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Kneipp J, Miller LM, Spassov S, Sokolowski F, Lasch P, Beekes M, Naumann D. Scrapie-infected cells, isolated prions, and recombinant prion protein: a comparative study. Biopolymers 2004; 74:163-7. [PMID: 15137116 DOI: 10.1002/bip.20064] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Fourier -transform infrared microscopic spectra of scrapie-infected nervous tissue measured at high spatial resolution (approximately 6 microm) were compared with those obtained from the purified, partly proteinase K digested scrapie isoform of the prion protein isolated from nervous tissue of hamsters infected with the same scrapie strain (263K) to elucidate similarities/dissimilarities between prion structure investigated in situ and ex vivo. A further comparison is drawn to the recombinant Syrian hamster prion protein SHaPrP(90-232) after in vitro conformational transition from the predominantly alpha-helical isoform to beta-sheet-rich structures. It is shown that prion protein structure can be investigated within tissue and that detectability of regions with elevated beta-sheet content as observed in microspectra of prion-infected tissue strongly depends on spatial resolution of the experiment.
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Dumas P, Jamin N, Teillaud JL, Miller LM, Beccard B. Imaging capabilities of synchrotron infrared microspectroscopy. Faraday Discuss 2004; 126:289-302; discussion 303-11. [PMID: 14992414 DOI: 10.1039/b305065c] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It has become increasingly clear that synchrotron infrared micro-spectroscopy is an extremely valuable analysis tool when determining the chemical composition of biological and biomedical samples, at the diffraction-limited spatial resolution. Highly resolved infrared micro-spectroscopy, together with the high signal-to-noise level of the recorded spectra, is essential in generating chemical and statistical (multivariate) images. This is illustrated in the case of individual cell and hair section studies. Unprecedented chemical images of lipid distribution and secondary structure relative concentration have been achieved using the synchrotron source. A comparison with a Focal plane Array imaging system, on the same hair section, shows that, despite the fast imaging processing and improved quality achieved with the focal plane array detectors, spectral quality is markedly superior in the case of the synchrotron source. It is clear that the two approaches could be very complementary if combined on the same sample area, in a synchrotron facility.
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Miller LM, Smith GD, Carr GL. Synchrotron-based Biological Microspectroscopy: From the Mid-Infrared through the Far-Infrared Regimes. J Biol Phys 2003; 29:219-30. [PMID: 23345838 PMCID: PMC3456407 DOI: 10.1023/a:1024401027599] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Infrared radiation from synchrotron storagerings serves as a high-brightness source fordiffraction-limited microspectroscopy inboth the mid- and far-infrared spectralranges. Mid-infrared absorption, due to localvibrational modes within complex molecules,is shown to be sensitive to small chemicalchanges associated with certain diseases.Farinfrared modes are believed to result from thefolding or twisting of larger, morecomplex molecules. The ability for thesynchrotron source to perform microscopy ata frequency of 1 THz is demonstrated.
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Marinkovic NS, Huang R, Bromberg P, Sullivan M, Toomey J, Miller LM, Sperber E, Moshe S, Jones KW, Chouparova E, Lappi S, Franzen S, Chance MR. Center for Synchrotron Biosciences' U2B beamline: an international resource for biological infrared spectroscopy. JOURNAL OF SYNCHROTRON RADIATION 2002; 9:189-197. [PMID: 12091724 DOI: 10.1107/s0909049502008543] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2002] [Accepted: 05/09/2002] [Indexed: 05/23/2023]
Abstract
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.
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Huang RY, Miller LM, Carlson CS, Chance MR. Characterization of bone mineral composition in the proximal tibia of cynomolgus monkeys: effect of ovariectomy and nandrolone decanoate treatment. Bone 2002; 30:492-7. [PMID: 11882463 DOI: 10.1016/s8756-3282(01)00691-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Life postmenopausal women, ovariectomized cynomolgus monkeys (Macaca fascicularis) experience accelerated loss of bone mass. Treatment of ovariectomized monkeys with nandrolone decanoate results in an increase in bone mass to levels comparable to those of intact animals. The changes in bone composition that occur with these treatments, however, are less well characterized. In the present study, we used synchrotron Fourier-transform infrared microspectroscopy (FT-IRM) and curve-fitting methods to monitor specific changes at cortical, subchondral, and trabecular bone regions in the proximal tibia. Four groups were studied: (1) sham-operated (sham); (2) ovariectomized and treated with placebo for 2 years (ovx); (3) ovx + nandrolone decanoate for 2 years (NAN); and (4) ovx + nandrolone decanoate beginning 1 year after ovx (dNAN). The results demonstrate that ovariectomy and nandrolone treatment did not affect the degree of mineralization as defined by the phosphate/protein ratio, but acid phosphate content (HPO(4)(2-)) in cortical and subchondral bone was increased by ovariectomy, suggesting this bone to be less mature due to increased remodeling that occurs after ovariectomy. In the subchondral and cortical bone regions, ovariectomized monkeys showed a lower total carbonate content (CO(3)(2-)/matrix ratio) than sham controls, specifically due to the decrease in labile carbonate content. In the trabecular region, no change of carbonate content was observed. Treatment with nandrolone decanoate was found to restore the loss in carbonate, where the resulting mineral had a larger quantity of type B carbonate. Finally, we correlated carbonate content with dual-energy X-ray absorptiometry measurements, and found a positive correlation between bone mineral density and type A carbonate in bone, which is stoichiometrically related to the amount of calcium in bone. Therefore, the results presented herein identify significant differences in bone chemistry after ovariectomy and nandrolone treatment, which may help explain previous findings that, although nandrolone decanoate treatment increased bone mass, it could not reverse the decrease in bone strength due to ovariectomy.
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Paszek AA, Wilkie PJ, Flickinger GH, Miller LM, Louis CF, Rohrer GA, Alexander LJ, Beattie CW, Schook LB. Interval mapping of carcass and meat quality traits in a divergent swine cross. Anim Biotechnol 2001; 12:155-65. [PMID: 11808631 DOI: 10.1081/abio-100108342] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
An autosomal scan of the swine genome with 119 polymorphic microsatellite (ms) markers and data from 116 F2 barrows of the University of Illinois Meishan x Yorkshire Swine Resource Families identified genomic regions with effects on variance in carcass composition and meat quality at nominal significance (p-value <0.05). Marker intervals on chromosomes 1, 6, 7, 8 and 12 (SSC1, SSC6, SSC7, SSC8, SSC12) with phenotypic effects on carcass length, 10th rib backfat thickness, average backfat thickness, leaf fat, loin eye area and intramuscular fat content confirm QTL effects identified previously based on genome wide significance (p-value <0.05). Several marker intervals included nominally significant (p-value <0.05) dominance effects on leaf fat, 10th rib backfat thickness, loin eye area, muscle pH and intramuscular fat content.
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Miller LM, Escabí MA, Schreiner CE. Feature selectivity and interneuronal cooperation in the thalamocortical system. J Neurosci 2001; 21:8136-44. [PMID: 11588186 PMCID: PMC6763836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2001] [Revised: 07/19/2001] [Accepted: 07/20/2001] [Indexed: 02/21/2023] Open
Abstract
Action potentials are a universal currency for fast information transfer in the nervous system, yet few studies address how some spikes carry more information than others. We focused on the transformation of sensory representations in the lemniscal (high-fidelity) auditory thalamocortical network. While stimulating with a complex sound, we recorded simultaneously from functionally connected cell pairs in the ventral medial geniculate body and primary auditory cortex. Thalamic action potentials that immediately preceded or potentially caused a cortical spike were more selective than the average thalamic spike for spectrotemporal stimulus features. This net improvement of thalamic signaling indicates that for some thalamic cells, spikes are not propagated through cortex independently but interact with other inputs onto the same target cell. We then developed a method to identify the spectrotemporal nature of these interactions and found that they could be cooperative or antagonistic to the average receptive field of the thalamic cell. The degree of cooperativity with the thalamic cell determined the increase in feature selectivity for potentially causal thalamic spikes. We therefore show how some thalamic spikes carry more receptive field information than average and how other inputs cooperate to constrain the information communicated through a cortical cell.
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Miller LM, Escabí MA, Read HL, Schreiner CE. Functional convergence of response properties in the auditory thalamocortical system. Neuron 2001; 32:151-60. [PMID: 11604146 DOI: 10.1016/s0896-6273(01)00445-7] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
One of the brain's fundamental tasks is to construct and transform representations of an animal's environment, yet few studies describe how individual neurons accomplish this. Our results from correlated pairs in the auditory thalamocortical system show that cortical excitatory receptive field regions can be directly inherited from thalamus, constructed from smaller inputs, and assembled by the cooperative activity of neuronal ensembles. The prevalence of functional thalamocortical connectivity is strictly governed by tonotopy, but connection strength is not. Finally, spectral and temporal modulation preferences in cortex may differ dramatically from the thalamic input. Our observations reveal a radical reconstruction of response properties from auditory thalamus to cortex, and illustrate how some properties are propagated with great fidelity while others are significantly transformed or generated intracortically.
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Tetenbaum J, Miller LM. A new spectroscopic approach to examining the role of disulfide bonds in the structure and unfolding of soybean trypsin inhibitor. Biochemistry 2001; 40:12215-9. [PMID: 11580297 DOI: 10.1021/bi010796u] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although it is well-known that disulfide bonds stabilize the secondary structure of many proteins, it is difficult to directly probe both disulfide bond formation/breakage and the resulting secondary structural changes during the course of the protein folding/unfolding process. In this work, we have used a new, real-time spectroscopic approach to examine how the reduction of two disulfide bonds affects the secondary structure of soybean trypsin inhibitor (STI). The disulfide bonds are reduced with tris(2-carboxyethyl)phosphine (TCEP) at 40 degrees C, and the reduction process is probed in real-time using sulfur X-ray absorption spectroscopy. Circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopies are used concurrently to determine the structural changes caused by reduction of the disulfide bonds. Results demonstrate a noncooperative reduction of the two disulfide bonds within 5 min, likely because they are located on the surface of the protein. The unfolding of STI lags behind; dramatic changes are not observed until 60-90 min after the reduction was initiated. The CD and FTIR spectra indicate a decrease in the amount of extended (hydrated) coil, suggesting that the STI structure slowly collapses after the disulfide bonds are reduced. Thus, although the disulfide bonds are not located near the active site of STI, they play a crucial role in stabilizing the protein structure, which is necessary to sustain enzymatic activity.
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Meng F, Cargile BJ, Miller LM, Forbes AJ, Johnson JR, Kelleher NL. Informatics and multiplexing of intact protein identification in bacteria and the archaea. Nat Biotechnol 2001; 19:952-7. [PMID: 11581661 DOI: 10.1038/nbt1001-952] [Citation(s) in RCA: 181] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Although direct fragmentation of protein ions in a mass spectrometer is far more efficient than exhaustive mapping of 1-3 kDa peptides for complete characterization of primary structures predicted from sequenced genomes, the development of this approach is still in its infancy. Here we describe a statistical model (good to within approximately 5%) that shows that the database search specificity of this method requires only three of four fragment ions to match (at +/-0.1 Da) for a 99.8% probability of being correct in a database of 5,000 protein forms. Software developed for automated processing of protein ion fragmentation data and for probability-based retrieval of whole proteins is illustrated by identification of 18 archaeal and bacterial proteins with simultaneous mass-spectrometric (MS) mapping of their entire primary structures. Dissociation of two or three proteins at once for such identifications in parallel is also demonstrated, along with retention and exact localization of a phosphorylated serine residue through the fragmentation process. These conceptual and technical advances should assist future processing of whole proteins in a higher throughput format for more robust detection of co- and post-translational modifications.
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Miller LM, Vairavamurthy V, Chance MR, Mendelsohn R, Paschalis EP, Betts F, Boskey AL. In situ analysis of mineral content and crystallinity in bone using infrared micro-spectroscopy of the nu(4) PO(4)(3-) vibration. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1527:11-9. [PMID: 11420138 DOI: 10.1016/s0304-4165(01)00093-9] [Citation(s) in RCA: 179] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Measurements of bone mineral content and composition in situ provide insight into the chemistry of bone mineral deposition. Infrared (IR) micro-spectroscopy is well suited for this purpose. To date, IR microscopic (including imaging) analyses of bone apatite have centered on the nu(1),nu(3) PO(4)(3-) contour. The nu(4) PO(4)(3-) contour (500-650 cm(-1)), which has been extensively used to monitor the crystallinity of hydroxyapatite in homogenized bone samples, falls in a frequency region below the cutoff of the mercury-cadmium-telluride detectors used in commercial IR microscopes, thereby rendering this vibration inaccessible for imaging studies. The current study reports the first IR micro-spectroscopy spectra of human iliac crest cross sections in the nu(4) PO(4)(3-) spectral regions, obtained with a synchrotron radiation source and a Cu-doped Ge detector coupled to an IR microscope. The acid phosphate (HPO(4)(2-)) content and mineral crystallite perfection (crystallinity) of a human osteon were mapped. To develop spectra-structure correlations, a combination of X-ray powder diffraction data and conventional Fourier transform IR spectra have been obtained from a series of synthetic hydroxyapatite crystals and natural bone powders of various species and ages. X-ray powder diffraction data demonstrate that there is an increase in average crystal size as bone matures, which correlates with an increase in the nu(4) PO(4)(3-) FTIR absorption peak ratio of two peaks (603/563 cm(-1)) within the nu(4) PO(4)(3-) contour. Additionally, the IR results reveal that a band near 540 cm(-1) may be assigned to acid phosphate. This band is present at high concentrations in new bone, and decreases as bone matures. Correlation of the nu(4) PO(4)(3-) contour with the nu(2) CO (3)(2-) contour also reveals that when acid phosphate content is high, type A carbonate content (i.e., carbonate occupying OH(-) sites in the hydroxyapatite lattice) is high. As crystallinity increases and acid phosphate content decreases, carbonate substitution shifts toward occupation of PO(4)(3-) sites in the hydroxyapatite lattice. Thus, IR microscopic analysis of the nu(4) PO(4)(3-) contour provides a straightforward index of both relative mineral crystallinity and acid phosphate concentration that can be applied to in situ IR micro-spectroscopic analysis of bone samples, which are of interest for understanding the chemical mechanisms of bone deposition in normal and pathological states.
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Foster WM, Walters DM, Longphre M, Macri K, Miller LM. Methodology for the measurement of mucociliary function in the mouse by scintigraphy. J Appl Physiol (1985) 2001; 90:1111-7. [PMID: 11181627 DOI: 10.1152/jappl.2001.90.3.1111] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The objective of the study was to develop a scintigraphic method for measurement of airway mucociliary clearance in small laboratory rodents such as the mouse. Previous investigations have characterized the secretory cell types present in the mouse airway, but analysis of the mucus transport system has been limited to in vitro examination of tissue explants or invasive in vivo measures of a single airway, the trachea. Three methods were used to deposit insoluble, radioisotopic colloidal particles: oropharyngeal aspiration, intratracheal instillation, and nose-only aerosol inhalation. The initial distribution of particles within the lower respiratory tract was visualized by gamma-camera, and clearance of particles was followed intermittently over 6 h and at the conclusion, 24 h postdelivery. Subsets of mice underwent lavage for evidence of tissue inflammation, and others were restudied for reproducibility of the methods. The aspiration and instillation methods of delivery led to greater distributions of deposited activity within the lungs, i.e., approximately 60--80% of the total respiratory tract radioactivity, whereas the nose-only aerosol technique attained a distribution of 32% to the lungs. However, the aerosol technique maximized the fraction of particles that cleared the airway over a 24-h period, i.e, deposited onto airway epithelial surfaces and cleared by mucociliary function such that lung retention at 24 h averaged 57% for delivery by aerosol inhalation and > or =80% for the aspiration or intratracheal instillation techniques. Particle delivery methods did not cause lung inflammation/injury with use of inflammatory cells and chemoattractant cytokines as criteria. Scintigraphy can discern particle deposition and clearance from the lower respiratory tract in the mouse, is noninvasive and reproducible, and includes the capability for restudy and lung lavage when time course or chronic treatments are being considered.
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O'Connor DT, Tyrell EA, Kailasam MT, Miller LM, Martinez JA, Henry RR, Parmer RJ, Gabbai FB. Early alteration in glomerular reserve in humans at genetic risk of essential hypertension: mechanisms and consequences. Hypertension 2001; 37:898-906. [PMID: 11244015 DOI: 10.1161/01.hyp.37.3.898] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Essential hypertension has a familial predisposition, but the phenotype of elevated blood pressure has delayed penetrance. Because the kidney is a crucial determinant of blood pressure homeostasis, we studied early glomerular alterations in still-normotensive young subjects at genetic risk of hypertension. Thirty-nine normotensive adults (mean age 29 to 31 years), stratified by genetic risk (parental family history [FH]) of hypertension (26 with positive FH [FH+], 13 with negative FH [FH-]), underwent intravenous infusion of mixed amino acids. Before and during amino acid administration, we measured glomerular filtration rate (GFR), putative second messengers of amino acids (nitric oxide [NO.] metabolites and cGMP), serum insulin and amino acid concentrations, and the FE(Li)+ as an index of renal proximal tubular reabsorption. The FH+ group had a blunted GFR rise in response to amino acids (2.43+/-8.16% versus 31.0+/-13.4% rise, P:=0.0126). The amino acid-induced change in GFR correlated (r=0.786, P:<0.01) with the change in urinary NO. metabolite excretion; a diminished rise in urinary NO. metabolite excretion in the FH+ group (P:=0.0105) suggested a biochemical mechanism for the different GFR responses between FH groups: a relative inability to convert arginine to NO. The FH+ group had a far lower initial cGMP excretion at baseline (261+/-21.1 versus 579+/-84.9 nmol. h(-1)/1.73 m(2), P:=0.001), although cGMP did not change during the amino acid infusion (P:=0.703). FH status, baseline GFR, and baseline serum insulin jointly predicted GFR response to amino acids (P:=0.0013), accounting for approximately 45% of the variance in GFR response. Decline in FE(Li)+, an inverse index of proximal tubular reabsorption, paralleled increase in GFR (r=-0.506, P:=0.01), suggesting differences in proximal tubular reabsorption during amino acids between the FH groups. GFR response to amino acid infusion was blunted in the FH+ group despite significantly higher serum concentrations of 6 amino acids (arginine, isoleucine, leucine, methionine, phenylalanine, and valine) in the FH+ group, suggesting a novel form of insulin resistance (to the amino acid-translocating action of insulin) in FH+ subjects. We conclude that blunted glomerular filtration reserve in response to amino acids is an early-penetrance phenotype seen even in still-normotensive subjects at genetic risk of hypertension and is linked to impaired formation of NO. in the kidney. Corresponding changes in GFR and fractional excretion of Li(+) suggest that altered proximal tubular reabsorption after amino acids is an early pathophysiologic mechanism. Resistance to the amino acid-translocating actions of insulin may play a role in the biological response to amino acids in this setting. This glomerular reserve phenotype may be useful in genetic studies of renal traits preceding or predisposing to hypertension.
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Chen X, Shao Z, Marinkovic NS, Miller LM, Zhou P, Chance MR. Conformation transition kinetics of regenerated Bombyx mori silk fibroin membrane monitored by time-resolved FTIR spectroscopy. Biophys Chem 2001; 89:25-34. [PMID: 11246743 DOI: 10.1016/s0301-4622(00)00213-1] [Citation(s) in RCA: 195] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The ethanol-induced conformation transition of regenerated Bombyx mori silk fibroin membrane from a poorly defined to the well ordered state was monitored by time-resolved Fourier transform infrared spectroscopy (FTIR) for the first time. From the analysis of FTIR difference spectra, taken on time scales as short as 6 s and up to 1 h after addition of ethanol, intensity vs. time plots of an increasing band at 1618 cm(-1) were observed indicating formation of a beta-sheet coincident with the loss of intensity of a band at 1668 cm(-1) indicating decreases of random coil and/or silk I structure. Both infrared markers were fitted with identical biphasic exponential decay functions, however, there was a clear burst phase occurring prior to the onset of the observed transitions. The conformation transition process is indicated to either proceed sequentially through (at least) two intermediate states that contain different levels of beta-sheet structure or to have parallel pathways of initial beta-sheet formation followed by a slower 'perfection' phase. The first observed process forms in a burst phase a few seconds after mixing (or even faster), prior to the collection of the first spectrum at 6 s. The second observed process occurs with a time constant of approximately 0.5 min, the intermediate present at this stage then continues with a time constant of 5.5 min completing the observed formation of the beta-sheet. The conformation transition of this slower intermediate is not only indicated by an analysis of the kinetics of the random coil and beta-sheet-specific bands discussed above, it roughly coincides with the appearance of an additional infrared marker at 1695 cm(-1), which may be a marker for beta-sheet structure specific to the formation of the perfected structure. The conformation transition of this protein analyzed by infrared spectroscopy provides insight into a part of the fascinating process of cocoon formation in B. mori.
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Miller LM, Hess HA, Doroquez DB, Andrews NM. Null mutations in the lin-31 gene indicate two functions during Caenorhabditis elegans vulval development. Genetics 2000; 156:1595-602. [PMID: 11102360 PMCID: PMC1461380 DOI: 10.1093/genetics/156.4.1595] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The lin-31 gene is required for the proper specification of vulval cell fates in the nematode Caenorhabditis elegans and encodes a member of the winged-helix family of transcription factors. Members of this important family have been identified in many organisms and are known to bind specific DNA targets involved in a variety of developmental processes. DNA sequencing of 13 lin-31 alleles revealed six nonsense mutations and two missense mutations within the DNA-binding domain, plus three deletions, one transposon insertion, and one frameshift mutation that all cause large-scale disruptions in the gene. The missense mutations are amino acid substitutions in the DNA-binding domain and probably disrupt interactions of the LIN-31 transcription factor with its DNA target. In addition, detailed phenotypic analysis of all 19 alleles showed similar penetrance for several characteristics examined. From our analysis we conclude: (1) the null phenotype of lin-31 is the phenotype displayed by almost all of the existing alleles, (2) the DNA-binding domain plays a critical role in LIN-31 function, and (3) direct screens for multivulva and vulvaless mutants will probably yield only null (or strong) alleles of lin-31.
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Miller LM, Schreiner CE. Stimulus-based state control in the thalamocortical system. J Neurosci 2000; 20:7011-6. [PMID: 10995846 PMCID: PMC6772827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2000] [Revised: 06/29/2000] [Accepted: 07/05/2000] [Indexed: 02/17/2023] Open
Abstract
Neural systems operate in various dynamic states that determine how they process information (Livingstone and Hubel, 1981; Funke and Eysel, 1992; Morrow and Casey, 1992; Abeles et al., 1995; Guido et al., 1995; Mukherjee and Kaplan, 1995; Kenmochi and Eggermont, 1997; Wörgötter et al., 1998; Kisley and Gerstein, 1999). To investigate the function of a brain area, it is therefore crucial to determine the state of that system. One grave difficulty is that even under well controlled conditions, the thalamocortical network may undergo random dynamic state fluctuations which alter the most basic spatial and temporal response properties of the neurons. These uncontrolled state changes hinder the evaluation of state-specific properties of neural processing and, consequently, the interpretation of thalamocortical function. Simultaneous extracellular recordings were made in the auditory thalamus and cortex of the ketamine-anesthetized cat under several stimulus conditions. By considering the cellular and network mechanisms that govern state changes, we develop a complex stimulus that controls the dynamic state of the thalamocortical network. Traditional auditory stimuli have ambivalent effects on thalamocortical state, sometimes eliciting an oscillatory state prevalent in sleeping animals and other times suppressing it. By contrast, our complex stimulus clamps the network in a dynamic state resembling that observed in the alert animal. It thus allows evaluation of neural information processing not confounded by uncontrolled variations. Stimulus-based state control illustrates a general and direct mechanism whereby the functional modes of the brain are influenced by structural features of the external world.
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Miller LM, Tibrewala J, Carlson CS. Examination of bone chemical composition in osteoporosis using fluorescence-assisted synchrotron infrared microspectroscopy. Cell Mol Biol (Noisy-le-grand) 2000; 46:1035-44. [PMID: 10976861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Although it is clear that osteoporosis is associated with a reduction in bone mass and a fragile skeleton, it is not understood whether the chemical composition of osteoporotic bone is different from normal bone. In this study, cynomolgus monkeys (Macaca fascicularis) were administered fluorochrome labels at one and two years after ovariectomy (Ovx) or Sham ovariectomy (intact), that were taken up into newly remodeled bone. Using fluorescence-assisted synchrotron infrared microspectroscopy, the chemical composition of bone from intact versus Ovx monkeys has been compared. Results from overall composition distributions (labeled + non-labeled bone) reveal similar carbonate/protein and phosphate/protein ratios, but increased acid phosphate content and different collagen structure in the Ovx animals. Analysis of the fluorochrome-labeled bone indicates similar degrees of mineralization in bone remodeled after one year, but decreased mineralization in Ovx bone remodeled two years after surgery. Thus, bone from monkeys with osteoporosis can be characterized as having abnormal collagen structure and reduced rates of mineralization. Coupled with factors such as trabecular architecture and bone shape and size, these ultrastructural factors may play a contributing role in the increased bone fragility in osteoporosis.
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Abstract
In hybrid studies, potential for error is high when classifying genealogical origins of individuals (e.g., parental, F1, F2) based on their genotypic arrays. For codominant markers, previous researchers have considered the probability of misclassification by genotypic inspection and proposed alternative maximum-likelihood approaches to estimating genealogical class frequencies. Recently developed dominant marker systems may significantly increase the number of diagnostic loci available for hybrid studies. I examine probabilities of classification error based on the number of dominant loci. As in earlier studies, I assume that only parental and first- and second-generation hybrid crosses between two taxa potentially exist. Thirteen loci with dominant expression from each parental taxon (i.e., 26 total loci) are needed to reduce classification error below 5% for F2 individuals, compared to 13 codominant loci for the same error rate. Use of loci in similar numbers from both taxa most efficiently increases power to characterize all genealogical classes. In contrast, classification of backcrosses to one parental taxon is wholly dependent on loci from the other taxon. Use of dominant diagnostic markers may increase the power and expand the use of maximum-likelihood methods for evaluating hybrid mixtures.
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Zhao F, Miller LM, Chardon P, Rogel-Gaillard C, Louis CF. Five new polymorphic microsatellite markers for pig chromosome 6p. Anim Genet 1999; 30:394-5. [PMID: 10582297 DOI: 10.1046/j.1365-2052.1999.00526-14.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Zhao F, Ambady S, Ponce de León FA, Miller LM, Lunney JK, Grimm DR, Schook LB, Louis CF. Microsatellite markers from a microdissected swine chromosome 6 genomic library. Anim Genet 1999; 30:251-5. [PMID: 10467699 DOI: 10.1046/j.1365-2052.1999.00502.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To develop additional microsatellite (MS) markers in the region of the porcine skeletal muscle ryanodine receptor gene (RYR1), a microdissected genomic library was generated from the proximal half of the q arm of swine chromosome 6. Purified DNA was restriction enzyme-digested, ligated to oligonucleotide adaptors and amplified by PCR using primers complementary to the adaptor sequences. The purity of the amplified products and boundaries of the microdissected chromosomal region were verified by fluorescence in situ hybridization. (CA)n-containing sequences were then identified in a small insert genomic library generated from the PCR-amplified microdissected DNA. Oligonucleotide primers were developed for the PCR amplification of 30 of the 46 (CA)n repeat-containing clones, which were subsequently used to amplify DNA isolated from unrelated pigs of different breeds to determine the informativeness of these MS markers. Twenty-two of these MS markers were genotyped on the University of Illinois Yorkshire x Meishan swine reference population. These 22 markers were all assigned within a 50.7-CM region of the swine chromosome 6 linkage map, indicating the specificity of the microdissected library.
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Anderson GM, Dallaire A, Miller LM, Miller CW. Peripheral nerve sheath tumor of the diaphragm with osseous differentiation in a one-year-old dog. J Am Anim Hosp Assoc 1999; 35:319-22. [PMID: 10416777 DOI: 10.5326/15473317-35-4-319] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A 12-month-old, spayed female German shepherd dog was referred to the Veterinary Teaching Hospital for repair of a diaphragmatic hernia. Abdominal exploration revealed an intact diaphragm, but thoracic exploration revealed a large mass originating from the diaphragm. Resection of the mass was incomplete and required reconstruction of the diaphragm. On histopathology, the mass was composed mainly of spindle-shaped cells with occasional areas of osseous and chondroid tissue. The tumor was diagnosed as a peripheral nerve sheath tumor (PNST) with chondro-osseous differentiation. The dog was released four days after surgery; however, she began having difficulty breathing seven days after discharge, and the owners elected euthanasia. A necropsy was not performed. This is the first known report of a PNST originating in the diaphragm of a dog.
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Hayward R, Ferrington DA, Kochanowski LA, Miller LM, Jaworsky GM, Schneider CM. Effects of dietary protein on enzyme activity following exercise-induced muscle injury. Med Sci Sports Exerc 1999; 31:414-20. [PMID: 10188746 DOI: 10.1097/00005768-199903000-00010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE The objective of this investigation was to determine the effects of varying levels of dietary protein on the postexercise increase in serum and muscle enzyme activity normally observed following exercise-induced muscle injury. METHODS Serum creatine kinase (CK), serum aspartate aminotransferase (AST), and muscle glucose-6-phosphate dehydrogenase (G-6-PD) activities were measured in rats fed for 10 d on high (50%), normal (12%), or low (4%) protein diets following a single bout of eccentric exercise (treadmill running at 16 m.min(-1), -16 degrees incline, 90 min). RESULTS The exercise intervention resulted in significant increases in serum CK and AST activities in all diet groups. Serum CK demonstrated peak activity immediately postexercise with increases reaching 910+/-94, 594+/-53, and 283+/-52 IU.L(-1) for animals on high, normal, and low protein diets, respectively. Similarly, peak postexercise AST activity for high, normal, and low protein diets reached 193+/-10, 147+/-3, and 162+/-9 IU.L(-1), respectively. The exercise intervention resulted in increases in muscle G-6-PD activity for all diet groups; however, LP rats demonstrated significantly lower values than NP or HP rats. CONCLUSIONS These data show that dietary protein intake can significantly effect both serum and muscle enzyme activity following acute exercise-induced muscle injury.
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Borer SO, Miller LM, Kapuscinski AR. Microsatellites in walleye Stizostedion vitreum. Mol Ecol 1999; 8:336-8. [PMID: 10065550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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George LA, Miller LM, Valberg SJ, Mickelson JR. Fourteen new polymorphic equine microsatellites. Anim Genet 1998; 29:469-70. [PMID: 9883525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Miller LM, Stine-Morrow EA. Aging and the effects of knowledge on on-line reading strategies. J Gerontol B Psychol Sci Soc Sci 1998; 53:P223-33. [PMID: 9679514 DOI: 10.1093/geronb/53b.4.p223] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The effects of knowledge on on-line reading strategies and the relation of these effects to subsequent memory performance among young and elderly adults were investigated. Participants read passages with vague, ill-defined content word-by-word on a computer screen for immediate recall and reading times were recorded. High-knowledge (HK) readers received passage titles that clarified the content and low-knowledge (LK) readers did not. Reading strategy was found to be related to age, knowledge, and subsequent recall performance. LK readers, particularly those who produced high levels of recall, spent differentially more time at intrasentence and sentence boundaries suggesting that they allocated more processing resources to consolidate the concepts in the seemingly disjointed text. HK readers, on the other hand, showed facilitation in this organizational processing. These beneficial effects were more pronounced for elderly readers than for younger readers, suggesting that older readers take special advantage of knowledge in the on-line processing of discourse. Moreover, older LK readers who were above average in recall were differentially slowed at boundaries showing that successful older readers who lacked a situation model with which to interpret text allocated differentially more time to organize and integrate text than did their younger counterparts.
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