bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pressure‐induced incipient amorphization of α‐quartz and transition to coesite in an eclogite from Antarctica: a first record and some consequences
Authors: PALMERI R. , FREZZOTTI M. L. , GODARD G. , DAVIES R. J. 
Published: September 2009

AbstractMonocrystalline quartz inclusions in garnet and omphacite from various eclogite samples from the Lanterman Range (Northern Victoria Land, Antarctica) have been investigated by cathodoluminescence (CL), Raman spectroscopy and imaging, and in situ X‐ray (XR) microdiffraction using the synchrotron. A few inclusions, with a clear‐to‐opalescent lustre, show ‘anomalous’ Raman spectra characterized by weak α‐quartz modes, the broadening of the main α‐quartz peak at 465 cm−1, and additional vibrations at 480–485, 520–523 and 608 cm−1. CL and Raman imaging indicate that this ‘anomalous’α‐quartz occurs as relicts within ordinary α‐quartz, and that it was preserved in the internal parts of small quartz inclusions. XR diffraction circular patterns display irregular and broad α‐quartz spots, some of which show an anomalous d‐spacing tightening of ∼2%. They also show some very weak, hazy clouds that have d‐spacing compatible with coesite but not with α‐quartz. Raman spectrometry and XR microdiffraction characterize the anomalies with respect to α‐quartz as (i) a pressure‐induced disordering and incipient amorphization, mainly revealed by the 480–485 and 608‐cm−1 Raman bands, together with (ii) a lattice densification, evidenced by d‐spacing tightening; (iii) the cryptic development of coesite, 520–523 cm−1 being the main Raman peak of coesite and (iv) Brazil micro‐twinning. This ‘anomalous’α‐quartz represents the first example of pressure‐induced incipient amorphization of a metastable phase in a crustal rock. This issue is really surprising because pressure‐induced amorphization of metastable α‐quartz, observed in impactites and known to occur between 15 and 32 GPa during ultrahigh‐pressure (UHP) experiments at room temperature, is in principle irrelevant under normal geological P–T conditions. A shock (due to a seism?) or a local overpressure at the inclusion scale (due to expansion mismatch between quartz and its host mineral) seem the only geological mechanisms that can produce such incipient amorphization in crustal rocks. This discovery throws new light on the modality of the quartz‐coesite transition and on the pressure regimes (non‐lithostatic v. lithostatic) during high‐pressure/UHP metamorphism. In particular, incipient amorphization of quartz could favour the quartz‐coesite transition, or allow the growth of metastable coesite, as already experimentally observed.
Strain‐dependent activation of the mouse immune response is correlated with Porphyromonas gingivalis‐induced experimental periodontitis
Authors: Wilensky Asaf , Polak David , Awawdi Suhair , Halabi Amal , Shapira Lior , Houri‐Haddad Yael 
Published: September 2009

AbstractAims: To evaluate the effect of oral infection with three Porphyromonas gingivalis strains on alveolar bone loss (ABL) and its correlation with the mouse immune response.Materials and Methods: Mice were orally infected with P. gingivalis strains 381, 33277 and 53977. After 42 days, maxillae were analysed for ABL using micro‐computed tomography and the serum for anti‐P.gingivalis IgG1 and IgG2a levels. The cytokine response to P. gingivalis was tested using the subcutaneous chamber model.Results: The P. gingivalis 53977‐infected group showed the highest ABL, which was significantly different from all other groups (p<0.001). In addition, the humoral response to P. gingivalis 53977 was significantly lower than the response to P. gingivalis 381 and 33277 (p0.01). The IgG2a/IgG1 ratio was higher in the P. gingivalis 33277‐infected group (1.6) compared with the P. gingivalis 381‐infected group (0.51). Four days post‐infection, interleukin (IL)‐1β levels remained significantly higher in the P. gingivalis 53977‐infected group only (1198.2±260.0, p<0.05), while IL‐4 levels remained significantly higher in the P. gingivalis 381‐infected group (265.8±131.6, p<0.05).Conclusions: The high levels of ABL induced by P. gingivalis 53977 were inversely correlated with the humoral response to this bacterium. In addition, ABL was correlated with an elevated pro‐inflammatory response.
Surface‐conditioned dental implants: an animal study on bone formation
Authors: Stadlinger Bernd , Lode Anna Theresa , Eckelt Uwe , Range Ursula , Schlottig Falko , Hefti Thomas , Mai Ronald 
Published: September 2009

AbstractAim: The aim of this study was to determine whether bone formation around surface‐conditioned implants is enhanced compared with non‐surface‐conditioned sandblasted acid‐etched titanium implants.Materials and Methods: One hundred and forty‐four implants were placed in the mandible of 18 minipigs. Before placement, implants were either surface conditioned in a solution containing hydroxide ions (conSF) or assigned to controls. Animals were euthanized after 2, 4 and 8 weeks of submerged healing, the 8‐week group receiving polyfluorochrome labelling at week 2, 4, 6 and 8. One jaw quadrant per animal was selected for histological and histomorphometrical evaluation of mineralized bone–implant contact (mBIC), osteoid–implant contact (OIC) and bone volume (BV) analysis.Results: Polyfluorochrome labelling showed no general differences in bone dynamics. mBIC showed the most pronounced differences after 2 weeks, reaching 65.5% for conSF compared with 48.1% for controls, p=0.270. Differences levelled out after 4 weeks (67.4% control, 65.7% conSF) and 8 weeks (64.0% control, 70.2% conSF). OIC levels were initially comparable, showing a slower decline for conSF after 4 weeks. BV was higher for conSF at all times. No significant differences could be found.Conclusion: A tendency towards increased mBIC was shown for surface‐conditioned implants after short‐term healing.
Individualized developmental care for a large sample of very preterm infants: health, neurobehaviour and neurophysiology
Authors: McAnulty G , Duffy FH , Butler S , Parad R , Ringer S , Zurakowski D , Als H 
Published: September 2009

AbstractAim:  To assess medical and neurodevelopmental effects of Newborn Individualized Developmental Care and Assessment Program (NIDCAP) for a large sample of very early‐born infants.Methods:  One hundred and seven singleton inborn preterm infants, <29 weeks gestational age (GA), <1250 g birth weight, enrolled in three consecutive phases, were randomized within phase to NIDCAP (treatment, E) or standard care (C). Treatment extended from admission to the Newborn Intensive Care Unit to 2 weeks corrected age (wCA). Outcome included medical, neurobehavioural and neurophysiological status at 2 wCA, and growth and neurobehavioural status at 9 months (m) CA.Results:  The C‐ and E‐group within each of the three consecutive phases and across the three phases were comparable in terms of all background measures; they therefore were treated as one sample. The results indicated for the E‐group significant reduction in major medical morbidities of prematurity as well as significantly improved neurodevelopmental (behaviour and electrophysiology) functioning at 2 wCA; significantly better neurobehavioural functioning was also found at 9 mCA.Conclusion:  The NIDCAP is an effective treatment for very early‐born infants. It reduces health morbidities and enhances neurodevelopment, functional competence and life quality for preterm infants at 2 w and 9 mCA.
A new cost‐distance model for human accessibility and an evaluation of accessibility bias in permanent vegetation plots in Great Smoky Mountains National Park, USA
Authors: Jobe R. Todd , White Peter S. 
Published: September 2009

AbstractQuestion: Can a new cost‐distance model help us to evaluate the potential for accessibility bias in ecological observations? How much accessibility bias is present in the vegetation monitoring plots accumulated over the last three decades in Great Smoky Mountains National Park?Location: Great Smoky Mountains National Park, North Carolina and Tennessee, USA.Methods: Distance, slope, stream crossings, and vegetation density were incorporated into a least‐cost model of energetic expenditure for human access to locations.Results: Estimated round‐trip energy costs for the park ranged from 0  to 1.62 × 105 J kg−1. The estimated round‐trip energetic expenditure for the surveys ranged from 53 to 1.51 × 105 J kg−1. Their distribution was more accessible than the random expectation. Ten (17%) of the vegetation types in the park are significantly under‐sampled relative to their area, and 16 (29%) are over‐sampled. Plots in 18 of the 40 vegetation types exhibited a significant positive correlation with accessibility.Conclusions: The least‐cost model is an improvement over previous attempts to quantify accessibility. The bias in plot locations suggests using a least‐cost model to test for bias in cases in which human accessibility is confounded with other sources of ecosystem variation.
Transformative Knowledge Transfer Through Empowering and Paying Community Researchers
Authors: Garnett Stephen T. , Crowley Gabriel M. , Hunter‐Xenie Hmalan , Kozanayi Witness , Sithole Bevlyne , Palmer Carol , Southgate Richard , Zander Kerstin K. 
Published: September 2009

ABSTRACTEnvironmental research is often conducted independently of the community in which the environment is situated, with transfer of results into policy and on‐ground action occurring independently of the community's interests or aspirations. Increasingly the need for greater community involvement in the research process has been recognized. For community members, however, such engagement usually involves trade‐offs. While it is often assumed that community members should participate voluntarily because they will gain from the research, any benefits from knowledge, understanding and a capacity to influence the research have to be offset against time and potential loss of unremunerated intellectual property. We argue, using case studies from tropical Australia and Africa, that a more effective means of engagement and knowledge transfer is training and remuneration of community members as coresearchers. This engagement is much more than payment for labor—it is investment in local intellectual property and requires researcher humility, power‐sharing and recognition that access to research funding provides no moral or intellectual authority. Further, we argue that, for effective adoption of research results, community members need to be part of negotiated agreements on the initial nature of the research to ensure it answers questions of genuine local relevance and that local researchers have the capacity to place locally conducted research into a wider context. We argue that immediate rewards for involvement not only secure engagement but, where appropriate, are likely to lead to effective implementation of research results, enhanced local capacity and greater equity in intellectual power‐sharing.
Thermotolerant Coliforms Are Not a Good Surrogate for
Campylobacter
spp. in Environmental Water
Authors: St-Pierre Karen , Lévesque Simon , Frost Eric , Carrier Nathalie , Arbeit Robert D. , Michaud Sophie 
Published: September 2009

ABSTRACT

This study aimed to assess the importance of quantitatively detecting
Campylobacter
spp. in environmental surface water. The prevalence and the quantity of
Campylobacter
spp., thermotolerant coliforms, and
Escherichia coli
in 2,471 samples collected weekly, over a 2-year period, from 13 rivers and 12 streams in the Eastern Townships, Québec, Canada, were determined. Overall, 1,071 (43%), 1,481 (60%), and 1,463 (59%) samples were positive for
Campylobacter
spp., thermotolerant coliforms, and
E. coli
, respectively. There were weak correlations between the weekly distributions of
Campylobacter
spp. and thermotolerant coliforms (Spearman's ρ coefficient = 0.27;
P
= 0.008) and between the quantitative levels of the two classes of organisms (Kendall tau-b correlation coefficient = 0.233;
P
< 0.0001). Well water samples from the Eastern Townships were also tested. Five (10%) of 53 samples from private surface wells were positive for
Campylobacter jejuni
, of which only 2 were positive for thermotolerant coliforms. These findings suggest that microbial monitoring of raw water by using only fecal indicator organisms is not sufficient for assessing the occurrence or the load of thermophilic
Campylobacter
spp. Insights into the role of environmental water as sources for sporadic
Campylobacter
infection will require genus-specific monitoring techniques.
Analysis of the Clonal Relationship of Serotype O26:H11 Enterohemorrhagic
Escherichia coli
Isolates from Cattle
Authors: Geue Lutz , Klare Sabrina , Schnick Christina , Mintel Birgit , Meyer Katharina , Conraths Franz J. 
Published: September 2009

ABSTRACT

Twelve cluster groups of
Escherichia coli
O26 isolates found in three cattle farms were monitored in space and time. Cluster analysis suggests that only some O26:H11 strains had the potential for long-term persistence in hosts and farms. As judged by their virulence markers, bovine enterohemorrhagic O26:H11 isolates may represent a considerable risk for human infection.
Metabolic Engineering of
Escherichia coli
for Efficient Conversion of Glycerol to Ethanol
Authors: Trinh Cong T. , Srienc Friedrich 
Published: September 2009

ABSTRACT

Based on elementary mode analysis, an
Escherichia coli
strain was designed for efficient conversion of glycerol to ethanol. By using nine gene knockout mutations, the functional space of the central metabolism of
E. coli
was reduced from over 15,000 possible pathways to a total of 28 glycerol-utilizing pathways that support cell function. Among these pathways are eight aerobic and eight anaerobic pathways that do not support cell growth but convert glycerol into ethanol with a theoretical yield of 0.50 g ethanol/g glycerol. The remaining 12 pathways aerobically coproduce biomass and ethanol from glycerol. The optimal ethanol production depends on the oxygen availability that regulates the two competing pathways for biomass and ethanol production. The coupling between cell growth and ethanol production enabled metabolic evolution of the designed strain through serial dilution that resulted in strains with improved ethanol yields and productivities. In defined medium, the evolved strain can convert 40 g/liter of glycerol to ethanol in 48 h with 90% of the theoretical ethanol yield. The performance of the designed strain is predicted by the property space of remaining elementary modes.
Negative Roles of a Novel Nitrogen Metabolite Repression-Related Gene,
TAR1
, in Laccase Production and Nitrate Utilization by the Basidiomycete
Cryptococcus neoformans
Authors: Jiang Nan , Xiao Dongguang , Zhang Defa , Sun Naiyu , Yan Bing , Zhu Xudong 
Published: September 2009

ABSTRACT

The multicopper oxidase laccase is widespread in fungi and has great industrial importance. One puzzle regarding laccase production in the basidiomycetous yeast
Cryptococcus neoformans
is that it is inhibited by high temperature (e.g., 37°C). In this paper, we report identification of a nitrogen metabolite repression-related gene,
TAR1
, which is responsible for laccase repression. Disruption of
TAR1
results in a significant increase in the level of
LAC1
mRNA at 37°C. The putative protein Tar1 shares a moderate level of similarity with the nitrogen metabolite repressors Nmr1 and NmrA from
Neurospora crassa
and
Aspergillus nidulans
, respectively. Likewise, Tar1 has a negative role in the utilization of nitrate. Furthermore, the structure of Tar1 is unique. Tar1 lacks the long C-terminal region of Nmr1 and NmrA. It contains the canonical Rossmann fold motif, GlyXXGlyXXGly, whereas Nmr1 and NmrA have variable residues at the Gly positions. Interestingly, the promoter region of
TAR1
contains three TTC/GAA repeats which are likely the heat shock factor (Hsf) binding sites, implying that Hsf has a role in laccase inhibition.
TAR1
mediation of temperature-associated repression of
LAC1
suggests a novel mechanism of laccase regulation and a new function for Nmr proteins. Our work may be helpful for industry in terms of promotion of laccase activity.
Mutations That Disrupt Either thepqqor thegdhGene ofRahnella aquatilisAbolish the Production of an Antibacterial Substance and Result in Reduced Biological Control of Grapevine Crown Gall
Authors: Guo Yan Bin , Li Jinyun , Li Lei , Chen Fan , Wu Wenliang , Wang Jianhui , Wang Huimin 
Published: September 2009

ABSTRACTRahnella aquatilisHX2, a biocontrol agent for grapevine crown gall caused byAgrobacterium vitis, produces an antibacterial substance that inhibits the growth ofA. vitisin vitro. In this study, we show that MH15 and MH16, two Tn5-induced mutants of HX2, have lost their abilities to inhibitA. vitisand have reduced biocontrol activities; they grow in logarithmic phase at a rate similar to that of the wild type and have single Tn5insertions. They are also impaired in producing pyrroloquinoline quinone (PQQ) or glucose dehydrogenase (GDH). Complementation of MH15 and MH16 with cosmid clones of CP465 and CP104 from an HX2 DNA library restored the antibiosis, biocontrol, and PQQ or GDH production phenotypes. A 6.7-kb BamHI fragment from CP465 that fully restored the MH15-affected phenotypes was cloned and sequenced. Sequence analysis of the mutated DNA region resulted in the identification of seven open reading frames (ORFs), six of which share significant homology with PQQ-synthesizing genes in other bacteria, designatedpqqAthroughpqqF. Meanwhile, A 5.5-kb PstI fragment from CP104 fully complemented the MH16 mutant and contained a single ORF highly similar to that of genes coding for GDHs. An in-framegdhdeletion mutant has the same phenotypes as the Tn5mutant of MH16. Complementation of both deletion and Tn5 gdhmutants restored the affected phenotypes to wild-type levels. Our results suggest that an antibacterial substance plays a role in biocontrol ofA. vitisby HX2.
The Complete Genome of
Comamonas testosteroni
Reveals Its Genetic Adaptations to Changing Environments
Authors: Ma Ying-Fei , Zhang Yun , Zhang Jia-Yue , Chen Dong-Wei , Zhu Yongqian , Zheng Huajun , Wang Sheng-Yue , Jiang Cheng-Ying , Zhao Guo-Ping , Liu Shuang-Jiang 
Published: September 2009

ABSTRACT

Members of the gram-negative, strictly aerobic genus
Comamonas
occur in various environments. Here we report the complete genome of
Comamonas testosteroni
strain CNB-2. Strain CNB-2 has a circular chromosome that is 5,373,643 bp long and has a G+C content of 61.4%. A total of 4,803 open reading frames (ORFs) were identified; 3,514 of these ORFs are functionally assigned to energy production, cell growth, signal transduction, or transportation, while 866 ORFs encode hypothetical proteins and 423 ORFs encode purely hypothetical proteins. The CNB-2 genome has many genes for transportation (22%) and signal transduction (6%), which allows the cells to respond and adapt to changing environments. Strain CNB-2 does not assimilate carbohydrates due to the lack of genes encoding proteins involved in glycolysis and pentose phosphate pathways, and it contains many genes encoding proteins involved in degradation of aromatic compounds. We identified 66 Tct and nine TRAP-T systems and a complete tricarboxylic acid cycle, which may allow CNB-2 to take up and metabolize a range of carboxylic acids. This nutritional bias for carboxylic acids and aromatic compounds enables strain CNB-2 to occupy unique niches in environments. Four different sets of terminal oxidases for the respiratory system were identified, and they putatively functioned at different oxygen concentrations. This study conclusively revealed at the genomic level that the genetic versatility of
C. testosteroni
is vital for competition with other bacteria in its special niches.
Use of Inorganic and Organic Nitrogen by
Synechococcus
spp. and Diatoms on the West Florida Shelf as Measured Using Stable Isotope Probing
Authors: Wawrik Boris , Callaghan Amy V. , Bronk Deborah A. 
Published: September 2009

ABSTRACT

The marine nitrogen (N) cycle is a complex network of biological transformations in different N pools. The linkages among these different reservoirs are often poorly understood. Traditional methods for measuring N uptake rely on bulk community properties and cannot provide taxonomic information.
15
N-based stable isotope probing (SIP), however, is a technique that allows detection of uptake of individual N sources by specific microorganisms. In this study we used
15
N SIP methodology to assess the use of different nitrogen substrates by
Synechococcus
spp. and diatoms on the west Florida shelf. Seawater was incubated in the presence of
15
N-labeled ammonium, nitrate, urea, glutamic acid, and a mixture of 16 amino acids. DNA was extracted and fractionated using CsCl density gradient centrifugation. Quantitative PCR was used to quantify the amounts of
Synechococcus
and diatom DNA as a function of density, and
15
N tracer techniques were used to measure rates of N uptake by the microbial community. The ammonium, nitrate, urea, and dissolved primary amine uptake rates were 0.077, 0.065, 0.013, and 0.055 μmol N liter
−1
h
−1
, respectively. SIP data indicated that diatoms and
Synechococcus
spp. actively incorporated N from [
15
N]nitrate, [
15
N]ammonium, and [
15
N]urea.
Synechococcus
also incorporated nitrogen from [
15
N]glutamate and
15
N-amino acids, but no evidence indicating uptake of labeled amino acids by diatoms was detected. These data suggest that N flow in communities containing
Synechococcus
spp. and diatoms has more plasticity than the new-versus-recycled production paradigm suggests and that these phytoplankters should not be viewed strictly as recycled and new producers, respectively.
High-Level Resistance of
Nosema ceranae
, a Parasite of the Honeybee, to Temperature and Desiccation
Authors: Fenoy S. , Rueda C. , Higes M. , Martín-Hernández R. , del Aguila C. 
Published: September 2009

ABSTRACT

Resistance of
Nosema ceranae
to different exposure conditions has been evaluated by using Sytox green and DAPI (4′,6-diamidino-2-phenylindole) to test spore viability. High thermotolerance at 60 and 35°C and resistance to desiccation were observed. However, a significant decrease in viability after freezing and a rapid degeneration of spores maintained at 4°C were also detected.
Diversity of
Frankia
Populations in Root Nodules of Geographically Isolated Arizona Alder Trees in Central Arizona (United States)
Authors: Welsh Allana K. , Dawson Jeffrey O. , Gottfried Gerald J. , Hahn Dittmar 
Published: September 2009

ABSTRACT

The diversity of uncultured
Frankia
populations in root nodules of
Alnus oblongifolia
trees geographically isolated on mountaintops of central Arizona was analyzed by comparative sequence analyses of
nifH
gene fragments. Sequences were retrieved from
Frankia
populations in nodules of four trees from each of three mountaintops (
n
= 162) and their levels of diversity compared using spatial genetic clustering methods and single-nucleotide or 1, 3, or 5% sequence divergence thresholds. With the single-nucleotide threshold level, 45 different sequences with significant differences between the mountaintops were retrieved, with the southern site partitioning in a separate population from the two other sites. Some of these sequences were identical in nodules from different mountaintops and to those of strains isolated from around the world. A high level of diversity that resulted in the assignment of 14 clusters of sequences was also found on the 1% divergence level. Single-nucleotide and 1% divergence levels thus demonstrate microdiversity of frankiae in root nodules of
A. oblongifolia
trees and suggest a partitioning of diversity by site. At the 3 and 5% divergence levels, however, diversity was reduced to three clusters or one cluster, respectively, with no differentiation by mountaintop. Only at the 5% threshold level do all
Frankia
strains previously assigned to one genomic group cluster together.