bluuebunny/crossref_metadata_2025 huggingface dataset:
Artificial selection for determinate growth habit in soybean
Authors: Tian Zhixi , Wang Xiaobo , Lee Rian , Li Yinghui , Specht James E. , Nelson Randall L. , McClean Phillip E. , Qiu Lijuan , Ma Jianxin
Published: April 2010

Determinacy is an agronomically important trait associated with the domestication in soybean (
Glycine max
). Most soybean cultivars are classifiable into indeterminate and determinate growth habit, whereas
Glycine soja
, the wild progenitor of soybean, is indeterminate. Indeterminate (
Dt1/Dt1
) and determinate (
dt1/dt1
) genotypes, when mated, produce progeny that segregate in a monogenic pattern. Here, we show evidence that
Dt1
is a homolog (designated as
GmTfl1
) of
Arabidopsis
terminal flower 1 (
TFL1
), a regulatory gene encoding a signaling protein of shoot meristems. The transition from indeterminate to determinate phenotypes in soybean is associated with independent human selections of four distinct single-nucleotide substitutions in the
GmTfl1
gene, each of which led to a single amino acid change. Genetic diversity of a minicore collection of Chinese soybean landraces assessed by simple sequence repeat (SSR) markers and allelic variation at the
GmTfl1
locus suggest that human selection for determinacy took place at early stages of landrace radiation. The
GmTfl1
allele introduced into a determinate-type
(tfl1/tfl1) Arabidopsis
mutants fully restored the wild-type
(TFL1/TFL1)
phenotype, but the
Gmtfl1
allele in
tfl1/tfl1
mutants did not result in apparent phenotypic change. These observations indicate that
GmTfl1
complements the functions of
TFL1
in
Arabidopsis
. However, the
GmTfl1
homeolog, despite its more recent divergence from
GmTfl1
than from
Arabidopsis TFL1
, appears to be sub- or neo-functionalized, as revealed by the differential expression of the two genes at multiple plant developmental stages and by allelic analysis at both loci.
Fast on-rates allow short dwell time ligands to activate T cells
Authors: Govern Christopher C. , Paczosa Michelle K. , Chakraborty Arup K. , Huseby Eric S.
Published: April 2010

Two contrasting theories have emerged that attempt to describe T-cell ligand potency, one based on the t
1/2
of the interaction and the other based on the equilibrium affinity (K
D
). Here, we have identified and studied an extensive set of T-cell receptor (TCR)-peptide-MHC (pMHC) interactions for CD4
+
cells that have differential K
D
s and kinetics of binding. Our data indicate that ligands with a short t
1/2
can be highly stimulatory if they have fast on-rates. Simple models suggest these fast kinetic ligands are stimulatory because the pMHCs bind and rebind the same TCR several times. Rebinding occurs when the TCR-pMHC on-rate outcompetes TCR-pMHC diffusion within the cell membrane, creating an aggregate t
1/2
(t
a
) that can be significantly longer than a single TCR-pMHC encounter. Accounting for t
a
, ligand potency is K
D
-based when ligands have fast on-rates (k
on
) and t
1/2
-dependent when they have slow k
on
. Thus, TCR-pMHC k
on
allow high-affinity short t
1/2
ligands to follow a kinetic proofreading model.
Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex
Authors: Cheung Iris , Shulha Hennady P. , Jiang Yan , Matevossian Anouch , Wang Jie , Weng Zhiping , Akbarian Schahram
Published: April 2010

Little is known about the regulation of neuronal and other cell-type specific epigenomes from the brain. Here, we map the genome-wide distribution of trimethylated histone H3K4 (H3K4me3), a mark associated with transcriptional regulation, in neuronal and nonneuronal nuclei collected from prefrontal cortex (PFC) of 11 individuals ranging in age from 0.5 to 69 years. Massively parallel sequencing identified 12,732–19,704 H3K4me3 enriched regions (peaks), the majority located proximal to (within 2 kb of) the transcription start site (TSS) of annotated genes. These included peaks shared by neurons in comparison with three control (lymphocyte) cell types, as well as peaks specific to individual subjects. We identified 6,213 genes that show highly enriched H3K4me3 in neurons versus control. At least 1,370 loci, including annotated genes and novel transcripts, were selectively tagged with H3K4me3 in neuronal but not in nonneuronal PFC chromatin. Our results reveal age-correlated neuronal epigenome reorganization, including decreased H3K4me3 at approximately 600 genes (many function in developmental processes) during the first year after birth. In comparison, the epigenome of aging (>60 years) PFC neurons showed less extensive changes, including increased H3K4me3 at 100 genes. These findings demonstrate that H3K4me3 in human PFC is highly regulated in a cell type- and subject-specific manner and highlight the importance of early childhood for developmentally regulated chromatin remodeling in prefrontal neurons.
Pcdp1 is a central apparatus protein that binds Ca2+-calmodulin and regulates ciliary motility
Authors: DiPetrillo Christen G. , Smith Elizabeth F.
Published: April 2010

For all motile eukaryotic cilia and flagella, beating is regulated by changes in intraciliary calcium concentration. Although the mechanism for calcium regulation is not understood, numerous studies have shown that calmodulin (CaM) is a key axonemal calcium sensor. Using anti-CaM antibodies and Chlamydomonas reinhardtii axonemal extracts, we precipitated a complex that includes four polypeptides and that specifically interacts with CaM in high [Ca2+]. One of the complex members, FAP221, is an orthologue of mammalian Pcdp1 (primary ciliary dyskinesia protein 1). Both FAP221 and mammalian Pcdp1 specifically bind CaM in high [Ca2+]. Reduced expression of Pcdp1 complex members in C. reinhardtii results in failure of the C1d central pair projection to assemble and significant impairment of motility including uncoordinated bends, severely reduced beat frequency, and altered waveforms. These combined results reveal that the central pair Pcdp1 (FAP221) complex is essential for control of ciliary motility.
A two-tiered mechanism of EGFR inhibition by RALT/MIG6 via kinase suppression and receptor degradation
Authors: Frosi Yuri , Anastasi Sergio , Ballarò Costanza , Varsano Giulia , Castellani Loriana , Maspero Elena , Polo Simona , Alemà Stefano , Segatto Oreste
Published: April 2010

Signaling by epidermal growth factor receptor (EGFR) must be controlled tightly because aberrant EGFR activity may cause cell transformation. Receptor-associated late transducer (RALT) is a feedback inhibitor of EGFR whose genetic ablation in the mouse causes phenotypes due to EGFR-driven excess cell proliferation. RALT inhibits EGFR catalytic activation by docking onto EGFR kinase domain. We report here an additional mechanism of EGFR suppression mediated by RALT, demonstrating that RALT-bound EGF receptors undergo endocytosis and eventual degradation into lysosomes. Moreover, RALT rescues the endocytic deficit of EGFR mutants unable to undergo either endocytosis (Dc214) or degradation (Y1045F) and mediates endocytosis via a domain distinct from that responsible for EGFR catalytic suppression. Consistent with providing a scaffolding function for endocytic proteins, RALT drives EGFR endocytosis by binding to AP-2 and Intersectins. These data suggest a model in which binding of RALT to EGFR integrates suppression of EGFR kinase with receptor endocytosis and degradation, leading to durable repression of EGFR signaling.
Structural and stratigraphic relationships of the Palaeocene mounds of the Utsira High
Authors: Wild John , Briedis Nowell
Published: April 2010

The Balder and Ringhorne Tertiary oilfields of the Utsira High are a cluster of prominent Palaeocene mounds, whose presence has confounded geologists since they were first observed on 2D seismic data back in the 1960s and 1970s. Until recently, the Balder Field geologic model consisted of distal, deep‐water Heimdal, Hermod and Balder Formation sandy‐debrite and turbidite sands, compensationally stacked along the flanks of the Utsira palaeo‐high, with intervening layers of hemipelagic shale. Remobilization of the sands by large‐scale fluidization accentuated the high‐relief mounds and sand injections linked reservoirs that were originally isolated. Reprocessed seismic data show strong primary reflectors that cannot be reconciled with this model; continuous sand bodies are observed to cross‐cut normal, biostratigraphically constrained sequence‐stratigraphic reflectors. The implication is that many, if not most, of the Hermod and Balder sands are not depositional, but were emplaced by injection. Furthermore, most of the Palaeocene mounds are associated with major ‘tears’ in the normally smooth Top Cretaceous chalk seismic reflector, and overlying chalk ‘rafts’. The chalk rafts were formerly thought to be detached glide‐blocks, shed from distant scarps to the east, but the improved data show that they are always positioned above matching depressions in the main Chalk, implying a local origin. Some of the rafts are immense, exceeding half a kilometre in width and millions of tonnes in mass. We believe the association of the chalk features with the mounds is more than a coincidence and suggest that they are genetically related. A number of driving mechanisms have been proposed for the formation of the Palaeocene mounds of the Utsira High, including normal post‐depositional compaction, fluidization by earthquakes, overpressuring due to gas migration and gravity‐sliding back into the Viking Graben. Our observations are, however, more consistent with the mounds resulting from episodic supra‐lithostatic pressure escape from beneath the Chalk.
A Numerical Study of Labyrinth Seal Flutter
Authors: di Mare L. , Imregun M. , Green J. S. , Sayma A. I.
Published: April 2010

A numerical study of a labyrinth-type turbine seal flutter in a large turbofan engine is described. The flutter analysis was conducted using a coupled fluid-structure interaction code, which was originally developed for turbomachinery blade applications. The flow model is based on an unstructured, implicit Reynolds-averaged Navier–Stokes solver. The solver is coupled to a modal model for the structure obtained from a standard structural finite element code. During the aeroelasticity computations, the aerodynamic grid is moved at each time step to follow the structural motion, which is due to unsteady aerodynamic forces applied onto the structure by the fluid. Such an integrated time-domain approach allows the direct computation of aeroelastic time histories from which the aerodynamic damping, and hence, the flutter stability, can be determined. Two different configurations of a large-diameter aeroengine labyrinth seal were studied. The first configuration is the initial design with four fins, which exhibited flutter instability during testing. The second configuration is a modified design with three fins and a stiffened ring. The steady-state flow was computed for both configurations, and good agreement was reached with available reference data. An aeroelasticity analysis was conducted next for both configurations, and the model was able to predict the observed flutter behavior in both cases. A flutter mechanism is proposed, based on the matching of the structural frequencies to the frequencies of waves traveling in the fluid, in the interfin cavities and in the high- and low-pressure cavities.
Computational Fluid Dynamics Simulation of Fouling on Axial Compressor Stages
Authors: Morini Mirko , Pinelli Michele , Spina Pier Ruggero , Venturini Mauro
Published: April 2010

Three-dimensional numerical simulations of the effect of fouling on an axial compressor stage were carried out. As a case study, the NASA Stage 37 was considered for the numerical investigation, which was performed by means of a commercial computational fluid dynamic code. The numerical model was validated against the experimental data available from literature. Computed performance maps and main flow field features showed a good agreement with the experimental data. The model was considered representative of a realistic compressor stage. The model was then used to simulate the occurrence of fouling by imposing different combinations of added thickness and surface roughness levels. The effect of fouling on compressor performances was studied. Reductions in the flow coefficient and in the pressure coefficient were found to be of the same order of magnitude of the experimental results found in literature. The model developed seems to overcome some of the limitations of other models found in literature that tend to significantly underestimate the actual values of performance reduction. The numerical results were also used to analyze and debug the stage performance scaling procedure used in stage-stacking models in order to represent fouling in multistage compressors. The analysis highlighted that scaling can adequately represent the behavior of the fouled stage in the choked flow region, but it does not capture the reduction in the maximum of the pressure coefficient, which is instead revealed by the numerical simulations. Finally, blockage due to fouling was investigated both qualitatively and quantitatively.
Parametric Thermodynamic Analysis of a Solid Oxide Fuel Cell Gas Turbine System Design Space
Authors: Tarroja Brian , Mueller Fabian , Maclay Jim , Brouwer Jacob
Published: April 2010

A parametric study of a solid oxide fuel cell-gas turbine (SOFC-GT) hybrid system design is conducted with the intention of determining the thermodynamically based design space constrained by modern material and operating limits. The analysis is performed using a thermodynamic model of a generalized SOFC-GT system where the sizing of all components, except the fuel cell, is allowed to vary. Effects of parameters such as pressure ratio, fuel utilization, oxygen utilization, and current density are examined. Operational limits are discussed in terms of maximum combustor exit temperature, maximum heat exchanger effectiveness, limiting current density, maximum hydrogen utilization, and fuel cell temperature rise. It was found that the maximum hydrogen utilization and combustor exit temperature were the most significant constraints on the system design space. The design space includes the use of cathode flow recycling and air preheating via a recuperator (heat exchanger). The effect on system efficiency of exhaust gas recirculation using an ejector versus using a blower is discussed, while both are compared with the base case of using a heat exchanger only. It was found that use of an ejector for exhaust gas recirculation caused the highest efficiency loss, and the base case was found to exhibit the highest overall system efficiency. The use of a cathode recycle blower allowed the largest downsizing of the heat exchanger, although avoiding cathode recycling altogether achieved the highest efficiency. Efficiencies in the range of 50–75% were found for variations in pressure ratio, fuel utilization, oxygen utilization, and current density. The best performing systems that fell within all design constraints were those that used a heat exchanger only to preheat air, moderate pressure ratios, low oxygen utilizations, and high fuel utilizations.
Three-Dimensional Simulation of Gaseous Fuel Injection Through a Hybrid Approach
Authors: Andreassi L. , Facci A. L. , Ubertini S.
Published: April 2010

Direct injection of gaseous fuel has emerged to be a high potential strategy to tackle both environmental and fuel economy requirements. However, since the electronic gaseous injection technology is rather new for automotive applications, limited experience exists on the optimum configuration of the injection system and the combustion chamber. To facilitate the development of these applications computer models are being developed to simulate gaseous injection, air entrainment, and the ensuing combustion. This paper introduces a new method for modeling the injection process of gaseous fuels in multidimensional simulations. The proposed model allows holding down grid requirements, thus, making it compatible with the three-dimensional simulation of an internal combustion engine.
Safety Features of a Pressurized Water Reactor Utilizing Coated Fuel Particles With a Novel Composition
Authors: Hussain Anwar , Xinrong Cao
Published: April 2010

In this research paper, a safety analysis has been carried out for the conceptual design of a compact sized pressurized water reactor (PWR) core that utilizes a tristructural-isotropic (TRISO) fuel particle with an inventive composition. The use of TRISO fuel in PWR technology improves integrity of the design due to its fission fragments retention ability, as this fuel provides first retention barrier within the fuel itself against the release fission fragments. Hence, addition of one more reliable barrier in well established PWR technology makes this design concept safer and environment friendly. A small amount of Pu-240 has been added in the fuel for excess reactivity control. This addition of Pu-240 in TRISO fuel reduces the number of burnable poison and control rods required for reactivity control, and completely eliminates the requirement of soluble boron system. The suggested design operates at much lower temperature and pressure than a standard PWR power reactor, and the presence of TRISO fuel ensures the retention of fission fragments at elevated temperatures. All reactivity coefficients were found negative for the designed core, and the shutdown margin has also been increased with the suggested TRISO fuel composition.
The Development of Impact Analysis Methodology for CEDM Missile of APR1400
Authors: Kang Tae Kyo , Park Jin Seok , Kim Hyun Min , Kim In Yong
Published: April 2010

An integrated head assembly (IHA) is equipped with the missile shield to absorb the missile energy from postulated control element drive mechanism (CEDM) missile during the dynamic event of accidental conditions. Once a CEDM nozzle breaks, reactor coolant jet discharges from the broken nozzle, then it impinges at the bottom of the CEDM, and gives a thrust force to the CEDM missile until it impacts on the missile shield. After the missile impacting on missile shield, it is necessary to evaluate the structural responses on the local area of the missile shield, as well as behaviors of overall IHA structure. The jet has been previously assumed to be a single-phase flow. However, in order to reduce excessive conservatism for the jet characteristic, the jet is assumed to be a two-phase critical flow, and accordingly Fauske slip equilibrium model is applied to estimate the jet velocity. In this paper, jet impingement models are proposed to estimate the missile velocity depending on jet expansions and size of objects. With the calculated missile velocities using the jet impingement models, the nonlinear CEDM missile impact analysis is performed to investigate structural responses of the missile shield of advanced power reactor 1400. Finally, the results show that the structural integrity of the missile shield and the IHA can be maintained due to CEDM missile impact.
An Analytical Model for the Basic Design Calculations of Journal Bearings
Authors: Naffin R. K. , Chang L.
Published: April 2010

This paper presents an analytical model for the basic design calculations of plain journal bearings. The model yields reasonable accuracy as compared with published numerical solutions under the same conditions. The principles and procedures of the formulations are presented along with accuracy analyses.
A Voronoi FE Fatigue Damage Model for Life Scatter in Rolling Contacts
Authors: Jalalahmadi Behrooz , Sadeghi Farshid
Published: April 2010

It has been widely accepted that the microstructure of bearing materials can significantly affect their rolling contact fatigue (RCF) lives. Hence, microlevel topological features of materials will be of significant importance to RCF investigation. In order to estimate the fatigue lives of bearing elements and account for the effects of topological randomness of the bearing materials, in this work, damage mechanics modeling approach is incorporated into a Voronoi finite element method recently developed by the authors. Contrary to most of the life models existing in the literature for estimating the RCF lives, the current model considers microcrack initiation, coalescence, and propagation stages. The proposed model relates the fatigue life to a damage parameter D, which is a measure of the gradual material degradation under cyclic loading. In this investigation, 40 semi-infinite domains with different microstructural distributions are subjected to a moving Hertzian pressure. Using the fatigue damage model developed, the initiation and total lives of the 40 domains are obtained. Also, the effects of initial material flaws and inhomogeneous material properties (in the form of normal distribution of the elastic modulus) on the fatigue lives are investigated. It is observed that the fatigue lives calculated and their Weibull slopes are in good agreement with previous experimental and analytical results. It is noted that introducing inhomogeneous material properties and initial flaws within the domains decreases the fatigue lives and increases their scatters.
Thermohydrodynamic Analyses of Bump Air Foil Bearings With Detailed Thermal Model of Foil Structures and Rotor
Authors: Lee Donghyun , Kim Daejong
Published: April 2010

A new thermohydrodynamic analysis model for bump air foil bearings with a detailed thermal model of bump foil structures and rotor is presented. In the developed model, temperatures of lubricating air film, top foil, bump foils, bearing sleeve, and rotor are calculated simultaneously through an iterative process. Reynolds equation and 3D energy equation were applied to the air film, and energy equations were applied to all the other structures around the bearing. Energy and momentum equations were applied to cooling channels to predict spatial temperature distribution along the cooling channels. The thermal growth of the rotor, foil structure, bearing sleeve, and centrifugal growth of the rotor are also considered. For the accuracy of the model, effective heat transfer resistance between the top foil and bearing sleeve was measured for various conditions and implemented into the thermal analysis around the cooling channels. The model was also bench marked with published experimental results for verifications. Using a developed model, parametric studies were performed with different bearing nominal clearances, applied loads, rotating speeds, and cooling conditions through channels.
Flying Clearance Distribution With Thermal Flying Height Control in Hard Disk Drives
Authors: Lee Sung-Chang , Tyndall George W. , Suk Mike
Published: April 2010

Flying clearance distribution with thermal flying height control (or thermomechanical actuation) is characterized. Especially, factors contributing to variation in the flying clearance are identified based on the flying height change profiles taken from the burn-in process of hard disk drives and Gage R&R (repeatability and reproducibility) test of touch down repeatability. In addition, the effect of static temperature compensation scheme on the flying clearance distribution is investigated, and the disadvantage of static adaptation to temperature change is identified. In order to avoid early catastrophic head-disk interface failures due to poor static temperature compensation, dynamic clearance adjustment is necessary whenever environmental condition changes. Otherwise, static temperature compensation using the individual temperature sensitivity values of each head needs to be applied.
Measurement of the Casimir effect under ultrahigh vacuum: Calibration method
Authors: Torricelli Gauthier , Thornton Stuart , Binns Chris , Pirozhenko Irina , Lambrecht Astrid
Published: April 2010

In this article, the authors present a strategy to measure the Casimir effect with an atomic force microscopy in an ultrahigh vacuum system. The key parameters including the absolute distance, the contact potential difference, and the calibration factor of the probe are determined by electrostatic interaction without contact. The strategy has been developed with the main purpose of performing a reliable relative measurement, that is, comparison of the Casimir force between different surfaces. As an example of the method, the authors estimate the accuracy and the precision of measurements performed on a Au sample.
Molecular beam epitaxy growth and characterization of self-assembled MnAs wires on highly oriented pyrolytic graphite
Authors: Hegde S. , Fraser E. , Kwon J. , Luo H.
Published: April 2010

The authors have grown MnAs on highly oriented pyrolytic graphite (HOPG), a strain-free and inert substrate, using molecular beam epitaxy. MnAs on HOPG grows in the form of particles, which self-assemble to form wirelike structures along the step edges on the HOPG surface. The MnAs particles have an average height of 42 nm and a diameter of 240 nm. Vibrating sample magnetometry studies indicate that the samples are ferromagnetic with no observable in-plane anisotropy, which is expected from a sample with a random distribution of particle orientations. Magnetic force microscopy (MFM) results indicate that the magnetic coupling between particles is less than that within each particle, and likely a dipole-dipole interaction, giving rise to magnetization patterns for the wires. Temperature dependent MFM measurements yield a Curie temperature of 330 K. Scanning tunneling microscopy and scanning tunneling spectroscopy were used to investigate the electronic density of states of MnAs, with the well-studied HOPG surface as a convenient reference.
Evolution of CASK into a Mg
2+
-Sensitive Kinase
Authors: Mukherjee Konark , Sharma Manu , Jahn Reinhard , Wahl Markus C. , Südhof Thomas C.
Published: April 2010

The atypical kinase CASK evolved from a conventional Mg
2+
-dependent kinase.
Tumor Suppression Through Metabolic Regulation
Authors: Gough Nancy R.
Published: April 2010

By inducing the expression and activity of a mitochondrial glutaminase, p53 limits reactive oxygen species production and maintains oxidative respiration.
How the Fruit Fly Got His Spots
Authors: Adler Elizabeth M.
Published: April 2010

Wingless determines the pattern of fruit fly wing pigmentation.
Substrate Selectivity and a Novel Role in Inhibitor Discrimination by Residue 237 in the KPC-2 β-Lactamase
Authors: Papp-Wallace Krisztina M. , Taracila Magdalena , Hornick John M. , Hujer Andrea M. , Hujer Kristine M. , Distler Anne M. , Endimiani Andrea , Bonomo Robert A.
Published: April 2010

β-Lactamase-mediated antibiotic resistance continues to challenge the contemporary treatment of serious bacterial infections. The KPC-2 β-lactamase, a rapidly emerging Gram-negative resistance determinant, hydrolyzes all commercially available β-lactams, including carbapenems and β-lactamase inhibitors; the amino acid sequence requirements responsible for this versatility are not yet known. To explore the bases of β-lactamase activity, we conducted site saturation mutagenesis at Ambler position 237. Only the T237S variant of the KPC-2 β-lactamase expressed in
Escherichia coli
DH10B maintained MICs equivalent to those of the wild type (WT) against all of the β-lactams tested, including carbapenems. In contrast, the T237A variant produced in
E. coli
DH10B exhibited elevated MICs for only ampicillin, piperacillin, and the β-lactam-β-lactamase inhibitor combinations. Residue 237 also plays a novel role in inhibitor discrimination, as 11 of 19 variants exhibit a clavulanate-resistant, sulfone-susceptible phenotype. We further showed that the T237S variant displayed substrate kinetics similar to those of the WT KPC-2 enzyme. Consistent with susceptibility testing, the T237A variant demonstrated a lower
k
cat
/

K
m

for imipenem, cephalothin, and cefotaxime; interestingly, the most dramatic reduction was with cefotaxime. The decreases in catalytic efficiency were driven by both elevated

K
m

values and decreased
k
cat
values compared to those of the WT enzyme. Moreover, the T237A variant manifested increased

K
i

s for clavulanic acid, sulbactam, and tazobactam, while the T237S variant displayed

K
i

s similar to those of the WT. To explain these findings, a molecular model of T237A was constructed and this model suggested that (i) the hydroxyl side chain of T237 plays an important role in defining the substrate profile of the KPC-2 β-lactamase and (ii) hydrogen bonding between the hydroxyl side chain of T237 and the

sp
2

-hybridized carboxylate of imipenem may not readily occur in the T237A variant. This stringent requirement for selected cephalosporinase and carbapenemase activity and the important role of T237 in inhibitor discrimination in KPC-2 are central considerations in the future design of β-lactam antibiotics and inhibitors.
Rapid Assessment of Antibacterial Activity against
Mycobacterium ulcerans
by Using Recombinant Luminescent Strains
Authors: Zhang Tianyu , Bishai William R. , Grosset Jacques H. , Nuermberger Eric L.
Published: April 2010

Mycobacterium ulcerans
causes Buruli ulcer, an emerging infectious disease for which antimicrobial therapy has only recently proven to be beneficial. The discovery and development of new drugs against
M. ulcerans
are severely impeded by its very slow growth. Recombinant bioluminescent strains have proven useful in drug development for other mycobacterial infections, but the ability of such strains to discriminate bacteriostatic from bactericidal activity has not been well demonstrated. We engineered recombinant
M. ulcerans
strains to express
luxAB
from
Vibrio harveyi
. In drug susceptibility tests employing a wide range of antimicrobial agents and concentrations, the relative light unit (RLU) count measured in real time was a reliable surrogate marker for CFU counts available 3 months later, indicating utility for the rapid determination of drug susceptibility and discrimination of bacteriostatic and bactericidal effects. A second important finding of this study is that the addition of subinhibitory concentrations of the ATP-binding cassette transporter inhibitor reserpine increases the susceptibility of
M. ulcerans
to tetracycline and erythromycin, indicating that drug efflux may explain at least part of the intrinsic resistance of
M. ulcerans
to these agents.
Daptomycin Is Effective for Treatment of Experimental Endocarditis Due to Methicillin-Resistant and Glycopeptide-Intermediate
Staphylococcus epidermidis
Authors: García-de-la-Mària C. , Marco F. , Armero Y. , Soy D. , Moreno A. , del Río A. , Almela M. , Cervera C. , Ninot S. , Falces C. , Mestres C. A. , Gatell J. M. , Jiménez de Anta M. T. , Miró J. M.
Published: April 2010

This study evaluated the daptomycin activity against two methicillin-resistant
Staphylococcus epidermidis
(MRSE) clinical isolates with different vancomycin susceptibilities: MRSE-375, with a vancomycin MIC of 2 μg/ml, and NRS6, a glycopeptide-intermediate
S. epidermidis
(GISE) strain with a vancomycin MIC of 8 μg/ml. The
in vivo
activity of daptomycin at two different doses (standard dose [SD-daptomycin], 6 mg/kg of body weight/day intravenously [i.v.]; high dose [HD-daptomycin], 10 mg/kg/day i.v.) was evaluated in a rabbit model of infective endocarditis and compared with that of a standard dose of vancomycin (SD-vancomycin; 1 g i.v. every 12 h) for 2 days. For the MRSE-375 strain, high-dose vancomycin (HD-vancomycin; 1 g i.v. every 6 h) was also studied. For MRSE-375, SD- and HD-daptomycin therapy sterilized significantly more vegetations than SD-vancomycin therapy (9/15 [60%] and 11/15 [73%] vegetations, respectively, versus 3/16 [19%] vegetations;
P
= 0.02 and
P
= 0.002, respectively). HD-daptomycin sterilized more vegetations than HD-vancomycin (11/15 [73%] versus 5/15 [33%] vegetations;
P
= 0.03) and was more effective than SD- and HD-vancomycin in reducing the density of bacteria in valve vegetations (0 log
10
CFU/g vegetation [interquartile range {IQR}, 0 to 1 log
10
CFU/g vegetation] versus 2 log
10
CFU/g vegetation [IQR, 2 to 2 log
10
CFU/g vegetation] and 2 log
10
CFU/g vegetation [IQR, 0 to 2.8 log
10
CFU/g vegetation];
P
= 0.002 and
P
= 0.01, respectively). For the NRS6 strain, SD- and HD-daptomycin were significantly more effective than vancomycin in reducing the density of bacteria in valve vegetations (3.7 log
10
CFU/g vegetation [IQR, 2 to 6 log
10
CFU/g vegetation] versus 7.1 log
10
CFU/g vegetation [IQR, 5.2 to 8.5 log
10
CFU/g vegetation];
P
= 0.02). In all treatment arms, isolates recovered from vegetations remained susceptible to daptomycin and vancomycin and had the same MICs. In conclusion, daptomycin at doses of 6 mg/kg/day or 10 mg/kg/day is more effective than vancomycin for the treatment of experimental endocarditis due to MRSE and GISE.
Deamplification of
pfmdr1
-Containing Amplicon on Chromosome 5 in
Plasmodium falciparum
Is Associated with Reduced Resistance to Artelinic Acid
In Vitro
Authors: Chen Nanhua , Chavchich Marina , Peters Jennifer M. , Kyle Dennis E. , Gatton Michelle L. , Cheng Qin
Published: April 2010

Amplification of the
Plasmodium falciparum
multidrug resistance 1 gene (
pfmdr1
) has been implicated in multidrug resistance, including
in vitro
resistance to artelinic acid (AL). The stability and fitness of having multiple copies of
pfmdr1
are important factors due to their potential effects on the resistance phenotype of parasites. These factors were investigated by using an AL-resistant line of
P. falciparum
(W2AL80) and clones originating from W2AL80. A rapid reduction in
pfmdr1
copy number (CN) was observed in the uncloned W2AL80 line; 63% of this population reverted to a CN of <3 without exposure to the drug. Deamplification of the
pfmdr1
amplicon was then determined in three clones, each initially containing three copies of
pfmdr1
. Interestingly, two outcomes were observed during 3 months without drug pressure. In one clone, parasites with fewer than 3 copies of
pfmdr1
emerged rapidly. In two other clones, the reversion was significantly delayed. In all subclones, the reduction in
pfmdr1
CN involved the deamplification of the entire amplicon (19 genes). Importantly, deamplification of the
pfmdr1
amplicon resulted in partial reversal of resistance to AL and increased susceptibility to mefloquine. These results demonstrate that multiple copies of the
pfmdr1
-containing amplicon in AL-resistant parasites are unstable when drug pressure is withdrawn and have practical implications for the maintenance and spread of parasites resistant to artemisinin derivatives.
Optimal CD8 T-Cell Response againstEncephalitozoon cuniculiIs Mediated by Toll-Like Receptor 4 Upregulation by Dendritic Cells
Authors: Lawlor Elizabeth M. , Moretto Magali M. , Khan Imtiaz A.
Published: April 2010

CD8+T-cell immunity has been shown to play an important role in the protective immune response againstEncephalitozoon cuniculi. Although earlier studies suggest that dendritic cells (DC) are important for the induction of this response, the factors responsible for initiation of the dendritic cell response against this pathogen have not been evaluated. In the current study, we demonstrate thatE. cuniculiinfection causes strong Toll-like receptor 4 (TLR4)-dependent dendritic cell activation and a blockade of this molecule reduces the ability of DC to prime an antigen-specific CD8+T-cell response. Pretreatment of DC with anti-TLR4 antibody causes a defect in bothin vitroandin vivoCD8+T-cell priming. These findings, for the first time, emphasize the contribution of TLR4 in the induction of CD8+T-cell immunity againstE. cuniculiinfection.
Pertactin Is Required forBordetellaSpecies To Resist Neutrophil-Mediated Clearance
Authors: Inatsuka Carol S. , Xu Qian , Vujkovic-Cvijin Ivan , Wong Sandy , Stibitz Scott , Miller Jeff F. , Cotter Peggy A.
Published: April 2010

Pertactin (PRN) is an autotransporter protein produced by all members of theBordetella bronchisepticacluster, which includesB. pertussis,B. parapertussis, andB. bronchiseptica. It is a primary component of acellular pertussis vaccines, and anti-PRN antibody titers correlate with protection.In vitrostudies have suggested that PRN functions as an adhesin and that an RGD motif located in the center of the passenger domain is important for this function. Two regions of PRN that contain sequence repeats (region 1 [R1] and R2) show polymorphisms among strains and have been implicated in vaccine-driven evolution. We investigated the role of PRN in pathogenesis usingB. bronchisepticaand natural-host animal models. A Δprnmutant did not differ from wild-typeB. bronchisepticain its ability to adhere to epithelial and macrophage-like cellsin vitroor to establish respiratory infection in rats but was cleared much faster than wild-type bacteria in a mouse lung inflammation model. Unlike wild-typeB. bronchiseptica, the Δprnmutant was unable to cause a lethal infection in SCID-Bg mice, but, like wild-type bacteria, it was lethal for neutropenic mice. These results suggest that PRN plays a critical role in allowingBordetellato resist neutrophil-mediated clearance. Mutants producing PRN proteins in which the RGD motif was replaced with RGE or in which R1 and R2 were deleted were indistinguishable from wild-type bacteria in all assays, suggesting that these sequences do not contribute to PRN function.
Safety of ProbioticEscherichia coliStrain Nissle 1917 Depends on Intestinal Microbiota and Adaptive Immunity of the Host
Authors: Gronbach Kerstin , Eberle Ute , Müller Martina , Ölschläger Tobias A. , Dobrindt Ulrich , Leithäuser Frank , Niess Jan Hendrik , Döring Gerd , Reimann Jörg , Autenrieth Ingo B. , Frick Julia-Stefanie
Published: April 2010

Probiotics are viable microorganisms that are increasingly used for treatment of a variety of diseases. Occasionally, however, probiotics may have adverse clinical effects, including septicemia. Here we examined the role of the intestinal microbiota and the adaptive immune system in preventing translocation of probiotics (e.g.,EscherichiacoliNissle). We challenged C57BL/6J mice raised under germfree conditions (GF-raised C57BL/6J mice) andRag1−/−mice raised under germfree conditions (GF-raisedRag1−/−mice) and under specific-pathogen-free conditions (SPF-raisedRag1−/−mice) with probioticE. colistrain Nissle 1917, strain Nissle 1917 mutants, the commensal strainE. colimpk, orBacteroides vulgatusmpk. Additionally, we reconstitutedRag1−/−mice with CD4+T cells.E. colitranslocation and dissemination and the mortality of mice were assessed. In GF-raisedRag1−/−mice, but not in SPF-raisedRag1−/−mice or GF-raised C57BL/6J mice, oral challenge withE. colistrain Nissle 1917, but not oral challenge withE. colimpk, resulted in translocation and dissemination. The mortality rate was significantly higher forE. colistrain Nissle 1917-challenged GF-raisedRag1−/−mice (100%;P< 0.001) than forE. colistrain Nissle 1917-challenged SPF-raisedRag1−/−mice (0%) and GF-raised C57BL/6J mice (0%). Translocation of and mortality due to strainE. coliNissle 1917 in GF-raisedRag1−/−mice were prevented when mice were reconstituted with T cells prior to strainE. coliNissle 1917 challenge, but not when mice were reconstituted with T cells afterE. colistrain Nissle 1917 challenge. Cocolonization experiments revealed thatE. colimpk could not prevent translocation of strainE. coliNissle 1917. Moreover, we demonstrated that neither lipopolysaccharide structure nor flagella play a role inE. colistrain Nissle 1917 translocation and dissemination. Our results suggest that if both the microbiota and adaptive immunity are defective, translocation across the intestinal epithelium and dissemination of the probioticE. colistrain Nissle 1917 may occur and have potentially severe adverse effects. Future work should define the possibly related molecular factors that promote probiotic functions, fitness, and facultative pathogenicity.
NalP-Mediated Proteolytic Release of Lactoferrin-Binding Protein B from the Meningococcal Cell Surface
Authors: Roussel-Jazédé Virginie , Jongerius Ilse , Bos Martine P. , Tommassen Jan , van Ulsen Peter
Published: April 2010

Bacteria have developed several mechanisms for iron uptake during colonization of mammalian hosts, where the availability of free iron is limiting for growth.
Neisseria meningitidis
expresses under iron-limiting conditions a receptor complex consisting of the lactoferrin-binding proteins A (LbpA) and LbpB to acquire iron from lactoferrin, which is abundantly present on the mucosal surfaces of the human nasopharynx. LbpA is an integral outer membrane-embedded iron transporter, whereas LbpB is a cell surface-exposed lipoprotein. In this study, we demonstrate that LbpB is also released into the culture medium. We identified NalP, an autotransporter known to be involved in the processing of other autotransporters, as the protease responsible for LbpB release. This release of LbpB reduced the complement-mediated killing of the bacteria when incubated with an LbpB-specific bactericidal antiserum. Since antibodies directed against LbpB are found in convalescent-patient sera, the release of an immunogenic protein as LbpB may represent a novel means for
N. meningitidis
to escape the human immune response.
Comparison of the Moonlighting Actions of the Two Highly Homologous Chaperonin 60 Proteins of
Mycobacterium tuberculosis
Authors: Cehovin Ana , Coates Anthony R. M. , Hu Yanmin , Riffo-Vasquez Yanira , Tormay Peter , Botanch Catherine , Altare Frederic , Henderson Brian
Published: April 2010

Evidence is emerging that the two chaperonin (Cpn) 60 proteins of
Mycobacterium tuberculosis
, Cpn60.1 and Cpn60.2, have moonlighting actions that may contribute to the pathology of tuberculosis. We studied the release of Cpn60.1 from
M. tuberculosis
and infected macrophagelike cells and compared recombinant Cpn60.1 and Cpn60.2 in a range of cell-based assays to determine how similar the actions of these highly homologous proteins are. We now establish that Cpns are similar as follows: (i) Cpn60.1, as it has been shown for Cpn60.2, is released by
M. tuberculosis
in culture, and Cpn60.1 is furthermore released when the bacterium is in quiescent, but not activated, macrophagelike cells, and (ii) both proteins only showed a partial requirement for MyD88 for the induction of proinflammatory cytokine production compared to lipopolysaccharide. However, we also found major differences in the cellular action of Cpns. (i) Cpn60.2 proved to be a more potent stimulator of whole blood leukocytes than Cpn60.1 and was the only one to induce tumor necrosis factor alpha synthesis. (ii) Cpn60.1 bound to ca. 90% of circulating monocytes compared to Cpn60.2, which bound <50% of these cells. Both chaperonins bound to different cell surface receptors, while monocyte activation by both proteins was completely abrogated in TLR4
−/−
mice, although Cpn60.2 also showed significant requirement for TLR2. Finally, an isogenic mutant lacking
cpn60.1
, but containing intact
cpn60.2
, was severely inhibited in generating multinucleate giant cells in an
in vitro
human granuloma assay. These results clearly show that, despite significant sequence homology,
M. tuberculosis
Cpn60 proteins interact in distinct ways with human or murine macrophages.
Performance of an Enzyme-Linked Immunosorbent Assay for Detection of
Clonorchis sinensis
Infestation in High- and Low-Risk Groups
Authors: Kim Young Jin , Lee Sun Min , Choi Go Eun , Hwang Sang Hyun , Kim Hyung Hoi , Lee Eun Yup , Chang Chulhun L.
Published: April 2010

Clonorchis sinensis
is still a common parasite in South Korea. An enzyme-linked immunosorbent assay (ELISA) was developed to replace the usual intradermal test, and its performance in an area of endemicity was evaluated. From 2004 to 2006, 182 adults were included. The patient group consisted of 51 adults; 43 patients showed fluke eggs by microscopy, and 8 had their disease diagnosed clinically. The negative-control group included 131 adults: 98 at low risk and 33 at high risk of infestation. Both intradermal testing and ELISA were performed for all patients, and the sensitivity and specificity were evaluated. Statistical analysis for specificity looked at two groups: those at high risk and those at low risk. The sensitivity of the
C. sinensis
ELISA was 80.4%, while that of the intradermal test was 56.9% (
P
= 0.019). The specificities of the
C. sinensis
ELISA in the low-risk and high-risk groups were 93.9% and 33.3%, respectively, while those of the intradermal test were 85.7% and 30.3%, respectively (
P
= 0.0968,
P
= 0.9979). The
C. sinensis
ELISA may be more useful than the intradermal test; however, because of its low specificity, it may not be used independently for the diagnosis of
C. sinensis
infestation or a prevalence survey in a high-risk group.
BREAST IMAGING SYSTEMS: A REVIEW AND COMPARATIVE STUDY
Authors: SREE S. VINITHA , NG EDDIE Y.-K. , ACHARYA U RAJENDRA , TAN WILLIAM
Published: April 2010

Due to the successful union between computational technologies and basic laws of physics and biological sciences, many biomedical imaging systems now find significant presence in clinical settings, aiding physicians in diagnosing most forms of human illness with more confidence. In the case of breast imaging, apart from the basic diagnosis, these imaging systems also help in locating the abnormal tissues for biopsy, identifying the exact margins of the lesion for good lumpectomy results, staging and restaging the cancer, detecting locations of metastases, and planning and following up treatment protocols. It is well known that early detection of cancer is the only way to increase the survival rate of the patient. Without such imaging systems, it would be hard and almost impossible for the physicians to determine the nature and extent of the disease by merely simple physical examinations and biopsies. This article presents a description of most of these invaluable breast-imaging systems. Moreover, a comparison of these modalities and a review of a few of the developments these devices have come across over the years are also given.
Great computing museums of the world, part two
Authors: Aspray William
Published: April 2010

The second of a two-part series highlighting several of the world's museums dedicated to preserving, exhibiting, and elucidating computing history.
Puzzled: Variations on the Ham Sandwich Theorum
Authors: Winkler Peter
Published: April 2010

Welcome to three new puzzles. Solutions to the first two will be published next month; the third is (as yet) unsolved. In each, the issue is how your intuition matches up with the mathematics.