bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constructing Semantic Representations From a Gradually Changing Representation of Temporal Context
Authors: Howard Marc W. , Shankar Karthik H. , Jagadisan Udaya K. K. 
Published: August 2010

AbstractComputational models of semantic memory exploit information about co‐occurrences of words in naturally occurring text to extract information about the meaning of the words that are present in the language. Such models implicitly specify a representation of temporal context. Depending on the model, words are said to have occurred in the same context if they are presented within a moving window, within the same sentence, or within the same document. The temporal context model (TCM), which specifies a particular definition of temporal context, has proved useful in the study of episodic memory. The predictive temporal context model (pTCM) uses the same definition of temporal context to generate semantic memory representations. Taken together pTCM and TCM may prove to be part of a general model of declarative memory.
Microbial metacommunities in the lichen–rock habitat
Authors: Bjelland Torbjørg , Grube Martin , Hoem Solveig , Jorgensen Steffen L. , Daae Frida Lise , Thorseth Ingunn H. , Øvreås Lise 
Published: August 2010

SummaryLichens are common as colonizers of bare rocks and contribute to weathering, but their associated bacterial communities have been poorly studied. In this study Hydropunctaria maura, Ophioparma ventosa, Pertusaria corallina and Rhizocarpon geographicum were analysed to determine the influence of lichens on lichen–rock‐associated microbial metacommunities. For the first time, Archaea were documented to be associated with rock‐inhabiting lichens. All the archaeal sequences obtained were affiliated with Crenarchaeota. The Bacteria detected in the lichen–rock samples were affiliated with the major lineages Acidobacteria, Actinobacteria, Alpha‐, Beta‐, Gammaproteobacteria, Bacteriodetes, Chloroflexi, Deinococcus, Firmicutes, Planctomycetes, Tenericutes and Cyanobacteria. The microbial communities of O. ventosa, P. corallina and R. geographicum were more similar to each other both terms of the number and types of different sequences, than to H. maura. A higher bacterial diversity was observed endolithically than within the epilithic lichen thalli directly above. The abundance of Archaea were also generally higher endolithically than in the epilithic lichen thalli, while the abundance of Bacteria was higher in the lichen thalli compared with within the rock. These results demonstrated that the lichen–rock interfaces are complex habitats, where the macroscopic lichens influence the composition of microbial metacommunities.
Non‐autonomous transposable elements associated with inactivation of microcystin gene clusters in strains of the genus Anabaena isolated from the Baltic Sea
Authors: Fewer David P. , Halinen Katrianna , Sipari Hanna , Bernardová Kateřina , Mänttäri Mia , Eronen Eeva , Sivonen Kaarina 
Published: August 2010

SummaryMicrocystins are potent peptide toxins produced by a range of distantly related cyanobacteria. They are assembled on a large enzyme complex encoded by the 55 kb microcystin synthetase (mcy) gene cluster. Here we report two strains of the genus Anabaena isolated from the Baltic Sea, which contain the entire mcy gene cluster but do not produce microcystins. Transcription analysis demonstrated that mcy genes were not expressed in these strains. We identified short insertion elements interrupting the mcyA, mcyD and mcyE genes in the two strains isolated in different years from different parts of the Baltic Sea. The 126–207 bp insertion elements encoded both terminal inverted repeats and direct repeats but lacked transposases. However, we found evidence for transposition of these elements despite the absence of genes encoding transposases, suggesting that they are non‐autonomous mobile miniature inverted‐repeat transposable elements (MITEs) recently described from cyanobacteria. The MITE insertion elements were present in mcyD genes amplified directly from the cyanobacterial community present in the Baltic Sea blooms from 2005. The results demonstrate that mcy gene cluster mutants can make up a stable proportion of the mcy gene pool in the Baltic Sea population.
A simple and efficient method for concentration of ocean viruses by chemical flocculation
Authors: John Seth G. , Mendez Carolina B. , Deng Li , Poulos Bonnie , Kauffman Anne Kathryn M. , Kern Suzanne , Brum Jennifer , Polz Martin F. , Boyle Edward A. , Sullivan Matthew B. 
Published: August 2010

SummaryOcean viruses alter ecosystems through host mortality, horizontal gene transfer and by facilitating remineralization of limiting nutrients. However, the study of wild viral populations is limited by inefficient and unreliable concentration techniques. Here, we develop a new technique to recover viruses from natural waters using iron‐based flocculation and large‐pore‐size filtration, followed by resuspension of virus‐containing precipitates in a pH 6 buffer. Recovered viruses are amenable to gene sequencing, and a variable proportion of phages, depending upon the phage, retain their infectivity when recovered. This Fe‐based virus flocculation, filtration and resuspension method (FFR) is efficient (> 90% recovery), reliable, inexpensive and adaptable to many aspects of marine viral ecology and genomics research.
Horizon-Specific Bacterial Community Composition of German Grassland Soils, as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes
Authors: Will Christiane , Thürmer Andrea , Wollherr Antje , Nacke Heiko , Herold Nadine , Schrumpf Marion , Gutknecht Jessica , Wubet Tesfaye , Buscot François , Daniel Rolf 
Published: August 2010

ABSTRACT

The diversity of bacteria in soil is enormous, and soil bacterial communities can vary greatly in structure. Here, we employed a pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to characterize the overall and horizon-specific (A and B horizons) bacterial community compositions in nine grassland soils, which covered three different land use types. The entire data set comprised 752,838 sequences, 600,544 of which could be classified below the domain level. The average number of sequences per horizon was 41,824. The dominant taxonomic groups present in all samples and horizons were the
Acidobacteria
,
Betaproteobacteria
,
Actinobacteria
,
Gammaproteobacteria
,
Alphaproteobacteria
,
Deltaproteobacteria
,
Chloroflexi
,
Firmicutes
, and
Bacteroidetes
. Despite these overarching dominant taxa, the abundance, diversity, and composition of bacterial communities were horizon specific. In almost all cases, the estimated bacterial diversity (
H
′) was higher in the A horizons than in the corresponding B horizons. In addition, the
H
′ was positively correlated with the organic carbon content, the total nitrogen content, and the C-to-N ratio, which decreased with soil depth. It appeared that lower land use intensity results in higher bacterial diversity. The majority of sequences affiliated with the
Actinobacteria
,
Bacteroidetes
,
Cyanobacteria
,
Fibrobacteres
,
Firmicutes
,
Spirochaetes
,
Verrucomicrobia
,
Alphaproteobacteria
,
Betaproteobacteria
, and
Gammaproteobacteria
were derived from A horizons, whereas the majority of the sequences related to
Acidobacteria
,
Chloroflexi
,
Gemmatimonadetes
,
Nitrospira
, TM7, and WS3 originated from B horizons. The distribution of some bacterial phylogenetic groups and subgroups in the different horizons correlated with soil properties such as organic carbon content, total nitrogen content, or microbial biomass.
Inhibition of the Activity of Both Domains of Lysostaphin through Peptidoglycan Modification by the Lysostaphin Immunity Protein
Authors: Gargis Shaw R. , Heath Harry E. , LeBlanc Paul A. , Dekker Linda , Simmonds Robin S. , Sloan Gary L. 
Published: August 2010

ABSTRACT
Resistance to lysostaphin, a staphylolytic glycylglycine endopeptidase, is due to a FemABX-like immunity protein that inserts serines in place of some glycines in peptidoglycan cross bridges. These modifications inhibit both binding of the recombinant cell wall targeting domain and catalysis by the recombinant catalytic domain of lysostaphin.
Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach
Authors: Cardenas Erick , Wu Wei-Min , Leigh Mary Beth , Carley Jack , Carroll Sue , Gentry Terry , Luo Jian , Watson David , Gu Baohua , Ginder-Vogel Matthew , Kitanidis Peter K. , Jardine Philip M. , Zhou Jizhong , Criddle Craig S. , Marsh Terence L. , Tiedje James M. 
Published: August 2010

ABSTRACTMassively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions.CastellaniellaandRhodanobactercharacterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio,Anaeromyxobacter, andDesulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducerGeobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.
Transmission of Plant-Pathogenic Bacteria by Nonhost Seeds without Induction of an Associated Defense Reaction at Emergence
Authors: Darrasse Armelle , Darsonval Arnaud , Boureau Tristan , Brisset Marie-Noëlle , Durand Karine , Jacques Marie-Agnès 
Published: August 2010

ABSTRACTAn understanding of the mechanisms involved in the different steps of bacterial disease epidemiology is essential to develop new control strategies. Seeds are the passive carriers of a diversified microbial cohort likely to affect seedling physiology. Among seed-borne plant-pathogenic bacteria, seed carriage in compatible situations is well evidenced. The aims of our work are to determine the efficiency of pathogen transmission to seeds of a nonhost plant and to evaluate bacterial and plant behaviors at emergence. Bacterial transmission from flowers to seeds and from seeds to seedlings was measured forXanthomonas campestrispv. campestris in incompatible interactions with bean. Transmissions from seeds to seedlings were compared forX. campestrispv. campestris, forXanthomonas citripv. phaseoli var. fuscans in compatible interactions with bean, and forEscherichia coli, a human pathogen, in null interactions with bean. The induction of defense responses was monitored by using reverse transcription and quantitative PCR (RT-qPCR) of genes representing the main signaling pathways and assaying defense-related enzymatic activities. Flower inoculations resulted in a high level of bean seed contamination byX. campestrispv. campestris, which transmitted efficiently to seedlings. Whatever the type of interaction tested, dynamics of bacterial population sizes were similar on seedlings, and no defense responses were induced evidencing bacterial colonization of seedlings without any associated defense response induction. Bacteria associated with the spermosphere multiply in this rich environment, suggesting that the colonization of seedlings relies mostly on commensalism. The transmission of plant-pathogenic bacteria to and by nonhost seeds suggests a probable role of seeds of nonhost plants as an inoculum source.
Association of
Campylobacter jejuni
Cj0859c Gene (
fspA
) Variants with Different
C. jejuni
Multilocus Sequence Types
Authors: de Haan C. P. A. , Kivistö R. , Hänninen M. L. 
Published: August 2010

ABSTRACT

Cj0859c variants
fspA1
and
fspA2
from 669 human, poultry, and bovine
Campylobacter jejuni
strains were associated with certain hosts and multilocus sequence typing (MLST) types. Among the human and poultry strains,
fspA1
was significantly (
P
< 0.001) more common than
fspA2
. FspA2 amino acid sequences were the most diverse and were often truncated.
A Mutation within the β Subunit ofEscherichia coliRNA Polymerase Impairs Transcription from Bacteriophage T4 Middle Promoters
Authors: James Tamara D. , Cashel Michael , Hinton Deborah M. 
Published: August 2010

ABSTRACTDuring infection ofEscherichia coli, bacteriophage T4 usurps the host transcriptional machinery, redirecting it to the expression of early, middle, and late phage genes. Middle genes, whose expression begins about 1 min postinfection, are transcribed both from the extension of early RNA into middle genes and by the activation of T4 middle promoters. Middle-promoter activation requires the T4 transcriptional activator MotA and coactivator AsiA, which are known to interact with σ70, the specificity subunit of RNA polymerase. T4motAamber [motA(Am)] orasiA(Am) phage grows poorly in wild-typeE. coli. However, previous work has found that T4motA(Am)does not grow in theE. colimutant strain TabG. We show here that the RNA polymerase in TabG contains two mutations within its β-subunit gene:rpoB(E835K) andrpoB(G1249D). We find that the G1249D mutation is responsible for restricting the growth of either T4motA(Am)orasiA(Am) and for impairing transcription from MotA/AsiA-activated middle promotersin vivo. With one exception, transcription from tested T4 early promoters is either unaffected or, in some cases, even increases, and there is no significant growth phenotype for therpoB(E835K G1249D) strain in the absence of T4 infection. In reported structures of thermophilic RNA polymerase, the G1249 residue is located immediately adjacent to a hydrophobic pocket, called the switch 3 loop. This loop is thought to aid in the separation of the RNA from the DNA-RNA hybrid as RNA enters the RNA exit channel. Our results suggest that the presence of MotA and AsiA may impair the function of this loop or that this portion of the β subunit may influence interactions among MotA, AsiA, and RNA polymerase.
Orientations of theBacteroides fragilisCapsular Polysaccharide Biosynthesis Locus Promoters during Symbiosis and Infection
Authors: Troy Erin B. , Carey Vincent J. , Kasper Dennis L. , Comstock Laurie E. 
Published: August 2010

ABSTRACTOrientations of the seven invertible polysaccharide biosynthesis locus promoters ofBacteroidesfragiliswere determined from bacteria grownin vitro, from feces of monoassociated and complex colonized mice, and fromB. fragilis-induced murine abscesses. Bacteria grownin vivohave greater variability in orientation of polysaccharide locus promoters than culture-grown organisms.
Characterization of the CDP-2-Glycerol Biosynthetic Pathway in
Streptococcus pneumoniae
Authors: Wang Quan , Xu Yanli , Perepelov Andrei V. , Xiong Wei , Wei Dongmei , Shashkov Alexander S. , Knirel Yuriy A. , Feng Lu , Wang Lei 
Published: August 2010

ABSTRACT

Capsule polysaccharide (CPS) plays an important role in the virulence of
Streptococcus pneumoniae
and is usually used as the pneumococcal vaccine target. Glycerol-2-phosphate is found in the CPS of
S. pneumoniae
types 15A and 23F and is rarely found in the polysaccharides of other bacteria. The biosynthetic pathway of the nucleotide-activated form of glycerol-2-phosphate (NDP-2-glycerol) has never been identified. In this study, three genes (
gtp1
,
gtp2
, and
gtp3
) from
S. pneumoniae
23F that have been proposed to be involved in the synthesis of NDP-2-glycerol were cloned and the enzyme products were expressed, purified, and assayed for their respective activities. Capillary electrophoresis was used to detect novel products from the enzyme-substrate reactions, and the structure of the product was elucidated using electrospray ionization mass spectrometry and nuclear magnetic resonance spectroscopy. Gtp1 was identified as a reductase that catalyzes the conversion of 1,3-dihydroxyacetone to glycerol, Gtp3 was identified as a glycerol-2-phosphotransferase that catalyzes the conversion of glycerol to glycerol-2-phosphate, and Gtp2 was identified as a cytidylyltransferase that transfers CTP to glycerol-2-phosphate to form CDP-2-glycerol as the final product. The kinetic parameters of Gtp1 and Gtp2 were characterized in depth, and the effects of temperature, pH, and cations on these two enzymes were analyzed. This is the first time that the biosynthetic pathway of CDP-2-glycerol has been identified biochemically; this pathway provides a method to enzymatically synthesize this compound.
Characterization of the RNA Degradosome ofPseudoalteromonas haloplanktis: Conservation of the RNase E-RhlB Interaction in the Gammaproteobacteria
Authors: Aït-Bara Soraya , Carpousis Agamemnon J. 
Published: August 2010

ABSTRACTThe degradosome is a multienzyme complex involved in mRNA degradation inEscherichia coli. The essential endoribonuclease RNase E contains a large noncatalytic region necessary for protein-protein interactions with other components of the RNA degradosome. Interacting proteins include the DEAD-box RNA helicase RhlB, the glycolytic enzyme enolase, and the exoribonuclease PNPase.Pseudoalteromonas haloplanktis, a psychrotolerant gammaproteobacterium distantly related toE. coli, encodes homologs of each component of the RNA degradosome. InP. haloplanktis, RNase E associates with RhlB and PNPase but not enolase. Plasmids expressingP. haloplanktisRNase E (Ph-RNase E) can complementE. colistrains lackingE. coliRNase E (Ec-RNase E). Ph-RNase E, however, does not confer a growth advantage toE. coliat low temperature. Ph-RNase E has a heterologous protein-protein interaction with Ec-RhlB but not with Ec-enolase or Ec-PNPase. The Ph-RNase E binding sites for RhlB and PNPase were mapped by deletion analysis. The PNPase binding site is located at the C-terminal end of Ph-RNase E at the same position as that in Ec-RNase E, but the sequence of the site is not conserved. The sequence of the RhlB binding site in Ph-RNase E is related to the sequence in Ec-RNase E. Together with the heterologous interaction between Ph-RNase E and Ec-RhlB, our results suggest that the underlying structural motif for the RNase E-RhlB interaction is conserved. Since the activity of Ec-RhlB requires its physical interaction with Ec-RNase E, conservation of the underlying structural motif over a large evolutionary distance could be due to constraints involved in the control of RhlB activity.
An Extreme Thermophile,Thermus thermophilus, Is a Polyploid Bacterium
Authors: Ohtani Naoto , Tomita Masaru , Itaya Mitsuhiro 
Published: August 2010

ABSTRACTAn extremely thermophilic bacterium,Thermus thermophilusHB8, is one of the model organisms for systems biology. Its genome consists of a chromosome (1.85 Mb), a megaplasmid (0.26 Mb) designated pTT27, and a plasmid (9.3 kb) designated pTT8, and the complete sequence is available. We show here thatT. thermophilusis a polyploid organism, harboring multiple genomic copies in a cell. In the case of the HB8 strain, the copy number of the chromosome was estimated to be four or five, and the copy number of the pTT27 megaplasmid seemed to be equal to that of the chromosome. It has never been discussed whetherT. thermophilusis haploid or polyploid. However, the finding that it is polyploid is not surprising, asDeinococcus radiodurans, an extremely radioresistant bacterium closely related toThermus, is well known to be a polyploid organism. As is the case forD. radioduransin the radiation environment, the polyploidy ofT. thermophilusmight allow for genomic DNA protection, maintenance, and repair at elevated growth temperatures. Polyploidy often complicates the recognition of an essential gene inT. thermophilusas a model organism for systems biology.
The Flagellar Basal Body-Associated Protein FlgT Is Essential for a Novel Ring Structure in the Sodium-Driven
Vibrio
Motor
Authors: Terashima Hiroyuki , Koike Masafumi , Kojima Seiji , Homma Michio 
Published: August 2010

ABSTRACT

In
Vibrio alginolyticus
, the flagellar motor can rotate at a remarkably high speed, ca. three to four times faster than the
Escherichia coli
or
Salmonella
motor. Here, we found a
Vibrio
-specific protein, FlgT, in the purified flagellar basal body fraction. Defects of FlgT resulted in partial Fla
−
and Mot
−
phenotypes, suggesting that FlgT is involved in formation of the flagellar structure and generating flagellar rotation. Electron microscopic observation of the basal body of Δ
flgT
cells revealed a smaller LP ring structure compared to the wild type, and most of the T ring was lost. His
6
-tagged FlgT could be coisolated with MotY, the T-ring component, suggesting that FlgT may interact with the T ring composed of MotX and MotY. From these lines of evidence, we conclude that FlgT associates with the basal body and is responsible to form an outer ring of the LP ring, named the H ring, which can be distinguished from the LP ring formed by FlgH and FlgI.
Vibrio
-specific structures, e.g., the T ring and H ring might contribute the more robust motor structure compared to that of
E. coli
and
Salmonella
.
Enterococcus faecalis rnjB
Is Required for Pilin Gene Expression and Biofilm Formation
Authors: Gao Peng , Pinkston Kenneth L. , Nallapareddy Sreedhar R. , van Hoof Ambro , Murray Barbara E. , Harvey Barrett R. 
Published: August 2010

ABSTRACT

Pili in Gram-positive bacteria play a major role in the colonization of host tissue and in the development of biofilms. They are promising candidates for vaccines or drug targets since they are highly immunogenic and share common structural and functional features among various Gram-positive pathogens. Numerous publications have helped build a detailed understanding of pilus surface assembly, yet regulation of pilin gene expression has not been well defined. Utilizing a monoclonal antibody developed against the
Enterococcus faecalis
major pilus protein EbpC, we identified mutants from a transposon (Tn) insertion library which lack surface-exposed Ebp pili. In addition to insertions in the
ebp
regulon, an insertion in
ef1184
(
dapA
) significantly reduced levels of EbpC. Analysis of in-frame
dapA
deletion mutants and mutants with the downstream gene
rnjB
deleted further demonstrated that
rnjB
was responsible for the deficiency of EbpC. Sequence analysis revealed that
rnjB
encodes a putative RNase J2. Subsequent quantitative real-time PCR (qRT-PCR) and Northern blotting demonstrated that the
ebpABC
mRNA transcript level was significantly decreased in the
rnjB
deletion mutant. In addition, using a reporter gene assay, we confirmed that
rnjB
affects the expression of the
ebpABC
operon. Functionally, the
rnjB
deletion mutant was attenuated in its ability to produce biofilm, similar to that of an
ebpABC
deletion mutant which lacks Ebp pili. Together, these results demonstrate the involvement of
rnjB
in
E. faecalis
pilin gene expression and provide insight into a novel mechanism of regulation of pilus production in Gram-positive pathogens.