bluuebunny/crossref_metadata_2025_split huggingface dataset:
S‐type asteroids, ordinary chondrites, and space weathering: The evidence from Galileo's fly‐bys of Gaspra and Ida
Authors: CHAPMAN Clark R. 
Published: August 2012

Abstract— New observations of the S‐type asteroids Gaspra and Ida, especially, by the Galileo spacecraft demonstrate that a “space weathering” process operates, which modifies the reflectance spectra of fresh material to be redder, straighter, and have shallower absorption bands. The weathering process appears similar to but less potent than that observed on the Moon. It operates in the sense that it would tend to convert spectra of ordinary chondrites (OC) to having the spectral traits of S‐type asteroids. These results appear to resolve the major obstacles of the long standing “S‐type conundrum” about the provenance of ordinary chondrite meteorites. A wide body of recent research, which is reviewed here, builds on previous meteoritical evidence to support a new, developing consensus that the larger S‐type asteroids are a diverse assortment of silicaceous assemblages, which includes the ordinary chrondite parent bodies. Recent fairly realistic laboratory simulations of space weathering processes have changed OC spectra to resemble S‐type spectra. J. F. Bell's highly regarded earlier paradigm that OC parent bodies would be found only among sub‐10 km main‐belt asteroids has been tested by an extensive observational survey by R. Binzel and his proteges; the result is that no small, main‐belt analog for the OCs has been found, not even the somewhat OC‐like object Boznemcová.This article reviews the history of the S‐type conundrum, which set the stage for Galileo's historic flybys. I review the findings about Gaspra and Ida, including results about their geology, their geophysical structure and probable origins, and about Ida's small moonlet, Dactyl. Density constraints on Ida set by Dactyl's orbit rule out (for Ida, at least) the classic view of S‐types as metallic, stripped cores of differentiated precursor asteroids. New analysis of the Galileo spectral images of Ida is presented that provides strong evidence that space weathering occurs on Ida, and that Ida, and the Koronis family asteroids in general, are plausibly OC‐like in composition. After reviewing 1990s developments on the S‐type conundrum, I advocate a new perspective that the ordinary chondrite parent bodies are among the S‐type asteroids, a diverse grouping that also contains other silicaceous and silicate/metal assemblages, presumably including various stony‐irons and primitive achondrites represented in meteorite collections; Gaspra may be such a metal‐rich assemblage.
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

SummaryYersinia 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.
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.
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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.