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The microbiota of chicken litter remains largely unexplored, despite its leading role in the formation of volatile odorants and unpleasant odors. One of the main components of the odor is hydrogen sulfide, which may be formed as a result of microbial sulfate reduction. The composition of the microbial community of poultry plant waste was investigated. Samples were collected at the Mezheninovskaya large poultry farm, 15 km from the city of Tomsk, Russia. The 16S rRNA gene profiling revealed sulfate-reducing Desulfovibrionaceae in the microbial community. Both their share in the community and sulfide production increased upon incubation of the waste in the medium with sulfate and lactate. The possible sulfate sources in the waste are gypsum and the feed additives introduced as sulfates, such as lysine sulfate.

Hydrogen is a key energy-yielding substrate for microbial processes in the deep biosphere. Fracture water of a deep gold mine in South Africa is a well-known example of the ecosystem based on a hydrogenotrophic sulfate reducer, “Candidatus Desulforudis audaxviator.” The present work reports the cultivation and pure culture isolation of a novel obligate chemolithotroph reducing sulfate during growth on hydrogen or formate. Phylogenetic analysis of the 16S rRNA gene of the strain Tu-874 showed its clusterization with its closest cultured relative, “Candidatus Desulforudis audaxviator.” However, the low 16S rRNA sequence similarity of 88.95% indicates that the organism represents a new taxonomic group above the species level.

There is still a lack of understanding of H2S formation in agricultural waste, which leads to poor odour prevention and control. Microbial sulfate reduction is a major process contributing to sulfide formation in natural and technogenic environments with high sulfate and low oxygen concentration. Agricultural waste can be considered a low-sulfate system with no obvious input of oxidised sulfur compounds. The purpose of this study was to characterise a microbial community participating in H2S production and estimate the microbial sulfate reduction rate (SRR) in manure slurry from a large-scale swine finishing facility in Western Siberia. In a series of manure slurry microcosms, we identified bacterial consortia by 16S rRNA gene profiling and metagenomic analysis and revealed that sulfate-reducing Desulfovibrio were key players responsible for H2S production. The SRR measured with radioactive sulfate in manure slurry was high and comprised 7.25 nmol S cm−3 day−1. Gypsum may be used as a solid-phase electron acceptor for sulfate reduction. Another plausible source of sulfate is a swine diet, which often contains supplements in the form of sulfates, including lysine sulfate. Low-sulfur diet, manure treatment with iron salts, and avoiding gypsum bedding are possible ways to mitigate H2S emissions from swine manure.

With ongoing climate warming, ice-rich permafrost, such as late Pleistocene Yedoma permafrost, is especially vulnerable to rapid and deep thaw processes. Such permafrost sediments contain a large organic matter storage that becomes increasingly accessible to microbes upon thaw. Only a few studies analysed organic matter in deep (>10 m) permafrost and thawed permafrost sediments. We studied Yedoma sediments from four sites in Yakutia in the Russian Federation: at the Arctic Ocean (Bykovsky Peninsula), inside the Lena Delta (Sobo-Sise Cliff), close to the northern hemisphere’s cold pole (Batagay) and in central Yakutia (Yukechi Alas). We measured biomarker concentrations of sediment cores taken from below thermokarst lakes and sediment samples taken from the headwall of a coastal bluff and a retrogressive thaw slump. In addition, we carried out incubation experiments to quantify greenhouse gas production in thawing permafrost. Here, we present the first molecular biomarker distributions (alkanes and fatty acids) and organic carbon turnover (anaerobic CO2 and CH4 production) data as well as insights in organic matter decomposition processes in deep frozen and thawed Yedoma sediments. We show that biomarker proxies are useful to assess the source and degree of degradation of permafrost organic matter. Furthermore, the organic matter in frozen Pleistocene Yedoma sediments was better preserved than in thawed Holocene sediments. These findings show the relevance of studying organic matter in deep permafrost sediments.

Evaporation of paraffin and ultra-high-molecular-weight polyethylene admixed with alumina powder for the slip casting and sintering process allowed the obtainment of segmented porous alumina ceramics with 50% total porosity, whose deformation behavior we studied. Structurally, these ceramic materials were composed of large and small pores, and a system of discontinuities subdividing the samples into segments. Using digital image correlation (DIC), strain distribution maps were obtained that allowed the observation of strain localization zones, where primary cracks propagated along the interblock discontinuities. Two stages were revealed to be responsible for different mechanisms that provided the sample with damage tolerance under compression loading: the first stage was crack propagation along the block boundaries, which was followed by the second stage of microcracking and fragmentation, consisting of filling of the free spaces with fragments, compaction band generation, and stabilization of the crack. Both stages comprise a cycle that is repeated again and again until the full volume of the sample is occupied by the compaction bands.

Permafrost region subsurface organic carbon (OC) pools are a major component of the terrestrial carbon cycle and vulnerable to a warming climate. Thermokarst lagoons are an important transition stage with complex depositional histories during which permafrost and lacustrine carbon pools are transformed along eroding Arctic coasts. The effects of temperature and salinity changes during thermokarst lake to lagoon transitions on thaw history and lagoon deposits are understudied. We analyzed two 30-m-long sediment cores from two thermokarst lagoons on the Bykovsky Peninsula, Northeast Siberia, using sedimentological, geochronological, hydrochemical, and biogeochemical techniques. Using remote sensing we distinguished between a semi-closed and a nearly closed lagoon. We (1) characterized the depositional history, (2) studied the impact of marine inundation on ice-bearing permafrost and taliks, and (3) quantified the OC pools for different stages of thermokarst lagoons. Fluvial and former Yedoma deposits were found at depth between 30 and 8.5 m, while lake and lagoon deposits formed the upper layers. The electrical conductivity of the pore water indicated hypersaline conditions for the semi-closed lagoon (max: 108 mS/cm), while fresh to brackish conditions were observed beneath a 5 m-thick surface saline layer at the nearly closed lagoon. The deposits had a mean OC content of 15 ± 2 kg/m3, with higher values in the semi-closed lagoon. Based on the cores we estimated a total OC pool of 5.7 Mt-C for the first 30 m of sediment below five mapped lagoons on the Bykovsky Peninsula. Our results suggest that paleo river branches shaped the middle Pleistocene landscape followed by late Pleistocene Yedoma permafrost accumulation and early Holocene lake development. Afterward, lake drainage, marine flooding, and bedfast ice formation caused the saline enrichment of pore water, which led to cryotic talik development. We find that the OC-pool of Arctic lagoons may comprise a substantial inventory of partially thawed and partially refrozen OC, which is available for microbial degradation processes at the Arctic terrestrial-marine interface. Climate change in the Arctic leading to sea level rise, permafrost thaw, coastal erosion, and sea ice loss may increase the rate of thermokarst lagoon formation and thus increase the importance of lagoons as biogeochemical processors of former permafrost OC.

The development of public-private partnership in the Russian economy is conditioned on the need to ensure stable economic growth and improve the quality of life of the population. Imperfection of the regulatory legislation of the private-public partnership, lack of clearly defined terms and concepts, proportion and strategic importance of private-public partnership projects have predetermined numerous theoretical studies, the results of which confirm the high terminological uncertainty of the characteristics and systematization of models, forms and mechanisms of private-public partnership implementation. The study of the modern conceptual and terminological apparatus of private-public partnership allowed to clarify the concepts of “private-public partnership PPP model”, “organizational and legal form of private-public partnership”, “mechanism of implementation” and their relationship, to justify the criteria of differentiation and to identify the models of organization, participation in capital and contractual model as priority areas of interaction between the state and business within private-public partnership, on the basis of which the organizational and legal forms of partnership and mechanisms of their implementation are systematized. There has been shown the classification of models, forms and mechanisms of private-public partnership; it has been stated that “a weak points” are mechanisms of private-public partnership realization, in terms of detail upkeep and operation order, which is stipulated by lack of imperfection of regulatory documents and methodological recommendations, as well as unique terms of arrangement and realization of a private-public partnership project. It has been recommended to develop realization mechanisms using current legislation and foreign practices, taking into account the Russian economic environment and the nature of a certain private-public partnership project. There have been revealed extra virtues that allow to unify terminological and conceptual apparatus of private-public partnership.

Thermal ecosystems associated with areas of underground burning coal seams are rare and poorly understood in comparison with geothermal objects. We studied the microbial communities associated with gas vents from the coal-fire in the mining wastes in the Kemerovo region of the Russian Federation. The temperature of the ground heated by the hot coal gases and steam coming out to the surface was 58 °C. Analysis of the composition of microbial communities revealed the dominance of Ktedonobacteria (the phylum Chloroflexi), known to be capable of oxidizing hydrogen and carbon monoxide. Thermophilic hydrogenotrophic Firmicutes constituted a minor part of the community. Among the well-known thermophiles, members of the phyla Aquificae, Deinococcus-Thermus and Bacteroidetes were also found. In the upper ground layer, Acidobacteria, Verrucomicrobia, Actinobacteria, Planctomycetes, as well as Proteobacteria of the alpha and gamma classes, typical of soils, were detected, their relative abundancies decreased with depth. The phylum Verrucomicrobia was dominated by Candidatus Udaeobacter, aerobic heterotrophs capable of generating energy through the oxidation of hydrogen present in the atmosphere in trace amounts. Archaea made up a small part of the communities and were represented by thermophilic ammonium-oxidizers. Overall, the community was dominated by bacteria, whose cultivated relatives are able to obtain energy through the oxidation of the main components of coal gases, hydrogen and carbon monoxide, under aerobic conditions.

AlMgB14-TiB2 composite materials were fabricated by self-propagating high-temperature synthesis (SHS) followed by spark plasma sintering of the obtained SHS products. It was found that, during the SHS, the AlMgB14 phase is formed at a donor (Ti + 2B) to acceptor (Al12Mg17-B) mass ratio of 3:7 and 4:6, respectively. The specimen sintered from the SHS powder with the donor:acceptor mass ratio of 5:5 at a temperature of 1470 °C has a uniform skeletal structure. The average hardness of the obtained specimen is 30.1 GPa.

Currently, metal–matrix composite materials are some of the most promising types of materials, and they combine the advantages of a metal matrix and reinforcing particles/fibres. Within the framework of this article, the high-temperature synthesis of metal–matrix composite materials based on the (Ni-Ti)-TiB2 system was studied. The selected approaches make it possible to obtain composite materials of various compositions without contamination and with a high degree of energy efficiency during production processes. Combustion processes in the samples of a 63.5 wt.% NiB + 36.5 wt.% Ti mixture and the phase composition and structure of the synthesis products were researched. It has been established that the synthesis process in the samples proceeds via the spin combustion mechanism. It has been shown that self-propagating high-temperature synthesis (SHS) powder particles have a composite structure and consist of a Ni-Ti matrix and TiB2 reinforcement inclusions that are uniformly distributed inside it. The inclusion size lies in the range between 0.1 and 4 µm, and the average particle size is 0.57 µm. The obtained metal-matrix composite materials can be used in additive manufacturing technologies as ligatures for heat-resistant alloys, as well as for the synthesis of composites using traditional methods of powder metallurgy.

The paper presents the main approaches and principles of planning and managing service promotion, as well as organizing effective production processes for maintaining cars in a safe and sound technical condition. The article presents a mathematical model for forecasting the supply and demand of services for servicing automobiles with justification of the required production capacities and another mathematical model for estimating the incoming flows to service enterprises, taking into account the intensity of operation of automobiles and their reliability, which varies over time, allowing optimization of the necessary production resources for the functioning of existing as well as emerging service enterprises. The conducted studies allow us to formulate and solve the problems of ensuring the possibility of assessing the optimal levels of profitability of the promoted projects for the development of service enterprises at specified time lags, considering market conditions and possible risks.

The article considers questions of introduction of modern instruments of management into practice of financial activity of the oil and gas company to optimize financial control. Characterisrtics of oil production markets and petroservices has been given. The results of the carried-out analysis revealed that for oil and gas branch of Kazakhstan at the moment the processes of restoration after the crisis of 2014-2015 are typical. The oil branch is important for economic development of Kazakhstan. Mangystaumunaygaz, JSC is one of the largest oil and gas extraction companies in Kazakhstan. The analysis of the key economic parameters of activity of Mangystaumunaygaz, JSC showed that for the observed period company developed successfully, despite the crisis phenomena in national economy. However, in the medium term there were observed fluctuations. For increase of efficiency of activity of the Mangystaumunaygaz, JSC company it is offered to introduce transformational financial model of management of assets based on modern instruments of management, such as: a system of separate account and a system of planning profit on strategic business units (budgeting), transition to the separate financial account of wells and their efficiency. It has been offered to apply one of means of coordination of commodity and financial streams - factoring. The main advantage of factoring consists in uninterrupted providing the oil and gas company with current assets right after delivery. In Kazakhstan operates the national factoring association, whose annual turn of participants in 2016 has made 28.1 billion tenges. The analysis of economic efficiency of factoring operation showed possibility of its influence on financial stability of the company.

Most of the world's permafrost is located in the Arctic, where its frozen organic carbon con-tent makes it a potentially important influence on the global climate system. The Arctic climate appears to be changing more rapidly than the lower latitudes, but observational data density in the region is low. Permafrost thaw and carbon release into the atmosphere is a positive feed-back mechanism that has the potential for climate warming. It is therefore particularly im-portant to understand the links between the energy balance, which can vary rapidly over hour-ly to annual time scales, and permafrost condition, which changes slowly on decadal to cen-tennial timescales. This requires long-term observational data such as that available from the Samoylov research site in northern Siberia, where meteorological parameters, energy balance, and subsurface observations have been recorded since 1998. This paper presents the temporal data set produced between 2002 and 2017, explaining the instrumentation, calibration, pro-cessing and data quality control. Additional data include a high-resolution digital terrain mod-el (DTM) obtained from terrestrial LiDAR laser scanning. Since the data provide observations of temporally variable parameters that influence energy fluxes between permafrost, active lay-er soils, and the atmosphere (such as snow depth and soil moisture content), they are suitable for calibrating and quantifying the dynamics of permafrost as a component in earth system models. The data also include soil properties beneath different microtopographic features (a polygon center, a rim, a slope, and a trough), yielding much-needed information on landscape heterogeneity for use in land surface modeling. For the record from 1998 to 2017, the average mean annual air temperature was − 12.3 °C, with mean monthly temperature of the warmest month (July) recorded as 9.5 °C and for the coldest month (February) − 32.7 °C. The average annual rainfall was 169 mm. The depth of zero annual amplitude niveau is at 20.8 m, and has warmed from − 9.1 °C in 2006 to − 7.7 °C in 2017. The presented data are available in the supplementary material of this paper and through the PANGAEA website (https://doi.org/10.1594/PANGAEA.891142).

Introduction. Nowadays ship hull diagnostics is carried out in dry-dock or using divers in the road. The both technologies are time consuming, labour and material resource demanding. Specialists from Bauman Moscow State Technical University have developed a diagnostics system that allows the ship hull underwater part inspection to be performed without calling at dry-dock and without divers. The system includes the following main elements: remotely operated vehicle that contains diagnostics tools; hydro acoustic navigation system; software; and diagnostics technology. Method. The technology is based on an acoustic method of non-destructive testing (NDT). SH-waves with elastic vibrations excitation by non-contact method are used without necessity of thorough surface preparation before testing. SH-waves are also used for flaw detection within damaged areas (areas of different thicknesses). As the research has shown, the mirror-shadow technique with bottom signal attenuation as a criterion for corrosion crack detection is most effective. The minimum detectable deep of the corrosion cracks is 1.5–2 mm. The proposed diagnostics technology uses electromagnetic acoustic transducers (EMAT) with a 5 MHz frequency. Results. The diagnostics system was successfully tested in the pool. The test results confirmed the system’s ability to perform automatic metal diagnostics with wall thickness measurements and defect detection within areas of corrosion. Discussions. Nowadays the system is under the process of Russian Maritime Register of Shipping approval. It is planned to develop a system with arc welding tools for underwater objects repair. Prospects of diagnostics system usage for the various underwater steel structures including ones located on the Russian Federation Arctic shelf are under consideration.

Summary Eukaryotic TIP49a (Pontin) and TIP49b (Reptin) AAA+ ATPases play essential roles in key cellular processes. How their weak ATPase activity contributes to their important functions remains largely unknown and difficult to analyze because of the divergent properties of TIP49a and TIP49b proteins and of their homo- and hetero-oligomeric assemblies. To circumvent these complexities, we have analyzed the single ancient TIP49 ortholog found in the archaeon Methanopyrus kandleri (mkTIP49). All-atom homology modeling and molecular dynamics simulations validated by biochemical assays reveal highly conserved organizational principles and identify key residues for ATP hydrolysis. An unanticipated crosstalk between Walker B and Sensor I motifs impacts the dynamics of water molecules and highlights a critical role of trans-acting aspartates in the lytic water activation step that is essential for the associative mechanism of ATP hydrolysis., Graphical Abstract, Highlights • We have studied the single TIP49 ortholog (mkTIP49) from the archaeon M. kandleri • We propose a model for assembly of the pre-transition state for ATP hydrolysis • Trans-aspartates downregulate ATP hydrolysis by mkTIP49 hexamers • Mutational analysis confirms a highly conserved mechanism for lytic water activation, Afanasyeva et al. combine computational and biochemical analysis to reveal conserved organizational principles and residues critical for ATP hydrolysis in the AAA+ ATPase TIP49 ortholog from archaea. They highlight a role of trans-aspartates in the lytic water activation step essential for ATP hydrolysis.

TIP49b (reptin) is an essential eukaryotic AAA+ ATPase involved in a variety of cellular processes, such as chromatin remodeling during double-strand break repair, transcriptional regulation, control of cell proliferation and small nucleolar RNA biogenesis. How it acts at the molecular level remains largely unknown. In the present study, we show that both human TIP49b and its yeast orthologue, Rvb2p, cooperatively bind single-stranded DNA as monomers. Binding stimulates a slow ATPase activity and supports a 3′- to 5′ DNA unwinding activity that requires a 3′-protruding tail ≥ 30 nucleotides. The data obtained indicate that DNA unwinding of 3′- to 5′ junctions is also constrained by the length of flanking duplex DNA. By contrast, TIP49b hexamers were found to be inactive for ATP hydrolysis and DNA unwinding, suggesting that, in cells, protein factors that remain unknown might be required to recycle these into an active form. Structured digital abstract • MINT-7804328: TIP49b (uniprotkb:Q4QQS4) and TIP49b (uniprotkb:Q4QQS4) bind (MI:0407) by electron microscopy (MI:0040) • MINT-7804638: tip49b (uniprotkb:Q4QQS4) and tip49b (uniprotkb:Q4QQS4) bind (MI:0407) by molecular sieving (MI:0071)

The great majority of the modern centrifugal stages utilize periodic stationary structures such as inlet guide vanes and/or diffuser vanes. To maximize the aerodynamic performance of the centrifugal stage, these vanes must be positioned at a close proximity of the centrifugal impeller. This arrangement results in a dramatic interaction between rotating impeller and stationary vanes due to reflection of the pressure waves from the periodic vanes back onto the impeller blades. The periodic nature of the reflected pressure waves may lead to an excitation of the impeller blade eigenmodes if the fundamental frequency (or, its multiple) of the external force matches with the natural frequency of the subject impeller. As the impeller blades provide very little to no damping, there is a strong possibility of the high cycle fatigue resonance failure of the impeller blades if the impeller design does not provide with a sufficient separation from the resonance modes. We should note that ensuring such a separation is not straightforward task for many stages with periodic exciters, and may not be even feasible for some practical design cases. This presentation focuses on a novel way to mitigate possible resonance issues for centrifugal impellers due to pressure reflection waves emanating from the diffuser blades. We propose to utilize non-periodic centrifugal diffuser together with the sculpting leading edges for the three-dimensional diffuser vanes. In order to demonstrate the attractiveness and feasibility of this approach, we have utilized Computational Fluid Dynamics (CFD) tools to perform time-accurate unsteady turbulent flow analyses in centrifugal stages and capture cyclic pressure waves acting on the impeller blades. The present work considers a regular periodic low-solidity diffuser with two-dimensional vanes, a three-dimensional periodic diffuser with a sculpted leading edge, and, finally, a non-periodic three-dimensional diffuser with an unequal, non-repeating stagger. We have utilized eighteen CFD pressure probes located on the impeller blade pressure and suction sides to monitor temporal variations of the static pressure that capture the pressure reflection waves from the diffuser vanes. The Fourier series decomposition facilitates detailed analyses of the pressure energy distribution over a wide range of frequencies. The results of the numerical studies demonstrate that even the use of the periodic diffuser with 3D sculpted leading edges help reduce the magnitude of the pressure oscillations at the dominant frequency and its integer multiples. However, the pressure energy distribution changes dramatically when using the non-periodic diffuser arrangement together with the sculpted leading edge vanes. The strength of the pressure waves associated with the dominant harmonics and its integer multiples are reduced about 30% to 85% and spread over the frequencies that constitute integer multiples of the fundamental impeller frequency. This pressure energy redistribution of the 3D non-periodic diffuser is a significant aid to the aerodynamicist. By significantly reducing the mechanical constraint compromises, the designer is allowed to focus more on aerodynamic component efficiency.

Recent changes in the global economy have significantly impacted the air separation market. Companies traditionally focused upon initial capital expenditures, have shifted their mindset towards total life cycle costs. As a primary component in the air separation process, the compressor has been recognized as a significant contributor to life cycle costs of an air separation facility. Accordingly, market expectations have shifted towards more efficient compressor designs to reduce the overall power consumption. This paper highlights the development efforts at Cameron’s Compression Systems to design advanced 3D cascade diffusers, leading to the development of compressors with higher aerodynamic efficiencies. While the concept of matching the diffuser design towards the local flow field is not new, the implementation of this concept has been significantly hindered by a lack of understanding with regard to impeller discharge conditions. Furthermore, the tools necessary to explore these specifics either did not exist, or where prohibitive in terms of both cost and time. Over the past 20 years, great advances have been made in the area of computational engineering. The advancements in Computational Fluid Dynamics (CFD) tools have led to a better understanding of the transitional impeller flow fields. Furthermore, the dramatic progress in cheaper high-end computers has facilitated the design and development of sculpted three-dimensional diffusers within reasonable time frames and at relatively low cost. Recently, Cameron has deployed advanced sculpted 3D diffusers on limited production designs. This process involves a heavy utilization of STAR-CCM+ for performance analyses of centrifugal stages with various diffuser geometries. The CFD analyses vary from relatively simple steady state analyses with single impeller and single diffuser passages using indirect (mixing plane) interfaces to full stage unsteady simulations involving full inlet, impeller, diffuser and volute with a discharge pipe. This paper discusses a range of issues involved in performing CFD analyses for complex diffuser geometries. We show how CFD analyses are used to improve the aerodynamic performance of stages with respect to the regular low solidity cascade 2D diffusers. The paper provides results of comparative studies of the computational analyses with the aerodynamically tested data for the stages using both the regular low solidity 2D diffusers and sculpted non-periodic 3D diffusers. The test results confirm predicted improvements in compressor efficiency using sculpted non-periodic 3D diffusers over regular 2D diffusers by as much as 2% for peak efficiency. The paper discusses stage improvements due to use of 3D sculpted non-periodic diffusers.

Finite Element Methods (FEM) have become a key tool to predict stresses, deformations, eigenfrequencies and eigenmodes in centrifugal impellers under centrifugal loads. Accurate prediction of values of principal stresses and natural frequencies is critical to avoiding field failures of impellers. Accurate prediction of maximum principal stresses in centrifugal impeller blades is a straightforward task using linear finite elements with a moderate mesh resolution. Centrifugal impeller failures due to high stresses have been virtually eliminated as a failure mode because of this level of analysis. However, the same level of analysis of natural frequencies does not always result in accurate predictions of higher frequency modes. It has been Cameron’s experience that the most common reason for impeller field failure has been a high frequency resonance resulting in a high cycle fatigue failure. Although there are a few commercially available tools for stress and modal analyses of centrifugal impellers, we are not aware of any that offers the flexibility, generality and, most importantly, accuracy in predicting high modal frequencies. The impeller designer has to find a solution that allows the impeller to survive with the exciters caused by diffuser vane pass frequencies and/or inlet guide vane pass frequencies and still meet the performance guarantee. Historically, design practice focused on stress levels and avoiding one time vane pass frequencies. In general, this approach has been very successful at eliminating stress and one-time vane pass frequency failures. However, it must be emphasized that current tools can incorrectly predict excitation modes due to twice the diffuser vane or inlet guide vane pass frequencies. It has been Cameron’s experience that most field failures are in this two times vane pass frequency range. The development of a custom in-house tool for accurate stress and modal analyses of centrifugal impellers has been a major task at Cameron in the past few years. This thrust resulted in Cameron’s cooperation with Pointwise, Inc. to develop a set of automated tools to utilize higher order finite element meshes for such analyses. Pointwise has established itself as the world-leading mesh generation software for Computational Fluid Dynamics (CFD) analysis. However, the flexibility and versatility of this meshing software also makes it a very attractive and powerful tool for generating Finite Element Analysis (FEA) meshes. This work focuses on a utilization of Pointwise for automated generation of higher order finite element meshes for centrifugal impeller blades. Pointwise-based automated tools generate a fully structured mesh of higher order elements that involves every detailed feature of the centrifugal impeller. The mesh retains geometric validity of the centrifugal impeller and maintains accurate geometrical resolution of the higher order surfaces associated with the impeller blade and hub. The structural and modal analyses are then automatically performed in ANSYS. We show that the Pointwise-based meshing tools are both general and robust. They allow for high quality, higher order finite element meshes for an entire range of applications that we encounter at Cameron Compression Systems on a daily basis. This work demonstrates the attractiveness of higher order finite element meshes for accurately predicting the natural frequencies for centrifugal impellers for an entire range of desired frequencies. We present finite element mesh convergence studies, and utilize a Pointwise based meshing tool together with ANSYS to accurately predict failure modes for impellers that have experienced field failures in the last decade.

Chromatin plays a critical role in regulating access to DNA by proteins that direct recombination and repair. The E. coli RuvAB protein complex promotes branch migration of the Holliday junction recombination intermediate. The ability of RuvAB to negotiate passage of the junction through nucleosomal DNA is examined. The model system involves the formation of a Holliday junction positioned upstream of a nucleosome. Unassisted, the junction is blocked by a histone octamer. In the presence of RuvAB and ATP, rapid branch migration through the nucleosome is observed. It results in disruption of the histone–DNA interactions leading to the removal of the octamer from the junction intermediate. These results suggest that eukaryotic DNA motor proteins analogous to RuvAB could function during recombination to promote branch migration through chromatin.

The Holliday junction is a key intermediate in genetic recombination. Here, we examine the effect of a nucleosome core on movement of the Holliday junction in vitro by spontaneous branch migration. Histone octamers consisting of H2A, H2B, H3, and H4 are reconstituted onto DNA duplexes containing an artificial nucleosome-positioning sequence consisting of a tandem array of an alternating AT-GC sequence motif. Characterization of the reconstituted branch migration substrates by micrococcal nuclease mapping and exonuclease III and hydroxyl radical footprinting reveal that 70% of the reconstituted octamers are positioned near the center of the substrate and the remaining 30% are located at the distal end, although in both cases some translational degeneracy is observed. Branch migration assays with the octamer-containing substrates reveal that the Holliday junction cannot migrate spontaneously through DNA organized into a nucleosomal core unless DNA-histone interactions are completely disrupted. Similar results are obtained with branch migration substrates containing an octamer positioned on a naturally occurring sequence derived from the yeast GLN3 locus. Digestion of Holliday junctions with T7 endonuclease I establishes that the junction is not trapped by the octamer but can branch migrate in regions free of histone octamers. Our findings suggest that migration of Holliday junctions during recombination and the recombinational repair of DNA damage requires proteins not only to accelerate the intrinsic rate of branch migration but also to facilitate the passage of the Holliday junction through a nucleosome.

Synthetic oligodeoxynucleotides represent promising tools for gene inhibition in live systems. Triple helix-forming oligonucleotides, which bind to double-stranded DNA, are of special interest since they are targeted to the gene itself rather than to its mRNA product, as in the antisense strategy. Triple helix-forming oligonucleotides can be coupled to DNA-modifying agents and used to introduce modifications in the DNA target in a highly sequence-specific manner. We have recently designed psoralen-oligonucleotide conjugates, which, upon binding to double-stranded DNA sequences via triple helix formation, may be cross-linked in vitro to both strands of the DNA following UV irradiation. A psoralen-oligonucleotide conjugate was targeted to the promoter of the alpha subunit of the interleukin 2 receptor (IL-2R alpha) gene. The triple helix site overlaps the binding site for the transcription factor NF-kappa B, which activates transcription from the IL-2R alpha promoter. After UV irradiation, the oligonucleotide conjugate becomes cross-linked to the target site and inhibits transcription of reporter plasmids transfected in live cells. Inhibition is observed when UV-induced cross-linking occurs both in vitro (before transfection) and in vivo (after transfection). We directly demonstrate that this inhibitory effect is due to triple helix formation at the target site, since a mutant of the promoter, to which oligonucleotide binding was inhibited, was not affected by the psoralen-oligonucleotide conjugate after UV irradiation. In addition, we demonstrate that site-specific cross-linking upstream of the promoter has no effect on transcription.

It has been well-known that many industrial applications that use centrifugal compressors have continuously demanded for more and more efficient machines in the past decade or so. However, the current market trend indicates that there is a strong demand among the end users for reduced delivery times of these efficient compressors. This, in turn, requires that the aerodynamic design of highly efficient centrifugal stages be completed within shorter time frames. In order to meet these challenges, it is mandatory to involve modern computational analysis tools such as Computational Fluid Dynamics (CFD) as a routine design tool for the aerodynamic engineer. This presentation discusses a hierological structure for CFD analysis along with an overview of limitations and benefits for each classification within this structure. Usage and results pertaining to the implementation of this structure at Cameron’s Compression System will also be covered. Accordingly, a discussion of aerodynamic design practices (both current and historical) will be offered. It should be obvious to the reader that the goal of design integration would require the primary focus to be towards validation of the commercial CFD code. Results presented were obtained using the StarCCM + CFD package developed by CD-Adapco. As mentioned earlier, CFD analysis can be described as a hierological structure consisting of 4 levels. At level 1, the analysis component consists of an impeller coupled with a vaneless diffuser region under a steady state flow condition. On level 2, the model involves an impeller and low solidity diffuser row analysis using a mixing plane interface. Level 3 facilitates the consideration of entire impeller and an entire diffuser with a full set of diffuser blades within a transient framework. These levels (1 through 3) include the assumption of a dump collector and imply a circumferential periodicity at the exit. Also, models for level 2 and level 3 incorporate the use of a 1-d modeling to predict overall stage performance. Level 4, the most sophisticated model, involves a full-stage analysis of an unsteady turbulent flow through the entire centrifugal stage, all the way from impeller inlet to the discharge of the scroll/volute/collector. At this level, the overall stage performance is predicted directly from the CFD analyses. The paper compares the results of each level of analyses with the test data and discusses the potential benefits as well as limitations of each level of analyses.Copyright © 2010 by ASME

Chromatin modifications and chromatin-modifying enzymes are believed to play a major role in the process of DNA repair. The histone acetyl transferase Tip60 is physically recruited to DNA DSBs (double-strand breaks) where it mediates histone acetylation. In the present study, we show, using a reporter system in mammalian cells, that Tip60 expression is required for homology-driven repair, strongly suggesting that Tip60 participates in DNA DSB repair through homologous recombination. Moreover, Tip60 depletion inhibits the formation of Rad50 foci following ionizing radiation, indicating that Tip60 expression is necessary for the recruitment of the DNA damage sensor MRN (Mre11–Rad50–Nbs1) complex to DNA DSBs. Moreover, we found that endogenous Tip60 physically interacts with endogenous MRN proteins in a complex which is distinct from the classical Tip60 complex. Taken together, our results describe a physical link between a DNA damage sensor and a histone-modifying enzyme, and provide important new insights into the role and mechanism of action of Tip60 in the process of DNA DSB repair.

International audience; Prp43p is a RNA helicase required for pre-mRNA splicing and for the synthesis of large and small ribosomal subunits. The molecular functions and modes of regulation of Prp43p during ribosome biogenesis remain unknown. We demonstrate that the G-patch protein Pfa1p, a component of pre-40S pre-ribosomal particles, directly interacts with Prp43p. We also show that lack of Gno1p, another G-patch protein associated with Prp43p, specifically reduces Pfa1p accumulation, whereas it increases the levels of the pre-40S pre-ribosomal particle component Ltv1p. Moreover, cells lacking Pfa1p and depleted for Ltv1p show strong 20S pre-rRNA accumulation in the cytoplasm and reduced levels of 18S rRNA. Finally, we demonstrate that Pfa1p stimulates the ATPase and helicase activities of Prp43p. Truncated Pfa1p variants unable to fully stimulate the activity of Prp43p fail to complement the 20S pre-rRNA processing defect of Deltapfa1 cells depleted for Ltv1p. Our results strongly suggest that stimulation of ATPase/helicase activities of Prp43p by Pfa1p is required for efficient 20S pre-rRNA-to-18S rRNA conversion.

The temperature dependencies of attenuation of: (i) longitudinal and shear waves in lithium niobate, (ii) longitudinal waves in ruby, and (iii) longitudinal and shear waves in magnesium aluminate spinel (spinel) at the frequency 36.5 GHz were measured. For the most crystals and wave types the temperature range was 78–∼150К, i.e. the strong attenuation did not allow to watch the echo-pulses at the room temperature. The exemption was the shear wave in spinel with the ratio of oxides 1∶2, for which we could confidently watch the echo-pulse at 300K delayed on 0.78 µs. The comparison of the attenuation of this wave at frequencies 36.5 GHz (54 dB/mks) and 9.4 GHz (3.5 dB/mks) at 300K showed the quadratic frequency dependency.

International audience; Bacterial chromosomes are organized in replichores of opposite sequence polarity. This conserved feature suggests a role in chromosome dynamics. Indeed, sequence polarity controls resolution of chromosome dimers in Escherichia coli. Chromosome dimers form by homologous recombination between sister chromosomes. They are resolved by the combined action of two tyrosine recombinases, XerC and XerD, acting at a specific chromosomal site, dif, and a DNA translocase, FtsK, which is anchored at the division septum and sorts chromosomal DNA to daughter cells. Evidences suggest that DNA motifs oriented from the replication origin towards dif provide FtsK with the necessary information to faithfully distribute chromosomal DNA to either side of the septum, thereby bringing the dif sites together at the end of this process. However, the nature of the DNA motifs acting as FtsK orienting polar sequences (KOPS) was unknown. Using genetics, bioinformatics and biochemistry, we have identified a family of DNA motifs in the E. coli chromosome with KOPS activity.

Branch migration of Holliday junctions is an important step of genetic recombination and DNA repair. In Escherichia coli , this process is driven by the RuvAB complex acting as a molecular motor. Using magnetic tweezers, we studied the RuvAB-directed migration of individual Holliday junctions formed between two ≈6-kb DNA molecules of identical sequence, and we measured the migration rate at 37°C and 1 mM ATP. We directly demonstrate that RuvAB is a highly processive DNA motor protein that is able to drive continuous and unidirectional branch migration of Holliday junctions at a well defined average speed over several kilobases through homologous sequences. We observed directional inversions of the migration at the DNA molecule boundaries leading to forth-and-back migration of the branch point and allowing us to measure the migration rate in the presence of negative or positive loads. The average migration rate at zero load was found to be ≈43 bp/sec. Furthermore, the load dependence of the migration rate is small, within the force range of –3.4 pN (hindering force) to +3.4 pN (assisting force).

The Holliday junction, the key intermediate of recombination, is generated by strand exchange resulting in a covalent connection between two recombining DNA molecules. Translocation of a Holliday junction along DNA, or branch migration, progressively exchanges one DNA strand for another and determines the amount of information that is transferred between two recombining partners. In Escherichia coli, the RuvAB protein complex promotes rapid and unidirectional branch migration of Holliday junctions. We have studied translocation of Holliday junctions using a quantitative biochemical system together with a 'single-molecule' branch migration assay. We demonstrate that RuvAB translocates the junctions through identical DNA sequences in a processive manner with a broad distribution of individual branch migration rates. However, when the complex encounters short heterologous sequences, translocation of the Holliday junctions is impeded. We conclude that translocation of the junctions through a sequence heterology occurs with a probability of bypass being determined both by the length of the heterologous region and the lifetime of the stalled RuvAB complex.

We describe a simple single-particle tracking approach for monitoring the length of DNA molecules in tethered particle motion experiments. In this method, the trajectory of a submicroscopic bead tethered by a DNA molecule to a glass surface is determined by videomicroscopy coupled to image analysis. The amplitude of motion of the bead is measured by the standard deviation of the distribution of successive positions of the bead in a given time interval. We were able to describe theoretically the variation of the equilibrium value of the amplitude of the bead motion with the DNA tether length for the entire applicable DNA length range (up to approximately 3500 bp). The sensitivity of the approach was illustrated by the evidence obtained for conformational changes introduced into a Holliday junction by the binding of the Escherichia coli RuvA protein. An advantage of this method is that the trajectory of the tethered bead, rather than its averaged motion, is measured, allowing analysis of the conformational dynamics of DNA chains at the single-molecule level.

Two 10-mer oligopyrimidine peptide nucleic acids (PNAs) were designed to interfere with IL-2R alpha promoter expression by binding to the regulatory sequences overlapping SRF and NF-kappa B transcription factor sites. Specific complexes were formed on each target sequence, and clearly involved (1) Hoogsteen hydrogen bonds as shown by experiments in which the purine strand of a single or double-stranded target was substituted with 7-deazadeoxyguanosine, (2) P-loop formation on double-helical DNA as evidenced by susceptibility to a single-strand-specific nuclease. When formed on a single-stranded DNA target, these highly stable complexes were responsible for efficient physical blockage of T7 DNA polymerase elongation on the template DNA containing the target oligopurine sequence. On a double-stranded target, these complexes only formed at low ionic strength and were slowly dissociated at physiological ionic strength (pH 6.5) with a t1/2 of 6.5-7 h. The salt-dependent instability of preformed complexes on a plasmid target was probably the critical factor responsible for their lack of significant sequence-specific effect on IL-2R alpha promoter activity inside living cells.

Eukaryotic genome is a highly compacted nucleoprotein complex organized in a hierarchical structure based on nucleosomes. Detailed organization of this structure remains unknown. In the present work we developed algorithms for geometry modeling of the supernucleosomal chromatin structure and for computing distance distribution functions and small-angle neutron scattering (SANS) spectra of the genome-scale (∼106 nucleosomes) chromatin structure at residue resolution. Our physical nucleosome model was based on the mononucleosome crystal structure. A nucleosome was assumed to be rigid within a local coordinate system. Interface parameters between nucleosomes can be set for each nucleosome independently. Pair distance distributions were computed with Monte Carlo simulation. SANS spectra were calculated with Fourier transformation of weighted distance distribution; the concentration of heavy water in solvent and probability of H/D exchange were taken into account. Two main modes of supernucleosomal structure generation were used. In a free generation mode all interface parameters were chosen randomly, whereas nucleosome self-intersections were not allowed. The second generation mode (generation in volume) enabled spherical or cubical wall restrictions. It was shown that calculated SANS spectra for a number of our models were in general agreement with available experimental data.

CArG boxes are cis-regulatory elements which are represented both in serum responsive and unresponsive promoters. Here we show that the RSV Long Terminal Repeat contains two CArG boxes, which were efficiently recognised by purified Serum Response Factor, although they remained unresponsive to serum in transient transfection assays. However, RSV CArG boxes were as efficient as c-fos Serum Response Element in mediating a Serum Response Factor-dependent transcription in vitro . Thus, the fact that a CArG box is able to bind Serum Response Factor in an active form is unsufficient for serum responsiveness in vivo .