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  • Articles  (17)
  • X-ray structure
  • hydrochemistry
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  • Springer  (17)
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  • 1
    ISSN: 1420-9055
    Keywords: Alpine lakes ; hydrochemistry ; acidification
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract During a four-year study (1988–1991), 413 lakes in the Central Alps (Italy, Switzerland and Austria) were investigated to quantify their acidification. The ionic content of the lakes was generally low: 68% of them had alkalinity values of less than 200 µeq 1−1 and were regarded as sensitive to acidification. Moreover, 36% of the lakes showed alkalinity values of less than 50 µeq 1−1. Redundancy Analysis was used to relate the hydrochemistry of 187 lakes to their catchment characteristics. Calcite weathering was the main factor influencing lake chemistry. The same analysis, applied to a subset of 101 lakes lying in watersheds exclusively composed of silicic rocks, showed that lake chemistry was influenced by silicate weathering and nitrogen uptake. These processes were found to be mainly related to lake altitude and the fraction of the watershed not covered by vegetation, i.e. controlled by temperature. The importance of these relations to explain the pH shift produced by climatic variation is also discussed.
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  • 2
    ISSN: 1432-1432
    Keywords: Two classes of aminoacyl-tRNA synthetases ; Sequence comparisons ; Homology ; X-ray structure ; Structure-function relationships ; Origin of aminoacyl-tRNA synthetases ; Two ancestral molecules ; Genetic code
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Previous sequence analyses have suggested the existence of two distinct classes of aminoacyl-tRNA synthetase. The partition was established on the basis of exclusive sets of sequence motifs (Eriani et al. [1990] Nature 347:203–306). X-ray studies have now well defined the structural basis of the two classes: the class I enzymes share with dehydrogenases and kinases the classic nucleotide binding fold called the Rossmann fold, whereas the class II enzymes possess a different fold, not found elsewhere, built around a six-stranded antiparallel β-sheet. The two classes of synthetases catalyze the same global reaction that is the attachment of an amino acid to the tRNA, but differ as to where on the terminal adenosine of the tRNA the amino acid is placed: class I enzymes act on the 2′ hydroxyl whereas the class II enzymes prefer the 3′ hydroxyl group. The three-dimensional structure of aspartyl-tRNA synthetase from yeast, a typical class II enzyme, is described here, in relation to its function. The crucial role of the sequence motifs in substrate binding and enzyme structure is high-lighted. Overall these results underline the existence of an intimate evolutionary link between the aminoacyl-tRNA synthetases, despite their actual structural diversity.
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  • 3
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    Electronic Resource
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    Mangroves and salt marshes 3 (1999), S. 105-115 
    ISSN: 1572-977X
    Keywords: dissolved Mn ; hydrochemistry ; particulate Mn ; sediments ; Sepetiba Bay ; tidal variation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract This study investigated the behavior of soluble and particulate manganese, during tidal cycles in a mangrove tidal creek and adjacent mud flats in SE Brazil. We identify the major processes affecting manganese transport to mangroves. The results showed that manganese variability occurs both seasonally, and over the tidal cycle, in response to changing redox potentials. Tidal water flooding mud flats are enriched in manganese, originating from upward migration of reduced species and further adsorption onto suspended particles under oxic conditions. During the tidal cycle, particulate manganese concentrations are higher during flood periods, whilst dissolved concentrations are higher during ebb periods. Although quantitatively different, this pattern occurs both in winter and summer. The dynamics of manganese characterized in this study suggest that this metal may play a significant role as a conveyor of trace metals to mangrove ecosystems, as suggested by earlier studies.
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  • 4
    ISSN: 1432-1327
    Keywords: Key words Ceruloplasmin ; Copper oxidase ; X-ray structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  The X-ray structure of human serum ceruloplasmin has been solved at a resolution of 3.1 Å. The structure reveals that the molecule is comprised of six plastocyanin-type domains arranged in a triangular array. There are six copper atoms; three form a trinuclear cluster sited at the interface of domains 1 and 6, and there are three mononuclear sites in domains 2, 4 and 6. Each of the mononuclear coppers is coordinated to a cysteine and two histidine residues, and those in domains 4 and 6 also coordinate to a methionine residue; in domain 2, the methionine is replaced by a leucine residue which may form van der Waals type contacts with the copper. The trinuclear centre and the mononuclear copper in domain 6 form a cluster essentially the same as that found in ascorbate oxidase, strongly suggesting an oxidase role for ceruloplasmin in the plasma.
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  • 5
    ISSN: 1432-1327
    Keywords: Key words Superoxide dismutase ; Propionibacterium shermanii ; X-ray structure ; Metal specificity ; Cambialism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  The first structure of a cambialistic superoxide dismutase (SOD) from Propionibacterium shermanii exhibiting similar activity with iron and with manganese was solved at a resolution of 1.6 Å and 1.9 Å respectively. Surprisingly, no obvious differences between the two SODs were observable. The protein crystallises as a homo dimer in the asymmetric unit. Because of the crystallographic symmetry, it forms a tetramer. Structures of both the manganese and the ferric form were solved using molecular replacement techniques and multiple isomorphous replacement. The tertiary structure is similar to that of the other superoxide dismutases, the metal being fivefold coordinated by three histidines, one aspartate and one water molecule. The second shell of residues consists of hydrophobic amino acids, histidines and two water molecules, which are assumed to be involved in both the catalytic activity and structural stability of this superoxide dismutase. This shell may also be responsible for the cambialistic behaviour. This work shows that the reason for the metal specificity is not trivial, although minor alterations in the metal environment might be responsible for this behaviour.
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  • 6
    ISSN: 1432-1327
    Keywords: Key words Dimeric dihaem cytochrome ; Stacked haem arrangement ; MAD phasing ; X-ray structure ; Novel fold
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  Haem-containing proteins are directly involved in electron transfer as well as in enzymatic functions. The "split-Soret" cytochrome (SSC) was isolated from the sulfate- and nitrate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 and has no significant nitrate or nitrite reductase activity. The protein received its name due its unusual spectral properties. It is a dimer containing two identical subunits of 26.3 kDa, each with two haem-c groups. A preliminary model for the three-dimensional structure of this cytochrome was derived using the Multiple Wavelength Anomalous Dispersion (MAD) phasing method. This model shows that SSC is indeed a dimer containing four haems at one end of the molecule. In each monomer the two haems have their edges overlapped within van der Waals contacts with an iron-to-iron distance of 9 Å. The polypeptide chain of each monomer supplies the sixth axial ligand to the haems of the other monomer. This work shows that SSC constitutes a new class of cytochrome. The stacking of the two haems in the monomer within van der Waals distances of each other, and also the short (van der Waals) distances between the two monomers in the dimeric molecule are unprecedented in hemoproteins. This particular haem arrangement is an excellent model for the spectral study (undertaken several years ago) of haem-haem interaction using the aggregated haem undecapeptide derived from mammalian cytochrome c.
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  • 7
    ISSN: 1432-1327
    Keywords: Key words Prismane ; Hybrid cluster ; Desulfovibrio ; X-ray structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  The three-dimensional structure of the native "putative prismane" protein from Desulfovibrio vulgaris (Hildenborough) has been solved by X-ray crystallography to a resolution of 1.72 Å. The molecule does not contain a [6Fe-6S] prismane cluster, but rather two 4Fe clusters some 12 Å apart and situated close to the interfaces formed by the three domains of the protein. Cluster 1 is a conventional [4Fe-4S] cubane bound, however, near the N-terminus by an unusual, sequential arrangement of four cysteine residues (Cys 3, 6, 15, 21). Cluster 2 is a novel 4Fe structure with two μ2-sulfido bridges, two μ2-oxo bridges, and a partially occupied, unidentified μ2 bridge X. The protein ligands of cluster 2 are widely scattered through the second half of the sequence and include three cysteine residues (Cys 312, 434, 459), one persulfido-cysteine (Cys 406), two glutamates (Glu 268, 494), and one histidine (His 244). With this unusual mixture of bridging and external type of ligands, cluster 2 is named the "hybrid" cluster, and its asymmetric, open structure suggests that it could be the site of a catalytic activity. X-ray absorption spectroscopy at the Fe K-edge is readily interpretable in terms of the crystallographic model when allowance is made for volume contraction at 10 K; no Fe··Fe distances beyond 3.1 Å could be identified. EPR, Mössbauer and MCD spectroscopy have been used to define the oxidation states and the magnetism of the clusters in relation to the crystallographic structure. Reduced cluster 1 is a [4Fe-4S]1+ cubane with S = 3/2; it is the first biological example of a "spin-admixed" iron-sulfur cluster. The hybrid cluster 2 has four oxidation states from (formally) all FeIII to three FeII plus one FeIII. The four iron ions are exchange coupled resulting in the system spins S = 0, 9/2, 0 (and 4), 1/2, respectively, for the four redox states. Resonance Raman spectroscopy suggests that the bridging ligand X which could not be identified unambiguously in the crystal structure is a solvent-exchangeable oxygen.
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  • 8
    ISSN: 1432-1327
    Keywords: Key words Recombinant horse apoferritin ; X-ray structure ; Stability ; Function
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  The X-ray structure of recombinant horse L-chain (rL) apoferritin, solved at 2.0 Å resolution with a final R factor of 17.9%, gives evidence that the residue at position 93 in the sequence is a proline and not a leucine, as found in earlier sequencing studies. The structure is isomorphous with other apoferritin structures, and we thus draw particular attention to those structural features which can be related to the stability and function of the protein. Analysis of hydrogen bonding and salt bridge interactions shows that dimers and tetramers are the most stable molecular entities within the protein shell: a result confirming earlier biophysical experiments. The stability of horse rL apoferritin to both dissociation into subunits at acidic pH values and to complete unfolding in guanidine chloride solutions is compared with that of other apoferritins. This emphasizes the role played by the salt bridge in the stability of this protein family. The horse rL apoferritin is significantly more resistant to denaturation than horse spleen ferritin, which in turn is more resistant than any human rH apoferritins, even those for which a salt bridge is restored. Finally, this structure determination not only establishes that a preformed pocket exists in L-chain apoferritin, at a site known to be able to bind porphyrin, but also underlines the particular function of a cluster of glutamic acids (E53, E56, E57 and E60) located at the entrance of this porphyrin-binding pocket.
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  • 9
    ISSN: 1573-4919
    Keywords: active site ; catalytic mechanism ; creatine kinase ; high-energy phosphate transport ; membrane binding ; metabolic channeling ; mitochondrial energetics ; octamer/dimer equilibrium ; X-ray structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Abstract Mitochondrial creatine kinase (Mi-CK) is a central enzyme in energy metabolism of tissues with high and fluctuating energy requirements. In this review, recent progress in the functional and structural characterization of Mi-CK is summarized with special emphasis on the solved X-ray structure of chicken Mib-CK octamer (Fritz-Wolf et al., Nature 381, 341-345, 1996). The new results are discussed in a historical context and related to the characteristics of CK isoforms as known from a large number of biophysical and biochemical studies. Finally, two hypothetical functional aspects of the Mi-CK structure are proposed: (i) putative membrane binding motifs at the top and bottom faces of the octamer and (ii) a possible functional role of the central 20 Å channel.
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  • 10
    Electronic Resource
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    Aquatic ecology 30 (1997), S. 331-337 
    ISSN: 1573-5125
    Keywords: restoration ; aquatic plants ; Chara ; seed bank ; hydrochemistry ; peat ; the Netherlands
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In the Netherlands peat was excavated for fuel until 1950. This gave rise to waterbodies (called turf ponds) which were then colonized by aquatic plants. Succession resulted in different aquatic plant communities and more terrestrialized stages such as floating fens. Nature conservation authorities started to excavate new turf ponds in 1990(ca. 2 ha y−1) with the aim to restore calcareous, mesotraphent ecosystems by totally setting back succession. A sequence of new species was revealed by mapping the aquatic vegetation from 1990 onwards.Chara spp. proved early colonizers, which was not expected because they have not been present in ditches and ponds in the area for the last 20 years. The denseChara vegetation prevents the resuspension of organic soil and contributes to keep the water column nutrient-poor and clear. ability of species such asStratiotes aloides to colonise the ponds from adjacent waterbodies is not possible because no open contact exists between a turf pond and a ditch. Management measures, such as re-introduction, have to be considered if the full-range of aquatic plant communities remains the goal.
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  • 11
    ISSN: 1573-5117
    Keywords: Lake Peipsi-Pihkva ; large shallow eutrophic lake ; hydrochemistry ; plankton ; macrozoobenthos ; macrophytes ; fishes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Lake Peipsi-Pihkva (3555 km2, mean depth 8.3 m), consisting of three parts, (L. Peipsi, L. Pihkva, L. Lämmijärv) is located on the border of Estonia and Russia. L. Peipsi belongs to unstratified eutrophic lakes with mesotrophic features, L. Lämmijärv has some dyseutrophic features, while L. Pihkva is strongly eutrophic. The total annual nutrient load is 15.57 tons N km−2 and 327 kgP km−2 with 74% of N and 39% of P originating from agriculture. The mean concentrations of total N and P in the lake are 876 mg m−3 and 46 mg m−3, respectively, both being the highest in L. Pihkva and the lowest in the northern part of L. Peipsi. Average pH is 8.14 and Secchi disk transparency 1.63 m. Diatoms and blue-green algae prevail in phytoplankton biomass. The blue-greens Gloeotrichia echinulata and Aphanizomenon flos-aquae dominate in summer causing the water-blooms. The concentration of Chla was the lowest in the northern part of L. Peipsi (mean 14.7 mg m−3) and the highest in the southern part of L. Pihkva (mean 47.9 mg m−3, median 16.3 mg m−3). An increase of Chla and decrease of Secchi depth could be noticed in 1983–1988, while in 1988–1994 the tendency was opposite. The long-term average primary production is 0.8 g C m−2 d−1. Zooplankton is remarkably rich in species, the average biomass in the vegetative period being 2–3 g m−3 and production 22 g C m−2. The role of rotifers in production is 53% followed by that of cladocerans (30%), copepods (16%) and Dreissena polymorpha larvae (1%). The total count of bacteria is 1–9 million cells per ml. Chironomus plumosus and Potamothrix hammoniensis are dominating in the profundal. The average abundance of macrozoobenthos (without big molluscs) 2617 ind. m−2, and their biomass 12.34 g m−2 are considered to be the highest among the large lakes of North Europe. Macroflora occupies a small percentage of the total lake area but is rich in species. Taxa forming communities are Potamogeton perfoliatus, Phragmites australis, Schoenoplectus laccustris, Potamogeton lucens, Eleocharis palustris, and Polygonum amphibium. Submerged vegetation occupies the first place amongst different growth forms, followed by emergent plants. The main commercial fishes are lake smelt, perch, ruff, roach, bream, pike, vendace and pikeperch. The stock of vendace has sharply decreased in the last years, while the amount of pikeperch has increased. Considering annual fish catches (9000–12000 tons or 25–34 kg ha−1), L. Peipsi-Pihkva exceeds all large lakes in North Europe.
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  • 12
    ISSN: 1573-5117
    Keywords: seasonality ; algae ; hydrochemistry ; ecology ; tropical river ; West Africa
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Seasonal studies were undertaken (August 1983–July 1984) toevaluate the algal distribution and ecology of the RiverDelimi, Jos Plateau, Nigeria at three stations: upstream, withlittle allochthonous input; midstream, receiving heavy domesticaffluents; downstream. A wide amplitude of variability wasdiscernible in physicochemical factors, and photosyntheticactivity and abundance of ‘suspended’ algae in relation to thedegree of pollution along the first 7-km stretch of the river.Conductivity (µS cm-1) showed a 9-fold increase fromupstream (x = 35) to downstream. The standing crop(Chl a) fluctuated markedly, with 6-times higher valuesfor a polluted midstream site (x = 18.2 mg m-3). Production rate measurements (mg C m-3 d-1) showed significant variability with relatively lowvalues (x = 610) recorded for the upstream andhighest (x = 1050) at the midstream site. Apositive correlation was obtained between production rates andChl a for the polluted midstream zone.
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  • 13
    ISSN: 1573-5117
    Keywords: pristine ; hydrochemistry ; podzol ; soil processes ; sulphate ; nitrogen
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract During the Surface Water Acidification Programme, ahydrochemical plot study was carried out at thepristine Høylandet study site during 1986–89. Theplot soils were acidic iron podzols (sensuKubiena), with a significant content of secondaryaluminium (Al), forming a potential major source oftoxic Al in streams and lakes. Rain and mist inputscontain small amounts of anthropogenic sulphate, withammonium inputs being enhanced during the summermonths. Vegetation canopy interactions, includingsorption and leaching, change input water chemistrybefore it reaches the soil, in which organicinteractions increase, especially during the summer.Amphibole in the soil parent material is probablyresponsible for the large mineral weathering ratedetermined and this source of base cations, alliedwith the small anthropogenic inputs, results in Alconcentrations in the streamwater being small incomparison with impacted sites.
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  • 14
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    International journal of salt lake research 4 (1995), S. 315-325 
    ISSN: 1573-8590
    Keywords: Argentina ; hydrochemistry ; inland waters
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geography
    Notes: Abstract The major ion chemistry of 639 aquatic localities in Argentina is presented and discussed. Salinities range from quite fresh (〈3 g L−1) to highly saline (〉300 g L−1); a variety of ion dominances occur but NaCl predominates in highly saline waters. The principal mechanisms controlling water chemistry are rock dominance and evaporation; atmospheric contributions are less important.
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  • 15
    ISSN: 1573-5028
    Keywords: Arabidopsis thaliana ; lignification ; monolignols ; plant peroxidase ; promoter ; X-ray structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Lignins are phenolic biopolymers synthesized by terrestrial, vascular plants for mechanical support and in response to pathogen attack. Peroxidases have been proposed to catalyse the dehydrogenative polymerization of monolignols into lignins, although no specific isoenzyme has been shown to be involved in lignin biosynthesis. Recently we isolated an extracellular anionic peroxidase, ATP A2, from rapidly lignifying Arabidopsis cell suspension culture and cloned its cDNA. Here we show that the Atp A2 promoter directs GUS reporter gene expression in lignified tissues of transgenic plants. Moreover, an Arabidopsis mutant with increased lignin levels compared to wild type shows increased levels of ATP A2 mRNA and of a mRNA encoding an enzyme upstream in the lignin biosynthetic pathway. The substrate specificity of ATP A2 was analysed by X-ray crystallography and docking of lignin precursors. The structure of ATP A2 was solved to 1.45 Å resolution at 100 K. Docking of p-coumaryl, coniferyl and sinapyl alcohol in the substrate binding site of ATP A2 were analysed on the basis of the crystal structure of a horseradish peroxidase C-CN-ferulic acid complex. The analysis indicates that the precursors p-coumaryl and coniferyl alcohols are preferred by ATP A2, while the oxidation of sinapyl alcohol will be sterically hindered in ATP A2 as well as in all other plant peroxidases due to an overlap with the conserved Pro-139. We suggest ATP A2 is involved in a complex regulation of the covalent cross-linking in the plant cell wall.
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  • 16
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    Photosynthesis research 55 (1998), S. 127-132 
    ISSN: 1573-5079
    Keywords: bacterial photosynthesis ; proton transfer ; Rhodobacter sphaeroides ; water clusters ; X-ray structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The structure of the reaction centre from Rhodobacter sphaeroides has been refined up to 2.4 Å resolution. Several clusters of firmly bound water molecules were found proximal to the primary and secondary quinones. They represent putative pathways for proton transfer.
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  • 17
    ISSN: 1573-5117
    Keywords: hydrochemistry ; coniferous forest ; temporal variation ; catchment ; acidity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A study of the spatio-temporal variation in hydrochemistry in the afforested catchment of the River Douglas, in the Araglin Valley, Co. Cork, Ireland, was undertaken over a two year period. The aim of the study was to examine the influence of afforestation on stream water quality both spatially and temporally. The catchment, one of the most westerly in Europe, with low atmospheric pollution, allowed the analysis of the interactions between conifer afforestation per se on stream chemistry. In contrast to most other studies, there was a general trend of increasing pH and related variables with distance from headwater despite increasing levels of catchment afforestation. In one tributary, pH and related variables increased rapidly as the stream entered the forest, with pH rising by 1.67 units over a distance of 1.2 km. Temporal fluctuations in most physico-chemical variables were minor and no acid pulses were noted during spate. Thus, the current level of afforestation within the River Douglas catchment does not appear to have negatively affected stream chemistry.
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