Publications
151 results found
Uchiyama K, Jokitalo E, Kano F, et al., 2002, VCIP135, a novel essential factor for p97/p47-mediated membrane fusion, is required for Golgi and ER assembly in vivo, Journal of Cell Biology, Vol: 159, Pages: 855-866, ISSN: 0021-9525
NSF and p97 are ATPases required for the heterotypic fusion of transport vesicles with their target membranes and the homotypic fusion of organelles. NSF uses ATP hydrolysis to dissociate NSF/SNAPs/SNAREs complexes, separating the v- and t-SNAREs, which are then primed for subsequent rounds of fusion. In contrast, p97 does not dissociate the p97/p47/SNARE complex even in the presence of ATP. Now we have identified a novel essential factor for p97/p47-mediated membrane fusion, named VCIP135 (valosin-containing protein [VCP][p97]/p47 complex-interacting protein, p135), and show that it binds to the p97/p47/syntaxin5 complex and dissociates it via p97 catalyzed ATP hydrolysis. In living cells, VCIP135 and p47 are shown to function in Golgi and ER assembly.
Zhang X, Chaney M, Wigneshweraraj SR, et al., 2002, Mechanochemical ATPases and transcriptional activation, MOLECULAR MICROBIOLOGY, Vol: 45, Pages: 895-903, ISSN: 0950-382X
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- Citations: 136
Zhang XD, Beuron F, Freemont PS, 2002, Machinery of protein folding and unfolding, CURRENT OPINION IN STRUCTURAL BIOLOGY, Vol: 12, Pages: 231-238, ISSN: 0959-440X
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- Citations: 44
Yuan XM, Shaw A, Zhang XD, et al., 2001, Solution structure and interaction surface of the C-terminal domain from p47: A major p97-cofactor involved in SNARE disassembly, JOURNAL OF MOLECULAR BIOLOGY, Vol: 311, Pages: 255-263, ISSN: 0022-2836
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- Citations: 74
Dulic A, Bates PA, Zhang XD, et al., 2001, BRCT domain interactions in the heterodimeric DNA repair protein XRCC1-DNA ligase III, BIOCHEMISTRY, Vol: 40, Pages: 5906-5913, ISSN: 0006-2960
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- Citations: 55
Zhang XD, Shaw A, Bates PA, et al., 2000, Structure of the AAA ATPase p97, MOLECULAR CELL, Vol: 6, Pages: 1473-1484, ISSN: 1097-2765
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- Citations: 363
Huyton T, Bates PA, Zhang XD, et al., 2000, The BRCA1 C-terminal domain: structure and function, MUTATION RESEARCH-DNA REPAIR, Vol: 460, Pages: 319-332, ISSN: 0921-8777
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- Citations: 126
Zhang XD, Rosenthal PB, Formanowski F, et al., 1999, X-ray crystallographic determination of the structure of the influenza C virus haemagglutinin-esterase-fusion glycoprotein, ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, Vol: 55, Pages: 945-961, ISSN: 2059-7983
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- Citations: 11
Zhang XD, Moréra S, Bates PA, et al., 1998, Structure of an XRCC1 BRCT domain:: a new protein-protein interaction module, EMBO JOURNAL, Vol: 17, Pages: 6404-6411, ISSN: 0261-4189
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- Citations: 208
Buckley CJ, Khaleque N, Bellamy SJ, et al., 1997, Mapping the organic and inorganic components of tissue using NEXAFS, 9th International Conference on X-Ray Absorption Fine Structure, Publisher: EDITIONS PHYSIQUE, Pages: 83-90, ISSN: 1155-4339
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- Citations: 16
Buckley CJ, Khaleque N, Bellamy SJ, et al., 1997, Mapping the organic and inorganic components of tissue Using NEXAFS, Journal De Physique. IV : JP, Vol: 7, ISSN: 1155-4339
A mapping technique which uses a scanning transmission soft X-ray microscope (STXM) is described. The technique has been developed and used to quantitatively map the calcium mineral and protein mass thicknesses in undemineralised, unstained, thin bone sections. Near complete femoral-neck sections of sibling normal and ovariectomised mice have been mapped. The results show the quantitative relationship between calcium and protein on the macro and microscopic scales for both tissues.
Jacobsen C, Chapman HN, Fu J, et al., 1996, Biological microscopy and soft x-ray optics at Stony Brook, 11th International Conference on Vacuum Ultraviolet Radiation Physics (VUV-11 Conference), Publisher: ELSEVIER SCIENCE BV, Pages: 337-341, ISSN: 0368-2048
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- Citations: 7
Zhang XD, Balhorn R, Mazrimas J, et al., 1996, Measuring DNA to protein ratios in mammalian sperm head by XANES imaging, JOURNAL OF STRUCTURAL BIOLOGY, Vol: 116, Pages: 335-344, ISSN: 1047-8477
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- Citations: 107
Williams S, Jacobsen C, Kirz J, et al., 1995, Instrumentation developments in scanning soft x-ray microscopy at the NSLS (invited), Review of Scientific Instruments, Vol: 66, Pages: 1271-1275, ISSN: 0034-6748
The Scanning Transmission Soft X-ray Microscope at the NSLS has been instrumented for the following new forms of imaging: (1) XANES microscopy for the mapping of chemical constituents and for absorption spectroscopy of small specimen areas; (2) luminescence microscopy for locating visible light emitting labels at the resolution determined by the size of the x-ray microprobe; and (3) dichroism microscopy for mapping the alignment of molecules whose absorption spectra are polarization dependent. Since the instrument is used mostly for the imaging of biological and other radiation sensitive materials, a cryostage is being planned to accommodate frozen hydrated specimens. © 1995 American Institute of Physics.
Buckley CJ, Bellamy SJ, Zhang X, et al., 1995, The NEXAFS of biological calcium phosphates, Review of Scientific Instruments, Vol: 66, Pages: 1322-1324, ISSN: 0034-6748
The absorption cross section of a number of calcium salts has been assessed at the calcium L edge by measuring the total electron yield (TEY) at the NSLS U13UA beamline. TEY was used because of distortions introduced by instrumentation when using a transmission signal. The effect of these distortions has been evaluated and is presented. The TEY signal was normalized to the incident beam using the signal from a new beam monitor which is detailed here. Comparative spectra are presented for some calcium salts associated with osteoarthritis. © 1995 American Institute of Physics.
Maser JM, Chapman HN, Jacobsen CJ, et al., 1995, Scanning transmission x-ray microscope at the NSLS: from XANES to cryo, Pages: 78-89, ISSN: 0277-786X
The Stony Brook scanning transmission x-ray microscope (STXM) has been operating at the X1A beamline at the NSLS since 1989. A large number of users have used it to study biological and material science samples. We report on changes that have been performed in the past year, and present recent results. To stabilize the position of the micro probe when doing spectral scans at high spatial resolution, we have constructed a piezo-driven flexure stage which carries out the focusing motion of the zone plate needed when changing the wavelength. To overcome our detector limitation set by saturation of our gas-flow counter at count rates around 1 MHz, we are installing an avalanche photo diode with an active quenching circuit which we expect to respond linearly to count rates in excess of 10 MHz. We have improved the enclosure for STXM to improve the stability of the Helium atmosphere while taking data. This reduces fluctuations of beam absorption and, therefore, noise in the image. A fast shutter has been installed in the beam line. We are also developing a cryo- STXM which is designed for imaging frozen hydrated samples at temperatures below 120 K. At low temperatures, radiation sensitive samples can tolerate a considerably higher radiation dose than at room temperature. This should improve the resolution obtainable from biological samples and should make recording of multiple images of the same sample area possible while minimizing the effects of radiation damage. This should enable us to perform elemental and chemical mapping at high resolution, and to record the large number of views needed for 3D reconstruction of the object.
JACOBSEN C, CHAPMAN H, KIRZ J, et al., 1995, CELL BIOLOGY APPLICATIONS OF A SCANNING-TRANSMISSION X-RAY MICROSCOPE, MOLECULAR BIOLOGY OF THE CELL, Vol: 6, Pages: 660-660, ISSN: 1059-1524
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- Citations: 3
ZHANG X, JACOBSEN C, LINDAAS S, et al., 1995, EXPOSURE STRATEGIES FOR POLYMETHYL METHACRYLATE FROM IN-SITU X-RAY-ABSORPTION NEAR-EDGE STRUCTURE SPECTROSCOPY, JOURNAL OF VACUUM SCIENCE & TECHNOLOGY B, Vol: 13, Pages: 1477-1483, ISSN: 1071-1023
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- Citations: 64
Williams S, Jacobsen C, Kirz J, et al., 1994, Metaphase chromosome DNA mass fraction is independent of species, Pages: 46-47
Metaphase chromosome DNA mass fraction from the broad bean Vicia faba has been measured in the study. The result indicates that the DNA mass faction value obtained is not a property of the preparation procedure. Since dry specimens are not subject to mass loss at these exposure levels, the mass results for both the wet and dry specimens is not an artifact caused by radiation damage. Metaphase chromosomes from other species have similar DNA mass fractions although the sizes, shapes and densities of the chromosomes are very different. The results suggest that, at some level, the method for packing chromatin within metaphase chromosomes is conserved.
Zhang X, Balhorn R, Jacobsen C, et al., 1994, Mapping DNA and protein in biological samples using the scanning transmission x-ray microscope, Pages: 50-51
The Scanning Transmission soft X-ray Microscope (STXM) at the X1A beamline at the National Synchrotron Light Source, Brookhaven National Library has been used to image wet biological samples using the natural absorption differences between carbon and water in the water window. The step-like jumps in the absorption of soft x-rays by materials as a function of energy have been used for elemental mapping. The paper examines the x-ray absorption fine structure spectra at the carbon absorption edge from DNA and bovine serum albumin taken using the STXM. Differences between the spectra of these two biologically important molecules can be used to distinguish DNA and proteins.
ZHANG X, ADE H, JACOBSEN C, et al., 1994, MICRO-XANES - CHEMICAL CONTRAST IN THE SCANNING-TRANSMISSION X-RAY MICROSCOPE, 8th National Conference on Synchrotron Radiation Instrumentation, Publisher: ELSEVIER SCIENCE BV, Pages: 431-435, ISSN: 0168-9002
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- Citations: 49
KIRZ J, ADE H, ANDERSON E, et al., 1994, NEW RESULTS IN SOFT-X-RAY MICROSCOPY, 16th International Conference on X-ray and Inner-Shell Process (X 93), Publisher: ELSEVIER SCIENCE BV, Pages: 92-97, ISSN: 0168-583X
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- Citations: 21
Zhang X, Ade H, Jacobsen C, et al., 1993, Chemical contrast in scanning transmission x-ray microscope, Pages: 648-649, ISSN: 0424-8201
Different wet, unstained biological samples were imaged at 55 nm spatial resolution by the use of scanning transmission X-ray microscope (STXM). The microscope has measured the modulation transfer function which agrees well with theoretical calculations. The chemical composition of the sample is localized by x-ray energy variation in which the beam is focused to one spot. Another technique is X-ray absorption near edge structure which is chemically sensitive thereby acting as a contrast mechanism for organic system imaging. Due to its sensitivity, it can be easily applied for chemical reaction investigations.
JACOBSEN C, LINDAAS S, WILLIAMS S, et al., 1993, SCANNING LUMINESCENCE X-RAY MICROSCOPY - IMAGING FLUORESCENCE DYES AT SUBOPTICAL RESOLUTION, JOURNAL OF MICROSCOPY-OXFORD, Vol: 172, Pages: 121-129, ISSN: 0022-2720
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- Citations: 35
WILLIAMS S, ZHANG X, JACOBSEN C, et al., 1993, MEASUREMENTS OF WET METAPHASE CHROMOSOMES IN THE SCANNING-TRANSMISSION X-RAY MICROSCOPE, JOURNAL OF MICROSCOPY-OXFORD, Vol: 170, Pages: 155-165, ISSN: 0022-2720
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- Citations: 72
Zhang X, Jacobsen CJ, Williams SP, 1993, Image enhancement through deconvolution, Pages: 251-259, ISSN: 0277-786X
Several groups have been developing x-ray microscopes for studies of biological and materials specimens at suboptical resolution. The X1A scanning transmission x-ray microscope at Brookhaven National Laboratory has achieved 55 nm Rayleigh resolution, and is limited by the 45 nm finest zone width of the zone plate used to focus the x rays. In principle, features as small as half the outermost zone width, or 23 nm, can be observed in the microscope, though with reduced contrast in the image. One approach to recover the object from the image is to deconvolve the image with the point spread function (PSF) of the optic system. Toward this end, the magnitude of the Fourier transform of the PSF, the modulation transfer function, has been experimentally determined and agrees reasonably well with the calculations using the known parameters of the microscope. To minimize artifacts in the deconvolved images, large signal to noise ratios are required in the original image, and high frequency filters can be used to reduce the noise at the expense of resolution. In this way we are able to recover the original contrast of high resolution features in our images.
Jacobsen CJ, Lindaas S, Oehler V, et al., 1993, Experiments in scanning luminescence x-ray microscopy, Pages: 223-231, ISSN: 0277-786X
Scanning luminescence x-ray microscopy is based on collecting visible light emission from a sample region illuminated by an x-ray microprobe. We have tested the resolution of the method using P31 phosphor grains, and have obtained luminescence images of dye-labelled polystyrene spheres and sodium salicylate crystals. However, we have observed no light emission from the dyes DAPI, ethidium bromide, Hoecst 33258, and rhodamine phalloidon. Present efforts are aimed at improving our understanding of the luminescence process so as to find appropriate dyes for imaging dye-labelled biological specimens.
Williams SP, Jacobsen CJ, Kirz J, et al., 1993, Radiation damage to chromosomes in the scanning transmission x-ray microscope, Pages: 318-324, ISSN: 0277-786X
Imaging with soft x rays having energies between the carbon and oxygen K edge (284 - 531 eV) yields large absorption contrast for wet organic specimens, but these soft x rays are known to be very effective in damaging biological specimens. The commonly used criterion of mass loss was employed for assessing radiation damage in the scanning transmission x-ray microscope. Multiple images of freeze-dried V. faba chromosomes show no significant mass loss after 150 Mrad. Experiments performed on fixed hydrated chromosomes revealed them to be radiation sensitive. The greater total mass loss observed in multiple low dose images compared to that incurred during a single high dose image suggests that the effects of radiation damage occur slower than the acquisition time for neighboring pixels. The radiation sensitivity of chromosomes depends critically on the fixative used, with damage minimized in glutaraldehyde fixed samples. Radiation damage to chromosomes is independent of ionic strength above 65 mM, but increases for ionic strengths below 65 mM. Using free radical scavengers in the buffer, and changing the design of the sample cell reduced the amount of damage incurred as a function of dose.
ADE H, ZHANG X, CAMERON S, et al., 1992, CHEMICAL CONTRAST IN X-RAY MICROSCOPY AND SPATIALLY RESOLVED XANES SPECTROSCOPY OF ORGANIC SPECIMENS, SCIENCE, Vol: 258, Pages: 972-975, ISSN: 0036-8075
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- Citations: 303
KIRZ J, ADE H, JACOBSEN C, et al., 1992, SOFT-X-RAY MICROSCOPY WITH COHERENT X-RAYS, 4TH INTERNATIONAL CONF ON SYNCHROTRON RADIATION INSTRUMENTATION, Publisher: AMER INST PHYSICS, Pages: 557-563, ISSN: 0034-6748
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- Citations: 41
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