bluuebunny/crossref_metadata_2025 huggingface dataset:
Constitutive Modeling of Coronary Arterial Media—Comparison of Three Model Classes
Authors: Hollander Yaniv , Durban David , Lu Xiao , Kassab Ghassan S. , Lanir Yoram
Published: June 2011

Accurate modeling of arterial elasticity is imperative for predicting pulsatile blood flow and transport to the periphery, and for evaluating the mechanical microenvironment of the vessel wall. The goal of the present study is to compare a recently developed structural model of porcine left anterior descending artery media to two commonly used typical representatives of phenomenological and structure-motivated invariant-based models, in terms of the number of model parameters, model descriptive and predictive powers, and requisite different test protocols for reliable parameter estimation. The three models were compared against 3D data of radial inflation, axial extension, and twist tests. Also checked are the models predictive capabilities to response data not used for estimation, including both tests outside the range of estimation database, as well as protocols of a different nature. The results show that the descriptive estimation error (model fit to estimation database), measured by the sum of squared residuals (SSE) between full 3D data and model predictions, was about twice as low for the structural (4.58%) model compared to the other two (9.71 and 8.99% for the phenomenological and structure-motivated models, respectively). Similar SSE ratios were obtained for the predictive capabilities. Prediction SSE at high stretch based on estimation of two low stretches yielded an SSE value of 2.81% for the structural model, and 10.54% and 7.87% for the phenomenological and structure-motivated models, respectively. For the prediction of twist from inflation-extension data, SSE values for the torsional stiffness was 1.76% for the structural model and 39.62 and 2.77% for the phenomenological and structure-motivated models. The required number of model parameters for the structural model is four, whereas the phenomenological model requires six to nine and the structure-motivated has four parameters. These results suggest that modeling based on the tissue structural features improves model reliability in describing given data and in predicting the tissue general response.
Stereoscopic Particle Image Velocimetry Analysis of Healthy and Emphysemic Alveolar Sac Models
Authors: Berg Emily J. , Robinson Risa J.
Published: June 2011

Emphysema is a progressive lung disease that involves permanent destruction of the alveolar walls. Fluid mechanics in the pulmonary region and how they are altered with the presence of emphysema are not well understood. Much of our understanding of the flow fields occurring in the healthy pulmonary region is based on idealized geometries, and little attention has been paid to emphysemic geometries. The goal of this research was to utilize actual replica lung geometries to gain a better understanding of the mechanisms that govern fluid motion and particle transport in the most distal regions of the lung and to compare the differences that exist between healthy and emphysematous lungs. Excised human healthy and emphysemic lungs were cast, scanned, graphically reconstructed, and used to fabricate clear, hollow, compliant models. Three dimensional flow fields were obtained experimentally using stereoscopic particle image velocimetry techniques for healthy and emphysematic breathing conditions. Measured alveolar velocities ranged over two orders of magnitude from the duct entrance to the wall in both models. Recirculating flow was not found in either the healthy or the emphysematic model, while the average flow rate was three times larger in emphysema as compared to healthy. Diffusion dominated particle flow, which is characteristic in the pulmonary region of the healthy lung, was not seen for emphysema, except for very small particle sizes. Flow speeds dissipated quickly in the healthy lung (60% reduction in 0.25 mm) but not in the emphysematic lung (only 8% reduction 0.25 mm). Alveolar ventilation per unit volume was 30% smaller in emphysema compared to healthy. Destruction of the alveolar walls in emphysema leads to significant differences in flow fields between the healthy and emphysemic lung. Models based on replica geometry provide a useful means to quantify these differences and could ultimately improve our understanding of disease progression.
Mechanical Properties of Orbital Fat and Its Encapsulating Connective Tissue
Authors: Chen Kinon , Weiland James D.
Published: June 2011

There is an increasing need to understand the mechanical properties of human orbital fat and its encapsulating connective tissue (OFCT), but such knowledge is not available in the current literature. The purpose of the present study is to examine the mechanical properties of the OFCT. From 5 pairs of 76- to 92-year-old Caucasian human eyes and 33 5- to 7-month-old porcine eyes, 5 human and 11 porcine OFCT samples were dissected at the posterior pole or adjacent to the pole in the vertical, horizontal, and radial directions. Sample dimensions were fixed or measured. Tensile tests were performed on the samples in body-temperature saline. The stress-strain relationship was first approximately linear and then became nonlinear. The linear, the neo-Hookean, and the Mooney–Rivlin constants are reported in Tables 1 and 2. No statistical difference was found among their properties in the different directions in either the human or the porcine samples. Statistical differences were found between the human and the porcine material constants in the horizontal and radial directions. Among our material models, only the Mooney–Rivlin model was able to capture the mechanical properties of the OFCT in large deformation properly. The Mooney–Rivlin model was especially adaptive to the human data. This is the first time the mechanical properties of the human and porcine OFCT have been examined in the literature. We believe our data will provide valuable information to others regarding designing implant biomaterials in orbital treatments and developing computer models to study orbital biomechanics.
Impact of Stents and Flow Diverters on Hemodynamics in Idealized Aneurysm Models
Authors: Seshadhri Santhosh , Janiga Gábor , Beuing Oliver , Skalej Martin , Thévenin Dominique
Published: June 2011

Cerebral aneurysms constitute a major medical challenge as treatment options are limited and often associated with high risks. Statistically, up to 3% of patients with a brain aneurysm may suffer from bleeding for each year of life. Eight percent of all strokes are caused by ruptured aneurysms. In order to prevent this rupture, endovascular stenting using so called flow diverters is increasingly being regarded as an alternative to the established coil occlusion method in minimally invasive treatment. Covering the neck of an aneurysm with a flow diverter has the potential to alter the hemodynamics in such a way as to induce thrombosis within the aneurysm sac, stopping its further growth, preventing its rupture and possibly leading to complete resorption. In the present study the influence of different flow diverters is quantified considering idealized patient configurations, with a spherical sidewall aneurysm placed on either a straight or a curved parent vessel. All important hemodynamic parameters (exchange flow rate, velocity, and wall shear stress) are determined in a quantitative and accurate manner using computational fluid dynamics when varying the key geometrical properties of the aneurysm. All simulations are carried out using an incompressible, Newtonian fluid with steady conditions. As a whole, 72 different cases have been considered in this systematic study. In this manner, it becomes possible to compare the efficiency of different stents and flow diverters as a function of wire density and thickness. The results show that the intra-aneurysmal flow velocity, wall shear stress, mean velocity, and vortex topology can be considerably modified thanks to insertion of a suitable implant. Intra-aneurysmal residence time is found to increase rapidly with decreasing stent porosity. Of the three different implants considered in this study, the one with the highest wire density shows the highest increase of intra-aneurysmal residence time for both the straight and the curved parent vessels. The best hemodynamic modifications are always obtained for a small aneurysm diameter.
A Wearable System to Assess Risk for Anterior Cruciate Ligament
Injury During Jump Landing: Measurements of Temporal Events, Jump Height, and
Sagittal Plane Kinematics
Authors: Dowling Ariel V. , Favre Julien , Andriacchi Thomas P.
Published: June 2011

The incidence of anterior cruciate ligament (ACL) injury remains high, and there is a need for simple, cost effective methods to identify athletes at a higher risk for ACL injury. Wearable measurement systems offer potential methods to assess the risk of ACL injury during jumping tasks. The objective of this study was to assess the capacity of a wearable inertial-based system to evaluate ACL injury risk during jumping tasks. The system accuracy for measuring temporal events (initial contact, toe-off), jump height, and sagittal plane angles (knee, trunk) was assessed by comparing results obtained with the wearable system to simultaneous measurements obtained with a marker-based optoelectronic reference system. Thirty-eight healthy participants (20 male and 18 female) performed drop jumps with bilateral and unilateral support landing. The mean differences between the temporal events obtained with both systems were below 5 ms, and the precisions were below 24 ms. The mean jump heights measured with both systems differed by less than 1 mm, and the associations (Pearson correlation coefficients) were above 0.9. For the discrete angle parameters, there was an average association of 0.91 and precision of 3.5° for the knee flexion angle and an association of 0.77 and precision of 5.5° for the trunk lean. The results based on the receiver-operating characteristic (ROC) also demonstrated that the proposed wearable system could identify movements at higher risk for ACL injury. The area under the ROC plots was between 0.89 and 0.99 for the knee flexion angle and between 0.83 and 0.95 for the trunk lean. The wearable system demonstrated good concurrent validity with marker-based measurements and good discriminative performance in terms of the known risk factors for ACL injury. This study suggests that a wearable system could be a simple cost-effective tool for conducting risk screening or for providing focused feedback.
Effect of Storage Duration on the Mechanical Behavior of Mouse Carotid Artery
Authors: Amin Mazyar , Kunkel Amber G. , Le Victoria P. , Wagenseil Jessica E.
Published: June 2011

Determining arterial mechanical properties is important for understanding the work done by the heart and how it changes with cardiovascular disease. Ex vivo tests are necessary to apply various loads to the artery and obtain data to model and predict the behavior under any load. Most ex vivo tests are performed within 24 h of dissection, so the tissue is still “alive.” For large elastic arteries; however, the passive mechanical behavior is attributed mostly to the very stable proteins, elastin, and collagen. If the testing equipment fails, is in use, or is located at another facility, it would be useful to store the vessels and postpone the tests until the equipment is available. The goal of this study is to determine the effects of storage time on the mechanical behavior of the common carotid artery from adult mice. Each artery was tested after storage for 1–28 days in physiologic saline at 4°C. There were no significant effects of storage time on the arterial diameter or force at each pressure, but there were significant effects on the stretch ratio and stress at each pressure. The significant effects on the stretch ratio and stress were due to decreases in the unloaded dimensions with storage time, when measured from cut arterial rings. When the unloaded dimensions were measured instead from histology sections, there were no significant changes with storage time. We conclude that histology sections yield a more consistent measurement of the unloaded dimensions and that there are no significant changes in the mechanical behavior of mouse carotid artery with storage up to 28 days.
Realization of uniform large-area pentacene thin film transistor arrays by roller vacuum thermal evaporation
Authors: Wang Liangmin , Li Dexing , Hu Yuanyuan , Jiang Chao
Published: June 2011

A conventional vacuum thermal evaporation (VTE) system has been extended to a roller-VTE system with a moving substrate-holder to realize large-area organic film deposition. The multidimensional movement of the substrate-holder guarantees excellent uniformity of the large-area pentacene thin films. An 85-nm-thick pentacene film with a relative standard deviation as low as 2.7% is demonstrated within a 300 mm × 500 mm area. Thin film transistor arrays are then fabricated using the uniform pentacene films. The average transistor mobility is up to 0.85 cm2/V s with a relative standard deviation of 10%.
Calculation of electron and isotopes dose point kernels with fluka Monte Carlo code for dosimetry in nuclear medicine therapy
Authors: Botta F. , Mairani A. , Battistoni G. , Cremonesi M. , Di Dia A. , Fassò A. , Ferrari A. , Ferrari M. , Paganelli G. , Pedroli G. , Valente M.
Published: June 2011

Purpose: The calculation of patient‐specific dose distribution can be achieved by Monte Carlo simulations or by analytical methods. In this study, fluka Monte Carlo code has been considered for use in nuclear medicine dosimetry. Up to now, fluka has mainly been dedicated to other fields, namely high energy physics, radiation protection, and hadrontherapy. When first employing a Monte Carlo code for nuclear medicine dosimetry, its results concerning electron transport at energies typical of nuclear medicine applications need to be verified. This is commonly achieved by means of calculation of a representative parameter and comparison with reference data. Dose point kernel (DPK), quantifying the energy deposition all around a point isotropic source, is often the one.Methods: fluka DPKs have been calculated in both water and compact bone for monoenergetic electrons (10–3 MeV) and for beta emitting isotopes commonly used for therapy (89Sr, 90Y, 131I, 153Sm, 177Lu, 186Re, and 188Re). Point isotropic sources have been simulated at the center of a water (bone) sphere, and deposed energy has been tallied in concentric shells. fluka outcomes have been compared to penelope v.2008 results, calculated in this study as well. Moreover, in case of monoenergetic electrons in water, comparison with the data from the literature (etran, geant4, mcnpx) has been done. Maximum percentage differences within 0.8·RCSDA and 0.9·RCSDA for monoenergetic electrons (RCSDA being the continuous slowing down approximation range) and within 0.8·X90 and 0.9·X90 for isotopes (X90 being the radius of the sphere in which 90% of the emitted energy is absorbed) have been computed, together with the average percentage difference within 0.9·RCSDA and 0.9·X90 for electrons and isotopes, respectively.Results: Concerning monoenergetic electrons, within 0.8·RCSDA (where 90%–97% of the particle energy is deposed), fluka and penelope agree mostly within 7%, except for 10 and 20 keV electrons (12% in water, 8.3% in bone). The discrepancies between fluka and the other codes are of the same order of magnitude than those observed when comparing the other codes among them, which can be referred to the different simulation algorithms. When considering the beta spectra, discrepancies notably reduce: within 0.9·X90, fluka and penelope differ for less than 1% in water and less than 2% in bone with any of the isotopes here considered. Complete data of fluka DPKs are given as Supplementary Material as a tool to perform dosimetry by analytical point kernel convolution.Conclusions: fluka provides reliable results when transporting electrons in the low energy range, proving to be an adequate tool for nuclear medicine dosimetry.
Verification of the linac isocenter for stereotactic radiosurgery using cine‐EPID imaging and arc delivery
Authors: Rowshanfarzad Pejman , Sabet Mahsheed , O'Connor Daryl J. , Greer Peter B.
Published: June 2011

Purpose:Verification of the mechanical isocenter position is required as part of comprehensive quality assurance programs for stereotactic radiosurgery/radiotherapy (SRS/SRT) treatments. Several techniques have been proposed for this purpose but each of them has certain drawbacks. In this paper, a new efficient and more comprehensive method using cine‐EPID images has been introduced for automatic verification of the isocenter with sufficient accuracy for stereotactic applications.Methods: Using a circular collimator fixed to the gantry head to define the field, EPID images of a Winston–Lutz phantom were acquired in cine‐imaging mode during 360° gantry rotations. A robust matlab code was developed to analyze the data by finding the center of the field and the center of the ball bearing shadow in each image with sub‐pixel accuracy. The distance between these two centers was determined for every image. The method was evaluated by comparison to results of a mechanical pointer and also by detection of a manual shift applied to the phantom position. The repeatability and reproducibility of the method were tested and it was also applied to detect couch and collimator wobble during rotation.Results:The accuracy of the algorithm was 0.03 ± 0.02 mm. The repeatability was less than 3 μm and the reproducibility was less than 86 μm. The time elapsed for the analysis of more than 100 cine images of Varian aS1000 and aS500 EPIDs were ∼65 and 20 s, respectively. Processing of images taken in integrated mode took 0.1 s. The output of the analysis software is printable and shows the isocenter shifts as a function of angle in both in‐plane and cross‐plane directions. It gives warning messages where the shifts exceed the criteria for SRS/SRT and provides useful data for the necessary adjustments in the system including bearing system and/or room lasers.Conclusions: The comprehensive method introduced in this study uses cine‐images, is highly accurate, fast, and independent of the observer. It tests all gantry angles and is suitable for pretreatment QA of the isocenter for stereotactic treatments.
Estimate of temperature and its uncertainty in small systems
Authors: Falcioni M. , Villamaina D. , Vulpiani A. , Puglisi A. , Sarracino A.
Published: June 2011

The energy of a finite system thermally connected to a thermal reservoir may fluctuate, while the temperature is a constant representing a thermodynamic property of the reservoir. The finite system can also be used as a thermometer for the reservoir. From such a perspective, the temperature has an uncertainty, which can be treated within the framework of estimation theory. We review the main results of this theory and clarify some controversial issues regarding temperature fluctuations. We also offer a simple example of a thermometer with a small number of particles. We discuss the relevance of the total observation time, which must be much longer than the decorrelation time.
Fission fizzles: Estimating the yield of a predetonated nuclear weapon
Authors: Cameron Reed B.
Published: June 2011

An undergraduate-level model is developed for estimating the fraction of the design yield that can be realized if a uranium or a plutonium fission bomb suffers an uncontrolled predetonation due to a spontaneous fission of the fissile material. The model is based on the combination of one published earlier for the predetonation probability and a yield model developed by Mark et al. [“Explosive properties of reactor-grade plutonium,” Sci. Global Secur. 17 (2), 170–185 (2009); a reprint of the same paper published in Sci. Global Secur. 4 (1), 111–128 (1993)].
Simplified model for the dynamics of a helical flagellum
Authors: de Lima Bernardo B. , Moraes Fernando
Published: June 2011

Several bacteria, such as Escherichia coli and Salmonella typhimurium, are self-propelled using their flagella in a very particular way. We analyze the mechanics of this phenomenon, taking into account the geometry of these propellers. The dependence of the speed of the bacterium on the configuration of the flagellum is found in a simple way. By using similar artifices, we also describe the mechanics of the opposite effect, that is, the rotation acquired by a helix when it is towed through a fluid in the axial direction at low Reynolds number.
Quantum Gaussian wells and barriers
Authors: Fernández Francisco M.
Published: June 2011

We apply the variational method to the ground-state and first-excited-state energies of a Gaussian well and show that the expansion of the approximate energy when the potential strength approaches zero does not agree with the exact result. We argue that a recent semiclassical approach to tunneling through a Gaussian barrier does not agree with an accurate calculation of the transmission probability. We point out the advantages of converting the Schrödinger equation into a dimensionless eigenvalue equation.
How to twirl a hula hoop
Authors: Seyranian Alexander P. , Belyakov Anton O.
Published: June 2011

We consider the twirling of a hula hoop when the waist of a gymnast moves along an elliptical trajectory close to a circle. For a circular trajectory, two families of exact solutions are obtained, corresponding to twirling of the hula hoop with a constant angular speed equal to the speed of the excitation. We show that one family of solutions is stable, and the other one is unstable. These exact solutions allow us to obtain approximate solutions for a slightly elliptical trajectory of the waist. We demonstrate that to twirl a hula hoop the waist needs to rotate with a phase difference between π/2 and π. An interesting effect of inverse twirling is described when the waist moves in a direction opposite to the hula hoop rotation. The approximate analytical solutions are compared with the results of a numerical calculation.
Anharmonic dynamics of a mass O-spring oscillator
Authors: Filipponi A. , Cavicchia D. R.
Published: June 2011

We investigate the dynamics of a one-dimensional oscillator made of a mass connected to a circular spring under uniaxial extension. The functional dependence of the elastic energy on the strain is obtained by solving the differential equations resulting from a variational formalism common to Euler’s elastica problem. The calculated nonlinear force agrees with the experiment, confirming the anharmonic nature of the oscillator.
Double well potentials and quantum gates
Authors: Foot C. J. , Shotter M. D.
Published: June 2011

A system of particles in a double well potential is a widely studied and useful example for understanding quantum mechanics. This simple system has recently been used in theoretical proposals and related experiments as a way to make quantum logic gates for ultracold atoms confined in optical lattices. Such quantum gates are the fundamental building blocks for quantum information processing; in these proposals, a regular array of cold atoms in an optical lattice serves as the quantum register. We explain how this research can be understood in terms of well-known principles for systems of identical particles.
A chain that speeds up, rather than slows, due to collisions: How compression can cause tension
Authors: Grewal Anoop , Johnson Phillip , Ruina Andy
Published: June 2011

When two nominally rigid objects collide, their velocities change in response to the compression force between them. The difference in the normal component of the velocities of the objects is thus generally eliminated or reversed. The nature of collisions for nonrigid objects is more subtle. Surprisingly, when a long chain moving lengthwise collides with a wall, the chain can be pulled into the wall (instead of pushed away) with the approach velocity between the wall and chain increasing in time rather than not changing or decreasing. We discuss theoretical limits on how much a chain can be pulled into an object with which it collides, some chain link designs that lead to these limits, and experimental results which show the pulling of one of these chain link designs into a wall.
High-Temperature Enzymatic Breakdown of Cellulose
Authors: Wang Hongliang , Squina Fabio , Segato Fernando , Mort Andrew , Lee David , Pappan Kirk , Prade Rolf
Published: June 2011

Cellulose is an abundant and renewable biopolymer that can be used for biofuel generation; however, structural entrapment with other cell wall components hinders enzyme-substrate interactions, a key bottleneck for ethanol production. Biomass is routinely subjected to treatments that facilitate cellulase-cellulose contacts. Cellulases and glucosidases act by hydrolyzing glycosidic bonds of linear glucose β-1,4-linked polymers, producing glucose. Here we describe eight high-temperature-operating cellulases (TCel enzymes) identified from a survey of thermobacterial and archaeal genomes. Three TCel enzymes preferentially hydrolyzed soluble cellulose, while two preferred insoluble cellulose such as cotton linters and filter paper. TCel enzymes had temperature optima ranging from 85°C to 102°C. TCel enzymes were stable, retaining 80% of initial activity after 120 h at 85°C. Two modes of cellulose breakdown, i.e., with endo- and exo-acting glucanases, were detected, and with two-enzyme combinations at 85°C, synergistic cellulase activity was observed for some enzyme combinations.
Allelic Diversity and Population Structure of Bacillus sphaericus as Revealed by Multilocus Sequence Typing
Authors: Ge Yong , Hu Xiaomin , Zheng Dasheng , Wu Yiming , Yuan Zhiming
Published: June 2011

The genetic diversity of 35
Bacillus sphaericus
strains was analyzed by a newly developed multilocus sequence typing (MLST) scheme, toxin gene pool survey, and mosquito bioassay. The results demonstrated that strains assigned to the same sequence type (ST) had the same occurrence of toxin genes. Further sequence analysis revealed that toxic strains presented a nearly clonal population structure, whereas nontoxic strains had a high level of heterogeneity and were significantly distinct from toxic strains.
Pseudomonas fluorescens F113 Mutant with Enhanced Competitive Colonization Ability and Improved Biocontrol Activity against Fungal Root Pathogens
Authors: Barahona Emma , Navazo Ana , Martínez-Granero Francisco , Zea-Bonilla Teresa , Pérez-Jiménez Rosa María , Martín Marta , Rivilla Rafael
Published: June 2011

Motility is one of the most important traits for efficient rhizosphere colonization by
Pseudomonas fluorescens
F113rif (F113). In this bacterium, motility is a polygenic trait that is repressed by at least three independent pathways, including the Gac posttranscriptional system, the Wsp chemotaxis-like pathway, and the SadB pathway. Here we show that the
kinB
gene, which encodes a signal transduction protein that together with AlgB has been implicated in alginate production, participates in swimming motility repression through the Gac pathway, acting downstream of the GacAS two-component system. Gac mutants are impaired in secondary metabolite production and are unsuitable as biocontrol agents. However, the
kinB
mutant and a triple mutant affected in
kinB
,
sadB
, and
wspR
(KSW) possess a wild-type phenotype for secondary metabolism. The KSW strain is hypermotile and more competitive for rhizosphere colonization than the wild-type strain. We have compared the biocontrol activity of KSW with those of the wild-type strain and a phenotypic variant (F113v35 [V35]) which is hypermotile and hypercompetitive but is affected in secondary metabolism since it harbors a
gacS
mutation. Biocontrol experiments in the
Fusarium oxysporum
f. sp.
radicis-lycopersici
/
Lycopersicum esculentum
(tomato) and
Phytophthora cactorum/Fragaria vesca
(strawberry) pathosystems have shown that the three strains possess biocontrol activity. Biocontrol activity was consistently lower for V35, indicating that the production of secondary metabolites was the most important trait for biocontrol. Strain KSW showed improved biocontrol compared with the wild-type strain, indicating that an increase in competitive colonization ability resulted in improved biocontrol and that the rational design of biocontrol agents by mutation is feasible.
2,3-Butanediol Production by Acetogenic Bacteria, an Alternative Route to Chemical Synthesis, Using Industrial Waste Gas
Authors: Köpke Michael , Mihalcea Christophe , Liew FungMin , Tizard Joseph H. , Ali Mohammed S. , Conolly Joshua J. , Al-Sinawi Bakir , Simpson Séan D.
Published: June 2011

2,3-Butanediol (23BD) is a high-value chemical usually produced petrochemically but which can also be synthesized by some bacteria. To date, the best microbial 23BD production rates have been observed using pathogenic bacteria in fermentation systems that depend on sugars as the carbon and energy sources for product synthesis. Here we present evidence of 23BD production by three nonpathogenic acetogenicClostridiumspecies—Clostridium autoethanogenum,C. ljungdahlii, andC. ragsdalei—using carbon monoxide-containing industrial waste gases or syngas as the sole source of carbon and energy. Through an analysis of theC. ljungdahliigenome, the complete pathway from carbon monoxide to 23BD has been proposed. Homologues of the genes involved in this pathway were also confirmed for the other two species investigated. A gene expression study demonstrates a correlation between mRNA accumulation from 23BD biosynthetic genes and the onset of 23BD production, while a broader expression study of Wood-Ljungdahl pathway genes provides a transcription-level view of one of the oldest existing biochemical pathways.
Rapid Detection and Enumeration of Giardia lamblia Cysts in Water Samples by Immunomagnetic Separation and Flow Cytometric Analysis
Authors: Keserue Hans-Anton , Füchslin Hans Peter , Egli Thomas
Published: June 2011

Giardia lamblia
is an important waterborne pathogen and is among the most common intestinal parasites of humans worldwide. Its fecal-oral transmission leads to the presence of cysts of this pathogen in the environment, and so far, quantitative rapid screening methods are not available for various matrices, such as surface waters, wastewater, or food. Thus, it is necessary to establish methods that enable reliable rapid detection of a single cyst in 10 to 100 liters of drinking water. Conventional detection relies on cyst concentration, isolation, and confirmation by immunofluorescence microscopy (IFM), resulting in low recoveries and high detection limits. Many different immunomagnetic separation (IMS) procedures have been developed for separation and cyst purification, so far with variable but high losses of cysts. A method was developed that requires less than 100 min and consists of filtration, resuspension, IMS, and flow cytometric (FCM) detection. MACS MicroBeads were used for IMS, and a reliable flow cytometric detection approach was established employing 3 different parameters for discrimination from background signals, i.e., green and red fluorescence (resulting from the distinct pattern emitted by the fluorescein dye) and sideward scatter for size discrimination. With spiked samples, recoveries exceeding 90% were obtained, and false-positive results were never encountered for negative samples. Additionally, the method was applicable to naturally occurring cysts in wastewater and has the potential to be automated.
Analysis of
bla
CTX-M
-Carrying Plasmids from Escherichia coli Isolates Collected in the BfT-GermVet Study
Authors: Schink Anne-Kathrin , Kadlec Kristina , Schwarz Stefan
Published: June 2011

In this study, 417
Escherichia coli
isolates from defined disease conditions of companion and farm animals collected in the BfT-GermVet study were investigated for the presence of extended-spectrum β-lactamase (ESBL) genes. Three ESBL-producing
E. coli
isolates were identified among the 100 ampicillin-resistant isolates. The
E. coli
isolates 168 and 246, of canine and porcine origins, respectively, harbored
bla
CTX-M-1
, and the canine isolate 913 harbored
bla
CTX-M-15
, as confirmed by PCR and sequence analysis. The isolates 168 and 246 belonged to the novel multilocus sequence typing (MLST) types ST1576 and ST1153, respectively, while isolate 913 had the MLST type ST410. The ESBL genes were located on structurally related IncN plasmids in isolates 168 and 246 and on an IncF plasmid in isolate 913. The
bla
CTX-M-1
upstream regions of plasmids pCTX168 and pCTX246 were similar, whereas the downstream regions showed structural differences. The genetic environment of the
bla
CTX-M-15
gene on plasmid pCTX913 differed distinctly from that of both
bla
CTX-M-1
genes. Detailed sequence analysis showed that the integration of insertion sequences, as well as interplasmid recombination events, accounted for the structural variability in the
bla
CTX-M
gene regions.
Environmental, Biogeographic, and Biochemical Patterns of Archaea of the Family Ferroplasmaceae
Authors: Golyshina Olga V.
Published: June 2011

About 10 years ago, a new family of cell wall-deficient, iron-oxidizing archaea,
Ferroplasmaceae
, within the large archaeal phylum
Euryarchaeota
, was described. In this minireview, I summarize the research progress achieved since then and report on the current status of taxonomy, biogeography, physiological diversity, biochemistry, and other research areas involving this exciting group of acidophilic archaea.
Systematic Search for Cultivatable Fungi That Best Deconstruct Cell Walls of Miscanthus and Sugarcane in the Field
Authors: Shrestha Prachand , Szaro Timothy M. , Bruns Thomas D. , Taylor John W.
Published: June 2011

The goals of our project were to document the diversity and distributions of cultivable fungi associated with decaying
Miscanthus
and sugarcane plants in nature and to further assess biodegradation of host plant cell walls by these fungi in pure cultures. Late in 2008 and early in 2009 we collected decaying
Miscanthus
and
Saccharum
from 8 sites in Illinois and 11 sites in Louisiana, respectively. To recover fungi that truly decay plants and to recover slow-growing fungi, we washed the plant material repeatedly to remove spores and cultivated fungi from plant fragments small enough to harbor at most one mycelium. We randomly selected 950 fungal colonies out of 4,560 microwell colonies and used molecular identification to discover that the most frequently recovered fungal species resided in
Hypocreales
(
Sordariomycetes
),
Pleosporales
(
Dothideomycetes
), and
Chaetothryiales
(
Eurotiomycetes
) and that only a few weedy species were recovered. We were particularly interested in
Pleosporales
and
Chaetothyriales
, groups that have not been mined for plant decay fungi. To confirm that we had truly recovered fungi that deconstruct plant cell walls, we assayed the capacity of the fungi to consume whole, alkali-pretreated, ground
Miscanthus
. Solid substrate cultures of the nine most commonly encountered
Ascomycota
resulted in
Miscanthus
weight loss of 8 to 13% over 4 weeks. This is the first systematic, high-throughput, isolation and biodegradation assessment of fungi isolated from decaying bioenergy grasses.
Increased Furfural Tolerance Due to Overexpression of NADH-Dependent Oxidoreductase FucO in Escherichia coli Strains Engineered for the Production of Ethanol and Lactate
Authors: Wang X. , Miller E. N. , Yomano L. P. , Zhang X. , Shanmugam K. T. , Ingram L. O.
Published: June 2011

Furfural is an important fermentation inhibitor in hemicellulose sugar syrups derived from woody biomass. The metabolism of furfural by NADPH-dependent oxidoreductases, such as YqhD (low

K
m

for NADPH), is proposed to inhibit the growth and fermentation of xylose in
Escherichia coli
by competing with biosynthesis for NADPH. The discovery that the NADH-dependent propanediol oxidoreductase (FucO) can reduce furfural provided a new approach to improve furfural tolerance. Strains that produced ethanol or lactate efficiently as primary products from xylose were developed. These strains included chromosomal mutations in
yqhD
expression that permitted the fermentation of xylose broths containing up to 10 mM furfural. Expression of
fucO
from plasmids was shown to increase furfural tolerance by 50% and to permit the fermentation of 15 mM furfural. Product yields with 15 mM furfural were equivalent to those of control strains without added furfural (85% to 90% of the theoretical maximum). These two defined genetic traits can be readily transferred to enteric biocatalysts designed to produce other products. A similar strategy that minimizes the depletion of NADPH pools by native detoxification enzymes may be generally useful for other inhibitory compounds in lignocellulosic sugar streams and with other organisms.
Rickettsia monteiroi sp. nov., Infecting the Tick Amblyomma incisum in Brazil
Authors: Pacheco Richard C. , Moraes-Filho Jonas , Marcili Arlei , Richtzenhain Leonardo J. , Szabó Matias P. J. , Catroxo Márcia H. B. , Bouyer Donald H. , Labruna Marcelo B.
Published: June 2011

Free-living adultAmblyomma incisumticks were collected in an Atlantic rainforest area at Intervales State Park, State of São Paulo, Brazil. From anA. incisumspecimen, rickettsiae were successfully isolated in Vero cell culture by the shell vial technique. Rickettsial isolation was confirmed by optical microscopy, transmission electron microscopy, and PCRs targeting portions of the rickettsial genesgltA,htrA,rrs, andsca1on infected cells. Fragments of 1,089, 457, 1,362, and 443 nucleotides of thegltA,htrA,rrs, andsca1genes, respectively, were sequenced. By BLAST analysis, the partial sequence ofrrsof theA. incisumrickettsial isolate was closest to the corresponding sequence ofRickettsia bellii(99.1% similarity). ThegltApartial sequence was closest to the corresponding sequences of “CandidatusRickettsia tarasevichiae” (96.1% similarity) andRickettsia canadensis(95.8% similarity). ThehtrApartial sequence was closest to the corresponding sequence ofR. canadensis(89.8% similarity). Thesca1partial sequence was closest to the corresponding sequence ofR. canadensis(95.2% similarity). Since our rickettsial isolate was genetically distinct from otherRickettsiaspecies, we propose a new species designatedRickettsia monteiroisp. nov. Phylogenetic analyses indicated thatR. monteiroibelongs to the canadensis group within the genusRickettsia, together with the speciesR. canadensisand “CandidatusR. tarasevichiae”. Little or no antibody cross-reaction was observed between sera ofR. monteiroi-inoculated guinea pigs andR. bellii-,Rickettsia rickettsii-, orR. canadensis-inoculated guinea pigs.
Variation among Plasmodium falciparum Strains in Their Reliance on Mitochondrial Electron Transport Chain Function
Authors: Ke Hangjun , Morrisey Joanne M. , Ganesan Suresh M. , Painter Heather J. , Mather Michael W. , Vaidya Akhil B.
Published: June 2011

Previous studies demonstrated that
Plasmodium falciparum
strain D10 became highly resistant to the mitochondrial electron transport chain (mtETC) inhibitor atovaquone when the mtETC was decoupled from the pyrimidine biosynthesis pathway by expressing the fumarate-dependent (ubiquinone-independent) yeast dihydroorotate dehydrogenase (yDHODH) in parasites. To investigate the requirement for decoupled mtETC activity in
P. falciparum
with different genetic backgrounds, we integrated a single copy of the yDHODH gene into the genomes of D10attB, 3D7attB, Dd2attB, and HB3attB strains of the parasite. The yDHODH gene was equally expressed in all of the transgenic lines. All four yDHODH transgenic lines showed strong resistance to atovaquone in standard short-term growth inhibition assays. During longer term growth with atovaquone, D10attB-yDHODH and 3D7attB-yDHODH parasites remained fully resistant, but Dd2attB-yDHODH and HB3attB-yDHODH parasites lost their tolerance to the drug after 3 to 4 days of exposure. No differences were found, however, in growth responses among all of these strains to the
Plasmodium
-specific DHODH inhibitor DSM1 in either short- or long-term exposures. Thus, DSM1 works well as a selective agent in all parasite lines transfected with the yDHODH gene, whereas atovaquone works for some lines. We found that the ubiquinone analog decylubiquinone substantially reversed the atovaquone inhibition of Dd2attB-yDHODH and HB3attB-yDHODH transgenic parasites during extended growth. Thus, we conclude that there are strain-specific differences in the requirement for mtETC activity among
P. falciparum
strains, suggesting that, in erythrocytic stages of the parasite, ubiquinone-dependent dehydrogenase activities other than those of DHODH are dispensable in some strains but are essential in others.
Genetic and Biochemical Analysis of PadR-
padC
Promoter Interactions during the Phenolic Acid Stress Response in Bacillus subtilis 168
Authors: Nguyen Thi Kim Chi , Tran Ngoc Phuong , Cavin Jean-François
Published: June 2011

Bacillus subtilis
168 is resistant to phenolic acids by expression of an inducible enzyme, the phenolic acid decarboxylase (PadC), that decarboxylates these acids into less toxic vinyl derivatives. In the phenolic acid stress response (PASR), the repressor of
padC
, PadR, is inactivated by these acids. Inactivation of PadR is followed by a strong expression of
padC
. To elucidate the functional interaction between PadR and the
padC
promoter, we performed (i) footprinting assays to identify the region protected by PadR, (ii) electrophoretic mobility shift assays (EMSAs) with a modified
padC
promoter protected region to determine the interacting sequences, and (iii) random mutagenesis of
padR
to identify amino acid residues essential for the function of PadR. We identified an important consensus dyad sequence called IR1-2 (ATGT-8N-ACAT) overlapping a second dyad element (GTGT-8N-ACAT) that we named dIR1-2bis. The entire dIR1-2bis/IR1-2 sequence permits binding of two PadR dimers in EMSAs, which may be observed for bacteria grown under noninduced conditions where the
padC
promoter is completely repressed. Three groups of modified PadRs giving a PASR phenotype were characterized
in vivo
. The DNA sequences of certain mutant
padR
alleles indicate that important residues are all located in the region containing the coiled-coil leucine zipper domain that is involved in dimerization. These substitutions reduce the affinity of PadR binding to the
padC
promoter. Of particular interest are residue L128, located at the center of the putative coiled-coil leucine zipper domain, and residue E97, which is conserved among all PadRs.
Refining the Binding of the Escherichia coli Flagellar Master Regulator, FlhD
4
C
2
, on a Base-Specific Level
Authors: Lee Yi-Ying , Barker Clive S. , Matsumura Philip , Belas Robert
Published: June 2011

The
Escherichia coli
flagellar master regulator, FlhD
4
C
2
, binds to the promoter regions of flagellar class II genes, yet, despite extensive analysis of the FlhD
4
C
2
-regulated promoter region, a detailed consensus sequence has not emerged. We used
in vitro
and
in vivo
experimental approaches to determine the nucleotides in the class II promoter,
fliAp
, required for the binding and function of FlhD
4
C
2
. FlhD
4
C
2
protects 48 bp (positions −76 to −29 relative to the σ
70
-dependent transcriptional start site) in the
fliA
promoter. We divided the 48-bp footprint region into 5 sections to determine the requirement of each DNA segment for the binding and function of FlhD
4
C
2
. Results from an
in vitro
binding competition assay between the wild-type FlhD
4
C
2
-protected fragment and DNA fragments possessing mutations in one section of the 48-bp protected region showed that only one-third of the 48 bp protected by FlhD
4
C
2
is required for FlhD
4
C
2
binding and
fliA
promoter activity. This
in vitro
binding result was also seen
in vivo
with
fliA
promoter-
lacZ
fusions carrying the same mutations. Only seven bases (A
12
, A
15
, T
34
, A
36
, T
37
, A
44
, and T
45
) are absolutely required for the promoter activity. Moreover, A
12
, A
15
, T
34
, T
37
, and T
45
within the 7 bases are highly specific to
fliA
promoter activity, and those bases form an asymmetric recognition site for FlhD
4
C
2
. The implications of the asymmetry of the FlhD
4
C
2
binding site and its potential impact on FlhD
4
C
2
are discussed.
Cooperativity and Interference of Germination Pathways in Bacillus anthracis Spores
Authors: Luu Helen , Akoachere Monique , Patra Manomita , Abel-Santos Ernesto
Published: June 2011

Spore germination is the first step to
Bacillus anthracis
pathogenicity. Previous work has shown that
B. anthracis
spores use germination (Ger) receptors to recognize amino acids and nucleosides as germinants. Genetic analysis has putatively paired each individual Ger receptor with a specific germinant. However, Ger receptors seem to be able to partially compensate for each other and recognize alternative germinants. Using kinetic analysis of
B. anthracis
spores germinated with inosine and
l
-alanine, we previously determined kinetic parameters for this germination process and showed binding synergy between the cogerminants. In this work, we expanded our kinetic analysis to determine kinetic parameters and binding order for every
B. anthracis
spore germinant pair. Our results show that germinant binding can exhibit positive, neutral, or negative cooperativity. Furthermore, different germinants can bind spores by either a random or an ordered mechanism. Finally, simultaneous triggering of multiple germination pathways shows that germinants can either cooperate or interfere with each other during the spore germination process. We postulate that the complexity of germination responses may allow
B. anthracis
spores to respond to different environments by activating different germination pathways.
The Requirement for Pneumococcal MreC and MreD Is Relieved by Inactivation of the Gene Encoding PBP1a
Authors: Land Adrian D. , Winkler Malcolm E.
Published: June 2011

MreC and MreD, along with the actin homologue MreB, are required to maintain the shape of rod-shaped bacteria. The depletion of MreCD in rod-shaped bacteria leads to the formation of spherical cells and the accumulation of suppressor mutations. Ovococcus bacteria, such as
Streptococcus pneumoniae
, lack MreB homologues, and the functions of the
S. pneumoniae
MreCD (MreCD

Spn

) proteins are unknown.
mreCD
are located upstream from the
pcsB
cell division gene in most
Streptococcus
species, but we found that
mreCD
and
pcsB
are transcribed independently. Similarly to rod-shaped bacteria, we show that
mreCD
are essential in the virulent serotype 2 D39 strain of
S. pneumoniae
, and the depletion of MreCD results in cell rounding and lysis. In contrast, laboratory strain R6 contains suppressors that allow the growth of Δ
mreCD
mutants, and bypass suppressors accumulate in D39 Δ
mreCD
mutants. One class of suppressors eliminates the function of class A penicillin binding protein 1a (PBP1a). Unencapsulated Δ
pbp1a
D39 mutants have smaller diameters than their
pbp1a
+
parent or Δ
pbp2a
and Δ
pbp1b
mutants, which lack other class A PBPs and do not show the suppression of Δ
mreCD
mutations. Suppressed Δ
mreCD
Δ
pbp1a
double mutants form aberrantly shaped cells, some with misplaced peptidoglycan (PG) biosynthesis compared to that of single Δ
pbp1a
mutants. Quantitative Western blotting showed that MreC

Spn

is abundant (≈8,500 dimers per cell), and immunofluorescent microscopy (IFM) located MreCD

Spn

to the equators and septa of dividing cells, similarly to the PBPs and PG pentapeptides indicative of PG synthesis. These combined results are consistent with a model in which MreCD

Spn

direct peripheral PG synthesis and control PBP1a localization or activity.