bluuebunny/crossref_metadata_2025 huggingface dataset:
The elemental abundances in interplanetary dust particles
Authors: ARNDT Peter , BOHSUNG Jörg , MAETZ Mischa , JESSBERGER Elmar K.
Published: August 2012

Abstract— We compiled a table of all major, minor, and trace‐element abundances in 89 interplanetary dust particles (IDPs) that includes data obtained with proton‐induced x‐ray emission (PIXE), synchroton x‐ray fluorescence (SXRF), and secondary ion mass spectrometry (SIMS). For the first time, the reliability of the trace‐element abundances in IDPs is tested by various crosschecks. We also report on the results of cluster analyses that we performed on IDP compositions. Because of the incompleteness of the data set, we included only the elements Cr, Mn, Ni, Cu, and Zn, normalized to Fe and CI chondrite abundances, that are determined in 73 IDPs. The data arrange themselves in four rather poorly defined groups that we discuss in relation to CI chondrites following the assumption that on the average CI abundances are most probable. The largest group (chondritic), with 44 members, has close to CI abundances for many refractory and moderately refractory elements (Na, Al, Si, P, K, Sc, Ti, V, Cr, Co, Ge, Sr). It is slightly depleted in Fe and more in Ca and S, while the volatile elements (Cl, Cu, Zn, Ga, Se, Rb) are enriched by =1.7 × CI and Br by 21 × CI. The low‐Zn group, with 12 members, is very similar to the chondritic group except for its Zn‐depletion, stronger Ca‐depletion and Fe‐enrichment. The low‐Ni group, with 11 members, has Ni/Fe = 0.03 × CI and almost CI‐like Ca, but its extraterrestrial origin is not established. The last group (6 members) contains non‐systematic particles of unknown origin. We found that Fe is inhomogeneously distributed on a micron scale. Furthermore, the abundances of elements that are measured near their limits of detection are easily overestimated. These biases involved, the incomplete data set and possible contaminating processes prevent us from obtaining information on the specific origin(s) of IDPs from elemental abundances.
Microstructure, chemistry, and origin of grain rims on ilmenite from the lunar soil finest fraction
Authors: CHRISTOFFERSEN Roy , McKay DAVID S. , KELLER Lindsay P.
Published: August 2012

Abstract— Analytical transmission electron microscope (TEM) observations reveal that ilmenite grains sampled from the sub‐10 μm size fraction of Apollo 11 (10084) and Apollo 16 (61221, 67701) soils have rims 10–300 nm thick that are chemically and microstructurally distinct from the host ilmenite. The rims have a thin outer sublayer 10–50 nm thick that contains the ilmenite‐incompatible elements Si, Al, Ca and S. This overlies a relatively thicker (50–250 nm) inner sublayer of nanocrystalline Ti‐oxide precipitates in a matrix of single‐crystal ilmenite that is structurally continuous with the underlying host grain. Microstructural information, as well as data from x‐ray spectrometry (EDS) and electron energy loss spectrometry (EELS) analysis of the inner sublayer, suggest that both the inner and outer sublayer assemblages are reduced and that the inner layer is depleted in Fe relative to the underlying ilmenite. The chemistry of the outer sublayer suggests that it is a surface deposit of sputtered or impact‐vaporized components from the bulk lunar soil. The inner sublayer is part of the original host grain that has been physically and chemically processed, but not amorphized, by solar ion irradiation and possibly some subsolidus heating. The fact that the deposited outer sublayer is consistently much thinner than the radiation‐altered inner sublayer indicates that only a minor fraction of the total rim volume is a product of vapor or sputter deposition. This finding is in contrast to recent descriptions of thick deposited layers on one‐third of regolith silicate grains and indicates that ilmenite and silicate rims as a group are different in the fraction of deposited material that they contain.
Lunar meteorite Queen Alexandra Range 93069 and the iron concentration of the lunar highlands surface
Authors: KOROTEV Randy L. , JOLLIFF Bradley L. , ROCKOW Kaylynn M.
Published: August 2012

Abstract— Lunar meteorite Queen Alexandra Range 93069 is a clast‐rich, glassy‐matrix regolith breccia of ferroan, highly aluminous bulk composition. It is similar in composition to other feldspathic lunar meteorites but differs in having higher concentrations of siderophile elements and incompatible trace elements. Based on electron microprobe analyses of the fusion crust, glassy matrix, and clasts, and instrumental neutron activation analysis of breccia fragments, QUE 93069 is dominated by nonmare components of ferroan, noriticanorthosite bulk composition. Thin section QUE 93069,31 also contains a large, impact‐melted, partially devitrified clast of magnesian, anorthositic‐norite composition. The enrichment in Fe, Sc, and Cr and lower Mg/Fe ratio of lunar meteorites Yamato 791197 and Yamato 82192/3 compared to other feldspathic lunar meteorites can be attributed to a small proportion (5–10%) of low‐Ti mare basalt. It is likely that the nonmare components of Yamato 82192/3 are similar to and occur in similar abundance to those of Yamato 86032, with which it is paired. There is a significant difference between the average FeO concentration of the lunar highlands surface as inferred from the feldspathic lunar meteorites (mean: ∼5.0%; range: 4.3–6.1%) and a recent estimate based on data from the Clementine mission (3.6%).
The Richfield LL3 chondrite
Authors: RUBIN Alan E. , BENOIT Paul , REED Blaine , EUGSTER Otto , POLNAU Ernst
Published: August 2012

Abstract— Richfield is a moderately shocked (shock stage S4) LL3.7 genomict breccia find consisting mainly of light‐colored recrystallized clasts and dark clasts exhibiting significant silicate darkening; a few impact‐melt‐rock clasts and LL5 chondrite clasts also occur. The cosmic‐ray exposure age of 14.5 Ma is indistinguishable from the main exposure peak for LL chondrites (15 Ma). Although the exposure ages indicate little He loss, the gas‐retention ages indicate high gas losses that must have occurred prior to or during ejection from the LL parent body.
Hfq‐dependent, co‐ordinate control of cyclic diguanylate synthesis and catabolism in the plague pathogen Yersinia pestis
Authors: Bellows Lauren E. , Koestler Benjamin J. , Karaba Sara M. , Waters Christopher M. , Lathem Wyndham W.
Published: August 2012

Yersinia pestis, the cause of the disease plague, forms biofilms to enhance flea‐to‐mammal transmission. Biofilm formation is dependent on exopolysaccharide synthesis and is controlled by the intracellular levels of the second messenger molecule cyclic diguanylate (c‐di‐GMP), but the mechanisms by which Y. pestis regulates c‐di‐GMP synthesis and turnover are not fully understood. Here we show that the small RNA chaperone Hfq contributes to the regulation of c‐di‐GMP levels and biofilm formation by modulating the abundance of both the c‐di‐GMP phosphodiesterase HmsP and the diguanylate cyclase HmsT. To do so, Hfq co‐ordinately promotes hmsP mRNA accumulation while simultaneously decreasing the stability of the hmsT transcript. Hfq‐dependent regulation of HmsP occurs at the transcriptional level while the regulation of HmsT is post‐transcriptional and is localized to the 5′ untranslated region/proximal coding sequence of the hmsT transcript. Decoupling HmsP from Hfq‐based regulation is sufficient to overcome the effects of Δhfq on c‐di‐GMP and biofilm formation. We propose that Y. pestis utilizes Hfq to link c‐di‐GMP levels to environmental conditions and that the disregulation of c‐di‐GMP turnover in the absence of Hfq may contribute to the severe attenuation of Y. pestis lacking this RNA chaperone in animal models of plague.
Altering the rest interval during high‐intensity interval training does not affect muscle or performance adaptations
Authors: Edge Johann , Eynon Nir , McKenna Michael J. , Goodman Craig A. , Harris Roger C. , Bishop David J.
Published: August 2012

New findings

What is the central question of this study?

Are exercise‐induced changes in metabolites and ions a crucial factor in the adaptation of contracting muscle? This was assessed by manipulating the rest period between high‐intensity intervals.

What is the main finding and its importance?

Our results suggest that the perturbation of muscle metabolites (specifically phophocreatine, lactate and H+) during high‐intensity interval training is not a crucial factor regulating related adaptations of the contracting muscle, when training intensity and volume are matched. This has implications for understanding the mechanisms that regulate muscle adaptations.

It has been hypothesized that exercise‐induced changes in metabolites and ions are crucial in the adaptation of contracting muscle. We tested this hypothesis by comparing adaptations to two different interval‐training protocols (differing only in the rest duration between intervals), which provoked different perturbations in muscle metabolites and acid–base status. Prior to and immediately after training, 12 women performed the following tests: (1) a graded exercise test to determine peak oxygen uptake (); (2) a high‐intensity exercise bout (followed 60 s later by a repeated‐sprint‐ability test; and (3) a repeat of the high‐intensity exercise bout alone with muscle biopsies pre‐exercise, immediately postexercise and after 60 s of recovery. Subjects performed 5 weeks (3 days per week) of training, with either a short (1 min; HIT‐1) or a long rest period (3 min; HIT‐3) between intervals; training intensity and volume were matched. Muscle [H+] (155 ± 15 versus 125 ± 8 nmol l−1; P < 0.05) and muscle lactate content (84.2 ± 7.9 versus 46.9 ± 3.1 mmol (g wet weight)−1) were both higher after HIT‐1, while muscle phosphocreatine (PCr) content (52.8 ± 8.3 versus 63.4 ± 9.8 mmol (g wet weight)−1) was lower. There were no significant differences between the two groups regarding the increases in , repeated‐sprint performance or muscle Na+,K+‐ATPase content. Following training, both groups had a significant decrease in postexercise muscle [H+] and lactate content, but not postexercise ATP or PCr. Postexercise PCr resynthesis increased following both training methods. In conclusion, intense interval training results in marked improvements in muscle Na+,K+‐ATPase content, PCr resynthesis and . However, manipulation of the rest period during intense interval training did not affect these changes.
A Damage Model for Adhesively Bonded Single-Lap Thick Composite Joints
Authors: Nassar Sayed A. , Mao Jianghui , Yang Xianjie , Templeton Douglas
Published: August 2012

A proposed damage model is used for investigating the deformation and interfacial failure behavior of an adhesively bonded single-lap thick joint made of S2 glass/SC-15 epoxy resin composite material. The bonding material is 3M Scotch-Weld Epoxy Adhesive DP405 Black. Continuum damage mechanics models are used to describe the damage initiation and final failure at or near the interface. The effect of adhesive overlap length, thickness, and plasticity on the interfacial shear and normal stresses is studied. Experimental and analytical data are used to validate the proposed damage models.
Optical and structural properties of low thickness lead zirconate titanate films on sapphire substrates prepared via sol-gel method
Authors: Garoli Denis , Natali Marco , Rigato Valentino , Romanato Filippo
Published: August 2012

Lead zirconate titanate (PZT) thin films in the range of 35–90 nm were deposited on a sapphire (1000) substrate using the sol-gel preparation method by diluting a PZT solution at different levels and using dichloromethane as the solvent. The microstructure, surface morphology, and stoichiometry of the films were studied by x-ray diffraction, atomic force microscopy, and Rutherford backscattering. Very smooth films characterized by single perovskite and mixed pyrochlore/perovskite polycrystalline phases were obtained and their optical properties were studied by spectroscopic ellipsometry in the ultraviolet–visible–near-infrared region. The refractive index was evaluated by analyzing the spectroscopic ellipsometry spectra. The ellipsometric data were also used to evaluate the bandgap energy of the films. The results show that the optical parameters of the films depend on the crystalline structure and demonstrate that higher bandgaps are obtained for perovskite films as compared to pyrochlore or mixed pyrochlore/perovskite structures. Data also confirm the higher bandgap of the amorphous structure compared to the polycrystalline PZT phases.
Magnetostatic focal spot correction for x‐ray tubes operating in strong magnetic fields using iterative optimization
Authors: Lillaney Prasheel , Shin Mihye , Conolly Steven M. , Fahrig Rebecca
Published: August 2012

Purpose:

Combining x‐ray fluoroscopy and MR imaging systems for guidance of interventional procedures has become more commonplace. By designing an x‐ray tube that is immune to the magnetic fields outside of the MR bore, the two systems can be placed in close proximity to each other. A major obstacle to robust x‐ray tube design is correcting for the effects of the magnetic fields on the x‐ray tube focal spot. A potential solution is to design active shielding that locally cancels the magnetic fields near the focal spot.

Methods:

An iterative optimization algorithm is implemented to design resistive active shielding coils that will be placed outside the x‐ray tube insert. The optimization procedure attempts to minimize the power consumption of the shielding coils while satisfying magnetic field homogeneity constraints. The algorithm is composed of a linear programming step and a nonlinear programming step that are interleaved with each other. The coil results are verified using a finite element space charge simulation of the electron beam inside the x‐ray tube. To alleviate heating concerns an optimized coil solution is derived that includes a neodymium permanent magnet. Any demagnetization of the permanent magnet is calculated prior to solving for the optimized coils. The temperature dynamics of the coil solutions are calculated using a lumped parameter model, which is used to estimate operation times of the coils before temperature failure.

Results:

For a magnetic field strength of 88 mT, the algorithm solves for coils that consume 588 A/cm2. This specific coil geometry can operate for 15 min continuously before reaching temperature failure. By including a neodymium magnet in the design the current density drops to 337 A/cm2, which increases the operation time to 59 min. Space charge simulations verify that the coil designs are effective, but for oblique x‐ray tube geometries there is still distortion of the focal spot shape along with deflections of approximately 3 mm in the radial and circumferential directions on the anode.

Conclusions:

Active shielding is an attractive solution for correcting the effects of magnetic fields on the x‐ray focal spot. If extremely long fluoroscopic exposure times are required, longer operation times can be achieved by including a permanent magnet with the active shielding design.
The Higgs Boson: Is the End in Sight?
Authors: Lincoln Don
Published: August 2012

This summer, perhaps while you were lounging around the pool in the blistering heat, the blogosphere was buzzing about data taken at the Large Hadron Collider1 at CERN. The buzz reached a crescendo in the first week of July when both Fermilab and CERN announced the results of their searches for the Higgs boson. Hard data confronted a theory nearly half a century old and the theory survived.
Sympathetic Resonance: A New Use for an Old Demonstration
Authors: Greenslade Thomas B.
Published: August 2012

I spent the 1972“73 academic year on sabbatical leave at the Kingston, Jamaica, campus of the University of the West Indies. One of my duties was to give Saturday morning enrichment lectures to the students, and the best one was on suspension bridges. The demonstration lecture then went on tour to high schools in Jamaica and the Cayman Islands. During the course of the talk, I “built ”the suspension bridge in Fig. 1; this picture was published in the January 1974 issue of The Physics Teacher.1
Measuring the axial magnetic field of a thin coil
Authors: Graf Erlend H.
Published: August 2012

A remarkably precise laboratory verification of the functional behavior of the magnetic field along the axis of a thin coil can be made with the apparatus described here and shown in Fig. 1.
Information fluency: Where to start
Authors: Viele Pat
Published: August 2012

There are many different definitions of information literacy, but perhaps the best succinct and comprehensive definition is: Information literacy (or fluency) is a set of abilities requiring individuals to “recognize when information is needed and have the ability to locate, evaluate, and use effectively the needed information.” This skill set will be invaluable throughout life in making informed decisions.
Cold-Inducible RNA-Binding Protein Modulates Circadian Gene Expression Posttranscriptionally
Authors: Morf Jörg , Rey Guillaume , Schneider Kim , Stratmann Markus , Fujita Jun , Naef Felix , Schibler Ueli
Published: August 2012

Transcription Around the Clock

The biological clock that controls daily rhythms in mammalian physiology and behavior is thought to be regulated in large part by transcriptional events (see the Perspective by

Doherty and Kay

).

Koike
et al.

(p.
349
; published online 30 August) produced a comprehensive analysis of these transcriptional events across the entire mouse liver genome over a 24-hour period. Only ∼22% of cycling messenger RNA transcripts were driven by de novo transcription, suggesting that posttranscriptional events also play an important regulatory role in the mammalian clock. Biological timing in organisms can also respond to rhythmic cues from the environment.

Morf
et al.

(p.
379
, published online 23 August) explored how one such cue, cycles in ambient temperature, influence circadian timing in mammalian cells. Cold-inducible RNA–binding protein (CIRP) accumulates when body temperature is low. A systematic search for binding partners of CIRP identified RNA encoding core components of the circadian clock. Loss of CIRP decreased the amplitude of circadian gene expression and cells lacking CIRP adapted more quickly to temperature cycles.
Synthesis and Characterization of a Rhodium(I) σ-Alkane Complex in the Solid State
Authors: Pike Sebastian D. , Thompson Amber L. , Algarra Andrés G. , Apperley David C. , Macgregor Stuart A. , Weller Andrew S.
Published: August 2012

Solid View of a Sigma Complex

For decades, it has been clear from kinetic studies that saturated hydrocarbons can also act as weak ligands, often just prior to bond cleavage reactions. These short-lived intermediates—termed “σ complexes” because the donated electrons reside in single (sigma symmetry) C-H bonds—have been glimpsed spectroscopically but have largely eluded full structural characterization.

Pike
et al.

(p.
1648
, published online 23 August) now present the crystallographic characterization of an alkane bound to rhodium, which they captured by direct hydrogenation of a more stable crystalline precursor incorporating an alkene.
Adhesion Functions in Cell Sorting by Mechanically Coupling the Cortices of Adhering Cells
Authors: Maître Jean-Léon , Berthoumieux Hélène , Krens Simon Frederik Gabriel , Salbreux Guillaume , Jülicher Frank , Paluch Ewa , Heisenberg Carl-Philipp
Published: August 2012

Embryonic Cell Sorting and Movement

Differential cell adhesion has long been thought to drive cell sorting.

Maître
et al.

(p.
253
, published online 23 August) show that cell sorting in zebrafish gastrulation is triggered by differences in the ability of cells to modulate cortex tension at cell-cell contacts, thereby controlling contact expansion. Cell adhesion functions in this process by mechanically coupling the cortices of adhering cells at their contacts, allowing cortex tension to control contact expansion. In zebrafish epiboly the enveloping cell layer (EVL)—a surface epithelium formed at the animal pole of the gastrula—gradually spreads over the entire yolk cell to engulf it at the end of gastrulation.

Behrndt
et al.

(p.
257
) show that an actomyosin ring connected to the epithelial margin triggers EVL spreading both by contracting around its circumference and by generating a pulling force through resistance against retrograde actomyosin flow.
Functional Analysis of Family GH36 α-Galactosidases from Ruminococcus gnavus E1: Insights into the Metabolism of a Plant Oligosaccharide by a Human Gut Symbiont
Authors: Cervera-Tison M. , Tailford L. E. , Fuell C. , Bruel L. , Sulzenbacher G. , Henrissat B. , Berrin J. G. , Fons M. , Giardina T. , Juge N.
Published: August 2012

Ruminococcus gnavus
belongs to the 57 most common species present in 90% of individuals. Previously, we identified an α-galactosidase (Aga1) belonging to glycoside hydrolase (GH) family 36 from
R. gnavus
E1 (M. Aguilera, H. Rakotoarivonina, A. Brutus, T. Giardina, G. Simon, and M. Fons, Res. Microbiol. 163:14–21, 2012). Here, we identified a novel GH36-encoding gene from the same strain and termed it
aga2
. Although
aga1
showed a very simple genetic organization,
aga2
is part of an operon of unique structure, including genes putatively encoding a regulator, a GH13, two phosphotransferase system (PTS) sequences, and a GH32, probably involved in extracellular and intracellular sucrose assimilation. The 727-amino-acid (aa) deduced Aga2 protein shares approximately 45% identity with Aga1. Both Aga1 and Aga2 expressed in
Escherichia coli
showed strict specificity for α-linked galactose. Both enzymes were active on natural substrates such as melibiose, raffinose, and stachyose. Aga1 and Aga2 occurred as homotetramers in solution, as shown by analytical ultracentrifugation. Modeling of Aga1 and Aga2 identified key amino acids which may be involved in substrate specificity and stabilization of the α-linked galactoside substrates within the active site. Furthermore, Aga1 and Aga2 were both able to perform transglycosylation reactions with α-(1,6) regioselectivity, leading to the formation of product structures up to [Hex]
12
and [Hex]
8
, respectively. We suggest that Aga1 and Aga2 play essential roles in the metabolism of dietary oligosaccharides and could be used for the design of galacto-oligosaccharide (GOS) prebiotics, known to selectively modulate the beneficial gut microbiota.
Genetic Linkage of Soil Carbon Pools and Microbial Functions in Subtropical Freshwater Wetlands in Response to Experimental Warming
Authors: Wang Hang , He Zhili , Lu Zhenmei , Zhou Jizhong , Van Nostrand Joy D. , Xu Xinhua , Zhang Zhijian
Published: August 2012

Rising climate temperatures in the future are predicted to accelerate the microbial decomposition of soil organic matter. A field microcosm experiment was carried out to examine the impact of soil warming in freshwater wetlands on different organic carbon (C) pools and associated microbial functional responses. GeoChip 4.0, a functional gene microarray, was used to determine microbial gene diversity and functional potential for C degradation. Experimental warming significantly increased soil pore water dissolved organic C and phosphorus (P) concentrations, leading to a higher potential for C emission and P export. Such losses of total organic C stored in soil could be traced back to the decomposition of recalcitrant organic C. Warming preferentially stimulated genes for degrading recalcitrant C over labile C. This was especially true for genes encoding cellobiase and
mnp
for cellulose and lignin degradation, respectively. We confirmed this with warming-enhanced polyphenol oxidase and peroxidase activities for recalcitrant C acquisition and greater increases in recalcitrant C use efficiency than in labile C use efficiency (average percentage increases of 48% versus 28%, respectively). The relative abundance of lignin-degrading genes increased by 15% under warming; meanwhile, soil fungi, as the primary decomposers of lignin, were greater in abundance by 27%. This work suggests that future warming may enhance the potential for accelerated fungal decomposition of lignin-like compounds, leading to greater microbially mediated C losses than previously estimated in freshwater wetlands.
Bioaugmentation of Syntrophic Acetate-Oxidizing Culture in Biogas Reactors Exposed to Increasing Levels of Ammonia
Authors: Westerholm Maria , Levén Lotta , Schnürer Anna
Published: August 2012

The importance of syntrophic acetate oxidation for process stability in methanogenic systems operating at high ammonia concentrations has previously been emphasized. In this study we investigated bioaugmentation of syntrophic acetate-oxidizing (SAO) cultures as a possible method for decreasing the adaptation period of biogas reactors operating at gradually increased ammonia concentrations (1.5 to 11 g NH
4
+
-N/liter). Whole stillage and cattle manure were codigested semicontinuously for about 460 days in four mesophilic anaerobic laboratory-scale reactors, and a fixed volume of SAO culture was added daily to two of the reactors. Reactor performance was evaluated in terms of biogas productivity, methane content, pH, alkalinity, and volatile fatty acid (VFA) content. The decomposition pathway of acetate was analyzed by isotopic tracer experiments, and population dynamics were monitored by quantitative PCR analyses. A shift in dominance from aceticlastic methanogenesis to SAO occurred simultaneously in all reactors, indicating no influence by bioaugmentation on the prevailing pathway. Higher abundances of
Clostridium ultunense
and
Tepidanaerobacter acetatoxydans
were associated with bioaugmentation, but no influence on
Syntrophaceticus schinkii
or the methanogenic population was distinguished. Overloading or accumulation of VFA did not cause notable dynamic effects on the population. Instead, the ammonia concentration had a substantial impact on the abundance level of the microorganisms surveyed. The addition of SAO culture did not affect process performance or stability against ammonia inhibition, and all four reactors deteriorated at high ammonia concentrations. Consequently, these findings further demonstrate the strong influence of ammonia on the methane-producing consortia and on the representative methanization pathway in mesophilic biogas reactors.
Detection of Botulinum Neurotoxin Serotype A, B, and F Proteolytic Activity in Complex Matrices with Picomolar to Femtomolar Sensitivity
Authors: Dunning F. Mark , Ruge Daniel R. , Piazza Timothy M. , Stanker Larry H. , Zeytin Füsûn N. , Tucker Ward C.
Published: August 2012

Rapid, high-throughput assays that detect and quantify botulinum neurotoxin (BoNT) activity in diverse matrices are required for environmental, clinical, pharmaceutical, and food testing. The current standard, the mouse bioassay, is sensitive but is low in throughput and precision. In this study, we present three biochemical assays for the detection and quantification of BoNT serotype A, B, and F proteolytic activities in complex matrices that offer picomolar to femtomolar sensitivity with small assay volumes and total assay times of less than 24 h. These assays consist of magnetic beads conjugated with BoNT serotype-specific antibodies that are used to purify BoNT from complex matrices before the quantification of bound BoNT proteolytic activity using the previously described BoTest reporter substrates. The matrices tested include human serum, whole milk, carrot juice, and baby food, as well as buffers containing common pharmaceutical excipients. The limits of detection were below 1 pM for BoNT/A and BoNT/F and below 10 pM for BoNT/B in most tested matrices using 200-μl samples and as low as 10 fM for BoNT/A with an increased sample volume. Together, these data describe rapid, robust, and high-throughput assays for BoNT detection that are compatible with a wide range of matrices.
Interspecies Electron Transfer via Hydrogen and Formate Rather than Direct Electrical Connections in Cocultures of Pelobacter carbinolicus and Geobacter sulfurreducens
Authors: Rotaru Amelia-Elena , Shrestha Pravin M. , Liu Fanghua , Ueki Toshiyuki , Nevin Kelly , Summers Zarath M. , Lovley Derek R.
Published: August 2012

Direct interspecies electron transfer (DIET) is an alternative to interspecies H
2
/formate transfer as a mechanism for microbial species to cooperatively exchange electrons during syntrophic metabolism. To understand what specific properties contribute to DIET, studies were conducted with
Pelobacter carbinolicus
, a close relative of
Geobacter metallireducens
, which is capable of DIET.
P. carbinolicus
grew in coculture with
Geobacter sulfurreducens
with ethanol as the electron donor and fumarate as the electron acceptor, conditions under which
G. sulfurreducens
formed direct electrical connections with
G. metallireducens
. In contrast to the cell aggregation associated with DIET,
P. carbinolicus
and
G. sulfurreducens
did not aggregate. Attempts to initiate cocultures with a genetically modified strain of
G. sulfurreducens
incapable of both H
2
and formate utilization were unsuccessful, whereas cocultures readily grew with mutant strains capable of formate but not H
2
uptake or vice versa. The hydrogenase mutant of
G. sulfurreducens
compensated, in cocultures, with significantly increased formate dehydrogenase gene expression. In contrast, the transcript abundance of a hydrogenase gene was comparable in cocultures with that for the formate dehydrogenase mutant of
G. sulfurreducens
or the wild type, suggesting that H
2
was the primary electron carrier in the wild-type cocultures. Cocultures were also initiated with strains of
G. sulfurreducens
that could not produce pili or OmcS, two essential components for DIET. The finding that
P. carbinolicus
exchanged electrons with
G. sulfurreducens
via interspecies transfer of H
2
/formate rather than DIET demonstrates that not all microorganisms that can grow syntrophically are capable of DIET and that closely related microorganisms may use significantly different strategies for interspecies electron exchange.
High-Salinity Growth Conditions Promote Tat-Independent Secretion of Tat Substrates in Bacillus subtilis
Authors: van der Ploeg René , Monteferrante Carmine G. , Piersma Sjouke , Barnett James P. , Kouwen Thijs R. H. M. , Robinson Colin , van Dijl Jan Maarten
Published: August 2012

The Gram-positive bacterium
Bacillus subtilis
contains two Tat translocases, which can facilitate transport of folded proteins across the plasma membrane. Previous research has shown that Tat-dependent protein secretion in
B. subtilis
is a highly selective process and that heterologous proteins, such as the green fluorescent protein (GFP), are poor Tat substrates in this organism. Nevertheless, when expressed in
Escherichia coli
, both
B. subtilis
Tat translocases facilitated exclusively Tat-dependent export of folded GFP when the twin-arginine (RR) signal peptides of the
E. coli
AmiA, DmsA, or MdoD proteins were attached. Therefore, the present studies were aimed at determining whether the same RR signal peptide-GFP precursors would also be exported Tat dependently in
B. subtilis
. In addition, we investigated the secretion of GFP fused to the full-length YwbN protein, a strict Tat substrate in
B. subtilis
. Several investigated GFP fusion proteins were indeed secreted in
B. subtilis
, but this secretion was shown to be completely Tat independent. At high-salinity growth conditions, the Tat-independent secretion of GFP as directed by the RR signal peptides from the
E. coli
AmiA, DmsA, or MdoD proteins was significantly enhanced, and this effect was strongest in strains lacking the TatAy-TatCy translocase. This implies that high environmental salinity has a negative influence on the avoidance of Tat-independent secretion of AmiA-GFP, DmsA-GFP, and MdoD-GFP. We conclude that as-yet-unidentified control mechanisms reject the investigated GFP fusion proteins for translocation by the
B. subtilis
Tat machinery and, at the same time, set limits to their Tat-independent secretion, presumably via the Sec pathway.
RcsB Contributes to the Distinct Stress Fitness among Escherichia coli O157:H7 Curli Variants of the 1993 Hamburger-Associated Outbreak Strains
Authors: Carter Michelle Q. , Parker Craig T. , Louie Jacqueline W. , Huynh Steven , Fagerquist Clifton K. , Mandrell Robert E.
Published: August 2012

Curli are adhesive fimbriae of
Enterobactericaeae
and are involved in surface attachment, cell aggregation, and biofilm formation. We reported previously that curli-producing (C
+
) variants of
E. coli
O157:H7 (EcO157) were much more acid sensitive than their corresponding curli-deficient (C
−
) variants; however, this difference was not linked to the curli fimbriae
per se
. Here, we investigated the underlying molecular basis of this phenotypic divergence. We identified large deletions in the
rcsB
gene of C
+
variants isolated from the 1993 U.S. hamburger-associated outbreak strains.
rcsB
encodes the response regulator of the RcsCDB two-component signal transduction system, which regulates curli biogenesis negatively but acid resistance positively. Further comparison of stress fitness revealed that C
+
variants were also significantly more sensitive to heat shock but were resistant to osmotic stress and oxidative damage, similar to C
−
variants. Transcriptomics analysis uncovered a large number of differentially expressed genes between the curli variants, characterized by enhanced expression in C
+
variants of genes related to biofilm formation, virulence, catabolic activity, and nutrient uptake but marked decreases in transcription of genes related to various types of stress resistance. Supplying C
+
variants with a functional
rcsB
restored resistance to heat shock and acid challenge in cells but blocked curli production, confirming that inactivation of RcsB in C
+
variants was the basis of fitness segregation within the EcO157 population. This study provides an example of how genome instability of EcO157 promotes intrapopulation diversification, generating subpopulations carrying an array of distinct phenotypes that may confer the pathogen with survival advantages in diverse environments.
Evidence of
In Vivo
Prophage Induction during Clostridium difficile Infection
Authors: Meessen-Pinard Mathieu , Sekulovic Ognjen , Fortier Louis-Charles
Published: August 2012

Prophages contribute to the evolution and virulence of most bacterial pathogens, but their role in
Clostridium difficile
is unclear. Here we describe the isolation of four
Myoviridae
phages, ϕMMP01, ϕMMP02, ϕMMP03, and ϕMMP04, that were recovered as free viral particles in the filter-sterilized stool supernatants of patients suffering from
C. difficile
infection (CDI). Furthermore, identical prophages were found in the chromosomes of
C. difficile
isolated from the corresponding fecal samples. We therefore provide, for the first time, evidence of
in vivo
prophage induction during CDI. We completely sequenced the genomes of ϕMMP02 and ϕMMP04, and bioinformatics analyses did not reveal the presence of virulence factors but underlined the unique character of ϕMMP04. We also studied the mobility of ϕMMP02 and ϕMMP04 prophages
in vitro
. Both prophages were spontaneously induced, with 4 to 5 log PFU/ml detected in the culture supernatants of the corresponding lysogens. When lysogens were grown in the presence of subinhibitory concentrations of ciprofloxacin, moxifloxacin, levofloxacin, or mitomycin C, the phage titers further increased, reaching 8 to 9 log PFU/ml in the case of ϕMMP04. In summary, our study highlights the extensive genetic diversity and mobility of
C. difficile
prophages. Moreover, antibiotics known to represent risk factors for CDI, such as quinolones, can stimulate prophage mobility
in vitro
and probably
in vivo
as well, which underscores their potential impact on phage-mediated horizontal gene transfer events and the evolution of
C. difficile
.
Dynamics and Innovations within Oomycete Genomes: Insights into Biology, Pathology, and Evolution
Authors: Judelson Howard S.
Published: August 2012

The eukaryotic microbes known as oomycetes are common inhabitants of terrestrial and aquatic environments and include saprophytes and pathogens. Lifestyles of the pathogens extend from biotrophy to necrotrophy, obligate to facultative pathogenesis, and narrow to broad host ranges on plants or animals. Sequencing of several pathogens has revealed striking variation in genome size and content, a plastic set of genes related to pathogenesis, and adaptations associated with obligate biotrophy. Features of genome evolution include repeat-driven expansions, deletions, gene fusions, and horizontal gene transfer in a landscape organized into gene-dense and gene-sparse sectors and influenced by transposable elements. Gene expression profiles are also highly dynamic throughout oomycete life cycles, with transcriptional polymorphisms as well as differences in protein sequence contributing to variation. The genome projects have set the foundation for functional studies and should spur the sequencing of additional species, including more diverse pathogens and nonpathogens.
The Three Clades of the Telomere-Associated
TLO
Gene Family of Candida albicans Have Different Splicing, Localization, and Expression Features
Authors: Anderson Matthew Z. , Baller Joshua A. , Dulmage Keely , Wigen Lauren , Berman Judith
Published: August 2012

Candida albicans
grows within a wide range of host niches, and this adaptability enhances its success as a commensal and as a pathogen. The telomere-associated
TLO
gene family underwent a recent expansion from one or two copies in other CUG clade members to 14 expressed copies in
C. albicans
. This correlates with increased virulence and clinical prevalence relative to those of other
Candida
clade species. The 14 expressed
TLO
gene family members have a conserved Med2 domain at the N terminus, suggesting a role in general transcription. The C-terminal half is more divergent, distinguishing three clades: clade α and clade β have no introns and encode proteins that localize primarily to the nucleus; clade γ sometimes undergoes splicing, and the gene products localize within the mitochondria as well as the nuclei. Additionally,
TLO
α genes are generally expressed at much higher levels than are
TLO
γ genes. We propose that expansion of the
TLO
gene family and the predicted role of Tlo proteins in transcription regulation provide
C. albicans
with the ability to adapt rapidly to the broad range of different environmental niches within the human host.
Functional Characterization of the RNA Chaperone Hfq in the Opportunistic Human Pathogen Stenotrophomonas maltophilia
Authors: Roscetto Emanuela , Angrisano Tiziana , Costa Valerio , Casalino Mariassunta , Förstner Konrad U. , Sharma Cynthia M. , Di Nocera Pier Paolo , De Gregorio Eliana
Published: August 2012

Hfq is an RNA-binding protein known to regulate a variety of cellular processes by interacting with small RNAs (sRNAs) and mRNAs in prokaryotes.
Stenotrophomonas maltophilia
is an important opportunistic pathogen affecting primarily hospitalized and immunocompromised hosts. We constructed an
hfq
deletion mutant (Δ
hfq
) of
S. maltophilia
and compared the behaviors of wild-type and Δ
hfq S. maltophilia
cells in a variety of assays. This revealed that
S. maltophilia
Hfq plays a role in biofilm formation and cell motility, as well as susceptibility to antimicrobial agents. Moreover, Hfq is crucial for adhesion to bronchial epithelial cells and is required for the replication of
S. maltophilia
in macrophages. Differential RNA sequencing analysis (dRNA-seq) of RNA isolated from
S. maltophilia
wild-type and Δ
hfq
strains showed that Hfq regulates the expression of genes encoding flagellar and fimbrial components, transmembrane proteins, and enzymes involved in different metabolic pathways. Moreover, we analyzed the expression of several sRNAs identified by dRNA-seq in wild-type and Δ
hfq
S. maltophilia
cells grown in different conditions on Northern blots. The accumulation of two sRNAs was strongly reduced in the absence of Hfq. Furthermore, based on our dRNA-seq analysis we provide a genome-wide map of transcriptional start sites in
S. maltophilia
.
Localization of Poly(3-Hydroxybutyrate) (PHB) Granule-Associated Proteins during PHB Granule Formation and Identification of Two New Phasins, PhaP6 and PhaP7, in Ralstonia eutropha H16
Authors: Pfeiffer Daniel , Jendrossek Dieter
Published: August 2012

Poly(3-hydroxybutyrate) (PHB) granules are covered by a surface layer consisting of mainly phasins and other PHB granule-associated proteins (PGAPs). Phasins are small amphiphilic proteins that determine the number and size of accumulated PHB granules. Five phasin proteins (PhaP1 to PhaP5) are known for
Ralstonia eutropha
. In this study, we identified three additional potential phasin genes (H16_B1988, H16_B2296, and H16_B2326) by inspection of the
R. eutropha
genome for sequences with “phasin 2 motifs.” To determine whether the corresponding proteins represent true PGAPs, fusions with eYFP (enhanced yellow fluorescent protein) were constructed. Similar fusions of eYFP with PhaP1 to PhaP5 as well as fusions with PHB synthase (PhaC1), an inactive PhaC1 variant (PhaC1-C319A), and PhaC2 were also made. All fusions were investigated in wild-type and PHB-negative backgrounds. Colocalization with PHB granules was found for all PhaC variants and for PhaP1 to PhaP5. Additionally, eYFP fusions with H16_B1988 and H16_B2326 colocalized with PHB. Fusions of H16_B2296 with eYFP, however, did not colocalize with PHB granules but did colocalize with the nucleoid region. Notably, all fusions (except H16_B2296) were soluble in a Δ
phaC1
strain. These data confirm that H16_B1988 and H16_B2326 but not H16_B2296 encode true PGAPs, for which we propose the designation PhaP6 (H16_B1988) and PhaP7 (H16_B2326). When localization of phasins was investigated at different stages of PHB accumulation, fusions of PhaP6 and PhaP7 were soluble in the first 3 h under PHB-permissive conditions, although PHB granules appeared after 10 min. At later time points, the fusions colocalized with PHB. Remarkably, PHB granules of strains expressing eYFP fusions with PhaP5, PhaP6, or PhaP7 localized predominantly near the cell poles or in the area of future septum formation. This phenomenon was not observed for the other PGAPs (PhaP1 to PhaP4, PhaC1, PhaC1-C319A, and PhaC2) and indicated that some phasins can have additional functions. A chromosomal deletion of
phaP6
or
phaP7
had no visible effect on formation of PHB granules.
Whole Surface Image of Mycoplasma mobile, Suggested by Protein Identification and Immunofluorescence Microscopy
Authors: Wu Heng Ning , Miyata Makoto
Published: August 2012

Mycoplasma mobile
, a freshwater fish pathogen featured with robust gliding motility, binds to the surface of the gill, where it then colonizes. Here, to obtain a whole image of its cell surface, we identified the proteins exposed on the surface using the following methods. (i) The cell surface was labeled with sulfosuccinimidyl-6-(biotinamido) hexanoate and recovered by an avidin column. (ii) The cells were subjected to phase partitioning using Triton X-114, and the hydrophobic proteins were recovered. (iii) The membrane fraction was analyzed by two-dimensional gel electrophoresis. These recovered proteins were subjected to peptide mass fingerprinting, and a final list of 36 expressed surface proteins was established. The ratio of identified proteins to whole surface proteins was estimated through two-dimensional gel electrophoresis of the membrane fraction. The localization of three newly found proteins, Mvsps C, E, and F, has been clarified by immunofluorescence microscopy. Integrating all information, a whole image of the cell surface showed that the proteins for gliding that were localized at the base of the protrusion of flask-shaped
M. mobile
account for more than 12% of all surface proteins and that Mvsps, surface variants that were localized at both parts other than the neck, account for 49% of all surface proteins.
Characterization of Novel Phages Isolated in Coagulase-Negative Staphylococci Reveals Evolutionary Relationships with Staphylococcus aureus Phages
Authors: Deghorain Marie , Bobay Louis-Marie , Smeesters Pierre R. , Bousbata Sabrina , Vermeersch Marjorie , Perez-Morga David , Drèze Pierre-Alexandre , Rocha Eduardo P. C. , Touchon Marie , Van Melderen Laurence
Published: August 2012

Despite increasing interest in coagulase-negative staphylococci (CoNS), little information is available about their bacteriophages. We isolated and sequenced three novel temperate
Siphoviridae
phages (StB12, StB27, and StB20) from the CoNS
Staphylococcus hominis
and
S. capitis
species. The genome sizes are around 40 kb, and open reading frames (ORFs) are arranged in functional modules encoding lysogeny, DNA metabolism, morphology, and cell lysis. Bioinformatics analysis allowed us to assign a potential function to half of the predicted proteins. Structural elements were further identified by proteomic analysis of phage particles, and DNA-packaging mechanisms were determined. Interestingly, the three phages show identical integration sites within their host genomes. In addition to this experimental characterization, we propose a novel classification based on the analysis of 85 phage and prophage genomes, including 15 originating from CoNS. Our analysis established 9 distinct clusters and revealed close relationships between
S. aureus
and CoNS phages. Genes involved in DNA metabolism and lysis and potentially in phage-host interaction appear to be widespread, while structural genes tend to be cluster specific. Our findings support the notion of a possible reciprocal exchange of genes between phages originating from
S. aureus
and CoNS, which may be of crucial importance for pathogenesis in staphylococci.
Three Mutations in Escherichia coli That Generate Transformable Functional Flagella
Authors: Wang Wenjing , Jiang Zhengzeng , Westermann Martin , Ping Liyan
Published: August 2012

Hydrodynamics predicts that swimming bacteria generate a propulsion force when a helical flagellum rotates because rotating helices necessarily translate at a low Reynolds number. It is generally believed that the flagella of motile bacteria are semirigid helices with a fixed pitch determined by hydrodynamic principles. Here, we report the characterization of three mutations in laboratory strains of
Escherichia coli
that produce different steady-state flagella without losing cell motility.
E. coli
flagella rotate counterclockwise during forward swimming, and the normal form of the flagella is a left-handed helix. A single amino acid exchange A45G and a double mutation of A48S and S110A change the resting flagella to right-handed helices. The stationary flagella of the triple mutant were often straight or slightly curved at neutral pH. Deprotonation facilitates the helix formation of it. The helical and curved flagella can be transformed to the normal form by torsion upon rotation and thus propel the cell. These mutations arose in the long-term laboratory cultivation. However, flagella are under strong selection pressure as extracellular appendages, and similar transformable flagella would be common in natural environments.