bluuebunny/crossref_metadata_2025_split huggingface dataset:
Questioning as thinking: a metacognitive framework to improve comprehension of expository text
Authors: Wilson Nance Speizman , Smetana Linda 
Published: July 2011

AbstractDespite a push to develop high levels of active engagement in learning by helping students reflect, refine and extend their ideas through effective questioning strategies, evidence suggests that teacher‐dominated interaction patterns permeate classroom instruction. This Initiate, Respond and Evaluate process leads students to maintain a passive stance towards learning and non‐engagement with text. As a result students fail to develop the strategies to solve comprehension problems and monitor their own learning with text. In contrast, effective, active instructional patterns provide students with opportunities to negotiate textual meaning. Through the use of the Question as Thinking framework we provide teachers with tools to enable pupils to reflect on their reading and understanding of expository texts. This article describes a framework for questioning designed to assist in the development of an active instructional pattern promoting the joint negotiation of meaning.
Temporal Variation and Host Association in the Campylobacter Population in a Longitudinal Ruminant Farm Study
Authors: Sproston Emma L. , Ogden Iain D. , MacRae Marion , Dallas John F. , Sheppard Samuel K. , Cody Alison J. , Colles Frances M. , Wilson Michael J. , Forbes Ken J. , Strachan Norval J. C. 
Published: July 2011

ABSTRACTCampylobacter jejuniandC. coliwere quantified and typed, using multilocus sequence typing (MLST), from fecal samples collected from a mixed cattle and sheep farm during summer. Cattle had a significantly higher prevalence than sheep (21.9% [74/338] and 14.0% [30/214], respectively), but both decreased over time. There were no differences in the averageCampylobacterconcentrations shed by cattle (600 CFU g−1) and sheep (820 CFU g−1), although sheep did show a significant temporal reduction in the number ofCampylobacterorganisms shed in their feces. A total of 21 different sequence types (STs) (97.7%C. jejuni, 2.3%C. coli) were isolated from cattle, and 9 different STs were isolated from sheep (40.6%C. jejuni, 59.4%C. coli). TheCampylobacterpopulation in cattle was relatively stable, and the frequencies of genotypes isolated showed little temporal variation. However, the composition of subtypes isolated from sheep did show significant temporal differences. The cattle and sheep consistently showed significant differences in their carriage ofCampylobacterspecies, STs, and CCs despite the fact that both were exposed to the same farming environment. This work has highlighted the patterns of aCampylobacterpopulation on a ruminant farm by identifying the existence of both temporal and between-host variations.
Biodiversity and Biogeography of Rhizobia Associated with Soybean Plants Grown in the North China Plain
Authors: Zhang Yan Ming , Li Ying , Chen Wen Feng , Wang En Tao , Tian Chang Fu , Li Qin Qin , Zhang Yun Zeng , Sui Xin Hua , Chen Wen Xin 
Published: July 2011

ABSTRACT

As the putative center of origin for soybean and the second largest region of soybean production in China, the North China Plain covers temperate and subtropical regions with diverse soil characteristics. However, the soybean rhizobia in this plain have not been sufficiently studied. To investigate the biodiversity and biogeography of soybean rhizobia in this plain, a total of 309 isolates of symbiotic bacteria from the soybean nodules collected from 16 sampling sites were studied by molecular characterization. These isolates were classified into 10 genospecies belonging to the genera
Sinorhizobium
and
Bradyrhizobium
, including four novel groups, with
S. fredii
(68.28%) as the dominant group. The phylogeny of symbiotic genes
nodC
and
nifH
defined four lineages among the isolates associated with
Sinorhizobium fredii
,
Bradyrhizobium
elkanii
,
B. japonicum
, and
B. yuanmingense
, demonstrating the different origins of symbiotic genes and their coevolution with the chromosome. The possible lateral transfer of symbiotic genes was detected in several cases. The association between soil factors (available N, P, and K and pH) and the distribution of genospecies suggest clear biogeographic patterns:
Sinorhizobium
spp. were superdominant in sampling sites with alkaline-saline soils, while
Bradyrhizobium
spp. were more abundant in neutral soils. This study clarified the biodiversity and biogeography of soybean rhizobia in the North China Plain.
Role of Alcohols in Growth, Lipid Composition, and Membrane Fluidity of Yeasts, Bacteria, and Archaea
Authors: Huffer Sarah , Clark Melinda E. , Ning Jonathan C. , Blanch Harvey W. , Clark Douglas S. 
Published: July 2011

ABSTRACT
Increased membrane fluidity, which causes cofactor leakage and loss of membrane potential, has long been documented as a cause for decreased cell growth during exposure to ethanol, butanol, and other alcohols. Reinforcement of the membrane with more complex lipid components is thus thought to be beneficial for the generation of more tolerant organisms. In this study, organisms with more complex membranes, namely, archaea, did not maintain high growth rates upon exposure to alcohols, indicating that more complex lipids do not necessarily fortify the membrane against the fluidizing effects of alcohols. In the presence of alcohols, shifts in lipid composition to more saturated and unbranched lipids were observed in most of the organisms tested, including archaea, yeasts, and bacteria. However, these shifts did not always result in a decrease in membrane fluidity or in greater tolerance of the organism to alcohol exposure. In general, organisms tolerating the highest concentrations of alcohols maintained membrane fluidity after alcohol exposure, whereas organisms that increased membrane rigidity were less tolerant. Altered lipid composition was a common response to alcohol exposure, with the most tolerant organisms maintaining a modestly fluid membrane. Our results demonstrate that increased membrane fluidity is not the sole cause of growth inhibition and that alcohols may also denature proteins within the membrane and cytosol, adversely affecting metabolism and decreasing cell growth.
Defining Components of the Chromosomal Origin of Replication of the Hyperthermophilic Archaeon Pyrococcus furiosus Needed for Construction of a Stable Replicating Shuttle Vector
Authors: Farkas Joel , Chung Daehwan , DeBarry Megan , Adams Michael W. W. , Westpheling Janet 
Published: July 2011

ABSTRACT

We report the construction of a series of replicating shuttle vectors that consist of a low-copy-number cloning vector for
Escherichia coli
and functional components of the origin of replication (
oriC
) of the chromosome of the hyperthermophilic archaeon
Pyrococcus furiosus
. In the process of identifying the minimum replication origin sequence required for autonomous plasmid replication in
P. furiosus
, we discovered that several features of the origin predicted by bioinformatic analysis and
in vitro
binding studies were not essential for stable autonomous plasmid replication. A minimum region required to promote plasmid DNA replication was identified, and plasmids based on this sequence readily transformed
P. furiosus
. The plasmids replicated autonomously and existed in a single copy. In contrast to shuttle vectors based on a plasmid from the closely related hyperthermophile
Pyrococcus abyssi
for use in
P. furiosus
, plasmids based on the
P. furiosus
chromosomal origin were structurally unchanged after transformation and were stable without selection for more than 100 generations.
Effective Antibiotic Resistance Mitigation during Cheese Fermentation
Authors: Li Xinhui , Li Yingli , Alvarez Valente , Harper Willis James , Wang Hua H. 
Published: July 2011

ABSTRACT
Controlling antibiotic-resistant (ART) bacteria in cheese fermentation is important for food safety and public health. A plant-maintained culture was found to be a potential source for ART bacterial contamination in cheese fermentation. Antibiotics had a detectable effect on the ART population from contamination in the finished product. The decrease in the prevalence of antibiotic resistance (AR) in retail cheese samples from 2010 compared to data from 2006 suggested the effectiveness of targeted AR mitigation in related products.
Detection of Coxiella burnetii in Complex Matrices by Using Multiplex Quantitative PCR during a Major Q Fever Outbreak in The Netherlands
Authors: de Bruin A. , de Groot A. , de Heer L. , Bok J. , Wielinga P. R. , Hamans M. , van Rotterdam B. J. , Janse I. 
Published: July 2011

ABSTRACT

Q fever, caused by
Coxiella burnetii
, is a zoonosis with a worldwide distribution. A large rural area in the southeast of the Netherlands was heavily affected by Q fever between 2007 and 2009. This initiated the development of a robust and internally controlled multiplex quantitative PCR (qPCR) assay for the detection of
C. burnetii
DNA in veterinary and environmental matrices on suspected Q fever-affected farms. The qPCR detects three
C. burnetii
targets (
icd
,
com1
, and IS
1111
) and one
Bacillus thuringiensis
internal control target (
cry1b
).
Bacillus thuringiensis
spores were added to samples to control both DNA extraction and PCR amplification. The performance of the qPCR assay was investigated and showed a high efficiency; a limit of detection of 13.0, 10.6, and 10.4 copies per reaction for the targets
icd
,
com1
, and IS
1111
, respectively; and no cross-reactivity with the nontarget organisms tested. Screening for
C. burnetii
DNA on 29 suspected Q fever-affected farms during the Q fever epidemic in 2008 showed that swabs from dust-accumulating surfaces contained higher levels of
C. burnetii
DNA than vaginal swabs from goats or sheep. PCR inhibition by coextracted substances was observed in some environmental samples, and 10- or 100-fold dilutions of samples were sufficient to obtain interpretable signals for both the
C. burnetii
targets and the internal control. The inclusion of an internal control target and three
C. burnetii
targets in one multiplex qPCR assay showed that complex veterinary and environmental matrices can be screened reliably for the presence of
C. burnetii
DNA during an outbreak.
Diversity and Plasticity of the Intracellular Plant Pathogen and Insect Symbiont “Candidatus Liberibacter asiaticus” as Revealed by Hypervariable Prophage Genes with Intragenic Tandem Repeats
Authors: Zhou Lijuan , Powell Charles A. , Hoffman Michele T. , Li Wenbin , Fan Guocheng , Liu Bo , Lin Hong , Duan Yongping 
Published: July 2011

ABSTRACT

“
Candidatus
Liberibacter asiaticus” is a psyllid-transmitted, phloem-limited alphaproteobacterium and the most prevalent species of “
Ca
. Liberibacter” associated with a devastating worldwide citrus disease known as huanglongbing (HLB). Two related and hypervariable genes (
hyv
I
and
hyv
II
) were identified in the prophage regions of the Psy62 “
Ca.
Liberibacter asiaticus” genome. Sequence analyses of the
hyv
I
and
hyv
II
genes in 35 “
Ca.
Liberibacter asiaticus” DNA isolates collected globally revealed that the
hyv
I
gene contains up to 12 nearly identical tandem repeats (NITRs, 132 bp) and 4 partial repeats, while
hyv
II
contains up to 2 NITRs and 4 partial repeats and shares homology with
hyv
I
. Frequent deletions or insertions of these repeats within the
hyv
I
and
hyv
II
genes were observed, none of which disrupted the open reading frames. Sequence conservation within the individual repeats but an extensive variation in repeat numbers, rearrangement, and the sequences flanking the repeat region indicate the diversity and plasticity of “
Ca.
Liberibacter asiaticus” bacterial populations in the world. These differences were found not only in samples of distinct geographical origins but also in samples from a single origin and even from a single “
Ca.
Liberibacter asiaticus”-infected sample. This is the first evidence of different “
Ca.
Liberibacter asiaticus” populations coexisting in a single HLB-affected sample. The Florida “
Ca.
Liberibacter asiaticus” isolates contain both
hyv
I
and
hyv
II
, while all other global “
Ca.
Liberibacter asiaticus” isolates contain either one or the other. Interclade assignments of the putative Hyv
I
and Hyv
II
proteins from Florida isolates with other global isolates in phylogenetic trees imply multiple “
Ca.
Liberibacter asiaticus” populations in the world and a multisource introduction of the “
Ca.
Liberibacter asiaticus” bacterium into Florida.
Low Relative Abundances of the Mucolytic Bacterium Akkermansia muciniphila and Bifidobacterium spp. in Feces of Children with Autism
Authors: Wang Lv , Christophersen Claus T. , Sorich Michael J. , Gerber Jacobus P. , Angley Manya T. , Conlon Michael A. 
Published: July 2011

ABSTRACT

Gastrointestinal disturbance is frequently reported for individuals with autism. We used quantitative real-time PCR analysis to quantify fecal bacteria that could influence gastrointestinal health in children with and without autism. Lower relative abundances of
Bifidobacteria
species and the mucolytic bacterium
Akkermansia muciniphila
were found in children with autism, the latter suggesting mucus barrier changes.
Isolation of Generalized Transducing Bacteriophages for Uropathogenic Strains of Escherichia coli
Authors: Battaglioli E. J. , Baisa G. A. , Weeks A. E. , Schroll R. A. , Hryckowian A. J. , Welch R. A. 
Published: July 2011

ABSTRACT

The traditional genetic procedure for random or site-specific mutagenesis in
Escherichia coli
K-12 involves mutagenesis, isolation of mutants, and transduction of the mutation into a clean genetic background. The transduction step reduces the likelihood of complications due to secondary mutations. Though well established, this protocol is not tenable for many pathogenic
E. coli
strains, such as uropathogenic strain CFT073, because it is resistant to known K-12 transducing bacteriophages, such as P1. CFT073 mutants generated via a technique such as lambda Red mutagenesis may contain unknown secondary mutations. Here we describe the isolation and characterization of transducing bacteriophages for CFT073. Seventy-seven phage isolates were acquired from effluent water samples collected from a wastewater treatment plant in Madison, WI. The phages were differentiated by a host sensitivity-typing scheme with a panel of
E. coli
strains from the ECOR collection and clinical uropathogenic isolates. We found 49 unique phage isolates. These were then examined for their ability to transduce antibiotic resistance gene insertions at multiple loci between different mutant strains of CFT073. We identified 4 different phages capable of CFT073 generalized transduction. These phages also plaque on the model uropathogenic
E. coli
strains 536, UTI89, and NU14. The highest-efficiency transducing phage, ΦEB49, was further characterized by DNA sequence analysis, revealing a double-stranded genome 47,180 bp in length and showing similarity to other sequenced phages. When combined with a technique like lambda Red mutagenesis, the newly characterized transducing phages provide a significant development in the genetic tools available for the study of uropathogenic
E. coli
.
Novel [NiFe]- and [FeFe]-Hydrogenase Gene Transcripts Indicative of Active Facultative Aerobes and Obligate Anaerobes in Earthworm Gut Contents
Authors: Schmidt Oliver , Wüst Pia K. , Hellmuth Susanne , Borst Katharina , Horn Marcus A. , Drake Harold L. 
Published: July 2011

ABSTRACTThe concomitant occurrence of molecular hydrogen (H2) and organic acids along the alimentary canal of the earthworm is indicative of ongoing fermentation during gut passage. Fermentative H2production is catalyzed by [FeFe]-hydrogenases and group 4 [NiFe]-hydrogenases in obligate anaerobes (e.g.,Clostridiales) and facultative aerobes (e.g.,Enterobacteriaceae), respectively, functional groups that might respond differently to contrasting redox conditions. Thus, the objectives of this study were to assess the redox potentials of the alimentary canal ofLumbricus terrestrisand analyze the hydrogenase transcript diversities of H2producers in glucose-supplemented gut content microcosms. Although redox potentials in the core of the alimentary canal were variable on an individual worm basis, average redox potentials were similar. The lowest redox potentials occurred in the foregut and midgut regions, averaging 40 and 110 mV, respectively. Correlation plots between hydrogenase amino acid sequences and 16S rRNA gene sequences indicated that closely related hydrogenases belonged to closely related taxa, whereas distantly related hydrogenases did not necessarily belong to distantly related taxa. Of 178 [FeFe]-hydrogenase gene transcripts, 177 clustered in 12Clostridiales-affiliated operational taxonomic units, the majority of which were indicative of heretofore unknown hydrogenases. Of 86 group 4 [NiFe]-hydrogenase gene transcripts, 79% and 21% were affiliated with organisms in theEnterobacteriaceaeandAeromonadaceae, respectively. The collective results (i) suggest that fermenters must cope with variable and moderately oxidative redox conditions along the alimentary canal, (ii) demonstrate that heretofore undetected hydrogenases are present in the earthworm gut, and (iii) corroborate previous findings implicatingClostridiaceaeandEnterobacteriaceaeas active fermentative taxa in earthworm gut content.
Unexpected Stress-Reducing Effect of PhaP, a Poly(3-Hydroxybutyrate) Granule-Associated Protein, in Escherichia coli
Authors: de Almeida Alejandra , Catone Mariela V. , Rhodius Virgil A. , Gross Carol A. , Pettinari M. Julia 
Published: July 2011

ABSTRACT

Phasins (PhaP) are proteins normally associated with granules of poly(3-hydroxybutyrate) (PHB), a biodegradable polymer accumulated by many bacteria as a reserve molecule. These proteins enhance growth and polymer production in natural and recombinant PHB producers. It has been shown that the production of PHB causes stress in recombinant
Escherichia coli
, revealed by an increase in the concentrations of several heat stress proteins. In this work, quantitative reverse transcription (qRT)-PCR analysis was used to study the effect of PHB accumulation, and that of PhaP from
Azotobacter
sp. strain FA8, on the expression of stress-related genes in PHB-producing
E. coli
. While PHB accumulation was found to increase the transcription of
dnaK
and
ibpA
, the expression of these genes and of
groES
,
groEL
,
rpoH
,
dps
, and
yfiD
was reduced, when PhaP was coexpressed, to levels even lower than those detected in the non-PHB-accumulating control. These results demonstrated the protective role of PhaP in PHB-synthesizing
E. coli
and linked the effects of the protein to the expression of stress-related genes, especially
ibpA
. The effect of PhaP was also analyzed in non-PHB-synthesizing strains, showing that expression of this heterologous protein has an unexpected protective effect in
E. coli
, under both normal and stress conditions, resulting in increased growth and higher resistance to both heat shock and superoxide stress by paraquat. In addition, PhaP expression was shown to reduce RpoH protein levels during heat shock, probably by reducing or titrating the levels of misfolded proteins.
Cell Wall Chitosan Is Necessary for Virulence in the Opportunistic Pathogen Cryptococcus neoformans
Authors: Baker Lorina G. , Specht Charles A. , Lodge Jennifer K. 
Published: July 2011

ABSTRACT

Cryptococcus neoformans
is an opportunistic fungal pathogen that causes meningoencephalitis. Its cell wall is composed of glucans, proteins, chitin, and chitosan. Multiple genetic approaches have defined a chitosan-deficient syndrome that includes slow growth and decreased cell integrity. Here we demonstrate chitosan is necessary for virulence and persistence in the mammalian host.
Pseudomonas aeruginosa tssC1
Links Type VI Secretion and Biofilm-Specific Antibiotic Resistance
Authors: Zhang Li , Hinz Aaron J. , Nadeau Jean-Paul , Mah Thien-Fah 
Published: July 2011

ABSTRACT

Biofilm-specific antibiotic resistance is influenced by multiple factors. We demonstrated that
Pseudomonas aeruginosa tssC1
, a gene implicated in type VI secretion (T6S), is important for resistance of biofilms to a subset of antibiotics. We showed that
tssC1
expression is induced in biofilms and confirmed that
tssC1
is required for T6S.
Proteolytic Cleavage Inactivates the Staphylococcus aureus Lipoteichoic Acid Synthase
Authors: Wörmann Mirka E. , Reichmann Nathalie T. , Malone Cheryl L. , Horswill Alexander R. , Gründling Angelika 
Published: July 2011

ABSTRACT

Lipoteichoic acid (LTA) is a crucial cell envelope component in Gram-positive bacteria. In
Staphylococcus aureus
, the polyglycerolphosphate LTA molecule is synthesized by LtaS, a membrane-embedded enzyme with five N-terminal transmembrane helices (5TM domain) that are connected via a linker region to the C-terminal extracellular enzymatic domain (eLtaS). The LtaS enzyme is processed during bacterial growth, and the eLtaS domain is released from the bacterial membrane. Here we provide experimental evidence that the proteolytic cleavage following residues
215
Ala-Leu-Ala
217
is performed by the essential
S. aureus
signal peptidase SpsB, as depletion of
spsB
results in reduced LtaS processing. In addition, the introduction of a proline residue at the +1 position with respect to the cleavage site, a substitution known to inhibit signal peptidase-dependent cleavage, abolished LtaS processing at this site. It was further shown that the 5TM domain is crucial for enzyme function. The observation that the construction of hybrid proteins between two functional LtaS-type enzymes resulted in the production of proteins unable to synthesize LTA suggests that specific interactions between the 5TM and eLtaS domains are required for function. No enzyme activity was detected upon expression of the 5TM and eLtaS domains as separate fragments, indicating that the two domains cannot assemble postsynthesis to form a functional enzyme. Taken together, our data suggest that only the full-length LtaS enzyme is active in the LTA synthesis pathway and that the proteolytic cleavage step is used as a mechanism to irreversibly inactivate the enzyme.
Putative Role of Cellulosomal Protease Inhibitors in Clostridium cellulovorans Based on Gene Expression and Measurement of Activities
Authors: Meguro Hirokazu , Morisaka Hironobu , Kuroda Kouichi , Miyake Hideo , Tamaru Yutaka , Ueda Mitsuyoshi 
Published: July 2011

ABSTRACTThis study is the first to demonstrate the activity of putative cellulosomal protease/peptidase inhibitors (named cyspins) ofClostridium cellulovorans, using theSaccharomyces cerevisiaedisplay system. Cyspins exhibited inhibitory activities against several representative plant proteases. This suggests that these inhibitors protect their microbe and cellulosome from external attack by plant proteases.