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  • 1
    ISSN: 1618-2650
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Bioscience reports 17 (1997), S. 335-342 
    ISSN: 1573-4935
    Keywords: oxygen receptors ; bacterial chemotaxis ; reactive oxygen species ; signal transduction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Bacteria, such as Escherichia coli and Azospirillum brasilense, avoid microenvironments with elevated oxygen concentrations, not by sensing reactive oxygen derivatives, but by sensing a metabolic down-shift that results from elevated oxygen levels. A novel protein, Aer, and the chemotaxis serine receptor, Tsr, have recently been identified as transducers for aerotaxis which monitor internal energy levels in the bacteria.
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  • 3
    ISSN: 1573-4943
    Keywords: ATP-AMP transphosphorylase ; adenylate kinase ; myokinase ; nucleotide-binding peptides and peptide fragments ; ligand binding ; peptide synthesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Two peptide fragments, derived from the head and tail of rabbit muscle myokinase, were found to possess remarkable and specific ligand-binding properties (Hamadaet al., 1979). By initiating systematic syntheses and measurements of equilibrium substrate-binding properties of these two sets of peptides, or portions thereof, which encompass the binding sites for (a) the magnesium complexes of the nucleotide substrates (MgATP2− and MgADP−) and (b) the uncomplexed nucleotide substrates (ADP3− and AMP2−) of rabbit muscle myokinase, some of the requirements for binding of the substrates to ATP-AMP transphosphorylase are being deduced and chemically outlined. One requirement for tight nucleotide binding appears to be a minimum peptide length of 15–25 residues. In addition, Lys-172 and/or Lys-194 may be involved in the binding of εAMP. The syntheses are described as a set of peptides corresponding to residues 31–45, 20–45, 5–45, and 1–45, and a set of peptides corresponding to residues 178–192, 178–194, and 172–194 of rabbit muscle adenylate kinase. The ligand-binding properties of the first set of synthetic peptides to the fluorescent ligands: εMgATP/εATP and εMgADP/εADP are quantitatively presented in terms of their intrinsic dissociation constants (K′d) and values ofN (maximal number of moles bound per mole of peptide); and compared with the peptide fragment MT-I (1–44) obtained from rabbit muscle myokinase (Kubyet al., 1984) and with the native enzyme (Hamadaet al., 1979). In addition, the values ofN andK′d are given for the second set of synthetic peptides to the fluorescent ligands εAMP and εADP as well as for the peptide fragments MT-XII(172–194) and CB-VI(126–194) (Kuby et al., 1984) and, in turn, compared with the native enzyme. A few miscellaneous dissociation constants which had been derived kinetically are also given for comparison (e.g., theK i for εAMP and the value of $$\bar K_{Mg\varepsilon ATP} $$ obtained for the native enzyme) (Hamada and Kuby, 1978), and theK'd measured for Cr3+ and the synthetic peptide I1–45 (Fryet al., 1985b).
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  • 4
    ISSN: 1432-1432
    Keywords: Simultaneous multiple alignments ; Amino acid sequences ; Globins ; Neurotoxins ; Protease inhibitors
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We describe an algorithm for the concurrent comparison of three or more amino acid sequences. The basis of the approach is a progressive evaluation of selected segments from each sequence. Only a small subset of all possible segments from each sequence is compared, and a minimum of information is retained for the trace-back of the alignment. As a result, this method has the advantage of being both rapid and minimally consumptive of computer memory when constructing an alignment. This being the case, there are no practical limits on the length of sequences that may be aligned. A computer program for the alignment of three sequences is described, and this method is compared with two three-sequence extensions of the Needleman and Wunsch variety, including a recently published approach. In addition, we have made simultaneous alignments of sets of four and five sequences with this selected-segment method.
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  • 5
    Publication Date: 2017-01-05
    Description: Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Biogeochemistry 105 (2011): 7-18, doi:10.1007/s10533-011-9597-8.
    Description: The flowpaths by which water moves from watersheds to streams has important consequences for the runoff dynamics and biogeochemistry of surface waters in the Amazon Basin. The clearing of Amazon forest to cattle pasture has the potential to change runoff sources to streams by shifting runoff to more surficial flow pathways. We applied end member mixing analysis (EMMA) to ten small watersheds throughout the Amazon in which solute composition of streamwater and groundwater, overland flow, soil solution, throughfall and rainwater were measured, largely as part of the Large-Scale Biosphere-Atmosphere Experiment in Amazonia. We found a range in the extent to which streamwater samples fell within the mixing space determined by potential flowpath end members, suggesting that some water sources to streams were not sampled. The contribution of overland flow as a source of stream flow was greater in pasture watersheds than in forest watersheds of comparable size. Increases in overland flow contribution to pasture streams ranged in some cases from 0% in forest to 27 to 28% in pasture and were broadly consistent with results from hydrometric sampling of Amazon forest and pasture watersheds that indicate 17- to 18-fold increase in the overland flow contribution to stream flow in pastures. In forest, overland flow was an important contribution to stream flow (45 to 57%) in ephemeral streams where flows were dominated by stormflow. Overland flow contribution to stream flow decreased in importance with increasing watershed area, from 21 to 57% in forest and 60 to 89% in pasture watersheds 〈10 ha to 0% in forest and 27 to 28% in pastures in watersheds 〉100 ha. Soil solution contributions to stream flow were similar across watershed area and groundwater inputs generally increased in proportion to decreases in overland flow. Application of EMMA across multiple watersheds indicated patterns across gradients of stream size and land cover that were consistent with patterns determined by detailed hydrometric sampling.
    Description: This work was supported by National Science Foundation (DEB-0315656, DEB-0640661), the NASA LBA Program (NCC5-686, NCC5-69, NCC5-705, NNG066E88A) and by grants from Brazilian agencies FAPESP (03/13172-2) and CNPq (20199/2005-5).
    Keywords: Cattle pasture ; Deforestation ; Flowpaths ; Principal components analysis ; Overland flow ; Soil solution
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
    Format: application/pdf
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  • 6
    Publication Date: 2017-01-07
    Description: Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of springer for personal use, not for redistribution. The definitive version was published in Biogeochemistry 105 (2011): 19-35, doi:10.1007/s10533-011-9574-2.
    Description: Stream discharge-concentration relationships are indicators of terrestrial ecosystem function. Throughout the Amazon and Cerrado regions of Brazil rapid changes in land use and land cover may be altering these hydrochemical relationships. The current analysis focuses on factors controlling the discharge-calcium (Ca) concentration relationship since previous research in these regions has demonstrated both positive and negative slopes in linear log10discharge-log10Ca concentration regressions. The objective of the current study was to evaluate factors controlling stream discharge-Ca concentration relationships including year, season, stream order, vegetation cover, land use, and soil classification. It was hypothesized that land use and soil class are the most critical attributes controlling discharge-Ca concentration relationships. A multilevel, linear regression approach was utilized with data from 28 streams throughout Brazil. These streams come from three distinct regions and varied broadly in watershed size (〈1 to 〉106 ha) and discharge (10-5.7 to 103.2 m3 sec-1). Linear regressions of log10Ca versus log10discharge in 13 streams have a preponderance of negative slopes with only two streams having significant positive slopes. An ANOVA decomposition suggests the effect of discharge on Ca concentration is large but variable. Vegetation cover, which incorporates aspects of land use, explains the largest proportion of the variance in the effect of discharge on Ca followed by season and year. In contrast, stream order, land use, and soil class explain most of the variation in stream Ca concentration. In the current data set, soil class, which is related to lithology, has an important effect on Ca concentration but land use, likely through its effect on runoff concentration and hydrology, has a greater effect on discharge-concentration relationships.
    Description: This research was supported by grant #’s NCC5-686 and NNG06GE88A of NASA’s Terrestrial Ecology Program as part of the Large-scale Biosphere-Atmosphere Experiment in Amazonia (LBA-ECO) project.
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 7
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature Publishing Group
    Nature 307 (1984), S. 558-560 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The EGFP precursor sequence was searched against 1,081 sequences (-120,000 residues) in the 1978 Dayhoff Atlas4 and about 800 sequences (-160,000 residues) in Newat5. The search identified bovine factors X and IX (in the Dayhoff Atlas), and human factors X and IX and bovine protein C (in Newat) as ...
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  • 8
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Integrin α1β1 is one of the main collagen receptors in many cell types. A fast large-scale production, purification and crystallization method for the integrin α1 I domain is reported here. The α1 I domain was crystallized using the vapour-diffusion method with a reservoir solution containing a mixture of PEG 4000, sodium acetate, glycerol and Tris–HCl buffer. The crystals beong to the C2 space group, with unit-cell parameters a = 74.5, b = 81.9, c = 37.3 Å, α = γ = 90.0, β = 90.8°. The crystals diffract to 2.0 Å and a 94.2% complete data set to 2.2 Å has been collected from a single crystal with an Rmerge of 5.8%.
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  • 9
    ISSN: 1432-1432
    Keywords: Key words:Diphyllobothrium dendriticum— Cestode — Actin cDNA — Polyadenylation signal — Multigene family — Molecular evolution — Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Five cDNAs (pDidact2–pDidact6), representing different actin genes, were isolated from a Diphyllobothrium dendriticum cDNA library, and the DNA as well as the putative amino acid sequences were determined. The corresponding Didact2 and Didact4 genes code for peptides 376 amino acids long, with molecular weights 41,772 and 41,744 Da, respectively, while the deduced Didact3 protein is 377 amino acids long and weighs 41,912 Da. The pDidact5 and -6 cDNAs lack nucleotides corresponding to three to six amino acids at the amino-terminus. Two of the five cDNAs contain the conventional AATAAA as the putative polyadenylation signal, one has the common variant ATTAAA, whereas the hexanucleotide AATAGA is found 15 and 18 nucleotides, respectively, upstream of the poly(A) site in two of the cDNAs. Phylogenetic studies including 102 actin protein sequences revealed that there are at least four different types of cestode actins. In this study three of these types were found to be expressed in the adult D. dendriticum tapeworm. Structurally the cestode actin groupings differ from each other to an extent seen only among the metazoan actins between the vertebrate muscle and cytoplasmic isoforms. In the phylogenetic trees constructed, cestode actins were seen to map to two different regions, one on the border of the metazoan actins and the other within this group. It is, however, difficult to say whether the cestode actins branched off early in the metazoan evolution or if this position in the phylogenetic tree only reflects upon differences in evolutionary rate.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1432-1432
    Keywords: Phyletic trees from x-ray crystal structures ; Sequences ; Globins ; Cytochromes ; Immunoglobulins ; Serine proteinases ; Eye-lens gamma crystallins ; Dinucleotide-binding proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A distance measure that reflects the dissimilarity among structures has been developed on the basis of the three-dimensional structures of similar proteins, this being totally independent of sequence in the sense that only the relative spatial positions of mainchain alpha-carbon atoms need be known. This procedure leads to phyletic relationships that are in general correlated with the sequence phylogenies based on residue type. Such relationships among known protein three-dimensional structures are also a useful aid to their classification and selection in knowledge-based modeling using homologous structures. We have applied this approach to six homologous sets of proteins: immunoglobulin fragments, globins, cytochromesc, serine proteinases, eye-lens gamma crystallins, and dinucleotide-binding domains.
    Type of Medium: Electronic Resource
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