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Grid cells

Christopher J Benjamin, Kyle J Wright, Scott C Bolton, Seok-Hee Hyun, Kyle Krynski, Mahima Grover, Guimei Yu, Fei Guo, Tamara L Kinzer-Ursem, Wen Jiang, David H Thompson
We report the fabrication of transmission electron microscopy (TEM) grids bearing graphene oxide (GO) sheets that have been modified with N(α), N(α)-dicarboxymethyllysine (NTA) and deactivating agents to block non-selective binding between GO-NTA sheets and non-target proteins. The resulting GO-NTA-coated grids with these improved antifouling properties were then used to isolate His6-T7 bacteriophage and His6-GroEL directly from cell lysates. To demonstrate the utility and simplified workflow enabled by these grids, we performed cryo-electron microscopy (cryo-EM) of His6-GroEL obtained from clarified E...
October 17, 2016: Scientific Reports
Yuting Zhou, Xiangming Xiao, Yuanwei Qin, Jinwei Dong, Geli Zhang, Weili Kou, Cui Jin, Jie Wang, Xiangping Li
Accurate and up-to-date information on the spatial distribution of paddy rice fields is necessary for the studies of trace gas emissions, water source management, and food security. The phenology-based paddy rice mapping algorithm, which identifies the unique flooding stage of paddy rice, has been widely used. However, identification and mapping of paddy rice in rice-wetland coexistent areas is still a challenging task. In this study, we found that the flooding/transplanting periods of paddy rice and natural wetlands were different...
April 2016: International Journal of Applied Earth Observation and Geoinformation: ITC Journal
Holger Dannenberg, James R Hinman, Michael E Hasselmo
Behavioral data suggest that cholinergic modulation may play a role in certain aspects of spatial memory, and neurophysiological data demonstrate neurons that fire in response to spatial dimensions, including grid cells and place cells that respond on the basis of location and running speed. These neurons show firing responses that depend upon the visual configuration of the environment, due to coding in visually-responsive regions of the neocortex. This review focuses on the physiological effects of acetylcholine that may influence the sensory coding of spatial dimensions relevant to behavior...
September 24, 2016: Journal of Physiology, Paris
Rui Liu, Yun Chen, Jianping Wu, Lei Gao, Damian Barrett, Tingbao Xu, Xiaojuan Li, Linyi Li, Chang Huang, Jia Yu
Regional flood risk caused by intensive rainfall under extreme climate conditions has increasingly attracted global attention. Mapping and evaluation of flood hazard are vital parts in flood risk assessment. This study develops an integrated framework for estimating spatial likelihood of flood hazard by coupling weighted naïve Bayes (WNB), geographic information system, and remote sensing. The north part of Fitzroy River Basin in Queensland, Australia, was selected as a case study site. The environmental indices, including extreme rainfall, evapotranspiration, net-water index, soil water retention, elevation, slope, drainage proximity, and density, were generated from spatial data representing climate, soil, vegetation, hydrology, and topography...
September 24, 2016: Risk Analysis: An Official Publication of the Society for Risk Analysis
Argo Ronk, Francesco de Bello, Pavel Fibich, Meelis Pärtel
Large-scale biodiversity studies can be more informative if observed diversity in a study site is accompanied by dark diversity, the set of absent although ecologically suitable species. Dark diversity methodology is still being developed and a comparison of different approaches is needed. We used plant data at two different scales (European and seven large regions) and compared dark diversity estimates from two mathematical methods: species co-occurrence (SCO) and species distribution modeling (SDM). We used plant distribution data from the Atlas Florae Europaeae (50 × 50 km grid cells) and seven different European regions (10 × 10 km grid cells)...
September 2016: Ecology and Evolution
Georgios Gerogiokas, Michelle W Y Southey, Michael P Mazanetz, Alexander Heifetz, Michael Bodkin, Richard J Law, Richard H Henchman, J Michel
Molecular dynamics simulations have been analyzed with the Grid Cell Theory (GCT) method to spatially resolve the binding enthalpies and entropies of water molecules at the interface of 17 structurally diverse proteins. Correlations between computed energetics and structural descriptors have been sought to facilitate the development of simple models of protein hydration. Little correlation was found between GCT-computed binding enthalpies and continuum electrostatics calculations. A simple count of contacts with functional groups in charged amino acids correlates well with enhanced water stabilization, but the stability of water near hydrophobic and polar residues depends markedly on its coordination environment...
October 13, 2016: Journal of Physical Chemistry. B
Corinna S Bazelet, Aileen C Thompson, Piotr Naskrecki
The use of endemism and vascular plants only for biodiversity hotspot delineation has long been contested. Few studies have focused on the efficacy of global biodiversity hotspots for the conservation of insects, an important, abundant, and often ignored component of biodiversity. We aimed to test five alternative diversity measures for hotspot delineation and examine the efficacy of biodiversity hotspots for conserving a non-typical target organism, South African katydids. Using a 1° fishnet grid, we delineated katydid hotspots in two ways: (1) count-based: grid cells in the top 10% of total, endemic, threatened and/or sensitive species richness; vs...
2016: PloS One
Marie Hébert, Antoine Anfray, Arnaud Chevilley, Sara Martinez de Lizarrondo, Aurélien Quenault, Morgane Louessard, Benoit D Roussel, Pauline Obiang, Etienne Save, Cyrille Orset, Eric Maubert, Denis Vivien, Véronique Agin
In humans, spatial cognition and navigation impairments are a frequent situation during physiological and pathological aging, leading to a dramatic deterioration in the quality of life. Despite the discovery of neurons with location-specific activity in rodents, that is, place cells in the hippocampus and later on grid cells in the entorhinal cortex (EC), the molecular mechanisms underlying spatial cognition are still poorly known. Our present data bring together in an unusual combination 2 molecules of primary biological importance: a major neuronal excitatory receptor, N-methyl-D-aspartate receptor (NMDAR), and an extracellular protease, tissue plasminogen activator (tPA), in the control of spatial navigation...
September 9, 2016: Cerebral Cortex
Yuanqing Li, Chong Liu, Yi Cui, Spencer S Walse, Ryan Olver, David Zilberman, William A Mitch
Due to concerns surrounding its ozone depletion potential, there is a need for technologies to capture and destroy methyl bromide (CH3Br) emissions from postharvest fumigations applied to control agricultural pests. Previously, we described a system in which CH3Br fumes vented from fumigation chambers could be captured by granular activated carbon (GAC). The GAC was converted to a cathode by submergence in a high ionic strength solution and connection to the electrical grid, resulting in reductive debromination of the sorbed CH3Br...
October 18, 2016: Environmental Science & Technology
Yvonne Roger, Luisa Marilena Schäck, Anastasia Koroleva, Sandra Noack, Kestutis Kurselis, Christian Krettek, Boris Chichkov, Thomas Lenarz, Athanasia Warnecke, Andrea Hoffmann
The use of autologous cells for the coating of implant surfaces presents a promising tool to attenuate foreign body reaction and inflammation. However, insertion forces that occur especially during implantation of electrodes into the narrow cochlea may strip off cells from the surface. Thus, implant surfaces should be ideally structured in a way that protects the cell coating from mechanical removal during implantation. The structuring of implant surfaces may also direct cells towards desired functions to further enhance their performance and clinical suitability...
June 16, 2016: Colloids and Surfaces. B, Biointerfaces
Masaki Makihara, Takashi Watanabe, Eiji Usukura, Kozo Kaibuchi, Akihiro Narita, Nobuo Tanaka, Jiro Usukura
An improved unroofing method consisting of tearing off the cell membrane using an adhesive electron microscopy (EM) grid instead of vitreous ice sectioning (cryo-sectioning) has enabled us to panoramically view the membrane cytoskeleton in its native state with extremely high contrast. Grids pre-treated with Alcian blue were placed on cells, and a portion of the dorsal plasma membrane was transferred onto the grid, which was then floated in buffer solution. These membrane fragments contained sufficient cytoskeleton and were of suitable thickness for observation by cryo-EM...
September 1, 2016: Microscopy
Fotis Georgiou, Maarten Hornikx
The pseudospectral time-domain method (PSTD) provides an efficient way to solve the linear acoustics equations. With regards to acoustic modeling and auralization, source directivity as well as head-related directivity have a clear influence on the perceived sound field and have to be included in computations. In this paper directive sources are implemented in the time-domain method PSTD. First, a given frequency dependent source directivity is decomposed onto spherical harmonic functions. The directive source is then implemented through spatial distributions in PSTD that relate to the spherical harmonic functions, and time-dependent functions are assigned to the spatial distributions in order to obtain the frequency content of the directivity...
August 2016: Journal of the Acoustical Society of America
Murray C Killingsworth, Yuri V Bobryshev
A method is described whereby quantum dot (QD) nanoparticles can be used for correlative immunocytochemical studies of human pathology tissue using widefield fluorescence light microscopy and transmission electron microscopy (TEM). To demonstrate the protocol we have immunolabeled ultrathin epoxy sections of human somatostatinoma tumor using a primary antibody to somatostatin, followed by a biotinylated secondary antibody and visualization with streptavidin conjugated 585 nm cadmium-selenium (CdSe) quantum dots (QDs)...
2016: Journal of Visualized Experiments: JoVE
Koen M Marien, Valerie Croons, Yannick Waumans, Ellen Sluydts, Stefanie De Schepper, Luc Andries, Wim Waelput, Erik Fransen, Peter B Vermeulen, Mark M Kockx, Guido R Y De Meyer
Despite all efforts made to develop predictive biomarkers for antiangiogenic therapies, no unambiguous markers have been identified so far. This is due to among others the lack of standardized tests. This study presents an improved microvessel density quantification method in tumor tissue based on stereological principles and using whole-slide images. Vessels in tissue sections of different cancer types were stained for CD31 by an automated and validated immunohistochemical staining method. The stained slides were digitized with a digital slide scanner...
2016: PloS One
Lidija Čomić, Benedek Nagy
Topological coordinate systems are used to address all cells of abstract cell complexes. In this paper, a topological coordinate system for cells in the diamond cubic grid is presented and some of its properties are detailed. Four dependent coordinates are used to address the voxels (triakis truncated tetrahedra), their faces (hexagons and triangles), their edges and the points at their corners. Boundary and co-boundary relations, as well as adjacency relations between the cells, can easily be captured by the coordinate values...
September 1, 2016: Acta Crystallographica. Section A, Foundations and Advances
Jacob Ls Bellmund, Lorena Deuker, Tobias Navarro Schröder, Christian F Doeller
Anticipating the future is a key motif of the brain, possibly supported by mental simulation of upcoming events. Rodent single-cell recordings suggest the ability of spatially tuned cells to represent subsequent locations. Grid-like representations have been observed in the human entorhinal cortex during virtual and imagined navigation. However, hitherto it remains unknown if grid-like representations contribute to mental simulation in the absence of imagined movement. Participants imagined directions between building locations in a large-scale virtual-reality city while undergoing fMRI without re-exposure to the environment...
2016: ELife
Iyad Kheirbek, Jay Haney, Sharon Douglas, Kazuhiko Ito, Thomas Matte
BACKGROUND: On-road vehicles are an important source of fine particulate matter (PM2.5) in cities, but spatially varying traffic emissions and vulnerable populations make it difficult to assess impacts to inform policy and the public. METHODS: We estimated PM2.5-attributable mortality and morbidity from on-road vehicle generated air pollution in the New York City (NYC) region using high-spatial-resolution emissions estimates, air quality modeling, and local health incidence data to evaluate variations in impacts by vehicle class, neighborhood, and area socioeconomic status...
2016: Environmental Health: a Global Access Science Source
B Samuel Thavamani, Molly Mathew, S P Dhanabal
BACKGROUND: Protein-ligand interaction plays a major role in identification of the possible mechanism by which a ligand can bind with the target and exerts the pharmacological action. OBJECTIVE: The aim is to identify the best candidate of Cocculus hirsutus which binds with the hepatocellular carcinoma (HCC) targets by docking studies. MATERIALS AND METHODS: The reported phytoconstituents such as coclaurine, hirsutine, cohirsine, cohirsinine, lirioresinol, cohirsitinine, haiderine, jamtinine, isotrilobine, shaheenine, jamtine, and cocsoline present in the plant, C...
May 2016: Pharmacognosy Magazine
Christoph Hönigsperger, Maximiliano J Nigro, Johan F Storm
The medial entorhinal cortex (mEC) is strongly involved in spatial navigation, memory, dementia and epilepsy. Although potassium channels shape neuronal activity, their roles in mEC are largely unknown. We used the new Kv2 blocker Guangxitoxin-1E (GTx, 10-100 nm) in rat brain slices to investigate Kv2 channel functions in mEC layer II stellate cells (SCs). These neurons project to the hippocampus and are thought to be grid cells representing space. Voltage clamp recordings from SCs nucleated patches showed that GTx inhibited a delayed rectifier K(+) current activating beyond -30 mV, but not transient, A-type current...
August 26, 2016: Journal of Physiology
Caterina Penone, Ben G Weinstein, Catherine H Graham, Thomas M Brooks, Carlo Rondinini, S Blair Hedges, Ana D Davidson, Gabriel C Costa
The taxonomic, phylogenetic and trait dimensions of beta diversity each provide us unique insights into the importance of historical isolation and environmental conditions in shaping global diversity. These three dimensions should, in general, be positively correlated. However, if similar environmental conditions filter species with similar trait values, then assemblages located in similar environmental conditions, but separated by large dispersal barriers, may show high taxonomic, high phylogenetic, but low trait beta diversity...
August 31, 2016: Proceedings. Biological Sciences
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