bluuebunny/crossref_metadata_2025 huggingface dataset:
Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps
Authors: Fischer Martin C. , Rellstab Christian , Tedder Andrew , Zoller Stefan , Gugerli Felix , Shimizu Kentaro K. , Holderegger Rolf , Widmer Alex
Published: September 2013

Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing environmental conditions. Here, we examine genomewide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps. Using a pooled population sequencing (Pool‐Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using FST‐based analyses. We tested only the most strongly differentiated SNPs for associations with a nonredundant set of environmental factors using partial Mantel tests to identify topo‐climatic factors that may underlie the observed footprints of selection. Possible functions of genes showing signatures of selection were identified by Gene Ontology analysis. We found 175 genes to be highly associated with one or more of the five tested topo‐climatic factors. Of these, 23.4% had unknown functions. Genetic variation in four candidate genes was strongly associated with site water balance and solar radiation, and functional annotations were congruent with these environmental factors. Our results provide a genomewide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.
Epigenetic programming of neuroendocrine systems during early life
Authors: Murgatroyd Chris
Published: September 2013

New findings

What is the topic of this review?

Behavioural epigenetics and its role in early‐life programming and adaptation is allowing us to understand how psychiatric diseases can develop through interactions of genes and environments.

What advances does it highlight?

The ability of methyl of Methyl‐CpG binding protein 2 to regulate Avp gene expression, in response to early‐life stress, and induce DNA methylation, occurs through the recruitment of components of the epigenetic machinery.

Arginine vasopressin plays a pivotal role in the control of long‐lasting effects of early‐life stress on the brain. We previously reported that maternal separation in mice persistently upregulates Avp gene expression associated with reduced DNA methylation of a region in the Avp enhancer. This early‐life stress‐responsive region serves as a binding site for the methyl‐CpG binding protein 2, which in turn is controlled through neuronal activity. We also found that the ability of methyl‐CpG binding protein 2 to regulate transcription of the Avp gene and induce DNA methylation occured through the recruitment of components of the epigenetic machinery. Understanding the sequential events involved in the epigenetic regulation of a gene should allow for targeted approaches aimed at reprogramming expression during development and possibly later life.
Mechanisms contributing to cluster formation in the inferior olivary nucleus in brainstem slices from postnatal mice
Authors: Kølvraa Mathias , Müller Felix C. , Jahnsen Henrik , Rekling Jens C.
Published: September 2013

Key points

One of the two main inputs to the cerebellum consists of climbing fibres from neurons in the inferior olivary nucleus (IO).

The IO spontaneously forms clusters of co‐active neurons in transverse brainstem slices from 1‐ to 2‐week‐old animals, coinciding with a critical time period in cerebellar development.

Here, we studied the cluster‐forming mechanisms, and find that randomly occurring spontaneous clusters overlap extensively, and contain 10 to hundreds of IO neurons with an average somatodendritic field size that is slightly smaller than the average IO cluster size.

Cluster formation is dependent on sodium action potentials and electrical coupling between IO neurons, and may spread with decreasing velocity and may involve active dendritic properties.

The results help us better understand the basic mechanism underlying cluster formation in the IO, which is an important feature in the generation of patterned input to the cerebellum.

Abstract  The inferior olivary nucleus (IO) in in vitro slices from postnatal mice (P5.5–P15.5) spontaneously generates clusters of neurons with synchronous calcium transients, and intracellular recordings from IO neurons suggest that electrical coupling between neighbouring IO neurons may serve as a synchronizing mechanism. Here, we studied the cluster‐forming mechanism and find that clusters overlap extensively with an overlap distribution that resembles the distribution for a random overlap model. The average somatodendritic field size of single curly IO neurons was ∼6400 μm2, which is slightly smaller than the average IO cluster size. Eighty‐seven neurons with overlapping dendrites were estimated to be contained in the principal olive mean cluster size, and about six non‐overlapping curly IO neurons could be contained within the largest clusters. Clusters could also be induced by iontophoresis with glutamate. Induced clusters were inhibited by tetrodotoxin, carbenoxelone and 18β‐glycyrrhetinic acid, suggesting that sodium action potentials and electrical coupling are involved in glutamate‐induced cluster formation, which could also be induced by activation of N‐methyl‐d‐aspartate and α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid receptors. Spikelets and a small transient depolarizing response were observed during glutamate‐induced cluster formation. Calcium transients spread with decreasing velocity during cluster formation, and somatic action potentials and cluster formation are accompanied by large dendritic calcium transients. In conclusion, cluster formation depends on gap junctions, sodium action potentials and spontaneous clusters occur randomly throughout the IO. The relative slow signal spread during cluster formation, combined with a strong dendritic influx of calcium, may signify that active dendritic properties contribute to cluster formation.
Experimental and Numerical Studies on High-Pressure Composite Cylinders Subjected to Localized and Engulfing Fire
Authors: Zheng Jinyang , Ou Kesheng , Hua Zhengli , Zhao Yongzhi , Hu Jun , Han Bing
Published: September 2013

Vehicle fires may lead to on-board high-pressure composite cylinders experiencing a term of localized and engulfing fire. During this period, the composite cylinder would be degraded and even burst before pressure relief device (PRD) could be activated to release internal high-pressure gas. In this paper, experimental investigation for such cylinders subjected to localized and engulfing fire was conducted on an aluminum liner composite cylinder filled with hydrogen. A three-dimensional computational fluid dynamics (CFD) model is developed to study the key factors influencing PRD activation time. The effects of hydrogen and compressed natural gas (CNG) as filling media, cylinder pressure and localized fire exposure time are analyzed in detail. The experimental results showed that pressure and temperature of internal gas rose very slowly during the localized fire. In addition, Hydrogen and CNG as filling media with different pressures have weak influence on the activation time of thermally activated PRD (TPRD), but have significant effect on the activation time of pressure-activated PRD (PPRD). TPRD can respond more quickly to protect the hydrogen composite cylinder than PPRD. PRD activation time increases as the localized fire exposure time is extended.
An Outdoor Experiment of a Lens-Walled Compound Parabolic Concentrator Photovoltaic Module on a Sunny Day in Nottingham
Authors: Li Guiqiang , Su Yuehong , Pei Gang , Zhou Hang , Yu Xu , Ji Jie , Riffat Saffa
Published: September 2013

A lens-walled compound parabolic concentrator (lens-walled CPC) has a larger half acceptance angle than a mirror CPC for the same geometrical concentration ratio of 2.5X, so it would be more suitable for the building-integrated application as a stationary solar concentrator. Based on our previous work, an outdoor experimental study of a sample trough lens-walled CPC PV module under sunny condition in Nottingham is described. The experimental results provide the verification of actual larger half acceptance angle obtained by the lens-walled CPC in comparison with a mirror CPC of the same size. Along with the analysis of the projected incidence angles, the experimental results also indicate that the lens-walled CPC of 2.5X orientated east–west may be a good choice for high latitude area as a stationary solar concentrator to give a satisfactory whole year performance.
Condition Monitoring the Drive Train of a Direct Drive Permanent Magnet Wind Turbine Using Generator Electrical Signals
Authors: Yang Wenxian
Published: September 2013

The benefit of wind turbine (WT) can be significantly improved through a well-organized condition-based maintenance strategy. However, such a target has not been fully achieved today. One of the major reasons is lack of an efficient WT condition monitoring system (CMS). The existing WT CMSs often involve high initial capital cost, with complex structure, suffer from inefficient management and show unsatisfactory hardware reliability. So, the operators still have desire for an economical, effective, and reliable CMS for their machines. The work reported in this paper is intended to meet such a demand. Because direct drive permanent magnet (PM) WTs are showing increased market share, but the existing WT CMSs are not designed to deal specifically with this new design, this paper reports on a CM technique dedicated to monitoring the drive train of direct drive WTs. Instead of taking the vibration analysis approach that is being popularly adopted by commercial WT CMSs, a novel CM strategy is researched in this paper by introducing generator electrical signals into WT CM and interpreting them by using a dedicated criterion named instantaneous variance (IV) and Teager–Huang transform (THT), i.e. the generator electrical signals will be evaluated first by using the IV, of which the fault detection capability can be further enhanced with the aid of empirical mode decomposition (EMD). Once an abnormality is detected, then detailed THT analysis of the signal will be conducted for further investigation. The technique has been verified experimentally on a specifically designed WT drive train test rig, on which a PM generator rotates at slow variable speed and is subjected to varying load like a real WT does. Considering the electric subassemblies and rotor blades of direct drive WTs are most vulnerable to damage in practice, rotor unbalance and generator winding faults were emulated on the test rig. Experimental results show that the proposed CM technique is effective in detecting both types of faults occurring in the drive train of direct drive PM WTs. In summary, the proposed CM technique can be identified by (i) the CM is accomplished through analyzing the generator electrical signals without resorting to any other information (e.g. vibro-acoustic). Hence, the data acquisition work will be eased off; (ii) no more transducer other than current and voltage sensors are required. Thus, the cost of the CMS will be significantly reduced; (iii) attributed to the distinguished superiorities of THT to traditional spectral analyses in processing nonlinear signals, the proposed technique is more reliable in interpreting WT CM signals; and (iv) the CM criterion IV has a simple computational algorithm. It is therefore suited to both online and offline WT CM applications.
Design for Thermo-Acoustic Stability: Modeling of Burner and Flame Dynamics
Authors: Bade S. , Wagner M. , Hirsch C. , Sattelmayer T. , Schuermans B.
Published: September 2013

A design for thermo-acoustic stability (DeTAS) procedure is presented that aims at selecting the most stable burner geometry for a given combustor. It is based on the premise that a thermo-acoustic stability model of the combustor can be formulated and that a burner design exists, which has geometric design parameters that sufficiently influence the dynamics of the flame. Describing the flame dynamics in dependence of the geometrical parameters, an optimization procedure involving a linear stability model of the target combustor, maximizes the damping and thereby yields the optimal geometrical parameters. To demonstrate the procedure on an existing annular combustor a generic burner design was developed that features significant variability of dynamical flame response in dependence of two geometrical parameters. In this paper the experimentally determined complex burner acoustics and complex flame responses are described in terms of physics-based parametric models with excellent agreement between experimental and model data. It is shown that these model parameters correlate uniquely with the variation of the burner geometrical parameters, allowing interpolating the model with respect to the geometrical parameters. The interpolation is validated with experimental data.
Performance Analysis of Organic Rankine Cycle With Preliminary Design of Radial Turbo Expander for Binary-Cycle Geothermal Plants
Authors: Wang Xing , Liu Xiaomin , Zhang Chuhua
Published: September 2013

In order to produce less emission of greenhouse gases, many studies have been done on the binary-cycle geothermal power plant to obtain better performance. The radial turbo expanders play an important role in the performance of the organic rankine cycle (ORC) for binary-cycle geothermal plants. However, few studies have investigated the effect of parameters of radial turbo expanders on the performance of the ORC. In this paper, a new thermodynamic model of the ORC coupled with the preliminary design of radial turbo expanders is developed. The effects of geothermal water temperature on the ORC performance parameters, such as power output and thermal efficiency are investigated by using the proposed thermodynamic model. The variation of radial turbo expanders’ parameters, such as specific rotational speed with geothermal water temperature is revealed. In the present study, the reasonable efficiency of radial turbo expanders by using the preliminary design is adopted to analyze the performance of the ORC, and an accurate reference about the effect of geothermal source on the parameters of radial turbo expanders is obtained.
Modeling and Technical-Economic Optimization of Electricity Supply Network by Three Photovoltaic Systems
Authors: Safarian Sahar , Khodaparast Pooya , Kateb Movaffaq
Published: September 2013

To attain an ongoing electricity economy, developing novel widespread electricity supply systems based on diverse energy resources are critically important. Several photovoltaic (PV) technologies exist, which cause various pathways to produce electricity from solar energy. This paper evaluates the competition between three influential solar technologies based on photovoltaic technique to find the optimal pathways for satisfying the electricity demand: (1) multicrystalline silicon; (2) copper, indium, gallium, and selenium (CIGS); and (3) multijunction. Besides the technical factors, there are other effective parameters such as cost, operability, feasibility, and capacity that should be considered when assessing the different pathways as optimal and viable long-term alternatives. To aid this decision-making process, a generic optimization-based model was developed for the long-range energy planning and design of future electricity supply system from solar energy. By applying dynamic programming techniques, the model is capable of identifying the optimal investment strategies and integrated supply system configurations from the many alternatives. The features and capabilities of the model were shown through application to Iran as a case study.
Control of a Supercritical CO2 Recompression Brayton Cycle Demonstration Loop
Authors: Conboy T. , Pasch J. , Fleming D.
Published: September 2013

The U.S. Department of Energy is currently focused on the development of next-generation nuclear power reactors, with an eye towards improved efficiency and reduced capital cost. To this end, reactors using a closed-Brayton power conversion cycle have been proposed as an attractive alternative to steam turbines. The supercritical-CO2 recompression cycle has been identified as a leading candidate for this application since it can achieve high efficiency at relatively low operating temperatures with extremely compact turbomachinery. Sandia National Laboratories has been a leader in hardware and component development for the supercritical-CO2 cycle. With contractor Barber-Nichols Inc., Sandia has constructed a megawatt-class S-CO2 cycle test-loop to investigate the key areas of technological uncertainty for this power cycle and to confirm model estimates of advantageous thermodynamic performance. Until recently, much of the work has centered on the simple S-CO2 cycle—a recuperated Brayton loop with a single turbine and compressor. However, work has recently progressed to a recompression cycle with split-shaft turbo-alternator-compressors, unlocking the potential for much greater efficiency power conversion, but introducing greater complexity in control operations. The following sections use testing experience to frame control actions made by test loop operators in bringing the recompression cycle from cold startup conditions through transition to power generation on both turbines, to the desired test conditions, and finally to a safe shutdown. During this process, considerations regarding the turbocompressor thrust state, CO2 thermodynamic state at the compressor inlet, compressor surge and stall, turbine u/c ratio, and numerous other factors must be taken into account. The development of these procedures on the Sandia test facility has greatly reduced the risk to industry in commercial development of the S-CO2 power cycle.
Presenilin Lets the Ca
2+
Out of the Bag
Authors: Berndt Jason D.
Published: September 2013

Presenilins promote synaptic potentiation by stabilizing ryanodine receptors.
Biological Evaluation of Benzothiazole Ethyl Urea Inhibitors of Bacterial Type II Topoisomerases
Authors: Stokes Neil R. , Thomaides-Brears Helena B. , Barker Stephanie , Bennett James M. , Berry Joanne , Collins Ian , Czaplewski Lloyd G. , Gamble Vicki , Lancett Paul , Logan Alastair , Lunniss Christopher J. , Peasley Hilary , Pommier Stéphanie , Price Daniel , Smee Carol , Haydon David J.
Published: September 2013

The type II topoisomerases DNA gyrase (GyrA/GyrB) and topoisomerase IV (ParC/ParE) are well-validated targets for antibacterial drug discovery. Because of their structural and functional homology, these enzymes are amenable to dual targeting by a single ligand. In this study, two novel benzothiazole ethyl urea-based small molecules, designated compound A and compound B, were evaluated for their biochemical, antibacterial, and pharmacokinetic properties. The two compounds inhibited the ATPase activity of GyrB and ParE with 50% inhibitory concentrations of <0.1 μg/ml. Prevention of DNA supercoiling by DNA gyrase was also observed. Both compounds potently inhibited the growth of a range of bacterial organisms, including staphylococci, streptococci, enterococci,
Clostridium difficile
, and selected Gram-negative respiratory pathogens. MIC
90
s against clinical isolates ranged from 0.015 μg/ml for
Streptococcus pneumoniae
to 0.25 μg/ml for
Staphylococcus aureus
. No cross-resistance with common drug resistance phenotypes was observed. In addition, no synergistic or antagonistic interactions between compound A or compound B and other antibiotics, including the topoisomerase inhibitors novobiocin and levofloxacin, were detected in checkerboard experiments. The frequencies of spontaneous resistance for
S. aureus
were <2.3 × 10
−10
with compound A and <5.8 × 10
−11
with compound B at concentrations equivalent to 8× the MICs. These values indicate a multitargeting mechanism of action. The pharmacokinetic properties of both compounds were profiled in rats. Following intravenous administration, compound B showed approximately 3-fold improvement over compound A in terms of both clearance and the area under the concentration-time curve. The measured oral bioavailability of compound B was 47.7%.
Thioridazine Pharmacokinetic-Pharmacodynamic Parameters “Wobble” during Treatment of Tuberculosis: a Theoretical Basis for Shorter-Duration Curative Monotherapy with Congeners
Authors: Musuka Sandirai , Srivastava Shashikant , Siyambalapitiyage Dona Chandima Wasana , Meek Claudia , Leff Richard , Pasipanodya Jotam , Gumbo Tawanda
Published: September 2013

Phenothiazines are being repurposed for treatment of tuberculosis. We examined time-kill curves of thioridazine and first-line drugs against log-growth-phase and semidormant bacilli under acidic conditions and nonreplicating persistent
Mycobacterium tuberculosis
. While both the potency and the efficacy of first-line drugs declined dramatically as
M. tuberculosis
replication rates decreased, those of thioridazine improved. The mutation prevalence to 3 times the thioridazine MIC was <1 × 10
−11
, better than for ≥2 first-line drugs combined. Hollow fiber system studies revealed that the relationship between sterilizing effect and pharmacodynamic indices (PDI) was characterized by an
r
2
of 0.88 for peak/MIC, an
r
2
of 0.47 for the area under the concentration-time curve (AUC) to MIC, and an
r
2
of 0.14 for the cumulative percentage of a 24-h period that the drug concentration exceeds the MIC under steady-state pharmacokinetic conditions (%
T
MIC
) at the end of the first week. However, the PDI linked to effect “wobbled” as the duration of therapy increased, so that by the fourth week the
r
2
was 0.88 for AUC/MIC, 0.78 for %T
MIC
, and 0.72 for peak/MIC. This “wobble” has implications on general pharmacokinetic/pharmacodynamic theory, whereby efficacy is linked to only one of the three PDIs in deterministic models. The potency changed 8.9-fold from the first to the fourth weeks. The non-protein-bound AUC/MIC associated with maximal kill at the end of therapy was 50.53 (protein binding = 99.5%). This thioridazine exposure was calculated to extinguish all three
M. tuberculosis
metabolic populations in human lungs in only 42.9 days of monotherapy. However, this concentration exceeds the 2- to 8-mg/liter thioridazine concentration in serum known to be lethal to humans. Therefore, the way forward for phenothiazine monotherapy that also reduces therapy duration is via synthesis of less toxic congeners.
In Vitro
Susceptibility of Aspergillus fumigatus to Isavuconazole: Correlation with Itraconazole, Voriconazole, and Posaconazole
Authors: Gregson Lea , Goodwin Joanne , Johnson Adam , McEntee Laura , Moore Caroline B. , Richardson Malcolm , Hope William W. , Howard Susan J.
Published: September 2013

Triazoles are first-line agents for treating aspergillosis. The prevalence of azole resistance in
Aspergillus fumigatus
is increasing, and cross-resistance is a growing concern. In this study, the susceptibilities of 40
A. fumigatus
clinical isolates were tested by using the CLSI method with amphotericin B, itraconazole, voriconazole, posaconazole, and the new triazole isavuconazole. Isavuconazole MICs were higher in strains with reduced susceptibilities to other triazoles, mirroring changes in voriconazole susceptibility. Isavuconazole MICs differed depending on the Cyp51A substitution.
Impacts of Labile Organic Carbon Concentration on Organic and Inorganic Nitrogen Utilization by a Stream Biofilm Bacterial Community
Authors: Ghosh Suchismita , Leff Laura G.
Published: September 2013

In aquatic ecosystems, carbon (C) availability strongly influences nitrogen (N) dynamics. One manifestation of this linkage is the importance in the dissolved organic matter (DOM) pool of dissolved organic nitrogen (DON), which can serve as both a C and an N source, yet our knowledge of how specific properties of DOM influence N dynamics are limited. To empirically examine the impact of labile DOM on the responses of bacteria to DON and dissolved inorganic nitrogen (DIN), bacterial abundance and community composition were examined in controlled laboratory microcosms subjected to various combinations of dissolved organic carbon (DOC), DON, and DIN treatments. Bacterial communities that had colonized glass beads incubated in a stream were treated with various glucose concentrations and combinations of inorganic and organic N (derived from algal exudate, bacterial protein, and humic matter). The results revealed a strong influence of C availability on bacterial utilization of DON and DIN, with preferential uptake of DON under low C concentrations. Bacterial DON uptake was affected by the concentration and by its chemical nature (labile versus recalcitrant). Labile organic N sources (algal exudate and bacterial protein) were utilized equally well as DIN as an N source, but this was not the case for the recalcitrant humic matter DON treatment. Clear differences in bacterial community composition among treatments were observed based on terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes. C, DIN, and DON treatments likely drove changes in bacterial community composition that in turn affected the rates of DON and DIN utilization under various C concentrations.
Characteristics of Cefotaxime-Resistant Escherichia coli from Wild Birds in The Netherlands
Authors: Veldman Kees , van Tulden Peter , Kant Arie , Testerink Joop , Mevius Dik
Published: September 2013

Cloacal swabs from carcasses of Dutch wild birds obtained in 2010 and 2011 were selectively cultured on media with cefotaxime to screen for the presence of extended-spectrum β-lactamase (ESBL)/AmpC-producing
Escherichia coli
. Subsequently, all cefotaxime-resistant
E. coli
isolates were tested by broth microdilution and microarray. The presence of ESBL/AmpC and coexisting plasmid-mediated quinolone resistance (PMQR) genes was confirmed by PCR and sequencing. To determine the size of plasmids and the location of ESBL and PMQR genes, S1 pulsed-field gel electrophoresis (PFGE) was performed on transformants, followed by Southern blot hybridization. The study included 414 cloacal swabs originating from 55 different bird species. Cefotaxime-resistant
E. coli
isolates were identified in 65 birds (15.7%) from 21 different species. In all, 65 cefotaxime-resistant
E. coli
ESBL/AmpC genes were detected, mainly comprising variants of
bla
CTX-M
and
bla
CMY-2
. Furthermore, PMQR genes [
aac(6
′
)-lb-cr
,
qnrB1
, and
qnrS1
] coincided in seven cefotaxime-resistant
E. coli
isolates. Overall, replicon typing of the ESBL/AmpC-carrying plasmids demonstrated the predominant presence of IncI1 (
n
= 31) and variants of IncF (
n
= 18). Our results indicate a wide dissemination of ESBL and AmpC genes in wild birds from The Netherlands, especially among aquatic-associated species (waterfowl, gulls, and waders). The identified genes and plasmids reflect the genes found predominantly in livestock animals as well as in humans.
Specific Midgut Region Controlling the Symbiont Population in an Insect-Microbe Gut Symbiotic Association
Authors: Kim Jiyeun Kate , Kim Na Hyang , Jang Ho Am , Kikuchi Yoshitomo , Kim Chan-Hee , Fukatsu Takema , Lee Bok Luel
Published: September 2013

Many insects possess symbiotic bacteria that affect the biology of the host. The level of the symbiont population in the host is a pivotal factor that modulates the biological outcome of the symbiotic association. Hence, the symbiont population should be maintained at a proper level by the host's control mechanisms. Several mechanisms for controlling intracellular symbionts of insects have been reported, while mechanisms for controlling extracellular gut symbionts of insects are poorly understood. The bean bug
Riptortus pedestris
harbors a betaproteobacterial extracellular symbiont of the genus
Burkholderia
in the midgut symbiotic organ designated the M4 region. We found that the M4B region, which is directly connected to the M4 region, also harbors
Burkholderia
symbiont cells, but the symbionts therein are mostly dead. A series of experiments demonstrated that the M4B region exhibits antimicrobial activity, and the antimicrobial activity is specifically potent against the
Burkholderia
symbiont but not the cultured
Burkholderia
and other bacteria. The antimicrobial activity of the M4B region was detected in symbiotic host insects, reaching its highest point at the fifth instar, but not in aposymbiotic host insects, which suggests the possibility of symbiont-mediated induction of the antimicrobial activity. This antimicrobial activity was not associated with upregulation of antimicrobial peptides of the host. Based on these results, we propose that the M4B region is a specialized gut region of
R. pedestris
that plays a critical role in controlling the population of the
Burkholderia
gut symbiont. The molecular basis of the antimicrobial activity is of great interest and deserves future study.
Species Co-Occurrence Patterns among Lyme Borreliosis Pathogens in the Tick Vector Ixodes ricinus
Authors: Herrmann Coralie , Gern Lise , Voordouw Maarten J.
Published: September 2013

Mixed infections have important consequences for the ecology and evolution of host-parasite interactions. In vector-borne diseases, interactions between pathogens occur in both the vertebrate host and the arthropod vector. Spirochete bacteria belonging to the
Borrelia burgdorferi
sensu lato
genospecies complex are transmitted by
Ixodes
ticks and cause Lyme borreliosis in humans. In Europe, there is a high diversity of
Borrelia
pathogens, and the main tick vector,
Ixodes ricinus
, is often infected with multiple
Borrelia
genospecies. In the present study, we characterized the pairwise interactions between five
B. burgdorferi
sensu lato
genospecies in a large data set of
I. ricinus
ticks collected from the same field site in Switzerland. We measured two types of pairwise interactions: (i) co-occurrence, whether double infections occurred more or less often than expected, and (ii) spirochete load additivity, whether the total spirochete load in double infections was greater or less than the sum of the single infections. Mixed infections of
Borrelia
genospecies specialized on different vertebrate reservoir hosts occurred less frequently than expected (negative co-occurrence) and had joint spirochete loads that were lower than the additive expectation (inhibition). In contrast, mixed infections of genospecies that share the same reservoir hosts were more common than expected (positive co-occurrence) and had joint spirochete loads that were similar to or greater than the additive expectation (facilitation). Our study suggests that the vertebrate host plays an important role in structuring the community of
B. burgdorferi
sensu lato
genospecies inside the tick vector.
Development of a Tiered Multilocus Sequence Typing Scheme for Members of the Lactobacillus acidophilus Complex
Authors: Ramachandran Padmini , Lacher David W. , Pfeiler Erika A. , Elkins Christopher A.
Published: September 2013

Members of the
Lactobacillus acidophilus
complex are associated with functional foods and dietary supplements because of purported health benefits they impart to the consumer. Many characteristics of these microorganisms are reported to be strain specific. Therefore, proper strain typing is essential for safety assessment and product labeling, and also for monitoring strain integrity for industrial production purposes. Fifty-two strains of the
L. acidophilus
complex (
L. acidophilus
,
L. amylovorus
,
L. crispatus
,
L. gallinarum
,
L. gasseri
, and
L. johnsonii
) were genotyped using two established methods and compared to a novel multilocus sequence typing (MLST) scheme. PCR restriction fragment length polymorphism (PCR-RFLP) analysis of the
hsp60
gene with AluI and TaqI successfully clustered 51 of the 52 strains into the six species examined, but it lacked strain-level discrimination. Random amplified polymorphic DNA PCR (RAPD-PCR) targeting the M13 sequence resulted in highly discriminatory profiles but lacked reproducibility. In this study, an MLST scheme was developed using the conserved housekeeping genes
fusA
,
gpmA
,
gyrA
,
gyrB
,
lepA
,
pyrG
, and
recA
, which identified 40 sequence types that successfully clustered all of the strains into the six species. Analysis of the observed alleles suggests that nucleotide substitutions within five of the seven MLST loci have reached saturation, a finding that emphasizes the highly diverse nature of the
L. acidophilus
complex and our unconventional application of a typically intraspecies molecular typing tool. Our MLST results indicate that this method could be useful for characterization and strain discrimination of a multispecies complex, with the potential for taxonomic expansion to a broader collection of
Lactobacillus
species.
Detection of Achromobacter xylosoxidans in Hospital, Domestic, and Outdoor Environmental Samples and Comparison with Human Clinical Isolates
Authors: Amoureux Lucie , Bador Julien , Fardeheb Sakina , Mabille Cédric , Couchot Charlyne , Massip Clémence , Salignon Anne-Lise , Berlie Guillaume , Varin Véronique , Neuwirth Catherine
Published: September 2013

Achromobacter xylosoxidans
is an aerobic nonfermentative Gram-negative rod considered an important emerging pathogen among cystic fibrosis (CF) patients worldwide and among immunocompromised patients. This increased prevalence remains unexplained, and to date no environmental reservoir has been identified. The aim of this study was to identify potential reservoirs of
A. xylosoxidans
in hospital, domestic, and outdoor environments and to compare the isolates with clinical ones. From 2011 to 2012, 339 samples were collected in Dijon's university hospital, in healthy volunteers' homes in the Dijon area, and in the outdoor environment in Burgundy (soil, water, mud, and plants). We designed a protocol to detect
A. xylosoxidans
in environmental samples based on a selective medium: MCXVAA (MacConkey agar supplemented with xylose, vancomycin, aztreonam, and amphotericin B). Susceptibility testing, genotypic analysis by pulsed-field gel electrophoresis, and
bla
OXA-114
sequencing were performed on the isolates. A total of 50 strains of
A. xylosoxidans
were detected in hospital (33 isolates), domestic (9 isolates), and outdoor (8 isolates) samples, mainly in hand washing sinks, showers, and water. Most of them were resistant to ciprofloxacin (49 strains). Genotypic analysis and
bla
OXA-114
sequencing revealed a wide diversity among the isolates, with 35 pulsotypes and 18 variants of oxacillinases. Interestingly, 10 isolates from hospital environment were clonally related to clinical isolates previously recovered from hospitalized patients, and one domestic isolate was identical to one recovered from a CF patient. These results indicate that
A. xylosoxidans
is commonly distributed in various environments and therefore that CF patients or immunocompromised patients are surrounded by these reservoirs.
Identification of CtpL as a Chromosomally Encoded Chemoreceptor for 4-Chloroaniline and Catechol in Pseudomonas aeruginosa PAO1
Authors: Vangnai Alisa S. , Takeuchi Kazuki , Oku Shota , Kataoka Naoya , Nitisakulkan Tisana , Tajima Takahisa , Kato Junichi
Published: September 2013

Bacterial chemotaxis influences the ability of bacteria to survive and thrive in most environments, including polluted ones. Despite numerous reports of the phenotypic characterization of chemotactic bacteria, only a few molecular details of chemoreceptors for aromatic pollutants have been described. In this study, the molecular basis of chemotaxis toward an environmentally toxic chlorinated aromatic pollutant, 4-chloroaniline (4CA), was evaluated. Among the three
Pseudomonas
spp. tested,
Pseudomonas aeruginosa
PAO1 exhibited positive chemotaxis both to the nonmetabolizable 4CA, where 4-chloroacetanilide was formed as a dead-end transformation product, and to the metabolizable catechol. Molecular analysis of all 26 mutants with a disrupted methyl-accepting chemotaxis gene revealed that CtpL, a chromosomally encoded chemoreceptor, was responsible for the positive chemotactic response toward 4CA. Since CtpL has previously been described to be a major chemoreceptor for inorganic phosphate at low concentrations in PAO1, this report describes a fortuitous ability of CtpL to function toward aromatic pollutants. In addition, its regulation not only was dependent on the presence of the chemoattractant inducer but also was regulated by conditions of phosphate starvation. These results expand the range of known chemotactic transducers and their function in the environmental bacterium PAO1.
Accumulation and Inactivation of Avian Influenza Virus by the Filter-Feeding Invertebrate Daphnia magna
Authors: Meixell Brandt W. , Borchardt Mark A. , Spencer Susan K.
Published: September 2013

The principal mode of avian influenza A virus (AIV) transmission among wild birds is thought to occur via an indirect fecal-oral route, whereby individuals are exposed to virus from the environment through contact with virus-contaminated water. AIV can remain viable for an extended time in water; however, little is known regarding the influence of the biotic community (i.e., aquatic invertebrates) on virus persistence and infectivity in aquatic environments. We conducted laboratory experiments to investigate the ability of an aquatic filter-feeding invertebrate,
Daphnia magna
, to accumulate virus from AIV-dosed water under the hypothesis that they represent a potential vector of AIV to waterfowl hosts. We placed live daphnids in test tubes dosed with low-pathogenicity AIV (H3N8 subtype isolated from a wild duck) and sampled
Daphnia
tissue and the surrounding water using reverse transcription-quantitative PCR (RT-qPCR) at 3- to 120-min intervals for up to 960 min following dosing. Concentrations of viral RNA averaged 3 times higher in
Daphnia
tissue than the surrounding water shortly after viral exposure, but concentrations decreased exponentially through time for both. Extracts from
Daphnia
tissue were negative for AIV by cell culture, whereas AIV remained viable in water without
Daphnia
present. Our results suggest daphnids can accumulate AIV RNA and effectively remove virus particles from water. Although concentrations of viral RNA were consistently higher in
Daphnia
tissue than the water, additional research is needed on the time scale of AIV inactivation after
Daphnia
ingestion to fully elucidate
Daphnia
's role as a potential vector of AIV infection to aquatic birds.
Regiospecificities and Prenylation Mode Specificities of the Fungal Indole Diterpene Prenyltransferases AtmD and PaxD
Authors: Liu Chengwei , Minami Atsushi , Noike Motoyoshi , Toshima Hiroaki , Oikawa Hideaki , Dairi Tohru
Published: September 2013

We recently reported the function of
paxD
, which is involved in the paxilline (compound 1) biosynthetic gene cluster in
Penicillium paxilli
. Recombinant PaxD catalyzed a stepwise regular-type diprenylation at the 21 and 22 positions of compound 1 with dimethylallyl diphosphate (DMAPP) as the prenyl donor. In this study,
atmD
, which is located in the aflatrem (compound 2) biosynthetic gene cluster in
Aspergillus flavus
and encodes an enzyme with 32% amino acid identity to PaxD, was characterized using recombinant enzyme. When compound 1 and DMAPP were used as substrates, two major products and a trace of minor product were formed. The structures of the two major products were determined to be reversely monoprenylated compound 1 at either the 20 or 21 position. Because compound 2 and β-aflatrem (compound 3), both of which are compound 1-related compounds produced by
A. flavus
, have the same prenyl moiety at the 20 and 21 position, respectively, AtmD should catalyze the prenylation in compound 2 and 3 biosynthesis. More importantly and surprisingly, AtmD accepted paspaline (compound 4), which is an intermediate of compound 1 biosynthesis that has a structure similar to that of compound 1, and catalyzed a regular monoprenylation of compound 4 at either the 21 or 22 position, though the reverse prenylation was observed with compound 1. This suggests that fungal indole diterpene prenyltransferases have the potential to alter their position and regular/reverse specificities for prenylation and could be applicable for the synthesis of industrially useful compounds.
Bacterial Persister Cell Formation and Dormancy
Authors: Wood Thomas K. , Knabel Stephen J. , Kwan Brian W.
Published: September 2013

Bacterial cells may escape the effects of antibiotics without undergoing genetic change; these cells are known as persisters. Unlike resistant cells that grow in the presence of antibiotics, persister cells do not grow in the presence of antibiotics. These persister cells are a small fraction of exponentially growing cells (due to carryover from the inoculum) but become a significant fraction in the stationary phase and in biofilms (up to 1%). Critically, persister cells may be a major cause of chronic infections. The mechanism of persister cell formation is not well understood, and even the metabolic state of these cells is debated. Here, we review studies relevant to the formation of persister cells and their metabolic state and conclude that the best model for persister cells is still dormancy, with the latest mechanistic studies shedding light on how cells reach this dormant state.
The Polyketide Synthase Gene
pks4
of Trichoderma reesei Provides Pigmentation and Stress Resistance
Authors: Atanasova Lea , Knox Benjamin P. , Kubicek Christian P. , Druzhinina Irina S. , Baker Scott E.
Published: September 2013

Species of the fungal genus
Trichoderma
(Hypocreales, Ascomycota) are well-known for their production of various secondary metabolites. Nonribosomal peptides and polyketides represent a major portion of these products. In a recent phylogenomic investigation of
Trichoderma
polyketide synthase (PKS)-encoding genes, the
pks4
from
T. reesei
was shown to be an orthologue of pigment-forming PKSs involved in synthesis of aurofusarin and bikaverin in
Fusarium
spp. In this study, we show that deletion of this gene in
T. reesei
results in loss of green conidial pigmentation and in pigmentation alteration of teleomorph structures. It also has an impact on conidial cell wall stability and the antagonistic abilities of
T. reesei
against other fungi, including formation of inhibitory metabolites. In addition, deletion of
pks4
significantly influences the expression of other PKS-encoding genes of
T. reesei
. To our knowledge, this is the first indication that a low-molecular-weight pigment-forming PKS is involved in defense, mechanical stability, and stress resistance in fungi.
Murine Models of Candida Gastrointestinal Colonization and Dissemination
Authors: Koh Andrew Y.
Published: September 2013

Ninety-five percent of infectious agents enter through exposed mucosal surfaces, such as the respiratory and gastrointestinal (GI) tracts. The human GI tract is colonized with trillions of commensal microbes, including numerous
Candida
spp. Some commensal microbes in the GI tract can cause serious human infections under specific circumstances, typically involving changes in the gut environment and/or host immune conditions. Therefore, utilizing animal models of fungal GI colonization and dissemination can lead to significant insights into the complex pathophysiology of transformation from a commensal organism to a pathogen and host-pathogen interactions. This paper will review the methodologic approaches used for modeling GI colonization versus dissemination, the insights learned from these models, and finally, possible future directions using these animal modeling systems.
Loss of Mitochondrial Protein Fus1 Augments Host Resistance to Acinetobacter baumannii Infection
Authors: Hood M. Indriati , Uzhachenko Roman , Boyd Kelli , Skaar Eric P. , Ivanova Alla V.
Published: September 2013

Fus1 is a tumor suppressor protein with recently described immunoregulatory functions. Although its role in sterile inflammation is being elucidated, its role in regulating immune responses to infectious agents has not been examined. We used here a murine model ofAcinetobacter baumanniipneumonia to identify the role of Fus1 in antibacterial host defenses. We found that the loss of Fus1 in mice results in significantly increased resistance toA. baumanniipneumonia. We observed earlier and more robust recruitment of neutrophils and macrophages to the lungs of infected Fus1−/−mice, with a concomitant increase in phagocytosis of invading bacteria and more rapid clearance. Such a prompt and enhanced immune response to bacterial infection in Fus1−/−mice stems from early activation of proinflammatory pathways (NF-κB and phosphatidylinositol 3-kinase/Akt/mammalian target of rapamycin [mTOR]), most likely due to significantly increased mitochondrial membrane potential and mitochondrial reactive oxygen species production. Significant early upregulation of interleukin-17 (IL-17) in Fus1−/−immune cells was also observed, together with significant downregulation of IL-10. Depletion of neutrophils eliminates the enhanced antibacterial defenses of the Fus1−/−mice, suggesting that ultimately it is the enhanced immune cell recruitment that mediates the increased resistance of Fus1−/−mice toA. baumanniipneumonia. Taken together, our data define the novel role for Fus1 in the immune response toA. baumanniipneumonia and highlight new avenues for immune modulating therapeutic targets for this treatment-resistant nosocomial pathogen.
The Sulfolobus Initiator Element Is an Important Contributor to Promoter Strength
Authors: Ao Xiang , Li Yingjun , Wang Fan , Feng Mingxia , Lin Yanxu , Zhao Shumiao , Liang Yunxiang , Peng Nan
Published: September 2013

Basal elements in archaeal promoters, except for putative initiator elements encompassing transcription start sites, are well characterized. Here, we employed the
Sulfolobus
araS
promoter as a model to study the function of the initiator element (Inr) in archaea. We have provided evidence for the presence of a third core promoter element, the
Sulfolobus
Inr, whose action depends on a TATA box and the TF
B
r
ecognition
e
lement (BRE). Substitution mutations in the
araS
Inr did not alter the location of the transcription start site. Using systematic mutagenesis, the most functional
araS
Inr was defined as +1 GAGAMK +6 (where M is A/C and K is G/T). Furthermore, WebLogo analysis of a subset of promoters with coding sequences for 5′ untranslated regions (UTRs) larger than 4 nucleotides (nt) in
Sulfolobus solfataricus
P2 identified an Inr consensus that exactly matches the functional
araS
Inr sequence. Moreover, mutagenesis of 3 randomly selected promoters confirmed the Inr sequences to be important for basal promoter strength in the subgroup. Importantly, the result of the
araS
Inr being added to the Inr-less promoters indicates that the
araS
Inr, the core promoter element, is able to enhance the strength of Inr-less promoters. We infer that transcription factor B (TFB) and subunits of RNA polymerase bind the Inr to enhance promoter strength. Taken together, our data suggest that the presence or absence of an Inr on basal promoters is important for global gene regulation in
Sulfolobus
.