bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization and Acceptor Preference of a Soluble Meningococcal Group C Polysialyltransferase
Authors: Peterson Dwight C. , Arakere Gayathri , Vionnet Justine , McCarthy Pumtiwitt C. , Vann Willie F. 
Published: January 2011

ABSTRACT

Vaccines against
Neisseria meningitidis
group C are based on its α-2,9-linked polysialic acid capsular polysaccharide. This polysialic acid expressed on the surface of
N. meningitidis
and in the absence of specific antibody serves to evade host defense mechanisms. The polysialyltransferase (PST) that forms the group C polysialic acid (NmC PST) is located in the cytoplasmic membrane. Until recently, detailed characterization of bacterial polysialyltransferases has been hampered by a lack of availability of soluble enzyme preparations. We have constructed chimeras of the group C polysialyltransferase that catalyzes the formation α-2,9-polysialic acid as a soluble enzyme. We used site-directed mutagenesis to determine the region of the enzyme necessary for synthesis of the α-2,9 linkage. A chimera of NmB and NmC PSTs containing only amino acids 1 to 107 of the NmB polysialyltransferase catalyzed the synthesis of α-2,8-polysialic acid. The NmC polysialyltransferase requires an exogenous acceptor for catalytic activity. While it requires a minimum of a disialylated oligosaccharide to catalyze transfer, it can form high-molecular-weight α-2,9-polysialic acid in a nonprocessive fashion when initiated with an α-2,8-polysialic acid acceptor.
De novo
synthesis
in vivo
requires an endogenous acceptor. We attempted to reconstitute
de novo
activity of the soluble group C polysialyltransferase with membrane components. We found that an acapsular mutant with a defect in the polysialyltransferase produces outer membrane vesicles containing an acceptor for the α-2,9-polysialyltransferase. This acceptor is an amphipathic molecule and can be elongated to produce polysialic acid that is reactive with group C-specific antibody.
The Main Virulence Determinant of Yersinia entomophaga MH96 Is a Broad-Host-Range Toxin Complex Active against Insects
Authors: Hurst Mark R. H. , Jones Sandra A. , Binglin Tan , Harper Lincoln A. , Jackson Trevor A. , Glare Travis R. 
Published: January 2011

ABSTRACT

Through transposon mutagenesis and DNA sequence analysis, the main disease determinant of the entomopathogenic bacterium
Yersinia entomophaga
MH96 was localized to an ∼32-kb pathogenicity island (PAI) designated PAI
Ye96
. Residing within PAI
Ye96
are seven open reading frames that encode an insecticidal toxin complex (TC), comprising not only the readily recognized toxin complex A (TCA), TCB, and TCC components but also two chitinase proteins that form a composite TC molecule. The central TC gene-associated region (∼19 kb) of PAI
Ye96
was deleted from the
Y. entomophaga
MH96 genome, and a subsequent bioassay of the ΔTC derivative toward
Costelytra zealandica
larvae showed it to be innocuous. Virulence of the ΔTC mutant strain could be restored by the introduction of a clone containing the entire PAI
Ye96
TC gene region. As much as 0.5 mg of the TC is released per 100 ml of Luria-Bertani broth at 25°C, while at 30 or 37°C, no TC could be detected in the culture supernatant. Filter-sterilized culture supernatants derived from
Y. entomophaga
MH96, but not from the ΔTC strain grown at temperatures of 25°C or less, were able to cause mortality. The 50% lethal doses (LD
50
s) of the TC toward diamondback moth
Plutella xylostella
and
C. zealandica
larvae were defined as 30 ng and 50 ng, respectively, at 5 days after ingestion. Histological analysis of the effect of the TC toward
P. xylostella
larva showed that within 48 h after ingestion of the TC, there was a general dissolution of the larval midgut.
EsaD, a Secretion Factor for the Ess Pathway inStaphylococcus aureus
Authors: Anderson Mark , Chen Yi-Hsing , Butler Emily K. , Missiakas Dominique M. 
Published: January 2011

ABSTRACTStaphylococcus aureusencodes the Sec-independent Ess secretion pathway, an ortholog of mycobacterial T7 secretion systems which is required for the virulence of this Gram-positive microbe. The Ess (ESXsecretion) pathway was previously defined as a genomic cluster of eight genes,esxA,esaA,essA,essB,esaB,essC,esaC, andesxB. essABCencode membrane proteins involved in the stable expression ofesxA,esxB, andesaC, genes specifying three secreted polypeptide substrates.esaB, which encodes a small cytoplasmic protein, represses the synthesis of EsaC but not that of EsxA and EsxB. Here we investigated a hitherto uncharacterized gene,esaD, located downstream ofesxB. Expression ofesaDis activated by mutations inesaBandessB. EsaD, the 617-amino-acid product ofesaD, is positioned in the membrane and is also accessible to EsaD-specific antibodies on the bacterial surface.S. aureusmutants lackingesaDare defective in the secretion of EsxA. Following intravenous inoculation of mice,S. aureus esaDmutants generate fewer abscesses with a reduced bacterial load compared to wild-type parent strain Newman. The chromosomes ofListeriaandBacillusspecies with Ess pathways also harboresaDhomologues downstream ofesxB, suggesting that the contributory role of EsaD in Ess secretion may be shared among Gram-positive pathogens.
The Three-Layered DNA Uptake Machinery at the Cell Pole in Competent
Bacillus subtilis
Cells Is a Stable Complex
Authors: Kaufenstein Miriam , van der Laan Martin , Graumann Peter L. 
Published: January 2011

ABSTRACT

Many bacteria possess the ability to actively take up DNA from the environment and incorporate it into the chromosome. RecA protein is the key protein achieving homologous recombination. Several of the proteins involved in the transport of DNA across the cell envelope assemble at a single or both cell poles in competent
Bacillus subtilis
cells. We show that the presumed structure that transports DNA across the cell wall, the pseudopilus, also assembles at a single or both cell poles, while the membrane receptor, ComEA, forms a mobile layer throughout the cell membrane. All other known Com proteins, including the membrane permease, localize again to the cell pole, revealing that the uptake machinery has three distinct layers. In cells having two uptake machineries, one complex is occasionally mobile, with pairs of proteins moving together, suggesting that a complete complex may lose anchoring and become mobile. Overall, the cell pole provides stable anchoring. Only one of two uptake machineries assembles RecA protein, suggesting that only one is competent for DNA transfer. FRAP (fluorescence recovery after photobleaching) analyses show that in contrast to known multiprotein complexes, the DNA uptake machinery forms a highly stable complex, showing little or no exchange with unbound molecules. When cells are converted into round spheroplasts, the structure persists, revealing that the assembly is highly stable and does not require the cell pole for its maintenance. High stability may be important to fulfill the mechanical function in pulling DNA across two cell layers.
Autogenous Transcriptional Regulation of the
regA
Gene, Encoding an AraC-Like, Essential Virulence Regulator in
Citrobacter rodentium
Authors: Tan Aimee , Yang Ji , Tauschek Marija , Praszkier Judyta , Robins-Browne Roy M. 
Published: January 2011

ABSTRACT

We identified several promoters responsible for the expression of
regA
, which encodes a global virulence regulator in
Citrobacter rodentium
. Expression of some of the promoters was strongly autoactivated by RegA in conjunction with bicarbonate. Biochemical and mutational analyses were used to determine the consensus sequence of the RegA-binding sites.
Retrospective Application of Transposon-Directed Insertion Site Sequencing to a Library of Signature-Tagged Mini-Tn
5
Km2 Mutants of
Escherichia coli
O157:H7 Screened in Cattle
Authors: Eckert Sabine E. , Dziva Francis , Chaudhuri Roy R. , Langridge Gemma C. , Turner Daniel J. , Pickard Derek J. , Maskell Duncan J. , Thomson Nicholas R. , Stevens Mark P. 
Published: January 2011

ABSTRACT

Massively parallel sequencing of transposon-flanking regions assigned the genotype and fitness score to 91% of
Escherichia coli
O157:H7 mutants previously screened in cattle by signature-tagged mutagenesis (STM). The method obviates the limitations of STM and markedly extended the functional annotation of the prototype
E. coli
O157:H7 genome without further animal use.
A Major Role for Nonenzymatic Antioxidant Processes in the Radioresistance ofHalobacterium salinarum
Authors: Robinson Courtney K. , Webb Kim , Kaur Amardeep , Jaruga Pawel , Dizdaroglu Miral , Baliga Nitin S. , Place Allen , DiRuggiero Jocelyne 
Published: January 2011

ABSTRACTOxidative stress occurs when the generation of reactive oxygen species (ROS) exceeds the capacity of the cell's endogenous systems to neutralize them. Our analyses of the cellular damage and oxidative stress responses of the archaeonHalobacterium salinarumexposed to ionizing radiation (IR) revealed a critical role played by nonenzymatic antioxidant processes in the resistance ofH. salinarumto IR. ROS-scavenging enzymes were essential for resistance to chemical oxidants, yet those enzymes were not necessary forH. salinarum's resistance to IR. We found that protein-free cell extracts fromH. salinarumprovided a high level of protection for protein activity against IRin vitrobut did not protect DNA significantly. Compared with cell extracts of radiation-sensitive bacteria,H. salinarumextracts were enriched in manganese, amino acids, and peptides, supporting an essential role in ROS scavenging for those small moleculesin vivo. With regard to chemical oxidants, we showed that the damage caused by gamma irradiation was mechanistically different than that produced by hydrogen peroxide or by the superoxide-generating redox-cycling drug paraquat. The data presented support the idea that IR resistance is most likely achieved by a “metabolic route,” with a combination of tightly coordinated physiological processes.
The Second RNA Chaperone, Hfq2, Is Also Required for Survival under Stress and Full Virulence of
Burkholderia cenocepacia
J2315
Authors: Ramos Christian G. , Sousa Sílvia A. , Grilo André M. , Feliciano Joana R. , Leitão Jorge H. 
Published: January 2011

ABSTRACT

Burkholderia cenocepacia
J2315 is a highly virulent and epidemic clinical isolate of the
B
.
cepacia
complex (Bcc), a group of bacteria that have emerged as important pathogens to cystic fibrosis patients. This bacterium, together with all Bcc strains and a few other prokaryotes, is unusual for encoding in its genome two distinct and functional Hfq-like proteins. In this work, we show results indicating that the 188-amino-acid Hfq2 protein is required for the full virulence and stress resistance of
B
.
cenocepacia
J2315, despite the presence on its genome of the functional 79-amino-acid Hfq protein encoded by the
hfq
gene. Similar to other Hfq proteins, Hfq2 is able to bind RNA. However, Hfq2 is unique in its ability to apparently form trimers
in vitro
. Maximal transcription of
hfq
was observed in
B
.
cenocepacia
J2315 cells in the early exponential phase of growth. In contrast,
hfq2
transcription reached maximal levels in cells in the stationary phase, depending on the CepR quorum-sensing regulator. These results suggest that tight regulation of the expression of these two RNA chaperones is required to maximize the fitness and virulence of this bacterium. In addition, the ability of Hfq2 to bind DNA, not observed for Hfq, suggests that Hfq2 might play additional roles besides acting as an RNA chaperone.
Genome Analyses of Icelandic Strains ofSulfolobus islandicus, Model Organisms for Genetic and Virus-Host Interaction Studies
Authors: Guo Li , Brügger Kim , Liu Chao , Shah Shiraz A. , Zheng Huajun , Zhu Yongqiang , Wang Shengyue , Lillestøl Reidun K. , Chen Lanming , Frank Jeremy , Prangishvili David , Paulin Lars , She Qunxin , Huang Li , Garrett Roger A. 
Published: January 2011

ABSTRACTThe genomes of twoSulfolobus islandicusstrains obtained from Icelandic solfataras were sequenced and analyzed. Strain REY15A is a host for a versatile genetic toolbox. It exhibits a genome of minimal size, is stable genetically, and is easy to grow and manipulate. Strain HVE10/4 shows a broad host range for exceptional crenarchaeal viruses and conjugative plasmids and was selected for studying their life cycles and host interactions. The genomes of strains REY15A and HVE10/4 are 2.5 and 2.7 Mb, respectively, and each genome carries a variable region of 0.5 to 0.7 Mb where major differences in gene content and gene order occur. These include gene clusters involved in specific metabolic pathways, multiple copies of VapBC antitoxin-toxin gene pairs, and in strain HVE10/4, a 50-kb region rich in glycosyl transferase genes. The variable region also contains most of the insertion sequence (IS) elements and high proportions of the orphanorfBelements and SMN1 miniature inverted-repeat transposable elements (MITEs), as well as the clustered regular interspaced short palindromic repeat (CRISPR)-based immune systems, which are complex and diverse in both strains, consistent with them having been mobilized both intra- and intercellularly. In contrast, the remainder of the genomes are highly conserved in their protein and RNA gene syntenies, closely resembling those of otherS. islandicusandSulfolobus solfataricusstrains, and they exhibit only minor remnants of a few genetic elements, mainly conjugative plasmids, which have integrated at a few tRNA genes lacking introns. This provides a possible rationale for the presence of the introns.
EAL Domain Protein YdiV Acts as an Anti-FlhD
4
C
2
Factor Responsible for Nutritional Control of the Flagellar Regulon in
Salmonella enterica
Serovar Typhimurium
Authors: Wada Takeo , Morizane Tomoe , Abo Tatsuhiko , Tominaga Akira , Inoue-Tanaka Kanako , Kutsukake Kazuhiro 
Published: January 2011

ABSTRACT

Flagellar operons are divided into three classes with respect to their transcriptional hierarchy in
Salmonella enterica
serovar Typhimurium. The class 1 gene products FlhD and FlhC act together in an FlhD
4
C
2
heterohexamer, which binds upstream of the class 2 promoters to facilitate binding of RNA polymerase. In this study, we showed that flagellar expression was much reduced in the cells grown in poor medium compared to those grown in rich medium. This nutritional control was shown to be executed at a step after class 1 transcription. We isolated five Tn
5
insertion mutants in which the class 2 expression was derepressed in poor medium. These insertions were located in the
ydiV
(
cdgR
) gene or a gene just upstream of
ydiV
. The
ydiV
gene is known to encode an EAL domain protein and to act as a negative regulator of flagellar expression. Gene disruption and complementation analyses revealed that the
ydiV
gene is responsible for nutritional control. Expression analysis of the
ydiV
gene showed that its translation, but not transcription, was enhanced by growth in poor medium. The
ydiV
mutation did not have a significant effect on either the steady-state level of
flhDC
mRNA or that of FlhC protein. Purified YdiV protein was shown
in vitro
to bind to FlhD
4
C
2
through interaction with FlhD subunit and to inhibit its binding to the class 2 promoter, resulting in inhibition of FlhD
4
C
2
-dependent transcription. Taking these data together, we conclude that YdiV is a novel anti-FlhD
4
C
2
factor responsible for nutritional control of the flagellar regulon.
Genome Sequence of
Taylorella equigenitalis
MCE9, the Causative Agent of Contagious Equine Metritis
Authors: Hébert Laurent , Moumen Bouziane , Duquesne Fabien , Breuil Marie-France , Laugier Claire , Batto Jean-Michel , Renault Pierre , Petry Sandrine 
Published: January 2011

ABSTRACT

Taylorella equigenitalis
is the causative agent of contagious equine metritis (CEM), a sexually transmitted infection of horses. We herein report the genome sequence of
T. equigenitalis
strain MCE9, isolated in 2005 from the urethral fossa of a 4-year-old stallion in France.
Prevalence of depression in granted and refused requests for euthanasia and assisted suicide: a systematic review
Authors: Levene Ilana , Parker Michael 
Published: January 2011

BackgroundThere is an established link between depression and interest in hastened death in patients who are seriously ill. Concern exists over the extent of depression in patients who actively request euthanasia/physician-assisted suicide (PAS) and those who have their requests granted.ObjectivesTo estimate the prevalence of depression in refused and granted requests for euthanasia/PAS and discuss these findings.MethodsA systematic review was performed in MEDLINE and PsycINFO in July 2010, identifying studies reporting rates of depression in requests for and cases of euthanasia/PAS. One author critically appraised the strength of the data using published criteria.Results21 studies were included covering four countries. There was considerable heterogeneity in methods of assessing depression and selecting patients. In the highest quality studies, in the Netherlands and Oregon, 8–47% of patients requesting euthanasia/PAS had depressive symptoms and 2–17% of completed euthanasia/PAS cases had depressive symptoms. In the Netherlands, depression was significantly higher in refused than granted requests, and there was no significant difference in the rate of depression between euthanasia cases and similar patients who had not made a request for euthanasia.ConclusionIt is unclear whether depression increases the probability of making a request for euthanasia/PAS, but in the Netherlands most requests in depressed patients are rejected, leaving a depression rate in cases that is similar to the surrounding population. Less evidence is available elsewhere, but some level of depression has been identified in patients undergoing euthanasia/PAS in all the countries studied. Whether the presence of depression is ever compatible with an ethical decision on euthanasia/PAS is discussed.
SELDI-TOF derived serum biomarkers failed to differentiate between patients with beryllium sensitisation and patients with chronic beryllium disease
Authors: Tooker B C , Bowler R P , Orcutt J M , Maier L A , Christensen H M , Newman L S 
Published: January 2011

BackgroundPeople exposed to beryllium may develop beryllium sensitisation (BeS) and, in some cases, progress to chronic beryllium disease (CBD).ObjectivesThe objective of this study was to test the ability of proteomic technology to identify patterns of serum protein biomarkers that allow differentiation between BeS and CBD and thus remove the need for invasive bronchoscopic procedures.MethodsInitially, SELDI-TOF methodology and analysis was performed on serum samples from 30 CBD and 31 BeS patients.ResultsThis ‘starter set’ yielded two distinct biomarker pattern sets with eight candidate proteins. The first set differentiated between BeS and CBD with 83.3% sensitivity and 82.3% specificity, with 10-fold cross-validation of 75% and 79%, respectively. The second set of biomarkers yielded higher sensitivity (90.0%) and higher specificity (90.3%), with 10-fold cross-validation of 71.7% and 82.3%, respectively. Due to its greater sensitivity and specificity, the second set of biomarkers was used as the framework for differentiating between CBD and BeS in a second set of serum samples from 450 patients with BeS and CBD. When this larger set of samples was subjected to the biomarker framework in a blinded fashion, it yielded a sensitivity of 43.53% and a specificity of 38.93%.ConclusionsDue to these low sensitivity and specificity values, we have concluded that, currently, the unique set of SELDI-TOF derived biomarkers does not possess the qualities that would allow it to differentiate between a CBD patient and a BeS patient using serum protein biomarkers. Future refinements in sample collection or proteomic technology may be needed to improve biomarker discovery.
Experience report
Authors: Pop Iustin 
Published: February 2011

In system administration, the languages of choice for solving automation tasks are scripting languages, owing to their flexibility, extensive library support and quick development cycle. Functional programming is more likely to be found in software development teams and the academic world.
This separation means that system administrators cannot use the most effective tool for a given problem; in an ideal world, we should be able to mix and match different languages, based on the problem at hand.
This experience report details our initial introduction and use of Haskell in a mature, medium size project implemented in Python. We also analyse the interaction between the two languages, and show how Haskell has excelled at solving a particular type of real-world problems
What can the GC compute efficiently?
Authors: Reichenbach Christoph , Immerman Neil , Smaragdakis Yannis , Aftandilian Edward E. , Guyer Samuel Z. 
Published: February 2011

We present the DeAL language for heap assertions that are efficiently evaluated during garbage collection time. DeAL is a rich, declarative, logic-based language whose programs are guaranteed to be executable with good whole-heap locality, i.e., within a single traversal over every live object on the heap and a finite neighborhood around each object. As a result, evaluating DeAL programs incurs negligible cost: for simple assertion checking at each garbage collection, the end-to-end execution slowdown is below 2%. DeAL is integrated into Java as a VM extension and we demonstrate its efficiency and expressiveness with several applications and properties from the past literature.
Compared to past systems for heap assertions, DeAL is distinguished by its very attractive expressiveness/efficiency tradeoff: it o ers a significantly richer class of assertions than what past systems could check with a single traversal. Conversely, past systems that can express the same (or more) complex assertions as DeAL do so only by su ering orders-of-magnitude higher costs.
Random testing for higher-order, stateful programs
Authors: Klein Casey , Flatt Matthew , Findler Robert Bruce 
Published: February 2011

Testing is among the most effective tools available for finding bugs. Still, we know of no automatic technique for generating test cases that expose bugs involving a combination of mutable state and callbacks, even though objects and method overriding set up exactly that combination. For such cases, a test generator must create callbacks or subclasses that aggressively exercise side-effecting operations using combinations of generated objects.
This paper presents a new algorithm for randomly testing programs that use state and callbacks. Our algorithm exploits a combination of contracts and environment bindings to guide the test-case generator toward interesting inputs. Our prototype implementation for Racket (formerly PLT Scheme) - which has a Java-like class system, but with first-class classes as well as gbeta-like augmentable methods - uncovered dozens of bugs in a well-tested and widely used text-editor library.
We describe our approach in a precise, formal notation, borrowing the techniques used to describe operational semantics and type systems. The formalism enables us to provide a compact and self-contained explanation of the core of our technique without the ambiguity usually present in pseudo-code descriptions.