Showing papers by "Russian Academy of Sciences published in 2010"

International network of cancer genome projects

Abstract: The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.

HITEMP, the high-temperature molecular spectroscopic database

Abstract: A new molecular spectroscopic database for high-temperature modeling of the spectra of molecules in the gas phase is described. This database, called HITEMP, is analogous to the HITRAN database but encompasses many more bands and transitions than HITRAN for the absorbers H2O, CO2, CO, NO, and OH. HITEMP provides users with a powerful tool for a great many applications: astrophysics, planetary and stellar atmospheres, industrial processes, surveillance, non-local thermodynamic equilibrium problems, and investigating molecular interactions, to name a few. The sources and implementation of the spectroscopic parameters incorporated into HITEMP are discussed.

Genetic history of an archaic hominin group from Denisova Cave in Siberia

Abstract: Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.

The Microarray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

Abstract: Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. In the MAQC-II project, 36 independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity in rodents, or of breast cancer, multiple myeloma or neuroblastoma in humans. In total, >30,000 models were built using many combinations of analytical methods. The teams generated predictive models without knowing the biological meaning of some of the endpoints and, to mimic clinical reality, tested the models on data that had not been used for training. We found that model performance depended largely on the endpoint and team proficiency and that different approaches generated models of similar performance. The conclusions and recommendations from MAQC-II should be useful for regulatory agencies, study committees and independent investigators that evaluate methods for global gene expression analysis.

Influence of spring and autumn phenological transitions on forest ecosystem productivity

Abstract: We use eddy covariance measurements of net ecosystem productivity (NEP) from 21 FLUXNET sites (153 site-years of data) to investigate relationships between phenology and productivity (in terms of both NEP and gross ecosystem photosynthesis, GEP) in temperate and boreal forests. Results are used to evaluate the plausibility of four different conceptual models. Phenological indicators were derived from the eddy covariance time series, and from remote sensing and models. We examine spatial patterns (across sites) and temporal patterns (across years); an important conclusion is that it is likely that neither of these accurately represents how productivity will respond to future phenological shifts resulting from ongoing climate change. In spring and autumn, increased GEP resulting from an 'extra' day tends to be offset by concurrent, but smaller, increases in ecosystem respiration, and thus the effect on NEP is still positive. Spring productivity anomalies appear to have carry-over effects that translate to productivity anomalies in the following autumn, but it is not clear that these result directly from phenological anomalies. Finally, the productivity of evergreen needleleaf forests is less sensitive to phenology than is productivity of deciduous broadleaf forests. This has implications for how climate change may drive shifts in competition within mixed-species stands.

Ancient human genome sequence of an extinct Palaeo-Eskimo

Abstract: We report here the genome sequence of an ancient human. Obtained from approximately 4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20x, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.

The complete mitochondrial DNA genome of an unknown hominin from southern Siberia

Abstract: With the exception of Neanderthals, from which DNA sequences of numerous individuals have now been determined 1 , the number and genetic relationships of other hominin lineages are largely unknown. Here we report a complete mitochondrial (mt) DNA sequence retrieved from a bone excavated in 2008 in Denisova Cave in the Altai Mountains in southern Siberia. It represents a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago. This indicates that it derives from a hominin migration out of Africa distinct from that of the ancestors of Neanderthals and of modern humans. The stratigraphy of the cave where the bone was found suggests that the

Consistent Extension of Horava Gravity

Abstract: We propose a natural extension of Horava's model for quantum gravity, which is free from the notorious pathologies of the original proposal. The new model endows the scalar graviton mode with a regular quadratic action and remains power-counting renormalizable. At low energies, it reduces to a Lorentz-violating scalar-tensor gravity theory. The deviations with respect to general relativity can be made weak by an appropriate choice of parameters.

Combined Measurement and QCD Analysis of the Inclusive e± p Scattering Cross Sections at HERA

Abstract: A combination is presented of the inclusive deep inelastic cross sections measured by the H1 and ZEUS Collaborations in neutral and charged current unpolarised e(+/-)p scattering at HERA during the period 1994-2000. The data span six orders of magnitude in negative four-momentum-transfer squared, Q(2), and in Bjorken x. The combination method used takes the correlations of systematic uncertainties into account, resulting in an improved accuracy. The combined data are the sole input in a NLO QCD analysis which determines a new set of parton distributions, HERAPDF1.0, with small experimental uncertainties. This set includes an estimate of the model and parametrisation uncertainties of the fit result.

Extensive Methane Venting to the Atmosphere from Sediments of the East Siberian Arctic Shelf

Abstract: Remobilization to the atmosphere of only a small fraction of the methane held in East Siberian Arctic Shelf (ESAS) sediments could trigger abrupt climate warming, yet it is believed that sub-sea permafrost acts as a lid to keep this shallow methane reservoir in place. Here, we show that more than 5000 at-sea observations of dissolved methane demonstrates that greater than 80% of ESAS bottom waters and greater than 50% of surface waters are supersaturated with methane regarding to the atmosphere. The current atmospheric venting flux, which is composed of a diffusive component and a gradual ebullition component, is on par with previous estimates of methane venting from the entire World Ocean. Leakage of methane through shallow ESAS waters needs to be considered in interactions between the biogeosphere and a warming Arctic climate.

Metal-catalyzed immortal ring-opening polymerization of lactones, lactides and cyclic carbonates.

Abstract: This Perspective article summarizes efforts paid in our group to develop efficient metal-based catalysts for the immortal ring-opening polymerization (iROP) of cyclic esters in the presence of large amounts of alcohols (ROH) as chain transfer agents. The catalyst systems reviewed include discrete organometallic complexes based on rare earths, magnesium, calcium and more specifically zinc, as well as simple systems employing metal triflate salts, notably Al(OTf)3, for the (stereo)controlled iROP of lactide (LA), β-butyrolactone (BBL) and trimethylenecarbonate (TMC). Special emphasis is given to systems that allow the use of minute amounts of metal catalysts and large loadings of both monomer and alcohol for the rapid and productive formation of functional polyesters (H–Pol–OR) with controlled molecular features.

Simulating present-day climate with the INMCM4.0 coupled model of the atmospheric and oceanic general circulations

Abstract: The INMCM3.0 climate model has formed the basis for the development of a new climate-model version: the INMCM4.0. It differs from the previous version in that there is an increase in its spatial resolution and some changes in the formulation of coupled atmosphere-ocean general circulation models. A numerical experiment was conducted on the basis of this new version to simulate the present-day climate. The model data were compared with observational data and the INMCM3.0 model data. It is shown that the new model adequately reproduces the most significant features of the observed atmospheric and oceanic climate. This new model is ready to participate in the Coupled Model Intercomparison Project Phase 5 (CMIP5), the results of which are to be used in preparing the fifth assessment report of the Intergovernmental Panel on Climate Change (IPCC).

Selective hydrogen gas nanosensor using individual ZnO nanowire with fast response at room temperature

Abstract: In this work, we report on a single ZnO nanowire-based nanoscale sensor fabricated using focused ion beam (FIB/SEM) instrument. We studied the diameter dependence of the gas response and selectivity of ZnO nanowires (NWs) synthesized by chemical vapor phase growth method. The photoluminescence (PL) measurements were used to determine the deep levels related to defects which are presented in the ZnO nanomaterial as well as to evaluate the effect of thermal treatment in H2 atmosphere on the emission from ZnO nanowires. We show that sample annealed in hydrogen leads to passivation of recombination centers thus modifying the NWs properties. We studied the gas response and selectivity of these ZnO nanowires to H2 ,N H 3, i-Butane, CH4 gases at room temperature. Our results indicated that zinc oxide NWs hold a high promise for nanoscale sensor applications due to its capability to operate at room-temperature and its ability to tune the gas response and selectivity by the defect concentration and the diameter of ZnO nanowire. A method is proposed to reduce the nanosensor’s recovery time through the irradiation with an ultraviolet radiation pulse. The sensing mechanisms of ZnO nanowires will be discussed.

What is stress? Concepts, definitions and applications in seed science.

Abstract: Summary ‘Stresses’ that impact upon seeds can affect plant reproduction and productivity, and, hence, agriculture and biodiversity. In the absence of a clear definition of plant stress, we relate concepts from physics, medicine and psychology to stresses that are specific to seeds. Potential ‘eustresses’ that enhance function and ‘distresses’ that have harmful effects are considered in relation to the seed life cycle. Taking a triphasic biomedical stress concept published in 1936, the ‘General Adaptation Syndrome’, to the molecular level, the ‘alarm’ response is defined by post-translational modifications and stress signalling through cross-talk between reactive oxygen and nitrogen species, and seed hormones, that result in modifications to the transcriptome. Protection, repair, acclimation and adaptation are viewed as the ‘building blocks’ of the ‘resistance’ response, which, in seeds, are the basis for their longevity over centuries. When protection and repair mechanisms eventually fail, depending on dose and time of exposure to stress, cell death and, ultimately, seed death are the result, corresponding to ‘exhaustion’. This proposed seed stress concept may have wider applicability to plants in general. Contents Summary 655 I. Definitions of stress 656 II. The seed life cycle revisited in view of the eustress‐distress concept 657

The genome-wide structure of the Jewish people

Abstract: Contemporary Jews comprise an aggregate of ethno-religious communities whose worldwide members identify with each other through various shared religious, historical and cultural traditions. Historical evidence suggests common origins in the Middle East, followed by migrations leading to the establishment of communities of Jews in Europe, Africa and Asia, in what is termed the Jewish Diaspora. This complex demographic history imposes special challenges in attempting to address the genetic structure of the Jewish people. Although many genetic studies have shed light on Jewish origins and on diseases prevalent among Jewish communities, including studies focusing on uniparentally and biparentally inherited markers, genome-wide patterns of variation across the vast geographic span of Jewish Diaspora communities and their respective neighbours have yet to be addressed. Here we use high-density bead arrays to genotype individuals from 14 Jewish Diaspora communities and compare these patterns of genome-wide diversity with those from 69 Old World non-Jewish populations, of which 25 have not previously been reported. These samples were carefully chosen to provide comprehensive comparisons between Jewish and non-Jewish populations in the Diaspora, as well as with non-Jewish populations from the Middle East and north Africa. Principal component and structure-like analyses identify previously unrecognized genetic substructure within the Middle East. Most Jewish samples form a remarkably tight subcluster that overlies Druze and Cypriot samples but not samples from other Levantine populations or paired Diaspora host populations. In contrast, Ethiopian Jews (Beta Israel) and Indian Jews (Bene Israel and Cochini) cluster with neighbouring autochthonous populations in Ethiopia and western India, respectively, despite a clear paternal link between the Bene Israel and the Levant. These results cast light on the variegated genetic architecture of the Middle East, and trace the origins of most Jewish Diaspora communities to the Levant.

Thick gas discs in faint dwarf galaxies

Abstract: We determine the intrinsic axial ratio distribution of the gas discs of extremely faint MB < −14.5 dwarf irregular galaxies. We start with the measured (beam corrected) distribution of apparent axial ratios in the H i 21-cm images of dwarf irregular galaxies observed as part of the Faint Irregular Galaxy GMRT Survey (FIGGS). Assuming that the discs can be approximated as oblate spheroids, the intrinsic axial ratio distribution can be obtained from the observed apparent axial ratio distribution. We use a variety of methods to do this, and our final results are based on using Lucy's deconvolution algorithm. This method is constrained to produce physically plausible distributions, and also has the added advantage of allowing for observational errors to be accounted for. While one might a priori expect that gas discs would be thin (because collisions between gas clouds would cause them to quickly settle down to a thin disc), we find that the H i discs of faint dwarf irregulars are quite thick, with mean axial ratio 〈q〉∼ 0.6. While this is substantially larger than the typical value of ∼0.2 for the stellar discs of large spiral galaxies, it is consistent with the much larger ratio of velocity dispersion to rotational velocity (σ/vc) in dwarf galaxy H i discs as compared to that in spiral galaxies. Our findings have implications for studies of the mass distribution and the Tully–Fisher relation for faint dwarf irregular galaxies, where it is often assumed that the gas is in a thin disc.

Biocompatible and Biodegradable Materials for Organic Field-Effect Transistors

Abstract: Biocompatible-ingestible electronic circuits and capsules for medical diagnosis and monitoring are currently based on traditional silicon technology Organic electronics has huge potential for developing biodegradable, biocompatible, bioresorbable, or even metabolizable products An ideal pathway for such electronic devices involves fabrication with materials from nature, or materials found in common commodity products Transistors with an operational voltage as low as 4–5 V, a source drain current of up to 05 μ A and an on-off ratio of 3–5 orders of magnitude have been fabricated with such materials This work comprises steps towards environmentally safe devices in lowcost, large volume, disposable or throwaway electronic applications, such as in food packaging, plastic bags, and disposable dishware In addition, there is signifi cant potential to use such electronic items in biomedical implants

Ionization induced trapping in a laser wakefield accelerator.

Abstract: Experimental studies of electrons produced in a laser wakefield accelerator indicate trapping initiated by ionization of target gas atoms. Targets composed of helium and controlled amounts of various gases were found to increase the beam charge by as much as an order of magnitude compared to pure helium at the same electron density and decrease the beam divergence from $5.1\ifmmode\pm\else\textpm\fi{}1.0$ to $2.9\ifmmode\pm\else\textpm\fi{}0.8\text{ }\text{ }\mathrm{mrad}$. The measurements are supported by particle-in-cell modeling including ionization. This mechanism should allow generation of electron beams with lower emittance and higher charge than in preionized gas.

FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence

Abstract: Motivation: Amyloidogenic regions in polypeptide chains are very important because such regions are responsible for amyloid formation and aggregation. It is useful to be able to predict positions of amyloidogenic regions in protein chains. Results: Two characteristics (expected probability of hydrogen bonds formation and expected packing density of residues) have been introduced by us to detect amyloidogenic regions in a protein sequence. We demonstrate that regions with high expected probability of the formation of backbone–backbone hydrogen bonds as well as regions with high expected packing density are mostly responsible for the formation of amyloid fibrils. Our method (FoldAmyloid) has been tested on a dataset of 407 peptides (144 amyloidogenic and 263 non-amyloidogenic peptides) and has shown good performance in predicting a peptide status: amyloidogenic or non-amyloidogenic. The prediction based on the expected packing density classified correctly 75% of amyloidogenic peptides and 74% of non-amyloidogenic ones. Two variants (averaging by donors and by acceptors) of prediction based on the probability of formation of backbone–backbone hydrogen bonds gave a comparable efficiency. With a hybrid-scale constructed by merging the above three scales, our method is correct for 80% of amyloidogenic peptides and for 72% of non-amyloidogenic ones. Prediction of amyloidogenic regions in proteins where positions of amyloidogenic regions are known from experimental data has also been done. In the proteins, our method correctly finds 10 out of 11 amyloidogenic regions. Availability: The FoldAmyloid server is available at http://antares.protres.ru/fold-amyloid/ Contact: ogalzit@vega.protres.ru

The Afterglows of Swift-era Gamma-ray Bursts. I. Comparing pre-Swift and Swift-era Long/Soft (Type II) GRB Optical Afterglows

Abstract: We have gathered optical photometry data from the literature on a large sample of Swift-era gamma-ray burst (GRB) afterglows including GRBs up to 2009 September, for a total of 76 GRBs, and present an additional three pre-Swift GRBs not included in an earlier sample. Furthermore, we publish 840 additional new photometry data points on a total of 42 GRB afterglows, including large data sets for GRBs 050319, 050408, 050802, 050820A, 050922C, 060418, 080413A, and 080810. We analyzed the light curves of all GRBs in the sample and derived spectral energy distributions for the sample with the best data quality, allowing us to estimate the host-galaxy extinction. We transformed the afterglow light curves into an extinction-corrected z = 1 system and compared their luminosities with a sample of pre-Swift afterglows. The results of a former study, which showed that GRB afterglows clustered and exhibited a bimodal distribution in luminosity space, are weakened by the larger sample. We found that the luminosity distribution of the two afterglow samples (Swift-era and pre-Swift) is very similar, and that a subsample for which we were not able to estimate the extinction, which is fainter than the main sample, can be explained by assuming a moderate amount of line-of-sight host extinction. We derived bolometric isotropic energies for all GRBs in our sample, and found only a tentative correlation between the prompt energy release and the optical afterglow luminosity at 1 day after the GRB in the z = 1 system. A comparative study of the optical luminosities of GRB afterglows with echelle spectra (which show a high number of foreground absorbing systems) and those without, reveals no indication that the former are statistically significantly more luminous. Furthermore, we propose the existence of an upper ceiling on afterglow luminosities and study the luminosity distribution at early times, which was not accessible before the advent of the Swift satellite. Most GRBs feature afterglows that are dominated by the forward shock from early times on. Finally, we present the first indications of a class of long GRBs, which form a bridge between the typical high-luminosity, high-redshift events and nearby low-luminosity events (which are also associated with spectroscopic supernovae) in terms of energetics and observed redshift distribution, indicating a continuous distribution overall.

Multiple roles of cytochrome c oxidase in mammalian cells under action of red and IR‐A radiation

Abstract: This article reviews the current knowledge in photobiology and photomedicine about the influence of monochromatic, quasimonochromatic, and bread-band radiation of red-to-near infrared (IR-A) part on solar spectrum upon mammalian cells and human skin. The role of cytochrome c oxidase as the photoacceptor and photosignal transducer is underlined and its photosensitivity at certain circumstances is discussed. The role of ATP as a critical signaling molecule is discussed.

GPS velocity field for the Tien Shan and surrounding regions

Abstract: [1] Measurements at ∼400 campaign-style GPS points and another 14 continuously recording stations in central Asia define variations in their velocities both along and across the Kyrgyz and neighboring parts of Tien Shan. They show that at the longitude of Kyrgyzstan the Tarim Basin converges with Eurasia at 20 ± 2 mm/yr, nearly two thirds of the total convergence rate between India and Eurasia at this longitude. This high rate suggests that the Tien Shan has grown into a major mountain range only late in the evolution of the India-Eurasia collision. Most of the convergence between Tarim and Eurasia within the upper crust of the Tien Shan presumably occurs by slip on faults on the edges of and within the belt, but 1–3 mm/yr of convergence is absorbed farther north, at the Dzungarian Alatau and at a lower rate with the Kazakh platform to the west. The Tarim Basin is thrust beneath the Tien Shan at ∼4–7 mm/yr. With respect to Eurasia, the Ferghana Valley rotates counterclockwise at ∼0.7° Myr−1 about an axis at the southwest end of the valley. Thus, GPS data place a bound of ∼4 mm/yr on the rate of crustal shortening across the Chatkal and neighboring ranges on the northwest margin of the Ferghana Valley, and they limit the present-day slip rate on the right-lateral Talas-Ferghana fault to less than ∼2 mm/yr. GPS measurements corroborate geologic evidence indicating that the northern margin of the Pamir overthrusts the Alay Valley and require a rate of at least 10 and possibly 15 mm/yr.

The design of artificial nestboxes for the study of secondary hole-nesting birds: a review of methodological inconsistencies and potential biases

Abstract: The widespread use of artificial nestboxes has led to significant advances in our knowledge of the ecology, behaviour and physiology of cavity nesting birds, especially small passerines. Nestboxes have made it easier to perform routine monitoring and experimental manipulation of eggs or nestlings, and also repeatedly to capture, identify and manipulate the parents. However, when comparing results across study sites the use of nestboxes may also introduce a potentially significant confounding variable in the form of differences in nestbox design amongst studies, such as their physical dimensions, placement height, and the way in which they are constructed and maintained. However, the use of nestboxes may also introduce an unconsidered and potentially significant confounding variable due to differences in nestbox design amongst studies, such as their physical dimensions, placement height, and the way in which they are constructed and maintained. Here we review to what extent the characteristics of artificial nestboxes (e.g. size, shape, construction material, colour) are documented in the 'methods' sections of publications involving hole-nesting passer- ine birds using natural or excavated cavities or artificial nestboxes for reproduction and roosting. Despite explicit previ- ous recommendations that authors describe in detail the characteristics of the nestboxes used, we found that the description of nestbox characteristics in most recent publications remains poor and insufficient. We therefore list the types of descriptive data that should be included in the methods sections of relevant manuscripts and justify this by discussing how variation in nestbox characteristics can affect or confound conclusions from nestbox studies. We also propose several recommendations to improve the reliability and usefulness of research based on long-term studies of any secondary hole-nesting species using artificial nestboxes for breeding or roosting.

Status of Biodiversity in the Baltic Sea

Abstract: The brackish Baltic Sea hosts species of various origins and environmental tolerances. These immigrated to the sea 10,000 to 15,000 years ago or have been introduced to the area over the relatively recent history of the system. The Baltic Sea has only one known endemic species. While information on some abiotic parameters extends back as long as five centuries and first quantitative snapshot data on biota (on exploited fish populations) originate generally from the same time, international coordination of research began in the early twentieth century. Continuous, annual Baltic Sea-wide long-term datasets on several organism groups (plankton, benthos, fish) are generally available since the mid-1950s. Based on a variety of available data sources (published papers, reports, grey literature, unpublished data), the Baltic Sea, incl. Kattegat, hosts altogether at least 6,065 species, including at least 1,700 phytoplankton, 442 phytobenthos, at least 1,199 zooplankton, at least 569 meiozoobenthos, 1,476 macrozoobenthos, at least 380 vertebrate parasites, about 200 fish, 3 seal, and 83 bird species. In general, but not in all organism groups, high sub-regional total species richness is associated with elevated salinity. Although in comparison with fully marine areas the Baltic Sea supports fewer species, several facets of the system's diversity remain underexplored to this day, such as micro-organisms, foraminiferans, meiobenthos and parasites. In the future, climate change and its interactions with multiple anthropogenic forcings are likely to have major impacts on the Baltic biodiversity.