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Cryo-EM Model of the Bullet-Shaped Vesicular Stomatitis Virus

SCIENCE 2010年第5966期327卷 689-693页

作者： Ge, Peng Tsao, Jun Schein, Stan Green, Todd J. Luo, Ming Zhou, Z. Hong Univ Calif Los Angeles Dept Microbiol Immunol & Mol Genet Los Angeles CA 90095 USA Univ Calif Los Angeles Calif NanoSyst Inst Los Angeles CA 90095 USA Baylor Coll Med Struct Computat Biol & Mol Biophys Program Houston TX 77030 USA Univ Texas Med Sch Houston Dept Pathol & Lab Med Houston TX 77030 USA Univ Alabama Dept Microbiol Birmingham AL 35294 USA Univ Calif Los Angeles Dept Psychol Los Angeles CA 90095 USA

Vesicular stomatitis virus (VSV) is a bullet-shaped rhabdovirus and a model system of negative-strand RNA viruses. Through direct visualization by means of cryo-electron microscopy, we show that each virion contains two nested, left-handed helices: an outer helix of matrix protein M and an inner helix of nucleoprotein N and RNA. M has a hub domain with four contact sites that link to neighboring M and N subunits, providing rigidity by clamping adjacent turns of the nucleocapsid. Side-by-side interactions between neighboring N subunits are critical for the nucleocapsid to form a bullet shape, and structure-based mutagenesis results support this description. Together, our data suggest a mechanism of VSV assembly in which the nucleocapsid spirals from the tip to become the helical trunk, both subsequently framed and rigidified by the M layer.

关键词： Cryoelectron Microscopy Crystallography, X-Ray image processing, computer-assisted Lipid Bilayers Models, Molecular Mutagenesis Nucleocapsid Proteins/chemistry Nucleocapsid Proteins/genetics Nucleocapsid Proteins/ultrastructure Protein Conformation Protein Structure, Secondary Protein Structure, Tertiary Protein Subunits/chemistry RNA, Viral/chemistry RNA, Viral/ultrastructure Vesiculovirus/chemistry Vesiculovirus/physiology Vesiculovirus/ultrastructure Viral Matrix Proteins/chemistry Viral Matrix Proteins/ultrastructure Virion/chemistry Virion/ultrastructure Virus Assembly

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XMSF: Structure-preserving noise reduction and pre-segmentation in microscope tomography

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BIOINFORMATICS 2010年第21期26卷 2786-2787页

作者： Bilbao-Castro, J. R. Sorzano, C. O. S. Garcia, I. Fernandez, J. J. Univ Almeria Dept Comp Architecture & Elect Almeria 04120 Spain Univ Autonoma Madrid Natl Ctr Biotechnol CSIC E-28049 Madrid Spain Univ Malaga Dept Comp Architecture E-29071 Malaga Spain

Interpretation of electron tomograms is difficult due to the high noise levels. Thus, denoising techniques are needed to improve the signal-to-noise ratio. XMSF (Microscopy Mean Shift Filtering) is a fast, user-friendly application that succeeds in filtering noise while preserving the structures of interest. It is based on the extension to 3D of a method widely applied in other image processing fields under very different scenarios. XMSF has been tested for a variety of tomograms, showing a great potential to become a state-of-the-art filtering program in electron tomography. Applied iteratively, the algorithm yields pre-segmented volumes facilitating posterior segmentation tasks. Moreover, execution times remain low thanks to parallel computing techniques to exploit current multicore computers.

关键词： Algorithms Electron Microscope Tomography/methods image processing, computer-assisted Imaging, Three-Dimensional/methods Sensitivity and Specificity Software

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From the Connectome to the Synaptome: An Epic Love Story

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SCIENCE 2010年第6008期330卷 1198-1201页

作者： DeFelipe, Javier CSIC Inst Cajal Madrid Spain Univ Politecn Madrid Ctr Tecnol Biomed Lab Circuitos Corticales E-28040 Madrid Spain

A major challenge in neuroscience is to decipher the structural layout of the brain. The term "connectome" has recently been proposed to refer to the highly organized connection matrix of the human brain. However, defining how information flows through such a complex system represents so difficult a task that it seems unlikely it could be achieved in the near future or, for the most pessimistic, perhaps ever. Circuit diagrams of the nervous system can be considered at different levels, although they are surely impossible to complete at the synaptic level. Nevertheless, advances in our capacity to marry macro-and microscopic data may help establish a realistic statistical model that could describe connectivity at the ultrastructural level, the "synaptome," giving us cause for optimism.

关键词： Animals Brain/anatomy & histology Brain/cytology Brain/physiology Brain/ultrastructure Brain Mapping Brain Mapping History, 19th Century History, 20th Century Humans image processing, computer-assisted Microscopy, Electron Neural Pathways/physiology Neural Pathways/ultrastructure Neurons/physiology Neurons/ultrastructure Synapses/physiology Synapses/ultrastructure

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Systems survey of endocytosis by multiparametric image analysis

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NATURE 2010年第7286期464卷 243-U123页

作者： Collinet, Claudio Stoeter, Martin Bradshaw, Charles R. Samusik, Nikolay Rink, Jochen C. Kenski, Denise Habermann, Bianca Buchholz, Frank Henschel, Robert Mueller, Matthias S. Nagel, Wolfgang E. Fava, Eugenio Kalaidzidis, Yannis Zerial, Marino MPI CBG Max Planck Inst Mol Cell Biol & Genet D-01307 Dresden Germany Tech Univ Dresden Ctr Informat Serv & High Performance Comp ZIH D-01062 Dresden Germany Moscow MV Lomonosov State Univ Belozersky Inst Physicochem Biol Moscow 119899 Russia

Endocytosis is a complex process fulfilling many cellular and developmental functions. Understanding how it is regulated and integrated with other cellular processes requires a comprehensive analysis of its molecular constituents and general design principles. Here, we developed a new strategy to phenotypically profile the human genome with respect to transferrin (TF) and epidermal growth factor (EGF) endocytosis by combining RNA interference, automated high-resolution confocal microscopy, quantitative multiparametric image analysis and high-performance computing. We identified several novel components of endocytic trafficking, including genes implicated in human diseases. We found that signalling pathways such as Wnt, integrin/cell adhesion, transforming growth factor (TGF)-beta and Notch regulate the endocytic system, and identified new genes involved in cargo sorting to a subset of signalling endosomes. A systems analysis by Bayesian networks further showed that the number, size, concentration of cargo and intracellular position of endosomes are not determined randomly but are subject to specific regulation, thus uncovering novel properties of the endocytic system.

关键词： Computing Methodologies Endocytosis/physiology Endosomes/metabolism Epidermal Growth Factor/metabolism Gene Expression Profiling/methods Genome-Wide Association Study Humans image processing, computer-assisted Metabolic Networks and Pathways/physiology Microscopy, Confocal Phenotype Protein Transport/physiology RNA Interference Signal Transduction/physiology Transferrin/metabolism Transferrin/metabolism

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Relationship between radiation dose reduction and image quality change in photostimulable phosphor luminescence X-ray imaging systems

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DENTOMAXILLOFACIAL RADIOLOGY 2010年第4期39卷 207-215页

作者： Sakurai, T. Kawamata, R. Kozai, Y. Kaku, Y. Nakamura, K. Saito, M. Wakao, H. Kashima, I. Kanagawa Dent Coll Dept Maxillofacial Diagnost Sci Div Radiol Yokosuka Kanagawa 238 Japan

Objectives: The aim of the study was to clarify the change in image quality upon X-ray dose reduction and to re-analyse the possibility of X-ray dose reduction in photostimulable phosphor luminescence (PSPL) X-ray imaging systems. In addition, the study attempted to verify the usefulness of multiobjective frequency processing (MFP) and flexible noise control (FNC) for X-ray dose reduction. Methods: Three PSPL X-ray imaging systems were used in this study. Modulation transfer function (MTF), noise equivalent number of quanta (NEQ) and detective quantum efficiency (DQE) were evaluated to compare the basic physical performance of each system. Subjective visual evaluation of diagnostic ability for normal anatomical structures was performed. The NEQ, DQE and diagnostic ability were evaluated at base X-ray dose, and 1/3, 1/10 and 1/20 of the base X-ray dose. Results: The MTF of the systems did not differ significantly. The NEQ and DQE did not necessarily depend on the pixel size of the system. The images from all three systems had a higher diagnostic utility compared with conventional film images at the base and 1/3 X-ray doses. The subjective image quality was better at the base X-ray dose than at 1/3 of the base dose in all systems. The MFP and FNC-processed images had a higher diagnostic utility than the images without MFP and FNC. Conclusions: The use of PSPL imaging systems may allow a reduction in the X-ray dose to one-third of that required for conventional film. It is suggested that MFP and FNC are useful for radiation dose reduction. Dentomaxillofacial Radiology (2010) 39, 207-215. doi: 10.1259/dmfr/44413341

关键词： dental digital radiography image processing, computer-assisted radiographic image enhancement

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The effect of different anesthetics on neurovascular coupling

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NEUROimage 2010年第4期51卷 1367-1377页

作者： Franceschini, Maria Angela Radhakrishnan, Harsha Thakur, Kiran Wu, Weicheng Ruvinskaya, Svetlana Carp, Stefan A. Boas, David A. Massachusetts Gen Hosp Athinoula A Martinos Ctr Biomed Imaging Charlestown MA 02129 USA

To date, the majority of neurovascular coupling studies focused on the thalamic afferents' activity in layer IV and the corresponding large spiking activity as responsible for functional hyperemia. This paper highlights the role of the secondary and late cortico-cortical transmission in neurovascular coupling. Simultaneous scalp electroencephalography (EEG) and diffuse optical imaging (DOI) measurements were obtained during multiple conditions of event-related electrical forepaw stimulation in 33 male Sprague-Dawley rats divided into 6 groups depending on the maintaining anesthetic - alpha-chloralose, pentobarbital, ketamine-xylazine, fentanyl-droperidol, isoflurane, or propofol. The somatosensory evoked potentials (SEP) were decomposed into four components and the question of which best predicts the hemodynamic responses was investigated. Results of the linear regression analysis show that the hemodynamic response is best correlated with the secondary and late cortico-cortical transmissions and not with the initial thalamic input activity in layer IV. Baseline cerebral blood flow (CBF) interacts with neural activity and influences the evoked hemodynamic responses. Finally, neurovascular coupling appears to be the same across all anesthetics used. (C) 2010 Elsevier Inc. All rights reserved.

关键词： Anesthetics/pharmacology Animals Blood Vessels/drug effects Blood Vessels/innervation Cerebral Cortex/drug effects Cerebral Cortex/physiology Cerebrovascular Circulation/drug effects Electric Stimulation Electroencephalography Evoked Potentials, Somatosensory/drug effects Forelimb/physiology Hemoglobins/metabolism Hypercapnia/physiopathology image processing, computer-assisted Male Neurons/physiology Rats Rats, Sprague-Dawley Synaptic Transmission/drug effects Synaptic Transmission/physiology Thalamus/drug effects Thalamus/physiology

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Brain activity during bladder filling is related to white matter structural changes in older women with urinary incontinence

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NEUROimage 2010年第4期51卷 1294-1302页

作者： Tadic, Stasa D. Griffiths, Derek Murrin, Andrew Schaefer, Werner Aizenstein, Howard J. Resnick, Neil M. Univ Pittsburgh Div Geriatr Med Pittsburgh PA USA Univ Pittsburgh Inst Aging Pittsburgh PA USA Univ Pittsburgh Dept Psychiat Pittsburgh PA USA

Evidence from longitudinal studies in community-dwelling elderly links complaints of urgency and urinary incontinence with structural white matter changes known as white matter hyperintensities (WMH). How WMH might lead to incontinence remains unknown, since information about how they relate to neural circuits involved in continence control is lacking. The aim of this study was to investigate the role of WMH in altered brain activity in older women with urgency incontinence. In a cross-sectional study, we measured WMH, globally and in specific white matter tracts, and correlated them with regional brain activity measured by fMRI (combined with simultaneous urodynamic monitoring) during bladder filling and reported 'urgency'. We postulated that increase in global WMH burden would be associated with changes (either attenuation or reinforcement) in responses to bladder filling in brain regions involved in bladder control. Secondly, we proposed that such apparent effects of global WMH burden might be specifically related to the burden in a few critical white matter pathways. The results showed that regional activations (e.g. medial/superior frontal gyrus adjacent to dorsal ACG) and deactivations (e.g. perigenual ACG adjacent to ventromedial prefrontal cortex) became more prominent with increased global WMH burden, suggesting that activity aimed at suppressing urgency was augmented. Secondary analyses confirmed that the apparent effect of global WMH burden might reflect the presence of WMH in specific pathways (anterior thalamic radiation and superior longitudinal fasciculus), thus affecting connections between key regions and suggesting possible mechanisms involved in continence control. (C) 2010 Elsevier Inc. All rights reserved.

关键词： Adaptation, Psychological/physiology Aged Brain/pathology Cross-Sectional Studies Female Humans image processing, computer-assisted Magnetic Resonance Imaging Middle Aged Neural Pathways/pathology Neural Pathways/physiology Urinary Bladder/physiology Urinary Incontinence/pathology Urinary Incontinence/pathology Urodynamics/physiology

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Effect of Tamsulosin on Bladder Microcirculation in a Rat Ischemia-reperfusion Model, Evaluated by Pencil Lens Charge-coupled Device Microscopy System

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UROLOGY 2010年第5期76卷 1266.e1-1266.e5页

作者： Mizuno, Hideki Yamamoto, Tokunori Okutsu, Hiroko Ohtake, Akiyoshi Sasamata, Masao Matsukawa, Yoshihisa Funahashi, Yasuhito Kato, Masashi Hattori, Ryohei Gotoh, Momokazu Nagoya Univ Dept Urol Grad Sch Med Nagoya Aichi 4668550 Japan Astellas Pharma Inc Appl Pharmacol Res Labs Drug Discovery Res Ibaraki Japan

OBJECTIVES To investigate the effect of tamsulosin hydrochloride on bladder microcirculation in a rat ischemia-reperfusion model using a pencil lens charge-coupled device microscopy system (PLCMS). METHODS Changes in blood flow through a submucosal capillary of the rat bladder were measured during bladder filling using the PLCMS. One week after starting infusion of either physiological saline or tamsulosin, blood flow in the bladder was halted by bladder overdistention via an infusion of physiological saline. The bladder was then emptied to be reperfused with blood. Changes in blood flow through a submucosal capillary of the bladder during ischemia and reperfusion were measured using a PLCMS, and the data obtained for the control group and tamsulosin group were compared. RESULTS As the bladder was distended, the velocity of red blood cell flow in a submucosal capillary of the bladder slowed and stopped altogether when the bladder became overdistended. In the control group, capillary blood flow improved over time after release from overdistention but failed to return to the baseline level, demonstrating that reperfusion injury to bladder microcirculation was caused by bladder overdistention and emptying. In the tamsulosin group, capillary blood flow rapidly returned to baseline after release from overdistention. CONCLUSIONS Using a PLCMS, bladder microcirculation was able to be visualized and quantitatively assessed by measuring the velocity of blood flow in a submucosal capillary of the bladder. Findings from the present study suggest that tamsulosin hydrochloride exerts a protective effect on blood flow in ischemia-reperfusion injury of the bladder. UROLOGY 76: 1266. e1-1266. e5, 2010. (c) 2010 Elsevier Inc.

关键词： Adrenergic alpha-1 Receptor Antagonists/pharmacology Animals Blood Flow Velocity/drug effects Capillaries Female image processing, computer-assisted Laser-Doppler Flowmetry Microcirculation/drug effects Microscopy, Video Rats Rats, Sprague-Dawley Reperfusion Injury/physiopathology Sulfonamides/pharmacology Urinary Bladder/blood supply

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Identical, but not the same: Intra-site and inter-site reproducibility of fractional anisotropy measures on two 3.0 T scanners

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NEUROimage 2010年第4期51卷 1384-1394页

作者： Vollmar, Christian O'Muircheartaigh, Jonathan Barker, Gareth J. Symms, Mark R. Thompson, Pamela Kumari, Veena Duncan, John S. Richardson, Mark P. Koepp, Matthias J. UCL Inst Neurol Dept Clin & Expt Epilepsy Natl Soc Epilepsy MRI Unit London WC1N 3BG England Kings Coll London Inst Psychiatry Dept Clin Neurosci London SE5 8AF England

Diffusion Tensor Imaging (DTI) is being increasingly used to assess white matter integrity and it is therefore paramount to address the test-retest reliability of DTI measures. In this study we assessed inter- and intra-site reproducibility of two nominally identical 3 T scanners at different sites in nine healthy controls using a DTI protocol representative of typical current "best practice" including cardiac gating, a multichannel head coil, parallel imaging and optimized diffusion gradient parameters. We calculated coefficients of variation (CV) and intraclass correlation coefficients (ICC) of fractional anisotropy (FA) measures for the whole brain, for three regions of interest (ROI) and for three tracts derived from these ROI by probabilistic tracking. We assessed the impact of affine, nonlinear and template based methods for spatially aligning FA maps on the reproducibility. The intra-site CV for FA ranged from 0.8% to 3.0% with ICC from 0.90 to 0.99, while the inter-site CV ranged from 1.0% to 4.1% with ICC of 0.82 to 0.99. Nonlinear image coregistration improved reproducibility compared to affine coregistration. Normalization to template space reduced the between-subject variation, resulting in lower ICC values and indicating a possibly reduced sensitivity. CV from probabilistic tractography were about 50% higher than for the corresponding seed ROI. Reproducibility maps of the whole scan volume showed a low variation of less than 5% in the major white matter tracts but higher variations of 10-15% in gray matter regions. One of the two scanners showed better intra-site reproducibility, while the intra-site CV for both scanners was significantly better than inter-site CV. However, when using nonlinear coregistration of FA maps, the average inter-site CV was below 2%. There was a consistent inter-site bias, FA values on site 2 were 1.0-1.5% lower than on site 1. Correction for this bias with a global scaling factor reduced the inter-site CV to the range of intr

关键词： Adult Anisotropy Brain/anatomy & histology Brain Mapping Brain Mapping Diffusion Magnetic Resonance Imaging/instrumentation Diffusion Magnetic Resonance Imaging/statistics & numerical data Female Humans image processing, computer-assisted Male Middle Aged Neural Pathways/anatomy & histology Nonlinear Dynamics Reproducibility of Results

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Categorical Speech Representation in Human Superior Temporal Gyrus

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NEUROSURGERY 2010年第6期67卷 N19-N20页

作者： Mikell, Charles B. McKhann, Guy M.

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