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  • 1
    Electronic Resource
    Electronic Resource
    1H, 13C, and 15N resonance assignments and secondary structure analysis of the HU protein from Bacillus stearothermophilus using two- and three-dimensional double- and triple-resonance heteronuclear magnetic resonance spectroscopy (1994)
    s.l. : American Chemical Society
    Biochemistry 33 (1994), S. 14858-14870 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00253a025
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  • 2
    Electronic Resource
    Electronic Resource
    Is humane slaughter of fish possible for industry? (2003)
    Oxford, UK : Blackwell Science Ltd
    Aquaculture research 34 (2003), S. 0 
    Details
    ISSN: 1365-2109
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The objective was to evaluate industrial and research slaughter methods for Atlantic salmon (Salmo salar), gilt-head seabream (Sparus auratus) and eel (Anguilla anguilla) with respect to welfare and quality. As a general term of reference, an optimal slaughter method should render fish unconscious until death without avoidable excitement, pain or suffering prior to killing. For Atlantic salmon, commercial slaughter methods (carbon dioxide stunning followed by gill cutting, and gill cutting alone) are not in conformity with the general term of reference, as the fish are not rendered unconscious immediately and possibly experience stress. Evaluation of automated percussive stunning remained unconclusive. More research should enable us to ascertain whether loss of consciousness is instantaneous. Electrical stunning can be humane if applied properly. However, because flesh of electrostunned fish was characterized by occasional bloodspots, optimization of the electrical parameters is required. Prototypes for percussive and electrical stunning of salmon have been recently developed. This implies that humane slaughter of salmon is feasible for industry. For gilt-head seabream, neither aphyxia in air nor transfer of the fish to an ice slurry were considered to be humane: the methods did not induce immediate brain dysfunction and vigorous attempts to escape occurred. Percussive and electrical stunning can be in conformity with the general term of reference. However, conditions for stunning whole batches of seabream have not been established. Quality of the fish slaughtered by percussive stunning was similar to that obtained by the industrial method, i.e. immersion in an ice slurry. Further work is required to establish optimal stunning conditions and to develop prototypes. For eel, desliming in a salt-bath followed by evisceration, electrical stunning performed under the conditions prescribed by the German legislation, and live chilling and freezing were not considered to be humane. In contrast, it was established that a 10–20 kg batch of eels in fresh water could be rendered unconscious immediately and until death by applying electricity in combination with nitrogen gas. The conditions used were 0.64 A dm−2 for 1 s, followed by 0.17 A dm−2 combined with nitrogen flushing for 5 min. A preliminary assessment of flesh quality suggests that it may be improved by application of the latter method, compared with the salt bath. The results clearly indicated that humane slaughter of eels is possible in practice.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2109.2003.00804.x
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  • 3
    Electronic Resource
    Electronic Resource
    Effect of the slaughter method on the quality of raw and smoked eels (Anguilla anguilla L.) (2003)
    Oxford, UK : Blackwell Science Ltd
    Aquaculture research 34 (2003), S. 0 
    Details
    ISSN: 1365-2109
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Eels (Anguilla anguilla L.) were slaughtered using two procedures. The commercial method consisted of desliming the fish in dry salt followed by evisceration. The alternative method consisted of stunning and killing in water with a combination of electricity and oxygen removal. Eels slaughtered as commercially exhibited aversive reactions and consequently a higher level of muscular activity before death. In raw fillets, differences appeared clearly between the two batches. The alternative slaughter by electricity and gas led to redder, firmer flesh with a higher pH. Myofibrillar proteolysis, lipid oxidation and loss of freshness (as evaluated by K-value) were reduced. After hot-smoking, which is a process that greatly modifies the fish flesh properties, differences between batches were less pronounced. However, eels slaughtered by the alternative method were characterized by a higher pH and a redder colour of the dark muscle, a desirable property form a commercial point of view. When assessed by sensory difference tests, appearance seemed to be the only attribute that allowed panellists to discriminate the two batches. Overall, it is concluded that slaughter by electricity and gas improved the quality of raw and smoked eels compared with the commercial method.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2109.2003.00754.x
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  • 4
    Electronic Resource
    Electronic Resource
    Mobility of NH bonds in DNA-binding protein HU of shape Bacillus stearothermophilus from reduced spectral density mapping analysis at multiple NMR fields (1998)
    Springer
    Journal of biomolecular NMR 11 (1998), S. 265-277 
    Details
    ISSN: 1573-5001
    Keywords: DNA-binding protein ; heteronuclear NMR relaxation ; model-free approach ; protein dynamics ; rotational diffusion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract The dynamics of the backbone NH bonds of protein HU from Bacillus stearothermophilus (HUBst) have been characterized using measurements of cross-relaxation, longitudinal and transverse relaxation rates $$({\text{R}}_{\text{N}} ({\text{H}}_{\text{z}} \leftrightarrow {\text{N}}_{\text{z}} ),{\text{R}}_{\text{N}} {\text{(N}}_{\text{z}} ){\text{ and R}}_{\text{N}} ({\text{N}}_{{\text{x,y}}} ))$$ at 11.7, 14.1 and 17.6 T. Linear regression of the values $$2{\text{R}}_{\text{N}} ({\text{N}}_{{\text{x,y}}} ) - {\text{R}}_{\text{N}} ({\text{N}}_{\text{Z}} )$$ with the squared Larmor frequency ω N 2 has revealed global exchange processes, which contributed on the order of 0.5–5.0 s-1to the transverse relaxation rate. Subsequently, the experimental values $${\text{R}}_{\text{N}} ({\text{N}}_{{\text{x,y}}} )$$ were corrected for these exchange contributions. A reduced spectral density mapping procedure has been employed with the experimental relaxation rates and seven values of the spectral density function J(ω) have been extracted. These spectral densities have been fitted within the framework of the model-free approach. The densities agree well with an axially symmetric rotational diffusion tensor with a diffusion anisotropy D_∥/D_⊥ of 1.15, indicating that the flexible arms of HUBst do not significantly contribute to the rotational diffusion. The overall correlation time is 8.9 ± 0.6 ns/rad. The fast internal motions of most of the NH bonds in the core display order parameters ranging between 0.74 and 0.83 and internal correlation times between 1 and 20 ps. For the residues in the DNA-binding β-arms, an extended version of the model function has been used. The slow internal motions show correlation times of 1–2 ns. The concomitant order parameters (0.3–0.6) are lower than those observed on the fast time scale, indicating that the flexibility of the β-arms is mainly determined by the slower internal motions. A substantial decrease of the generalized order parameters in the β-arms starting at residues Arg55 and Ser74, opposite on both strands of the β-ribbon arms, has been explained as a ‘hinge’ motion. A comparison of the order parameters for free and DNA-bound protein has demonstrated that the slow hinge motions largely disappear when HU binds DNA.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008208615714
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  • 5
    Electronic Resource
    Electronic Resource
    Use of graph theory for secondary structure recognition and sequential assignment in heteronuclear (13C, 15N) NMR spectra: Application to HU protein from Bacillus stearothermophilus (1996)
    New York : Wiley-Blackwell
    Biopolymers 39 (1996), S. 691-707 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A computer-assisted procedure, based upon a branch of mathematics known as graph theory, has been developed to recognize secondary structure elements in proteins from their corresponding nuclear Overhauser effect spectroscopy (NOESY)-type spectra and to carry out their sequential assignment. In the method, NOE connectivity templates characteristic of regular secondary structures are identified in the spectra. Resonance assignment is then achieved by connecting these NOE patterns of secondary structure together, and thereby matching connected spin systems to specific parts of the primary sequence. The range of NOE-graph templates of secondary structure motifs, incorporating α-helices and β-strand motifs, has been examined for reliability and extent of secondary structure identification in a data base composed of the high resolution structures of 20 proteins. The analysis identified several robust NOE-graph templates and supports the implementation of an ordered search strategy. The method, known as SERENDIPITY, has been applied to the analysis of nuclear Overhauser effect data from a three-dimensional time-shared nuclear Overhauser effect spectroscopy (13C, 15N) heteronuclear single quantum correlation spectrum of the (α + β) type protein HU from Bacillus stearothermophilus. The arrangement of the elucidated elements of secondary structure is very similar to that of the x-ray and nmr structures of HU. In addition, our analysis revealed a pattern of interstrand nuclear Overhauser effect in the β-arm region (residues 53-76) of HU, which suggest irregularities, not reported in the x-ray structure, in both strands of the β-arm at Ala57 and Pro72, respectively. At these residues, both strands of the β-arm appear to flip inside out before continuing as a regular antiparallel β-sheet. © 1996 John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Structure and dynamics of the DNA binding protein HU from Bacillus stearothermophilus by NMR spectroscopy (1996)
    New York : Wiley-Blackwell
    Biopolymers 40 (1996), S. 553-559 
    Details
    ISSN: 0006-3525
    Keywords: protein structure ; protein dynamics ; protein-DNA complex ; heteronuclear relaxation measurements ; triple-resonance nmr ; photo-CIDNP ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The DNA-binding protein HU from Bacillus stearothermophilus (HUBst) is a dimer with a molecular weight of 19.5 kDa that is capable of bending DNA. An x-ray structure has been determined previously [Tanaka et al. (1984) Nature, Vol. 310, pp. 376-381], but no structure could be established for a large part of the supposed DNA-binding β-arms. Distance geometry and restrained molecular dynamics using nmr restraints were used to generate a set of 25 structures. These structures display a backbone rms deviation (RMSD) of 0.36 Å for the well-defined region (residues 2-54 and 75-90). The structure of the core is very similar to that observed in the x-ray structure, with a pairwise RMSD of 1.06 Å. The structure of the β-hairpin arm contains a double flip-over at the prolines in the two strands of the β-arm. Heteronuclear 15N relaxation measurements indicate that the β-arm and the tip of the β-arm is flexible. This explains the disorder observed in the solution and x-ray structures of the β-arm with respect to the core of the protein. Overlayed onto itself the β-arm is better defined, with an backbone RMSD of 1.0 Å calculated for residues 54-59 and 69-74. The tip of the arm adopts a well-defined 4 : 6 β-hairpin conformation. Changes in amide 15N and 1H chemical shifts upon titrating DNA are most pronounced for the residues in the β-hairpin arm and for the residues in the second half of the third α-helix. Heteronuclear 15N relaxation data for free and complexed HUBst show that the arms become structured upon DNA binding. Together with chemically induced nuclear polarization measurements on a mutant HUBst (M69Y; V76Y) this shows that the β-hairpin arm is involved in direct DNA interaction. © 1997 John Wiley & Sons, Inc. Biopoly 40: 553-559, 1996
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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