Brookhaven National Laboratory (brookhaven + national_laboratory)

Distribution by Scientific Domains


Selected Abstracts


Atomic force microscopic analysis of hydrogen peroxide bleached kraft northern black spruce fibres

JOURNAL OF MICROSCOPY, Issue 2 2005
M. A. POGGI
Summary Hydrogen peroxide is a potent, relatively inexpensive oxidant that chemically degrades chromophoric components in pulps and textiles. Oxidation of cellulose is a byproduct of this process step that decreases the tensile strength of individual fibres. The residence time of pulp in the bleaching reactor must be optimized to achieve the desired brightness and minimizing fibre degradation. To evaluate the impact of peroxide bleaching at the microfibrillar level, a single black spruce tree was chosen and kraft pulped. Peroxide bleaching was conducted via benchtop polyethylene bag bleaching in a temperature-controlled waterbath. Atomic force microscopy (AFM) topographical images acquired before and after the bleaching step show dramatic changes in fibre structure consistent with delignification and defects in the surface topography. This was further verified by X-ray work at Brookhaven National Laboratory, NY, U.S.A. [source]


The Beamline X28C of the Center for Synchrotron Biosciences: a National Resource for Biomolecular Structure and Dynamics Experiments Using Synchrotron Footprinting

JOURNAL OF SYNCHROTRON RADIATION, Issue 3 2007
Sayan Gupta
Structural mapping of proteins and nucleic acids with high resolution in solution is of critical importance for understanding their biological function. A wide range of footprinting technologies have been developed over the last ten years to address this need. Beamline X28C, a white-beam X-ray source at the National Synchrotron Light Source of Brookhaven National Laboratory, functions as a platform for synchrotron footprinting research and further technology development in this growing field. An expanding set of user groups utilize this national resource funded by the National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health. The facility is operated by the Center for Synchrotron Biosciences and the Center for Proteomics of Case Western Reserve University. The facility includes instrumentation suitable for conducting both steady-state and millisecond time-resolved footprinting experiments based on the production of hydroxyl radicals by X-rays. Footprinting studies of nucleic acids are routinely conducted with X-ray exposures of tens of milliseconds, which include studies of nucleic acid folding and their interactions with proteins. This technology can also be used to study protein structure and dynamics in solution as well as protein,protein interactions in large macromolecular complexes. This article provides an overview of the X28C beamline technology and defines protocols for its adoption at other synchrotron facilities. Lastly, several examples of published results provide illustrations of the kinds of experiments likely to be successful using these approaches. [source]


Center for Synchrotron Bioşsciences' U2B beamline: an international resource for biological infrared spectroscopy

JOURNAL OF SYNCHROTRON RADIATION, Issue 4 2002
N. S. Marinkovic
A synchrotron infrared (IR) beamline, U2B, dedicated to the biomedical and biological sciences has been constructed and is in operation at the National Synchrotron Light Source (NSLS) of Brookhaven National Laboratory. The facility is operated by the Center for Synchrotron Biosciences of the Albert Einstein College of Medicine in cooperation with the NSLS. Owing to the broadband nature of the synchrotron beam with brightness 1000 times that of conventional sources, Fourier transform IR spectroscopy experiments are feasible on diffraction-limited sample areas at high signal-to-noise ratios and with relatively short data-acquisition times. A number of synchrotron IR microscopy experiments that have been performed in the mid-IR spectral range (500,5000,cm,1) are summarized, including time-resolved protein-folding studies in the microsecond time regime, IR imaging of neurons, bone and other biological tissues, as well as imaging of samples of interest in the chemical and environmental sciences. Owing to the high flux output of this beamline in the far-IR region (50,500,cm,1), investigations of hydrogen bonding and dynamic molecular motions of biomolecules have been carried out from 10 to 300,K using a custom-made cryostat and an evacuated box. This facility is intended as an international resource for biological IR spectroscopy fully available to outside users based on competitive proposal. [source]


THE HISTORY OF THE BROOKHAVEN NATIONAL LABORATORY PROJECT IN ARCHAEOLOGICAL CHEMISTRY, AND APPLYING NUCLEAR METHODS TO THE FINE ARTS

ARCHAEOMETRY, Issue 2 2007
G. HARBOTTLE
This paper traces the events leading up to the formation of a project in 1954, in the Chemistry Department at Brookhaven National Laboratory, dedicated to the application of those new developments that were rapidly transforming postwar nuclear science to the parallel humanistic disciplines of archaeology and the fine arts. The further evolution of this effort involved the enlightened support of the Department of Energy (then AEC and ERDA) coupled with the lively interests of the archaeological, fine-arts and art-historical communities, their professional academics and the many graduate and undergraduate students who participated in the Brookhaven project. But more than new scientific methodologies, concepts and instrumentation were deployed. What developed was a large-scale, truly interdisciplinary effort, where scholars of the humanities and sciences worked side by side in a remarkable way, each led by the other, to the mutual benefit and increase of their knowledge and understanding. A paradigm of co-operation between arts and sciences was initiated: this paper presents a record of the process and its outcome, a novel blending of science and humanism that is very much taken for granted by research workers today. [source]


Crystallization and preliminary X-ray analysis of Borrelia burgdorferi outer surface protein C (OspC)

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2001
D. Kumaran
Single crystals of the outer surface protein C (OspC) from Borrelia burgdorferi HB19 have been obtained by the vapor-diffusion method. These crystals belong to space group P21, with unit-cell parameters a = 66.218, b = 46.113, c = 112.079,┼, , = 99.30░, and diffract to at least 2.2,┼ resolution. Native data have been collected from flash-frozen crystals at the National Synchrotron facility of Brookhaven National Laboratory. There are two dimers per asymmetric unit, related by a non-crystallographic twofold axis and a pseudo-translational symmetry. [source]


Crystallization and preliminary X-ray analysis of Clostridium botulinum neurotoxin type B

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2000
S. Swaminathan
Single crystals of Clostridium botulinum neurotoxin type B have been obtained by the vapor-diffusion method. These crystals belong to space group P21, with unit-cell parameters a = 76.08, b = 123.11, c = 95.86,┼, , = 113.03░ and diffract to at least 1.8,┼ resolution. Native data have been collected from flash-frozen crystals at the National Synchrotron facility of Brookhaven National Laboratory. These crystals often tend to be non-isomorphic. [source]


Molecular chemical structure of barley proteins revealed by ultra-spatially resolved synchrotron light sourced FTIR microspectroscopy: Comparison of barley varieties

BIOPOLYMERS, Issue 4 2007
Peiqiang Yu
Abstract Barley protein structure affects the barley quality, fermentation, and degradation behavior in both humans and animals among other factors such as protein matrix. Publications show various biological differences among barley varieties such as Valier and Harrington, which have significantly different degradation behaviors. The objectives of this study were to reveal the molecular structure of barley protein, comparing various varieties (Dolly, Valier, Harrington, LP955, AC Metcalfe, and Sisler), and quantify protein structure profiles using Gaussian and Lorentzian methods of multi-component peak modeling by using the ultra-spatially resolved synchrotron light sourced Fourier transform infrared microspectroscopy (SFTIRM). The items of the protein molecular structure revealed included protein structure ,-helices, ,-sheets, and others such as ,-turns and random coils. The experiment was performed at the National Synchrotron Light Source in Brookhaven National Laboratory (BNL, US Department of Energy, NY). The results showed that with the SFTIRM, the molecular structure of barley protein could be revealed. Barley protein structures exhibited significant differences among the varieties in terms of proportion and ratio of model-fitted ,-helices, ,-sheets, and others. By using multi-component peaks modeling at protein amide I region of 1710,1576 cm,1, the results show that barley protein consisted of approximately 18,34% of ,-helices, 14,25% of ,-sheets, and 44,69% others. AC Metcalfe, Sisler, and LP955 consisted of higher (P < 0.05) proportions of ,-helices (30,34%) than Dolly and Valier (,-helices 18,23%). Harrington was in between which was 25%. For protein ,-sheets, AC Metcalfe, and LP955 consisted of higher proportions (22,25%) than Dolly and Valier (13,17%). Different barley varieties contained different ,-helix to ,-sheet ratios, ranging from 1.4 to 2.0, although the difference were insignificant (P > 0.05). The ratio of ,-helices to others (0.3 to 1.0, P < 0.05) and that of ,-sheets to others (0.2 to 0.8, P < 0.05) were different among the barley varieties. It needs to be pointed out that using a multi-peak modeling for protein structure analysis is only for making relative estimates and not exact determinations and only for the comparison purpose between varieties. The principal component analysis showed that protein amide I Fourier self-deconvolution spectra were different among the barley varieties, indicating that protein internal molecular structure differed. The above results demonstrate the potential of the SFTIRM to localize relatively pure protein areas in barley tissues and reveal protein molecular structure. The results indicated relative differences in protein structures among the barley varieties, which may partly explain the biological differences among the barley varieties. Further study is needed to understand the relationship between barley molecular chemical structure and biological features in terms of nutrient availability and digestive behavior. ę 2006 Wiley Periodicals, Inc. Biopolymers 85:308,317, 2007. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source]


Expression, purification, crystallization and preliminary X-ray analysis of Pseudomonas fluorescens AlgK

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2007
Carrie-Lynn Keiski
AlgK is an outer-membrane lipoprotein involved in the biosynthesis of alginate in Pseudomonads and Azotobacter vinelandii. A recombinant form of Pseudomonas fluorescens AlgK with a C-terminal polyhistidine affinity tag has been expressed and purified from the periplasm of Escherichia coli cells and diffraction-quality crystals of AlgK have been grown using the hanging-drop vapour-diffusion method. The crystals grow as flat plates with unit-cell parameters a = 79.09, b = 107.85, c = 119.15,┼, , = 96.97░. The crystals exhibit the symmetry of space group P21 and diffract to a minimum d -spacing of 2.5,┼ at Station X29 of the National Synchrotron Light Source, Brookhaven National Laboratory. On the basis of the Matthews coefficient (VM = 2.53,┼3,Da,1), four protein molecules are estimated to be present in the asymmetric unit. [source]


Expression, purification, crystallization and preliminary X-ray crystallographic studies of a novel acetylcitrulline deacetylase from Xanthomonas campestris

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2005
Dashuang Shi
A novel N -acetyl- l -citrulline deacetylase that is able to catalyze the hydrolysis of N -acetyl- l -citrulline to acetate and citrulline was identified from Xanthomonas campestris. The protein was overexpressed, purified and crystallized. The crystals belong to the monoclinic space group C2 and diffract to 1.75,┼ resolution, with unit-cell parameters a = 94.13, b = 95.23, c = 43.61,┼, , = 93.76░. Since attempts to use homologous structural models to solve the structure via molecular replacement were unsuccessful, the selenomethionine-substituted protein was prepared using an overnight auto-induction overexpression system. Selenomethionine incorporation into the protein was verified by MALDI,TOF/TOF mass-spectroscopic analysis after trypsin digestion. The crystals of the selenomethionine-substituted protein were prepared using crystallization conditions similar to those for the native protein. Multiple anomalous dispersion (MAD) data were collected at Brookhaven National Laboratory. Structure determination is under way using the MAD phasing method. [source]