bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure-Specific Nuclease Activities of
Pyrococcus abyssi
RNase HII
Authors: Le Laz Sébastien , Le Goaziou Audrey , Henneke Ghislaine 
Published: May 2010

ABSTRACT

Faithful DNA replication involves the removal of RNA residues from genomic DNA prior to the ligation of nascent DNA fragments in all living organisms. Because the physiological roles of archaeal type 2 RNase H are not fully understood, the substrate structure requirements for the detection of RNase H activity need further clarification. Biochemical characterization of a single RNase H detected within the genome of
Pyrococcus abyssi
showed that this type 2 RNase H is an Mg- and alkaline pH-dependent enzyme.
Pab
RNase HII showed RNase activity and acted as a specific endonuclease on RNA-DNA/DNA duplexes. This specific cleavage, 1 nucleotide upstream of the RNA-DNA junction, occurred on a substrate in which RNA initiators had to be fully annealed to the cDNA template. On the other hand, a 5′ RNA flap Okazaki fragment intermediate impaired
Pab
RNase HII endonuclease activity. Furthermore, introduction of mismatches into the RNA portion near the RNA-DNA junction decreased both the specificity and the efficiency of cleavage by
Pab
RNase HII. Additionally,
Pab
RNase HII could cleave a single ribonucleotide embedded in a double-stranded DNA. Our data revealed
Pab
RNase HII as a dual-function enzyme likely required for the completion of DNA replication and DNA repair.
Frequency and Rate of Pilin Antigenic Variation of
Neisseria meningitidis
Authors: Helm R. Allen , Seifert H. Steven 
Published: May 2010

ABSTRACT

The rates of pilin antigenic variation (Av) of two strains of
Neisseria meningitidis
were determined using an unbiased DNA sequencing assay. Strain MC58 underwent pilin Av at a rate similar to that of
N. gonorrhoeae
strain MS11 but lower than that of
N. gonorrhoeae
strain FA1090. Pilin Av was undetectable in strain FAM18.
The Response Regulator SprE (RssB) Is Required for Maintaining Poly(A) Polymerase I-Degradosome Association during Stationary Phase
Authors: Carabetta Valerie J. , Silhavy Thomas J. , Cristea Ileana M. 
Published: May 2010

ABSTRACTPoly(A) polymerase I (PAP I) is the enzyme responsible for the addition of poly(A) tails onto RNA molecules inEscherichia coli. Polyadenylation is believed to facilitate the destruction of such RNAs by the mRNA degradosome. Recently, it was discovered that the stationary-phase regulatory protein SprE (RssB) has a second function in the control of polyadenylation that is distinct from its known function in the regulated proteolysis of RpoS. In the work presented herein, we used a targeted proteomic approach to further investigate SprE's involvement in the polyadenylation pathway. Specifically, we used cryogenic cell lysis, immunopurifications on magnetic beads, and mass spectrometry to identify interacting partners of PAP I-green fluorescent protein. We provide the firstin vivoevidence that PAP I interacts with the mRNA degradosome during both exponential and stationary phases and find that the degradosome can contain up to 10 different proteins under certain conditions. Moreover, we demonstrate that the majority of these PAP I interactions are formed via protein-protein interactions and that SprE plays an important role in the maintenance of the PAP I-degradosome association during stationary phase.
Redundant Function ofcmaA2andmmaA2inMycobacterium tuberculosis cisCyclopropanation of Oxygenated Mycolates
Authors: Barkan Daniel , Rao Vivek , Sukenick George D. , Glickman Michael S. 
Published: May 2010

ABSTRACTTheMycobacterium tuberculosiscell envelope contains a wide variety of lipids and glycolipids, including mycolic acids, long-chain branched fatty acids that are decorated by cyclopropane rings. Genetic analysis of the mycolate methyltransferase family has been a powerful approach to assign functions to each of these enzymes but has failed to reveal the origin ofciscyclopropanation of the oxygenated mycolates. Here we examine potential redundancy between mycolic acid methyltransferases by generating and analyzingM. tuberculosisstrains lackingmmaA2andcmaA2,mmaA2andcmaA1, ormmaA1alone.M. tuberculosislacking bothcmaA2andmmaA2cannotciscyclopropanate methoxymycolates or ketomycolates, phenotypes not shared by themmaA2andcmaA2single mutants. In contrast, a combined loss ofcmaA1andmmaA2had no effect on mycolic acid modification compared to results with a loss ofmmaA2alone. Deletion ofmmaA1fromM. tuberculosisabolishestranscyclopropanation without accumulation oftrans-unsaturated oxygenated mycolates, placing MmaA1 in the biosynthetic pathway fortrans-cyclopropanated oxygenated mycolates before CmaA2. These results define new functions for the mycolic acid methyltransferases ofM. tuberculosisand indicate a substantial redundancy of function for MmaA2 and CmaA2, the latter of which can function as both acisandtranscyclopropane synthase for the oxygenated mycolates.
The
Yersinia pestis
Chromosome Encodes Active Addiction Toxins
Authors: Goulard Céline , Langrand Sophie , Carniel Elisabeth , Chauvaux Sylvie 
Published: May 2010

ABSTRACT

Toxin-antitoxin (TA) loci consist of two genes in an operon, encoding a stable toxin and an unstable antitoxin. The expression of toxin leads to cell growth arrest and sometimes bacterial death, while the antitoxin prevents the cytotoxic activity of the toxin. In this study, we show that the chromosome of
Yersinia pestis
, the causative agent of plague, carries 10 putative TA modules and two solitary antitoxins that belong to five different TA families (HigBA, HicAB, RelEB, Phd/Doc, and MqsRA). Two of these toxin genes (
higB2
and
hicA1
) could not be cloned in
Escherichia coli
unless they were coexpressed with their cognate antitoxin gene, indicating that they are highly toxic for this species. One of these toxin genes (
higB2
) could, however, be cloned directly and expressed in
Y. pestis
, where it was highly toxic, while the other one (
hicA1
) could not, probably because of its extreme toxicity. All eight other toxin genes were successfully cloned into the expression vector pBAD-TOPO. For five of them (
higB1
,
higB3
,
higB5
,
hicA2
, and
tox
), no toxic activity was detected in either
E. coli
or
Y. pestis
despite their overexpression. The three remaining toxin genes (
relE1
,
higB4
, and
doc
) were toxic for
E. coli
, and this toxic activity was abolished when the cognate antitoxin was coexpressed, showing that these three TA modules are functional in
E. coli
. Curiously, only one of these three toxins (RelE1) was active in
Y. pestis
. Cross-interaction between modules of the same family was observed but occurred only when the antitoxins were almost identical. Therefore, our study demonstrates that of the 10 predicted TA modules encoded by the
Y. pestis
chromosome, at least 5 are functional in
E. coli
and/or in
Y. pestis
. This is the first demonstration of active addiction toxins produced by the plague agent.
Factors Affecting Variability in Time between Addition of Nutrient Germinants and Rapid Dipicolinic Acid Release during Germination of Spores of
Bacillus
Species
Authors: Zhang Pengfei , Garner Will , Yi Xuan , Yu Ji , Li Yong-qing , Setlow Peter 
Published: May 2010

ABSTRACT

The simultaneous nutrient germination of hundreds of individual wild-type spores of three
Bacillus
species and a number of
Bacillus subtilis
strains has been measured by two new methods, and rates of release of the great majority of the large pool of dipicolinic acid (DPA) from individual spores of
B. subtilis
strains has been measured by Raman spectroscopy with laser tweezers. The results from these analyses and published data have allowed a number of significant conclusions about the germination of spores of
Bacillus
species as follows. (i) The time needed for release of the great majority of a
Bacillus
spore's DPA once rapid DPA release had begun (Δ
T
release
) during nutrient germination was independent of the concentration of nutrient germinant used, the level of the germinant receptors (GRs) that recognize nutrient germinants used and heat activation prior to germination. Values for Δ
T
release
were generally 0.5 to 3 min at 25 to 37°C for individual wild-type spores. (ii) Despite the conclusion above, germination of individual spores in populations was very heterogeneous, with some spores in wild-type populations completing germination ≥15-fold slower than others. (iii) The major factor in the heterogeneity in germination of individual spores in populations was the highly variable lag time,
T
lag
, between mixing spores with nutrient germinants and the beginning of Δ
T
release
. (iv) A number of factors decrease spores'
T
lag
values including heat activation, increased levels of GRs/spore, and higher levels of nutrient germinants. These latter factors appear to affect the level of activated GRs/spore during nutrient germination. (v) The conclusions above lead to the simple prediction that a major factor causing heterogeneity in
Bacillus
spore germination is the number of functional GRs in individual spores, a number that presumably varies significantly between spores in populations.
Complete Genome Sequence of the Aerobic Facultative Methanotroph
Methylocella silvestris
BL2
Authors: Chen Yin , Crombie Andrew , Rahman M. Tanvir , Dedysh Svetlana N. , Liesack Werner , Stott Matthew B. , Alam Maqsudul , Theisen Andreas R. , Murrell J. Colin , Dunfield Peter F. 
Published: May 2010

ABSTRACT

Methylocella silvestris
BL2 is an aerobic methanotroph originally isolated from an acidic forest soil in Germany. It is the first fully authenticated facultative methanotroph. It grows not only on methane and other one-carbon (C
1
) substrates, but also on some compounds containing carbon-carbon bonds, such as acetate, pyruvate, propane, and succinate. Here we report the full genome sequence of this bacterium.
Genome Sequence of the Novel Marine Member of the
Gammaproteobacteria
Strain HTCC5015
Authors: Thrash J. Cameron , Stingl Ulrich , Cho Jang-Cheon , Ferriera Steve , Johnson Justin , Vergin Kevin L. , Giovannoni Stephen J. 
Published: May 2010

ABSTRACT

HTCC5015 is a novel, highly divergent marine member of the
Gammaproteobacteria
, currently without a cultured representative with greater than 89% 16S rRNA gene identity to itself. The organism was isolated from water collected from Hydrostation S south of Bermuda using high-throughput dilution-to-extinction culturing techniques. Here we present the genome sequence of the unique
Gammaproteobacterium
strain HTCC5015.
Genome Sequences of Strains HTCC2148 and HTCC2080, Belonging to the OM60/NOR5 Clade of the
Gammaproteobacteria
Authors: Thrash J. Cameron , Cho Jang-Cheon , Ferriera Steve , Johnson Justin , Vergin Kevin L. , Giovannoni Stephen J. 
Published: May 2010

ABSTRACT

Organisms in the OM60/NOR5 clade of the
Gammaproteobacteria
are ubiquitous in the world's oceans and can make up as much as 11% of bacterial cells in certain areas. Isolated from coastal Oregon water,
Gammaproteobacteria
HTCC2148 and HTCC2080 are two members of this important clade. Here we present the genome sequences of the OM60
Gammaproteobacteria
HTCC2148 and HTCC2080.
Synthetic Effects ofsecGandsecY2Mutations on Exoproteome Biogenesis inStaphylococcus aureus
Authors: Sibbald Mark J. J. B. , Winter Theresa , van der Kooi-Pol Magdalena M. , Buist G. , Tsompanidou E. , Bosma Tjibbe , Schäfer Tina , Ohlsen Knut , Hecker Michael , Antelmann Haike , Engelmann Susanne , van Dijl Jan Maarten 
Published: May 2010

ABSTRACTThe Gram-positive pathogenStaphylococcus aureussecretes various proteins into its extracellular milieu. Bioinformatics analyses have indicated that most of these proteins are directed to the canonical Sec pathway, which consists of the translocation motor SecA and a membrane-embedded channel composed of the SecY, SecE, and SecG proteins. In addition,S. aureuscontains an accessory Sec2 pathway involving the SecA2 and SecY2 proteins. Here, we have addressed the roles of the nonessential channel components SecG and SecY2 in the biogenesis of the extracellular proteome ofS. aureus. The results show that SecG is of major importance for protein secretion byS. aureus.Specifically, the extracellular accumulation of nine abundant exoproteins and seven cell wall-bound proteins was significantly affected in ansecGmutant. No secretion defects were detected for strains with asecY2single mutation. However, deletion ofsecY2exacerbated the secretion defects ofsecGmutants, affecting the extracellular accumulation of one additional exoprotein and one cell wall protein. Furthermore, ansecG secY2double mutant displayed a synthetic growth defect. This might relate to a slightly elevated expression ofsraP, encoding the only known substrate for the Sec2 pathway, in cells lacking SecG. Additionally, the results suggest that SecY2 can interact with the Sec1 channel, which would be consistent with the presence of a single set ofsecEandsecGgenes inS. aureus.
Transcriptional Analysis of the
grlRA
Virulence Operon from
Citrobacter rodentium
Authors: Tauschek Marija , Yang Ji , Hocking Dianna , Azzopardi Kristy , Tan Aimee , Hart Emily , Praszkier Judyta , Robins-Browne Roy M. 
Published: May 2010

ABSTRACT

The locus for enterocyte effacement (LEE) is the virulence hallmark of the attaching-and-effacing (A/E) intestinal pathogens, namely, enteropathogenic
Escherichia coli
, enterohemorrhagic
E. coli
, and
Citrobacter rodentium
. The LEE carries more than 40 genes that are arranged in several operons, e.g.,
LEE1
to
LEE5
. Expression of the various transcriptional units is subject to xenogeneic silencing by the histone-like protein H-NS. The
LEE1
-encoded regulator, Ler, plays a key role in relieving this repression at several major LEE promoters, including
LEE2
to
LEE5
. To achieve appropriate intracellular concentrations of Ler in different environments, A/E pathogens have evolved a sophisticated regulatory network to control
ler
expression. For example, the LEE-encoded GrlA and GrlR proteins work as activator and antiactivator, respectively, of
ler
transcription. Thus, control of the transcriptional activities of the
LEE1
(
ler
) promoter and the
grlRA
operon determines the rate of transcription of all of the LEE-encoded virulence factors. To date, only a single promoter has been identified for the
grlRA
operon. In this study, we showed that the non-LEE-encoded AraC-like regulatory protein RegA of
C. rodentium
directly stimulates transcription of the
grlRA
promoter by binding to an upstream region in the presence of bicarbonate ions. In addition,
in vivo
and
in vitro
transcription assays revealed a σ
70
promoter that is specifically responsible for transcription of
grlA
. Expression from this promoter was strongly repressed by H-NS and its paralog StpA but was activated by Ler. DNase I footprinting demonstrated that Ler binds to a region upstream of the
grlA
promoter, whereas H-NS interacts specifically with a region extending from the
grlA
core promoter into its coding sequence. Together, these findings provide new insights into the environmental regulation and differential expressions of the
grlR
and
grlA
genes of
C. rodentium
.
Transcriptional Activation of the
tad
Type IVb Pilus Operon by PypB in
Yersinia enterocolitica
Authors: Schilling Jennifer , Wagner Karin , Seekircher Stephanie , Greune Lilo , Humberg Verena , Schmidt M. Alexander , Heusipp Gerhard 
Published: May 2010

ABSTRACT

Type IV pili are virulence factors in various bacteria and mediate, among other functions, the colonization of diverse surfaces. Various subclasses of type IV pili have been identified, but information on pilus expression, biogenesis, and the associated phenotypes is sparse for the genus
Yersinia
. We recently described the identification of PypB as a transcriptional regulator in
Yersinia enterocolitica
. Here we show that the
pypB
gene is associated with the
tad
locus, a genomic island that is widespread among bacterial and archaeal species. The genetic linkage of
pypB
with the
tad
locus is conserved throughout the yersiniae but is not found among other bacteria carrying the
tad
locus. We show that the genes of the
tad
locus form an operon in
Y. enterocolitica
that is controlled by PypB and that
pypB
is part of this operon. The
tad
genes encode functions necessary for the biogenesis of the Flp subfamily of type IVb pili initially described for
Aggregatibacter actinomycetemcomitans
to mediate a tight-adherence phenotype. In
Y. enterocolitica
, the Flp pilin protein shows some peculiarities in its amino acid sequence that imply similarities as well as differences compared to typical motifs found in the Flp subtype of type IVb pili. Flp is expressed and processed after PypB overproduction, resulting in microcolony formation but not in increased adherence to biotic or abiotic surfaces. Our data describe the transcriptional regulation of the
tad
type IVb pilus operon by PypB in
Y. enterocolitica
but fail to show most previously described phenotypes associated with this type of pilus in other bacteria.
How cost-effective is ‘No Smoking Day’?: Figure 1
Authors: Kotz D , Stapleton J A , Owen L , West R 
Published: May 2010

ObjectiveTo obtain a more rigorous estimate of the cost-effectiveness of No Smoking Day (NSD), an annual UK-wide campaign to encourage smokers to quit, than has been possible hitherto.DesignComparison of reported quit attempts in the month following NSD for three consecutive years with adjacent months using repeated national surveys of quit attempts.SettingEngland.ParticipantsA total of 1309 adults who had smoked in the past year who responded to the surveys in the month following NSD (April 2007–2009) and a comparison group of 2672 adults who smoked in the past year who responded to the survey in the two adjacent months (March and May 2007–2009).Main outcome measuresThe number of additional smokers who quit permanently in response to NSD was estimated from the survey results. The incremental cost-effectiveness ratio (ICER) was calculated by combining this estimate with established estimates of life years gained and the known costs of NSD.ResultsThe rate of quit attempts was 2.8 percentage points higher in the months following NSD (120/1309) compared with the adjacent months (170/2672; 95% CI 0.99% to 4.62%), leading to an estimated additional 0.07% of the 8.5 million smokers in England quitting permanently in response to NSD. The cost of NSD per smoker was £0.088. The discounted life years gained per smoker in the modal age group 35–44 years was 0.00107, resulting in an ICER of £82.24 (95% CI 49.7 to 231.6). ICER estimates for other age groups were similar.ConclusionsNSD emerges as an extremely cost-effective public health intervention.
Tobacco point-of-sale displays in England: a snapshot survey of current practices
Authors: Rooke Catriona , Cheeseman Hazel , Dockrell Martin , Millward Deborah , Sandford Amanda 
Published: May 2010

BackgroundTobacco displays at the point of sale (PoS) are an important means for the tobacco industry to communicate with consumers. With regulations prohibiting PoS displays recently having come into force in Ireland, passed into law in England, Wales and Northern Ireland and some Australian states, and being considered in New Zealand, Finland and Brazil, this is an increasingly important issue. This study explores the nature of displays, the extent to which they are tobacco industry funded, and the relation between the tobacco companies and retailers.MethodsThree areas were chosen to gain a snapshot of PoS displays in England. Over 100 retailers were visited, with interviews taking place on site. Information was gathered on the type and size of tobacco display, who was paying for the display, requirements and incentives, and visits by industry representatives.ResultsThe majority of retailers had gantries provided by tobacco companies. A minority of these were fitted with automated dispensers called retail vending machines. Attractive lighting and colour were often used to highlight particular products. Most retailers were being visited by industry representatives who checked displays. Some retailers also reported incentives offered to them for displaying products.ConclusionsThe results suggest that the tobacco industry presence and control in the retail environment is significant. Tobacco companies overwhelmingly provided tobacco gantries in the shops surveyed and influenced displays through a combination of requirements and incentives. The extensive involvement of tobacco companies in providing and monitoring retail displays suggests the importance of implementing policies to end this form of advertising.
Targeting the Mitogen-Activated Protein Kinase Pathway: Physiological Feedback and Drug Response
Authors: Pratilas Christine A. , Solit David B. 
Published: May 2010

Abstract
Mitogen-activated protein kinase (MAPK) pathway activation is a frequent event in human cancer and is often the result of activating mutations in the BRAF and RAS oncogenes. Targeted inhibitors of BRAF and its downstream effectors are in various stages of preclinical and clinical development. These agents offer the possibility of greater efficacy and less toxicity than current therapies for tumors driven by oncogenic mutations in the MAPK pathway. Early clinical results with the BRAF-selective inhibitor PLX4032 suggest that this strategy will prove successful in a select group of patients whose tumors are driven by V600E BRAF. Relief of physiologic feedback upon pathway inhibition may, however, attenuate drug response and contribute to the development of acquired resistance. An improved understanding of the adaptive response of cancer cells to MAPK pathway inhibition may thus aid in the identification of those patients most likely to respond to targeted pathway inhibitors and provide a rational basis for tailored combination strategies. Clin Cancer Res; 16(13); 3329–34. ©2010 AACR.
Rapid and Robust Transgenic High-Grade Glioma Mouse Models for Therapy Intervention Studies
Authors: de Vries Nienke A. , Bruggeman Sophia W. , Hulsman Danielle , de Vries Hilda I. , Zevenhoven John , Buckle Tessa , Hamans Bob C. , Leenders William P. , Beijnen Jos H. , van Lohuizen Maarten , Berns Anton J.M. , van Tellingen Olaf 
Published: May 2010

Abstract
Purpose: To develop a transgenic mouse model of glioma that can be conveniently used for testing therapy intervention strategies. High-grade glioma is a devastating and uniformly fatal disease for which better therapy is urgently needed. Typical for high-grade glioma is that glioma cells infiltrate extensively into surrounding pivotal brain structures, thereby rendering current treatments largely ineffective. Evaluation of novel therapies requires the availability of appropriate glioma mouse models.
Experimental Design: High-grade gliomas were induced by stereotactic intracranial injection of lentiviral GFAP-Cre or CMV-Cre vectors into compound LoxP-conditional mice, resulting in K-Rasv12 expression and loss of p16Ink4a/p19Arf with or without concomitant loss of p53 or Pten.
Results: Tumors reproduced many of the features that are characteristic for human high-grade gliomas, including invasiveness and blood-brain barrier functionality. Especially, CMV-Cre injection into p53;Ink4a/Arf;K-Rasv12 mice resulted in high-grade glioma with a short tumor latency (2-3 weeks) and full penetrance. Early detection and follow-up was accomplished by noninvasive bioluminescence imaging, and the practical utility for therapy intervention was shown in a study with temozolomide.
Conclusion: We have developed a realistic high-grade glioma model that can be used with almost the same convenience as traditional xenograft models, thus allowing its implementation at the forefront of preclinical evaluation of new treatments. Clin Cancer Res; 16(13); 3431–41. ©2010 AACR.