bluuebunny/crossref_metadata_2025 huggingface dataset:
Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants
Authors: Gompert Zachariah , Lucas Lauren K. , Buerkle C. Alex , Forister Matthew L. , Fordyce James A. , Nice Chris C.
Published: May 2014

Detailed information about the geographic distribution of genetic and genomic variation is necessary to better understand the organization and structure of biological diversity. In particular, spatial isolation within species and hybridization between them can blur species boundaries and create evolutionary relationships that are inconsistent with a strictly bifurcating tree model. Here, we analyse genome‐wide DNA sequence and genetic ancestry variation in Lycaeides butterflies to quantify the effects of admixture and spatial isolation on how biological diversity is organized in this group. We document geographically widespread and pervasive historical admixture, with more restricted recent hybridization. This includes evidence supporting previously known and unknown instances of admixture. The genome composition of admixed individuals varies much more among than within populations, and tree‐ and genetic ancestry‐based analyses indicate that multiple distinct admixed lineages or populations exist. We find that most genetic variants in Lycaeides are rare (minor allele frequency <0.5%). Because the spatial and taxonomic distributions of alleles reflect demographic and selective processes since mutation, rare alleles, which are presumably younger than common alleles, were spatially and taxonomically restricted compared with common variants. Thus, we show patterns of genetic variation in this group are multifaceted, and we argue that this complexity challenges simplistic notions concerning the organization of biological diversity into discrete, easily delineated and hierarchically structured entities.
Growth with Unused Capacity and Endogenous Capital Depreciation
Authors: Patriarca Fabrizio , Sardoni Claudio
Published: May 2014

The paper contributes to the debate on growth and distribution in a non‐mainstream perspective. It looks at the role that capacity utilization plays in the process of growth under the hypothesis that the rate of capital depreciation is a function of the degree of capacity utilization. Our hypothesis implies results partly different from those obtained by other models in which capacity utilization plays a key role. In particular, a varying rate of depreciation affects the conditions under which distributional changes in favor of wages affect the rate of growth positively.
Xanthomonas campestris RpfB is a fatty Acyl‐CoA ligase required to counteract the thioesterase activity of the RpfF diffusible signal factor (DSF) synthase
Authors: Bi Hongkai , Yu Yonghong , Dong Huijuan , Wang Haihong , Cronan John E.
Published: May 2014

In Xanthomonas campestris pv. campestris (Xcc), the proteins encoded by the rpf (regulator of pathogenicity factor) gene cluster produce and sense a fatty acid signal molecule called diffusible signalling factor (DSF, 2(Z)‐11‐methyldodecenoic acid). RpfB was reported to be involved in DSF processing and was predicted to encode an acyl‐CoA ligase. We report that RpfB activates a wide range of fatty acids to their CoA esters in vitro. Moreover, RpfB can functionally replace the paradigm bacterial acyl‐CoA ligase, Escherichia coli FadD, in the E. coli ß‐oxidation pathway and deletion of RpfB from the Xcc genome results in a strain unable to utilize fatty acids as carbon sources. An essential RpfB function in the pathogenicity factor pathway was demonstrated by the properties of a strain deleted for both the rpfB and rpfC genes. The ΔrpfB ΔrpfC strain grew poorly and lysed upon entering stationary phase. Deletion of rpfF, the gene encoding the DSF synthetic enzyme, restored normal growth to this strain. RpfF is a dual function enzyme that synthesizes DSF by dehydration of a 3‐hydroxyacyl‐acyl carrier protein (ACP) fatty acid synthetic intermediate and also cleaves the thioester bond linking DSF to ACP. However, the RpfF thioesterase activity is of broad specificity and upon elimination of its RpfC inhibitor RpfF attains maximal activity and its thioesterase activity proceeds to block membrane lipid synthesis by cleavage of acyl‐ACP intermediates. This resulted in release of the nascent acyl chains to the medium as free fatty acids. This lack of acyl chains for phospholipid synthesis results in cell lysis unless RpfB is present to counteract the RpfF thioesterase activity by catalysing uptake and activation of the free fatty acids to give acyl‐CoAs that can be utilized to restore membrane lipid synthesis. Heterologous expression of a different fatty acid activating enzyme, the Vibrio harveyi acyl‐ACP synthetase, replaced RpfB in counteracting the effects of high level RpfF thioesterase activity indicating that the essential role of RpfB is uptake and activation of free fatty acids.
Memory deficits correlate with tau and spine pathology in P301S MAPT transgenic mice
Authors: Xu Hong , Rösler Thomas W. , Carlsson Thomas , de Andrade Anderson , Bruch Julius , Höllerhage Matthias , Oertel Wolfgang H. , Höglinger Günter U.
Published: May 2014

Aim

P301S MAPT transgenic mice (P301S mice) are a widely used model of frontotemporal dementia and parkinsonism linked to chromosome 17 with tau pathology (FTDP‐17‐tau). However, a systematic correlation between cognitive deficits and cellular tau pathology at different ages is still missing. Therefore, our study investigated memory deficits of P301S mice in relation to pathological tau species and dendritic spine pathology throughout adulthood.

Methods

We analysed P301S mice behaviourally with the novel open field, rotarod, and Morris water maze tests to measure deficits in locomotion, balance and cognition, respectively; immunohistochemically with different tau antibodies for specific tau species; and with Golgi staining for dendritic spine pathology.

Results

We confirmed the occurrence of locomotor deficits at an age of 5 months and newly report memory deficits from 2.5 months of age onwards. At this early age, MC1 and CP13, but not AT180 immunoreactivity, was prominent in the hippocampus of P301S mice. Neuronal cell loss in the hippocampus of P301S mice was not observed to occur till 6 months of age. However, there was a significant reduction in the density of dendritic spines from young adulthood onwards in hippocampal pyramidal neurones.

Conclusion

In P301S mice, memory deficits precede the onset of locomotor dysfunction and coincide with the appearance of conformationally changed, S202‐phosphorylated tau and reduced spine density in the absence of neuronal cell loss in the hippocampus. Our finding provides insights into the toxic effects of different tau species in vivo and may facilitate the development of new therapies against neurodegenerative tauopathies.
Investigation of a freshwater acrochaetioid alga (Rhodophyta) with molecular and morphological methods
Authors: Chen Le , Feng Jia , Han Xiao‐Jing , Xie Shu‐Lian
Published: May 2014

An enigmatic acrochaetioid alga was collected from Niangziguan spring in Shanxi Province, northern China. Morphological data indicated that this alga reproduces exclusively asexually by monosporangia and its morphological characteristics suggested that it might be referred to Audouinella heterospora. To ascertain its phylogenetic position, phylogenetic trees were reconstructed using partial sequences of the plastid‐encoded gene (rbcL) and the nuclear‐encoded gene (SSU rDNA) applying Bayesian inference (BI), maximum parsimony (MP) and maximum likelihood (ML). However, phylogenetic reconstructions showed that this acrochaetioid alga does not belong in a clade with the genus Audouinella, but forms a clade with Thorea hispida (Thoreales). Based on this analysis it is concluded that A. heterospora represents the ‘chantransia’ stage of T. hispida.
Glochidion kingii sp. nov. (Phyllanthaceae) from Saddle Peak National Park, Andaman and Nicobar Islands, India
Authors: Venkat Ramana M. , Sanjappa M. , Venu P. , Chorghe Alok
Published: May 2014

Glochidion kingii M. V. Ramana, Sanjappa, Venu & Alok Chorghe, a new species from the scrub forests of North Andaman Islands, is described and illustrated. Its morphological similarities/dissimilarities in relation to G. rubrum Blume from the Malay Peninsula and Sumatra is discussed and information about the distribution and conservation status for the new species is provided.
The putative Agrobacterium transcriptional activator‐like virulence protein VirD5 may target T‐complex to prevent the degradation of coat proteins in the plant cell nucleus
Authors: Wang Yafei , Peng Wei , Zhou Xu , Huang Fei , Shao Lingyun , Luo Meizhong
Published: May 2014

Agrobacterium exports at least five virulence proteins (VirE2, VirE3, VirF, VirD2, VirD5) into host cells and hijacks some host plant factors to facilitate its transformation process.

Random DNA binding selection assays (RDSAs), electrophoretic mobility shift assays (EMSAs) and yeast one‐hybrid systems were used to identify protein‐bound DNA elements. Bimolecular fluorescence complementation, glutathione S‐transferase pull‐down and yeast two‐hybrid assays were used to detect protein interactions. Protoplast transformation, coprecipitation, competitive binding and cell‐free degradation assays were used to analyze the relationships among proteins.

We found that Agrobacterium VirD5 exhibits transcriptional activation activity in yeast, is located in the plant cell nucleus, and forms homodimers. A specific VirD5‐bound DNA element designated D5RE (VirD5 response element) was identified. VirD5 interacted directly with Arabidopsis VirE2 Interacting Protein 1 (AtVIP1). However, the ternary complex of VirD5–AtVIP1–VirE2 could be detected, whereas that of VirD5–AtVIP1–VBF (AtVIP1 Binding F‐box protein) could not. We demonstrated that VirD5 competes with VBF for binding to AtVIP1 and stabilizes AtVIP1 and VirE2 in the cell‐free degradation system.

Our results indicated that VirD5 may act as both a transcriptional activator‐like effector to regulate host gene expression and a protector preventing the coat proteins of the T‐complex from being quickly degraded by the host's ubiquitin proteasome system (UPS).
Powers, Non‐Consent and Freedom
Authors: Mumford Stephen , Anjum Rani Lill
Published: May 2014

There are a number of dispositionalist solutions to the free will problem based on freedom consisting in the agent's exercise of a power. But if a subject a is free when they exercise their power P, there is an objection to be overcome from the possibility of power implantation. A brainwasher, rather than directly manipulating a subject's movements, can instead implant in them a desire, to be understood as a disposition to act, and allow the subject to exercise such a power. It seems that, according to the dispositionalist theory of freedom, such an agent would still count as acting freely. There is a strong non‐consent intuition that a is not free in such a case because they did not consent to having the power P—the desire in question. Filling out this intuition is not straightforward. But it can be done in terms of the exercise of P being regulated by higher‐order powers of self‐reflection. Such regulation is what allows an agent to either take ownership of a power or to reject it.
Imaginative Attitudes
Authors: Langland‐Hassan Peter
Published: May 2014

The point of this paper is to reveal a dogma in the ordinary conception of sensory imagination, and to suggest another way forward. The dogma springs from two main sources: a too close comparison of mental imagery to perceptual experience, and a too strong division between mental imagery and the traditional propositional attitudes (such as belief and desire). The result is an unworkable conception of the correctness conditions of sensory imaginings—one lacking any link between the conditions under which an imagining aids human action and inference and the conditions under which it is veridical. The proposed solution is, first, to posit a variety ofimaginative attitudes—akin to the traditional propositional attitudes—which have different associated correctness (or satisfaction) conditions. The second part of the solution is to allow for imaginings with “hybrid” contents, in the sense that both mental images and representations with language‐like constituent structure contribute to the content of imaginings.
A new look at the corporate capability of personalized medicine development in the pharmaceutical industry
Authors: Haruya Mei , Kano Shingo
Published: May 2014

Despite the recent rise in academic and practitioner interest in the development of personalized medicine in the pharmaceutical industry, no study has yet assessed the corporate capability of such development. This study thus develops a model to illustrate the corporate capability of personalized medicine development (PMD capability) in the pharmaceutical industry. First, we define three key influencing factors for PMD capability, namely new product development (NPD) capability, External drug–CoDx co‐development (CoDxD) capability [i.e. the capability of drug–CoDx (companion diagnostics) co‐development with external companies], and Internal CoDxD capability (i.e. the capability of drug–CoDx co‐development with an internal organization). Then, a research model is developed, and by carrying out a structural equation modeling analysis, we successfully find a good fit of the model and that the critical path to contribute to PMD capability runs from NPD capability via External CoDxD capability rather than via Internal CoDxD capability.
Novel applications of fluid inclusions and isotope geochemistry in unravelling the genesis of fossil travertine systems
Authors: Desouky Hamdy El , Soete Jeroen , Claes Hannes , Özkul Mehmet , Vanhaecke Frank , Swennen Rudy
Published: May 2014

The Denizli Basin is a fault‐bounded Neogene–Quaternary depression located in the Western Anatolian Extensional Province, Western Turkey. The basin is a unique geological site with abundant active and fossil (Quaternary) travertine and tufa deposits. Fluid inclusion microthermometry and isotopic analysis were applied to study the genesis of the Ballık fossil travertine deposits, located in the south‐eastern part of the basin. Microthermometry on fluid inclusions indicates that the main travertine precipitating and cementing fluids are characterized by low salinity (<0·7 wt% NaCl equivalent) and variable temperatures that cluster at <50°C and ca 100°C. Fluids of meteoric origin have been heated by migration to the deeper subsurface, possibly in a local high geothermal gradient setting. A later uncommon cementation phase is related to a fluid with a significantly higher salinity (25·5 to 26·0 wt% bulk). The fluid obtained its salinity by interaction with Late Triassic evaporite layers. Strontium isotopes indicate that the parent carbonate source rock of the different travertine precipitates is very likely to be the Triassic limestone of the Lycian Nappes. Carbon isotopes suggest that the parent CO2 gas originated from thermal decarbonation of the Lycian limestones with minor contributions of magmatic degassing and organic soil CO2. Oxygen isotopes confirm the meteoric origin of the fluids and indicate disequilibrium precipitation because of evaporation and degassing. Results were integrated within the available geological data of the Denizli Basin in a generalized travertine precipitation model, which enhanced the understanding of fossil travertine systems. The study highlights the novel application of fluid inclusion research in unravelling the genesis of continental carbonates and provides several recommendations for hydrocarbon exploration in travertine‐bearing sedimentary basins. The findings suggest that travertine bodies and their parent carbonate source rocks have the potential to constitute interesting subsurface hydrocarbon reservoirs.
Documenting, Dramatizing, and Representing China's Porcelain World in Broken Pots Broken Dreams
Authors: Gillette Maris
Published: May 2014

In this essay, I argue that a successful ethnographic film, like a good story, responds both to its film subjects and to its audience's expectations. I discuss why I made a film about Jingdezhen's porcelain workers (as opposed to a text) and the relationships, goals, ideas, and constraints that influenced the final film. I contextualize my process in a broader discussion of documentary and ethnographic filmmaking, looking at representation in documentary, sensory anthropology, and the conventions of Western dramatic writing.
IMAGING DIAGNOSIS—DISSEMINATED PERITONEAL LEIOMYOMATOSIS IN A DOG
Authors: Isaac Markay L. , Spaulding Kathy A. , Goodrich Zachary J.
Published: May 2014

A 17‐month‐old male Labrador retriever presented for evaluation of an abdominal mass felt during abdominal palpation. Multiple variably sized cystic masses were identified on sonographic and radiographic images. Exploratory laparotomy revealed multiple peritoneal masses that exhibited atypical contractions and lacked an identifiable organ of origin. Histology and immunohistochemistry of multiple surgically excised masses was consistent with benign tumors of smooth muscle origin (leiomyomas). The presence of multiple peritoneal leiomyomas in this dog is consistent with disseminated peritoneal leiomyomatosis. Two years after diagnosis and multiple surgical interventions, continual insidious enlargement of leiomyomas was identified on ultrasound and CT.
The biochemical relationships in anaerobic digestion after thermal hydrolysis at Davyhulme
Authors: Jolly Martin , Belshaw Dave , Telfer Jack
Published: May 2014

The commissioning of the largest thermal hydrolysis plant in the world at Davyhulme, Manchester involved detailed analysis of the digestion process. The plant consists of eight digesters, 20 thermal hydrolysis reactors and a maximum throughput of 121 000 tDS/year.

The plant was converted from conventional digestion with a loading rate of 1.25 kgVS/m3/day to digestion fed with thermally hydrolysed sludge with a loading rate of 4.16 kgVS/m3/day. At the start of the commissioning and ramp‐up of the loading rate, control actions were based on acid/alkalinity, pH and foaming; however, it was found that the methane concentration was the parameter that changed quickest during digester instability. The monitoring was changed during commissioning to use methane concentration as the primary control parameter.

It was found that the rate of increased organic loading is dependent on the availability of seed biomass already acclimatised to thermally hydrolysed feed sludge and the presence of a high alkalinity buffer.
Journal Bearing Stiffness and Damping Coefficients Using Nanomagnetorheological Fluids and Stability Analysis
Authors: Bompos D. A. , Nikolakopoulos P. G.
Published: May 2014

The integrity and reliability of a rotor depend significantly on the dynamic characteristics of its bearings. Bearing design has evolved in many ways in order to achieve higher damping and stiffness. A promising field in terms of vibrations control and overall performance improvement for the journal bearings is the use of smart lubricants. Smart lubricants are fluids with controllable properties. A suitable excitation, such as an electric or a magnetic field, is applied to the lubricant volume and changes its properties. Magnetorheological (MR) fluids consist one category of lubricants with controllable properties. Magnetic particles inside the MR fluid volume are coerced by a magnetic field. These particles form chains which hinder the flow of the base fluid and alter its apparent viscosity. According to the magnetic particle size, there are two subcategories of magnetorheological fluids: the regular MR fluids with particles sizing some tens of micrometers and the nanomagnetorheological (NMR) fluids with a particle size of a few nanometers. The change of magnetorheological fluid's viscosity is an efficient way of control of the dynamic characteristics of the journal bearing system. In this work, the magnetic field intensity inside the volume of lubricant is calculated through finite element analysis. The calculated value of the magnetic field intensity is used to define the apparent viscosity of both the MR and the NMR fluids. Using computational fluid dynamics (CFD) method, the pressure developed inside the journal bearing is found. Through this simulation with the use of a suitable algorithm, the stiffness and damping coefficients are calculated and stability charts of Newtonian, MR, and NMR fluid are presented and discussed.
Elastohydrodynamic Lubrication Analysis of Point Contacts With Consideration of Material Inhomogeneity
Authors: Shengguang Zhang , Wenzhong Wang , Ziqiang Zhao
Published: May 2014

Inhomogeneities in matrix may significantly affect the performance of mechanical elements, such as possible fatigue life reduction for rolling bearing due to stress concentration induced by inhomogeneities; on the other hand, most components operate under lubrication environment. So far the numerical algorithms to solve lubrication problems without the consideration of inhomogeneities or inclusions are well developed. In this paper, the combination of elastohydrodynamic lubrication (EHL) and inclusion problem is realized to consider the effect of material inhomogeneity on the lubrication performance and subsurface stress distribution, etc. The matrix inhomogeneity will induce disturbed displacement, which will modify the film thickness and consequently result in the change of lubricated contact pressure distribution, etc. The matrix inhomogeneity is treated as the homogeneous inclusion with equivalent eigenstrain according to equivalent inclusion method (EIM), and the disturbed displacement is calculated by semi-analytical method (SAM). While the pressure and film thickness distributions are obtained by solving Reynolds equation. The iterative process is realized to consider the interaction between lubrication behavior and material response. The results show the inhomogeneity in contacting body will greatly influence the lubricated contact performance. The influences are different between compliant and stiff inhomogeneity. It is also found that different sizes and positions of inhomogeneity can significantly affect the contact characteristic parameters.
Generation of High-Intensity Focused Ultrasound by Carbon Nanotube Opto-Acoustic Lens
Authors: Tong L. H. , Lim C. W. , Li Y. C.
Published: May 2014

A new model of high-intensity focused ultrasound generation by radiation from a composite nanothinfilm made of carbon nanotubes (CNTs) and elastomeric polymer is presented in this paper. The composite nanothinfilm is deposited to the surface of a concave lens and the performance of focused ultrasound generated by an incident pulsed laser onto the lens is analyzed. The analysis and results are verified by comparing with published experimental data and very good agreement is recorded. The opto-acoustic pressure on the symmetric axis and the lateral focal plane are investigated analytically and the result indicates that excellent acoustic performance is found to be present in the vicinity of the focus region. The temporal performance of the focused lens is also investigated both at the focal point and the prefocal zone and very good agreement comparing with experiment is obtained. Conclusively, it is demonstrated theoretically that there exists an optimal input frequency for a pulsed laser at which the performance of the focused lens can be tremendously enhanced. In general, this new analytical model provides new guidelines in the design of high-intensity ultrasound lens, hence opening up promising applications to medical ultrasonography treatment.
Bifurcation Analysis of Forming Limits for an Orthotropic Sheet Metal
Authors: Li Shuhui , He Ji , Cedric Xia Z. , Zeng Danielle , Hou Bo
Published: May 2014

A bifurcation analysis of forming limits for an orthotropic sheet metal is presented in this paper. The approach extends Stören and Rice's (S–R) bifurcation analysis for isotropic materials, with materials following a vertex theory of plasticity at the onset of localized necking. The sheet orthotropy is represented by the Hill’48 yield criterion with three r-values in the rolling (r0), the transverse (r90) and the diagonal direction (r45). The emphasis of the study is on the examination of r-value effect on the sheet metal forming limit, expressed as a combination of the average r-value raverage and the planar anisotropy (Δr). Forming limits under both zero extension assumption and minimum extension assumption as well as necking band orientation evolution are investigated in detail. The comparison between the experimental result and predicted forming limit diagram (FLD) is presented to validate the extended bifurcation analysis. The r-value effect is observed under uniaxial and equal-biaxial loadings. However, no difference is found under plane strain condition in strain-based FLD which is consistent with Hill's theory. The force maximum criterion is also used to analyze FLD for verification.
Laser-induced acoustic point source for accurate impulse response measurements within the audible bandwidth
Authors: Gómez Bolaños Javier , Delikaris-Manias Symeon , Pulkki Ville , Eskelinen Joona , Hæggström Edward
Published: May 2014

Laser induced air breakdown is proposed as a sound source for accurate impulse response measurements. Within the audible bandwidth, the source is repeatable, broadband, and omnidirectional. The applicability of the source was evaluated by measuring the impulse response of a room. The proposed source provides a more accurate temporal and spatial representation of room reflections than conventional loudspeakers due to its omnidirectionality, negligible size and short pulse duration.
Driving Convergence with Human Diversity
Authors: DeSimone Joseph M. , Farrell Crista L.
Published: May 2014

Convergent science will require human diversity—individuals with different backgrounds and life experiences—to drive it forward.
Tumor Archaeology: Tracking Leukemic Evolution to Its Origins
Authors: Dick John E.
Published: May 2014

Unearthing of the BRAF mutation in hematopoietic stem cells reveals an unexpected origin for a mature B cell malignancy and a new therapeutic target.
Angiotensin Blockade—A Double-Edged Sword in Renal Failure
Authors: Chitalia Vipul
Published: May 2014

Angiotensin receptor suppression in macrophages infiltrating damaged kidneys exacerbates renal fibrosis.
A Maternal Microbial Gift for the Baby
Authors: Dela Cruz Charles S.
Published: May 2014

Alteration of the neonatal gut microbiome with antibiotics can impair neutrophil function and increase susceptibility to bacterial sepsis.
Bordetella pertussis Lipid A Glucosamine Modification Confers Resistance to Cationic Antimicrobial Peptides and Increases Resistance to Outer Membrane Perturbation
Authors: Shah Nita R. , Hancock Robert E. W. , Fernandez Rachel C.
Published: May 2014

Bordetella pertussis
, the causative agent of whooping cough, has many strategies for evading the human immune system. Lipopolysaccharide (LPS) is an important Gram-negative bacterial surface structure that activates the immune system via Toll-like receptor 4 and enables susceptibility to cationic antimicrobial peptides (CAMPs). We show modification of the lipid A region of LPS with glucosamine increased resistance to numerous CAMPs, including LL-37. Furthermore, we demonstrate that this glucosamine modification increased resistance to outer membrane perturbation.
Activity of Daptomycin or Linezolid in Combination with Rifampin or Gentamicin against Biofilm-Forming Enterococcus faecalis or E. faecium in an
In Vitro
Pharmacodynamic Model Using Simulated Endocardial Vegetations and an
In Vivo
Survival Assay Using Galleria mellonella Larvae
Authors: Luther Megan K. , Arvanitis Marios , Mylonakis Eleftherios , LaPlante Kerry L.
Published: May 2014

Enterococci are the third most frequent cause of infective endocarditis. A high-inoculum stationary-phase
in vitro
pharmacodynamic model with simulated endocardial vegetations was used to simulate the human pharmacokinetics of daptomycin at 6 or 10 mg/kg of body weight/day or linezolid at 600 mg every 12 h (q12h), alone or in combination with gentamicin at 1.3 mg/kg q12h or rifampin at 300 mg q8h or 900 mg q24h. Biofilm-forming, vancomycin-susceptible
Enterococcus faecalis
and vancomycin-resistant
Enterococcus faecium
(vancomycin-resistant enterococcus [VRE]) strains were tested. At 24, 48, and 72 h, all daptomycin-containing regimens demonstrated significantly more activity (decline in CFU/g) than any linezolid-containing regimen against biofilm-forming
E. faecalis
. The addition of gentamicin to daptomycin (at 6 or 10 mg/kg) in the first 24 h significantly improved bactericidal activity. In contrast, the addition of rifampin delayed the bactericidal activity of daptomycin against
E. faecalis
, and the addition of rifampin antagonized the activities of all regimens against VRE at 24 h. Also, against VRE, the addition of gentamicin to linezolid at 72 h improved activity and was bactericidal. Rifampin significantly antagonized the activity of linezolid against VRE at 72 h. In
in vivo
Galleria mellonella
survival assays, linezolid and daptomycin improved survival. Daptomycin at 10 mg/kg improved survival significantly over that with linezolid against
E. faecalis
. The addition of gentamicin improved the efficacy of daptomycin against
E. faecalis
and those of linezolid and daptomycin against VRE. We conclude that in enterococcal infection models, daptomycin has more activity than linezolid alone. Against biofilm-forming
E. faecalis
, the addition of gentamicin in the first 24 h causes the most rapid decline in CFU/g. Of interest, the addition of rifampin decreased the activity of daptomycin against both
E. faecalis
and VRE.
β-Lactam Resistance in Methicillin-Resistant Staphylococcus aureus USA300 Is Increased by Inactivation of the ClpXP Protease
Authors: Bæk Kristoffer T. , Gründling Angelika , Mogensen René G. , Thøgersen Louise , Petersen Andreas , Paulander Wilhelm , Frees Dorte
Published: May 2014

Methicillin-resistant
Staphylococcus aureus
(MRSA) has acquired the
mecA
gene encoding a peptidoglycan transpeptidase, penicillin binding protein 2a (PBP2a), which has decreased affinity for β-lactams. Quickly spreading and highly virulent community-acquired (CA) MRSA strains recently emerged as a frequent cause of infection in individuals without exposure to the health care system. In this study, we found that the inactivation of the components of the ClpXP protease substantially increased the β-lactam resistance level of a CA-MRSA USA300 strain, suggesting that the proteolytic activity of ClpXP controls one or more pathways modulating β-lactam resistance. These pathways do not involve the control of
mecA
expression, as the cellular levels of PBP2a were unaltered in the
clp
mutants. An analysis of the cell envelope properties of the
clpX
and
clpP
mutants revealed a number of distinct phenotypes that may contribute to the enhanced β-lactam tolerance. Both mutants displayed significantly thicker cell walls, increased peptidoglycan cross-linking, and altered composition of monomeric muropeptide species compared to those of the wild types. Moreover, changes in Sle1-mediated peptidoglycan hydrolysis and altered processing of the major autolysin Atl were observed in the
clp
mutants. In conclusion, the results presented here point to an important role for the ClpXP protease in controlling cell wall metabolism and add novel insights into the molecular factors that determine strain-dependent β-lactam resistance.
Interspecies Mixed-Effect Pharmacokinetic Modeling of Penicillin G in Cattle and Swine
Authors: Li Mengjie , Gehring Ronette , Tell Lisa , Baynes Ronald , Huang Qingbiao , Riviere Jim E.
Published: May 2014

Extralabel drug use of penicillin G in food-producing animals may cause an excess of residues in tissue which will have the potential to damage human health. Of all the antibiotics, penicillin G may have the greatest potential for producing allergic responses to the consumer of food animal products. There are, however, no population pharmacokinetic studies of penicillin G for food animals. The objective of this study was to develop a population pharmacokinetic model to describe the time-concentration data profile of penicillin G across two species. Data were collected from previously published pharmacokinetic studies in which several formulations of penicillin G were administered to diverse populations of cattle and swine. Liver, kidney, and muscle residue data were also used in this study. Compartmental models with first-order absorption and elimination were fit to plasma and tissue concentrations using a nonlinear mixed-effect modeling approach. A 3-compartment model with extra tissue compartments was selected to describe the pharmacokinetics of penicillin G. Typical population parameter estimates (interindividual variability) were central volumes of distribution of 3.45 liters (12%) and 3.05 liters (8.8%) and central clearance of 105 liters/h (32%) and 16.9 liters/h (14%) for cattle and swine, respectively, with peripheral clearance of 24.8 liters/h (13%) and 9.65 liters/h (23%) for cattle and 13.7 liters/h (85%) and 0.52 liters/h (40%) for swine. Body weight and age were the covariates in the final pharmacokinetic models. This study established a robust model of penicillin for a large and diverse population of food-producing animals which could be applied to other antibiotics and species in future analyses.
Plasmodium falciparum Founder Populations in Western Cambodia Have Reduced Artemisinin Sensitivity
In Vitro
Authors: Amaratunga Chanaki , Witkowski Benoit , Dek Dalin , Try Vorleak , Khim Nimol , Miotto Olivo , Ménard Didier , Fairhurst Rick M.
Published: May 2014

Reduced
Plasmodium falciparum
sensitivity to short-course artemisinin (ART) monotherapy manifests as a long parasite clearance half-life. We recently defined three parasite founder populations with long half-lives in Pursat, western Cambodia, where reduced ART sensitivity is prevalent. Using the ring-stage survival assay, we show that these founder populations have reduced ART sensitivity
in vitro
at the early ring stage of parasite development and that a genetically admixed population contains subsets of parasites with normal or reduced ART sensitivity.
Alternative Screening Approaches for Discovery of Middle East Respiratory Syndrome Coronavirus Inhibitors
Authors: LaFemina Robert L.
Published: May 2014

Two coronaviruses causing severe respiratory disease and high mortality rates emerging within the past dozen years reinforces the need for clinically efficacious antivirals targeting coronaviruses. Alternative screening approaches for antivirals against the recently emergent Middle East respiratory syndrome coronavirus (MERS-CoV) may provide lead compounds to address this need. Two
Antimicrobial Agents and Chemotherapy
(AAC) papers screened libraries of approved compounds that may potentially be repurposed as MERS-CoV antivirals. A third AAC paper showed that a previously described severe acute respiratory syndrome coronavirus (SARS-CoV) helicase inhibitor also has activity against MERS-CoV.
Nuclear Factor of Activated T Cells Regulates Neutrophil Recruitment, Systemic Inflammation, and T-Cell Dysfunction in Abdominal Sepsis
Authors: Zhang Su , Luo Lingtao , Wang Yongzhi , Gomez Maria F. , Thorlacius Henrik
Published: May 2014

The signaling mechanisms regulating neutrophil recruitment, systemic inflammation, and T-cell dysfunction in polymicrobial sepsis are not clear. This study explored the potential involvement of the calcium/calcineurin-dependent transcription factor, nuclear factor of activated T cells (NFAT), in abdominal sepsis. Cecal ligation and puncture (CLP) triggered NFAT-dependent transcriptional activity in the lung, spleen, liver, and aorta in NFAT-luciferase reporter mice. Treatment with the NFAT inhibitor A-285222 prior to CLP completely prevented sepsis-induced NFAT activation in all these organs. Inhibition of NFAT activity reduced sepsis-induced formation of CXCL1, CXCL2, and CXCL5 chemokines and edema as well as neutrophil infiltration in the lung. Notably, NFAT inhibition efficiently reduced the CLP-evoked increases in HMBG1, interleukin 6 (IL-6), and CXCL5 levels in plasma. Moreover, administration of A-285222 restored sepsis-induced T-cell dysfunction, as evidenced by markedly decreased apoptosis and restored proliferative capacity of CD4 T cells. Along these lines, treatment with A-285222 restored gamma interferon (IFN-γ) and IL-4 levels in the spleen, which were markedly reduced in septic mice. CLP-induced formation of regulatory T cells (CD4
+
CD25
+
Foxp3
+
) in the spleen was also abolished in A-285222-treated animals. All together, these novel findings suggest that NFAT is a powerful regulator of pathological inflammation and T-cell immune dysfunction in abdominal sepsis. Thus, our data suggest that NFAT signaling might be a useful target to protect against respiratory failure and immunosuppression in patients with sepsis.
CD14 Influences Host Immune Responses and Alternative Activation of Macrophages during Schistosoma mansoni Infection
Authors: Tundup Smanla , Srivastava Leena , Nagy Tamas , Harn Donald
Published: May 2014

Antigen-presenting cell (APC) plasticity is critical for controlling inflammation in metabolic diseases and infections. The roles that pattern recognition receptors (PRRs) play in regulating APC phenotypes are just now being defined. We evaluated the expression of PRRs on APCs in mice infected with the helminth parasite
Schistosoma mansoni
and observed an upregulation of CD14 expression on macrophages. Schistosome-infected
Cd14
−/−
mice showed significantly increased alternative activation of (M2) macrophages in the livers compared to infected wild-type (wt) mice. In addition, splenocytes from infected
Cd14
−/−
mice exhibited increased production of CD4
+
-specific interleukin-4 (IL-4), IL-5, and IL-13 and CD4
+
Foxp3
+
IL-10
+
regulatory T cells compared to cells from infected wt mice.
S. mansoni
-infected
Cd14
−/−
mice also presented with smaller liver egg granulomas associated with increased collagen deposition compared to granulomas in infected wt mice. The highest expression of CD14 was found on liver macrophages in infected mice. To determine if the
Cd14
−/−
phenotype was in part due to increased M2 macrophages, we adoptively transferred wt macrophages into
Cd14
−/−
mice and normalized the M2 and CD4
+
Th cell balance close to that observed in infected wt mice. Finally, we demonstrated that CD14 regulates STAT6 activation, as
Cd14
−/−
mice had increased STAT6 activation
in vivo
, suggesting that lack of CD14 impacts the IL-4Rα-STAT6 pathway, altering macrophage polarization during parasite infection. Collectively, these data identify a previously unrecognized role for CD14 in regulating macrophage plasticity and CD4
+
T cell biasing during helminth infection.
The Borrelia hermsii Factor H Binding Protein FhbA Is Not Required for Infectivity in Mice or for Resistance to Human Complement
In Vitro
Authors: Fine Lindy M. , Miller Daniel P. , Mallory Katherine L. , Tegels Brittney K. , Earnhart Christopher G. , Marconi Richard T.
Published: May 2014

The primary causative agent of tick-borne relapsing fever in North America is
Borrelia hermsii
. It has been hypothesized that
B. hermsii
evades complement-mediated destruction by binding factor H (FH), a host-derived negative regulator of complement.
In vitro
,
B. hermsii
produces a single FH binding protein designated FhbA (FH binding protein A). The properties and ligand binding activity of FhbA suggest that it plays multiple roles in pathogenesis. It binds plasminogen and has been identified as a significant target of a B1b B cell-mediated IgM response in mice. FhbA has also been explored as a potential diagnostic antigen for
B. hermsii
infection in humans. The ability to test the hypothesis that FhbA is a critical virulence factor
in vivo
has been hampered by the lack of well-developed systems for the genetic manipulation of the relapsing fever spirochetes. In this report, we have successfully generated a
B. hermsii
fhbA
deletion mutant (the
B. hermsii
YORΔ
fhbA
strain) through allelic exchange mutagenesis. Deletion of
fhbA
abolished FH binding by the YORΔ
fhbA
strain and eliminated cleavage of C3b on the cell surface. However, the YORΔ
fhbA
strain remained infectious in mice and retained resistance to killing
in vitro
by human complement. Collectively, these results indicate that
B. hermsii
employs an FhbA/FH-independent mechanism of complement evasion that allows for resistance to killing by human complement and persistence in mice.
Functional Genomics with a Comprehensive Library of Transposon Mutants for the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20
Authors: Kuehl Jennifer V. , Price Morgan N. , Ray Jayashree , Wetmore Kelly M. , Esquivel Zuelma , Kazakov Alexey E. , Nguyen Michelle , Kuehn Raquel , Davis Ronald W. , Hazen Terry C. , Arkin Adam P. , Deutschbauer Adam
Published: May 2014

The genomes of sulfate-reducing bacteria remain poorly characterized, largely due to a paucity of experimental data and genetic tools. To meet this challenge, we generated an archived library of 15,477 mapped transposon insertion mutants in the sulfate-reducing bacterium
Desulfovibrio alaskensis
G20. To demonstrate the utility of the individual mutants, we profiled gene expression in mutants of six regulatory genes and used these data, together with 1,313 high-confidence transcription start sites identified by tiling microarrays and transcriptome sequencing (5′ RNA-Seq), to update the regulons of Fur and Rex and to confirm the predicted regulons of LysX, PhnF, PerR, and Dde_3000, a histidine kinase. In addition to enabling single mutant investigations, the
D. alaskensis
G20 transposon mutants also contain DNA bar codes, which enables the pooling and analysis of mutant fitness for thousands of strains simultaneously. Using two pools of mutants that represent insertions in 2,369 unique protein-coding genes, we demonstrate that the hypothetical gene
Dde_3007
is required for methionine biosynthesis. Using comparative genomics, we propose that Dde_3007 performs a missing step in methionine biosynthesis by transferring a sulfur group to
O
-phosphohomoserine to form homocysteine. Additionally, we show that the entire choline utilization cluster is important for fitness in choline sulfate medium, which confirms that a functional microcompartment is required for choline oxidation. Finally, we demonstrate that Dde_3291, a MerR-like transcription factor, is a choline-dependent activator of the choline utilization cluster. Taken together, our data set and genetic resources provide a foundation for systems-level investigation of a poorly studied group of bacteria of environmental and industrial importance.

IMPORTANCE
Sulfate-reducing bacteria contribute to global nutrient cycles and are a nuisance for the petroleum industry. Despite their environmental and industrial significance, the genomes of sulfate-reducing bacteria remain poorly characterized. Here, we describe a genetic approach to fill gaps in our knowledge of sulfate-reducing bacteria. We generated a large collection of archived, transposon mutants in
Desulfovibrio alaskensis
G20 and used the phenotypes of these mutant strains to infer the function of genes involved in gene regulation, methionine biosynthesis, and choline utilization. Our findings and mutant resources will enable systematic investigations into gene function, energy generation, stress response, and metabolism for this important group of bacteria.
Enhanced Specialized Transduction Using Recombineering in Mycobacterium tuberculosis
Authors: Tufariello JoAnn M. , Malek Adel A. , Vilchèze Catherine , Cole Laura E. , Ratner Hannah K. , González Pablo A. , Jain Paras , Hatfull Graham F. , Larsen Michelle H. , Jacobs William R.
Published: May 2014

G
enetic engineering has contributed greatly to our understanding of
Mycobacterium tuberculosis
biology and has facilitated antimycobacterial and vaccine development. However, methods to generate
M. tuberculosis
deletion mutants remain labor-intensive and relatively inefficient. Here, methods are described that significantly enhance the efficiency (greater than 100-fold) of recovering deletion mutants by the expression of mycobacteriophage recombineering functions during the course of infection with specialized transducing phages delivering allelic exchange substrates. This system has been successfully applied to the CDC1551 strain of
M. tuberculosis
, as well as to a Δ
recD
mutant generated in the CDC1551 parental strain. The latter studies were undertaken as there were precedents in both the
Escherichia coli
literature and mycobacterial literature for enhancement of homologous recombination in strains lacking RecD. In combination, these measures yielded a dramatic increase in the recovery of deletion mutants and are expected to facilitate construction of a comprehensive library of mutants with every nonessential gene of
M. tuberculosis
deleted. The findings also open up the potential for sophisticated genetic screens, such as synthetic lethal analyses, which have so far not been feasible for the slow-growing mycobacteria.

IMPORTANCE
Genetic manipulation of
M. tuberculosis
is hampered by laborious and relatively inefficient methods for generating deletion mutant strains. The combined use of phage-based transduction and recombineering methods greatly enhances the efficiency by which knockout strains can be generated. The additional elimination of
recD
further enhances this efficiency. The methods described herein will facilitate the construction of comprehensive gene knockout libraries and expedite the isolation of previously difficult to recover mutants, promoting antimicrobial and vaccine development.
Calyceal diverticulum: a benign imitator of serious pathology
Authors: Pareek Anuj , Laursen Christian B , Graumann Ole
Published: May 2014

A 72-year-old man with lung cancer underwent positron emission tomography CT (PET-CT) as a part of cancer staging. As an incidental finding, the PET-CT revealed a renal mass with metabolic and morphological characteristics of a malignant tumour. A diagnostic CT scan revealed a Bosniak III renal cyst, and malignancy could not be excluded. For correct Bosniak classification, a multiphasic contrast-enhanced CT was performed and the renal mass was finally diagnosed as a calyceal diverticulum. This case report summarises how calyceal diverticula may mimic serious pathology, leading to diagnostic difficulties.
Giant dumbbell-shaped schwannoma but not transforaminal: transdiaphragmatic
Authors: Cuce Ferhat , Kara Kemal , Asker Muntecep , Sonmez Guner
Published: May 2014

A 31-year-old man reported a 3-month history of right upper abdominal pain and effort dyspnoea. The laboratory data demonstrated no abnormality. On abdominal ultrasound, a gross solid lesion with smooth borders was seen behind the liver. CT scan revealed a huge tumour, 23×17×15 cm in size, it was in the right posterior mediastinum and extended to the right retroperitoneum. In sagittal plane CT images, the lesion was like a dumbbell shape. CT-guided biopsy revealed a spindle cell tumour.
Syringocysadenoma papilliferum of the vulva: a rarity in gynaecology
Authors: Steshenko Oleksandr , Chandrasekaran Nirmala , Lawton Frank
Published: May 2014

A case of syringocystadenoma papilliferum of the vulva in a 36-year-old woman is reported .The patient presented with a single cystic lesion on the left labia minora of 8 years duration with a recent increase in size and redness around the lesion. Examination revealed a polypoid cystic lesion with no regional lymphadenopathy. An excision biopsy was performed under general anaesthesia and the specimen was subjected to histological examination. Histopathology revealed closely excised syringocystadenoma papilliferum. On follow-up, the patient was asymptomatic and the wound had healed well.