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  • 1
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1573-5052
    Keywords: Cistus ; Germinability ; Halimium ; Physical dormancy ; Physical separation method ; Seedling emergence method
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The impact of fire on hard-coated Cistaceae (Halimium ocymoides, Cistus ladanifer, and C. salvifolius) soil seed banks in a Mediterranean 'maquis' shrubland, and its effect on seed germinability were studied. The study also contrasts the effectiveness of two widely used techniques for quantifying seed banks, the seedling emergence and the physical separation methods, in relation to fire. The null hypothesis that a massive enhancement of physically-dormant Cistaceae seed germination by fire would make use of the time-consuming physical separation technique unnecessary was tested. Fire reduced Cistaceae seed banks in the 0–2 cm deep soil layer by both seed fire-consumption and lethal temperatures, revealed by the significant decreasing of the seed bank density and by the increase of apparently-intact but soft-unviable seeds, respectively. In contrast, no damage was recorded in the 2–5 cm soil layer. A dramatic seed bank depletion (〉 90%) in both soil layers was recorded one year after fire in the burnt area, coinciding with a significant increase of seedling density confined to the first post-fire year. The ecological consequences of this massive post-fire seed bank input are discussed. A germinability test revealed that germination of surviving Cistaceae seeds was significantly enhanced in all cases except for the C. salvifolious seed bank in the deeper soil layer. However, final germination levels (60–75%) did not correspond to the magnitude of seed bank depletion, especially for C. salvifolious, which suggests that other environmental factors not exclusively associated with fire may also be important in softening Cistaceae seeds. Germination enhancement by fire soil-heating was not high enough to reject the physical separation technique, at least in the deeper soil layer. The simultaneous use of both seedling emergence and physical separation is recommended for reliable seed bank estimates when a physically-dormant hard-seeded component can be expected in the soil, as in many Mediterranean ecosystems, regardless of fire occurrence.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 0749-1581
    Keywords: Peptide group proton shift effects ; Proton chemical shift computation ; Protein backbone conformation ; Solution peptide and protein structures ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: It has been found that protein NH protons on top of a peptide group plane experience large upfield conformation shifts. The joint analysis of this effect and other known effects of the peptide group on proton chemical shifts has led to a two-term empirical expression for peptide group proton chemical shift computation as a function of protein backbone conformation. Both terms are expressed by McConnell's point-dipole shielding expressions, one referred to an axis perpendicular to the peptide plane and origin in the coordinate centre of the OCN atoms and the other referred to an axis along the carbonyl bond and origin close to the oxygen atom. Values for the two constants have been determined by least-squares fitting of the C-α, H and amide NH chemical shifts of the protein ubiquitin. As a cross-check on the validity of the expression, the C-α, H and NH shifts of ribonuclease and BPTI (basic pancreatic trypsin inhibitor) have been computed. The general agreement between the observed and computed shifts and the correlation coefficients found (0.72 on average) indicate that the expression accounts for the main physical effects of the protein peptide group on the proton chemical shifts. It is shown that, together with ring current shifts, the expression explains the main characteristics of the C-α, H and amide NH chemical shifts in proteins.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1573-5001
    Keywords: RNase A solution structure ; 2D1H NMR ; RNase A active center ; Crystal and solution protein structures ; Method to generate starting structures
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary A method is proposed to generate initial structures in cases where the distance geometry method may fail, such as when the set of1H NMR NOE-based distance constraints is small in relation to the size of the protein. The method introduces an initial correlation between the φ and ψ backbone angles (based on empirical observations) which is relaxed in later stages of the calculation. The obtained initial structures are refined by well-established methods of energy minimization and restrained molecular dynamics. The method is applied to determine the solution structure of Ribonuclease A (124 residues) from a NOE basis consisting of 467 NOE cross-correlations (97 intra-residue, 206 sequential, 23 medium-range and 141 long-range) obtained at 360 MHz. The global shape and backbone overall fold of the eight final refined structures are close to those shown by the crystal structure. A meaningful difference in the positioning of the catalytically important His119 side chain in the solution and crystal structures has been detected.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1573-5052
    Keywords: Hardseedness ; Heat ; Leguminosae ; Seed germination
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The influence of high temperatures (dry heat and hot water) on germination of seven Mediterranean Leguminosae species typical of fire-prone ecosystems in southern Spain is analyzed, in order to know the response of seeds to wildfires and the possible implications in their regeneration after this disturbance. Seeds were heated to a range of temperatures (50 °–150 °C) and exposure times (1–60 min) similar to those registered in the upper soil layers during wildfires. Germination tests were carried out in plastic Petri dishes over 60 days. In general, the degree of seed germination promotion by dry heat treatments showed a wide interspecific variation, although the final germination level was increased in all the studied species except for Scorpiurus muricatus. The thermal pretreatment of 50 °C, however, was not effective for germination in any species, and rising the temperature to 70 °C only slightly enhanced the germination in Cytisus patens. The preheatings of 90 °C (5 and 10 min), 120 °C (5 and 10 min), and 150 °C (1 min) were the most effective in promoting seed germination. Hot water (100 °C) scarification also increased the final germination level in all cases, with the exception of C. patens. The germination rates after preheating were much lower than in mechanically scarified seeds and closely resembled those of the untreated seeds, except for C. reverchonii, whose seed germination rate decreased with heat. The response of species to heat shock had no clear relationship with life trait or with the specific post-fire regeneration strategy (obligate seeder or facultative resprouter). Those species coexisting in the same habitats had different heat optimal requirements for seed germination, an strategy suggested by some authors as minimizing interspecific competition in the secondary succession started after fire.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solution structure of a peptide fragment corresponding to the 38-59 region of porcine phospholipase A2 has been investigated using CD, nmr chemical shifts, and nuclear over-hauser effects (NOEs). This isolated fragment of phospholipase forms an α-helix spanning residues 38-55, very similar to the one found in the native protein, except for residues 56-58, which were helical in the crystal but found random in solution. Addition of triflouro-ethanol (TFE) merely increased helix population but it did not redefine helix limits. To investigate how the folding information, in particular that concerning eventual helix start and stop signals, was coded in this particular amino acid sequence, the helices formed by synthetic peptides reproducing sections of this phospholipase 38-59 fragment, namely 40-59, 42-59, 38-50, and 45-57, were characterized using NOEs and helix populations quantitatively evaluated on different peptide chain segments using nmr chemical shifts in two solvents (H2O and 30% TFE/H2O). A set of nmr spectra was also recorded and assigned under denaturing conditions (6Murea) to obtain reliable values for the chemical shifts of each peptide in the random state. Based on chemical shift data, it was concluded that the helix formed by the phospholipase 38-59 fragment was not abruptly, but progressively, destabilized all along its length by successive elimination of residues at the N end, while the removal of residues at the C end affected helix stability more locally and to a lesser extent. These results are consistent with the idea that there are not single residues responsible for helix initiation or helix stability, and they also evidence an asymmetry for contributions to helix stability by residues located at the two chain ends. The restriction of molecular mobility caused by linking with a disulphide bridge at Cys 51 two identical 38-59 peptide chains did not increase helix stability. The helix formed by the covalently formed homodimer was very similar in length and population to that formed by the monomer. © 1994 John Wiley & Sons, Inc.
    Additional Material: 10 Ill.
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  • 8
    Publication Date: 2018-11-02
    Description: Metabolic reprogramming plays an important role in cancer development and progression and is a well-established hallmark of cancer. Despite its inherent complexity, cellular metabolism can be decomposed into functional modules that represent fundamental metabolic processes. Here, we performed a pan-cancer study involving 9,428 samples from 25 cancer types to reveal metabolic modules whose individual or coordinated activity predict cancer type and outcome, in turn highlighting novel therapeutic opportunities. Integration of gene expression levels into metabolic modules suggests that the activity of specific modules differs between cancers and the corresponding tissues of origin. Some modules may cooperate, as indicated by the positive correlation of their activity across a range of tumors. The activity of many metabolic modules was significantly associated with prognosis at a stronger magnitude than any of their constituent genes. Thus, modules may be classified as tumor suppressors and oncomodules according to their potential impact on cancer progression. Using this modeling framework, we also propose novel potential therapeutic targets that constitute alternative ways of treating cancer by inhibiting their reprogrammed metabolism. Collectively, this study provides an extensive resource of predicted cancer metabolic profiles and dependencies.Significance: Combining gene expression with metabolic modules identifies molecular mechanisms of cancer undetected on an individual gene level and allows discovery of new potential therapeutic targets. Cancer Res; 78(21); 6059–72. ©2018 AACR.
    Print ISSN: 0008-5472
    Electronic ISSN: 1538-7445
    Topics: Medicine
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