Showing papers by "Russian Academy of Sciences published in 2008"

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

Abstract: There are currently few therapeutic options for patients with pancreatic cancer, and new insights into the pathogenesis of this lethal disease are urgently needed. Toward this end, we performed a comprehensive genetic analysis of 24 pancreatic cancers. We first determined the sequences of 23,219 transcripts, representing 20,661 protein-coding genes, in these samples. Then, we searched for homozygous deletions and amplifications in the tumor DNA by using microarrays containing probes for approximately 10(6) single-nucleotide polymorphisms. We found that pancreatic cancers contain an average of 63 genetic alterations, the majority of which are point mutations. These alterations defined a core set of 12 cellular signaling pathways and processes that were each genetically altered in 67 to 100% of the tumors. Analysis of these tumors' transcriptomes with next-generation sequencing-by-synthesis technologies provided independent evidence for the importance of these pathways and processes. Our data indicate that genetically altered core pathways and regulatory processes only become evident once the coding regions of the genome are analyzed in depth. Dysregulation of these core pathways and processes through mutation can explain the major features of pancreatic tumorigenesis.

Freshwater Ecoregions of the World: A New Map of Biogeographic Units for Freshwater Biodiversity Conservation

Abstract: We present a new map depicting the first global biogeographic regionalization of Earth's freshwater systems. This map of freshwater ecoregions is based on the distributions and compositions of freshwater fish species and incorporates major ecological and evolutionary patterns. Covering virtually all freshwater habitats on Earth, this ecoregion map, together with associated species data, is a useful tool for underpinning global and regional conservation planning efforts (particularly to identify outstanding and imperiled freshwater systems); for serving as a logical framework for large-scale conservation strategies; and for providing a global-scale knowledge base for increasing freshwater biogeographic literacy. Preliminary data for fish species compiled by ecoregion reveal some previously unrecognized areas of high biodiversity, highlighting the benefit of looking at the world's freshwaters through a new framework.

Mechanisms of real and apparent priming effects and their dependence on soil microbial biomass and community structure: critical review

Abstract: The number of studies on priming effects (PE) in soil has strongly increased during the last years. The information regarding real versus apparent PE as well as their mechanisms remains controversial. Based on a meta-analysis of studies published since 1980, we evaluated the intensity, direction, and the reality of PE in dependence on the amount and quality of added primers, the microbial biomass and community structure, enzyme activities, soil pH, and aggregate size. The meta-analysis allowed revealing quantitative relationships between the amounts of added substrates as related to microbial biomass C and induced PE. Additions of easily available organic C up to 15% of microbial biomass C induce a linear increase of extra CO2. When the added amount of easily available organic C is higher than 50% of the microbial biomass C, an exponential decrease of the PE or even a switch to negative values is often observed. A new approach based on the assessment of changes in the production of extracellular enzymes is suggested to distinguish real and apparent PE. To distinguish real and apparent PE, we discuss approaches based on the C budget. The importance of fungi for long-term changes of SOM decomposition is underlined. Priming effects can be linked with microbial community structure only considering changes in functional diversity. We conclude that the PE involves not only one mechanism but a succession of processes partly connected with succession of microbial community and functions. An overview of the dynamics and intensity of these processes as related to microbial biomass changes and C and N availability is presented.

Heat stress: an overview of molecular responses in photosynthesis

Abstract: The primary targets of thermal damage in plants are the oxygen evolving complex along with the associated cofactors in photosystem II (PSII), carbon fixation by Rubisco and the ATP generating system. Recent investigations on the combined action of moderate light intensity and heat stress suggest that moderately high temperatures do not cause serious PSII damage but inhibit the repair of PSII. The latter largely involves de novo synthesis of proteins, particularly the D1 protein of the photosynthetic machinery that is damaged due to generation of reactive oxygen species (ROS), resulting in the reduction of carbon fixation and oxygen evolution, as well as disruption of the linear electron flow. The attack of ROS during moderate heat stress principally affects the repair system of PSII, but not directly the PSII reaction center (RC). Heat stress additionally induces cleavage and aggregation of RC proteins; the mechanisms of such processes are as yet unclear. On the other hand, membrane linked sensors seem to trigger the accumulation of compatible solutes like glycinebetaine in the neighborhood of PSII membranes. They also induce the expression of stress proteins that alleviate the ROS-mediated inhibition of repair of the stress damaged photosynthetic machinery and are required for the acclimation process. In this review we summarize the recent progress in the studies of molecular mechanisms involved during moderate heat stress on the photosynthetic machinery, especially in PSII.

Radius of gyration as an indicator of protein structure compactness

Abstract: Identification and study of the main principles underlying the kinetics and thermodynamics of protein folding generate a new insight into the factors that control this process. Statistical analysis of the radius of gyration for 3769 protein domains of four major classes (α, β, α/β, and α + β) showed that each class has a characteristic radius of gyration that determines the protein structure compactness. For instance, α proteins have the highest radius of gyration throughout the protein size range considered, suggesting a less tight packing as compared with β-and (α + β)-proteins. The lowest radius of gyration and, accordingly, the tightest packing are characteristic of α/β-proteins. The protein radius of gyration normalized by the radius of gyration of a ball with the same volume is independent of the protein size, in contrast to compactness and the number of contacts per residue.

The unfoldomics decade: an update on intrinsically disordered proteins

Abstract: Our first predictor of protein disorder was published just over a decade ago in the Proceedings of the IEEE International Conference on Neural Networks (Romero P, Obradovic Z, Kissinger C, Villafranca JE, Dunker AK (1997) Identifying disordered regions in proteins from amino acid sequence. Proceedings of the IEEE International Conference on Neural Networks, 1: 90–95). By now more than twenty other laboratory groups have joined the efforts to improve the prediction of protein disorder. While the various prediction methodologies used for protein intrinsic disorder resemble those methodologies used for secondary structure prediction, the two types of structures are entirely different. For example, the two structural classes have very different dynamic properties, with the irregular secondary structure class being much less mobile than the disorder class. The prediction of secondary structure has been useful. On the other hand, the prediction of intrinsic disorder has been revolutionary, leading to major modifications of the more than 100 year-old views relating protein structure and function. Experimentalists have been providing evidence over many decades that some proteins lack fixed structure or are disordered (or unfolded) under physiological conditions. In addition, experimentalists are also showing that, for many proteins, their functions depend on the unstructured rather than structured state; such results are in marked contrast to the greater than hundred year old views such as the lock and key hypothesis. Despite extensive data on many important examples, including disease-associated proteins, the importance of disorder for protein function has been largely ignored. Indeed, to our knowledge, current biochemistry books don't present even one acknowledged example of a disorder-dependent function, even though some reports of disorder-dependent functions are more than 50 years old. The results from genome-wide predictions of intrinsic disorder and the results from other bioinformatics studies of intrinsic disorder are demanding attention for these proteins. Disorder prediction has been important for showing that the relatively few experimentally characterized examples are members of a very large collection of related disordered proteins that are wide-spread over all three domains of life. Many significant biological functions are now known to depend directly on, or are importantly associated with, the unfolded or partially folded state. Here our goal is to review the key discoveries and to weave these discoveries together to support novel approaches for understanding sequence-function relationships. Intrinsically disordered protein is common across the three domains of life, but especially common among the eukaryotic proteomes. Signaling sequences and sites of posttranslational modifications are frequently, or very likely most often, located within regions of intrinsic disorder. Disorder-to-order transitions are coupled with the adoption of different structures with different partners. Also, the flexibility of intrinsic disorder helps different disordered regions to bind to a common binding site on a common partner. Such capacity for binding diversity plays important roles in both protein-protein interaction networks and likely also in gene regulation networks. Such disorder-based signaling is further modulated in multicellular eukaryotes by alternative splicing, for which such splicing events map to regions of disorder much more often than to regions of structure. Associating alternative splicing with disorder rather than structure alleviates theoretical and experimentally observed problems associated with the folding of different length, isomeric amino acid sequences. The combination of disorder and alternative splicing is proposed to provide a mechanism for easily "trying out" different signaling pathways, thereby providing the mechanism for generating signaling diversity and enabling the evolution of cell differentiation and multicellularity. Finally, several recent small molecules of interest as potential drugs have been shown to act by blocking protein-protein interactions based on intrinsic disorder of one of the partners. Study of these examples has led to a new approach for drug discovery, and bioinformatics analysis of the human proteome suggests that various disease-associated proteins are very rich in such disorder-based drug discovery targets.

Constraints on the Self-Interaction Cross Section of Dark Matter from Numerical Simulations of the Merging Galaxy Cluster 1E 0657?56

Abstract: We compare recent results from X-ray, strong lensing, weak lensing, and optical observations with numerical simulations of the merging galaxy cluster 1E 0657–56. X-ray observations reveal a bullet-like subcluster with a prominent bow shock, which gives an estimate for the merger velocity of 4700 km s−1, while lensing results show that the positions of the total mass peaks are consistent with the centroids of the collisionless galaxies (and inconsistent with the X-ray brightness peaks). Previous studies, based on older observational data sets, have placed upper limits on the self-interaction cross section of dark matter per unit mass, σ/m, using simplified analytic techniques. In this work, we take advantage of new, higher quality observational data sets by running full N-body simulations of 1E 0657–56 that include the effects of self-interacting dark matter, and comparing the results with observations. Furthermore, the recent data allow for a new independent method of constraining σ/m, based on the nonobservation of an offset between the bullet subcluster mass peak and galaxy centroid. This new method places an upper limit (68% confidence) of σ/m < 1.25 cm2 g−1. If we make the assumption that the subcluster and the main cluster had equal mass-to-light ratios prior to the merger, we derive our most stringent constraint of σ/m < 0.7 cm2 g−1, which comes from the consistency of the subcluster's observed mass-to-light ratio with the main cluster's, and with the universal cluster value, ruling out the possibility of a large fraction of dark matter particles being scattered away due to collisions. Our limit is a slight improvement over the previous result from analytic estimates, and rules out most of the 0.5-5 cm2 g−1 range invoked to explain inconsistencies between the standard collisionless cold dark matter model and observations.

A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring.

Abstract: The recent discovery of ammonia-oxidizing archaea (AOA) dramatically changed our perception of the diversity and evolutionary history of microbes involved in nitrification. In this study, a moderately thermophilic (46°C) ammonia-oxidizing enrichment culture, which had been seeded with biomass from a hot spring, was screened for ammonia oxidizers. Although gene sequences for crenarchaeotal 16S rRNA and two subunits of the ammonia monooxygenase (amoA and amoB) were detected via PCR, no hints for known ammonia-oxidizing bacteria were obtained. Comparative sequence analyses of these gene fragments demonstrated the presence of a single operational taxonomic unit and thus enabled the assignment of the amoA and amoB sequences to the respective 16S rRNA phylotype, which belongs to the widely distributed group I.1b (soil group) of the Crenarchaeota. Catalyzed reporter deposition (CARD)–FISH combined with microautoradiography (MAR) demonstrated metabolic activity of this archaeon in the presence of ammonium. This finding was corroborated by the detection of amoA gene transcripts in the enrichment. CARD-FISH/MAR showed that the moderately thermophilic AOA is highly active at 0.14 and 0.79 mM ammonium and is partially inhibited by a concentration of 3.08 mM. The enriched AOA, which is provisionally classified as “Candidatus Nitrososphaera gargensis,” is the first described thermophilic ammonia oxidizer and the first member of the crenarchaeotal group I.1b for which ammonium oxidation has been verified on a cellular level. Its preference for thermophilic conditions reinvigorates the debate on the thermophilic ancestry of AOA.

Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners.

Abstract: Proteins are involved in many interactions with other proteins leading to networks that regulate and control a wide variety of physiological processes. Some of these proteins, called hub proteins or hubs, bind to many different protein partners. Protein intrinsic disorder, via diversity arising from structural plasticity or flexibility, provide a means for hubs to associate with many partners (Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN: Flexible Nets: The roles of intrinsic disorder in protein interaction networks. FEBS J 2005, 272:5129-5148). Here we present a detailed examination of two divergent examples: 1) p53, which uses different disordered regions to bind to different partners and which also has several individual disordered regions that each bind to multiple partners, and 2) 14-3-3, which is a structured protein that associates with many different intrinsically disordered partners. For both examples, three-dimensional structures of multiple complexes reveal that the flexibility and plasticity of intrinsically disordered protein regions as well as induced-fit changes in the structured regions are both important for binding diversity. These data support the conjecture that hub proteins often utilize intrinsic disorder to bind to multiple partners and provide detailed information about induced fit in structured regions.

The mechanism of the oxidative polymerization of aniline and the formation of supramolecular polyaniline structures

Abstract: Polyaniline is one of the most important conducting and responsive polymers. A molecular mechanism for the oxidation of aniline is proposed. This mechanism explains the specific features of aniline oligomerization and polymerization in various acidity ranges. The formation of polyaniline precipitates, colloids and thin films is reviewed and discussed on the basis of the chemistry of aniline oxidation. The generation of nanostructures, i.e. granules, nanotubes, nanowires and microspheres, is also considered. Oligomers containing phenazine constitutional units play an important role in self-assembly to form templates. Polyaniline chains then grow from these templates and produce the various individual morphologies. Copyright © 2008 Society of Chemical Industry

Strong magneto-chiral dichroism in enantiopure chiral ferromagnets

Abstract: As materials science is moving towards the synthesis, the study and the processing of new materials exhibiting well-defined and complex functions, the synthesis of new multifunctional materials is one of the important challenges. One of these complex physical properties is magneto-chiral dichroism which arises, at second order, from the coexistence of spatial asymmetry and magnetization in a material. Herein we report the first measurement of strong magneto-chiral dichroism in an enantiopure chiral ferromagnet. The ab initio synthesis of the enantiopure chiral ferromagnet is based on an enantioselective self-assembly, where a resolved chiral quaternary ammonium cation imposes the absolute configurations of the metal centres within chromium-manganese two-dimensional oxalate layers. The ferromagnetic interaction between Cr(III) and Mn(II) ions leads to a Curie temperature of 7 K. The magneto-chiral dichroic effect is enhanced by a factor of 17 when entering into the ferromagnetic phase.

Mitochondrial signaling in mammalian cells activated by red and near-IR radiation.

Abstract: Mitochondrial signaling is an information channel between the mitochondrial respiratory chain and the nucleus for the transduction signals regarding the functional state of the mitochondria. The present review examines the question whether radiation of visible and near-IR (IR-A) radiation can activate this retrograde-type cellular signaling pathway. Experimental data about modulation of elements of mitochondrial retrograde signaling by the irradiation (mitochondrial membrane potential DeltaPsi(m), reactive oxygen species ROS, Ca(2+), NO, pH(i), fission-fusion homeostasis of mitochondria) are reviewed. The terminal enzyme of the mitochondrial respiratory chain cytochrome c oxidase is considered as the photoacceptor. Functions of cytochrome c oxidase as a signal generator as well as a signal transducer in irradiated cells are outlined.

Metabolic aspects of aerobic obligate methanotrophy.

Abstract: Publisher Summary This chapter discusses the metabolic aspects of aerobic obligate methanotrophy. Aerobic methanotrophs are a unique group of gram-negative bacteria that use methane as carbon and energy source. Methanotrophs have been studied intensively over the past 40 years since these bacteria possess significant metabolic potential for practical use in the biotransformation of a variety of organic substrates, bioremediation of pollutants the production of single-cell protein (SCP), and value-added products. They also play a vital role in the global methane cycle, mitigating the emissions and green-house effects of methane on the Earth's climate. Methanotrophs build all of their cell constituents from C1 compounds by employing special biosynthetic pathways for phosphotrioses, which are different from those of heterotrophic bacteria.

Mode-locked 1.93 μm thulium fiber laser with a carbon nanotube absorber

Abstract: We report a ring-cavity thulium fiber laser mode locked with a single-wall carbon nanotube absorber used in transmission. A carboxymethyl cellulose polymer film with incorporated carbon nanotubes synthesized by the arc discharge method has an absorption coinciding with in the amplification bandwidth of a Tm-doped fiber. This laser is pumped by an erbium fiber laser at 1.57 μm wavelength and produces a 37 MHz train of mode-locked 1.32 ps pulses at 1.93 μm wavelength with an average output power of 3.4 mW.

Bottom-up organic integrated circuits

Abstract: Self-assembly—the autonomous organization of components into patterns and structures1—is a promising technology for the mass production of organic electronics. Making integrated circuits using a bottom-up approach involving self-assembling molecules was proposed2 in the 1970s. The basic building block of such an integrated circuit is the self-assembled-monolayer field-effect transistor (SAMFET), where the semiconductor is a monolayer spontaneously formed on the gate dielectric. In the SAMFETs fabricated so far, current modulation has only been observed in submicrometre channels3–5, the lack of efficient charge transport in longer channels being due to defects and the limited intermolecular p–p coupling between the molecules in the selfassembled monolayers. Low field-effect carrier mobility, low yield and poor reproducibility have prohibited the realization of bottom-up integrated circuits. Here we demonstrate SAMFETs with long-range intermolecular p–p coupling in the monolayer. We achieve dense packing by using liquid-crystalline molecules consisting of a p-conjugated mesogenic core separated by a long aliphatic chain from a monofunctionalized anchor group. The resulting SAMFETs exhibit a bulk-like carrier mobility, large current modulation and high reproducibility. As a first step towards functional circuits, we combine the SAMFETs into logic gates as inverters; the small parameter spread then allows us to combine the inverters into ring oscillators. We demonstrate real logic functionality by constructing a 15-bit code generator in which hundreds of SAMFETs are addressed simultaneously. Bridging the gap between discrete monolayer transistors and functional selfassembled integrated circuits puts bottom-up electronics in a new perspective.

Protein-calcium carbonate coprecipitation: a tool for protein encapsulation.

Abstract: A new approach of encapsulation of proteins in polyelectrolyte microcapsules has been developed using porous calcium carbonate microparticles as microsupports for layer-by-layer (LbL) polyelectrolyte assembling. Two different ways were used to prepare protein-loaded CaCO3 microparticles: (i) physical adsorption--adsorption of proteins from the solutions onto preformed CaCO3 microparticles, and (ii) coprecipitation--protein capture by CaCO3 microparticles in the process of growth from the mixture of aqueous solutions of CaCl2 and Na2CO3. The latter was found to be about five times more effective than the former (approximately 100 vs approximately 20 mug of captured protein per 1 mg of CaCO3). The procedure is rather mild; the revealed enzymatic activity of alpha-chymotrypsin captured initially by CaCO3 particles during their growth and then recovered after particle dissolution in EDTA was found to be about 85% compared to the native enzyme. Core decomposition and removal after assembly of the required number of polyelectrolyte layers resulted in release of protein into the interior of polyelectrolyte microcapsules (PAH/PSS)5 thus excluding the encapsulated material from direct contact with the surrounding. The advantage of the suggested approach is the possibility to control easily the concentration of protein inside the microcapsules and to minimize the protein immobilization within the capsule walls. Moreover, it is rather universal and may be used for encapsulation of a wide range of macromolecular compounds and bioactive species.

TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorder.

Abstract: Intrinsically disordered proteins carry out various biological functions while lacking ordered secondary and/or tertiary structure. In order to find general intrinsic properties of amino acid residues that are responsible for the absence of ordered structure in intrinsically disordered proteins we surveyed 517 amino acid scales. Each of these scales was taken as an independent attribute for the subsequent analysis. For a given attribute value X, which is averaged over a consecutive string of amino acids, and for a given data set having both ordered and disordered segments, the conditional probabilities P(so | x) and P(sd | x) for order and disorder, respectively, can be determined for all possible values of X. Plots of the conditional probabilities P(so | x) and P(sd | x) versus X give a pair of curves. The area between these two curves divided by the total area of the graph gives the area ratio value (ARV), which is proportional to the degree of separation of the two probability curves and, therefore, provides a measure of the given attribute’s power to discriminate between order and disorder. As ARV falls between zero and one, larger ARV corresponds to the better discrimination between order and disorder. Starting from the scale with the highest ARV, we applied a simulated annealing procedure to search for alternative scale values and have managed to increase the ARV by more than 10%. The ranking of the amino acids in this new TOP-IDP scale is as follows (from order promoting to disorder promoting): W, F, Y, I, M, L, V, N, C, T, A, G, R, D, H, Q, K, S, E, P. A web-based server has been created to apply the TOP-IDP scale to predict intrinsically disordered proteins (http://www.disprot.org/dev/disindex.php).

Infrared-modified gravities and massive gravitons

Abstract: We review some theoretical and phenomenological aspects of massive gravities in 4 dimensions. We start from the Fierz–Pauli theory with Lorentz-invariant mass terms and then proceed to Lorentz-violating masses. Unlike the former theory, some models with Lorentz violation have no pathologies in the spectrum in flat and nearly flat backgrounds and lead to an interesting phenomenology.

Sequencing the nuclear genome of the extinct woolly mammoth

Abstract: In 1994, two independent groups extracted DNA from several Pleistocene epoch mammoths and noted differences among individual specimens. Subsequently, DNA sequences have been published for a number of extinct species. However, such ancient DNA is often fragmented and damaged, and studies to date have typically focused on short mitochondrial sequences, never yielding more than a fraction of a per cent of any nuclear genome. Here we describe 4.17 billion bases (Gb) of sequence from several mammoth specimens, 3.3 billion (80%) of which are from the woolly mammoth (Mammuthus primigenius) genome and thus comprise an extensive set of genome-wide sequence from an extinct species. Our data support earlier reports that elephantid genomes exceed 4 Gb. The estimated divergence rate between mammoth and African elephant is half of that between human and chimpanzee. The observed number of nucleotide differences between two particular mammoths was approximately one-eighth of that between one of them and the African elephant, corresponding to a separation between the mammoths of 1.5-2.0 Myr. The estimated probability that orthologous elephant and mammoth amino acids differ is 0.002, corresponding to about one residue per protein. Differences were discovered between mammoth and African elephant in amino-acid positions that are otherwise invariant over several billion years of combined mammalian evolution. This study shows that nuclear genome sequencing of extinct species can reveal population differences not evident from the fossil record, and perhaps even discover genetic factors that affect extinction.