bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical Investigation on the Plastic Response of a Small-Scale Laterally Impacted Tanker Double Hull Structure
Authors: Villavicencio Richard , Kim Young-Hun , Cho Sang-Rai , Soares C. Guedes
Published: August 2013

Numerical simulations are presented, on the dynamic response of a one-tenth scaled tanker double hull structure struck laterally by a knife edge indenter. The small stiffeners of the full-scale prototype are smeared in the small-scale model by increasing the thicknesses of the corresponding plates. The dynamic response is evaluated at an impact velocity of 7.22 m/s and the impact point is chosen between two frames to assure damage to the outer shell plating and stringers. The simulations are performed by LS-DYNA finite element solver. They aim at evaluating the influence of strain hardening and strain rate hardening on the global impact response of the structure, following different models proposed in the literature. Moreover, the numerical model is scaled to its full-scale prototype, summarizing the governing scaling laws for collision analysis and evaluating the effect of the material strain rate on the plastic response of large scaled numerical models.
Stability Analysis Hinged Vertical Flat Plate Rotation in a Uniform Flow
Authors: Sefat Sina Mirzaei , Fernandes Antonio Carlos
Published: August 2013

The free falling of objects is a phenomenon that has been observed in the nature. The Pendulous Installation Method (PIM) of heavy devices is an example of free falling which occurs in the installation of heavy offshore devices on sea bed. Hence, the motivation of the present research is to study the fluttering and tumbling (autorotation) motions that may occur during the free fall of object. The fluttering is a periodic or chaotic oscillation of body about a vertical axis. On the other hand, the tumbling is end-over-end rotation of body. In order to access the main physical aspects, the present work decided to attack a more fundamental problem and describes the investigations on fluttering and autorotation motions of the interaction of uniform current and freely rotating plate about a fixed vertical axis.

A quasi-steady model is suggested to model the trajectories of flow induced rotation phenomenon and a stability analysis performed to gain insight into the nature of the bifurcation from fluttering to autorotation. At first, the fixed points for different models of motion is obtained and each point analyzed by using the linearized equation. Secondly, the phase diagrams as a function of angular velocity and angle of rotation have been presented for different dynamic models.
Scaling of Flexural and Compressive Ice Failure
Authors: Jordaan Ian , Taylor Rocky , Derradji-Aouat Ahmed
Published: August 2013

Physical model tests are a powerful means of obtaining solutions to a variety of engineering problems. The applications in hydraulics and aerospace engineering are prominent, where the use of similitude and dimensionless numbers is well developed. The first step is to understand the mechanics of the process. In the case of ice, the theory has not been developed to the same degree as in fluid mechanics. The use of scale models in test basins has often focused on resistance to ship motion and on flexural failure of the ice. This has been reasonably well addressed. The properties of the model ice have often been modified to permit scaling of flexural strength as well as elastic modulus to achieve appropriate behaviour.

Extension of testing to situations where ice fails in compression or combined flexure and crushing leads to additional complication. At low rates of loading, ice creeps and also demonstrates enhanced rates of creep if the stress is sufficient to cause damage (microstructural change) in the ice. At higher rates of loading, fracture processes result in a localization of loading, and in the formation of high-pressure zones, which have their own special failure process.

In the paper a review of scaled ice testing is given, with associated mechanics including flexural failure. This is followed by a discussion of the failure processes in compression and related mechanics such as creep, damage and fracture. Suggestions as to scaling of these processes are made. An important aspect that is considered is the randomness of ice loads as measured in the full scale. Modelling this aspect and determination of appropriate extreme values is discussed. The Weibull modulus is suggested as an appropriate parameter.
Study for Modification Lattice Boltzmann Model Application to Flow Characteristics for Gas Hydrate Decomposition in Sediment
Authors: Yu Xichong , Liu Yu , Pang Weixin , Bai Yuhu , Zhao Jiafei
Published: August 2013

In this paper, based on sediment with gas hydrate and flow characteristics for gas hydrate decomposition, the interaction and density difference between the phases are considered, conventional lattice Boltzmann model is modified to new lattice Boltzmann model then is applied to study flow characteristics for gas hydrate decomposition in sediment. The method is the mesoscopic model between macro and micro methods between. Modification lattice Boltzmann model is applied to carry out a complex micro-channel single-phase, multiphase flow simulation analysis, single-phase flow in porous media for gas hydrate decomposition. The results show that complex micro-channel flow field depends on the micro-channel roughness, bending degree, surface wet ability, fluid properties and other media. Single-phase flow in porous media depends on the pore diameter (saturation) and permeability of the sediment and the hydrate formation in the sediment so greatly reduces the permeability of porous media.
Vibration Analysis and Evaluation for the Offshore Structure Using Simplified Model and RSS Method
Authors: Lee Chan Hui , Song Keun Bok , Kim Heui Won
Published: August 2013

The evaluation of the vibration characteristics of offshore structure in the design stage is important to ensure the safety of structure, equipment and worker. Conventionally, the vibration analysis of the offshore structure is carried out according to its own analysis procedure including the selection of vibrating equipment, FE modeling, evaluation of excitation forces and criteria. The efficient modeling of the vibration equipment and the consideration of the phase of excitation forces are necessary to reduce the calculation time and to increase the accuracy of analysis.

In this paper, the efficient and accurate vibration analysis method is introduced including the simplified model of equipment and the RSS (root squared summation) method. The vibration equipment was modeled as the simplified model of which mesh size is reduced by 90%, however, its vibration characteristics such as natural frequency and vibration modes are not changed. In addition, the RSS method was applied in the forced vibration analysis to consider appropriate phase of excitation forces. As the RSS method is the summation of all the vibration response with respect to each excitation forces, it presents more reasonable and conservative vibration evaluation. The proposed vibration analysis method has been confirmed by conducting various offshore projects and is expected to be more efficient for the design of offshore structure.
Comprehensive Riser VIV Model Tests in Uniform and Sheared Flow
Authors: Lie Halvor , Braaten Henning , Jhingran Vikas Gopal , Sequeiros Octavio E. , Vandiver Kim
Published: August 2013

Despite of considerable research activity during the last decades considerable uncertainties still remain in prediction of Vortex Induced Vibrations (VIV) of risers. Model tests of risers subjected to current have been shown to be a useful method for investigation of the VIV behavior of risers with and without suppression devices.

In order to get further insight on VIV of risers, an extensive hydrodynamic test program of riser models subjected to vortex-induced vibrations was undertaken during the winter 2010 by Shell Oil Company.

The VIV-model test campaign was performed in the MARINTEK Offshore Basin Laboratory. A new test rig was constructed and showed to give good test conditions. Three different 38m long riser models were towed horizontally at different speeds, simulating uniform and linearly varying sheared current. Measurements were made In-Line (IL) and Cross-Flow (CF) of micro bending strains and accelerations along the risers. The test program compromised about 400 tests, which give a rich test material for further studies.

In the present paper the test set-up and program are presented and selected results are reported.
Is the Vertical Variability of the Ocean in Santos Bight, Brazil, Dominated by the Western Boundary Current Meanders?
Authors: Ceccopieri Wellington , da Silveira Ilson C. A.
Published: August 2013

The Brazil Current (CB) flows southwestward as vertically stratified and organized western boundary jet in the Brazilian shelf-break region ranging from 20–40° S, where the CB’s mass transport grows vertically. This geographical band show intense mesoescale activity due to passageway of eddies and meanders, superimposed over oceanic large-scale recirculation features which influence the oceanic circulation in the Santos Bight Pre-salt cluster area 300 km offshore. Based on 2-year observed data series of an oceanographic mooring array at Lula Field, and based on repeated hydrographic data (seawater temperature, salinity and N2 profiles) we used statistical and dynamical orthogonal modes in order to approach the local vertical current profile variability. We verified that it is 85 % explained by EOF-1. This variability is essentially of 1st baroclinic mode. Great part of it occupies the first 400–600 m water depth, with no predominant direction. We also found remarkable water column seasonal stratification. Albeit of relative weaker mean flows (0.1–0.2 m s−1), the study area is eddy dominated which are geostrophically adjusted to the 1st baroclinic mode. Furthermore, we observed that the significant directional variability over the São Paulo Plateau occurs far away from the mean current jets that flow parallel to the continental shelf-break geometry.
Ratcheting of Corroded Pipes
Authors: Lourenço Marcelo Igor , Netto Theodoro A.
Published: August 2013

Corroded pipes for oil transportation can eventually experience Ratcheting after some years of operation. The evaluation of the defects caused by corrosion in these pipes is important when deciding for the repair of the line or continuity in operation. Under normal operational conditions, these pipes are subject to constant internal pressure and cyclic load due to bending and/or tension. Under such loading conditions, the region in the pipes with thickness reduction due to corrosion could experience the phenomenon known as ratcheting. The objective of this paper is to present a revision of the available numerical models to treat the ratcheting phenomenon. Experimental tests were developed allowing the evaluation of occurrence of ratcheting in corroded pipes under typical operational load conditions as well as small-scale cyclic tests to obtain the material parameters. Numerical and experimental tests results are compared. Shakedown models are also investigated as a practical tool for ratcheting prediction.
Artificial Lift Management: Recommendations for Unconventional Oilfields
Authors: Hirschfeldt Clemente Marcelo , Avila Fernando Flores , Cáliz Jaime Granados
Published: August 2013

This paper presents concepts and recommendations regarding Artificial Lift Systems (ALS’s) management during productive life of oil fields, envisioning: selection, acquisition, installation, monitoring and evaluation criteria, as well as subsequent inspection thereof, and highlighting the more important that applies particularly to unconventional oil fields. Issues analyzed herein involve definitions of roles, functions and competencies related to operator as well as service companies and sectors involved or required to live up to the challenges posed by these systems. Two scenarios that represent Latin American region real cases are presented and illustrated with the analysis of these ALS’s management topics; one of them, the oldest productive basin in Argentina, as an example of conventional oilfields with experience in Artificial Lift Management and the other, an unconventional field recently re-activated with an accelerated development pace, being exploited in Mexico. Conclusions are presented in terms of that ALS’s Integral management should be taken with strategic and integrated vision, in accordance with current level of development, future plans, and complexity of the field; not only focused on maximum oil production, but also on optimizing production costs; and contemplate all parts commitment that add value to the whole process.
Numerical Simulation on Natural Gas Production From Gas Hydrate Dissociation by Depressurization
Authors: Yu Tao , Liu Weiguo , Zhao Jiafei , Song Yongchen , Liu Yu
Published: August 2013

The paper presented a numerical model on the gas hydrate production by depressurization. During the simulation a one-dimensional dissociation model applied to a gas hydrate reservoir was set up to simulate the process of gas hydrate production by depressurization. Based on the calculation results, influences of the gas pressure, saturation, porosity and absolute permeability on the production effect were studied respectively. The results obtained from the sensitivity analysis provide theoretical supported for the actual gas hydrate production.
Fractional Flow Analysis of Displacement in a CO2 Enhanced Gas Recovery Process for Carbonate Reservoirs
Authors: Odi Uchenna , Gupta Anuj
Published: August 2013

This paper presents fractional flow analysis of displacement of gas/condensate in a wet/condensate gas reservoir by CO2 that includes interactions between CO2 and condensate.

Phase behavior affects the performance of carbon dioxide enhanced oil/ gas recovery processes in a significant manner. It also controls the effectiveness of carbon dioxide sequestration processes. In the past, there has been a focus on understanding interactions of CO2 with matrix and other fluids in oil reservoirs by various researchers. However, there is now an increasing interest in understanding carbon dioxide interactions in gas condensate reservoirs so that CO2 can be used to increase recovery. For a carbonate reservoir containing gas-condensates, this new focus requires a fundamental understanding of the interactions of carbon dioxide with condensate and gas phases. This paper describes the relative effect that these mechanisms have by conducting a fractional flow analysis for Enhanced Gas Recovery. These mechanisms include miscibility and partitioning of CO2 in various phases. Understanding these mechanisms is essential to modeling Enhanced Oil/Gas Recovery using CO2.

The analysis honors the material balance and accounts for miscibility between carbon dioxide and condensate. The results of the fractional flow analysis are important for validation of computer simulation of the comparable processes. This work is expected to serve as a foundation work in understanding the mechanisms involved in CO2 assisted enhanced oil and gas recovery.
Pore-Pressure Accumulation and Soil Softening Around Pile Foundations for Offshore Wind Turbines
Authors: Cuéllar Pablo , Baeßler Matthias , Rücker Werner
Published: August 2013

The foundation of offshore wind turbines usually involves the installation of large-diameter steel piles in the seabed, either in monopile or multi-pile configurations (jacket, tripod, etc…), which have to ensure a proper fixity of the turbine during its whole service life-time.

However, such foundations raise several challenges and novel questions, partly due to the special characteristics of the offshore environment (for instance, the large numbers of load cycles from wind and waves and the possible influence of transient changes of pore water pressure around the pile) and aggravated by their large diameter, reduced slenderness and elevated ratio of lateral to vertical loads (see Fig. 1).

This paper studies the effects of cyclic lateral loading on the offshore piles focusing on the possibility of a progressive accumulation of residual pore water pressure within the saturated embedding soil. As it will be shown, this can lead to significant changes of their behaviour under external loading, which can potentially compromise the foundation’s stability or serviceability.

The paper will also analyse some singular effects of an irregular loading (e.g. cyclic loading with variable amplitude), in particular the so-called “order effects” and the phenomena arising during a realistic storm of moderate magnitude, and discuss their potential for transient damages to the foundation’s stiffness.

All these phenomena, which can lead to a loss of serviceability of the structure, have been investigated by the authors by means of a coupled bi-phasic analytical model of the offshore foundation featuring a versatile constitutive law suitable for the soil. The constitutive model, in the frame of the theory of Generalized Plasticity, can reproduce some complex features of cyclic soil behaviour such as the tendency for a progressive densification under cyclic loading, which is responsible for the soil liquefaction phenomena in undrained conditions.

Finally, some implications of these issues for the practical design of offshore monopiles will be discussed and some specific recommendations for the design procedures will be outlined.
Modelling Pore Continuity and Durability of Cementitious Sealing Material
Authors: Koenders E. A. B. , Hansen W. , Toledo Filho R. D. , van Breugel K.
Published: August 2013

In this paper the latest developments of the hydration simulation model Hymostruc are discussed while evaluating pore connectivity and the influence on permeability and durability of cementitious sealing material for carbon sequestration projects. The numerical model Hymostruc is used to quantify and visualize this phenomenon and to show the contribution of capillary pores to the continuity of the capillary pore system throughout an evolving microstructure. Once the capillary pores are blocked by ongoing hydration the transport of CO2 gasses are restricted to migrate through the microstructure and avoid leakage of the sealing material. A blockage of the capillary pore system during evolution of the microstructure (pore discontinuity or depercolation) is, therefore, indispensable for a sound cementitious sealing material and must be one of the main objectives for the slurry design. The numerical model Hymostruc is used to evaluate existing literature-based slurry compositions on their ability achieve full depercolation of the capillary pore system in relation to the hardening conditions. Potential compositions of slurries are proposed and microstructural properties show the performance of optimized microstructures that comply with pore discontinuity. A durability evaluation regarding the CO2 ingress is conducted as well. The pore continuity analysis shows the relevance to control of the capillary pore structure inside an evolving microstructure in relation to its permeability and it ease to leak gaseous phases through the sealing material.
A Comprehensive Approach for Assessing the Impacts of Wettability on Oil Production in Carbonate Reservoirs
Authors: Faerstein Marcos , Couto Paulo , Alves José
Published: August 2013

This paper discusses the impacts that rock wettability may have upon the production and recovery of oil with waterflooding in carbonate reservoirs and how it should be modeled. A broad review of the state of the art has been conducted surveying existing disagreements and knowledge gaps, basic definitions, as well as the correct understanding of the physical phenomena and identification of the characteristics of the various wettability scenarios.

Case studies conducted with a black oil reservoir simulator evaluated the impact of different wettability scenarios on oil production and recovery. A comprehensive approach considering all the parameters involved in the wettability modeling was applied to the case studies, showing how the behavior of the reservoir varies as a function of their wettability.

This paper shows how relative permeability and capillary pressure should be varied to correctly represent different wettability scenarios and consequently assess its impacts on oil production and recovery.

The case studies show that the evaluation of the volume of oil in the reservoir is impacted by wettability through the irreducible water saturation and primary drainage capillary pressure and must be considered in the analyses. In long term analyses, mixed-wet scenarios have a higher oil production and recovery. In medium and short term, the water-wet scenarios have the higher recovery, but in relation to oil production, these scenarios are negatively influenced by the smaller volume of oil in place.

The main contribution of this paper is the simultaneous analyses of all the parameters involved in the modeling of wettability showing how they impact the behavior of a reservoir. It shows how the parameters must be varied in a heterogeneous reservoir and how heterogeneity impacts the relevance of wettability in the studies.
Energy, Environment, and Economical Advantages of Solar Thermal Cracking of Natural Gas
Authors: Ozalp Nesrin
Published: August 2013

Among all fossil fuels, natural gas is probably the most attractive one because of its higher heating value, and approximately 97% methane content, which creates less hazardous emissions during power generation. Considering these important facts and the demand for natural gas in the world market, it would be unlikely to think of converting natural gas. However, if we want to utilize our planet’s limited natural gas resources better, then we need to explore alternative ways. A way to achieve that goal is direct cracking of natural gas via solar thermal processing. This paper describes advantages of solar cracking of natural gas from energy, environment and economic point of view. Results show that products of natural gas decomposition contain 8% more energy per mole compared to natural gas itself, while the decomposition process does not emit any hazardous emissions to the environment. As for the economics, once the decomposition products of natural gas, namely hydrogen and carbon black, are sold separately, it is possible to make up to three times more revenue than the selling of natural gas. The products of natural gas decomposition have a very wide use in chemical and petroleum industries. For example, hydrogen is a crucial commodity to refine crude oil, while carbon black is the fundamental component in car tire, battery, conveyer belt, and printer ink manufacturing industries. Currently, petroleum industry produces hydrogen via steam reforming of methane and the chemical industry produces carbon black from coal or natural gas combustion in furnace, which are both highly toxic and global warming emissive processes. With solar cracking of natural gas, these two important commodities can be produced without any emissions to the environment.
Loss Circulation and Formation Damage Control on Overbalanced Drilling With Different Formulations of Water Based Drill-In Fluids on Sandstone Reservoir
Authors: Lopes Leandro F. , Silveira Bruno O. , Moreno Rosângela B. Z. L.
Published: August 2013

The oil well drilling should not damage formation, mainly the interest region: the reservoir. Drilling without damaging the reservoir is a hard challenge, and therefore the development of technologies and optimization process, including, for example, the design of fluids in order to minimize damage, is been stimulated. Drilling fluids may interact with reservoir rocks resulting on permeability impairment, which reduces well productivity. It has been reported that a detailed fluid management plan can help to minimize formation damage and improve well productivity. This work is focused on formation damage analysis due to drilling fluids invasion in high permeability sandstone oil reservoir. Water-based fluids were prepared with the following components: distilled water, salt (NaI), polymer (Partially Hydrolyzed Polyacrylamide - HPAM, and Xanthan Gum - XG) and clay (Bentonite). Samples were submitted to an invasion process, simulating an overbalanced drilling, and to an oil reverse flow, simulating oil production beginning. Results showed that all fluids containing clay presented less deep invasion than the fluids prepared with polymer only. Moreover, clay concentration influenced on permeability impairment and productivity ratio return results. HPAM fluids, when injected, invaded more deeply the samples than XG fluids, but productivity ratio return was also higher.
Experimental Study of the Impact of Drilling Fluid Contamination on the Integrity of Cement-Formation Interface
Authors: Agbasimalo Nnamdi , Radonjic Mileva
Published: August 2013

Primary cementing is performed during drilling and completion of wells mainly to provide zonal isolation. Ideally, 100% drilling fluid displacement should be achieved during cementing. This is difficult to achieve and some mud is left on the wellbore walls. This study investigates the effect of the undisplaced mud on the integrity of the cement-formation interface. Flow-through experiments were conducted at 14.48 MPa (2100 psi) overburden pressure and temperature of 22° C (72° F) with cement-sandstone composite cores and brine at a flow rate of 1 ml/min. The cement-sandstone composite cores had 0% and 10% drilling mud contamination respectively. Variations in the permeability of the composite cores were recorded throughout the flow-through experiments by measuring the pressure drop across the composite cores. The composite cores were characterized before and after the flow-through experiments to delineate the alterations in the composite cores due to the flow-through experiments. Higher pH values were observed in the effluent brine from the 10% mud contaminated core than the 0% mud contaminated core due to increased dissolution of cement. Microtomography revealed higher porosity at the interface zone of the 10% mud contaminated core. These show that mud contamination has a deleterious effect on the cement-sandstone interface and may create pathways for inter-zonal communication.
Tensile Strain Models for Strain-Based Design of Pipelines
Authors: Wang Yong-Yi , Liu Ming , Song Yaxin , Horsley David
Published: August 2013

This paper covers the development of tensile strain design models using a multidisciplinary approach, including fundamental fracture mechanics, small-scale material characterization tests, and large-scale tests of full-size pipes. The tensile strain design models are formulated in a four-level format. The Level 1 procedure provides estimated tensile strain capacity (TSC) in a tabular format for quick initial assessment. The initiation toughness alternatively termed apparent toughness is estimated from upper shelf Charpy impact energy. The Level 2 procedure contains a set of parametric equations based on an initiation-control limit state. The tensile strain capacity can be computed from these equations with the input of a pipe’s dimensional and material property parameters. The apparent toughness is estimated from either upper shelf Charpy energy or upper shelf toughness of standard CTOD test specimens. The Level 3 procedure uses the same set of equations as in Level 2 and the toughness values are obtained from low-constraint tests. In the Level 3 procedure, two limit states based on either initiation control or ductile instability can be used. The Level 4 procedure allows the use of direct FEA calculation to develop crack driving force relations. The same limit states as those in Level 3 may be used. The Level 4 procedures should only be used by seasoned experts in special circumstances where lower level procedures are judged inappropriate.

The tensile strain design models may be used for the following purposes:

(1) The determination of tensile strain capacity for a given set of material properties and flaw size.

(2) The determination of acceptable flaw sizes for a given set of material properties and target tensile strain capacity.

(3) The selection of material properties to achieve a target strain capacity for a given flaw size.

(4) The optimization of the tensile strain capacity by balancing the requirements of material parameters, such as weld strength (thus weld strength mismatch level) versus toughness.

The application of the tensile strain design models is given in a companion paper.
Third Party HIL Testing of Safety Critical Control System Software on Ships and Rigs
Authors: Smogeli Øyvind , Augustson Trond
Published: August 2013

The drilling industry is characterized by a rapid and up front technology development to conquer larger water and drilling depths. The level of automation has been steadily increasing over several decades, growing from manually operated sledge-hammer technology to space-age computer-based integrated systems. Most of the automation systems on today’s vessels are put into operation without independent testing. This is a paradox considering that a single control system may be more complex than all the mechanical systems onboard. It is also a paradox that the automation systems often contain safety-critical failure handling functionality that may be difficult or dangerous to test onboard the real vessel, and therefore is not properly tested until it is activated during an emergency situation. These automation systems are essential for the safety, reliability, and performance of the vessels. Examples are the Dynamic Positioning (DP) systems, Power Management systems, Drilling Control Systems, BOP control systems, Managed Pressure Drilling (MPD) systems, and crane control systems. Hardware-In-the-Loop (HIL) testing is a well proven test methodology from automotive, avionics, and space industries, and is now also gaining recognition in the marine and offshore industries. The aim of this paper is to clarify what HIL testing is, how third party HIL testing can be applied to safety critical control system software on drilling ships and rigs, and why this is an important contribution to technical safety, reliability and profitability of offshore operations.
The Molecular Trigger for High-Speed Wing Beats in a Bee
Authors: Iwamoto H. , Yagi N.
Published: August 2013

At a Stretch

Insect flight muscles are operationally similar to vertebrate skeletal muscles in many ways; however, they are specialized for high-speed, small amplitude oscillations and are activated not by the release and re-uptake of calcium, but rather through stretch-activation.
Iwamoto and Yagi
(p.
1243
, published online 22 August) use a pair of ultrafast cameras to record diffraction patterns and wing beats in the flight muscles of bumblebees and find that stretch activation is a result of myosin and actin dynamics.
Conserved Regulation of Cardiac Calcium Uptake by Peptides Encoded in Small Open Reading Frames
Authors: Magny Emile G. , Pueyo Jose Ignacio , Pearl Frances M.G. , Cespedes Miguel Angel , Niven Jeremy E. , Bishop Sarah A. , Couso Juan Pablo
Published: August 2013

smORFing for Calcium

Genomes contain thousands of small open reading frames (smORFs), short DNA sequences coding for peptides of less than 100 amino acids.

Magny
et al.

(p.
1116
, published on 22 August) describe two smORF-encoded peptides of less than 30 amino acids regulating calcium transport and, hence, regular heart contraction, in the fruit fly
Drosophila
. These peptides seem to have been conserved for more than 550 million years in a range of species from flies to humans, where they have been implicated in severe heart diseases. Such conservation suggests that smORFs might be an ancient part of our functional genome.
An Atomic Clock with 10
–18
Instability
Authors: Hinkley N. , Sherman J. A. , Phillips N. B. , Schioppo M. , Lemke N. D. , Beloy K. , Pizzocaro M. , Oates C. W. , Ludlow A. D.
Published: August 2013

Tick, Tick, Tick…

Many aspects of everyday life from communication to navigation rely on the precise ticking of the microwave transitions of the atoms in atomic clocks. Optical transitions occur at much higher frequency and so offer the opportunity to reduce the scale of the ticks even more.

Hinkley
et al.

(p.
1215
, published online 22 August; see the Perspective by

Margolis

) compare the ticking of two optical clocks and report an instability near the 10
−18
level. Such performance will improve tests of general relativity and pave the way for a redefinition of the second.
Stationary Phase and Nutrient Levels Trigger Transcription of a Genomic Locus Containing a Novel Peptide (TM1316) in the Hyperthermophilic Bacterium Thermotoga maritima
Authors: Frock Andrew D. , Montero Clemente I. , Blumer-Schuette Sara E. , Kelly Robert M.
Published: August 2013

The genome of the hyperthermophilic bacterium
Thermotoga maritima
encodes numerous putative peptides/proteins of 100 amino acids or less. While most of these open reading frames (ORFs) are transcribed during growth, their corresponding physiological roles are largely unknown. The onset of stationary phase in
T. maritima
was accompanied by significant morphological changes and upregulation of several ORFs located in the TM1298-TM1336 genome locus. This region contains putative HicAB toxin-antitoxin pairs, hypothetical proteins, radical
S
-adenosylmethionine (SAM) enzymes, and ABC transporters. Of particular note was the TM1315-TM1319 operon, which includes a putative 31-amino-acid peptide (TM1316) that was the most highly transcribed gene in the transcriptome during stationary phase. Antibodies directed against a synthetic version of TM1316 were used to track its production, which correlated closely with transcriptomic data. Immunofluorescence microscopy revealed that TM1316 was localized to the cell envelope and prominent in cell aggregates formed during stationary phase. The only functionally characterized locus with an organization similar to that of TM1315-TM1319 is in
Bacillus subtilis
, which contains subtilosin A, a cyclic peptide with Cys–to–α-carbon linkages that functions as an antilisterial bacteriocin. While the organization of TM1316 resembled that of the
Bacillus
peptide (e.g., in its number of amino acids and spacing of Cys residues), preparations containing high levels of TM1316 affected the growth of neither
Thermotoga
species nor
Pyrococcus furiosus
, a hyperthermophilic archaeon isolated from the same locale as
T. maritima
. Several other putative Cys-rich peptides could be identified in the TM1298-TM1336 locus, and while their roles are also unclear, they merit examination as potential antimicrobial agents in hyperthermophilic biotopes.
Development of a DNA Microarray Method for Detection and Identification of All 15 Distinct O-Antigen Forms of Legionella pneumophila
Authors: Cao Boyang , Yao Fangfang , Liu Xiangqian , Feng Lu , Wang Lei
Published: August 2013

Legionella
is ubiquitous in many environments. At least 50 species and 70 serogroups of the Gram-negative bacterium have been identified. Of the 50 species, 20 are pathogenic, and
Legionella pneumophila
is responsible for the great majority (approximately 90%) of the Legionnaires' disease cases that occur. Furthermore, of the 15
L. pneumophila
serogroups identified, O1 alone causes more than 84% of the Legionnaires' disease cases that occur worldwide. Rapid and reliable assays for the detection and identification of
L. pneumophila
in water, environmental, and clinical samples are in great demand.
L. pneumophila
bacteria are traditionally identified by their O antigens by immunological methods. We have recently developed an O serogroup-specific DNA microarray for the detection of all 15 distinct O-antigen forms of
L. pneumophila
, including serogroups O1 to O15. A total of 35 strains were used to verify the specificity of the microarray, including 15
L. pneumophila
O-antigen standard reference strains and seven
L. pneumophila
clinical isolates as target strains, seven reference strains of other non-
pneumophila Legionella
species as closely related strains, and six non-
Legionella
bacterial species as nonrelated strains. The detection sensitivity was 1 ng of genomic DNA or 0.4 CFU/ml in water samples with filter enrichment and plate culturing. This study demonstrated that the microarray allows specific, sensitive, and reproducible detection of
L. pneumophila
serogroups. To the best of our knowledge, this is the first report of a microarray serotyping method for all 15 distinct O-antigen forms of
L. pneumophila
.
Streptomycin Application Has No Detectable Effect on Bacterial Community Structure in Apple Orchard Soil
Authors: Shade Ashley , Klimowicz Amy K. , Spear Russell N. , Linske Matthew , Donato Justin J. , Hogan Clifford S. , McManus Patricia S. , Handelsman Jo
Published: August 2013

Streptomycin is commonly used to control fire blight disease on apple trees. Although the practice has incited controversy, little is known about its nontarget effects in the environment. We investigated the impact of aerial application of streptomycin on nontarget bacterial communities in soil beneath streptomycin-treated and untreated trees in a commercial apple orchard. Soil samples were collected in two consecutive years at 4 or 10 days before spraying streptomycin and 8 or 9 days after the final spray. Three sources of microbial DNA were profiled using tag-pyrosequencing of 16S rRNA genes: uncultured bacteria from the soil (culture independent) and bacteria cultured on unamended or streptomycin-amended (15 μg/ml) media. Multivariate tests for differences in community structure, Shannon diversity, and Pielou's evenness test results showed no evidence of community response to streptomycin. The results indicate that use of streptomycin for disease management has minimal, if any, immediate effect on apple orchard soil bacterial communities. This study contributes to the profile of an agroecosystem in which antibiotic use for disease prevention appears to have minimal consequences for nontarget bacteria.
Engineered Escherichia coli with Periplasmic Carbonic Anhydrase as a Biocatalyst for CO2Sequestration
Authors: Jo Byung Hoon , Kim Im Gyu , Seo Jeong Hyun , Kang Dong Gyun , Cha Hyung Joon
Published: August 2013

Carbonic anhydrase is an enzyme that reversibly catalyzes the hydration of carbon dioxide (CO2). It has been suggested recently that this remarkably fast enzyme can be used for sequestration of CO2, a major greenhouse gas, making this a promising alternative for chemical CO2mitigation. To promote the economical use of enzymes, we engineered the carbonic anhydrase fromNeisseria gonorrhoeae(ngCA) in the periplasm ofEscherichia coli, thereby creating a bacterial whole-cell catalyst. We then investigated the application of this system to CO2sequestration by mineral carbonation, a process with the potential to store large quantities of CO2.ngCA was highly expressed in the periplasm ofE. coliin a soluble form, and the recombinant bacterial cell displayed the distinct ability to hydrate CO2compared with its cytoplasmicngCA counterpart and previously reported whole-cell CA systems. The expression ofngCA in the periplasm ofE. coligreatly accelerated the rate of calcium carbonate (CaCO3) formation and exerted a striking impact on the maximal amount of CaCO3produced under conditions of relatively low pH. It was also shown that the thermal stability of the periplasmic enzyme was significantly improved. These results demonstrate that the engineered bacterial cell with periplasmicngCA can successfully serve as an efficient biocatalyst for CO2sequestration.
Bimodular Peptide Synthetase SidE Produces Fumarylalanine in the Human Pathogen Aspergillus fumigatus
Authors: Steinchen Wieland , Lackner Gerald , Yasmin Sabiha , Schrettl Markus , Dahse Hans-Martin , Haas Hubertus , Hoffmeister Dirk
Published: August 2013

The filamentous mold
Aspergillus fumigatus
causes invasive aspergillosis, a potentially life-threatening infectious disease, in humans. The
sidE
gene encodes a bimodular peptide synthetase and was shown previously to be strongly upregulated during initiation of murine lung infection. In this study, we characterized the two adenylation domains of SidE with the ATP-[
32
P]pyrophosphate exchange assay
in vitro
, which identified fumarate and
l
-alanine, respectively, as the preferred substrates. Using full-length
holo
-SidE, fumarylalanine (FA) formation was observed
in vitro
. Furthermore, FA was identified in
A. fumigatus
culture supernatants under inducing conditions, unless
sidE
was genetically inactivated. As FA is structurally related to established pharmaceutical products exerting immunomodulatory activity, this work may contribute to our understanding of the virulence of
A. fumigatus
.
Evidence for a Bacterial Lipopolysaccharide-Recognizing G-Protein-Coupled Receptor in the Bacterial Engulfment by Entamoeba histolytica
Authors: Brewer Matthew T. , Agbedanu Prince N. , Zamanian Mostafa , Day Tim A. , Carlson Steve A.
Published: August 2013

Entamoeba histolytica
is the causative agent of amoebic dysentery, a worldwide protozoal disease that results in approximately 100,000 deaths annually. The virulence of
E. histolytica
may be due to interactions with the host bacterial flora, whereby trophozoites engulf colonic bacteria as a nutrient source. The engulfment process depends on trophozoite recognition of bacterial epitopes that activate phagocytosis pathways.
E. histolytica
GPCR-1 (EhGPCR-1) was previously recognized as a putative G-protein-coupled receptor (GPCR) used by
Entamoeba histolytica
during phagocytosis. In the present study, we attempted to characterize EhGPCR-1 by using heterologous GPCR expression in
Saccharomyces cerevisiae
. We discovered that bacterial lipopolysaccharide (LPS) is an activator of EhGPCR-1 and that LPS stimulates EhGPCR-1 in a concentration-dependent manner. Additionally, we demonstrated that
Entamoeba histolytica
prefers to engulf bacteria with intact LPS and that this engulfment process is sensitive to suramin, which prevents the interactions of GPCRs and G-proteins. Thus, EhGPCR-1 is an LPS-recognizing GPCR that is a potential drug target for treatment of amoebiasis, especially considering the well-established drug targeting to GPCRs.
Complete Genome Sequence for Lactobacillus helveticus CNRZ 32, an Industrial Cheese Starter and Cheese Flavor Adjunct
Authors: Broadbent Jeff R. , Hughes Joanne E. , Welker Dennis L. , Tompkins Thomas A. , Steele James L.
Published: August 2013

Lactobacillus helveticus
is a lactic acid bacterium widely used in the manufacture of cheese and for production of bioactive peptides from milk proteins. We present the complete genome sequence for
L. helveticus
CNRZ 32, a strain particularly recognized for its ability to reduce bitterness and accelerate flavor development in cheese.
Complete Genome Sequence Analysis of a Reassortant Strain of Bluetongue Virus Serotype 16 from Italy
Authors: Lorusso Alessio , Costessi Adalberto , Pirovano Walter , Marcacci Maurilia , Cammà Cesare , Savini Giovanni
Published: August 2013

The complete genome sequence of a reassortant field strain of bluetongue virus serotype 16 (BTV-16), isolated from cattle in the Apulia region of Italy in 2002, has been determined by Illumina sequencing. Sequence comparisons of segment 1 (Seg-1) to Seg-10, except Seg-5, show that BTV-16 strain ITL2002 belongs to the major eastern topotype of BTV.
Full Genome Sequence of Egg Drop Syndrome Virus Strain FJ12025 Isolated from Muscovy Duckling
Authors: Fu Guanghua , Chen Hongmei , Huang Yu , Cheng Longfei , Fu Qiuling , Shi Shaohua , Wan Chunhe , Chen Cuiteng , Lin Jiansheng
Published: August 2013

Egg drop syndrome virus (EDSV) strain FJ12025 was isolated from a 9-day-old Muscovy duckling. The results of the sequence showed that the genome of strain FJ12025 is 33,213 bp in length, with a G+C content of 43.03%. When comparing the genome sequence of strain FJ12025 to that of laying duck original strain AV-127, we found 50 single-nucleotide polymorphisms (SNPs) between the two viral genome sequences. A genomic sequence comparison of FJ12025 and AV-127 will help to understand the phenotypic differences between the two viruses.
Genome Sequence of the Quorum-Quenching Agrobacterium tumefaciens Strain WRT31
Authors: Mondy Samuel , Lalouche Ouaghlis , Dessaux Yves , Faure Denis
Published: August 2013

Agrobacterium tumefaciens
strain WRT31 is a quorum-sensing signal-degrading bacterium that has been isolated from the rhizosphere of tobacco plants. This strain belongs to
A. tumefaciens
genomovar G1, is avirulent on various putative host plants, devoid of Ti plasmid, and contains the
blcC
gene encoding a gamma-butyrolactonase.
Complete Genome Sequence of the Arcobacter butzleri Cattle Isolate 7h1h
Authors: Merga J. Yvette , Winstanley Craig , Williams Nicola J. , Yee Emma , Miller William G.
Published: August 2013

Arcobacter butzleri
strain 7h1h was isolated in the United Kingdom from the feces of a clinically healthy dairy cow. The genome of this isolate was sequenced to completion. Here, we present the annotation and analysis of the completed 7h1h genome, along with a comparison of this genome to the existing
A. butzleri
genomes.
Draft Genome Sequence of Lactobacillus hominis Strain CRBIP 24.179
T
, Isolated from Human Intestine
Authors: Cousin Sylvie , Creno Sophie , Ma Laurence , Clermont Dominique , Loux Valentin , Bizet Chantal , Bouchier Christiane
Published: August 2013

We report the draft genome sequence of the strain
Lactobacillus hominis
CRBIP 24.179
T
, isolated from a human clinical sample. The total length of the 28 contigs is about 1.9 Mb, with a G+C content of 37% and 1,983 coding sequences.
Dimerization of the Pseudomonas aeruginosa Translocator Chaperone PcrH Is Required for Stability, Not Function
Authors: Tomalka Amanda G. , Zmina Stephanie E. , Stopford Charles M. , Rietsch Arne
Published: August 2013

Type III secretion systems rely on hydrophobic translocator proteins that form a pore in the host cell membrane to deliver effector proteins into targeted host cells. These translocator proteins are stabilized in the cytoplasm and targeted for export with the help of specific chaperone proteins. In
Pseudomonas aeruginosa
, the chaperone of the pore-forming translocator proteins is PcrH. Although all translocator chaperones dimerize, the location of the dimerization interface is in dispute. Moreover, it has been reported that interfering with dimerization interferes with chaperone function. However, binding of
P. aeruginosa
chaperone PcrH to its cognate secretion substrate, PopD, results in dissociation of the PcrH dimer
in vitro
, arguing that dimerization of PcrH is likely not important for substrate binding or targeting translocators for export. We demonstrate that PcrH dimerization occurs
in vivo
in
P. aeruginosa
and used a genetic screen to identify a dimerization mutant of PcrH. The mutant protein is fully functional in that it can both stabilize PopB and PopD in the cytoplasm and promote their export via the type III secretion system. The location of the mutation suggests that the dimerization interface of PcrH mirrors that of the
Yersinia
homolog SycD and not the dimerization interface that had previously been reported for PcrH based on crystallographic evidence. Finally, we present data that the dimerization mutant of PcrH is less stable than the wild-type protein in
P. aeruginosa
, suggesting that the function of dimerization is stabilization of PcrH in the absence of its cognate cargo.