bluuebunny/crossref_metadata_2025 huggingface dataset:
The Deep-Water-Horizon Spill: Flow-Rate Estimation Based on Satellite Images
Authors: Giraldo Diego Garcia , Yeung Ronald W.
Published: August 2013

The “Deep Water Horizon” Mobil Offshore Drilling Unit (MODU) is one of several classes of floatable drilling machines. As a consequence of the accident on April 20, 2010, the worst ecological disaster with regard to oil spills in the US history was generated in the Gulf of Mexico, causing extensive damage to marine and wildlife habitats, as well as the Gulf’s fishing and tourism industries. Since that moment, experts are trying to estimate the total amount of oil being lost into the sea. The objective of this presentation is to report a procedure developed in the first author’s thesis1 an independent and logical estimate of the oil flow rate into the Gulf of Mexico produced by the rupture in this rig. There are a number of possible approaches to estimate the flow rate of oil spilling into the Gulf of Mexico. The Plume Modeling Team has developed an approach by observing video image of the oil/gas mixture escaping from the kinks in the riser and the end of the riser pipe. The Mass Balance Team has developed a range of values using USGS (US Geological Survey) and NOAA (National Oceanic and Atmospheric Administration) data analysis collected from NASA’s (National Aeronautics and Space Administration) Airborne Visible InfraRed Imaging Spectrometer (AVIRIS). Finally, a reality-check estimate was based on the amount of oil collected by the Riser Insertion Tube Tool (RITT) plus the estimate of how much oil is escaping from the RITT, and from the kink in the riser. However, there are several limitations in each of these techniques.
Stability Analysis of a Yawing Flat Plate Into the Water Current
Authors: Armandei Mohammadmehdi , Fernandes Antonio Carlos
Published: August 2013

The present study deals with the stability analysis of an oscillating flat plate into the water current. The flat plate, which is attached to a torsion spring and located vertically in the water current, has only 1 DOF that is yawing motion. The experiments have shown that as the current velocity exceeds a special threshold, the flat plate becomes unstable and begins to oscillate. This oscillation can be utilized to extract energy. A free vibration experimental technique is used in this study. The experimental results are analyzed using the flutter derivative theory, in which the flutter derivatives of the motion are extracted using GLS (General Least-Square) method. The results confirm that the flat plate becomes dynamically unstable. Also, there is a Liapunov stable fixed point on the origin at the phase portrait of the yawing motion.
Characterization of Matrix Wettability and Mass Transfer From Matrix to Fractures in Carbonate Reservoirs
Authors: Gupta Anuj
Published: August 2013

This paper presents results of an experimental investigation, supported by numerical analysis, to characterize oil recovery from fractured carbonate reservoirs. Imbibition recovery of oil is measured as a function of time for samples with varying wettability and shape factors. One of the objectives of this study is to verify the validity of exponential transfer function for matrix-fracture systems with varying wettability and flow-boundary conditions. Another objective is to establish the possibility of quantitatively determining the wettability of a sample based on history-matching of cumulative imbibition recovery and recovery rate data.

The productivity of most carbonate oil and gas reservoirs is closely tied to the natural or stimulated fracture system present in the reservoir. Further, the recovery from naturally fractured reservoirs, in presence of aquifer drive or waterflooding is closely tied to the wettability of the matrix. The approach presented in this paper offers means to evaluate how recovery factor in a fractured system can be affected by wettability. A detailed understanding of rock-fluid interactions and wettability alterations at the fracturing face should help design improved strategies for exploiting naturally fractured carbonate reservoirs.
Hydrodynamic Interaction Forces on Ship Hulls Equipped With Propulsors
Authors: Sutulo Serge , Guedes Soares C.
Published: August 2013

Typically, study of hydrodynamic interaction between vessels navigating in close proximity to each other is limited to hydrodynamics of bare hulls. Meanwhile, ship propulsors, especially heavily loaded, which may happen in accelerating motion, can alter substantially the flow and distribution of pressure on the hulls which can be viewed as generalization of the thrust deduction phenomenon.

The 3D doubled body potential interaction code based on the source panel method developed earlier by the authors has been enhanced to include the effect of a propeller on each of the interacting ships under the assumption that the propeller jets (slipstreams) are not involved into the interaction. Each propeller is simulated by a disk of sinks further approximated with a polygon composed of identical triangular panels with identical constant sink density linked to the thrust of the propulsor according to the actuator disk theory.

Comparative computations were carried out for two identical tanker vessels in the close-proximity overtaking manoeuvre at various values of the loading coefficient of each propeller. The loading coefficient is not supposed to be necessarily defined by the steady propulsion point. Numerical results demonstrate that a heavily loaded propeller substantially modifies the pressure distribution on both hulls resulting in alteration of the hydrodynamic interaction loads, especially of the surge force and yaw moment.
Drilling Vessels’ Hurricane Evasion in the Gulf of Mexico
Authors: Wishahy Momen A. , Weinzapfel Bob A. , Diaz Dante C. , Eyre Devin J.
Published: August 2013

A study was carried out to determine the probability of avoiding severe weather conditions generated by historical hurricanes to improve the management of dynamically-positioned (DP) drilling vessels operating in the Gulf of Mexico during hurricane season. Rather than staying on location during an approaching hurricane, DP drilling vessels secure well operations, pull riser, and evade the hurricane.

The study considers several factors affecting the measure of success including inherent errors in forecasting hurricane strength, track and speed of advance; types and speeds of vessels; vessel sensitivity to wind and wave conditions; evasion time and direction of evasion; location of the drilling site relative to the hurricane track; and escape route water depth limitations.

The results provide a statistical basis for the required evasion time and would be part of the Hurricane Evacuation Plan that stakeholders agree upon to achieve acceptable risk. The simulations could also be used in a training program for captains and considered in the tactical decision-making process regarding when to leave the site and in which direction to go.
Elastic Characteristics of TLP Type Offshore Wind Turbine
Authors: Nihei Yasunori , Kozen Minori , Iijima Kazuhiro
Published: August 2013

In this paper, we will discuss about structural problems affecting TLP type offshore wind turbines under wind and wave conditions. For TLP type offshore windturbines, structural problems haven’t been found yet, however when talking about the use of wind turbines on a TLP structure we come to realize certain problems. For example the bending vibration of the tower and the blades, the bending moments and inertia of the upper structure under heavy sea conditions that might affect the mooring lines. Those are pressing issues and it is therefore important to take them into consideration. So, in this study, we will perform some experiments using appropriate “elastic model” of TLP type offshore wind turbines to observe those effects. We have not only measured the loads on tension legs in waves and wind but also the bending stresses acting on the tower and blades. We observed some phenomenon that will be reported later on, in this study.
Development of a Six-Component Blade Load Measurement Test Setup for Propeller-Ice Impact
Authors: Hagesteijn G. , Brouwer J. , Bosman R.
Published: August 2013

The impact of ice on a propeller is a complex process, which most likely results into a milling or crushing process, or a combination. The highly dynamic forces during an impact can change rapidly in amplitude as well as direction. Little information can be deducted from classic test setups with rigid propellers, especially forces on the individual blades are seldom successfully measured. The presented paper will outline the challenges which need to be overcome to measure these impacts more accurately and elaborate on a measurement setup which has proven to capture the impact loads of actual ice impacts in great detail.

Classic designs for propeller testing involve rigid propellers with force measurements located at the base of the propeller. From this type of setup, immediately two problems arise. First of all, when impacting relatively large ice blocks, it will be hard to derive which part of the measured forces contributes to one blade and which part to the other. Secondly, in practical test situations the natural frequency of the entire propeller mounted on a force transducer can be relatively low. Impacts are suspected to contain forces with high frequency components, causing the entire propeller assembly to vibrate and thereby obscuring a correct measurement of the impact loads.

A measurement setup has been designed to overcome both problems. Rather than measuring the forces on a complete propeller, only a single blade is mounted on a force transducer. This particular transducer is capable of measuring forces in x-, y- and z-directions as well as moments around the x-, y- and z-axis. The other propeller blades are mounted directly on the shaft drive. This measurement setup reduces the first problem, any impact visible in the measurements signals are solely due to forces on the instrumented ‘key-blade’.
Effective Estimation of Water Waves Scattering by Double-Row Pile Breakwaters
Authors: Nejadkazem Omid , Gharabaghi Ahmad Reza Mostafa
Published: August 2013

This paper describes various hydraulic characteristic of double-row pile breakwaters (DPB). Applying an eigenfunction expansion method, a numerical method have been developed that can compute wave transmission, reflection, and other hydraulic characteristics. To verify the validity of developed prediction, laboratory experiments of Isaascson et al. (1999) have been utilized. Then for an efficient calculation, optimum number of necessary evanescent waves for an effective and efficient prediction is discussed for various hydraulic quantities of interest. In a nutshell, for an effective and efficient performance of the DPB, intermediate water wave and porosity range of [0.2 0.3] are recommended. Relative distance between two barriers must be set depending on significant wave length of design.
Sea Level Rise and Implication on Coastal Process: A Review
Authors: Akib Shatirah , Jahangirzadeh Afshin , Kamali Babak , Mamat Noor Liana
Published: August 2013

The purpose of this review paper is to summarise the literature on sea level rise and its implication on coastal process. Sea level rise is the increase of volume of water in the oceans and seas relative to increase in height when compared to the ground level. Sea water covers increase when the sea level raises increase. Coastal process is the set of mechanisms that operate along a coastline, bringing about various combinations of erosion and deposition. Impacts in vulnerable regions of the Earth will be expected to have far reaching and dramatic by an accelerated global sea level rise. The other impacts of rising sea level are changes in salinity distribution in estuaries alteration in coastal circulation patterns, destruction of transportation infrastructure in low lying areas, and increase in pressure on coastal levee systems. The causes of a sea level rise are global warming and excessive extraction of groundwater in some areas.
Rheological Characterization and Mechanical Behavior of Polymer Powder Modified-Cement Pastes and Wollastonite Fibers Reinforced Cement Pastes
Authors: de C. Vitorino Fabrício , Toledo Filho Romildo D.
Published: August 2013

In the design of oil wells subjected to temperature variations and imposed deformations, the fracture toughness of the cement pastes is a very important property. In order to obtain higher toughness values and adequate rheological properties, cement pastes modified by polymer and reinforced by wollastonite microfibers were developed and studied. In the present case, the redispersible polymer powder used was the styrene-butadiene rubber (SBR). The pastes were mechanically characterized by the evaluation of compressive strength, Young’s modulus, Poisson’s ratio and strain capacity. The rheological properties, such as plastic viscosity, yield point and gel strength, were obtained in a Couette coaxial cylinder rotational viscometer.
Optimizing the Location of Platforms and Manifolds
Authors: Rosa Vinícius Ramos , Martins Ferreira Filho Virgilio José
Published: August 2013

This paper presents a general method for optimize platform and manifold location in offshore projects, by maximizing their net present value. Finding the best offshore facilities locations is further than minimize the total pipelines length. The distances between wells and platform are related to their productivity, the farther the distance the less production. Each well has a particular response to pressure loss along the pipelines due to fluids and reservoir characteristics. Therefore, not only costs related to distances must be taken in account, but also revenues from the oil production, which are a function of flow conditions in the reservoir, tubing and pipelines. Moreover, to locate a manifold also means choose which wells will be linked with it. Every possible combination of wells leads to a different production rate. Again, petroleum engineering expertise it is needed to optimize the project, working together numerical techniques. A simple optimization method is proposed and to testify it a small example model was built.
Workshop on Verification and Validation of CFD for Offshore Flows
Authors: Eça L. , Vaz G.
Published: August 2013

This document introduces the Workshop on Verification and Validation (V&V) of CFD for Offshore Flows, to be held during OMAE2012. It presents a brief introduction to the purpose of Verification and Validation with the identification of the goals of code and solution verification and validation. Within this context, three test-cases are proposed: Case-I of code verification, Case-II of solution verification and Case-III of solution verification and validation. Case-I consists on a 3D manufactured solution of an unsteady turbulent flow. Case-II is an exercise on the canonical problem of the infinite smooth circular cylinder flow at different Reynolds numbers. Case-III is a more complex flow around a straked-riser. The participants are asked to perform at least one of these test-cases. The objectives for the three proposed test-cases are presented, together with a detailed description of the numerical settings to be used, and the results to be obtained and sent to the Workshop organization. At the end some considerations on general conditions, paper submission, deadlines, and encouragements are stated.
Aspects of Importance Related to Arctic DP Operations
Authors: Gürtner Arne , Baardson Bror Henrik Heier , Kaasa Glenn-Ole , Lundin Erik
Published: August 2013

International operators are seeking, investigating and pursuing new business opportunities in the Arctic. While operating in the Arctic, there will be a considerable need for vessels to keep their position during various operations which may include lifting, installation, crew change, evacuation, and maybe drilling. Opposed to open water, the drifting ice poses severe limitations as to how stationkeeping operations may be carried out. Dynamic positioning systems are currently developed aiding stationkeeping without mooring systems. There is a considerable need to enhance the open water DP systems for use in a new forcing environment. Essentially a new technology has to be developed with time. For that reason, considerable knowledge is required concerning current limitations and boundary conditions. This paper addresses some of the generic challenges related to DP operations in ice together with relevant learnings which are employed in mentioned DP enhancements.
Tensile Strain Capacity of X80 and X100 Welds
Authors: Wang Yong-Yi , Zhang Fan , Liu Ming , Cho Woo-Yeon , Seo Dong-Han
Published: August 2013

High-strength pipelines (API 5L grade X70 and above) provide viable economic options for large-diameter and high-pressure transmission of energy products. To facilitate the understanding and potential use of high-strength pipelines, the tensile strain capacity (TSC) of X80 and X100 girth welds was evaluated through a series of mechanical tests and analytical/computational modeling. The experimental tests include tensile, Charpy, SENT, and curved-wide-plate (CWP) tests. The TSC measured from CWP tests is compared with the prediction from TSC models developed at CRES. The TSC of the girth welds is assessed by comparing experimentally measured values with the expected TSC from similar welds. The assessment confirms that this particular set of X80 and X100 girth welds provide very good tensile strain capacity.
Field Observation of Tide-Induced Loading Upon Undersea Tunnel
Authors: Chen Nan , Ye Guan-lin , Chen Jin-jian , Xia Xiao-he
Published: August 2013

Many shallow undersea tunnels have been built to circulate the cooling water for the thermal or nuclear power stations in recent years. In current study, a field monitoring of tide-influenced earth pressure on the tunnel was carried out by using the pad type pressure transducers. The variation of tidal level was also recorded carefully. The measured results of earth pressures and the tidal height were analyzed qualitatively and quantitatively. It can be found that there is a linear relation between the variation of load and tidal height. The computed values of the loadings based on tunnel pressure theory are almost the same with measurements.
Study on Strength of Shanghai Marine Clay by True Triaxial Test
Authors: Sheng Jia-ren , Wu Chao-jun , Ye Guan-lin , Wang Jian-hua
Published: August 2013

Shanghai locates on the east tip of Yangtze River Delta facing the East China Sea. Shanghai marine clay owns some particular properties. However, the report on the mechanical properties of Shanghai marine clay is rather rare. The three-dimensional strength and deformation characteristics of soft soil are dependent on the stress conditions. In this study, a series of isotropic consolidated drained true triaxial tests are carried out with an automatically controlled mixed rigid-flexible boundary true triaxial apparatus. Undisturbed soil sample is prepared by the block sampling method. 5 drained tests with stress path in the same π plane along different Lode angles are performed. Tests results show that the intermediate stress has large influence on the yielding and failure of Shanghai marine clay. Three dimensional strength of Shanghai marine clay generally obeys the SMP failure criteria.
Numerical Simulation of Contaminant Transport in Unsaturated Deformable Soils
Authors: Zuo Z. B. , Zhang L. L. , Cheng Y. , Wang J. H.
Published: August 2013

Transport of contaminant or solute in saturated or unsaturated soils has been widely investigated in the literature. The soils are usually assumed to be rigid. However, there are cases where soils may be deformable and the deformation of the soils may influence the transport of contaminant. In this paper, a finite element model for contaminant transport in unsaturated deformable soils is established based on the governing equations of solute transport, flow and deformation in unsaturated soils. Transport of solute in a hypothetical landfill liner is used as an illustrative example. Numerical analyses are performed to investigate the transport of contaminant and the deformation of the unsaturated landfill clay liner. Effects of the soil compressibility, the level of water table, unsaturated hydraulic parameters are investigated in the parametric study. It is found that with a lower initial water level, the settlement at the surface at the clay liner is initially larger during the consolidation period and the breakthrough time of the liner is longer. However, the final settlement of the clay is smaller with a lower initial water level. If a soil is more compressible, the breakthrough time of solute transport is shorter. With the increase of saturated hydraulic conductivity, the settlement of clay increases and the breakthrough time decreases. With a larger α value, the final steady state dimensionless concentration at liner base is greater and the consolidation rate is larger during the consolidation period.
Time-Domain VIV Prediction of Marine Risers
Authors: Ma Peter , Qiu Wei , Spencer Don
Published: August 2013

Vortex Induced Vibration (VIV) of marine risers poses a significant challenge as the offshore oil and gas industry moves into deep water. A time-domain analysis tool has been developed to predict the VIV of marine risers based on a forcing algorithm and by making full use of the available high Reynolds number experimental data. In the formulation, the hydrodynamic damping is not treated as a special case but simply an extension of the experimentally derived lift curves. The forcing algorithm was integrated into a mooring analysis program based on the global-coordinate based finite element method. At each time step, the added mass, lifting force and drag force coefficients and their corresponding loads are computed for each element. Validation studies have been carried out for a full-scale rigid riser segment and a model-scale flexible riser. The numerical results were compared with experimental data and solutions by other programs.
Fatigue of Friction Stir and GTAW Welded AZ31B Magnesium Alloy
Authors: Ávila J. A. , Jaramillo H. E. , Franco F.
Published: August 2013

The mechanical behavior of butt welds made on AZ31B magnesium alloy plates by solid-state friction stir welding (FSW) and gas tungsten arc welding (GTAW) is presented. Fatigue, tensile strength, and hardness tests were performed. Also, fractographic analyses of the weld microstructures were conducted. Tests results show that the fatigue performance of FSW joints was superior to that of conventional welding (GTAW).
On the Efficiency of Oscillating Water Column (OWC) Devices in Converting Ocean Wave Energy to Electricity Under Weakly Nonlinear Waves
Authors: Nader Jean-Roch , Zhu Song-Ping , Cooper Paul
Published: August 2013

Oscillating Water Column (OWC) devices are regarded as one of the most promising systems developed to harness ocean wave energy. In this paper, we present some preliminary results of our most recent effort in the research of trying to improve the efficiency of OWCs with a focus on the comparison of incident waves being in the linear and weekly nonlinear regimes. As the results show, the counted-in nonlinearity at the second order could contribute to more than a 50% increase in the maximum mean power output.
STC (Spar-Torus Combination): A Combined Spar-Type Floating Wind Turbine and Large Point Absorber Floating Wave Energy Converter — Promising and Challenging
Authors: Muliawan Made Jaya , Karimirad Madjid , Moan Torgeir , Gao Zhen
Published: August 2013

This paper deals with a novel concept by combining a spar-type floating wind turbine (FWT) and a Torus (donutshaped) point absorber-type wave energy converter (WEC) that is referred as the ‘Spar-Torus Combination’ (STC) herein. Concept feasibility study has been carried out by doing numerical simulations. It showed that the STC results in a positive synergy between wind and wave energy generation in terms of both capital investment and power production. As a novel concept, the STC concept is considered a simple compact combination of two technologies that have had high technology readiness level (TRL). It is suitable for deep water deployment and is not sensitive to seabed conditions and wave directions. Therefore, it is interesting to pursue a further development of this concept. The paper presents the technical information about the STC and highlights some challenging areas of the STC that should be carefully looked at to make it a proven concept.
Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit
Authors: Preheim Sarah P. , Perrotta Allison R. , Martin-Platero Antonio M. , Gupta Anika , Alm Eric J.
Published: August 2013

16S rRNA sequencing, commonly used to survey microbial communities, begins by grouping individual reads into operational taxonomic units (OTUs). There are two major challenges in calling OTUs: identifying bacterial population boundaries and differentiating true diversity from sequencing errors. Current approaches to identifying taxonomic groups or eliminating sequencing errors rely on sequence data alone, but both of these activities could be informed by the distribution of sequences across samples. Here, we show that using the distribution of sequences across samples can help identify population boundaries even in noisy sequence data. The logic underlying our approach is that bacteria in different populations will often be highly correlated in their abundance across different samples. Conversely, 16S rRNA sequences derived from the same population, whether slightly different copies in the same organism, variation of the 16S rRNA gene within a population, or sequences generated randomly in error, will have the same underlying distribution across sampled environments. We present a simple OTU-calling algorithm (distribution-based clustering) that uses both genetic distance and the distribution of sequences across samples and demonstrate that it is more accurate than other methods at grouping reads into OTUs in a mock community. Distribution-based clustering also performs well on environmental samples: it is sensitive enough to differentiate between OTUs that differ by a single base pair yet predicts fewer overall OTUs than most other methods. The program can decrease the total number of OTUs with redundant information and improve the power of many downstream analyses to describe biologically relevant trends.
Characterization of a Potential Listeria monocytogenes Virulence Factor Associated with Attachment to Fresh Produce
Authors: Bae Dongryeoul , Seo Keun Seok , Zhang Ting , Wang Chinling
Published: August 2013

A study to determine the attachment of
L. monocytogenes
serotype 4b strain F2365 on vegetables and fruits was conducted. In an initial study, we screened 32 genes encoding surface proteins and lipases of the strain to find highly expressed genes on lettuce leaves. The results showed that transcription levels of LMOf2365_0413, LMOf2365_0498, LMOf2365_0859, LMOf2365_2052, and LMOf2365_2812 were significantly upregulated on lettuce leaves.
In silico
analysis showed that LMOf2365_0859 contains a putative cellulose binding domain. Thus, we hypothesized that this gene may be involved in an attachment to vegetables, and named it
lcp
(gene encoding
Listeria
cellulose binding protein [LCP]).
lcp
mutant (Δ
lcp
) and
lcp
complement (F2365::pMAD::
cat
::
lcp
) strains were generated by homologous recombination. The abilities of a wild-type (WT) strain, the Δ
lcp
strain, and the complemented strain to attach to lettuce leaves were evaluated, which indicated that the attachment of the Δ
lcp
strain to lettuce was significantly less than that of the WT and the complemented strains. Similar results were observed for baby spinach and cantaloupe. Fluorescence microscopy and field emission scanning microscopy analysis further supported these findings. The binding of
L. monocytogenes
to cellulose was determined using cellulose acetate-coated plates. The results showed that a binding ability of the Δ
lcp
strain was significantly lower than that of the wild type. Combined, these results strongly suggest that LCP plays an important role in an attachment to vegetables and fruits.
Design and Optimization of Short DNA Sequences That Can Be Used as 5′ Fusion Partners for High-Level Expression of Heterologous Genes in Escherichia coli
Authors: Kucharova Veronika , Skancke Jørgen , Brautaset Trygve , Valla Svein
Published: August 2013

The 5′ terminal nucleotide sequence of a gene is often a bottleneck in recombinant protein production. The

ifn-α2b
S

gene is poorly expressed in
Escherichia coli
unless a translocation signal sequence (
pelB
) is fused to the 5′ end of the gene. A combined
in silico
and
in vivo
analysis reported here further indicates that the

ifn-α2b
S

5′ coding sequence is suboptimal for efficient gene expression.

ifn-α2b
S

therefore presents a suitable model gene for describing properties of 5′ fusions promoting expression. We show that short DNA sequences corresponding to the 5′ end of the highly expressed
celB
gene, whose protein product is cytosolic, can functionally replace
pelB
as a 5′ fusion partner for efficient

ifn-α2b
S

expression.
celB
fusions of various lengths (corresponding to a minimum of 8 codons) led to more than 7- and 60-fold stimulation of expression at the transcript and protein levels, respectively. Moreover, the presence of a
celB
-based fusion partner was found to moderately reduce the decay rate of the corresponding transcript. The 5′ fusions thus appear to act by enhancing translation, and bound ribosomes may accordingly contribute to increased mRNA stability and reduced mRNA decay. However, other effects, such as altered protein stability, cannot be excluded. We also developed an experimental protocol that enabled us to identify improved variants of the
celB
fusion, and one of these (
celB
D11
) could be used to additionally increase

ifn-α2b
S

expression more than 4-fold at the protein level. Interestingly,
celB
D11
also stimulated greater protein production of three other medically important human genes than the wild-type
celB
fragment.
Molecular and Phenotypic Characterization of Escherichia coli O26:H8 among Diarrheagenic E. coli O26 Strains Isolated in Brazil
Authors: Piazza Roxane M. F. , Delannoy Sabine , Fach Patrick , Saridakis Halha O. , Pedroso Margareth Z. , Rocha Letícia B. , Gomes Tânia A. T. , Vieira Mônica A. M. , Beutin Lothar , Guth Beatriz E. C.
Published: August 2013

Escherichia coli
strains of serogroup O26 comprise two distinct groups of pathogens, characterized as enteropathogenic
E. coli
(EPEC) and enterohemorrhagic
E. coli
(EHEC). Among the several genes related to type III secretion system-secreted effector proteins,
espK
was found to be highly specific for EHEC O26:H11 and its
stx
-negative derivative strains isolated in European countries.
E. coli
O26 strains isolated in Brazil from infant diarrhea, foods, and the environment have consistently been shown to lack
stx
genes and are thus considered atypical EPEC. However, no further information related to their genetic background is known. Therefore, in this study, we aimed to discriminate and characterize these Brazilian O26
stx
-negative strains by phenotypic, genetic, and biochemical approaches. Among 44 isolates confirmed to be O26 isolates, most displayed flagellar antigen H11 or H32. Out of the 13 nonmotile isolates, 2 tested positive for
fliC
H11
, and 11 were
fliC
H8
positive. The identification of genetic markers showed that several O26:H11 and all O26:H8 strains tested positive for
espK
and could therefore be discriminated as EHEC derivatives. The presence of H8 among EHEC O26 and its
stx
-negative derivative isolates is described for the first time. The interaction of three isolates with polarized Caco-2 cells and with intestinal biopsy specimen fragments
ex vivo
confirmed the ability of the O26 strains analyzed to cause attaching-and-effacing (A/E) lesions. The O26:H32 strains, isolated mostly from meat, were considered nonvirulent. Knowledge of the virulence content of
stx
-negative O26 isolates within the same serotype helped to avoid misclassification of isolates, which certainly has important implications for public health surveillance.
Probing 3-Hydroxyflavone for
In Vitro
Glycorandomization of Flavonols by YjiC
Authors: Pandey Ramesh Prasad , Parajuli Prakash , Koirala Niranjan , Park Je Won , Sohng Jae Kyung
Published: August 2013

The glycosylation of five different flavonols, fisetin, quercetin, myricetin, kaempferol, and 3-hydroxyflavone, was achieved by applying YjiC. 3-Hydroxyflavone was selected as a probe for
in vitro
glycorandomization of all flavonols using diverse nucleotide diphosphate-
d/l
-sugars. This study unlocked the possibilities of the glycodiversification of flavonols and the generation of novel compounds as future therapeutics.
Differential Gene Expression in Pycnoporus coccineus during Interspecific Mycelial Interactions with Different Competitors
Authors: Arfi Yonathan , Levasseur Anthony , Record Eric
Published: August 2013

Fungi compete against each other for environmental resources. These interspecific combative interactions encompass a wide range of mechanisms. In this study, we highlight the ability of the white-rot fungus
Pycnoporus coccineus
to quickly overgrow or replace a wide range of competitor fungi, including the gray-mold fungus
Botrytis cinerea
and the brown-rot fungus
Coniophora puteana
. To gain a better understanding of the mechanisms deployed by
P. coccineus
to compete against other fungi and to assess whether common pathways are used to interact with different competitors, differential gene expression in
P. coccineus
during cocultivation was assessed by transcriptome sequencing and confirmed by quantitative reverse transcription-PCR analysis of a set of 15 representative genes. Compared with the pure culture, 1,343 transcripts were differentially expressed in the interaction with
C. puteana
and 4,253 were differentially expressed in the interaction with
B. cinerea
, but only 197 transcripts were overexpressed in both interactions. Overall, the results suggest that a broad array of functions is necessary for
P. coccineus
to replace its competitors and that different responses are elicited by the two competitors, although a portion of the mechanism is common to both. However, the functions elicited by the expression of specific transcripts appear to converge toward a limited set of roles, including detoxification of secondary metabolites.
Occurrence and Genetic Diversity of Arcobacter butzleri in an Artisanal Dairy Plant in Italy
Authors: Giacometti Federica , Lucchi Alex , Manfreda Gerardo , Florio Daniela , Zanoni Renato Giulio , Serraino Andrea
Published: August 2013

The present study aimed to investigate the presence, distribution, and persistence of
Arcobacter
spp. in an artisanal dairy plant and to test the isolates to determine their different genotypes in the processing plant and in foods. Samples were collected in an artisanal cheese factory on four occasions between October and December 2012. Food samples (raw milk, ricotta cheese, mozzarella cheese, and conditioning liquid), water samples, and environmental samples were analyzed by the culture method; isolates were identified by multiplex PCR and genotyped by pulsed-field gel electrophoresis (PFGE) analysis.
Arcobacter butzleri
was isolated from 29 out of 59 samples (46.6%), 22 of which were from environmental samples and 7 of which were from food samples. Cluster analysis divided the strains into 47 PFGE patterns: 14 PFGE clusters and 33 unique types. Our findings indicate that the plant harbored numerous
A. butzleri
pulsotypes and that the manual cleaning and sanitation in the studied dairy plant do not effectively remove
Arcobacter
. The recurrent isolation of
A. butzleri
suggests that the environmental conditions in the dairy plant constitute a good ecological niche for the colonization of this microorganism. In some cases, the presence of indistinguishable strains isolated from the same facilities on different sampling days showed that these strains were persistent in the processing environment.
Mapping of Heavy Metal Ion Sorption to Cell-Extracellular Polymeric Substance-Mineral Aggregates by Using Metal-Selective Fluorescent Probes and Confocal Laser Scanning Microscopy
Authors: Hao Likai , Li Jianli , Kappler Andreas , Obst Martin
Published: August 2013

Biofilms, organic matter, iron/aluminum oxides, and clay minerals bind toxic heavy metal ions and control their fate and bioavailability in the environment. The spatial relationship of metal ions to biomacromolecules such as extracellular polymeric substances (EPS) in biofilms with microbial cells and biogenic minerals is complex and occurs at the micro- and submicrometer scale. Here, we review the application of highly selective and sensitive metal fluorescent probes for confocal laser scanning microscopy (CLSM) that were originally developed for use in life sciences and propose their suitability as a powerful tool for mapping heavy metals in environmental biofilms and cell-EPS-mineral aggregates (CEMAs). The benefit of using metal fluorescent dyes in combination with CLSM imaging over other techniques such as electron microscopy is that environmental samples can be analyzed in their natural hydrated state, avoiding artifacts such as aggregation from drying that is necessary for analytical electron microscopy. In this minireview, we present data for a group of sensitive fluorescent probes highly specific for Fe
3+
, Cu
2+
, Zn
2+
, and Hg
2+
, illustrating the potential of their application in environmental science. We evaluate their application in combination with other fluorescent probes that label constituents of CEMAs such as DNA or polysaccharides and provide selection guidelines for potential combinations of fluorescent probes. Correlation analysis of spatially resolved heavy metal distributions with EPS and biogenic minerals in their natural, hydrated state will further our understanding of the behavior of metals in environmental systems since it allows for identifying bonding sites in complex, heterogeneous systems.
Nitrogen Source-Dependent Capsule Induction in Human-Pathogenic Cryptococcus Species
Authors: Frazzitta Aubrey E. , Vora Haily , Price Michael S. , Tenor Jennifer L. , Betancourt-Quiroz Marisol , Toffaletti Dena L. , Cheng Nan , Perfect John R.
Published: August 2013

Cryptococcus neoformans
and
C. gattii
cause meningoencephalitis and are an increasing human health threat. These pathogenic
Cryptococcus
species are neurotropic and persist in the cerebrospinal fluid (CSF) of the mammalian host during infection. In order to survive in the host, pathogenic fungi must procure nutrients, such as carbon and nitrogen, from the CSF. To enhance our understanding of nutrient acquisition during central nervous system infection by
Cryptococcus
species, we examined the utilization of nitrogen sources available in CSF. We screened for the growth and capsule production of 817 global environmental and clinical isolates on various sources of nitrogen. Both environmental and clinical strains grew robustly on uric acid, Casamino Acids, creatinine, and asparagine as sole nitrogen sources. Urea induced the greatest magnitude of capsule induction. This induction was greater in
Cryptococcus gattii
than in
C. neoformans
. We confirmed the ability of nonpreferred nitrogen sources to increase capsule production in pathogenic species of
Cryptococcus
. Since urea is metabolized to ammonia and CO
2
(a known signal for capsule induction), we examined urea metabolism mutants for their transcriptional response to urea regarding capsule production. The transcriptional profile of
C. neoformans
under urea-supplemented conditions revealed both similar and unique responses to other capsule-inducing conditions, including both intra- and extracellular urea utilization. As one of the most abundant nitrogen sources in the CSF, the ability of
Cryptococcus
to import urea and induce capsule production may substantially aid this yeast's survival and propagation in the host.
The Function of the Na
+
-Driven Flagellum of Vibrio cholerae Is Determined by Osmolality and pH
Authors: Halang Petra , Leptihn Sebastian , Meier Thomas , Vorburger Thomas , Steuber Julia
Published: August 2013

Vibrio cholerae
is motile by its polar flagellum, which is driven by a Na
+
-conducting motor. The stators of the motor, composed of four PomA and two PomB subunits, provide access for Na
+
to the torque-generating unit of the motor. To characterize the Na
+
pathway formed by the PomAB complex, we studied the influence of chloride salts (chaotropic, Na
+
, and K
+
) and pH on the motility of
V. cholerae
. Motility decreased at elevated pH but increased if a chaotropic chloride salt was added, which rules out a direct Na
+
and H
+
competition in the process of binding to the conserved PomB D23 residue. Cells expressing the PomB S26A/T or D42N variants lost motility at low Na
+
concentrations but regained motility in the presence of 170 mM chloride. Both PomA and PomB were modified by
N
,
N
′-dicyclohexylcarbodiimide (DCCD), indicating the presence of protonated carboxyl groups in the hydrophobic regions of the two proteins. Na
+
did not protect PomA and PomB from this modification. Our study shows that both osmolality and pH have an influence on the function of the flagellum from
V. cholerae
. We propose that D23, S26, and D42 of PomB are part of an ion-conducting pathway formed by the PomAB stator complex.
Roles of HynAB and Ech, the Only Two Hydrogenases Found in the Model Sulfate Reducer
Desulfovibrio gigas
Authors: Morais-Silva Fabio O. , Santos Catia I. , Rodrigues Rute , Pereira Inês A. C. , Rodrigues-Pousada Claudina
Published: August 2013

Sulfate-reducing bacteria are characterized by a high number of hydrogenases, which have been proposed to contribute to the overall energy metabolism of the cell, but exactly in what role is not clear.
Desulfovibrio
spp. can produce or consume H
2
when growing on organic or inorganic substrates in the presence or absence of sulfate. Because of the presence of only two hydrogenases encoded in its genome, the periplasmic HynAB and cytoplasmic Ech hydrogenases,
Desulfovibrio gigas
is an excellent model organism for investigation of the specific function of each of these enzymes during growth. In this study, we analyzed the physiological response to the deletion of the genes that encode the two hydrogenases in
D. gigas
, through the generation of Δ
echBC
and Δ
hynAB
single mutant strains. These strains were analyzed for the ability to grow on different substrates, such as lactate, pyruvate, and hydrogen, under respiratory and fermentative conditions. Furthermore, the expression of both hydrogenase genes in the three strains studied was assessed through quantitative reverse transcription-PCR. The results demonstrate that neither hydrogenase is essential for growth on lactate-sulfate, indicating that hydrogen cycling is not indispensable. In addition, the periplasmic HynAB enzyme has a bifunctional activity and is required for growth on H
2
or by fermentation of pyruvate. Therefore, this enzyme seems to play a dominant role in
D. gigas
hydrogen metabolism.
Flexibility of Syntrophic Enzyme Systems in Desulfovibrio Species Ensures Their Adaptation Capability to Environmental Changes
Authors: Meyer Birte , Kuehl Jennifer V. , Deutschbauer Adam M. , Arkin Adam P. , Stahl David A.
Published: August 2013

The mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers obligately linked by interspecies metabolite exchange in syntrophic consortia that may include sulfate reducing species such as
Desulfovibrio
. To evaluate the metabolic flexibility of syntrophic
Desulfovibrio
to adapt to naturally fluctuating methanogenic environments, we studied
Desulfovibrio alaskensis
strain G20 grown in chemostats under respiratory and syntrophic conditions with alternative methanogenic partners,
Methanococcus maripaludis
and
Methanospirillum hungatei
, at different growth rates. Comparative whole-genome transcriptional analyses, complemented by G20 mutant strain growth experiments and physiological data, revealed a significant influence of both energy source availability (as controlled by dilution rate) and methanogen on the electron transfer systems, ratios of interspecies electron carriers, energy generating systems, and interspecies physical associations. A total of 68 genes were commonly differentially expressed under syntrophic versus respiratory lifestyle. Under low-energy (low-growth-rate) conditions, strain G20 further had the capacity to adapt to the metabolism of its methanogenic partners, as shown by its differing gene expression of enzymes involved in the direct metabolic interactions (e.g., periplasmic hydrogenases) and the ratio shift in electron carriers used for interspecies metabolite exchange (hydrogen/formate). A putative monomeric [Fe-Fe] hydrogenase and Hmc (high-molecular-weight-cytochrome
c
3
) complex-linked reverse menaquinone (MQ) redox loop become increasingly important for the reoxidation of the lactate-/pyruvate oxidation-derived redox pair, DsrC
red
and Fd
red
, relative to the Qmo-MQ-Qrc (quinone-interacting membrane-bound oxidoreductase; quinone-reducing complex) loop. Together, these data underscore the high enzymatic and metabolic adaptive flexibility that likely sustains
Desulfovibrio
in naturally fluctuating methanogenic environments.
Complementation of the F
o
c
Subunit of Escherichia coli with That of Streptococcus mutans and Properties of the Hybrid F
o
F
1
ATP Synthase
Authors: Araki Makoto , Hoshi Kazuya , Fujiwara Masasuke , Sasaki Yuka , Yonezawa Hideo , Senpuku Hidenobu , Iwamoto-Kihara Atsuko , Maeda Masatomo
Published: August 2013

The
c
subunit of
Streptococcus mutans
ATP synthase (F
o
F
1
) is functionally exchangeable with that of
Escherichia coli
, since
E. coli
with a hybrid F
o
F
1
is able to grow on minimum succinate medium through oxidative phosphorylation.
E. coli
F
1
bound to the hybrid F
o
with the
S. mutans
c
subunit showed N,N′-dicyclohexylcarbodiimide-sensitive ATPase activity similar to that of
E. coli
F
o
F
1
. Thus, the
S. mutans
c
subunit assembled into a functional F
o
together with the
E. coli
a
and
b
subunits, forming a normal F
1
binding site. Although the H
+
pathway should be functional, as was suggested by the growth on minimum succinate medium, ATP-driven H
+
transport could not be detected with inverted membrane vesicles
in vitro
. This observation is partly explained by the presence of an acidic residue (Glu-20) in the first transmembrane helix of the
S. mutans
c
subunit, since the site-directed mutant carrying Gln-20 partly recovered the ATP-driven H
+
transport. Since
S. mutans
is recognized to be a primary etiological agent of human dental caries and is one cause of bacterial endocarditis, our system that expresses hybrid F
o
with the
S. mutans
c
subunit would be helpful to find antibiotics and chemicals specifically directed to
S. mutans
.
Measurements of mRNA Degradation in Borrelia burgdorferi
Authors: Archambault Linda , Borchert J. Simmons , Bergeron Jennifer , Snow Santina , Schlax Paula Jean
Published: August 2013

The importance of gene regulation in the enzootic cycle of
Borrelia burgdorferi
, the spirochete that causes Lyme disease, is well established.
B. burgdorferi
regulates gene expression in response to changes in environmental stimuli associated with changing hosts. In this study, we monitored mRNA decay in
B. burgdorferi
following transcriptional arrest with actinomycin D. The time-dependent decay of transcripts encoding RNA polymerase subunits (
rpoA
and
rpoS
), ribosomal proteins (
rpsD
,
rpsK
,
rpsM
,
rplQ
, and
rpsO
), a nuclease (
pnp
), outer surface lipoproteins (
ospA
and
ospC
), and a flagellar protein (
flaB
) have different profiles and indicate half-lives ranging from approximately 1 min to more than 45 min in cells cultured at 35°C. Our results provide a first step in characterizing mRNA decay in
B. burgdorferi
and in investigating its role in gene expression and regulation.