabilis may be used to collect nutrients, perform colonization, and squeeze out competitors. The movement characteristics of P. mirabilis are vital to the organism's biological adaptability to the surrounding environment. Copyright © 2013 Elsevier Ltd. All rights reserved.

Multimodal analysis of diamond crystals and layers using RISE microscopy

Czech Academy of Sciences Publication Activity Database

Váňa, R.; Dluhoš, J.; Varga, Marián; Schmid, Ch.; Kromka, Alexander

2017-01-01

Roč. 23, Aug (2017), s. 2280-2281 ISSN 1431-9276 R&D Projects: GA MŠk(CZ) LD15003 Institutional support: RVO:68378271 Keywords : diamond * RISE microscopy Subject RIV: BH - Optics, Masers, Lasers OBOR OECD: Optics (including laser optics and quantum optics) Impact factor: 1.891, year: 2016

Correlating Intravital Multi-Photon Microscopy to 3D Electron Microscopy of Invading Tumor Cells Using Anatomical Reference Points

Science.gov (United States)

Karreman, Matthia A.; Mercier, Luc; Schieber, Nicole L.; Shibue, Tsukasa; Schwab, Yannick; Goetz, Jacky G.

2014-01-01

Correlative microscopy combines the advantages of both light and electron microscopy to enable imaging of rare and transient events at high resolution. Performing correlative microscopy in complex and bulky samples such as an entire living organism is a time-consuming and error-prone task. Here, we investigate correlative methods that rely on the use of artificial and endogenous structural features of the sample as reference points for correlating intravital fluorescence microscopy and electron microscopy. To investigate tumor cell behavior in vivo with ultrastructural accuracy, a reliable approach is needed to retrieve single tumor cells imaged deep within the tissue. For this purpose, fluorescently labeled tumor cells were subcutaneously injected into a mouse ear and imaged using two-photon-excitation microscopy. Using near-infrared branding, the position of the imaged area within the sample was labeled at the skin level, allowing for its precise recollection. Following sample preparation for electron microscopy, concerted usage of the artificial branding and anatomical landmarks enables targeting and approaching the cells of interest while serial sectioning through the specimen. We describe here three procedures showing how three-dimensional (3D) mapping of structural features in the tissue can be exploited to accurately correlate between the two imaging modalities, without having to rely on the use of artificially introduced markers of the region of interest. The methods employed here facilitate the link between intravital and nanoscale imaging of invasive tumor cells, enabling correlating function to structure in the study of tumor invasion and metastasis. PMID:25479106

A multispectral scanner survey of the Rocky Flats Environmental Technology Site and surrounding area, Golden, Colorado

International Nuclear Information System (INIS)

Brewster, S.B. Jr.; Brickey, D.W.; Ross, S.L.; Shines, J.E.

1997-04-01

Aerial multispectral scanner imagery was collected of the Rocky Flats Environmental Technology Site in Golden, Colorado, on June 3, 5, 6, and 7, 1994, using a Daedalus AADS1268 multispectral scanner and coincident aerial color and color infrared photography. Flight altitudes were 4,500 feet (1372 meters) above ground level to match prior 1989 survey data; 2,000 feet (609 meters) above ground level for sitewide vegetation mapping; and 1,000 feet (304 meters) above ground level for selected areas of special interest. A multispectral survey was initiated to improve the existing vegetation classification map, to identify seeps and springs, and to generate ARC/INFO Geographic Information System compatible coverages of the vegetation and wetlands for the entire site including the buffer zone. The multispectral scanner imagery and coincident aerial photography were analyzed for the detection, identification, and mapping of vegetation and wetlands. The multispectral scanner data were processed digitally while the color and color infrared photography were manually photo-interpreted to define vegetation and wetlands. Several standard image enhancement techniques were applied to the multispectral scanner data to assist image interpretation. A seep enhancement was applied and a color composite consisting of multispectral scanner channels 11, 7, and 5 (thermal infrared, mid-infrared, and red bands, respectively) proved most useful for detecting seeps, seep zones, and springs. The predawn thermal infrared data were also useful in identifying and locating seeps. The remote sensing data, mapped wetlands, and ancillary Geographic Information System compatible data sets were spatially analyzed for seeps

Automated analysis of high-content microscopy data with deep learning.

Science.gov (United States)

Kraus, Oren Z; Grys, Ben T; Ba, Jimmy; Chong, Yolanda; Frey, Brendan J; Boone, Charles; Andrews, Brenda J

2017-04-18

Existing computational pipelines for quantitative analysis of high-content microscopy data rely on traditional machine learning approaches that fail to accurately classify more than a single dataset without substantial tuning and training, requiring extensive analysis. Here, we demonstrate that the application of deep learning to biological image data can overcome the pitfalls associated with conventional machine learning classifiers. Using a deep convolutional neural network (DeepLoc) to analyze yeast cell images, we show improved performance over traditional approaches in the automated classification of protein subcellular localization. We also demonstrate the ability of DeepLoc to classify highly divergent image sets, including images of pheromone-arrested cells with abnormal cellular morphology, as well as images generated in different genetic backgrounds and in different laboratories. We offer an open-source implementation that enables updating DeepLoc on new microscopy datasets. This study highlights deep learning as an important tool for the expedited analysis of high-content microscopy data. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

Comparative analysis of imaging configurations and objectives for Fourier microscopy.

Science.gov (United States)

Kurvits, Jonathan A; Jiang, Mingming; Zia, Rashid

2015-11-01

Fourier microscopy is becoming an increasingly important tool for the analysis of optical nanostructures and quantum emitters. However, achieving quantitative Fourier space measurements requires a thorough understanding of the impact of aberrations introduced by optical microscopes that have been optimized for conventional real-space imaging. Here we present a detailed framework for analyzing the performance of microscope objectives for several common Fourier imaging configurations. To this end, we model objectives from Nikon, Olympus, and Zeiss using parameters that were inferred from patent literature and confirmed, where possible, by physical disassembly. We then examine the aberrations most relevant to Fourier microscopy, including the alignment tolerances of apodization factors for different objective classes, the effect of magnification on the modulation transfer function, and vignetting-induced reductions of the effective numerical aperture for wide-field measurements. Based on this analysis, we identify an optimal objective class and imaging configuration for Fourier microscopy. In addition, the Zemax files for the objectives and setups used in this analysis have been made publicly available as a resource for future studies.

Species distribution and population connectivity of deep-sea mussels at hydrocarbon seeps in the Gulf of Mexico.

Directory of Open Access Journals (Sweden)

Baptiste Faure

Full Text Available Hydrocarbon seepage is widespread and patchy in the Gulf of Mexico, and six species of symbiont containing bathymodiolin mussels are found on active seeps over wide and overlapping depth and geographic ranges. We use mitochondrial genes to discriminate among the previously known and a newly discovered species and to assess the connectivity among populations of the same species in the northern Gulf of Mexico (GoM. Our results generally validate the morphologically based distribution of the three previously known GoM species of Bathymodiolus, although we found that approximately 10% of the morphologically based identifications were incorrect and this resulted in some inaccuracies with respect to their previously assigned depth and geographical distribution patterns. These data allowed us to confirm that sympatry of two species of Bathymodiolus within a single patch of mussels is common. A new species of bathymodiolin, Bathymodiolus sp. nov., closely related to B. heckerae was also discovered. The two species live at the same depths but have not been found in sympatry and both have small effective population sizes. We found evidence for genetic structure within populations of the three species of Bathymodiolinae for which we had samples from multiple sites and suggest limited connectivity for populations at some sites. Despite relatively small sample sizes, genetic diversity indices suggest the largest population sizes for B. childressi and Tamu fisheri and the smallest for B. heckerae and B. sp. nov. among the GoM bathymodiolins. Moreover, we detected an excess of rare variants indicating recent demographic changes and population expansions for the four species of bathymodiolins from the Gulf of Mexico.

Collaborative Computational Project for Electron cryo-Microscopy

Energy Technology Data Exchange (ETDEWEB)

Wood, Chris; Burnley, Tom [Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA (United Kingdom); Patwardhan, Ardan [European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD (United Kingdom); Scheres, Sjors [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom); Topf, Maya [University of London, Malet Street, London WC1E 7HX (United Kingdom); Roseman, Alan [University of Manchester, Oxford Road, Manchester M13 9PT (United Kingdom); Winn, Martyn, E-mail: martyn.winn@stfc.ac.uk [Science and Technology Facilities Council, Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA (United Kingdom)

2015-01-01

The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) is a new initiative for the structural biology community, following the success of CCP4 for macromolecular crystallography. Progress in supporting the users and developers of cryoEM software is reported. The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has recently been established. The aims of the project are threefold: to build a coherent cryoEM community which will provide support for individual scientists and will act as a focal point for liaising with other communities, to support practising scientists in their use of cryoEM software and finally to support software developers in producing and disseminating robust and user-friendly programs. The project is closely modelled on CCP4 for macromolecular crystallography, and areas of common interest such as model fitting, underlying software libraries and tools for building program packages are being exploited. Nevertheless, cryoEM includes a number of techniques covering a large range of resolutions and a distinct project is required. In this article, progress so far is reported and future plans are discussed.

Collaborative Computational Project for Electron cryo-Microscopy

International Nuclear Information System (INIS)

Wood, Chris; Burnley, Tom; Patwardhan, Ardan; Scheres, Sjors; Topf, Maya; Roseman, Alan; Winn, Martyn

2015-01-01

The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) is a new initiative for the structural biology community, following the success of CCP4 for macromolecular crystallography. Progress in supporting the users and developers of cryoEM software is reported. The Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has recently been established. The aims of the project are threefold: to build a coherent cryoEM community which will provide support for individual scientists and will act as a focal point for liaising with other communities, to support practising scientists in their use of cryoEM software and finally to support software developers in producing and disseminating robust and user-friendly programs. The project is closely modelled on CCP4 for macromolecular crystallography, and areas of common interest such as model fitting, underlying software libraries and tools for building program packages are being exploited. Nevertheless, cryoEM includes a number of techniques covering a large range of resolutions and a distinct project is required. In this article, progress so far is reported and future plans are discussed

Atomic Force Microscopy Based Cell Shape Index

Science.gov (United States)

Adia-Nimuwa, Usienemfon; Mujdat Tiryaki, Volkan; Hartz, Steven; Xie, Kan; Ayres, Virginia

2013-03-01

Stellation is a measure of cell physiology and pathology for several cell groups including neural, liver and pancreatic cells. In the present work, we compare the results of a conventional two-dimensional shape index study of both atomic force microscopy (AFM) and fluorescent microscopy images with the results obtained using a new three-dimensional AFM-based shape index similar to sphericity index. The stellation of astrocytes is investigated on nanofibrillar scaffolds composed of electrospun polyamide nanofibers that has demonstrated promise for central nervous system (CNS) repair. Recent work by our group has given us the ability to clearly segment the cells from nanofibrillar scaffolds in AFM images. The clear-featured AFM images indicated that the astrocyte processes were longer than previously identified at 24h. It was furthermore shown that cell spreading could vary significantly as a function of environmental parameters, and that AFM images could record these variations. The new three-dimensional AFM-based shape index incorporates the new information: longer stellate processes and cell spreading. The support of NSF PHY-095776 is acknowledged.

Sputum Microscopy With Fluorescein Diacetate Predicts Tuberculosis Infectiousness.

Science.gov (United States)

Datta, Sumona; Sherman, Jonathan M; Tovar, Marco A; Bravard, Marjory A; Valencia, Teresa; Montoya, Rosario; Quino, Willi; D'Arcy, Nikki; Ramos, Eric S; Gilman, Robert H; Evans, Carlton A

2017-09-01

Sputum from patients with tuberculosis contains subpopulations of metabolically active and inactive Mycobacterium tuberculosis with unknown implications for infectiousness. We assessed sputum microscopy with fluorescein diacetate (FDA, evaluating M. tuberculosis metabolic activity) for predicting infectiousness. Mycobacterium tuberculosis was quantified in pretreatment sputum of patients with pulmonary tuberculosis using FDA microscopy, culture, and acid-fast microscopy. These 35 patients' 209 household contacts were followed with prevalence surveys for tuberculosis disease for 6 years. FDA microscopy was positive for a median of 119 (interquartile range [IQR], 47-386) bacteria/µL sputum, which was 5.1% (IQR, 2.4%-11%) the concentration of acid-fast microscopy-positive bacteria (2069 [IQR, 1358-3734] bacteria/μL). Tuberculosis was diagnosed during follow-up in 6.4% (13/209) of contacts. For patients with lower than median concentration of FDA microscopy-positive M. tuberculosis, 10% of their contacts developed tuberculosis. This was significantly more than 2.7% of the contacts of patients with higher than median FDA microscopy results (crude hazard ratio [HR], 3.8; P = .03). This association maintained statistical significance after adjusting for disease severity, chemoprophylaxis, drug resistance, and social determinants (adjusted HR, 3.9; P = .02). Mycobacterium tuberculosis that was FDA microscopy negative was paradoxically associated with greater infectiousness. FDA microscopy-negative bacteria in these pretreatment samples may be a nonstaining, slowly metabolizing phenotype better adapted to airborne transmission. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America.

The evolution of hot-stage microscopy to aid solid-state characterizations of pharmaceutical solids

International Nuclear Information System (INIS)

Vitez, I.M.; Davidovich, M.; Newman, A.W.; Kiesnowski, C.

1998-01-01

A variety of techniques can be used to characterize the physical properties of pharmaceutical solids, including thermal analysis, hot-stage microscopy, X-ray powder diffraction, spectroscopic and micromeritic analysis. Comprehensive characterizations of the physical properties of pharmaceutical solids require a multi-disciplinary approach, since no single technique is capable of characterizing the materials completely.The combination of traditional hot-stage microscopy with new technologies such as high-resolution micrography, image capture, storage manipulation, and presentation, have permitted more comprehensive physical property characterizations to be conducted. As a result of these technological advances, it is possible to present the results of these microscopic analyses, as they were initially collected by the microscopist, outside of the laboratory.An evolutionary trail detailing the use of hot-stage microscopy in the Materials Science Group, from a simple melting point apparatus to the current hot-stage DSC microscopy instrument, will be presented. Examples of materials characterized using the hot-stage microscopy system will also be presented. (Copyright (c) 1998 Elsevier Science B.V., Amsterdam. All rights reserved.)

High-precision correlative fluorescence and electron cryo microscopy using two independent alignment markers

International Nuclear Information System (INIS)

Schellenberger, Pascale; Kaufmann, Rainer; Siebert, C. Alistair; Hagen, Christoph; Wodrich, Harald; Grünewald, Kay

2014-01-01

Correlative light and electron microscopy (CLEM) is an emerging technique which combines functional information provided by fluorescence microscopy (FM) with the high-resolution structural information of electron microscopy (EM). So far, correlative cryo microscopy of frozen-hydrated samples has not reached better than micrometre range accuracy. Here, a method is presented that enables the correlation between fluorescently tagged proteins and electron cryo tomography (cryoET) data with nanometre range precision. Specifically, thin areas of vitrified whole cells are examined by correlative fluorescence cryo microscopy (cryoFM) and cryoET. Novel aspects of the presented cryoCLEM workflow not only include the implementation of two independent electron dense fluorescent markers to improve the precision of the alignment, but also the ability of obtaining an estimate of the correlation accuracy for each individual object of interest. The correlative workflow from plunge-freezing to cryoET is detailed step-by-step for the example of locating fluorescence-labelled adenovirus particles trafficking inside a cell. - Highlights: • Vitrified mammalian cell were imaged by fluorescence and electron cryo microscopy. • TetraSpeck fluorescence markers were added to correct shifts between cryo fluorescence channels. • FluoSpheres fiducials were used as reference points to assign new coordinates to cryoEM images. • Adenovirus particles were localised with an average correlation precision of 63 nm

High-precision correlative fluorescence and electron cryo microscopy using two independent alignment markers

Energy Technology Data Exchange (ETDEWEB)

Schellenberger, Pascale [Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Kaufmann, Rainer [Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU (United Kingdom); Siebert, C. Alistair; Hagen, Christoph [Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Wodrich, Harald [Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, University of Bordeaux SEGALEN, 146 rue Leo Seignat, 33076 Bordeaux (France); Grünewald, Kay, E-mail: kay@strubi.ox.ac.uk [Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom)

2014-08-01

Correlative light and electron microscopy (CLEM) is an emerging technique which combines functional information provided by fluorescence microscopy (FM) with the high-resolution structural information of electron microscopy (EM). So far, correlative cryo microscopy of frozen-hydrated samples has not reached better than micrometre range accuracy. Here, a method is presented that enables the correlation between fluorescently tagged proteins and electron cryo tomography (cryoET) data with nanometre range precision. Specifically, thin areas of vitrified whole cells are examined by correlative fluorescence cryo microscopy (cryoFM) and cryoET. Novel aspects of the presented cryoCLEM workflow not only include the implementation of two independent electron dense fluorescent markers to improve the precision of the alignment, but also the ability of obtaining an estimate of the correlation accuracy for each individual object of interest. The correlative workflow from plunge-freezing to cryoET is detailed step-by-step for the example of locating fluorescence-labelled adenovirus particles trafficking inside a cell. - Highlights: • Vitrified mammalian cell were imaged by fluorescence and electron cryo microscopy. • TetraSpeck fluorescence markers were added to correct shifts between cryo fluorescence channels. • FluoSpheres fiducials were used as reference points to assign new coordinates to cryoEM images. • Adenovirus particles were localised with an average correlation precision of 63 nm.

Three axis vector magnet set-up for cryogenic scanning probe microscopy

International Nuclear Information System (INIS)

Galvis, J. A.; Herrera, E.; Buendía, A.; Guillamón, I.; Vieira, S.; Suderow, H.; Azpeitia, J.; Luccas, R. F.; Munuera, C.; García-Hernandez, M.

2015-01-01

We describe a three axis vector magnet system for cryogenic scanning probe microscopy measurements. We discuss the magnet support system and the power supply, consisting of a compact three way 100 A current source. We obtain tilted magnetic fields in all directions with maximum value of 5T along z-axis and of 1.2T for XY-plane magnetic fields. We describe a scanning tunneling microscopy-spectroscopy (STM-STS) set-up, operating in a dilution refrigerator, which includes a new high voltage ultralow noise piezodrive electronics and discuss the noise level due to vibrations. STM images and STS maps show atomic resolution and the tilted vortex lattice at 150 mK in the superconductor β-Bi 2 Pd. We observe a strongly elongated hexagonal lattice, which corresponds to the projection of the tilted hexagonal vortex lattice on the surface. We also discuss Magnetic Force Microscopy images in a variable temperature insert

Three axis vector magnet set-up for cryogenic scanning probe microscopy

Energy Technology Data Exchange (ETDEWEB)

Galvis, J. A. [Laboratorio de Bajas Temperaturas, Departamento de Física de la Materia Condensada, Instituto de Ciencia de Materiales Nicolás Cabrera, Condensed Matter Physics Center (IFIMAC), Facultad de Ciencias Universidad Autónoma de Madrid, 28049 Madrid (Spain); Departamento de Ciencias Naturales Facultad de Ingeniería Universidad Central, Bogotá (Colombia); Herrera, E.; Buendía, A. [Laboratorio de Bajas Temperaturas, Departamento de Física de la Materia Condensada, Instituto de Ciencia de Materiales Nicolás Cabrera, Condensed Matter Physics Center (IFIMAC), Facultad de Ciencias Universidad Autónoma de Madrid, 28049 Madrid (Spain); Guillamón, I.; Vieira, S.; Suderow, H. [Laboratorio de Bajas Temperaturas, Departamento de Física de la Materia Condensada, Instituto de Ciencia de Materiales Nicolás Cabrera, Condensed Matter Physics Center (IFIMAC), Facultad de Ciencias Universidad Autónoma de Madrid, 28049 Madrid (Spain); Unidad Asociada de Bajas Temperaturas y Altos Campos Magnéticos, UAM, CSIC, Cantoblanco, E-28049 Madrid (Spain); Azpeitia, J.; Luccas, R. F.; Munuera, C.; García-Hernandez, M. [Unidad Asociada de Bajas Temperaturas y Altos Campos Magnéticos, UAM, CSIC, Cantoblanco, E-28049 Madrid (Spain); Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas (ICMM-CSIC), Sor Juana Inés de la Cruz 3, 28049 Madrid (Spain); and others

2015-01-15

We describe a three axis vector magnet system for cryogenic scanning probe microscopy measurements. We discuss the magnet support system and the power supply, consisting of a compact three way 100 A current source. We obtain tilted magnetic fields in all directions with maximum value of 5T along z-axis and of 1.2T for XY-plane magnetic fields. We describe a scanning tunneling microscopy-spectroscopy (STM-STS) set-up, operating in a dilution refrigerator, which includes a new high voltage ultralow noise piezodrive electronics and discuss the noise level due to vibrations. STM images and STS maps show atomic resolution and the tilted vortex lattice at 150 mK in the superconductor β-Bi{sub 2}Pd. We observe a strongly elongated hexagonal lattice, which corresponds to the projection of the tilted hexagonal vortex lattice on the surface. We also discuss Magnetic Force Microscopy images in a variable temperature insert.

Scanning probe microscopy in material science and biology

International Nuclear Information System (INIS)

Cricenti, A; Colonna, S; Girasole, M; Gori, P; Ronci, F; Longo, G; Dinarelli, S; Luce, M; Rinaldi, M; Ortenzi, M

2011-01-01

A review of the activity of scanning probe microscopy at our Institute is presented, going from instrumentation to software development of scanning tunnelling microscopy, atomic force microscopy and scanning near-field optical microscopy (SNOM). Some of the most important experiments in material science and biology performed by our group through the years with these SPM techniques will be presented. Finally, infrared applications by coupling a SNOM with a free electron laser will also be presented.

Nanoparticle sizing: a comparative study using atomic force microscopy, transmission electron microscopy, and ferromagnetic resonance

International Nuclear Information System (INIS)

Lacava, L.M.; Lacava, B.M.; Azevedo, R.B.; Lacava, Z.G.M.; Buske, N.; Tronconi, A.L.; Morais, P.C.

2001-01-01

Atomic force microscopy (AFM), transmission electron microscopy (TEM), and ferromagnetic resonance (FMR) were used to unfold the nanoparticle size of a ferrofluid sample. Compared to TEM, the AFM method showed a nanoparticle diameter (D m ) reduction of 20% and standard deviation (σ) increase of 15%. The differences in D m and σ were associated with the AFM tip and the nanoparticle concentration on the substrate

Developments in Scanning Hall Probe Microscopy

Science.gov (United States)

Chouinard, Taras; Chu, Ricky; David, Nigel; Broun, David

2009-05-01

Low temperature scanning Hall probe microscopy is a sensitive means of imaging magnetic structures with high spatial resolution and magnetic flux sensitivity approaching that of a Superconducting Quantum Interference Device. We have developed a scanning Hall probe microscope with novel features, including highly reliable coarse positioning, in situ optimization of sensor-sample alignment and capacitive transducers for linear, long range positioning measurement. This has been motivated by the need to reposition accurately above fabricated nanostructures such as small superconducting rings. Details of the design and performance will be presented as well as recent progress towards time-resolved measurements with sub nanosecond resolution.

Electron microscopy - principles of radiation protection

International Nuclear Information System (INIS)

1990-01-01

This 8 minute programme explains the nature of the possible radiation hazard in Electron Microscopy and outlines the ways in which modern equipment is designed and made so that in normal use the worker is not exposed to radiation. The interlock principle is explained and illustrated by an example from the field of X-ray crystallography. By filming machines while they were dismantled for servicing, details of several internal safety devices have been included. In this way workers who normally use the equipment as a 'black box' get some insight into the principles and practice of radiation protection in the field. (author)

X-ray microscopy of human malaria

International Nuclear Information System (INIS)

Magowan, C.; Brown, J.T.; Mohandas, N.; Meyer-Ilse, W.

1997-01-01

Associations between intracellular organisms and host cells are complex and particularly difficult to examine. X-ray microscopy provides transmission images of subcellular structures in intact cells at resolutions superior to available methodologies. The spatial resolution is 50-60nm with a 1 micron depth of focus, superior to anything achievable with light microscopy. Image contrast is generated by differences in photoelectric absorption by the atoms in different areas (i.e. subcellular structures) throughout the full thickness of the sample. Absorption due to carbon dominates among all the elements in the sample at 2.4 nm x-ray wavelength. Thus images show features or structures, in a way not usually seen by other types of microscopy. The authors used soft x-ray microscopy to investigate structural development of Plasmodium falciparum malaria parasites in normal and genetically abnormal erythrocytes, and in infected erythrocytes treated with compounds that have anti-malarial effects. X-ray microscopy showed newly elaborated structures in the cytosol of unstained, intact erythrocytes, redistribution of mass (carbon) in infected erythrocytes, and aberrant parasite morphology. Better understanding of the process of intracellular parasite maturation and the interactions between the parasite and its host erythrocyte can help define new approaches to the control of this deadly disease

X-ray microscopy of human malaria

Energy Technology Data Exchange (ETDEWEB)

Magowan, C.; Brown, J.T.; Mohandas, N.; Meyer-Ilse, W. [Ernest Orlando Lawrence Berkeley National Lab., CA (United States)

1997-04-01

Associations between intracellular organisms and host cells are complex and particularly difficult to examine. X-ray microscopy provides transmission images of subcellular structures in intact cells at resolutions superior to available methodologies. The spatial resolution is 50-60nm with a 1 micron depth of focus, superior to anything achievable with light microscopy. Image contrast is generated by differences in photoelectric absorption by the atoms in different areas (i.e. subcellular structures) throughout the full thickness of the sample. Absorption due to carbon dominates among all the elements in the sample at 2.4 nm x-ray wavelength. Thus images show features or structures, in a way not usually seen by other types of microscopy. The authors used soft x-ray microscopy to investigate structural development of Plasmodium falciparum malaria parasites in normal and genetically abnormal erythrocytes, and in infected erythrocytes treated with compounds that have anti-malarial effects. X-ray microscopy showed newly elaborated structures in the cytosol of unstained, intact erythrocytes, redistribution of mass (carbon) in infected erythrocytes, and aberrant parasite morphology. Better understanding of the process of intracellular parasite maturation and the interactions between the parasite and its host erythrocyte can help define new approaches to the control of this deadly disease.

Scanning Capacitance Microscopy | Materials Science | NREL

Science.gov (United States)

obtained using scanning capacitance microscopy. Top Right: Image of p-type and n-type material, obtained 'fingers' of light-colored n-type material on a yellow and blue background representing p-type material material, obtained using scanning capacitance microscopy, in a sample semiconductor device; the image shows

Analysis of incomplete excisions of basal-cell carcinomas after breadloaf microscopy compared with 3D-microscopy: a prospective randomized and blinded study.

Science.gov (United States)

Boehringer, Alexandra; Adam, Patrick; Schnabl, Saskia; Häfner, Hans-Martin; Breuninger, Helmut

2015-08-01

Basal-cell carcinomas may show irregular, asymmetric subclinical growth. This study analyzed the efficacy of 'breadloaf' microscopy (serial sectioning) and three-dimensional (3D) microscopy in detecting positive tumor margins. Two hundred eighty-three (283) tumors (51.2%) were put into the breadloaf microscopy group; 270 tumors (48.8%) into the 3D microscopy group. The position of any detected tumor outgrowths was identified in clock face fashion. The time required for cutting and embedding the specimens and the examination of the microscopic slides was measured. Patient/tumor characteristics and surgical margins did not differ significantly. Tumor outgrowths at the excision margin were found in 62 of 283 cases (21.9%) in the breadloaf microscopy group and in 115 of 270 cases (42.6%) in the 3D microscopy group, constituting a highly significant difference (p < 0.001). This difference held true with incomplete excision of fibrosing (infiltrative/sclerosing/morpheaform) tumors [32.9% in the breadloaf microscopy group and 57.5% in the 3D microscopy group (p = 0.003)] and also with solid (nodular) tumors [16.1 and 34.2%, respectively (p < 0.001)]. The mean overall examination time required showed no important difference. In summary, for detection of tumor outgrowths, 3D microscopy has almost twice the sensitivity of breadloaf microscopy, particularly in the situation of aggressive/infiltrative carcinomas. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Whole Slide Imaging Versus Microscopy for Primary Diagnosis in Surgical Pathology: A Multicenter Blinded Randomized Noninferiority Study of 1992 Cases (Pivotal Study).

Science.gov (United States)

Mukhopadhyay, Sanjay; Feldman, Michael D; Abels, Esther; Ashfaq, Raheela; Beltaifa, Senda; Cacciabeve, Nicolas G; Cathro, Helen P; Cheng, Liang; Cooper, Kumarasen; Dickey, Glenn E; Gill, Ryan M; Heaton, Robert P; Kerstens, René; Lindberg, Guy M; Malhotra, Reenu K; Mandell, James W; Manlucu, Ellen D; Mills, Anne M; Mills, Stacey E; Moskaluk, Christopher A; Nelis, Mischa; Patil, Deepa T; Przybycin, Christopher G; Reynolds, Jordan P; Rubin, Brian P; Saboorian, Mohammad H; Salicru, Mauricio; Samols, Mark A; Sturgis, Charles D; Turner, Kevin O; Wick, Mark R; Yoon, Ji Y; Zhao, Po; Taylor, Clive R

2018-01-01

Most prior studies of primary diagnosis in surgical pathology using whole slide imaging (WSI) versus microscopy have focused on specific organ systems or included relatively few cases. The objective of this study was to demonstrate that WSI is noninferior to microscopy for primary diagnosis in surgical pathology. A blinded randomized noninferiority study was conducted across the entire range of surgical pathology cases (biopsies and resections, including hematoxylin and eosin, immunohistochemistry, and special stains) from 4 institutions using the original sign-out diagnosis (baseline diagnosis) as the reference standard. Cases were scanned, converted to WSI and randomized. Sixteen pathologists interpreted cases by microscopy or WSI, followed by a wash-out period of ≥4 weeks, after which cases were read by the same observers using the other modality. Major discordances were identified by an adjudication panel, and the differences between major discordance rates for both microscopy (against the reference standard) and WSI (against the reference standard) were calculated. A total of 1992 cases were included, resulting in 15,925 reads. The major discordance rate with the reference standard diagnosis was 4.9% for WSI and 4.6% for microscopy. The difference between major discordance rates for microscopy and WSI was 0.4% (95% confidence interval, -0.30% to 1.01%). The difference in major discordance rates for WSI and microscopy was highest in endocrine pathology (1.8%), neoplastic kidney pathology (1.5%), urinary bladder pathology (1.3%), and gynecologic pathology (1.2%). Detailed analysis of these cases revealed no instances where interpretation by WSI was consistently inaccurate compared with microscopy for multiple observers. We conclude that WSI is noninferior to microscopy for primary diagnosis in surgical pathology, including biopsies and resections stained with hematoxylin and eosin, immunohistochemistry and special stains. This conclusion is valid across a wide

Advanced Electron Microscopy in Materials Physics

International Nuclear Information System (INIS)

Zhu, Y.; Jarausch, K.

2009-01-01

Aberration correction has opened a new frontier in electron microscopy by overcoming the limitations of conventional round lenses, providing sub-angstrom-sized probes and extending information limits. The imaging and analytical performance of these corrector-equipped microscopes affords an unprecedented opportunity to study structure-property relationships of matter at the atomic scale. This new generation of microscopes is able to retrieve high-quality structural information comparable to neutron and synchrotron x-ray experiments, but with local atomic resolution. These advances in instrumentation are accelerating the research and development of various functional materials ranging from those for energy generation, conversion, transportation and storage to those for catalysis and nano-device applications. The dramatic improvements in electron-beam illumination and detection also present a host of new challenges for the interpretation and optimization of experiments. During 7-9 November 2007, a workshop, entitled 'Aberration Corrected Electron Microscopy in Material Physics', was convened at the Center for Functional Nanomaterials, Brookhaven National Laboratories (BNL) to address these opportunities and challenges. The workshop was co-sponsored by Hitachi High Technologies, a leader in electron microscopy instrumentation, and BNL's Institute of Advanced Electron Microscopy, a leader in materials physics research using electron microscopy. The workshop featured presentations by internationally prominent scientists working at the frontiers of electron microscopy, both on developing instrumentation and applying it in materials physics. The meeting, structured to stimulate scientific exchanges and explore new capabilities, brought together ∼100 people from over 10 countries. This special issue complies many of the advances in instrument performance and materials physics reported by the invited speakers and attendees at the workshop.

A review of cellphone microscopy for disease detection.

Science.gov (United States)

Dendere, R; Myburg, N; Douglas, T S

2015-12-01

The expansion in global cellphone network coverage coupled with advances in cellphone imaging capabilities present an opportunity for the advancement of cellphone microscopy as a low-cost alternative to conventional microscopy for disease detection in resource-limited regions. The development of cellphone microscopy has also benefitted from the availability of low-cost miniature microscope components such as low-power light-emitting diodes and ball lenses. As a result, researchers are developing hardware and software techniques that would enable such microscopes to produce high-resolution, diagnostic-quality images. This approach may lead to more widespread delivery of diagnostic services in resource-limited areas where there is a shortage of the skilled labour required for conventional microscopy and where prevalence of infectious and other diseases is still high. In this paper, we review current techniques, clinical applications and challenges faced in the field of cellphone microscopy. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Microbial communities in methane- and short chain alkane-rich hydrothermal sediments of Guaymas Basin

Directory of Open Access Journals (Sweden)

Frederick eDowell

2016-01-01

Full Text Available The hydrothermal sediments of Guaymas Basin, an active spreading center in the Gulf of California (Mexico, are rich in porewater methane, short-chain alkanes, sulfate and sulfide, and provide a model system to explore habitat preferences of microorganisms, including sulfate-dependent, methane- and short chain alkane-oxidizing microbial communities. In this study, sediments (above 60˚C covered with sulfur-oxidizing microbial mats surrounding a hydrothermal mound (termed Mat Mound were characterized by porewater geochemistry of methane, C2-C6 short-chain alkanes, sulfate, sulfide, sulfate reduction rate measurements, in-situ temperature gradients, bacterial and archaeal 16S rRNA gene clone libraries and V6 tag pyrosequencing. The most abundantly detected groups in the Mat mound sediments include anaerobic methane-oxidizing archaea of the ANME-1 lineage and its sister clade ANME-1Guaymas, the uncultured bacterial groups SEEP-SRB2 within the Deltaproteobacteria and the separately branching HotSeep-1 Group; these uncultured bacteria are candidates for sulfate-reducing alkane oxidation and for sulfate-reducing syntrophy with ANME archaea. The archaeal dataset indicates distinct habitat preferences for ANME-1, ANME-1-Guaymas and ANME-2 archaea in Guaymas Basin hydrothermal sediments. The bacterial groups SEEP-SRB2 and HotSeep-1 co-occur with ANME-1 and ANME-1Guaymas in hydrothermally active sediments underneath microbial mats in Guaymas Basin. We propose the working hypothesis that this mixed bacterial and archaeal community catalyzes the oxidation of both methane and short-chain alkanes, and constitutes a microbial community signature that is characteristic for hydrothermal and/or cold seep sediments containing both substrates.

The Electron Microscopy Outreach Program: A Web-based resource for research and education.

Science.gov (United States)

Sosinsky, G E; Baker, T S; Hand, G; Ellisman, M H

1999-01-01

We have developed a centralized World Wide Web (WWW)-based environment that serves as a resource of software tools and expertise for biological electron microscopy. A major focus is molecular electron microscopy, but the site also includes information and links on structural biology at all levels of resolution. This site serves to help integrate or link structural biology techniques in accordance with user needs. The WWW site, called the Electron Microscopy (EM) Outreach Program (URL: http://emoutreach.sdsc.edu), provides scientists with computational and educational tools for their research and edification. In particular, we have set up a centralized resource containing course notes, references, and links to image analysis and three-dimensional reconstruction software for investigators wanting to learn about EM techniques either within or outside of their fields of expertise. Copyright 1999 Academic Press.

Unconventional methods of imaging: computational microscopy and compact implementations

Science.gov (United States)

McLeod, Euan; Ozcan, Aydogan

2016-07-01

In the past two decades or so, there has been a renaissance of optical microscopy research and development. Much work has been done in an effort to improve the resolution and sensitivity of microscopes, while at the same time to introduce new imaging modalities, and make existing imaging systems more efficient and more accessible. In this review, we look at two particular aspects of this renaissance: computational imaging techniques and compact imaging platforms. In many cases, these aspects go hand-in-hand because the use of computational techniques can simplify the demands placed on optical hardware in obtaining a desired imaging performance. In the first main section, we cover lens-based computational imaging, in particular, light-field microscopy, structured illumination, synthetic aperture, Fourier ptychography, and compressive imaging. In the second main section, we review lensfree holographic on-chip imaging, including how images are reconstructed, phase recovery techniques, and integration with smart substrates for more advanced imaging tasks. In the third main section we describe how these and other microscopy modalities have been implemented in compact and field-portable devices, often based around smartphones. Finally, we conclude with some comments about opportunities and demand for better results, and where we believe the field is heading.

Coherent Raman Scattering Microscopy in Biology and Medicine

Science.gov (United States)

Zhang, Chi; Zhang, Delong; Cheng, Ji-Xin

2016-01-01

Advancements in coherent Raman scattering (CRS) microscopy have enabled label-free visualization and analysis of functional, endogenous biomolecules in living systems. When compared with spontaneous Raman microscopy, a key advantage of CRS microscopy is the dramatic improvement in imaging speed, which gives rise to real-time vibrational imaging of live biological samples. Using molecular vibrational signatures, recently developed hyperspectral CRS microscopy has improved the readout of chemical information available from CRS images. In this article, we review recent achievements in CRS microscopy, focusing on the theory of the CRS signal-to-noise ratio, imaging speed, technical developments, and applications of CRS imaging in bioscience and clinical settings. In addition, we present possible future directions that the use of this technology may take. PMID:26514285

High resolution, high speed ultrahigh vacuum microscopy

International Nuclear Information System (INIS)

Poppa, Helmut

2004-01-01

The history and future of transmission electron microscopy (TEM) is discussed as it refers to the eventual development of instruments and techniques applicable to the real time in situ investigation of surface processes with high resolution. To reach this objective, it was necessary to transform conventional high resolution instruments so that an ultrahigh vacuum (UHV) environment at the sample site was created, that access to the sample by various in situ sample modification procedures was provided, and that in situ sample exchanges with other integrated surface analytical systems became possible. Furthermore, high resolution image acquisition systems had to be developed to take advantage of the high speed imaging capabilities of projection imaging microscopes. These changes to conventional electron microscopy and its uses were slowly realized in a few international laboratories over a period of almost 40 years by a relatively small number of researchers crucially interested in advancing the state of the art of electron microscopy and its applications to diverse areas of interest; often concentrating on the nucleation, growth, and properties of thin films on well defined material surfaces. A part of this review is dedicated to the recognition of the major contributions to surface and thin film science by these pioneers. Finally, some of the important current developments in aberration corrected electron optics and eventual adaptations to in situ UHV microscopy are discussed. As a result of all the path breaking developments that have led to today's highly sophisticated UHV-TEM systems, integrated fundamental studies are now possible that combine many traditional surface science approaches. Combined investigations to date have involved in situ and ex situ surface microscopies such as scanning tunneling microscopy/atomic force microscopy, scanning Auger microscopy, and photoemission electron microscopy, and area-integrating techniques such as x-ray photoelectron

Is vaginal microscopy an essential tool for the management of women presenting with vaginal discharge?

Science.gov (United States)

Lascar, R M; Devakumar, H; Jungmann, E; Copas, A; Arthur, G; Mercey, D

2008-12-01

Point-of-care microscopy is the gold standard for the diagnosis of vaginal discharge in genitourinary (GU) medicine clinics but not used in primary care settings and reproductive health clinics to which many patients present. In our GU medicine clinic setting, we conducted an audit to assess the utility of microscopy of vaginal secretions versus clinical diagnosis alone for the differential diagnosis of uncomplicated lower vaginal infections. Clinical diagnosis (including pH) of bacterial vaginosis had a sensitivity between 85% and 88% at two clinic sites. Our results suggest that it may be safe and more cost-effective to restrict vaginal microscopy to a subgroup of women presenting with vaginal discharge.

CARS microscopy of Alzheimer's diseased brain tissue

Science.gov (United States)

Enejder, Annika; Kiskis, Juris; Fink, Helen; Nyberg, Lena; Thyr, Jakob; Li, Jia-Yi

2014-02-01

Alzheimer's disease (AD) is a progressive neurodegenerative disorder currently without cure, characterized by the presence of extracellular plaques surrounded by dystrophic neurites. In an effort to understand the underlying mechanisms, biochemical analysis (protein immunoblot) of plaque extracts reveals that they consist of amyloid-beta (Aβ) peptides assembled as oligomers, protofibrils and aggregates. Their spatial distribution has been confirmed by Thioflavin-S or immuno-staining with fluorescence microscopy. However, it is increasingly understood that the protein aggregation is only one of several mechanism that causes neuronal dysfunction and death. This raises the need for a more complete biochemical analysis. In this study, we have complemented 2-photon fluorescence microscopy of Thioflavin-S and Aβ immuno-stained human AD plaques with CARS microscopy. We show that the chemical build-up of AD plaques is more complex and that Aβ staining does not provide the complete picture of the spatial distribution or the molecular composition of AD plaques. CARS images provide important complementary information to that obtained by fluorescence microscopy, motivating a broader introduction of CARS microscopy in the AD research field.

Applications of microscopy in Salmonella research.

Science.gov (United States)

Malt, Layla M; Perrett, Charlotte A; Humphrey, Suzanne; Jepson, Mark A

2015-01-01

Salmonella enterica is a Gram-negative enteropathogen that can cause localized infections, typically resulting in gastroenteritis, or systemic infection, e.g., typhoid fever, in humans and many other animals. Understanding the mechanisms by which Salmonella induces disease has been the focus of intensive research. This has revealed that Salmonella invasion requires dynamic cross-talk between the microbe and host cells, in which bacterial adherence rapidly leads to a complex sequence of cellular responses initiated by proteins translocated into the host cell by a type 3 secretion system. Once these Salmonella-induced responses have resulted in bacterial invasion, proteins translocated by a second type 3 secretion system initiate further modulation of cellular activities to enable survival and replication of the invading pathogen. Elucidation of the complex and highly dynamic pathogen-host interactions ultimately requires analysis at the level of single cells and single infection events. To achieve this goal, researchers have applied a diverse range of microscopy techniques to analyze Salmonella infection in models ranging from whole animal to isolated cells and simple eukaryotic organisms. For example, electron microscopy and high-resolution light microscopy techniques such as confocal microscopy can reveal the precise location of Salmonella and its relationship to cellular components. Widefield light microscopy is a simpler approach with which to study the interaction of bacteria with host cells and often has advantages for live cell imaging, enabling detailed analysis of the dynamics of infection and cellular responses. Here we review the use of imaging techniques in Salmonella research and compare the capabilities of different classes of microscope to address specific types of research question. We also provide protocols and notes on some microscopy techniques used routinely in our own research.

Differentiating the two main histologic categories of fibroadenoma tissue from normal breast tissue by using multiphoton microscopy.

Science.gov (United States)

Nie, Y T; Wu, Y; Fu, F M; Lian, Y E; Zhuo, S M; Wang, C; Chen, J X

2015-04-01

Multiphoton microscopy has become a novel biological imaging technique that allows cellular and subcellular microstructure imaging based on two-photon excited fluorescence and second harmonic generation. In this work, we used multiphoton microscopy to obtain the high-contrast images of human normal breast tissue and two main histologic types of fibroadenoma (intracanalicular, pericanalicular). Moreover, quantitative image analysis was performed to characterize the changes of collagen morphology (collagen content, collagen orientation). The results show that multiphoton microscopy combined with quantitative method has the ability to identify the characteristics of fibroadenoma including changes of the duct architecture and collagen morphology in stroma. With the advancement of multiphoton microscopy, we believe that the technique has great potential to be a real-time histopathological diagnostic tool for intraoperative detection of fibroadenoma in the future. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Fluorescence microscopy for the characterization of structural integrity

Science.gov (United States)

Street, Kenneth W.; Leonhardt, Todd A.

1991-01-01

The absorption characteristics of light and the optical technique of fluorescence microscopy for enhancing metallographic interpretation are presented. Characterization of thermally sprayed coatings by optical microscopy suffers because of the tendency for misidentification of the microstructure produced by metallographic preparation. Gray scale, in bright field microscopy, is frequently the only means of differentiating the actual structural details of porosity, cracking, and debonding of coatings. Fluorescence microscopy is a technique that helps to distinguish the artifacts of metallographic preparation (pullout, cracking, debonding) from the microstructure of the specimen by color contrasting structural differences. Alternative instrumentation and the use of other dye systems are also discussed. The combination of epoxy vacuum infiltration with fluorescence microscopy to verify microstructural defects is an effective means to characterize advanced materials and to assess structural integrity.

Handheld Fluorescence Microscopy based Flow Analyzer.

Science.gov (United States)

Saxena, Manish; Jayakumar, Nitin; Gorthi, Sai Siva

2016-03-01

Fluorescence microscopy has the intrinsic advantages of favourable contrast characteristics and high degree of specificity. Consequently, it has been a mainstay in modern biological inquiry and clinical diagnostics. Despite its reliable nature, fluorescence based clinical microscopy and diagnostics is a manual, labour intensive and time consuming procedure. The article outlines a cost-effective, high throughput alternative to conventional fluorescence imaging techniques. With system level integration of custom-designed microfluidics and optics, we demonstrate fluorescence microscopy based imaging flow analyzer. Using this system we have imaged more than 2900 FITC labeled fluorescent beads per minute. This demonstrates high-throughput characteristics of our flow analyzer in comparison to conventional fluorescence microscopy. The issue of motion blur at high flow rates limits the achievable throughput in image based flow analyzers. Here we address the issue by computationally deblurring the images and show that this restores the morphological features otherwise affected by motion blur. By further optimizing concentration of the sample solution and flow speeds, along with imaging multiple channels simultaneously, the system is capable of providing throughput of about 480 beads per second.

Multidirectional Image Sensing for Microscopy Based on a Rotatable Robot

Directory of Open Access Journals (Sweden)

Yajing Shen

2015-12-01

Full Text Available Image sensing at a small scale is essentially important in many fields, including microsample observation, defect inspection, material characterization and so on. However, nowadays, multi-directional micro object imaging is still very challenging due to the limited field of view (FOV of microscopes. This paper reports a novel approach for multi-directional image sensing in microscopes by developing a rotatable robot. First, a robot with endless rotation ability is designed and integrated with the microscope. Then, the micro object is aligned to the rotation axis of the robot automatically based on the proposed forward-backward alignment strategy. After that, multi-directional images of the sample can be obtained by rotating the robot within one revolution under the microscope. To demonstrate the versatility of this approach, we view various types of micro samples from multiple directions in both optical microscopy and scanning electron microscopy, and panoramic images of the samples are processed as well. The proposed method paves a new way for the microscopy image sensing, and we believe it could have significant impact in many fields, especially for sample detection, manipulation and characterization at a small scale.

Electron Microscopy Center (EMC)

Data.gov (United States)

Federal Laboratory Consortium — The Electron Microscopy Center (EMC) at Argonne National Laboratory develops and maintains unique capabilities for electron beam characterization and applies those...

Electron microscopy of intermediate filaments: teaming up with atomic force and confocal laser scanning microscopy.

Science.gov (United States)

Kreplak, Laurent; Richter, Karsten; Aebi, Ueli; Herrmann, Harald

2008-01-01

Intermediate filaments (IFs) were originally discovered and defined by electron microscopy in myoblasts. In the following it was demonstrated and confirmed that they constitute, in addition to microtubules and microfilaments, a third independent, general filament system in the cytoplasm of most metazoan cells. In contrast to the other two systems, IFs are present in cells in two principally distinct cytoskeletal forms: (i) extended and free-running filament arrays in the cytoplasm that are integrated into the cytoskeleton by associated proteins of the plakin type; and (ii) a membrane- and chromatin-bound thin 'lamina' of a more or less regular network of interconnected filaments made from nuclear IF proteins, the lamins, which differ in several important structural aspects from cytoplasmic IF proteins. In man, more than 65 genes code for distinct IF proteins that are expressed during embryogenesis in various routes of differentiation in a tightly controlled manner. IF proteins exhibit rather limited sequence identity implying that the different types of IFs have distinct biochemical properties. Hence, to characterize the structural properties of the various IFs, in vitro assembly regimes have been developed in combination with different visualization methods such as transmission electron microscopy of fixed and negatively stained samples as well as methods that do not use staining such as scanning transmission electron microscopy (STEM) and cryoelectron microscopy as well as atomic force microscopy. Moreover, with the generation of both IF-type specific antibodies and chimeras of fluorescent proteins and IF proteins, it has become possible to investigate the subcellular organization of IFs by correlative fluorescence and electron microscopic methods. The combination of these powerful methods should help to further develop our understanding of nuclear architecture, in particular how nuclear subcompartments are organized and in which way lamins are involved.

Light microscopy - Methods and protocols

Directory of Open Access Journals (Sweden)

CarloAlberto Redi

2011-11-01

Full Text Available The first part of the book (six chapters is devoted to some selected applications of bright-field microscopy while the second part (eight chapters to some fluorescence microscopy studies. Both animal and plant biology investigations are presented covering multiple fields like immunology, cell signaling, cancer biology and, surprisingly to me, ecology. This chapter is titled: Light microscopy in aquatic ecology: Methods for plankton communities studies and it is due to Maria Carolina S. Soares and colleagues from the Laboratory of Aquatic Ecology, Dept. of Biology, Federal University of Juiz de Fora (Brazil. Here they present methods to quantify the different component of planktonic communities in a step-by-step manner so that virus, bacteria, algae and animals pertaining to different taxa can be recognized and the contribution they made to the plankton composition evaluated. It descends that even how the plankton composition is changing due to environmental variations can be accurately determined....

Confocal microscopy for astrocyte in vivo imaging: Recycle and reuse in microscopy

Science.gov (United States)

Pérez-Alvarez, Alberto; Araque, Alfonso; Martín, Eduardo D.

2013-01-01

In vivo imaging is one of the ultimate and fundamental approaches for the study of the brain. Two-photon laser scanning microscopy (2PLSM) constitutes the state-of-the-art technique in current neuroscience to address questions regarding brain cell structure, development and function, blood flow regulation and metabolism. This technique evolved from laser scanning confocal microscopy (LSCM), which impacted the field with a major improvement in image resolution of live tissues in the 1980s compared to widefield microscopy. While nowadays some of the unparalleled features of 2PLSM make it the tool of choice for brain studies in vivo, such as the possibility to image deep within a tissue, LSCM can still be useful in this matter. Here we discuss the validity and limitations of LSCM and provide a guide to perform high-resolution in vivo imaging of the brain of live rodents with minimal mechanical disruption employing LSCM. We describe the surgical procedure and experimental setup that allowed us to record intracellular calcium variations in astrocytes evoked by sensory stimulation, and to monitor intact neuronal dendritic spines and astrocytic processes as well as blood vessel dynamics. Therefore, in spite of certain limitations that need to be carefully considered, LSCM constitutes a useful, convenient, and affordable tool for brain studies in vivo. PMID:23658537

French Society of Microscopies, 11. Colloquium. SFM Paris 2009. Compilation of summaries

International Nuclear Information System (INIS)

2009-06-01

The 11. conference of the SFM (French Society of Microscopies), held in Paris in 2009, was divided into 14 symposiums, 4 GN-MEBA symposiums, and 10 workshops. The titles of the symposiums are: homage to Nicolas Boisset, advanced microscopies, alternative microscopies, new optical and plasmonic imaging microscopies, dynamic and quantitative microscopy of the living matter, photonic and correlative electronic microscopy, near field microscopy, molecular and cellular electronic cryo-microscopy, cellular compartmentation and dynamics (CFPU), microscopy and materials, dynamical microscopy in materials science, minerals/bio-minerals and environment, structure and properties of nano-materials, sub-eV and sub-nm chemical bonds imaging. The titles of the GN-MEBA symposiums are: microscopy and metals, microscopy and minerals, microscopy and living beings, microscopy and new materials. The titles of the workshops are: Correlative Light and Electron Microscopy (CLEM), Cryo and electronic tomography in cellular biology, Cryo electronic microscopy of vitreous sections (CEMOVIS), Atomic Force Microscopy (AFM), ULTRASTEM, Digital Micrograph programming, Cryo-Microscopy and molecular tomography, Cryo-ultra-microtomy and immuno-marking, FIB, ASTAR(EBSD-MET) - rapid mapping of crystalline orientations and phases

Scanning probe recognition microscopy investigation of tissue scaffold properties

Science.gov (United States)

Fan, Yuan; Chen, Qian; Ayres, Virginia M; Baczewski, Andrew D; Udpa, Lalita; Kumar, Shiva

2007-01-01

Scanning probe recognition microscopy is a new scanning probe microscopy technique which enables selective scanning along individual nanofibers within a tissue scaffold. Statistically significant data for multiple properties can be collected by repetitively fine-scanning an identical region of interest. The results of a scanning probe recognition microscopy investigation of the surface roughness and elasticity of a series of tissue scaffolds are presented. Deconvolution and statistical methods were developed and used for data accuracy along curved nanofiber surfaces. Nanofiber features were also independently analyzed using transmission electron microscopy, with results that supported the scanning probe recognition microscopy-based analysis. PMID:18203431

Tracking an oil slick from multiple natural sources, Coal Oil Point, California

International Nuclear Information System (INIS)

Leifer, Ira; Luyendyk, Bruce; Broderick, Kris

2006-01-01

Oil slicks on the ocean surface emitted from natural marine hydrocarbon seeps offshore from Coal Oil Point in the Santa Barbara Channel, California were tracked and sampled over a 2-h period. The objectives were to characterize the seep oil and to track its composition over time using a new sampling device, a catamaran drum sampler (CATDRUMS). The sampler was designed and developed at UCSB. Chromatograms showed that oil originating from an informally named, very active seep area, Shane Seep, primarily evolved during the first hour due to mixing with oil originating from a convergence zone slick surrounding Shane Seep. (author)

Tracking an oil slick from multiple natural sources, Coal Oil Point, California

Energy Technology Data Exchange (ETDEWEB)

Leifer, Ira [Marine Sciences Institute, University of California, Santa Barbara, CA 93106 (United States); Luyendyk, Bruce [Department of Geological Sciences, University of California, Santa Barbara, CA 93106 (United States); Broderick, Kris [Exxon/Mobil Exploration Company, 13401 N. Freeway, Houston, TX 77060 (United States)

2006-06-15

Oil slicks on the ocean surface emitted from natural marine hydrocarbon seeps offshore from Coal Oil Point in the Santa Barbara Channel, California were tracked and sampled over a 2-h period. The objectives were to characterize the seep oil and to track its composition over time using a new sampling device, a catamaran drum sampler (CATDRUMS). The sampler was designed and developed at UCSB. Chromatograms showed that oil originating from an informally named, very active seep area, Shane Seep, primarily evolved during the first hour due to mixing with oil originating from a convergence zone slick surrounding Shane Seep. (author)

Nanoscale Laser Terahertz Emission Microscopy

DEFF Research Database (Denmark)

Klarskov, Pernille; Kim, Hyewon; Colvin, Vicki L.

2017-01-01

Laser terahertz emission microscopy (LTEM) has become a powerful tool for studying ultrafast dynamics and local fields in many different types of materials. This technique, which relies on acceleration of charge carriers in a material upon femtosecond excitation, can provide insight into the phys......Laser terahertz emission microscopy (LTEM) has become a powerful tool for studying ultrafast dynamics and local fields in many different types of materials. This technique, which relies on acceleration of charge carriers in a material upon femtosecond excitation, can provide insight...

Atomic resolution three-dimensional electron diffraction microscopy

International Nuclear Information System (INIS)

Miao Jianwei; Ohsuna, Tetsu; Terasaki, Osamu; Hodgson, Keith O.; O'Keefe, Michael A.

2002-01-01

We report the development of a novel form of diffraction-based 3D microscopy to overcome resolution barriers inherent in high-resolution electron microscopy and tomography. By combining coherent electron diffraction with the oversampling phasing method, we show that the 3D structure of a nanocrystal can be determined ab initio at a resolution of 1 Angstrom from 29 simulated noisy diffraction patterns. This new form of microscopy can be used to image the 3D structures of nanocrystals and noncrystalline samples, with resolution limited only by the quality of sample diffraction

Confocal Raman Microscopy; applications in tissue engineering

NARCIS (Netherlands)

van Apeldoorn, Aart A.

2005-01-01

This dissertation describes the use of confocal Raman microscopy and spectroscopy in the field of tissue engineering. Moreover, it describes the combination of two already existing technologies, namely scanning electron microscopy and confocal Raman spectroscopy in one apparatus for the enhancement

Laboratory soft x-ray microscopy and tomography

International Nuclear Information System (INIS)

Bertilson, Michael

2011-01-01

Soft x-ray microscopy in the water-window (λ = 2.28 nm - 4.36 nm) is based on zone-plate optics and allows high-resolution imaging of, e.g., cells and soils in their natural or near-natural environment. Three-dimensional imaging is provided via tomographic techniques, soft x-ray cryo tomography. However, soft x-ray microscopes with such capabilities have been based on large-scale synchrotron x-ray facilities, thereby limiting their accessibility for a wider scientific community. This Thesis describes the development of the Stockholm laboratory soft x-ray microscope to three-dimensional cryo tomography and to new optics-based contrast mechanisms. The microscope relies on a methanol or nitrogen liquid-jet laser-plasma source, normal-incidence multilayer or zone-plate condenser optics, in-house fabricated zone-plate objectives, and allows operation at two wavelengths in the water-window, λ = 2.48 nm and λ = 2.48 nm. With the implementation of a new state-of-the-art normal-incidence multilayer condenser for operation at λ = 2.48 nm and a tiltable cryogenic sample stage the microscope now allows imaging of dry, wet or cryo-fixed samples. This arrangement was used for the first demonstration of laboratory soft x-ray cryo microscopy and tomography. The performance of the microscope has been demonstrated in a number of experiments described in this Thesis, including, tomographic imaging with a resolution of 140 nm, cryo microscopy and tomography of various cells and parasites, and for studies of aqueous soils and clays. The Thesis also describes the development and implementation of single-element differential-interference and Zernike phase-contrast zone-plate objectives. The enhanced contrast provided by these optics reduce exposure times or lowers the dose in samples and are of major importance for harder x-ray microscopy. The implementation of a high-resolution 50 nm compound zone-plate objective for sub-25-nm resolution imaging is also described. All experiments

Super-resolution fluorescence microscopy by stepwise optical saturation

Science.gov (United States)

Zhang, Yide; Nallathamby, Prakash D.; Vigil, Genevieve D.; Khan, Aamir A.; Mason, Devon E.; Boerckel, Joel D.; Roeder, Ryan K.; Howard, Scott S.

2018-01-01

Super-resolution fluorescence microscopy is an important tool in biomedical research for its ability to discern features smaller than the diffraction limit. However, due to its difficult implementation and high cost, the super-resolution microscopy is not feasible in many applications. In this paper, we propose and demonstrate a saturation-based super-resolution fluorescence microscopy technique that can be easily implemented and requires neither additional hardware nor complex post-processing. The method is based on the principle of stepwise optical saturation (SOS), where M steps of raw fluorescence images are linearly combined to generate an image with a M-fold increase in resolution compared with conventional diffraction-limited images. For example, linearly combining (scaling and subtracting) two images obtained at regular powers extends the resolution by a factor of 1.4 beyond the diffraction limit. The resolution improvement in SOS microscopy is theoretically infinite but practically is limited by the signal-to-noise ratio. We perform simulations and experimentally demonstrate super-resolution microscopy with both one-photon (confocal) and multiphoton excitation fluorescence. We show that with the multiphoton modality, the SOS microscopy can provide super-resolution imaging deep in scattering samples. PMID:29675306

Multiparallel Three-Dimensional Optical Microscopy

Science.gov (United States)

Nguyen, Lam K.; Price, Jeffrey H.; Kellner, Albert L.; Bravo-Zanoquera, Miguel

2010-01-01

Multiparallel three-dimensional optical microscopy is a method of forming an approximate three-dimensional image of a microscope sample as a collection of images from different depths through the sample. The imaging apparatus includes a single microscope plus an assembly of beam splitters and mirrors that divide the output of the microscope into multiple channels. An imaging array of photodetectors in each channel is located at a different distance along the optical path from the microscope, corresponding to a focal plane at a different depth within the sample. The optical path leading to each photodetector array also includes lenses to compensate for the variation of magnification with distance so that the images ultimately formed on all the photodetector arrays are of the same magnification. The use of optical components common to multiple channels in a simple geometry makes it possible to obtain high light-transmission efficiency with an optically and mechanically simple assembly. In addition, because images can be read out simultaneously from all the photodetector arrays, the apparatus can support three-dimensional imaging at a high scanning rate.

Visualizing radiofrequency-skin interaction using multiphoton microscopy in vivo.

Science.gov (United States)

Tsai, Tsung-Hua; Lin, Sung-Jan; Lee, Woan-Ruoh; Wang, Chun-Chin; Hsu, Chih-Ting; Chu, Thomas; Dong, Chen-Yuan

2012-02-01

Redundant skin laxity is a major feature of aging. Recently, radiofrequency has been introduced for nonablative tissue tightening by volumetric heating of the deep dermis. Despite the wide range of application based on this therapy, the effect of this technique on tissue and the subsequent tissue remodeling have not been investigated in detail. Our objective is to evaluate the potential of non-linear optics, including multiphoton autofluorescence and second harmonic generation (SHG) microscopy, as a non-invasive imaging modality for the real-time study of radiofrequency-tissue interaction. Electro-optical synergy device (ELOS) was used as the radiofrequency source in this study. The back skin of nude mouse was irradiated with radiofrequency at different passes. We evaluated the effect on skin immediately and 1 month after treatment with multiphoton microscopy. Corresponding histology was performed for comparison. We found that SHG is negatively correlated to radiofrequency passes, which means that collagen structural disruption happens immediately after thermal damage. After 1 month of collagen remodeling, SHG signals increased above baseline, indicating that collagen regeneration has occurred. Our findings may explain mechanism of nonablative skin tightening and were supported by histological examinations. Our work showed that monitoring the dermal heating status of RF and following up the detailed process of tissue reaction can be imaged and quantified with multiphoton microscopy non-invasively in vivo. Copyright © 2011. Published by Elsevier Ireland Ltd.

35 years of electron microscopy in Costa Rica

International Nuclear Information System (INIS)

Hernandez Chavarria, Francisco

2011-01-01

Electron microscopy has celebrated in 2009 the XXXV anniversary in Costa Rica. The history of the electron microscopy was initiated with the donation of a microscope by Japan and the establishment of the Unidad de Microscopia Electronica (UME), which later, has been consolidated as the Centro de Investigacion en Estructuras Microscopicas (CIEMic) of the Universidad de Costa Rica (UCR). This center has realized its own research and has gave support to different units of the UCR, state universities and the private sector. Currently, the CIEMic has had two transmission electron microscopes (TEM) and two scanning electron microscopes (SEM), besides of optical microscopy equipment, including a laser confocal microscope. The two fundamental types of electron microscopes (TEM and SEM) have generated different images. While the first has had a resolution that has allowed to analyze virus, usually their images have been flat; however, with some special techniques can obtain three-dimensional images. The image in the TEM is generated by electrons that have passed through the sample, and to interact with its atoms have changed its energy and trajectory. This, at the end, has impacted on a photosensitive screen that has become in flashes, whose intensity has depended on its energy and form the image. Meanwhile, in the MER, the image has been normal type, although with less resolution. The electrons in the MER are focused on a small area of the sample in which have interacted with the atoms of this, and has generated a a series of signals, including the most used were the secondary electrons and characteristic X-rays. In both cases, an electron from beam has generated in the filament a collision against an electron of the sample and has given part of its energy to the degree of release of its atom and issued out of the sample; this has been called secondary electrons. X-rays have been generated when an electron of the same atom that has lost the secondary electron, but in an

Scanning electron microscopy and transmission electron microscopy study of hot-deformed gamma-TiAl-based alloy microstructure.

Science.gov (United States)

Chrapoński, J; Rodak, K

2006-09-01

The aim of this work was to assess the changes in the microstructure of hot-deformed specimens made of alloys containing 46-50 at.% Al, 2 at.% Cr and 2 at.% Nb (and alloying additions such as carbon and boron) with the aid of scanning electron microscopy and transmission electron microscopy techniques. After homogenization and heat treatment performed in order to make diverse lamellae thickness, the specimens were compressed at 1000 degrees C. Transmission electron microscopy examinations of specimens after the compression test revealed the presence of heavily deformed areas with a high density of dislocation. Deformation twins were also observed. Dynamically recrystallized grains were revealed. For alloys no. 2 and no. 3, the recovery and recrystallization processes were more extensive than for alloy no. 1.

Integrated Photoacoustic and Fluorescence Confocal Microscopy

OpenAIRE

Wang, Yu; Maslov, Konstantin; Kim, Chulhong; Hu, Song; Wang, Lihong V.

2010-01-01

We have developed a dual-modality imaging system by integrating optical-resolution photoacoustic microscopy and fluorescence confocal microscopy to provide optical absorption and fluorescence contrasts simultaneously. By sharing the same laser source and objective lens, intrinsically registered photoacoustic and fluorescence images are acquired in a single scan. The micrometer resolution allows imaging of both blood and lymphatic vessels down to the capillary level. Simultaneous photoacoustic...

In vivo Diagnosis of Basal Cell Carcinoma Subtype by Reflectance Confocal Microscopy

NARCIS (Netherlands)

Peppelman, M.; Wolberink, E.A.W.; Blokx, W.A.M.; Kerkhof, P.C.M. van de; Erp, P.E.J. van; Gerritsen, M.J.P.

2013-01-01

Background: Reflectance confocal microscopy (RCM) is a noninvasive imaging technique. Currently, RCM is mainly used for the diagnosis of melanoma and nonmelanoma skin cancer including basal cell carcinoma (BCC). Until now, it has not been possible to distinguish between subtypes of BCC using RCM.

Two-Photon Fluorescence Microscopy Developed for Microgravity Fluid Physics

Science.gov (United States)

Fischer, David G.; Zimmerli, Gregory A.; Asipauskas, Marius

2004-01-01

Recent research efforts within the Microgravity Fluid Physics Branch of the NASA Glenn Research Center have necessitated the development of a microscope capable of high-resolution, three-dimensional imaging of intracellular structure and tissue morphology. Standard optical microscopy works well for thin samples, but it does not allow the imaging of thick samples because of severe degradation caused by out-of-focus object structure. Confocal microscopy, which is a laser-based scanning microscopy, provides improved three-dimensional imaging and true optical sectioning by excluding the out-of-focus light. However, in confocal microscopy, out-of-focus object structure is still illuminated by the incoming beam, which can lead to substantial photo-bleaching. In addition, confocal microscopy is plagued by limited penetration depth, signal loss due to the presence of a confocal pinhole, and the possibility of live-cell damage. Two-photon microscopy is a novel form of laser-based scanning microscopy that allows three-dimensional imaging without many of the problems inherent in confocal microscopy. Unlike one-photon microscopy, it utilizes the nonlinear absorption of two near-infrared photons. However, the efficiency of two-photon absorption is much lower than that of one-photon absorption because of the nonlinear (i.e., quadratic) electric field dependence, so an ultrafast pulsed laser source must typically be employed. On the other hand, this stringent energy density requirement effectively localizes fluorophore excitation to the focal volume. Consequently, two-photon microscopy provides optical sectioning and confocal performance without the need for a signal-limiting pinhole. In addition, there is a reduction in photo-damage because of the longer excitation wavelength, a reduction in background fluorescence, and a 4 increase in penetration depth over confocal methods because of the reduction in Rayleigh scattering.

Selective plane illumination microscopy (SPIM) with time-domain fluorescence lifetime imaging microscopy (FLIM) for volumetric measurement of cleared mouse brain samples

Science.gov (United States)

Funane, Tsukasa; Hou, Steven S.; Zoltowska, Katarzyna Marta; van Veluw, Susanne J.; Berezovska, Oksana; Kumar, Anand T. N.; Bacskai, Brian J.

2018-05-01

We have developed an imaging technique which combines selective plane illumination microscopy with time-domain fluorescence lifetime imaging microscopy (SPIM-FLIM) for three-dimensional volumetric imaging of cleared mouse brains with micro- to mesoscopic resolution. The main features of the microscope include a wavelength-adjustable pulsed laser source (Ti:sapphire) (near-infrared) laser, a BiBO frequency-doubling photonic crystal, a liquid chamber, an electrically focus-tunable lens, a cuvette based sample holder, and an air (dry) objective lens. The performance of the system was evaluated with a lifetime reference dye and micro-bead phantom measurements. Intensity and lifetime maps of three-dimensional human embryonic kidney (HEK) cell culture samples and cleared mouse brain samples expressing green fluorescent protein (GFP) (donor only) and green and red fluorescent protein [positive Förster (fluorescence) resonance energy transfer] were acquired. The results show that the SPIM-FLIM system can be used for sample sizes ranging from single cells to whole mouse organs and can serve as a powerful tool for medical and biological research.

Aspects on gametogenesis, fertilization and embryogenesis of two deep-sea polychaetes from Eastern Atlantic cold seeps

Science.gov (United States)

Gaudron, S. M.; Hourdez, S.; Olu, K.

2017-11-01

We investigated two gonochoristic species of annelid polychaetes (one siboglinid and one polynoid) from cold seeps that ranged from 525 m to 3300 m in depth (Guiness, Worm Hole and Regab pockmarks) on the Gabon and Congo continental margins (Gulf of Guinea). Different aspects of gametogenesis (oocyte diameter, presence of ovisac, spermatozoa shape, and fecundity), fertilization (in vitro fertilization experiments: IVF) and embryogenesis (cleavage rate) were studied. The sampled siboglinid was a new species of Lamellibrachia and the second population of this genus in the Eastern Atlantic. Mean oocyte diameter was about 100 μm and fully-grown primary oocytes were stored in an ovisac, as in other studied siboglinids. The presence of a single spermatozoon was noted within an oviduct, indicating a possible internal fertilization. The rate of cell division at 6 °C was one cleavage every 20 h. Embryos developed normally to the blastula stage after 5-d post-fertilization at atmospheric pressure suggesting some pressure tolerance. The second polychaete was the scale-worm Branchipolynoe cf. seepensis that lives in commensalism in the mantle cavity of Bathymodiolus aff. boomerang. Anatomical reproductive features were similar to those described in B. seepensis from hydrothermal vents on Mid-Atlantic Ridge, with lecithotrophic larval development and continuous gametogenesis. We performed the first IVF carried out on gametes for any deep-sea polynoid species. Fertilization and development occurred but a number of abnormalities were observed demonstrating a limitation to embryogenesis at atmospheric pressure. The rate of cell division was three times faster at 8 °C than at 4 °C with a maximum stage of 8-cells reached after 72 h post-fertilization. We surprisingly observed some oocytes from the negative seawater control during IVF experiments cleaved to the 2-cell stage, demonstrating the possible occurrence of internal fertilization prior to IVF experiment or the accidental

New developments in transmission electron microscopy for nanotechnology

International Nuclear Information System (INIS)

Wang, Z.L.

2003-01-01

High-resolution transmission electron microscopy (HRTEM) is one of the most powerful tools used for characterizing nanomaterials, and it is indispensable for nanotechnology. This paper reviews some of the most recent developments in electron microscopy techniques for characterizing nanomaterials. The review covers the following areas: in-situ microscopy for studying dynamic shape transformation of nanocrystals; in-situ nanoscale property measurements on the mechanical, electrical and field emission properties of nanotubes/nanowires; environmental microscopy for direct observation of surface reactions; aberration-free angstrom-resolution imaging of light elements (such as oxygen and lithium); high-angle annular-dark-field scanning transmission electron microscopy (STEM); imaging of atom clusters with atomic resolution chemical information; electron holography of magnetic materials; and high-spatial resolution electron energy-loss spectroscopy (EELS) for nanoscale electronic and chemical analysis. It is demonstrated that the picometer-scale science provided by HRTEM is the foundation of nanometer-scale technology. (Abstract Copyright [2003], Wiley Periodicals, Inc.)

Digital differential confocal microscopy based on spatial shift transformation.

Science.gov (United States)

Liu, J; Wang, Y; Liu, C; Wilson, T; Wang, H; Tan, J

2014-11-01

Differential confocal microscopy is a particularly powerful surface profilometry technique in industrial metrology due to its high axial sensitivity and insensitivity to noise. However, the practical implementation of the technique requires the accurate positioning of point detectors in three-dimensions. We describe a simple alternative based on spatial transformation of a through-focus series of images obtained from a homemade beam scanning confocal microscope. This digital differential confocal microscopy approach is described and compared with the traditional Differential confocal microscopy approach. The ease of use of the digital differential confocal microscopy system is illustrated by performing measurements on a 3D standard specimen. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.

Electron microscopy of primary cell cultures in solution and correlative optical microscopy using ASEM

International Nuclear Information System (INIS)

Hirano, Kazumi; Kinoshita, Takaaki; Uemura, Takeshi; Motohashi, Hozumi; Watanabe, Yohei; Ebihara, Tatsuhiko; Nishiyama, Hidetoshi; Sato, Mari; Suga, Mitsuo; Maruyama, Yuusuke; Tsuji, Noriko M.; Yamamoto, Masayuki; Nishihara, Shoko; Sato, Chikara

2014-01-01

Correlative light-electron microscopy of cells in a natural environment of aqueous liquid facilitates high-throughput observation of protein complex formation. ASEM allows the inverted SEM to observe the wet sample from below, while an optical microscope observes it from above quasi-simultaneously. The disposable ASEM dish with a silicon nitride (SiN) film window can be coated variously to realize the primary-culture of substrate-sensitive cells in a few milliliters of culture medium in a stable incubator environment. Neuron differentiation, neural networking, proplatelet-formation and phagocytosis were captured by optical or fluorescence microscopy, and imaged at high resolution by gold-labeled immuno-ASEM with/without metal staining. Fas expression on the cell surface was visualized, correlated to the spatial distribution of F-actin. Axonal partitioning was studied using primary-culture neurons, and presynaptic induction by GluRδ2-N-terminus-linked fluorescent magnetic beads was correlated to the presynaptic-marker Bassoon. Further, megakaryocytes secreting proplatelets were captured, and P-selectins with adherence activity were localized to some of the granules present by immuno-ASEM. The phagocytosis of lactic acid bacteria by dendritic cells was also imaged. Based on these studies, ASEM correlative microscopy promises to allow the study of various mesoscopic-scale dynamics in the near future. - Highlights: • In situ correlative light electron microscopy of samples in open solution by ASEM. • Primary cultures for in-solution CLEM by developing SiN-film coating methods • First visualization of fluorescent magnetic beads in aqueous solution by CLEM. • Presynaptic induction of neurons by GluRδ2-N-terminus-coated beads studied by CLEM. • Axonal partitioning, bacterial phagocytosis, platelet formation imaged by CLEM

Electron microscopy of primary cell cultures in solution and correlative optical microscopy using ASEM

Energy Technology Data Exchange (ETDEWEB)

Hirano, Kazumi; Kinoshita, Takaaki [Laboratory of Cell Biology, Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577 (Japan); Uemura, Takeshi [Department of Molecular Neurobiology and Pharmacology, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 (Japan); Motohashi, Hozumi [Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-cho, Aoba-ku, Sendai 980-8575 (Japan); Watanabe, Yohei; Ebihara, Tatsuhiko [Biomedical Research Institute, National Institute of Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566 (Japan); Nishiyama, Hidetoshi [JEOL Ltd., 1-2 Musashino 3-chome, Akishima, Tokyo 196-8558 (Japan); Sato, Mari [Biomedical Research Institute, National Institute of Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566 (Japan); Suga, Mitsuo [JEOL Ltd., 1-2 Musashino 3-chome, Akishima, Tokyo 196-8558 (Japan); Maruyama, Yuusuke; Tsuji, Noriko M. [Biomedical Research Institute, National Institute of Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566 (Japan); Yamamoto, Masayuki [Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai 980-8575 (Japan); Nishihara, Shoko, E-mail: shoko@soka.ac.jp [Laboratory of Cell Biology, Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577 (Japan); Sato, Chikara, E-mail: ti-sato@aist.go.jp [Biomedical Research Institute, National Institute of Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566 (Japan)

2014-08-01

Correlative light-electron microscopy of cells in a natural environment of aqueous liquid facilitates high-throughput observation of protein complex formation. ASEM allows the inverted SEM to observe the wet sample from below, while an optical microscope observes it from above quasi-simultaneously. The disposable ASEM dish with a silicon nitride (SiN) film window can be coated variously to realize the primary-culture of substrate-sensitive cells in a few milliliters of culture medium in a stable incubator environment. Neuron differentiation, neural networking, proplatelet-formation and phagocytosis were captured by optical or fluorescence microscopy, and imaged at high resolution by gold-labeled immuno-ASEM with/without metal staining. Fas expression on the cell surface was visualized, correlated to the spatial distribution of F-actin. Axonal partitioning was studied using primary-culture neurons, and presynaptic induction by GluRδ2-N-terminus-linked fluorescent magnetic beads was correlated to the presynaptic-marker Bassoon. Further, megakaryocytes secreting proplatelets were captured, and P-selectins with adherence activity were localized to some of the granules present by immuno-ASEM. The phagocytosis of lactic acid bacteria by dendritic cells was also imaged. Based on these studies, ASEM correlative microscopy promises to allow the study of various mesoscopic-scale dynamics in the near future. - Highlights: • In situ correlative light electron microscopy of samples in open solution by ASEM. • Primary cultures for in-solution CLEM by developing SiN-film coating methods • First visualization of fluorescent magnetic beads in aqueous solution by CLEM. • Presynaptic induction of neurons by GluRδ2-N-terminus-coated beads studied by CLEM. • Axonal partitioning, bacterial phagocytosis, platelet formation imaged by CLEM.

Identification and quantitive analysis of calcium phosphate microparticles in intestinal tissue by nuclear microscopy

International Nuclear Information System (INIS)

Gomez-Morilla, Inmaculada; Thoree, Vinay; Powell, Jonathan J.; Kirkby, Karen J.; Grime, Geoffrey W.

2006-01-01

Microscopic particles (0.5-2 μm diameter), rich in calcium and phosphorus, are found in the lumen of the mid-distal gut of all mammals investigated, including humans, and these may play a role in immuno-surveillance and immune regulation of antigens from food and symbiotic bacteria that are contained in the gut. Whether these particles can cross in to tissue of the intestinal mucosa is unclear. If so, characterising their morphology and chemical composition is an important task in elucidating their function. The analysis of calcium phosphate in biological tissues has been approached in several ways including optical microscopy, scanning electron microscopy and, most recently in this work, with nuclear microscopy. In this paper, we describe the use of microPIXE and microRBS to locate these particles and to determine, accurately, the ratio of phosphorus to calcium using the information on sample thickness obtained from RBS to allow the PIXE ratios to be corrected. A commercial sample of hydroxy apatite was used to demonstrate accuracy and precision of the technique. Then, in a pilot study on intestinal tissue of mice, we demonstrated the presence of calcium phosphate microparticles, consistent with confocal microscopy observations, and we identified the average molar P:Ca molar ratio as 1.0. Further work will confirm the exact chemical speciation of these particles and will examine the influence of differing calcium containing diets on the formation of these microparticles

Identification and quantitive analysis of calcium phosphate microparticles in intestinal tissue by nuclear microscopy

Energy Technology Data Exchange (ETDEWEB)

Gomez-Morilla, Inmaculada [Advanced Technology Institute, University of Surrey, Guildford GU2 7XH (United Kingdom)]. E-mail: i.gomez-morilla@surrey.ac.uk; Thoree, Vinay [Gastrointestinal Laboratory, Rayne Institute, St. Thomas' Hospital, London SE1 7EH (United Kingdom); Powell, Jonathan J. [MRC Human Nutrition Research, Elsie Widdowson Laboratory, Fulbourn Road, Cambridge CB1 9NL (United Kingdom); Kirkby, Karen J. [Advanced Technology Institute, University of Surrey, Guildford GU2 7XH (United Kingdom); Grime, Geoffrey W. [Department of Physics, University of Surrey, GU2 7XH (United Kingdom)

2006-08-15

Microscopic particles (0.5-2 {mu}m diameter), rich in calcium and phosphorus, are found in the lumen of the mid-distal gut of all mammals investigated, including humans, and these may play a role in immuno-surveillance and immune regulation of antigens from food and symbiotic bacteria that are contained in the gut. Whether these particles can cross in to tissue of the intestinal mucosa is unclear. If so, characterising their morphology and chemical composition is an important task in elucidating their function. The analysis of calcium phosphate in biological tissues has been approached in several ways including optical microscopy, scanning electron microscopy and, most recently in this work, with nuclear microscopy. In this paper, we describe the use of microPIXE and microRBS to locate these particles and to determine, accurately, the ratio of phosphorus to calcium using the information on sample thickness obtained from RBS to allow the PIXE ratios to be corrected. A commercial sample of hydroxy apatite was used to demonstrate accuracy and precision of the technique. Then, in a pilot study on intestinal tissue of mice, we demonstrated the presence of calcium phosphate microparticles, consistent with confocal microscopy observations, and we identified the average molar P:Ca molar ratio as 1.0. Further work will confirm the exact chemical speciation of these particles and will examine the influence of differing calcium containing diets on the formation of these microparticles.

Paleomagnetic Analysis Using SQUID Microscopy

Science.gov (United States)

Weiss, Benjamin P.; Lima, Eduardo A.; Fong, Luis E.; Baudenbacher, Franz J.

2007-01-01

Superconducting quantum interference device (SQUID) microscopes are a new generation of instruments that map magnetic fields with unprecedented spatial resolution and moment sensitivity. Unlike standard rock magnetometers, SQUID microscopes map magnetic fields rather than measuring magnetic moments such that the sample magnetization pattern must be retrieved from source model fits to the measured field data. In this paper, we presented the first direct comparison between paleomagnetic analyses on natural samples using joint measurements from SQUID microscopy and moment magnetometry. We demonstrated that in combination with apriori geologic and petrographic data, SQUID microscopy can accurately characterize the magnetization of lunar glass spherules and Hawaiian basalt. The bulk moment magnitude and direction of these samples inferred from inversions of SQUID microscopy data match direct measurements on the same samples using moment magnetometry. In addition, these inversions provide unique constraints on the magnetization distribution within the sample. These measurements are among the most sensitive and highest resolution quantitative paleomagnetic studies of natural remanent magnetization to date. We expect that this technique will be able to extend many other standard paleomagnetic techniques to previously inaccessible microscale samples.

Combined frequency modulated atomic force microscopy and scanning tunneling microscopy detection for multi-tip scanning probe microscopy applications

International Nuclear Information System (INIS)

Morawski, Ireneusz; Spiegelberg, Richard; Korte, Stefan; Voigtländer, Bert

2015-01-01

A method which allows scanning tunneling microscopy (STM) tip biasing independent of the sample bias during frequency modulated atomic force microscopy (AFM) operation is presented. The AFM sensor is supplied by an electronic circuit combining both a frequency shift signal and a tunneling current signal by means of an inductive coupling. This solution enables a control of the tip potential independent of the sample potential. Individual tip biasing is specifically important in order to implement multi-tip STM/AFM applications. An extensional quartz sensor (needle sensor) with a conductive tip is applied to record simultaneously topography and conductivity of the sample. The high resonance frequency of the needle sensor (1 MHz) allows scanning of a large area of the surface being investigated in a reasonably short time. A recipe for the amplitude calibration which is based only on the frequency shift signal and does not require the tip being in contact is presented. Additionally, we show spectral measurements of the mechanical vibration noise of the scanning system used in the investigations

Combined frequency modulated atomic force microscopy and scanning tunneling microscopy detection for multi-tip scanning probe microscopy applications

Energy Technology Data Exchange (ETDEWEB)

Morawski, Ireneusz [Peter Grünberg Institut (PGI-3) and JARA-Fundamentals of Future Information Technology, Forschungszentrum Jülich, 52425 Jülich (Germany); Institute of Experimental Physics, University of Wrocław, pl. M. Borna 9, 50-204 Wrocław (Poland); Spiegelberg, Richard; Korte, Stefan; Voigtländer, Bert [Peter Grünberg Institut (PGI-3) and JARA-Fundamentals of Future Information Technology, Forschungszentrum Jülich, 52425 Jülich (Germany)

2015-12-15

A method which allows scanning tunneling microscopy (STM) tip biasing independent of the sample bias during frequency modulated atomic force microscopy (AFM) operation is presented. The AFM sensor is supplied by an electronic circuit combining both a frequency shift signal and a tunneling current signal by means of an inductive coupling. This solution enables a control of the tip potential independent of the sample potential. Individual tip biasing is specifically important in order to implement multi-tip STM/AFM applications. An extensional quartz sensor (needle sensor) with a conductive tip is applied to record simultaneously topography and conductivity of the sample. The high resonance frequency of the needle sensor (1 MHz) allows scanning of a large area of the surface being investigated in a reasonably short time. A recipe for the amplitude calibration which is based only on the frequency shift signal and does not require the tip being in contact is presented. Additionally, we show spectral measurements of the mechanical vibration noise of the scanning system used in the investigations.

Deep-water chemosynthetic ecosystem research during the Census of Marine Life decade and beyond: A proposed deep-ocean road map.

Digital Repository Service at National Institute of Oceanography (India)

German, C.R.; Ramirez-Llodra, E.; Baker, M.C.; Tyler, P.A.; Baco-Taylor, A.; Boetius, A.; Bright, M.; de Siqueira, L.C.; Cordes, E.E.; Desbruyeres, D.; Dubilier, N.; Fisher, C.R.; Fujiwara, Y.; Gaill, F.; Gebruk, A.; Juniper, K.; Levin, L.A.; Lokabharathi, P.A.; Metaxas, A.; Rowden, A.A.; Santos, R.S.; Shank, T.M.; Smith, C.R.; Van Dover, C.L.; Young, C.M.; Waren, A.

West Africa, encompassing a very large region around the Equator, from 15uS to 30uN. The key sites include the Costa Rica cold seeps, the Gulf of Mexico cold seeps, the ultra-slow spreading Mid Cayman Rise, the Barbados Accretionary Prism, hydrothermal... and those present in the Americas – along the Atlantic margin, the Barbados Accretionary Prism, the Gulf of Mexico and, in the extreme, along the Pacific margin of Costa Rica which would also have Census Chemosynthetic Ecosystem Research & Beyond PLoS ONE...

Multimodal nonlinear microscopy: A powerful label-free method for supporting standard diagnostics on biological tissues

Directory of Open Access Journals (Sweden)

Riccardo Cicchi

2014-09-01

Full Text Available The large use of nonlinear laser scanning microscopy in the past decade paved the way for potential clinical application of this imaging technique. Modern nonlinear microscopy techniques offer promising label-free solutions to improve diagnostic performances on tissues. In particular, the combination of multiple nonlinear imaging techniques in the same microscope allows integrating morphological with functional information in a morpho-functional scheme. Such approach provides a high-resolution label-free alternative to both histological and immunohistochemical examination of tissues and is becoming increasingly popular among the clinical community. Nevertheless, several technical improvements, including automatic scanning and image analysis, are required before the technique represents a standard diagnostic method. In this review paper, we highlight the capabilities of multimodal nonlinear microscopy for tissue imaging, by providing various examples on colon, arterial and skin tissues. The comparison between images acquired using multimodal nonlinear microscopy and histology shows a good agreement between the two methods. The results demonstrate that multimodal nonlinear microscopy is a powerful label-free alternative to standard histopathological methods and has the potential to find a stable place in the clinical setting in the near future.

Single spin stochastic optical reconstruction microscopy

OpenAIRE

Pfender, Matthias; Aslam, Nabeel; Waldherr, Gerald; Wrachtrup, Jörg

2014-01-01

We experimentally demonstrate precision addressing of single quantum emitters by combined optical microscopy and spin resonance techniques. To this end we utilize nitrogen-vacancy (NV) color centers in diamond confined within a few ten nanometers as individually resolvable quantum systems. By developing a stochastic optical reconstruction microscopy (STORM) technique for NV centers we are able to simultaneously perform sub diffraction-limit imaging and optically detected spin resonance (ODMR)...

Nanoscale surface characterization using laser interference microscopy

Science.gov (United States)

Ignatyev, Pavel S.; Skrynnik, Andrey A.; Melnik, Yury A.

2018-03-01

Nanoscale surface characterization is one of the most significant parts of modern materials development and application. The modern microscopes are expensive and complicated tools, and its use for industrial tasks is limited due to laborious sample preparation, measurement procedures, and low operation speed. The laser modulation interference microscopy method (MIM) for real-time quantitative and qualitative analysis of glass, metals, ceramics, and various coatings has a spatial resolution of 0.1 nm for vertical and up to 100 nm for lateral. It is proposed as an alternative to traditional scanning electron microscopy (SEM) and atomic force microscopy (AFM) methods. It is demonstrated that in the cases of roughness metrology for super smooth (Ra >1 nm) surfaces the application of a laser interference microscopy techniques is more optimal than conventional SEM and AFM. The comparison of semiconductor test structure for lateral dimensions measurements obtained with SEM and AFM and white light interferometer also demonstrates the advantages of MIM technique.

3rd International Multidisciplinary Microscopy and Microanalysis Congress

CERN Document Server

Oral, Zehra

2017-01-01

The 3rd International Multidisciplinary Microscopy Congress (InterM2015), held from 19 to 23 October 2015, focused on the latest developments concerning applications of microscopy in the biological, physical and chemical sciences at all dimensional scales, advances in instrumentation, techniques in and educational materials on microscopy. These proceedings gather 17 peer-reviewed technical papers submitted by leading academic and research institutions from nine countries and representing some of the most cutting-edge research available.

Multiphoton microscopy imaging of developing tooth germs

Directory of Open Access Journals (Sweden)

Pei-Yu Pan

2014-01-01

Conclusion: In this study, a novel multiphoton microscopy database of images from developing tooth germs in mice was set up. We confirmed that multiphoton laser microscopy is a powerful tool for investigating the development of tooth germ and is worthy for further application in the study of tooth regeneration.

Magnetic force microscopy : Quantitative issues in biomaterials

NARCIS (Netherlands)

Passeri, D.; Dong, C.; Reggente, M.; Angeloni, L.; Barteri, M.; Scaramuzzo, F.A.; De Angelis, F.; Marinelli, F.; Antonelli, F.; Rinaldi, F.; Marianecci, C.; Carafa, M.; Sorbo, A.; Sordi, D.; Arends, I.W.C.E.; Rossi, M.

2014-01-01

Magnetic force microscopy (MFM) is an atomic force microscopy (AFM) based technique in which an AFM tip with a magnetic coating is used to probe local magnetic fields with the typical AFM spatial resolution, thus allowing one to acquire images reflecting the local magnetic properties of the samples

New directions in scanning-tunneling microscopy

International Nuclear Information System (INIS)

Ferrell, T.L.; Warmack, R.J.; Reddick, R.C.

1989-01-01

The tunneling of electrons in scanning-tunneling microscopy (STM) has permitted imaging of the electronic distribution about individual atoms on surfaces. The need for use of conducting surfaces in STM limits its applicability, and new forms of scanning microscopy have emerged as a result of interest in poorly conducting samples. Atomic force microscopy has demonstrated that the force between a surface and a probe tip can be used to image selected materials. Now being developed are magnetic probe STM's and photon tunneling microscopes in which the probe is a sharpened optical fiber. Also of great interest presently is the measurement of differential conductance of surfaces using electron STM's. This method supplies spectral information and contrast enhancement in images. At present there remains much theoretical work to be carried out in order to better characterize related data on inelastic electron tunneling, and valuable insight may be gained from data being gathered on the local work function of materials. As matters stand today, the key problems lie in determining tip and contamination effects, preparation of samples, and understanding conductivity mechanisms in very thin materials on conducting substrates. Resolution of these problems and introduction of new forms of scanning microscopy may permit novel and important applications in biology as well as surface science

AutoMicromanager: A microscopy scripting toolkit for LABVIEW and other programming environments

Science.gov (United States)

Ashcroft, Brian Alan; Oosterkamp, Tjerk

2010-11-01

We present a scripting toolkit for the acquisition and analysis of a wide variety of imaging data by integrating the ease of use of various programming environments such as LABVIEW, IGOR PRO, MATLAB, SCILAB, and others. This toolkit is designed to allow the user to quickly program a variety of standard microscopy components for custom microscopy applications allowing much more flexibility than other packages. Included are both programming tools as well as graphical user interface classes allowing a standard, consistent, and easy to maintain scripting environment. This programming toolkit allows easy access to most commonly used cameras, stages, and shutters through the Micromanager project so the scripter can focus on their custom application instead of boilerplate code generation.

AutoMicromanager: a microscopy scripting toolkit for LABVIEW and other programming environments.

Science.gov (United States)

Ashcroft, Brian Alan; Oosterkamp, Tjerk

2010-11-01

We present a scripting toolkit for the acquisition and analysis of a wide variety of imaging data by integrating the ease of use of various programming environments such as LABVIEW, IGOR PRO, MATLAB, SCILAB, and others. This toolkit is designed to allow the user to quickly program a variety of standard microscopy components for custom microscopy applications allowing much more flexibility than other packages. Included are both programming tools as well as graphical user interface classes allowing a standard, consistent, and easy to maintain scripting environment. This programming toolkit allows easy access to most commonly used cameras, stages, and shutters through the Micromanager project so the scripter can focus on their custom application instead of boilerplate code generation.

Musculature of Notholca acuminata (Rotifera : Ploima : Brachionidae) revealed by confocal scanning laser microscopy

DEFF Research Database (Denmark)

Sørensen, M.V.; Funch, P.; Hooge, M.

2003-01-01

The body-wall and visceral musculature of Notholca acuminata was visualized using phalloidin-linked fluorescent dye under confocal laser scanning microscopy. The body-wall musculature includes dorsal, lateral, and ventral pairs of longitudinally oriented body retractor muscles, two pairs of head...

Ultrafast Science Opportunities with Electron Microscopy

Energy Technology Data Exchange (ETDEWEB)

DURR, HERMANN; Wang, X.J., ed.

2016-04-28

X-rays and electrons are two of the most fundamental probes of matter. When the Linac Coherent Light Source (LCLS), the world’s first x-ray free electron laser, began operation in 2009, it transformed ultrafast science with the ability to generate laser-like x-ray pulses from the manipulation of relativistic electron beams. This document describes a similar future transformation. In Transmission Electron Microscopy, ultrafast relativistic (MeV energy) electron pulses can achieve unsurpassed spatial and temporal resolution. Ultrafast temporal resolution will be the next frontier in electron microscopy and can ideally complement ultrafast x-ray science done with free electron lasers. This document describes the Grand Challenge science opportunities in chemistry, material science, physics and biology that arise from an MeV ultrafast electron diffraction & microscopy facility, especially when coupled with linac-based intense THz and X-ray pump capabilities.

Scanning fluorescent microscopy is an alternative for quantitative fluorescent cell analysis.

Science.gov (United States)

Varga, Viktor Sebestyén; Bocsi, József; Sipos, Ferenc; Csendes, Gábor; Tulassay, Zsolt; Molnár, Béla

2004-07-01

Fluorescent measurements on cells are performed today with FCM and laser scanning cytometry. The scientific community dealing with quantitative cell analysis would benefit from the development of a new digital multichannel and virtual microscopy based scanning fluorescent microscopy technology and from its evaluation on routine standardized fluorescent beads and clinical specimens. We applied a commercial motorized fluorescent microscope system. The scanning was done at 20 x (0.5 NA) magnification, on three channels (Rhodamine, FITC, Hoechst). The SFM (scanning fluorescent microscopy) software included the following features: scanning area, exposure time, and channel definition, autofocused scanning, densitometric and morphometric cellular feature determination, gating on scatterplots and frequency histograms, and preparation of galleries of the gated cells. For the calibration and standardization Immuno-Brite beads were used. With application of shading compensation, the CV of fluorescence of the beads decreased from 24.3% to 3.9%. Standard JPEG image compression until 1:150 resulted in no significant change. The change of focus influenced the CV significantly only after +/-5 microm error. SFM is a valuable method for the evaluation of fluorescently labeled cells. Copyright 2004 Wiley-Liss, Inc.

Resolution improvement by nonconfocal theta microscopy.

Science.gov (United States)

Lindek, S; Stelzer, E H

1999-11-01

We present a novel scanning fluorescence microscopy technique, nonconfocal theta microscopy (NCTM), that provides almost isotropic resolution. In NCTM, multiphoton absorption from two orthogonal illumination directions is used to induce fluorescence emission. Therefore the point-spread function of the microscope is described by the product of illumination point-spread functions with reduced spatial overlap, which provides the resolution improvement and the more isotropic observation volume. We discuss the technical details of this new method.

Superresolution Microscopy of the Nuclear Envelope and Associated Proteins.

Science.gov (United States)

Xie, Wei; Horn, Henning F; Wright, Graham D

2016-01-01

Superresolution microscopy is undoubtedly one of the most exciting technologies since the invention of the optical microscope. Capable of nanometer-scale resolution to surpass the diffraction limit and coupled with the versatile labeling techniques available, it is revolutionizing the study of cell biology. Our understanding of the nucleus, the genetic and architectural center of the cell, has gained great advancements through the application of various superresolution microscopy techniques. This chapter describes detailed procedures of multichannel superresolution imaging of the mammalian nucleus, using structured illumination microscopy and single-molecule localization microscopy.

Boundary segmentation for fluorescence microscopy using steerable filters

Science.gov (United States)

Ho, David Joon; Salama, Paul; Dunn, Kenneth W.; Delp, Edward J.

2017-02-01

Fluorescence microscopy is used to image multiple subcellular structures in living cells which are not readily observed using conventional optical microscopy. Moreover, two-photon microscopy is widely used to image structures deeper in tissue. Recent advancement in fluorescence microscopy has enabled the generation of large data sets of images at different depths, times, and spectral channels. Thus, automatic object segmentation is necessary since manual segmentation would be inefficient and biased. However, automatic segmentation is still a challenging problem as regions of interest may not have well defined boundaries as well as non-uniform pixel intensities. This paper describes a method for segmenting tubular structures in fluorescence microscopy images of rat kidney and liver samples using adaptive histogram equalization, foreground/background segmentation, steerable filters to capture directional tendencies, and connected-component analysis. The results from several data sets demonstrate that our method can segment tubular boundaries successfully. Moreover, our method has better performance when compared to other popular image segmentation methods when using ground truth data obtained via manual segmentation.

Electron microscopy characterization of Ni-Cr-B-Si-C laser deposited coatings.

Science.gov (United States)

Hemmati, I; Rao, J C; Ocelík, V; De Hosson, J Th M

2013-02-01

During laser deposition of Ni-Cr-B-Si-C alloys with high amounts of Cr and B, various microstructures and phases can be generated from the same chemical composition that results in heterogeneous properties in the clad layer. In this study, the microstructure and phase constitution of a high-alloy Ni-Cr-B-Si-C coating deposited by laser cladding were analyzed by a combination of several microscopy characterization techniques including scanning electron microscopy in secondary and backscatter imaging modes, energy dispersive spectroscopy (EDS), electron backscatter diffraction (EBSD), and transmission electron microscopy (TEM). The combination of EDS and EBSD allowed unequivocal identification of micron-sized precipitates as polycrystalline orthorhombic CrB, single crystal tetragonal Cr5B3, and single crystal hexagonal Cr7C3. In addition, TEM characterization showed various equilibrium and metastable Ni-B, Ni-Si, and Ni-Si-B eutectic products in the alloy matrix. The findings of this study can be used to explain the phase formation reactions and to tune the microstructure of Ni-Cr-B-Si-C coatings to obtain the desired properties.

Platinum replica electron microscopy: Imaging the cytoskeleton globally and locally.

Science.gov (United States)

Svitkina, Tatyana M

2017-05-01

Structural studies reveal how smaller components of a system work together as a whole. However, combining high resolution of details with full coverage of the whole is challenging. In cell biology, light microscopy can image many cells in their entirety, but at a lower resolution, whereas electron microscopy affords very high resolution, but usually at the expense of the sample size and coverage. Structural analyses of the cytoskeleton are especially demanding, because cytoskeletal networks are unresolvable by light microscopy due to their density and intricacy, whereas their proper preservation is a challenge for electron microscopy. Platinum replica electron microscopy can uniquely bridge the gap between the "comfort zones" of light and electron microscopy by allowing high resolution imaging of the cytoskeleton throughout the entire cell and in many cells in the population. This review describes the principles and applications of platinum replica electron microscopy for studies of the cytoskeleton. Copyright © 2017 Elsevier Ltd. All rights reserved.

Super-resolution microscopy reveals cell wall dynamics and peptidoglycan architecture in ovococcal bacteria.

Science.gov (United States)

Wheeler, Richard; Mesnage, Stéphane; Boneca, Ivo G; Hobbs, Jamie K; Foster, Simon J

2011-12-01

Cell morphology and viability in Eubacteria is dictated by the architecture of peptidoglycan, the major and essential structural component of the cell wall. Although the biochemical composition of peptidoglycan is well understood, how the peptidoglycan architecture can accommodate the dynamics of growth and division while maintaining cell shape remains largely unknown. Here, we elucidate the peptidoglycan architecture and dynamics of bacteria with ovoid cell shape (ovococci), which includes a number of important pathogens, by combining biochemical analyses with atomic force and super-resolution microscopies. Atomic force microscopy analysis showed preferential orientation of the peptidoglycan network parallel to the short axis of the cell, with distinct architectural features associated with septal and peripheral wall synthesis. Super-resolution three-dimensional structured illumination fluorescence microscopy was applied for the first time in bacteria to unravel the dynamics of peptidoglycan assembly in ovococci. The ovococci have a unique peptidoglycan architecture and growth mode not observed in other model organisms. © 2011 Blackwell Publishing Ltd.

Atomic Force Microscopy Based Nanorobotics Modelling, Simulation, Setup Building and Experiments

CERN Document Server

Xie, Hui; Régnier, Stéphane; Sitti, Metin

2012-01-01

The atomic force microscope (AFM) has been successfully used to perform nanorobotic manipulation operations on nanoscale entities such as particles, nanotubes, nanowires, nanocrystals, and DNA since 1990s. There have been many progress on modeling, imaging, teleoperated or automated control, human-machine interfacing, instrumentation, and applications of AFM based nanorobotic manipulation systems in literature. This book aims to include all of such state-of-the-art progress in an organized, structured, and detailed manner as a reference book and also potentially a textbook in nanorobotics and any other nanoscale dynamics, systems and controls related research and education. Clearly written and well-organized, this text introduces designs and prototypes of the nanorobotic systems in detail with innovative principles of three-dimensional manipulation force microscopy and parallel imaging/manipulation force microscopy.

Analysis of ancient pigments by Raman microscopy

International Nuclear Information System (INIS)

Zuo Jian; Xu Cunyi

1999-01-01

Raman microscopy can be applied for the spatial resolution, and non-destructive in situ analysis of inorganic pigments in pottery, manuscripts and paintings. Compared with other techniques, it is the best single technique for this purpose. An overview is presented of the applications of Raman microscopy in the analysis of ancient pigments

Local crystallography analysis for atomically resolved scanning tunneling microscopy images

International Nuclear Information System (INIS)

Lin, Wenzhi; Li, Qing; Belianinov, Alexei; Gai, Zheng; Baddorf, Arthur P; Pan, Minghu; Jesse, Stephen; Kalinin, Sergei V; Sales, Brian C; Sefat, Athena

2013-01-01

Scanning probe microscopy has emerged as a powerful and flexible tool for atomically resolved imaging of surface structures. However, due to the amount of information extracted, in many cases the interpretation of such data is limited to being qualitative and semi-quantitative in nature. At the same time, much can be learned from local atom parameters, such as distances and angles, that can be analyzed and interpreted as variations of local chemical bonding, or order parameter fields. Here, we demonstrate an iterative algorithm for indexing and determining atomic positions that allows the analysis of inhomogeneous surfaces. This approach is further illustrated by local crystallographic analysis of several real surfaces, including highly ordered pyrolytic graphite and an Fe-based superconductor FeTe 0.55 Se 0.45 . This study provides a new pathway to extract and quantify local properties for scanning probe microscopy images. (paper)

Phenol-ammonium sulfate microscopy method for diagnosis of pulmonary tuberculosis

Directory of Open Access Journals (Sweden)

Ritu Singhal

2013-01-01

Conclusion: Sputum microscopy with PhAS solution is a safe, reliable and inexpensive alternative for direct microscopy. This method can be conveniently applied for usage in microscopy centers with limited bio-safety facilities.

Environmental cell assembly for use in for use in spectroscopy and microscopy applications

Science.gov (United States)

Stowe, Ashley Clinton; Smyrl, Norman; Hallman, Jr., Russell L.

2014-09-02

An environmental cell assembly for use in microscopy and spectroscopy applications, including: an environmentally sealed body assembly configured to selectively hold and contain a sample; a plurality of ports manufactured into one or more surfaces of the body assembly for one or more of evacuating the body assembly and injecting a gas into or removing a gas from the body assembly; a port manufactured into a surface of the body assembly for receiving a translating stage configured to move the sample within the body assembly; and a port manufactured into a surface of the body assembly for receiving one or more lenses utilized in a microscopy or spectroscopy application; wherein the one or more lenses are disposed adjacent the sample without intervening structures disposed there between. The cell assembly also includes a port manufactured into a surface of the body assembly for retaining a window and providing visualization of the sample.

Aberrations and adaptive optics in super-resolution microscopy

Science.gov (United States)

Booth, Martin; Andrade, Débora; Burke, Daniel; Patton, Brian; Zurauskas, Mantas

2015-01-01

As one of the most powerful tools in the biological investigation of cellular structures and dynamic processes, fluorescence microscopy has undergone extraordinary developments in the past decades. The advent of super-resolution techniques has enabled fluorescence microscopy – or rather nanoscopy – to achieve nanoscale resolution in living specimens and unravelled the interior of cells with unprecedented detail. The methods employed in this expanding field of microscopy, however, are especially prone to the detrimental effects of optical aberrations. In this review, we discuss how super-resolution microscopy techniques based upon single-molecule switching, stimulated emission depletion and structured illumination each suffer from aberrations in different ways that are dependent upon intrinsic technical aspects. We discuss the use of adaptive optics as an effective means to overcome this problem. PMID:26124194

Illuminating Electron Microscopy of Photocatalysts

DEFF Research Database (Denmark)

Cavalca, Filippo

.1% of the surface of the planet with a device that converts solar energy into a useable form at 10% efficiency would give more than the present worldwide consumption of fossil energy. Photocatalysts are of fundamental interest for sustainable energy research because they provide a viable route for converting solar...... energy into chemical bonds. By means of Transmission Electron Microscopy (TEM) it is possible to gain insight in the fundamentals of their reaction mechanisms, chemical behaviour, structure and morphology before, during and after reaction using in situ investigations. In particular, the environmental TEM...... the microscope that allows electron microscopy under nonconventional TEM conditions and new kinds of in situ spectroscopy....

Atomic force microscopy as a tool for the investigation of living cells.

Science.gov (United States)

Morkvėnaitė-Vilkončienė, Inga; Ramanavičienė, Almira; Ramanavičius, Arūnas

2013-01-01

Atomic force microscopy is a valuable and useful tool for the imaging and investigation of living cells in their natural environment at high resolution. Procedures applied to living cell preparation before measurements should be adapted individually for different kinds of cells and for the desired measurement technique. Different ways of cell immobilization, such as chemical fixation on the surface, entrapment in the pores of a membrane, or growing them directly on glass cover slips or on plastic substrates, result in the distortion or appearance of artifacts in atomic force microscopy images. Cell fixation allows the multiple use of samples and storage for a prolonged period; it also increases the resolution of imaging. Different atomic force microscopy modes are used for the imaging and analysis of living cells. The contact mode is the best for cell imaging because of high resolution, but it is usually based on the following: (i) image formation at low interaction force, (ii) low scanning speed, and (iii) usage of "soft," low resolution cantilevers. The tapping mode allows a cell to behave like a very solid material, and destructive shear forces are minimized, but imaging in liquid is difficult. The force spectroscopy mode is used for measuring the mechanical properties of cells; however, obtained results strongly depend on the cell fixation method. In this paper, the application of 3 atomic force microscopy modes including (i) contact, (ii) tapping, and (iii) force spectroscopy for the investigation of cells is described. The possibilities of cell preparation for the measurements, imaging, and determination of mechanical properties of cells are provided. The applicability of atomic force microscopy to diagnostics and other biomedical purposes is discussed.

Application of multiphoton microscopy in dermatological studies: A mini-review

Directory of Open Access Journals (Sweden)

Elijah Yew

2014-09-01

Full Text Available This review summarizes the historical and more recent developments of multiphoton microscopy, as applied to dermatology. Multiphoton microscopy offers several advantages over competing microscopy techniques: there is an inherent axial sectioning, penetration depths that compete well with confocal microscopy on account of the use of near-infrared light, and many two-photon contrast mechanisms, such as second-harmonic generation, have no analogue in one-photon microscopy. While the penetration depths of photons into tissue are typically limited on the order of hundreds of microns, this is of less concern in dermatology, as the skin is thin and readily accessible. As a result, multiphoton microscopy in dermatology has generated a great deal of interest, much of which is summarized here. The review covers the interaction of light and tissue, as well as the various considerations that must be made when designing an instrument. The state of multiphoton microscopy in imaging skin cancer and various other diseases is also discussed, along with the investigation of aging and regeneration phenomena, and finally, the use of multiphoton microscopy to analyze the transdermal transport of drugs, cosmetics and other agents is summarized. The review concludes with a look at potential future research directions, especially those that are necessary to push these techniques into widespread clinical acceptance.

Functional photoacoustic microscopy of pH.

Science.gov (United States)

Chatni, Muhammad Rameez; Yao, Junjie; Danielli, Amos; Favazza, Christopher P; Maslov, Konstantin I; Wang, Lihong V

2011-10-01

pH is a tightly regulated indicator of metabolic activity. In mammalian systems, an imbalance of pH regulation may result from or result in serious illness. In this paper, we report photoacoustic microscopy (PAM) of a commercially available pH-sensitive fluorescent dye (SNARF-5F carboxylic acid) in tissue phantoms. We demonstrated that PAM is capable of pH imaging in absolute values at tissue depths of up to 2.0 mm, greater than possible with other forms of optical microscopy.

Secondary sulfate minerals from Alum Cave Bluff: Microscopy and microanalysis

Energy Technology Data Exchange (ETDEWEB)

Lauf, R.J.

1997-07-01

Microcrystals of secondary sulfate minerals from Alum Cave Bluff, Great Smoky Mountains National Park, were examined by scanning electron microscopy and identified by X-ray fluorescence (XRF) in the SEM. Among the samples the author discovered three new rare-earth sulfates: coskrenite-(Ce), levinsonite-(Y), and zugshunstite-(Ce). Other minerals illustrated in this report include sulfur, tschermigite, gypsum, epsomite, melanterite, halotrichite, apjohnite, jarosite, slavikite, magnesiocopiapite, and diadochite. Additional specimens whose identification is more tentative include pickeringite, aluminite, basaluminite, and botryogen. Alum Cave is a ``Dana locality`` for apjohnite and potash alum, and is the first documented North American occurrence of slavikite.

Data Validation Package April 2016 Groundwater and Surface Water Sampling at the Monticello, Utah, Disposal and Processing Sites August 2016

Energy Technology Data Exchange (ETDEWEB)

Nguyen, Jason [USDOE Office of Legacy Management, Washington, DC (United States); Smith, Fred [Navarro Research and Engineering, Oak Ridge, TN (United States)

2016-08-01

This semiannual event includes sampling groundwater and surface water at the Monticello Disposal and Processing Sites. Sampling and analyses were conducted as specified in the Sampling and Analysis Plan for U.S. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated) and Program Directive MNT-2016-01. Complete sample sets were collected from 42 of 48 planned locations (9 of 9 former mill site wells, 13 of 13 downgradient wells, 7 of 9 downgradient permeable reactive barrier wells, 4 of 7 seeps and wetlands, and 9 of 10 surface water locations). Planned monitoring locations are shown in Attachment 1, Sampling and Analysis Work Order. Locations R6-M3, SW00-01, Seep 1, Seep 2, and Seep 5 were not sampled due to insufficient water availability. A partial sample was collected at location R4-M3 due to insufficient water. All samples from the permeable reactive barrier wells were filtered as specified in the program directive. Duplicate samples were collected from surface water location Sorenson and from monitoring wells 92-07 and RlO-Ml. Water levels were measured at all sampled wells and an additional set of wells. See Attachment2, Trip Report for additional details. The contaminants of concern (COCs) for the Monticello sites are arsenic, manganese, molybdenum, nitrate+ nitrite as nitrogen (nitrate+ nitrite as N), selenium, uranium, and vanadium. Locations with COCs that exceeded remediation goals are listed in Table 1 and Table 2. Time-concentration graphs of the COCs for all groundwater and surface water locations are included in Attachment 3, Data Presentation. An assessment of anomalous data is included in Attachment 4.

Fluctuation microscopy: a probe of medium range order

International Nuclear Information System (INIS)

Treacy, M M J; Gibson, J M; Fan, L; Paterson, D J; McNulty, I

2005-01-01

Fluctuation microscopy is a hybrid diffraction-imaging technique that detects medium range order in amorphous materials by examining spatial fluctuations in coherent scattering. These fluctuations appear as speckle in images and diffraction patterns. The volume of material contributing to the speckle is determined by the point-spread function (the resolution) of the imaging optics and the sample thickness. The spatial periodicities being probed are related to the diffraction vector. Statistical analysis of the speckle allows the random and non-random (ordered) contributions to be discriminated. The image resolution that gives the maximum speckle contrast, as determined by the normalized variance of the image intensity, is determined by the characteristic length scale of the ordering. Because medium range ordering length scales can extend out to about the tenth coordination shell, fluctuation microscopy tends to be a low image resolution technique. This review presents the kinematical scattering theory underpinning fluctuation microscopy and a description of fluctuation electron microscopy as it has been employed in the transmission electron microscope for studying amorphous materials. Recent results using soft x-rays for studying nanoscale materials are also presented. We summarize outstanding issues and point to possible future directions for fluctuation microscopy as a technique

Electron transparent graphene windows for environmental scanning electron microscopy in liquids and dense gases.

Science.gov (United States)

Stoll, Joshua D; Kolmakov, Andrei

2012-12-21

Due to its ultrahigh electron transmissivity in a wide electron energy range, molecular impermeability, high electrical conductivity and excellent mechanical stiffness, suspended graphene membranes appear to be a nearly ideal window material for in situ (in vivo) environmental electron microscopy of nano- and mesoscopic objects (including bio-medical samples) immersed in liquids and/or in dense gaseous media. In this paper, taking advantage of a small modification of the graphene transfer protocol onto metallic and SiN supporting orifices, reusable environmental cells with exchangeable graphene windows have been designed. Using colloidal gold nanoparticles (50 nm) dispersed in water as model objects for scanning electron microscopy in liquids as proof of concept, different conditions for imaging through the graphene membrane were tested. Limiting factors for electron microscopy in liquids, such as electron beam induced water radiolysis and damage of the graphene membrane at high electron doses, are discussed.

Application of Confocal Laser Scanning Microscopy in Biology and Medicine

OpenAIRE

I. A. Volkov; N. V. Frigo; L. F. Znamenskaya; O. R. Katunina

2014-01-01

Fluorescence confocal laser scanning microscopy and reflectance confocal laser scanning microscopy are up-to-date highend study methods. Confocal microscopy is used in cell biology and medicine. By using confocal microscopy, it is possible to study bioplasts and localization of protein molecules and other compounds relative to cell or tissue structures, and to monitor dynamic cell processes. Confocal microscopes enable layer-by-layer scanning of test items to create demonstrable 3D models. As...

In vivo studies of transdermal nanoparticle delivery with microneedles using photoacoustic microscopy

Science.gov (United States)

Moothanchery, Mohesh; Seeni, Razina Z.; Xu, Chenjie; Pramanik, Manojit

2017-01-01

Microneedle technology allows micron-sized conduits to be formed within the outermost skin layers for both localized and systemic delivery of therapeutics including nanoparticles. Histological methods are often employed for characterization, and unfortunately do not allow for the in vivo visualization of the delivery process. This study presents the utilization of optical resolution-photoacoustic microscopy to characterize the transdermal delivery of nanoparticles using microneedles. Specifically, we observe the in vivo transdermal delivery of gold nanoparticles using microneedles in mice ear and study the penetration, diffusion, and spatial distribution of the nanoparticles in the tissue. The promising results reveal that photoacoustic microscopy can be used as a potential imaging modality for the in vivo characterization of microneedles based drug delivery. PMID:29296482

Recent achievements in multi-keV x-ray microscopy

International Nuclear Information System (INIS)

Susini, J.; Barrett, R.; Salome, M.; Kaulich, B.

2002-01-01

X-ray microscopy (XRM) techniques are emerging as powerful and complementary tools for sub-micron investigations. Soft XRM traditionally offers the possibility to form direct images of thick hydrated biological material in near-native environments, at a spatial resolution well beyond that achievable with visible light microscopy. Natural contrast is available in the soft X-ray region, in the so-called 'water-window', due to the presence of absorption edges of the major constituents (C,N,O). Recent advances in manufacturing techniques have enlarged the accessible energy range of micro-focusing optics and offer new applications in a broad range of disciplines. XRM in the 1-20 keV energy range is better suited to map trace elements in fluorescence yield, 3-D tomographic imaging and in micro-diffraction. After a brief introduction to the principles and methods, the main attributes of X-ray microscopy will be presented. This presentation will be biased towards sub-micron microscopy developed at the ESRF in the 2-10 keV energy. Strengths and weaknesses of X-ray microscopy and spectro-microscopy techniques will be discussed and illustrated by examples in biology, materials sciences and geology. (authors)

NDE Acoustic Microscopy Research Laboratory

Data.gov (United States)

Federal Laboratory Consortium — The purpose is to develop advanced, more effective high-resolution micro-NDE materials characterization methods using scanning acoustic microscopy. The laboratory's...

Ballistic hole magnetic microscopy

NARCIS (Netherlands)

Haq, E.; Banerjee, T.; Siekman, M.H.; Lodder, J.C.; Jansen, R.

2005-01-01

A technique to study nanoscale spin transport of holes is presented: ballistic hole magnetic microscopy. The tip of a scanning tunneling microscope is used to inject hot electrons into a ferromagnetic heterostructure, where inelastic decay creates a distribution of electron-hole pairs.

The Open Microscopy Environment: open image informatics for the biological sciences

Science.gov (United States)

Blackburn, Colin; Allan, Chris; Besson, Sébastien; Burel, Jean-Marie; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gault, David; Gillen, Kenneth; Leigh, Roger; Leo, Simone; Li, Simon; Lindner, Dominik; Linkert, Melissa; Moore, Josh; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Swedlow, Jason R.

2016-07-01

Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. While the open FITS file format is ubiquitous in astronomy, astronomical imaging shares many challenges with biological imaging, including the need to share large image sets using secure, cross-platform APIs, and the need for scalable applications for processing and visualization. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges. OME tools include: an open data model for multidimensional imaging (OME Data Model); an open file format (OME-TIFF) and library (Bio-Formats) enabling free access to images (5D+) written in more than 145 formats from many imaging domains, including FITS; and a data management server (OMERO). The Java-based OMERO client-server platform comprises an image metadata store, an image repository, visualization and analysis by remote access, allowing sharing and publishing of image data. OMERO provides a means to manage the data through a multi-platform API. OMERO's model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high content screening, digital pathology and recently into applications using non-image data from clinical and genomic studies. This is made possible using the Bio-Formats library. The current release includes a single mechanism for accessing image data of all types, regardless of original file format, via Java, C/C++ and Python and a variety of applications and environments (e.g. ImageJ, Matlab and R).

Second harmonic generation microscopy

DEFF Research Database (Denmark)

Brüggemann, Dagmar Adeline; Brewer, Jonathan R.; Risbo, Jens

2010-01-01

Myofibers and collagen show non-linear optical properties enabling imaging using second harmonic generation (SHG) microscopy. The technique is evaluated for use as a tool for real-time studies of thermally induced changes in thin samples of unfixed and unstained pork. The forward and the backward...... scattered SHG light reveal complementary features of the structures of myofibers and collagen fibers. Upon heating the myofibers show no structural changes before reaching a temperature of 53 °C. At this temperature the SHG signal becomes extinct. The extinction of the SHG at 53 °C coincides with a low......-temperature endotherm peak observable in the differential scanning calorimetry (DSC) thermograms. DSC analysis of epimysium, the connective tissue layer that enfold skeletal muscles, produces one large endotherm starting at 57 °C and peaking at 59.5 °C. SHG microscopy of collagen fibers reveals a variability of thermal...

Transmission Electron Microscopy and Diffractometry of Materials

CERN Document Server

Fultz, Brent

2013-01-01

This book explains concepts of transmission electron microscopy (TEM) and x-ray diffractometry (XRD) that are important for the characterization of materials. The fourth edition adds important new techniques of TEM such as electron tomography, nanobeam diffraction, and geometric phase analysis. A new chapter on neutron scattering completes the trio of x-ray, electron and neutron diffraction. All chapters were updated and revised for clarity. The book explains the fundamentals of how waves and wavefunctions interact with atoms in solids, and the similarities and differences of using x-rays, electrons, or neutrons for diffraction measurements. Diffraction effects of crystalline order, defects, and disorder in materials are explained in detail. Both practical and theoretical issues are covered. The book can be used in an introductory-level or advanced-level course, since sections are identified by difficulty. Each chapter includes a set of problems to illustrate principles, and the extensive Appendix includes la...

Biostatistical analysis of quantitative immunofluorescence microscopy images.

Science.gov (United States)

Giles, C; Albrecht, M A; Lam, V; Takechi, R; Mamo, J C

2016-12-01

Semiquantitative immunofluorescence microscopy has become a key methodology in biomedical research. Typical statistical workflows are considered in the context of avoiding pseudo-replication and marginalising experimental error. However, immunofluorescence microscopy naturally generates hierarchically structured data that can be leveraged to improve statistical power and enrich biological interpretation. Herein, we describe a robust distribution fitting procedure and compare several statistical tests, outlining their potential advantages/disadvantages in the context of biological interpretation. Further, we describe tractable procedures for power analysis that incorporates the underlying distribution, sample size and number of images captured per sample. The procedures outlined have significant potential for increasing understanding of biological processes and decreasing both ethical and financial burden through experimental optimization. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Magnetic Resonance Force Microscopy System

Data.gov (United States)

Federal Laboratory Consortium — The Magnetic Resonance Force Microscopy (MRFM) system, developed by ARL, is the world's most sensitive nuclear magnetic resonance (NMR) spectroscopic analysis tool,...

SISGR: Room Temperature Single-Molecule Detection and Imaging by Stimulated Emission Microscopy

Energy Technology Data Exchange (ETDEWEB)

Xie, Xiaoliang Sunney [Harvard Univ., Cambridge, MA (United States). Dept. of Chemistry and Chemical Biology

2017-03-13

Single-molecule spectroscopy has made considerable impact on many disciplines including chemistry, physics, and biology. To date, most single-molecule spectroscopy work is accomplished by detecting fluorescence. On the other hand, many naturally occurring chromophores, such as retinal, hemoglobin and cytochromes, do not have detectable fluorescence. There is an emerging need for single-molecule spectroscopy techniques that do not require fluorescence. In the last proposal period, we have successfully demonstrated stimulated emission microscopy, single molecule absorption, and stimulated Raman microscopy based on a high-frequency modulation transfer technique. These first-of-a- kind new spectroscopy/microscopy methods tremendously improved our ability to observe molecules that fluorescence weakly, even to the limit of single molecule detection for absorption measurement. All of these methods employ two laser beams: one (pump beam) excites a single molecule to a real or virtual excited state, and the other (probe beam) monitors the absorption/emission property of the single. We extract the intensity change of the probe beam with high sensitivity by implementing a high-frequency phase-sensitive detection scheme, which offers orders of magnitude improvement in detection sensitivity over direct absorption/emission measurement. However, single molecule detection based on fluorescence or absorption is fundamentally limited due to their broad spectral response. It is important to explore other avenues in single molecule detection and imaging which provides higher molecular specificity for studying a wide variety of heterogeneous chemical and biological systems. This proposal aimed to achieve single-molecule detection sensitivity with near resonance stimulated Raman scattering (SRS) microscopy. SRS microscopy was developed in our lab as a powerful technique for imaging heterogeneous samples based on their intrinsic vibrational contrasts, which provides much higher molecular

QUANTITATIVE CONFOCAL LASER SCANNING MICROSCOPY

Directory of Open Access Journals (Sweden)

Merete Krog Raarup

2011-05-01

Full Text Available This paper discusses recent advances in confocal laser scanning microscopy (CLSM for imaging of 3D structure as well as quantitative characterization of biomolecular interactions and diffusion behaviour by means of one- and two-photon excitation. The use of CLSM for improved stereological length estimation in thick (up to 0.5 mm tissue is proposed. The techniques of FRET (Fluorescence Resonance Energy Transfer, FLIM (Fluorescence Lifetime Imaging Microscopy, FCS (Fluorescence Correlation Spectroscopy and FRAP (Fluorescence Recovery After Photobleaching are introduced and their applicability for quantitative imaging of biomolecular (co-localization and trafficking in live cells described. The advantage of two-photon versus one-photon excitation in relation to these techniques is discussed.

All-optical optoacoustic microscopy based on probe beam deflection technique

Directory of Open Access Journals (Sweden)

Saher M. Maswadi

2016-09-01

Full Text Available Optoacoustic (OA microscopy using an all-optical system based on the probe beam deflection technique (PBDT for detection of laser-induced acoustic signals was investigated as an alternative to conventional piezoelectric transducers. PBDT provides a number of advantages for OA microscopy including (i efficient coupling of laser excitation energy to the samples being imaged through the probing laser beam, (ii undistorted coupling of acoustic waves to the detector without the need for separation of the optical and acoustic paths, (iii high sensitivity and (iv ultrawide bandwidth. Because of the unimpeded optical path in PBDT, diffraction-limited lateral resolution can be readily achieved. The sensitivity of the current PBDT sensor of 22 μV/Pa and its noise equivalent pressure (NEP of 11.4 Pa are comparable with these parameters of the optical micro-ring resonator and commercial piezoelectric ultrasonic transducers. Benefits of the present prototype OA microscope were demonstrated by successfully resolving micron-size details in histological sections of cardiac muscle.

All-optical optoacoustic microscopy based on probe beam deflection technique.

Science.gov (United States)

Maswadi, Saher M; Ibey, Bennett L; Roth, Caleb C; Tsyboulski, Dmitri A; Beier, Hope T; Glickman, Randolph D; Oraevsky, Alexander A

2016-09-01

Optoacoustic (OA) microscopy using an all-optical system based on the probe beam deflection technique (PBDT) for detection of laser-induced acoustic signals was investigated as an alternative to conventional piezoelectric transducers. PBDT provides a number of advantages for OA microscopy including (i) efficient coupling of laser excitation energy to the samples being imaged through the probing laser beam, (ii) undistorted coupling of acoustic waves to the detector without the need for separation of the optical and acoustic paths, (iii) high sensitivity and (iv) ultrawide bandwidth. Because of the unimpeded optical path in PBDT, diffraction-limited lateral resolution can be readily achieved. The sensitivity of the current PBDT sensor of 22 μV/Pa and its noise equivalent pressure (NEP) of 11.4 Pa are comparable with these parameters of the optical micro-ring resonator and commercial piezoelectric ultrasonic transducers. Benefits of the present prototype OA microscope were demonstrated by successfully resolving micron-size details in histological sections of cardiac muscle.

High spatial resolution Kelvin probe force microscopy with coaxial probes

International Nuclear Information System (INIS)

Brown, Keith A; Westervelt, Robert M; Satzinger, Kevin J

2012-01-01

Kelvin probe force microscopy (KPFM) is a widely used technique to measure the local contact potential difference (CPD) between an AFM probe and the sample surface via the electrostatic force. The spatial resolution of KPFM is intrinsically limited by the long range of the electrostatic interaction, which includes contributions from the macroscopic cantilever and the conical tip. Here, we present coaxial AFM probes in which the cantilever and cone are shielded by a conducting shell, confining the tip–sample electrostatic interaction to a small region near the end of the tip. We have developed a technique to measure the true CPD despite the presence of the shell electrode. We find that the behavior of these probes agrees with an electrostatic model of the force, and we observe a factor of five improvement in spatial resolution relative to unshielded probes. Our discussion centers on KPFM, but the field confinement offered by these probes may improve any variant of electrostatic force microscopy. (paper)

Electron microscopy study of advanced heterostructures for optoelectronics

NARCIS (Netherlands)

Katcki, J.; Ratajczak, J.; Phillipp, F.; Muszalski, J.; Bugajski, M.; Chen, J.X.; Fiore, A.

2003-01-01

The application of cross-sectional transmission electron microscopy and SEM to the investigation of optoelectronic devices are reviewed. Special attention was paid to the electron microscopy assessment of the growth perfection of such crucial elements of the devices like quantum wells, quantum dots,

Optimisation-based wavefront sensorless adaptive optics for microscopy

NARCIS (Netherlands)

Antonello, J.

2014-01-01

Microscopy is an essential tool for life sciences. Thanks to the development of confocal and multiphoton microscopy, scientists are able to obtain high-resolution 3D views of biological specimens. Nevertheless, spatial variations in the index of refraction within specimens cause aberrations that

Nonlinear Polarimetric Microscopy for Biomedical Imaging

Science.gov (United States)

Samim, Masood

A framework for the nonlinear optical polarimetry and polarimetric microscopy is developed. Mathematical equations are derived in terms of linear and nonlinear Stokes Mueller formalism, which comprehensively characterize the polarization properties of the incoming and outgoing radiations, and provide structural information about the organization of the investigated materials. The algebraic formalism developed in this thesis simplifies many predictions for a nonlinear polarimetry study and provides an intuitive understanding of various polarization properties for radiations and the intervening medium. For polarimetric microscopy experiments, a custom fast-scanning differential polarization microscope is developed, which is also capable of real-time three-dimensional imaging. The setup is equipped with a pair of high-speed resonant and galvanometric scanning mirrors, and supplemented by advanced adaptive optics and data acquisition modules. The scanning mirrors when combined with the adaptive optics deformable mirror enable fast 3D imaging. Deformable membrane mirrors and genetic algorithm optimization routines are employed to improve the imaging conditions including correcting the optical aberrations, maximizing signal intensities, and minimizing point-spread-functions of the focal volume. A field-programmable-gate array (FPGA) chip is exploited to rapidly acquire and process the multidimensional data. Using the nonlinear optical polarimetry framework and the home-built polarization microscope, a few biologically important tissues are measured and analyzed to gain insight as to their structure and dynamics. The structure and distribution of muscle sarcomere myosins, connective tissue collagen, carbohydrate-rich starch, and fruit fly eye retinal molecules are characterized with revealing polarization studies. In each case, using the theoretical framework, polarization sensitive data are analyzed to decipher the molecular orientations and nonlinear optical

Determination of processed animal proteins, including meat and bone meal, in animal feed

NARCIS (Netherlands)

Gizzi, G.; Holst, von C.; Baeten, V.; Berben, G.; Raamsdonk, van L.W.D.

2004-01-01

The presence of processed animal proteins (PAP), including meat and bone meal (MBM) from various species, in animal feed was investigated. It was demonstrated that microscopy is the most reliable method for enforcing the current total MBM ban in the European Uion (EU). It was shown that near

Observation of self-assembled fluorescent beads by scanning near-field optical microscopy and atomic force microscopy

International Nuclear Information System (INIS)

Oh, Y.J.; Jo, W.; Kim, Min-Gon; Kyu Park, Hyun; Hyun Chung, Bong

2006-01-01

Optical response and topography of fluorescent latex beads both on flat self-assembled monolayer and on a micron-patterned surface with poly(dimethylsiloxane) are studied. Scanning near-field optical microscopy and atomic force microscopy were utilized together for detecting fluorescence and imaging topography of the patterned latex beads, respectively. As a result, the micro-patterned latex beads where a specific chemical binding occurred show a strong signal, whereas no signals are observed in the case of nonspecific binding. With fluorescein isothiocyanate (FITC), it is convenient to measure fluorescence signal from the patterned beads allowing us to monitor the small balls of fluorescent latex

Cryo-Scanning Electron Microscopy (SEM) and Scanning Transmission Electron Microscopy (STEM)-in-SEM for Bio- and Organo-Mineral Interface Characterization in the Environment.

Science.gov (United States)

Wille, Guillaume; Hellal, Jennifer; Ollivier, Patrick; Richard, Annie; Burel, Agnes; Jolly, Louis; Crampon, Marc; Michel, Caroline

2017-12-01

Understanding biofilm interactions with surrounding substratum and pollutants/particles can benefit from the application of existing microscopy tools. Using the example of biofilm interactions with zero-valent iron nanoparticles (nZVI), this study aims to apply various approaches in biofilm preparation and labeling for fluorescent or electron microscopy and energy dispersive X-ray spectrometry (EDS) microanalysis for accurate observations. According to the targeted microscopy method, biofilms were sampled as flocs or attached biofilm, submitted to labeling using 4',6-diamidino-2-phenylindol, lectins PNA and ConA coupled to fluorescent dye or gold nanoparticles, and prepared for observation (fixation, cross-section, freezing, ultramicrotomy). Fluorescent microscopy revealed that nZVI were embedded in the biofilm structure as aggregates but the resolution was insufficient to observe individual nZVI. Cryo-scanning electron microscopy (SEM) observations showed nZVI aggregates close to bacteria, but it was not possible to confirm direct interactions between nZVI and cell membranes. Scanning transmission electron microscopy in the SEM (STEM-in-SEM) showed that nZVI aggregates could enter the biofilm to a depth of 7-11 µm. Bacteria were surrounded by a ring of extracellular polymeric substances (EPS) preventing direct nZVI/membrane interactions. STEM/EDS mapping revealed a co-localization of nZVI aggregates with lectins suggesting a potential role of EPS in nZVI embedding. Thus, the combination of divergent microscopy approaches is a good approach to better understand and characterize biofilm/metal interactions.

Soft X-ray microscopy and lithography with synchrotron radiation

International Nuclear Information System (INIS)

Gudat, W.

1977-12-01

Considerable progress in the technique microscopy with soft X-ray radiation has been achieved in particular through the application of synchrotron radiation. Various methods which are currently being studied theoretically or already being used practically will be described briefly. Attention is focussed on the method of contact microscopy. Various biological specimens have been investigated by this method with a resolution as good as 100 A. X-ray lithography which in the technical procedure is very similar to contact microscopy gives promise for the fabrication of high quality submicron structures in electronic device production. Important factors limiting the resolution and determining the performance of contact microscopy and X-ray lithography will be discussed. (orig.) [de

Nuclear microscopy in biomedical analysis with special emphasis on clinical metal biology

Science.gov (United States)

Lindh, Ulf; Frisk, Peter; Nyström, Joakim; Danersund, Antero; Hudecek, Romuald; Lindvall, Anders; Thunell, Stig

1997-07-01

Nuclear microscopy based upon developments in high energy ion beam techniques is by now an accepted technique in many fields of research. The advancements into the biomedical field have, however, been slower than expected. A major factor explaining this tendency is the availability of nuclear microscopy. This paper reviews briefly the biomedical work using nuclear microscopy that has been carried out since the 4 th International Conference on Nuclear Microprobe Technology and Applications held in Shanghai. Nuclear microscopy of isolated individual blood cells from patients adversely affected by metal exposure from dental amalgam has been performed both before and after removal of the metallic fillings. The elemental profile of blood cells was more or less normalised after treatment. Some of these results will be presented to illustrate a medical application. Results from bulk analysis by ICP-MS of erythrocytes and plasma before and after treatment will also be presented to illustrate the difference in information content between these two approaches as well as the need for complementary information in solving biomedical problems. As part of a larger study of acute porphyria, nuclear microscopy of blood cells was included among the 78 laboratory tests. The approach in this study was unbiased in the sense that no hypothesis was formulated as to which laboratory parameters would be the most explanatory for health or disease. Multivariate discriminant analysis was applied to the large amounts of data acquired. This approach led to the hypothesis that oxidative stress increased the synthesis of manganese-dependent superoxide dismutase in the mitochondria of polymorphonuclear leukocytes, explaining the increase of manganese in these cells. Antioxidant therapy was therefore applied to a couple of patients with porphyria, however, without clinical success.

Scanning transmission electron microscopy imaging and analysis

CERN Document Server

Pennycook, Stephen J

2011-01-01

Provides the first comprehensive treatment of the physics and applications of this mainstream technique for imaging and analysis at the atomic level Presents applications of STEM in condensed matter physics, materials science, catalysis, and nanoscience Suitable for graduate students learning microscopy, researchers wishing to utilize STEM, as well as for specialists in other areas of microscopy Edited and written by leading researchers and practitioners

Raman Microscopy: A Noninvasive Method to Visualize the Localizations of Biomolecules in the Cornea.

Science.gov (United States)

Kaji, Yuichi; Akiyama, Toshihiro; Segawa, Hiroki; Oshika, Tetsuro; Kano, Hideaki

2017-11-01

In vivo and in situ visualization of biomolecules without pretreatment will be important for diagnosis and treatment of ocular disorders in the future. Recently, multiphoton microscopy, based on the nonlinear interactions between molecules and photons, has been applied to reveal the localizations of various molecules in tissues. We aimed to use multimodal multiphoton microscopy to visualize the localizations of specific biomolecules in rat corneas. Multiphoton images of the corneas were obtained from nonlinear signals of coherent anti-Stokes Raman scattering, third-order sum frequency generation, and second-harmonic generation. The localizations of the adhesion complex-containing basement membrane and Bowman layer were clearly visible in the third-order sum frequency generation images. The fine structure of type I collagen was observed in the corneal stroma in the second-harmonic generation images. The localizations of lipids, proteins, and nucleic acids (DNA/RNA) was obtained in the coherent anti-Stokes Raman scattering images. Imaging technologies have progressed significantly and been applied in medical fields. Optical coherence tomography and confocal microscopy are widely used but do not provide information on the molecular structure of the cornea. By contrast, multiphoton microscopy provides information on the molecular structure of living tissues. Using this technique, we successfully visualized the localizations of various biomolecules including lipids, proteins, and nucleic acids in the cornea. We speculate that multiphoton microscopy will provide essential information on the physiological and pathological conditions of the cornea, as well as molecular localizations in tissues without pretreatment.

Scanning photoemission microscopy with synchrotron radiation

Science.gov (United States)

Ade, Harald W.

1992-08-01

Progress in photoemission spectro-microscopy at various synchrotron radiation facilities is reviewed. Microprobe devices such as MAXIMUM at the SRC in Wisconsin, the X1-SPEM at the NSLS at BNL, as well as the ellipsoidal ring mirror microscope at DESY in Hamburg, recorded first images during the last few years. The present status of these devices which achieve their lateral resolution by focusing X-rays to a small spot is the primary focus of this paper, but work representing other approaches to spectro-microscopy is also discussed.

Single-wavelength functional photoacoustic microscopy in biological tissue.

Science.gov (United States)

Danielli, Amos; Favazza, Christopher P; Maslov, Konstantin; Wang, Lihong V

2011-03-01

Recently, we developed a reflection-mode relaxation photoacoustic microscope, based on saturation intensity, to measure picosecond relaxation times using a nanosecond laser. Here, using the different relaxation times of oxygenated and deoxygenated hemoglobin molecules, both possessing extremely low fluorescence quantum yields, the oxygen saturation was quantified in vivo with single-wavelength photoacoustic microscopy. All previous functional photoacoustic microscopy measurements required imaging with multiple-laser-wavelength measurements to quantify oxygen saturation. Eliminating the need for multiwavelength measurements removes the influence of spectral properties on oxygenation calculations and improves the portability and cost-effectiveness of functional or molecular photoacoustic microscopy.

Intermittent contact atomic force microscopy in electrochemical environment