Showing papers by "Russian Academy of Sciences published in 2000"
TL;DR: Analysis of amino acid sequences, based on the normalized net charge and mean hydrophobicity, has been applied to two sets of proteins and shows that “natively unfolded” proteins are specifically localized within a unique region of charge‐hydrophobia phase space.
Abstract: "Natively unfolded" proteins occupy a unique niche within the protein kingdom in that they lack ordered structure under conditions of neutral pH in vitro. Analysis of amino acid sequences, based on the normalized net charge and mean hydrophobicity, has been applied to two sets of proteins: small globular folded proteins and "natively unfolded" ones. The results show that "natively unfolded" proteins are specifically localized within a unique region of charge-hydrophobicity phase space and indicate that a combination of low overall hydrophobicity and large net charge represent a unique structural feature of "natively unfolded" proteins.
2,029 citations
1,992 citations
TL;DR: It is suggested that while large-scale trends show considerable geographical and temporal variability, amphibian populations are in fact declining—and that this decline has been happening for several decades.
Abstract: Although there is growing concern that amphibian populations are declining globally, much of the supporting evidence is either anecdotal or derived from short-term studies at small geographical scales. This raises questions not only about the difficulty of detecting temporal trends in populations which are notoriously variable, but also about the validity of inferring global trends from local or regional studies. Here we use data from 936 populations to assess large-scale temporal and spatial variations in amphibian population trends. On a global scale, our results indicate relatively rapid declines from the late 1950s/early 1960s to the late 1960s, followed by a reduced rate of decline to the present. Amphibian population trends during the 1960s were negative in western Europe (including the United Kingdom) and North America, but only the latter populations showed declines from the 1970s to the late 1990s. These results suggest that while large-scale trends show considerable geographical and temporal variability, amphibian populations are in fact declining--and that this decline has been happening for several decades.
1,297 citations
TL;DR: In this paper, the authors investigated the accuracy limits of putative universal templates for visual pigment absorbance spectra, and if possible to amend the templates to overcome the limitations, and concluded that the idea of universal templates remains valid and useful at the present level of accuracy of data on photoreceptor absorbance.
Abstract: Absorbance spectra were recorded by microspectrophotometry from 39 different rod and cone types representing amphibians, reptiles, and fishes, with A1- or A2-based visual pigments and λmax ranging from 357 to 620 nm. The purpose was to investigate accuracy limits of putative universal templates for visual pigment absorbance spectra, and if possible to amend the templates to overcome the limitations. It was found that (1) the absorbance spectrum of frog rhodopsin extract very precisely parallels that of rod outer segments from the same individual, with only a slight hypsochromic shift in λmax, hence templates based on extracts are valid for absorbance in situ; (2) a template based on the bovine rhodopsin extract data of Partridge and De Grip (1991) describes the absorbance of amphibian rod outer segments excellently, contrary to recent electrophysiological results; (3) the λmax/λ invariance of spectral shape fails for A1 pigments with small λmax and for A2 pigments with large λmax, but the deviations are systematic and can be readily incorporated into, for example, the Lamb (1995) template. We thus propose modified templates for the main “α-band” of A1 and A2 pigments and show that these describe both absorbance and spectral sensitivities of photoreceptors over the whole range of λmax. Subtraction of the α-band from the full absorbance spectrum leaves a “β-band” described by a λmax-dependent Gaussian. We conclude that the idea of universal templates (one for A1- and one for A2-based visual pigments) remains valid and useful at the present level of accuracy of data on photoreceptor absorbance and sensitivity. The sum of our expressions for the α- and β-band gives a good description for visual pigment spectra with λmax > 350 nm.
985 citations
TL;DR: A significant correlation between the NRY haplotype data and principal components based on 95 protein markers was observed, indicating the effectiveness of NRY binary polymorphisms in the characterization of human population composition and history.
Abstract: A genetic perspective of human history in Europe was derived from 22 binary markers of the nonrecombining Y chromosome (NRY). Ten lineages account for >95% of the 1007 European Y chromosomes studied. Geographic distribution and age estimates of alleles are compatible with two Paleolithic and one Neolithic migratory episode that have contributed to the modern European gene pool. A significant correlation between the NRY haplotype data and principal components based on 95 protein markers was observed, indicating the effectiveness of NRY binary polymorphisms in the characterization of human population composition and history.
743 citations
TL;DR: In this article, the possibility of fabricating a wide class of free-standing nano-objects based on few monolayers thick scrolled heterostructures was shown, using an ultra-thin film (1 ML GaAs:1 ML InAs).
Abstract: The possibility is shown to fabricate a wide class of free-standing nano-objects based on few monolayers thick scrolled heterostructures. Using an ultra-thin film (1 ML GaAs:1 ML InAs), nanotubes with an inside diameter of ≈2 nm have been obtained, which constitutes the limiting size for this system. Molecular-beam-expitaxy overgrown structures with nanotubes embedded into GaAs have been obtained.
723 citations
TL;DR: A combination of phylogenetic analysis and FISH was used to reveal 16 globally distributed sequence clusters and to confirm the broad distribution, abundance, and high biomass of members of the class Actinobacteria in freshwater ecosystems.
Abstract: (FISH) with probes specific for the hgcI cluster showed abundances of up to 1.7 3 10 5 cells ml 21 in Lake Gossenkollesee, with strong seasonal fluctuations, and high abundances in the two other lakes investigated. Cell size measurements revealed that Actinobacteria in Lake Gossenkollesee can account for up to 63% of the bacterioplankton biomass. A combination of phylogenetic analysis and FISH was used to reveal 16 globally distributed sequence clusters and to confirm the broad distribution, abundance, and high biomass of members of the class Actinobacteria in freshwater ecosystems.
617 citations
TL;DR: Protein microchips were used in immunoassays for detection of antigens or antibodies, as well as to carry out enzymatic reactions and to measure their kinetics in the absence or presence of an inhibitor.
608 citations
Abstract: Analytic properties of the reflection coefficient of a multilayer metal-backed slab are considered. The result is a new form of the dispersion relationship, which characterizes the integral of the reflectance over wavelength in terms of the total thickness and averaged static permeability of the slab. The relation may be transformed to an inequality, which produces the least thickness to bandwidth ratio achievable for a physically realizable radar absorber. The particular cases of broad-band and narrow-band absorbers are discussed. The least thickness of a 10-dB broad-band dielectric radar absorber is shown to be 1/17 of the largest operating wavelength. The discussion also involves the results of a numerical study.
608 citations
TL;DR: It is suggested that the stationary phase, which is generally considered to be reached when the availability of nutrients becomes limiting, was brought on under conditions by the formation of diffusion barriers in the thin layers of unfrozen water known to be present in permafrost soils, the thickness of which depends on temperature.
Abstract: Metabolic activity was measured in the laboratory at temperatures between 5 and -20 degrees C on the basis of incorporation of (14)C-labeled acetate into lipids by samples of a natural population of bacteria from Siberian permafrost (permanently frozen soil). Incorporation followed a sigmoidal pattern similar to growth curves. At all temperatures, the log phase was followed, within 200 to 350 days, by a stationary phase, which was monitored until the 550th day of activity. The minimum doubling times ranged from 1 day (5 degrees C) to 20 days (-10 degrees C) to ca. 160 days (-20 degrees C). The curves reached the stationary phase at different levels, depending on the incubation temperature. We suggest that the stationary phase, which is generally considered to be reached when the availability of nutrients becomes limiting, was brought on under our conditions by the formation of diffusion barriers in the thin layers of unfrozen water known to be present in permafrost soils, the thickness of which depends on temperature.
562 citations
TL;DR: In this paper, Chandra data was used to map the gas temperature in the central region of the merging cluster A2142 and showed that the cluster is markedly nonisothermal; it appears that the central cooling flow has been disturbed but not destroyed by a merger.
Abstract: We use Chandra data to map the gas temperature in the central region of the merging cluster A2142. The cluster is markedly nonisothermal; it appears that the central cooling flow has been disturbed but not destroyed by a merger. The X-ray image exhibits two sharp, bow-shaped, shocklike surface brightness edges or gas density discontinuities. However, temperature and pressure profiles across these edges indicate that these are not shock fronts. The pressure is reasonably continuous across these edges, while the entropy jumps in the opposite sense to that in a shock (i.e., the denser side of the edge has lower temperature, and hence lower entropy). Most plausibly, these edges delineate the dense subcluster cores that have survived a merger and ram pressure stripping by the surrounding shock-heated gas.
TL;DR: Functioning of α‐LA requires its interactions with membranes, proteins, peptides and low molecular weight substrates and products, and it was shown that these interactions are modulated by the binding of metal cations.
TL;DR: Using a combination of the quartz crystal microbalance and surface plasmon resonance techniques, the spontaneous formation of supported lipid bilayers from small unilamellar vesicles is studied for the first time.
Abstract: Using a combination of the quartz crystal microbalance and surface plasmon resonance techniques, we have studied the spontaneous formation of supported lipid bilayers from small (approximately 25 nm) unilamellar vesicles. Together these experimental methods measure the amount of lipid adsorbed on the surface and the amount of water trapped by the lipid. With this approach, we have, for the first time, been able to observe in detail the progression from the adsorption of intact vesicles to rupture and bilayer formation. Monte Carlo simulations reproduce the data.
24 Jan 2000
TL;DR: It is demonstrated that the excited state transitions arise from lateral quantization and that tuning through the inhomogeneous distribution of dot energies can be achieved by variation of electric field.
Abstract: New information on the electron-hole wave functions in InAs-GaAs self-assembled quantum dots is deduced from Stark effect spectroscopy. Most unexpectedly it is shown that the hole is localized towards the top of the dot, above the electron, an alignment that is inverted relative to the predictions of all recent calculations. We are able to obtain new information on the structure and composition of buried quantum dots from modeling of the data. We also demonstrate that the excited state transitions arise from lateral quantization and that tuning through the inhomogeneous distribution of dot energies can be achieved by variation of electric field.
TL;DR: In this paper, the normal spectral absorptance of a number of metal, ceramic and polymer powders susceptible to be utilised for selective laser sintering (SLS) technique was experimentally determined.
Abstract: The normal spectral absorptance of a number of metal, ceramic and polymer powders susceptible to be utilised for selective laser sintering (SLS) technique was experimentally determined. The measurements were performed with two laser wavelengths of 1.06μm and 10.6μm obtained by using two lasers – Nd‐YAG and CO2 respectively. The change in the powder absorptance with time during laser processing was also investigated. The effect of the absorptance characteristics on the sintering process is discussed.
TL;DR: The path of the nucleic acids through a transcription elongation complex was tracked by mapping cross-links between bacterial RNA polymerase and transcript RNA or template DNA onto the x-ray crystal structure and the resulting model provides insight into the functional properties of the transcription complex.
Abstract: The path of the nucleic acids through a transcription elongation complex was tracked by mapping cross-links between bacterial RNA polymerase (RNAP) and transcript RNA or template DNA onto the x-ray crystal structure. In the resulting model, the downstream duplex DNA is nestled in a trough formed by the β′ subunit and enclosed on top by the β subunit. In the RNAP channel, the RNA/DNA hybrid extends from the enzyme active site, along a region of the β subunit harboring rifampicin resistance mutations, to the β′ subunit “rudder.” The single-stranded RNA is then extruded through another channel formed by the β-subunit flap domain. The model provides insight into the functional properties of the transcription complex.
TL;DR: Comparison of double-stranded RNA regions and positions of proteins identified in both cryo-EM and X-ray maps indicates good overall agreement but points to rearrangements of ribosomal components required for the subunit association.
TL;DR: Results from molecular dynamics free energy perturbation calculations that both establish the nature of the multiple ion conduction mechanism and yield the correct ion selectivity of the K+ channel are reported.
Abstract: Ion-selective channels enable the specific permeation of ions through cell membranes and provide the basis of several important biological functions; for example, electric signalling in the nervous system1. Although a large amount of electrophysiological data is available1,2, the molecular mechanisms by which these channels can mediate ion transport remain a significant unsolved problem. With the recently determined crystal structure of the representative K+ channel (KcsA) from Streptomyces lividans3, it becomes possible to examine ion conduction pathways on a microscopic level. K+ channels utilize multi-ion conduction mechanisms1,2,4,5,6, and the three-dimensional structure also shows several ions present in the channel. Here we report results from molecular dynamics free energy perturbation calculations that both establish the nature of the multiple ion conduction mechanism and yield the correct ion selectivity of the channel. By evaluating the energetics of all relevant occupancy states of the selectivity filter, we find that the favoured conduction pathway involves transitions only between two main states with a free difference of about 5 kcal mol-1. Other putative permeation pathways can be excluded because they would involve states that are too high in energy.
TL;DR: A method for quantitating proteins and peptides in the low picomole and sub-picomole range has been developed using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) with internal (18)O-labeled standards.
Abstract: A method for quantitating proteins and peptides in the low picomole and sub-picomole range has been developed using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) with internal (18)O-labeled standards. A simple procedure is proposed to produce such internal standards for the tested sample by enzymatic hydrolysis of the same sample (with known concentration) in (18)O-water. A mathematical algorithm was developed which uses the isotopic patterns of the substance, the internal standard, and the substance/internal standard mixture for accurate quantitation of the substance. A great advantages of the proposed method is the absence of molecular weight limitation for the protein quantitation and the possibility of quantitation without previous fractionation of proteins and peptides. Using this strategy, the peptide angiotensinogen and two proteins, RNase and its protein inhibitor, were quantified by MALDI-time-of-flight (TOF) mass spectrometry.
TL;DR: In vivo labeling with E5 is used to measure expression from the heat shock-dependent promoter in Caenorhabditis elegans and from the Otx-2 promoter in developing Xenopus embryos to monitor both activation and down-regulation of target promoters on the whole-organism scale.
Abstract: We generated a mutant of the red fluorescent protein drFP583. The mutant (E5) changes its fluorescence from green to red over time. The rate of color conversion is independent of protein concentration and therefore can be used to trace time-dependent expression. We used in vivo labeling with E5 to measure expression from the heat shock-dependent promoter in Caenorhabditis elegans and from the Otx-2 promoter in developing Xenopus embryos. Thus, E5 is a "fluorescent timer" that can be used to monitor both activation and down-regulation of target promoters on the whole-organism scale.
TL;DR: The discovery of exotic, strontium-enriched melt inclusions in Mauna Loa olivines demonstrates that the former gabbro can retain much of its original chemical identity through the convective cycle without completely mixing with other portions of the former oceanic crust.
Abstract: The hypothesis that mantle plumes contain recycled oceanic crust1 is now widely accepted. Some specific source components of the Hawaiian plume have been inferred to represent recycled oceanic basalts2, pelagic sediments3,4 or oceanic gabbros5. Bulk lava compositions, however, retain the specific trace-element fingerprint of the original crustal component in only a highly attenuated form. Here we report the discovery of exotic, strontium-enriched melt inclusions in Mauna Loa olivines. Their complete trace-element patterns strongly resemble those of layered gabbros found in ophiolites, which are characterized by cumulus plagioclase with very high strontium abundances6. The major-element compositions of these melts indicate that their composition cannot be the result of the assimilation of present-day oceanic crust through which the melts have travelled. Instead, the gabbro has been transformed into a (high-pressure) eclogite by subduction and recycling, and this eclogite has then been incorporated into the Hawaiian mantle plume. The trace-element signature of the original plagioclase is present only as a ‘ghost’ signature, which permits specific identification of the recycled rock type. The ‘ghost plagioclase’ trace-element signature demonstrates that the former gabbro can retain much of its original chemical identity through the convective cycle without completely mixing with other portions of the former oceanic crust.
Book•
01 Jan 2000TL;DR: Lightning Physics and Lightning Protection as mentioned in this paper provides a comprehensive and up-to-date review of lightning, including its hazards and protection techniques, and provides technical advice and practical recommendations, and explores the prospects for the preventive control of a lightning leader.
Abstract: Lightning Physics and Lightning Protection presents a comprehensive and up-to-date review of lightning, including its hazards and protection techniques. The authors first discuss the effectiveness of conventional protective measures, supply technical advice and practical recommendations, and explore the prospects for the preventive control of a lightning leader, followed by a discussion of the initiation of a leader and return stroke and subsequent components. After including measurements useful for understanding lightning and its effects, the book describes the mechanism of lightning discharge processes. It then examines the effects of large aircraft, high-voltage lines, and other high-altitude constructions on lightning trajectory and leader attraction. The book concludes by studying the action of lightning's electrical and magnetic fields and the lightning current on industrial premises, power transmission lines, underground communications, aircraft and their electrical circuits, and the induction of a dangerous overvoltage.A clear, straightforward, and systematic presentation of complicated material, Lightning Physics and Lightning Protection provides deep insight into the physics of lightning, simple analytical estimates, and a detailed illustration of effects by computer simulation, making this resource essential for those who investigate lightning phenomena and who have to solve practical protection problems.
Book•
21 Dec 2000TL;DR: In this paper, the authors studied the behavior of discontinuities under vanishing viscosity and dispersion in nonlinear hyperbolic systems and applied it to magnetohydrodynamic equations, nonlinear waves in elastic media, and electromagnetic wave propagation in magnetics.
Abstract: A number of physical phenomena are described by nonlinear hyperbolic equations Presence of discontinuous solutions motivates the necessity of development of reliable numerical methods based on the fundamental mathematical properties of hyperbolic systems Construction of such methods for systems more complicated than the Euler gas dynamic equations requires the investigation of existence and uniqueness of the self-similar solutions to be used in the development of discontinuity-capturing high-resolution numerical methods This frequently necessitates the study of the behavior of discontinuities under vanishing viscosity and dispersion We discuss these problems in the application to the magnetohydrodynamic equations, nonlinear waves in elastic media, and electromagnetic wave propagation in magnetics
TL;DR: There is a broad overlap in energy partitioning between Arctic and boreal ecosystems, although Arctic ecosystems and light taiga generally have higher ground heat flux because there is less leaf and stem area to shade the ground surface, and the thermal gradient from the surface to permafrost is steeper.
Abstract: This paper summarizes and analyses available data on the surface energy balance of Arctic tundra and boreal forest. The complex interactions between ecosystems and their surface energy balance are also examined, including climatically induced shifts in ecosystem type that might amplify or reduce the effects of potential climatic change. High latitudes are characterized by large annual changes in solar input. Albedo decreases strongly from winter, when the surface is snow-covered, to summer, especially in nonforested regions such as Arctic tundra and boreal wetlands. Evapotranspiration (QE) of high-latitude ecosystems is less than from a freely evaporating surface and decreases late in the season, when soil moisture declines, indicating stomatal control over QE, particularly in evergreen forests. Evergreen conifer forests have a canopy conductance half that of deciduous forests and consequently lower QE and higher sensible heat flux (QH). There is a broad overlap in energy partitioning between Arctic and boreal ecosystems, although Arctic ecosystems and light taiga generally have higher ground heat flux because there is less leaf and stem area to shade the ground surface, and the thermal gradient from the surface to permafrost is steeper. Permafrost creates a strong heat sink in summer that reduces surface temperature and therefore heat flux to the atmosphere. Loss of permafrost would therefore amplify climatic warming. If warming caused an increase in productivity and leaf area, or fire caused a shift from evergreen to deciduous forest, this would increase QE and reduce QH. Potential future shifts in vegetation would have varying climate feedbacks, with largest effects caused by shifts from boreal conifer to shrubland or deciduous forest (or vice versa) and from Arctic coastal to wet tundra. An increase of logging activity in the boreal forests appears to reduce QE by roughly 50% with little change in QH, while the ground heat flux is strongly enhanced.
01 Oct 2000
TL;DR: In this article, a polycrystalline Nd-doped Y3Al5O12 ceramics was used for the first time to achieve highly efficient laser oscillation at 1064 nm.
Abstract: Optical absorption, emission spectra have been measured for polycrystalline Nd-doped Y3Al5O12 ceramics. Fluorescence lifetimes of 257.6 μs, 237.6 μs, 184.2 μs and 95.6 μs have been obtained for 0.6%, 1%, 2% and 4% neodymium-doped YAG ceramics, respectively. For the first time, highly efficient laser oscillation at 1064 nm has been obtained with this kind of ceramics. Slope efficiency of 53% has been achieved on a uncoated 4.8-mm thick 1% Nd:YAG ceramics sample. Optical to optical conversion efficiency is 47.6%. Laser oscillation has also been obtained with a 2% Nd:YAG ceramics. The optical properties and laser output results have been compared with that of Nd:YAG single crystal grown by the Czochralski method. Almost identical results have been achieved including laser experiments results. But fabrication of Nd:YAG ceramics is much easier compared to the single-crystal growth method. And also large size (now of about 400 mm diameter×5 mm is available) and high-concentration (>1%) Nd:YAG ceramics can be fabricated. The results show that this kind of Nd:YAG ceramics is a very good alternative to Nd:YAG single crystal.
TL;DR: A naturally nonfluorescent homolog of GFP is found to determine strong purple coloration of tentacles in the sea anemone Anemonia sulcata, demonstrating that long wavelength fluorescence is attainable in GFP-like fluorescent proteins.
TL;DR: Radiocarbon-dated macrofossils are used to document Holocene treeline history across northern Russia (including Siberia), and Boreal forest development in this region commenced by 10,000 yr B.P..
TL;DR: It is shown that a phenomenologically acceptable range of validity of four-dimensional gravity extending from microscopic to cosmological scales is obtained without strong fine-tuning of parameters in models with infinite extra dimensions.
Abstract: The standard picture of viable higher-dimensional theories is that direct manifestations of extra dimensions occur at short distances only, whereas long-distance physics is effectively four-dimensional We show that this is not necessarily true in models with infinite extra dimensions As an example, we consider a five-dimensional scenario with three 3-branes in which gravity is five dimensional at both short- and very long-distance scales, with conventional four-dimensional gravity operating at intermediate length scales A phenomenologically acceptable range of validity of four-dimensional gravity extending from microscopic to cosmological scales is obtained without strong fine-tuning of parameters
TL;DR: The nature of genetic variation for Drosophila longevity in a population of recombinant inbred lines was investigated, providing support for the pleiotropy theory of senescence and the hypothesis that variation for longevity might be maintained by opposing selection pressures in males and females and variable environments.
Abstract: The nature of genetic variation for Drosophila longevity in a population of recombinant inbred lines was investigated by estimating quantitative genetic parameters and mapping quantitative trait loci (QTL) for adult life span in five environments: standard culture conditions, high and low temperature, and heat-shock and starvation stress. There was highly significant genetic variation for life span within each sex and environment. In the analysis of variance of life span pooled over sexes and environments, however, the significant genetic variation appeared in the genotype x sex and genotype x environment interaction terms. The genetic correlation of longevity across the sexes and environments was not significantly different from zero in these lines. We estimated map positions and effects of QTL affecting life span by linkage to highly polymorphic roo transposable element markers, using a multiple-trait composite interval mapping procedure. A minimum of 17 QTL were detected; all were sex and/or environment-specific. Ten of the QTL had sexually antagonistic or antagonistic pleiotropic effects in different environments. These data provide support for the pleiotropy theory of senescence and the hypothesis that variation for longevity might be maintained by opposing selection pressures in males and females and variable environments. Further work is necessary to assess the generality of these results, using different strains, to determine heterozygous effects and to map the life span QTL to the level of genetic loci.
TL;DR: In this paper, the second-order Doppler (SOD) shift has been used to determine the reduced isotopic partition function ratio (β-factor) for a wide range of minerals.