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https://www.readbyqxmd.com/read/27788689/combined-small-angle-x-ray-solution-scattering-with-atomic-force-microscopy-for-characterizing-radiation-damage-on-biological-macromolecules
#1
Luca Costa, Alexander Andriatis, Martha Brennich, Jean-Marie Teulon, Shu-Wen W Chen, Jean-Luc Pellequer, Adam Round
BACKGROUND: Synchrotron radiation facilities are pillars of modern structural biology. Small-Angle X-ray scattering performed at synchrotron sources is often used to characterize the shape of biological macromolecules. A major challenge with high-energy X-ray beam on such macromolecules is the perturbation of sample due to radiation damage. RESULTS: By employing atomic force microscopy, another common technique to determine the shape of biological macromolecules when deposited on flat substrates, we present a protocol to evaluate and characterize consequences of radiation damage...
October 27, 2016: BMC Structural Biology
https://www.readbyqxmd.com/read/27756898/the-room-temperature-crystal-structure-of-a-bacterial-phytochrome-determined-by-serial-femtosecond-crystallography
#2
Petra Edlund, Heikki Takala, Elin Claesson, Léocadie Henry, Robert Dods, Heli Lehtivuori, Matthijs Panman, Kanupriya Pande, Thomas White, Takanori Nakane, Oskar Berntsson, Emil Gustavsson, Petra Båth, Vaibhav Modi, Shatabdi Roy-Chowdhury, James Zook, Peter Berntsen, Suraj Pandey, Ishwor Poudyal, Jason Tenboer, Christopher Kupitz, Anton Barty, Petra Fromme, Jake D Koralek, Tomoyuki Tanaka, John Spence, Mengning Liang, Mark S Hunter, Sebastien Boutet, Eriko Nango, Keith Moffat, Gerrit Groenhof, Janne Ihalainen, Emina A Stojković, Marius Schmidt, Sebastian Westenhoff
Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser...
October 19, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27735069/x-ray-microtomography-observations-of-xylem-embolism-in-stems-of-laurus-nobilis-are-consistent-with-hydraulic-measurements-of-percentage-loss-of-conductance
#3
Andrea Nardini, Tadeja Savi, Adriano Losso, Giai Petit, Serena Pacilè, Giuliana Tromba, Stefan Mayr, Patrizia Trifilò, Maria A Lo Gullo, Sebastiano Salleo
Drought-induced xylem embolism is a serious threat to plant survival under future climate scenarios. Hence, accurate quantification of species-specific vulnerability to xylem embolism is a key to predict the impact of climate change on vegetation. Low-cost hydraulic measurements of embolism rate have been suggested to be prone to artefacts, thus requiring validation by direct visualization of the functional status of xylem conduits using nondestructive imaging techniques, such as X-ray microtomography (microCT)...
October 13, 2016: New Phytologist
https://www.readbyqxmd.com/read/27693754/resolving-colocalization-of-bacteria-and-metal-loid-s-on-plant-root-surfaces-by-combining-fluorescence-in-situ-hybridization-fish-with-multiple-energy-micro-focused-x-ray-fluorescence-me-%C3%AE-xrf
#4
Linnea K Honeker, Robert A Root, Jon Chorover, Raina M Maier
Metal(loid)-contamination of the environment due to anthropogenic activities is a global problem. Understanding the fate of contaminants requires elucidation of biotic and abiotic factors that influence metal(loid) speciation from molecular to field scales. Improved methods are needed to assess micro-scale processes, such as those occurring at biogeochemical interfaces between plant tissues, microbial cells, and metal(loid)s. Here we present an advanced method that combines fluorescence in situ hybridization (FISH) with synchrotron-based multiple-energy micro-focused X-ray fluorescence microprobe imaging (ME μXRF) to examine colocalization of bacteria and metal(loid)s on root surfaces of plants used to phytostabilize metalliferous mine tailings...
December 2016: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/27647420/x-rays-and-virtual-taphonomy-resolve-the-first-cissus-vitaceae-macrofossils-from-africa-as-early-diverging-members-of-the-genus
#5
Neil F Adams, Margaret E Collinson, Selena Y Smith, Marion K Bamford, Félix Forest, Panagiota Malakasi, Federica Marone, Dan Sykes
PREMISE OF THE STUDY: Fossilized seeds similar to Cissus (Vitaceae) have been recognized from the Miocene of Kenya, though some were previously assigned to the Menispermaceae. We undertook a comparative survey of extant African Cissus seeds to identify the fossils and consider their implications for the evolution and biogeography of Cissus and for African early Miocene paleoenvironments. METHODS: Micro-computed tomography (µCT) and synchrotron-based X-ray tomographic microscopy (SRXTM) were used to study seed morphology and anatomy...
September 2016: American Journal of Botany
https://www.readbyqxmd.com/read/27557457/evaluation-of-aggregate-microstructures-following-natural-regeneration-in-bauxite-residue-as-characterized-by-synchrotron-based-x-ray-micro-computed-tomography
#6
Feng Zhu, Jiaxin Liao, Shengguo Xue, William Hartley, Qi Zou, Hao Wu
Bauxite residue often has poor physical conditions which impede plant growth. Native plant encroachment on a bauxite residue disposal area in Central China reveals that natural regeneration may improve its physicochemical properties. Residue samples collected from three different disposal ages were assessed to evaluate residue micromorphology and three-dimensional (3D) aggregate microstructure under natural regeneration. The residue aggregates in different disposal ages were divided in two sections: macro-aggregate (2-1mm) and micro-aggregate (0...
December 15, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/27539601/in-vivo-dynamic-analysis-of-water-refilling-in-embolized-xylem-vessels-of-intact-zea-mays-leaves
#7
Jeongeun Ryu, Bae Geun Hwang, Sang Joon Lee
BACKGROUND AND AIMS: The refilling of embolized xylem vessels under tension is a major issue in water transport among vascular plants. However, xylem embolism and refilling remain poorly understood because of technical limitations. Direct observation of embolism repair in intact plants is essential to understand the biophysical aspects of water refilling in embolized xylem vessels. This paper reports on details of the water refilling process in leaves of the intact herbaceous monocot plant Zea mays and its refilling kinetics obtained by a direct visualization technique...
August 18, 2016: Annals of Botany
https://www.readbyqxmd.com/read/27476512/effect-of-phytosterols-on-the-crystallization-behavior-of-oil-in-water-milk-fat-emulsions
#8
Lisa M Zychowski, Amy Logan, Mary Ann Augustin, Alan L Kelly, Alexandru Zabara, James A O'Mahony, Charlotte E Conn, Mark A E Auty
Milk has been used commercially as a carrier for phytosterols, but there is limited knowledge on the effect of added plant sterols on the properties of the system. In this study, phytosterols dispersed in milk fat at a level of 0.3 or 0.6% were homogenized with an aqueous dispersion of whey protein isolate (WPI). The particle size, morphology, ζ-potential, and stability of the emulsions were investigated. Emulsion crystallization properties were examined through the use of differential scanning calorimetry (DSC) and Synchrotron X-ray scattering at both small and wide angles...
August 31, 2016: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/27475903/practical-review-on-the-use-of-synchrotron-based-micro-and-nano-x-ray-fluorescence-mapping-and-x-ray-absorption-spectroscopy-to-investigate-the-interactions-between-plants-and-engineered-nanomaterials
#9
Hiram A Castillo-Michel, Camille Larue, Ana E Pradas Del Real, Marine Cotte, Geraldine Sarret
The increased use of engineered nanomaterials (ENMs) in commercial products and the continuous development of novel applications, is leading to increased intentional and unintentional release of ENMs into the environment with potential negative impacts. Particularly, the partition of nanoparticles (NPs) to waste water treatment plant (WWTP) sludge represents a potential threat to agricultural ecosystems where these biosolids are being applied as fertilizers. Moreover, several applications of ENMs in agriculture and soil remediation are suggested...
July 20, 2016: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/27446168/vulnerability-of-protoxylem-and-metaxylem-vessels-to-embolisms-and-radial-refilling-in-a-vascular-bundle-of-maize-leaves
#10
Bae Geun Hwang, Jeongeun Ryu, Sang Joon Lee
Regulation of water flow in an interconnected xylem vessel network enables plants to survive despite challenging environment changes that can cause xylem embolism. In this study, vulnerability to embolisms of xylem vessels and their water-refilling patterns in vascular bundles of maize leaves were experimentally investigated by employing synchrotron X-ray micro-imaging technique. A vascular bundle in maize consisted of a protoxylem vessel with helical thickenings between two metaxylem vessels with single perforation plates and nonuniformly distributed pits...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27445995/cell-wall-biomolecular-composition-plays-a-potential-role-in-the-host-type-ii-resistance-to-fusarium-head-blight-in-wheat
#11
Rachid Lahlali, Saroj Kumar, Lipu Wang, Li Forseille, Nicole Sylvain, Malgorzata Korbas, David Muir, George Swerhone, John R Lawrence, Pierre R Fobert, Gary Peng, Chithra Karunakaran
Fusarium head blight (FHB) is a serious disease of wheat worldwide. Cultivar resistance to FHB depends on biochemical factors that confine the pathogen spread in spikes. Breeding for cultivar resistance is considered the most practical way to manage this disease. In this study, different spectroscopy and microscopy techniques were applied to discriminate resistance in wheat genotypes against FHB. Synchrotron-based spectroscopy and imaging techniques, including focal plane array infrared and X-ray fluorescence (XRF) spectroscopy were used to understand changes in biochemical and nutrients in rachis following FHB infection...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27385767/cadmium-accumulation-is-enhanced-by-ammonium-compared-to-nitrate-in-two-hyperaccumulators-without-affecting-speciation
#12
Miaomiao Cheng, Peng Wang, Peter M Kopittke, Anan Wang, Peter W G Sale, Caixian Tang
Nitrogen fertilization could improve the efficiency of Cd phytoextraction in contaminated soil and thus shorten the remediation time. However, limited information is available on the effect of N form on Cd phytoextraction and associated mechanisms in plants. This study examined the effect of N form on Cd accumulation, translocation, and speciation in Carpobrotus rossii and Solanum nigrum Plants were grown in nutrient solution with 5-15 μM Cd in the presence of 1000 µM NH4 (+) or NO3 (-) Plant growth and Cd uptake were measured, and Cd speciation was analyzed using synchrotron-based X-ray absorption spectroscopy...
September 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/27380126/silver-nanoparticles-entering-soils-via-the-wastewater-sludge-soil-pathway-pose-low-risk-to-plants-but-elevated-cl-concentrations-increase-ag-bioavailability
#13
Peng Wang, Neal W Menzies, Paul G Dennis, Jianhua Guo, Christian Forstner, Ryo Sekine, Enzo Lombi, Peter Kappen, Paul M Bertsch, Peter M Kopittke
The widespread use of silver nanoparticles (Ag-NPs) results in their movement into wastewater treatment facilities and subsequently to agricultural soils via application of contaminated sludge. On-route, the chemical properties of Ag may change, and further alterations are possible upon entry to soil. In the present study, we examined the long-term stability and (bio)availability of Ag along the "wastewater-sludge-soil" pathway. Synchrotron-based X-ray absorption spectroscopy (XAS) revealed that ca. 99% of Ag added to the sludge reactors as either Ag-NPs or AgNO3 was retained in sludge, with ≥79% of this being transformed to Ag2S, with the majority (≥87%) remaining in this form even after introduction to soils at various pH values and Cl concentrations for up to 400 days...
August 2, 2016: Environmental Science & Technology
https://www.readbyqxmd.com/read/27359142/synchrotron-x-ray-microfluorescence-measurement-of-metal-distributions-in-phragmites-australis-root-system-in-the-yangtze-river-intertidal-zone
#14
Huan Feng, Weiguo Zhang, Yu Qian, Wenliang Liu, Lizhong Yu, Shinjae Yoo, Jun Wang, Jia Jun Wang, Christopher Eng, Chang Jun Liu, Ryan Tappero
This study investigates the distributions of Br, Ca, Cl, Cr, Cu, K, Fe, Mn, Pb, Ti, V and Zn in Phragmites australis root system and the function of Fe nanoparticles in scavenging metals in the root epidermis using synchrotron X-ray microfluorescence, synchrotron transmission X-ray microscope measurement and synchrotron X-ray absorption near-edge structure techniques. The purpose of this study is to understand the mobility of metals in wetland plant root systems after their uptake from rhizosphere soils. Phragmites australis samples were collected in the Yangtze River intertidal zone in July 2013...
July 2016: Journal of Synchrotron Radiation
https://www.readbyqxmd.com/read/27266296/a-barrier-to-metal-movement-synchrotron-study-of-iron-plaque-on-roots-of-wetland-plants
#15
Iris Koch, Michelle M Nearing
No abstract text is available yet for this article.
June 2016: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/27140160/synchrotron-x-ray-phase-contrast-imaging-of-leaf-venation-in-soybean-glycine-max-after-exclusion-of-solar-uv-280-400%C3%A2-nm-radiation
#16
A Fatima, S Kataria, K N Guruprasad, A K Agrawal, B Singh, P S Sarkar, T Shripathi, Y Kashyap, A Sinha
The hydraulic efficiency of a leaf depends on its vascular structure as this is responsible for transport activities. To investigate the effect of exclusion of UVAB and UVB radiation from the solar spectrum on the micro-structure of leaves of soybean (Glycine max, variety JS-335), a field experiment was conducted using synchrotron-based phase contrast imaging (PCI). Plants were grown in specially designed UV exclusion chambers, and wrapped with filters that excluded UVB (280-315 nm) or UVAB (280-400 nm), or transmitted all the ambient solar UV (280-400 nm) radiation (filter control)...
May 2016: Journal of Synchrotron Radiation
https://www.readbyqxmd.com/read/27120684/reconstruction-of-the-disassembly-pathway-of-an-icosahedral-viral-capsid-and-shape-determination-of-two-successive-intermediates
#17
Didier Law-Hine, Anil K Sahoo, Virginie Bailleux, Mehdi Zeghal, Sylvain Prevost, Prabal K Maiti, Stéphane Bressanelli, Doru Constantin, Guillaume Tresset
Viral capsids derived from an icosahedral plant virus widely used in physical and nanotechnological investigations were fully dissociated into dimers by a rapid change of pH. The process was probed in vitro at high spatiotemporal resolution by time-resolved small-angle X-ray scattering using a high brilliance synchrotron source. A powerful custom-made global fitting algorithm allowed us to reconstruct the most likely pathway parametrized by a set of stoichiometric coefficients and to determine the shape of two successive intermediates by ab initio calculations...
September 3, 2015: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/27098521/photo-spectroscopy-of-mixtures-of-catalyst-particles-reveals-their-age-and-type
#18
M M Kerssens, A Wilbers, J Kramer, P de Peinder, G Mesu, B J Nelissen, E T C Vogt, B M Weckhuysen
Within a fluid catalytic cracking (FCC) unit, a mixture of catalyst particles that consist of either zeolite Y (FCC-Y) or ZSM-5 (FCC-ZSM-5) is used in order to boost the propylene yield when processing crude oil fractions. Mixtures of differently aged FCC-Y and FCC-ZSM-5 particles circulating in the FCC unit, the so-called equilibrium catalyst (Ecat), are routinely studied to monitor the overall efficiency of the FCC process. In this study, the age of individual catalyst particles is evaluated based upon photographs after selective staining with substituted styrene molecules...
July 4, 2016: Faraday Discussions
https://www.readbyqxmd.com/read/27015946/observation-of-yttrium-oxide-nanoparticles-in-cabbage-brassica-oleracea-through-dual-energy-k-edge-subtraction-imaging
#19
Yunyun Chen, Carlos Sanchez, Yuan Yue, Mauricio de Almeida, Jorge M González, Dilworth Y Parkinson, Hong Liang
BACKGROUND: The potential transfer of engineered nanoparticles (ENPs) from plants into the food chain has raised widespread concerns. In order to investigate the effects of ENPs on plants, young cabbage plants (Brassica oleracea) were exposed to a hydroponic system containing yttrium oxide (yttria) ENPs. The objective of this study was to reveal the impacts of NPs on plants by using K-edge subtraction imaging technique. RESULTS: Using synchrotron dual-energy X-ray micro-tomography with K-edge subtraction technique, we studied the uptake, accumulation, distribution and concentration mapping of yttria ENPs in cabbage plants...
March 25, 2016: Journal of Nanobiotechnology
https://www.readbyqxmd.com/read/27004874/vuv-and-soft-x-ray-ionization-of-a-plant-volatile-vanillin-c8h8o3
#20
A Moreno Betancourt, L H Coutinho, R B Bernini, C E V de Moura, A B Rocha, G G B de Souza
Plant volatiles are emitted by plants in response to several forms of stress, including interaction with energetic photons. In the present work, we discuss the interaction of extreme UV and soft X-ray photons with a plant volatile, vanillin. The single and double (multiple) ionization of the vanillin molecule have been studied for the first time using time-of-flight mass spectrometry and VUV and soft X-ray photons (synchrotron radiation, at 12.0 eV, 21.2 eV, 130 eV, 310 eV, 531 eV, and 550 eV). At 12.0 and 21...
March 21, 2016: Journal of Chemical Physics
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